Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold171
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: 2364178
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 278680 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:1260312 original size:51 final size:52
Alignment explanation
Indices: 1260184--1260334 Score: 207
Period size: 51 Copynumber: 2.9 Consensus size: 52
1260174 GATGGTGAAA
* *
1260184 AAAATTGGTGCTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGG
1 AAAATTGGTG-TTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATTAAAGG
* * *
1260237 AAAATTGGTGTTTT-AGAAATAAAATCGGAGTTAGAGTATCCCCGATTATA-G
1 AAAATTGGTGTTTTGA-AAATAAAATCGGAGATGGAGTATCCCCGATTAAAGG
* *
1260288 AAAATTAGTGTTTTGAAAATAAAATCGGAGATGGAATATCCCCGATT
1 AAAATTGGTGTTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATT
1260335 GCGGAGAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 42 0.48
52 36 0.41
53 10 0.11
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (52 bp):
AAAATTGGTGTTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATTAAAGG
Found at i:1262829 original size:21 final size:22
Alignment explanation
Indices: 1262803--1262860 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1262793 GTTGGGACCC
* *
1262803 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
1262824 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
1262845 TGTATCGATACATTTG
1 TGTATCGATACATTTG
1262861 GATAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:1263777 original size:27 final size:27
Alignment explanation
Indices: 1263637--1263777 Score: 67
Period size: 28 Copynumber: 5.1 Consensus size: 27
1263627 TGTGGGCTTT
*
1263637 GAAAGGCGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
** * *
1263663 GAAAGGTG-CCACCAACTTGTGTAGG-CTT
1 GAAAGGTGTCCTGC-TCTT-TG-AGGACTG
*
1263691 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1263719 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1263747 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
1263774 GAAA
1 GAAA
1263778 ATGCCACCAA
Statistics
Matches: 79, Mismatches: 24, Indels: 23
0.63 0.19 0.18
Matches are distributed among these distances:
25 6 0.08
26 15 0.19
27 18 0.23
28 21 0.27
29 13 0.16
30 6 0.08
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1263841 original size:60 final size:60
Alignment explanation
Indices: 1263590--1264601 Score: 1153
Period size: 55 Copynumber: 17.4 Consensus size: 60
1263580 ATAAAGTGTA
* ** * *
1263590 TCCTGCTCATTGAGGACTAAAAAGTGCCATCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
1263645 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTAGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
1263700 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
1263755 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
1263815 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
1263875 TCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
1263934 TCCTGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
1263989 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGCGTGGGCTTTAAGAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AAGAAAAGGCG
* * * *
1264050 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGGAGAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAA-AGAAAAGGCG
* * *
1264111 T-CTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* * *
1264171 TCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
1264226 TCCTGCTCTTTGAGGATTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* * *
1264287 TCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * * *
1264342 TCGTGCTTTTTGAGGATTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCA
1 TCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
*
1264403 TCCGGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGCG
1 TCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
1264458 TCCTGTTGTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGCG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
*
1264518 TCCTGCTTTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAG--AAAAGGCG
1264580 TCCTGCTCTTTGAGGACTGGAA
1 TCCTGCTCTTTGAGGACTGGAA
1264602 GGGCTAAAAG
Statistics
Matches: 845, Mismatches: 61, Indels: 93
0.85 0.06 0.09
Matches are distributed among these distances:
53 3 0.00
54 30 0.04
55 295 0.35
56 8 0.01
57 1 0.00
59 56 0.07
60 216 0.26
61 207 0.24
62 27 0.03
64 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:1264081 original size:116 final size:116
Alignment explanation
Indices: 1263590--1264567 Score: 1250
Period size: 116 Copynumber: 8.4 Consensus size: 116
1263580 ATAAAGTGTA
* ** * * *
1263590 TCCTGCTCATTGAGGACTAAAAAGTGCCATCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* *
1263655 TGAGGACT-GAAAGGTGCCACCAACTTGTGTAGGCTTT----A-AG-AGGTG
66 TGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
* * *
1263700 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* * *
1263765 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
66 TGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
* *
1263815 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGCGTCCTG
* *
1263880 CTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
61 CTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
* * * *
1263934 TCCTGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* * *
1263999 TGAGGACT-GAAAGGTGCCACCAACTTGCGTGGGCTTTAAGAGGAGAAGGCG
66 TGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
* *
1264050 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGGAGAAGGCAT-CT
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT--A---A-AAGGCGTCCT
* * *
1264114 ACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
60 GCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
* * *
1264171 TCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* *
1264236 TGAGGATTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
66 TGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
* * * * *
1264287 TCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCGTGCTTTT
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* * *
1264352 TGAGGATTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCA
66 TGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
* * *
1264403 TCCGGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGTTGT
1 TCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCT
* * * *
1264467 TTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGCG
65 TTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
*
1264518 TCCTGCTTTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAA
1264568 AGAAAAAAGG
Statistics
Matches: 786, Mismatches: 58, Indels: 44
0.89 0.07 0.05
Matches are distributed among these distances:
110 88 0.11
111 4 0.01
113 3 0.00
114 56 0.07
115 132 0.17
116 287 0.37
117 2 0.00
118 1 0.00
119 85 0.11
120 23 0.03
121 97 0.12
122 8 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (116 bp):
TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
TGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCG
Found at i:1269502 original size:32 final size:33
Alignment explanation
Indices: 1269427--1269505 Score: 115
Period size: 35 Copynumber: 2.4 Consensus size: 33
1269417 CATTTAATAG
* *
1269427 TGTATCAATACATCTGGGCAAATTTGCCTGCATAA
1 TGTATCGATACATCTGGGCAAATTTCCCTGC--AA
1269462 TGTATCGATACATCTGGGCAAATTTCCCTGC-A
1 TGTATCGATACATCTGGGCAAATTTCCCTGCAA
1269494 TGTATCGATACA
1 TGTATCGATACA
1269506 AAGATCAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
32 13 0.31
35 29 0.69
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATCTGGGCAAATTTCCCTGCAA
Found at i:1269532 original size:13 final size:13
Alignment explanation
Indices: 1269514--1269538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1269504 CAAAGATCAG
1269514 TGTATCGATACAA
1 TGTATCGATACAA
1269527 TGTATCGATACA
1 TGTATCGATACA
1269539 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1269616 original size:33 final size:33
Alignment explanation
Indices: 1269579--1269645 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1269569 AGTAGGTTAA
1269579 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1269612 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1269645 A
1 A
1269646 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1269619 original size:13 final size:13
Alignment explanation
