Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 73 of 318
Found at i:25254894 original size:3 final size:3
Alignment explanation
Indices: 25254857--25254881 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25254847 ATTGTAGATC
25254857 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
25254882 ATACTCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25265538 original size:37 final size:37
Alignment explanation
Indices: 25265477--25265622 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
25265467 TACGTATGAT
* *
25265477 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
25265512 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
25265549 CACTTATCACTTTGTTTCTTGATCAGATAAGTGCAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
25265586 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
25265623 TAAAACTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:25265639 original size:46 final size:46
Alignment explanation
Indices: 25265586--25265802 Score: 272
Period size: 46 Copynumber: 4.6 Consensus size: 46
25265576 TAAGTGCAGC
* * * *
25265586 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAACTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
* *
25265632 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
*
25265678 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
* * * *
25265724 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
*
25265776 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
25265803 AGTACTCAAA
Statistics
Matches: 153, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
46 111 0.73
48 1 0.01
50 1 0.01
52 40 0.26
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
Found at i:25265754 original size:52 final size:52
Alignment explanation
Indices: 25265675--25265788 Score: 158
Period size: 52 Copynumber: 2.2 Consensus size: 52
25265665 TAGCCGAAGC
* **
25265675 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTT-TCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
* *
25265728 TATCACTTTCCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTT-CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
25265780 TATCACTTT
1 TATCACTTT
25265789 ATCACTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 44 0.80
53 11 0.20
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (52 bp):
TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
Found at i:25277363 original size:44 final size:44
Alignment explanation
Indices: 25277312--25277403 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
25277302 CTGAAGTATC
*
25277312 AGTAACAGTACGAGACACA-AAGTGCCTCATCGACACAAAGTCGA
1 AGTAACAGTACGACAC-CATAAGTGCCTCATCGACACAAAGTCGA
* * *
25277356 AGTAACAGTACGACACCATTAGTGCCTCATCGACTCAAGGTCGA
1 AGTAACAGTACGACACCATAAGTGCCTCATCGACACAAAGTCGA
25277400 AGTA
1 AGTA
25277404 TCCTGAACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 2 0.05
44 41 0.95
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (44 bp):
AGTAACAGTACGACACCATAAGTGCCTCATCGACACAAAGTCGA
Found at i:25287832 original size:8 final size:8
Alignment explanation
Indices: 25287821--25287864 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
25287811 CTTTTATGTT
25287821 TTATTATA
1 TTATTATA
25287829 TTATT-TAA
1 TTATTAT-A
25287837 TTATTATA
1 TTATTATA
*
25287845 TTAATATA
1 TTATTATA
25287853 TTATTATA
1 TTATTATA
25287861 TTAT
1 TTAT
25287865 ATAGTTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 1 0.03
8 30 0.94
9 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATTATA
Found at i:25287840 original size:16 final size:17
Alignment explanation
Indices: 25287821--25287867 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
25287811 CTTTTATGTT
*
25287821 TTATTATATTATTTA-A
1 TTATTATATTATATATA
25287837 TTATTATATTA-ATATA
1 TTATTATATTATATATA
