Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003552.1 Hibiscus syriacus cultivar Beakdansim tig00007497_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: 297196
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:5582 original size:20 final size:20
Alignment explanation
Indices: 5541--5643 Score: 68
Period size: 20 Copynumber: 5.1 Consensus size: 20
5531 TAACGCGAAC
* * *
5541 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACTCAATT
5561 TCCAAATTCGCAACTCAATT
1 TCCAAATTCGCAACTCAATT
* *
5581 TCTGC-AA-TCGCAACGCGATT
1 TC--CAAATTCGCAACTCAATT
* * *
5601 TTCAAATTCGCAATATAGAATT
1 TCCAAATTCGCAA-CT-CAATT
*
5623 T-CAAATTCGCAACTCGATT
1 TCCAAATTCGCAACTCAATT
5642 TC
1 TC
5644 TGAATTCCAA
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.02
19 6 0.10
20 38 0.60
21 13 0.21
22 5 0.08
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (20 bp):
TCCAAATTCGCAACTCAATT
Found at i:5654 original size:19 final size:21
Alignment explanation
Indices: 5565--5664 Score: 68
Period size: 20 Copynumber: 5.0 Consensus size: 21
5555 ACAGTTTCCA
*
5565 AATTCGCAACTC-AATTTCTG
1 AATTCGCAACGCGAATTTCTG
* *
5585 CAA-TCGCAACGCGATTTTC-A
1 -AATTCGCAACGCGAATTTCTG
*** *
5605 AATTCGCAATATAGAATTTC-A
1 AATTCGCAA-CGCGAATTTCTG
*
5626 AATTCGCAACTCG-ATTTCTG
1 AATTCGCAACGCGAATTTCTG
5646 AATTC-CAACGCGAATTTCT
1 AATTCGCAACGCGAATTTCT
5665 TTTTCGCAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
19 13 0.21
20 27 0.43
21 23 0.37
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (21 bp):
AATTCGCAACGCGAATTTCTG
Found at i:5712 original size:39 final size:39
Alignment explanation
Indices: 5669--5757 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 39
5659 ATTTCTTTTT
*
5669 CGCAACACAAGTTCCTTTTCGCAACAAGATTTTCTAAAC
1 CGCAACACAAGTTCCTTTTCGCAACAAGATTTTCGAAAC
* ** ** **
5708 CGCAACACGAATTTTGTTTTCGCAACTCGATTTTCGAATT
1 CGCAACAC-AAGTTCCTTTTCGCAACAAGATTTTCGAAAC
5748 CGCAACACAA
1 CGCAACACAA
5758 ATTTTAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (39 bp):
CGCAACACAAGTTCCTTTTCGCAACAAGATTTTCGAAAC
Found at i:5731 original size:20 final size:20
Alignment explanation
Indices: 5708--5774 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
5698 TTTTCTAAAC
*
5708 CGCAACACGAATTTTGTTTT
1 CGCAACACGAATTTTGATTT
* *
5728 CGCAACTCG-ATTTTCGAATT
1 CGCAACACGAATTTT-GATTT
* *
5748 CGCAACACAAATTTTAATTT
1 CGCAACACGAATTTTGATTT
5768 CGCAACA
1 CGCAACA
5775 GCTTTATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (20 bp):
CGCAACACGAATTTTGATTT
Found at i:5740 original size:40 final size:40
Alignment explanation
Indices: 5684--5774 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 40
5674 CACAAGTTCC
* * *
5684 TTTTCGCAACAAGATTTTCTAAACCGCAACACGAATTTTG
1 TTTTCGCAACAAGATTTTCGAAACCGCAACACAAATTTTA
** **
5724 TTTTCGCAACTCGATTTTCGAATTCGCAACACAAATTTTA
1 TTTTCGCAACAAGATTTTCGAAACCGCAACACAAATTTTA
*
5764 ATTTCGCAACA
1 TTTTCGCAACA
5775 GCTTTATTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (40 bp):
TTTTCGCAACAAGATTTTCGAAACCGCAACACAAATTTTA
Found at i:10114 original size:23 final size:22
Alignment explanation
Indices: 10066--10114 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
10056 ACAGAATGTC
*
10066 AAGG-GGGAACTGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
10087 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
10110 AAGGA
1 AAGGA
10115 AAATTGTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:11998 original size:98 final size:98
Alignment explanation
Indices: 11689--11990 Score: 477
Period size: 97 Copynumber: 3.1 Consensus size: 98
11679 GGGTCTACGC
11689 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATG---TCTTTGGAACATGTGTGAAGTCTGGTGAG--ACATACTTGAT
11754 CCTTGGCATATGTATATGATTCTTAAGGAATG--ATGT
61 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
*
11790 GGTCCTTCGGGACATATAT-TCTTTGGAACATGTGTGAAGTTTGGTGA-ACATACTTGATCCTTG
1 GGTCCTTCGGGACATATATGTCTTTGGAACATGTGTGAAGTCTGGTGAGACATACTTGATCCTTG
*
11853 GCATATGTATATGATTCTTAAAGAATGATATGT
66 GCATATGTATATGATTCTTAAGGAATGATATGT
* *
11886 GGTCCTTCGGGACATATATGTCTTTGGAACATGTGTGAAGTCTGGTGAGACATACTTGATCCCTA
1 GGTCCTTCGGGACATATATGTCTTTGGAACATGTGTGAAGTCTGGTGAGACATACTTGATCCTTG
*
11951 GTATATGTATATGATTCTTAAGGAATGATATGT
66 GCATATGTATATGATTCTTAAGGAATGATATGT
*
11984 AGTCCTT
1 GGTCCTT
11991 ATGGACATTA
Statistics
Matches: 189, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
94 42 0.22
96 23 0.12
97 54 0.29
98 51 0.27
101 19 0.10
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (98 bp):
GGTCCTTCGGGACATATATGTCTTTGGAACATGTGTGAAGTCTGGTGAGACATACTTGATCCTTG
GCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:12040 original size:23 final size:23
Alignment explanation
Indices: 12007--12058 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
11997 ATTATTATAT
12007 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
12030 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
12053 GGCACT
1 GGCACT
12059 TCAGTACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.31, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:12068 original size:23 final size:23
Alignment explanation
Indices: 12019--12074 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
12009 CACTACGGTG
* *
12019 CAATTCTACGCGGCACTCCGGTG
1 CAATTCTACGCGGCACTCCAGTA
* *
12042 CAATTCTACGTGGCACTTCAGTA
1 CAATTCTACGCGGCACTCCAGTA
*
12065 CAATTATACG
1 CAATTCTACG
12075 AGTTGTGTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (23 bp):
CAATTCTACGCGGCACTCCAGTA
Found at i:16776 original size:20 final size:21
Alignment explanation
Indices: 16751--16795 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
16741 AACTTCATAA
* *
16751 TTTAAATATAT-GAACTTTAT
1 TTTAAAGATATAGAACATTAT
*
16771 TTTAAAGATATAGCACATTAT
1 TTTAAAGATATAGAACATTAT
16792 TTTA
1 TTTA
16796 TTACATCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTAAAGATATAGAACATTAT
Found at i:28828 original size:14 final size:14
Alignment explanation
Indices: 28795--28828 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28785 TGTAAATATT
*
28795 TATTATAATTTGAA
1 TATTATAATTTCAA
28809 TATTATAATTTCAA
1 TATTATAATTTCAA
*
28823 TTTTAT
1 TATTAT
28829 TTTCAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTATAATTTCAA
Found at i:30572 original size:13 final size:13
Alignment explanation
Indices: 30554--30578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30544 ATCCAACTCA
30554 GATAAAAATAAAC
1 GATAAAAATAAAC
30567 GATAAAAATAAA
1 GATAAAAATAAA
30579 TCAACAACTC
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:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
GATAAAAATAAAC
Found at i:35264 original size:24 final size:24
Alignment explanation
Indices: 35232--35299 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
35222 CAAATATATA
*
35232 AAATATGAAATAATTTTATTTTAT
1 AAATTTGAAATAATTTTATTTTAT
35256 AAATTTGAAATAATTTTATTTTAT
1 AAATTTGAAATAATTTTATTTTAT
35280 AAATTTGAAATTTAATTTTA
1 AAATTTGAAA--TAATTTTA
35300 AAGTAGAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 33 0.80
26 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
AAATTTGAAATAATTTTATTTTAT
Found at i:35337 original size:2 final size:2
Alignment explanation
Indices: 35330--35370 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35320 AATTAATTCC
35330 AT AT AT 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 AT AT AT A
35371 ATTAACACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38171 original size:42 final size:40
Alignment explanation
Indices: 38120--38197 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 40
38110 TTCTCTAAAT
*
38120 ATATTTTTATTTTATTTATTTTA-ATTTTTACTCATCTCTATG
1 ATATTTTTA-TTGATTTATTTTATATTTTT--TCATCTCTATG
*
38162 ATATTTTTATTGATTTTTTTTATATTTTTTCATCTC
1 ATATTTTTATTGATTTATTTTATATTTTTTCATCTC
38198 AATTGTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 7 0.21
41 11 0.33
42 15 0.45
ACGTcount: A:0.22, C:0.09, G:0.03, T:0.67
Consensus pattern (40 bp):
ATATTTTTATTGATTTATTTTATATTTTTTCATCTCTATG
Found at i:38340 original size:22 final size:22
Alignment explanation
Indices: 38315--38366 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
38305 AAATTCGTAG
38315 AAAAATAACTTTCAAATGAGAT
1 AAAAATAACTTTCAAATGAGAT
38337 AAAAATAACTTTCAAATGAGAT
1 AAAAATAACTTTCAAATGAGAT
38359 AAAAATAA
1 AAAAATAA
38367 AAAAAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (22 bp):
AAAAATAACTTTCAAATGAGAT
Found at i:39354 original size:42 final size:41
Alignment explanation
Indices: 39308--39646 Score: 238
Period size: 41 Copynumber: 8.2 Consensus size: 41
39298 GACATATAAC
*
39308 GGCGTTTTTACAACAAACGCCGCAATAGAGTGGTAA-ATTAGT
1 GGCGTTTTTACCACAAACGCCGCAATAGA-T-GTAACATTAGT
*
39350 GGCGTTTATACCACAAACGCCGCAATAGAT-TAACATATAGT
1 GGCGTTTTTACCACAAACGCCGCAATAGATGTAACAT-TAGT
* *
39391 GGCG-TTTTAGCCA-AAACGTCGCAATAGATCGGTAA-ATTAGC
1 GGCGTTTTTA-CCACAAACGCCGCAATAGAT--GTAACATTAGT
* * *
39432 GGCATTTATACCACAAACGCCGTAATAGAT-TACACATATAGT
1 GGCGTTTTTACCACAAACGCCGCAATAGATGTA-ACAT-TAGT
* * * * * *
39474 GGCATTTATT-CTTA-AAACGCCGCAATAGTTATAATAAATAGT
1 GGCGTTT-TTAC-CACAAACGCCGCAATAGATGTAA-CATTAGT
* *
39516 GGCGTTTTTA-GACAAACGCCGCAATAG-TGTTAATCAATAGT
1 GGCGTTTTTACCACAAACGCCGCAATAGATG-TAA-CATTAGT
* * * * *
39557 GGCGTTTTTA-CAAAAACGCCGTAATAGTTTTAATCAATAGT