Indices: 1269601--1269625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1269591 CAAAAAAATA
1269601 TGTATCGATACAT
1 TGTATCGATACAT
1269614 TGTATCGATACA
1 TGTATCGATACA
1269626 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1270434 original size:13 final size:13
Alignment explanation
Indices: 1270418--1270442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1270408 AAAATAAATG
1270418 CATAAAAAGAAAC
1 CATAAAAAGAAAC
1270431 CATAAAAAGAAA
1 CATAAAAAGAAA
1270443 GGACGATCAA
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:0.72, C:0.12, G:0.08, T:0.08
Consensus pattern (13 bp):
CATAAAAAGAAAC
Found at i:1270925 original size:51 final size:52
Alignment explanation
Indices: 1270797--1270947 Score: 216
Period size: 51 Copynumber: 2.9 Consensus size: 52
1270787 GATTGTGAAA
* *
1270797 AAAATTGGTGTTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGG
1 AAAATTGGTG-TTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATTAAAGG
* *
1270850 AAAATTGGTGTTTT-AGAAATAAAATCGGAGGTGGAGTATCCCCGATTATA-G
1 AAAATTGGTGTTTTGA-AAATAAAATCGGAGATGGAGTATCCCCGATTAAAGG
* *
1270901 AAAATTAGTGTTTTGAAAATAAAATCGGAGATGGAATATCCCCGATT
1 AAAATTGGTGTTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATT
1270948 GCGGAGAATT
Statistics
Matches: 90, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
51 43 0.48
52 37 0.41
53 10 0.11
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (52 bp):
AAAATTGGTGTTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATTAAAGG
Found at i:1273320 original size:21 final size:21
Alignment explanation
Indices: 1273294--1273343 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1273284 GTAAACTTCC
1273294 TAGATGTATCAATACAAAGAA
1 TAGATGTATCAATACAAAGAA
* *
1273315 TAGATGTATCGATACACAGAA
1 TAGATGTATCAATACAAAGAA
*
1273336 -AAATGTAT
1 TAGATGTAT
1273344 TGATACATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (21 bp):
TAGATGTATCAATACAAAGAA
Found at i:1273343 original size:20 final size:21
Alignment explanation
Indices: 1273297--1273350 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1273287 AACTTCCTAG
* *
1273297 ATGTATCAATACAAAGAATAG
1 ATGTATCGATACAAAGAATAA
*
1273318 ATGTATCGATACACAGAA-AA
1 ATGTATCGATACAAAGAATAA
*
1273338 ATGTATTGATACA
1 ATGTATCGATACA
1273351 TTCCCTTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (21 bp):
ATGTATCGATACAAAGAATAA
Found at i:1278697 original size:34 final size:32
Alignment explanation
Indices: 1278654--1278719 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 32
1278644 TACAAGCCAA
1278654 TGTATCGATACAAT-TTGGTCATGTATCGATACAT
1 TGTATCGATAC-ATCTT-GT-ATGTATCGATACAT
1278688 TGTATCGATACATCTTGTATGTATCGATACAT
1 TGTATCGATACATCTTGTATGTATCGATACAT
1278720 ACATTTAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.45
33 4 0.13
34 13 0.42
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGTATGTATCGATACAT
Found at i:1278707 original size:15 final size:13
Alignment explanation
Indices: 1278675--1278700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1278665 AATTTGGTCA
1278675 TGTATCGATACAT
1 TGTATCGATACAT
1278688 TGTATCGATACAT
1 TGTATCGATACAT
1278701 CTTGTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1278802 original size:20 final size:20
Alignment explanation
Indices: 1278779--1278849 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
1278769 ACATTTGGTC
1278779 ATGTATCGATATTGTGCATT
1 ATGTATCGATATTGTGCATT
1278799 ATGTATCGATATTGTGCATT
1 ATGTATCGATATTGTGCATT
*
1278819 ATGTATCGATACTGTGCATT
1 ATGTATCGATATTGTGCATT
1278839 ATGTATCGATA
1 ATGTATCGATA
1278850 CATCTGAAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (20 bp):
ATGTATCGATATTGTGCATT
Found at i:1278864 original size:40 final size:40
Alignment explanation
Indices: 1278779--1278870 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
1278769 ACATTTGGTC
* * * **
1278779 ATGTATCGATATTGTGCATTATGTATCGATATTGTGCATT
1 ATGTATCGATACTGTGCATTATGTATCGATAATCTGCAAG
1278819 ATGTATCGATACTGTGCATTATGTATCGATACATCTG-AAG
1 ATGTATCGATACTGTGCATTATGTATCGATA-ATCTGCAAG
*
1278859 GTGTATCGATAC
1 ATGTATCGATAC
1278871 ATTAGAGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 42 0.93
41 3 0.07
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (40 bp):
ATGTATCGATACTGTGCATTATGTATCGATAATCTGCAAG
Found at i:1281304 original size:13 final size:13
Alignment explanation
Indices: 1281286--1281324 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1281276 ATAAACCCTT
*
1281286 TGTATCGATACAC
1 TGTATCGATACAA
1281299 TGTATCGATACAA
1 TGTATCGATACAA
1281312 TGTATCGATACAA
1 TGTATCGATACAA
1281325 AGAATACTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1296296 original size:404 final size:404
Alignment explanation
Indices: 1295547--1296346 Score: 1422
Period size: 404 Copynumber: 2.0 Consensus size: 404
1295537 AGATTGAACT
1295547 GCTGCCTCTGCTGGTTCGCACCTAGATTGTTTAGTGCAGTAGGGTTGGTATTTAGGTTAGCCTAG
1 GCTGCCTCTGCTGGTTCGCACCTAGATTGTTTAGTGCAGTAGGGTTGGTATTTAGGTTAGCCTAG
**
1295612 GATTGGTTAGTTCGTGGTGGATGCAGCAGGACAGTAAGGGATGGGCTATAGGTTGCAGCATACAC
66 GATTGGTTAGTTCGTGGTGGACACAGCAGGACAGTAAGGGATGGGCTATAGGTTGCAGCATACAC
* *
1295677 TGGTTGAGAATGTATCATGACTGGGCCTAGGTATGGTGCACTTGAGTAACAAGGACCGGGTGTTA
131 TGGTTGAGAATGTATCATGACTAGGCCTAGGTACGGTGCACTTGAGTAACAAGGACCGGGTGTTA
1295742 ATGTTGTCTCAATTGTGTTGGGTTGGCATAACTGATGGCATTGGCCTCTCCCTTCTTTTTCTTGT
196 ATGTTGTCTCAATTGTGTTGGGTTGGCATAACTGATGGCATTGGCCTCTCCCTTCTTTTTCTTGT
* * * *
1295807 TAGCAGTGGCTTTCTTACTCGATTCAGATGACTCTTCTATAGATATTTTGTCACTTTTAATTGAT
261 TAGCAGTGGCCTTCTTACTCAATTCAGATGACTCTCCTATAGATATTTTGCCACTTTTAATTGAT
* *
1295872 GCAGCAATTATTTTGCCATATAAAACCAAATCGGTAAACTTTTTCGTGGCATTTCATACAAGCTT
326 GCAGCAATTATTTTGCCATATAAAACAAAATCGATAAACTTTTTCGTGGCATTTCATACAAGCTT
1295937 CTCAAACCAAATCG
391 CTCAAACCAAATCG
* *
1295951 GCTGCCTCTGCTGGTTTGCACCTAGATTGTTTAGTGCAGTAGGGTTGGTATTTAGGTTAGCCTGG
1 GCTGCCTCTGCTGGTTCGCACCTAGATTGTTTAGTGCAGTAGGGTTGGTATTTAGGTTAGCCTAG
*
1296016 GATTGGTTAGTTCGTGGTGGACATAGCAGGACAGTAAGGGATGGGCTATAGGTTGCAGCATACAC
66 GATTGGTTAGTTCGTGGTGGACACAGCAGGACAGTAAGGGATGGGCTATAGGTTGCAGCATACAC
1296081 TGGTTGAGAATGTATCATGACTAGGCCTAGGTACGGTGCACTTGAGTAACAAGGACCGGGTGCTT
131 TGGTTGAGAATGTATCATGACTAGGCCTAGGTACGGTGCACTTGAGTAACAAGGACCGGGTG-TT
1296146 AATGTTGTCTCAATTGTGTTGGGTTGGCATAAC-GATGGCATTGGCCTCTCCCTTCTTTTTCTTG
195 AATGTTGTCTCAATTGTGTTGGGTTGGCATAACTGATGGCATTGGCCTCTCCCTTCTTTTTCTTG
* *
1296210 TTAGCAGTGGCCTTCTTACTCAATTCGGATGACTCTCCTATAGATATTTTGCCACTTTTAATTGC
260 TTAGCAGTGGCCTTCTTACTCAATTCAGATGACTCTCCTATAGATATTTTGCCACTTTTAATTGA
* * *
1296275 TGCATCAATTATTTTGCCATATAAAACAAAATCGATAAACTTTTTCTTGGCATTTCCTACAAGCT
325 TGCAGCAATTATTTTGCCATATAAAACAAAATCGATAAACTTTTTCGTGGCATTTCATACAAGCT
1296340 TCTCAAA
390 TCTCAAA
1296347 GTAAAGAGCA
Statistics
Matches: 377, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
404 342 0.91
405 35 0.09
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (404 bp):
GCTGCCTCTGCTGGTTCGCACCTAGATTGTTTAGTGCAGTAGGGTTGGTATTTAGGTTAGCCTAG
GATTGGTTAGTTCGTGGTGGACACAGCAGGACAGTAAGGGATGGGCTATAGGTTGCAGCATACAC
TGGTTGAGAATGTATCATGACTAGGCCTAGGTACGGTGCACTTGAGTAACAAGGACCGGGTGTTA
ATGTTGTCTCAATTGTGTTGGGTTGGCATAACTGATGGCATTGGCCTCTCCCTTCTTTTTCTTGT
TAGCAGTGGCCTTCTTACTCAATTCAGATGACTCTCCTATAGATATTTTGCCACTTTTAATTGAT
GCAGCAATTATTTTGCCATATAAAACAAAATCGATAAACTTTTTCGTGGCATTTCATACAAGCTT
CTCAAACCAAATCG
Found at i:1297486 original size:43 final size:43
Alignment explanation
Indices: 1297425--1297511 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1297415 ATGATAGTGG
* *
1297425 ATATGATAATGAATGACTAGTGATATGGATGCGTGATCAAGAC
1 ATATGATAATGAATGACTAGTGATATGGATGCATAATCAAGAC
*
1297468 ATATGATAATGAATGACTAGTGATGTGGATGCATAATCAAGAC
1 ATATGATAATGAATGACTAGTGATATGGATGCATAATCAAGAC
1297511 A
1 A
1297512 ATTAAATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (43 bp):
ATATGATAATGAATGACTAGTGATATGGATGCATAATCAAGAC
Found at i:1299712 original size:20 final size:20
Alignment explanation
Indices: 1299689--1299761 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1299679 ACAATTCAAA
1299689 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1299709 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1299730 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
1299750 GTATCAATACAT
1 GTATCGATACAT
1299762 AAAAAAGATG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1299733 original size:21 final size:21
Alignment explanation