25287853 TTATTATATTATATA
1 TTATTATATTATATA
25287868 GTTAAGTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 2 0.07
16 23 0.82
17 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTATATTATATATA
Found at i:25287863 original size:24 final size:24
Alignment explanation
Indices: 25287825--25287872 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
25287815 TATGTTTTAT
25287825 TATATTATTTAATTATTATA-TTAA
1 TATATTATTTAATTA-TATAGTTAA
25287849 TATATTA-TTATATTATATAGTTAA
1 TATATTATTTA-ATTATATAGTTAA
25287873 GTCTTAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATTATTTAATTATATAGTTAA
Found at i:25303125 original size:21 final size:21
Alignment explanation
Indices: 25303091--25303130 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25303081 AGATGAAAAT
*
25303091 AAAAACTAAACCTCGAAACAC
1 AAAAACTAAACCTCAAAACAC
25303112 AAAAAC-AAACCCTCAAAAC
1 AAAAACTAAA-CCTCAAAAC
25303131 GTAAACACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.60, C:0.30, G:0.03, T:0.07
Consensus pattern (21 bp):
AAAAACTAAACCTCAAAACAC
Found at i:25304649 original size:45 final size:45
Alignment explanation
Indices: 25304583--25304672 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
25304573 GAAAAATTTA
* *
25304583 GTAAAAATATCCATCATCTGATCTCTGATTTGCAATAAATCAGTT
1 GTAAAAATATCCATCACCTGATCTCTGATTTGCAATAAACCAGTT
** *
25304628 GTAAAAATATCTGTCACCTGATCTTTGATTTGCAATAAACCAGTT
1 GTAAAAATATCCATCACCTGATCTCTGATTTGCAATAAACCAGTT
25304673 TCTTCAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (45 bp):
GTAAAAATATCCATCACCTGATCTCTGATTTGCAATAAACCAGTT
Found at i:25309109 original size:19 final size:18
Alignment explanation
Indices: 25309046--25309109 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
25309036 GTTCGGAAAA
*
25309046 TTTTATAAATTTTTAATT
1 TTTTATAATTTTTTAATT
* * *
25309064 AGTCTATAATTTTTTTATT
1 -TTTTATAATTTTTTAATT
*
25309083 TTAATATAATTTTTATAATT
1 TT-TTATAATTTTT-TAATT
25309103 TTTTATA
1 TTTTATA
25309110 GAGAAAAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 1 0.03
19 28 0.80
20 6 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTATAATTTTTTAATT
Found at i:25320682 original size:75 final size:75
Alignment explanation
Indices: 25320559--25320709 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
25320549 GCGAGAATGA
* ** *
25320559 ACTCACCTCCAAGAGGGGACCACCAAGGAGTCACTAGGGTGTAACATTGTACTACCTCAGCCAAT
1 ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCCAAG
25320624 GGAATGTTAG
66 GGAATGTTAG
*
25320634 ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCTAAG
1 ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCCAAG
25320699 GGAATGTTAG
66 GGAATGTTAG
25320709 A
1 A
25320710 ACAATACCAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.19
Consensus pattern (75 bp):
ACTCACCTCCAAAAGGGGACCACCAAGGAACCACTAGGGTGTAACATTGTACTACCTCAGCCAAG
GGAATGTTAG
Found at i:25330270 original size:16 final size:15
Alignment explanation
Indices: 25330239--25330278 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
25330229 TTTCTTACAT
25330239 TCTTTTTCTTTTTCA
1 TCTTTTTCTTTTTCA
25330254 TCTTTTTC-TTTTC-
1 TCTTTTTCTTTTTCA
*
25330267 TCATTTTCTTTT
1 TCTTTTTCTTTT
25330279 CACTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 7 0.30
14 8 0.35
15 8 0.35
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (15 bp):
TCTTTTTCTTTTTCA
Found at i:25330275 original size:13 final size:14
Alignment explanation
Indices: 25330242--25330280 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
25330232 CTTACATTCT
*
25330242 TTTTCTTTTTCATCT
1 TTTTC-TTTTCATCA
25330257 TTTTCTTTTC-TCA
1 TTTTCTTTTCATCA
25330270 TTTTCTTTTCA
1 TTTTCTTTTCA
25330281 CTTTCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 5 0.23
15 5 0.23
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTTCATCA
Found at i:25330346 original size:18 final size:17