1 GGCGTTTTTACCACAAACGCCGCAATAGATGTAA-CATTAGT
* *
39598 GGCGTTTTTTA--ACAAACGCCACAATA-ATGTAATCAATAGT
1 GGCG-TTTTTACCACAAACGCCGCAATAGATGTAA-CATTAGT
39638 GGCGTTTTT
1 GGCGTTTTT
39647 TTGTATAAAC
Statistics
Matches: 248, Mismatches: 29, Indels: 43
0.77 0.09 0.13
Matches are distributed among these distances:
39 10 0.04
40 40 0.16
41 100 0.40
42 90 0.36
43 8 0.03
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
GGCGTTTTTACCACAAACGCCGCAATAGATGTAACATTAGT
Found at i:39668 original size:41 final size:40
Alignment explanation
Indices: 39488--39668 Score: 184
Period size: 41 Copynumber: 4.4 Consensus size: 40
39478 TTTATTCTTA
* * * *
39488 AAACGCCGCAATAGTTATAATAAATAGTGGCGTTTTTAGAC
1 AAACGCCGCAATA-ATGTAATCAATAGTGGCGTTTTTTGAC
* ** *
39529 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTACAA
1 AAACGCCGCAATAATG-TAATCAATAGTGGCGTTTTTTGAC
* * * *
39570 AAACGCCGTAATAGTTTTAATCAATAGTGGCGTTTTTTAAC
1 AAACGCCGCAATA-ATGTAATCAATAGTGGCGTTTTTTGAC
* *
39611 AAACGCCACAATAATGTAATCAATAGTGGCGTTTTTTTGTAT
1 AAACGCCGCAATAATGTAATCAATAGTGGCG-TTTTTTG-AC
39653 AAACGCCGCAA-AATGT
1 AAACGCCGCAATAATGT
39669 TAAATATATA
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
40 17 0.14
41 89 0.75
42 12 0.10
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (40 bp):
AAACGCCGCAATAATGTAATCAATAGTGGCGTTTTTTGAC
Found at i:40280 original size:42 final size:42
Alignment explanation
Indices: 40171--40595 Score: 492
Period size: 42 Copynumber: 10.2 Consensus size: 42
40161 TTGTATCTAG
* * *
40171 AAACGCCGCTATAGA-TC-TGACATTTTGTGGCG-TTTGTATCCAA
1 AAACGCCGCTATAGACTCGT-AC-TTTAGTGGCGTTTTGAAT--AC
* * *
40214 AAACGCCGCTATAAACTC-TACTTTAGTGGTGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* * * * * *
40255 AAACGCCTCTAAAGACTCGTACTTTAGTAGTGTTTT-TATAT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* * * *
40296 AAACACCGCTATAGACTAGTACTTTAGTGGTGTTTT-TATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* *
40337 AAACGCTGCTATATACTCGTACTTTAGTGGCGTTTTGAATGA-
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAAT-AC
40379 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* * *
40421 AAACGCTGCTA-ATGACTCGTACTTCAGTGGCGTTTT-TATAC
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTTTGAATAC
*
40462 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
40504 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* *
40546 AAACGCTGCTA-ATGACTCGTACTTTAGTGGCGTTTGTAAATAC
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTT-TGAATAC
40589 AAACGCC
1 AAACGCC
40596 ACAATTTTAC
Statistics
Matches: 333, Mismatches: 38, Indels: 22
0.85 0.10 0.06
Matches are distributed among these distances:
41 122 0.37
42 173 0.52
43 35 0.11
44 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (42 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
Found at i:40329 original size:83 final size:84
Alignment explanation
Indices: 40214--40595 Score: 483
Period size: 83 Copynumber: 4.6 Consensus size: 84
40204 TTGTATCCAA
* * *
40214 AAACGCCGCTATAAACTC-TACTTTAGTGGTGTTTTGAATGCAAACGCCT-CTAAAGACTCGTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCCTGCTAAAGACTCGTAC
* * *
40277 TTTAGTAGTGTTTTTATAT
66 TTTAGTGGCGTTTTTATAC
* * * * * *
40296 AAACACCGCTATAGACTAGTACTTTAGTGGTGTTTT-TATACAAACG-CTGCTATATACTCGTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCCTGCTAAAGACTCGTAC
*
40359 TTTAGTGGCGTTTTGAATGA-
66 TTTAGTGGCGTTTT-TAT-AC
*
40379 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACG-CTGCTAATGACTCGTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCCTGCTAAAGACTCGTAC
*
40443 TTCAGTGGCGTTTTTATAC
66 TTTAGTGGCGTTTTTATAC
* *
40462 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATGCAAACGCC-GCTATAGACTCGTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCCTGCTAAAGACTCGTAC
*
40526 TTTAGTGGCGTTTTGAATAC
66 TTTAGTGGCGTTTT-TATAC
* *
40546 AAACGCTGCTA-ATGACTCGTACTTTAGTGGCGTTTGTAAATACAAACGCC
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTT-TGAATACAAACGCC
40596 ACAATTTTAC
Statistics
Matches: 263, Mismatches: 27, Indels: 17
0.86 0.09 0.06
Matches are distributed among these distances:
81 2 0.01
82 48 0.18
83 127 0.48
84 74 0.28
85 12 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (84 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCCTGCTAAAGACTCGTAC
TTTAGTGGCGTTTTTATAC
Found at i:40490 original size:125 final size:125
Alignment explanation
Indices: 40214--40595 Score: 563
Period size: 125 Copynumber: 3.1 Consensus size: 125
40204 TTGTATCCAA
* * *
40214 AAACGCCGCTATAAACTC-TACTTTAGTGGTGTTTTGAATGCAAACGCCTCTAAAGACTCGTACT
1 AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACT
* * * * * * * *
40278 TTAGTAGTGTTTT-TATATAAACACCGCT-ATAGACTAGTACTTTAGTGGTGTTTTTATAC
66 TTAGTGGCGTTTTGAATACAAACGCTGCTAAT-GACTCGTACTTTAGTGGCGTTTTTATAC
* * *
40337 AAACGCTGCTATATACTCGTACTTTAGTGGCGTTTTGAATGAAAACGCCGCTATAGACTCGTACT
1 AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACT
*
40402 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTCAGTGGCGTTTTTATAC
66 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTTTTATAC
*
40462 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACT
1 AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACT
*
40527 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTTGTAAATAC
66 TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTT-T-TATAC
40589 AAACGCC
1 AAACGCC
40596 ACAATTTTAC
Statistics
Matches: 234, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
123 16 0.07
124 53 0.23
125 151 0.65
126 3 0.01
127 11 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (125 bp):
AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACT
TTAGTGGCGTTTTGAATACAAACGCTGCTAATGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:43474 original size:21 final size:21
Alignment explanation
Indices: 43443--43516 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
43433 AGCATCAGCC
* * *
43443 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAG
*
43464 AAAGAAGCAGCGGCAGCACAG
1 AGAGAAGCAGCGGCAGCACAG
43485 AGAGAAGCAGCGGCAGCACAG
1 AGAGAAGCAGCGGCAGCACAG
43506 AGAGAAGCAGC
1 AGAGAAGCAGC
43517 ATATCAGAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.38, T:0.00
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAG
Found at i:43960 original size:43 final size:43
Alignment explanation
Indices: 43913--44223 Score: 136
Period size: 43 Copynumber: 7.2 Consensus size: 43
43903 AGACCTGTAC
* *
43913 CGGCGTTTTTAGCAGAAACACCGCAAAACATCAATACCTACTG
1 CGGCGTTTTTAGCAAAAACACCGCAAAACATCAACACCTACTG
* * * * *
43956 CGGCGTTTGT-GAAAAAAATATCGCAAGACATCAACACCTACTG
1 CGGCGTTTTTAG-CAAAAACACCGCAAAACATCAACACCTACTG
* * * *
43999 CGGCG-TTTTAGCGAAAAACGCCGCTAAACATCATA-ACTTATTG
1 CGGCGTTTTTAGC-AAAAACACCGCAAAACATCA-ACACCTACTG
* * * * * * *
44042 CGACGTTTGTCT-G-AAAAACGCTGCTAAATATTAACACCTATTG
1 CGGCGTTT-T-TAGCAAAAACACCGCAAAACATCAACACCTACTG
* * * ** * * *
44085 CGACATTTTTATG-ACAAACGTCGCTAAATATCAACACCTATTG
1 CGGCGTTTTTA-GCAAAAACACCGCAAAACATCAACACCTACTG
* * * * *
44128 CAGCGTTTGTCT-G-AAAAACACTGCTAAATATCAACACCTATTG
1 CGGCGTTT-T-TAGCAAAAACACCGCAAAACATCAACACCTACTG
* * * * * * *
44171 CGGCGTTTGTCA-CACAAACGCCGCTAAATATCAATACCTATTG
1 CGGCGTTT-TTAGCAAAAACACCGCAAAACATCAACACCTACTG
44214 CGGCGTTTTT
1 CGGCGTTTTT
44224 TATATCAACA
Statistics
Matches: 214, Mismatches: 40, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
41 1 0.00
42 7 0.03
43 198 0.93
44 4 0.02
45 3 0.01
46 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
CGGCGTTTTTAGCAAAAACACCGCAAAACATCAACACCTACTG
Found at i:44234 original size:86 final size:85
Alignment explanation
Indices: 43913--44221 Score: 306
Period size: 86 Copynumber: 3.6 Consensus size: 85
43903 AGACCTGTAC
* * * * * * *
43913 CGGCGTTTTTAGCAGAAACACCGCAAAACATCAATACCTACTGCGGCGTTTG--TGAAAAAAATA
1 CGGCG-TTTTAGCACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTTGTCTGAAAAACA-C
* *
43976 TCGC-AAGACATCAACACCTACTG
64 T-GCTAA-ATATCAACACCTATTG
* * * * *
43999 CGGCGTTTTAGCGAAAAACGCCGCTAAACATC-ATAACTTATTGCGACGTTTGTCTGAAAAACGC
1 CGGCGTTTTAGC-ACAAACGCCGCTAAATATCAAT-ACCTATTGCGGCGTTTGTCTGAAAAACAC
*
44063 TGCTAAATATTAACACCTATTG
64 TGCTAAATATCAACACCTATTG
* * * * *
44085 CGACATTTTTATG-ACAAACGTCGCTAAATATCAACACCTATTGCAGCGTTTGTCTGAAAAACAC
1 CGGC-GTTTTA-GCACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTTGTCTGAAAAACAC
44149 TGCTAAATATCAACACCTATTG
64 TGCTAAATATCAACACCTATTG
44171 CGGCGTTTGTCA-CACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
1 CGGCGTTT-T-AGCACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
44222 TTTATATCAA
Statistics
Matches: 184, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
85 12 0.07
86 154 0.84
87 10 0.05
88 8 0.04
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (85 bp):
CGGCGTTTTAGCACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTTGTCTGAAAAACACTG
CTAAATATCAACACCTATTG
Found at i:44268 original size:70 final size:70
Alignment explanation
Indices: 44155--44294 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
44145 ACACTGCTAA
44155 ATATCAACACCTATTGCGGCGTTTGTCACACAAACGCCGCTAAATATCAATACCTATTGCGGCGT
1 ATATCAACACCTATTGCGGCGTTTGTCACACAAACGCCGCTAAATATCAATACCTATTGCGGCGT
44220 TTTTT
66 TTTTT
* *
44225 ATATCAACACCTATTGCGGCGTTTGTCACATAAACGCCGCTAAATATCAATACCTATTGCGGCTT
