Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 8 of 18
Found at i:1187729 original size:6 final size:6
Alignment explanation
Indices: 1187718--1187743 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1187708 AAAAATATAC
1187718 TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TA
1187744 TAAAGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:1189613 original size:2 final size:2
Alignment explanation
Indices: 1189606--1189637 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1189596 TTTCTATAAG
1189606 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
1189638 AGTGATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1190178 original size:9 final size:9
Alignment explanation
Indices: 1190157--1190192 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
1190147 AGTCGAATAA
1190157 AATCAATTTT
1 AATCAA-TTT
1190167 AATCAATTT
1 AATCAATTT
1190176 AATCAATTT
1 AATCAATTT
*
1190185 AATTAATT
1 AATCAATT
1190193 CAATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 19 0.76
10 6 0.24
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (9 bp):
AATCAATTT
Found at i:1190791 original size:19 final size:18
Alignment explanation
Indices: 1190769--1190805 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
1190759 TTTATTAATA
1190769 TTTTATATAATTAAATTTAT
1 TTTTAT-TAATT-AATTTAT
1190789 TTTTATTAATTAATTTA
1 TTTTATTAATTAATTTA
1190806 CAGTTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATTAATTAATTTAT
Found at i:1191931 original size:15 final size:15
Alignment explanation
Indices: 1191911--1191963 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
1191901 AAACAATTTA
1191911 AAAAAATCTATTTTT
1 AAAAAATCTATTTTT
*
1191926 AAAAAATAT-TTTTT
1 AAAAAATCTATTTTT
1191940 AAAAAAT-TATTTTT
1 AAAAAATCTATTTTT
1191954 CATAAAAATC
1 -A-AAAAATC
1191964 AAAATCAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.03
14 17 0.52
15 9 0.27
16 6 0.18
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAAATCTATTTTT
Found at i:1197389 original size:97 final size:97
Alignment explanation
Indices: 1197219--1197415 Score: 263
Period size: 97 Copynumber: 2.0 Consensus size: 97
1197209 GATGCTCACA
* *
1197219 CCAGAACAAACCACTCCTGGATTCATCAATTCAACAGCATCTCGGCAAAATCACAACAACCATAT
1 CCAGAACAAACCACTCCTGGATTCATCAATTCAACAGCATCTCAGCAAAATCACAACAACCACAT
* * * *
1197284 CTCGGCTAA-ATATATTGCACTGTCAAGCTCAG
66 CTCAGCTAACA-AGATCGCACTCTCAAGCTCAG
* * **
1197316 CCAGAAC-AACCACTCCTGGGATTCATCAGTTCAACAGCATCTCAGCAAAATCACAACAGCTGCA
1 CCAGAACAAACCACTCCT-GGATTCATCAATTCAACAGCATCTCAGCAAAATCACAACAACCACA
*
1197380 TCTCAGCTAACAAGATCGCACTCTCAAGCTTAG
65 TCTCAGCTAACAAGATCGCACTCTCAAGCTCAG
1197413 CCA
1 CCA
1197416 CAATTGTTAG
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 10 0.11
97 76 0.87
98 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.20
Consensus pattern (97 bp):
CCAGAACAAACCACTCCTGGATTCATCAATTCAACAGCATCTCAGCAAAATCACAACAACCACAT
CTCAGCTAACAAGATCGCACTCTCAAGCTCAG
Found at i:1201597 original size:38 final size:35
Alignment explanation
Indices: 1201554--1201677 Score: 112
Period size: 38 Copynumber: 3.5 Consensus size: 35
1201544 ATATAATATC
1201554 TTAAAATGAATTATGATAATTAATTAATTAAATTTGAA
1 TTAAAATGAATT-T-ATAATTAATTAATTAAATTT-AA
* * * *
1201592 GTAAAATGAATTT-TAA-TAATTAATTTAATAT-C
1 TTAAAATGAATTTATAATTAATTAATTAAATTTAA
1201624 TTAAAATGAATTGTAATAATTAATTAAATTAAATTTAAA
1 TTAAAATGAATT-T-ATAATTAATT-AATTAAATTT-AA
*
1201663 TTAAAAT-ATTTTATA
1 TTAAAATGAATTTATA
1201678 TCTTTAATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
32 11 0.16
33 1 0.01
34 13 0.19
35 6 0.09
36 8 0.11
37 10 0.14
38 14 0.20
39 7 0.10
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.44
Consensus pattern (35 bp):
TTAAAATGAATTTATAATTAATTAATTAAATTTAA
Found at i:1201621 original size:70 final size:71
Alignment explanation
Indices: 1201532--1201669 Score: 206
Period size: 70 Copynumber: 2.0 Consensus size: 71
1201522 TTGTAATATT
* *
1201532 TTTTAAAAATAAATATAATATCTTAAAATGAATTATGATAATTAATT-AATTAAATTTGAAGTAA
1 TTTTAAAAATAAATATAATATCTTAAAATGAATTATAATAATTAATTAAATTAAATTTAAAGTAA
1201596 AATGAA
66 AATGAA
* * * * *
1201602 TTTTAATAATTAATTTAATATCTTAAAATGAATTGTAATAATTAATTAAATTAAATTTAAATTAA
1 TTTTAAAAATAAATATAATATCTTAAAATGAATTATAATAATTAATTAAATTAAATTTAAAGTAA
1201667 AAT
66 AAT
1201670 ATTTTATATC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
70 42 0.70
71 18 0.30
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (71 bp):
TTTTAAAAATAAATATAATATCTTAAAATGAATTATAATAATTAATTAAATTAAATTTAAAGTAA
AATGAA
Found at i:1201633 original size:32 final size:32
Alignment explanation
Indices: 1201532--1201648 Score: 108
Period size: 32 Copynumber: 3.5 Consensus size: 32
1201522 TTGTAATATT
* * *
1201532 TTTTAAAAATAAATATAATATCTTAAAATGAA
1 TTTTAATAATTAATTTAATATCTTAAAATGAA
* * **
1201564 TTATGATAATTAATTAATTAAATTTGAAGTAAAATGAA
1 TT-T--TAA-TAATTAATTTAATAT--CTTAAAATGAA
1201602 TTTTAATAATTAATTTAATATCTTAAAATGAA
1 TTTTAATAATTAATTTAATATCTTAAAATGAA
*
1201634 TTGTAATAATTAATT
1 TTTTAATAATTAATT
1201649 AAATTAAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
32 25 0.37
33 1 0.01
34 13 0.19
35 6 0.09
36 10 0.15
37 1 0.01
38 11 0.16
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (32 bp):
TTTTAATAATTAATTTAATATCTTAAAATGAA
Found at i:1207355 original size:18 final size:16
Alignment explanation
Indices: 1207332--1207365 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
1207322 AAATATAAAC
1207332 TTTTTAAATATATATTAA
1 TTTTTAAA-ATA-ATTAA
1207350 TTTTTAAAATAATTAA
1 TTTTTAAAATAATTAA
1207366 ATTTAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTTAAAATAATTAA
Found at i:1207368 original size:17 final size:19
Alignment explanation
Indices: 1207327--1207369 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
1207317 TATAAAAATA
1207327 TAAACTTTTTAAATATATAT
1 TAAA-TTTTTAAATATATAT
1207347 T-AATTTTTAAA-ATA-AT
1 TAAATTTTTAAATATATAT
1207363 TAAATTT
1 TAAATTT
1207370 AATTACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 8 0.36
19 2 0.09
20 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAATTTTTAAATATATAT
Found at i:1208430 original size:2 final size:2
Alignment explanation
Indices: 1208423--1208471 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1208413 AAAGAAAAAG
1208423 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1208465 GA GA GA G
1 GA GA GA G
1208472 TACGAATGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1213652 original size:10 final size:9
Alignment explanation
Indices: 1213618--1213651 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1213608 ACATATTGAA
*
1213618 TATTTTAAT
1 TATTTTATT
1213627 TATTTTATAT
1 TATTTTAT-T
1213637 TATTTTATT
1 TATTTTATT
1213646 TATTTT
1 TATTTT
1213652 TTAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTTTATT
Found at i:1217979 original size:10 final size:10
Alignment explanation
Indices: 1217958--1218008 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
1217948 CAACTCAATT
1217958 AAAAATAT-A
1 AAAAATATAA
1217967 AAAAATATAA
1 AAAAATATAA
1217977 AAAAATAATATCA
1 AAAAAT-ATA--A
*
1217990 AATAATATAA
1 AAAAATATAA
1218000 AATAAATAT
1 AA-AAATAT
1218009 TTACCTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.23
10 10 0.29
11 8 0.23
12 3 0.09
13 6 0.17
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAAATATAA
Found at i:1218467 original size:28 final size:28
Alignment explanation
Indices: 1218436--1218492 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1218426 AAAAGAATTA
* *
1218436 AAAAATT-ATTTTATATTAATATATTTTT
1 AAAAATTAATTTTA-ATAAAAATATTTTT
*
1218464 AAAATTTAATTTTAATAAAAATATTTTT
1 AAAAATTAATTTTAATAAAAATATTTTT
1218492 A
1 A
1218493 TTAATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAAAATTAATTTTAATAAAAATATTTTT
Found at i:1223072 original size:12 final size:12
Alignment explanation
Indices: 1223055--1223082 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1223045 GATTGAATTA
1223055 TTTATTTTATTT
1 TTTATTTTATTT
1223067 TTTATTTTATTT