Alignment explanation
Indices: 25330303--25330346 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
25330293 GTTTTTCCTC
25330303 TCTTTTTCTCATTTTTAT
1 TCTTTTT-TCATTTTTAT
25330321 T-TTCTTTTACATTTTTAT
1 TCTT-TTTT-CATTTTTAT
25330339 TCTTTTTT
1 TCTTTTTT
25330347 TTTCTCTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.13
18 18 0.78
19 2 0.09
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTTTTTTCATTTTTAT
Found at i:25332826 original size:74 final size:74
Alignment explanation
Indices: 25332714--25332863 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 74
25332704 TAAGTATAAA
* * *
25332714 GATAGGTAATGGAAATAGGTTCAAAATTGGCTAAGTATAAGTTGATTAGGTTCGGCTAACAAAGA
1 GATAGGTAATAGAAATAGGTTCAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA
25332779 AAGTAAATT
66 AAGTAAATT
*
25332788 GATAGGTAATAGAAATAGGTTTAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA
1 GATAGGTAATAGAAATAGGTTCAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA
25332853 AAGTAAATT
66 AAGTAAATT
25332862 GA
1 GA
25332864 ATAGTTTAGA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29
Consensus pattern (74 bp):
GATAGGTAATAGAAATAGGTTCAAAATTGGATAAGTATAAGTTGATTAGGTTCGACTAACAAAGA
AAGTAAATT
Found at i:25334130 original size:10 final size:10
Alignment explanation
Indices: 25334103--25334132 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
25334093 AGAAATAAAG
*
25334103 ATGAGCTCAA
1 ATGAGCTGAA
25334113 ATGAGCTGAA
1 ATGAGCTGAA
25334123 ATGAGCTGAA
1 ATGAGCTGAA
25334133 CTAAGCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (10 bp):
ATGAGCTGAA
Found at i:25342261 original size:29 final size:29
Alignment explanation
Indices: 25342219--25342277 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
25342209 TCAAGATGAG
25342219 GAATTTAATGAAATGATTACATTATCTAT
1 GAATTTAATGAAATGATTACATTATCTAT
*
25342248 GAATTTAATGAAATGATTACATTCTCTAT
1 GAATTTAATGAAATGATTACATTATCTAT
25342277 G
1 G
25342278 TATTAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (29 bp):
GAATTTAATGAAATGATTACATTATCTAT
Found at i:25342290 original size:29 final size:29
Alignment explanation
Indices: 25342219--25342290 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
25342209 TCAAGATGAG
* *
25342219 GAATTTAATGAAATGATTACATTATCTAT
1 GAATTAAATAAAATGATTACATTATCTAT
* * *
25342248 GAATTTAATGAAATGATTACATTCTCTAT
1 GAATTAAATAAAATGATTACATTATCTAT
*
25342277 GTATTAAATAAAAT
1 GAATTAAATAAAAT
25342291 ACTATTAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (29 bp):
GAATTAAATAAAATGATTACATTATCTAT
Found at i:25342703 original size:12 final size:14
Alignment explanation
Indices: 25342666--25342732 Score: 63
Period size: 11 Copynumber: 5.0 Consensus size: 14
25342656 TTTTAATTTG
*
25342666 TTAAATTGATTATGAT
1 TTAAATTAATTAT--T
25342682 TTAAATTAATT-TT
1 TTAAATTAATTATT
25342695 TTAAA-TAATTATT
1 TTAAATTAATTATT
25342708 TT---TTAATTATT
1 TTAAATTAATTATT
*
25342719 TTGAATTAATTATT
1 TTAAATTAATTATT
25342733 ATACAAATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
11 10 0.22
12 5 0.11
13 10 0.22
14 9 0.20
15 1 0.02
16 10 0.22
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.58
Consensus pattern (14 bp):
TTAAATTAATTATT
Found at i:25343685 original size:18 final size:17
Alignment explanation
Indices: 25343635--25343689 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
25343625 TTTCTTAGAA
*
25343635 TTTTGT-ATCTCGTAACT
1 TTTTGTAATCTCATAA-T
*
25343652 TTTTGTATTC-CATAAT
1 TTTTGTAATCTCATAAT
25343668 TATTTGTAATCTCATAAT
1 T-TTTGTAATCTCATAAT
25343686 TTTT
1 TTTT
25343690 AGTATGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.06
17 21 0.66
18 9 0.28
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTTGTAATCTCATAAT
Found at i:25344872 original size:49 final size:48
Alignment explanation