1 ATATCAACACCTATTGCGGCGTTTGTCACACAAACGCCGCTAAATATCAATACCTATTGCGGCGT
44290 TTTTT
66 TTTTT
44295 GTGAAAAAAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (70 bp):
ATATCAACACCTATTGCGGCGTTTGTCACACAAACGCCGCTAAATATCAATACCTATTGCGGCGT
TTTTT
Found at i:51223 original size:29 final size:30
Alignment explanation
Indices: 51150--51223 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
51140 TAATTAAAGG
51150 TTTTTTGTCAAAAT-TAATATCTAAAGTTA
1 TTTTTTGTCAAAATATAATATCTAAAGTTA
* * *
51179 TCTTTTGATTAAAATAT-ATATTTAAAG-TA
1 TTTTTTG-TCAAAATATAATATCTAAAGTTA
51208 TTTTTTTGTCAAAATA
1 -TTTTTTGTCAAAATA
51224 GGTACCTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 15 0.41
30 21 0.57
31 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (30 bp):
TTTTTTGTCAAAATATAATATCTAAAGTTA
Found at i:57366 original size:23 final size:22
Alignment explanation
Indices: 57336--57379 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
57326 GAATACATAT
*
57336 ATCTTTAAAATTTTATAAATTA
1 ATCTTTAAAATTATATAAATTA
*
57358 ATCTCTTAACATTATATAAATT
1 ATCT-TTAAAATTATATAAATT
57380 TTAAAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (22 bp):
ATCTTTAAAATTATATAAATTA
Found at i:59183 original size:16 final size:16
Alignment explanation
Indices: 59162--59195 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
59152 TTACTATTCA
*
59162 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
59178 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
59194 CG
1 CG
59196 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:65874 original size:5 final size:5
Alignment explanation
Indices: 65864--65901 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
65854 ACATTAAAAG
65864 TGGGA TGGGA TGGGA TGGGA TGGGA TGGGA TGGGA TGG
1 TGGGA TGGGA TGGGA TGGGA TGGGA TGGGA TGGGA TGG
65902 TTGCAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (5 bp):
TGGGA
Found at i:69447 original size:21 final size:21
Alignment explanation
Indices: 69423--69467 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
69413 TCTTTAATGG
69423 TCTCTTGTGGTTTACTATTAT
1 TCTCTTGTGGTTTACTATTAT
69444 TCTCTTGTGGTTTACTATTAT
1 TCTCTTGTGGTTTACTATTAT
69465 TCT
1 TCT
69468 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (21 bp):
TCTCTTGTGGTTTACTATTAT
Found at i:70100 original size:12 final size:10
Alignment explanation
Indices: 70068--70098 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
70058 TTTATCACAC
70068 CAAATTCTCT
1 CAAATTCTCT
70078 CAAATTCTCT
1 CAAATTCTCT
*
70088 CAAATACTCT
1 CAAATTCTCT
70098 C
1 C
70099 TCTTTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:71808 original size:51 final size:51
Alignment explanation
Indices: 71729--71858 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 51
71719 CCCGTACATG
* * * * * *
71729 GCGTATAGCGCGG-AGTAGGGGGCACGCTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGTA-CAGGGGGCGCGCTACACCCCACGTGGAACCAAATCA
* **
71780 GCGTATAGCGCGGTACAGGGGGCGCGCTACACTCCACGTGGCGCCAAATCA
1 GCGTATAGCGCGGTACAGGGGGCGCGCTACACCCCACGTGGAACCAAATCA
* *
71831 GCATATAGCGCGGTTCAGGGGGCGCGCT
1 GCGTATAGCGCGGTACAGGGGGCGCGCT
71859 TTACTGCTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
51 66 0.99
52 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.15
Consensus pattern (51 bp):
GCGTATAGCGCGGTACAGGGGGCGCGCTACACCCCACGTGGAACCAAATCA
Found at i:73451 original size:21 final size:21
Alignment explanation
Indices: 73425--73475 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
73415 CTCATAACAT
73425 GGTGCATCGGTGCACTATCAA
1 GGTGCATCGGTGCACTATCAA
73446 GGTGCATCGGTGCACTATCAA
1 GGTGCATCGGTGCACTATCAA
73467 GGTGCATCG
1 GGTGCATCG
73476 ATACCCCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (21 bp):
GGTGCATCGGTGCACTATCAA
Found at i:73641 original size:21 final size:21
Alignment explanation
Indices: 73615--73668 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
73605 ACTAGTGGCA
*
73615 GGTGCATGGATGGACTGCAGG
1 GGTGCATGGATGGACTGCAAG
73636 GGTGCATGGATGGACTGCAAG
1 GGTGCATGGATGGACTGCAAG
73657 GGTGCATGGATG
1 GGTGCATGGATG
73669 AACTTTAACA
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:0.20, C:0.13, G:0.46, T:0.20
Consensus pattern (21 bp):
GGTGCATGGATGGACTGCAAG
Found at i:73920 original size:21 final size:21
Alignment explanation
Indices: 73896--73935 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
73886 ATGTTTAATG
73896 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
73917 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
73936 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:75629 original size:14 final size:15
Alignment explanation
Indices: 75610--75640 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
75600 TTCTTTTTGT
75610 TTTTCTTC-TCTTCC
1 TTTTCTTCTTCTTCC
75624 TTTTCTTCTTCTTCC
1 TTTTCTTCTTCTTCC
75639 TT
1 TT
75641 CACCATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTCTTCTTCTTCC
Found at i:79862 original size:198 final size:195
Alignment explanation
Indices: 79519--79925 Score: 557
Period size: 198 Copynumber: 2.1 Consensus size: 195
79509 AGTACGAGGG
* * * * *
79519 TCTTGAGTTGATGTTCATGCTTTATACAGATCTCACTCGCTTATATTTACATATGTACTCTATTT
1 TCTTGAGTTGATGTTCATACTTTATACAGATCTCACTCGCATAGATTTACACATGTACTCTATGT
* *
79584 CACCGATATTCTGTTGTGTGTTGCTATGACAAGGATGTCCAGACGTTCACTAGGAAACAGCAACG
66 CACCGATATTCTGTTGTATGTTGCTATGACAAGGATGTCCAGACATTCACTAGGAAACAGCAACG
* ** * *
79649 AGAGTACAGGAGGCAAAACTGTTCTCAAATGTTGTTGTTGTCTGAT-GTTTTCTGTAATGCAAGG
131 AGAGTACAAGAGGCAAAACTGTTCTCAAATGTTGTCATTGTCTGATCATTTT-TGCAATGCAAGG
79713 C
195 C
*
79714 TCTTGAGTTGATGTTCATACTTTATACAGATCTCACTCGCATAGATTTACACATGTACTTTATGT
1 TCTTGAGTTGATGTTCATACTTTATACAGATCTCACTCGCATAGATTTACACATGTACTCTATGT
* * * *
79779 CACCGGTATTCTGCTGCTGTATGTTGCTGTTG-CGAGGATGTCTAGACATTCACTAGGAAACAGC
66 CACCGATATTCTG-T--TGTATGTTGCT-ATGACAAGGATGTCCAGACATTCACTAGGAAACAGC
* * *
79843 AACGAGAGTATAAGAGGCAAAACTGTTCTCGAATGTTGTCATTGTCTGATCATTTTTGCAATTCA
127 AACGAGAGTACAAGAGGCAAAACTGTTCTCAAATGTTGTCATTGTCTGATCATTTTTGCAATGCA
79908 AGGC
192 AGGC
* *
79912 TCTGGAGTAGATGT
1 TCTTGAGTTGATGT
79926 CCACTCTTTG
Statistics
Matches: 185, Mismatches: 22, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
195 71 0.38
196 1 0.01
198 107 0.58
199 6 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (195 bp):
TCTTGAGTTGATGTTCATACTTTATACAGATCTCACTCGCATAGATTTACACATGTACTCTATGT
CACCGATATTCTGTTGTATGTTGCTATGACAAGGATGTCCAGACATTCACTAGGAAACAGCAACG
AGAGTACAAGAGGCAAAACTGTTCTCAAATGTTGTCATTGTCTGATCATTTTTGCAATGCAAGGC
Found at i:80941 original size:2 final size:2
Alignment explanation
Indices: 80936--80973 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
80926 ATATGATGAA
80936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80974 GGGTTAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85087 original size:81 final size:81
Alignment explanation
Indices: 84980--85139 Score: 266
Period size: 81 Copynumber: 2.0 Consensus size: 81
84970 TCGATTTGTG
* *
84980 AAATTCACGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAATTTCCATGT
1 AAATTCACGTTGCGAATAGCTGTGTTTACCTATATCGGTAATTAGCGTTGCAAAAATTTCCATGT
85045 TCGAGTTGCGAATTCC
66 TCGAGTTGCGAATTCC
* * * *
85061 AAATTCGCGTTGCGAATAGCTGTGTTTACCTATATCGGTAATTCGTGTTGCAAAAATTTTCATGT
1 AAATTCACGTTGCGAATAGCTGTGTTTACCTATATCGGTAATTAGCGTTGCAAAAATTTCCATGT
85126 TCGAGTTGCGAATT
66 TCGAGTTGCGAATT
85140 TGGAAACTGT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (81 bp):
AAATTCACGTTGCGAATAGCTGTGTTTACCTATATCGGTAATTAGCGTTGCAAAAATTTCCATGT
TCGAGTTGCGAATTCC
Found at i:85734 original size:18 final size:18
Alignment explanation
Indices: 85685--85736 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
85675 GAATATTTTT
* * *
85685 TAATTAAAAAACAATTTA
1 TAATTATAAAATAATATA
*
85703 TAATTAATTTAAATAATATA
1 TAATT-A-TAAAATAATATA
85723 TAATTATAAAATAA
1 TAATTATAAAATAA
85737 AAATTTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.44
19 2 0.07
20 13 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATTATAAAATAATATA
Found at i:89228 original size:10 final size:10
Alignment explanation
Indices: 89213--89299 Score: 66
Period size: 10 Copynumber: 7.7 Consensus size: 10
89203 ATAAACGAAT
89213 ACGAACATAA
1 ACGAACATAA
*
89223 ACGAACACAA
1 ACGAACATAA
89233 ACAAATGAACATAA
1 AC----GAACATAA
89247 ACGAACATAATAA
1 ACGAAC---ATAA
*
89260 ATGAACATAA
1 ACGAACATAA
89270 ACGAACGCAATAA
1 ACGAA--C-ATAA
89283 ACGAACATAA
1 ACGAACATAA
89293 ACGAACA
1 ACGAACA
89300 ACACAAACAC
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
10 34 0.54
11 1 0.02
12 1 0.02
13 18 0.29
14 9 0.14
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (10 bp):
ACGAACATAA
Found at i:89265 original size:13 final size:13
Alignment explanation
Indices: 89243--89292 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
89233 ACAAATGAAC
89243 ATAAACGAACATA
1 ATAAACGAACATA
*
89256 ATAAATGAAC---
1 ATAAACGAACATA
**
89266 ATAAACGAACGCA
1 ATAAACGAACATA
89279 ATAAACGAACATA
1 ATAAACGAACATA
89292 A
1 A
89293 ACGAACAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 9 0.30
13 21 0.70
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.14
Consensus pattern (13 bp):
ATAAACGAACATA
Found at i:89265 original size:23 final size:23
Alignment explanation
