Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008194.1 Hibiscus syriacus cultivar Beakdansim tig00110813_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2426039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1479075 original size:20 final size:20
Alignment explanation
Indices: 1479050--1479099 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1479040 ATTATTTATT
1479050 TCCCTAAATTCAAGGTTTAA
1 TCCCTAAATTCAAGGTTTAA
1479070 TCCCTAAATTCAAGGTTTAA
1 TCCCTAAATTCAAGGTTTAA
1479090 TCCCTAAATT
1 TCCCTAAATT
1479100 TCATACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (20 bp):
TCCCTAAATTCAAGGTTTAA
Found at i:1479193 original size:18 final size:18
Alignment explanation
Indices: 1479166--1479203 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1479156 ATCAACCAAA
1479166 TTAATATATAATTTTTAT
1 TTAATATATAATTTTTAT
*
1479184 TTAATTTATAATTTTTAT
1 TTAATATATAATTTTTAT
1479202 TT
1 TT
1479204 TAAAATGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTAATATATAATTTTTAT
Found at i:1484545 original size:40 final size:40
Alignment explanation
Indices: 1484494--1484581 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
1484484 CGTTTTTTGA
1484494 ACAAACGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
1 ACAAACGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
* * * *
1484534 ACAAACGCCGCAAAAGATCTTACTTTAGTGGCGTTTGTAT
1 ACAAACGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
1484574 ACAAACGC
1 ACAAACGC
1484582 TGCTAAAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (40 bp):
ACAAACGCCGCAAAAAACCTAACTTTAGAGGCGTTTGTAT
Found at i:1484683 original size:41 final size:41
Alignment explanation
Indices: 1484476--1484940 Score: 394
Period size: 41 Copynumber: 11.3 Consensus size: 41
1484466 TAGCGGTATT
* * *
1484476 TTTAGCGGCGTTTTT-TGAACAAACGCCGCAAAAAAC-C-TAAC
1 TTTAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTCGT-AC
* * * *
1484517 TTTAGAGGCGTTTGTATACAAACGCCGCAAAAGA-TCTTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
1484557 TTTAGTGGCGTTTGTATACAAACGCTGCTAAAGATTAGTA-
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * * *
1484597 TTGTAGTGGCGTTTTTACACAAACGTCGGTATAGAATCGTTC
1 TT-TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
*
1484639 TTTAAG-GGCGCTTTTATACAAACGCCGCTAAAGACTCGTAC
1 TTT-AGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * *
1484680 TTTAGTGGCGTTTTTATA-AAAGCGCTGCTATA-ACTCATAC
1 TTTAGTGGCGTTTTTATACAAA-CGCCGCTAAAGACTCGTAC
* * * * *
1484720 TTTACTGGCGTTTTTATAAAAACGCTGCTATA-ACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
1484760 TTTAGTGGCGTTTTTGTTTACAAATGCCGCTATAGACTCATAC
1 TTTAGTGGCG-TTTT-TATACAAACGCCGCTAAAGACTCGTAC
* * * *
1484803 TTTAGTGGCGTTTTTGTTTACAAACGTCGCTATAGACTTGTAC
1 TTTAGTGGCG-TTTT-TATACAAACGCCGCTAAAGACTCGTAC
*
1484846 TTTAGTGGCGTTTTTATAAAAACGCCG-TAAAAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCT-AAAGACTCGTAC
** *
1484887 GCTAGTGGCGTTTTTATACAAACGCCG-TAAAAGAATCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCT-AAAGACTCGTAC
*
1484928 TTTTGTGGCGTTT
1 TTTAGTGGCGTTT
1484941 GTACCGCAAA
Statistics
Matches: 360, Mismatches: 50, Indels: 28
0.82 0.11 0.06
Matches are distributed among these distances:
40 109 0.30
41 171 0.47
42 23 0.06
43 57 0.16
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:1487609 original size:43 final size:42
Alignment explanation
Indices: 1487548--1487825 Score: 247
Period size: 43 Copynumber: 6.5 Consensus size: 42
1487538 ATGGTAATTA
1487548 GCGGCGTTTGTATCCAAAAACGCCGCTATATATCCGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATATATCCGACCTTTT
* * *
1487591 GCGGCGTTTGTGTCCAAAAACGCCACTATATGTCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATATATCCGACCTTTT
* * * ** ** *
1487634 ACGACGTTTGTTCTAAAAACGCCAG-TATAGGTCTTATCTTTT
1 GCGGCGTTTGTTCCAAAAACGCC-GCTATATATCCGACCTTTT
* * *
1487676 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-CTATCATTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATATATCCGA-CCTTTT
* * * * * ** *
1487719 GCGACGTTTTTTCTAGAAACGCTGCTATATATCATAACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATATATC-CGACCTTTT
*
1487762 GCGGCGTTTATTCCAAAAACGCCGCTATAGATAT-CGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTAT--ATATCCGACCTTTT
*
1487805 GCGGCGTTTGTTCAAAAAACG
1 GCGGCGTTTGTTCCAAAAACG
1487826 TCGTAATAGA
Statistics
Matches: 190, Mismatches: 37, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
42 54 0.28
43 131 0.69
44 1 0.01
45 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATATATCCGACCTTTT
Found at i:1487724 original size:85 final size:84
Alignment explanation
Indices: 1487552--1487825 Score: 252
Period size: 85 Copynumber: 3.2 Consensus size: 84
1487542 TAATTAGCGG
* * * ** * *
1487552 CGTTTGTATCCAAAAACGCCGCTATATATCCGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCAC
1 CGTTTGT-TCTAAAAACGCAGCTATAGATCATAACTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* *
1487617 TATATG-TCTGA-CCTTTTACGA
64 TATA-GATCT-ATCATTTTGCGA
* * *
1487638 CGTTTGTTCTAAAAACGCCAG-TATAGGTCTTATCTTTTGCGGCGTTTGTATCCAAAAACGCCGC
1 CGTTTGTTCTAAAAACG-CAGCTATAGATCATAACTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
1487702 TATAGATCTATCATTTTGCGA
64 TATAGATCTATCATTTTGCGA
* * * * *
1487723 CGTTTTTTCTAGAAACGCTGCTATATATCATAACTTTTTGCGGCGTTTATTCCAAAAACGCCGCT
1 CGTTTGTTCTAAAAACGCAGCTATAGATCATAAC-TTTTGCGGCGTTTGTTCCAAAAACGCCGCT
*
1487788 ATAGA--TATCGACCTTTTGCGG
65 ATAGATCTATC-A--TTTTGCGA
*
1487809 CGTTTGTTCAAAAAACG
1 CGTTTGTTCTAAAAACG
1487826 TCGTAATAGA
Statistics
Matches: 157, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
83 4 0.03
84 5 0.03
85 104 0.66
86 44 0.28
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (84 bp):
CGTTTGTTCTAAAAACGCAGCTATAGATCATAACTTTTGCGGCGTTTGTTCCAAAAACGCCGCTA
TAGATCTATCATTTTGCGA
Found at i:1487780 original size:128 final size:129
Alignment explanation
Indices: 1487548--1487825 Score: 305
Period size: 128 Copynumber: 2.2 Consensus size: 129
1487538 ATGGTAATTA
* * *
1487548 GCGGCGTTTGTATCCAAAAACGCCGCTATATATCCGACCTTTTGCGGCGTTTGTGTCCAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCCGACATTTTGCGACGTTTGTGTCCAAAAACG
* * * * * * * *
1487613 CCACTATATGTCTGACCTTTTACGACGTTTGTTCTAAAAACGCCAG-TATAGGTCT-TATCTTTT
66 CCACTATATATCTAACCTTTTACGACGTTTATTCCAAAAACGCC-GCTATAGATATCGACCTTTT
* * * *
1487676 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-CTATCATTTTGCGACGTTT-TTTCTAGAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCCGA-CATTTTGCGACGTTTGTGTCCAAAAAC
** * * *
1487739 GCTGCTATATATCATAACTTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATATCGACCTTT
65 GCCACTATATATC-TAACCTTTTACGACGTTTATTCCAAAAACGCCGCTATAGATATCGACCTTT
1487804 T
129 T
*
1487805 GCGGCGTTTGT-TCAAAAAACG
1 GCGGCGTTTGTATCCAAAAACG
1487826 TCGTAATAGA
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
127 21 0.17
128 87 0.70
129 17 0.14
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (129 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCCGACATTTTGCGACGTTTGTGTCCAAAAACG
CCACTATATATCTAACCTTTTACGACGTTTATTCCAAAAACGCCGCTATAGATATCGACCTTTT
Found at i:1487835 original size:43 final size:43
Alignment explanation
Indices: 1487548--1487856 Score: 190
Period size: 43 Copynumber: 7.2 Consensus size: 43
1487538 ATGGTAATTA
* *
1487548 GCGGCGTTTGTATCCAAAAACGCCGCTAT--ATATCCGACCTTTT
1 GCGGCGTTTAT-TCAAAAAACGCCGCTATAGATAT-CGACCTTTT
* * * *
1487591 GCGGCGTTTGTGTCCAAAAACGCCACTAT--ATGTCTGACCTTTT
1 GCGGCGTTTAT-TCAAAAAACGCCGCTATAGATATC-GACCTTTT
* * * * * * * *
1487634 ACGACGTTTGTTCTAAAAACGCCAG-TATAGGTCT-TATCTTTT
1 GCGGCGTTTATTCAAAAAACGCC-GCTATAGATATCGACCTTTT
* *
1487676 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTATC-A--TTTT
1 GCGGCGTTTAT-TCAAAAAACGCCGCTATAGA--TATCGACCTTTT
* * * * * * * *
1487719 GCGACGTTTTTTCTAGAAACGCTGCTATATATCAT-AACTTTTT
1 GCGGCGTTTATTCAAAAAACGCCGCTATAGAT-ATCGACCTTTT
*
1487762 GCGGCGTTTATTCCAAAAACGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTATTCAAAAAACGCCGCTATAGATATCGACCTTTT
* * * *
1487805 GCGGCGTTTGTTCAAAAAACGTCG-TAATAGATATTGACCTATT
1 GCGGCGTTTATTCAAAAAACGCCGCT-ATAGATATCGACCTTTT
1487848 GCGGCGTTT
1 GCGGCGTTT
1487857 TTTGTTCTCA
Statistics
Matches: 216, Mismatches: 35, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
40 1 0.00
41 3 0.01
42 50 0.23
43 157 0.73
44 2 0.01
45 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTATTCAAAAAACGCCGCTATAGATATCGACCTTTT
Found at i:1487952 original size:18 final size:18
Alignment explanation
Indices: 1487929--1487967 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1487919 TTCCTATCGT
1487929 CGCAAATACTTTTAGCGG
1 CGCAAATACTTTTAGCGG
1487947 CGCAAATACTTTTAGCGG
1 CGCAAATACTTTTAGCGG
1487965 CGC
1 CGC
1487968 TTAAAAACGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (18 bp):
CGCAAATACTTTTAGCGG
Found at i:1488522 original size:21 final size:21
Alignment explanation
Indices: 1488498--1488558 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1488488 AACTTTGAAA
1488498 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1488519 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
1488533 AAATAGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1488554 AAATG
1 AAATG
1488559 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1488604 original size:36 final size:36
Alignment explanation
Indices: 1488490--1488608 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
1488480 TGGTAACCAA
*
1488490 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1488527 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
