Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold947.1
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: 644213
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.32
Warning! 26822 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:217486 original size:23 final size:21
Alignment explanation
Indices: 217444--217488 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
217434 GAGGTGAGAT
**
217444 AAAATTTTAAATTTTATATTA
1 AAAATTTTAAATTAAATATTA
217465 AAAATATTTAAATTAAATTATTA
1 AAAAT-TTTAAATTAAA-TATTA
217488 A
1 A
217489 CATAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 9 0.45
23 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTTTAAATTAAATATTA
Found at i:218166 original size:6 final size:6
Alignment explanation
Indices: 218151--218184 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
218141 GGATCAAATT
*
218151 GAAAAA -AAAAA GAAAAA AAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
218185 CTCACACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:220734 original size:21 final size:21
Alignment explanation
Indices: 220672--220771 Score: 71
Period size: 21 Copynumber: 4.9 Consensus size: 21
220662 GTACATCGTT
* *
220672 AACAGAAGCTC-GAA-AGCTA
1 AACAGAAGCTCATAAGAGCTG
* * *
220691 AACAGAAACCCATAAG-GTTTG
1 AACAGAAGCTCATAAGAG-CTG
**
220712 AACAGAAGCTTGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * *
220733 AACGGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
*
220754 AACAAAAGCTCATAAGAG
1 AACAGAAGCTCATAAGAG
220772 TCGAACTCAT
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
19 9 0.15
20 3 0.05
21 46 0.78
22 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:220747 original size:42 final size:42
Alignment explanation
Indices: 220672--220814 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 42
220662 GTACATCGTT
* * *
220672 AACAGAAGCTCG-AA-AGCTAAACAGAAACCCATAAGGTTTG
1 AACAAAAGCTCGTAAGAGCTAAACGGAAACTCATAAGGTTTG
* * *
220712 AACAGAAGCTTGTAAGAGCTGAACGGAAACTCATAAGAG-TTG
1 AACAAAAGCTCGTAAGAGCTAAACGGAAACTCATAAG-GTTTG
* *
220754 AACAAAAGCTCATAAGAG-T---C-G-AACTCATAAGATTTG
1 AACAAAAGCTCGTAAGAGCTAAACGGAAACTCATAAGGTTTG
220790 AACAAAAGCTCGTAAGAGCTAAACG
1 AACAAAAGCTCGTAAGAGCTAAACG
220815 AAAAGTAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
36 30 0.35
37 2 0.02
38 1 0.01
40 12 0.14
41 3 0.04
42 36 0.42
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
AACAAAAGCTCGTAAGAGCTAAACGGAAACTCATAAGGTTTG
Found at i:220772 original size:21 final size:21
Alignment explanation
Indices: 220701--220807 Score: 68
Period size: 21 Copynumber: 5.4 Consensus size: 21
220691 AACAGAAACC
*
220701 CATAAG-GTTTGAACAGAAGCT
1 CATAAGAG-TTGAACAAAAGCT
** * *
220722 TGTAAGAGCTGAACGGAAA-CT
1 CATAAGAGTTGAAC-AAAAGCT
220743 CATAAGAGTTGAACAAAAGCT
1 CATAAGAGTTGAACAAAAGCT
*
220764 CATAAGAG-T---C-GAA-CT
1 CATAAGAGTTGAACAAAAGCT
*
220779 CATAAGATTTGAACAAAAGCT
1 CATAAGAGTTGAACAAAAGCT
*
220800 CGTAAGAG
1 CATAAGAG
220808 CTAAACGAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
15 9 0.14
16 3 0.05
17 1 0.02
19 1 0.02
20 6 0.10
21 40 0.63
22 3 0.05
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (21 bp):
CATAAGAGTTGAACAAAAGCT
Found at i:220791 original size:36 final size:36
Alignment explanation
Indices: 220739--220807 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
220729 GCTGAACGGA
220739 AACTCATAAGAGTTGAACAAAAGCTCATAAGAGTCG
1 AACTCATAAGAGTTGAACAAAAGCTCATAAGAGTCG
* *
220775 AACTCATAAGATTTGAACAAAAGCTCGTAAGAG
1 AACTCATAAGAGTTGAACAAAAGCTCATAAGAG
220808 CTAAACGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (36 bp):
AACTCATAAGAGTTGAACAAAAGCTCATAAGAGTCG
Found at i:226013 original size:29 final size:30
Alignment explanation
Indices: 225969--226026 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
225959 CGAAACTTAT
* *
225969 TTGATTCTTTTTAATAGTATAAA-AATTAAA
1 TTGATTCTATTTAATAATA-AAATAATTAAA
225999 TTGATTC-ATTTAATAATAAAATAATTAA
1 TTGATTCTATTTAATAATAAAATAATTAA
226027 TTTAATCCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (30 bp):
TTGATTCTATTTAATAATAAAATAATTAAA
Found at i:228242 original size:24 final size:24
Alignment explanation
Indices: 228206--228253 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
228196 GATTTTCTAG
228206 AAAAGCTGATATTTTCTAATGTTT
1 AAAAGCTGATATTTTCTAATGTTT
*
228230 AAAAGCTGTTATTTTCTAATGTTT
1 AAAAGCTGATATTTTCTAATGTTT
228254 GAATTATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (24 bp):
AAAAGCTGATATTTTCTAATGTTT
Found at i:229284 original size:47 final size:47
Alignment explanation
Indices: 229215--229312 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
229205 GTGAACCCAA
229215 TTAAATTCTTGGTTACAAAAAAAAAATAAATCAATTGGCCCCTTTCT
1 TTAAATTCTTGGTTACAAAAAAAAAATAAATCAATTGGCCCCTTTCT
229262 TTAAATTCTTGGTTACAAAAAAAAAATAAATCAATTGGCCCCTTTCT
1 TTAAATTCTTGGTTACAAAAAAAAAATAAATCAATTGGCCCCTTTCT
229309 TTAA
1 TTAA
229313 TAGAAATCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (47 bp):
TTAAATTCTTGGTTACAAAAAAAAAATAAATCAATTGGCCCCTTTCT
Found at i:230718 original size:21 final size:21
Alignment explanation
Indices: 230688--230729 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
230678 TACAGTCTAC
*
230688 CCATACGGCCGTGTTTCTCAG
1 CCATACGGCCGTGTCTCTCAG
*
230709 CCATATGGCCGTGTCTCTCAG
1 CCATACGGCCGTGTCTCTCAG
230730 GCACATGGTT
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:0.14, C:0.33, G:0.24, T:0.29
Consensus pattern (21 bp):
CCATACGGCCGTGTCTCTCAG
Found at i:230737 original size:21 final size:21
Alignment explanation
Indices: 230694--230737 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
230684 CTACCCATAC
* *
230694 GGCCGTGTTTCTCAGCCATAT
1 GGCCGTGTCTCTCAGCCACAT
*
230715 GGCCGTGTCTCTCAGGCACAT
1 GGCCGTGTCTCTCAGCCACAT
230736 GG
1 GG
230738 TTGTGTATTC
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:0.14, C:0.30, G:0.30, T:0.27
Consensus pattern (21 bp):
GGCCGTGTCTCTCAGCCACAT
Found at i:232898 original size:47 final size:45
Alignment explanation
Indices: 232797--232898 Score: 109
Period size: 47 Copynumber: 2.2 Consensus size: 45
232787 ATCATTTTCA
*
232797 GATACAGAATCAATACAGATATACAGAATCAGACATAATTATTTTG
1 GATACA-AATCAATACAGATATACAGAATCAGACATAAGTATTTTG
* *
232843 AATAACAAATTCAATACGGATATACAGAATCGAAGACACT-AGTA-TTTG
1 GAT-ACAAA-TCAATACAGATATACAGAATC--AGACA-TAAGTATTTTG
232891 GATACAAA
1 GATACAAA
232899 ATAACGGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
46 4 0.09
47 28 0.60
48 6 0.13
49 8 0.17
50 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (45 bp):
GATACAAATCAATACAGATATACAGAATCAGACATAAGTATTTTG
Found at i:233209 original size:30 final size:30
Alignment explanation
Indices: 233175--233232 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
233165 TATCTAAGTA
*
233175 GCACAT-GAACATGTGAACCGCCCGTGTGCG
1 GCACATAG-ACATGTCAACCGCCCGTGTGCG
* *
233205 GCACATAGCCATGTCAACCGCTCGTGTG
1 GCACATAGACATGTCAACCGCCCGTGTG
233233 ATCCAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (30 bp):
GCACATAGACATGTCAACCGCCCGTGTGCG
Found at i:237742 original size:5 final size:5
Alignment explanation
Indices: 237724--237756 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
237714 AAATAGGCTA
*
237724 CATA- CATAC TATAC CATAC CATAC CATAC CATA
1 CATAC CATAC CATAC CATAC CATAC CATAC CATA
237757 TATACATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.24
Consensus pattern (5 bp):
CATAC
Found at i:241491 original size:47 final size:49
Alignment explanation
Indices: 241402--241497 Score: 162
Period size: 47 Copynumber: 2.0 Consensus size: 49
241392 AGAACAAGGA
241402 AGAGGTACGACCTCATCAGTTTTTTTTTAGAATGTCTTGATTGCGTTTT
1 AGAGGTACGACCTCATCAGTTTTTTTTTAGAATGTCTTGATTGCGTTTT
241451 AGAGGTACGA-C-C-TCAGTTTGTTTTTTAGAATGTCTTGATTGCGTTTT
1 AGAGGTACGACCTCATCAGTTT-TTTTTTAGAATGTCTTGATTGCGTTTT
241498 CATTAATTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