1 TTTATTTTATTT
1223079 TTTA
1 TTTA
1223083 CTTTGATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:1223902 original size:2 final size:2
Alignment explanation
Indices: 1223895--1223953 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
1223885 CCATCTCATA
* * *
1223895 AT AT AT AT AT AT AT AT AT AT AT CT -T TT AT AA 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
* *
1223936 AT AT GT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1223954 TAATTTTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1225149 original size:17 final size:16
Alignment explanation
Indices: 1225119--1225195 Score: 50
Period size: 17 Copynumber: 4.7 Consensus size: 16
1225109 TTACGATAAT
*
1225119 AAAATAACACAAATATA
1 AAAATAA-ATAAATATA
*
1225136 AAAATAATATAAATACA
1 AAAATAA-ATAAATATA
* ** *
1225153 TAAATATTTTTAA-AT-
1 AAAATA-AATAAATATA
1225168 AAAATAAATAACATATA
1 AAAATAAATAA-ATATA
1225185 AAAATAAATAA
1 AAAATAAATAA
1225196 TATTATGATT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 2 0.05
15 6 0.14
16 3 0.07
17 33 0.75
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATAAATAAATATA
Found at i:1235202 original size:21 final size:20
Alignment explanation
Indices: 1235164--1235207 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1235154 AAAAAAAAAT
1235164 TTAAAATTTTAATATATCATA
1 TTAAAATTTTAATATATCA-A
*
1235185 TTAAAA-TTTAATTTTATCAA
1 TTAAAATTTTAA-TATATCAA
1235205 TTA
1 TTA
1235208 TTTAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAATTTTAATATATCAA
Found at i:1236941 original size:21 final size:22
Alignment explanation
Indices: 1236917--1236958 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1236907 TTAAAAAATT
1236917 ATTTATAA-TTGTTAAATTTAA
1 ATTTATAACTTGTTAAATTTAA
*
1236938 ATTTATAACTTTTTAAATTTA
1 ATTTATAACTTGTTAAATTTA
1236959 TATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTATAACTTGTTAAATTTAA
Found at i:1239391 original size:29 final size:29
Alignment explanation
Indices: 1239359--1239418 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1239349 CTTTTATGGC
*
1239359 AATAATTGAAGACACTTCCTGATCCTATT
1 AATAATTAAAGACACTTCCTGATCCTATT
*
1239388 AATAATTAAAGAGACTTCCTGATCCTATT
1 AATAATTAAAGACACTTCCTGATCCTATT
1239417 AA
1 AA
1239419 CTTTTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (29 bp):
AATAATTAAAGACACTTCCTGATCCTATT
Found at i:1241021 original size:2 final size:2
Alignment explanation
Indices: 1241014--1241049 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1241004 CTTTTATGCT
1241014 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
1241050 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1241054 original size:2 final size:2
Alignment explanation
Indices: 1241049--1241094 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1241039 ATATATATAT
1241049 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1241090 AG AG A
1 AG AG A
1241095 TGGGGACAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1241251 original size:22 final size:24
Alignment explanation
Indices: 1241226--1241272 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
1241216 TGATAATTTT
*
1241226 AAATATGAT-ATGAAAA-AATATA
1 AAATATGATAATAAAAATAATATA
1241248 AAATATGATAATAAAAATAATATA
1 AAATATGATAATAAAAATAATATA
1241272 A
1 A
1241273 TATGATGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 6 0.27
24 7 0.32
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (24 bp):
AAATATGATAATAAAAATAATATA
Found at i:1243932 original size:45 final size:45
Alignment explanation
Indices: 1243868--1243954 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 45
1243858 ATCATTCAAA
*
1243868 AATATTTTAATGACTAAAACCTT-AAGACTCAAAACCAATCATTCG
1 AATATTTTAATGACTAAAA-CTTGAAGACTCAAAACAAATCATTCG
*
1243913 AATATTTT-ATGATTAAAAACTTGAAGACTCAAAACAAATCAT
1 AATATTTTAATGACT-AAAACTTGAAGACTCAAAACAAATCAT
1243955 GCAAATGCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 8 0.21
45 30 0.79
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (45 bp):
AATATTTTAATGACTAAAACTTGAAGACTCAAAACAAATCATTCG
Found at i:1245328 original size:258 final size:259
Alignment explanation
Indices: 1244834--1245330 Score: 617
Period size: 258 Copynumber: 1.9 Consensus size: 259
1244824 GCAAAAAGCG
* * ** **
1244834 AACCCCAGAAATCACCGGTTACAACCCAGAAACTTCTTTTGCCAGCCAACAAAAGAAACAACAAC
1 AACCCCAGAAATCACCAGTAACAACCCAGAAACCACCCTTGCCAGCCAACAAAAGAAACAACAAC
* * * *
1244899 AGTGTGGAAGAAAGCGTAGAAAGTGGCAATGAATCGCTGGTAAATCCAATCCCCCCGCCGCCACC
66 AATGTGGAAGAAAACGTAGAAAGTGGCAATGAATCGCCGGTAAATCCAATCCCCCCACCGCCACC
* * *
1244964 TCTTCCGCCATTTAAAATGAAGCCGTGCTAATTCGAACAGCACGGAGATTTTGTTAGAGTAAAAA
131 TCCTCCGCCATTTAAAATGAAGCCGTGC-AATTCGAACAGCACGAAGATTTTGTTAGACTAAAAA
*
1245029 GCTTTAACTGGTCACAAAGCAGCTCACAGGATTTGGATGATCCACCAGCATCACCAGTAACAAAA
195 GCTTTAACAGGTCACAAAGCAGCTCACAGGATTTGGATGATCCACCAGCATCACCAGTAACAAAA
* * * *
1245094 AACCCCATAAATCATCAGTAACAACCCAGAAACCACCCTTGCCAGCCAACATGAA-AAAC-TCAA
1 AACCCCAGAAATCACCAGTAACAACCCAGAAACCACCCTTGCCAGCCAACA-AAAGAAACAACAA
* * * *
1245157 CAATGTGGAA-AAGAACGTCGAAAGTGGCAATGAGTCGCCGTTAAATCCAATCCCCCCACGGCCA
65 CAATGTGGAAGAA-AACGTAGAAAGTGGCAATGAATCGCCGGTAAATCCAATCCCCCCACCGCCA
* * * *
1245221 CCTCCTCCGCCATTT-AAATGAAGCCGTTG-AAGTTTGAACGGCGCGAAGATTTTGTTAGACTGA
129 CCTCCTCCGCCATTTAAAATGAAGCCG-TGCAA-TTCGAACAGCACGAAGATTTTGTTAGACTAA
* *** ** *
1245284 AAAGCTTTAACAGTTCATGGAGCAGCTTGCCGGATTTGGATGATCCA
192 AAAGCTTTAACAGGTCACAAAGCAGCTCACAGGATTTGGATGATCCA
1245331 TTGAGCGGTG
Statistics
Matches: 200, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
257 2 0.01
258 77 0.38
259 72 0.36
260 47 0.23
261 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (259 bp):
AACCCCAGAAATCACCAGTAACAACCCAGAAACCACCCTTGCCAGCCAACAAAAGAAACAACAAC
AATGTGGAAGAAAACGTAGAAAGTGGCAATGAATCGCCGGTAAATCCAATCCCCCCACCGCCACC
TCCTCCGCCATTTAAAATGAAGCCGTGCAATTCGAACAGCACGAAGATTTTGTTAGACTAAAAAG
CTTTAACAGGTCACAAAGCAGCTCACAGGATTTGGATGATCCACCAGCATCACCAGTAACAAAA
Found at i:1255161 original size:39 final size:39
Alignment explanation
Indices: 1255088--1255162 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
1255078 ATATTTAATT
*
1255088 AAAATATATGTATATAGAATAAATAATTAAAAATTATTA
1 AAAATATATGTATATAGAATAAATAAATAAAAATTATTA
* *
1255127 AAAATATATTTATATTA-AAT-AATAAAATATAAATTA
1 AAAATATATGTATA-TAGAATAAAT-AAATAAAAATTA
1255163 AATAATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 3 0.10
39 26 0.84
40 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (39 bp):
AAAATATATGTATATAGAATAAATAAATAAAAATTATTA
Found at i:1255227 original size:35 final size:34
Alignment explanation
Indices: 1255186--1255280 Score: 95
Period size: 37 Copynumber: 2.7 Consensus size: 34
1255176 AATCATCAAA
*
1255186 TATATTTATATTAAATGA-TAAAACATAAATAAAAT
1 TATATTTATATTAAATAATTAAAA-ATAAA-AAAAT
* *
1255221 TATATTTATATTGAATAATAATTAAAAATTAAAAATT
1 TATATTTATATT--A-AATAATTAAAAATAAAAAAAT
*
1255258 TATATTTATATTAAA-AAATAAAA
1 TATATTTATATTAAATAATTAAAA
1255281 TTTTAAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
33 7 0.13
34 2 0.04
35 13 0.25
37 17 0.33
38 8 0.15
39 5 0.10
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (34 bp):
TATATTTATATTAAATAATTAAAAATAAAAAAAT
Found at i:1255273 original size:26 final size:25
Alignment explanation
Indices: 1255241--1255294 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1255231 TTGAATAATA
* *
1255241 ATTAAAAATTAAAAATTTATATTTAT
1 ATTAAAAAATAAAAATTTA-AATTAT
*
1255267 ATTAAAAAATAAAATTTTAAATTAT
1 ATTAAAAAATAAAAATTTAAATTAT
1255292 ATT
1 ATT
1255295 TATTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAAAAAATAAAAATTTAAATTAT
Found at i:1255306 original size:29 final size:30
Alignment explanation
Indices: 1255131--1255318 Score: 111
Period size: 29 Copynumber: 6.1 Consensus size: 30
1255121 TTATTAAAAA
*
1255131 TATATTTATATTAAATAATAAAATATAAAT
1 TATATTTATATTAAAAAATAAAATATAAAT
* * * * *
1255161 TA-AATAATAAGTTAAAATCATCAAATAT-ATT
1 TATATTTAT-A-TTAAAA-AATAAAATATAAAT
* *
1255192 TATA-TTAAATGATAAAACAT-AAATA-AAAT
1 TATATTTATAT--TAAAAAATAAAATATAAAT