1488562 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
1488599 -GTTGAAAAAT
1 CTTTGAAAAAT
1488609 GATAATGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 16 0.21
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1493077 original size:21 final size:21
Alignment explanation
Indices: 1493053--1493113 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1493043 AACTTTGAAA
1493053 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1493074 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1493088 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1493109 AAATG
1 AAATG
1493114 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1493144 original size:37 final size:37
Alignment explanation
Indices: 1493045--1493163 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
1493035 TGGTAACCAA
1493045 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1493082 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1493117 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1493154 -GTTGAAAAAT
1 CTTTGAAAAAT
1493164 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1494730 original size:19 final size:19
Alignment explanation
Indices: 1494702--1494740 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1494692 AAGTGATGCT
*
1494702 TAAAAATTATATATTGATA
1 TAAAAATTATATATCGATA
*
1494721 TAAAATTTATATATCGATA
1 TAAAAATTATATATCGATA
1494740 T
1 T
1494741 GAGTAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (19 bp):
TAAAAATTATATATCGATA
Found at i:1494996 original size:38 final size:38
Alignment explanation
Indices: 1494954--1495027 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
1494944 TGTCGGAGTC
*
1494954 GGTGG-AAGATATACATTTTTCAGGCCGGGTCGGGTTCG
1 GGTGGTAAG-TATACATTTTTCAGGCCGGGTAGGGTTCG
* * * *
1494992 GGTGGTATGTATATATTTTTCTGGTCGGGTAGGGTT
1 GGTGGTAAGTATACATTTTTCAGGCCGGGTAGGGTT
1495028 TACAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 28 0.93
39 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.36, T:0.36
Consensus pattern (38 bp):
GGTGGTAAGTATACATTTTTCAGGCCGGGTAGGGTTCG
Found at i:1511123 original size:20 final size:20
Alignment explanation
Indices: 1511077--1511137 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
1511067 TTCCCCTGTG
*
1511077 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCAATT-CCC-TC-AA
*
1511100 GGGGGAATCGATTCCCTCAA
1 GGGGGAATCAATTCCCTCAA
*
1511120 GGGGGGATCAATTCCCTC
1 GGGGGAATCAATTCCCTC
1511138 TGTACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.53
21 2 0.06
22 3 0.09
23 11 0.32
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (20 bp):
GGGGGAATCAATTCCCTCAA
Found at i:1513701 original size:3 final size:3
Alignment explanation
Indices: 1513693--1513753 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
1513683 TTCATTTTAA
** * * *
1513693 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT AAT AGT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1513741 ATT ATTT ATT ATT
1 ATT A-TT ATT ATT
1513754 TAAATATTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1514582 original size:13 final size:13
Alignment explanation
Indices: 1514564--1514591 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1514554 CCACCGTTAT
1514564 GGTGGTCGGCGGC
1 GGTGGTCGGCGGC
1514577 GGTGGTCGGCGGC
1 GGTGGTCGGCGGC
1514590 GG
1 GG
1514592 AGTACGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.64, T:0.14
Consensus pattern (13 bp):
GGTGGTCGGCGGC
Found at i:1515301 original size:35 final size:35
Alignment explanation
Indices: 1515226--1515301 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
1515216 TTACTTAATT
*
1515226 TTTATTATTTTAATATATTTTAAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACTTTA
* * *
1515261 ATTATTGTTTTACTATATTATAAAT-ATATA-TATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACT-TTA
1515296 TTTATT
1 TTTATT
1515302 TAATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACTTTA
Found at i:1522546 original size:83 final size:83
Alignment explanation
Indices: 1522402--1522743 Score: 548
Period size: 83 Copynumber: 4.1 Consensus size: 83
1522392 AAATGTAATG
1522402 TGCTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCA
1 TGCT-CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCA
* *
1522466 TTGAATTTGGAAGATGAATA
64 TTGAATTTAGAAGATGAATT
*
1522486 TGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCAT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCAT
*
1522550 TTAATTTAGAAGATGAATT
65 TGAATTTAGAAGATGAATT
1522569 TGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
*
1522633 GGAATTTAGAAGATGAATT
65 TGAATTTAGAAGATGAATT
*
1522652 TGC-CAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
*
1522716 TGAATTTGGAAGATGAATT
65 TGAATTTAGAAGATGAATT
1522735 TGCTCATAG
1 TGCTCATAG
1522744 TAGAAATAAG
Statistics
Matches: 244, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
82 1 0.00
83 234 0.96
84 9 0.04
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (83 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
GAATTTAGAAGATGAATT
Found at i:1526039 original size:76 final size:76
Alignment explanation
Indices: 1525913--1526600 Score: 1216
Period size: 76 Copynumber: 9.0 Consensus size: 76
1525903 CTATTTCTCA
* *
1525913 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAGGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1525978 ATCCTTCGGGT
66 AACCTTCGGGT
*
1525989 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1526054 AGCCTTCGGGT
66 AACCTTCGGGT
*
1526065 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1526130 ATCCTTCGGGT
66 AACCTTCGGGT
1526141 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1526206 AACCTTTGGGT
66 AACCTTCGGGT
*
1526217 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1526282 AAACCTTCGGGT
65 AAACCTTCGGGT
*
1526294 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1526359 ATCCTTCGGGT
66 AACCTTCGGGT
1526370 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1526435 AACCTTCGGGT
66 AACCTTCGGGT
1526446 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1526511 AGCCTTCGGGT
66 AACCTTCGGGT
* *
1526522 CATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1526586 AACCCTCAGGGT
66 AACCTTC-GGGT
1526598 CAT
1 CAT
1526601 TCATAAGACC
Statistics
Matches: 592, Mismatches: 18, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
75 6 0.01
76 513 0.87
77 73 0.12
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGT
Found at i:1526463 original size:305 final size:305
Alignment explanation
Indices: 1525913--1526600 Score: 1247
Period size: 305 Copynumber: 2.3 Consensus size: 305
1525903 CTATTTCTCA
* *
1525913 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGAGGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1525977 AATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1526042 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
131 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
1526107 CGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
196 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
*
1526172 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTTGGGT
261 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
*
1526217 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1526282 AAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1526347 TGATGTTTTCAAATCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
131 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1526412 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
196 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
*
1526477 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
261 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
*
1526522 CATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAA-CCTTCGGGAGCTTTTTGATGTTTTC-
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1526585 AAACCCTCAGGGTCAT
66 AAACCTTC-GGGTCAT
1526601 TCATAAGACC
Statistics
Matches: 370, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
303 7 0.02
304 62 0.17
305 301 0.81
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (305 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
Found at i:1526764 original size:3 final size:3
Alignment explanation
Indices: 1526756--1526828 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
1526746 TTCATTTTAA
**
1526756 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1526804 ATT ATT AGT AAT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT
1526829 TAAATATTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1526772 original size:15 final size:15
Alignment explanation
Indices: 1526754--1526837 Score: 89
Period size: 15 Copynumber: 5.6 Consensus size: 15
1526744 TTTTCATTTT
1526754 AAATTATTATTATTA
1 AAATTATTATTATTA
1526769 AAATTATTATTATTA
1 AAATTATTATTATTA
**
1526784 TTATTATTATTATTA
1 AAATTATTATTATTA
** *
1526799 TTATTATTATTAGTA
1 AAATTATTATTATTA
* *
1526814 ATATTATTTATTATTT
1 AAATTA-TTATTATTA
1526830 AAA-TATTA
1 AAATTATTA
1526838 CAAAGCCCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
14 3 0.05
15 49 0.80
16 9 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:1528343 original size:54 final size:52
Alignment explanation
Indices: 1528242--1528345 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 52
1528232 ATAATTTTAC
* * * *
1528242 ATTTATTATTATTTTATTTATTTATAGTCATTGTTTAGTTATTTTTTACTTA
1 ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTTTTTACTTA
1528294 ATTT-TTATTATTTTAATATATTT-TAAATCATTACTTTAATTATTGTTTTACT
1 ATTTATTATTATTTT-ATATATTTAT-AATCATT-CTTTAATTATT-TTTTACT