Indices: 25344806--25344900 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
25344796 TGTGACACAC
* * *
25344806 CCGTGTGAGGTGGCTTAGGACGTGTTTAGAGTCTGCTAAATAGACACGG
1 CCGTGTGAGGTGACTTAGGACGTG-TTACAATCTGCTAAATAGACACGG
* *
25344855 CCGTGTG-GTGTGACTTAGGCCGTGTTACAATCTGTTAAATAGACAC
1 CCGTGTGAG-GTGACTTAGGACGTGTTACAATCTGCTAAATAGACAC
25344901 AGGTGTGTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
48 20 0.50
49 20 0.50
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (48 bp):
CCGTGTGAGGTGACTTAGGACGTGTTACAATCTGCTAAATAGACACGG
Found at i:25350165 original size:20 final size:20
Alignment explanation
Indices: 25350075--25350181 Score: 64
Period size: 20 Copynumber: 5.3 Consensus size: 20
25350065 TACTTCACAA
*
25350075 ATATATACATATACT-AAAAT
1 ATATATA-ATATAATAAAAAT
*
25350095 ATACATAATA-ATATATAAAAT
1 ATATATAATATA-ATA-AAAAT
*
25350116 ATA-AT-AT-TAAAAAACACAT
1 ATATATAATATAATAAA-A-AT
* *
25350135 GTATATGATAT-ATGAAAAAT
1 ATATATAATATAAT-AAAAAT
25350155 ATATATAATATAATAAAAAT
1 ATATATAATATAATAAAAAT
*
25350175 ACATATA
1 ATATATA
25350182 TATGTAATAC
Statistics
Matches: 68, Mismatches: 8, Indels: 22
0.69 0.08 0.22
Matches are distributed among these distances:
17 2 0.03
18 4 0.06
19 11 0.16
20 33 0.49
21 14 0.21
22 4 0.06
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.33
Consensus pattern (20 bp):
ATATATAATATAATAAAAAT
Found at i:25350180 original size:22 final size:22
Alignment explanation
Indices: 25350114--25350183 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
25350104 AATATATAAA
* *
25350114 ATATAATATTA-AAAAACACAT
1 ATATAATATAATAAAAATACAT
*
25350135 GTAT-ATGATATATGAAAAAT--AT
1 ATATAAT-ATA-AT-AAAAATACAT
25350157 ATATAATATAATAAAAATACAT
1 ATATAATATAATAAAAATACAT
25350179 ATATA
1 ATATA
25350184 TGTAATACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
20 8 0.21
21 7 0.18
22 16 0.42
23 2 0.05
24 5 0.13
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATAATATAATAAAAATACAT
Found at i:25350623 original size:3 final size:3
Alignment explanation
Indices: 25350615--25350655 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
25350605 GAAATATACT
* *
25350615 TAA TAA TAA TAA GAA TAA TAG TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25350656 ACATATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:25350663 original size:17 final size:17
Alignment explanation
Indices: 25350615--25350655 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
25350605 GAAATATACT
*
25350615 TAATAATAATAAGAATAA
1 TAATAATAAT-ATAATAA
*
25350633 TAGTAATAATATAATAA
1 TAATAATAATATAATAA
25350650 TAATAA
1 TAATAA
25350656 ACATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:25351156 original size:18 final size:19
Alignment explanation
Indices: 25351133--25351186 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
25351123 AAAGAAAAAA
25351133 AAAGAGA-AGAAGGGAGAG
1 AAAGAGAGAGAAGGGAGAG
*
25351151 AAAGAGAGAGGAGGGAGAAGGG
1 AAAGAGAGAGAAGGGAG-A--G
25351173 AAAG-GAGAGAAGGG
1 AAAGAGAGAGAAGGG
25351187 GGGCTACCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 7 0.23
19 8 0.27
20 1 0.03
21 9 0.30
22 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (19 bp):
AAAGAGAGAGAAGGGAGAG
Found at i:25351167 original size:19 final size:18
Alignment explanation
Indices: 25351133--25351168 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25351123 AAAGAAAAAA
25351133 AAAGAGAAGAAGGGAGAG
1 AAAGAGAAGAAGGGAGAG
*
25351151 AAAGAGAGAGGAGGGAGA
1 AAAGAGA-AGAAGGGAGA
25351169 AGGGAAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (18 bp):
AAAGAGAAGAAGGGAGAG
Found at i:25359118 original size:19 final size:21
Alignment explanation
Indices: 25359076--25359118 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25359066 TTACTCAAAG
25359076 AAAGCCGATTGATCCATCTCA
1 AAAGCCGATTGATCCATCTCA
25359097 AAAGCCGGATT-ATCC-T-TCA