*
1255221 TATATTTATATTGAATAATAATTAAAAATTAAAAATT
1 TATATTTATATT-AA-AA-AA-T-AAAA-TATAAA-T
*
1255258 TATATTTATATTAAAAAATAAAATTTTAAAT
1 TATATTTATATTAAAAAATAAAA-TATAAAT
*
1255289 TATA-TT-TATTAAATAATAAAATATAAAT
1 TATATTTATATTAAAAAATAAAATATAAAT
1255317 TA
1 TA
1255319 AAAACTAAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 36
0.71 0.08 0.20
Matches are distributed among these distances:
28 9 0.07
29 32 0.25
30 16 0.13
31 22 0.17
32 19 0.15
33 1 0.01
34 5 0.04
35 4 0.03
36 5 0.04
37 13 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
TATATTTATATTAAAAAATAAAATATAAAT
Found at i:1255361 original size:16 final size:17
Alignment explanation
Indices: 1255331--1255371 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1255321 AACTAAAATT
*
1255331 TATAA-TTATATT-AAA
1 TATAATTTACATTAAAA
*
1255346 TATTATTTACATTAAAA
1 TATAATTTACATTAAAA
1255363 TATAATTTA
1 TATAATTTA
1255372 ATAAAAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATTTACATTAAAA
Found at i:1256631 original size:24 final size:24
Alignment explanation
Indices: 1256599--1256644 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1256589 TCCTCTGCAC
*
1256599 ATTGACAAGTTAAAAAGTTTCCAG
1 ATTGACAAGCTAAAAAGTTTCCAG
1256623 ATTGACAAGCTAAAAAGTTTCC
1 ATTGACAAGCTAAAAAGTTTCC
1256645 GGATAAGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (24 bp):
ATTGACAAGCTAAAAAGTTTCCAG
Found at i:1259203 original size:19 final size:18
Alignment explanation
Indices: 1259176--1259211 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1259166 AATTTTATAA
1259176 AAAATAATAATAATAATT
1 AAAATAATAATAATAATT
*
1259194 AAAATAAATATTAATAAT
1 AAAAT-AATAATAATAAT
1259212 CAATCATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAATAATAATAATT
Found at i:1259641 original size:8 final size:8
Alignment explanation
Indices: 1259628--1259666 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1259618 AAAATATGTT
*
1259628 TAAAATAA
1 TAAAATTA
1259636 TAAAATT-
1 TAAAATTA
1259643 TAAAATTA
1 TAAAATTA
1259651 TAAAAATTA
1 T-AAAATTA
1259660 TAAAATT
1 TAAAATT
1259667 TCAATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.25
8 13 0.46
9 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:1259646 original size:15 final size:16
Alignment explanation
Indices: 1259626--1259665 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1259616 AAAAAATATG
1259626 TTTAAAATAAT-AAAA
1 TTTAAAATAATAAAAA
*
1259641 TTTAAAATTATAAAAA
1 TTTAAAATAATAAAAA
1259657 TTATAAAAT
1 TT-TAAAAT
1259666 TTCAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 6 0.27
17 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAAATAATAAAAA
Found at i:1259678 original size:24 final size:23
Alignment explanation
Indices: 1259628--1259686 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1259618 AAAATATGTT
*
1259628 TAAAATAATAAAATTTAAAATTA
1 TAAAATTATAAAATTTAAAATTA
* *
1259651 TAAAAATTATAAAATTT-CAATTT
1 T-AAAATTATAAAATTTAAAATTA
*
1259674 TTAAATTATAAAA
1 TAAAATTATAAAA
1259687 ATTTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 11 0.35
23 6 0.19
24 14 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAATTATAAAATTTAAAATTA
Found at i:1261659 original size:3 final size:3
Alignment explanation
Indices: 1261651--1261675 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1261641 ATTTGATGAA
1261651 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1261676 TTATTATTAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1262923 original size:6 final size:6
Alignment explanation
Indices: 1262912--1262936 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1262902 ATTTATTTAA
1262912 ATATTT ATATTT ATATTT ATATTT A
1 ATATTT ATATTT ATATTT ATATTT A
1262937 ATACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:1263594 original size:16 final size:18
Alignment explanation
Indices: 1263554--1263598 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1263544 GAATTTTTTT
*
1263554 AAATTTTAATTAGTATCA
1 AAATTTTAATTAGAATCA
1263572 TAAATTTTAATTA-AATC-
1 -AAATTTTAATTAGAATCA
1263589 AAATTTTAAT
1 AAATTTTAAT
1263599 ACAAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 10 0.40
18 3 0.12
19 12 0.48
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (18 bp):
AAATTTTAATTAGAATCA
Found at i:1263703 original size:25 final size:23
Alignment explanation
Indices: 1263661--1263738 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 23
1263651 AAACAAATAC
*
1263661 AATTTAATTTTTATTTTAAATTA
1 AATTTAATTTTTAATTTAAATTA
1263684 AATTTCAATTTTTACATTTAAATTA
1 AATTT-AATTTTTA-ATTTAAATTA
1263709 AA-TTAATTAATTTAATTTAAATTTA
1 AATTTAATT--TTTAATTTAAA-TTA
1263734 AATTT
1 AATTT
1263739 TAAATCAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
23 9 0.19
24 17 0.35
25 20 0.42
26 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTAATTTTTAATTTAAATTA
Found at i:1263712 original size:19 final size:18
Alignment explanation
Indices: 1263674--1263750 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 18
1263664 TTAATTTTTA
* *
1263674 TTTTAAATTAAATTTCAAT
1 TTTTAATTTAAA-TTAAAT
1263693 TTTTACATTTAAATTAAAT
1 TTTTA-ATTTAAATTAAAT
* *
1263712 TAATTAATTTAATTTAAA-
1 T-TTTAATTTAAATTAAAT
* *
1263730 TTTAAATTTTAAATCAAAT
1 TTTTAA-TTTAAATTAAAT
1263749 TT
1 TT
1263751 AACCTTTTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
17 3 0.07
18 10 0.22
19 24 0.52
20 9 0.20
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTAATTTAAATTAAAT
Found at i:1265513 original size:3 final size:3
Alignment explanation
Indices: 1265505--1265546 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1265495 AATGAGAATG
*
1265505 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA CTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
1265547 ACAATAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:1266514 original size:20 final size:19
Alignment explanation
Indices: 1266486--1266525 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1266476 GGAAGATAAA
*
1266486 AAAATAAAATATAAATATT
1 AAAATAAAATATAAAAATT
*
1266505 AAAATCAAAATTTAAAAATT
1 AAAAT-AAAATATAAAAATT
1266525 A
1 A
1266526 TTAAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAAAATATAAAAATT
Found at i:1270758 original size:3 final size:3
Alignment explanation
Indices: 1270750--1270774 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1270740 AAGTGCATAC
1270750 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1270775 GATAATGAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1271725 original size:16 final size:17
Alignment explanation
Indices: 1271690--1271742 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
1271680 ATTTATATAC
*
1271690 TTATTTTATATTACCATAT
1 TTATTTT-TA-TATCATAT
1271709 TTATTTTTA-ATCATA-
1 TTATTTTTATATCATAT
*
1271724 TTATTTTTATATTATAT
1 TTATTTTTATATCATAT
1271741 TT
1 TT
1271743 TTAATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 9 0.30
16 10 0.33
17 2 0.07
18 2 0.07
19 7 0.23
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTTTTATATCATAT
Found at i:1271880 original size:2 final size:2
Alignment explanation
Indices: 1271873--1271910 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1271863 AAATTTAAGC
1271873 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
1271911 CACACACACA
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):
TA
Found at i:1275797 original size:2 final size:2
Alignment explanation
Indices: 1275790--1275825 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1275780 TTTTAAACTG
1275790 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
1275826 TTCGCCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1276318 original size:27 final size:27
Alignment explanation
Indices: 1276272--1276339 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
1276262 TATTTTTATT
1276272 TTTAAAT-AATTAAAATTATTAAAAAAA
1 TTTAAATAAATT-AAATTATTAAAAAAA
* *
1276299 TTTAAATAAAATTAAA-TATTTATAAAA
1 TTTAAAT-AAATTAAATTATTAAAAAAA
*
1276326 TTTAATTATAATTA
1 TTTAAATA-AATTA
