Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007864.1 Hibiscus syriacus cultivar Beakdansim tig00110236_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: 1537186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:195289 original size:29 final size:30
Alignment explanation
Indices: 195209--195290 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
195199 TTTCGGAAAA
*
195209 TGAATTACT-GAAATTTGAATTACTGAAATT
1 TGAATTACTGGAAA-ATGAATTACTGAAATT
*
195239 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
*
195269 TGAATT-TTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
195291 ATTTCCGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.31
30 29 0.60
31 4 0.08
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGAAATT
Found at i:195478 original size:19 final size:20
Alignment explanation
Indices: 195451--195489 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
195441 TATTTTAAAA
195451 TATTAAAATAATTTATTTAT
1 TATTAAAATAATTTATTTAT
195471 TATT-AAATAATTTATTTAT
1 TATTAAAATAATTTATTTAT
195490 AATTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAAAATAATTTATTTAT
Found at i:195802 original size:50 final size:51
Alignment explanation
Indices: 195686--195802 Score: 141
Period size: 50 Copynumber: 2.3 Consensus size: 51
195676 AAAAATTATT
* *
195686 ATATATTATTAAAATAAAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAACT--AAAAATATAATA-CTTATATTATTATAATATAATTAA
*
195740 TTATATTATTAAACTAAAAATATAATA-TTATATTATTATAAATATTAA-TAA
1 ATATATTATTAAACTAAAAATATAATACTTATATTATTAT-AATA-TAATTAA
195791 ATATATT-TTAAA
1 ATATATTATTAAA
195803 TATTTTAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
50 17 0.30
51 12 0.21
52 15 0.26
54 13 0.23
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (51 bp):
ATATATTATTAAACTAAAAATATAATACTTATATTATTATAATATAATTAA
Found at i:197107 original size:117 final size:118
Alignment explanation
Indices: 196982--197223 Score: 459
Period size: 119 Copynumber: 2.1 Consensus size: 118
196972 CTCAACTCGA
196982 ACTCAAAACTCGAATT-AAAAAAATTCAAAATCTCAATTAAAACTTGAGACTCAAACTCGATTAG
1 ACTCAAAACTCGAATTAAAAAAAATTCAAAATCTCAATTAAAACTTGAGACTCAAACTCGATTAG
197046 ACTCAATTTTGAGCTCGATCCTCCCCTGAAGCAAACTACTATGAAAGGTTTTC
66 ACTCAATTTTGAGCTCGATCCTCCCCTGAAGCAAACTACTATGAAAGGTTTTC
197099 ACTCAAAACTCGAATTCAAAAAAAATTCAAAATCTCAATTAAAACTTGAGACTCAAACTCGATTA
1 ACTCAAAACTCGAATT-AAAAAAAATTCAAAATCTCAATTAAAACTTGAGACTCAAACTCGATTA
*
197164 GACTTAATTTTGAGCTCGATCCTCCCCTGAAGCAAACTACTATGAAAGGTTTTC
65 GACTCAATTTTGAGCTCGATCCTCCCCTGAAGCAAACTACTATGAAAGGTTTTC
197218 ACTCAA
1 ACTCAA
197224 TTTTGAGTCG
Statistics
Matches: 122, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
117 16 0.13
119 106 0.87
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (118 bp):
ACTCAAAACTCGAATTAAAAAAAATTCAAAATCTCAATTAAAACTTGAGACTCAAACTCGATTAG
ACTCAATTTTGAGCTCGATCCTCCCCTGAAGCAAACTACTATGAAAGGTTTTC
Found at i:197790 original size:33 final size:34
Alignment explanation
Indices: 197753--197816 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
197743 ATTTACAACT
197753 TCGATGACATTGTTAATTGGTTTTCA-TTAAACA
1 TCGATGACATTGTTAATTGGTTTTCACTTAAACA
197786 TCGATGACATTGTTAATTGGTTTTCACTTAA
1 TCGATGACATTGTTAATTGGTTTTCACTTAA
197817 TCTTTGTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (34 bp):
TCGATGACATTGTTAATTGGTTTTCACTTAAACA
Found at i:198336 original size:33 final size:33
Alignment explanation
Indices: 198294--198360 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
198284 GTTTTACTGA
*
198294 TTCCCATGTCTATTCCTGTCCTGTAACCAGGTT
1 TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
198327 TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
1 TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
198360 T
1 T
198361 GCCAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.15, C:0.30, G:0.16, T:0.39
Consensus pattern (33 bp):
TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
Found at i:199200 original size:157 final size:159
Alignment explanation
Indices: 198994--199328 Score: 532
Period size: 157 Copynumber: 2.1 Consensus size: 159
198984 GAATACTACA
* *
198994 TTTAGGGTTTAGGGTTTATGATTAGTCAAAATAATTAAAATGTTCATTCTTTAATTTGGGAGTTT
1 TTTATGGTTTAGGGTTTATGATTAGCCAAAATAATTAAAATGTTCATTCTTTAATTTGGGAGTTT
*
199059 AGGGTTTATGGTTAGTCAAAATCTAATAAGGAAATATGG-T-T-AAAATAGTCAACCAGAAAAAC
66 AGGGTTTATGGTTAGTCAAAATCCAATAAGGAAATATGGTTATCAAAATAGTCAACCA-AAAAAC
*
199121 AGTTGAAATGTTCATTCATCAGTTTGGGAG
130 AGTTGAAATGTTCATTCATCAGTTCGGGAG
* * *
199151 TTTATGGTTTAAGGTTTATGATTAGCCAAAATAATTGAAATGTTCATTCTTTATTTTGGGAGTTT
1 TTTATGGTTTAGGGTTTATGATTAGCCAAAATAATTAAAATGTTCATTCTTTAATTTGGGAGTTT
* *
199216 AGGGTTTATGGTTAGTCAAAATCCAATCAGGAAATATGGTTAGTCAAAATAGTCAACCAAAAAAT
66 AGGGTTTATGGTTAGTCAAAATCCAATAAGGAAATATGGTTA-TCAAAATAGTCAACCAAAAAAC
*
199281 AGTTGAAATGTTCATTCATCAGTTCGTGAG
130 AGTTGAAATGTTCATTCATCAGTTCGGGAG
*
199311 TTTATGATTTAGGGTTTA
1 TTTATGGTTTAGGGTTTA
199329 AAGTTCATGT
Statistics
Matches: 162, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
157 97 0.60
158 1 0.01
160 50 0.31
161 14 0.09
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (159 bp):
TTTATGGTTTAGGGTTTATGATTAGCCAAAATAATTAAAATGTTCATTCTTTAATTTGGGAGTTT
AGGGTTTATGGTTAGTCAAAATCCAATAAGGAAATATGGTTATCAAAATAGTCAACCAAAAAACA
GTTGAAATGTTCATTCATCAGTTCGGGAG
Found at i:199342 original size:21 final size:21
Alignment explanation
Indices: 199309--199349 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
199299 TCAGTTCGTG
*
199309 AGTTTATGATTTAGGGTTTAA
1 AGTTCATGATTTAGGGTTTAA
*
199330 AGTTCATGTTTTAGGGTTTA
1 AGTTCATGATTTAGGGTTTA
199350 GGGTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (21 bp):
AGTTCATGATTTAGGGTTTAA
Found at i:199869 original size:11 final size:11
Alignment explanation
Indices: 199853--199915 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
199843 GTATTATAAA
199853 ATTTTTAATAT
1 ATTTTTAATAT
199864 ATTTTTAA-A-
1 ATTTTTAATAT
199873 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
199884 ATCAATAGTGT
1 ATTTTTAATAT
199895 ATTTTTAATAT
1 ATTTTTAATAT
199906 ATTTTTAATA
1 ATTTTTAATA
199916 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:206109 original size:19 final size:22
Alignment explanation
Indices: 206075--206121 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
206065 ATTTAACGTG
206075 ATTTAATTTATAATTTTAT-AA
1 ATTTAATTTATAATTTTATAAA
206096 ATTTAA-TT-TAATTTTATAAA
1 ATTTAATTTATAATTTTATAAA
206116 ATTTAA
1 ATTTAA
206122 AGTGTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.36
20 10 0.40
21 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTAATTTATAATTTTATAAA
Found at i:207492 original size:3 final size:3
Alignment explanation
Indices: 207484--207557 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
207474 TGTGCAGAGG
207484 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
207532 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
207558 TGCCCAGCTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:209812 original size:55 final size:55
Alignment explanation
Indices: 209721--209843 Score: 219
Period size: 55 Copynumber: 2.2 Consensus size: 55
209711 ACCCACCCGA
*
209721 ACCAGCGCAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
1 ACCAGCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
*
209776 ACCATCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
1 ACCAGCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
*
209831 ACCAGCGCAGCAT
1 ACCAGCACAGCAT
209844 TAGGTATGTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (55 bp):
ACCAGCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
Found at i:215558 original size:14 final size:14
Alignment explanation
Indices: 215536--215570 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
215526 CATCCAAACA
215536 CTAGAAAATATTTT
1 CTAGAAAATATTTT
*
215550 CTTGAAAATATTTT
1 CTAGAAAATATTTT
215564 CTAGAAA
1 CTAGAAA
215571 TGTAATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (14 bp):
CTAGAAAATATTTT
Found at i:216274 original size:31 final size:31
Alignment explanation
Indices: 216236--216301 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
216226 ACACAACTAC
216236 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
1 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
216267 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
1 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
216298 GAAC
1 GAAC
216302 TTATAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (31 bp):
GAACGTAGGATTTTAAGTTTGGAGAAAACTT
Found at i:216701 original size:16 final size:17
Alignment explanation
Indices: 216670--216702 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
216660 TATGTCGTTG
*
216670 AGCCAATGTTTTGAAAT
1 AGCCAATGTCTTGAAAT
216687 AGCCAATG-CTTGAAAT
1 AGCCAATGTCTTGAAAT
216703 CTTGTGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (17 bp):
AGCCAATGTCTTGAAAT
Found at i:220629 original size:2 final size:2
Alignment explanation
Indices: 220617--220657 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
220607 CCACATGCAC
* *
