Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009633.1 Hibiscus syriacus cultivar Beakdansim tig00117032_pilon, whole genome shotgun sequence
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: 2608659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:934424 original size:21 final size:21
Alignment explanation
Indices: 934398--934439 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
934388 TCAAAGTTTT
* *
934398 ATGCATTGGTGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
*
934419 ATGCATCGATGCTCTGTAGCA
1 ATGCATCGATGCACTGTAGCA
934440 CTGTAACACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:937395 original size:14 final size:14
Alignment explanation
Indices: 937378--937420 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
937368 TTTTGCACAA
*
937378 TTTTGTTTTTTTTC
1 TTTTATTTTTTTTC
*
937392 TTTTCTTTTTTTTTC
1 TTTT-ATTTTTTTTC
937407 TTTTATTTTTTTTC
1 TTTTATTTTTTTTC
937421 ACTGAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.86
Consensus pattern (14 bp):
TTTTATTTTTTTTC
Found at i:937401 original size:15 final size:15
Alignment explanation
Indices: 937383--937419 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
937373 CACAATTTTG
*
937383 TTTTTTTTCTTTTCT
1 TTTTTTTTCTTTTAT
937398 TTTTTTTTCTTTTAT
1 TTTTTTTTCTTTTAT
937413 TTTTTTT
1 TTTTTTT
937420 CACTGAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTCTTTTAT
Found at i:947561 original size:20 final size:20
Alignment explanation
Indices: 947536--947610 Score: 150
Period size: 20 Copynumber: 3.8 Consensus size: 20
947526 CAAAATTGAA
947536 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
947556 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
947576 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
947596 GGTGCATCGATGCAT
1 GGTGCATCGATGCAT
947611 AGGAATTTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (20 bp):
GGTGCATCGATGCATTAAGG
Found at i:948061 original size:30 final size:30
Alignment explanation
Indices: 948027--948095 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
948017 TTATATGAGT
* *
948027 TATGTGATAAAGGTATGTAAATGATATGTC
1 TATGTGATAAAGGTATGGAAATAATATGTC
948057 TATGTGATAAAGGTATGGAAATAATATGTC
1 TATGTGATAAAGGTATGGAAATAATATGTC
*
948087 TATGCGATA
1 TATGTGATA
948096 TGACATACGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATAATATGTC
Found at i:948359 original size:23 final size:23
Alignment explanation
Indices: 948329--948374 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
948319 GACATATTAT
948329 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
* *
948352 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTACGGTGCAATTCTAC
948375 GCGGTCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:949054 original size:20 final size:20
Alignment explanation
Indices: 949029--949067 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
949019 GTGCACTGTA
*
949029 GCATTGTAGCACTATTCACG
1 GCATTGTACCACTATTCACG
*
949049 GCATTGTACCACTGTTCAC
1 GCATTGTACCACTATTCAC
949068 AGTACTGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (20 bp):
GCATTGTACCACTATTCACG
Found at i:949562 original size:164 final size:162
Alignment explanation
Indices: 949293--949614 Score: 511
Period size: 164 Copynumber: 2.0 Consensus size: 162
949283 GTGATTAATT
* * * *
949293 TTTTATTTTCAAAATTTTAATGAAAAACGAAAACTTACTCAAATATTATTGATCATTTATGTAAT
1 TTTTATTTTCAAAATTTTAATGAAAAACAAAAACTTAATCAAACATTAATGATCATTTATGTAAT
* *
949358 TTATCCTTTCAATATAATAGATAAAGAAATTGTATGTTACTTTCTCATGTTTCCGTTAGCACTTG
66 TTATCCTTTCAATATAATAGATAAAGAAATTGTATGTTACTTTCTCATGTTTCCGGTAGCAATTG
949423 CTGAAATTTATGACGAAATAAGCCAATGAATA
131 CTGAAATTTATGACGAAATAAGCCAATGAATA
*
949455 TTTTATTTTTAAAATTTTAATGAAAAACAAAAAACTTAATCAAACATTAATGATCATTTATGTAA
1 TTTTATTTTCAAAATTTTAATGAAAAAC-AAAAACTTAATCAAACATTAATGATCATTTATGTAA
* * * *
949520 TTTACTCTTTTTAATATAATATG-TTAAGAAATTGTATGTTACTTTCTCATGTTTCCGGTGGCAA
65 TTTA-TCCTTTCAATATAATA-GATAAAGAAATTGTATGTTACTTTCTCATGTTTCCGGTAGCAA
949584 TTGCTGAAATTTATGACGAAATAAGCCAATG
128 TTGCTGAAATTTATGACGAAATAAGCCAATG
949615 CCAGAAAGGA
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
162 27 0.18
163 36 0.25
164 82 0.56
165 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (162 bp):
TTTTATTTTCAAAATTTTAATGAAAAACAAAAACTTAATCAAACATTAATGATCATTTATGTAAT
TTATCCTTTCAATATAATAGATAAAGAAATTGTATGTTACTTTCTCATGTTTCCGGTAGCAATTG
CTGAAATTTATGACGAAATAAGCCAATGAATA
Found at i:950669 original size:36 final size:36
Alignment explanation
Indices: 950629--950711 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
950619 ATCATCAGCG
* * *
950629 CTTTCGATTCAA-AATGAACGGAAGGAAGTATCGGCA
1 CTTTCGATTCAAGAA-GAACGAAAGGAAGTAACGACA
*
950665 CTTTCGTTTCAAGAAGAACGAAAGGAAGTAACGACA
1 CTTTCGATTCAAGAAGAACGAAAGGAAGTAACGACA
950701 CTTTCGATTCA
1 CTTTCGATTCA
950712 GGGAGAGAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
36 39 0.95
37 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (36 bp):
CTTTCGATTCAAGAAGAACGAAAGGAAGTAACGACA
Found at i:952608 original size:36 final size:35
Alignment explanation
Indices: 952561--952685 Score: 142
Period size: 36 Copynumber: 3.5 Consensus size: 35
952551 CAAAATGAAA
*
952561 CATCGGCACTTTCGATTCAAAGTGAATGGAAGGAAG
1 CATCGGCACTTTCGATTC-AAGTGAACGGAAGGAAG
* *
952597 CATCGGCACTTTCGATTCAAGAAGAACGAAAGGAAG
1 CATCGGCACTTTCGATTCAAG-TGAACGGAAGGAAG
* * * *
952633 CAACGACACTTTCGATTCAAGTGAACGGAATGAAT
1 CATCGGCACTTTCGATTCAAGTGAACGGAAGGAAG
***
952668 CATCATTACTTTCGATTC
1 CATCGGCACTTTCGATTC
952686 GATTGTTCAT
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
35 27 0.36
36 48 0.64
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (35 bp):
CATCGGCACTTTCGATTCAAGTGAACGGAAGGAAG
Found at i:952644 original size:72 final size:71
Alignment explanation
Indices: 952543--952685 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 71
952533 GAAGGTGAAT
* * * * *
952543 AAGAAGAACAAAATGAAACATCGGCACTTTCGATTCAAAGTGAATGGAAGGAAGCATCGGCACTT
1 AAGAAGAACAAAAGGAAACAACGACACTTTCGATTC-AAGTGAACGGAAGGAAGCATCAGCACTT
952608 TCGATTC
65 TCGATTC
* * * * **
952615 AAGAAGAACGAAAGGAAGCAACGACACTTTCGATTCAAGTGAACGGAATGAATCATCATTACTTT
1 AAGAAGAACAAAAGGAAACAACGACACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTT
952680 CGATTC
66 CGATTC
952686 GATTGTTCAT
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
71 29 0.48
72 31 0.52
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (71 bp):
AAGAAGAACAAAAGGAAACAACGACACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTT
CGATTC
Found at i:955563 original size:2 final size:2
Alignment explanation
Indices: 955556--955585 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
955546 ACTAAAATTA
955556 AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
955586 TATTGTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:961229 original size:16 final size:16
Alignment explanation
Indices: 961208--961245 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
961198 TTGGGGAGTG
961208 TCTTCCCGCTTTGTTA
1 TCTTCCCGCTTTGTTA
961224 TCTTCCCGCTTTGTTA
1 TCTTCCCGCTTTGTTA
961240 TCTTCC
1 TCTTCC
961246 AGTAGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.05, C:0.34, G:0.11, T:0.50
Consensus pattern (16 bp):
TCTTCCCGCTTTGTTA
Found at i:963304 original size:15 final size:15
Alignment explanation
Indices: 963284--963322 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
963274 GAGATTGGGC
963284 TTTGAAGAAAATCAA
1 TTTGAAGAAAATCAA
963299 TTTGAAGAAAATCAA
1 TTTGAAGAAAATCAA
963314 TTTGAAGAA
1 TTTGAAGAA
963323 GTCGGATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28
Consensus pattern (15 bp):
TTTGAAGAAAATCAA
Found at i:965441 original size:17 final size:18
Alignment explanation
Indices: 965416--965449 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
965406 ATTATATTTT
*
965416 CCAGTGAAAACA-ATTAA
1 CCAGAGAAAACATATTAA
965433 CCAGAGAAAACATATTA
1 CCAGAGAAAACATATTA
965450 GGTAGCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAGAGAAAACATATTAA
Found at i:966868 original size:2 final size:2
Alignment explanation
Indices: 966855--966887 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
966845 AGCATATTCA
*
966855 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
966888 CTTATGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:966963 original size:2 final size:2
Alignment explanation
Indices: 966950--967012 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
966940 TACACCTGTA
*
966950 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
966992 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
967013 AGTTAAACAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:968957 original size:9 final size:9
Alignment explanation
Indices: 968940--968993 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
968930 AAAAATGTAA
968940 TAATAATAT
1 TAATAATAT
*
968949 TAATGATA-
1 TAATAATAT
*
968957 TAATAATAA
1 TAATAATAT
968966 TAAT-ATA-