1276340 TACGTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 1 0.03
27 27 0.77
28 3 0.09
29 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAAATAAATTAAATTATTAAAAAAA
Found at i:1279528 original size:45 final size:43
Alignment explanation
Indices: 1279469--1279552 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
1279459 GGATTTTTTT
* * *
1279469 AAAAAAATTTAAATATTTAATATTTGAATTAATTTATTTATATA
1 AAAAAAATTGAAATATTTAA-ATTTAAATTAATATATTTATATA
*
1279513 AAAATAAATTGAAATATTTAAATTTAAATTTATATATTTA
1 AAAA-AAATTGAAATATTTAAATTTAAATTAATATATTTA
1279553 ATTCTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
44 20 0.57
45 15 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (43 bp):
AAAAAAATTGAAATATTTAAATTTAAATTAATATATTTATATA
Found at i:1279534 original size:20 final size:20
Alignment explanation
Indices: 1279511--1279553 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1279501 TTTATTTATA
1279511 TAAAAATAAATTGAAATATT
1 TAAAAATAAATTGAAATATT
** * *
1279531 TAAATTTAAATTTATATATT
1 TAAAAATAAATTGAAATATT
1279551 TAA
1 TAA
1279554 TTCTTTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAAAATAAATTGAAATATT
Found at i:1280009 original size:3 final size:3
Alignment explanation
Indices: 1280001--1280030 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1279991 TTAATGGGCA
1280001 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1280031 TTATTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1280301 original size:2 final size:2
Alignment explanation
Indices: 1280294--1280345 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1280284 GTTCAAAAGA
*
1280294 AG AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1280336 AG AG AG AG AG
1 AG AG AG AG AG
1280346 GGGGGGGGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1286038 original size:21 final size:20
Alignment explanation
Indices: 1286004--1286044 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1285994 TTTTTAAAAT
1286004 AATATATTTATATATTTTATA
1 AATATATTT-TATATTTTATA
*
1286025 AATATCATTTTATAATTTAT
1 AATAT-ATTTTATATTTTAT
1286045 TATTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AATATATTTTATATTTTATA
Found at i:1286652 original size:9 final size:9
Alignment explanation
Indices: 1286638--1286664 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1286628 TAATAACCAA
1286638 TATATATAT
1 TATATATAT
1286647 TATATATAT
1 TATATATAT
1286656 TATATATAT
1 TATATATAT
1286665 ATTTTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATATAT
Found at i:1287421 original size:75 final size:75
Alignment explanation
Indices: 1287270--1287423 Score: 168
Period size: 75 Copynumber: 2.1 Consensus size: 75
1287260 TCTTATATTC
* * * *
1287270 TGATTGTCAATATTCACTCTGACTGTTAGATCTGTATTCGTTATTTAAATTTTAGTCATAAAAAA
1 TGATTGTCAACATTCACTCTGACTATTAGATCTGTACTCGTTACTTAAATTTTAGTCATAAAAAA
* *
1287335 AACGAAGTCT
66 AACAAAATCT
** * *
1287345 TGATTGTCAACATTCACTCTGGTTATTAGATTTGTGCTCGTTACTTAAATTTT-GAT-AGTAAAA
1 TGATTGTCAACATTCACTCTGACTATTAGATCTGTACTCGTTACTTAAATTTTAG-TCA-TAAAA
* *
1287408 AAGATAAAATCT
64 AAAACAAAATCT
1287420 TGAT
1 TGAT
1287424 CTTCAATACT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
74 2 0.03
75 63 0.97
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (75 bp):
TGATTGTCAACATTCACTCTGACTATTAGATCTGTACTCGTTACTTAAATTTTAGTCATAAAAAA
AACAAAATCT
Found at i:1287577 original size:26 final size:26
Alignment explanation
Indices: 1287548--1287602 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1287538 TTGTCAGTGA
* * *
1287548 CACCATGGCACTCCCATCCTGATTGC
1 CACCATAGCACTCACATCCTGATCGC
*
1287574 CACCATAGCACTTACATCCTGATCGC
1 CACCATAGCACTCACATCCTGATCGC
1287600 CAC
1 CAC
1287603 ATTAGTATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.22
Consensus pattern (26 bp):
CACCATAGCACTCACATCCTGATCGC
Found at i:1287770 original size:104 final size:104
Alignment explanation
Indices: 1287548--1287774 Score: 262
Period size: 104 Copynumber: 2.2 Consensus size: 104
1287538 TTGTCAGTGA
* * * * *
1287548 CACCATGGCACTCCCATCCTGATTGCCACCATAGCACTTACATCCTGATCGCCACATTAGTATCA
1 CACCATGGCACTTCGATCCGGATCGCCACCATAGCACTTACATCCTGATCGCCACATTAGCATCA
* *
1287613 ATACTGTCAGTGACACGAAGTCACTCCGATCCTGATTGT
66 ATACTGTCAGTGACACCAAGGCACTCCGATCCTGATTGT
*** * * * * *
1287652 CATGGTGGCGCTTCGATCCGGATCGTCACCATAGCACTCT-CATCCTGATCGTCACTTTGGCATC
1 CACCATGGCACTTCGATCCGGATCGCCACCATAGCACT-TACATCCTGATCGCCACATTAGCATC
*
1287716 AATACTGTCAGTGACACCACGGCACTCTC-ATCCTGATTG-
65 AATACTGTCAGTGACACCAAGGCACTC-CGATCCTGATTGT
1287755 CTACCATGGCACTTCGATCC
1 C-ACCATGGCACTTCGATCC
1287775 TAATCGCCTC
Statistics
Matches: 100, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
103 1 0.01
104 97 0.97
105 2 0.02
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (104 bp):
CACCATGGCACTTCGATCCGGATCGCCACCATAGCACTTACATCCTGATCGCCACATTAGCATCA
ATACTGTCAGTGACACCAAGGCACTCCGATCCTGATTGT
Found at i:1287904 original size:52 final size:51
Alignment explanation
Indices: 1287764--1287945 Score: 181
Period size: 52 Copynumber: 3.5 Consensus size: 51
1287754 GCTACCATGG
* * * * *
1287764 CACTTCGATCCTAATCG-CCTCATGGCATCAATATTATCAGTGACGTCGATT
1 CACTTCGATCCTGATCGTCATCATGGCATCAATACTATCAGTGACCT-GAGT
* * * * * * *
1287815 CATTTTGATCTTGATCATC-GCATGGCTTTAATACTATCAGTGACACTGAGT
1 CACTTCGATCCTGATCGTCATCATGGCATCAATACTATCAGTGAC-CTGAGT
1287866 CACTTCGATCCTGATCGTCATCATGGCATCAATACTATCAGTGATGCC-GAGT
1 CACTTCGATCCTGATCGTCATCATGGCATCAATACTATCAGTGA--CCTGAGT
* *
1287918 CACTTCGATCCTGATTGTCACCATGGCA
1 CACTTCGATCCTGATCGTCATCATGGCA
1287946 CTTTGATCTT
Statistics
Matches: 106, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
51 51 0.48
52 53 0.50
53 1 0.01
54 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (51 bp):
CACTTCGATCCTGATCGTCATCATGGCATCAATACTATCAGTGACCTGAGT
Found at i:1287909 original size:180 final size:180
Alignment explanation
Indices: 1287709--1288301 Score: 796
Period size: 180 Copynumber: 3.3 Consensus size: 180
1287699 ATCGTCACTT
* ** * *
1287709 TGGCATCAATACTGTCAGTGACACC-ACGGCACTCTC-ATCCTGATTGCTACCATGGCACTTCGA
1 TGGCATCAATACTATCAGTGATGCCGA-GTCACT-TCGATCCTGATTGCTACCATGGCACTTTGA
* *
1287772 TCCTAATCGCCTCATGGCATCAATATTATCAGTGACGTCGATTCATTTTGATCTTGATCATCGCA
64 TCCTAATCGCCTCATGGCATCAATATTATCAGTGACGTCGATTCACTTTGATCTTGATCGTCGCA
* * * *
1287837 TGGCTTTAATACTATCAGTGACACTGAGTCACTTCGATCCTGATCGTCATCA
129 TGGCATTAATACTATCAGTGACGCCGAGTCACTTCGATCCTGATCGCCATCA
1287889 TGGCATCAATACTATCAGTGATGCCGAGTCACTTCGATCCTGATTG-TCACCATGGCACTTTGAT
1 TGGCATCAATACTATCAGTGATGCCGAGTCACTTCGATCCTGATTGCT-ACCATGGCACTTTGAT
* * * * * *
1287953 CTTAATCGCCTCATGGCATCAATATTATCAGTGACATCGAGTCACTTCGATCTTAATCGGCGCAT
65 CCTAATCGCCTCATGGCATCAATATTATCAGTGACGTCGATTCACTTTGATCTTGATCGTCGCAT
* *
1288018 GGCATTAATACTATCAGTGACGCCGAGTCACTTCGATCTTGATCACCATCA
130 GGCATTAATACTATCAGTGACGCCGAGTCACTTCGATCCTGATCGCCATCA
* * * * *
1288069 TGGCATCAATACCATCAGTGATGCCGAGTCACTTCGATCCTAATCGCCAACATGGCACTTTGATC
1 TGGCATCAATACTATCAGTGATGCCGAGTCACTTCGATCCTGATTGCTACCATGGCACTTTGATC
* * * * *
1288134 CTAATCGCCTCATGGTATCAATACTATCAGTGAAGTCGATTTACTTTGATCCTGATCGTCGCATG
66 CTAATCGCCTCATGGCATCAATATTATCAGTGACGTCGATTCACTTTGATCTTGATCGTCGCATG
* * *
1288199 ACATTAATACTATCAATGACGCCGAGTCACTTCAATCCTGATCGCCATCA
131 GCATTAATACTATCAGTGACGCCGAGTCACTTCGATCCTGATCGCCATCA
* * * * * *
1288249 TGGCATTAATACTATCAGTGATGCCGAGTGACTTTGATCTTGATCGCCACCAT
1 TGGCATCAATACTATCAGTGATGCCGAGTCACTTCGATCCTGATTGCTACCAT
1288302 TGCATCAATA
Statistics
Matches: 362, Mismatches: 47, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
179 3 0.01
180 358 0.99
181 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (180 bp):
TGGCATCAATACTATCAGTGATGCCGAGTCACTTCGATCCTGATTGCTACCATGGCACTTTGATC
CTAATCGCCTCATGGCATCAATATTATCAGTGACGTCGATTCACTTTGATCTTGATCGTCGCATG
GCATTAATACTATCAGTGACGCCGAGTCACTTCGATCCTGATCGCCATCA
Found at i:1288071 original size:128 final size:129
Alignment explanation
Indices: 1287835--1288073 Score: 329
Period size: 128 Copynumber: 1.9 Consensus size: 129
1287825 TTGATCATCG
* * * * *
