Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 126 of 161
Found at i:39824235 original size:120 final size:121
Alignment explanation
Indices: 39824096--39824392 Score: 469
Period size: 120 Copynumber: 2.5 Consensus size: 121
39824086 ATTTAATCAT
*
39824096 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * * *
39824161 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
39824218 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
39824281 AATAAAATTCTTCTATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
39824337 ATTTCAA-ATAATTAATATTAAATATGATT-TAATT-AAATATATGATTTAATAAAATT
1 ATTTCAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATT
39824393 TAAAATTATT
Statistics
Matches: 165, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
119 24 0.15
120 133 0.81
121 7 0.04
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:39824266 original size:14 final size:15
Alignment explanation
Indices: 39824217--39824268 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
39824207 GTAAAATATA
39824217 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
39824232 TATTAAATATATTAT
1 AATTAAATATATTAT
39824247 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
39824260 AATTTAATA
1 AATTAAATA
39824269 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:39824283 original size:44 final size:43
Alignment explanation
Indices: 39824194--39824284 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
39824184 CTCAAATCAT
* * *
39824194 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
39824237 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
39824281 AATA
1 AATA
39824285 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:39824319 original size:59 final size:59
Alignment explanation
Indices: 39824136--39824319 Score: 155
Period size: 59 Copynumber: 3.1 Consensus size: 59
39824126 TAATTAAAAT
*
39824136 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * *
39824195 ATAT-ATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-ATAA-TATTCTTATATGA-ATT-TACTCAAATCA
39824255 T-
58 TA
* *
39824256 ATATAATTTAATAAAATTCTTAATAAATAAAATTCTTCTATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
39824315 ATATA
1 ATATA
39824320 TGATACTATA
Statistics
Matches: 92, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 8 0.09
61 14 0.15
62 8 0.09
63 12 0.13
64 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
Found at i:39824373 original size:15 final size:15
Alignment explanation
Indices: 39824353--39824391 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
39824343 AATAATTAAT
39824353 ATTAAATATGATTTA
1 ATTAAATATGATTTA
39824368 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
39824385 ATAAAAT
1 ATTAAAT
39824392 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:39824378 original size:17 final size:17
Alignment explanation
Indices: 39824358--39824391 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39824348 TTAATATTAA
*
39824358 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
39824375 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
39824392 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:39824534 original size:93 final size:92
Alignment explanation
Indices: 39824424--39824618 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
39824414 GATTATAGTT
* * *
39824424 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
39824487 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
39824517 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
39824582 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
39824609 TATGAATTTA
1 TATGAATTTA
39824619 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:39826218 original size:34 final size:34
Alignment explanation
Indices: 39826180--39826247 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
39826170 TCTGAAATTC
39826180 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
1 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
39826214 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
1 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
39826248 CTACATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (34 bp):
AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
Found at i:39829565 original size:21 final size:20
Alignment explanation
Indices: 39829540--39829580 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39829530 ACCGTCAGAG
39829540 CCAACAACCACCTCTCCAAAA
1 CCAACAA-CACCTCTCCAAAA
*
39829561 CCAACGACACCTCTCCAAAA
1 CCAACAACACCTCTCCAAAA
39829581 TAATGGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.41, C:0.46, G:0.02, T:0.10
Consensus pattern (20 bp):
CCAACAACACCTCTCCAAAA
Found at i:39832986 original size:7 final size:7
Alignment explanation
Indices: 39832974--39833005 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
39832964 CGTGTTTTGA
39832974 GGTTTTC
1 GGTTTTC
39832981 GGTTTTC
1 GGTTTTC
39832988 GGTTTTC
1 GGTTTTC
39832995 GGTTTTC
1 GGTTTTC
39833002 GGTT
1 GGTT
39833006 GATTTCCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.31, T:0.56
Consensus pattern (7 bp):
GGTTTTC
Found at i:39833206 original size:8 final size:8
Alignment explanation
Indices: 39833195--39833229 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
39833185 TAAATGATGA
*
39833195 TATGTATG
1 TATGCATG
39833203 TATGCATG
1 TATGCATG
39833211 TATGCATG
1 TATGCATG
*
39833219 CATGCATG
1 TATGCATG
39833227 TAT
1 TAT
39833230 TCCTTCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (8 bp):
TATGCATG
Found at i:39833213 original size:12 final size:12
Alignment explanation
Indices: 39833196--39833229 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39833186 AAATGATGAT
39833196 ATGTATGTATGC
1 ATGTATGTATGC
*
39833208 ATGTATGCATGC
1 ATGTATGTATGC
*
39833220 ATGCATGTAT
1 ATGTATGTAT
39833230 TCCTTCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (12 bp):
ATGTATGTATGC
Found at i:39837780 original size:18 final size:19
Alignment explanation
Indices: 39837737--39837786 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
39837727 AACTATATTA
39837737 AAAAATATTTTATTAATTTTT
1 AAAAATA-TTTA-TAATTTTT
*
39837758 -TAAATATTTAT-ATTTTT
1 AAAAATATTTATAATTTTT
39837775 AAAAATATTTAT
1 AAAAATATTTAT
39837787 CAATAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 4 0.15
20 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAAATATTTATAATTTTT
Found at i:39838119 original size:21 final size:21
Alignment explanation
Indices: 39838093--39838137 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
39838083 AATTACAAGC
39838093 AATTTAAACAATTACAATTAA
1 AATTTAAACAATTACAATTAA
39838114 AATTTAAACAATTACAATTAA
1 AATTTAAACAATTACAATTAA
39838135 AAT
1 AAT
39838138 CAAAGGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAACAATTACAATTAA
Found at i:39843978 original size:20 final size:21
Alignment explanation
Indices: 39843949--39843994 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
39843939 AATTATTTTC
* *
39843949 TATAATTTTTTTA-ATATTAT
1 TATAAATTTTTTATATAATAT
39843969 TATAAATTTTTTATATAATAT
1 TATAAATTTTTTATATAATAT
39843990 T-TAAA
1 TATAAA
39843995 ATTATTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATAAATTTTTTATATAATAT
Found at i:39845893 original size:16 final size:16
Alignment explanation
Indices: 39845872--39845923 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
39845862 TTTGGTTCGC
39845872 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39845888 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
39845904 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
39845920 TGTA
1 TGTA
39845924 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39845970 original size:45 final size:44
Alignment explanation
Indices: 39845904--39845998 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
39845894 GGATTAGAGG
* * *
39845904 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
39845949 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
39845993 TGTAAT
1 TGTAAT
39845999 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:39846181 original size:18 final size:17
Alignment explanation
Indices: 39846160--39846194 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39846150 TTATTATTTA
*
39846160 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39846178 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39846195 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39846188 original size:28 final size:27
Alignment explanation
Indices: 39846118--39846190 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
39846108 TTTATTATCA
*
39846118 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
39846146 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
39846173 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
39846191 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:39846307 original size:144 final size:147
Alignment explanation
Indices: 39846079--39846350 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
39846069 ATGATTATTG
39846079 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
39846144 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
39846209 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
39846228 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
39846290 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
39846351 ANNNNNNNNN
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:39846325 original size:18 final size:17
Alignment explanation
Indices: 39846304--39846338 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39846294 TTATTATTAA
*
39846304 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39846322 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39846339 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39853832 original size:17 final size:16
Alignment explanation
Indices: 39853806--39853841 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
39853796 AACATTCATG
*
39853806 ATTGATTTTAAGTTGA
1 ATTGATTTTAAGTCGA
39853822 ATTGAATTTTAAGTCGA
1 ATTG-ATTTTAAGTCGA
39853839 ATT
1 ATT
39853842 TACATGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (16 bp):
ATTGATTTTAAGTCGA
Found at i:39855419 original size:3 final size:3
Alignment explanation
Indices: 39855411--39855453 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
39855401 GCCACCGCCC
39855411 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
39855454 TGGTTCCAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:39861315 original size:21 final size:22
Alignment explanation
Indices: 39861278--39861320 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39861268 CAGTAAAATG
*
39861278 ATTTTTAGAAAATAATTTATTT
1 ATTTTTAGAAAATAATTAATTT
*
39861300 ATTTTTTGAAAA-AATTAATTT
1 ATTTTTAGAAAATAATTAATTT
39861321 TTTCTAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
ATTTTTAGAAAATAATTAATTT
Found at i:39862904 original size:30 final size:30
Alignment explanation
Indices: 39862870--39862941 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
39862860 CGGTTCAATT
39862870 TAATTCAAATAACCAT-AACACAATTCAACC
1 TAATTCAAATAACCATGAA-ACAATTCAACC
* *
39862900 TAATTCAAATAATCATGAAACAATTCAATC
1 TAATTCAAATAACCATGAAACAATTCAACC
39862930 TAATTCAAATAA
1 TAATTCAAATAA
39862942 ACATCAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.28
Consensus pattern (30 bp):
TAATTCAAATAACCATGAAACAATTCAACC
Found at i:39866697 original size:127 final size:126
Alignment explanation
Indices: 39866330--39866704 Score: 486
Period size: 127 Copynumber: 3.0 Consensus size: 126
39866320 TTTTTATTGA
* * * * * *
39866330 AGAAAACGTGAACGGAATTTTAAAAAGATATTTGATTATTT-GGCTAAACAGAAA-ATCGAAACC
1 AGAAAACGCGGACGAAATTTT-AAAGGAAATTTGATTATTTAGAC-AAAC-GAAAGATCGAAACC
* * * * * *
39866393 CAGGACGTTAGGGCACGATTTCC-CGAATTCCCAAACATCAATCATTGCCTCTATTTTAAAGTTT
63 CAGCACGTTAGGGCACGA-TCCCTCGAATTTCTAAACATCAATCATCGCCTTTATTTTAAAGTTT
* * *
39866457 AGAAAACGTGGACGAAATTTTAAAGGAAAATTTGATTATTTAGACAAACGAAAGATCAAAACCTA
1 AGAAAACGCGGACGAAATTTTAAAGG-AAATTTGATTATTTAGACAAACGAAAGATCGAAACCCA
* *
39866522 GCACGTTAGGGCGCAATCCCTCGAATTTCTAAACATCAATCATCGCCTTTATTTTAAAGTTT
65 GCACGTTAGGGCACGATCCCTCGAATTTCTAAACATCAATCATCGCCTTTATTTTAAAGTTT
*
39866584 AGAAAATGCGGACGAAATTTTAAAGTGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCA
1 AGAAAACGCGGACGAAATTTTAAAG-GAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCA
* * *
39866649 GTACGTTAGGGCACGATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTTA
65 GCACGTTAGGGCACGATCCCTCGAATTTCTAAACATCAATCATCGCCTTTATTTTA
39866705 TAAAGTCGAC
Statistics
Matches: 219, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
126 11 0.05
127 205 0.94
128 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (126 bp):
AGAAAACGCGGACGAAATTTTAAAGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAG
CACGTTAGGGCACGATCCCTCGAATTTCTAAACATCAATCATCGCCTTTATTTTAAAGTTT
Found at i:39869280 original size:44 final size:44
Alignment explanation
Indices: 39869035--39870124 Score: 563
Period size: 44 Copynumber: 23.9 Consensus size: 44
39869025 TTTAATCTAT
* * *** * * *
39869035 TCCATTGCAACTTCAGGGAAATAAGATCCACTATCTTCAGTCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-CTTGTAACTTCAATCTGC
* *
39869080 TCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTCTA-CTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATC-TGC
* * * * *
39869124 CCCACTGCAACCTCAGAGG-GATTAGGTTTGCGACCTGTAGCTTCAATCTG-