1 TAATAATAT
968973 TAATTAATAT
1 TAA-TAATAT
*
968983 TTATAATAT
1 TAATAATAT
968992 TA
1 TA
968994 TTTTAATCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.08
8 11 0.30
9 21 0.57
10 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
TAATAATAT
Found at i:968959 original size:17 final size:16
Alignment explanation
Indices: 968939--968983 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
968929 CAAAAATGTA
968939 ATAATAATATTAATGAT
1 ATAATAATATTAAT-AT
*
968956 ATAATAATAATAATAT
1 ATAATAATATTAATAT
968972 ATAATTAATATT
1 ATAA-TAATATT
968984 TATAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATAATAATATTAATAT
Found at i:968980 original size:20 final size:21
Alignment explanation
Indices: 968937--968991 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
968927 AACAAAAATG
* *
968937 TAATAATAATATTA-ATGATA
1 TAATAATAATAATATATAATA
968957 TAATAATAATAATATATAAT-
1 TAATAATAATAATATATAATA
* *
968977 TAATATTTATAATAT
1 TAATAATAATAATAT
968992 TATTTTAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATAATAATAATATATAATA
Found at i:969360 original size:135 final size:135
Alignment explanation
Indices: 969119--969459 Score: 490
Period size: 135 Copynumber: 2.5 Consensus size: 135
969109 TTGTTGGATT
* * * * *
969119 GAACAAGTTATTCTTATTATGAACTTATTCTCTCT-TATGGACGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCTATGGATGAGTTCTTCTCATTATGAACTC
* * *
969183 TTCACTAAAAATGTTGATCCCTCAAGCGAGGCATTACTGATTCGAAATGCCGTAAATCGAGTGAT
66 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCATGACTGATTCGAAATGCCATAAATCGAGTGAT
969248 AGGTC
131 AGGTC
969253 GAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGT-TGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTC-TATGGATGAGTTCTTCTCATTATGAACT
* * * *
969317 CTTCACTGAAAATGTTGATTCCTCAAGCGAGGCGTGACTGATTCGAAATGTCATGAATCGAGTGA
65 CTTCACTGAAAATGTTGATCCCTCAAGCGAGGCATGACTGATTCGAAATGCCATAAATCGAGTGA
969382 TAGGTC
130 TAGGTC
* * * *
969388 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATAAATT-TTCTCATTATAAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCTAT-GGATGAGTTCTTCTCATTATGAACT
*
969452 CTCCACTG
65 CTTCACTG
969460 GAAACACTGA
Statistics
Matches: 186, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
134 32 0.17
135 146 0.78
136 8 0.04
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCTATGGATGAGTTCTTCTCATTATGAACTC
TTCACTGAAAATGTTGATCCCTCAAGCGAGGCATGACTGATTCGAAATGCCATAAATCGAGTGAT
AGGTC
Found at i:970364 original size:64 final size:64
Alignment explanation
Indices: 970275--970428 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 64
970265 TTGAAGGTGT
* *
970275 ATCGATGCACT-AGGTAGTGCATCGATGCACT-CTTTCAA-AATATAAACATCGAATGCA-ATTA
1 ATCGATGCA-TAAGG-AATGCATCGATGCACTCCATT-AATAATA-AAACATCGAATGCATATTA
970336 GTGC
62 -TGC
* * *
970340 ATCGATGCATAAGGCATGCATCGATGCATTCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGGAATGCATCGATGCACTCCATTAATAATAAAACATCGAATGCATATTATGC
* * *
970404 ACCGATGCACAAGTAATGCATCGAT
1 ATCGATGCATAAGGAATGCATCGAT
970429 ACATACCTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
64 54 0.71
65 22 0.29
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAAGGAATGCATCGATGCACTCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:977252 original size:64 final size:64
Alignment explanation
Indices: 977182--977337 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 64
977172 TTGAAGGTGT
***
977182 ATCGATGCACAGGTAGTGCATCGATGCACTGTTTTAA-AATATAAACATCGAATGCA-ATTAGTG
1 ATCGATGCACAGGTAGTGCATCGATGCACTCCATTAATAATA-AAACATCGAATGCATATTA-TG
977245 C
64 C
* * * *
977246 ATCGATGCATAAGGCA-TGCATCGATGCATTCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCACTCCATTAATAATAAAACATCGAATGCATATTATGC
* *
977310 ACCGATGCACAAGTAGTGCATCGATGCA
1 ATCGATGCACAGGTAGTGCATCGATGCA
977338 TACCTTCATT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
63 3 0.04
64 63 0.82
65 11 0.14
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCACTCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:977754 original size:29 final size:29
Alignment explanation
Indices: 977715--977795 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
977705 TATGTGATAT
977715 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
977745 GAGAAATGACATGAGCTACATGATCATAA
1 GAGAAATGACATGAGCTACATGATCACAA
977774 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
977796 ACATATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:982533 original size:2 final size:2
Alignment explanation
Indices: 982526--982586 Score: 56
Period size: 2 Copynumber: 31.0 Consensus size: 2
982516 AATTAATTTT
* * *
982526 TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA CA TA TA TGA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
982568 -A TA TGA TA TA -A TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA
982587 AACGGCATAG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
1 3 0.06
2 46 0.88
3 3 0.06
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (2 bp):
TA
Found at i:982880 original size:2 final size:2
Alignment explanation
Indices: 982873--982901 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
982863 AGCATATTCA
982873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
982902 ATACATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:983522 original size:13 final size:13
Alignment explanation
Indices: 983504--983528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
983494 CGCCGTTATC
983504 CTCTTTTTTTTCA
1 CTCTTTTTTTTCA
983517 CTCTTTTTTTTC
1 CTCTTTTTTTTC
983529 TTCGACCGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
CTCTTTTTTTTCA
Found at i:984897 original size:17 final size:16
Alignment explanation
Indices: 984877--984921 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
984867 CAAAAATGTA
984877 ATAATAATATTAATGAT
1 ATAATAATATTAAT-AT
*
984894 ATAATAATAATAATAT
1 ATAATAATATTAATAT
984910 ATAATTAATATT
1 ATAA-TAATATT
984922 TATAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATAATAATATTAATAT
Found at i:984918 original size:20 final size:21
Alignment explanation
Indices: 984875--984929 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
984865 AACAAAAATG
* *
984875 TAATAATAATATTA-ATGATA
1 TAATAATAATAATATATAATA
984895 TAATAATAATAATATATAAT-
1 TAATAATAATAATATATAATA
* *
984915 TAATATTTATAATAT
1 TAATAATAATAATAT
984930 TTTTTTAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATAATAATAATATATAATA
Found at i:986359 original size:12 final size:12
Alignment explanation
Indices: 986344--986374 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
986334 GTCAACAGGC
986344 ATGTCAACGAGA
1 ATGTCAACGAGA
986356 ATGTCAACGAGA
1 ATGTCAACGAGA
*
986368 AGGTCAA
1 ATGTCAA
986375 AGTCAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (12 bp):
ATGTCAACGAGA
Found at i:988834 original size:31 final size:31
Alignment explanation
Indices: 988799--989020 Score: 381
Period size: 31 Copynumber: 7.2 Consensus size: 31
988789 GATCACAATA
988799 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
988830 TAAACGGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
988861 CAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
988892 TAAACTGTTAATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
988923 TAAACTGCTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
988954 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
988985 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
989016 TAAAC
1 TAAAC
989021 CCTCGACTCT
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 179 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:992084 original size:31 final size:31
Alignment explanation
Indices: 992044--992265 Score: 381
Period size: 31 Copynumber: 7.2 Consensus size: 31
992034 GATCACAATA
992044 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
992075 TAAATTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
992106 CAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
992137 TAAACTGTTAATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
992168 TAAACTGCTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
992199 TAAACTGTTCGTATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
992230 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
992261 TAAAC
1 TAAAC
992266 CCTCGACTCT
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 177 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:992136 original size:16 final size:16
Alignment explanation
Indices: 992115--992168 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
992105 ACAAACTGTT
992115 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
992131 CATATGTAAACTGTT--A
1 CATATGT-GCCT-TTAAA
992147 -ATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
992162 CATATGT
1 CATATGT
992169 AAACTGCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 7 0.24
16 14 0.48
17 2 0.07
18 2 0.07