Indices: 89215--89300 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
89205 AAACGAATAC
*
89215 GAACATAAACGAACACAAACAAAT
1 GAACATAAACGAACA-AAATAAAT
*
89239 GAACATAAACGAACATAATAAAT
1 GAACATAAACGAACAAAATAAAT
** *
89262 GAACATAAACGAACGCAATAAAC
1 GAACATAAACGAACAAAATAAAT
89285 GAACATAAACGAACAA
1 GAACATAAACGAACAA
89301 CACAAACACA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 40 0.73
24 15 0.27
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.10
Consensus pattern (23 bp):
GAACATAAACGAACAAAATAAAT
Found at i:89580 original size:14 final size:14
Alignment explanation
Indices: 89561--89598 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
89551 GCCCTCTGTT
89561 CGAACATAAATGAA
1 CGAACATAAATGAA
89575 CGAACATAAATGAA
1 CGAACATAAATGAA
89589 CGAACATAAA
1 CGAACATAAA
89599 CAAACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:96836 original size:3 final size:3
Alignment explanation
Indices: 96828--96908 Score: 117
Period size: 3 Copynumber: 27.0 Consensus size: 3
96818 TTTGATTTAT
* * * *
96828 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA GTA TTA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
96876 TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
96909 AATATATATA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:98276 original size:20 final size:21
Alignment explanation
Indices: 98230--98276 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
98220 CTGCTTTTAA
*
98230 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
98251 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
98270 ATATATT
1 ATATATT
98277 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:99066 original size:28 final size:27
Alignment explanation
Indices: 98991--99068 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 27
98981 TTAAAATTTC
98991 ATATATTAATTTATAATTTT-TTTATAT
1 ATATATTAATTT-TAATTTTATTTATAT
* * **
99018 ACATATT-ATTTTTATAGTATTTATAT
1 ATATATTAATTTTAATTTTATTTATAT
*
99044 ATATATTAATATTTCATTTTATTTA
1 ATATATTAAT-TTTAATTTTATTTA
99069 CAAGTATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
25 4 0.10
26 17 0.43
27 8 0.20
28 11 0.28
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (27 bp):
ATATATTAATTTTAATTTTATTTATAT
Found at i:102366 original size:15 final size:15
Alignment explanation
Indices: 102346--102377 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
102336 ATCAATACCT
102346 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
102361 TTTTGCATACATTCA
1 TTTTGCATACATGCA
102376 TT
1 TT
102378 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:109722 original size:10 final size:10
Alignment explanation
Indices: 109701--109754 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
109691 ATGCTTGAAG
109701 AGAAAAAGAAA
1 AGAAAAA-AAA
109712 AGAAAAAAAA
1 AGAAAAAAAA
109722 AGAGAAAAAAA
1 AGA-AAAAAAA
* *
109733 AGGAGAAAAA
1 AGAAAAAAAA
*
109743 AGAAGAAAAA
1 AGAAAAAAAA
109753 AG
1 AG
109755 GGGGGGGTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
10 23 0.59
11 16 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:109727 original size:12 final size:12
Alignment explanation
Indices: 109698--109753 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
109688 ATTATGCTTG
*
109698 AAGAGAAAAAGA
1 AAGAGAAAAAAA
109710 AA-AGAAAAAAA
1 AAGAGAAAAAAA
109721 AAGAGAAAAAAA
1 AAGAGAAAAAAA
* *
109733 AGGAGAAAAAAG
1 AAGAGAAAAAAA
109745 AAGA-AAAAA
1 AAGAGAAAAA
109754 GGGGGGGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
11 15 0.38
12 24 0.62
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAGAGAAAAAAA
Found at i:111023 original size:83 final size:83
Alignment explanation
Indices: 110897--111186 Score: 436
Period size: 83 Copynumber: 3.5 Consensus size: 83
110887 GTACTCATAG
* * *
110897 CATCTTCTGGAAGTGTTCTTTGATTTATCTGACCTGGTTTGGTAAAACCAATCATTGAATTTGAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGA
110962 AGATGAATGTGCTAATAA
66 AGATGAATGTGCTAATAA
* *
110980 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGA
*
111045 AGAGGAATGTGCTAATAA
66 AGATGAATGTGCTAATAA
* *
111063 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGA
* * * *
111128 AGATAAATGCGCTCATAG
66 AGATGAATGTGCTAATAA
* * * *
111146 CATCTTCTGGAAATGTTCTTTGAATTCTCTGATTTGGTTTG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
111187 ATATAAAACC
Statistics
Matches: 187, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 187 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (83 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGA
AGATGAATGTGCTAATAA
Found at i:112113 original size:113 final size:112
Alignment explanation
Indices: 111915--112457 Score: 853
Period size: 113 Copynumber: 4.8 Consensus size: 112
111905 GCAAAGATTT
* * *
111915 AAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCAAAATGAGAAGAACTTATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
111980 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
65 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
* *
112028 AAATCCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATATGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGAAG
*
112093 GAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
65 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
*
112141 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
112206 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
65 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
* * *
112254 AAATCCATTACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAATAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * **
112319 AAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTATGCTC
65 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
*
112367 AAATCCATCA-TTCGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTG-A-
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAG
*
112429 -A-GAAGAAGAAGTTCATAATGAGAAGAATT
65 GAGGAAGAAGAAATTCATAATGAGAAGAATT
112458 CATCTGAAAA
Statistics
Matches: 400, Mismatches: 26, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
108 25 0.06
109 1 0.00
111 1 0.00
112 31 0.08
113 338 0.85
114 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGG
AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
Found at i:112443 original size:36 final size:38
Alignment explanation
Indices: 112399--112494 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 38
112389 GCTTTTCCAG
*
112399 AGAAGTTCATAATAAGAAGAACTCATCTG-AAG-AAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAAGAAAGA
*
112435 AGAAGTTCATAATGAGAAGAATTCATCTGAAAAAGAAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTG--AAAGAAAGA
*
112475 AAAAGTTCATAATGAGAAGA
1 AGAAGTTCATAATGAGAAGA
112495 GCTTATTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 27 0.51
39 3 0.06
40 23 0.43
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (38 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAAAGAAAGA
Found at i:112757 original size:3 final size:3
Alignment explanation
Indices: 112749--112811 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
112739 TTTGATTTAT
* * * * *
112749 TTA TTA TTA TTA TCA TTA TTA TTA GTA TTA TTA TTA TAA ATA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
112797 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
112812 AATATATATA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:112768 original size:12 final size:11
Alignment explanation
Indices: 112745--112867 Score: 74
Period size: 14 Copynumber: 10.3 Consensus size: 11
112735 CCATTTTGAT
112745 TTATT-TATTA
1 TTATTATATTA
112755 TTATTATCATTA
1 TTATTAT-ATTA
112767 TTATTAGTATTA
1 TTATTA-TATTA
112779 TTATTATA--A
1 TTATTATATTA
*
112788 ATATTACTATTA
1 TTATTA-TATTA
112800 TTATTATTATTAA
1 TTATTA-TATT-A
*
112813 ATATATATATATA
1 TTAT-TATAT-TA
112826 TATATATATATATA
1 T-TAT-TATAT-TA
112840 TATATATATATGTA
1 T-TAT-TATAT-TA
112854 TATATTA-ATTA
1 T-TATTATATTA
112865 TTA
1 TTA
112868 CAAGCCCAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
9 6 0.06
10 9 0.09
11 6 0.06
12 32 0.33
13 11 0.11
14 33 0.34
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTATTATATTA
Found at i:112820 original size:2 final size:2
Alignment explanation
Indices: 112813--112858 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
112803 TTATTATTAA
*
112813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112855 AT AT
1 AT AT
112859 TAATTATTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119225 original size:27 final size:27
Alignment explanation
Indices: 119183--119250 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
119173 CTGTAGGAAT
119183 TATAGAG--ATGATTTGTTACCATTTC-
1 TATAGAGATATGATTTGTTACCA-TTCA
*
119208 TATAGAGATATGATTTGTTATCATTCA
1 TATAGAGATATGATTTGTTACCATTCA
119235 TATAGAGATATGATTT
1 TATAGAGATATGATTT
119251 CTATAATCCC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 7 0.18
26 3 0.08
27 29 0.74
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCA
Found at i:122981 original size:27 final size:27
Alignment explanation
Indices: 122939--123006 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
122929 GTCTAGGAAT
* *
122939 TATAGAG--ATGATTTGTTGCCATTCC
1 TATAGAGATATGATTTGTTACCATTCA
122964 TATAGAGATATGATTTGTTACCATTCA