1528346 ATATTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
51 11 0.25
52 17 0.39
53 9 0.20
54 7 0.16
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (52 bp):
ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTTTTTACTTA
Found at i:1528372 original size:35 final size:35
Alignment explanation
Indices: 1528297--1528372 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
1528287 TTACTTAATT
*
1528297 TTTATTATTTTAATATATTTTAAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACTTTA
* * *
1528332 ATTATTGTTTTACTATATTATAAAT-ATATA-TATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACT-TTA
1528367 TTTATT
1 TTTATT
1528373 TAATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACTTTA
Found at i:1532527 original size:23 final size:23
Alignment explanation
Indices: 1532501--1532592 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 23
1532491 TTTTATACGG
*
1532501 TCCTTCGGGATATTTCTACGTGA
1 TCCTTCGGGACATTTCTACGTGA
* * * ** *
1532524 TCCTTCAGGACAATACTATATGG
1 TCCTTCGGGACATTTCTACGTGA
*
1532547 TCCTTCGGGACATTTCTATGTGA
1 TCCTTCGGGACATTTCTACGTGA
1532570 -CACTTCGGTG-CAATTTCTACGTG
1 TC-CTTCGG-GAC-ATTTCTACGTG
1532593 GCACTCCGGT
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.02
23 41 0.77
24 11 0.21
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (23 bp):
TCCTTCGGGACATTTCTACGTGA
Found at i:1532588 original size:24 final size:24
Alignment explanation
Indices: 1532558--1532609 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1532548 CCTTCGGGAC
* *
1532558 ATTTCTATGTGACACTTCGGTGCA
1 ATTTCTACGTGACACTCCGGTGCA
* *
1532582 ATTTCTACGTGGCACTCCGGTGTA
1 ATTTCTACGTGACACTCCGGTGCA
1532606 ATTT
1 ATTT
1532610 ATACAAACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
ATTTCTACGTGACACTCCGGTGCA
Found at i:1532764 original size:31 final size:31
Alignment explanation
Indices: 1532729--1532789 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1532719 CATAATGGAA
*
1532729 TATGTCATTATTGGTTAAATATATGATGATG
1 TATGTCATTATTGATTAAATATATGATGATG
* * *
1532760 TATGTTATTGTTGATTAGATATATGATGAT
1 TATGTCATTATTGATTAAATATATGATGAT
1532790 TCCTATACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (31 bp):
TATGTCATTATTGATTAAATATATGATGATG
Found at i:1536241 original size:13 final size:13
Alignment explanation
Indices: 1536223--1536254 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1536213 AATTACCGAA
1536223 ACATTTGAAGTAT
1 ACATTTGAAGTAT
1536236 ACATTTGAAGTAT
1 ACATTTGAAGTAT
*
1536249 GCATTT
1 ACATTT
1536255 TTGGGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (13 bp):
ACATTTGAAGTAT
Found at i:1549442 original size:32 final size:32
Alignment explanation
Indices: 1549406--1549518 Score: 113
Period size: 32 Copynumber: 3.5 Consensus size: 32
1549396 TTGGGGCGTG
* * *
1549406 AGAGCCTACCTAAGGGAGTTCCTTAGGGCATA
1 AGAGCCTACCCAAGGAAGTACCTTAGGGCATA
* *
1549438 AGAGCCTACCCAAGGAAGTACCTTGGGGCCTTA
1 AGAGCCTACCCAAGGAAGTACCTTAGGG-CATA
* * *
1549471 A-AGCCTATCCAAGGAAGTACCTTGGGGCCTTA
1 AGAGCCTACCCAAGGAAGTACCTTAGGG-CATA
*
1549503 A-AGCCTATCCAAGGAA
1 AGAGCCTACCCAAGGAA
1549519 ATGCCTTGGG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
32 70 0.95
33 4 0.05
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (32 bp):
AGAGCCTACCCAAGGAAGTACCTTAGGGCATA
Found at i:1549526 original size:32 final size:32
Alignment explanation
Indices: 1549440--1549548 Score: 173
Period size: 32 Copynumber: 3.4 Consensus size: 32
1549430 AGGGCATAAG
*
1549440 AGCCTACCCAAGGAAGTACCTTGGGGCCTTAA
1 AGCCTATCCAAGGAAGTACCTTGGGGCCTTAA
1549472 AGCCTATCCAAGGAAGTACCTTGGGGCCTTAA
1 AGCCTATCCAAGGAAGTACCTTGGGGCCTTAA
* * *
1549504 AGCCTATCCAAGGAAATGCCTTGGGGCCTCAA
1 AGCCTATCCAAGGAAGTACCTTGGGGCCTTAA
*
1549536 AGCCTAACCAAGG
1 AGCCTATCCAAGG
1549549 TCACCTTAGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (32 bp):
AGCCTATCCAAGGAAGTACCTTGGGGCCTTAA
Found at i:1553797 original size:23 final size:23
Alignment explanation
Indices: 1553746--1553800 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1553736 CAAACGAAAG
*
1553746 CGTGTCATAGAGGTAGAGAAAAA
1 CGTGTTATAGAGGTAGAGAAAAA
1553769 CGTGTTATAGAGGTAGAGAAAAA
1 CGTGTTATAGAGGTAGAGAAAAA
1553792 CGTGTTATA
1 CGTGTTATA
1553801 AATACAGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (23 bp):
CGTGTTATAGAGGTAGAGAAAAA
Found at i:1570632 original size:3 final size:3
Alignment explanation
Indices: 1570624--1570656 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1570614 AAAAATATAT
*
1570624 TTA TTA TTA -TA ATA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1570657 AAAAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1576029 original size:20 final size:19
Alignment explanation
Indices: 1575989--1576035 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1575979 TATAGCAAAA
*
1575989 AGAAAAAAATATAAAATAG
1 AGAAAAAAATATAAAAGAG
1576008 AGAAAAGAAATA-AATAAGAG
1 AGAAAA-AAATATAA-AAGAG
1576028 AGATAAAA
1 AGA-AAAA
1576036 GAAAGCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.33
20 13 0.54
21 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (19 bp):
AGAAAAAAATATAAAAGAG
Found at i:1576062 original size:17 final size:19
Alignment explanation
Indices: 1576032--1576069 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1576022 TAAGAGAGAT
1576032 AAAAGAAAGCAAGAAAGAA
1 AAAAGAAAGCAAGAAAGAA
*
1576051 AAAAG-AAG-AAGAAATAA
1 AAAAGAAAGCAAGAAAGAA
1576068 AA
1 AA
1576070 TAGATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAGAAAGCAAGAAAGAA
Found at i:1578233 original size:54 final size:53
Alignment explanation
Indices: 1578146--1578584 Score: 391
Period size: 54 Copynumber: 8.1 Consensus size: 53
1578136 CCAAACAATA
* * * * * *
1578146 TGATGTCTTCAAATAAATGTTTAAAAAAGCTAAGCTAGATTTTTAGGGATTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAATCTAAGCTA-ATTTTTAGGGGTTTCT
* *
1578200 TGATGTTTTCAAAAGAATTTTTAAAGAATCTAAGTTTAATTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAATCTAAG-CTAATTTTTAGGGGTTTCT
* * * ** *
1578254 TGATATTTTCAAATGAATGTTTAAAGGAGATAAGCTTAAATTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAATCTAAGC-TAATTTTTAGGGGTTTCT
* * * * *
1578308 TGATGTTTTCAAATGAATGTTTAAAGAAGT-TAAGCATGATTTTCAAGGGTTTTT
1 TGATGTTTTCAAATGAATTTTTAAAGAA-TCTAAGC-TAATTTTTAGGGGTTTCT
* * * * **
1578362 TGATGTTTTCAAATAAATTTTTAAAGGATATAAGCTTGATTTTCGGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAATCTAAGC-TAATTTTTAGGGGTTTCT
* * * * *
1578416 TAATGTTTACAAATGGATTTTGAAATAAGT-TAAGCCTAA-TTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAA-TCTAAG-CTAATTTTTAGGGGTTTCT
* * * * * *
1578469 AGATGTTTTCAAATGAATTTATAAAGGAGCTAAGCTTGATTTTTAGGGGTTTTTT
1 TGATGTTTTCAAATGAATTTTTAAAGAATCTAAGC-TAATTTTTAGGGG-TTTCT
*
1578524 TGATGTCTTT-AAATGAATTTTTAAAAGAAACTAAGCCTAATTTTTTAGGGGTTTCT
1 TGATGT-TTTCAAATGAATTTTT-AAAGAATCTAAG-CTAA-TTTTTAGGGGTTTCT
1578580 TGATG
1 TGATG
1578585 ATAACTATAA
Statistics
Matches: 312, Mismatches: 59, Indels: 26
0.79 0.15 0.07
Matches are distributed among these distances:
52 1 0.00
53 39 0.12
54 213 0.68
55 24 0.08
56 24 0.08
57 11 0.04
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (53 bp):
TGATGTTTTCAAATGAATTTTTAAAGAATCTAAGCTAATTTTTAGGGGTTTCT
Found at i:1578298 original size:108 final size:108
Alignment explanation
Indices: 1578146--1578584 Score: 458
Period size: 108 Copynumber: 4.0 Consensus size: 108
1578136 CCAAACAATA
* ** * * *
1578146 TGATGTCTTCAAATAAATGTTTAAAAAAGCTAAGC-TAGATTTTTAGGGATTTCTTGATGTTTTC
1 TGATGTTTTCAAATAAATGTTTAAAGGAGATAAGCTTA-AATTTTAGGGGTTTCTTGATGTTTTC
* **
1578210 AAAAGAATTTTTAAAGAA-TCTAAGTTTAATTTTTAGGGGTTTCT
65 AAATGAATTTTTAAAGAAGT-TAAGCCTAATTTTTAGGGGTTTCT
* *
1578254 TGATATTTTCAAATGAATGTTTAAAGGAGATAAGCTTAAATTTTAGGGGTTTCTTGATGTTTTCA
1 TGATGTTTTCAAATAAATGTTTAAAGGAGATAAGCTTAAATTTTAGGGGTTTCTTGATGTTTTCA
* * * * * *
1578319 AATGAATGTTTAAAGAAGTTAAGCATGATTTTCAAGGGTTTTT
66 AATGAATTTTTAAAGAAGTTAAGCCTAATTTTTAGGGGTTTCT
* * * * * *
1578362 TGATGTTTTCAAATAAATTTTTAAAGGATATAAGCTT-GATTTTCGGGGGTTTCTTAATGTTTAC
1 TGATGTTTTCAAATAAATGTTTAAAGGAGATAAGCTTAAATTTT-AGGGGTTTCTTGATGTTTTC
* * *
1578426 AAATGGATTTTGAAATAAGTTAAGCCTAA-TTTTAGGGGTTTCT
65 AAATGAATTTTTAAAGAAGTTAAGCCTAATTTTTAGGGGTTTCT
* * * * * *
1578469 AGATGTTTTCAAATGAAT-TTATAAAGGAGCTAAGCTTGATTTTTAGGGGTTTTTTTGATGTCTT
1 TGATGTTTTCAAATAAATGTT-TAAAGGAGATAAGCTTAAATTTTAGGGG-TTTCTTGATGT-TT
**
1578533 T-AAATGAATTTTTAAAAGAAACTAAGCCTAATTTTTTAGGGGTTTCT
63 TCAAATGAATTTTT-AAAGAAGTTAAGCCTAA-TTTTTAGGGGTTTCT
1578580 TGATG
1 TGATG
1578585 ATAACTATAA
Statistics
Matches: 272, Mismatches: 49, Indels: 17
0.80 0.14 0.05
Matches are distributed among these distances:
106 2 0.01
107 50 0.18
108 183 0.67
109 19 0.07
111 18 0.07
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (108 bp):
TGATGTTTTCAAATAAATGTTTAAAGGAGATAAGCTTAAATTTTAGGGGTTTCTTGATGTTTTCA
AATGAATTTTTAAAGAAGTTAAGCCTAATTTTTAGGGGTTTCT
Found at i:1578526 original size:162 final size:161
Alignment explanation
Indices: 1578147--1578580 Score: 484
Period size: 162 Copynumber: 2.7 Consensus size: 161
1578137 CAAACAATAT
* * * * *
1578147 GATGTCTTCAAATAAATGTTTAAAAAAGCTAAGCTAGATTTTTAGGGATTTCTTGATGTTTTCAA
1 GATGTTTTCAAATGAATGTTTAAAGAAGCTAAGCTTGATTTTTAGGG-TTTTTTGATGTTTTCAA
* * * * *
1578212 A-AGAATTTTTAAAGAATCTAAGTTTAATTTTTAGGGGTTTCTTGATATTTTCAAATGAATGTTT
65 ATA-AATTTTTAAAGAATATAAGCTTAATTTTCAGGGGTTTCTTAATATTTACAAATGAATGTTT
* * *
1578276 AAAGGAGATAAGCTTAAATTTTAGGGGTTTCTT
129 AAAGAAGATAAGCCTAAATTTTAGGGGTTTCTA
* * *
1578309 GATGTTTTCAAATGAATGTTTAAAGAAGTTAAGCATGATTTTCAAGGGTTTTTTGATGTTTTCAA
1 GATGTTTTCAAATGAATGTTTAAAGAAGCTAAGCTTGATTTT-TAGGGTTTTTTGATGTTTTCAA
* * * * *