220617 CT CT GT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
220658 AACCTTTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.05, T:0.49
Consensus pattern (2 bp):
CT
Found at i:221755 original size:15 final size:15
Alignment explanation
Indices: 221735--221766 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
221725 GAGACCATCC
221735 TCTTCACTTCTATAT
1 TCTTCACTTCTATAT
*
221750 TCTTCACTTTTATAT
1 TCTTCACTTCTATAT
221765 TC
1 TC
221767 CTCGTTATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTTCACTTCTATAT
Found at i:223187 original size:2 final size:2
Alignment explanation
Indices: 223180--223213 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
223170 CAATTTTGTA
223180 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
223214 GAATTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:224179 original size:37 final size:37
Alignment explanation
Indices: 224110--224445 Score: 372
Period size: 37 Copynumber: 9.2 Consensus size: 37
224100 ACACATAGTG
* * *
224110 TATATAATATATAGTGTTGAAAGCATTTTTTTTCAAAAATA
1 TATATAATATATAGTTTTGAAAACA---TTTTT-GAAAATA
* * *
224151 TATCTAATATATAGTTTTGAGAAA-TTTTTTAAAAATA
1 TATATAATATATAGTTTTGA-AAACATTTTTGAAAATA
*
224188 TATATAATATATAG-TTTAAAAACATTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
* *
224224 TATATAGTACATAGTTTTGAAAACATTTTTG-----A
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
224256 -ATAT-ATATATAGTTTTGAAAACATTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
224291 TATATAATATATAGTTTTGAAAACATTTTTGAAAATATA
1 TATATAATATATAGTTTTGAAAACATTTTTG-AAA-ATA
* *
224330 TATATAATATATAATTTTGTAAACATTTTTCGAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTT-GAAAATA
224368 TATATAATATATAGTTTT-AAAACATTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
** * *
224404 TATAT-A-ATATAGTTTCAAAAAACATTTTCGAAAATT
1 TATATAATATATAGTTT-TGAAAACATTTTTGAAAATA
224440 TATATA
1 TATATA
224446 TAGCTTTTTT
Statistics
Matches: 259, Mismatches: 20, Indels: 36
0.82 0.06 0.11
Matches are distributed among these distances:
30 23 0.09
31 4 0.02
32 1 0.00
34 9 0.03
35 5 0.02
36 64 0.25
37 70 0.27
38 28 0.11
39 34 0.13
40 1 0.00
41 18 0.07
42 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
Found at i:224287 original size:67 final size:68
Alignment explanation
Indices: 224189--224445 Score: 286
Period size: 67 Copynumber: 3.6 Consensus size: 68
224179 TTAAAAATAT
* * *
224189 ATATAATATATAG-TTTAAAAACATTTTTGAAAATATATATAGTACATAGTTTTGAAAACATTTT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
224253 TGA
66 TGA
224256 ATAT-ATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
224320 TGAAAATATA
66 TG-------A
* *
224330 TATATAATATATAATTTTGTAAACATTTTTCGAAAATATATATAATATATAGTTTT-AAAACATT
1 -ATATAATATATAGTTTTGAAAACATTTTT-GAAAATATATATAATATATAGTTTTGAAAACATT
224394 TTTGAAA
64 TTTG--A
** * *
224401 ATATATATAATATAGTTTCAAAAAACATTTTCGAAAATTTATATA
1 ATATA-AT-ATATAGTTT-TGAAAACATTTTTGAAAATATATATA
224446 TAGCTTTTTT
Statistics
Matches: 164, Mismatches: 12, Indels: 23
0.82 0.06 0.12
Matches are distributed among these distances:
66 8 0.05
67 54 0.33
70 5 0.03
71 4 0.02
72 20 0.12
73 9 0.05
74 1 0.01
75 4 0.02
76 34 0.21
77 25 0.15
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (68 bp):
ATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
TGA
Found at i:224341 original size:76 final size:75
Alignment explanation
Indices: 224256--224414 Score: 268
Period size: 76 Copynumber: 2.1 Consensus size: 75
224246 ACATTTTTGA
*
224256 ATATATATATAGTTTTGAAAACATTTTT-GAAAATATATATAATATATAGTTTTGAAAACATTTT
1 ATATATATATAATTTTGAAAACATTTTTCGAAAATATATATAATATATAGTTTT-AAAACATTTT
224320 TGAAAATATAT
65 TGAAAATATAT
*
224331 ATATAATATATAATTTTGTAAACATTTTTCGAAAATATATATAATATATAGTTTTAAAACATTTT
1 ATAT-ATATATAATTTTGAAAACATTTTTCGAAAATATATATAATATATAGTTTTAAAACATTTT
224396 TGAAAATATAT
65 TGAAAATATAT
224407 ATA-ATATA
1 ATATATATA
224415 GTTTCAAAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
74 5 0.06
75 4 0.05
76 46 0.57
77 25 0.31
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (75 bp):
ATATATATATAATTTTGAAAACATTTTTCGAAAATATATATAATATATAGTTTTAAAACATTTTT
GAAAATATAT
Found at i:224461 original size:36 final size:36
Alignment explanation
Indices: 224182--224445 Score: 158
Period size: 36 Copynumber: 7.3 Consensus size: 36
224172 AAATTTTTTA
*
224182 AAAATATATATAATATATAGTTT--AAAAACATTTTTG
1 AAAATATATAT-A-ATATAGTTTCAAAAAACATTTTCG
* ** *
224218 AAAATATATATAGTACATAGTTT-TGAAAACATTTTTG
1 AAAATATATATA--ATATAGTTTCAAAAAACATTTTCG
** *
224255 ---A-ATATAT-ATATAGTTT-TGAAAACATTTTTG
1 AAAATATATATAATATAGTTTCAAAAAACATTTTCG
** *
224285 AAAATATATATAATATATAGTTT-TGAAAACATTTTTG
1 AAAATATATAT-A-ATATAGTTTCAAAAAACATTTTCG
****
224322 AAAATATATATATAATATA-TAATTTTGTAAACATTTTTCG
1 -AAA-ATATATATAATATAGT--TTCAAAAAACA-TTTTCG
* *
224362 AAAATATATATAATATATAGTTT--TAAAACATTTTTG
1 AAAATATATAT-A-ATATAGTTTCAAAAAACATTTTCG
224398 AAAATATATATAATATAGTTTCAAAAAACATTTTCG
1 AAAATATATATAATATAGTTTCAAAAAACATTTTCG
*
224434 AAAATTTATATA
1 AAAATATATATA
224446 TAGCTTTTTT
Statistics
Matches: 197, Mismatches: 11, Indels: 40
0.79 0.04 0.16
Matches are distributed among these distances:
30 22 0.11
33 7 0.04
34 16 0.08
35 2 0.01
36 59 0.30
37 45 0.23
38 14 0.07
39 21 0.11
40 10 0.05
41 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (36 bp):
AAAATATATATAATATAGTTTCAAAAAACATTTTCG
Found at i:225702 original size:13 final size:13
Alignment explanation
Indices: 225684--225708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225674 CTCTTAACAT
225684 TTTTTTCTTTCTA
1 TTTTTTCTTTCTA
225697 TTTTTTCTTTCT
1 TTTTTTCTTTCT
225709 TTCAAAATTC
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:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTCTTTCTA
Found at i:226609 original size:6 final size:6
Alignment explanation
Indices: 226598--226642 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
226588 TCAACAAATC
226598 CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG CTA
1 CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG CTA
226643 GGCGCGTGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (6 bp):
CTATGG
Found at i:230601 original size:21 final size:21
Alignment explanation
Indices: 230537--230605 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
230527 GTGCGGCGGT
* *
230537 GGACGGTGGTCGGAAGACGGC
1 GGACGATGGTCGGAGGACGGC
* * * *
230558 GAACGGTGGTTGGAGGTCGGC
1 GGACGATGGTCGGAGGACGGC
*
230579 GGATGATGGTCGGAGGACGGC
1 GGACGATGGTCGGAGGACGGC
230600 GGACGA
1 GGACGA
230606 CAAGCGACTG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.19, C:0.16, G:0.52, T:0.13
Consensus pattern (21 bp):
GGACGATGGTCGGAGGACGGC
Found at i:243975 original size:361 final size:361
Alignment explanation
Indices: 243311--244033 Score: 1446
Period size: 361 Copynumber: 2.0 Consensus size: 361
243301 TAACTTAGAT
243311 TTCGCAAAAATTTCCCTGCAACAGAACCTATTGTTAGAGAAGGAGTTTACGGAAGATGAGATTTG
1 TTCGCAAAAATTTCCCTGCAACAGAACCTATTGTTAGAGAAGGAGTTTACGGAAGATGAGATTTG
243376 GGGGACCATTAATTCTTGTGATAGTAATAAAGCCCCTGGGCCAGATGGGTTGAACATGGGTTTTT
66 GGGGACCATTAATTCTTGTGATAGTAATAAAGCCCCTGGGCCAGATGGGTTGAACATGGGTTTTT
243441 TTAAGAACTTCTGGCTTAGCTTGAAAGGTGATATATTGAAATTCTTCCACAACTTCTATTTGGGT
131 TTAAGAACTTCTGGCTTAGCTTGAAAGGTGATATATTGAAATTCTTCCACAACTTCTATTTGGGT
243506 AAGGAGTGGGAGCATGGTATTAACCATTCCTTCTTAACTCTCATCCCGAAAGGTTCTAATGTTGG
196 AAGGAGTGGGAGCATGGTATTAACCATTCCTTCTTAACTCTCATCCCGAAAGGTTCTAATGTTGG
243571 GAGTTTAGATGATTTCAGACCTATTTCCCTTGTAGGTGGGATGTATAAGATCCTATCTAAGTGCC
261 GAGTTTAGATGATTTCAGACCTATTTCCCTTGTAGGTGGGATGTATAAGATCCTATCTAAGTGCC
243636 TCGCGAGAAGATTGAGATGTTGCATCAATGATATAA
326 TCGCGAGAAGATTGAGATGTTGCATCAATGATATAA
243672 TTCGCAAAAATTTCCCTGCAACAGAACCTATTGTTAGAGAAGGAGTTTACGGAAGATGAGATTTG
1 TTCGCAAAAATTTCCCTGCAACAGAACCTATTGTTAGAGAAGGAGTTTACGGAAGATGAGATTTG
243737 GGGGACCATTAATTCTTGTGATAGTAATAAAGCCCCTGGGCCAGATGGGTTGAACATGGGTTTTT
66 GGGGACCATTAATTCTTGTGATAGTAATAAAGCCCCTGGGCCAGATGGGTTGAACATGGGTTTTT
243802 TTAAGAACTTCTGGCTTAGCTTGAAAGGTGATATATTGAAATTCTTCCACAACTTCTATTTGGGT
131 TTAAGAACTTCTGGCTTAGCTTGAAAGGTGATATATTGAAATTCTTCCACAACTTCTATTTGGGT
243867 AAGGAGTGGGAGCATGGTATTAACCATTCCTTCTTAACTCTCATCCCGAAAGGTTCTAATGTTGG
196 AAGGAGTGGGAGCATGGTATTAACCATTCCTTCTTAACTCTCATCCCGAAAGGTTCTAATGTTGG
243932 GAGTTTAGATGATTTCAGACCTATTTCCCTTGTAGGTGGGATGTATAAGATCCTATCTAAGTGCC
261 GAGTTTAGATGATTTCAGACCTATTTCCCTTGTAGGTGGGATGTATAAGATCCTATCTAAGTGCC
243997 TCGCGAGAAGATTGAGATGTTGCATCAATGATATAA
326 TCGCGAGAAGATTGAGATGTTGCATCAATGATATAA
244033 T
1 T
244034 CAGTGAGTCT
Statistics
Matches: 362, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
361 362 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (361 bp):
TTCGCAAAAATTTCCCTGCAACAGAACCTATTGTTAGAGAAGGAGTTTACGGAAGATGAGATTTG
GGGGACCATTAATTCTTGTGATAGTAATAAAGCCCCTGGGCCAGATGGGTTGAACATGGGTTTTT
TTAAGAACTTCTGGCTTAGCTTGAAAGGTGATATATTGAAATTCTTCCACAACTTCTATTTGGGT
AAGGAGTGGGAGCATGGTATTAACCATTCCTTCTTAACTCTCATCCCGAAAGGTTCTAATGTTGG
GAGTTTAGATGATTTCAGACCTATTTCCCTTGTAGGTGGGATGTATAAGATCCTATCTAAGTGCC
TCGCGAGAAGATTGAGATGTTGCATCAATGATATAA
Found at i:248339 original size:18 final size:18