1 AAAGCC-GATTGATCCATCTCA
25359116 AAA
1 AAA
25359119 CTGAAGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 10 0.48
22 4 0.19
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (21 bp):
AAAGCCGATTGATCCATCTCA
Found at i:25362690 original size:22 final size:21
Alignment explanation
Indices: 25362652--25362695 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
25362642 CTTTTCTCTC
*
25362652 TATTCTCTTGTTATTTACTGT
1 TATTCTCTTGTTATTTAATGT
25362673 TATT-TCTTGTTTATTTTAATGT
1 TATTCTCTTG-TTA-TTTAATGT
25362695 T
1 T
25362696 TTTTATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.66
Consensus pattern (21 bp):
TATTCTCTTGTTATTTAATGT
Found at i:25364266 original size:14 final size:15
Alignment explanation
Indices: 25364247--25364276 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25364237 TTTATTTATT
25364247 ATTTTTAT-GTTTTA
1 ATTTTTATCGTTTTA
25364261 ATTTTTATCGTTTTA
1 ATTTTTATCGTTTTA
25364276 A
1 A
25364277 AACTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (15 bp):
ATTTTTATCGTTTTA
Found at i:25373927 original size:40 final size:41
Alignment explanation
Indices: 25373875--25373966 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 41
25373865 TAATATTCTG
* *
25373875 ATCTGCATTCTATATTTGATAGGACTGAGGCCCTA-ATATAT
1 ATCTG-ATTCTATATCTGATAGGACTAAGGCCCTATATATAT
* * *
25373916 TTCTGATTCTATATCTGATTGGGCTAAGGCCCTATTATATAT
1 ATCTGATTCTATATCTGATAGGACTAAGGCCCTA-TATATAT
25373958 ATCTGATTC
1 ATCTGATTC
25373967 GGCATCCGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
40 25 0.58
41 4 0.09
42 14 0.33
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (41 bp):
ATCTGATTCTATATCTGATAGGACTAAGGCCCTATATATAT
Found at i:25378406 original size:20 final size:20
Alignment explanation
Indices: 25378381--25378419 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
25378371 TAATTTTTAA
25378381 ATATAAAATTTTCATCAATT
1 ATATAAAATTTTCATCAATT
25378401 ATATAAAATTTTCATCAAT
1 ATATAAAATTTTCATCAAT
25378420 AAACTCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATAAAATTTTCATCAATT
Found at i:25384817 original size:18 final size:18
Alignment explanation
Indices: 25384794--25384831 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25384784 AATATATATT
25384794 AACCCAAGTACCCAACCC
1 AACCCAAGTACCCAACCC
*
25384812 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
25384830 AA
1 AA
25384832 TCATAAAAAT
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:0.42, C:0.47, G:0.03, T:0.08
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:25384824 original size:13 final size:13
Alignment explanation
Indices: 25384808--25384832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25384798 CAAGTACCCA
25384808 ACCCAACCCAATT
1 ACCCAACCCAATT
25384821 ACCCAACCCAAT
1 ACCCAACCCAAT
25384833 CATAAAAATT
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:25384912 original size:18 final size:18
Alignment explanation
Indices: 25384889--25384957 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
25384879 TTTATACAAA
25384889 TAATTCGGTTAATTTAGT
1 TAATTCGGTTAATTTAGT
** *
25384907 TAATTCAGG-TAATTCGGG
1 TAATTC-GGTTAATTTAGT
*
25384925 TAATTCGGTTAA-TTCGAT
1 TAATTCGGTTAATTTAG-T
25384943 TAATTCGGTTAATTT
1 TAATTCGGTTAATTT
25384958 TATACTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 4 0.10
18 33 0.80
19 4 0.10
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (18 bp):
TAATTCGGTTAATTTAGT
Found at i:25384928 original size:27 final size:27
Alignment explanation
Indices: 25384889--25384957 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
25384879 TTTATACAAA
25384889 TAATTCGGTTAATTTAGTTAATTC-AGG
1 TAATTCGGTTAATTTAGTTAATTCGA-G
* ** *
25384916 TAATTCGGGTAATTCGGTTAATTCGAT
1 TAATTCGGTTAATTTAGTTAATTCGAG
25384943 TAATTCGGTTAATTT
1 TAATTCGGTTAATTT