1578374 ATAAATTTTTAAAGGATATAAGCTTGATTTTCGGGGGTTTCTTAATGTTTACAAATGGAT-TTTG
65 ATAAATTTTTAAAGAATATAAGCTTAATTTTCAGGGGTTTCTTAATATTTACAAATGAATGTTT-
* *
1578438 AAATAAGTTAAGCCT-AATTTTAGGGGTTTCTA
129 AAAGAAGATAAGCCTAAATTTTAGGGGTTTCTA
*
1578470 GATGTTTTCAAATGAAT-TTATAAAGGAGCTAAGCTTGATTTTTAGGGGTTTTTTTGATGTCTTT
1 GATGTTTTCAAATGAATGTT-TAAAGAAGCTAAGCTTGATTTTTA-GGG-TTTTTTGATGT-TTT
* * *
1578534 -AAATGAATTTTTAAAAGAA-ACTAAGCCTAATTTTTTAGGGGTTTCTT
62 CAAATAAATTTTT-AAAGAATA-TAAGCTTAA-TTTTCAGGGGTTTCTT
1578581 GATGATAACT
Statistics
Matches: 229, Mismatches: 33, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
160 3 0.01
161 58 0.25
162 134 0.59
163 20 0.09
164 14 0.06
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.43
Consensus pattern (161 bp):
GATGTTTTCAAATGAATGTTTAAAGAAGCTAAGCTTGATTTTTAGGGTTTTTTGATGTTTTCAAA
TAAATTTTTAAAGAATATAAGCTTAATTTTCAGGGGTTTCTTAATATTTACAAATGAATGTTTAA
AGAAGATAAGCCTAAATTTTAGGGGTTTCTA
Found at i:1578907 original size:12 final size:14
Alignment explanation
Indices: 1578871--1578929 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
1578861 TCGGGTCGGG
*
1578871 TATATATATTTAAA
1 TATATATATATAAA
*
1578885 T-TAAATATATAAA
1 TATATATATATAAA
*
1578898 -ATATTATATATATA
1 TATA-TATATATAAA
*
1578912 TATATATATATTAA
1 TATATATATATAAA
1578926 TATA
1 TATA
1578930 AATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
13 12 0.33
14 21 0.58
15 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATATATATAAA
Found at i:1582039 original size:118 final size:119
Alignment explanation
Indices: 1581770--1582086 Score: 456
Period size: 118 Copynumber: 2.7 Consensus size: 119
1581760 TCTGTTGAAG
* * * *
1581770 GGTTCGTAATGAGAATAAATCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTATTCA
1 GGTTCGTAATGAGAAGAACTCATCCGATGAGGGAAAATAAGTTCATAATGAGAAGAACTTATTCA
* * * * * * *
1581835 ACCTTAACTTGATTTCATCATAAAAAGTAGGTGGATCAAGATTTCCAATAGAAG
66 ACCTTAGCTCGATTCCATCATAAAAAGAAAGTGGATCAACATTTCCAATAGAAA
* * *
1581889 GGTTCGTAATGAGAAGAACTCATCCGATGAGGGATAATAAGTTCATAAGGAGAAGAATTTATTCA
1 GGTTCGTAATGAGAAGAACTCATCCGATGAGGGAAAATAAGTTCATAATGAGAAGAACTTATTCA
* *
1581954 ACCTTAGCTCGATTCCATCA-CAAAAGAAAGTGGATCAACATTTCCAATGGAAA
66 ACCTTAGCTCGATTCCATCATAAAAAGAAAGTGGATCAACATTTCCAATAGAAA
* * *
1582007 GGTTCGTAATAAGAAGAACTCATCCGAAGAGGGAAAATAATTTCATAATGAGAAGAACTTATTCA
1 GGTTCGTAATGAGAAGAACTCATCCGATGAGGGAAAATAAGTTCATAATGAGAAGAACTTATTCA
1582072 ACCTTAGCTCGATTC
66 ACCTTAGCTCGATTC
1582087 TATTACATAA
Statistics
Matches: 177, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
118 101 0.57
119 76 0.43
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (119 bp):
GGTTCGTAATGAGAAGAACTCATCCGATGAGGGAAAATAAGTTCATAATGAGAAGAACTTATTCA
ACCTTAGCTCGATTCCATCATAAAAAGAAAGTGGATCAACATTTCCAATAGAAA
Found at i:1582118 original size:43 final size:43
Alignment explanation
Indices: 1582070--1582195 Score: 114
Period size: 43 Copynumber: 3.0 Consensus size: 43
1582060 AGAACTTATT
* *
1582070 CAACCTTAGC-TCGATTCTATTACATAAGGAGTTGGAACAACAC
1 CAACCTTAGCTTC-ATTCCATCACATAAGGAGTTGGAACAACAC
** * * *
1582113 CAACCTTTTCTTCATTCCATCATATTAGGAGTTGGAACAACAT
1 CAACCTTAGCTTCATTCCATCACATAAGGAGTTGGAACAACAC
* * * * *
1582156 CGACCTTGGC-TCA-TCCATCGCATAAGGAGGTGGATCAACA
1 CAACCTTAGCTTCATTCCATCACATAAGGAGTTGGAACAACA
1582196 TCATTACTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 22 0.33
42 3 0.04
43 40 0.60
44 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
CAACCTTAGCTTCATTCCATCACATAAGGAGTTGGAACAACAC
Found at i:1597677 original size:23 final size:23
Alignment explanation
Indices: 1597651--1597705 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1597641 TGGTGCAAGA
* *
1597651 GGTATCGATACCC-CCTTTGCATG
1 GGTATCGATACCCTAC-TTGAATG
* *
1597674 GGTACCAATACCCTACTTGAATG
1 GGTATCGATACCCTACTTGAATG
1597697 GGTATCGAT
1 GGTATCGAT
1597706 TGTAACACCC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (23 bp):
GGTATCGATACCCTACTTGAATG
Found at i:1597849 original size:36 final size:36
Alignment explanation
Indices: 1597809--1597879 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
1597799 ATTTAAGAAA
1597809 GTGAGTATTTTACATTAATAATTACAATCAAATTGG
1 GTGAGTATTTTACATTAATAATTACAATCAAATTGG
1597845 GTGAGTATTTTACATTAATAATTACAATCAAATTG
1 GTGAGTATTTTACATTAATAATTACAATCAAATTG
1597880 TTTCTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (36 bp):
GTGAGTATTTTACATTAATAATTACAATCAAATTGG
Found at i:1601830 original size:21 final size:21
Alignment explanation
Indices: 1601806--1601848 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1601796 ATGGAGACAT
*
1601806 TTGACTTACGGTTTGCATCCA
1 TTGACTTACGGTTTACATCCA
*
1601827 TTGATTTACGGTTTACATCCA
1 TTGACTTACGGTTTACATCCA
1601848 T
1 T
1601849 AGAGTTCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (21 bp):
TTGACTTACGGTTTACATCCA
Found at i:1602415 original size:13 final size:12
Alignment explanation
Indices: 1602373--1602416 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 12
1602363 GGAGTAATAA
1602373 TTTTCTCAAAATTG
1 TTTTCT-AAAA-TG
1602387 TTTTCTAAAATG
1 TTTTCTAAAATG
1602399 TTTTCTAAAATG
1 TTTTCTAAAATG
1602411 ATTTTC
1 -TTTTC
1602417 AATAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 14 0.48
13 9 0.31
14 6 0.21
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (12 bp):
TTTTCTAAAATG
Found at i:1602784 original size:19 final size:20
Alignment explanation
Indices: 1602743--1602784 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1602733 AAGACAGATT
*
1602743 CCCCATAGGGTACCGAAACC
1 CCCCAGAGGGTACCGAAACC
*
1602763 CCCCAGAGGGTACCGATACC
1 CCCCAGAGGGTACCGAAACC
1602783 CC
1 CC
1602785 TATGAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.43, G:0.21, T:0.10
Consensus pattern (20 bp):
CCCCAGAGGGTACCGAAACC
Found at i:1606155 original size:31 final size:33
Alignment explanation
Indices: 1606107--1606185 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
1606097 TTTAAATAGT
* *
1606107 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTTTTATTAAATAATATTTATATAAA
*
1606139 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
1606173 TATTATTTATTTA
1 TATTATTTTTTTA
1606186 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:1606177 original size:34 final size:31
Alignment explanation
Indices: 1606097--1606185 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
1606087 TTAGTATTTT
* * *
1606097 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
1606129 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
1606163 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
1606186 GAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:1606346 original size:17 final size:17
Alignment explanation
Indices: 1606324--1606377 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1606314 AATGTTAATA
1606324 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1606341 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1606358 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1606375 TTT
1 TTT
1606378 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1614780 original size:27 final size:26
Alignment explanation
Indices: 1614714--1614791 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
1614704 ACGATGCAAC
*
1614714 AAAAAATTAAAAAGAACTAAATAATA
1 AAAAAATTAAAAACAACTAAATAATA
* * *
1614740 AAAATAATT-CAAACAATTAAGTAATA
1 AAAA-AATTAAAAACAACTAAATAATA
*
1614766 AAAAAATTAAGAAACAAAATAAATAA
1 AAAAAATTAA-AAAC-AACTAAATAA
1614792 AAATCTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
25 4 0.10
26 21 0.51
27 8 0.20
28 8 0.20
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.21
Consensus pattern (26 bp):
AAAAAATTAAAAACAACTAAATAATA
Found at i:1614976 original size:3 final size:3
Alignment explanation
Indices: 1614968--1615003 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1614958 CTCCTCACTC
* *
1614968 TCA TCA TCA TCA TCG TCA TCA TCA TCA ACA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1615004 ATAACATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:1617782 original size:12 final size:12
Alignment explanation
Indices: 1617749--1617793 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1617739 TAAAAAGGTT
*
1617749 AATATTTTTTAA
1 AATATTATTTAA
* *
1617761 TAT-TTTTTTAA
1 AATATTATTTAA
1617772 AATATTATTTAA
1 AATATTATTTAA
1617784 AATATTATTT
1 AATATTATTT
1617794 TTTTTATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AATATTATTTAA
Found at i:1618333 original size:2 final size:2
Alignment explanation
Indices: 1618326--1618360 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1618316 ATAGAATGAA
1618326 AT AT AT 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 AT AT AT A
1618361 GTTTTCTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1618825 original size:21 final size:23
Alignment explanation
Indices: 1618786--1618829 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 23
1618776 TACCACTTAC
1618786 AAATAATATTACTATATTTTAAAA
1 AAATAATATTACTATA-TTTAAAA
1618810 AAAT-ATATTA-TA-ATTTAAAA
1 AAATAATATTACTATATTTAAAA
1618830 TTTTGATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 2 0.10
23 6 0.30
24 4 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAATATTACTATATTTAAAA
Found at i:1619920 original size:18 final size:18
Alignment explanation
Indices: 1619894--1619928 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1619884 TATCATGTGA
*
1619894 CATACTAAAAAAGTATTG
1 CATAATAAAAAAGTATTG
*
1619912 CATAATAAAAAATTATT
1 CATAATAAAAAAGTATT
1619929 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (18 bp):
CATAATAAAAAAGTATTG
Found at i:1620030 original size:23 final size:22