1 TCCACTGCAACTTCAG-GGAGA-TA------AGACTTGTAACTTCAATCTGC
* * * * * *
39869174 TCCCACTGCGACTTTAGTGAGATAAGA-TTCACTATCTTCCATCTG-
1 T-CCACTGCAACTTCAGGGAGATAAGACTT--GTAACTTCAATCTGC
** * *
39869219 TCCCACTGTGACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
1 T-CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGC
* *
39869264 TCCACTGCAACCTCAGGGAGATAAGACTTGTAACTTCCA-CTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATC-TGC
* * * * *
39869308 CCCACTGTAACCTCAGGGAGATAAGAATTGTAACTTCCA-CTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATC-TGC
* * * * *
39869352 CCCACTGCAACCTCAGAGG-GATTAGGTTTGCGACCTGTAGCTTCAATCTG-
1 TCCACTGCAACTTCAG-GGAGA-TA------AGACTTGTAACTTCAATCTGC
* * * **
39869402 TCCCACTGCGACTTTAGTGAGATAAGA-TTCGCTGTCTTCAATCTG-
1 T-CCACTGCAACTTCAGGGAGATAAGACTT-G-TAACTTCAATCTGC
* * *
39869447 TCCCACTGCGACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
1 T-CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGC
* * * *
39869492 TCCACTGCAACTTTAGGGAGATAAGA-TTCACTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTT--GTAACTTCAATCTGC
* *
39869537 TCCACTGTAACCTT-AGGGAGATAAGACTTGTAACTTCCA-CTTGC
1 TCCACTGCAA-CTTCAGGGAGATAAGACTTGTAACTTCAATC-TGC
* * *** * *
39869581 -CCTACAGCAACCTCAAAAAGATTAGGTTTGTGACTTGTAGCTTCAATCTGC
1 TCC-ACTGCAACTTCAGGGAGA-TA------AGACTTGTAACTTCAATCTGC
* ** *
39869632 CCCACTGCAACTTCAGGGAGATAAGA-TTCGCTGTCTTCAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGACTT-G-TAACTTCAATCTGC
* * *
39869677 TCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGC
* * ** *
39869721 TCCACTGCAACTTTAGGGAGATAAG-GTTAGTGGCTTCGATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAATCTGC
* * ** **
39869765 CCCACTACAACTTCAGGGAGATAAGTTTTGCTGTCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTCAATCTGC
* * * * *
39869810 TCTACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGC
* ** *
39869854 TCCACTGCAACTTCAGGGAGATAAG-GTTAGTGGCTTCGATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAATCTGC
* * *
39869898 TCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTT-G-TAACTTCAATCTGC
*
39869943 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCTA-CTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATC-TGC
* * * * *
39869987 CCCAC-ACAAGC-TCAGAGAGATTAGGTTTGTGACTTGTAGCTTCAATCTGC
1 TCCACTGCAA-CTTCAGGGAGA-TA------AGACTTGTAACTTCAATCTGC
* **
39870037 CCCACTGCAACTTCAGGGAGATAAGA-TTCGCTGTCTTCAATCT-C
1 TCCACTGCAACTTCAGGGAGATAAGACTT-G-TAACTTCAATCTGC
*
39870081 TTCACTTCACTGCAACTTCAGGGAAATAAGACTTGTAACTTCAA
1 -T--C--CACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAA
39870125 CCTATGCTTA
Statistics
Matches: 812, Mismatches: 155, Indels: 153
0.73 0.14 0.14
Matches are distributed among these distances:
43 31 0.04
44 342 0.42
45 259 0.32
46 13 0.02
47 1 0.00
48 7 0.01
49 24 0.03
50 34 0.04
51 96 0.12
52 5 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGC
Found at i:39869286 original size:89 final size:88
Alignment explanation
Indices: 39869159--39869979 Score: 488
Period size: 89 Copynumber: 9.1 Consensus size: 88
39869149 GTTTGCGACC
* * * * * *
39869159 TGTAGCTTCAATCTG-TCCCACTGCGACTTTAGTGAGATAAGATTCACTATCTTCCATCTGTCCC
1 TGTAACTTCAATCTGCT-CCACTGCAACTTCAGGGAGATAAGATT-ACTAACTTCAATCTGTCCC
**
39869223 ACTGTGACTTCAGGGAGATAAGACT
64 ACTGCAACTTCAGGGAGATAAGACT
* * * * * *
39869248 TATAACTTCAACCTGCTCCACTGCAACCTCAGGGAGATAAGACTT-GTAACTTCCA-CTTGCCCC
1 TGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTACTAACTTCAATC-TGTCCC
* * *
39869311 ACTGTAACCTCAGGGAGATAAGAAT
64 ACTGCAACTTCAGGGAGATAAGACT
* * * * * *
39869336 TGTAACTTCCA-CTTGCCCCACTGCAACCTCAGAGG-GATTAGGTTTGCGACCTGTAGCTTCAAT
1 TGTAACTTCAATC-TGCTCCACTGCAACTTCAG-GGAGA-TAAGATT---A-C--TAACTTCAAT
* * *
39869399 CTGTCCCACTGCGACTTTAGTGAGATAAGA-T
57 CTGTCCCACTGCAACTTCAGGGAGATAAGACT
** * *
39869430 TCGCTGTCTTCAATCTG-TCCCACTGCGACTTCAGGGAGATAAGACTTA-TAACTTCAACCTG-C
1 T-G-TAACTTCAATCTGCT-CCACTGCAACTTCAGGGAGATAAGA-TTACTAACTTCAATCTGTC
*
39869492 TCCACTGCAACTTTAGGGAGATAAGA-T
62 -CCACTGCAACTTCAGGGAGATAAGACT
* * * * * *
39869519 TCACTATCTTCAGTCTGCTCCACTGTAACCTT-AGGGAGATAAGACTT-GTAACTTCCA-CT-TG
1 T--GTAACTTCAATCTGCTCCACTGCAA-CTTCAGGGAGATAAGA-TTACTAACTTCAATCTGT-
* * *** *
39869580 CCCTACAGCAACCTCAAAAAGATTAGGTTTGTGACT
61 CCC-ACTGCAACTTCAGGGAGA-TA------AGACT
* * * ** * *
39869616 TGTAGCTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGTTCTA
1 TGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-ACTAACTTCAATCTGTCCCA
39869681 CTGCAACTTCAGGGAGATAAGACT
65 CTGCAACTTCAGGGAGATAAGACT
* * * * * ** * *
39869705 TGTAACTTTAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTAGTGGCTTCGATCTGCCCCAC
1 TGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTAACTTCAATCTGTCCCAC
* **
39869770 TACAACTTCAGGGAGATAAGTTT
66 TGCAACTTCAGGGAGATAAGACT
** * * ** * *
39869793 TGCTGTCTTCAATCTGCTCTACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAACCT-ACTCC
1 TG-TAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTAACTTCAATCTGTC-CC
*
39869857 ACTGCAACTTCAGGGAGATAAG-GT
64 ACTGCAACTTCAGGGAGATAAGACT
** * * * * *
39869881 TAGTGGCTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTTAATCTG-CTC
1 T-GTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-ACTAACTTCAATCTGTC-C
39869945 CACTGCAACTTCAGGGAGATAAGACT
63 CACTGCAACTTCAGGGAGATAAGACT
39869971 TGTAACTTC
1 TGTAACTTC
39869980 TACTTGCCCC
Statistics
Matches: 572, Mismatches: 113, Indels: 94
0.73 0.15 0.12
Matches are distributed among these distances:
87 2 0.00
88 148 0.26
89 279 0.49
90 11 0.02
93 1 0.00
94 7 0.01
95 70 0.12
96 47 0.08
97 6 0.01
98 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (88 bp):
TGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTACTAACTTCAATCTGTCCCAC
TGCAACTTCAGGGAGATAAGACT
Found at i:39869489 original size:228 final size:228
Alignment explanation
Indices: 39869035--39869789 Score: 1021
Period size: 228 Copynumber: 3.3 Consensus size: 228
39869025 TTTAATCTAT
* * * * * * * * * * *
39869035 TCCATTGCAACTTCAGGGAAATAAGATCCACTATCTTCAGTCTACTCTACTGCAACTTCAGGGAG
1 TCCACTGCAACTTTAGGGAGATAAGAT-TACTAACTTCACTCTGCCCCACTGTAACCTCAGGGAG
*
39869100 ATAAGACTTGTAACTTCTACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAGC
65 ATAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAGC
* * * *
39869165 TTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCACTATCTTCCATCTGTCCCACTGTGA
130 TTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCGA
39869230 CTTCAGGGAGATAAGACTTATAACTTCAACCTGC
195 CTTCAGGGAGATAAGACTTATAACTTCAACCTGC
* * *
39869264 TCCACTGCAACCTCAGGGAGATAAGACTT-GTAACTTCCACT-TGCCCCACTGTAACCTCAGGGA
1 TCCACTGCAACTTTAGGGAGATAAGA-TTACTAACTT-CACTCTGCCCCACTGTAACCTCAGGGA
*
39869327 GATAAGAATTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAG
64 GATAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAG
39869392 CTTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCG
129 CTTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCG
39869457 ACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
194 ACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
* * * *
39869492 TCCACTGCAACTTTAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGTAACCTTAGGGAG
1 TCCACTGCAACTTTAGGGAGATAAGATT-ACTAACTTCACTCTGCCCCACTGTAACCTCAGGGAG
* * * ** * *
39869557 ATAAGACTTGTAACTTCCACTTGCCCTACAGCAACCTCAAAAAGATTAGGTTTGTGACTTGTAGC
65 ATAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAGC
* * * * * * *
39869622 TTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGTTCTACTGCAA
130 TTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCGA
* *
39869687 CTTCAGGGAGATAAGACTTGTAACTTTAACCTGC
195 CTTCAGGGAGATAAGACTTATAACTTCAACCTGC
* * ** ** *
39869721 TCCACTGCAACTTTAGGGAGATAAGGTTAGTGGCTTCGA-TCTGCCCCACTACAACTTCAGGGAG
1 TCCACTGCAACTTTAGGGAGATAAGATTACTAACTTC-ACTCTGCCCCACTGTAACCTCAGGGAG
39869785 ATAAG
65 ATAAG
39869790 TTTTGCTGTC
Statistics
Matches: 469, Mismatches: 51, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
227 2 0.00
228 239 0.51
229 227 0.48
230 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (228 bp):
TCCACTGCAACTTTAGGGAGATAAGATTACTAACTTCACTCTGCCCCACTGTAACCTCAGGGAGA
TAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAGCT
TCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCGAC
TTCAGGGAGATAAGACTTATAACTTCAACCTGC
Found at i:39869659 original size:229 final size:229
Alignment explanation
Indices: 39869035--39869745 Score: 1043
Period size: 229 Copynumber: 3.1 Consensus size: 229
39869025 TTTAATCTAT
* * * * * *
39869035 TCCATTGCAACTTCAGGGAAATAAGATCCACTATCTTCAGTCTACTCTACTGCAA-CTTCAGGGA
1 TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGTAACCTT-AGGGA
*
39869099 GATAAGACTTGTAACTTCTACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAG
65 GATAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAG
* * * *
39869164 CTTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCACTATCTTCCATCTGTCCCACTGTG
130 CTTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCG
39869229 ACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
195 ACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
* * * * * *
39869264 TCCACTGCAACCTCAGGGAGATAAGACTT--GTAACTTCCACT-TGCCCCACTGTAACCTCAGGG
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCACTATCTT-CAGTCTGCTCCACTGTAACCTTAGGG
*
39869326 AGATAAGAATTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTA
64 AGATAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTA
39869391 GCTTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGC
129 GCTTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGC
39869456 GACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
194 GACTTCAGGGAGATAAGACTTATAACTTCAACCTGC
*
39869492 TCCACTGCAACTTTAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGTAACCTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGTAACCTTAGGGAG
* * * ** * *
39869557 ATAAGACTTGTAACTTCCACTTGCCCTACAGCAACCTCAAAAAGATTAGGTTTGTGACTTGTAGC
66 ATAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAGC
* * * * * * *
39869622 TTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGTTCTACTGCAA
131 TTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCGA
* *
39869687 CTTCAGGGAGATAAGACTTGTAACTTTAACCTGC
196 CTTCAGGGAGATAAGACTTATAACTTCAACCTGC
*
39869721 TCCACTGCAACTTTAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
39869746 GTTAGTGGCT
Statistics
Matches: 434, Mismatches: 42, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
227 2 0.00
228 205 0.47
229 226 0.52
230 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (229 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGTAACCTTAGGGAG
ATAAGACTTGTAACTTCCACTTGCCCCACTGCAACCTCAGAGGGATTAGGTTTGCGACCTGTAGC
TTCAATCTGTCCCACTGCGACTTTAGTGAGATAAGATTCGCTGTCTTCAATCTGTCCCACTGCGA
CTTCAGGGAGATAAGACTTATAACTTCAACCTGC
Found at i:39869800 original size:133 final size:133
Alignment explanation
Indices: 39869209--39870127 Score: 741
Period size: 133 Copynumber: 6.7 Consensus size: 133
39869199 GATTCACTAT
* * ** * ** * *
39869209 CTTCCATCTGTCCCACTGTGACTTCAGGGAGATAAGACTT--ATAACTTCAACCTGCTCCACTGC
1 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGA-TTCGCTGTCTTCAATCTGCTCTACTGC
* * * * * * *
39869272 AACCTCAGGGAGATAAGACTTGTAACTTCCACTTGCCCCACTGTAACCTCAGGGAGATAAGAATT
65 AACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG-GTT
**
39869337 -GTAA
129 AGTGG
* * * *
39869341 CTTCCA-CTTGCCCCACTGCAACCTCAGAGG-GATTAGGTTTGCGACCTGTAGCTTCAATCTG-T
1 CTTCAATC-TGCCCCACTGCAACTTCAG-GGAGA-TAAGATT-CG--CTGT--CTTCAATCTGCT
* * * * ** * *
39869403 CCCACTGCGACTTTAGTGAGATAAGA-TTCGCTGTCTTCAATCTG-TCCCACTGCGACTTCAGGG
58 -CTACTGCAACTTCAGGGAGATAAGACTT-G-TAACTTCAACCTGCT-CCACTGCAACTTCAGGG
* **
39869466 AGATAAGACTTA-TAA
119 AGATAAG-GTTAGTGG
* * * * * * * *
39869481 CTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGATTCACTATCTTCAGTCTGCTCCACTGTA
1 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGCTCTACTGCA
* * * * *** *
39869546 ACCTT-AGGGAGATAAGACTTGTAACTTCCACTTGC-CCTACAGCAACCTCAAAAAGATTAGGTT
66 A-CTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCC-ACTGCAACTTCAGGGAGATAAGG--
*
39869609 TGTGACTTGTAG
127 T-T-A---GTGG
*
39869621 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGTTCTACTGCA
1 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGCTCTACTGCA
* *
39869686 ACTTCAGGGAGATAAGACTTGTAACTTTAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTAG
66 ACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTAG
39869751 TGG
131 TGG
* * * *
39869754 CTTCGATCTGCCCCACTACAACTTCAGGGAGATAAGTTTTGCTGTCTTCAATCTGCTCTACTGCA
1 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGCTCTACTGCA
* * *
39869819 ACTTTAGGGAGATAAGATTTGTAACTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTAG
66 ACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTAG
39869884 TGG
131 TGG
* * ** * *
39869887 CTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTTAATCTGCTCCACTGCA
1 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGCTCTACTGCA
* * * * * *
39869952 ACTTCAGGGAGATAAGACTTGTAACTTCTACTTGCCCCAC-ACAAGC-TCAGAGAGATTAGGTTT
66 ACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAA-CTTCAGGGAGATAAGG--T
*
39870015 GTGACTTGTAG
128 -T-A---GTGG
39870026 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCT-CTTCACTTCA
1 CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGC-T--C-T-A
*
39870090 CTGCAACTTCAGGGAAATAAGACTTGTAACTTCAACCT
61 CTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCT
39870128 ATGCTTATGC
Statistics
Matches: 635, Mismatches: 107, Indels: 79
0.77 0.13 0.10
Matches are distributed among these distances:
131 1 0.00
132 42 0.07
133 246 0.39
134 30 0.05
135 8 0.01
136 6 0.01
137 2 0.00
138 6 0.01
139 94 0.15
140 160 0.25
141 4 0.01
143 36 0.06
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (133 bp):
CTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCGCTGTCTTCAATCTGCTCTACTGCA
ACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTAG
TGG
Found at i:39877448 original size:31 final size:31
Alignment explanation
Indices: 39877410--39877473 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
39877400 GGTTTCTGAA
39877410 TTATGACTCTCGACGCCATTTACATTCCTGC
1 TTATGACTCTCGACGCCATTTACATTCCTGC
*
39877441 TTATGACTCTCGACGCTATTTACATTCCTGC
1 TTATGACTCTCGACGCCATTTACATTCCTGC
39877472 TT
1 TT
39877474 CATTTTTCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (31 bp):
TTATGACTCTCGACGCCATTTACATTCCTGC
Found at i:39879240 original size:24 final size:24
Alignment explanation
Indices: 39879192--39879236 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39879182 TATTTTAGCT
* *
39879192 AATTGCTCTTGCATCTGCGCTTGC
1 AATTGCTCTTGCATATGCCCTTGC
39879216 AATTGCTCTTGCATAT-CCCTT
1 AATTGCTCTTGCATATGCCCTT
39879237 TGCATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.40
Consensus pattern (24 bp):
AATTGCTCTTGCATATGCCCTTGC
Found at i:39879433 original size:20 final size:20
Alignment explanation
Indices: 39879391--39879430 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
39879381 AATGCATATC
**
39879391 ATGAAATGTAATGCAAATGA
1 ATGAAATGTAATGCAAAAAA
39879411 ATGAAATG-AATGCAAAAAA
1 ATGAAATGTAATGCAAAAAA
39879430 A
1 A
39879431 ATGCGTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (20 bp):
ATGAAATGTAATGCAAAAAA
Found at i:39888945 original size:127 final size:125
Alignment explanation
Indices: 39888671--39889122 Score: 500
Period size: 127 Copynumber: 3.6 Consensus size: 125
39888661 GTTATTCGGT
* * **
39888671 CAAACGATAAATCGAAACCCAGCATGTTAGGGCACAATTTCTCGAATTTCCAAACA-CGAAAT-A
1 CAAACGA-AAATCGAAACCCAGCACGTTAGGGCACGATCCCTCGAATTTCCAAACATC--AATCA
* ** * * ** *
39888734 TTGCCTTATTTTTTTTA-TTGAAGAAAACGTGGGCTGAATTTTAAAGGGATATTTGATTATTT-G
63 TCGCCTTA--TTTTAAAGTT-TAGAAAACGTGGACAAAATTTTAAAGGGAAATTTGATTATTTAG
*
39888797 G
125 A
* * *
39888798 CTAAATAGAAAATCGAAACCCAGCACGTTAGGGCACGATTTCC-CGAATTCCCAAACATCAATCA
1 C-AAA-CGAAAATCGAAACCCAGCACGTTAGGGCACGA-TCCCTCGAATTTCCAAACATCAATCA
*
39888862 TCGCCTCTATTTTAAAGTTTAGAAAACGTGGACAAAATTTTAAAGGAAAATTTGATTATTTAGA
63 TCGCCT-TATTTTAAAGTTTAGAAAACGTGGACAAAATTTTAAAGGGAAATTTGATTATTTAGA
* * *
39888926 CAAACGAAAGATCGAAACCCAGCAAGTTAGGGCGCGATCCCTCGAATTTCTAAACATCAATCATC
1 CAAACGAAA-ATCGAAACCCAGCACGTTAGGGCACGATCCCTCGAATTTCCAAACATCAATCATC
* * * *
39888991 GCCTTTGTTTTAAAGTTTAGAAAATGCGGACGAAATTTTAAAGGGAAATTTGATTATTTAGA
65 GCC-TTATTTTAAAGTTTAGAAAACGTGGACAAAATTTTAAAGGGAAATTTGATTATTTAGA
* * * *
39889053 CAAACGAAAGATCGAAACCCAACACGTTAGGGCACGATCCCTCAAATTTCTAAACATCAAACATC
1 CAAACGAAA-ATCGAAACCCAGCACGTTAGGGCACGATCCCTCGAATTTCCAAACATCAATCATC
39889118 GCCTT
65 GCCTT
39889123 TGTTTTATAA
Statistics
Matches: 283, Mismatches: 31, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
126 9 0.03
127 212 0.75
128 54 0.19
129 8 0.03
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (125 bp):
CAAACGAAAATCGAAACCCAGCACGTTAGGGCACGATCCCTCGAATTTCCAAACATCAATCATCG
CCTTATTTTAAAGTTTAGAAAACGTGGACAAAATTTTAAAGGGAAATTTGATTATTTAGA
Found at i:39889123 original size:127 final size:127
Alignment explanation
Indices: 39888770--39889129 Score: 519
Period size: 127 Copynumber: 2.8 Consensus size: 127
39888760 ACGTGGGCTG
* * *
39888770 AATTTTAAAGGGATATTTGATTATTT-GGCTAAATAGAAA-ATCGAAACCCAGCACGTTAGGGCA
1 AATTTTAAAGGGAAATTTGATTATTTAGAC-AAA-CGAAAGATCGAAACCCAGCACGTTAGGGCA
* * * * * *
39888833 CGATTTCC-CGAATTCCCAAACATCAATCATCGCCTCTATTTTAAAGTTTAGAAAACGTGGACAA
64 CGA-TCCCTCGAATTTCTAAACATCAATCATCGCCTTTGTTTTAAAGTTTAGAAAACGCGGACAA
* * *
39888897 AATTTTAAAGGAAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAGCAAGTTAGGGCGCG
1 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAGCACGTTAGGGCACG
* *
39888962 ATCCCTCGAATTTCTAAACATCAATCATCGCCTTTGTTTTAAAGTTTAGAAAATGCGGACGA
66 ATCCCTCGAATTTCTAAACATCAATCATCGCCTTTGTTTTAAAGTTTAGAAAACGCGGACAA
*
39889024 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAACACGTTAGGGCACG
1 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAGCACGTTAGGGCACG
* *
39889089 ATCCCTCAAATTTCTAAACATCAAACATCGCCTTTGTTTTA
66 ATCCCTCGAATTTCTAAACATCAATCATCGCCTTTGTTTTA
39889130 TAAAGCTGAC
Statistics
Matches: 210, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
126 7 0.03
127 201 0.96
128 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (127 bp):
AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAGCACGTTAGGGCACG
ATCCCTCGAATTTCTAAACATCAATCATCGCCTTTGTTTTAAAGTTTAGAAAACGCGGACAA
Found at i:39892869 original size:23 final size:24
Alignment explanation
Indices: 39892813--39892871 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
39892803 AACTTAATTA
*
39892813 TTTTATTACAAGTGTACATATATC
1 TTTTATTACAAATGTACATATATC
39892837 TATTTATTACAAATGTACCA-ATAT-
1 T-TTTATTACAAATGTA-CATATATC
39892861 TTTTATTACAA
1 TTTTATTACAA
39892872 TTGTCATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 10 0.31
24 2 0.06
25 18 0.56
26 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTTATTACAAATGTACATATATC
Found at i:39894875 original size:23 final size:21
Alignment explanation
Indices: 39894849--39894894 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
39894839 CCACCCTAGC
39894849 CTTGTCAGCCACCTGCTCCACCA
1 CTTGTCAGCCACCTG-T-CACCA
*
39894872 CTTGTCAGCTACCTGTCACCA
1 CTTGTCAGCCACCTGTCACCA
39894893 CT
1 CT
39894895 ACTTGCACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.17, C:0.43, G:0.13, T:0.26
Consensus pattern (21 bp):
CTTGTCAGCCACCTGTCACCA
Found at i:39895992 original size:23 final size:26
Alignment explanation
Indices: 39895944--39896227 Score: 86
Period size: 24 Copynumber: 11.6 Consensus size: 26
39895934 CTATTATTAT
39895944 TATTATTATTATTATACATTAGTGTA
1 TATTATTATTATTATACATTAGTGTA
39895970 TATTATT-TT-TTATTACA-TA-TGTA
1 TATTATTATTATTA-TACATTAGTGTA
* *
39895993 TATGTATATATTTTTATACA-TAGTAT-
1 TAT-TAT-TATTATTATACATTAGTGTA
** * * * *
39896019 TA-T-TTCCTAAT-TACTTTATTTTAA
1 TATTATTATTATTATACATTAGTGT-A
* * **
39896043 TATTTTTATTATATTTAC-TTTTTGTA
1 TATTATTATTAT-TATACATTAGTGTA
* *
39896069 T-TTCAATATTATTAT-TATTA-T-TA
1 TATT-ATTATTATTATACATTAGTGTA
*
39896092 TTATTATTATTATTAT-TATTA-T-TA
1 -TATTATTATTATTATACATTAGTGTA
*
39896116 TTATTATTATTATTAT-TATTA-T-TA
1 -TATTATTATTATTATACATTAGTGTA
*
39896140 TTATTATTATTATTAT-TATTA-T-TA
1 -TATTATTATTATTATACATTAGTGTA
*
39896164 TTATTATTATTATTAT-TATTA-T-TA
1 -TATTATTATTATTATACATTAGTGTA
*
39896188 TTATTATTATTATTAT-TATTA-T-TA
1 -TATTATTATTATTATACATTAGTGTA
39896212 TTATTATTATTATTAT
1 -TATTATTATTATTAT
39896228 TATTATTATT
Statistics
Matches: 222, Mismatches: 19, Indels: 36
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.01
22 7 0.03
23 10 0.05
24 143 0.64
25 16 0.07
26 29 0.13
27 11 0.05
28 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTATTATTATTATACATTAGTGTA
Found at i:39896009 original size:142 final size:140
Alignment explanation
Indices: 39895799--39896101 Score: 446
Period size: 143 Copynumber: 2.1 Consensus size: 140
39895789 TTACTTTTAC
* * *
39895799 TATTATTGTTATTATTATTATATAGTAGTGCATACTTTTTATTATATACGTATATGTATATATAT
1 TATTATTATTATTATTATTATACAGTAGTGCATACTTTTTATTACATACGTATATGTATATATAT
* * * *
39895864 TTATATATAGTATTATTT-TTTATTACTTTATTTTAATATTTTAATTATATTTTCTTTTTGTATT
66 TTATACATAGTATTATTTCCTAATTACTTTATTTTAATATTTTAATTATATTTACTTTTTGTATT
39895928 TCAATACTAT
131 TCAATACTAT
* * * *
39895938 TATTATTATTATTATTATTATACATTAGTGTATATTATTTTTTATTACATATGTATATGTATATA
1 TATTATTATTATTATTATTATACAGTAGTG--CA-TACTTTTTATTACATACGTATATGTATATA
* *
39896003 TTTTTATACATAGTATTATTTCCTAATTACTTTATTTTAATATTTTTATTATATTTACTTTTTGT
63 TATTTATACATAGTATTATTTCCTAATTACTTTATTTTAATATTTTAATTATATTTACTTTTTGT
*
39896068 ATTTCAATATTAT
128 ATTTCAATACTAT
39896081 TATTATTATTATTATTATTAT
1 TATTATTATTATTATTATTAT
39896102 TATTATTATT
Statistics
Matches: 146, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
139 27 0.18
141 1 0.01
142 46 0.32
143 72 0.49
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (140 bp):
TATTATTATTATTATTATTATACAGTAGTGCATACTTTTTATTACATACGTATATGTATATATAT
TTATACATAGTATTATTTCCTAATTACTTTATTTTAATATTTTAATTATATTTACTTTTTGTATT
TCAATACTAT
Found at i:39896059 original size:9 final size:8
Alignment explanation
Indices: 39896034--39896240 Score: 175
Period size: 9 Copynumber: 23.6 Consensus size: 8
39896024 CCTAATTACT
39896034 TTATTTTA
1 TTATTTTA
*
39896042 ATATTTTTA
1 TTA-TTTTA
39896051 TTATATTTA
1 TTAT-TTTA
*
39896060 CT-TTTT-
1 TTATTTTA
* *
39896066 GTATTTCA
1 TTATTTTA
*
39896074 ATATTATTA
1 TTATT-TTA
39896083 TTATTATTA
1 TTATT-TTA
39896092 TTATTATTA
1 TTATT-TTA
39896101 TTATTATTA
1 TTATT-TTA
39896110 TTATTATTA
1 TTATT-TTA
39896119 TTATTATTA
1 TTATT-TTA
39896128 TTATTATTA
1 TTATT-TTA
39896137 TTATTATTA
1 TTATT-TTA
39896146 TTATTATTA
1 TTATT-TTA
39896155 TTATTATTA
1 TTATT-TTA
39896164 TTATTATTA
1 TTATT-TTA
39896173 TTATTATTA
1 TTATT-TTA
39896182 TTATTATTA
1 TTATT-TTA
39896191 TTATTATTA
1 TTATT-TTA
39896200 TTATTATTA
1 TTATT-TTA
39896209 TTATTATTA
1 TTATT-TTA
39896218 TTATTATTA
1 TTATT-TTA
39896227 TTATTATTA
1 TTATT-TTA
39896236 TTATT
1 TTATT
39896241 ATTACTTTAT
Statistics
Matches: 186, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
6 1 0.01
7 6 0.03
8 8 0.04
9 171 0.92
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATTTTA
Found at i:39896263 original size:3 final size:3
Alignment explanation
Indices: 39896075--39896244 Score: 340
Period size: 3 Copynumber: 56.7 Consensus size: 3
39896065 TGTATTTCAA
39896075 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39896123 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39896171 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39896219 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
39896245 CTTTATTGTG
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 167 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39896274 original size:9 final size:9
Alignment explanation
Indices: 39896075--39896274 Score: 177
Period size: 9 Copynumber: 22.0 Consensus size: 9
39896065 TGTATTTCAA
*
39896075 TATTATTAT
1 TATTATTGT
*
39896084 TATTATTAT
1 TATTATTGT
*
39896093 TATTATTAT
1 TATTATTGT
*
39896102 TATTATTAT
1 TATTATTGT
*
39896111 TATTATTAT
1 TATTATTGT
*
39896120 TATTATTAT
1 TATTATTGT
*
39896129 TATTATTAT
1 TATTATTGT
*
39896138 TATTATTAT
1 TATTATTGT
*
39896147 TATTATTAT
1 TATTATTGT
*
39896156 TATTATTAT
1 TATTATTGT
*
39896165 TATTATTAT
1 TATTATTGT
*
39896174 TATTATTAT
1 TATTATTGT
*
39896183 TATTATTAT
1 TATTATTGT
*
39896192 TATTATTAT
1 TATTATTGT
*
39896201 TATTATTAT
1 TATTATTGT
*
39896210 TATTATTAT
1 TATTATTGT
*
39896219 TATTATTAT
1 TATTATTGT
*
39896228 TATTATTAT
1 TATTATTGT
**
39896237 TATTATTAC
1 TATTATTGT
39896246 T-TTATTGT
1 TATTATTGT
39896254 GAATATTATTGT
1 ---TATTATTGT
*
39896266 TATTTTTGT
1 TATTATTGT
39896275 GCTAATATTA
Statistics
Matches: 183, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
8 5 0.03
9 170 0.93
11 1 0.01
12 7 0.04
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.66
Consensus pattern (9 bp):
TATTATTGT
Found at i:39899846 original size:24 final size:24
Alignment explanation
Indices: 39899819--39899978 Score: 148
Period size: 24 Copynumber: 6.6 Consensus size: 24
39899809 GAAATGACCT
*
39899819 TGGCACTATGTGTGCAGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
39899843 TGGCACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGGATTTGAA
*
39899867 TAGCACTATGTGTGCGGATTT-ATA
1 TGGCACTATGTGTGCGGATTTGA-A
*
39899891 CGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* ** *
39899915 TCGTCGA-TATGTGTATGGATTATTAA
1 T-GGC-ACTATGTGTGCGGATT-TGAA
* *
39899941 -GGCACTATGTGTGCGG-GTTAACA
1 TGGCACTATGTGTGCGGATTTGA-A
*
39899964 TGGCACTATGGGTGC
1 TGGCACTATGTGTGC
39899979 AAATTTCCTT
Statistics
Matches: 111, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 87 0.78
25 15 0.14
26 4 0.04
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.34
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:39899969 original size:73 final size:72
Alignment explanation
Indices: 39899819--39899984 Score: 185
Period size: 73 Copynumber: 2.3 Consensus size: 72
39899809 GAAATGACCT
*
39899819 TGGCACTATGTGTGCAGATTTGAATGGCACTATGTGTGCGGATTTGTATAGCACTATGTGTGCGG
1 TGGCACTATGTGTGCAGATTTGAATGGCACTATGTGTACGGATTTGTATAGCACTATGTGTGCGG
* *
39899884 ATTTATA
66 ATTAACA
* * * *
39899891 CGGCACTATGTGTGCGGATTTGAATCGTCGA-TATGTGTATGGATTAT-TA-AGGCACTATGTGT
1 TGGCACTATGTGTGCAGATTTGAAT-GGC-ACTATGTGTACGGATT-TGTATA-GCACTATGTGT
*
39899953 GCGGGTTAACA
62 GCGGATTAACA
* *
39899964 TGGCACTATGGGTGCAAATTT
1 TGGCACTATGTGTGCAGATTT
39899985 CCTTGATGGA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
72 24 0.31
73 52 0.67
74 2 0.03
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (72 bp):
TGGCACTATGTGTGCAGATTTGAATGGCACTATGTGTACGGATTTGTATAGCACTATGTGTGCGG
ATTAACA
Found at i:39904230 original size:19 final size:19
Alignment explanation
Indices: 39904206--39904242 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39904196 TTAATGTGCG
*
39904206 AATATATGTATATGTGTGT
1 AATATATATATATGTGTGT