1 TATAGAGATATGATTTGTTACCATTCA
122991 TATAGAGATATGATTT
1 TATAGAGATATGATTT
123007 CTATAATCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 7 0.18
27 32 0.82
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCA
Found at i:123902 original size:100 final size:100
Alignment explanation
Indices: 123729--123930 Score: 368
Period size: 100 Copynumber: 2.0 Consensus size: 100
123719 GCAAATTTAA
* *
123729 AGACAATGGTAGTTTGGGAGTGATGGATCTCAACCTAATGAATAGAGCTCTTTTAGGGAAATGGT
1 AGACAATAGTAGTTTGGGAGTGATAGATCTCAACCTAATGAATAGAGCTCTTTTAGGGAAATGGT
123794 CTTGGAAGTTTGCAAATGAAAAGGATTATGAGTGG
66 CTTGGAAGTTTGCAAATGAAAAGGATTATGAGTGG
*
123829 AGACAATAGTGGTTTGGGAGTGATAGATCTCAACCTAATGAATAGAGCTCTTTTAGGGAAATGGT
1 AGACAATAGTAGTTTGGGAGTGATAGATCTCAACCTAATGAATAGAGCTCTTTTAGGGAAATGGT
*
123894 CTTGGAAGTTTGCAAATGAAAAGGATTCTGAGTGG
66 CTTGGAAGTTTGCAAATGAAAAGGATTATGAGTGG
123929 AG
1 AG
123931 GAAGTTGATT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (100 bp):
AGACAATAGTAGTTTGGGAGTGATAGATCTCAACCTAATGAATAGAGCTCTTTTAGGGAAATGGT
CTTGGAAGTTTGCAAATGAAAAGGATTATGAGTGG
Found at i:133730 original size:23 final size:25
Alignment explanation
Indices: 133686--133732 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
133676 ATTGATTATT
* *
133686 TAATTTTGCATCCCCTGGAATTTTA
1 TAATTTCGCATCCCCTGAAATTTTA
133711 TAATTTCGCA-CCCCT-AAATTTT
1 TAATTTCGCATCCCCTGAAATTTT
133733 TTAACATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (25 bp):
TAATTTCGCATCCCCTGAAATTTTA
Found at i:135373 original size:16 final size:17
Alignment explanation
Indices: 135352--135383 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
135342 TGCTAATGAT
135352 AAAAATTCTT-TGTGGA
1 AAAAATTCTTATGTGGA
135368 AAAAATTCTTATGTGG
1 AAAAATTCTTATGTGG
135384 CAAACACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (17 bp):
AAAAATTCTTATGTGGA
Found at i:138693 original size:15 final size:15
Alignment explanation
Indices: 138673--138704 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
138663 CATTCCATAA
138673 AATATCCAATAAAAC
1 AATATCCAATAAAAC
138688 AATATCCAATAAAAC
1 AATATCCAATAAAAC
138703 AA
1 AA
138705 ATACATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (15 bp):
AATATCCAATAAAAC
Found at i:158498 original size:24 final size:25
Alignment explanation
Indices: 158445--158500 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
158435 CACGAAAACT
* *
158445 TTGTTTATTGTCTCATTTATAAGTC
1 TTGTTTACTGACTCATTTATAAGTC
* *
158470 -CGTTTACTGACTCGTTTATAA-TC
1 TTGTTTACTGACTCATTTATAAGTC
158493 TTGTTTAC
1 TTGTTTAC
158501 ACGGTTCTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (25 bp):
TTGTTTACTGACTCATTTATAAGTC
Found at i:158712 original size:23 final size:23
Alignment explanation
Indices: 158685--158747 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
158675 TAGCAAACAT
*
158685 TTAAAAGAACATGTTCGTGAATG
1 TTAAACGAACATGTTCGTGAATG
* *
158708 TTAAACGAATATGTTTGTGAATG
1 TTAAACGAACATGTTCGTGAATG
158731 TTAAACGAACATGTTCG
1 TTAAACGAACATGTTCG
158748 CAAACGCTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (23 bp):
TTAAACGAACATGTTCGTGAATG
Found at i:159344 original size:60 final size:60
Alignment explanation
Indices: 159257--159375 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
159247 AAATTGGACT
* * * * **
159257 TTAAACTTTTGAATATTTTAATTTCATCCCCAAATTATGATTATCGTTCTAAATTAGTCC
1 TTAAACTTTTGAACATTTCAATATCATCCCCAAACTATGAACATCGTTCTAAATTAGTCC
* * *
159317 TTAAACTTGTT-AACATTTCAATATCATCCCTAAACTATGAACCTCTTTCTAAATTAGTC
1 TTAAACTT-TTGAACATTTCAATATCATCCCCAAACTATGAACATCGTTCTAAATTAGTC
159376 TCTGAACTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (60 bp):
TTAAACTTTTGAACATTTCAATATCATCCCCAAACTATGAACATCGTTCTAAATTAGTCC
Found at i:159628 original size:60 final size:60
Alignment explanation
Indices: 159542--159689 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
159532 ATAGTTAGGA
* * * * *
159542 ATGAAATTGGAATGTTCAAAAAGTTTAGAA-ACTAATTTAGAGTGA-AGGTCATAGTTTGGGG
1 ATGAAATTGAAATGTT-TAAAAGTTTA-AAGACTAATTTAGAATGATA-ATCATAATTTGGGG
*
159603 ATGAAATTGAAATGTTTAAAAGTTTAAAGACTAATTTAGAATGATAATCATAATTTTGGG
1 ATGAAATTGAAATGTTTAAAAGTTTAAAGACTAATTTAGAATGATAATCATAATTTGGGG
* **
159663 ATAAAATTGAAATCCTTAAAAGTTTAA
1 ATGAAATTGAAATGTTTAAAAGTTTAA
159690 GGACCAATGT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
59 2 0.03
60 58 0.76
61 16 0.21
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
ATGAAATTGAAATGTTTAAAAGTTTAAAGACTAATTTAGAATGATAATCATAATTTGGGG
Found at i:184196 original size:93 final size:92
Alignment explanation
Indices: 184032--184338 Score: 350
Period size: 93 Copynumber: 3.3 Consensus size: 92
184022 ACCGGGCTTG
* * * * *
184032 ATGCAGTTTCATCTGATTCTCCAGATGATAGTCCTCTTCGGCAGCCTCGGAGGATTCCGAGAAGT
1 ATGCAGTTTCATCTGATTCTCCGGATGACAGT-CTCTTCAGCAGCCTCAGAGAATTCCGAGAAGT
* * *
184097 AAGCAAACTGAA-ATT-CTTGGGAGGGAAA
65 AAGCAAAC-CAAGATTGC-CGAGAGGGAAA
* *
184125 ATGCTGTTTCATCTGATTCTCCGGATGACAGCTCTCTTCAGCAGCCTCAGAGAATTCCGAGAAAT
1 ATGCAGTTTCATCTGATTCTCCGGATGACAG-TCTCTTCAGCAGCCTCAGAGAATTCCGAGAAGT
* *
184190 AAGCAAACCAAGATTGCCGAGATGGAAG
65 AAGCAAACCAAGATTGCCGAGAGGGAAA
* * *
184218 ATGCAGTTTCATCTGATTCTCCGGATGACAGTTCTCTTCAGCAACATCAGAGAATTCCGAGAAGC
1 ATGCAGTTTCATCTGATTCTCCGGATGACAG-TCTCTTCAGCAGCCTCAGAGAATTCCGAGAAGT
** *
184283 AAGCAAACCAAGATTGTTGAGAGGGAAG
65 AAGCAAACCAAGATTGCCGAGAGGGAAA
* **
184311 ATGAAGTTTCAGATGATTCGT-CGGATGA
1 ATGCAGTTTCATCTGATTC-TCCGGATGA
184339 TACTTCTCAT
Statistics
Matches: 186, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
92 2 0.01
93 181 0.97
94 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (92 bp):
ATGCAGTTTCATCTGATTCTCCGGATGACAGTCTCTTCAGCAGCCTCAGAGAATTCCGAGAAGTA
AGCAAACCAAGATTGCCGAGAGGGAAA
Found at i:187864 original size:2 final size:2
Alignment explanation
Indices: 187847--187879 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
187837 TTGGGTGGCC
187847 AT AT A- AT AT A- 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
187880 ATAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:187892 original size:12 final size:13
Alignment explanation
Indices: 187847--187895 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 13
187837 TTGGGTGGCC
187847 ATATAAT-ATAAT
1 ATATAATAATAAT
187859 ATATATATATATATAT
1 ATATA-ATA-ATA-AT
187875 ATATAATAATAAT
1 ATATAATAATAAT
187888 A-ATAATAA
1 ATATAATAA
187896 ATCATTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.36
13 5 0.15
14 3 0.09
15 6 0.18
16 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:188670 original size:72 final size:73
Alignment explanation
Indices: 188577--188711 Score: 211
Period size: 73 Copynumber: 1.9 Consensus size: 73
188567 CCATATATTT
* *
188577 GACAAATTAGGTATTTGACAAA-CCCCAATCCCAATTGCTAATAATCTAAGCCTAATCATATACT
1 GACAAATTAGGTATTTGACAAATCCCCAAACCCAATTGCTAATAACCTAAGCCTAATCATATACT
188641 TATGTATC
66 TATGTATC
* *
188649 GACAAATT-GGATATTTGACAAATCCCCAAAGCTAATTGCTAATAACCTAAGCCTAATCATATA
1 GACAAATTAGG-TATTTGACAAATCCCCAAACCCAATTGCTAATAACCTAAGCCTAATCATATA
188712 TTCTATTGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
71 2 0.04
72 19 0.33
73 36 0.63
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (73 bp):
GACAAATTAGGTATTTGACAAATCCCCAAACCCAATTGCTAATAACCTAAGCCTAATCATATACT
TATGTATC
Found at i:189735 original size:20 final size:20
Alignment explanation
Indices: 189712--189779 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
189702 AGTTTCCAAT
* *
189712 TTCGCAACGCGATAGTCAAA
1 TTCGCAACACGAAAGTCAAA
*
189732 TTCGGAACACGAAAGTCAAA
1 TTCGCAACACGAAAGTCAAA
* **
189752 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACACGAAAGTCAAA
189771 TTCGCAACA
1 TTCGCAACA
189780 GGTTTTAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.40
20 24 0.60
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (20 bp):
TTCGCAACACGAAAGTCAAA
Found at i:190545 original size:12 final size:12
Alignment explanation
Indices: 190524--190557 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
190514 ACCACATTTC
*
190524 CAATACCAAACA
1 CAATATCAAACA
190536 CAATATCAAACA
1 CAATATCAAACA
*
190548 CAATCTCAAA
1 CAATATCAAA
190558 GCCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:193365 original size:20 final size:20
Alignment explanation
Indices: 193342--193397 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
193332 AATCGCAAAC
193342 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* *
193362 CGAATTTGACATTCGCGTTT
1 CGAATTTGACTTTCGCGTTG
*
193382 CGAATTTGACTATCGC
1 CGAATTTGACTTTCGC
193398 AACGCTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:193526 original size:25 final size:25
Alignment explanation
Indices: 193488--193537 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
193478 AAATCAATTA
*
193488 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
193513 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
193538 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:193944 original size:18 final size:18
Alignment explanation
Indices: 193923--193959 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
193913 GTAATTGGAG
193923 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
193941 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
193959 T
1 T
193960 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:193966 original size:24 final size:24