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:992881 original size:64 final size:65
Alignment explanation
Indices: 992773--992981 Score: 219
Period size: 64 Copynumber: 3.3 Consensus size: 65
992763 TAATGAAGGT
* * * ** ** * **
992773 ATGCATCGATGCACTACTGATACATCGGTGCATAAAAGGTATTCGATGTAAT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGG
* *
992837 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGG
** * * **
992901 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGG
992964 AGTGCATCGATGCACTAC
1 A-TGCATCGATGCACTAC
992982 CAATGCATTT
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 116 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTAATCATTATTAATGGG
Found at i:995387 original size:31 final size:31
Alignment explanation
Indices: 995352--995573 Score: 381
Period size: 31 Copynumber: 7.2 Consensus size: 31
995342 GGTCACAATA
995352 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
995383 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
995414 CAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
995445 TAAACTGTTAATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
995476 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
995507 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
995538 TAAATTGTTCATATGTACCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
995569 TAAAC
1 TAAAC
995574 CCTCGACTCT
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 179 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:996191 original size:64 final size:65
Alignment explanation
Indices: 996083--996306 Score: 249
Period size: 64 Copynumber: 3.5 Consensus size: 65
996073 TAATGAAGGT
* * ** * *
996083 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAAT-ATTATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATTATTAATGGG
* ** *
996147 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATTATTAATGGG
* * * **
996211 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATTATTAATGGG
** *
996274 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
996307 CATTCAAACA
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 130 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAATCATTATTAATGGG
Found at i:1002614 original size:14 final size:15
Alignment explanation
Indices: 1002595--1002629 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
1002585 CCCATCACCC
1002595 AATGCAGGGGAAGG-
1 AATGCAGGGGAAGGA
1002609 AATGCAGGGGAAGGA
1 AATGCAGGGGAAGGA
1002624 AATGCA
1 AATGCA
1002630 TACACTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.40, C:0.09, G:0.43, T:0.09
Consensus pattern (15 bp):
AATGCAGGGGAAGGA
Found at i:1007736 original size:9 final size:9
Alignment explanation
Indices: 1007724--1007781 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
1007714 ACAAAACACG
1007724 TAAAAATAA
1 TAAAAATAA
1007733 TAAAAATAAA
1 TAAAAAT-AA
1007743 TAAAAATAA
1 TAAAAATAA
1007752 -ACAAAATGAA
1 TA-AAAAT-AA
*
1007762 T-AAAATAT
1 TAAAAATAA
1007770 TAAAAA-AA
1 TAAAAATAA
1007778 TAAA
1 TAAA
1007782 GATACAGATA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.19
9 23 0.55
10 11 0.26
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
TAAAAATAA
Found at i:1007746 original size:19 final size:18
Alignment explanation
Indices: 1007724--1007781 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 18
1007714 ACAAAACACG
1007724 TAAAAATAATAAAAATAAA
1 TAAAAATAA-AAAAATAAA
*
1007743 TAAAAATAAACAAAATGAA
1 TAAAAATAAA-AAAATAAA
1007762 TAAAATATTAAAAAAATAAA
1 TAAAA-A-TAAAAAAATAAA
1007782 GATACAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 21 0.62
20 8 0.24
21 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
TAAAAATAAAAAAATAAA
Found at i:1007843 original size:18 final size:17
Alignment explanation
Indices: 1007810--1007857 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1007800 ATATTAATGG
1007810 AGTAAAAAAATAAAAAA
1 AGTAAAAAAATAAAAAA
*
1007827 AGTAAAATAAATTAAAAA
1 AGTAAAA-AAATAAAAAA
1007845 AG-AATAAAAATAA
1 AGTAA-AAAAATAA
1007858 TGTATACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AGTAAAAAAATAAAAAA
Found at i:1008056 original size:39 final size:39
Alignment explanation
Indices: 1007995--1008082 Score: 113
Period size: 39 Copynumber: 2.3 Consensus size: 39
1007985 AATATAATAT
* *
1007995 ATATAAATAAATAAAAACAAAAAATAAAATATTAAGAAA
1 ATATATATATATAAAAACAAAAAATAAAATATTAAGAAA
* * * *
1008034 ATATATATATATAAACATAAAAAATATAATATTATGAAA
1 ATATATATATATAAAAACAAAAAATAAAATATTAAGAAA
*
1008073 AAATATATAT
1 ATATATATAT
1008083 GCATAGTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (39 bp):
ATATATATATATAAAAACAAAAAATAAAATATTAAGAAA
Found at i:1008113 original size:2 final size:2
Alignment explanation
Indices: 1008106--1008170 Score: 77
Period size: 2 Copynumber: 34.5 Consensus size: 2
1008096 AGAAAAATTA
1008106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
*
1008147 AG AT AT AT AT A- AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1008171 AATAAAAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
1 5 0.09
2 49 0.88
3 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1008214 original size:21 final size:22
Alignment explanation
Indices: 1008160--1008214 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
1008150 TATATATAAT
1008160 AATATAATATAAATAAAAAAAAG
1 AATATAAT-TAAATAAAAAAAAG
* *
1008183 AATAT-AGTAAATAAATAAAA-
1 AATATAATTAAATAAAAAAAAG
1008203 AATATAATTAAA
1 AATATAATTAAA
1008215 AGTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.18
21 17 0.61
22 1 0.04
23 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (22 bp):
AATATAATTAAATAAAAAAAAG
Found at i:1008965 original size:71 final size:71
Alignment explanation
Indices: 1008824--1008957 Score: 268
Period size: 71 Copynumber: 1.9 Consensus size: 71
1008814 TTTGAACAAC
1008824 GTTGGTTGTTGTTAGAGGAGTCGAGTTCTCAGACAACTCGTTTTGATTATTGCCCCCCCCCCCCC
1 GTTGGTTGTTGTTAGAGGAGTCGAGTTCTCAGACAACTCGTTTTGATTATTGCCCCCCCCCCCCC
1008889 TTCTCT
66 TTCTCT
1008895 GTTGGTTGTTGTTAGAGGAGTCGAGTTCTCAGACAACTCGTTTTGATTATTGCCCCCCCCCCC
1 GTTGGTTGTTGTTAGAGGAGTCGAGTTCTCAGACAACTCGTTTTGATTATTGCCCCCCCCCCC
1008958 TTCTCTCTCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.34
Consensus pattern (71 bp):
GTTGGTTGTTGTTAGAGGAGTCGAGTTCTCAGACAACTCGTTTTGATTATTGCCCCCCCCCCCCC
TTCTCT
Found at i:1010295 original size:2 final size:2
Alignment explanation
Indices: 1010288--1010349 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1010278 CTTCATCTGT
1010288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1010330 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1010350 CTAAATTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1027969 original size:16 final size:16
Alignment explanation
Indices: 1027948--1027980 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1027938 CAGGTTGGCC
1027948 TAATAATACTGGTGTT
1 TAATAATACTGGTGTT
1027964 TAATAATACTGGTGTT
1 TAATAATACTGGTGTT
1027980 T
1 T
1027981 CTGGCTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (16 bp):
TAATAATACTGGTGTT
Found at i:1035549 original size:31 final size:31
Alignment explanation
Indices: 1035484--1035564 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
1035474 TCAAATAGCA
* * *
1035484 ATAAGTTTTAGAACCATTTTATAACAGTTCG
1 ATAAGTTTAAGAACCATTCTATAACAATTCG
* *
1035515 ATAAGTTTAAGAACCATTCTATAATAATTTG
1 ATAAGTTTAAGAACCATTCTATAACAATTCG
1035546 ATAAAGTTTAATG-ACCATT
1 AT-AAGTTTAA-GAACCATT
1035565 TTGTAACCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 28 0.65
32 14 0.33
33 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (31 bp):
ATAAGTTTAAGAACCATTCTATAACAATTCG
Found at i:1037441 original size:2 final size:2
Alignment explanation
Indices: 1037386--1037425 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1037376 CTAGTTCCCG
1037386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1037426 GGTATGGCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1043657 original size:2 final size:2
Alignment explanation
Indices: 1043650--1043695 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1043640 TACTTGCATG
1043650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1043692 TA TA
1 TA TA
1043696 AGTGAAACTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1055272 original size:20 final size:20
Alignment explanation
Indices: 1055247--1055287 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1055237 ACATATTGAG
*
1055247 CTTGTTCAAGTTTCTTTTCC
1 CTTGTTCAAGTCTCTTTTCC
1055267 CTTGTTCAAGTCTCTTTTCC
1 CTTGTTCAAGTCTCTTTTCC
1055287 C
1 C
1055288 ACTTTCGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.51
Consensus pattern (20 bp):
CTTGTTCAAGTCTCTTTTCC
Found at i:1068709 original size:25 final size:25
Alignment explanation
Indices: 1068677--1068724 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1068667 TTTTTTCATT
* *
1068677 TAAATACTTCAAG-TATTTTTTTGG
1 TAAATACTTAAAGTTATATTTTTGG
1068701 TAAAGTACTTAAAGTTATATTTTT