Indices: 1299707--1299782 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1299697 ACATGTTGCA
1299707 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1299728 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
* *
1299748 ATGTATCAATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1299769 ATGTATCGATACAT
1 ATGTATCGATACAT
1299783 TTCTTGGCAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1299740 original size:41 final size:41
Alignment explanation
Indices: 1299689--1299782 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1299679 ACAATTCAAA
* *
1299689 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
1299730 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
1299771 GTATCGATACAT
1 GTATCGATACAT
1299783 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
Found at i:1299839 original size:13 final size:13
Alignment explanation
Indices: 1299821--1299846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1299811 TACAGCAAGT
1299821 ATGTATCGATACA
1 ATGTATCGATACA
1299834 ATGTATCGATACA
1 ATGTATCGATACA
1299847 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1303929 original size:15 final size:15
Alignment explanation
Indices: 1303909--1303939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1303899 TAAAAATGTC
*
1303909 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1303924 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1303939 C
1 C
1303940 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1306032 original size:20 final size:21
Alignment explanation
Indices: 1305953--1306031 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1305943 AATGTCCAAA
*
1305953 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
1305973 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
1305998 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
1306018 TTGTATCGATACAT
1 ATGTATCGATACAT
1306032 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:1306036 original size:13 final size:13
Alignment explanation
Indices: 1306018--1306056 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1306008 ACATTTTTCT
1306018 TTGTATCGATACA
1 TTGTATCGATACA
1306031 TTGTATCGATACA
1 TTGTATCGATACA
*
1306044 CTGTATCGATACA
1 TTGTATCGATACA
1306057 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1308519 original size:20 final size:20
Alignment explanation
Indices: 1308496--1308568 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1308486 ACAATTCAAA
1308496 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1308516 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1308537 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
1308557 GTATCAATACAT
1 GTATCGATACAT
1308569 AAAAAAGATG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1308540 original size:21 final size:21
Alignment explanation
Indices: 1308514--1308589 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1308504 ACATGTTGCA
1308514 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1308535 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
* *
1308555 ATGTATCAATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1308576 ATGTATCGATACAT
1 ATGTATCGATACAT
1308590 TTCTTGGCAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1308547 original size:41 final size:41
Alignment explanation
Indices: 1308496--1308589 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1308486 ACAATTCAAA
* *
1308496 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
1308537 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
1308578 GTATCGATACAT
1 GTATCGATACAT
1308590 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
Found at i:1308646 original size:13 final size:13
Alignment explanation
Indices: 1308628--1308653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1308618 TACAGCAAGT
1308628 ATGTATCGATACA
1 ATGTATCGATACA
1308641 ATGTATCGATACA
1 ATGTATCGATACA
1308654 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1310956 original size:18 final size:18
Alignment explanation
Indices: 1310933--1310969 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1310923 GTATGGAGAC
1310933 ATCTGAATGACTTGGGAT
1 ATCTGAATGACTTGGGAT
1310951 ATCTGAATGACTTGGGAT
1 ATCTGAATGACTTGGGAT
1310969 A
1 A
1310970 AAACCTGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (18 bp):
ATCTGAATGACTTGGGAT
Found at i:1311805 original size:43 final size:43
Alignment explanation
Indices: 1311755--1311855 Score: 184
Period size: 43 Copynumber: 2.3 Consensus size: 43
1311745 CCAGAAGCAC
*
1311755 CTTTTCAATCTTACCTTTCTTTCAAAGGAAATGCTTAGCTTAG
1 CTTTTCAATCTTACCTTTCCTTCAAAGGAAATGCTTAGCTTAG
1311798 CTTTTCAATCTTACCTTTCCTTCAAAGGAAATGCTTAGCTTAG
1 CTTTTCAATCTTACCTTTCCTTCAAAGGAAATGCTTAGCTTAG
*
1311841 CTTTTCAATCATACC
1 CTTTTCAATCTTACC
1311856 AATCCCAACA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.41
Consensus pattern (43 bp):
CTTTTCAATCTTACCTTTCCTTCAAAGGAAATGCTTAGCTTAG
Found at i:1312825 original size:2 final size:2
Alignment explanation
Indices: 1312820--1312846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1312810 TTTTGTGTTT
1312820 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1312847 CCTGCTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1313333 original size:16 final size:16
Alignment explanation
Indices: 1313300--1313337 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1313290 TCAATTTTTT
*
1313300 TAAAAAAATTAACCAC
1 TAAAAAAATTAACAAC
1313316 TAAAAAAATT-ACTAAC
1 TAAAAAAATTAAC-AAC
1313332 TAAAAA
1 TAAAAA
1313338 TTTACTACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAAAATTAACAAC
Found at i:1316609 original size:163 final size:163
Alignment explanation
Indices: 1316296--1316718 Score: 566
Period size: 163 Copynumber: 2.6 Consensus size: 163
1316286 ATTTAAACAT
* *
1316296 TTTTGAAAAATCCATTTATTTTTATGAGATTTTCATTTTTTTCTTTGAAAATCTCTTATTTTCGA
1 TTTTGAAAAATCCATTTATTTTTATGAGTTTTTCA--TTTTTCTTTGAAAATCTCCTATTTTCGA
* **
1316361 AAAATTGAGTTTTCTATTTCATAAATATTTTTGGGGAGGGTTTCTCAGTTCAAAATTTTTAATAT
64 AAAATTGAGTTTT-TATTCCATAAATATTTTCAGGGAGGGTTTCTCAGTTCAAAATTTTTAATAT
* *
1316426 TCATCAAATATCATCATTTAAATTATAGTAAACCAG
128 TCATCAAATATCATCATTTAAATCATAGTAAACCAA
*
1316462 TTTTGAAAAATCCATTTATTTTTATGAGTTTTTCATTTTTCTTTGAAAATCTCCTA-TTTCTAAA
1 TTTTGAAAAATCCATTTATTTTTATGAGTTTTTCATTTTTCTTTGAAAATCTCCTATTTTC-GAA
* * * ** *
1316526 AAACTGAATTTTTAATTCCATAAATGTTTTCAGGG-GTTTTTCTCGGTTCAAAATTTTTAATATT
65 AAATTGAGTTTTT-ATTCCATAAATATTTTCAGGGAGGGTTTCTCAGTTCAAAATTTTTAATATT
*
1316590 CATCAAATATCATCATTTAAATCATAGTAAATCAA
129 CATCAAATATCATCATTTAAATCATAGTAAACCAA
* * * * *
1316625 TTTTGAAAAATTCATTT-CTTTCATGAGTTTTTCATTTATTCCTTG-AAATTTCCTTATTTTCGA
1 TTTTGAAAAATCCATTTATTTTTATGAGTTTTTCATTT-TTCTTTGAAAATCTCC-TATTTTCGA
1316688 AAAATTGAGTTTTTTATTCCATAAATATTTT
64 AAAATTGAG-TTTTTATTCCATAAATATTTT
1316719 TGGGGGAATT
Statistics
Matches: 227, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
162 25 0.11
163 110 0.48
164 58 0.26
166 34 0.15
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (163 bp):
TTTTGAAAAATCCATTTATTTTTATGAGTTTTTCATTTTTCTTTGAAAATCTCCTATTTTCGAAA
AATTGAGTTTTTATTCCATAAATATTTTCAGGGAGGGTTTCTCAGTTCAAAATTTTTAATATTCA
TCAAATATCATCATTTAAATCATAGTAAACCAA
Found at i:1317546 original size:13 final size:13
Alignment explanation
Indices: 1317528--1317553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1317518 ACACATCCAG
1317528 ATGTATCGATACA
1 ATGTATCGATACA
1317541 ATGTATCGATACA
1 ATGTATCGATACA
1317554 TGTTCATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1319849 original size:19 final size:21
Alignment explanation
Indices: 1319821--1319860 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1319811 AATGCGCTTA
*
1319821 AGAAAGGAAAA-AA-CGAATT
1 AGAAAAGAAAATAACCGAATT
1319840 AGAAAAGAAAATAACCGAATT
1 AGAAAAGAAAATAACCGAATT
1319861 GCAATTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.12
Consensus pattern (21 bp):
AGAAAAGAAAATAACCGAATT
Found at i:1329624 original size:13 final size:13
Alignment explanation
Indices: 1329606--1329645 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1329596 ACAATATTCC
1329606 TTGTATCAATACA
1 TTGTATCAATACA
*
1329619 TTGTATCCATACA
1 TTGTATCAATACA
*
1329632 TTGTATCGATACA
1 TTGTATCAATACA
1329645 T
1 T
1329646 AGGGTACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:1332283 original size:13 final size:13
Alignment explanation