Alignment explanation
Indices: 193915--193967 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
193905 TTTCATATGT
* * *
193915 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
193939 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
193963 AATTT
1 AATTT
193968 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:194315 original size:40 final size:40
Alignment explanation
Indices: 194271--194346 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
194261 TCCGATGCTC
*
194271 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAAAAA
1 ATCAAAATCCAAAGCCCATATGGTGCCAAGCAAAAAAAAA
*
194311 ATCAAAATCCAAATCCCATATGGTGCCAAGCAAAAA
1 ATCAAAATCCAAAGCCCATATGGTGCCAAGCAAAAA
194347 GATATCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (40 bp):
ATCAAAATCCAAAGCCCATATGGTGCCAAGCAAAAAAAAA
Found at i:194562 original size:20 final size:20
Alignment explanation
Indices: 194534--194596 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
194524 ATGTTGCGAT
*
194534 CAACGCGAAAGTTAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
194554 CAACACGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
194574 CGACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
194594 CAA
1 CAA
194597 ACCAAAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:194630 original size:20 final size:20
Alignment explanation
Indices: 194604--194648 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
194594 CAAACCAAAA
194604 ATCGCGTTGCAAATTTGACT
1 ATCGCGTTGCAAATTTGACT
* *
194624 TTCGCGTTGCGAATTTGACT
1 ATCGCGTTGCAAATTTGACT
194644 ATCGC
1 ATCGC
194649 AACGCTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (20 bp):
ATCGCGTTGCAAATTTGACT
Found at i:194839 original size:47 final size:49
Alignment explanation
Indices: 194732--194830 Score: 139
Period size: 52 Copynumber: 2.0 Consensus size: 49
194722 TTTTAAAACA
*
194732 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTT
1 ACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTT
*
194784 ACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTT
1 ACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTT
194831 CCTCATCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
47 17 0.38
48 3 0.07
52 25 0.56
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (49 bp):
ACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTT
Found at i:196257 original size:21 final size:21
Alignment explanation
Indices: 196233--196328 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
196223 GACAGAACCA
*
196233 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
196254 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
196275 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
*
196296 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
196317 CTTGAATGATGA
1 CTTGAACGATGA
196329 TAGGTGCATT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:196311 original size:42 final size:42
Alignment explanation
Indices: 196233--196328 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
196223 GACAGAACCA
* * * * *
196233 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
*
196275 CTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCGCCT
1 CTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
196317 CTTGAATGATGA
1 CTTGAATGATGA
196329 TAGGTGCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (42 bp):
CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
Found at i:197890 original size:29 final size:30
Alignment explanation
Indices: 197843--197914 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
197833 CCCGAAGGAC
* *
197843 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCATAGGTCACAAAGAACCCCGGCAA
* * *
197872 CTATCCATAGGTTATAAAGAACCTCGGCAA
1 CTATCCATAGGTCACAAAGAACCCCGGCAA
*
197902 CTGTCCATAGGTC
1 CTATCCATAGGTC
197915 CCGACGAACC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCCCGGCAA
Found at i:197938 original size:31 final size:31
Alignment explanation
Indices: 197900--197972 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
197890 GAACCTCGGC
*
197900 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
197931 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
197962 AACTGTCCATA
1 AACTGTCCATA
197973 TGTCTCAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:197994 original size:31 final size:31
Alignment explanation
Indices: 197900--197995 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
197890 GAACCTCGGC
** * * *
197900 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCAAAAGAACATAAGTA
** * *
197931 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCAAAAGAACATAAGTA
*
197962 AACTGTCCATATGTCTCAAAAG-ACATAAGTA
1 AACTGTCCATAGGTC-CAAAAGAACATAAGTA
197993 AAC
1 AAC
197996 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 54 0.93
32 4 0.07
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCCAAAAGAACATAAGTA
Found at i:198972 original size:20 final size:20
Alignment explanation
Indices: 198947--199001 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
198937 TTCCCCTTGA
198947 AGTGCATCGATGCATGCTAT
1 AGTGCATCGATGCATGCTAT
198967 AGTGCATCGATGCATGCTAT
1 AGTGCATCGATGCATGCTAT
198987 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
199002 TCTTTAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATGCTAT
Found at i:199081 original size:64 final size:63
Alignment explanation
Indices: 199012--199152 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 63
199002 TCTTTAACAT
* *
199012 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * ** * * * * *
199075 GATGCATCAATGCACTTCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
199139 GTGCATCGATGCAC
1 GTGCATCGATGCAC
199153 ATTCAATATG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 18 0.28
64 46 0.72
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:201695 original size:22 final size:22
Alignment explanation
Indices: 201664--201715 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
201654 ATATGGAGAT
*
201664 AGACGAATTTCGTCGGAAATGG
1 AGACGGATTTCGTCGGAAATGG
*
201686 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGTCGGAAATGG
*
201708 GGACGGAT
1 AGACGGAT
201716 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.38, T:0.21
Consensus pattern (22 bp):
AGACGGATTTCGTCGGAAATGG
Found at i:201868 original size:20 final size:20
Alignment explanation
Indices: 201843--201907 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
201833 GCGTAAAAAC
201843 ATTTGACTTTCGCTTTGCGA
1 ATTTGACTTTCGCTTTGCGA
*
201863 ATTTGACTTTTG-TGTTGCGA
1 ATTTGACTTTCGCT-TTGCGA
* * *
201883 ATTTGACTATCGCGTTGTGA
1 ATTTGACTTTCGCTTTGCGA
201903 ATTTG
1 ATTTG
201908 GAAAATCACA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (20 bp):
ATTTGACTTTCGCTTTGCGA
Found at i:202130 original size:27 final size:27
Alignment explanation
Indices: 202100--202151 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
202090 CTAAATTATA
*
202100 GTTTAGTCCTTATACTATAATTTAAGG
1 GTTTAATCCTTATACTATAATTTAAGG
* * *
202127 GTTTAATCTTTATATTTTAATTTAA
1 GTTTAATCCTTATACTATAATTTAA
202152 TATAATAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.52
Consensus pattern (27 bp):
GTTTAATCCTTATACTATAATTTAAGG
Found at i:204150 original size:22 final size:22
Alignment explanation
Indices: 204117--204169 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
204107 ATCAATTTAG
204117 ACAAACAA-ATAACACTATA-AAA
1 ACAAA-AATATAA-ACTATATAAA
*
204139 ACAAAAATATAAGCTATATAAA
1 ACAAAAATATAAACTATATAAA
*
204161 ATAAAAATA
1 ACAAAAATA
204170 AAGATATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.19
Consensus pattern (22 bp):
ACAAAAATATAAACTATATAAA
Found at i:207276 original size:32 final size:32
Alignment explanation
Indices: 207220--207307 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
207210 ACATGTTACG
* * **
207220 TCACTAAAATTGATGACATAATATGTGTCATA
1 TCACTAAAAGTGATGACATGATATGCATCATA
* *
207252 TCA-TCAAAAGTGATGACATGATATGCATCGTG
1 TCACT-AAAAGTGATGACATGATATGCATCATA
*
207284 TCACTAAAAGTGATGACACGATAT
1 TCACTAAAAGTGATGACATGATAT
207308 TTTTAACTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.02
32 45 0.96
33 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (32 bp):
TCACTAAAAGTGATGACATGATATGCATCATA
Found at i:207437 original size:2 final size:2
Alignment explanation
Indices: 207426--207471 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
207416 CAAAATGAAA
207426 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
207467 AT AT A
1 AT AT A
207472 ATCACGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:213648 original size:41 final size:41
Alignment explanation
Indices: 213566--213649 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
213556 TCTTGGTGAC
*
213566 ATAGGACTAGATTCCAGGTTTAGGGTTTAGGGACTTGTGAT
1 ATAGGACTAGATTCCAGGTTTAGGGTTTAGGGACTTATGAT
* *
213607 ATAGGACTA-AGTTTCAGGTTTAGGGTTTA-TGACCTTATGAT
1 ATAGGACTAGA-TTCCAGGTTTAGGGTTTAGGGA-CTTATGAT
213648 AT
1 AT
213650 GTTCATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 3 0.08
41 35 0.92
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.37
Consensus pattern (41 bp):
ATAGGACTAGATTCCAGGTTTAGGGTTTAGGGACTTATGAT
Found at i:213820 original size:34 final size:34
Alignment explanation