25384958 TATACTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (27 bp):
TAATTCGGTTAATTTAGTTAATTCGAG
Found at i:25388000 original size:20 final size:20
Alignment explanation
Indices: 25387975--25388012 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
25387965 ATGAGGTTTA
25387975 AAAAATGGGTTAAAAACCAC
1 AAAAATGGGTTAAAAACCAC
25387995 AAAAATGGGTTAAAAACC
1 AAAAATGGGTTAAAAACC
25388013 CCATTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAAATGGGTTAAAAACCAC
Found at i:25400567 original size:18 final size:18
Alignment explanation
Indices: 25400536--25400593 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
25400526 TCTATTATAA
25400536 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
25400554 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
* *
25400572 TATTATTTAATAAAAAAT
1 TATTAATTAATAAAATAT
25400590 TATT
1 TATT
25400594 TGAAAGTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:25401707 original size:39 final size:40
Alignment explanation
Indices: 25401612--25401708 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 40
25401602 CTTTGATTAG
* *
25401612 CCGATGATGCACTATGTGCTAGTATATTTACTTCGTTTAT
1 CCGATGATGCACTATATGCTAGTATATTTACTTCGTATAT
* *
25401652 -CTATGATGCACTTATATGCTAGTATA-TTGCTTCGATATAT
1 CCGATGATGCAC-TATATGCTAGTATATTTACTTCG-TATAT
25401692 CCGATGATGCA-TATATG
1 CCGATGATGCACTATATG
25401709 TTCCAATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
39 23 0.47
40 17 0.35
41 9 0.18
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (40 bp):
CCGATGATGCACTATATGCTAGTATATTTACTTCGTATAT
Found at i:25412944 original size:15 final size:15
Alignment explanation
Indices: 25412926--25412991 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
25412916 TATTACAAAA
25412926 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
25412941 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
25412960 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
25412975 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
25412988 ATTT
1 ATTT
25412992 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:25413041 original size:16 final size:16
Alignment explanation
Indices: 25413010--25413046 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
25413000 ATGTGAATAA
25413010 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
25413026 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
25413042 TATTA
1 TATTA
25413047 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:25413098 original size:22 final size:22
Alignment explanation
Indices: 25413058--25413113 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
25413048 AATAAAATTG
*
25413058 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
25413078 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
25413100 TATTAATAATTTAT
1 AAATAATAAATTAT
25413114 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:25417825 original size:20 final size:21
Alignment explanation
Indices: 25417802--25417851 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
25417792 ATTTTAATAT
25417802 TATATTATATATAT-TTTTCA
1 TATATTATATATATGTTTTCA
*
25417822 TATATTATATATATGTTTTTA
1 TATATTATATATATGTTTTCA
25417843 -ATATTATAT
1 TATATTATAT
25417852 TTTATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TATATTATATATATGTTTTCA
Found at i:25417862 original size:34 final size:37
Alignment explanation
Indices: 25417807--25417887 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 37
25417797 AATATTATAT
*
25417807 TATATATATTTTTCATATATTA-TATATATGTTTTTAA
1 TATATATA-TTTTCATATATTATTATATATATTTTTAA
* *
25417844 TAT-TATATTTT-ATATATTATTATGTATATTTTTAG
1 TATATATATTTTCATATATTATTATATATATTTTTAA
25417879 TATATATAT
1 TATATATAT
25417888 ATTTGTGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.21
35 19 0.49
36 9 0.23
37 3 0.08
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (37 bp):