Indices: 1332265--1332323 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
1332255 CATGGTGCAA
1332265 TGTATCGATACAT
1 TGTATCGATACAT
1332278 TGTATCGATACA-
1 TGTATCGATACAT
1332290 TG-AT-G--AC-T
1 TGTATCGATACAT
1332298 TGTATCGATACAT
1 TGTATCGATACAT
1332311 TGTATCGATACAT
1 TGTATCGATACAT
1332324 GATGACTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 2 0.05
12 4 0.10
13 26 0.65
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1332286 original size:33 final size:33
Alignment explanation
Indices: 1332244--1332343 Score: 166
Period size: 33 Copynumber: 3.0 Consensus size: 33
1332234 CTACCACTGT
* *
1332244 TTGTATCGATACATGGTG-CAATGTATCGATACA
1 TTGTATCGATACATGATGAC-TTGTATCGATACA
1332277 TTGTATCGATACATGATGACTTGTATCGATACA
1 TTGTATCGATACATGATGACTTGTATCGATACA
1332310 TTGTATCGATACATGATGACTTGTATCGATACA
1 TTGTATCGATACATGATGACTTGTATCGATACA
1332343 T
1 T
1332344 AGCTTGTAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 63 0.98
34 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGACTTGTATCGATACA
Found at i:1332302 original size:20 final size:20
Alignment explanation
Indices: 1332277--1332343 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1332267 TATCGATACA
1332277 TTGTATCGATACATGATGAC
1 TTGTATCGATACATGATGAC
1332297 TTGTATCGATAC------A-
1 TTGTATCGATACATGATGAC
1332310 TTGTATCGATACATGATGAC
1 TTGTATCGATACATGATGAC
1332330 TTGTATCGATACAT
1 TTGTATCGATACAT
1332344 AGCTTGTAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.30
14 1 0.03
19 1 0.03
20 26 0.65
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAC
Found at i:1336162 original size:20 final size:19
Alignment explanation
Indices: 1336136--1336220 Score: 92
Period size: 20 Copynumber: 4.6 Consensus size: 19
1336126 ACCACTGTTC
1336136 GTATCGATACATGACACATT
1 GTATCGATACATGACA-ATT
*
1336156 ATATCG----AT-ACAA-T
1 GTATCGATACATGACAATT
1336169 GTATCGATACATGACGAATT
1 GTATCGATACATGAC-AATT
1336189 GTATCGATACATGACAAATT
1 GTATCGATACATGAC-AATT
1336209 GTATCGATACAT
1 GTATCGATACAT
1336221 TGCTTCAAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
13 6 0.11
14 1 0.02
15 3 0.05
16 2 0.04
17 2 0.04
18 2 0.04
19 2 0.04
20 37 0.67
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (19 bp):
GTATCGATACATGACAATT
Found at i:1336178 original size:33 final size:33
Alignment explanation
Indices: 1336136--1336199 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
1336126 ACCACTGTTC
1336136 GTATCGATACATGAC-ACATTATATCGATACAAT
1 GTATCGATACATGACGA-ATTATATCGATACAAT
*
1336169 GTATCGATACATGACGAATTGTATCGATACA
1 GTATCGATACATGACGAATTATATCGATACA
1336200 TGACAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (33 bp):
GTATCGATACATGACGAATTATATCGATACAAT
Found at i:1337012 original size:11 final size:11
Alignment explanation
Indices: 1336996--1337035 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
1336986 TCAACAAGTG
1336996 GAGAAAAAAAA
1 GAGAAAAAAAA
1337007 GAGAAAAAATAA
1 GAGAAAAAA-AA
1337019 -AGAAAAAAAA
1 GAGAAAAAAAA
1337029 GAGAAAA
1 GAGAAAA
1337036 TAGAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (11 bp):
GAGAAAAAAAA
Found at i:1338656 original size:13 final size:13
Alignment explanation
Indices: 1338638--1338668 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1338628 ACATTTCTTC
1338638 ATGTATCGATACA
1 ATGTATCGATACA
1338651 ATGTATCGATACA
1 ATGTATCGATACA
*
1338664 TTGTA
1 ATGTA
1338669 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1338657 original size:33 final size:33
Alignment explanation
Indices: 1338620--1338684 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1338610 TACAAGCTAC
1338620 GTATCGATACATT-T-CTTCATGTATCGATACAAT
1 GTATCGATACATTGTAC--CATGTATCGATACAAT
1338653 GTATCGATACATTGTACCATGTATCGATACAA
1 GTATCGATACATTGTACCATGTATCGATACAA
1338685 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (33 bp):
GTATCGATACATTGTACCATGTATCGATACAAT
Found at i:1338758 original size:19 final size:19
Alignment explanation
Indices: 1338713--1338769 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1338703 CTGCCAGTTT
**
1338713 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1338734 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1338753 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1338770 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.56
21 15 0.44
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1338772 original size:13 final size:13
Alignment explanation
Indices: 1338754--1338780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1338744 TACAATGAAC
1338754 ATGTATCGATACA
1 ATGTATCGATACA
1338767 ATGTATCGATACA
1 ATGTATCGATACA
1338780 A
1 A
1338781 AGCAACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1338794 original size:33 final size:32
Alignment explanation
Indices: 1338735--1338799 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1338725 CAATTTGTCC
*
1338735 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
1338767 ATGTATCGATACAAAGCAACATTTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1338800 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1339386 original size:22 final size:22
Alignment explanation
Indices: 1339333--1339388 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1339323 CCTTAAAAAA
1339333 TTCTCCCCCTTAAACGAATATC
1 TTCTCCCCCTTAAACGAATATC
* *
1339355 TTCACCCCCTTAAAC-AATTATT
1 TTCTCCCCCTTAAACGAA-TATC
*
1339377 TTCTCACCCTTA
1 TTCTCCCCCTTA
1339389 TGTAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.27, C:0.36, G:0.02, T:0.36
Consensus pattern (22 bp):
TTCTCCCCCTTAAACGAATATC
Found at i:1340858 original size:150 final size:150
Alignment explanation
Indices: 1340587--1340883 Score: 585
Period size: 150 Copynumber: 2.0 Consensus size: 150
1340577 AAACAACCTT
1340587 CGAAGAAGGTTTGGTTTTGCGAATTTGAGGAGGAGGCACCTCGAGGACGTCGTTGTGCGGTTAAT
1 CGAAGAAGGTTTGGTTTTGCGAATTTGAGGAGGAGGCACCTCGAGGACGTCGTTGTGCGGTTAAT
*
1340652 TTCATCCGATGAGCCATTGGACGAGTTAAAGAAAAGTTTGGTGAAAAATTGAAAAGTTTTAGGTG
66 TTCATCCGATGAGCCATTGGACGAGTTAAAGAAAAGTTTGGTGAAAAATCGAAAAGTTTTAGGTG
1340717 TTCTAGGCGATAGGTGTAGG
131 TTCTAGGCGATAGGTGTAGG
1340737 CGAAGAAGGTTTGGTTTTGCGAATTTGAGGAGGAGGCACCTCGAGGACGTCGTTGTGCGGTTAAT
1 CGAAGAAGGTTTGGTTTTGCGAATTTGAGGAGGAGGCACCTCGAGGACGTCGTTGTGCGGTTAAT
1340802 TTCATCCGATGAGCCATTGGACGAGTTAAAGAAAAGTTTGGTGAAAAATCGAAAAGTTTTAGGTG
66 TTCATCCGATGAGCCATTGGACGAGTTAAAGAAAAGTTTGGTGAAAAATCGAAAAGTTTTAGGTG
1340867 TTCTAGGCGATAGGTGT
131 TTCTAGGCGATAGGTGT
1340884 GGGGGCTGCC
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 146 1.00
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.29
Consensus pattern (150 bp):
CGAAGAAGGTTTGGTTTTGCGAATTTGAGGAGGAGGCACCTCGAGGACGTCGTTGTGCGGTTAAT
TTCATCCGATGAGCCATTGGACGAGTTAAAGAAAAGTTTGGTGAAAAATCGAAAAGTTTTAGGTG
TTCTAGGCGATAGGTGTAGG
Found at i:1341385 original size:13 final size:13
Alignment explanation
Indices: 1341367--1341406 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1341357 ATAGTACCCT
*
1341367 ATGTATCCATACA
1 ATGTATCGATACA
1341380 ATGTATCGATACA
1 ATGTATCGATACA
1341393 ATGTATCGATACA
1 ATGTATCGATACA
1341406 A
1 A
1341407 GGAATATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1347883 original size:3 final size:3
Alignment explanation
Indices: 1347875--1347907 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1347865 TCAACCATCA
*
1347875 ATG ATG ATG AAG ATG AT- ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1347908 AATTGACTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:1347897 original size:17 final size:17
Alignment explanation
Indices: 1347875--1347907 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1347865 TCAACCATCA
1347875 ATGATGATGAAGATGAT
1 ATGATGATGAAGATGAT
*
1347892 ATGATGATGATGATGA
1 ATGATGATGAAGATGA
1347908 AATTGACTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (17 bp):
ATGATGATGAAGATGAT
Found at i:1352342 original size:20 final size:20
Alignment explanation
Indices: 1352317--1352354 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1352307 GAAATTCCCA
*
1352317 CAATGTATCTATATATTATT
1 CAATGTATCGATATATTATT
1352337 CAATGTATCGATATATTA
1 CAATGTATCGATATATTA
1352355 CATCTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
CAATGTATCGATATATTATT
Found at i:1352411 original size:13 final size:13
Alignment explanation
Indices: 1352393--1352417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1352383 AAGTTCTTTA
1352393 TATCGATACATTG
1 TATCGATACATTG
1352406 TATCGATACATT