1287835 CATGGCTTTAATACTATCAGTGACACTGAGTCACTTCGATCCTGATCGTCATCATGGCATCAATA
1 CATGGCATCAATACTATCAGTGACACTGAGTCACTTCGATCCTAATCGGCAGCATGGCATCAATA
* ***
1287900 CTATCAGTGATGCCGAGTCACTTCGATCCTGATTGTCACCATGGCACTTTGATCTTAATCGCCT
66 CTATCAGTGACGCCGAGTCACTTCGATCCTGATCACCACCATGGCACTTTGATCTTAATCGCCT
* * *
1287964 CATGGCATCAATATTATCAGTGACA-TCGAGTCACTTCGATCTTAATCGGC-GCATGGCATTAAT
1 CATGGCATCAATACTATCAGTGACACT-GAGTCACTTCGATCCTAATCGGCAGCATGGCATCAAT
* *
1288027 ACTATCAGTGACGCCGAGTCACTTCGATCTTGATCACCATCATGGCA
65 ACTATCAGTGACGCCGAGTCACTTCGATCCTGATCACCACCATGGCA
1288074 TCAATACCAT
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
128 53 0.56
129 42 0.44
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (129 bp):
CATGGCATCAATACTATCAGTGACACTGAGTCACTTCGATCCTAATCGGCAGCATGGCATCAATA
CTATCAGTGACGCCGAGTCACTTCGATCCTGATCACCACCATGGCACTTTGATCTTAATCGCCT
Found at i:1288089 original size:52 final size:51
Alignment explanation
Indices: 1287944--1288125 Score: 229
Period size: 51 Copynumber: 3.5 Consensus size: 51
1287934 GTCACCATGG
* * **
1287944 CACTTTGATCTTAATCGCCTCATGGCATCAATATTATCAGTGACATCGAGT
1 CACTTCGATCTTAATCGCCTCATGGCATCAATACTATCAGTGACGCCGAGT
* * *
1287995 CACTTCGATCTTAATCGGCGCATGGCATTAATACTATCAGTGACGCCGAGT
1 CACTTCGATCTTAATCGCCTCATGGCATCAATACTATCAGTGACGCCGAGT
* * * *
1288046 CACTTCGATCTTGATCACCATCATGGCATCAATACCATCAGTGATGCCGAGT
1 CACTTCGATCTTAATCGCC-TCATGGCATCAATACTATCAGTGACGCCGAGT
* *
1288098 CACTTCGATCCTAATCGCCAACATGGCA
1 CACTTCGATCTTAATCGCC-TCATGGCA
1288126 CTTTGATCCT
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 60 0.54
52 52 0.46
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (51 bp):
CACTTCGATCTTAATCGCCTCATGGCATCAATACTATCAGTGACGCCGAGT
Found at i:1288208 original size:51 final size:51
Alignment explanation
Indices: 1288124--1288369 Score: 201
Period size: 52 Copynumber: 4.8 Consensus size: 51
1288114 GCCAACATGG
* * * * *
1288124 CACTTTGATCCTAATCGCCTCATGGTATCAATACTATCAGTGAAGTCGATT
1 CACTTTGATCCTGATCGCCTCATGGCATTAATACTATCAGTGAAGCCGAGT
* * * * * *
1288175 TACTTTGATCCTGATCGTCGCATGACATTAATACTATCAATGACGCCGAGT
1 CACTTTGATCCTGATCGCCTCATGGCATTAATACTATCAGTGAAGCCGAGT
** *
1288226 CACTTCAATCCTGATCGCCATCATGGCATTAATACTATCAGTGATGCCGAGT
1 CACTTTGATCCTGATCGCC-TCATGGCATTAATACTATCAGTGAAGCCGAGT
* * * * * *
1288278 GACTTTGATCTTGATCGCCACCATTGCATCAATACTATCAATG-A-CACGAAGT
1 CACTTTGATCCTGATCGCC-TCATGGCATTAATACTATCAGTGAAGC-CG-AGT
* ** *
1288330 CACTCAT-ATCCTGATAACCATCATGGCATCAATACTATCA
1 CACT-TTGATCCTGATCGCC-TCATGGCATTAATACTATCA
1288370 ATGACACGAA
Statistics
Matches: 156, Mismatches: 35, Indels: 7
0.79 0.18 0.04
Matches are distributed among these distances:
50 1 0.01
51 57 0.37
52 97 0.62
53 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
CACTTTGATCCTGATCGCCTCATGGCATTAATACTATCAGTGAAGCCGAGT
Found at i:1288351 original size:104 final size:103
Alignment explanation
Indices: 1288143--1288369 Score: 280
Period size: 104 Copynumber: 2.2 Consensus size: 103
1288133 CCTAATCGCC
* * * * * * *
1288143 TCATGGTATCAATACTATCAGTGAAGTCGATTTACTTTGATCCTGATCGTCGCATGACATTAATA
1 TCATGGCATCAATACTATCAGTGAAGCCGAGTGACTTTGATCCTGATCGCCCCATGACATCAATA
* **
1288208 CTATCAATGACGCCGAGTCACTTCAATCCTGATCGCCA
66 CTATCAATGACGACGAGTCACTTCAATCCTGATAACCA
* * *
1288246 TCATGGCATTAATACTATCAGTGATGCCGAGTGACTTTGATCTTGATCGCCACCATTG-CATCAA
1 TCATGGCATCAATACTATCAGTGAAGCCGAGTGACTTTGATCCTGATCGCC-CCA-TGACATCAA
1288310 TACTATCAATGAC-ACGAAGTCAC-TCATATCCTGATAACCA
64 TACTATCAATGACGACG-AGTCACTTCA-ATCCTGATAACCA
1288350 TCATGGCATCAATACTATCA
1 TCATGGCATCAATACTATCA
1288370 ATGACACGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
103 48 0.45
104 56 0.53
105 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (103 bp):
TCATGGCATCAATACTATCAGTGAAGCCGAGTGACTTTGATCCTGATCGCCCCATGACATCAATA
CTATCAATGACGACGAGTCACTTCAATCCTGATAACCA
Found at i:1288594 original size:156 final size:155
Alignment explanation
Indices: 1288204--1288599 Score: 461
Period size: 156 Copynumber: 2.5 Consensus size: 155
1288194 GCATGACATT
* * * * *
1288204 AATACTATCAATGACGCCG-AGTCACTTCAATCCTGATCGCCATCATGGCATTAATACTATCAGT
1 AATACTATCAATGAC-ACGAAGTCACTCCGATCTTGATCGCCACCATGGCATTAATACTATCAGT
* * * * * *
1288268 GATGCCGAGTGACTTTGATCTTGATCGCCACCATTGCATCAATACTATCAATGACACGAAGTCAC
65 GA-CCCAAGTCACTTAGATCTTGATCGCCACCATTACATCAATACTATCAAGGACACGAAGTCAC
* * *
1288333 TCATATCCTGATAACCATCATGGCATC
129 TCAAATCCTGATAACCACCATCGCATC
* * ** * *
1288360 AATACTATCAATGACACGAAGTTACTCCGATCTTGATCGTCACCATGGTTTTAATATTATTAGTG
1 AATACTATCAATGACACGAAGTCACTCCGATCTTGATCGCCACCATGGCATTAATACTATCAGTG
* * * * **
1288425 ACCCCACGCCACTTAGATCTTGATCGCTACCATTACATCAATACTATCAGGGACATTAAGTCACT
66 A-CCCAAGTCACTTAGATCTTGATCGCCACCATTACATCAATACTATCAAGGACACGAAGTCACT
* **
1288490 CAAATCTTGATCGCCACCATCGCATC
130 CAAATCCTGATAACCACCATCGCATC
* * *
1288516 AATACTATCAATGACACGAAGTCACTCCGATCTTGATCGCCACCATGGCATCAATACTATCAATT
1 AATACTATCAATGACACGAAGTCACTCCGATCTTGATCGCCACCATGGCATTAATACTATCAGTG
1288581 ACCCTAAGTCACTTAGATC
66 ACCC-AAGTCACTTAGATC
1288600 CTAATCACCA
Statistics
Matches: 197, Mismatches: 41, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
155 5 0.03
156 192 0.97
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (155 bp):
AATACTATCAATGACACGAAGTCACTCCGATCTTGATCGCCACCATGGCATTAATACTATCAGTG
ACCCAAGTCACTTAGATCTTGATCGCCACCATTACATCAATACTATCAAGGACACGAAGTCACTC
AAATCCTGATAACCACCATCGCATC
Found at i:1288612 original size:52 final size:52
Alignment explanation
Indices: 1288195--1288599 Score: 350
Period size: 52 Copynumber: 7.8 Consensus size: 52
1288185 CTGATCGTCG
* * * * *
1288195 CATGACATTAATACTATCAATGACGCCG-AGTCACTTCA-ATCCTGATCGCCAT
1 CATGGCATCAATACTATCAATGAC-ACGAAGTCAC-TCAGATCTTGATCGCCAC
* * * **
1288247 CATGGCATTAATACTATCAGTGATGC-CG-AGTGACTTTGATCTTGATCGCCAC
1 CATGGCATCAATACTATCAATGA--CACGAAGTCACTCAGATCTTGATCGCCAC
* * * ** *
1288299 CATTGCATCAATACTATCAATGACACGAAGTCACTCATATCCTGATAACCAT
1 CATGGCATCAATACTATCAATGACACGAAGTCACTCAGATCTTGATCGCCAC
* * *
1288351 CATGGCATCAATACTATCAATGACACGAAGTTACTCCGATCTTGATCGTCAC
1 CATGGCATCAATACTATCAATGACACGAAGTCACTCAGATCTTGATCGCCAC
** * * * * * * * * * *
1288403 CATGGTTTTAATATTATTAGTGACCCCACGCCACTTAGATCTTGATCGCTAC
1 CATGGCATCAATACTATCAATGACACGAAGTCACTCAGATCTTGATCGCCAC
** ** ** *
1288455 CATTACATCAATACTATCAGGGACATTAAGTCACTCAAATCTTGATCGCCAC
1 CATGGCATCAATACTATCAATGACACGAAGTCACTCAGATCTTGATCGCCAC
* *
1288507 CATCGCATCAATACTATCAATGACACGAAGTCACTCCGATCTTGATCGCCAC
1 CATGGCATCAATACTATCAATGACACGAAGTCACTCAGATCTTGATCGCCAC
* * * *
1288559 CATGGCATCAATACTATCAATTACCCTAAGTCACTTAGATC
1 CATGGCATCAATACTATCAATGACACGAAGTCACTCAGATC
1288600 CTAATCACCA
Statistics
Matches: 276, Mismatches: 72, Indels: 10
0.77 0.20 0.03
Matches are distributed among these distances:
50 1 0.00
51 3 0.01
52 271 0.98
54 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (52 bp):
CATGGCATCAATACTATCAATGACACGAAGTCACTCAGATCTTGATCGCCAC
Found at i:1289429 original size:75 final size:75
Alignment explanation
Indices: 1289255--1289431 Score: 232
Period size: 75 Copynumber: 2.4 Consensus size: 75
1289245 CAATTGTTAT
* * *
1289255 ATCTTGATTGCCAACACTCACTT-T-ACTGCAAGACCTGTGCTCGCCACTTAAATCTTGGCCGCC
1 ATCTTGATTGCCAACACTCA-TTCTGGCTGCAAGACCTGAGCTCACCACTTAAATCTTGGCCGCC
*
1289318 GGAAAGACGAA
65 AGAAAGACGAA
* * * *
1289329 ATCTTGATTGCCAACACTTACTCTGGTTGCAAGACCTGAGCTCACCACTTAAATCTTGGCTGCCA
1 ATCTTGATTGCCAACACTCATTCTGGCTGCAAGACCTGAGCTCACCACTTAAATCTTGGCCGCCA
* *
1289394 GAAGGACGGA
66 GAAAGACGAA
*
1289404 ATCTTGATCGCCAACACTCATTCTGGCT
1 ATCTTGATTGCCAACACTCATTCTGGCT
1289432 ACTAGACTTG
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
73 1 0.01
74 20 0.23
75 66 0.76
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (75 bp):
ATCTTGATTGCCAACACTCATTCTGGCTGCAAGACCTGAGCTCACCACTTAAATCTTGGCCGCCA
GAAAGACGAA
Found at i:1291046 original size:3 final size:3
Alignment explanation
Indices: 1291040--1291081 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1291030 AATAATAATA
*