1 TAAA-TACTTAAAGTTATATTTTT
1068725 AGTCAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 8 0.40
26 8 0.40
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (25 bp):
TAAATACTTAAAGTTATATTTTTGG
Found at i:1068918 original size:28 final size:28
Alignment explanation
Indices: 1068861--1068929 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 28
1068851 GAATTTTTTT
** *
1068861 AATACTTTAGGTACTTATTTTGACAAAA
1 AATACTTTAAATATTTATTTTGACAAAA
* *
1068889 AATAATTTTAAATATTTATTTTGA-TAAA
1 AAT-ACTTTAAATATTTATTTTGACAAAA
1068917 AATACTTTAAATA
1 AATACTTTAAATA
1068930 CTTAAATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 9 0.26
28 9 0.26
29 16 0.47
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (28 bp):
AATACTTTAAATATTTATTTTGACAAAA
Found at i:1071389 original size:2 final size:2
Alignment explanation
Indices: 1071382--1071406 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1071372 TAAGTTAATT
1071382 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1071407 GAGAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1074203 original size:2 final size:2
Alignment explanation
Indices: 1074196--1074224 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1074186 ACTGGAAGGG
1074196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1074225 TGATTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1079752 original size:28 final size:30
Alignment explanation
Indices: 1079702--1079769 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
1079692 TAAACTATAT
1079702 ATTATATATAATTTCAAAAATGTTTT-AAA
1 ATTATATATAATTTCAAAAATGTTTTAAAA
*
1079731 ATTATATATATTTTC-AAAATGTTTTCAAAA
1 ATTATATATAATTTCAAAAATGTTTT-AAAA
*
1079761 ACTATATAT
1 ATTATATAT
1079770 TATATATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 10 0.29
29 14 0.40
30 11 0.31
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (30 bp):
ATTATATATAATTTCAAAAATGTTTTAAAA
Found at i:1079770 original size:28 final size:28
Alignment explanation
Indices: 1079704--1079770 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
1079694 AACTATATAT
*
1079704 TATATATAATTTCAAAAATGTTTTAAAA
1 TATATATATTTTCAAAAATGTTTTAAAA
1079732 TTATATATATTTTC-AAAATGTTTTCAAAA
1 -TATATATATTTTCAAAAATGTTTT-AAAA
1079761 -ACTATATATT
1 TA-TATATATT
1079771 ATATATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 1 0.03
28 18 0.51
29 16 0.46
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (28 bp):
TATATATATTTTCAAAAATGTTTTAAAA
Found at i:1079814 original size:38 final size:39
Alignment explanation
Indices: 1079733--1079814 Score: 130
Period size: 38 Copynumber: 2.1 Consensus size: 39
1079723 GTTTTAAAAT
1079733 TATATATATTTTCAAAATGTTTTCAAAAACTATATATTA
1 TATATATATTTTCAAAATGTTTTCAAAAACTATATATTA
* * *
1079772 TATATATTTTTTCAAAATG-TTTCCAAAATTATATATTA
1 TATATATATTTTCAAAATGTTTTCAAAAACTATATATTA
1079810 TATAT
1 TATAT
1079815 TTCAAAACCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 22 0.55
39 18 0.45
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (39 bp):
TATATATATTTTCAAAATGTTTTCAAAAACTATATATTA
Found at i:1079890 original size:37 final size:38
Alignment explanation
Indices: 1079846--1079921 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
1079836 ACTATACACG
*
1079846 TTTTCAAAAAATATGTTTTAAAAACATATA-ATATATA
1 TTTTCAAAAAATATGTTTGAAAAACATATATATATATA
* * *
1079883 TTTTCAAAAATTATGTTTGAAATATATATATATATATA
1 TTTTCAAAAAATATGTTTGAAAAACATATATATATATA
1079921 T
1 T
1079922 ATATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
37 26 0.76
38 8 0.24
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (38 bp):
TTTTCAAAAAATATGTTTGAAAAACATATATATATATA
Found at i:1079911 original size:2 final size:2
Alignment explanation
Indices: 1079904--1079946 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
1079894 TATGTTTGAA
1079904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
1079946 A
1 A
1079947 ATAATACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1097065 original size:3 final size:3
Alignment explanation
Indices: 1097059--1097099 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
1097049 TTTTTATTTG
1097059 ATT ATT ATT -TAT ATT ATT ATT ATT ATT ATAT ATT ATT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT ATT ATT A
1097100 AATAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1098470 original size:16 final size:16
Alignment explanation
Indices: 1098451--1098506 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
1098441 TTACTTTTTA
1098451 TATTTAATTTTAATTT
1 TATTTAATTTTAATTT
1098467 TATTT-ATTTTACTCATTGTT
1 TATTTAATTTTA---A-T-TT
1098487 TATTTATATTTTAATTT
1 TATTTA-ATTTTAATTT
1098504 TAT
1 TAT
1098507 ATGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 5 0.15
18 2 0.06
19 2 0.06
20 7 0.21
22 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTAATTTTAATTT
Found at i:1100877 original size:7 final size:7
Alignment explanation
Indices: 1100861--1100902 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
1100851 TTTTCATACA
1100861 TGCA-TT
1 TGCATTT
1100867 TGCATTT
1 TGCATTT
1100874 TGCATCTT
1 TGCAT-TT
1100882 TGCATTT
1 TGCATTT
*
1100889 TTCATTT
1 TGCATTT
1100896 TGCATTT
1 TGCATTT
1100903 ATACTCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 4 0.12
7 21 0.66
8 7 0.22
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (7 bp):
TGCATTT
Found at i:1100885 original size:15 final size:14
Alignment explanation
Indices: 1100861--1100902 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
1100851 TTTTCATACA
1100861 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
1100874 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
*
1100889 TTCATTTTGCATTT
1 TGCATTTTGCATTT
1100903 ATACTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 13 0.50
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1104320 original size:14 final size:14
Alignment explanation
Indices: 1104297--1104357 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
1104287 GCAAAGAAAG
*
1104297 AAGAAGAAGAAAAA
1 AAGAAAAAGAAAAA
1104311 AAGAAAAAGAAAACA
1 AAGAAAAAGAAAA-A
*
1104326 AA-AACAAAAACAAAA
1 AAGAA-AAAGA-AAAA
*
1104341 AACAAAAAGGAAAAA
1 AAGAAAAA-GAAAAA
1104356 AA
1 AA
1104358 AAAGAAGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 14 0.36
15 19 0.49
16 6 0.15
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAAAAA
Found at i:1104328 original size:17 final size:18
Alignment explanation
Indices: 1104307--1104359 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
1104297 AAGAAGAAGA
*
1104307 AAAAAAGAAAAAGAAAAC
1 AAAAACGAAAAAGAAAAC
* *
1104325 AAAAACAAAAACAAAAAAC
1 AAAAACGAAAA-AGAAAAC
*
1104344 AAAAAGGAAAAA-AAAA
1 AAAAACGAAAAAGAAAA
1104360 AGAAGGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 15 0.52
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAACGAAAAAGAAAAC
Found at i:1104329 original size:12 final size:11
Alignment explanation
Indices: 1104300--1104363 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
1104290 AAGAAAGAAG
*
1104300 AAGAAGAAAAA
1 AAGAAAAAAAA
*
1104311 AAGAAAAAGAA
1 AAGAAAAAAAA
*
1104322 AACAAAAACAAA
1 AAGAAAAA-AAA
*
1104334 AACAAAAAACAAA
1 AA-GAAAAA-AAA
1104347 AAGGAAAAAAAA
1 AA-GAAAAAAAA
1104359 AAGAA
1 AAGAA
1104364 GGAAAATTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 19 0.43
12 9 0.20
13 16 0.36
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1106911 original size:92 final size:93
Alignment explanation
Indices: 1106517--1107252 Score: 1049
Period size: 92 Copynumber: 8.0 Consensus size: 93
1106507 GAACAAATAC
*
1106517 AATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1106574 A-AACCAATCATTGAATTT-GAAAGATG
66 AGAACCAATCATTGAATTTAGAAAGATG
1106600 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-CC-
* * *
1106665 AAAAAACCAATCATTAAATTT-GAAAGATG
64 ACAGAACCAATCATTGAATTTAGAAAGATG
* * *
1106694 AATGTGTTAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCA
* *
1106759 CAAAACCAATCATTGGATATTA-AAAGATG
65 CAGAACCAATCATTGAAT-TTAGAAAGATG
1106788 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
* *
1106853 AGAACCAGTTATTGAATTTAG-AAGATG
66 AGAACCAATCATTGAATTTAGAAAGATG
*
1106880 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCA
*
1106945 CAAAACCAATCATTGGAATTT-GAAAGATG
65 CAGAACCAATCATT-GAATTTAGAAAGATG
1106974 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
* *
1107039 AGAACCAGTTATTGAATTTAG-AAGATG
66 AGAACCAATCATTGAATTTAGAAAGATG
1107066 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
* * *
1107131 AGAACCAGTTATTG-ATTTTGAAAGATG
66 AGAACCAATCATTGAATTTAGAAAGATG
* * * * * * * *
1107158 AATATGCTAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATTTGGTTTGATATAAAACGC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1107223 AGAACCAATCATTGGAA-TTA-AAAGATG
66 AGAACCAATCATT-GAATTTAGAAAGATG
1107250 AAT
1 AAT
1107253 TGCATGATCG
Statistics
Matches: 596, Mismatches: 35, Indels: 35
0.89 0.05 0.05