1 TATCGATACATT
1352418 ATAAAATGTA
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:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1355318 original size:11 final size:11
Alignment explanation
Indices: 1355302--1355326 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1355292 AAATAAGCTC
1355302 CAACAAGTCAA
1 CAACAAGTCAA
1355313 CAACAAGTCAA
1 CAACAAGTCAA
1355324 CAA
1 CAA
1355327 TGGCTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.28, G:0.08, T:0.08
Consensus pattern (11 bp):
CAACAAGTCAA
Found at i:1364627 original size:13 final size:13
Alignment explanation
Indices: 1364609--1364635 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1364599 ACAAAGATCA
1364609 AATGTATCGATAC
1 AATGTATCGATAC
1364622 AATGTATCGATAC
1 AATGTATCGATAC
1364635 A
1 A
1364636 CTAAGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1364631 original size:34 final size:32
Alignment explanation
Indices: 1364588--1364655 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 32
1364578 AAACTTCCCA
1364588 AATGTATCGATACA-AAGATCAAATGTATCGATAC
1 AATGTATCGATACACAAG-T--AATGTATCGATAC
1364622 AATGTATCGATACACTAAGTAATGTATCGATAC
1 AATGTATCGATACAC-AAGTAATGTATCGATAC
1364655 A
1 A
1364656 TTTCCTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 14 0.44
34 14 0.44
35 1 0.03
36 3 0.09
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (32 bp):
AATGTATCGATACACAAGTAATGTATCGATAC
Found at i:1365689 original size:166 final size:166
Alignment explanation
Indices: 1365502--1365805 Score: 445
Period size: 166 Copynumber: 1.8 Consensus size: 166
1365492 TTCTTCTTCG
1365502 TAAATTTTTTCGAGAGGA-TTTTCATGGGTTTAAAATTTTGAAAATTCATCAAATATTATTATTT
1 TAAATTTTTTCGAGAGGATTTTTC-TGGGTTTAAAATTTTGAAAATTCATCAAATATTATTATTT
* * * *
1365566 AATTCATATTAAATC-CTTTTTTAAAAATTAATTTATTTTTATGAGTTTTTGAATTTTTT-TTGA
65 AATTCATATTAAATCAC-TTTTCAAAAATTAATTCATCTTCATGAGTTTTTGAATTTTTTCTTGA
1365629 AATTCTCTTATTTTCAAAATACGGAGTTTTCTACTCTA
129 AATTCTCTTATTTTCAAAATACGGAGTTTTCTACTCTA
* ** * *
1365667 TAAATTTTTTTC-AGAGGGATTTTTCTTGGTTTTTATTTTTTAAAATTCATCAAATATTATTATT
1 TAAA-TTTTTTCGAGA-GGATTTTTCTGGGTTTAAAATTTTGAAAATTCATCAAATATTATTATT
*
1365731 TATTTCATATTAAATCACTTTTCAAAAATTAATTCATCTTCATGAGTTTTTGAATTTTTTCCTTG
64 TAATTCATATTAAATCACTTTTCAAAAATTAATTCATCTTCATGAGTTTTTGAATTTTTT-CTTG
1365796 AAATTCTCTT
128 AAATTCTCTT
1365806 TTTCTGAAAA
Statistics
Matches: 123, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
165 7 0.06
166 97 0.79
167 6 0.05
168 13 0.11
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (166 bp):
TAAATTTTTTCGAGAGGATTTTTCTGGGTTTAAAATTTTGAAAATTCATCAAATATTATTATTTA
ATTCATATTAAATCACTTTTCAAAAATTAATTCATCTTCATGAGTTTTTGAATTTTTTCTTGAAA
TTCTCTTATTTTCAAAATACGGAGTTTTCTACTCTA
Found at i:1368255 original size:79 final size:79
Alignment explanation
Indices: 1368125--1368703 Score: 423
Period size: 79 Copynumber: 7.3 Consensus size: 79
1368115 CTGATGGTGG
** * *** * * * *
1368125 AAAATCGATGTTTT-GATAATAAAATTGAGGTTGGGGTATCGCCTCAGAAATAATGGGGTTGGAG
1 AAAATCGATGTTTTGGA-AATAAAACCGAGATTAAAGTATCCCCTCAAAAATAACGGGGTTAGAG
* *
1368189 TATCCCCAATTATGA
65 TATCCCCGATTGTGA
* * * * ** *
1368204 AAAATCGATGTTTTAGAAATAAAGCCGAGATTAAAGCATCCCCTCGAAAATAATAGGATTAGAGT
1 AAAATCGATGTTTTGGAAATAAAACCGAGATTAAAGTATCCCCTCAAAAATAACGGGGTTAGAGT
1368269 ATCCCCGATTGTGA
66 ATCCCCGATTGTGA
* * * * * * *
1368283 AAAATC-AGTGTTTTAGAAATAAAAACTAGGGGTTAGAGTATCCCCTC-GAAATAACAGGGTTAG
1 AAAATCGA-TGTTTTGGAAAT-AAAAC-CGAGATTAAAGTATCCCCTCAAAAATAACGGGGTTAG
* *
1368346 ATTATCCCCGATGGTGA
63 AGTATCCCCGATTGTGA
* * * * * *
1368363 AAAATCGATGTTTTGGAAATAAAATCGGGGTTGAAGTATCCCCTTAAAAATAATGGGGTTAGAGT
1 AAAATCGATGTTTTGGAAATAAAACCGAGATTAAAGTATCCCCTCAAAAATAACGGGGTTAGAGT
* *
1368428 ATCCTCGATGGTGA
66 ATCCCCGATTGTGA
* * *
1368442 AAAATCGATGTTTTGGAAATAAAACCG-GAGTTAAAGTATCCTCTAAAAAATAACGGGGTTGGAG
1 AAAATCGATGTTTTGGAAATAAAACCGAGA-TTAAAGTATCCCCTCAAAAATAACGGGGTTAGAG
* * * *
1368506 TATCCTCAATTATTAA
65 TATCCCCGATT-GTGA
* * * ** * *
1368522 AAAATC-ATTTTTTTGGAAACAAAACC-AAAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGA
1 AAAATCGA-TGTTTTGGAAATAAAACCGAGA-TTAAAGTATCCCCTCAAAAATAACGGGGTTAGA
*
1368585 GTATCCTCGATTGTGA
64 GTATCCCCGATTGTGA
* * * * * ** * *** *** *
1368601 AAAATCGGTATTTTGGAAATAAAACTGGGGTTGGAGTATCCCTTTGGAAATAATAAGGTTGGAGT
1 AAAATCGATGTTTTGGAAATAAAACCGAGATTAAAGTATCCCCTCAAAAATAACGGGGTTAGAGT
*
1368666 ATCCCTGATTGTGA
66 ATCCCCGATTGTGA
* *
1368680 AAAATTGGTGTTTTGGAAATAAAA
1 AAAATCGATGTTTTGGAAATAAAA
1368704 ACATGAATGA
Statistics
Matches: 411, Mismatches: 77, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
78 18 0.04
79 261 0.64
80 116 0.28
81 16 0.04
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
AAAATCGATGTTTTGGAAATAAAACCGAGATTAAAGTATCCCCTCAAAAATAACGGGGTTAGAGT
ATCCCCGATTGTGA
Found at i:1368574 original size:238 final size:237
Alignment explanation
Indices: 1368112--1368703 Score: 645
Period size: 238 Copynumber: 2.5 Consensus size: 237
1368102 TGGAGTACAT
* * * * * * *
1368112 TCCCTGATGGTGGAAAATCGATGTTTT-GATAATAAAATTGAGGTTGGGGTATCGCCTCAGAAAT
1 TCCCCGATGGTGAAAAATCGATGTTTTGGA-AATAAAATCGGGGTTGGAGTATCCCCTTAGAAAT
* * * *
1368176 AATGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTAGAAATAAAGCCGAGATTAAAGC
65 AATGGGGTTGGAGTAT-CCCGATTGTGAAAAATCGATGTTTTGGAAATAAAACCGAGATTAAAGC
** * * *
1368241 ATCCCCTCGAAAATAATAGGATTAGAGTATCCCCGATTGTGAAAAATCAGTGTTTTAGAAATAAA
129 ATCCCCTAAAAAATAACAGGATTAGAGTATCCCCAATTGTAAAAAATCAGTGTTTTAGAAATAAA
* ** *
1368306 AACTAGGGGTTAGAGTATCCCCTCGAAATAACAGGGTTAGATTA
194 AACCAGAAGTTAGAGTATCCCCTCGAAATAACAGGGTTAGAGTA
* *
1368350 TCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGAAGTATCCCCTTAAAAATA
1 TCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAGAAATA
* * *
1368415 ATGGGGTTAGAGTATCCTCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCG-GAGTTAAAGT
66 ATGGGGTTGGAGTATCC-CGATTGTGAAAAATCGATGTTTTGGAAATAAAACCGAGA-TTAAAGC
* * * * * * * * * *
1368479 ATCCTCTAAAAAATAACGGGGTTGGAGTATCCTCAATTATTAAAAAATCATTTTTTTGGAAA-CA
129 ATCCCCTAAAAAATAACAGGATTAGAGTATCCCCAATT-GTAAAAAATCAGTGTTTTAGAAATAA
* * *
1368543 AAACCA-AAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTA
193 AAACCAGAAGTTAGAGTATCCCCTC-GAAATAACAGGGTTAGAGTA
* * * * * *
1368588 TCCTCGATTGTGAAAAATCGGTATTTTGGAAATAAAA-CTGGGGTTGGAGTATCCCTTTGGAAAT
1 TCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAATC-GGGGTTGGAGTATCCCCTTAGAAAT
** * *
1368652 AATAAGGTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAA
65 AATGGGGTTGGAGTATCCC-GATTGTGAAAAATCGATGTTTTGGAAATAAAA
1368704 ACATGAATGA
Statistics
Matches: 295, Mismatches: 52, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
237 21 0.07
238 254 0.86
239 20 0.07
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (237 bp):
TCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAGAAATA
ATGGGGTTGGAGTATCCCGATTGTGAAAAATCGATGTTTTGGAAATAAAACCGAGATTAAAGCAT
CCCCTAAAAAATAACAGGATTAGAGTATCCCCAATTGTAAAAAATCAGTGTTTTAGAAATAAAAA
CCAGAAGTTAGAGTATCCCCTCGAAATAACAGGGTTAGAGTA
Found at i:1368705 original size:159 final size:157
Alignment explanation
Indices: 1368125--1368703 Score: 506
Period size: 159 Copynumber: 3.6 Consensus size: 157
1368115 CTGATGGTGG
* * * * * * **
1368125 AAAATCGATGTTTT-GATAATAAAATTGAGGTTGGGGTATCGCCTCAGAAATAATGGGGTTGGAG
1 AAAATCGGTGTTTTGGA-AATAAAACTGGGGTTAGAGTATC-CCTCTGAAATAATAAGGTTGGAG
** * * * * * * *
1368189 TATCCCCAATTATGAAAAATCGATGTTTTAGAAATAAAGCC-GAGATTAAAGCATCCCCTCGAAA
64 TATCCCTGATTGTGAAAAATCGATGTTTTGGAAATAAAACCAAAG-TTGAAGTATCCCCTCAAAA
** * *
1368253 ATAATAGGATTAGAGTATCCCCGATTGTGA
128 ATAACGGGGTTAGAGTATCCTCGATTGTGA
* * * * *
1368283 AAAATCAGTGTTTTAGAAATAAAAACTAGGGGTTAGAGTATCCC-CTCGAAATAACAGGGTTAGA
1 AAAATCGGTGTTTTGGAAAT-AAAACT-GGGGTTAGAGTATCCCTCT-GAAATAATAAGGTTGGA
* * * * *** *
1368347 TTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAATCGGGGTTGAAGTATCCCCTTAAAA
63 GTATCCCTGATTGTGAAAAATCGATGTTTTGGAAATAAAACCAAAGTTGAAGTATCCCCTCAAAA
* *
1368412 ATAATGGGGTTAGAGTATCCTCGATGGTGA
128 ATAACGGGGTTAGAGTATCCTCGATTGTGA
* * * * *
1368442 AAAATCGATGTTTTGGAAATAAAACCGGAGTTAAAGTAT-CCTCT-AAAAAATAACGGGGTTGGA
1 AAAATCGGTGTTTTGGAAATAAAACTGGGGTTAGAGTATCCCTCTGAAATAATAA---GGTTGGA
* * * * * *
1368505 GTAT-CCTCAATTATTAAAAAATC-ATTTTTTTGGAAACAAAACCAAAGTTGGAGTATCCCCTCA
63 GTATCCCT-GATT-GTGAAAAATCGA-TGTTTTGGAAATAAAACCAAAGTTGAAGTATCCCCTCA
* *
1368568 GAAATAACGGGGTTGGAGTATCCTCGATTGTGA
125 AAAATAACGGGGTTAGAGTATCCTCGATTGTGA