39904225 AATATATATATATGTGTG
1 AATATATATATATGTGTG
39904243 GATCGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
AATATATATATATGTGTGT
Found at i:39904516 original size:41 final size:41
Alignment explanation
Indices: 39904454--39904793 Score: 536
Period size: 41 Copynumber: 8.3 Consensus size: 41
39904444 GTTTGGAATT
* *
39904454 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
39904495 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
39904536 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
39904577 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
39904618 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
39904659 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
39904700 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
39904741 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
39904782 GGTGATCCGAAT
1 GGTGATCTGAAT
39904794 ATGATGAATT
Statistics
Matches: 271, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 271 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:39904591 original size:82 final size:82
Alignment explanation
Indices: 39904454--39904787 Score: 659
Period size: 82 Copynumber: 4.1 Consensus size: 82
39904444 GTTTGGAATT
39904454 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
39904519 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
39904536 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
39904601 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
39904618 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
39904683 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
*
39904700 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
39904765 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
39904782 GGTGAT
1 GGTGAT
39904788 CCGAATATGA
Statistics
Matches: 251, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 251 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:39910295 original size:24 final size:24
Alignment explanation
Indices: 39910268--39910359 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
39910258 AATGACCTTG
39910268 GCACTATGTGTGCGGATTTGTATA
1 GCACTATGTGTGCGGATTTGTATA
39910292 GCACTATGTGTGCGGATTTGTATA
1 GCACTATGTGTGCGGATTTGTATA
* * * **
39910316 GCAGTAAGTGTGCGGATTTATACG
1 GCACTATGTGTGCGGATTTGTATA
39910340 GCACTATGTGTGCGGATTTG
1 GCACTATGTGTGCGGATTTG
39910360 AATCGTCGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.35
Consensus pattern (24 bp):
GCACTATGTGTGCGGATTTGTATA
Found at i:39910401 original size:49 final size:48
Alignment explanation
Indices: 39910275--39910403 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 48
39910265 TTGGCACTAT
* * *
39910275 GTGTGCGGATTTGTATA-GCACTATGTGTGCGGATTTGTATAGCAGTAA
1 GTGTACGGATTTATA-AGGCACTATGTGTGCGGATTTGAATAGCAGTAA
* * * *
39910323 GTGTGCGGATTTATACGGCACTATGTGTGCGGATTTGAATCGTC-GATAT
1 GTGTACGGATTTATAAGGCACTATGTGTGCGGATTTGAATAG-CAG-TAA
*
39910372 GTGTATGGA-TTATTAAGGCACTATGTGTGCGG
1 GTGTACGGATTTA-TAAGGCACTATGTGTGCGG
39910404 GTTAACATGG
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
48 41 0.59
49 28 0.41
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.35
Consensus pattern (48 bp):
GTGTACGGATTTATAAGGCACTATGTGTGCGGATTTGAATAGCAGTAA
Found at i:39921418 original size:77 final size:77
Alignment explanation
Indices: 39921259--39921433 Score: 217
Period size: 77 Copynumber: 2.3 Consensus size: 77
39921249 TTGGTATCCT
* * ** *
39921259 GATATTTT-TATTTCTATTTTTTGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 GATATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGG
* ** *
39921323 ATCAGGCGCCGA
66 ACCACACGCCAA
* *
39921335 GGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGACCCTCGG
1 GATATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGG
* *
39921400 GCCACATGCCAA
66 ACCACACGCCAA
*
39921412 GATATTTTCAATTTTTGTTTTT
1 GATATTTTCAATTTCTGTTTTT
39921434 TAATTTTTTC
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
76 7 0.08
77 76 0.92
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (77 bp):
GATATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGG
ACCACACGCCAA
Found at i:39923600 original size:3 final size:3
Alignment explanation
Indices: 39923450--39923583 Score: 268
Period size: 3 Copynumber: 44.7 Consensus size: 3
39923440 TGTATTTCAA
39923450 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39923498 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39923546 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39923584 GTGTATATGT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 131 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39923613 original size:25 final size:25
Alignment explanation
Indices: 39923548--39923616 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
39923538 ATTATTATTA
*
39923548 TTATTATTATTATTA-T-TAT-T-A
1 TTATTATTATTATTAGTGTATATGT
39923569 TTATTATTATTATTAGTGTATATGT
1 TTATTATTATTATTAGTGTATATGT
39923594 TTATTA-TATATATATA-TGTATAT
1 TTATTATTAT-TAT-TAGTGTATAT
39923617 TTATATATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 15 0.37
22 1 0.02
23 3 0.07
24 4 0.10
25 16 0.39
26 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (25 bp):
TTATTATTATTATTAGTGTATATGT
Found at i:39923623 original size:16 final size:16
Alignment explanation
Indices: 39923602--39923634 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39923592 GTTTATTATA
39923602 TATATATATGTA-TATT
1 TATATATA-GTACTATT
39923618 TATATATAGTACTATT
1 TATATATAGTACTATT
39923634 T
1 T
39923635 TTAGTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (16 bp):
TATATATAGTACTATT
Found at i:39925101 original size:55 final size:55
Alignment explanation
Indices: 39925042--39925152 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
39925032 TTTATTTCTC
39925042 TATACATACATTGTTATATGCTTCTACGTTTAGAGTATTATTATTATTATTATTA
1 TATACATACATTGTTATATGCTTCTACGTTTAGAGTATTATTATTATTATTATTA
*
39925097 TATACATACATTGTTATATGCTTCTACGTTTCGAGTATTATTATTATTATTATTA
1 TATACATACATTGTTATATGCTTCTACGTTTAGAGTATTATTATTATTATTATTA
39925152 T
1 T
39925153 TATTTTTCTG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (55 bp):
TATACATACATTGTTATATGCTTCTACGTTTAGAGTATTATTATTATTATTATTA
Found at i:39925140 original size:3 final size:3
Alignment explanation
Indices: 39925132--39925192 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
39925122 ACGTTTCGAG
* *
39925132 TAT TAT TAT TAT TAT TAT TAT TAT T-T T-T CTGT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* *
39925176 TAG TAGA TAT TAT TAT T
1 TAT TA-T TAT TAT TAT T
39925193 TCTATTAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.06
3 43 0.88
4 3 0.06
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:39925323 original size:3 final size:3
Alignment explanation
Indices: 39925315--39925350 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39925305 ACTCATGTCG
39925315 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39925351 AACTGATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39930671 original size:6 final size:7
Alignment explanation
Indices: 39930655--39930697 Score: 59
Period size: 7 Copynumber: 5.7 Consensus size: 7
39930645 CGTTTAAGTC
39930655 AAAATTA
1 AAAATTA
39930662 AAAATTA
1 AAAATTA
39930669 AAAATCTGA
1 AAAAT-T-A
39930678 AAAATATA
1 AAAAT-TA
39930686 AAAATTA
1 AAAATTA
39930693 AAAAT
1 AAAAT
39930698 AATCATATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 19 0.58
8 7 0.21
9 7 0.21
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:39935338 original size:132 final size:130
Alignment explanation
Indices: 39935078--39935566 Score: 383
Period size: 132 Copynumber: 3.7 Consensus size: 130
39935068 TTCACGATTA
* * * * * * * * * **
39935078 TTTAAAACGAATGCGATATTCGATATTTGACAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTT
1 TTTAAAACGAAGGCAATGTTCGATGTTTGGCGATTCG-GGAATCATGCCCTATCGTGCTGGGTCG
* * ** ** * ** * *
39935143 CAATTTCTCGTTTGCTCAAAGTAATCGAA-AGTCCCTTCAAAATTTCACTCATATCTTCCAAAAA
65 CGATTTCTCATTTATTCAAAACAATCGAAGA-TCCCTTCAGAATTTCACTCACGTTTTCTAAAAA
39935207 TCC
129 -CC
** * * * *
39935210 TTTAAAACGAAGGCAATACTCGGTGTTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTCGT
1 TTTAAAACGAAGGCAATGTTCGATGTTTGGCGATTCGGGAATCATGCCCTATCGTGCTGGGTCGC
* * * * ** *
39935275 GATTTCTCATTTATTCAAAAACAATCGAATATTCTTTTAGGTTTTCACTCATGTTTAT-TAAAAA
66 GATTTCTCATTTATTC-AAAACAATCGAAGATCCCTTCAGAATTTCACTCACGTTT-TCTAAAAA
39935339 CC
129 CC
* * * * * * *
39935341 TTTCAAAACAAAGGCGATGTTCTATGTTTGGCGATTTGAGAATCGTGCCCTATCGTGCTGGGTTG
1 TTT-AAAACGAAGGCAATGTTCGATGTTTGGCGATTCGGGAATCATGCCCTATCGTGCTGGGTCG
* * * * *
39935406 CGCTTTTTCATTTATTCTAAACGATCGAAGATCCCTTCAGAATTTCATTCACGTTTTCTAAAAAC
65 CGATTTCTCATTTATTCAAAACAATCGAAGATCCCTTCAGAATTTCACTCACGTTTTCTAAAAAC
39935471 C
130 C
* *
39935472 ATTTAAAACGAAAGAAATGTTCGATGTTTGGCGATTCGGGGAAT-AGTGCCCTATCGTGCTGGGT
1 -TTTAAAACGAAGGCAATGTTCGATGTTTGGCGATTC-GGGAATCA-TGCCCTATCGTGCTGGGT
* * * *
39935536 TGCAATTTC-CAGTTTGTTCAAAATAATCGAA
63 CGCGATTTCTCA-TTTATTCAAAACAATCGAA
39935567 TGTTTCTTTG
Statistics
Matches: 282, Mismatches: 66, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
130 1 0.00
131 105 0.37
132 174 0.62
133 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (130 bp):
TTTAAAACGAAGGCAATGTTCGATGTTTGGCGATTCGGGAATCATGCCCTATCGTGCTGGGTCGC
GATTTCTCATTTATTCAAAACAATCGAAGATCCCTTCAGAATTTCACTCACGTTTTCTAAAAACC
Found at i:39936776 original size:13 final size:14
Alignment explanation
Indices: 39936755--39936788 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
39936745 CGCTGAGGTA
39936755 TTTTCAATTTATG-
1 TTTTCAATTTATGC
*
39936768 TTTTTAATTTATGC
1 TTTTCAATTTATGC
39936782 TTTTCAA
1 TTTTCAA
39936789 AAATCAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTTCAATTTATGC
Found at i:39936876 original size:89 final size:89
Alignment explanation
Indices: 39936701--39937780 Score: 1604
Period size: 89 Copynumber: 12.4 Consensus size: 89
39936691 GCTTTTCAAA
* * *
39936701 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTCAATTTA
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-
39936766 T-G---TTTTTAATTTATGCTTTTC
65 TCGTTTTTTTTAATTTATGCTTTTC
* * *
39936787 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
39936852 CGTTTTTTTTAATTTATGCTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
39936876 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
39936941 CGTTTTTTTTAATTTATGCTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
39936965 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
39937030 CGTTTTTTTTAATTTATGCTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
39937054 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
39937119 CGTTTTTTTTAATTTATGCTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
39937143 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
39937208 CGTTTTTTTTAATTTATGCTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
39937232 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA-TTT
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
39937296 C-TGTTTTTTTAATTTATGCTTTTC
66 CGT-TTTTTTTAATTTATGCTTTTC
* * * * *
39937320 AAAAATCAACTCATACTGCGAGATGTGAATTGAGCCTTAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
*
39937385 CG---TTTTTAATTTATGTTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
* * *
39937406 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
*
39937471 CG---TTTTTAATTTATGTTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
* * * *
39937492 AAAAATCAACTCATATTGC-A-A---GA---G-G--TGA-GACACGCTGAGGCATTTTCAATTTC
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
*
39937545 CTTTTTTTTTTAATTTATGCTTTTC
66 C-GTTTTTTTTAATTTATGCTTTTC
* *
39937570 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTCAA-TTT
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
* ** *
39937634 C-TGTTTTCCAATTTCTGCTTTTC
66 CGTTTTTTTTAATTTATGCTTTTC
39937657 AAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 --AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
* * *
39937722 TCCG--TTTTTCAATTTATGCTTTTA
64 TTCGTTTTTTTTAATTTATGCTTTTC
* * * * *
39937746 AAAAACCAACCCATATTGTGAGAAGTGAGTTGAGC
1 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGC
39937781 ATTGGCTCAC
Statistics
Matches: 925, Mismatches: 42, Indels: 53
0.91 0.04 0.05
Matches are distributed among these distances:
74 25 0.03
75 2 0.00
77 1 0.00
78 37 0.04
79 1 0.00
80 1 0.00
81 2 0.00
83 2 0.00
84 1 0.00
85 2 0.00
86 181 0.20
87 50 0.05
88 82 0.09
89 517 0.56
90 21 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (89 bp):
AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
CGTTTTTTTTAATTTATGCTTTTC
Found at i:39937537 original size:74 final size:75
Alignment explanation
Indices: 39937446--39937598 Score: 227
Period size: 78 Copynumber: 2.0 Consensus size: 75
39937436 TGAGCCTCAG
* * *
39937446 GACACGCTGAGGTATTTTCAATTTCC-GTTTTTAATTTATGTTTTTCAAAAATCAACTCATATTG
1 GACACGCTGAGGCATTTTCAATTTCCTGTTTTTAATTTATGCTTTTCAAAAATCAACTCATACTG
39937510 CAAGAGGTGA
66 CAAGAGGTGA
*
39937520 GACACGCTGAGGCATTTTCAATTTCCTTTTTTTTTTAATTTATGCTTTTCAAAAATCAACTCATA
1 GACACGCTGAGGCATTTTCAATTTCC---TGTTTTTAATTTATGCTTTTCAAAAATCAACTCATA
*
39937585 CTGCGAGAGGTGA
63 CTGCAAGAGGTGA
39937598 G
1 G
39937599 TTGAGCCTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
74 25 0.36
78 45 0.64
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (75 bp):
GACACGCTGAGGCATTTTCAATTTCCTGTTTTTAATTTATGCTTTTCAAAAATCAACTCATACTG
CAAGAGGTGA