46 7 0.15
47 28 0.61
48 1 0.02
49 10 0.22
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.45
Consensus pattern (49 bp):
AGAGGTACGACCTCATCAGTTTTTTTTTAGAATGTCTTGATTGCGTTTT
Found at i:252348 original size:47 final size:47
Alignment explanation
Indices: 252292--252385 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
252282 TAATTACACA
252292 CATTCATTTATAGTTACTGGAACACTATAAATATTTGAAAATGTTCC
1 CATTCATTTATAGTTACTGGAACACTATAAATATTTGAAAATGTTCC
*
252339 CATTCATTTATAGTTATTGGAACACTATAAATATTTGAAAATGTTCC
1 CATTCATTTATAGTTACTGGAACACTATAAATATTTGAAAATGTTCC
252386 AACAATCTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (47 bp):
CATTCATTTATAGTTACTGGAACACTATAAATATTTGAAAATGTTCC
Found at i:254999 original size:19 final size:19
Alignment explanation
Indices: 254975--255015 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
254965 TTACTTTAGT
*
254975 TTCCTTATTAGGAACTCTA
1 TTCCTTATTAGAAACTCTA
254994 TTCCTTATTAGAAACTCTA
1 TTCCTTATTAGAAACTCTA
255013 TTC
1 TTC
255016 AATATATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (19 bp):
TTCCTTATTAGAAACTCTA
Found at i:255739 original size:39 final size:40
Alignment explanation
Indices: 255685--255772 Score: 162
Period size: 39 Copynumber: 2.2 Consensus size: 40
255675 ATACCCTTCA
255685 CCTACAAAAATTCCTCCCTTAAACAAAATAAACTTATTT-
1 CCTACAAAAATTCCTCCCTTAAACAAAATAAACTTATTTG
255724 CCTACAAAAATTCCTCCCTTAAACAAAATAAACTTATTTG
1 CCTACAAAAATTCCTCCCTTAAACAAAATAAACTTATTTG
255764 CCT-CAAAAA
1 CCTACAAAAA
255773 AAGTTTGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 45 0.94
40 3 0.06
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.28
Consensus pattern (40 bp):
CCTACAAAAATTCCTCCCTTAAACAAAATAAACTTATTTG
Found at i:257536 original size:67 final size:67
Alignment explanation
Indices: 257428--257561 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
257418 ACTATTCAAA
*
257428 TAAAATTATTTAAATAGTTATAATTTTTTTTCAAAAAATCAAACAATATAATCTTTTGATTTATT
1 TAAAATTATTTAAATAGTTATAATTTTTTTTCAAAAAATCAAACAATATAATCTTTTGATTAATT
257493 AC
66 AC
257495 TAAAATTATTTAAATAGTTATAATTTTTTTTCAAAAAATCAAACAATATAATCTTTTGATTAATT
1 TAAAATTATTTAAATAGTTATAATTTTTTTTCAAAAAATCAAACAATATAATCTTTTGATTAATT
257560 AC
66 AC
257562 ACACATTCAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (67 bp):
TAAAATTATTTAAATAGTTATAATTTTTTTTCAAAAAATCAAACAATATAATCTTTTGATTAATT
AC
Found at i:264842 original size:20 final size:19
Alignment explanation
Indices: 264800--264842 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
264790 GGTCACCTAA
* * *
264800 TAAAACATTTTGTTTCACT
1 TAAAACATTTTGGTCCACG
264819 TAAAACAATTTTGGTCCACG
1 TAAAAC-ATTTTGGTCCACG
264839 TAAA
1 TAAA
264843 TTTAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TAAAACATTTTGGTCCACG
Found at i:269266 original size:31 final size:31
Alignment explanation
Indices: 269231--269297 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
269221 AAAAAACCTT
*
269231 AATAGC-CTAATGACTTAAATAAAAACTTTTA
1 AATAGCTC-AATGACTTAAATAAAAAATTTTA
* * *
269262 AATAGTTCAGTGACTTAAATAAAAAATTTTG
1 AATAGCTCAATGACTTAAATAAAAAATTTTA
269293 AATAG
1 AATAG
269298 TTCACTGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (31 bp):
AATAGCTCAATGACTTAAATAAAAAATTTTA
Found at i:269298 original size:31 final size:31
Alignment explanation
Indices: 269241--269301 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
269231 AATAGCCTAA
*
269241 TGACTTAAATAAAAACTTTTAAATAGTTCAG
1 TGACTTAAATAAAAAATTTTAAATAGTTCAG
*
269272 TGACTTAAATAAAAAATTTTGAATAGTTCA
1 TGACTTAAATAAAAAATTTTAAATAGTTCA
269302 CTGATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTTAAATAGTTCAG
Found at i:279970 original size:26 final size:26
Alignment explanation
Indices: 279939--280046 Score: 146
Period size: 26 Copynumber: 4.2 Consensus size: 26
279929 TGAAATGCCC
279939 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
279965 ATCATGGAATATTTACC-AAACCCATT
1 ATCATGGAACATTTACCTAAA-CCATT
* * *
279991 ACCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
280017 ATCATGGACCATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
280043 ATCA
1 ATCA
280047 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
25 3 0.04
26 68 0.93
27 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:280016 original size:52 final size:52
Alignment explanation
Indices: 279941--280043 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
279931 AAATGCCCAT
*
279941 CATGGAACATTTACCTAAACCATTATCATGGAATATTTACCAAACCCATTAC
1 CATGGAACATTTACCTAAACCATTATCATGGAACATTTACCAAACCCATTAC
* * * *
279993 CATGGAATATTTACCTAATCCATTATCATGGACCATTTACCTAACCCATTA
1 CATGGAACATTTACCTAAACCATTATCATGGAACATTTACCAAACCCATTA
280044 TCAATTTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (52 bp):
CATGGAACATTTACCTAAACCATTATCATGGAACATTTACCAAACCCATTAC
Found at i:285810 original size:236 final size:236
Alignment explanation
Indices: 285397--285867 Score: 879
Period size: 236 Copynumber: 2.0 Consensus size: 236
285387 ACATTGAAGT
285397 GTTCAAAACATTTTATATTGTTAATCCAGAAAAACTTACTTAGTGTTTTAAAAGATAATTTCATT
1 GTTCAAAACATTTTATATTGTTAATCCAGAAAAACTTACTTAGTGTTTTAAAAGATAATTTCATT
* * *
285462 ATAGTTTAAAGTGAATGAAAGCTGTGCACCAGGTAGGAAATCGAAAAAGAGGTGGTGAGTCTATC
66 ATAGGTTAAAGTGAATGAAAGCTGTGCACCAGGTAGGAAACCGAAAAAGAGGTGGTGAGTCCATC
* *
285527 GGACTGCTTAAGTACCAAGCTCCCTTCGGATCTAATCCTAGACATGCATACCGCCATTGCTACAC
131 GGACTGCTTAAGTACCAAGCTCCCTTCGGATCCAATCCTAGACATGCATACCGCCATTGCCACAC
285592 CTTAACGTCATGGATATTTCTAGGAAACCGATTTGATTAAC
196 CTTAACGTCATGGATATTTCTAGGAAACCGATTTGATTAAC
*
285633 GTTCAAAACATTTTATATTGTTGATCCAGAAAAACTTACTTAGTGTTTTAAAAGATAATTTCATT
1 GTTCAAAACATTTTATATTGTTAATCCAGAAAAACTTACTTAGTGTTTTAAAAGATAATTTCATT
*
285698 ATAGGTTAAAGTGAATGAAAGTTGTGCACCAGGTAGGAAACCGAAAAAGAGGTGGTGAGTCCATC
66 ATAGGTTAAAGTGAATGAAAGCTGTGCACCAGGTAGGAAACCGAAAAAGAGGTGGTGAGTCCATC
285763 GGACTGCTTAAGTACCAAGCTCCCTTCGGATCCAATCCTAGACATGCATACCGCCATTGCCACAC
131 GGACTGCTTAAGTACCAAGCTCCCTTCGGATCCAATCCTAGACATGCATACCGCCATTGCCACAC
285828 CTTAACGTCATGGATATTTCTAGGAAACCGATTTGATTAA
196 CTTAACGTCATGGATATTTCTAGGAAACCGATTTGATTAA
285868 GTCATTTTTA
Statistics
Matches: 228, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
236 228 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (236 bp):
GTTCAAAACATTTTATATTGTTAATCCAGAAAAACTTACTTAGTGTTTTAAAAGATAATTTCATT
ATAGGTTAAAGTGAATGAAAGCTGTGCACCAGGTAGGAAACCGAAAAAGAGGTGGTGAGTCCATC
GGACTGCTTAAGTACCAAGCTCCCTTCGGATCCAATCCTAGACATGCATACCGCCATTGCCACAC
CTTAACGTCATGGATATTTCTAGGAAACCGATTTGATTAAC
Found at i:286189 original size:89 final size:89
Alignment explanation
Indices: 286068--286245 Score: 320
Period size: 89 Copynumber: 2.0 Consensus size: 89
286058 AACTTCAAAT
*
286068 GTAAATAAAAGGATGTCCAGTTCACTAGAAAAAAAAATCAAACTTTCAGAACGGGTGGCCACTCC
1 GTAAATAAAAGGATGTCCAGTTCACCAGAAAAAAAAATCAAACTTTCAGAACGGGTGGCCACTCC
* *
286133 GAATTCTCTCACAGCTCTAAGCCC
66 GAATTCCCTCACAGCTCCAAGCCC
286157 GTAAATAAAAGGATGTCCAGTTCACCAGAAAAAAAAATCAAACTTTCAGAACGGGTGGCCACTCC
1 GTAAATAAAAGGATGTCCAGTTCACCAGAAAAAAAAATCAAACTTTCAGAACGGGTGGCCACTCC
*
286222 GAATTCCCTCGCAGCTCCAAGCCC
66 GAATTCCCTCACAGCTCCAAGCCC
286246 ACTATGGTTG
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (89 bp):
GTAAATAAAAGGATGTCCAGTTCACCAGAAAAAAAAATCAAACTTTCAGAACGGGTGGCCACTCC
GAATTCCCTCACAGCTCCAAGCCC
Found at i:298447 original size:40 final size:40
Alignment explanation
Indices: 298392--298472 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
298382 CGGGATTTGA
*
298392 AAGATATCATGCATTAGCATATCCCATCAATTCTAACTTT
1 AAGATATCATGCATTAGCATATCCCATCAAGTCTAACTTT
298432 AAGATATCATGCATTAGCATATCCCATCAAGTCTAACTTT
1 AAGATATCATGCATTAGCATATCCCATCAAGTCTAACTTT
298472 A
1 A
298473 CTCCATTTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (40 bp):
AAGATATCATGCATTAGCATATCCCATCAAGTCTAACTTT
Found at i:302484 original size:7 final size:7
Alignment explanation