* * *
1368601 AAAATCGGTATTTTGGAAATAAAACTGGGGTTGGAGTATCCCTTTGGAAATAATAAGGTTGGAGT
1 AAAATCGGTGTTTTGGAAATAAAACTGGGGTTAGAGTATCCCTCT-GAAATAATAAGGTTGGAGT
* *
1368666 ATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAA
65 ATCCCTGATTGTGAAAAATCGATGTTTTGGAAATAAAA
1368704 ACATGAATGA
Statistics
Matches: 335, Mismatches: 69, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
155 6 0.02
156 2 0.01
157 15 0.04
158 54 0.16
159 230 0.69
160 20 0.06
162 8 0.02
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (157 bp):
AAAATCGGTGTTTTGGAAATAAAACTGGGGTTAGAGTATCCCTCTGAAATAATAAGGTTGGAGTA
TCCCTGATTGTGAAAAATCGATGTTTTGGAAATAAAACCAAAGTTGAAGTATCCCCTCAAAAATA
ACGGGGTTAGAGTATCCTCGATTGTGA
Found at i:1371057 original size:50 final size:50
Alignment explanation
Indices: 1371003--1371133 Score: 192
Period size: 50 Copynumber: 2.6 Consensus size: 50
1370993 AAAATGCCTA
* * *
1371003 AATGTATCGATACATTG-AGAAATGTATCGATACATCTATGTAAAACCCAT
1 AATGTATCGATACAATGAAG-AATGTATCGATACATCTAGGTAAAACCCAG
* *
1371053 AATGTGTCGATACAATGAAGAATGTATTGATACATCTAGGTAAAACCCAG
1 AATGTATCGATACAATGAAGAATGTATCGATACATCTAGGTAAAACCCAG
*
1371103 AATGTATCGATACAATGAAGGATGTATCGAT
1 AATGTATCGATACAATGAAGAATGTATCGAT
1371134 GCAAATTGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 70 0.97
51 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (50 bp):
AATGTATCGATACAATGAAGAATGTATCGATACATCTAGGTAAAACCCAG
Found at i:1373788 original size:46 final size:46
Alignment explanation
Indices: 1373721--1373812 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
1373711 ATCAAGTTCT
*
1373721 TATCCCTCTTTGAAGGAAATGTTTTGCTGTGACGGGACCATTAACA
1 TATCCCTCTTTGAAGGAAATGTTTTGCTATGACGGGACCATTAACA
*
1373767 TATCCCTCTTTGAAGGAAATGTTTTGCTATGATGGGACCATTAACA
1 TATCCCTCTTTGAAGGAAATGTTTTGCTATGACGGGACCATTAACA
1373813 ATTCAGGTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (46 bp):
TATCCCTCTTTGAAGGAAATGTTTTGCTATGACGGGACCATTAACA
Found at i:1374772 original size:122 final size:122
Alignment explanation
Indices: 1374546--1374776 Score: 345
Period size: 122 Copynumber: 1.9 Consensus size: 122
1374536 TCATCTTGTC
* * * * *
1374546 TGATCTTTTTGGGAGCCATGTCTACCGCCATGACGCTACGTAAATGGGACTTTCTCTTGGATCTG
1 TGATCTTTTTGGAAGCCATGTCTACCACCATAACGCTACGTAAATGAGACTTTCTCTTGGATCTC
* ** * *
1374611 CTAACAGCCCATTCTTCAGTCATGCCTACTATGATATTGATAATGCCAATAACTATT
66 CTAACAGCCCATTCCTCAGTCACACCCACTATGACATTGATAATGCCAATAACTATT
* *
1374668 TGATTTTTTTGGAAGCCATGTCTACCACCATAATGCTACGTAAATGAGACTTTCTCTTGGATCTC
1 TGATCTTTTTGGAAGCCATGTCTACCACCATAACGCTACGTAAATGAGACTTTCTCTTGGATCTC
*
1374733 CTAGCAGCCCATTCCTCAGTCACACCCACTATGACATTGATAAT
66 CTAACAGCCCATTCCTCAGTCACACCCACTATGACATTGATAAT
1374777 AACAGGGTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
122 96 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (122 bp):
TGATCTTTTTGGAAGCCATGTCTACCACCATAACGCTACGTAAATGAGACTTTCTCTTGGATCTC
CTAACAGCCCATTCCTCAGTCACACCCACTATGACATTGATAATGCCAATAACTATT
Found at i:1376846 original size:21 final size:21
Alignment explanation
Indices: 1376813--1376853 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1376803 CAAAGTAAAA
*
1376813 ATACATATTGTATCGATACAT
1 ATACATATTGTATCAATACAT
1376834 ATAC-TATTGGTATCAATACA
1 ATACATATT-GTATCAATACA
1376854 CAAGGTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
ATACATATTGTATCAATACAT
Found at i:1377000 original size:10 final size:10
Alignment explanation
Indices: 1376987--1377027 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
1376977 ATCTTATTTT
1376987 TCACTATTCA
1 TCACTATTCA
1376997 TCACTATTCA
1 TCACTATTCA
1377007 TCACTATTCA
1 TCACTATTCA
* *
1377017 TAACTGTTCA
1 TCACTATTCA
1377027 T
1 T
1377028 GTATCGATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.41
Consensus pattern (10 bp):
TCACTATTCA
Found at i:1379234 original size:21 final size:21
Alignment explanation
Indices: 1379183--1379267 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
1379173 TAATATTCTG
* *
1379183 GAAAAGAAATTAAATGAATTA
1 GAAAAGAAAATAAATGAGTTA
** * *
1379204 GAGGACAAAATGAATGAGTTA
1 GAAAAGAAAATAAATGAGTTA
*
1379225 GAAAAGAAAAAAAATGAGTT-
1 GAAAAGAAAATAAATGAGTTA
*
1379245 GCAAAATGAAAAT-GATGAGTTA
1 G-AAAA-GAAAATAAATGAGTTA
1379267 G
1 G
1379268 CTAATAAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 5
0.73 0.20 0.08
Matches are distributed among these distances:
20 1 0.02
21 41 0.85
22 6 0.12
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.20
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAGTTA
Found at i:1388079 original size:17 final size:17
Alignment explanation
Indices: 1388038--1388081 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1388028 ATTCTTGTCT
* *
1388038 TAAATAAATATTTATTC
1 TAAATAAATATATATCC
1388055 -AAATTAAATATATATCC
1 TAAA-TAAATATATATCC
1388072 TAAATAAATA
1 TAAATAAATA
1388082 ATACAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAAATATATATCC
Found at i:1391508 original size:16 final size:16
Alignment explanation
Indices: 1391479--1391529 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1391469 TTTCATAGAT
**
1391479 AAAAGAAACCAAAGAA
1 AAAAGAAAAAAAAGAA
1391495 AAAA-AATAAAAAAGACA
1 AAAAGAA-AAAAAAGA-A
1391512 AAAAGGAAAAAAAAGAA
1 AAAA-GAAAAAAAAGAA
1391529 A
1 A
1391530 GGAGTTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 2 0.07
16 10 0.34
17 7 0.24
18 8 0.28
19 2 0.07
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAAAAGAA
Found at i:1392440 original size:20 final size:21
Alignment explanation
Indices: 1392415--1392467 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1392405 ATCGATACAT
*
1392415 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
* *
1392435 TGTATCAATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
1392456 TGTATCGATACA
1 TGTATCGATACA
1392468 GGTGATTGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:1392529 original size:15 final size:14
Alignment explanation
Indices: 1392509--1392541 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1392499 GTATCGATAC
1392509 ATACAAGATGTATCG
1 ATACAA-ATGTATCG
1392524 ATAC-AATGTATCG
1 ATACAAATGTATCG
1392537 ATACA
1 ATACA
1392542 TGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ATACAAATGTATCG
Found at i:1392534 original size:13 final size:13
Alignment explanation
Indices: 1392516--1392541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1392506 TACATACAAG
1392516 ATGTATCGATACA
1 ATGTATCGATACA
1392529 ATGTATCGATACA
1 ATGTATCGATACA
1392542 TGACCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1392560 original size:34 final size:32
Alignment explanation
Indices: 1392498--1392562 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
1392488 CTTAACTGTT
1392498 TGTATCGATACATACAAGATGTATCGATACAA
1 TGTATCGATACATACAAGATGTATCGATACAA
1392530 TGTATCGATACATGACCAA-ATTGTATCGATACA
1 TGTATCGATACAT-A-CAAGA-TGTATCGATACA
1392563 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 2 0.07
34 15 0.50
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATACAAGATGTATCGATACAA
Found at i:1398702 original size:13 final size:13
Alignment explanation
Indices: 1398684--1398708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1398674 CAGTATTCTC
1398684 TGTATCGATACAG
1 TGTATCGATACAG
1398697 TGTATCGATACA
1 TGTATCGATACA
1398709 AAAGGTTTAT
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1399187 original size:21 final size:21
Alignment explanation
Indices: 1399143--1399184 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1399133 TCTCTAGGCA
*
1399143 GCACTCACCAGGTCGCGACCG
1 GCACTCACCAGGTCGCAACCG
1399164 GCACTC-CCAGGTCGCAACCG
1 GCACTCACCAGGTCGCAACCG
1399184 G
1 G
1399185 GCAGCCCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.19, C:0.43, G:0.29, T:0.10
Consensus pattern (21 bp):
GCACTCACCAGGTCGCAACCG
Found at i:1400616 original size:22 final size:22
Alignment explanation
Indices: 1400570--1400612 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
1400560 TGATTAAAGA
1400570 AAATTGTTTTATTAAGGGGGAG
1 AAATTGTTTTATTAAGGGGGAG
1400592 AAATT-TTTT-TTAAGGGGGAG
1 AAATTGTTTTATTAAGGGGGAG
1400612 A
1 A
1400613 GAAAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.57
21 4 0.19
22 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (22 bp):
AAATTGTTTTATTAAGGGGGAG
Found at i:1401164 original size:13 final size:13
Alignment explanation
Indices: 1401146--1401170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1401136 ATAATGCACA