1291040 ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1291082 CTGCTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1298399 original size:15 final size:14
Alignment explanation
Indices: 1298376--1298410 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1298366 TAATATTAAA
1298376 AATATTTTATAATT
1 AATATTTTATAATT
1298390 AATATATTTATAATT
1 AATAT-TTTATAATT
1298405 AA-ATTT
1 AATATTT
1298411 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 7 0.35
15 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTTTATAATT
Found at i:1300272 original size:2 final size:2
Alignment explanation
Indices: 1300265--1300309 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1300255 TAGAATTATA
*
1300265 TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1300307 TC T
1 TC T
1300310 ATATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1306669 original size:24 final size:22
Alignment explanation
Indices: 1306642--1306689 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1306632 TATTTGATGA
*
1306642 ATTTTAATATTTATAATATTTTTT
1 ATTTTAATA-TTACAAT-TTTTTT
*
1306666 ATTTTTATATTACAATTTTTTT
1 ATTTTAATATTACAATTTTTTT
1306688 AT
1 AT
1306690 CTATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 6 0.27
24 8 0.36
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTAATATTACAATTTTTTT
Found at i:1307116 original size:38 final size:38
Alignment explanation
Indices: 1307030--1307117 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
1307020 TTTCTTTATT
1307030 TTTAATATAAATATAATTTTCTTAATTTTTAATTCTTA
1 TTTAATATAAATATAATTTTCTTAATTTTTAATTCTTA
* *
1307068 TTTAACATAAATATAATTTT-TATCATTTTTAATTCTTA
1 TTTAATATAAATATAATTTTCT-TAATTTTTAATTCTTA
*
1307106 TTTATTATAAAT
1 TTTAATATAAAT
1307118 TTTATATGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.02
38 44 0.98
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (38 bp):
TTTAATATAAATATAATTTTCTTAATTTTTAATTCTTA
Found at i:1307382 original size:4 final size:4
Alignment explanation
Indices: 1307365--1307396 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1307355 TTCAAAAAAT
*
1307365 ATTA ATTA AGTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1307397 CTTTTCGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:1312780 original size:2 final size:2
Alignment explanation
Indices: 1312773--1312800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1312763 GACTTGCATT
1312773 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
1312801 CTTGTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1313463 original size:30 final size:30
Alignment explanation
Indices: 1313428--1313488 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
1313418 GCTTTAAAGC
1313428 TGGATGGCACAATTC-GGTTTGGGCTGGGCT
1 TGGATGGCACAA-TCAGGTTTGGGCTGGGCT
*
1313458 TGGATGGCAGAATCAGGTTTGGGCTGGGCT
1 TGGATGGCACAATCAGGTTTGGGCTGGGCT
1313488 T
1 T
1313489 ATCTCAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.30
Consensus pattern (30 bp):
TGGATGGCACAATCAGGTTTGGGCTGGGCT
Found at i:1314182 original size:2 final size:2
Alignment explanation
Indices: 1314175--1314215 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1314165 TGTGACCGAA
1314175 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A- 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
1314215 A
1 A
1314216 AAAGTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1314199 original size:19 final size:19
Alignment explanation
Indices: 1314175--1314215 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1314165 TGTGACCGAA
1314175 ATATATATATAATATATAT
1 ATATATATATAATATATAT
1314194 ATATATATATAATATATAT
1 ATATATATATAATATATAT
1314213 ATA
1 ATA
1314216 AAAGTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATATATAATATATAT
Found at i:1314320 original size:3 final size:3
Alignment explanation
Indices: 1314312--1314353 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1314302 TATATAACTC
1314312 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1314354 CATGTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1321163 original size:3 final size:3
Alignment explanation
Indices: 1321155--1321209 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1321145 AATTTACATG
1321155 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1321203 TAT TAT T
1 TAT TAT T
1321210 TATGAGTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1322066 original size:30 final size:30
Alignment explanation
Indices: 1322030--1322090 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
1322020 GAATTGAGAT
1322030 AAGCCCAGCCCAAACCTG-ATTCTGCCATCC
1 AAGCCCAGCCCAAACC-GAATTCTGCCATCC
*
1322060 AAGCCCAGCCCAAACCGAATTGTGCCATCC
1 AAGCCCAGCCCAAACCGAATTCTGCCATCC
1322090 A
1 A
1322091 GCTTTAAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (30 bp):
AAGCCCAGCCCAAACCGAATTCTGCCATCC
Found at i:1322773 original size:22 final size:22
Alignment explanation
Indices: 1322748--1322792 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1322738 AAATATATGT
* *
1322748 TTTATAAAATATAATAAAAAAA
1 TTTATAAAAAATAACAAAAAAA
*
1322770 TTTATAAAAAATAACATAAAAA
1 TTTATAAAAAATAACAAAAAAA
1322792 T
1 T
1322793 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TTTATAAAAAATAACAAAAAAA
Found at i:1323715 original size:25 final size:24
Alignment explanation
Indices: 1323669--1323717 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1323659 ATTTTTGTGA
*
1323669 AAAAAAATTATAATTTTAAAATAT
1 AAAAAAATTATAATATTAAAATAT
*
1323693 AAAAAAATTATAAATATTGAAATAT
1 AAAAAAATTAT-AATATTAAAATAT
1323718 CATATTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAAAATTATAATATTAAAATAT
Found at i:1324082 original size:19 final size:19
Alignment explanation
Indices: 1324037--1324089 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1324027 ATGTTTTTAT
*
1324037 ATATTATAATTATATTTAAA
1 ATATTATAATT-TATATAAA
1324057 ATATTATAATTTATATAAA
1 ATATTATAATTTATATAAA
* *
1324076 TTTTTATAATTTAT
1 ATATTATAATTTAT
1324090 TAATTTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATAATTTATATAAA
Found at i:1324819 original size:16 final size:17
Alignment explanation
Indices: 1324772--1324820 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
1324762 TTTATTATTC
*
1324772 ATTATATTATTAAAATAT
1 ATTATA-TATTAAATTAT
*
1324790 ATTTTATATT-AATTAT
1 ATTATATATTAAATTAT
1324806 ATTATA-ATTAAATTA
1 ATTATATATTAAATTA
1324821 ATATAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.11
16 15 0.56
17 4 0.15
18 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATATTAAATTAT
Found at i:1326360 original size:39 final size:38
Alignment explanation
Indices: 1326280--1326374 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 38
1326270 ATTTTTATTT
* * *
1326280 ATATATAA-TAT-AAATAAAATATATTTATACAATAAT
1 ATATATAATTATAAAATATAATATATATATACAATAAA
*
1326316 TTATATAATTATAAAATATAATATATCATATACAATAAA
1 ATATATAATTATAAAATATAATATAT-ATATACAATAAA
* *
1326355 ATATATAATAATATAATATA
1 ATATATAATTATAAAATATA
1326375 TATTTTTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 7 0.14
37 3 0.06
38 12 0.24
39 27 0.55
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (38 bp):
ATATATAATTATAAAATATAATATATATATACAATAAA
Found at i:1326400 original size:26 final size:26
Alignment explanation
Indices: 1326371--1326420 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1326361 AATAATATAA
*
1326371 TATATATTTTTTA-TTATTTAATTTAT
1 TATA-ATTTTTGATTTATTTAATTTAT
*
1326397 TATACTTTTTGATTTATTTAATTT
1 TATAATTTTTGATTTATTTAATTT
1326421 TTGAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (26 bp):
TATAATTTTTGATTTATTTAATTTAT
Found at i:1326423 original size:16 final size:17
Alignment explanation
Indices: 1326391--1326424 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1326381 TTATTATTTA
*
1326391 ATTTATTATACTTTTTG
1 ATTTATTATAATTTTTG
1326408 ATTTATT-TAATTTTTG
1 ATTTATTATAATTTTTG
1326424 A
1 A
1326425 AATTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (17 bp):
ATTTATTATAATTTTTG
Found at i:1327047 original size:20 final size:20
Alignment explanation