Matches are distributed among these distances:
83 54 0.09
85 1 0.00
91 5 0.01
92 243 0.41
93 73 0.12
94 218 0.37
95 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (93 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
AGAACCAATCATTGAATTTAGAAAGATG
Found at i:1106948 original size:186 final size:185
Alignment explanation
Indices: 1106517--1107252 Score: 1068
Period size: 186 Copynumber: 4.0 Consensus size: 185
1106507 GAACAAATAC
*
1106517 AATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-------
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCAC
*
1106573 AAAACCAATCATTGAAT-TTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAG
66 AAAACCAATCATTGGATATTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAG
* * *
1106637 TTATCTGATCTGGTTTGGTATGAACCCTAAAAAACCAATCATTAAATTT-GAAAGATG
131 TTATCTGATCTGGTTTGGTATGAA-CC-ACAGAACCAATCATTGAATTTAG-AAGATG
* * *
1106694 AATGTGTTAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AAACCA
*
1106759 CAAAACCAATCATTGGATATTAAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
65 CAAAACCAATCATTGGATATTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
* *
1106824 GTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTAGAAGATG
130 GTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATTGAATTTAGAAGATG
1106880 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AAACCA
1106945 CAAAACCAATCATTGGA-ATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTG
65 CAAAACCAATCATTGGATA-TTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTG
* *
1107009 AGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTAGAAGATG
129 AGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATTGAATTTAGAAGATG
*
1107066 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCAC
* * * * * * *
1107131 AGAACCAGTTATT-GATTTTGAAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTAAG
66 AAAACCAATCATTGGATATTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAG
* * * * * *
1107195 TTATCTGATTTGGTTTGATATAAAACGCAGAACCAATCATTGGAA-TTAAAAGATG
131 TTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATT-GAATTTAGAAGATG
1107250 AAT
1 AAT
1107253 TGCATGATCG
Statistics
Matches: 512, Mismatches: 32, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
177 51 0.10
179 1 0.00
184 92 0.18
185 20 0.04
186 259 0.51
187 19 0.04
188 70 0.14
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (185 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCAC
AAAACCAATCATTGGATATTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAG
TTATCTGATCTGGTTTGGTATGAACCACAGAACCAATCATTGAATTTAGAAGATG
Found at i:1108339 original size:113 final size:112
Alignment explanation
Indices: 1107974--1108544 Score: 745
Period size: 112 Copynumber: 5.1 Consensus size: 112
1107964 TGTCAGTTAG
*
1107974 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
* *
1108039 AACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
66 AACTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTGCCAGAAAA
* *
1108086 AGTTCATAATAAGAAGAACTCATCTGAAG-AGAGAATAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-GAAGAAGAAGTTCATAATAAGAAGAACTTGTT
* *
1108150 CAACTTTTGCTTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAA
65 CAACTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTGCCAGAAAA
* * * *
1108198 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
* * * * *
1108263 AACTTTTTGCTCAAATCCATCACTTGATGGATTATCTTCT-CCAGAAAA
66 AAC-TTTTGCTTAAATTCATCATTTGATGGATCAGCTT-TGCCAGAAAA
* *
1108311 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGACGAAGAAGTTCATAATGAA-AAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-AAGAAGAACTTGTT
* * ** *
1108375 CAACCTTTTGTTTAAATTCATCATTTGATGGATCAGCATCCCCAGTGAAAG
65 CAA-CTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTGCCA--GAAAA
* * *
1108426 AGTTCATAATGAGAAAAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
* * * * * * *
1108491 AACTTTTCGCTCAAATTCATCACTCGATAGATCAACTTT-TCAGAAAG
66 AACTTTT-GCTTAAATTCATCATTTGATGGATCAGCTTTGCCAGAAAA
1108538 AGTTCAT
1 AGTTCAT
1108545 CTGAAGAAAG
Statistics
Matches: 407, Mismatches: 41, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
111 1 0.00
112 180 0.44
113 128 0.31
114 12 0.03
115 86 0.21
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
AACTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTGCCAGAAAA
Found at i:1108693 original size:17 final size:17
Alignment explanation
Indices: 1108646--1108695 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1108636 TTCCGGAAAG
*
1108646 AGTTCACAATGAGAAGA
1 AGTTCATAATGAGAAGA
* *
1108663 A-CTCAT-TTGAAGAAGA
1 AGTTCATAATG-AGAAGA
1108679 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
1108696 GCTTGTTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.08
16 10 0.40
17 11 0.44
18 2 0.08
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (17 bp):
AGTTCATAATGAGAAGA
Found at i:1108928 original size:3 final size:3
Alignment explanation
Indices: 1108922--1108968 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
1108912 TTTTTATTTG
1108922 ATT ATT ATT -TAT ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
1108968 A
1 A
1108969 AATAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.02
3 36 0.88
4 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1108938 original size:9 final size:10
Alignment explanation
Indices: 1108915--1108967 Score: 67
Period size: 9 Copynumber: 5.5 Consensus size: 10
1108905 ACTAGTTTTT
1108915 TTATTTGATTA
1 TTATTT-ATTA
1108926 TTATTTA-TA
1 TTATTTATTA
1108935 TTA-TTATTA
1 TTATTTATTA
1108944 TTA-TTATTA
1 TTATTTATTA
*
1108953 TTATATATTA
1 TTATTTATTA
1108963 TTATT
1 TTATT
1108968 AAATAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
8 3 0.08
9 19 0.50
10 10 0.26
11 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTATTTATTA
Found at i:1116507 original size:64 final size:64
Alignment explanation
Indices: 1116371--1116530 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
1116361 ATTGTTCAGT
* * * *
1116371 GTGTATCGATGCACAGGAAATGCATCGATGCA-CCCATTAAAATGGAAACATCGAATGCAATTA
1 GTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGGCAATTA
* * ** *
1116434 GTGCATCGATGCATAAGG-AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTG
1 GTGTATCGATGCAT-AGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGGCAATTA
* *
1116498 GTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 GTGTATCGATGCATAGGAAGTGCATCGATGCAC
1116531 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 27 0.33
64 56 0.67
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (64 bp):
GTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGGCAATTA
Found at i:1119438 original size:64 final size:64
Alignment explanation
Indices: 1119303--1119440 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
1119293 GTTCAGTGTG
* * * * *
1119303 TATCGATGCA-CAGGAAGTGCATTGATGCACCCATTAAAATGGAAACATCGAATGCAATTAGTG
1 TATCGATGCATAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTA
* * * ** *
1119366 CATTGATGCATAAGG-AGTGCATCGATGCACCCTCTTAAAATGAAAACATCGAAGGTGATTGGTA
1 TATCGATGCATAAGGAAGTGCATCGATGCACCC-ATTAAAATGAAAACATCGAAGGCAATTAGTA
1119430 TATCGATGCAT
1 TATCGATGCAT
1119441 GGATAGTGTG
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
63 24 0.40
64 36 0.60
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (64 bp):
TATCGATGCATAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTA
Found at i:1119492 original size:20 final size:20
Alignment explanation
Indices: 1119467--1119504 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1119457 CACATGTTAA
1119467 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
* *
1119487 AGAATGTATTGATGCACT
1 AGAATGCATCGATGCACT
1119505 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:1123601 original size:23 final size:23
Alignment explanation
Indices: 1123557--1123601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1123547 AGTAAGTATG
* *
1123557 GGTTGGACGTTAACCTGCTGACA
1 GGTTAGACGTTAACATGCTGACA
*
1123580 GGTTAGACGTTAACATGTTGAC
1 GGTTAGACGTTAACATGCTGAC
1123602 CGGGATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (23 bp):
GGTTAGACGTTAACATGCTGACA
Found at i:1138288 original size:15 final size:15
Alignment explanation
Indices: 1138268--1138297 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1138258 AACTCAAGAA
1138268 TTTTTATCTAAAACT
1 TTTTTATCTAAAACT
1138283 TTTTTATCTAAAACT
1 TTTTTATCTAAAACT
1138298 GGTCATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTATCTAAAACT
Found at i:1138895 original size:21 final size:21
Alignment explanation
Indices: 1138862--1138901 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1138852 AGTCTAAATG
* *
1138862 TACCAAGTGTTTTATTAAACA
1 TACCAAGTCTTTTAATAAACA
*
1138883 TACCAATTCTTTTAATAAA
1 TACCAAGTCTTTTAATAAA
1138902 ATAATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
TACCAAGTCTTTTAATAAACA
Found at i:1139724 original size:11 final size:11