Alignment explanation
Indices: 248312--248352 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
248302 TCTTCTTCGT
*
248312 CATCTGCATCCTCATCTC
1 CATCTCCATCCTCATCTC
*
248330 CATCTCCATCCTCATCTT
1 CATCTCCATCCTCATCTC
248348 CATCT
1 CATCT
248353 TCGTCTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.44, G:0.02, T:0.37
Consensus pattern (18 bp):
CATCTCCATCCTCATCTC
Found at i:249903 original size:39 final size:39
Alignment explanation
Indices: 249860--249937 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
249850 CGTTGGACTT
249860 TGAGACGTTGGACTTTGCCTACTCTTAAACAATTTTCTC
1 TGAGACGTTGGACTTTGCCTACTCTTAAACAATTTTCTC
*
249899 TGAGACGTTGGACTTTGCCTACTCTTGAACAATTTTCTC
1 TGAGACGTTGGACTTTGCCTACTCTTAAACAATTTTCTC
249938 GTCTAGTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (39 bp):
TGAGACGTTGGACTTTGCCTACTCTTAAACAATTTTCTC
Found at i:250410 original size:6 final size:6
Alignment explanation
Indices: 250399--250434 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
250389 TTAACGTTAT
250399 TTTAAA TTTAAA -TT-AA TTTAAA TTTAAA -TTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
250435 TTCTCATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 2 0.07
5 9 0.33
6 16 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:250420 original size:16 final size:16
Alignment explanation
Indices: 250399--250430 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
250389 TTAACGTTAT
250399 TTTAAATTTAAATTAA
1 TTTAAATTTAAATTAA
250415 TTTAAATTTAAATTAA
1 TTTAAATTTAAATTAA
250431 ATTTTTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATTAA
Found at i:256554 original size:3 final size:3
Alignment explanation
Indices: 256546--256570 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
256536 TTCTACACTA
256546 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
256571 ACGTGGGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:262860 original size:20 final size:21
Alignment explanation
Indices: 262815--262867 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 21
262805 CCTAGGGGGA
262815 TATCGATACCATAGCATAGAGG
1 TATCGATACCATA-CATAGAGG
262837 TATCGATACCATA-AT-GAGGG
1 TATCGATACCATACATAGA-GG
262857 TATCGATACCA
1 TATCGATACCA
262868 GTTATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
22 13 0.43
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (21 bp):
TATCGATACCATACATAGAGG
Found at i:262863 original size:94 final size:91
Alignment explanation
Indices: 262741--262963 Score: 241
Period size: 94 Copynumber: 2.4 Consensus size: 91
262731 CAAGCAATGT
* ** * *
262741 GGTATCAATACCATGGTAAGGGTATCGATACCAGTAAACATCGAATCTAATTTTAGTATCGATAC
1 GGTATCGATACCATAATAAGGGTATCGATACCAGT-AACATCAAAGCTAATTTTAGTATCGATAC
262806 CT-AGGGGGATATCGATACCATAGCATAGA
65 CTAAGGGGG-TATCGATACCATA--ATAGA
* * * * * *
262835 GGTATCGATACCATAATGAGGGTATCGATACCAGTTATATTAAAGCTAATTTTGGTATCGATACT
1 GGTATCGATACCATAATAAGGGTATCGATACCAGTAACATCAAAGCTAATTTTAGTATCGATACC
* *
262900 TGAAGGGGGTATCGATACCCTAATAGG
66 T-AAGGGGGTATCGATACCATAATAGA
*
262927 GTAGTATCGATACCATAAGTAAGGGTATAGATACCAG
1 G--GTATCGATACCATAA-TAAGGGTATCGATACCAG
262964 AGGGCCAGAA
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
92 5 0.05
93 24 0.22
94 58 0.53
95 22 0.20
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (91 bp):
GGTATCGATACCATAATAAGGGTATCGATACCAGTAACATCAAAGCTAATTTTAGTATCGATACC
TAAGGGGGTATCGATACCATAATAGA
Found at i:263453 original size:79 final size:79
Alignment explanation
Indices: 263322--263526 Score: 338
Period size: 79 Copynumber: 2.6 Consensus size: 79
263312 AAACTAATTA
* *
263322 ATAAAAGAATAATGCATATGGGTGCATTAGTGGAATGAAAAGATGCCTTAGCTAATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTAATATGTATATG
263387 GGTACAATATCGGC
66 GGTACAATATCGGC
*
263401 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTAATATGTATATG
*
263466 GGTACATTATCGGC
66 GGTACAATATCGGC
* * * *
263480 ATAACATAATAATGCATATAGGTGCATTATTGGCATGAAAGGATGCC
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCC
263527 AGAGTTGAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 118 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTAATATGTATATG
GGTACAATATCGGC
Found at i:263544 original size:79 final size:79
Alignment explanation
Indices: 263322--263555 Score: 335
Period size: 79 Copynumber: 3.0 Consensus size: 79
263312 AAACTAATTA
* *
263322 ATAAAAGAATAATGCATATGGGTGCATTAGTGGAATGAAAAGATGCCTTAGCT-AATATGTATAT
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGAA-ATGTATAT
*
263386 GGGTACAATATCGGC
65 GGGTACATTATCGGC
*
263401 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGAAATGTATATG
263466 GGTACATTATCGGC
66 GGTACATTATCGGC
* * * * ** * *
263480 ATAACATAATAATGCATATAGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGAAATGTATATG
*
263545 GGTGCATTATC
66 GGTACATTATC
263556 AACAGAAAAA
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
79 139 0.99
80 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGAAATGTATATG
GGTACATTATCGGC
Found at i:263578 original size:45 final size:45
Alignment explanation
Indices: 263529--263745 Score: 292
Period size: 45 Copynumber: 4.8 Consensus size: 45
263519 AGGATGCCAG
* *
263529 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTAC
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
** * *
263574 AGTTGAAATGCATATAAGTGCATTATCAACAGAAAAGTATGCTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * *
263619 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATATTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * * * *
263664 GGTT-AAGATGTATATGGGTACATTATCAACATAAAAGTACACTAT
1 AGTTGAA-ATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
263709 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
263746 ATGTTAGAGT
Statistics
Matches: 150, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
44 2 0.01
45 146 0.97
46 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (45 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
Found at i:263643 original size:90 final size:89
Alignment explanation
Indices: 263490--263744 Score: 305
Period size: 90 Copynumber: 2.8 Consensus size: 89
263480 ATAACATAAT
*** * *
263490 AATGCATATAGGTGCATTATTGGCATG-AAAGGATGCCAGAGTTGAAATGCATATGGGTGCATTA
1 AATGCATATAGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTA
263554 TCAACAGAAAAATATACTACAGTTGA
65 TCAACAGAAAAATATACTACAGTT-A
* * *
263580 AATGCATATAAGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTAT
1 AATGCATATAGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
* * **
263645 CAACAGAAAAGTATATTATGGTTA
66 CAACAGAAAAATATACTACAGTTA
* * * * ** *
263669 AGATGTATATGGGTACATTATCAACATAAAAGTACACTATAGTTGAAATGCATATGGGTGCATTA
1 A-ATGCATATAGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTA
263734 TCAACAGAAAA
65 TCAACAGAAAA
263745 GATGTTAGAG
Statistics
Matches: 141, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
89 3 0.02
90 138 0.98
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.28
Consensus pattern (89 bp):
AATGCATATAGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
CAACAGAAAAATATACTACAGTTA
Found at i:267109 original size:24 final size:24
Alignment explanation
Indices: 267082--267169 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
267072 TTCTATTATA
* *
267082 ATACCTGACTTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
267106 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* * *
267130 ATACTTGACTTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
267154 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
267170 ATGTTTTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:268641 original size:44 final size:46
Alignment explanation
Indices: 268573--268665 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 46
268563 CAACCAGACA
* *
268573 ATAAAAGGCATGAAATGATGCCATAAAT-GAAAT-GTATAATAGTGT
1 ATAAAAGGCATGAAATGATACCAT-AATGGAAATGGTATAAGAGTGT
*
268618 ATAAAA-GCATGAAA-GAATACCATAATGGAAATGGTATAAGGGTGT
1 ATAAAAGGCATGAAATG-ATACCATAATGGAAATGGTATAAGAGTGT
268663 ATA
1 ATA
268666 TTAAGCACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
43 4 0.10
44 19 0.45
45 19 0.45
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (46 bp):
ATAAAAGGCATGAAATGATACCATAATGGAAATGGTATAAGAGTGT
Found at i:271390 original size:2 final size:2
Alignment explanation
Indices: 271383--271407 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
271373 AAAAAGAAAG
271383 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
271408 GTGGTGATGG
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:275930 original size:23 final size:23
Alignment explanation
Indices: 275904--275990 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
275894 GGTTCTAAGC
275904 GGTCCTTCGGGACAAATCTATGT
1 GGTCCTTCGGGACAAATCTATGT
* * *
275927 GGTCATTCGAGACAATTCTATGT
1 GGTCCTTCGGGACAAATCTATGT
* * * *
275950 GGTCCTTCAGGACAAATTCGACGC
1 GGTCCTTCGGGACAAA-TCTATGT
275974 GGTCCTTCGGGACAAAT
1 GGTCCTTCGGGACAAAT
275991 TTTAAGTGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 33 0.63
24 19 0.37
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (23 bp):
GGTCCTTCGGGACAAATCTATGT