Indices: 302474--302500 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
302464 ACTCCAAACT
302474 CAAAATA
1 CAAAATA
302481 CAAAATA
1 CAAAATA
302488 CAAAATA
1 CAAAATA
302495 CAAAAT
1 CAAAAT
302501 TTTCCTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (7 bp):
CAAAATA
Found at i:309524 original size:156 final size:156
Alignment explanation
Indices: 309240--309551 Score: 606
Period size: 156 Copynumber: 2.0 Consensus size: 156
309230 ACAATATGGG
309240 CTGCGATAAAGGCTTAAAAGTGTTCGAAAATACGAGGCATACTCCACAGTTAACATATTCAATTT
1 CTGCGATAAAGGCTTAAAAGTGTTCGAAAATACGAGGCATACTCCACAGTTAACATATTCAATTT
309305 TTGATCTTATGTTTTTTGAAATAAAAGAGTAAAAGTAAGACAAAAATAAAATAAAATATTACGAA
66 TTGATCTTATGTTTTTTGAAATAAAAGAGTAAAAGTAAGACAAAAATAAAATAAAATATTACGAA
309370 AGGAAACAACAAATAAATTTAGAAAA
131 AGGAAACAACAAATAAATTTAGAAAA
*
309396 CTGCGATAAAGGCTTAAAAGTGTTCGAAAATACGATGCATACTCCACAGTTAACATATTCAATTT
1 CTGCGATAAAGGCTTAAAAGTGTTCGAAAATACGAGGCATACTCCACAGTTAACATATTCAATTT
309461 TTGATCTTATGTTTTTTGAAATAAAAGAGTAAAAGTAAGACAAAAATAAAATAAAATATTACGAA
66 TTGATCTTATGTTTTTTGAAATAAAAGAGTAAAAGTAAGACAAAAATAAAATAAAATATTACGAA
*
309526 AGGAAACAACAATTAAATTTAGAAAA
131 AGGAAACAACAAATAAATTTAGAAAA
309552 TATAATGAAA
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 154 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.28
Consensus pattern (156 bp):
CTGCGATAAAGGCTTAAAAGTGTTCGAAAATACGAGGCATACTCCACAGTTAACATATTCAATTT
TTGATCTTATGTTTTTTGAAATAAAAGAGTAAAAGTAAGACAAAAATAAAATAAAATATTACGAA
AGGAAACAACAAATAAATTTAGAAAA
Found at i:309790 original size:24 final size:24
Alignment explanation
Indices: 309744--309792 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
309734 TTTGATATGG
*
309744 AATTTTTTAAATTATAAGGATTTT
1 AATTTTTTAAATTATAAGAATTTT
* * *
309768 AATTTTTTTAATTTTAATAATTTT
1 AATTTTTTAAATTATAAGAATTTT
309792 A
1 A
309793 TGCTTTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTTTTTAAATTATAAGAATTTT
Found at i:309940 original size:21 final size:23
Alignment explanation
Indices: 309915--309958 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
309905 TTTCACCTAA
*
309915 TTATAATTT-TA-AAAATAATTT
1 TTATAATTTCTAGAAAAAAATTT
309936 TTATAATTTCTAGAAAAAAATTT
1 TTATAATTTCTAGAAAAAAATTT
309959 ATGAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTATAATTTCTAGAAAAAAATTT
Found at i:314765 original size:57 final size:57
Alignment explanation
Indices: 314677--314791 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
314667 GGCATGTGCC
314677 ACTTGGTAGTGGTTGGAAGTGGGTGGTTGAGGCTTGCGGCTAGGGGTTCTAATTTCT
1 ACTTGGTAGTGGTTGGAAGTGGGTGGTTGAGGCTTGCGGCTAGGGGTTCTAATTTCT
*
314734 ACTTGGTAGTGGTTGGAAGTGGGTGGTTGAGGCTTGCGGCTAGGGTTTCTAATTTCT
1 ACTTGGTAGTGGTTGGAAGTGGGTGGTTGAGGCTTGCGGCTAGGGGTTCTAATTTCT
314791 A
1 A
314792 AAAATAGGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.15, C:0.10, G:0.39, T:0.36
Consensus pattern (57 bp):
ACTTGGTAGTGGTTGGAAGTGGGTGGTTGAGGCTTGCGGCTAGGGGTTCTAATTTCT
Found at i:315610 original size:205 final size:205
Alignment explanation
Indices: 315256--315837 Score: 1044
Period size: 205 Copynumber: 2.8 Consensus size: 205
315246 AAATCTATTT
* *
315256 CTTCGATTTGTTCCCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
315321 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
315386 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGTTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGTTATGTGTCTGCTCTCCATCAAAGTGA
*
315451 AGATGCCAAA
196 AGATGACAAA
315461 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
315526 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* *
315591 GGATCTGCTTCAATGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGTTATGTGTCTGCTCTCCATCAAAGTGA
315656 AGATGACAAA
196 AGATGACAAA
* *
315666 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGC-TCCATCGTAATCA
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTC-TCGTAATCA
*
315730 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCT
65 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCT
*
315795 TGGATCTGCTTCAGT-ATAA-CATCTGAAGGCCAGATCTGTTATG
130 TGGATCTGCTTCAGTGA-AATCATCTGAAGGCGAGATCTGTTATG
315838 CTGCGGCCTA
Statistics
Matches: 364, Mismatches: 11, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
204 25 0.07
205 339 0.93
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGTTATGTGTCTGCTCTCCATCAAAGTGA
AGATGACAAA
Found at i:323828 original size:13 final size:15
Alignment explanation
Indices: 323798--323828 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
323788 TTCCAGATTT
323798 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
323813 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
323828 T
1 T
323829 GGAAAGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTTCTACCTCTC
Found at i:327868 original size:40 final size:39
Alignment explanation
Indices: 327715--327870 Score: 242
Period size: 39 Copynumber: 4.0 Consensus size: 39
327705 GATTCCACTC
* * * *
327715 CCCCCATGCTACTTTGTTTTATTATTAATTAAAACTACT
1 CCCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
*
327754 CCCCCATACTATTTTGTTTTATTATTAATTAAAACTATT
1 CCCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
327793 -CCCCATACTATTTTGTTTTCATTATTAATTAAAACCATT
1 CCCCCATACTATTTTGTTTT-ATTATTAATTAAAACCATT
327832 CCCCCATACTATTTTGTTTTTATTATTAATTAAAACCAT
1 CCCCCATACTATTTTG-TTTTATTATTAATTAAAACCAT
327871 ACTTTATTTT
Statistics
Matches: 110, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
38 19 0.17
39 54 0.49
40 33 0.30
41 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (39 bp):
CCCCCATACTATTTTGTTTTATTATTAATTAAAACCATT
Found at i:330715 original size:30 final size:30
Alignment explanation
Indices: 330681--330743 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
330671 ACTTATTTTA
330681 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
330711 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
330741 TTG
1 TTG
330744 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:330897 original size:12 final size:12
Alignment explanation
Indices: 330867--330899 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
330857 TATATATTTT
330867 AAAATT-ATATA
1 AAAATTAATATA
330878 AAAA-TAATATA
1 AAAATTAATATA
330889 AAAATTAATAT
1 AAAATTAATAT
330900 GGGCGAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:331202 original size:18 final size:19
Alignment explanation
Indices: 331168--331203 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
331158 TTTTTTTGTT
*
331168 TAAATTTAATTATAAAATA
1 TAAATTTAATGATAAAATA
331187 TAAATTTAA-GATAAAAT
1 TAAATTTAATGATAAAAT
331204 TAATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TAAATTTAATGATAAAATA
Found at i:331935 original size:13 final size:13
Alignment explanation
Indices: 331917--331953 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
331907 CAAAAGCCTC
331917 TCTTTTGTTTTTT
1 TCTTTTGTTTTTT
*
331930 TCTTTTG-TCTTT
1 TCTTTTGTTTTTT
331942 TCTTTT-TTTTTT
1 TCTTTTGTTTTTT
331954 GGTAAAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (13 bp):
TCTTTTGTTTTTT
Found at i:335382 original size:17 final size:17
Alignment explanation
Indices: 335360--335406 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
335350 ACTTTGAACA
* *
335360 TATATTTATTATTATAC
1 TATATTTATGAATATAC
*
335377 TATATTTATGAATATAT
1 TATATTTATGAATATAC
335394 TATATTTAT-AATA
1 TATATTTATGAATA
335407 GTGAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TATATTTATGAATATAC
Found at i:335442 original size:24 final size:24
Alignment explanation
Indices: 335410--335462 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
335400 TATAATAGTG
* *
335410 AATTTTTAAAAAATATATATATAA
1 AATTTTTAAAAAATAAATAAATAA
*
335434 CATTTTTAAAAAATAAATAAATAA
1 AATTTTTAAAAAATAAATAAATAA
335458 AATTT
1 AATTT
335463 CAAATTTAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTTTTAAAAAATAAATAAATAA
Found at i:353489 original size:36 final size:36
Alignment explanation
Indices: 353448--353520 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
353438 GGTTAATGTA
353448 AAAATAGTAGTGACGGTAAGATTAGATACTATAGCG
1 AAAATAGTAGTGACGGTAAGATTAGATACTATAGCG
353484 AAAATAGTAGTGACGGTAAGATTAGATACTATAGCG
1 AAAATAGTAGTGACGGTAAGATTAGATACTATAGCG
353520 A
1 A
353521 TATTGTAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (36 bp):
AAAATAGTAGTGACGGTAAGATTAGATACTATAGCG
Found at i:354702 original size:51 final size:51
Alignment explanation
Indices: 354634--354741 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
354624 CCCCTCAAAG
* * *
354634 TTTACACATTCTATCAATTCCGTCTTTGATTTAACAGATTTACCT-TCAACA
1 TTTACACATTCTATCAATTCAGTC-TTGATTTAACAAATTTACCTAGCAACA
* * * *
354685 TTTACACATTTTGTCAATTTAGTCTTGATTTAACAAATTTAGCTAGCAACA
1 TTTACACATTCTATCAATTCAGTCTTGATTTAACAAATTTACCTAGCAACA
354736 TTTACA
1 TTTACA
354742 AACTATACCA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
50 18 0.37
51 31 0.63
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.42
Consensus pattern (51 bp):
TTTACACATTCTATCAATTCAGTCTTGATTTAACAAATTTACCTAGCAACA
Found at i:356462 original size:22 final size:22
Alignment explanation
Indices: 356424--356472 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
356414 ATAAAAAATT
*
356424 TAAA-AATAATTTGTTAAATAA
1 TAAATAATAATTTGTTAAACAA
*
356445 TAAATAATAAATTT-TTAAACAG
1 TAAATAAT-AATTTGTTAAACAA
356467 TAAATA
1 TAAATA
356473 TTAACTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 15 0.62
23 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
TAAATAATAATTTGTTAAACAA
Found at i:356661 original size:21 final size:21
Alignment explanation
Indices: 356636--356734 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 21
356626 AATTACTTCG
*
356636 TTAATATTTTAATAATTATTA
1 TTAATATTTTAATAATTTTTA
*
356657 TTAATAGTTTTAA-ATTTTTTA
1 TTAATA-TTTTAATAATTTTTA
* * *
356678 TT-ATTTTTTTATTATTTTTA
1 TTAATATTTTAATAATTTTTA
*
356698 -TAA-ATTTTAAATAATTTTATT
1 TTAATATTTT-AATAATTTT-TA
*
356719 TTAAATTTTTTAATAA
1 TT-AATATTTTAATAA
356735 ATTTCAATCA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
19 10 0.17
20 16 0.27
21 15 0.25
22 7 0.12
23 7 0.12
24 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (21 bp):
TTAATATTTTAATAATTTTTA
Found at i:356687 original size:11 final size:11
Alignment explanation
Indices: 356671--356696 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
356661 TAGTTTTAAA
356671 TTTTTTATTAT
1 TTTTTTATTAT
356682 TTTTTTATTAT
1 TTTTTTATTAT
356693 TTTT
1 TTTT
356697 ATAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:359067 original size:12 final size:12
Alignment explanation
Indices: 359041--359080 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
359031 AAATTGAGAA
359041 TTTTTCTGATTT
1 TTTTTCTGATTT
*
359053 TTTTTTTGCTATTT
1 TTTTTCTG--ATTT
359067 TTTTTCTGATTT
1 TTTTTCTGATTT
359079 TT
1 TT
359081 CCTGTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTCTGATTT
Found at i:360199 original size:20 final size:21
Alignment explanation
Indices: 360146--360199 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
360136 AAATATCGTC
360146 ATGTCTCGAGACAATGTTCCCT
1 ATGTCTCGAGACAATG-TCCCT
* *
360168 ATCTCTCAAGACAATG-CCACT
1 ATGTCTCGAGACAATGTCC-CT
360189 -TGTCTCGAGAC
1 ATGTCTCGAGAC
360200 CCTGGACCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 11 0.41
21 2 0.07
22 14 0.52
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (21 bp):
ATGTCTCGAGACAATGTCCCT
Found at i:361410 original size:18 final size:18
Alignment explanation
Indices: 361381--361428 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
361371 TTTCTAATAG
361381 TTTTTATAAATTTTAATCT
1 TTTTTAT-AATTTTAATCT
*
361400 TTTTTATAATTTTAATGT
1 TTTTTATAATTTTAATCT
361418 TTTTTA-AATTT
1 TTTTTATAATTT
361429 ACTTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 5 0.18
18 16 0.57
19 7 0.25
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTATAATTTTAATCT
Found at i:363717 original size:14 final size:15
Alignment explanation
Indices: 363698--363730 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
363688 TTCCTTATGG
363698 TTTTCTGTTTC-TTC
1 TTTTCTGTTTCTTTC
*
363712 TTTTCTTTTTCTTTC
1 TTTTCTGTTTCTTTC
363727 TTTT
1 TTTT
363731 AATGTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTCTGTTTCTTTC
Found at i:369325 original size:25 final size:26
Alignment explanation
Indices: 369273--369327 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
369263 TTTATTTTAT
* *
369273 ATTATATTAATAATTTTAAAAATTAA
1 ATTAAATTAATAATTTTAAAAATAAA
* *
369299 ATTAAATTAA-AATTTTATATATAAA
1 ATTAAATTAATAATTTTAAAAATAAA
369324 ATTA
1 ATTA
369328 TATGTTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTAAATTAATAATTTTAAAAATAAA
Found at i:369710 original size:24 final size:24
Alignment explanation
Indices: 369678--369726 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
369668 AGTTAACATA
369678 ACTTTCAACTCTTGACCCGAACTT
1 ACTTTCAACTCTTGACCCGAACTT
369702 ACTTTCAACTCTTGACCCGAACTT
1 ACTTTCAACTCTTGACCCGAACTT
369726 A
1 A
369727 AGAAATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.33
Consensus pattern (24 bp):
ACTTTCAACTCTTGACCCGAACTT
Found at i:372271 original size:17 final size:18
Alignment explanation
Indices: 372233--372273 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
372223 TGTTGAAAAT
* *
372233 TTAAATTTATATATATTT
1 TTAAATTTATATAAATTA
372251 TTAAATTT-TATAAATTA
1 TTAAATTTATATAAATTA
372268 TTAAAT
1 TTAAAT
372274 CAATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAATTTATATAAATTA
Found at i:378773 original size:31 final size:31
Alignment explanation
Indices: 378738--378809 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
378728 GTTAAAATGG
* *
378738 TCAAATAAAGATTTAA-TATTTTTAAAAGTAC
1 TCAAATAAAGACTCAACT-TTTTTAAAAGTAC
* * *
378769 TCAAATAATGGCTCAACTTTTTTAAAAGTGC
1 TCAAATAAAGACTCAACTTTTTTAAAAGTAC
378800 TCAAATAAAG
1 TCAAATAAAG
378810 GCTTTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (31 bp):
TCAAATAAAGACTCAACTTTTTTAAAAGTAC
Found at i:381298 original size:3 final size:3
Alignment explanation
Indices: 381290--381329 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
381280 AACAAGTAAG
381290 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
381330 AGTGGCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:382120 original size:4 final size:4
Alignment explanation
Indices: 382113--382139 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
382103 TCAAAAAAAA
382113 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
382140 AATGTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:382743 original size:18 final size:18
Alignment explanation
Indices: 382716--382757 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
382706 AAAATAAAAA
*
382716 ATTATAAAATAATT-AATT
1 ATTATTAAAT-ATTAAATT
*
382734 ATTATTAAATTTTAAATT
1 ATTATTAAATATTAAATT
382752 ATTATT
1 ATTATT
382758 TTTAGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATTAAATATTAAATT
Found at i:382916 original size:25 final size:23
Alignment explanation
Indices: 382879--382939 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
382869 ATTATAAATT
*
382879 ATAAATTTCATTTTAATAGAAATCAA
1 ATAAATAT-ATTTTAAT-GAAAT-AA
* *
382905 ATATATATATTTTTATGAAATAA
1 ATAAATATATTTTAATGAAATAA
*
382928 GTAAATATATTT
1 ATAAATATATTT
382940 AATTTTAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 12 0.40
24 5 0.17
25 7 0.23
26 6 0.20
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (23 bp):
ATAAATATATTTTAATGAAATAA
Found at i:383034 original size:18 final size:18
Alignment explanation
Indices: 383011--383050 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
383001 AAAAATCGAC
* *
383011 AAATAAAAATACATATAT
1 AAATAAAAATAAAGATAT
*
383029 AAATAATAATAAAGATAT
1 AAATAAAAATAAAGATAT