Alignment explanation
Indices: 1620000--1620045 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1619990 ATATTTGATA
*
1620000 ATTTTGAATTATTTATATATTTT
1 ATTTTGAATT-TTTACATATTTT
*
1620023 ATTTTGAATTTTTACATTTTTT
1 ATTTTGAATTTTTACATATTTT
1620045 A
1 A
1620046 AAGAAATTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
ATTTTGAATTTTTACATATTTT
Found at i:1622059 original size:26 final size:26
Alignment explanation
Indices: 1622023--1622073 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1622013 CTGGTAGTTG
*
1622023 ATTTGAGTAGTTGGTTTGACTAACTT
1 ATTTGAGTAGTTGATTTGACTAACTT
* *
1622049 ATTTGATTAGTTGATTTGATTAACT
1 ATTTGAGTAGTTGATTTGACTAACT
1622074 GTTTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.06, G:0.20, T:0.49
Consensus pattern (26 bp):
ATTTGAGTAGTTGATTTGACTAACTT
Found at i:1622068 original size:13 final size:13
Alignment explanation
Indices: 1622017--1622070 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1622007 TAATAGCTGG
*
1622017 TAGTTGATTTGAG
1 TAGTTGATTTGAT
*
1622030 TAGTTGGTTTGACT
1 TAGTTGATTTGA-T
* *
1622044 AACTT-ATTTGAT
1 TAGTTGATTTGAT
1622056 TAGTTGATTTGAT
1 TAGTTGATTTGAT
1622069 TA
1 TA
1622071 ACTGTTTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
12 4 0.12
13 25 0.78
14 3 0.09
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.50
Consensus pattern (13 bp):
TAGTTGATTTGAT
Found at i:1622279 original size:20 final size:21
Alignment explanation
Indices: 1622254--1622294 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1622244 TTTTTTTAAA
1622254 GAAAATTATT-GA-ATATTTTT
1 GAAAATT-TTGGATATATTTTT
1622274 GAAAATTTTGGATATATTTTT
1 GAAAATTTTGGATATATTTTT
1622295 TAAATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 9 0.47
21 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
GAAAATTTTGGATATATTTTT
Found at i:1624466 original size:6 final size:6
Alignment explanation
Indices: 1624420--1624464 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
1624410 AGATTTATGA
* *
1624420 TGATGG TGATGC TGATGC TGATGC TGATGC TGATGC TGAAGC TGA
1 TGATGC TGATGC TGATGC TGATGC TGATGC TGATGC TGATGC TGA
1624465 AGAGGGAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (6 bp):
TGATGC
Found at i:1625151 original size:30 final size:29
Alignment explanation
Indices: 1625117--1625192 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
1625107 TTAATCAAAA
* *
1625117 TATTAATTATTAAAATATTTAAAATATATT
1 TATTAA-TATTATAATATATAAAATATATT
*
1625147 TATTAATATTTATAATAATATAATATATATT
1 TATTAATA-TTATAAT-ATATAAAATATATT
1625178 TA-TAATATTATAATA
1 TATTAATATTATAATA
1625193 AAATAATCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.02
29 9 0.22
30 17 0.41
31 14 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TATTAATATTATAATATATAAAATATATT
Found at i:1625156 original size:21 final size:21
Alignment explanation
Indices: 1625130--1625219 Score: 78
Period size: 21 Copynumber: 4.2 Consensus size: 21
1625120 TAATTATTAA
* * *
1625130 AATATTTAAAATATATTTATT
1 AATATTTATAATATATATAAT
1625151 AATATTTATAATA-ATATAAT
1 AATATTTATAATATATATAAT
1625171 ATATATTTATAATAT-TATAAT
1 A-ATATTTATAATATATATAAT
* *
1625192 AA-AATAATCAATTATATTATAAT
1 AATATTTAT-AA-TATA-TATAAT
1625215 AATAT
1 AATAT
1625220 AAGATATTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.07
20 9 0.16
21 34 0.61
23 8 0.14
24 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATTTATAATATATATAAT
Found at i:1625157 original size:10 final size:9
Alignment explanation
Indices: 1625142--1625192 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
1625132 TATTTAAAAT
1625142 ATATTTATTA
1 ATATTTA-TA
1625152 ATATTTATA
1 ATATTTATA
*
1625161 ATAATATAATA
1 AT-AT-TTATA
1625172 TATATTTATA
1 -ATATTTATA
1625182 ATA-TTATA
1 ATATTTATA
1625190 ATA
1 ATA
1625193 AAATAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 8 0.22
9 7 0.19
10 13 0.36
11 6 0.17
12 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATTTATA
Found at i:1625170 original size:8 final size:8
Alignment explanation
Indices: 1625157--1625221 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
1625147 TATTAATATT
1625157 TATAATAA
1 TATAATAA
1625165 TATAAT-A
1 TATAATAA
*
1625172 TAT-AT-T
1 TATAATAA
*
1625178 TATAATAT
1 TATAATAA
1625186 TATAATAA
1 TATAATAA
*
1625194 AATAATCAA
1 TATAAT-AA
*
1625203 T-T-ATAT
1 TATAATAA
1625209 TATAATAA
1 TATAATAA
1625217 TATAA
1 TATAA
1625222 GATATTATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
6 7 0.15
7 9 0.20
8 28 0.61
9 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
TATAATAA
Found at i:1625172 original size:29 final size:28
Alignment explanation
Indices: 1625139--1625264 Score: 95
Period size: 29 Copynumber: 4.6 Consensus size: 28
1625129 AAATATTTAA
1625139 AATATATTTATTAATATTTATAATAATAT
1 AATATATTTATTAATA-TTATAATAATAT
1625168 AATATATATT-TATAATATTATAAT-A-A-
1 AATATAT-TTAT-TAATATTATAATAATAT
**
1625194 AATA-ATCAATT-ATATTATAATAATAT
1 AATATATTTATTAATATTATAATAATAT
* ** *
1625220 AAGATATTATATTTTTATTTTAATAATATT
1 AATATATT-TATTAATATTATAATAATA-T
*
1625250 AATA-AATTATTAATA
1 AATATATTTATTAATA
1625265 AAAGTTATAT
Statistics
Matches: 76, Mismatches: 11, Indels: 21
0.70 0.10 0.19
Matches are distributed among these distances:
23 10 0.13
24 2 0.03
25 4 0.05
26 7 0.09
27 3 0.04
28 10 0.13
29 29 0.38
30 11 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATATTTATTAATATTATAATAATAT
Found at i:1625215 original size:31 final size:29
Alignment explanation
Indices: 1625140--1625221 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 29
1625130 AATATTTAAA
*
1625140 ATATATTTATTAATATTTATAATAATATAAT
1 ATATATTTA-TAATA-TTATAATAAAATAAT
1625171 ATATATTTATAATATTATAATAAAATAAT
1 ATATATTTATAATATTATAATAAAATAAT
*
1625200 CA-ATTATATTATAATAATATAA
1 -ATA-TAT-TTATAATATTATAA
1625222 GATATTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 15 0.33
30 9 0.20
31 22 0.48
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATATTTATAATATTATAATAAAATAAT
Found at i:1625244 original size:52 final size:52
Alignment explanation
Indices: 1625156--1625259 Score: 124
Period size: 52 Copynumber: 2.0 Consensus size: 52
1625146 TTATTAATAT
*
1625156 TTATAATAATATAATATATATTTATAATATTATAATAA-AATAATCAATTATA
1 TTATAATAATATAATATATATTTAT-ATATTATAATAATAATAATAAATTATA
* *
1625208 TTATAATAATATAAGATATTATATTT-T-TATTTTAATAATATTAATAAATTAT
1 TTATAATAATAT-A-ATA-TATATTTATATATTATAATAATAATAATAAATTAT
1625260 TAATAAAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
52 22 0.49
53 12 0.27
54 4 0.09
55 7 0.16
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (52 bp):
TTATAATAATATAATATATATTTATATATTATAATAATAATAATAAATTATA
Found at i:1625368 original size:23 final size:23
Alignment explanation
Indices: 1625340--1625393 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1625330 ATTTAATATA
**
1625340 AAAATATTTTAATAAATATATTT
1 AAAATATACTAATAAATATATTT
* *
1625363 AAAATATACTAATTAATATTTTT
1 AAAATATACTAATAAATATATTT
1625386 AAAATATA
1 AAAATATA
1625394 ATATAACACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATATACTAATAAATATATTT
Found at i:1625538 original size:20 final size:20
Alignment explanation
Indices: 1625492--1625542 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1625482 TAAAAATTAT
1625492 AAAAATAATATTTAATAATA
1 AAAAATAATATTTAATAATA
* *
1625512 AATAAATTAT-TTTAATATTTA
1 AA-AAATAATATTTAATA-ATA
1625533 AAAAATAATA
1 AAAAATAATA
1625543 ATATTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATAATATTTAATAATA
Found at i:1625695 original size:15 final size:14
Alignment explanation
Indices: 1625663--1625693 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1625653 AAACATCGTT
1625663 AAATATTTTCCAGA
1 AAATATTTTCCAGA
*
1625677 AAATATTTTTCAGA
1 AAATATTTTCCAGA
1625691 AAA
1 AAA
1625694 ATGTAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (14 bp):
AAATATTTTCCAGA
Found at i:1629884 original size:36 final size:36
Alignment explanation
Indices: 1629807--1629964 Score: 194
Period size: 36 Copynumber: 4.4 Consensus size: 36
1629797 AAAGATGAAC
* * * *
1629807 ACTTGAAACGAAAGTG-CGATACATCATTCCATTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCATTCG
*
1629842 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCATTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCATTCG
* * *
1629878 AATTGAATC-AGAAGTGTCGATGCTTCATTCCGTTCG
1 ACTTGAATCGA-AAGTGTCGATGCTTCCTTCCATTCG
* **
1629914 ACTTGAATCGAAAGTGCCGATGCTTCCTTCTGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCCTTCCATTCG
1629950 ACTTGAATCGAAAGT
1 ACTTGAATCGAAAGT
1629965 ACCGATGTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
35 14 0.13
36 92 0.86
37 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGTCGATGCTTCCTTCCATTCG
Found at i:1631818 original size:3 final size:3
Alignment explanation
Indices: 1631812--1631876 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
1631802 TTAAAATATA
* ** *
1631812 ATT ATT ATT ATT AAT ATT ATT AGA ATT ATT AGT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
* * *
1631858 AAT ATT AAT GTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
1631877 CATATATTTT
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1631829 original size:9 final size:9
Alignment explanation
Indices: 1631795--1631864 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
1631785 CCAGGTAAAA
1631795 AATATTATT
1 AATATTATT
*
1631804 AAAATATAATT
1 --AATATTATT
*
1631815 ATTATTATT
1 AATATTATT
1631824 AATATTATT
1 AATATTATT
1631833 AGA-ATTATT
1 A-ATATTATT
*
1631842 AGTATTATT
1 AATATTATT
1631851 --TATTATT
1 AATATTATT
1631858 AATATTA
1 AATATTA