Found at i:285551 original size:22 final size:23
Alignment explanation
Indices: 285525--285586 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
285515 TTAGTGCAGA
* *
285525 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATACCCCCTTTAAAG
*
285547 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATACCCCCTTTAAAG
285570 GGGAACCCGATACCCCC
1 GGGAA-CCGATACCCCC
285587 CTGGGGTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 14 0.41
23 10 0.29
24 10 0.29
ACGTcount: A:0.26, C:0.34, G:0.24, T:0.16
Consensus pattern (23 bp):
GGGAACCGATACCCCCTTTAAAG
Found at i:305579 original size:10 final size:10
Alignment explanation
Indices: 305564--305590 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
305554 TTTTATTATC
305564 TTTATTTGTT
1 TTTATTTGTT
305574 TTTATTTGTT
1 TTTATTTGTT
305584 TTTATTT
1 TTTATTT
305591 ATTACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.81
Consensus pattern (10 bp):
TTTATTTGTT
Found at i:309572 original size:14 final size:14
Alignment explanation
Indices: 309543--309622 Score: 59
Period size: 14 Copynumber: 6.1 Consensus size: 14
309533 CGTTCGTGAA
309543 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
309559 CGTTCATTTA---T
1 CGTTCATTTATGTT
*
309570 -GTTCATTTGTGTT
1 CGTTCATTTATGTT
*
309583 CGTTAATTTATG--
1 CGTTCATTTATGTT
309595 C--TCATTTATGTT
1 CGTTCATTTATGTT
*
309607 TGTTCATTTATGTT
1 CGTTCATTTATGTT
309621 CG
1 CG
309623 AACAGAGGGT
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
10 16 0.32
11 1 0.02
12 1 0.02
13 1 0.02
14 23 0.46
15 3 0.06
16 5 0.10
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.55
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:309591 original size:24 final size:24
Alignment explanation
Indices: 309544--309621 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
309534 GTTCGTGAAC
309544 GTTCGATTATATGTTCGTTCATTTAT
1 GTTC-ATT-TATGTTCGTTCATTTAT
* *
309570 GTTCATTTGTGTTCGTTAATTTAT
1 GTTCATTTATGTTCGTTCATTTAT
* *
309594 GCTCATTTATGTTTGTTCATTTAT
1 GTTCATTTATGTTCGTTCATTTAT
309618 GTTC
1 GTTC
309622 GAACAGAGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 38 0.84
25 3 0.07
26 4 0.09
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTCATTTAT
Found at i:309929 original size:10 final size:10
Alignment explanation
Indices: 309914--309953 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
309904 TATTATGTTC
*
309914 GTTCGTTTGT
1 GTTCGTTTAT
*
309924 GTTCGTTTAC
1 GTTCGTTTAT
309934 GTTCGTTTAT
1 GTTCGTTTAT
309944 GTTCGTTTAT
1 GTTCGTTTAT
309954 CATTTAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.57
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:309932 original size:27 final size:26
Alignment explanation
Indices: 309881--309932 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
309871 TTTTTTTGTC
*
309881 TATGTTGTTCGTTTATGTTTATTTAT
1 TATGTTGTTCGTTTATGTTCATTTAT
* *
309907 TATGTTCGTTCGTTTGTGTTCGTTTA
1 TATGTT-GTTCGTTTATGTTCATTTA
309933 CGTTCGTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.12, C:0.08, G:0.19, T:0.62
Consensus pattern (26 bp):
TATGTTGTTCGTTTATGTTCATTTAT
Found at i:309938 original size:20 final size:20
Alignment explanation
Indices: 309913--309952 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
309903 TTATTATGTT
*
309913 CGTTCGTTTGTGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
309933 CGTTCGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
309953 TCATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.15, G:0.23, T:0.55
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:312424 original size:12 final size:12
Alignment explanation
Indices: 312407--312440 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
312397 GAAAATAAAG
312407 AAAACTTAATGT
1 AAAACTTAATGT
*
312419 AAAACTTGATGT
1 AAAACTTAATGT
312431 AAAAC-TAATG
1 AAAACTTAATG
312441 GCCCTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:316115 original size:34 final size:32
Alignment explanation
Indices: 316053--316122 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
316043 CCTTACAAAC
* *
316053 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
316085 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
316119 TCCC
1 TCCC
316123 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:316429 original size:21 final size:21
Alignment explanation
Indices: 316403--316444 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
316393 CCATAATGGG
*
316403 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
316424 GGGAATCGATGCCCCTTCATA
1 GGGAATCGATACCCCTTCATA
316445 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:316506 original size:21 final size:21
Alignment explanation
Indices: 316480--316523 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
316470 CTGTTGAACA
316480 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
316501 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
316522 GG
1 GG
316524 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:316575 original size:21 final size:21
Alignment explanation
Indices: 316549--316628 Score: 82
Period size: 21 Copynumber: 4.1 Consensus size: 21
316539 GCTTTAGACA
*
316549 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
316570 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
316587 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
316606 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
316627 GG
1 GG
316629 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 31 0.63
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:316590 original size:15 final size:15
Alignment explanation
Indices: 316572--316601 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
316562 ACCCCCTGGG
316572 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
316587 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
316602 CCTGGGGGGG
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:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:316607 original size:36 final size:36
Alignment explanation
Indices: 316551--316622 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
316541 TTTAGACAGG
* *
316551 GGGGAATCGGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTATACCC
* *
316587 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTATACCC
316623 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTATACCC
Found at i:319749 original size:21 final size:21
Alignment explanation
Indices: 319723--319764 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
319713 CCATAATGGG
*
319723 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
319744 GGGAATCGATGCCCCTTCATA
1 GGGAATCGATACCCCTTCATA
319765 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:319827 original size:21 final size:21
Alignment explanation
Indices: 319801--319844 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
319791 TGTTGAACAA
319801 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
319822 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
319843 GG
1 GG
319845 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:319896 original size:21 final size:21
Alignment explanation
Indices: 319870--319949 Score: 82
Period size: 21 Copynumber: 4.1 Consensus size: 21
319860 GCTTTAGACA
*
319870 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
319891 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
319908 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
319927 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
319948 GG
1 GG
319950 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 31 0.63
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:319911 original size:15 final size:15
Alignment explanation
Indices: 319893--319922 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
319883 ACCCCCTGGG
319893 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
319908 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
319923 CCTGGGGGGG
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:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:319928 original size:36 final size:36
Alignment explanation
Indices: 319872--319943 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
319862 TTTAGACAGG
* *
319872 GGGGAATCGGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTATACCC
* *
319908 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTATACCC
319944 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTATACCC
Found at i:321463 original size:85 final size:82
Alignment explanation
Indices: 321314--321497 Score: 296
Period size: 85 Copynumber: 2.2 Consensus size: 82
321304 AAAAAAATGG
* * *
321314 TTTAGGATATTATTTTAAATATTATATTTTATCTTTGTTTTCGGAATTTTAGTTTAAATGGTTTT
1 TTTAGGATATTATTTTAAATATTATATTTTATCTTTGTTTTAGGAATTTTAGTTAAAATAGTTTT
321379 AAGTGTTTTAATTAGGA
66 AAGTGTTTTAATTAGGA
*
321396 TTTAGGATATTATTTTAAATATTATTTTATTTTATCTTTGTTTTAGGTATTTTAGTTAAAATAGT
1 TTTAGGATATTATTTTAAATATTA---TATTTTATCTTTGTTTTAGGAATTTTAGTTAAAATAGT
321461 TTTAAGTGTTTTAATTAGGA
63 TTTAAGTGTTTTAATTAGGA
*
321481 TTTAAGATATTATTTTA
1 TTTAGGATATTATTTTA