383047 AAAT
1 AAAT
383051 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATAAAAATAAAGATAT
Found at i:386996 original size:29 final size:29
Alignment explanation
Indices: 386963--387020 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
386953 GGGAATAATG
386963 CCAAGCTAAAGGGAGAAGTAAACCATTAC
1 CCAAGCTAAAGGGAGAAGTAAACCATTAC
386992 CCAAGCTAAAGGGAGAAGTAAACCATTAC
1 CCAAGCTAAAGGGAGAAGTAAACCATTAC
387021 TCATATGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (29 bp):
CCAAGCTAAAGGGAGAAGTAAACCATTAC
Found at i:387701 original size:24 final size:24
Alignment explanation
Indices: 387655--387701 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
387645 TGAATTAATT
* *
387655 TTTTTCTTTTAAAAATTTTATCTA
1 TTTTTATTTTAAAAATTTGATCTA
387679 TTTTTATTATTAAAAA-TTGATCT
1 TTTTTATT-TTAAAAATTTGATCT
387702 TTGTGCCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTATTTTAAAAATTTGATCTA
Found at i:388047 original size:10 final size:10
Alignment explanation
Indices: 388032--388073 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
388022 TTCATCTCTC
388032 TATACATATA
1 TATACATATA
388042 TATACATATA
1 TATACATATA
388052 TATACATACATGA
1 TATACAT--AT-A
388065 TATACATAT
1 TATACATAT
388074 CACTATGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 17 0.59
11 2 0.07
12 2 0.07
13 8 0.28
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (10 bp):
TATACATATA
Found at i:392597 original size:32 final size:30
Alignment explanation
Indices: 392536--392603 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 30
392526 TGGGGTCTAA
*
392536 TTAAAATTTTTGTGAGATCAATGAGAATTT
1 TTAAAATTTTTGTGAGATCAATGAAAATTT
* * *
392566 TTAAAATTTTTAAGTGAGGTTAATTAAAATTT
1 TTAAAATTTTT--GTGAGATCAATGAAAATTT
*
392598 TCAAAA
1 TTAAAA
392604 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 11 0.35
32 20 0.65
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (30 bp):
TTAAAATTTTTGTGAGATCAATGAAAATTT
Found at i:394953 original size:15 final size:15
Alignment explanation
Indices: 394935--394981 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
394925 TTTGAAAAAA
394935 ATATTTATATTATTT
1 ATATTTATATTATTT
394950 ATATTTAATATT-TTT
1 ATATTT-ATATTATTT
*
394965 ATATATT-TTTTATTT
1 ATAT-TTATATTATTT
394980 AT
1 AT
394982 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.11
15 18 0.64
16 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATTTATATTATTT
Found at i:394976 original size:26 final size:25
Alignment explanation
Indices: 394940--394994 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
394930 AAAAAATATT
394940 TATATTATTTA-TATTTAATATTTTTA
1 TATATTATTTATTATTTAA-A-TTTTA
*
394966 TATATTTTTTATTTATTTAAATTTTA
1 TATATTATTTA-TTATTTAAATTTTA
394992 TAT
1 TAT
394995 TTAAGCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 18 0.69
27 1 0.04
28 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TATATTATTTATTATTTAAATTTTA
Found at i:394989 original size:17 final size:17
Alignment explanation
Indices: 394938--394997 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
394928 GAAAAAAATA
394938 TTTATA-TTATTTATAT
1 TTTATATTTATTTATAT
*
394954 TTAATATTT-TTATATAT
1 TTTATATTTATT-TATAT
* *
394971 TTTTTATTTATTTAAAT
1 TTTATATTTATTTATAT
394988 TTTATATTTA
1 TTTATATTTA
394998 AGCATATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 7 0.19
17 27 0.75
18 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATTTATTTATAT
Found at i:395086 original size:19 final size:18
Alignment explanation
Indices: 395022--395092 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
395012 TTTTTAACAT
*
395022 TTACATTATAGTATTATATA
1 TTACA-TATA-TATTATAAA
* *
395042 TTAC-TATAGATT-TAAT
1 TTACATATATATTATAAA
*
395058 TTATATATATATTATAAA
1 TTACATATATATTATAAA
*
395076 TTACATAATATAATATA
1 TTACAT-ATATATTATA
395093 TCATAAACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
16 5 0.12
17 10 0.25
18 12 0.30
19 9 0.22
20 4 0.10
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (18 bp):
TTACATATATATTATAAA
Found at i:398515 original size:31 final size:30
Alignment explanation
Indices: 398471--398549 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
398461 CAGCTTAGTG
398471 ACTTAAATAAAAACTTTTAAATAGTT-AAGTA
1 ACTTAAAT-AAAACTTTTAAATAGTTCAA-TA
* * *
398502 ATTTAAATGAAAACTTTTGAATTGTTCAATA
1 ACTTAAAT-AAAACTTTTAAATAGTTCAATA
*
398533 ACTTAAATAGAACTTTT
1 ACTTAAATAAAACTTTT
398550 TGAATAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 8 0.20
31 31 0.76
32 2 0.05
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.39
Consensus pattern (30 bp):
ACTTAAATAAAACTTTTAAATAGTTCAATA
Found at i:398937 original size:17 final size:16
Alignment explanation
Indices: 398896--398958 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
398886 GCAAATTATT
398896 AATTATAAAATTTTAAA
1 AATTA-AAAATTTTAAA
* * *
398913 AAATAAAATTTTTTAA
1 AATTAAAAATTTTAAA
*
398929 AATTAAAAA-ATTAAA
1 AATTAAAAATTTTAAA
*
398944 AATTACAAGATTTTA
1 AATTA-AAAATTTTA
398959 GCAAGCTAAC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
15 9 0.26
16 19 0.54
17 7 0.20
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTAAAAATTTTAAA
Found at i:400210 original size:15 final size:15
Alignment explanation
Indices: 400192--400267 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 15
400182 TCGTTTGTTC
*
400192 CCTTGTCATCTGTGT
1 CCTTGTCATTTGTGT
* * *
400207 CCTTGCCGTTCAGT-T
1 CCTTGTCATT-TGTGT
*
400222 CCTTCTCATTTGTGT
1 CCTTGTCATTTGTGT
* * *
400237 CCTTGCCGTTTGTTT
1 CCTTGTCATTTGTGT
400252 CCTTGTCATTTGTGT
1 CCTTGTCATTTGTGT
400267 C
1 C
400268 TTTCTGCTGG
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
14 2 0.05
15 40 0.91
16 2 0.05
ACGTcount: A:0.05, C:0.28, G:0.18, T:0.49
Consensus pattern (15 bp):
CCTTGTCATTTGTGT
Found at i:400236 original size:30 final size:30
Alignment explanation
Indices: 400183--400267 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
400173 CCTTCAATGT
* * *
400183 CGTTTGTTCCCTTGTCATCTGTGTCCTTGC
1 CGTTAGTTTCCTTGTCATTTGTGTCCTTGC
*
400213 CGTTCAG-TTCCTTCTCATTTGTGTCCTTGC
1 CGTT-AGTTTCCTTGTCATTTGTGTCCTTGC
*
400243 CGTTTGTTTCCTTGTCATTTGTGTC
1 CGTTAGTTTCCTTGTCATTTGTGTC
400268 TTTCTGCTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.96
31 1 0.02
ACGTcount: A:0.05, C:0.27, G:0.19, T:0.49
Consensus pattern (30 bp):
CGTTAGTTTCCTTGTCATTTGTGTCCTTGC
Found at i:402795 original size:19 final size:19
Alignment explanation
Indices: 402759--402797 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
402749 AATATTTAGC
*
402759 ATGTTAAAAAGTATTATTA
1 ATGTTAAAAAGTAGTATTA
**
402778 ATGTTAAAATTTAGTATTA
1 ATGTTAAAAAGTAGTATTA
402797 A
1 A
402798 AATAAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (19 bp):
ATGTTAAAAAGTAGTATTA
Found at i:402910 original size:22 final size:19
Alignment explanation
Indices: 402864--402910 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
402854 ATATTCGATT
*
402864 TATTATATATTATTTTAAA
1 TATTAAATATTATTTTAAA
402883 TA-TAAATATTTATTTTAATAA
1 TATTAAATA-TTATTTT-A-AA
402904 TATTAAA
1 TATTAAA
402911 AAAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 1 0.04
21 4 0.17
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAAATATTATTTTAAA
Found at i:408950 original size:14 final size:15
Alignment explanation
Indices: 408901--408952 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
408891 TTTATCAGAC
408901 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
408916 TATTAAATATATTAT
1 AATTAAATATATTAT
408931 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
408944 AATTTAATA
1 AATTAAATA
408953 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:409124 original size:101 final size:93
Alignment explanation
Indices: 409018--409300 Score: 317
Period size: 91 Copynumber: 3.0 Consensus size: 93
409008 ACTATAAAAG
* * * *
409018 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT---