1401146 GTATCGATACATT
1 GTATCGATACATT
1401159 GTATCGATACAT
1 GTATCGATACAT
1401171 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1403926 original size:2 final size:2
Alignment explanation
Indices: 1403919--1403950 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1403909 ACTAATTTGC
*
1403919 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1403951 TTTTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1404125 original size:2 final size:2
Alignment explanation
Indices: 1404120--1404148 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1404110 ACGCTCTCTG
1404120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1404149 ATCACAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1405023 original size:20 final size:22
Alignment explanation
Indices: 1404986--1405027 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1404976 TGCATTACCA
1404986 AAAATATTTAACTATTTTAATT
1 AAAATATTTAACTATTTTAATT
*
1405008 AAAATTTTTAA-T-TTTTAATT
1 AAAATATTTAACTATTTTAATT
1405028 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AAAATATTTAACTATTTTAATT
Found at i:1405412 original size:24 final size:24
Alignment explanation
Indices: 1405378--1405449 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
1405368 TTAATTACAT
1405378 TTAATTAAATTGAGTTTAAAAAAAA
1 TTAA-TAAATTGAGTTTAAAAAAAA
* * * *
1405403 TT-ATCAAATTGGGCTCAAATAAAA
1 TTAAT-AAATTGAGTTTAAAAAAAA
* *
1405427 TTAATAAGTTGAATTTAAAAAAA
1 TTAATAAATTGAGTTTAAAAAAA
1405450 GATCAAATTC
Statistics
Matches: 35, Mismatches: 10, Indels: 5
0.70 0.20 0.10
Matches are distributed among these distances:
23 1 0.03
24 30 0.86
25 4 0.11
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (24 bp):
TTAATAAATTGAGTTTAAAAAAAA
Found at i:1409171 original size:20 final size:21
Alignment explanation
Indices: 1409138--1409178 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1409128 TATATACTTC
*
1409138 ATAAATATATAAATAT-ATAA
1 ATAAATATACAAATATGATAA
*
1409158 ATAAATATGCAAATATGATAA
1 ATAAATATACAAATATGATAA
1409179 CTAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
ATAAATATACAAATATGATAA
Found at i:1410291 original size:18 final size:18
Alignment explanation
Indices: 1410265--1410328 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
1410255 AGAGGACATC
*
1410265 AAAAATAATAAATAAGAT
1 AAAATTAATAAATAAGAT
* ***
1410283 AAAATTAATATATTTTAT
1 AAAATTAATAAATAAGAT
**
1410301 TGAATTAAATAAATAAGAT
1 AAAATT-AATAAATAAGAT
1410320 AAAATTAAT
1 AAAATTAAT
1410329 TGATAATAAT
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAATTAATAAATAAGAT
Found at i:1410362 original size:83 final size:83
Alignment explanation
Indices: 1410272--1410515 Score: 263
Period size: 90 Copynumber: 2.9 Consensus size: 83
1410262 ATCAAAAATA
* * *
1410272 ATAAATAAGATAAAATTAATATATTTTATTGAATTAAATAAATAAGATAAAATTAATTGATAATA
1 ATAAATAAGATAAAATTAATATATTTTATTAAATTAAATGAATGAGATAAAATTAATTGATAATA
* *
1410337 ATTTTTATATTATGCACT
66 ATTTTTATATTATGAACC
* * * * **
1410355 GTGAATAATATAAAATTAATATATGTTATTAAATTCTATGAATGAGATAAAATTAATTGATAATA
1 ATAAATAAGATAAAATTAATATATTTTATTAAATTAAATGAATGAGATAAAATTAATTG---AT-
*
1410420 AAAATTAATTTTTATATTGTGAACC
62 --AA-TAATTTTTATATTATGAACC
* * * * * *
1410445 ATAAATAAGATAAAATTAATATATTATATTAAATTTAATGATTGAGAGAAAATTAATTGGTACTA
1 ATAAATAAGATAAAATTAATATATTTTATTAAATTAAATGAATGAGATAAAATTAATTGATAATA
1410510 ATTTTT
66 ATTTTT
1410516 TTGTGATAAA
Statistics
Matches: 131, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
83 58 0.44
84 1 0.01
86 2 0.02
87 1 0.01
89 2 0.02
90 67 0.51
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (83 bp):
ATAAATAAGATAAAATTAATATATTTTATTAAATTAAATGAATGAGATAAAATTAATTGATAATA
ATTTTTATATTATGAACC
Found at i:1412104 original size:42 final size:43
Alignment explanation
Indices: 1412045--1412129 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 43
1412035 ATAAACTTGT
1412045 ATGTAACTCTCTTATGTTTATGTTAG-TTTTCTTATTTTAAGC
1 ATGTAACTCTCTTATGTTTATGTTAGTTTTTCTTATTTTAAGC
1412087 ATGTAACTCTCTTATGTTTATGTTAGTTTTTCTTATTTTAAGC
1 ATGTAACTCTCTTATGTTTATGTTAGTTTTTCTTATTTTAAGC
1412130 TTTGTTCTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 26 0.62
43 16 0.38
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (43 bp):
ATGTAACTCTCTTATGTTTATGTTAGTTTTTCTTATTTTAAGC
Found at i:1413145 original size:10 final size:11
Alignment explanation
Indices: 1413124--1413152 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1413114 ATATGAGCAT
1413124 GAAAAGAATGG
1 GAAAAGAATGG
1413135 GAAAA-AATGG
1 GAAAAGAATGG
1413145 GAAAAGAA
1 GAAAAGAA
1413153 CCATAACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (11 bp):
GAAAAGAATGG
Found at i:1418202 original size:1 final size:1
Alignment explanation
Indices: 1418196--1418247 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
1418186 AAATCTTCAC
* * * ***
1418196 TTTTTTTTTGTTTTTTTTGTTTTTTCTTTTTTTTTACCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1418248 ACAATTGCCA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.02, C:0.06, G:0.04, T:0.88
Consensus pattern (1 bp):
T
Found at i:1418224 original size:26 final size:26
Alignment explanation
Indices: 1418195--1418247 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1418185 CAAATCTTCA
*
1418195 CTTTTTTTTT-GTTTTTTTTGTTTTTT
1 CTTTTTTTTTACTTTTTTTT-TTTTTT
1418221 CTTTTTTTTTACCTTTTTTTTTTTTTT
1 CTTTTTTTTTA-CTTTTTTTTTTTTTT
1418248 ACAATTGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 6 0.25
28 8 0.33
ACGTcount: A:0.02, C:0.08, G:0.04, T:0.87
Consensus pattern (26 bp):
CTTTTTTTTTACTTTTTTTTTTTTTT
Found at i:1418237 original size:18 final size:17
Alignment explanation
Indices: 1418216--1418249 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
1418206 TTTTTTTTGT
1418216 TTTTTCTTTTTTTTTACC
1 TTTTT-TTTTTTTTTACC
1418234 TTTTTTTTTTTTTTAC
1 TTTTTTTTTTTTTTAC
1418250 AATTGCCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTTTACC
Found at i:1422939 original size:24 final size:23
Alignment explanation
Indices: 1422904--1422948 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1422894 GCTAACCTGC
* *
1422904 TAAGAAAAAGAGGTGTAGGAGTG
1 TAAGAAAAAGAGATGAAGGAGTG
1422927 TAAGAAGAAAGAGATGAAGGAG
1 TAAGAA-AAAGAGATGAAGGAG
1422949 GATCGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (23 bp):
TAAGAAAAAGAGATGAAGGAGTG
Found at i:1423253 original size:21 final size:21
Alignment explanation
Indices: 1423200--1423253 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1423190 GATGCTTGTC
*
1423200 CTTGTTTCCTGAATGTTGGCT
1 CTTGTTTCCTGTATGTTGGCT
1423221 CTTGTTTCCTGTATGTTGGCT
1 CTTGTTTCCTGTATGTTGGCT
1423242 CTTGTTTCCTGT
1 CTTGTTTCCTGT
1423254 TGAAATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.06, C:0.20, G:0.22, T:0.52
Consensus pattern (21 bp):
CTTGTTTCCTGTATGTTGGCT
Found at i:1426289 original size:33 final size:32
Alignment explanation
Indices: 1426233--1426299 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
1426223 GTTACAAGCT
1426233 ATGTATCGATACATTTCTTCATGTATCCATACA
1 ATGTATCGATACATTTC-TCATGTATCCATACA
*
1426266 ATGTATCGATACATTGTAC-CATGTATCGATACA
1 ATGTATCGATACATT-T-CTCATGTATCCATACA
1426299 A
1 A
1426300 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCCATACA
Found at i:1426373 original size:19 final size:19
Alignment explanation
Indices: 1426328--1426384 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1426318 CTGCCAATTT
**
1426328 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1426349 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1426368 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1426385 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.56
21 15 0.44
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1426387 original size:13 final size:13
Alignment explanation
Indices: 1426369--1426395 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1426359 TACAATGAAC
1426369 ATGTATCGATACA
1 ATGTATCGATACA
1426382 ATGTATCGATACA
1 ATGTATCGATACA
1426395 A
1 A
1426396 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1426410 original size:33 final size:32
Alignment explanation
Indices: 1426350--1426414 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1426340 CAATTTGTCC
*
1426350 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
1426382 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1426415 TTCAAGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1426934 original size:17 final size:17