321498 GGAATTATCT
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
82 24 0.26
85 70 0.74
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (82 bp):
TTTAGGATATTATTTTAAATATTATATTTTATCTTTGTTTTAGGAATTTTAGTTAAAATAGTTTT
AAGTGTTTTAATTAGGA
Found at i:323895 original size:23 final size:22
Alignment explanation
Indices: 323869--323917 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
323859 AAGTAAAGCG
323869 AAAATATCCAGAGAT-AAATCCTA
1 AAAATATCCA-A-ATAAAATCCTA
*
323892 AAAATATTCAAATAAAATCCTA
1 AAAATATCCAAATAAAATCCTA
323914 AAAA
1 AAAA
323918 CAAGTGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 2 0.08
22 13 0.54
23 9 0.38
ACGTcount: A:0.59, C:0.14, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAATATCCAAATAAAATCCTA
Found at i:324296 original size:14 final size:14
Alignment explanation
Indices: 324277--324305 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
324267 AACCTTATTT
324277 GTTACCCTTTTTCA
1 GTTACCCTTTTTCA
324291 GTTACCCTTTTTCA
1 GTTACCCTTTTTCA
324305 G
1 G
324306 GCCCCGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.10, T:0.48
Consensus pattern (14 bp):
GTTACCCTTTTTCA
Found at i:324443 original size:22 final size:21
Alignment explanation
Indices: 324414--324464 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
324404 TTTTCTAATT
324414 TCCC-AATTCTCTGACCCACAA
1 TCCCTAATTCT-TGACCCACAA
*
324435 TCCCTAATTCTTGACCCCCAA
1 TCCCTAATTCTTGACCCACAA
324456 TCCCTAATT
1 TCCCTAATT
324465 TTTCATCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.25, C:0.41, G:0.04, T:0.29
Consensus pattern (21 bp):
TCCCTAATTCTTGACCCACAA
Found at i:325874 original size:18 final size:18
Alignment explanation
Indices: 325853--325894 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
325843 AAATTAATAG
*
325853 TAAATTAATGGTGATATA
1 TAAACTAATGGTGATATA
325871 TAAACTAATGGTGATATA
1 TAAACTAATGGTGATATA
325889 TAAACT
1 TAAACT
325895 TGAACATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (18 bp):
TAAACTAATGGTGATATA
Found at i:326338 original size:3 final size:3
Alignment explanation
Indices: 326330--326356 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
326320 TTTATTAATG
326330 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
326357 AATAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:333846 original size:90 final size:90
Alignment explanation
Indices: 333697--333866 Score: 227
Period size: 90 Copynumber: 1.9 Consensus size: 90
333687 ATTATTATTA
* * *
333697 TATATGCAATAAAGCTTGAATTGTCCCTCTAGAACAATTGGTTAATAACCCCGGCTTTATGGATA
1 TATATGCAATAAAGATTGAATTGTCCCTATAGAACAATTGGTTAATAACCCCGGATTTATGGATA
*
333762 A-TATTCAGCTAGCTTATTATACTAT
66 AGT-TTCACCTAGCTTATTATACTAT
* ** * *
333787 TATATGTAATAAAGATTGAGA-TGTCCCTATAGAGTAATTGGTTAATAGCTCCGGATTTATGGAT
1 TATATGCAATAAAGATTGA-ATTGTCCCTATAGAACAATTGGTTAATAACCCCGGATTTATGGAT
333851 AAGTTTCACCTAGCTT
65 AAGTTTCACCTAGCTT
333867 GATAAATGTG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 67 0.97
91 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (90 bp):
TATATGCAATAAAGATTGAATTGTCCCTATAGAACAATTGGTTAATAACCCCGGATTTATGGATA
AGTTTCACCTAGCTTATTATACTAT
Found at i:335070 original size:51 final size:51
Alignment explanation
Indices: 335012--335157 Score: 229
Period size: 51 Copynumber: 2.9 Consensus size: 51
335002 AAGGTCCATA
** **
335012 TAATCCATGTGGGGCATCTTGAAGGCTCACTTCATTATGAAAAGACAGAAG
1 TAATCCATGTGGGGCATCTTGAAGGCTCACACCAGCATGAAAAGACAGAAG
*
335063 TAATCCATGTGGGGCATCTTGAAGGCTCACACCAGCATGAAAAGATAGAAG
1 TAATCCATGTGGGGCATCTTGAAGGCTCACACCAGCATGAAAAGACAGAAG
* *
335114 TAATCCATGTGGAGCATCTTGAAGGCTCACACCAGCATAAAAAG
1 TAATCCATGTGGGGCATCTTGAAGGCTCACACCAGCATGAAAAG
335158 GTTGGGATAT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 88 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (51 bp):
TAATCCATGTGGGGCATCTTGAAGGCTCACACCAGCATGAAAAGACAGAAG
Found at i:336668 original size:123 final size:123
Alignment explanation
Indices: 336521--336954 Score: 544
Period size: 123 Copynumber: 3.6 Consensus size: 123
336511 CACTCGATGG
* * * *
336521 ATCAACATTTCCAG-AAGAAGTTCGTAATAAAAAGAACTTATTTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAAG-AGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCAT
* * ** * *
336585 AATCTAAAGAACTTATTCAACCTTTTGTTTGATTCTATCATAGAAGGAGATAGACCATC
65 AATCTAAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAGAAGGAGATAGAGCAAC
* * * *
336644 ACCAACATTTCCAG-AAGACGTTCGTAATAAGAAGAACTCATCTGGAGAGAAAGAAAAAGTTAAT
1 ATCAACATTTCCAGAAAGA-GTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCAT
* * *
336708 AATTTGAAGAACTTATTCAACCTTTTGCTAGACTT-TATCGCAGAAGGATATAGAGCAGA-
65 AATCTAAAGAACTTATTCAACCTTTTGCTAGA-TTCTATCGCAGAAGGAGATAGAGCA-AC
*
336767 ATCAACATTTCCAGAAAGAGTTCGTAATGAGAAGAACTCATCTGAAGAG-AA-AA-AAGTTCATA
1 ATCAACATTTCCAGAAAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATA
* * *
336829 ATCTAAAGAACTTATTCAATCTTTTGCTAGA--CTATCGCAAAATGAGATAGAGCAAC
66 ATCTAAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAGAAGGAGATAGAGCAAC
* * * *
336885 ATCAATATTTCAAGAAAGAGTTCGTAATAAGAAGAACTAATCTGAAGAGAAAAAAGAAGTTCATA
1 ATCAACATTTCCAGAAAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATA
336950 ATCTA
66 ATCTA
336955 GAAGGAGTTT
Statistics
Matches: 271, Mismatches: 31, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
117 1 0.00
118 64 0.24
119 2 0.01
120 38 0.14
121 16 0.06
122 3 0.01
123 141 0.52
124 6 0.02
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGAAAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATA
ATCTAAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAGAAGGAGATAGAGCAAC
Found at i:336990 original size:57 final size:57
Alignment explanation
Indices: 336897--337014 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 57
336887 CAATATTTCA
* *
336897 AGAAAGAGTTCGTAATAAGAAGAACTAATCTGAAGAGAAAAAAGAAGTTCATAATCT
1 AGAAGGAGTTCGTAATAAGAAGAACTAATCTAAAGAGAAAAAAGAAGTTCATAATCT
* * * * *
336954 AGAAGGAGTTTGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTTATAATCT
1 AGAAGGAGTTCGTAATAAGAAGAACTAATCTAAAGAGAAAAAAGAAGTTCATAATCT
337011 -GAAG
1 AGAAG
337015 AACGTATTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 4 0.07
57 50 0.93
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.22
Consensus pattern (57 bp):
AGAAGGAGTTCGTAATAAGAAGAACTAATCTAAAGAGAAAAAAGAAGTTCATAATCT
Found at i:337093 original size:180 final size:175
Alignment explanation
Indices: 336779--337137 Score: 477
Period size: 180 Copynumber: 2.0 Consensus size: 175
336769 CAACATTTCC
* * * *
336779 AGAAAGAGTTCGTAATGAGAAGAACTCATCTGAAGAGAAAAAAGTTCATAATCTAAAGAACTTAT
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTAAAGAGAAAAAAGTTCATAATCTAAAGAACGTAT
* * *
336844 TCAATCTTTTGCTAGACTATCGCAAAATGAGATAGAGCAACATCAATATTTCAAGAAAGAGTTCG
66 TCAACCTTTTGCTAGACTATCACAAAATGAGATAGAGCAACATCAACATTTCAAGAAAGAGTTCG
*
336909 TAATAAGAAGAACTAATCTGAAGAGAAAAAAGAAGTTCATAATCT
131 TAATAAGAAGAACTAATCTGAAGAGAAAAAAGAAATTCATAATCT
* * *
336954 AGAAGGAGTTTGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTTATAATCTGAAGAACG
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTAAAGA-GAA-AA-AAGTTCATAATCTAAAGAACG
* * * * * * *
337019 TATTCAACCTTTTTCTCGATTCTGTCACAGAATGAGATAGAGCAGCATCAACATTTCCAGAAGGA
63 TATTCAACCTTTTGCTAGA--CTATCACAAAATGAGATAGAGCAACATCAACATTTCAAGAAAGA
* * *
337084 GTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATCT
126 GTTCGTAATAAGAAGAACTAATCTGAAGAGAAAAAAGAAATTCATAATCT
337134 -GAAG
1 AGAAG
337138 AACTTATTCA
Statistics
Matches: 158, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
175 32 0.20
176 3 0.02
177 2 0.01
178 34 0.22
179 4 0.03
180 83 0.53
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (175 bp):
AGAAGGAGTTCGTAATAAGAAGAACTCATCTAAAGAGAAAAAAGTTCATAATCTAAAGAACGTAT
TCAACCTTTTGCTAGACTATCACAAAATGAGATAGAGCAACATCAACATTTCAAGAAAGAGTTCG
TAATAAGAAGAACTAATCTGAAGAGAAAAAAGAAATTCATAATCT
Found at i:337173 original size:123 final size:123
Alignment explanation
Indices: 336954--337472 Score: 734
Period size: 123 Copynumber: 4.2 Consensus size: 123
336944 TTCATAATCT
* * * *
336954 AGAAGGAGTTTGTAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTTATAATCTGAAGAACG
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACT
* * * * * *
337019 TATTCAACCTTTTTCTCGATTCTGTCACAGAATGAGATAGAGCAGCATCAACATTTCC
66 TATTCAACCTTTTGCTCGACTCTATCGCAGAAAGAGATAGAGCAACATCAACATTTCC
*
337077 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATCTGAAGAACT
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACT
* * * *
337142 TATTCAACCTTTTGCTCGACTCTATTGCAGAAAGAGATAGAG-AAGCACCAATATTTTC
66 TATTCAACCTTTTGCTCGACTCTATCGCAGAAAGAGATAGAGCAA-CATCAACATTTCC
* *
337200 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAATAATT
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACT
** * * *
337265 TAAACAACCTTTTGCTTGACTCTATCGCAGAAAGAGATAGAGCAACATAAACATTTCA
66 TATTCAACCTTTTGCTCGACTCTATCGCAGAAAGAGATAGAGCAACATCAACATTTCC
*
337323 AGAAGGAGTTTGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACT
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACT
* * * * * **