Found at i:39937584 original size:164 final size:162
Alignment explanation
Indices: 39937362--39937687 Score: 476
Period size: 164 Copynumber: 2.0 Consensus size: 162
39937352 AGCCTTAGGG
* * *
39937362 CACGCTGAGGTATTTTCAATTTCCGTTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGCAA
1 CACGCTGAGGCATTTTCAATTTCCGTTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCAA
* * *
39937427 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCCGTTTT-TAATTTATGTTTTT
66 GAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATTTCCGTTTTCCAATTTATGCTTTT
*
39937491 C-AAAAATCAACTCATATTGCAAGAGGTGAGA
131 CAAAAAATCAACTCATACTGCAAGAGGTGAGA
*
39937522 CACGCTGAGGCATTTTCAATTTCCTTTTTTTTTTAATTTATGCTTTTCAAAAATCAACTCATACT
1 CACGCTGAGGCATTTTCAATTTCC----GTTTTTAATTTATGCTTTTCAAAAATCAACTCATACT
* * * *
39937587 GCGAGAGGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGC
62 GCAAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATTTCCGTTTTCCAATTTATGC
*
39937652 TTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAG
127 TTTTC-AAAAAATCAACTCATACTGCAAGAGGTGAG
39937688 TTGAGCCTCA
Statistics
Matches: 146, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
160 23 0.16
164 84 0.58
165 12 0.08
167 27 0.18
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (162 bp):
CACGCTGAGGCATTTTCAATTTCCGTTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCAA
GAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTCAATTTCCGTTTTCCAATTTATGCTTTT
CAAAAAATCAACTCATACTGCAAGAGGTGAGA
Found at i:39937647 original size:14 final size:15
Alignment explanation
Indices: 39937624--39937656 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39937614 CGCCGAGGTA
39937624 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39937637 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39937652 TTTTC
1 TTTTC
39937657 AAAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39937797 original size:89 final size:87
Alignment explanation
Indices: 39937520--39937868 Score: 353
Period size: 89 Copynumber: 3.9 Consensus size: 87
39937510 CAAGAGGTGA
* * * *
39937520 GACACGCTGAGGCATTTTCAATTTCCTTTTTTTTTTAATTTATGCTTTTCAAAAATCAACTCATA
1 GACACGCTGAGGTATTTTCAATTTCC---GTTTTTCAATTTATGCTTTTAAAAAATCAACTCATA
39937585 CTGCGAGAGGTGAGTTGAGCCTCAG
63 CTGCGAGAGGTGAGTTGAGCCTCAG
* * * * *
39937610 GGCACGCCGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTCAAAAAAATCAACTCATAC
1 GACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTTT--AAAAAATCAACTCATAC
39937675 TGCGAGAGGTGAGTTGAGCCTCAG
64 TGCGAGAGGTGAGTTGAGCCTCAG
* * *
39937699 GACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTTTAAAAAACCAACCCATATTG
1 GACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTTTAAAAAATCAACTCATACTG
* * * *
39937764 TGAGAAGTGAGTTGAGCAT-TG
66 CGAGAGGTGAGTTGAGCCTCAG
* * * * * * * *
39937785 GCTCACGTGCTGAGCTATTTTCAATTTCTGTTTTT-AATGTCTG-TATTTAAAGAGTCAATTCAT
1 G-ACAC--GCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCT-TTTAAAAAATCAACTCAT
* **
39937848 ATTGCGAGAAATGAGTTGAGC
62 ACTGCGAGAGGTGAGTTGAGC
39937869 TCAAGATCAC
Statistics
Matches: 220, Mismatches: 33, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
86 2 0.01
87 52 0.24
88 38 0.17
89 106 0.48
90 22 0.10
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (87 bp):
GACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTTTAAAAAATCAACTCATACTG
CGAGAGGTGAGTTGAGCCTCAG
Found at i:39939682 original size:25 final size:25
Alignment explanation
Indices: 39939651--39939700 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
39939641 TTTTTGTTTC
*
39939651 ATTATTAAAAATTGTTATTATTATT
1 ATTATTAAAAATTGTCATTATTATT
*
39939676 ATTATTAAATATTGTCATTATTATT
1 ATTATTAAAAATTGTCATTATTATT
39939701 CTAATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
ATTATTAAAAATTGTCATTATTATT
Found at i:39939688 original size:19 final size:20
Alignment explanation
Indices: 39939666--39939712 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
39939656 TAAAAATTGT
39939666 TATTATTATTATTATT-AAA
1 TATTATTATTATTATTCAAA
* * *
39939685 TATTGTCATTATTATTCTAA
1 TATTATTATTATTATTCAAA
39939705 TATTATTA
1 TATTATTA
39939713 ATGTTATCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTATTATTATTATTCAAA
Found at i:39939998 original size:23 final size:23
Alignment explanation
Indices: 39939960--39940028 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
39939950 TATTATACAT
39939960 GTATATATAT-ATATATATTTTTA
1 GTATAT-TATCATATATATTTTTA
39939983 GTA-ATTATCATA-ATATTTTCTTA
1 GTATATTATCATATATA-TTT-TTA
* * *
39940006 TTATATTATTATGTATATTTTTA
1 GTATATTATCATATATATTTTTA
39940029 ATACCATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
21 6 0.16
22 8 0.21
23 11 0.29
24 10 0.26
25 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (23 bp):
GTATATTATCATATATATTTTTA
Found at i:39951154 original size:18 final size:18
Alignment explanation
Indices: 39951131--39951166 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39951121 GATTCTCAAT
39951131 GAGATGGATGGGAAAGAG
1 GAGATGGATGGGAAAGAG
39951149 GAGATGGATGGGAAAGAG
1 GAGATGGATGGGAAAGAG
39951167 TTACCGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.50, T:0.11
Consensus pattern (18 bp):
GAGATGGATGGGAAAGAG
Found at i:39952362 original size:87 final size:81
Alignment explanation
Indices: 39952316--39953005 Score: 694
Period size: 87 Copynumber: 8.0 Consensus size: 81
39952306 TGCGAGAGGT
* *
39952316 GAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTTTTCCAATTTCTGCTT
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA---TT-TTTT--AATTTATGCTT
* *
39952381 TTCAAAAAAATCAACTCATATTAC
60 TTC--AAAAATCAACTCATACTGC
*
39952405 AAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCCGTTTTTTTAATTTATGCT
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA-------TTTTTTAATTTATGCT
*
39952470 TTTCAAAAATCGACTCATACTGC
59 TTTCAAAAATCAACTCATACTGC
* *
39952493 GAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC--------AATTTCTGCTTTTCAAA
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTTAATTTATGCTTTTC--A
*
39952550 AAAATTCAACTCATATTGC
64 AAAA-TCAACTCATACTGC
*
39952569 AAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCCATTTTTAATTTATGCTTT
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA--T---TTTTTAATTTATGCTTT
*
39952634 TCAAAAATCAACTCATATTGC
61 TCAAAAATCAACTCATACTGC
* *
39952655 AAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCCAATTTCCGTTTTTTTAATTTATGCT
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA-------TTTTTTAATTTATGCT
39952720 TTTCAAAAATCAACTCATACTGC
59 TTTCAAAAATCAACTCATACTGC
* *
39952743 GAGAGGTGAGTTGAGCCTCAGGATACGCTGATGTATTTTCAATTTCCGTTTTTTAATTTATGCTT
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA------TTTTTTAATTTATGCTT
*
39952808 TTCAAAAATCGACTCATACTGC
60 TTCAAAAATCAACTCATACTGC
* *
39952830 GAGAGGTGAGTTGAGCCTCAGGATACGCTGATGTATTTTCAATTTCCGTTTTTTAATTTATGCTT
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA------TTTTTTAATTTATGCTT
*
39952895 TTCAAAAATCGACTCATACTGC
60 TTCAAAAATCAACTCATACTGC
* *
39952917 GAGAGGTGAGTTGAGCCTCAGGATACGCTGATGTATTTTCAATTTCCGTTTTTTAATTTATGCTT
1 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA------TTTTTTAATTTATGCTT
*
39952982 TTCAAAAATCGACTCATACTGC
60 TTCAAAAATCAACTCATACTGC
39953004 GA
1 GA
39953006 TTTTCCAATT
Statistics
Matches: 549, Mismatches: 27, Indels: 52
0.87 0.04 0.08
Matches are distributed among these distances:
73 13 0.02
75 5 0.01
76 50 0.09
86 55 0.10
87 222 0.40
88 129 0.23
89 53 0.10
90 13 0.02
91 2 0.00
92 4 0.01
93 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (81 bp):
GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTTAATTTATGCTTTTCAAA
AATCAACTCATACTGC
Found at i:39952520 original size:88 final size:88
Alignment explanation
Indices: 39952185--39952548 Score: 466
Period size: 88 Copynumber: 4.1 Consensus size: 88
39952175 TGCCGAGGTA
* *
39952185 TTTTCAATTTATG--TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATAC
1 TTTTCAATTTATGCTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
39952248 GCTGATGTATTTTCAATTTCCGT
66 GCTGAGGTATTTTCAATTTCCGT
*
39952271 TTTTTAATTTATGCTTTTC-AAAAATCAACTCATACTGCGAGAGGTGAGAGGTGAGTTGAGCCTC
1 TTTTCAATTTATGCTTTTCAAAAAATCAACTCATACTGC-------GAGAGGTGAGTTGAGCCTC
* **
39952335 AGGGCACGCTGAGGTATTTTCAATTTTTGT
59 AGGACACGCTGAGGTATTTTCAATTTCCGT
* * * * *
39952365 TTTCCAATTTCTGCTTTTCAAAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTATGCTTTTC-AAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACA
39952430 CGCTGAGGTATTTTCAATTTCCGTT
65 CGCTGAGGTATTTTCAATTTCCG-T
* * *
39952455 TTTTTAATTTATGCTTTTC-AAAAATCGACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TTTTCAATTTATGCTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *
39952519 GCTGAGGTATTTTCAATTTCTGC
66 GCTGAGGTATTTTCAATTTCCGT
39952542 TTTTCAA
1 TTTTCAA
39952549 AAAAATTCAA
Statistics
Matches: 239, Mismatches: 27, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
86 12 0.05
87 24 0.10
88 65 0.27
89 44 0.18
90 17 0.07
94 60 0.25
96 17 0.07
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (88 bp):
TTTTCAATTTATGCTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTATTTTCAATTTCCGT
Found at i:39952583 original size:76 final size:75
Alignment explanation
Indices: 39952455--39952700 Score: 271
Period size: 86 Copynumber: 3.1 Consensus size: 75
39952445 AATTTCCGTT
* * * * * *
39952455 TTTTTAATTTATGCTTTTC--AAAAATCGACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACA
39952518 CGCTGAGGTA
66 CGCTGAGGTA
39952528 TTTTCAATTTCTGCTTTTCAAAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGAC
1 TTTTCAATTTCTGCTTTTCAAAAAAA-TCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGAC
39952593 ACGCTGAGGTA
65 ACGCTGAGGTA
** **
39952604 TTTTCAATTTCCATTTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGA
1 TTTTCAATTT-C-----TGCTTT-T-C---AAAAAAATCAACTCATATTGCAAGAGGTGAGTTGA
39952669 GCCTCAGGACACGCTGAGGTA
55 GCCTCAGGACACGCTGAGGTA
*
39952690 TTTCCAATTTC
1 TTTTCAATTTC
39952701 CGTTTTTTTA
Statistics
Matches: 148, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
73 17 0.11
75 5 0.03
76 55 0.37
77 1 0.01
82 4 0.03
83 1 0.01
84 1 0.01
85 1 0.01
86 58 0.39
87 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (75 bp):
TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTA
Found at i:39952771 original size:88 final size:87
Alignment explanation
Indices: 39952528--39953005 Score: 778
Period size: 87 Copynumber: 5.5 Consensus size: 87
39952518 CGCTGAGGTA
* * * * *
39952528 TTTTCAATTTCTGCTTTTCAAAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGAC
1 TTTTTAATTTATGCTTTTC--AAAAA-TCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGAT
* *
39952593 ACGCTGAGGTATTTTCAATTTCC-A
63 ACGCTGATGTATTTTCAATTTCCGT
* * *
39952617 TTTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
* *
39952682 CTGAGGTATTTCCAATTTCCGTT
66 CTGATGTATTTTCAATTTCCG-T
39952705 TTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
1 TTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
39952770 CTGATGTATTTTCAATTTCCGT
66 CTGATGTATTTTCAATTTCCGT
*
39952792 TTTTTAATTTATGCTTTTCAAAAATCGACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
1 TTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
39952857 CTGATGTATTTTCAATTTCCGT
66 CTGATGTATTTTCAATTTCCGT
*
39952879 TTTTTAATTTATGCTTTTCAAAAATCGACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
1 TTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
39952944 CTGATGTATTTTCAATTTCCGT
66 CTGATGTATTTTCAATTTCCGT
*
39952966 TTTTTAATTTATGCTTTTCAAAAATCGACTCATACTGCGA
1 TTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGA
39953006 TTTTCCAATT
Statistics
Matches: 377, Mismatches: 10, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
86 60 0.16
87 219 0.58
88 81 0.21
89 17 0.05
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (87 bp):
TTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACG
CTGATGTATTTTCAATTTCCGT
Found at i:39953192 original size:14 final size:15
Alignment explanation
Indices: 39953169--39953201 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39953159 CGATGAGGTA
39953169 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39953182 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39953197 TTTTC
1 TTTTC
39953202 AAAAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39953200 original size:217 final size:218
Alignment explanation
Indices: 39952811--39953206 Score: 643
Period size: 217 Copynumber: 1.8 Consensus size: 218
39952801 TATGCTTTTC
* * * * *
39952811 AAAAATCGACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGATACGCTGATGTATTTTCAATTTC
1 AAAAATCAACTCATACTACAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
39952876 CGTTTTTTAATTTATGCTTTTCAAAAATCGACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGAT
66 CGATTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGAT
* * **
39952941 ACGCTGATGTATTTTCAATTTCCGTTTTTTAATTTATGCTTTTCAAAAATCGACTCATACTGCGA
131 ACGATGAGGTATTTTCAATTTCCGTTTTCCAATTTATGCTTTTCAAAAATCGACTCATACTGCGA
39953006 TTTTCCAATTTCTGCTTTTCAAA
196 TTTTCCAATTTCTGCTTTTCAAA
*
39953029 AAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATACTACAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
39953094 C-ATTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG-
66 CGATTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTC-AGGA
* *
39953157 TACGATGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTCAAAAA
130 TACGATGAGGTATTTTCAATTTCCGTTTTCCAATTTATGCTTTTCAAAAA
39953207 AAATCAACTC
Statistics
Matches: 163, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
217 100 0.61
218 63 0.39
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (218 bp):
AAAAATCAACTCATACTACAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
CGATTTTTAATTTATGCTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGAT
ACGATGAGGTATTTTCAATTTCCGTTTTCCAATTTATGCTTTTCAAAAATCGACTCATACTGCGA
TTTTCCAATTTCTGCTTTTCAAA
Found at i:39953344 original size:88 final size:87
Alignment explanation
Indices: 39953029--39954849 Score: 2288
Period size: 88 Copynumber: 20.4 Consensus size: 87
39953019 GCTTTTCAAA
*
39953029 AAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*
39953094 C-ATTTTTAATTTATGCTTTTC
66 CGTTTTTTAATTTATGCTTTTC
* * * *
39953115 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG-TACGATGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTT
* ** *
39953179 CTGTTTTCCAATTTCTGCTTTTC
65 CCGTTTTTTAATTTATGCTTTTC
*
39953202 AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCCAAT
1 ---AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
39953267 TTCCGTTTTTTTAATTTATGCTTTTC
63 TTCCG-TTTTTTAATTTATGCTTTTC
* * *
39953293 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG-CACGATGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTT
* ** *
39953357 CTGTTTTCCAATTTCTGCTTTTC
65 CCGTTTTTTAATTTATGCTTTTC
* *
39953380 AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGATACGCTAAGGTATTTTCAAT
1 ---AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
39953445 TTCCGTTTTTTTAATTTATGCTTTTC
63 TTCCG-TTTTTTAATTTATGCTTTTC
* * *
39953471 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
39953536 CGTTTTTTTAATTTATGCTTTTC
66 CG-TTTTTTAATTTATGCTTTTC
* * *
39953559 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
39953624 CGTTTTTTTAATTTATGCTTTTC
66 CG-TTTTTTAATTTATGCTTTTC
* * *
39953647 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGATACGCTAAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
39953712 CGTTTTTTTAATTTATGCTTTTC
66 CG-TTTTTTAATTTATGCTTTTC
* * * *
39953735 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG-TACGATGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTT
* ** *
39953799 CTGTTTTCCAATTTCTGCTTTTC
65 CCGTTTTTTAATTTATGCTTTTC
*
39953822 AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCCAAT
1 ---AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
39953887 TTCCGTTTTTTTAATTTATGCTTTTC
63 TTCCG-TTTTTTAATTTATGCTTTTC
* * * *
39953913 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG-TACGATGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTT
* ** *
39953977 CTGTTTTCCAATTTCTGCTTTTC
65 CCGTTTTTTAATTTATGCTTTTC
*
39954000 AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCCCAGTTGAGCCTCAGGACACGCTGAT
1 ---AAAAATCAACTCATATTGCAAGA---G-G-T--G----AGTTGAGCCTCAGGACACGCTGAG
39954065 GTATTTTCAATTTCCG-TTTTTAATTTATGCTTTTC
52 GTATTTTCAATTTCCGTTTTTTAATTTATGCTTTTC
* * *
39954100 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
39954165 CGTTTTTTTAATTTATGCTTTTC
66 CG-TTTTTTAATTTATGCTTTTC
* * * ** *
39954188 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGGCTTGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* ** *
39954253 TGTTTTCCAATTTCTGCTTTTC
66 CGTTTTTTAATTTATGCTTTTC
*
39954275 AAAAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
1 ----AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
* ** *
39954340 TTTCTGTTTTCCAATTTCTGCTTTTC
62 TTTCCGTTTTTTAATTTATGCTTTTC
*
39954366 AAAAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
1 ----AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
39954431 TTTCCGTTTTTTTTTAATTTATGCTTTTC
62 TTTCCG---TTTTTTAATTTATGCTTTTC
* * * * *
39954460 AAAAATTAACTCATACTGCGAGAGGTGAGTTGAGCCTAAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* ** *
39954525 TGTTTTCCAATTTCTGCTTTTC
66 CGTTTTTTAATTTATGCTTTTC
* *
39954547 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 --AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
39954612 TCCGTTTTTTTTTAATTTATGCTTTTC
64 TCCG---TTTTTTAATTTATGCTTTTC
* * * * *
39954639 AAAAATTAACTCATACTGCGAGAGGTGAGTTGAGCCTAAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* ** *
39954704 TGTTTTCCAATTTCTGCTTTTC
66 CGTTTTTTAATTTATGCTTTTC
* *
39954726 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 --AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
39954791 TCCGTTTTTCAATTTATGCTTTTC
64 TCCGTTTTTTAATTTATGCTTTTC
* * *
39954815 AAAAACCAA-TCCATATTGCGAGAAGTGAGTTGAGC
1 AAAAATCAACT-CATATTGCAAGAGGTGAGTTGAGC
39954850 ATTGGCTCAC
Statistics
Matches: 1539, Mismatches: 144, Indels: 103
0.86 0.08 0.06
Matches are distributed among these distances:
86 94 0.06
87 151 0.10
88 507 0.33
89 158 0.10
90 314 0.20
91 201 0.13
92 18 0.01
93 1 0.00
94 19 0.01
95 1 0.00
97 24 0.02
100 19 0.01
101 32 0.02
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
CGTTTTTTAATTTATGCTTTTC
Found at i:39953361 original size:178 final size:175
Alignment explanation
Indices: 39953029--39954849 Score: 2273
Period size: 178 Copynumber: 10.2 Consensus size: 175
39953019 GCTTTTCAAA
*
39953029 AAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * * *
39953094 CATTTT-TAATTTATGCTTTTC-AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG
66 CGTTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGG
* * ** *
39953157 -TACGATGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTC
130 ACACGCTGAGGTATTTTCAATTTCTGTTTTTTAATTTATGCTTTTC
*
39953202 AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCCAAT
1 ---AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
** * *
39953267 TTCCGTTTTTTTAATTTATGCTTTTC-AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTC
63 TTCCG-TTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
* ** *
39953331 AAGG-CACGATGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTC
127 -AGGACACGCTGAGGTATTTTCAATTTCTGTTTTTTAATTTATGCTTTTC
* *
39953380 AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGATACGCTAAGGTATTTTCAAT
1 ---AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
** *
39953445 TTCCGTTTTTTTAATTTATGCTTTTC-AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTC
63 TTCCG-TTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
*
39953509 AGGACACGCTAAGGTATTTTCAATTT-TCGTTTTTTTAATTTATGCTTTTC
127 AGGACACGCTGAGGTATTTTCAATTTCT-G-TTTTTTAATTTATGCTTTTC
* * *
39953559 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
** *
39953624 CGTTTTTTTAATTTATGCTTTTC-AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGG
66 CG-TTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG
* * *
39953688 ATACGCTAAGGTATTTTCAATTTCCGTTTTTTTAATTTATGCTTTTC
130 ACACGCTGAGGTATTTTCAATTTCTG-TTTTTTAATTTATGCTTTTC
* * * *
39953735 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG-TACGATGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTT
* *
39953799 CTGTTTTCCAATTTCTGCTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCA
65 CCGTTTTCCAATTTATGCTTTTC--AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCA
* *
39953864 GGACACGCTGAGGTATTTCCAATTTCCGTTTTTTTAATTTATGCTTTTC
128 GGACACGCTGAGGTATTTTCAATTTCTG-TTTTTTAATTTATGCTTTTC
* * * *
39953913 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAAGG-TACGATGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTT
* *
39953977 CTGTTTTCCAATTTCTGCTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCCCA
65 CCGTTTTCCAATTTATGCTTTTC--AAAAAATCAACTCATATTGCAAGA---G-G-T--G----A
* *
39954042 GTTGAGCCTCAGGACACGCTGATGTATTTTCAATTTCCG-TTTTTAATTTATGCTTTTC
117 GTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTTAATTTATGCTTTTC
* * *
39954100 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
** * *
39954165 CGTTTTTTTAATTTATGCTTTTC-AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGG
66 CG-TTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG
* ** * ** *
39954229 GCTTGTTGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTC
130 ACACGCTGAGGTATTTTCAATTTCTGTTTTTTAATTTATGCTTTTC
*
39954275 AAAAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
1 ----AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
* * *
39954340 TTTCTGTTTTCCAATTTCTGCTTTTCAAAAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGC
62 TTTCCGTTTTCCAATTTATGCTTTTC---AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGC
*
39954405 CTCAGGACACGCTGAGGTATTTTCAATTTCCGTTTTTTTTTAATTTATGCTTTTC
124 CTCAGGACACGCTGAGGTATTTTCAATTT-C--TGTTTTTTAATTTATGCTTTTC
* * * * *
39954460 AAAAATTAACTCATACTGCGAGAGGTGAGTTGAGCCTAAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * * *
39954525 TGTTTTCCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG
66 CGTTTTCCAATTTATGCTTTTC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG
*
39954590 ACACGCTGAGGTATTTTCAATTTCCGTTTTTTTTTAATTTATGCTTTTC
130 ACACGCTGAGGTATTTTCAATTT-C--TGTTTTTTAATTTATGCTTTTC
* * * * *
39954639 AAAAATTAACTCATACTGCGAGAGGTGAGTTGAGCCTAAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * * *
39954704 TGTTTTCCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG
66 CGTTTTCCAATTTATGCTTTTC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG
* *
39954769 ACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTTTC
130 ACACGCTGAGGTATTTTCAATTTCTGTTTTTTAATTTATGCTTTTC
* * *
39954815 AAAAACCAA-TCCATATTGCGAGAAGTGAGTTGAGC
1 AAAAATCAACT-CATATTGCAAGAGGTGAGTTGAGC
39954850 ATTGGCTCAC
Statistics
Matches: 1515, Mismatches: 94, Indels: 72
0.90 0.06 0.04
Matches are distributed among these distances:
174 34 0.02
175 34 0.02
176 337 0.22
177 11 0.01
178 461 0.30
179 321 0.21
180 1 0.00
181 83 0.05
182 59 0.04
183 2 0.00
185 40 0.03
186 3 0.00
187 74 0.05
188 17 0.01
189 38 0.03
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (175 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
CGTTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGA
CACGCTGAGGTATTTTCAATTTCTGTTTTTTAATTTATGCTTTTC
Found at i:39953370 original size:14 final size:15
Alignment explanation
Indices: 39953347--39953379 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39953337 CGATGAGGTA
39953347 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39953360 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39953375 TTTTC
1 TTTTC
39953380 AAAAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39953812 original size:14 final size:15
Alignment explanation
Indices: 39953789--39953821 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39953779 CGATGAGGTA
39953789 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39953802 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39953817 TTTTC
1 TTTTC
39953822 AAAAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39953990 original size:14 final size:15
Alignment explanation
Indices: 39953967--39953999 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39953957 CGATGAGGTA
39953967 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39953980 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39953995 TTTTC
1 TTTTC
39954000 AAAAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39954265 original size:14 final size:15
Alignment explanation
Indices: 39954242--39954274 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39954232 TGTTGAGGTA
39954242 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39954255 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39954270 TTTTC
1 TTTTC
39954275 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39954356 original size:14 final size:15
Alignment explanation
Indices: 39954333--39954365 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39954323 CGCTGAGGTA
39954333 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39954346 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39954361 TTTTC
1 TTTTC
39954366 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39954537 original size:14 final size:15
Alignment explanation
Indices: 39954514--39954546 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39954504 CGCTGAGGTA
39954514 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39954527 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39954542 TTTTC
1 TTTTC
39954547 AAAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39954716 original size:14 final size:15
Alignment explanation
Indices: 39954693--39954725 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39954683 CGCTGAGGTA
39954693 TTTT-CAATTTCTG-
1 TTTTCCAATTTCTGC
39954706 TTTTCCAATTTCTGC
1 TTTTCCAATTTCTGC
39954721 TTTTC
1 TTTTC
39954726 AAAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCCAATTTCTGC
Found at i:39954888 original size:89 final size:87
Alignment explanation
Indices: 39954041--39954937 Score: 1061
Period size: 89 Copynumber: 10.1 Consensus size: 87
39954031 GTTGAGCCCC
* *
39954041 AGTTGAGCCTCAGGACACGCTGATGTATTTTCAATTTCCGTTTTT-AATTTATGCTTTTCAAAAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCTTTTCAAAAA
* *
39954105 TCAACTCATATTGCAAGAGATG
66 TCAACTCATATTGCGAGAGGTG
* *
39954127 AGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTT-TCGTTTTTTTAATTTATGCTTTTCAAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-G-TTTTTCAATTTATGCTTTTCAAA
*
39954191 AATCAACTCATACTGCGAGAGGTG
64 AATCAACTCATATTGCGAGAGGTG
* ** * * *
39954215 AGTTGAGCCTCAGGGCTTGTTGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTCAAAAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCTTTTC----A