Alignment explanation
Indices: 1426912--1426969 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
1426902 GTTTTTGTTT
1426912 TTCTCCCCTTAAAAATA
1 TTCTCCCCTTAAAAATA
*
1426929 TTCTCCCCCTTAAACGAT-
1 TTCT-CCCCTTAAA-AATA
*
1426947 TATCTCCTCTTAAAAA-A
1 T-TCTCCCCTTAAAAATA
1426964 TTCTCC
1 TTCTCC
1426970 TCTTTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 18 0.53
19 5 0.15
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (17 bp):
TTCTCCCCTTAAAAATA
Found at i:1427048 original size:41 final size:40
Alignment explanation
Indices: 1426972--1427048 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
1426962 AATTCTCCTC
* *
1426972 TTTTTATATCTTCTCCCCCTTTTTTATATATAAAAATTTA
1 TTTTCATATCTTCTCCCCCTTTTTTATATAAAAAAATTTA
1427012 TTTTCATATACTTCTCCCCCTTTTTGT-TATAAAAAAA
1 TTTTCATAT-CTTCTCCCCCTTTTT-TATATAAAAAAA
1427049 GTAATAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 8 0.24
41 24 0.73
42 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.01, T:0.51
Consensus pattern (40 bp):
TTTTCATATCTTCTCCCCCTTTTTTATATAAAAAAATTTA
Found at i:1435040 original size:13 final size:13
Alignment explanation
Indices: 1435022--1435052 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1435012 GCATTTCTTC
1435022 ATGTATCGATACA
1 ATGTATCGATACA
1435035 ATGTATCGATACA
1 ATGTATCGATACA
*
1435048 TTGTA
1 ATGTA
1435053 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1438619 original size:21 final size:21
Alignment explanation
Indices: 1438586--1438630 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1438576 TTGCAAGTTG
*
1438586 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1438608 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1438628 AAA
1 AAA
1438631 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1440455 original size:15 final size:15
Alignment explanation
Indices: 1440435--1440465 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1440425 TAAAAATGTC
*
1440435 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1440450 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1440465 C
1 C
1440466 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1442534 original size:13 final size:13
Alignment explanation
Indices: 1442516--1442541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1442506 ATATTTTTCT
1442516 TTGTATCGATACA
1 TTGTATCGATACA
1442529 TTGTATCGATACA
1 TTGTATCGATACA
1442542 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1442705 original size:20 final size:20
Alignment explanation
Indices: 1442662--1442707 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1442652 AAATCTTTTG
1442662 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1442683 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1442703 CAAAA
1 CAAAA
1442708 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1445114 original size:13 final size:13
Alignment explanation
Indices: 1445096--1445121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1445086 TACAGCAAGT
1445096 ATGTATCGATACA
1 ATGTATCGATACA
1445109 ATGTATCGATACA
1 ATGTATCGATACA
1445122 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1447372 original size:21 final size:21
Alignment explanation
Indices: 1447339--1447383 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1447329 TTGCAAGTTG
*
1447339 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1447361 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1447381 AAA
1 AAA
1447384 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1449208 original size:15 final size:15
Alignment explanation
Indices: 1449188--1449218 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1449178 TAAAAATGTC
*
1449188 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1449203 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1449218 C
1 C
1449219 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1451311 original size:20 final size:20
Alignment explanation
Indices: 1451232--1451311 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1451222 AATGTCCAAA
*
1451232 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1451252 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1451277 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1451297 TTGTATCGATACATT
1 ATGTATCGATACATT
1451312 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1451315 original size:13 final size:13
Alignment explanation
Indices: 1451297--1451322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1451287 ACATTTTTCT
1451297 TTGTATCGATACA
1 TTGTATCGATACA
1451310 TTGTATCGATACA
1 TTGTATCGATACA
1451323 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1451486 original size:20 final size:20
Alignment explanation
Indices: 1451443--1451488 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1451433 AAATCTTTTG
1451443 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1451464 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1451484 CAAAA
1 CAAAA
1451489 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1453895 original size:13 final size:13
Alignment explanation
Indices: 1453877--1453902 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1453867 TACAGCAAGT
1453877 ATGTATCGATACA
1 ATGTATCGATACA
1453890 ATGTATCGATACA
1 ATGTATCGATACA
1453903 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1455638 original size:21 final size:21
Alignment explanation
Indices: 1455597--1455640 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1455587 CTCCCCTTTA
* *
1455597 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1455618 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1455639 TC
1 TC
1455641 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1457463 original size:13 final size:13
Alignment explanation
Indices: 1457445--1457470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1457435 ATAATCACCC
1457445 TGTATCGATACAA
1 TGTATCGATACAA
1457458 TGTATCGATACAA
1 TGTATCGATACAA
1457471 AGAAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1459569 original size:15 final size:15
Alignment explanation
Indices: 1459549--1459579 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1459539 ATTTCGTTTG
*
1459549 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1459564 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1459579 G
1 G
1459580 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1460976 original size:20 final size:20
Alignment explanation
Indices: 1460953--1461025 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1460943 ACAATTCAAA
1460953 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1460973 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1460994 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1461014 GTATCGATACAT
1 GTATCGATACAT
1461026 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1460997 original size:21 final size:21
Alignment explanation
Indices: 1460971--1461046 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1460961 ACATGTTGCA
1460971 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1460992 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1461012 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1461033 ATGTATCGATACAT
1 ATGTATCGATACAT
1461047 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1461004 original size:41 final size:41
Alignment explanation
Indices: 1460953--1461046 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1460943 ACAATTCAAA
*
1460953 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1460994 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1461035 GTATCGATACAT
1 GTATCGATACAT
1461047 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1461103 original size:13 final size:13
Alignment explanation
Indices: 1461085--1461110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1461075 TACAGCAAGT
1461085 ATGTATCGATACA
1 ATGTATCGATACA
1461098 ATGTATCGATACA
1 ATGTATCGATACA
1461111 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1465192 original size:15 final size:15
Alignment explanation
Indices: 1465172--1465210 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1465162 TAAAAATGTC
*
1465172 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1465187 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
1465202 CCAAATGAA
1 CAAAATGAA
1465211 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Done.