337388 TATTCAACCTTTTGCTTGACTCTATTGCAGAAAGAAATATAACAACATCAGTATTTCC
66 TATTCAACCTTTTGCTCGACTCTATCGCAGAAAGAGATAGAGCAACATCAACATTTCC
* *
337446 AGAAAGAGTTCATAATAAGAAGAACTC
1 AGAAGGAGTTCGTAATAAGAAGAACTC
337473 GTACGAAGAA
Statistics
Matches: 351, Mismatches: 43, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
122 1 0.00
123 348 0.99
124 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACT
TATTCAACCTTTTGCTCGACTCTATCGCAGAAAGAGATAGAGCAACATCAACATTTCC
Found at i:338964 original size:5 final size:5
Alignment explanation
Indices: 338956--338981 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
338946 TAGTTTTCTA
338956 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
338982 ATCATTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:344206 original size:3 final size:3
Alignment explanation
Indices: 344198--344268 Score: 72
Period size: 3 Copynumber: 23.0 Consensus size: 3
344188 CATTTCATTT
** * *
344198 TTA TTA TTA TTA AAA TTA TTA TTA TTG TTA TTA ATA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
344244 -TA TATA TATA TTA TTA TTA TTA TTA
1 TTA T-TA T-TA TTA TTA TTA TTA TTA
344269 AATAAATAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.79
4 10 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:344251 original size:13 final size:14
Alignment explanation
Indices: 344214--344268 Score: 59
Period size: 13 Copynumber: 4.4 Consensus size: 14
344204 TTATTAAAAT
*
344214 TATTAT-TATTGT-
1 TATTATATATTATA
344226 TATTA-ATATTATA
1 TATTATATATTATA
344239 TATTATATA-TATA
1 TATTATATATTATA
344252 TATTAT-TATTAT-
1 TATTATATATTATA
344264 TATTA
1 TATTA
344269 AATAAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 17 0.45
13 18 0.47
14 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TATTATATATTATA
Found at i:345782 original size:12 final size:11
Alignment explanation
Indices: 345760--345789 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
345750 TTAAATATAG
345760 TATTTTTTATT
1 TATTTTTTATT
345771 TATTTATTTATT
1 TATTT-TTTATT
345783 TATTTTT
1 TATTTTT
345790 ATTCACTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:346110 original size:2 final size:2
Alignment explanation
Indices: 346103--346142 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
346093 AAAACCCTAA
346103 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
346143 TTTTCCTTAG
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):
AT
Found at i:347234 original size:46 final size:48
Alignment explanation
Indices: 347162--347251 Score: 130
Period size: 46 Copynumber: 1.9 Consensus size: 48
347152 GATTTTATTT
* * * *
347162 TTTTTCTAAATAAATGCATGTGAACTAGAAATCATGTAGTTAGGTTAA
1 TTTTTCCAAACAAATGCATGTGAACTAGAAAGCATGAAGTTAGGTTAA
347210 TTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAAGTTAGG
1 TTTTTCCAAACAAATGCATGTGAACTAGAAAGCATGAAGTTAGG
347252 ATTTATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 21 0.55
47 5 0.13
48 12 0.32
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (48 bp):
TTTTTCCAAACAAATGCATGTGAACTAGAAAGCATGAAGTTAGGTTAA
Found at i:349042 original size:22 final size:20
Alignment explanation
Indices: 349017--349070 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
349007 TTTTTCATTA
* *
349017 CATTTGTATTTTTTTATGTTT
1 CATTTGCATTTTTATAT-TTT
349038 GCATTTGCATTTTTATATTTT
1 -CATTTGCATTTTTATATTTT
*
349059 CATTTACATTTT
1 CATTTGCATTTT
349071 CATTTTTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 15 0.52
ACGTcount: A:0.19, C:0.09, G:0.07, T:0.65
Consensus pattern (20 bp):
CATTTGCATTTTTATATTTT
Found at i:349050 original size:20 final size:20
Alignment explanation
Indices: 349027--349090 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
349017 CATTTGTATT
*
349027 TTTTTATGTTTGCATTTGCA
1 TTTTTATATTTGCATTTGCA
* *
349047 TTTTTATATTTTCATTTACA
1 TTTTTATATTTGCATTTGCA
* *
349067 TTTTCATTTTTGCACCTTTGCA
1 TTTTTATATTTGCA--TTTGCA
349089 TT
1 TT
349091 GCACAGTTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 28 0.80
22 7 0.20
ACGTcount: A:0.17, C:0.14, G:0.08, T:0.61
Consensus pattern (20 bp):
TTTTTATATTTGCATTTGCA
Found at i:352263 original size:18 final size:17
Alignment explanation
Indices: 352209--352257 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
352199 TTGGACCCTT
*
352209 AGTGCATCGGTGCACTAA
1 AGTGCATCGGTGCA-TCA
352227 GAGTGCATCGGTGCATCA
1 -AGTGCATCGGTGCATCA
352245 AGTGCATTCGGTG
1 AGTGCA-TCGGTG
352258 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (17 bp):
AGTGCATCGGTGCATCA
Found at i:355104 original size:20 final size:21
Alignment explanation
Indices: 355036--355107 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
355026 GACCCTGTGC
* * *
355036 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
355057 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
355079 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
355099 ATCGATGCA
1 ATCGATGCA
355108 TGAAGCACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 11 0.26
21 19 0.44
22 13 0.30
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:360922 original size:65 final size:64
Alignment explanation
Indices: 360838--360983 Score: 172
Period size: 65 Copynumber: 2.2 Consensus size: 64
360828 TTCACTAAGA
* *
360838 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAATCCTCA-GTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGAT-TTTTAATAAAAT--TCAGGTGCATCGATGCATGGAT
360901 AT-
63 -TG
* **
360903 GTGCATCGATGCATGAAATGCATTCGATTTTTAATTTAATTCATGGTGCATCGATGCATGGATTG
1 GTGCATCGATGCATCAAATGCATTCGATTTTTAATAAAATTCA-GGTGCATCGATGCATGGATTG
*
360968 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
360984 CTCTGAAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
62 3 0.04
64 26 0.37
65 41 0.59
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATTTTTAATAAAATTCAGGTGCATCGATGCATGGATTG
Found at i:363462 original size:132 final size:131
Alignment explanation
Indices: 363300--363562 Score: 490
Period size: 132 Copynumber: 2.0 Consensus size: 131
363290 TAGATTATGT
363300 TAGTTTAATACTAGCATATACCTTGAACATTTTATGTTATTATATGATGTCGCCAGACCTCAATA
1 TAGTTTAATACTAGCATATACCTTGAACATTTTATGTTATTATATGATGTCGCCAGACCTCAATA
* *
363365 AATCTAGTGATCCAAGTAACACAAAAAAGATGGAAAAATGCAAAAATTGAGAATATTATCGAGGA
66 AATCTAGTGATCCAAGTAACAAAAAAAAGAAGGAAAAATGC-AAAATTGAGAATATTATCGAGGA
363430 GA
130 GA
*
363432 TAGTTTAATATTAGCATATACCTTGAACATTTTATGTTATTATATGATGTCGCCAGACCTCAATA
1 TAGTTTAATACTAGCATATACCTTGAACATTTTATGTTATTATATGATGTCGCCAGACCTCAATA
363497 AATCTAGTGATCCAAGTAACAAAAAAAAGAAGGAAAAATGCAAAATTGAGAATATTATCGAGGAG
66 AATCTAGTGATCCAAGTAACAAAAAAAAGAAGGAAAAATGCAAAATTGAGAATATTATCGAGGAG
363562 A
131 A
363563 ATATTCGGCA
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
131 25 0.20
132 103 0.80
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (131 bp):
TAGTTTAATACTAGCATATACCTTGAACATTTTATGTTATTATATGATGTCGCCAGACCTCAATA
AATCTAGTGATCCAAGTAACAAAAAAAAGAAGGAAAAATGCAAAATTGAGAATATTATCGAGGAG
A
Found at i:368871 original size:14 final size:14
Alignment explanation
Indices: 368852--368889 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
368842 TCACAACAGC
368852 TAACATCTTAGTGA
1 TAACATCTTAGTGA
368866 TAACATCTTAGTGA
1 TAACATCTTAGTGA
368880 TAACATCTTA
1 TAACATCTTA
368890 ATTAAAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (14 bp):
TAACATCTTAGTGA
Found at i:379307 original size:2 final size:2
Alignment explanation
Indices: 379300--379337 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
379290 TTAATTATGC
379300 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
379338 GATGTTATTT
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:381057 original size:28 final size:26
Alignment explanation
Indices: 381026--381077 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
381016 TAAATTGAGA
*
381026 AAATAACAATAAAAATGTTAAGAAAAAT
1 AAATAAAAATAAAAA--TTAAGAAAAAT
381054 AAATAAAAATAAAAATTAAGAAAA
1 AAATAAAAATAAAAATTAAGAAAA
381078 TATTCAGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
28 14 0.61
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (26 bp):
AAATAAAAATAAAAATTAAGAAAAAT
Found at i:381774 original size:15 final size:15
Alignment explanation
Indices: 381750--381782 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
381740 CCCCTCTTTC
381750 TTTCCTCTTTTT-TT
1 TTTCCTCTTTTTGTT
381764 TTTCTCTCTTTTTGTT
1 TTTC-CTCTTTTTGTT
381780 TTT
1 TTT
381783 ATTTCTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTCCTCTTTTTGTT
Found at i:387344 original size:22 final size:23
Alignment explanation
Indices: 387279--387354 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 23
387269 TATCTCACAT
387279 GAAA-GAAAATTAATATTCAAAAG
1 GAAATGAAAATTAA-ATTCAAAAG
* *
387302 GAAATG-AAA-TAAAGTACAAAAT
1 GAAATGAAAATTAAA-TTCAAAAG
*
387324 GAAA-GAAAATTAAATTTAAAAG
1 GAAATGAAAATTAAATTCAAAAG
387346 GAAATGAAA
1 GAAATGAAA
387355 TGAAACAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.05
22 25 0.58
23 15 0.35
24 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.14, T:0.20
Consensus pattern (23 bp):
GAAATGAAAATTAAATTCAAAAG
Found at i:390831 original size:21 final size:21