Alignment explanation
Indices: 1139705--1139739 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1139695 TAATTTTTTT
1139705 TAGTAAAATGA
1 TAGTAAAATGA
*
1139716 TAGTGAAATGA
1 TAGTAAAATGA
1139727 TAGTAAAATGA
1 TAGTAAAATGA
1139738 TA
1 TA
1139740 AACAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (11 bp):
TAGTAAAATGA
Found at i:1140815 original size:15 final size:15
Alignment explanation
Indices: 1140768--1140818 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
1140758 GAGACATTAC
1140768 CCGCCCCGCATCCGT
1 CCGCCCCGCATCCGT
* *
1140783 CCACCCCGCATCTGT
1 CCGCCCCGCATCCGT
*
1140798 CCGCCCCACATCCGT
1 CCGCCCCGCATCCGT
1140813 CCGCCC
1 CCGCCC
1140819 AGCTAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.10, C:0.61, G:0.16, T:0.14
Consensus pattern (15 bp):
CCGCCCCGCATCCGT
Found at i:1149625 original size:51 final size:51
Alignment explanation
Indices: 1149543--1149639 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
1149533 ACATATATTT
* *
1149543 TATTATATTTATATGTTGATGTGGGTCTATGTGTATGCATATATACCTATA
1 TATTATATTCATATGTTGATGTGGCTCTATGTGTATGCATATATACCTATA
* *
1149594 TATTATATTCATATGGTT-ATGTAGGCT-TATGTTTATGTATATATAC
1 TATTATATTCATAT-GTTGATGT-GGCTCTATGTGTATGCATATATAC
1149640 AAATGTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
51 34 0.85
52 6 0.15
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.48
Consensus pattern (51 bp):
TATTATATTCATATGTTGATGTGGCTCTATGTGTATGCATATATACCTATA
Found at i:1149656 original size:2 final size:2
Alignment explanation
Indices: 1149651--1149677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1149641 AATGTAATTT
1149651 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1149678 TAGTGGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1156062 original size:108 final size:108
Alignment explanation
Indices: 1155873--1156071 Score: 335
Period size: 108 Copynumber: 1.8 Consensus size: 108
1155863 ATTCATGACA
* *
1155873 GAGAATGAAAGAAAAGAGGGAGAGAATTGAGACAAGTAGAGAGCGGCTGGGGAGTTAGGGTTAGA
1 GAGAATGAAAGAAAAGAGGGAGAGAATTGAGACAAGGAGAGAGCGGCTAGGGAGTTAGGGTTAGA
1155938 TTTTTACCCATTATAACCCATATATTCGGTGGCCGGCGTGAAG
66 TTTTTACCCATTATAACCCATATATTCGGTGGCCGGCGTGAAG
* * * *
1155981 GAGAATGAAAGAAAAGAGGGAGGGAGTTGAGAGAAGGAGAGAGCGGTTAGGGAGTTAGGGTTAGA
1 GAGAATGAAAGAAAAGAGGGAGAGAATTGAGACAAGGAGAGAGCGGCTAGGGAGTTAGGGTTAGA
*
1156046 TTTTTACCCATTATAACCCTTATATT
66 TTTTTACCCATTATAACCCATATATT
1156072 TGGTTTCCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 84 1.00
ACGTcount: A:0.34, C:0.10, G:0.33, T:0.23
Consensus pattern (108 bp):
GAGAATGAAAGAAAAGAGGGAGAGAATTGAGACAAGGAGAGAGCGGCTAGGGAGTTAGGGTTAGA
TTTTTACCCATTATAACCCATATATTCGGTGGCCGGCGTGAAG
Found at i:1156884 original size:2 final size:2
Alignment explanation
Indices: 1156877--1156914 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1156867 TTCCATGTTA
1156877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1156915 CCTTTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1158564 original size:10 final size:10
Alignment explanation
Indices: 1158551--1158610 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
1158541 CGTTCGATTA
1158551 TATGTTCGTT
1 TATGTTCGTT
1158561 TATGTTCGTT
1 TATGTTCGTT
* *
1158571 CAT-TTATGTT
1 TATGTT-CGTT
1158581 TATGTTCGTT
1 TATGTTCGTT
* *
1158591 CAT-TTATGTT
1 TATGTT-CGTT
1158601 TATGTTCGTT
1 TATGTTCGTT
1158611 CATTTATGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:1158583 original size:20 final size:20
Alignment explanation
Indices: 1158558--1158620 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
1158548 TTATATGTTC
1158558 GTTTATGTTCGTTCATTTAT
1 GTTTATGTTCGTTCATTTAT
1158578 GTTTATGTTCGTTCATTTAT
1 GTTTATGTTCGTTCATTTAT
1158598 GTTTATGTTCGTTCATTTAT
1 GTTTATGTTCGTTCATTTAT
1158618 GTT
1 GTT
1158621 CGAGCTGAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.60
Consensus pattern (20 bp):
GTTTATGTTCGTTCATTTAT
Found at i:1159438 original size:2 final size:2
Alignment explanation
Indices: 1159431--1159455 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1159421 TGCAATCATC
1159431 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1159456 CAAGCTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1159552 original size:2 final size:2
Alignment explanation
Indices: 1159545--1159588 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1159535 CAAGTAATGA
1159545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1159587 AT
1 AT
1159589 TTCAATTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1170052 original size:26 final size:26
Alignment explanation
Indices: 1170023--1170083 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
1170013 AAATAGTGTG
1170023 GGGACTGGGGGAGGACAAATCCATAA
1 GGGACTGGGGGAGGACAAATCCATAA
1170049 GGGACTGGGGGAGGACAAATCCATAA
1 GGGACTGGGGGAGGACAAATCCATAA
1170075 GGGACTGGG
1 GGGACTGGG
1170084 ACAAGTCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.43, T:0.11
Consensus pattern (26 bp):
GGGACTGGGGGAGGACAAATCCATAA
Found at i:1180760 original size:222 final size:220
Alignment explanation
Indices: 1180366--1180849 Score: 783
Period size: 222 Copynumber: 2.2 Consensus size: 220
1180356 TATATTGTAA
* * * *
1180366 AGTATCTATCCTTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAATATATTTATTACCTTT
1 AGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTACATTT
*
1180431 GGTTAATATTGTTAAATTTAAATTCTCAATAATATTTTATAAAATATCAAAACAATCAAATAATT
66 GGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATT
* *
1180496 TTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAGAA
131 TTTTGCGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAA
1180561 ATTGAAACATAAATTACATAACTTT
196 ATTGAAACATAAATTACATAACTTT
*
1180586 -GTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATTAT
1 AGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATA--T-TTATTAC
*
1180650 ATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAAT
62 ATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT
1180714 AATTTTTTGCGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
127 AATTTTTTGCGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
1180779 AAAAATTGAAACATAAATTACATAACTTT
192 AAAAATTGAAACATAAATTACATAACTTT
1180808 AAAAAAAGTATATATCATTTTTATAAAAGTGTCCATACTTAT
1 ------AGTATATATCATTTTTATAAAAGTGTCCATACTTAT
1180850 AAAAGTAATA
Statistics
Matches: 244, Mismatches: 9, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
219 40 0.16
220 9 0.04
222 104 0.43
223 56 0.23
229 35 0.14
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (220 bp):
AGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTACATTT
GGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATT
TTTTGCGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAA
ATTGAAACATAAATTACATAACTTT
Found at i:1180862 original size:15 final size:15
Alignment explanation
Indices: 1180842--1180871 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1180832 AAAAGTGTCC
1180842 ATACTTATAAAAGTA
1 ATACTTATAAAAGTA
1180857 ATACTTATAAAAGTA
1 ATACTTATAAAAGTA
1180872 GGTCTAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
ATACTTATAAAAGTA
Found at i:1181166 original size:20 final size:19
Alignment explanation
Indices: 1181143--1181189 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1181133 CGATATACCA
1181143 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1181163 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1181183 GGTAAAA
1 GGTAAAA
1181190 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1181267 original size:181 final size:182
Alignment explanation
Indices: 1180931--1181403 Score: 700
Period size: 181 Copynumber: 2.6 Consensus size: 182
1180921 GATCCAAATT
* * * *
1180931 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
1180995 AAAACCGATAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
1181060 CGTGAATTTAAAAGAGAAACAGTTTTAAATCCTATAA-AGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAATA-TGTCGATACTTTAA
*
1181113 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
1181178 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* **
1181242 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATATGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAATATGTCGATACTTTAA
* * * *
1181294 AAAAATATATCGATCCACAACGATAAAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
*
1181359 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1181404 CGTAAGTACG
Statistics
Matches: 265, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
181 167 0.63
182 98 0.37
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAATATGTCGATACTTTAA
Found at i:1181340 original size:20 final size:19
Alignment explanation
Indices: 1181315--1181370 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1181305 GATCCACAAC
*
1181315 GATAAAACAGGTAAAAATAT
1 GATAAAACCGGTAAAAA-AT
*
1181335 GATAAAACCGGTATCAAAAT
1 GATAAAACCGGTA-AAAAAT