* *
409082 ATAATTATAACTAATAAATTATCTTATATGAATTTGT
62 -T--CT-TAA-TAATAAATTATCTTATATGAATTTAT
* *
409119 ATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
* *
409182 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTATCTTATATGAATTTAT
* *
409210 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
409273 AATAATAAAATGT-TCTTATATGAATTTA
66 AATAAT-AAAT-TATCTTATATGAATTTA
409301 CTAAAATCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
91 88 0.54
92 21 0.13
93 2 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 48 0.29
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
AATAATAAATTATCTTATATGAATTTAT
Found at i:409147 original size:26 final size:28
Alignment explanation
Indices: 409118--409178 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
409108 TATGAATTTG
*
409118 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
409144 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
409172 TAAAATT
1 TATAATT
409179 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:409176 original size:47 final size:46
Alignment explanation
Indices: 409125--409268 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
409115 TTGTATAATT
409125 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
409172 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
409216 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
409263 TAAAAT
1 TAAAAT
409269 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:409188 original size:91 final size:90
Alignment explanation
Indices: 409093--409300 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 90
409083 TAATTATAAC
* * * *
409093 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
409158 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
409184 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
409249 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
409275 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
409301 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
91 87 0.81
92 21 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:409260 original size:44 final size:43
Alignment explanation
Indices: 409118--409260 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
409108 TATGAATTTG
* *
409118 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
409162 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
409209 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
409253 TATAATTT
1 TATAATTT
409261 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:409275 original size:47 final size:47
Alignment explanation
Indices: 409143--409281 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
409133 TTATTATTAC
* *
409143 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
409190 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
409234 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
409281 A
1 A
409282 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:413882 original size:116 final size:117
Alignment explanation
Indices: 413678--413917 Score: 403
Period size: 116 Copynumber: 2.1 Consensus size: 117
413668 ATGATTTAGC
* *
413678 ATGGAATTATAGTTTTAAATTGTTTATATGCTGATTTTATTGAAAGAATTGAATAGAAAGTGAAT
1 ATGGAATTAGAGCTTTAAATTGTTTATATGCTGATTTTATTGAAAGAATTGAATAGAAAGTGAAT
* *
413743 GTTTGGGACCTAATTGTAAAAGAGTTTGAAGATAGAG-TTTATGTGGAAATT
66 GTTTGGGACCTAATGGTAAAAGAGTTTAAAGATAGAGTTTTATGTGGAAATT
413794 ATGGAATTAGAGCTTTAAATTGTTTATATGCTGATTTTATTGAAAGAATTGAATAGAAAGTGAAT
1 ATGGAATTAGAGCTTTAAATTGTTTATATGCTGATTTTATTGAAAGAATTGAATAGAAAGTGAAT
* * *
413859 GTTTGGGACCTAATGGTGAAAGAGTTTAAAGTTAGGGTTTTATGTGGAAATT
66 GTTTGGGACCTAATGGTAAAAGAGTTTAAAGATAGAGTTTTATGTGGAAATT
413911 AT-GAATT
1 ATGGAATT
413918 TAAATAATTT
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
116 100 0.86
117 16 0.14
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.38
Consensus pattern (117 bp):
ATGGAATTAGAGCTTTAAATTGTTTATATGCTGATTTTATTGAAAGAATTGAATAGAAAGTGAAT
GTTTGGGACCTAATGGTAAAAGAGTTTAAAGATAGAGTTTTATGTGGAAATT
Found at i:415118 original size:51 final size:50
Alignment explanation
Indices: 414959--415115 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
414949 ACTTCTGATC
* *
414959 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
415010 AGTGACAAGCGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
415060 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
415111 AGTGA
1 AGTGA
415116 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:418443 original size:15 final size:15
Alignment explanation
Indices: 418423--418464 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
418413 AATTTTTTTT
418423 CTTTCTTTCTTCCTC
1 CTTTCTTTCTTCCTC
418438 CTTTCTTTCTT--TC
1 CTTTCTTTCTTCCTC
*
418451 CTTT-TTTTTTCCTC
1 CTTTCTTTCTTCCTC
418465 TTATTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 5 0.21
13 6 0.25
14 2 0.08
15 11 0.46
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTCTTTCTTCCTC
Found at i:426276 original size:11 final size:10
Alignment explanation
Indices: 426262--426312 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 10
426252 AAAGAGAATG
426262 GAAAATAAAGA
1 GAAAATAAA-A
*
426273 GAAAAAAAAA
1 GAAAATAAAA
426283 GAAAATTAAAA
1 GAAAA-TAAAA
*
426294 GAACATAAAA
1 GAAAATAAAA
426304 GAAAA-AAAA
1 GAAAATAAAA
426313 TTAAATTGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 4 0.11
10 15 0.43
11 16 0.46
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.08
Consensus pattern (10 bp):
GAAAATAAAA
Found at i:426286 original size:21 final size:21
Alignment explanation
Indices: 426262--426308 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
426252 AAAGAGAATG
426262 GAAAA-TAAAGAGAAAAAAAAA
1 GAAAATTAAA-AGAAAAAAAAA
* *
426283 GAAAATTAAAAGAACATAAAA
1 GAAAATTAAAAGAAAAAAAAA
426304 GAAAA
1 GAAAA
426309 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.09
Consensus pattern (21 bp):
GAAAATTAAAAGAAAAAAAAA
Found at i:428529 original size:27 final size:27
Alignment explanation
Indices: 428476--428529 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
428466 ACGATTACTT
*
428476 AATTATTTAAAATTTAAAAATTCAAAA
1 AATTATTTAAAATTTAAAAACTCAAAA
428503 AATTATTTAAAAATTTAAAAACT-AAAA
1 AATTATTT-AAAATTTAAAAACTCAAAA
428530 TTTATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (27 bp):
AATTATTTAAAATTTAAAAACTCAAAA
Found at i:433793 original size:111 final size:111
Alignment explanation
Indices: 433599--433822 Score: 412
Period size: 111 Copynumber: 2.0 Consensus size: 111
433589 CCGTGATTCA
*
433599 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGACGTGGTCTGCATGCATAT
1 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGACGTAGTCTGCATGCATAT
433664 CTTATTAAGTAGGCTTTCTTTAATTGGATATGAAATATTTCTCCTG
66 CTTATTAAGTAGGCTTTCTTTAATTGGATATGAAATATTTCTCCTG
* *
433710 TTGGCTATTGAAATGTAAATAACGTGTTTGACATTGTTTCAGAGTGATGTAGTCTGCATGCATAT
1 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGACGTAGTCTGCATGCATAT
*
433775 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
66 CTTATTAAGTAGGCTTTCTTTAATTGGATATGAAATATTTCTCCTG
433821 TT
1 TT
433823 ATCTTGTTAA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42
Consensus pattern (111 bp):
TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGACGTAGTCTGCATGCATAT
CTTATTAAGTAGGCTTTCTTTAATTGGATATGAAATATTTCTCCTG
Found at i:444678 original size:17 final size:18
Alignment explanation
Indices: 444658--444694 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
444648 CAAAATTCCT
444658 TATTTAAAAAAATAA-AA
1 TATTTAAAAAAATAATAA
*
444675 TATTTAAATAAATAATAA
1 TATTTAAAAAAATAATAA
444693 TA
1 TA
444695 ATTACTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATTTAAAAAAATAATAA
Found at i:448298 original size:33 final size:34
Alignment explanation
Indices: 448248--448315 Score: 129
Period size: 33 Copynumber: 2.0 Consensus size: 34