Alignment explanation
Indices: 390805--390859 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
390795 TTATGAGGAT
390805 GAGGTAAGTCCAATGCTTAGG
1 GAGGTAAGTCCAATGCTTAGG
*
390826 GAGGTAAGTCCAATGCTTGGG
1 GAGGTAAGTCCAATGCTTAGG
* *
390847 GTGGTATGTCCAA
1 GAGGTAAGTCCAA
390860 CATTTTTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (21 bp):
GAGGTAAGTCCAATGCTTAGG
Found at i:395476 original size:19 final size:19
Alignment explanation
Indices: 395424--395490 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
395414 GACCTGAACC
*
395424 AAAATAAAAAATAAT-AAT
1 AAAATAAATAATAATAAAT
*
395442 AAAAATGAACT-A-AATAAAT
1 -AAAAT-AAATAATAATAAAT
*
395461 AAAATAAATAATAATATAT
1 AAAATAAATAATAATAAAT
395480 AATAA-AAATAA
1 AA-AATAAATAA
395491 AAACTATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
17 3 0.08
18 9 0.23
19 23 0.59
20 4 0.10
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (19 bp):
AAAATAAATAATAATAAAT
Found at i:395610 original size:37 final size:37
Alignment explanation
Indices: 395542--395799 Score: 319
Period size: 37 Copynumber: 7.0 Consensus size: 37
395532 AAAAAAATAT
* *
395542 TATATGTTTCAAAACCT-TTTTAAAAACTATATATTATA
1 TATAT-TTTCAAAA-ATGTTTTCAAAACTATATATTATA
* * *
395580 TACATATTCAAAAATGTTTTCAAAAGTATATATTATA
1 TATATTTTCAAAAATGTTTTCAAAACTATATATTATA
* * *
395617 TATGTTTTCAAAAATGTTTTCCATACTATATA-T-TA
1 TATATTTTCAAAAATGTTTTCAAAACTATATATTATA
*
395652 TATATTTTC-AAAACGTTTT-AAAACTATATATTATA
1 TATATTTTCAAAAATGTTTTCAAAACTATATATTATA
* *
395687 TATTTTTTCAAAAATGTTTCCAAAACTATATATTATA
1 TATATTTTCAAAAATGTTTTCAAAACTATATATTATA
*
395724 TATATGTTCAAAATATGTTTTCAAAACTATATATTATA
1 TATATTTTCAAAA-ATGTTTTCAAAACTATATATTATA
* * *
395762 TATATTTTCAAAAATATTCTCAAAACTATATAATATA
1 TATATTTTCAAAAATGTTTTCAAAACTATATATTATA
395799 T
1 T
395800 GTTTTTTAAC
Statistics
Matches: 189, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
33 9 0.05
34 10 0.05
35 20 0.11
36 10 0.05
37 101 0.53
38 39 0.21
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATTTTCAAAAATGTTTTCAAAACTATATATTATA
Found at i:396609 original size:30 final size:31
Alignment explanation
Indices: 396573--396638 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
396563 ATCATATTCG
* *
396573 ATTTAAAAT-ACTTAAATAGCAAAAATAGAC
1 ATTTAAAATGACTAAAATAACAAAAATAGAC
* *
396603 ATTT-AAATGACTAAAATAACAAAAATATAT
1 ATTTAAAATGACTAAAATAACAAAAATAGAC
396633 ATTTAA
1 ATTTAA
396639 GGGACTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 4 0.13
30 25 0.83
31 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.30
Consensus pattern (31 bp):
ATTTAAAATGACTAAAATAACAAAAATAGAC
Found at i:396645 original size:30 final size:30
Alignment explanation
Indices: 396586--396854 Score: 140
Period size: 30 Copynumber: 9.1 Consensus size: 30
396576 TAAAATACTT
* *
396586 AAATAGCAAAAATAGACATTTAAATGACTA
1 AAATAACAAAAATAGACATTTAAAGGACTA
* * *
396616 AAATAACAAAAATATATATTTAAGGGACTA
1 AAATAACAAAAATAGACATTTAAAGGACTA
** * * *
396646 AAATGATATTAACATA-A-ACTAAAAGGACTA
1 AAAT-A-ACAAAAATAGACATTTAAAGGACTA
** * * *
396676 ACAA-AGTAAAAATAGAAATTTAAAAGAATA
1 A-AATAACAAAAATAGACATTTAAAGGACTA
** * * * *
396706 AAATGGCAAAAATAGAAACTTAATGGTCTA
1 AAATAACAAAAATAGACATTTAAAGGACTA
* ** *
396736 AAA-CAGTAAAATAGAAATTTAAAGGACTA
1 AAATAACAAAAATAGACATTTAAAGGACTA
** * *
396765 AAATGGCAAAATATA-A-ACTTAAAGGTCT-
1 AAATAACAAAA-ATAGACATTTAAAGGACTA
* *
396793 AAATAA-AAATACAGACATTTAAAGGACTA
1 AAATAACAAAAATAGACATTTAAAGGACTA
* * *
396822 AAATAACAAAAACATACATTTAAGGGACTA
1 AAATAACAAAAATAGACATTTAAAGGACTA
396852 AAA
1 AAA
396855 GTGTATTAAC
Statistics
Matches: 180, Mismatches: 47, Indels: 24
0.72 0.19 0.10
Matches are distributed among these distances:
26 2 0.01
27 4 0.02
28 20 0.11
29 42 0.23
30 99 0.55
31 7 0.04
32 6 0.03
ACGTcount: A:0.57, C:0.09, G:0.12, T:0.22
Consensus pattern (30 bp):
AAATAACAAAAATAGACATTTAAAGGACTA
Found at i:396757 original size:29 final size:29
Alignment explanation
Indices: 396714--396795 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
396704 TAAAATGGCA
* *
396714 AAAATAGAAACTTAATGGTCTAAAACAGT
1 AAAATAGAAACTTAAAGGTCTAAAACAGC
* * **
396743 AAAATAGAAATTTAAAGGACTAAAATGGC
1 AAAATAGAAACTTAAAGGTCTAAAACAGC
*
396772 AAAATATAAACTTAAAGGTCTAAA
1 AAAATAGAAACTTAAAGGTCTAAA
396796 TAAAAATACA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (29 bp):
AAAATAGAAACTTAAAGGTCTAAAACAGC
Found at i:396767 original size:59 final size:56
Alignment explanation
Indices: 396683--396825 Score: 180
Period size: 59 Copynumber: 2.5 Consensus size: 56
396673 CTAACAAAGT
* * *
396683 AAAAATAGAAATTTAAAAGAATAAAATGGCAAAAATAGAAACTTAATGGTCTAAA-A
1 AAAAATAGAAATTTAAAGGACTAAAATGGC-AAAATAGAAACTTAAAGGTCTAAATA
*
396739 CAGTAAAATAGAAATTTAAAGGACTAAAATGGCAAAATATAAACTTAAAGGTCTAAATA
1 -A--AAAATAGAAATTTAAAGGACTAAAATGGCAAAATAGAAACTTAAAGGTCTAAATA
* *
396798 AAAATACAGACATTTAAAGGACTAAAAT
1 AAAA-ATAGAAATTTAAAGGACTAAAAT
396826 AACAAAAACA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
56 3 0.04
57 22 0.29
58 23 0.30
59 28 0.37
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.22
Consensus pattern (56 bp):
AAAAATAGAAATTTAAAGGACTAAAATGGCAAAATAGAAACTTAAAGGTCTAAATA
Found at i:399552 original size:18 final size:18
Alignment explanation
Indices: 399529--399565 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
399519 AATTCCTGAC
*
399529 AGATTCCAATTCCTTCAT
1 AGATTCCAATTCCCTCAT
399547 AGATTCCAATTCCCTCAT
1 AGATTCCAATTCCCTCAT
399565 A
1 A
399566 AATATTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (18 bp):
AGATTCCAATTCCCTCAT
Found at i:399762 original size:3 final size:3
Alignment explanation
Indices: 399754--399813 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
399744 TGTAAACATA
* *
399754 AAT AAT AAT AAT AAT AAT AA- AAT AAC GAT AAT AAT AATT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
399798 ATAT AAT -AT AAT AAT A
1 A-AT AAT AAT AAT AAT A
399814 TTTTTGGTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
2 5 0.10
3 39 0.81
4 4 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:400417 original size:28 final size:29
Alignment explanation
Indices: 400377--400432 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
400367 AGGGGCGAAT
* *
400377 TTGAAATTTTAAAATT-TCAAGGGTGAAC
1 TTGAAATTATAAAATTGTAAAGGGTGAAC
*
400405 TTGAACTTATAAAATTGTAAAGGGTGAA
1 TTGAAATTATAAAATTGTAAAGGGTGAA
400433 AGCATATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
TTGAAATTATAAAATTGTAAAGGGTGAAC
Found at i:401125 original size:21 final size:21
Alignment explanation
Indices: 401083--401130 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
401073 TCCTGGAAGG
*
401083 GGAATTAGGGATTAGGGGTGA
1 GGAATTAGGGATTAGGGATGA
401104 GGAATTAGGGATT-GGTGATGA
1 GGAATTAGGGATTAGG-GATGA
401125 GAGAAT
1 G-GAAT
401131 GGGGGAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (21 bp):
GGAATTAGGGATTAGGGATGA
Found at i:406220 original size:21 final size:21
Alignment explanation
Indices: 406178--406225 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
406168 TACTGGAAGG
*
406178 GGAATTAGGGATTAGGGGTGA
1 GGAATTAGGGATTAGGGATGA
406199 GGAATTAGGGATT-GGTGATGA
1 GGAATTAGGGATTAGG-GATGA
406220 GAGAAT
1 G-GAAT
406226 GGGGGAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (21 bp):
GGAATTAGGGATTAGGGATGA
Found at i:410240 original size:50 final size:50
Alignment explanation
Indices: 410179--410285 Score: 169
Period size: 50 Copynumber: 2.1 Consensus size: 50
410169 TTTTTGTCTG
* *
410179 ACATTATCAAGGAATTCAAAGAGGAAAAGACGTCTTTTATTTATCTTTGA
1 ACATTAACAAGGAATTCAAAGAGGAAAAGACGTCTTTTATATATCTTTGA
* *
410229 ACATTAACAAGGAATTCAAAGAGGAAAGGACGTCTTTTATATGTCTTTGA
1 ACATTAACAAGGAATTCAAAGAGGAAAAGACGTCTTTTATATATCTTTGA
*
410279 ATATTAA
1 ACATTAA
410286 GCGTTGGGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (50 bp):
ACATTAACAAGGAATTCAAAGAGGAAAAGACGTCTTTTATATATCTTTGA
Found at i:410448 original size:21 final size:21
Alignment explanation
Indices: 410423--410466 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
410413 TGAAATGTTA
* * *
410423 AAAAATATTGATATTTTTGAT
1 AAAAATAATAATATTTTAGAT
410444 AAAAATAATAATATTTTAGAT
1 AAAAATAATAATATTTTAGAT
410465 AA
1 AA
410467 TTTTTATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
AAAAATAATAATATTTTAGAT
Found at i:410795 original size:105 final size:105
Alignment explanation
Indices: 410680--410895 Score: 414
Period size: 105 Copynumber: 2.1 Consensus size: 105
410670 AAAAGTTATC
*
410680 AAATATAGTAACATAATAATTTGTACATAAAATATTATAACGGTAAGAAAATAAGTTATAAATAA
1 AAATATAGTAACATAATAATTTGTACATAAAACATTATAACGGTAAGAAAATAAGTTATAAATAA
410745 TACATGTTATGAGTATTATTAAAATTTTAGATTGTGTTTA
66 TACATGTTATGAGTATTATTAAAATTTTAGATTGTGTTTA
*
410785 AAATATAGTAACATAATAATTTGTACATAAAACATTATAACGGTACGAAAATAAGTTATAAATAA
1 AAATATAGTAACATAATAATTTGTACATAAAACATTATAACGGTAAGAAAATAAGTTATAAATAA
410850 TACATGTTATGAGTATTATTAAAATTTTAGATTGTGTTTA
66 TACATGTTATGAGTATTATTAAAATTTTAGATTGTGTTTA
410890 AAATAT
1 AAATAT
410896 TAATAGAATT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 109 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.38
Consensus pattern (105 bp):