1181355 GATAAAACCGGTAAAA
1 GATAAAACCGGTAAAA
1181371 TGATACCGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 27 0.84
21 3 0.09
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (19 bp):
GATAAAACCGGTAAAAAAT
Found at i:1181372 original size:17 final size:19
Alignment explanation
Indices: 1181333--1181375 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1181323 AGGTAAAAAT
1181333 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1181353 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1181370 ATGATA
1 ATGATA
1181376 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1183615 original size:21 final size:21
Alignment explanation
Indices: 1183591--1183634 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1183581 AAGACAATCA
1183591 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1183612 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1183633 AG
1 AG
1183635 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1183710 original size:33 final size:33
Alignment explanation
Indices: 1183668--1183733 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1183658 AAATAGATGG
*
1183668 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1183701 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1183734 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1185549 original size:19 final size:19
Alignment explanation
Indices: 1185525--1185573 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1185515 AATGTATGGT
1185525 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1185544 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1185563 TATTTTTGTAT
1 TAATTTTGTAT
1185574 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1186183 original size:199 final size:199
Alignment explanation
Indices: 1185692--1187062 Score: 2415
Period size: 199 Copynumber: 6.9 Consensus size: 199
1185682 CAAAATGGCC
*
1185692 AACAGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
1185757 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
1185822 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
1185887 TGGAA
195 TGGAA
1185892 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
1185957 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
1186022 GAATATGTCTAAATAATGTGTCGACA-TTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
1186086 TGGAA
195 TGGAA
* *
1186091 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAATGGCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
*
1186156 CCAAAAGGT-TAATGTAATATATAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
65 CCAAAA-GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
* * *
1186220 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCAATATTTTTGGTCCATAATGA
129 AGAATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
1186285 ATGGAA
194 ATGGAA
* *
1186291 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAATGGCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
1186356 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACAGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* * ****
1186421 AATATGTCTAAATAATGTGTCGACACCATTTAAAAAAGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
1186486 GGAA
196 GGAA
1186490 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1186555 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
1186620 AATATGTCTAAATAATGTGTCGACACGTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
1186685 GGAA
196 GGAA
1186689 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
1186754 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGATAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* * ****
1186819 AATATGTCTAAATAATGTGTCGACACCATTTAAAAAAGTGTCGATATTTTTGGTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
1186884 GGAA
196 GGAA
* * *
1186888 AACAGTGTGCAGCCATAAGGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
1186953 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
1187018 AATATGTCTAAATAATGTGTCGACA-CTTTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATA
1187063 CTAATTTAAA
Statistics
Matches: 1122, Mismatches: 46, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
198 16 0.01
199 847 0.75
200 259 0.23
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (199 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
GGAA
Found at i:1188547 original size:12 final size:12
Alignment explanation
Indices: 1188525--1188618 Score: 107
Period size: 12 Copynumber: 7.8 Consensus size: 12
1188515 CAAGCGGTCA
*
1188525 ATGAAGATGAAG
1 ATGACGATGAAG
*
1188537 CTGACGATGAAG
1 ATGACGATGAAG
*
1188549 ATGACGATGATG
1 ATGACGATGAAG
1188561 ATGACGATGAAG
1 ATGACGATGAAG
*
1188573 CTGACGATGAAG
1 ATGACGATGAAG
* *
1188585 ATGATGATGATG
1 ATGACGATGAAG
* *
1188597 ATGATGATGATG
1 ATGACGATGAAG
*
1188609 ATGATGATGA
1 ATGACGATGA
1188619 TGATCCAAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 73 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.23
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1188562 original size:3 final size:3
Alignment explanation
Indices: 1188542--1188622 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
1188532 TGAAGCTGAC
* * * * * * *
1188542 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1188590 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1188623 CCAAACAAGT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:1188577 original size:36 final size:36
Alignment explanation
Indices: 1188525--1188606 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
1188515 CAAGCGGTCA
1188525 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
* *
1188561 ATGACGATGAAGCTGACGATGAAGATGATGATGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
*
1188597 ATGATGATGA
1 ATGAAGATGA
1188607 TGATGATGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (36 bp):
ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
Found at i:1188599 original size:18 final size:18
Alignment explanation
Indices: 1188525--1188618 Score: 107
Period size: 18 Copynumber: 5.2 Consensus size: 18
1188515 CAAGCGGTCA
* *
1188525 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGATG
*
1188543 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGATG
* * *
1188561 ATGACGATGAAGCTGACG
1 ATGAAGATGAAGATGATG
*
1188579 ATGAAGATGATGATGATG
1 ATGAAGATGAAGATGATG
* *
1188597 ATGATGATGATGATGATG
1 ATGAAGATGAAGATGATG
1188615 ATGA
1 ATGA
1188619 TGATCCAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.23
Consensus pattern (18 bp):
ATGAAGATGAAGATGATG
Found at i:1189839 original size:16 final size:16
Alignment explanation
Indices: 1189818--1189851 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1189808 TATCCACAAC
*
1189818 AAAGTGTCGATTTAAA
1 AAAGTGTCGATTGAAA
1189834 AAAGTGTCGATTGAAA
1 AAAGTGTCGATTGAAA
1189850 AA
1 AA
1189852 TGTAATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (16 bp):
AAAGTGTCGATTGAAA
Found at i:1190244 original size:23 final size:23
Alignment explanation
Indices: 1190213--1190285 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1190203 ATAGGTAAAA
*
1190213 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1190236 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1190259 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1190282 ATAT
1 ATAT
1190286 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1190675 original size:23 final size:23
Alignment explanation
Indices: 1190644--1190716 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1190634 ATAGGTAAAA
*
1190644 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* **
1190667 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1190690 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1190713 ATAT
1 ATAT
1190717 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1190821 original size:431 final size:431
Alignment explanation
Indices: 1190005--1191491 Score: 2755
Period size: 431 Copynumber: 3.5 Consensus size: 431
1189995 CTTTGGTTAA
* * *
1190005 TATTGTTAAATT-TAAATTCTAAATATTATTTTATAAAATATCAAAATAATCAAATAATTTTTTG
1 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
*
1190069 TGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTA-TTAAAAAAAATTG
66 TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACA-TACTTAAAAAAAATTG
* * *
1190133 AAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCA
130 AAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCA
1190198 ATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAT
195 ATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAT
*
1190263 AATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAATGTCTATACTTTTT
260 AATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTT
1190328 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
325 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
*
1190393 TATAGACGTCTAATGATTTCTTTTTTACGTTACGATATATAT