Indices: 213782--213925 Score: 152
Period size: 34 Copynumber: 4.3 Consensus size: 34
213772 TCAGATTTAG
* *
213782 GGTTTAGGGTCTTGTGATATATGATTA-TTTCCTA
1 GGTTTAGGGTCTTGTGATATAGGATTAGGTT-CTA
* **
213816 GGTTTAGGGT-TTGTGACAT-GTTTTAGGTT-TA
1 GGTTTAGGGTCTTGTGATATAGGATTAGGTTCTA
** *
213847 GGGTTTAGGACCTTTTGATATAGGATTAGGTTCTA
1 -GGTTTAGGGTCTTGTGATATAGGATTAGGTTCTA
* *
213882 GGTTTAGGGTATTGTGATATAGGACTAGGTTCTA
1 GGTTTAGGGTCTTGTGATATAGGATTAGGTTCTA
213916 GGTTTAGGGT
1 GGTTTAGGGT
213926 TTATAGCCTT
Statistics
Matches: 89, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
31 2 0.02
32 11 0.12
33 17 0.19
34 57 0.64
35 2 0.02
ACGTcount: A:0.20, C:0.06, G:0.31, T:0.43
Consensus pattern (34 bp):
GGTTTAGGGTCTTGTGATATAGGATTAGGTTCTA
Found at i:213847 original size:66 final size:67
Alignment explanation
Indices: 213761--213898 Score: 190
Period size: 66 Copynumber: 2.1 Consensus size: 67
213751 GTTCCAGGCA
** * *
213761 TGTGACATGTTTCAGATTTAGGGTTTAGGGTCTTGTGATATATGATTA-TTTCCTAGGTTTAGGG
1 TGTGACATGTTTCAGATTTAGGGTTTAGGACCTTGTGATATAGGATTAGGTT-CTAGGTTTAGGG
213825 T-T
65 TAT
* * *
213827 TGTGACATGTTTTAGGTTTAGGGTTTAGGACCTTTTGATATAGGATTAGGTTCTAGGTTTAGGGT
1 TGTGACATGTTTCAGATTTAGGGTTTAGGACCTTGTGATATAGGATTAGGTTCTAGGTTTAGGGT
213892 AT
66 AT
213894 TGTGA
1 TGTGA
213899 TATAGGACTA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
66 55 0.87
67 8 0.13
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.44
Consensus pattern (67 bp):
TGTGACATGTTTCAGATTTAGGGTTTAGGACCTTGTGATATAGGATTAGGTTCTAGGTTTAGGGT
AT
Found at i:214241 original size:30 final size:30
Alignment explanation
Indices: 214217--214322 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
214207 AAGTCGTCGG
* *
214217 GAACATAGTGTGTCTTCGAAAAGTCGCTGA
1 GAACACAGTGCGTCTTCGAAAAGTCGCTGA
* *
214247 GAAGACAGTGCGTCTTCGAAAAGTCGCTAA
1 GAACACAGTGCGTCTTCGAAAAGTCGCTGA
* * *
214277 GAAGACAGTGCGTCTTAGAAAAGTCGCTAA
1 GAACACAGTGCGTCTTCGAAAAGTCGCTGA
* *
214307 GAAGACAGTGTGTCTT
1 GAACACAGTGCGTCTT
214323 TAGTTTTGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (30 bp):
GAACACAGTGCGTCTTCGAAAAGTCGCTGA
Found at i:217192 original size:19 final size:19
Alignment explanation
Indices: 217170--217208 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
217160 TATATACACA
*
217170 AATATTATAATTGATTAAT
1 AATATTATAACTGATTAAT
217189 AATATTATAACTGATTAAT
1 AATATTATAACTGATTAAT
217208 A
1 A
217209 TGTGGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (19 bp):
AATATTATAACTGATTAAT
Found at i:218955 original size:2 final size:2
Alignment explanation
Indices: 218950--218994 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
218940 CCATCCATCC
218950 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218991 AT AT
1 AT AT
218995 CCTTCCCTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:221545 original size:3 final size:3
Alignment explanation
Indices: 221537--221562 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
221527 AATATTAATA
221537 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
221563 ATTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:223011 original size:2 final size:2
Alignment explanation
Indices: 223004--223030 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
222994 CATGAACAAG
223004 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
223031 GTTTATGTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:223138 original size:2 final size:2
Alignment explanation
Indices: 223131--223201 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
223121 TAATGTTTTA
* *
223131 AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
223173 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
223202 AAAGATCTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:224834 original size:32 final size:32
Alignment explanation
Indices: 224797--224858 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
224787 TTTCACCAGT
*
224797 ACTAA-CTAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACCT-ATTTCTTTTCTTTTGATTGTGTAC
224829 ACTAACCTATTTCTTTTCTTTTGATTGTGT
1 ACTAACCTATTTCTTTTCTTTTGATTGTGT
224859 CATTTCTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (32 bp):
ACTAACCTATTTCTTTTCTTTTGATTGTGTAC
Found at i:228089 original size:2 final size:2
Alignment explanation
Indices: 228082--228135 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
228072 TCATTTATCC
*
228082 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
228124 AT AT AT AT AT AT
1 AT AT AT AT AT AT
228136 TCCTTATTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231810 original size:403 final size:403
Alignment explanation
Indices: 231063--231869 Score: 1578
Period size: 403 Copynumber: 2.0 Consensus size: 403
231053 ATTTCGAAGG
231063 AAGTGGATGCCAAACTGGGAAGGTTCTTATGTTATAAAAAAGGCCTTTTTAGAAGGAGCTTTAGT
1 AAGTGGATGCCAAACTGGGAAGGTTCTTATGTTATAAAAAAGGCCTTTTTAGAAGGAGCTTTAGT
231128 TTTGACTAAAATGGATGGAGAAGATTTGCCTAATCCTGTGAATTCTGACTCAGTCAAGCAATATT
66 TTTGACTAAAATGGATGGAGAAGATTTGCCTAATCCTGTGAATTCTGACTCAGTCAAGCAATATT
231193 ACACTTGAAGAAGAAAAAAAGAAAAGAAAAGCAAAGAAAAATGGACGAGACTCAAGTCAAATAGC
131 ACACTTGAAGAAGAAAAAAAGAAAAGAAAAGCAAAGAAAAATGGACGAGACTCAAGTCAAATAGC
231258 GTATCAAATTTCAAACCATGAGATTGATCATGCACAATTATTCCAGAATCACTTCACTCGAAGAT
196 GTATCAAATTTCAAACCATGAGATTGATCATGCACAATTATTCCAGAATCACTTCACTCGAAGAT
231323 CATAGAACATCAAAAGAGAGACACATACAAGCATATTCAAATTGAGCAAGACATGATTGAAGGCA
261 CATAGAACATCAAAAGAGAGACACATACAAGCATATTCAAATTGAGCAAGACATGATTGAAGGCA
*
231388 TCATAATGAATTGATCCTTGGTTCAATACCCTGAAACACTTGTTTTGGCCTATTTATCCTTTTCT
326 TCATAATGAATTGATCCTTGGTTCAATACCCTGAAACACTTGTTTGGGCCTATTTATCCTTTTCT
231453 TTCATAACCGTGA
391 TTCATAACCGTGA
* *
231466 AAGTGGATGCCAAACTGGGAAGGTTCTTATGTTGTAAAAAAGGCCTTTTTAGGAGGAGCTTTAGT
1 AAGTGGATGCCAAACTGGGAAGGTTCTTATGTTATAAAAAAGGCCTTTTTAGAAGGAGCTTTAGT
231531 TTTGACTAAAATGGATGGAGAAGATTTGCCTAATCCTGTGAATTCTGACTCAGTCAAGCAATATT
66 TTTGACTAAAATGGATGGAGAAGATTTGCCTAATCCTGTGAATTCTGACTCAGTCAAGCAATATT
*
231596 ACACTTGAAGAAGAAAAAAAGAAAAGAAAAGCAAAGAAAAATGGACGAGACTCAAGTCAAATGGC
131 ACACTTGAAGAAGAAAAAAAGAAAAGAAAAGCAAAGAAAAATGGACGAGACTCAAGTCAAATAGC
231661 GTATCAAATTTCAAACCATGAGATTGATCATGCACAATTATTCCAGAATCACTTCACTCGAAGAT
196 GTATCAAATTTCAAACCATGAGATTGATCATGCACAATTATTCCAGAATCACTTCACTCGAAGAT
231726 CATAGAACATCAAAAGAGAGACACATACAAGCATATTCAAATTGAGCAAGACATGATTGAAGGCA
261 CATAGAACATCAAAAGAGAGACACATACAAGCATATTCAAATTGAGCAAGACATGATTGAAGGCA
231791 TCATAATGAATTGATCCTTGGTTCAATACCCTGAAACACTTGTTTGGGCCTATTTATCCTTTTCT
326 TCATAATGAATTGATCCTTGGTTCAATACCCTGAAACACTTGTTTGGGCCTATTTATCCTTTTCT
231856 TTCATAACCGTGA
391 TTCATAACCGTGA
231869 A
1 A
231870 CCATTGCCTA
Statistics
Matches: 400, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
403 400 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (403 bp):
AAGTGGATGCCAAACTGGGAAGGTTCTTATGTTATAAAAAAGGCCTTTTTAGAAGGAGCTTTAGT
TTTGACTAAAATGGATGGAGAAGATTTGCCTAATCCTGTGAATTCTGACTCAGTCAAGCAATATT
ACACTTGAAGAAGAAAAAAAGAAAAGAAAAGCAAAGAAAAATGGACGAGACTCAAGTCAAATAGC
GTATCAAATTTCAAACCATGAGATTGATCATGCACAATTATTCCAGAATCACTTCACTCGAAGAT
CATAGAACATCAAAAGAGAGACACATACAAGCATATTCAAATTGAGCAAGACATGATTGAAGGCA
TCATAATGAATTGATCCTTGGTTCAATACCCTGAAACACTTGTTTGGGCCTATTTATCCTTTTCT
TTCATAACCGTGA
Found at i:232695 original size:32 final size:33
Alignment explanation
Indices: 232653--232730 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
232643 TGAGGAACAC
*
232653 TGGAGACATCTTTAAAG-ATTCAAAATCGAATAT
1 TGGAG-CATCTTTAAAGCAATCAAAATCGAATAT
* * *
232686 TGGAGCATCTTTGAGGCAATCAACATCGAATAT
1 TGGAGCATCTTTAAAGCAATCAAAATCGAATAT
*
232719 AGGAGCATCTTT
1 TGGAGCATCTTT
232731 GGGGATTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 9 0.23
33 30 0.77
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (33 bp):
TGGAGCATCTTTAAAGCAATCAAAATCGAATAT
Found at i:232714 original size:33 final size:32
Alignment explanation
Indices: 232672--232744 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
232662 CTTTAAAGAT
* *
232672 TCAAAATCGAATATTGGAGCATCTTTGAGGCAA
1 TCAACATCGAATATAGGAGCATCTTTG-GGCAA
* *
232705 TCAACATCGAATATAGGAGCATCTTTGGGGAT
1 TCAACATCGAATATAGGAGCATCTTTGGGCAA
232737 TCAACATC
1 TCAACATC
232745 CTGATGCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 11 0.31
33 25 0.69
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (32 bp):
TCAACATCGAATATAGGAGCATCTTTGGGCAA
Found at i:233185 original size:34 final size:34
Alignment explanation
Indices: 233137--233203 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
233127 TGATGGTGTT
233137 TTTCTAAAATCAAATTTTGCCTCACTTGAGACAA
1 TTTCTAAAATCAAATTTTGCCTCACTTGAGACAA
**
233171 TTTCTCAAAA-CAAATTTTGTTTCACTTGAGACA
1 TTTCT-AAAATCAAATTTTGCCTCACTTGAGACA
233204 TTTTTCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.37
Consensus pattern (34 bp):
TTTCTAAAATCAAATTTTGCCTCACTTGAGACAA
Found at i:233449 original size:15 final size:15
Alignment explanation
Indices: 233401--233449 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
233391 TTTAATATCG
233401 TTTCTTTTGAAACGAA
1 TTTCTTTTGAAAC-AA
*
233417 TTTCGTCTCTTGAGACAA
1 TTTC-T-T-TTGAAACAA
233435 TTTCTTTTGAAACAA
1 TTTCTTTTGAAACAA
233450 AAATCATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 8 0.29
16 5 0.18
17 2 0.07
18 7 0.25
19 6 0.21
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (15 bp):