Indices: 1327022--1327071 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1327012 TTATTAATAT
*
1327022 TATTTTTATATATCTTTAAA
1 TATTTTTATATATATTTAAA
*
1327042 TATTTTAATA-ATATTTAAA
1 TATTTTTATATATATTTAAA
1327061 T-TATTTTATAT
1 TAT-TTTTATAT
1327072 TTTTATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 15 0.60
20 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTATATATATTTAAA
Found at i:1327058 original size:19 final size:21
Alignment explanation
Indices: 1327015--1327068 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1327005 ACTCGTATTA
* *
1327015 TTAATATTATTTTTATATATCT
1 TTAA-ATTATTTTAATATATAT
1327037 TTAAA-TATTTTAATA-ATAT
1 TTAAATTATTTTAATATATAT
1327056 TTAAATTATTTTA
1 TTAAATTATTTTA
1327069 TATTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.28
20 16 0.55
21 1 0.03
22 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAATTATTTTAATATATAT
Found at i:1328284 original size:18 final size:17
Alignment explanation
Indices: 1328263--1328297 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1328253 GGTTTTCTCT
1328263 TTTTAAAAAAATTTTATA
1 TTTT-AAAAAATTTTATA
*
1328281 TTTTAAATAATTTTATA
1 TTTTAAAAAATTTTATA
1328298 ATTAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAAAAATTTTATA
Found at i:1328304 original size:16 final size:17
Alignment explanation
Indices: 1328272--1328306 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1328262 TTTTTAAAAA
*
1328272 AATTTTATATTTTAAAT
1 AATTTTATATATTAAAT
1328289 AATTTTATA-ATTAAAT
1 AATTTTATATATTAAAT
1328305 AA
1 AA
1328307 AAAAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTTATATATTAAAT
Found at i:1328708 original size:24 final size:24
Alignment explanation
Indices: 1328680--1328727 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1328670 ATAATTTTTT
* *
1328680 TAATTTTTAATTTATATTAAAATA
1 TAATTTTAAATTTAAATTAAAATA
*
1328704 TAATTTTAAATTTAAATTTAAATA
1 TAATTTTAAATTTAAATTAAAATA
1328728 ATTTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATTTTAAATTTAAATTAAAATA
Found at i:1328746 original size:22 final size:23
Alignment explanation
Indices: 1328716--1328764 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1328706 ATTTTAAATT
1328716 TAAATTTAAATAATTTA-TTAAAA
1 TAAATTT-AATAATTTATTTAAAA
*
1328739 TAAA-TTAATATTTTATTTAAAA
1 TAAATTTAATAATTTATTTAAAA
1328761 TAAA
1 TAAA
1328765 AATTTACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 12 0.50
23 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATTTAATAATTTATTTAAAA
Found at i:1328770 original size:17 final size:17
Alignment explanation
Indices: 1328750--1328808 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1328740 AAATTAATAT
1328750 TTTATTTAAAATAAAAA
1 TTTATTTAAAATAAAAA
* *
1328767 TTTACTT-AAATATAAA
1 TTTATTTAAAATAAAAA
** *
1328783 TCAAATTAATAA-AAAAA
1 TTTATTTAA-AATAAAAA
1328800 TTTATTTAA
1 TTTATTTAA
1328809 TTATAAATAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
16 12 0.39
17 17 0.55
18 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATTTAAAATAAAAA
Found at i:1328831 original size:29 final size:31
Alignment explanation
Indices: 1328759--1328846 Score: 99
Period size: 33 Copynumber: 2.8 Consensus size: 31
1328749 TTTTATTTAA
* *
1328759 AATAAAAATTTACTTAAATATAAATCAAATT
1 AATAAAAATTTATTTAAATATAAATCAAAGT
*
1328790 AATAAAAAAATTTATTTAATTATAAAT-AAAGT
1 AAT--AAAAATTTATTTAAATATAAATCAAAGT
*
1328822 -ATAAAAATTTATTTTAAAAATAAAT
1 AATAAAAATTTA-TTTAAATATAAAT
1328847 AATTCAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 11 0.22
31 5 0.10
32 4 0.08
33 20 0.41
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (31 bp):
AATAAAAATTTATTTAAATATAAATCAAAGT
Found at i:1329450 original size:7 final size:7
Alignment explanation
Indices: 1329433--1329462 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1329423 GAGAGAGAGC
1329433 TTTTTTA
1 TTTTTTA
1329440 -TTTTTA
1 TTTTTTA
1329446 TTTTTTA
1 TTTTTTA
1329453 TTTTTTA
1 TTTTTTA
1329460 TTT
1 TTT
1329463 ATCCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:1329647 original size:2 final size:2
Alignment explanation
Indices: 1329640--1329670 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1329630 GCTCGGTATT
1329640 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1329671 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1329675 original size:2 final size:2
Alignment explanation
Indices: 1329670--1329699 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1329660 TCTCTCTCTC
1329670 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
1329700 CACACACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1329704 original size:2 final size:2
Alignment explanation
Indices: 1329699--1329729 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1329689 ATATATATAT
1329699 AC AC AC AC A- AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1329730 GTTTTTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1339972 original size:22 final size:22
Alignment explanation
Indices: 1339947--1339989 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1339937 ATAAGTATGA
1339947 AAATATAATTTTT-TTAAATATT
1 AAATAT-ATTTTTATTAAATATT
1339969 AAATATATTTTTATTAAATAT
1 AAATATATTTTTATTAAATAT
1339990 ATATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATATATTTTTATTAAATATT
Found at i:1339983 original size:15 final size:16
Alignment explanation
Indices: 1339965--1340013 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 16
1339955 TTTTTTTAAA
1339965 TATTAAATATAT-TTT
1 TATTAAATATATATTT
1339980 TATTAAATATATATTT
1 TATTAAATATATATTT
* *
1339996 ATATTTAATATATGTTT
1 -TATTAAATATATATTT
1340013 T
1 T
1340014 TAAGTTCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 12 0.40
16 4 0.13
17 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTAAATATATATTT
Found at i:1343747 original size:24 final size:23
Alignment explanation
Indices: 1343707--1343752 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1343697 ATTTTTATAG
*
1343707 TTAAATATAAATAAAATTTATTA
1 TTAAATATAAATAAAATATATTA
* *
1343730 TTAAATAATAATTTAAATATATT
1 TTAAAT-ATAAATAAAATATATT
1343753 TATATTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAATATAAATAAAATATATTA
Found at i:1343788 original size:11 final size:12
Alignment explanation
Indices: 1343751--1343793 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1343741 TTTAAATATA
1343751 TTTATATTATTT
1 TTTATATTATTT
* *
1343763 TTAATATTATAT
1 TTTATATTATTT
1343775 TTTA-ATTATTTT
1 TTTATATTA-TTT
1343787 TTTATAT
1 TTTATAT
1343794 CAAACTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 4 0.16
12 19 0.76
13 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:1346212 original size:2 final size:2
Alignment explanation
Indices: 1346205--1346237 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1346195 TTAATCACTT
1346205 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 T
1346238 GAATGAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1347142 original size:20 final size:21
Alignment explanation
Indices: 1347117--1347157 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1347107 ATATAAACAT
1347117 ATATATAATAAA-A-TTATTTA
1 ATATATAA-AAATATTTATTTA
1347137 ATATATAAAAATATTTATTTA
1 ATATATAAAAATATTTATTTA
1347158 TTATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 9 0.47
21 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATATAAAAATATTTATTTA
Found at i:1347146 original size:17 final size:18
Alignment explanation
Indices: 1347119--1347153 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1347109 ATAAACATAT
*
1347119 ATATAATAAAATTATTTA
1 ATATAATAAAAATATTTA
1347137 ATAT-ATAAAAATATTTA
1 ATATAATAAAAATATTTA
1347154 TTTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATAAAAATATTTA
Found at i:1352568 original size:20 final size:19
Alignment explanation
Indices: 1352545--1352619 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 19
1352535 AAAAATTTGA
1352545 ATATATTAATAATTTATATT
1 ATATATTAAT-ATTTATATT
* *
1352565 ATATATAAATATGTA-ATT