448238 CATTATGCCA
448248 AAATATATTTTTTTTGTAATAATCTGAAGTAAAC
1 AAATATATTTTTTTTGTAATAATCTGAAGTAAAC
448282 AAATATA-TTTTTTTGTAATAATCTGAAGTAAAC
1 AAATATATTTTTTTTGTAATAATCTGAAGTAAAC
448315 A
1 A
448316 TTATAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (34 bp):
AAATATATTTTTTTTGTAATAATCTGAAGTAAAC
Found at i:449388 original size:31 final size:31
Alignment explanation
Indices: 449352--449420 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
449342 TAACAGCCCA
*
449352 AATGACTTAAATAAAAACTTTTGAAAAGTTG
1 AATGACTTAAATAAAAACTTTCGAAAAGTTG
* * *
449383 AATGACTTAAATGAAAACTTTCGAATAGTTT
1 AATGACTTAAATAAAAACTTTCGAAAAGTTG
449414 AATGACT
1 AATGACT
449421 ATTTTGTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCGAAAAGTTG
Found at i:457008 original size:10 final size:10
Alignment explanation
Indices: 456993--457020 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
456983 CATTTAACCG
456993 AATTAATCAA
1 AATTAATCAA
457003 AATTAATCAA
1 AATTAATCAA
457013 AATTAATC
1 AATTAATC
457021 GAATTGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTAATCAA
Found at i:462092 original size:16 final size:16
Alignment explanation
Indices: 462068--462102 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
462058 TTACTATAAA
*
462068 AGGCGCTTTACCTTTT
1 AGGCACTTTACCTTTT
462084 AGGCACTTTACCTTTT
1 AGGCACTTTACCTTTT
462100 AGG
1 AGG
462103 TTTAGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (16 bp):
AGGCACTTTACCTTTT
Found at i:462628 original size:21 final size:20
Alignment explanation
Indices: 462598--462640 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
462588 TAAATAAATT
*
462598 TCAAATATA-AAAATATTAA
1 TCAATTATATAAAATATTAA
*
462617 TCAATTATATAAAATATTTA
1 TCAATTATATAAAATATTAA
462637 TCAA
1 TCAA
462641 CAAACTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (20 bp):
TCAATTATATAAAATATTAA
Found at i:464453 original size:23 final size:25
Alignment explanation
Indices: 464427--464473 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
464417 TATCATTCAT
*
464427 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
464450 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
464474 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:464794 original size:46 final size:46
Alignment explanation
Indices: 464729--464903 Score: 181
Period size: 46 Copynumber: 4.0 Consensus size: 46
464719 TTATCTTTGA
* * * * *
464729 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACTATGGTCTTACACA-TTTCATAT
*
464775 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATAT
*
464821 CAGGTTGCCATGGTATCTTTCAACTATGGTCTT--ACA---C--A-
1 CATGTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATAT
* *
464859 CAGGTTGCCATGGTATCTTTCAA-TGTTGGTCTTACACATTTCATA
1 CATGTTGCCATGGTATCTTTCAACT-ATGGTCTTACACATTTCATA
464904 AGTCCAGGCT
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
37 1 0.01
38 30 0.27
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 5 0.05
46 66 0.59
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATAT
Found at i:464872 original size:38 final size:38
Alignment explanation
Indices: 464821--464896 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
464811 CATTTCATAT
464821 CAGGTTGCCATGGTATCTTTCAACT-ATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAA-TGATGGTCTTACACA
*
464859 CAGGTTGCCATGGTATCTTTCAATGTTGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAATGATGGTCTTACACA
464897 TTTCATAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAATGATGGTCTTACACA
Found at i:487216 original size:21 final size:22
Alignment explanation
Indices: 487184--487231 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
487174 CCTTATTCTA
*
487184 TTTTAAATTTTTTTATCTATTT
1 TTTTAAATTTTTCTATCTATTT
* *
487206 TTTTAAA-TTTTCTATGTTTTT
1 TTTTAAATTTTTCTATCTATTT
487227 TTTTA
1 TTTTA
487232 TGATTTAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTAAATTTTTCTATCTATTT
Found at i:500986 original size:13 final size:13
Alignment explanation
Indices: 500968--500992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500958 TGCCCGATGC
500968 AACAGATATGAGT
1 AACAGATATGAGT
500981 AACAGATATGAG
1 AACAGATATGAG
500993 CCAAAATAAT
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:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (13 bp):
AACAGATATGAGT
Found at i:501337 original size:20 final size:19
Alignment explanation
Indices: 501312--501368 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 19
501302 AAAATTACAA
*
501312 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAAT-ATTTAT
501332 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
501351 -AAAATTTAAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
501368 A
1 A
501369 TATATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.18
18 10 0.29
19 5 0.15
20 13 0.38
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:501362 original size:19 final size:20
Alignment explanation
Indices: 501312--501363 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
501302 AAAATTACAA
* *
501312 AAAAATTCAAAATAATTTTT
1 AAAAATTAAAAATAATTTAT
*
501332 AAAAATTCAAAAT-ATTTAT
1 AAAAATTAAAAATAATTTAT
*
501351 AAAATTTAAAAAT
1 AAAAATTAAAAAT
501364 TTATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTAAAAATAATTTAT
Found at i:501370 original size:19 final size:18
Alignment explanation
Indices: 501333--501402 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 18
501323 ATAATTTTTA
* * *
501333 AAAATTCAAAATATTTAT
1 AAAATTTAAAAAATATAT
*
501351 AAAATTTAAAAATTTATAT
1 AAAATTTAAAAA-ATATAT
** *
501370 ATATTTTTAAAAAATATAA
1 A-AAATTTAAAAAATATAT
501389 AAAATTTTAAAAAA
1 AAAA-TTTAAAAAA
501403 ATTCTAAAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
18 11 0.28
19 19 0.49
20 9 0.23
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTTAAAAAATATAT
Found at i:502765 original size:11 final size:11
Alignment explanation
Indices: 502749--502784 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
502739 TATTATTTAT
*
502749 TATTTTGCTAC
1 TATTTTACTAC
502760 TATTTTACTAC
1 TATTTTACTAC
*
502771 TATGTTACTAC
1 TATTTTACTAC
502782 TAT
1 TAT
502785 ATTGTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (11 bp):
TATTTTACTAC
Found at i:504097 original size:47 final size:47
Alignment explanation
Indices: 503988--504098 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
503978 CCGGGATAAG
* *
503988 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
504035 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
504082 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
504099 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:504872 original size:4 final size:4
Alignment explanation
Indices: 504863--504891 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
504853 TCCTTTTCTA
504863 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
504892 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:507936 original size:20 final size:20
Alignment explanation
Indices: 507911--507949 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
507901 AGCAGAATAC
507911 AAAAGAAAACCAAAAAACAG
1 AAAAGAAAACCAAAAAACAG
* *
507931 AAAAGAAAAGCAGAAAACA
1 AAAAGAAAACCAAAAAACA
507950 AGCAGCTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAGAAAACCAAAAAACAG
Found at i:510818 original size:3 final size:3
Alignment explanation
Indices: 510810--510957 Score: 71
Period size: 3 Copynumber: 49.3 Consensus size: 3
510800 TTAATTGATC
* *
510810 ATT ATT ATT ATT AAT ATT AGTGT ATA ATT -TT ATT ATAT ATGT ATGT
1 ATT ATT ATT ATT ATT ATT A-T-T ATT ATT ATT ATT AT-T AT-T AT-T
* * *
510856 AGT ATT ATT -TT TTT ATT ATT -TT ATT -TT AGT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
510900 A-T ATTT ACTT ATT -TGT GTT -TC ATT ATT ATT -TCT AGT ATT ATT ATT
1 ATT A-TT A-TT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