TTTCTTTTGAAACAA
Found at i:234252 original size:123 final size:125
Alignment explanation
Indices: 233907--234256 Score: 587
Period size: 126 Copynumber: 2.8 Consensus size: 125
233897 ATGTCACCCC
* *
233907 TAGATAACCAACCGTACCCATCAGAGTGAAACCATGTTATCACCTTTAGATGTCCAAGACTCATG
1 TAGATAACCAACCGTCCCCATCAGAGTGGAACCATGTTATCACCTTTAGATGTCCAAGACTCATG
* * *
233972 AACAGATGAGCAGTGTCATCACATGACCAGATTTTCTCATTATATAGGAGTTGTGTCAACT
66 AACAGATGAGCAGTGTCATCACATGACCAGA-TCTCTCATTATATAGGAGCTCTGTCAACT
234033 TAGATAACCAACCGTCCCCATCAGAGTGGAACCATGTTATCACCTTTAGATGTCCAAGACTCATG
1 TAGATAACCAACCGTCCCCATCAGAGTGGAACCATGTTATCACCTTTAGATGTCCAAGACTCATG
* *
234098 AACAGATGAGCAGTGTCATCACATGATCAGATCTC-CATTATGTAGGAGCTCTGTCAACT
66 AACAGATGAGCAGTGTCATCACATGACCAGATCTCTCATTATATAGGAGCTCTGTCAACT
* * *
234157 TAGATAACCAGCCGTCCCCATCAGAGTGGAA-CGTGTTATCACCTTTAGATGTCCAAGACTCATT
1 TAGATAACCAACCGTCCCCATCAGAGTGGAACCATGTTATCACCTTTAGATGTCCAAGACTCATG
234221 AACAGATGAGCAGTGTCATCACATGACCAGATCTCT
66 AACAGATGAGCAGTGTCATCACATGACCAGATCTCT
234257 TCATCACGTA
Statistics
Matches: 212, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
123 65 0.31
124 51 0.24
125 3 0.01
126 93 0.44
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (125 bp):
TAGATAACCAACCGTCCCCATCAGAGTGGAACCATGTTATCACCTTTAGATGTCCAAGACTCATG
AACAGATGAGCAGTGTCATCACATGACCAGATCTCTCATTATATAGGAGCTCTGTCAACT
Found at i:234396 original size:40 final size:40
Alignment explanation
Indices: 234341--234663 Score: 195
Period size: 40 Copynumber: 7.6 Consensus size: 40
234331 TGGCTTGACG
*
234341 TCCTCATCACGTAGGAACCGTGTCATCACCCGACCTGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCACCCGACCTGATC
* ** * *
234381 TCCTCATCACTTAGGAGCCGTGTCAATC-CTTGATAACCAGAAC
1 TCCTCATCACGTAGGAGCCGTGTC-ATCACCCG---ACCTGATC
* * * * * *
234424 TCTTCATCATGTATGAGCCATGTTATCACCTTTAGATGGCCTGA-C
1 TCCTCATCACGTAGGAGCCGTGTCATCACC---CGA---CCTGATC
*
234469 GTCCTCATCACGTAGGAACCGTGTCATCACCCGACCTGATC
1 -TCCTCATCACGTAGGAGCCGTGTCATCACCCGACCTGATC
* ** * *
234510 TCGTCATCACGTAGGAGCCGTGTCCATC-CTTGATAACCAGAAC
1 TCCTCATCACGTAGGAGCCGTGT-CATCACCCG---ACCTGATC
* * * * *
234553 TCTTCATCATGTATGAGCCGTGTTATCACCTTTAGATGGCCTGA-C
1 TCCTCATCACGTAGGAGCCGTGTCATCACC---CGA---CCTGATC
* *
234598 GTCCTCATCACATAGGAACCGTGTCATCACCCGACCTGATC
1 -TCCTCATCACGTAGGAGCCGTGTCATCACCCGACCTGATC
234639 TCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAGCCGTGTCA
234664 ATCCTTGATA
Statistics
Matches: 213, Mismatches: 44, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
40 80 0.38
41 9 0.04
42 6 0.03
43 58 0.27
45 2 0.01
46 58 0.27
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (40 bp):
TCCTCATCACGTAGGAGCCGTGTCATCACCCGACCTGATC
Found at i:234442 original size:43 final size:42
Alignment explanation
Indices: 234384--234694 Score: 161
Period size: 43 Copynumber: 7.2 Consensus size: 42
234374 CCTGATCTCC
*
234384 TCATCACTTAGGAGCCGTGTCAATCCTTGATAACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTC-ATCCTTGATAACCAGAACTCT
* * * * ** * *
234427 TCATCATGTATGAGCCATGTTATCACCTTTAGATGGCCTG-ACGTCC
1 TCATCACGTAGGAGCCGTGTCAT--CC-TT-GATAACCAGAAC-TCT
* ** * * *
234473 TCATCACGTAGGAACCGTGTCATCACCCG---ACCTGATCTCG
1 TCATCACGTAGGAGCCGTGTCATC-CTTGATAACCAGAACTCT
234513 TCATCACGTAGGAGCCGTGTCCATCCTTGATAACCAGAACTCT
1 TCATCACGTAGGAGCCGTGT-CATCCTTGATAACCAGAACTCT
* * * ** * *
234556 TCATCATGTATGAGCCGTGTTATCACCTTTAGATGGCCTG-ACGTCC
1 TCATCACGTAGGAGCCGTGTCAT--CC-TT-GATAACCAGAAC-TCT
* * ** * * *
234602 TCATCACATAGGAACCGTGTCATCACCCG---ACCTGATCTCC
1 TCATCACGTAGGAGCCGTGTCATC-CTTGATAACCAGAACTCT
*
234642 TCATCACGTAGGAGCCGTGTCAATCCTTGATAACCAGAACTTT
1 TCATCACGTAGGAGCCGTGTC-ATCCTTGATAACCAGAACTCT
234685 TCATCACGTA
1 TCATCACGTA
234695 TGAGTCATGT
Statistics
Matches: 197, Mismatches: 49, Indels: 44
0.68 0.17 0.15
Matches are distributed among these distances:
40 55 0.28
41 9 0.05
42 4 0.02
43 61 0.31
44 6 0.03
45 10 0.05
46 52 0.26
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (42 bp):
TCATCACGTAGGAGCCGTGTCATCCTTGATAACCAGAACTCT
Found at i:234483 original size:129 final size:129
Alignment explanation
Indices: 234233--234711 Score: 727
Period size: 129 Copynumber: 3.7 Consensus size: 129
234223 CAGATGAGCA
** * * * * *
234233 GTGTCATCACATGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCCTGGATAACTA-AGA-
1 GTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAGCCGTGTCAATCCTTGATAACCAGA-AC
* *
234296 --TTCATCATAGTATGAG-TAGTGTTATCA-CTCTTAGATGGCTTGACGTCCTCATCACGTAGGA
65 TCTTCATCAT-GTATGAGCCA-TGTTATCACCT-TTAGATGGCCTGACGTCCTCATCACGTAGGA
234357 ACC
127 ACC
*
234360 GTGTCATCACCCGACCTGATCTCCTCATCACTTAGGAGCCGTGTCAATCCTTGATAACCAGAACT
1 GTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAGCCGTGTCAATCCTTGATAACCAGAACT
234425 CTTCATCATGTATGAGCCATGTTATCACCTTTAGATGGCCTGACGTCCTCATCACGTAGGAACC
66 CTTCATCATGTATGAGCCATGTTATCACCTTTAGATGGCCTGACGTCCTCATCACGTAGGAACC
* *
234489 GTGTCATCACCCGACCTGATCTCGTCATCACGTAGGAGCCGTGTCCATCCTTGATAACCAGAACT
1 GTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAGCCGTGTCAATCCTTGATAACCAGAACT
* *
234554 CTTCATCATGTATGAGCCGTGTTATCACCTTTAGATGGCCTGACGTCCTCATCACATAGGAACC
66 CTTCATCATGTATGAGCCATGTTATCACCTTTAGATGGCCTGACGTCCTCATCACGTAGGAACC
234618 GTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAGCCGTGTCAATCCTTGATAACCAGAACT
1 GTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAGCCGTGTCAATCCTTGATAACCAGAACT
* * *
234683 TTTCATCACGTATGAGTCATGTTATCACC
66 CTTCATCATGTATGAGCCATGTTATCACC
234712 CTTCCTAAAG
Statistics
Matches: 325, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
127 53 0.16
128 1 0.00
129 260 0.80
130 11 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (129 bp):
GTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAGCCGTGTCAATCCTTGATAACCAGAACT
CTTCATCATGTATGAGCCATGTTATCACCTTTAGATGGCCTGACGTCCTCATCACGTAGGAACC
Found at i:237338 original size:2 final size:2
Alignment explanation
Indices: 237331--237371 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
237321 CGAGTTTTAT
237331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
237372 TGAGACGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:239205 original size:23 final size:23
Alignment explanation
Indices: 239179--239237 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
239169 ACATACATTA
* *
239179 TTTTTCTTTGTCTTTATGACATG
1 TTTTTCTATGTCTTTATGACACG
* *
239202 TTTTTCTATATTTTTATGACACG
1 TTTTTCTATGTCTTTATGACACG
*
239225 TTTTTCTCTGTCT
1 TTTTTCTATGTCT
239238 GTTGGCACAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.14, C:0.15, G:0.10, T:0.61
Consensus pattern (23 bp):
TTTTTCTATGTCTTTATGACACG
Found at i:241031 original size:3 final size:3
Alignment explanation
Indices: 241025--241062 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
241015 AAGCCATCAT
*
241025 CAC CAC CAA CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
241063 TCCAACACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:244189 original size:19 final size:20
Alignment explanation
Indices: 244160--244197 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
244150 AGAAATTTGC
244160 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
244180 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
244198 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:244240 original size:63 final size:62
Alignment explanation
Indices: 244165--244323 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 62
244155 TTTGCTGAAG
* * *
244165 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GAAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
* ** **
244228 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGAAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
244291 GTGCATCGATGCATCAGAAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGAAGTGCATCGATGCAT
244324 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGAAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:244957 original size:149 final size:149
Alignment explanation
Indices: 244779--245081 Score: 570
Period size: 149 Copynumber: 2.0 Consensus size: 149
244769 GGATAGAGGG
*
244779 TCTACGCGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACACGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
*
244844 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATAATATGTGGTCCTTATGGACATTATTA
244909 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
244928 TCTACACGGTCTTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACACGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
244993 ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATAATATGTGGTCCTTATGGACATTATTA
245058 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
245077 TCTAC
1 TCTAC
245082 GTGGCACTTC
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (149 bp):
TCTACACGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:245097 original size:23 final size:23
Alignment explanation
Indices: 245060--245105 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
245050 CATTATTATA
* *
245060 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGATGCAATTATACG
*
245083 TGGCACTTCGATGCAATTATACG
1 TGGCACTACGATGCAATTATACG
245106 AGCTGTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTACGATGCAATTATACG
Done.