**
39954280 AAAATCAACTCATATTGTAAGAGGTG
62 AAAATCAACTCATATTGCGAGAGGTG
* *
39954306 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTCAAAAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCTTTTC----A
**
39954371 AAAATCAACTCATATTGTAAGAGGTG
62 AAAATCAACTCATATTGCGAGAGGTG
* *
39954397 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCCGTTTTTTTTTAATTTATGCTTTTCAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-C--TGTTTTTCAATTTATGCTTTTCAA
* *
39954462 AAATTAACTCATACTGCGAGAGGTG
63 AAATCAACTCATATTGCGAGAGGTG
* * * *
39954487 AGTTGAGCCTAAGGGCACGCTGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTCAAAAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCTTTTC--AAA
*
39954552 AATCAACTCATATTGCGAGAGGCG
64 AATCAACTCATATTGCGAGAGGTG
* *
39954576 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCCGTTTTTTTTTAATTTATGCTTTTCAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-C--TGTTTTTCAATTTATGCTTTTCAA
* *
39954641 AAATTAACTCATACTGCGAGAGGTG
63 AAATCAACTCATATTGCGAGAGGTG
* * * *
39954666 AGTTGAGCCTAAGGGCACGCTGAGGTATTTTCAATTTCTGTTTTCCAATTTCTGCTTTTCAAAAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCTTTTC--AAA
*
39954731 AATCAACTCATATTGCGAGAGGCG
64 AATCAACTCATATTGCGAGAGGTG
*
39954755 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATTTATGCTTTTCAAAAA
1 AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCTTTTCAAAAA
* *
39954820 CCAA-TCCATATTGCGAGAAGTG
66 TCAACT-CATATTGCGAGAGGTG
* * * * * *
39954842 AGTTGAGCAT-TGGCTCACGTGCTGAGCTATTTTCAATTTCTGTTTTT-AATGTCTG-TATTT-A
1 AGTTGAGCCTCAGG-ACAC--GCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCT-TTTCA
* * **
39954903 AAGAGTCAATTCATATTGCGAGAAATG
62 AA-AATCAACTCATATTGCGAGAGGTG
39954930 AGTTGAGC
1 AGTTGAGC
39954938 TCAAGATCAC
Statistics
Matches: 712, Mismatches: 74, Indels: 48
0.85 0.09 0.06
Matches are distributed among these distances:
86 39 0.05
87 96 0.13
88 107 0.15
89 167 0.23
90 118 0.17
91 148 0.21
92 19 0.03
94 18 0.03
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (87 bp):
AGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGCTTTTCAAAAA
TCAACTCATATTGCGAGAGGTG
Found at i:39956755 original size:16 final size:16
Alignment explanation
Indices: 39956716--39956771 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
39956706 TGTTTTCAAC
*
39956716 ATTATTATTATGTATGT
1 ATTA-TATTATGTAAGT
*
39956733 A-TATATTATGTAAAT
1 ATTATATTATGTAAGT
39956748 ATTATATTATGTAAGT
1 ATTATATTATGTAAGT
39956764 ATGTATAT
1 AT-TATAT
39956772 ATATATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.32
16 17 0.50
17 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (16 bp):
ATTATATTATGTAAGT
Found at i:39958561 original size:6 final size:6
Alignment explanation
Indices: 39958550--39958577 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39958540 TATTGGGTCT
39958550 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
39958578 GGTATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:39963469 original size:22 final size:21
Alignment explanation
Indices: 39963435--39963484 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
39963425 TTTAAAAATA
39963435 TTTTTTTTAATTATTT-TATT
1 TTTTTTTTAATTATTTCTATT
*
39963455 TTTTCTTTTACATTATTTCTCTT
1 TTTT-TTTTA-ATTATTTCTATT
39963478 TTTTTTT
1 TTTTTTT
39963485 CTTTTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 10 0.38
23 7 0.27
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTTTAATTATTTCTATT
Found at i:39969019 original size:22 final size:21
Alignment explanation
Indices: 39968991--39969058 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 21
39968981 AGACTCACCA
39968991 TAGCTCGTATGAGCTTACTGTT
1 TAGCTCG-ATGAGCTTACTGTT
*
39969013 TAGCTCGATAGAGCTTACCGTT
1 TAGCTCGAT-GAGCTTACTGTT
*
39969035 TCAGCTCAATGAAGCTTACTGTT
1 T-AGCTCGATG-AGCTTACTGTT
39969058 T
1 T
39969059 TCAGCTCACC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 2 0.05
22 20 0.50
23 18 0.45
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (21 bp):
TAGCTCGATGAGCTTACTGTT
Found at i:39969145 original size:23 final size:23
Alignment explanation
Indices: 39969001--39969155 Score: 121
Period size: 23 Copynumber: 6.9 Consensus size: 23
39968991 TAGCTCGTAT
*
39969001 GAGCTTACTGTTT-AGCTCGATA
1 GAGCTTACTGTTTCAGCTCAATA
*
39969023 GAGCTTACCGTTTCAGCTCAAT-
1 GAGCTTACTGTTTCAGCTCAATA
**
39969045 GAAGCTTACTGTTTTCAGCTC-ACC
1 G-AGCTTACTG-TTTCAGCTCAATA
**
39969069 GAAGCTTACCATTTCA--T--AT-
1 G-AGCTTACTGTTTCAGCTCAATA
39969088 GAGCTTACTG-TTCAGCTCAATA
1 GAGCTTACTGTTTCAGCTCAATA
* *
39969110 GAGCTTACCGTTTCAGCTTAATA
1 GAGCTTACTGTTTCAGCTCAATA
*
39969133 GAGCTTATTGTTTATCAGCTCAA
1 GAGCTTACTG-TT-TCAGCTCAA
39969156 GAAGAACTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
17 4 0.04
18 7 0.07
19 2 0.02
20 1 0.01
21 3 0.03
22 22 0.21
23 40 0.37
24 20 0.19
25 8 0.07
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (23 bp):
GAGCTTACTGTTTCAGCTCAATA
Found at i:39973533 original size:30 final size:31
Alignment explanation
Indices: 39973474--39973537 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
39973464 ACTTAACAAG
39973474 CAAATGCTTCTAAAATAATAAAAAAAATTAA
1 CAAATGCTTCTAAAATAATAAAAAAAATTAA
*
39973505 CAAATGCCTT-TAAAATAAT-AAGAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAAAATTAA
39973535 CAA
1 CAA
39973538 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 13 0.42
31 15 0.48
32 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAAAAAAAATTAA
Found at i:39980102 original size:29 final size:31
Alignment explanation
Indices: 39980041--39980102 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
39980031 ATAATTTAAT
* **
39980041 TTGGTCATTTTGAATTTTTGTATTTTTTGAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCAAA
*
39980072 TTGGTCATTTT-TA-TTCTGTATTTTTCAAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCAAA
39980101 TT
1 TT
39980103 TTAAACTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.56
30 1 0.04
31 11 0.41
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (31 bp):
TTGGTCATTTTGAATTTCTGTATTTTTCAAA
Found at i:39983076 original size:23 final size:23
Alignment explanation
Indices: 39983036--39983080 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39983026 ATAGAAAAAG
*
39983036 ATATATATGCAACGATATATATT
1 ATATATATGAAACGATATATATT
39983059 ATATATTATGAAAC-ATATATAT
1 ATATA-TATGAAACGATATATAT
39983081 ATTAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (23 bp):
ATATATATGAAACGATATATATT
Found at i:39989826 original size:50 final size:50
Alignment explanation
Indices: 39989758--39989857 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
39989748 GTTTTTAATG
* *
39989758 AAAACGCCACTATGAAATCAAATTTTCTTAAAAACGGTGCCGTTTTGATA
1 AAAACGCCACTATCAAATCAAATTTTCTTAAAAACGGCGCCGTTTTGATA
39989808 AAAACGCCACTATCAAATCAAATTTTCTTAAAAACGGCGCCGTTTTGATA
1 AAAACGCCACTATCAAATCAAATTTTCTTAAAAACGGCGCCGTTTTGATA
39989858 TTCCTTAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (50 bp):
AAAACGCCACTATCAAATCAAATTTTCTTAAAAACGGCGCCGTTTTGATA
Found at i:39989962 original size:28 final size:28
Alignment explanation
Indices: 39989896--39989950 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
39989886 AATATATAGT
* *
39989896 ACTAATAATTATAAATTTTAGTGTTTTC
1 ACTAATATTTTTAAATTTTAGTGTTTTC
39989924 ACTAATATTTTTAAATTTTAGTGTTTT
1 ACTAATATTTTTAAATTTTAGTGTTTT
39989951 TATTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (28 bp):
ACTAATATTTTTAAATTTTAGTGTTTTC
Found at i:39993896 original size:16 final size:17
Alignment explanation
Indices: 39993875--39993906 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39993865 AAATATGCAA
39993875 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
39993891 TCACATAACTTCATAT
1 TCACATAACTTCATAT
39993907 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:39994133 original size:43 final size:43
Alignment explanation
Indices: 39994065--39994235 Score: 192
Period size: 43 Copynumber: 4.0 Consensus size: 43
39994055 AAGACTCGTA
*
39994065 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATAT
* *
39994108 CAATGCC-ACTGTCCCAAACAG-GGTCTTACACG-AATCAAATA-
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATAT
* * * *
39994149 CGATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA-T
*
39994192 CGATGCCAACGTCCCAGACGTGGTCTTACACGATAA-CACATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACG-TAATCACATAT
39994235 C
1 C
39994236 GGAAATCCTA
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
41 26 0.24
42 16 0.15
43 61 0.56
44 5 0.05
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATAT
Found at i:39994217 original size:84 final size:84
Alignment explanation
Indices: 39994067--39994224 Score: 214
Period size: 84 Copynumber: 1.9 Consensus size: 84
39994057 GACTCGTACA
* * *
39994067 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCAATGCCACTGTCCCAAACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAAACAGGGT
39994132 CTTACACGAATCAAATACG
66 CTTACACGAATCAAATACG
* * *
39994151 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGAC-GT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCAATGCC-ACTGTCCCAAACAG-
39994213 GGTCTTACACGA
63 GGTCTTACACGA
39994225 TAACACATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 2 0.03
84 61 0.94
85 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAAACAGGGT
CTTACACGAATCAAATACG
Found at i:40006901 original size:196 final size:196
Alignment explanation
Indices: 40006567--40006958 Score: 748
Period size: 196 Copynumber: 2.0 Consensus size: 196
40006557 CATCAATACC
40006567 ACATCTAAGGTTCTAAGCCGGAAATCAATTTATGTTGAACTCCTTTTTAACTTATAATTCGCTGA
1 ACATCTAAGGTTCTAAGCCGGAAATCAATTTATGTTGAACTCCTTTTTAACTTATAATTCGCTGA
*
40006632 CACATTTCTAAATTTCACAACTTCATTATATATACATTTATTTAGCCTCTAATTCATCTATCAAC
66 CACATTTCTAAATTTCACAACTTCATTATATAAACATTTATTTAGCCTCTAATTCATCTATCAAC
40006697 AGTTCATTACGTGATAAGATCAATCACGTATTCATCGCCCAATCAAAATATCCGAAACTTTAATC
131 AGTTCATTACGTGATAAGATCAATCACGTATTCATCGCCCAATCAAAATATCCGAAACTTTAATC
40006762 A
196 A
* *
40006763 ACATCTAAGGTTCTAAGCCGGAATTTAATTTATGTTGAACTCCTTTTTAACTTATAATTCGCTGA
1 ACATCTAAGGTTCTAAGCCGGAAATCAATTTATGTTGAACTCCTTTTTAACTTATAATTCGCTGA
*
40006828 CACATTTCTAAATTTCACAACTTCATTGTATAAACATTTATTTAGCCTCTAATTCATCTATCAAC
66 CACATTTCTAAATTTCACAACTTCATTATATAAACATTTATTTAGCCTCTAATTCATCTATCAAC
40006893 AGTTCATTACGTGATAAGATCAATCACGTATTCATCGCCCAATCAAAATATCCGAAACTTTAATC
131 AGTTCATTACGTGATAAGATCAATCACGTATTCATCGCCCAATCAAAATATCCGAAACTTTAATC
40006958 A
196 A
40006959 TTTTCCTCGG
Statistics
Matches: 192, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
196 192 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (196 bp):
ACATCTAAGGTTCTAAGCCGGAAATCAATTTATGTTGAACTCCTTTTTAACTTATAATTCGCTGA
CACATTTCTAAATTTCACAACTTCATTATATAAACATTTATTTAGCCTCTAATTCATCTATCAAC
AGTTCATTACGTGATAAGATCAATCACGTATTCATCGCCCAATCAAAATATCCGAAACTTTAATC
A
Found at i:40007539 original size:54 final size:54
Alignment explanation
Indices: 40007457--40007563 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
40007447 ACTCAATTAC
*
40007457 CTTTTGAAACAAATAATTCAAATTCGACTAAACCACTAAATCAGTCTTTTCGAT
1 CTTTTCAAACAAATAATTCAAATTCGACTAAACCACTAAATCAGTCTTTTCGAT
40007511 CTTTTCAAACAAATAATTCAAATTCGACTAAACCACTAAATCAGTCTTTTCGA
1 CTTTTCAAACAAATAATTCAAATTCGACTAAACCACTAAATCAGTCTTTTCGA
40007564 ATGAATCTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (54 bp):
CTTTTCAAACAAATAATTCAAATTCGACTAAACCACTAAATCAGTCTTTTCGAT
Found at i:40011318 original size:16 final size:17
Alignment explanation
Indices: 40011297--40011328 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40011287 AAATATGCAA
40011297 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
40011313 TCACATAACTTCATAT
1 TCACATAACTTCATAT
40011329 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:40011548 original size:43 final size:43
Alignment explanation
Indices: 40011487--40011657 Score: 201
Period size: 43 Copynumber: 4.0 Consensus size: 43
40011477 AAGACTCGTA
*
40011487 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATAT
*
40011530 CAATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AATCAAATA-
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATAT
* * * *
40011571 CGATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA-T
*
40011614 CGATGCCAACGTCCCAGACGTGGTCTTACACGATAA-CACATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACG-TAATCACATAT
40011657 C
1 C
40011658 GGAAATCCTA
Statistics
Matches: 110, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
41 27 0.25
42 16 0.15
43 62 0.56
44 5 0.05
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATAT
Found at i:40011630 original size:84 final size:84
Alignment explanation
Indices: 40011489--40011646 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
40011479 GACTCGTACA
* * *
40011489 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCAATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGAC-GTGG
40011553 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
* *
40011573 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCAATGCC-ACTGTCCCAGACGTG
40011636 GTCTTACACGA
64 GTCTTACACGA
40011647 TAACACATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 2 0.03
84 62 0.94
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:40012447 original size:247 final size:247
Alignment explanation
Indices: 40012005--40012497 Score: 923
Period size: 247 Copynumber: 2.0 Consensus size: 247
40011995 TGTCATATCA