390 TATAGGCGTCTAATGATTTCTTTTTTACGTTACGATATATAT
1190435 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
1 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
*
1190500 TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTAA
66 TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGA
* *
1190565 AACATAAATTATATAACTTTAAAAGAAGTATCGATCATTTTAATAAAAAGTATGGACACTTTCAA
131 AACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAA
*
1190630 TATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCATTTATATA
196 TATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATA
1190695 ATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTT
261 ATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTT
1190760 CACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATT
326 CACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATT
1190825 ATAGGCGTCTAATGATTTCTTTTTTACGTTACGATATATAT
391 ATAGGCGTCTAATGATTTCTTTTTTACGTTACGATATATAT
1190866 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAA-AAGTCAAATAATTTTTT
1 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAA-TCAAATAATTTTTT
*
1190930 GTGCAAATGAAATTATTAAATTAATATTGTAGGCGGAAAACATGAAACATACTTAAAAAAAATTG
65 GTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTG
1190995 AAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCA
130 AAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCA
1191060 ATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAT
195 ATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAT
*
1191125 AATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCTATACTTTTT
260 AATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTT
1191190 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
325 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
* *
1191255 TATAGGCGTCTAATGATTTATTTTTTACGTTACAATATATAT
390 TATAGGCGTCTAATGATTTCTTTTTTACGTTACGATATATAT
1191297 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
1 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
*
1191362 TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAATATACTTAAAAAAAATTGA
66 TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGA
* *
1191427 AACATAAATTACATAACTTTAAAAGAAGTATCAATCCTTTTTATAAAAAGTATGGACACTTTCAA
131 AACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAA
1191492 CATATTATAA
Statistics
Matches: 1028, Mismatches: 25, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
430 15 0.01
431 1011 0.98
432 2 0.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (431 bp):
TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGA
AACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAA
TATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATA
ATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTT
CACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATT
ATAGGCGTCTAATGATTTCTTTTTTACGTTACGATATATAT
Found at i:1191106 original size:23 final size:23
Alignment explanation
Indices: 1191075--1191147 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1191065 ATAGGTAAAA
*
1191075 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1191098 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1191121 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1191144 ATAT
1 ATAT
1191148 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1194476 original size:23 final size:23
Alignment explanation
Indices: 1194445--1194517 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1194435 ATAGGTAAAA
*
1194445 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1194468 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1194491 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1194514 ATAT
1 ATAT
1194518 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1195736 original size:2 final size:2
Alignment explanation
Indices: 1195729--1195769 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1195719 TTCATTCATT
1195729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1195770 TAATTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1205910 original size:48 final size:48
Alignment explanation
Indices: 1205852--1205964 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 48
1205842 TTATAATTCA
* * *
1205852 AACTCCTAATCTTACTTGAGGGATTTTAGTTGCAAATGTCAGAATTTG
1 AACTCCTAATCTTACTTAAGGGATTTTAGTTACAAACGTCAGAATTTG
* * *
1205900 AACTCTTAATCTTATTTAAGGGATTTTAGTTACAAACGTTAGAATTTG
1 AACTCCTAATCTTACTTAAGGGATTTTAGTTACAAACGTCAGAATTTG
*
1205948 AA-T--TAATATTACTTAAG
1 AACTCCTAATCTTACTTAAG
1205965 ATATTTAGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
45 12 0.21
47 1 0.02
48 44 0.77
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (48 bp):
AACTCCTAATCTTACTTAAGGGATTTTAGTTACAAACGTCAGAATTTG
Found at i:1206565 original size:2 final size:2
Alignment explanation
Indices: 1206558--1206592 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1206548 ATTTACAGTG
1206558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1206593 CCTTTAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1213057 original size:16 final size:15
Alignment explanation
Indices: 1213032--1213083 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
1213022 ATGGATGGTT
1213032 GTGATTGGTTAACTG
1 GTGATTGGTTAACTG
1213047 GTGACTTGG-T---T-
1 GTGA-TTGGTTAACTG
1213058 GTGATTGGTTAACTG
1 GTGATTGGTTAACTG
1213073 GTGACTTGGTT
1 GTGA-TTGGTT
1213084 GTGAGTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
10 4 0.13
11 5 0.17
12 1 0.03
14 1 0.03
15 9 0.30
16 10 0.33
ACGTcount: A:0.15, C:0.08, G:0.35, T:0.42
Consensus pattern (15 bp):
GTGATTGGTTAACTG
Found at i:1213063 original size:26 final size:26
Alignment explanation
Indices: 1213027--1213087 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
1213017 CTGAGATGGA
1213027 TGGTTGTGATTGGTTAACTGGTGACT
1 TGGTTGTGATTGGTTAACTGGTGACT
1213053 TGGTTGTGATTGGTTAACTGGTGACT
1 TGGTTGTGATTGGTTAACTGGTGACT
1213079 TGGTTGTGA
1 TGGTTGTGA
1213088 GTTTCAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.15, C:0.07, G:0.36, T:0.43
Consensus pattern (26 bp):
TGGTTGTGATTGGTTAACTGGTGACT
Found at i:1213346 original size:18 final size:18
Alignment explanation
Indices: 1213323--1213360 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1213313 AAGCATAAGA
1213323 ATTTATTTAAAA-TTAATT
1 ATTTA-TTAAAATTTAATT
1213341 ATTTATTAAAATTTAATT
1 ATTTATTAAAATTTAATT
1213359 AT
1 AT
1213361 AATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTATTAAAATTTAATT
Found at i:1214882 original size:36 final size:36
Alignment explanation
Indices: 1214842--1214944 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
1214832 ACGGTGCTGG
1214842 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
* *
1214878 ACATTGATACACGAATATACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1214914 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1214945 ATACTCAACT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:1222859 original size:36 final size:36
Alignment explanation
Indices: 1222819--1222921 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
1222809 ACAGTGCTGG
*
1222819 ACATTGATACACGAATGTACCAAAACTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
1222855 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
1222891 ACATTGATACACGAATATACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1222922 ATACTCAACT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:1224444 original size:26 final size:26
Alignment explanation
Indices: 1224408--1224460 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1224398 AAGAGAAATT
1224408 CATGTAGGTTATTTTATCTTTAATAA
1 CATGTAGGTTATTTTATCTTTAATAA
1224434 CATGTAGGTTATTTTATCTTTAATAA
1 CATGTAGGTTATTTTATCTTTAATAA
1224460 C
1 C
1224461 CTAACTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (26 bp):
CATGTAGGTTATTTTATCTTTAATAA
Found at i:1229612 original size:13 final size:13
Alignment explanation
Indices: 1229596--1229651 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
1229586 TCAAAGGAAC
1229596 AATAAAAAAATAA
1 AATAAAAAAATAA
*
1229609 AATAAAATAAT-A
1 AATAAAAAAATAA
*
1229621 AATCAAAAGAAAAAA
1 AAT-AAAA-AAATAA
1229636 TAATAATAAAAATAA
1 -AATAA-AAAAATAA
1229651 A
1 A
1229652 TCAAAGAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 4 0.12
13 14 0.41
14 3 0.09
15 8 0.24
16 5 0.15
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (13 bp):
AATAAAAAAATAA
Found at i:1229668 original size:33 final size:30
Alignment explanation
Indices: 1229600--1229656 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1229590 AGGAACAATA
1229600 AAAAAATAAAATAAAATAATAAATCAAAAG
1 AAAAAATAAAATAAAATAATAAATCAAAAG
1229630 AAAAAATAATAAT-AAA-AATAAATCAAA
1 AAAAAATAA-AATAAAATAATAAATCAAA
1229657 GAGGAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.42
30 12 0.46
31 3 0.12
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18
Consensus pattern (30 bp):
AAAAAATAAAATAAAATAATAAATCAAAAG
Done.