*
510945 ATT ATT AAT ATT A
1 ATT ATT ATT ATT A
510958 GTGTATGTTT
Statistics
Matches: 113, Mismatches: 17, Indels: 30
0.71 0.11 0.19
Matches are distributed among these distances:
2 15 0.13
3 79 0.70
4 17 0.15
5 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:511034 original size:143 final size:143
Alignment explanation
Indices: 510843--511186 Score: 415
Period size: 143 Copynumber: 2.4 Consensus size: 143
510833 ATAATTTTAT
* * * *
510843 TATATATGTATGTAGTATTATTTTTTTATTATTTTATTTTAGTATTATTATTATATTATATTTAC
1 TATATATTTATATAGTATTA-TTTTTAATTATTTTATTTTAATATTATTATTATATTATATTTAC
* * * * **
510908 TTATTTGTGTTTCATTATTATTTCTAGTATTATTATTATTATTAATATTAGTGTATG-TTTTA-T
65 TTATTTGTATTTCAATATTATTACTAGTATTATTATCATTATTAATA-TAGTAAATGTTTTTATT
* *
510971 -TATATGTATATATG
129 ATATATGCATATATA
* *
510985 TATATATTTACATATAGTATTATTTCTAATTATTTTATTTTAATATTATTATTATGTTATATTTA
1 TATATATTT--ATATAGTATTATTTTTAATTATTTTATTTTAATATTATTATTATATTATATTTA
* * * *
511050 CTTTTTTGTATTTTAATATTATTACTATTATTATTATCATTGTTAATATAGTAAATGTTTTTATT
64 CTTATTTGTATTTCAATATTATTACTAGTATTATTATCATTATTAATATAGTAAATGTTTTTATT
511115 ATATATGCATATATA
129 ATATATGCATATATA
* * ** * *
511130 TATGTATTTATATAGTAGTATTTTTAATTACCTTATTTTAAGATTATTGTTATATTA
1 TATATATTTATATAGTATTATTTTTAATTATTTTATTTTAATATTATTATTATATTA
511187 GACACTTTCC
Statistics
Matches: 171, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
142 15 0.09
143 125 0.73
144 11 0.06
145 20 0.12
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (143 bp):
TATATATTTATATAGTATTATTTTTAATTATTTTATTTTAATATTATTATTATATTATATTTACT
TATTTGTATTTCAATATTATTACTAGTATTATTATCATTATTAATATAGTAAATGTTTTTATTAT
ATATGCATATATA
Found at i:511036 original size:14 final size:16
Alignment explanation
Indices: 511002--511037 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
510992 TTACATATAG
511002 TATTATTTCTAATTAT
1 TATTATTTCTAATTAT
511018 T-TTATTT-TAA-TAT
1 TATTATTTCTAATTAT
511031 TATTATT
1 TATTATT
511038 ATGTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.21
14 8 0.42
15 6 0.32
16 1 0.05
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTCTAATTAT
Found at i:511256 original size:3 final size:3
Alignment explanation
Indices: 511242--511312 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
511232 TTAATTTAAC
* * * *
511242 TTA TTAA TTA TTA TTA TCA TTA TCA CTA TTG TTA -TA TTTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
511288 TTA CTT- TTA TTA TAA TTA TTA TTA T
1 TTA -TTA TTA TTA TTA TTA TTA TTA T
511313 AGCTTTTCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
2 4 0.08
3 42 0.79
4 7 0.13
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:511319 original size:24 final size:24
Alignment explanation
Indices: 511214--511312 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
511204 GTTTATTTAT
511214 TTATTAC-TTTATTACTAATTA--A
1 TTATTACTTTTATTA-TAATTATTA
* * *
511236 TT-TAACTTATTAATTATTATTATCA
1 TTATTACTT-TT-ATTATAATTATTA
* * * *
511261 TTATCACTATTGTTATATTTATTA
1 TTATTACTTTTATTATAATTATTA
511285 TTATTACTTTTATTATAATTATTA
1 TTATTACTTTTATTATAATTATTA
511309 TTAT
1 TTAT
511313 AGCTTTTCTT
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
21 3 0.05
22 3 0.05
23 7 0.12
24 37 0.63
25 5 0.08
26 4 0.07
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (24 bp):
TTATTACTTTTATTATAATTATTA
Found at i:512239 original size:8 final size:8
Alignment explanation
Indices: 512226--512251 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
512216 CTGAAATTCT
512226 ATTTTCAA
1 ATTTTCAA
512234 ATTTTCAA
1 ATTTTCAA
512242 ATTTTCAA
1 ATTTTCAA
512250 AT
1 AT
512252 AATTACCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTTCAA
Found at i:515644 original size:7 final size:8
Alignment explanation
Indices: 515627--515660 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
515617 AAACATTCGG
*
515627 AAAAAGTA
1 AAAAAGAA
515635 AAAAAG-A
1 AAAAAGAA
515642 AAAAAGAA
1 AAAAAGAA
515650 AAAAAGAA
1 AAAAAGAA
515658 AAA
1 AAA
515661 GAGAGCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:515645 original size:15 final size:15
Alignment explanation
Indices: 515627--515660 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
515617 AAACATTCGG
*
515627 AAAAAGTAAAAAAGA
1 AAAAAGAAAAAAAGA
515642 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
515657 AAAA
1 AAAA
515661 GAGAGCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:516548 original size:21 final size:19
Alignment explanation
Indices: 516523--516605 Score: 50
Period size: 21 Copynumber: 4.4 Consensus size: 19
516513 AGAAAATTTT
516523 ATTATTTGATATATTAGGTTG
1 ATTATTT-ATATATT-GGTTG
* *
516544 ATTATTTAAATATT--TTCA
1 ATTATTTATATATTGGTT-G
*
516562 ACTA-TT-TAT-TTGGTTG
1 ATTATTTATATATTGGTTG
*
516578 ATTATTTAATTTATTAGGTTG
1 ATTATTT-ATATATT-GGTTG
516599 ATTATTT
1 ATTATTT
516606 GATTATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
15 2 0.04
16 5 0.11
17 8 0.17
18 3 0.06
19 2 0.04
20 8 0.17
21 19 0.40
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (19 bp):
ATTATTTATATATTGGTTG
Found at i:516627 original size:55 final size:55
Alignment explanation
Indices: 516523--516663 Score: 135
Period size: 55 Copynumber: 2.6 Consensus size: 55
516513 AGAAAATTTT
* * * * * **
516523 ATTATTTGATATATTAGGTTGATTATTTAAATATTTTCAACTATTTATTTGGTTG
1 ATTATTTAATTTATTAGGTTGATTATTTGATTATTTTCAACAAAATATTTGGTTG
* *
516578 ATTATTTAATTTATTAGGTTGATTATTTGATTATTTTTAGA-AAAATATTTTGTTG
1 ATTATTTAATTTATTAGGTTGATTATTTGATTATTTTCA-ACAAAATATTTGGTTG
* * *
516633 ATT-GTTCATTTATTAGG-TGATTTAGTTGATT
1 ATTATTTAATTTATTAGGTTGA-TTATTTGATT
516664 GTAATTATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
53 3 0.04
54 21 0.29
55 47 0.65
56 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.55
Consensus pattern (55 bp):
ATTATTTAATTTATTAGGTTGATTATTTGATTATTTTCAACAAAATATTTGGTTG
Found at i:520807 original size:25 final size:25
Alignment explanation
Indices: 520778--520830 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
520768 TAGACTTTCA
520778 TTTAATGTCTTTTTTACTTTAGGTG
1 TTTAATGTCTTTTTTACTTTAGGTG
520803 TTTAATGTCTTTTTTACTTTAGGTG
1 TTTAATGTCTTTTTTACTTTAGGTG
520828 TTT
1 TTT
520831 TCTATGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (25 bp):
TTTAATGTCTTTTTTACTTTAGGTG
Found at i:521034 original size:18 final size:19
Alignment explanation
Indices: 520994--521035 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
520984 TTAAACTCAA
**
520994 AAATTAACTTAAACCGATT
1 AAATTAACTTAAACCGAAC
*
521013 AAATTAA-TTAAATCGAAC
1 AAATTAACTTAAACCGAAC
521031 AAATT
1 AAATT
521036 GTACAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (19 bp):
AAATTAACTTAAACCGAAC
Found at i:521215 original size:14 final size:15
Alignment explanation
Indices: 521196--521230 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
521186 TTTAATTTTC
*
521196 AAAATTTCAAAAA-A
1 AAAATTTAAAAAATA
521210 AAAATTTAAAAAATA
1 AAAATTTAAAAAATA
521225 AAAATT
1 AAAATT
521231 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTAAAAAATA
Found at i:521260 original size:30 final size:31
Alignment explanation
Indices: 521226--521327 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
521216 TAAAAAATAA
*
521226 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
521256 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
521286 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
521316 AAATTTCATTTT
1 AAATTTCATTTT
521328 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:521723 original size:3 final size:3
Alignment explanation
Indices: 521715--521786 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
521705 GCTAGACTTT
*
521715 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
521762 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
521787 ATAATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Done.