1631865 ATGTTATTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
7 7 0.14
9 34 0.68
10 1 0.02
11 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
AATATTATT
Found at i:1633369 original size:17 final size:17
Alignment explanation
Indices: 1633347--1633388 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1633337 GTTTAAAATA
1633347 TTATTAT-AATAAATATT
1 TTATTATCAATAAAT-TT
*
1633364 TTATTATTCAATATATTT
1 TTATTA-TCAATAAATTT
1633382 TTATTAT
1 TTATTAT
1633389 TTTATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTATCAATAAATTT
Found at i:1636334 original size:6 final size:6
Alignment explanation
Indices: 1636312--1636362 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
1636302 ATCAACATTT
* *
1636312 TTTGCA TATGCA TTTTTGCT TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA
1 TTTGCA TTTGCA --TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA
1636362 T
1 T
1636363 CTTTGCATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 35 0.90
8 4 0.10
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (6 bp):
TTTGCA
Found at i:1639549 original size:10 final size:10
Alignment explanation
Indices: 1639534--1639604 Score: 87
Period size: 10 Copynumber: 7.3 Consensus size: 10
1639524 CTCATAGAAG
1639534 GAAGAAAAAA
1 GAAGAAAAAA
1639544 GAAGAAAAAA
1 GAAGAAAAAA
1639554 GAAG-AAAAA
1 GAAGAAAAAA
1639563 GAAGAAAAAA
1 GAAGAAAAAA
1639573 GAA-AAAGAAA
1 GAAGAAA-AAA
1639583 G-AG-AAAAA
1 GAAGAAAAAA
*
1639591 GAAAAAAGAAA
1 GAAGAAA-AAA
1639602 GAA
1 GAA
1639605 TAAGTAATAA
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
8 4 0.07
9 16 0.30
10 28 0.52
11 6 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
GAAGAAAAAA
Found at i:1639569 original size:29 final size:28
Alignment explanation
Indices: 1639534--1639604 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
1639524 CTCATAGAAG
1639534 GAAGAAAAAAGAAGAAA-AAAGAAGAAAAA
1 GAAGAAAAAAGAA-AAAGAAAG-AGAAAAA
1639563 GAAGAAAAAAGAAAAAGAAAGAGAAAAA
1 GAAGAAAAAAGAAAAAGAAAGAGAAAAA
*
1639591 GAAAAAAGAAAGAA
1 GAAGAAA-AAAGAA
1639605 TAAGTAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 16 0.41
29 23 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (28 bp):
GAAGAAAAAAGAAAAAGAAAGAGAAAAA
Found at i:1639577 original size:6 final size:6
Alignment explanation
Indices: 1639539--1639601 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
1639529 AGAAGGAAGA
* *
1639539 AAAAAG AAGAAA- AAAGAAG AAAAAG -AAGA- AAAAAG AAAAAG AAAGAG
1 AAAAAG AA-AAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1639586 AAAAAG AAAAAAG AAA
1 AAAAAG -AAAAAG AAA
1639602 GAATAAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
5 7 0.15
6 28 0.60
7 12 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1639596 original size:19 final size:18
Alignment explanation
Indices: 1639535--1639604 Score: 92
Period size: 19 Copynumber: 3.9 Consensus size: 18
1639525 TCATAGAAGG
1639535 AAGAAAAAAG-AAGAAAA
1 AAGAAAAAAGAAAGAAAA
1639552 AAGAAGAAAA-AGAAGAAAA
1 AAGAA-AAAAGA-AAGAAAA
1639571 AAG-AAAAAGAAAGAGAAA
1 AAGAAAAAAGAAAGA-AAA
1639589 AAGAAAAAAGAAAGAA
1 AAGAAAAAAGAAAGAA
1639605 TAAGTAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
17 13 0.28
18 13 0.28
19 21 0.45
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAGAAAGAAAA
Found at i:1641105 original size:54 final size:54
Alignment explanation
Indices: 1641016--1641173 Score: 197
Period size: 47 Copynumber: 3.0 Consensus size: 54
1641006 AGCTTCGCTG
*
1641016 ACAAGAAATCT-AGGCAGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTTTT
1 ACAA-AAATCTGA-GCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTT
* *
1641071 ACAAAAATCTGAGCAGAAGCCATAGGAAAGGATGAATGTGTTGTCAAATG----
1 ACAAAAATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTT
* *
1641121 ---AAAATCTGGGCAGAAGCCACAGGAAATGATAAATGTGTTGTCAAATGTTTT
1 ACAAAAATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTT
1641172 AC
1 AC
1641174 GAACCAATGA
Statistics
Matches: 89, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
47 43 0.48
54 41 0.46
55 5 0.06
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (54 bp):
ACAAAAATCTGAGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTT
Found at i:1642202 original size:55 final size:54
Alignment explanation
Indices: 1642094--1642213 Score: 136
Period size: 55 Copynumber: 2.2 Consensus size: 54
1642084 TGGGTTTTTT
* * * *
1642094 AGAAACTAAGTCTGATTTTTATAAGTTTCTTGACGATTTTTAAGTAAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGAC-ATTTTTAAATAAGATTTTAA
*
1642149 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-TTTTTCTCAAATGAA-ATTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACATTTT-T-AAAT-AAGATTTTAA
*
1642204 ATAAACTAAG
1 AGAAACTAAG
1642214 CCTTCGGGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
53 4 0.07
54 1 0.02
55 49 0.88
56 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (54 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACATTTTTAAATAAGATTTTAA
Found at i:1642506 original size:177 final size:178
Alignment explanation
Indices: 1642206--1642608 Score: 675
Period size: 177 Copynumber: 2.3 Consensus size: 178
1642196 AATTTTAAAT
*
1642206 AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCCTCAGTGC
1 AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCCTCAGTAC
* *
1642271 AGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTTTTAATTATCTCAAAATA
66 AGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTCTTAATTATCTCAAAAGA
*
1642336 GTTGTT-AAAGGAAGCTAAG-TCTTTTAAGGGGTTCCTTGATAACTAAG
131 GTTGTTAAAAGGAAGCTAAGCT-TTTTAAGGGGTTCCTTGACAACTAAG
* * * * *
1642383 AAATTAAGCCTTCGAGGGTTTCTTAATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTAC
1 AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCCTCAGTAC
1642448 AGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTCTTAATTATCTCAAAAGA
66 AGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTCTTAATTATCTCAAAAGA
1642513 GTTGTTAAAAGGAAGCTAAGCTTTTTAAGGGGTTCCTTGACAACTAAG
131 GTTGTTAAAAGGAAGCTAAGCTTTTTAAGGGGTTCCTTGACAACTAAG
* * *
1642561 AAACAAAGCCTTCGGGGGTTTCTTGATTTTTAAATCCTTCGGGTCATC
1 AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATC
1642609 AGTAAGTCTT
Statistics
Matches: 208, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
177 128 0.62
178 79 0.38
179 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (178 bp):
AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCCTCAGTAC
AGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTCTTAATTATCTCAAAAGA
GTTGTTAAAAGGAAGCTAAGCTTTTTAAGGGGTTCCTTGACAACTAAG
Found at i:1642649 original size:42 final size:42
Alignment explanation
Indices: 1642590--1642672 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1642580 TTCTTGATTT
* *
1642590 TTAAATCCTTCGGGTCATCAGTAAGTCTTTAGAGCATGATGC
1 TTAAATCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGC
* *
1642632 TTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAAGATG
1 TTAAATCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATG
1642673 ATAAGTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (42 bp):
TTAAATCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGC
Found at i:1643094 original size:95 final size:95
Alignment explanation
Indices: 1642930--1643126 Score: 288
Period size: 95 Copynumber: 2.1 Consensus size: 95
1642920 CCAATGAGGA
* *
1642930 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTAAGGCTATCACAGAATGAGGTGG
1 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTGGTTTAAGGCCATCACAGAATGAGGTGG
1642995 ATCAACA-TTTTCAATGGAGAGTTCATAATG
66 ATCAA-ATTTTTCAATGGAGAGTTCATAATG
* * * ** *
1643025 AGAAGAAATTCATTATGAGAAGGACTTGTTCAACCTTGGTTTGATTCCATCACAGAATGAGGTGT
1 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTGGTTTAAGGCCATCACAGAATGAGGTGG
**
1643090 ATCAAATTTTTTTATGGAGAGTTCATAATG
66 ATCAAATTTTTCAATGGAGAGTTCATAATG
1643120 AGAAGAA
1 AGAAGAA
1643127 CTCATCCAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 1 0.01
95 90 0.99
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (95 bp):
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTGGTTTAAGGCCATCACAGAATGAGGTGG
ATCAAATTTTTCAATGGAGAGTTCATAATG
Found at i:1643146 original size:117 final size:116
Alignment explanation
Indices: 1643025--1643401 Score: 594
Period size: 117 Copynumber: 3.2 Consensus size: 116
1643015 GTTCATAATG
* * * *
1643025 AGAAGAAATTCATTATGAGAAGGACTTGTTCAACCTTGGTTTGATTCCATCACAGAATGAGGTGT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAA-GAGGTGG
** *
1643090 ATCAA-ATTTTTTTATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGA
65 ATCAACA-TTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGA
* *
1643142 AGAAGAATTTCATAATGAGAAGAACTTGTTCAAACTTGGTTTGATTCCATCACAGAAGTAGGTGG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAAG-AGGTGG
* *
1643207 ATCAACATTTTCAATTGAGAGTTCATAATGAGAAGAACTTATCCAATGAGGA
65 ATCAACATTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGA
*
1643259 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGAGGTGG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAA-GAGGTGG
*
1643324 GTCAACATTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGA
65 ATCAACATTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGA
1643376 AGAAGAAGTTCATAATGAGAAGAACT
1 AGAAGAAGTTCATAATGAGAAGAACT
1643402 CATCCAACAA
Statistics
Matches: 242, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
116 1 0.00
117 239 0.99
118 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (116 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAAGAGGTGGA
TCAACATTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGA
Found at i:1643289 original size:20 final size:20
Alignment explanation
Indices: 1643227--1643290 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1643217 TCAATTGAGA
1643227 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * ***
1643247 -ATC-CAATGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACTT
1643266 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1643286 GTTCA
1 GTTCA
1643291 ACCTTGGTTC
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 13 0.42
21 5 0.16
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1643386 original size:39 final size:39
Alignment explanation
Indices: 1643343--1643440 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
1643333 TTCAATAGAG
**
1643343 AGTTCATAATGAGAAGAACTCATCCAATGAG-GAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCAACAAGAG-AGAAGA
1643382 AGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGA
1643421 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1643441 TGTTCAATCC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
39 55 0.98
40 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGA
Found at i:1643398 original size:17 final size:17
Alignment explanation
Indices: 1643376--1643438 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
1643366 CCAATGAGGA
1643376 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* * *
1643393 AGAAGAACTCATCCAACAAGAG
1 AGAAGAAGT--T-C-ATAA-TG
1643415 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
1643432 AGAAGAA
1 AGAAGAA
1643439 CTTGTTCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 16 0.46
18 3 0.09
19 2 0.06
20 2 0.06
21 3 0.09
22 9 0.26
ACGTcount: A:0.51, C:0.11, G:0.22, T:0.16
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:1643624 original size:3 final size:3
Alignment explanation
Indices: 1643618--1643673 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
1643608 TTAAAATATA
* * * *
1643618 ATT ATT ATT ATT AGT ATT ATT AGT ATT ATTT ATT ATT AAT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
*
1643664 GTT ATT ATT A
1 ATT ATT ATT A
1643674 CATATATTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1645316 original size:21 final size:20
Alignment explanation
Indices: 1645292--1645333 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1645282 AATGTCGAGA
1645292 TTTCT-TTTCATATTAAATAAT
1 TTTCTCTTTCA-ATT-AATAAT
*
1645313 TTTCTCTTTTAATTAATAAT
1 TTTCTCTTTCAATTAATAAT
1645333 T
1 T
1645334 CGAAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTCTTTCAATTAATAAT
Found at i:1645794 original size:45 final size:45
Alignment explanation
Indices: 1645744--1645835 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1645734 CAATAGTATC
1645744 ATGCACAAAATGATATCGAACATCAACGGTTTCATCTAACATTTG
1 ATGCACAAAATGATATCGAACATCAACGGTTTCATCTAACATTTG
1645789 ATGCACAAAATGATATCGAACATCAACGGTTTCATCTAACATTTG
1 ATGCACAAAATGATATCGAACATCAACGGTTTCATCTAACATTTG
1645834 AT
1 AT
1645836 CCTTTATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (45 bp):
ATGCACAAAATGATATCGAACATCAACGGTTTCATCTAACATTTG
Found at i:1646392 original size:39 final size:39
Alignment explanation
Indices: 1646338--1646416 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
1646328 CTCCAAAGAG
** *
1646338 AGAAATGCGAATAGTATAGTTTCGAAGAGCGAGCCGTGT
1 AGAAATGCGAATAGTATAGCATCGAAGAGCAAGCCGTGT
*
1646377 AGAAATGCGAATAGTATAGCATCGAAGAGCAAGTCGTGT
1 AGAAATGCGAATAGTATAGCATCGAAGAGCAAGCCGTGT
1646416 A
1 A
1646417 ACTTCAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.22
Consensus pattern (39 bp):
AGAAATGCGAATAGTATAGCATCGAAGAGCAAGCCGTGT
Found at i:1646468 original size:21 final size:21
Alignment explanation
Indices: 1646415--1646472 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
1646405 GCAAGTCGTG
*
1646415 TAACTTCAAGAACGAACAATA
1 TAACTTCAAGAACGAAAAATA
1646436 TAA-TTCCGAAGAAC-AAAAATA
1 TAACTT-C-AAGAACGAAAAATA
1646457 TAACTTCAAAGAACGA
1 TAACTTC-AAGAACGA
1646473 GTCGTATAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 2 0.06
21 20 0.65
22 9 0.29
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.19
Consensus pattern (21 bp):
TAACTTCAAGAACGAAAAATA
Found at i:1646842 original size:14 final size:14
Alignment explanation
Indices: 1646819--1646862 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
1646809 TTCGATTATA
*
1646819 TGTTCGTTTATGTT
1 TGTTCATTTATGTT
1646833 TGTTCATTTATGTT
1 TGTTCATTTATGTT
*
1646847 CGTTCATTTATGTT
1 TGTTCATTTATGTT
1646861 TG
1 TG
1646863 AACAGAGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (14 bp):
TGTTCATTTATGTT
Found at i:1647152 original size:10 final size:10
Alignment explanation
Indices: 1647137--1647205 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
1647127 TCGTTTATTG
1647137 TGTTCGTTTA
1 TGTTCGTTTA
*
1647147 TGTTCGTCTA
1 TGTTCGTTTA
1647157 TGTTCG-TT-
1 TGTTCGTTTA
* **
1647165 CGTTTATGTT-
1 TGTTCGT-TTA
* *
1647175 CGTTCGTTTG
1 TGTTCGTTTA
1647185 TGTTCGTTTA
1 TGTTCGTTTA
1647195 TGTTCGTTTA
1 TGTTCGTTTA
1647205 T
1 T
1647206 TATTTAAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 41 0.87
ACGTcount: A:0.07, C:0.13, G:0.22, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1647167 original size:14 final size:14
Alignment explanation
Indices: 1647116--1647202 Score: 79
Period size: 13 Copynumber: 6.9 Consensus size: 14
1647106 TTTTTTGTGT
*
1647116 GTTTGTGTT-GTTC
1 GTTTATGTTCGTTC
1647129 GTTTAT-TGT-GTTC
1 GTTTATGT-TCGTTC
1647142 GTTTATGTTCG-TC
1 GTTTATGTTCGTTC
1647155 ---TATGTTCGTTC
1 GTTTATGTTCGTTC
1647166 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
1647180 G-TT-TG-T-GTTC
1 GTTTATGTTCGTTC
1647190 GTTTATGTTCGTT
1 GTTTATGTTCGTT
1647203 TATTATTTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 21
0.74 0.01 0.25
Matches are distributed among these distances:
10 13 0.21
11 5 0.08
12 5 0.08
13 22 0.35
14 17 0.27
ACGTcount: A:0.06, C:0.11, G:0.24, T:0.59
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:1647202 original size:24 final size:23
Alignment explanation
Indices: 1647124--1647202 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 23
1647114 GTGTTTGTGT
1647124 TGTTCGTT-TATTGTGTTCGTTTA
1 TGTTCGTTCT-TTGTGTTCGTTTA
*
1647147 TGTTCG-TCTATGTTCGTTCGTTTA
1 TGTTCGTTCTTTG-T-GTTCGTTTA
1647171 TGTTCGTTCGTTTGTGTTCGTTTA
1 TGTTCGTTC-TTTGTGTTCGTTTA
1647195 TGTTCGTT
1 TGTTCGTT
1647203 TATTATTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
22 3 0.06
23 8 0.16
24 32 0.65
25 3 0.06
26 3 0.06
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (23 bp):
TGTTCGTTCTTTGTGTTCGTTTA
Found at i:1648954 original size:3 final size:3
Alignment explanation
Indices: 1648946--1649007 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
1648936 TTTTTTCATT
* *
1648946 TTA TTA TTA TTA TTA -AA TTTA TCA TTA TTA TTA TGTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T-TA TTA TTA T-TA
1648992 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
1649008 AAAATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 3 0.06
3 36 0.72
4 11 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1650586 original size:3 final size:3
Alignment explanation
Indices: 1650564--1650603 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1650554 TATTTTATAA
*
1650564 ATT ATAT ATT AAT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1650604 GAAAAATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1663007 original size:35 final size:35
Alignment explanation
Indices: 1662958--1663028 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1662948 CGATTTATCG
*
1662958 AAAGTTGTTCCTTAAAAATATTGAATAATGCAGTT
1 AAAGTTATTCCTTAAAAATATTGAATAATGCAGTT
* *
1662993 AAAGTTATTTCTTAAAAATATTGAATGATGCAGTT
1 AAAGTTATTCCTTAAAAATATTGAATAATGCAGTT
1663028 A
1 A
1663029 TTTGTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (35 bp):
AAAGTTATTCCTTAAAAATATTGAATAATGCAGTT
Found at i:1668258 original size:20 final size:20
Alignment explanation
Indices: 1668233--1668285 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1668223 TATATATATT
*
1668233 GAAAGCAGATAAACTGCGAG
1 GAAAGCAGAGAAACTGCGAG
*
1668253 GAAAGCAGAGAAATTGCGAG
1 GAAAGCAGAGAAACTGCGAG
*
1668273 GAAAACAGAGAAA
1 GAAAGCAGAGAAA
1668286 GATCAACCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.30, T:0.08
Consensus pattern (20 bp):
GAAAGCAGAGAAACTGCGAG
Found at i:1672286 original size:17 final size:17
Alignment explanation
Indices: 1672238--1672286 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
1672228 TGAAAAATAT
* *
1672238 AAAATATGACTTTTCAA
1 AAAATTTGACTTTTTAA
1672255 AAAATTTGACTTTTTAA
1 AAAATTTGACTTTTTAA
* *
1672272 ACATTTTGACTTTTT
1 AAAATTTGACTTTTT
1672287 GGTCAAGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAAATTTGACTTTTTAA
Found at i:1682161 original size:44 final size:44
Alignment explanation
Indices: 1682020--1682161 Score: 103
Period size: 44 Copynumber: 3.2 Consensus size: 44
1682010 CATCCAAATA
1682020 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCAC
1 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCAC
* * * * * * ****
1682064 AATTTTACAT-AGATTATAAACTAACCAGTTGAA---AAGAAATGACATTT
1 AATTTTA-ATCAG-CT-GACACT-TCAAATT-AATGCAA-AAA-GACCCAC
1682111 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCAC
1 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCAC
1682155 AATTTTA
1 AATTTTA
1682162 CATAGATTAT
Statistics
Matches: 67, Mismatches: 20, Indels: 22
0.61 0.18 0.20
Matches are distributed among these distances:
43 2 0.03
44 23 0.34
45 12 0.18
46 12 0.18
47 16 0.24
48 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (44 bp):
AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCAC
Found at i:1682175 original size:91 final size:91
Alignment explanation
Indices: 1682020--1682202 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
1682010 CATCCAAATA
1682020 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCACAATTTTACATAGATTATAAAC
1 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCACAATTTTACATAGATTATAAAC
1682085 TAACCAGTTGAAAAGAAATGACATTT
66 TAACCAGTTGAAAAGAAATGACATTT
1682111 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCACAATTTTACATAGATTATAAAC
1 AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCACAATTTTACATAGATTATAAAC
1682176 TAACCAGTTGAAAAGAAATGACATTT
66 TAACCAGTTGAAAAGAAATGACATTT
1682202 A
1 A
1682203 CAACCCACAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (91 bp):
AATTTTAATCAGCTGACACTTCAAATTAATGCAAAAAGACCCACAATTTTACATAGATTATAAAC
TAACCAGTTGAAAAGAAATGACATTT
Found at i:1691326 original size:8 final size:8
Alignment explanation
Indices: 1691314--1691351 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1691304 TTGTAAATTT
*
1691314 AAAAAAAT
1 AAAAAAAC
1691322 AAAAAAA-
1 AAAAAAAC
1691329 AAAAAATAC
1 AAAAAA-AC
1691338 AAAAAAAC
1 AAAAAAAC
1691346 AAAAAA
1 AAAAAA
1691352 TTAGTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.21
8 16 0.57
9 6 0.21
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1691331 original size:14 final size:15
Alignment explanation
Indices: 1691314--1691350 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1691304 TTGTAAATTT
1691314 AAAAAAATA-AAAAA
1 AAAAAAATACAAAAA
1691328 AAAAAAATACAAAAA
1 AAAAAAATACAAAAA
1691343 AACAAAAA
1 AA-AAAAA
1691351 ATTAGTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.43
15 7 0.33
16 5 0.24
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (15 bp):
AAAAAAATACAAAAA
Found at i:1701873 original size:2 final size:2
Alignment explanation
Indices: 1701866--1701904 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1701856 CTTTAAACTA
*
1701866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1701905 GTTCAATGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1708657 original size:21 final size:21
Alignment explanation
Indices: 1708631--1708671 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1708621 GGTAAAAAAT
* *
1708631 TACCTAAAATATTATTATTTA
1 TACCTAAAACATTAATATTTA
1708652 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
1708672 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTA
Found at i:1708792 original size:27 final size:27
Alignment explanation
Indices: 1708754--1708818 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
1708744 GATATGTTAT
*
1708754 CAAAACTGGTAAAGAGCCCAATAATAA
1 CAAAACCGGTAAAGAGCCCAATAATAA
1708781 CAAAACCGGTAAAGAGCCCAATAATAA
1 CAAAACCGGTAAAGAGCCCAATAATAA
1708808 CAAAACCGGTA
1 CAAAACCGGTA
1708819 GAAATAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (27 bp):
CAAAACCGGTAAAGAGCCCAATAATAA
Found at i:1711820 original size:61 final size:62
Alignment explanation
Indices: 1711725--1711847 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 62
1711715 TTCGACATGA
1711725 TATGTTCATTTTTTATTATTATTCTGAAGATGTTCATATATTTAGAGGGTCTT-GGAGGGTC
1 TATGTTCATTTTTTATTATTATTCTGAAGATGTTCATATATTTAGAGGGTCTTGGGAGGGTC
1711786 TATGTTCATTTTTTATTATTATTCTGAAGATGTTCATATATTTAGAGGGTCTTGGGAGGGTC
1 TATGTTCATTTTTTATTATTATTCTGAAGATGTTCATATATTTAGAGGGTCTTGGGAGGGTC
1711848 AGTTCACACA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 53 0.87
62 8 0.13
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.47
Consensus pattern (62 bp):
TATGTTCATTTTTTATTATTATTCTGAAGATGTTCATATATTTAGAGGGTCTTGGGAGGGTC
Found at i:1716455 original size:8 final size:8
Alignment explanation
Indices: 1716442--1716471 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
1716432 TATACTATTA
1716442 AAAATAAT
1 AAAATAAT
1716450 AAAATAAT
1 AAAATAAT
1716458 AAAATAAT
1 AAAATAAT
1716466 AAAATA
1 AAAATA
1716472 GAAAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:1721382 original size:3 final size:3
Alignment explanation
Indices: 1721362--1721431 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
1721352 TTTAAAGTCG
* *
1721362 ATA ATG ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1721410 ATA ATA ATA ATA AT- ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
1721432 GATGATGATG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1721436 original size:3 final size:3
Alignment explanation
Indices: 1721430--1721479 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1721420 TAATATAATA
1721430 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1721478 AT
1 AT
1721480 AATAATAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1725086 original size:3 final size:3
Alignment explanation
Indices: 1725072--1725117 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1725062 AAATAAGTAT
* * *
1725072 TAA TAA -AA TAA TAA TAA TAC TTA TAA TAA TAA TAA -AT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1725118 ATGAGAACCT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1725539 original size:40 final size:41
Alignment explanation
Indices: 1725436--1725541 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 41
1725426 TTTGAAGACA
* * *
1725436 ACATGGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGTTG
1 ACATTGTTCCTACGTGATGAGGAAATCTGG-T-TCGAAGGATG
* * * * **
1725479 ACGTTGTTCATACGTAATGAGGAGATCTGG-TCGGTGGATG
1 ACATTGTTCCTACGTGATGAGGAAATCTGGTTCGAAGGATG
1725519 ACATTGTTCCTACGTGATGAGGA
1 ACATTGTTCCTACGTGATGAGGA
1725542 CGTCTAGCCA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
40 26 0.51
43 25 0.49
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (41 bp):
ACATTGTTCCTACGTGATGAGGAAATCTGGTTCGAAGGATG
Found at i:1725687 original size:140 final size:140
Alignment explanation
Indices: 1725431--1725848 Score: 586
Period size: 140 Copynumber: 3.0 Consensus size: 140
1725421 GTAAATTTGA
* *
1725431 AGACAACATGGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGTTGACGTTG-TTCATACGTA
1 AGACAACATGGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGATGACGTTGCTTC-TACGTG
*
1725495 ATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGA
65 ATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGG
*
1725560 GATAGTTTGGG
130 GATAATTTGGG
* * * * * *
1725571 AGACAATATGATTCTTACGTGATGAGGAATTCTGGTTCTCTAAGGATGACGCTGCTTCTACGTGA
1 AGACAACATGGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGATGACGTTGCTTCTACGTGA
* * **
1725636 TGAGGAGATCTGGTCGGTGGATGGCATTGTTCCTACGTGATGAGGATGTCTAGTAATCTTTAGGG
66 TGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGG
1725701 ATAATTTGGG
131 ATAATTTGGG
* * * * * * *
1725711 AAATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGAGGTTGCTCCTACATGA
1 AGACAACATGGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGATGACGTTGCTTCTACGTGA
* * * * *
1725776 TGAGGAGATCTGGTCAGTGGATGACATTGTTCCTATGTGATGTGAACGTCTAGCCATTTTTAGGG
66 TGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGG
1725841 ATAATTTG
131 ATAATTTG
1725849 TTTCAAGAGA
Statistics
Matches: 242, Mismatches: 35, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
140 239 0.99
141 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (140 bp):
AGACAACATGGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGATGACGTTGCTTCTACGTGA
TGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGG
ATAATTTGGG
Found at i:1726145 original size:66 final size:65
Alignment explanation
Indices: 1726068--1726235 Score: 169
Period size: 67 Copynumber: 2.5 Consensus size: 65
1726058 TTGAGAACAA
** * * *
1726068 TCTCAAGTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAA-ATTTGTATTTCTATGGGAA-A
1 TCTCAAGTGAGATAAA-TTTGTTTCAAGAAAAACAATATCAAATATTTGTATCT-TA-AGGAAGA
1726131 TTG
63 TTG
* * *
1726134 TCTCAAGTGAGATGAAATTTGTTTTTAAGAAAAACAATATCAAATGTTTGTGTCTTAAGGAAGAT
1 TCTCAAGTGAGAT-AAATTTG-TTTCAAGAAAAACAATATCAAATATTTGTATCTTAAGGAAGAT
1726199 TG
64 TG
* *
1726201 TCTCAAGTGAGAAAAAATTTGTTTTTAAGAAAAAC
1 TCTCAAGTGAG-ATAAATTTG-TTTCAAGAAAAAC
1726236 TATCTCAAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
66 21 0.24
67 59 0.67
68 8 0.09
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.36
Consensus pattern (65 bp):
TCTCAAGTGAGATAAATTTGTTTCAAGAAAAACAATATCAAATATTTGTATCTTAAGGAAGATTG
Found at i:1726242 original size:37 final size:38
Alignment explanation
Indices: 1726201--1726287 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 38
1726191 AGGAAGATTG
* ** *
1726201 TCTCAAGTGAGAAAAAATTTGTTTTTA-AGAAAAACTA
1 TCTCAAGTGAGAAAAAATTTATTTCAAGAGAAAAACAA
* * *
1726238 TCTCAAGCGAGACAAAATTTATTTCAAGAGAAAAAGAA
1 TCTCAAGTGAGAAAAAATTTATTTCAAGAGAAAAACAA
1726276 TCTCAAGTGAGA
1 TCTCAAGTGAGA
1726288 TCAATTTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 22 0.54
38 19 0.46
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (38 bp):
TCTCAAGTGAGAAAAAATTTATTTCAAGAGAAAAACAA
Found at i:1726301 original size:38 final size:36
Alignment explanation
Indices: 1726201--1726303 Score: 98
Period size: 38 Copynumber: 2.8 Consensus size: 36
1726191 AGGAAGATTG
* ** *
1726201 TCTCAAGTGAGAAAAAATTTGTTTTTAAGAAAAACTA
1 TCTCAAGTGAG-ACAAATTTGTTTCAAAGAAAAACAA
* * *
1726238 TCTCAAGCGAGACAAAATTTATTTCAAGAGAAAAAGAA
1 TCTCAAGTGAGAC-AAATTTGTTTCAA-AGAAAAACAA
*
1726276 TCTCAAGTGAGATCAATTTTGTTTCAAA
1 TCTCAAGTGAGA-CAAATTTGTTTCAAA
1726304 AAATTTCAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
36 1 0.02
37 21 0.40
38 30 0.57
39 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.30
Consensus pattern (36 bp):
TCTCAAGTGAGACAAATTTGTTTCAAAGAAAAACAA
Done.