40012005 GATTGAATCTCAATCTCTGTGGGACTAATCACATGTGAAGGATTACATAGGTATCTATGGAGCAT
1 GATTGAATCTCAATCTCTGTGGGACTAATCACATGTGAAGGATTACATAGGTATCTATGGAGCAT
*
40012070 CGAAACATGGAATACATTAAGAATCTTTTCTAGCTCAGGTGGCAACTACAATCTATAAGCAACCA
66 CGAAACATGGAATACATTAAGAATCTTTTCTAGCTCAGGTGGCAACTACAATCTATAAGAAACCA
40012135 GCCCGATACGCTCTATAATCTCATACGACCCAATAAATCTCACACTCAATTTCTTTTAACGATCA
131 GCCCGATACGCTCTATAATCTCATACGACCCAATAAATCTCACACTCAATTTCTTTTAACGATCA
40012200 AATCTAAGTATTTTCTTCCACTGTGATACCTACAAAAAGACTTTATCTCCAG
196 AATCTAAGTATTTTCTTCCACTGTGATACCTACAAAAAGACTTTATCTCCAG
* *
40012252 GATTGCATCTCAATCTCTGTGGGACTAATCACATGTGAAGGATTAGATAGGTATCTATGGAGCAT
1 GATTGAATCTCAATCTCTGTGGGACTAATCACATGTGAAGGATTACATAGGTATCTATGGAGCAT
**
40012317 CGAAACATGGAATACATTGTGAATCTTTTCTAGCTCAGGTGGCAACTACAATCTATAAGAAACCA
66 CGAAACATGGAATACATTAAGAATCTTTTCTAGCTCAGGTGGCAACTACAATCTATAAGAAACCA
*
40012382 GCCCGATACGCTCTATAATCTCATACGACCCAATAAATCTCACACTCAATTTCTTTTTACGATCA
131 GCCCGATACGCTCTATAATCTCATACGACCCAATAAATCTCACACTCAATTTCTTTTAACGATCA
*
40012447 AATCTAAGTATTTTCTTCCAGTGTGATACCTACAAAAAGACTTTATCTCCA
196 AATCTAAGTATTTTCTTCCACTGTGATACCTACAAAAAGACTTTATCTCCA
40012498 CACGCCTATG
Statistics
Matches: 239, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
247 239 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (247 bp):
GATTGAATCTCAATCTCTGTGGGACTAATCACATGTGAAGGATTACATAGGTATCTATGGAGCAT
CGAAACATGGAATACATTAAGAATCTTTTCTAGCTCAGGTGGCAACTACAATCTATAAGAAACCA
GCCCGATACGCTCTATAATCTCATACGACCCAATAAATCTCACACTCAATTTCTTTTAACGATCA
AATCTAAGTATTTTCTTCCACTGTGATACCTACAAAAAGACTTTATCTCCAG
Found at i:40022744 original size:40 final size:40
Alignment explanation
Indices: 40022689--40022995 Score: 533
Period size: 40 Copynumber: 7.7 Consensus size: 40
40022679 AGCATTGGAT
40022689 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
40022729 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
40022769 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
40022809 TATATCCGGGCTAAGACCCGAAGGCAACTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
** *
40022849 TATATCCGGGCTGTGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
** *
40022889 TATATCCGGGCTGTGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
40022929 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
40022969 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
40022996 ATGTGTTTGC
Statistics
Matches: 257, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 257 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:40033462 original size:26 final size:26
Alignment explanation
Indices: 40033437--40033498 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 26
40033427 TATTATATAT
40033437 TTATATATATAAAAAATATG-AGATA
1 TTATATATATAAAAAATATGAAGATA
* *
40033462 TTAT-TAT-TAAAAAAATTTGAAGTTAA
1 TTATATATAT-AAAAAATATGAAGAT-A
40033488 TTATATATATA
1 TTATATATATA
40033499 TATACATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
23 1 0.03
24 12 0.40
25 7 0.23
26 5 0.17
27 4 0.13
28 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (26 bp):
TTATATATATAAAAAATATGAAGATA
Found at i:40034036 original size:89 final size:89
Alignment explanation
Indices: 40033885--40034469 Score: 839
Period size: 89 Copynumber: 6.6 Consensus size: 89
40033875 GCTATCTTTA
* * * * * *
40033885 ATCTGCTTTCTTCGATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTGTCTTTGATCTAC
1 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
*
40033950 TTCACGCCAATA-AGTGAAGACAAG
66 TTCACGCCAGTACA-TGAAGACAAG
* * * *
40033974 ATCTGTTCTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGGTATCTTCGATCTAC
1 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
* *
40034039 TTCATGCCAGTATATGAAGACAAG
66 TTCACGCCAGTACATGAAGACAAG
* *
40034063 ATCTATTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGGTATCTTTGATCTAC
1 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
40034128 TTCACGCCAGTACATGAAGACAAG
66 TTCACGCCAGTACATGAAGACAAG
40034152 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
1 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
*
40034217 TTCACCCCAGTACATGAAGACAAG
66 TTCACGCCAGTACATGAAGACAAG
* * *
40034241 ATCTGTTTTCTTCGATCTACTCCACCACTAGTATGGGGAGACAAGATCTGATATCTTTGATCTAC
1 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
*
40034306 TTCACGCCAGTACGTGAAGACAAG
66 TTCACGCCAGTACATGAAGACAAG
* * * * * * * *
40034330 ATCTGTTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATTTGTTATTTTTGATCTAC
1 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
*
40034395 TTCACGCTAGTACATGAAGACAAG
66 TTCACGCCAGTACATGAAGACAAG
* * * * * *
40034419 ATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGG
1 ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGG
40034470 GTCAAAGATA
Statistics
Matches: 454, Mismatches: 41, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
89 453 1.00
90 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
ATCTGTTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTAC
TTCACGCCAGTACATGAAGACAAG
Found at i:40034753 original size:44 final size:46
Alignment explanation
Indices: 40034690--40034787 Score: 141
Period size: 44 Copynumber: 2.2 Consensus size: 46
40034680 CAGTGGAATC
* *
40034690 GATC-GAAGAAAGCAGATCTTGTCTTCATGTATTGGT-GTGAAGTA
1 GATCGGAAGAAAGCAGATCTTGTCTTCATATACTGGTGGTGAAGTA
*
40034734 GATCGGAA-AAAGCAGATCTTGTCTTCCTATACTGGTGGTGAAGTA
1 GATCGGAAGAAAGCAGATCTTGTCTTCATATACTGGTGGTGAAGTA
40034779 GATC-GAAGA
1 GATCGGAAGA
40034788 TACAAGCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 32 0.67
45 16 0.33
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (46 bp):
GATCGGAAGAAAGCAGATCTTGTCTTCATATACTGGTGGTGAAGTA
Found at i:40036351 original size:21 final size:21
Alignment explanation
Indices: 40036325--40036365 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40036315 CTATTGTTGT
*
40036325 TTTTTTTATTTGTTTTATTTG
1 TTTTTTTATTTGGTTTATTTG
40036346 TTTTTTTATTTGGTTTATTT
1 TTTTTTTATTTGGTTTATTT
40036366 TTTGTTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (21 bp):
TTTTTTTATTTGGTTTATTTG
Found at i:40040406 original size:25 final size:25
Alignment explanation
Indices: 40040376--40040431 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
40040366 TTAAAGGGGC
* *
40040376 AATCAAATCAATTTGATTAAAATAA
1 AATCAAATCAATTAGAATAAAATAA
** *
40040401 AATCAAATTGATTAGAATCAAATAA
1 AATCAAATCAATTAGAATAAAATAA
40040426 AATCAA
1 AATCAA
40040432 GATATATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (25 bp):
AATCAAATCAATTAGAATAAAATAA
Found at i:40040423 original size:20 final size:20
Alignment explanation
Indices: 40040376--40040428 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
40040366 TTAAAGGGGC
*
40040376 AATCAAATCAATTTGATTAA
1 AATCAAATCAAATTGATTAA
* *
40040396 AATAAAATCAAATTGATTAG
1 AATCAAATCAAATTGATTAA
*
40040416 AATCAAATAAAAT
1 AATCAAATCAAAT
40040429 CAAGATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.30
Consensus pattern (20 bp):
AATCAAATCAAATTGATTAA
Found at i:40044137 original size:81 final size:81
Alignment explanation
Indices: 40043934--40044201 Score: 383
Period size: 82 Copynumber: 3.2 Consensus size: 81
40043924 AGTCTTCTTG
* **
40043934 TTTGGAAACAAAATCAAAATCGAATAAAATATGTTAAACGATTGGAATAAATCCTGAAACAGATT
1 TTTGGAAACAAAATTAAAATCGAATAAAATATGTTAAACGGCTGGAATAAATCCTGAAACAGATT
*
40043999 ATTCAATTTAATTCTA
66 ATTCAATTTAATTTTA
* **
40044015 TTTTGGAAACAAAATTAAAATCAAATAAAATATGTTAAACGGCTGGAATAAATCCCAAAACAGAT
1 -TTTGGAAACAAAATTAAAATCGAATAAAATATGTTAAACGGCTGGAATAAATCCTGAAACAGAT
40044080 TATTCAATTTAATTTTA
65 TATTCAATTTAATTTTA
* *
40044097 TTTGGAAACAAAATTAAAATCGAATAAAATCTGTTAAACGGCAGGAATAAATCCTGAAACAGATT
1 TTTGGAAACAAAATTAAAATCGAATAAAATATGTTAAACGGCTGGAATAAATCCTGAAACAGA--
*
40044162 TTATTTAATTTTAATTTCTCA
64 TTATTCAA-TTTAATTT-T-A
*
40044183 TTTGGAAACAAAATAAAAA
1 TTTGGAAACAAAATTAAAA
40044202 AATGGAATCA
Statistics
Matches: 167, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
81 58 0.35
82 74 0.44
83 7 0.04
84 8 0.05
85 1 0.01
86 19 0.11
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (81 bp):
TTTGGAAACAAAATTAAAATCGAATAAAATATGTTAAACGGCTGGAATAAATCCTGAAACAGATT
ATTCAATTTAATTTTA
Found at i:40044232 original size:88 final size:81
Alignment explanation
Indices: 40043871--40044257 Score: 375
Period size: 82 Copynumber: 4.6 Consensus size: 81
40043861 ACAAAATCAA
* ** * ** *
40043871 AATAAAATCTGTTAAGCGACGAGAATAAATCCCGAAACATAATTATTTGA-TTAAGTCTTCTTGT
1 AATAAAATCTGTTAAACGGTG-GAATAAATCCCGAAACA-GATTATTCAATTTAA-T-TTC-TAT
*
40043935 TTGGAAACAAAATCAAAATCG
61 TTGGAAACAAAATTAAAATCG
* * *
40043956 AATAAAATATGTTAAACGATTGGAATAAATCCTGAAACAGATTATTCAATTTAA-TTCTATTTTG
1 AATAAAATCTGTTAAACG-GTGGAATAAATCCCGAAACAGATTATTCAATTTAATTTCTA-TTTG
*
40044020 GAAACAAAATTAAAATCA
64 GAAACAAAATTAAAATCG
* *
40044038 AATAAAATATGTTAAACGGCTGGAATAAATCCCAAAACAGATTATTCAATTTAATTT-TATTTGG
1 AATAAAATCTGTTAAACGG-TGGAATAAATCCCGAAACAGATTATTCAATTTAATTTCTATTTGG
40044102 AAACAAAATTAAAATCG
65 AAACAAAATTAAAATCG
* * *
40044119 AATAAAATCTGTTAAACGGCAGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTTCTCAT
1 AATAAAATCTGTTAAACGG-TGGAATAAATCCCGAAACAGA--TTATTCAA-TTTAATTTCT-AT
* *
40044184 TTGGAAACAAAATAAAAAAATGG
61 TTGGAAACAAAAT--TAAAATCG
* * * * *
40044207 AATCAAATCTGATGATCGGTGGGAATAAATCCCGAAATAGATATTATTCAA
1 AATAAAATCTGTTAAACGGT-GGAATAAATCCCGAAACAG--ATTATTCAA
40044258 AGATAGAATA
Statistics
Matches: 257, Mismatches: 30, Indels: 27
0.82 0.10 0.09
Matches are distributed among these distances:
81 59 0.23
82 75 0.29
83 9 0.04
84 15 0.06
85 37 0.14
86 16 0.06
88 45 0.18
90 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (81 bp):
AATAAAATCTGTTAAACGGTGGAATAAATCCCGAAACAGATTATTCAATTTAATTTCTATTTGGA
AACAAAATTAAAATCG
Found at i:40044929 original size:20 final size:20
Alignment explanation
Indices: 40044886--40044929 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40044876 AGAGGCAATT
*
40044886 AAATCAATTTGATTAAAATC
1 AAATCAATTTGATTAAAATA
*
40044906 AAATCAAATTT-ATTAGAATA
1 AAATC-AATTTGATTAAAATA
40044926 AAAT
1 AAAT
40044930 AAAACCAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATCAATTTGATTAAAATA
Found at i:40046474 original size:27 final size:27
Alignment explanation
Indices: 40046444--40046556 Score: 147
Period size: 27 Copynumber: 4.2 Consensus size: 27
40046434 GGTATAATAG
40046444 TCATTTTACCCTAT-GAGGGTATTTCGA
1 TCATTTTACCCTATAG-GGGTATTTCGA
*
40046471 TCATTTTACCTTATAGGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGA
* * *
40046498 TCATTCTACCTTATGGGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGA
** *
40046525 TTGTTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCGA
40046552 TCATT
1 TCATT
40046557 ATTTTAGTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 73 0.99
28 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTTCGA
Found at i:40046488 original size:54 final size:54
Alignment explanation
Indices: 40046430--40046546 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 54
40046420 TTTCATCTCC
* *
40046430 TAGGGGTATAATAG-TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCTTA
1 TAGGGGTAT-ATAGATCATTCTACCCTATGAGGGTATTTCGATCATTTTACCCTA
* * * * **
40046484 TAGGGGTATTTCGATCATTCTACCTTATGGGGGTATTTCGATTGTTTTACCCTA
1 TAGGGGTATATAGATCATTCTACCCTATGAGGGTATTTCGATCATTTTACCCTA
40046538 TAGGGGTAT
1 TAGGGGTAT
40046547 TTCGGTCATT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
53 2 0.04
54 52 0.96
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (54 bp):
TAGGGGTATATAGATCATTCTACCCTATGAGGGTATTTCGATCATTTTACCCTA
Found at i:40046547 original size:54 final size:54
Alignment explanation
Indices: 40046444--40046556 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
40046434 GGTATAATAG
* *
40046444 TCATTTTACCCTATGAGGGTATTTCGATCATTTTACCTTATAGGGGTATTTCGA
1 TCATTCTACCCTATGAGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGA
* * ** *
40046498 TCATTCTACCTTATGGGGGTATTTCGATTGTTTTACCCTATAGGGGTATTTCGG
1 TCATTCTACCCTATGAGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGA
40046552 TCATT
1 TCATT
40046557 ATTTTAGTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (54 bp):
TCATTCTACCCTATGAGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGA
Found at i:40056514 original size:40 final size:36
Alignment explanation
Indices: 40056454--40056539 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
40056444 AAACTAGTAT
* * *
40056454 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
40056490 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
40056530 TATTATTATT
1 TATTATTATT
40056540 TTCATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:40060700 original size:28 final size:27
Alignment explanation
Indices: 40060652--40060705 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
40060642 TACATACATA
40060652 TGTATAATAAAAATAATTTAATATAGGT
1 TGTATAATAAAAATAATTTAA-ATAGGT
40060680 TGTATACAT-AAAA-AATATTAAATAGG
1 TGTATA-ATAAAAATAAT-TTAAATAGG
40060706 GATATTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 8 0.33
28 14 0.58
29 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (27 bp):
TGTATAATAAAAATAATTTAAATAGGT
Found at i:40060776 original size:18 final size:16
Alignment explanation
Indices: 40060753--40060788 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
40060743 AAAATGGCTT
40060753 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
40060771 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
40060787 TA
1 TA
40060789 TATTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Done.