AAATATAGTAACATAATAATTTGTACATAAAACATTATAACGGTAAGAAAATAAGTTATAAATAA
TACATGTTATGAGTATTATTAAAATTTTAGATTGTGTTTA
Found at i:411128 original size:164 final size:165
Alignment explanation
Indices: 410930--411234 Score: 416
Period size: 164 Copynumber: 1.9 Consensus size: 165
410920 ATGATTTTTA
** * * * * ***
410930 CACAATAACAAAATAAGTTAAAAAGCTTAAAATGTAATGAATATCTATAATAAATATGGTTACA-
1 CACAATAACAAAATAAAATAAAAAACTGAAAATGTAATGAATATATACAATAAATACAATTACAG
* * ** *
410994 CTCAAGAATGTCATGATTCACTAAGAAAGTATGTTATGATCTGGAATGTT-AATATTTTTATTAA
66 CT-AAGAATGTCATGATTCACTAAGAAAGTAGGTTACGATCTGGAACATTAAAAATTTTTATTAA
411058 TAAAATGAGTTGAGCTGGTGGAGCCTTAGATTTTCC
130 TAAAATGAGTTGAGCTGGTGGAGCCTTAGATTTTCC
* *
411094 CACAATAACAAAATAAAATAAAAAACTGAAAATGTTATGAATATATACAATAAATACAATTGCAG
1 CACAATAACAAAATAAAATAAAAAACTGAAAATGTAATGAATATATACAATAAATACAATTACAG
* *
411159 CTAAGAATGTCATGATTCACTAAGAAAGTAGGTTGCGTTCTGGAACATTAAAAATTTTTATTAAT
66 CTAAGAATGTCATGATTCACTAAGAAAGTAGGTTACGATCTGGAACATTAAAAATTTTTATTAAT
*
411224 AAAATGGGTTG
131 AAAATGAGTTG
411235 CGTATACAAT
Statistics
Matches: 120, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
164 94 0.78
165 26 0.22
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.31
Consensus pattern (165 bp):
CACAATAACAAAATAAAATAAAAAACTGAAAATGTAATGAATATATACAATAAATACAATTACAG
CTAAGAATGTCATGATTCACTAAGAAAGTAGGTTACGATCTGGAACATTAAAAATTTTTATTAAT
AAAATGAGTTGAGCTGGTGGAGCCTTAGATTTTCC
Found at i:416283 original size:19 final size:21
Alignment explanation
Indices: 416259--416297 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
416249 TTGCTCAATC
416259 GAAATAAAA-T-AAAATAAAT
1 GAAATAAAATTAAAAATAAAT
416278 GAAATAAAATTAAAAATAAA
1 GAAATAAAATTAAAAATAAA
416298 CAATGGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (21 bp):
GAAATAAAATTAAAAATAAAT
Found at i:420355 original size:22 final size:23
Alignment explanation
Indices: 420309--420362 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
420299 TTGCTTGTTC
*
420309 ATATTTTCTTATTAGTTACCTTA
1 ATATTTTCTTATTACTTACCTTA
* *
420332 ATATTTT-TTTTTACTTTCCTTA
1 ATATTTTCTTATTACTTACCTTA
420354 AT-TTTTCTT
1 ATATTTTCTT
420363 CATTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 16 0.59
23 7 0.26
ACGTcount: A:0.20, C:0.13, G:0.02, T:0.65
Consensus pattern (23 bp):
ATATTTTCTTATTACTTACCTTA
Found at i:424747 original size:22 final size:23
Alignment explanation
Indices: 424722--424765 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
424712 AATTAAGTTT
424722 TAATCTTA-AAAAAATTTCAAAA
1 TAATCTTACAAAAAATTTCAAAA
* **
424744 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAAAATTTCAAA
424766 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAAAAATTTCAAAA
Found at i:440165 original size:12 final size:12
Alignment explanation
Indices: 440148--440184 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
440138 CGGATTCACC
440148 TGAATTTGATTA
1 TGAATTTGATTA
*
440160 TGAATTAGATTA
1 TGAATTTGATTA
*
440172 TGGATTTGATTA
1 TGAATTTGATTA
440184 T
1 T
440185 TGTCTCCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (12 bp):
TGAATTTGATTA
Found at i:440534 original size:18 final size:18
Alignment explanation
Indices: 440511--440555 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
440501 GGGGGGGGTT
440511 TGGTAAAAATATATTAAA
1 TGGTAAAAATATATTAAA
440529 TGGTAAAAATATATTAAA
1 TGGTAAAAATATATTAAA
*
440547 TAGTAAAAA
1 TGGTAAAAA
440556 GTAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (18 bp):
TGGTAAAAATATATTAAA
Found at i:442791 original size:21 final size:21
Alignment explanation
Indices: 442766--442805 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
442756 TCGATACTGT
*
442766 AAGGG-AGTATCGGTACCATAG
1 AAGGGTAGTAT-GATACCATAG
442787 AAGGGTAGTATGATACCAT
1 AAGGGTAGTATGATACCAT
442806 GTTAAGGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (21 bp):
AAGGGTAGTATGATACCATAG
Found at i:442905 original size:20 final size:20
Alignment explanation
Indices: 442866--442918 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
442856 CCAGGAAGGG
*
442866 GTATCGGTACTCTAGTGTAGAA
1 GTATCGGTA--CTAGGGTAGAA
*
442888 GTATCGGTACTAGGGTAGTA
1 GTATCGGTACTAGGGTAGAA
*
442908 GTATCGATACT
1 GTATCGGTACT
442919 TTGGAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.68
22 9 0.32
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.32
Consensus pattern (20 bp):
GTATCGGTACTAGGGTAGAA
Found at i:443539 original size:45 final size:45
Alignment explanation
Indices: 443328--443561 Score: 281
Period size: 45 Copynumber: 5.2 Consensus size: 45
443318 AGATAATACT
* ** * * * *
443328 AATGCATATGGGTGCATTATCGGCATG-AAAGGATGCCATATTTGA
1 AATGCATATGGGTACATTATCAACA-GAAAAGTATACTATAGTTGA
*
443373 AATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGA
* * *
443418 AATGTATATAGGTACATTATCAATAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGA
* * *
443463 AATGTATATGTGTACATTATCAATAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGA
* * * *
443508 AATGCATATGGGTGCATTATCAACAAAAAAGTATGCTATAGTTTA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGA
443553 AAGTGCATA
1 AA-TGCATA
443562 ATGGTGCCTT
Statistics
Matches: 168, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
44 1 0.01
45 161 0.96
46 6 0.04
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:457389 original size:61 final size:61
Alignment explanation
Indices: 457284--457461 Score: 221
Period size: 61 Copynumber: 2.9 Consensus size: 61
457274 TGCACAAAGC
* * * * * * * * *
457284 TTACGCTCTAGTGCTAATTCGAATATGAAACATAAGGTCGTGCCCATCACCTATATTAGGT
1 TTACACTCTAGTGTTGATCCGAATATGACACATAAGGTCATGCCCACCACCTACACTAGGT
*
457345 TTACACTCTAGTGTTGATCTGAATATGACACATAAGGTCATGCCCACCACCTACACTAGGT
1 TTACACTCTAGTGTTGATCCGAATATGACACATAAGGTCATGCCCACCACCTACACTAGGT
* ** * *
457406 TTACACTCTAGTGTTGATCCGGATATGACACATAAGGTTGTTCTCACCACCTACAC
1 TTACACTCTAGTGTTGATCCGAATATGACACATAAGGTCATGCCCACCACCTACAC
457462 CTAGTGTCCT
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 101 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (61 bp):
TTACACTCTAGTGTTGATCCGAATATGACACATAAGGTCATGCCCACCACCTACACTAGGT
Found at i:457679 original size:22 final size:22
Alignment explanation
Indices: 457639--457680 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
457629 CCGAAGTAAC
*
457639 ATTCATAATAAATAGCATATAT
1 ATTCATAATAAAAAGCATATAT
* *
457661 ATTCATGATAAAAATCATAT
1 ATTCATAATAAAAAGCATAT
457681 TTATAATAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTCATAATAAAAAGCATATAT
Found at i:458920 original size:27 final size:27
Alignment explanation
Indices: 458872--458923 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
458862 CATCACCACT
*
458872 TTGAACTTGAAACTCCATAGCATCACA
1 TTGAACTTGAAACTCCACAGCATCACA
* *
458899 TTGAACTTGAAAGTCTACAGCATCA
1 TTGAACTTGAAACTCCACAGCATCA
458924 AGATCTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (27 bp):
TTGAACTTGAAACTCCACAGCATCACA
Found at i:464135 original size:15 final size:15
Alignment explanation
Indices: 464115--464145 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
464105 AAAGTTGATA
464115 AAAATATCAAAATTT
1 AAAATATCAAAATTT
*
464130 AAAATATCAATATTT
1 AAAATATCAAAATTT
464145 A
1 A
464146 TATGATGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATATCAAAATTT
Found at i:464164 original size:73 final size:73
Alignment explanation
Indices: 464073--464239 Score: 185
Period size: 74 Copynumber: 2.3 Consensus size: 73
464063 ACGATGCTTA
* * *
464073 ATATATGATGATCGATACTTTTAAATATTGA-AAAAGTTGATAAAAAT-ATCAAAATTTAAAATA
1 ATATATGATGTTCAATACTTTTAAATATTGAGAAAA-TTGATAAAAATGATCAAAAGTTAAAATA
**
464136 TCAATATTT
65 TCAATACAT
* * * * *
464145 ATATGATGATGTTCAATACTTTTATATATTGAGAAAATTGATGAAGATGATCGATAGTTAAAATA
1 ATAT-ATGATGTTCAATACTTTTAAATATTGAGAAAATTGATAAAAATGATCAAAAGTTAAAATA
*
464210 TCTATACAT
65 TCAATACAT
*
464219 ATATCATGATGTTCAAAACTT
1 ATAT-ATGATGTTCAATACTT
464240 GCTATGGTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
72 4 0.05
73 33 0.42
74 42 0.53
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (73 bp):
ATATATGATGTTCAATACTTTTAAATATTGAGAAAATTGATAAAAATGATCAAAAGTTAAAATAT
CAATACAT
Found at i:466709 original size:19 final size:19
Alignment explanation
Indices: 466685--466723 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
466675 ATGACCAACA
*
466685 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
466704 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
466723 A
1 A
466724 GTATCGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:466853 original size:21 final size:21
Alignment explanation
Indices: 466827--466923 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
466817 CGAATATGTA
*
466827 AATCGCAAAGCGATAATACAT
1 AATCGCAACGCGATAATACAT
* **
466848 AATCGCAACGTGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
*
466869 -ATCGCAACTCGATAATACAT
1 AATCGCAACGCGATAATACAT
*
466889 AATCGCAACGCGATAATACAA
1 AATCGCAACGCGATAATACAT
*
466910 AATCGCAATGCGAT
1 AATCGCAACGCGAT
466924 TTTCAAAGCG
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 13 0.21
21 45 0.73
22 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Done.