1 ATATATTAATATTTATATT
*
1352583 ATATTTTAATTATTT-TATT
1 ATATATTAA-TATTTATATT
* *
1352602 -TATA-TCATGTTTATATT
1 ATATATTAATATTTATATT
1352619 A
1 A
1352620 CAATCAAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
16 4 0.09
17 6 0.14
18 13 0.30
19 11 0.26
20 9 0.21
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (19 bp):
ATATATTAATATTTATATT
Found at i:1353722 original size:31 final size:32
Alignment explanation
Indices: 1353686--1353752 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
1353676 AAAATAAAAA
*
1353686 ATAATATAAATATAAT-ATCTATT-AAATTTAT
1 ATAATA-AAATATAATAATATATTAAAATTTAT
* *
1353717 ATAATAAAATTTATTAATATATTAAAATTTAT
1 ATAATAAAATATAATAATATATTAAAATTTAT
1353749 ATAA
1 ATAA
1353753 ATATTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 12 0.39
32 12 0.39
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (32 bp):
ATAATAAAATATAATAATATATTAAAATTTAT
Found at i:1353728 original size:14 final size:15
Alignment explanation
Indices: 1353709--1353752 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
1353699 AATATCTATT
1353709 AAATTTATATAA-TA
1 AAATTTATATAATTA
1353723 AAATTTATTAATATATTA
1 AAATTTA-T-ATA-ATTA
1353741 AAATTTATATAA
1 AAATTTATATAA
1353753 ATATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.27
15 2 0.08
16 6 0.23
17 2 0.08
18 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTATATAATTA
Found at i:1353756 original size:18 final size:18
Alignment explanation
Indices: 1353715--1353757 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1353705 TATTAAATTT
*
1353715 ATATAATAAAATTTATTA
1 ATATATTAAAATTTATTA
1353733 ATATATTAAAATTTATATA
1 ATATATTAAAATTTAT-TA
1353752 A-ATATT
1 ATATATT
1353758 TATTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATATTAAAATTTATTA
Found at i:1354261 original size:26 final size:27
Alignment explanation
Indices: 1354226--1354281 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
1354216 CTACCCAATG
*
1354226 AAATTTTTA-TCTAAGTAATTTA-TTTA
1 AAATTGTTATTCTAA-TAATTTATTTTA
*
1354252 AAATTGTTATTTTAATAATTTATTTTA
1 AAATTGTTATTCTAATAATTTATTTTA
1354279 AAA
1 AAA
1354282 ATTACGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (27 bp):
AAATTGTTATTCTAATAATTTATTTTA
Found at i:1354577 original size:34 final size:34
Alignment explanation
Indices: 1354514--1354578 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1354504 TATTATTTTT
*
1354514 AATAATAAAAAAATTATATAAATTTATAATTATA
1 AATAATAAAAAAATTATATAAATTAATAATTATA
*
1354548 AATAATATAAAATAATT-TTTAAA-TAATAATT
1 AATAATA-AAAA-AATTATATAAATTAATAATT
1354579 CAAATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 14 0.52
35 9 0.33
36 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AATAATAAAAAAATTATATAAATTAATAATTATA
Found at i:1354731 original size:3 final size:3
Alignment explanation
Indices: 1354723--1354748 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1354713 AGGGAAATCG
1354723 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1354749 CAAGAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1356896 original size:16 final size:16
Alignment explanation
Indices: 1356843--1356898 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1356833 GATGAATTTT
1356843 ATTTTAATATTATTAA
1 ATTTTAATATTATTAA
* * *
1356859 ATTATAAATAATATTTA
1 ATT-TTAATATTATTAA
*
1356876 TTTTTAATATTATTAA
1 ATTTTAATATTATTAA
1356892 ATTTTAA
1 ATTTTAA
1356899 AATAAAAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAATATTATTAA
Found at i:1356911 original size:33 final size:33
Alignment explanation
Indices: 1356844--1356913 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
1356834 ATGAATTTTA
**
1356844 TTTTAATATTATTAAATTATAAATAATATTTAT
1 TTTTAATATTATTAAATTATAAATAATAAATAT
*
1356877 TTTTAATATTATTAAATTTTAAAATAA-AAATAT
1 TTTTAATATTATTAAATTAT-AAATAATAAATAT
1356910 TTTT
1 TTTT
1356914 TATGTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTTTAATATTATTAAATTATAAATAATAAATAT
Found at i:1357373 original size:19 final size:21
Alignment explanation
Indices: 1357335--1357373 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1357325 TTTTTAAATA
*
1357335 AATATAAATAAAATTTATTTC
1 AATATAAATAAAATTAATTTC
1357356 AATA-AAATAAAA-TAATTT
1 AATATAAATAAAATTAATTT
1357374 AATTCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATAAATAAAATTAATTTC
Found at i:1364900 original size:34 final size:34
Alignment explanation
Indices: 1364861--1364971 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
1364851 AATATTTTAA
1364861 ATATTAAATAAAAATATATTAAATATATCATATT
1 ATATTAAATAAAAATATATTAAATATATCATATT
* *** * * *
1364895 ATATTATCAT-CGTATTTATTAAATATATCGTTTT
1 ATATTA-AATAAAAATATATTAAATATATCATATT
* * *
1364929 TTATATAACACAATAAATATATTAAATATACCATATT
1 ATAT-TAA-ATAA-AAATATATTAAATATATCATATT
1364966 ATATTA
1 ATATTA
1364972 TTATCATATT
Statistics
Matches: 54, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
34 27 0.50
35 5 0.09
36 2 0.04
37 20 0.37
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (34 bp):
ATATTAAATAAAAATATATTAAATATATCATATT
Found at i:1364955 original size:71 final size:71
Alignment explanation
Indices: 1364872--1365008 Score: 220
Period size: 71 Copynumber: 1.9 Consensus size: 71
1364862 TATTAAATAA
* * * *
1364872 AAATATATTAAATATATCATATTATATTATCATCGTATTTATTAAATATATCGTTTTTTATATAA
1 AAATATATTAAATATACCATATTATATTATCATCATATTTATTAAACATATCATTTTTTATATAA
1364937 CACAAT
66 CACAAT
* *
1364943 AAATATATTAAATATACCATATTATATTATTATCATATTTATTAAACATATCATTTTTTATGTAA
1 AAATATATTAAATATACCATATTATATTATCATCATATTTATTAAACATATCATTTTTTATATAA
1365008 C
66 C
1365009 GTATAAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (71 bp):
AAATATATTAAATATACCATATTATATTATCATCATATTTATTAAACATATCATTTTTTATATAA
CACAAT
Found at i:1366360 original size:2 final size:2
Alignment explanation
Indices: 1366353--1366384 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1366343 GTCATAAAAT
1366353 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
1366385 AAAGGGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1367225 original size:17 final size:17
Alignment explanation
Indices: 1367190--1367230 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1367180 TTTAAAAGTT
1367190 TTTAATAAAAATATTAAA
1 TTTAA-AAAAATATTAAA
1367208 TTTAAAAAAA-ATTAAAA
1 TTTAAAAAAATATT-AAA
1367225 TTTAAA
1 TTTAAA
1367231 TCTCGTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.14
17 14 0.64
18 5 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTAAAAAAATATTAAA
Found at i:1367414 original size:100 final size:99
Alignment explanation
Indices: 1367301--1367698 Score: 456
Period size: 99 Copynumber: 4.0 Consensus size: 99
1367291 TTTTATATAA
* * * * *
1367301 AAATATGAATAAATTTGTACGAATTTAACTAATATTTTTCATATATATATTGAGTCCGAATGTAA
1 AAATATGAATAAATTTATACAAATTTAAATAATATTTTTCAAATATA-ACTGAGTCCGAATGTAA
* *
1367366 AAAATTTTGCTCATATTTTATAAAGGATTGAGGCT
65 AAAATTTTGCTCATACTTTATAAAGGACTGAGGCT
* * *
1367401 AAATACGAATAAATTTATACAAATTTAACTAATATTTTTCATATATATATATTGAGTCCGAATGT
1 AAATATGAATAAATTTATACAAATTTAAATAATATTTTTCA-A-ATATA-ACTGAGTCCGAATGT
* * *
1367466 AAAAAATTTTGCTCATGCTTTATAAAGGATTGAGGTT
63 AAAAAATTTTGCTCATACTTTATAAAGGACTGAGGCT
* * * * * * *
1367503 GAATATGGATGAATTTATATAAATTTAAATAATATTTTTTAAATATAACTGTGTCTGAATGTAAA
1 AAATATGAATAAATTTATACAAATTTAAATAATATTTTTCAAATATAACTGAGTCCGAATGTAAA
* *
1367568 AAATTTTGCTTATACTTTATAAAGGACTGAAGCT
66 AAATTTTGCTCATACTTTATAAAGGACTGAGGCT
* * * * * **
1367602 AGATATGGATGAATTTATACGAATTTAAATAATAATTTTT-AAATATAACTGAATCTAAATGTAA
1 AAATATGAATAAATTTATACAAATTTAAATAAT-ATTTTTCAAATATAACTGAGTCCGAATGTAA
* * *
1367666 AAAACTTTCCTCATACTTTATAAAAGACTGAGG
65 AAAATTTTGCTCATACTTTATAAAGGACTGAGG
1367699 GGATAATAAG
Statistics
Matches: 261, Mismatches: 34, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
99 122 0.47
100 49 0.19
101 1 0.00
102 89 0.34
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (99 bp):
AAATATGAATAAATTTATACAAATTTAAATAATATTTTTCAAATATAACTGAGTCCGAATGTAAA
AAATTTTGCTCATACTTTATAAAGGACTGAGGCT
Done.