TATATATATTTTCATATATTATTATATATATTTTTAA
Found at i:25418815 original size:15 final size:15
Alignment explanation
Indices: 25418797--25418830 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25418787 TTTATACTAT
*
25418797 GTATATATATATTTA
1 GTATATATATATTCA
*
25418812 GTATGTATATATTCA
1 GTATATATATATTCA
25418827 GTAT
1 GTAT
25418831 TATTATGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (15 bp):
GTATATATATATTCA
Found at i:25418837 original size:21 final size:20
Alignment explanation
Indices: 25418777--25418837 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
25418767 ATTCCTAATA
25418777 TATATATTCAT-TTATACTATG
1 TATATATTCATATTAT--TATG
*
25418798 TATATA-T-ATATTTAGTATG
1 TATATATTCATA-TTATTATG
25418817 TATATATTCAGTATTATTATG
1 TATATATTCA-TATTATTATG
25418838 CGTGTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
19 12 0.36
20 2 0.06
21 17 0.52
22 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.52
Consensus pattern (20 bp):
TATATATTCATATTATTATG
Found at i:25422708 original size:16 final size:16
Alignment explanation
Indices: 25422687--25422722 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
25422677 GTATAACTAA
25422687 CATTCATTTATGCATT
1 CATTCATTTATGCATT
*
25422703 CATTCATTTATTCATT
1 CATTCATTTATGCATT
25422719 CATT
1 CATT
25422723 GCATATCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
CATTCATTTATGCATT
Found at i:25431147 original size:68 final size:74
Alignment explanation
Indices: 25431025--25431207 Score: 234
Period size: 68 Copynumber: 2.6 Consensus size: 74
25431015 TATTTCTGTT
* * ** * *
25431025 TTCAAAATTCGACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAAAAGTTGAGGTATTTTC-A-
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAAAAGCTGAGGTAATTTCAAT
25431088 A-T-T-TTG
66 ATTCTATTG
* * *
25431094 TT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAAAAGCTGAGGTAATTTCAAT
*
25431158 ATTCTATTT
66 ATTCTATTG
25431167 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
25431208 GGCTCACATG
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
68 50 0.51
69 3 0.03
70 1 0.01
71 1 0.01
72 1 0.01
73 4 0.04
74 38 0.39
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (74 bp):
TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAAAAGCTGAGGTAATTTCAAT
ATTCTATTG
Found at i:25431401 original size:171 final size:164
Alignment explanation
Indices: 25431096--25431408 Score: 412
Period size: 171 Copynumber: 1.9 Consensus size: 164
25431086 CAATTTTGTT
* *
25431096 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTAATTTCAAAATT
* * *
25431161 CTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTTGAGGTA
66 CTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGCTA
*
25431226 TTTTCAGTTTCTGTTTTTTTAATTTATATTTTTC
131 TTTTCAATTTCTGTTTTTTTAATTTATATTTTTC
* * * * * *
25431260 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAATCTCGGGTCATATGTTGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGG--ACACGCTGAGGTAATTTCAAAA
* * *
25431325 TCTGCTTTTAAGTTTCAAAAAACCAACTCATATTGCG-GAGGTGAGTTGAGCCTTGGCTCACGTG
64 T-T-CTATT---TTTC-AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG
25431389 CTGAGCTATTTTCAATTTCT
123 CTGAGCTATTTTCAATTTCT
25431409 ACTTTAATGT
Statistics
Matches: 126, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
164 38 0.30
166 18 0.14
167 1 0.01
168 4 0.03
171 46 0.37
172 19 0.15
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (164 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTAATTTCAAAATT
CTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGCTA
TTTTCAATTTCTGTTTTTTTAATTTATATTTTTC
Found at i:25432536 original size:21 final size:21
Alignment explanation
Indices: 25432506--25432556 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
25432496 CCACCGGAAA
25432506 TCCCCTTCTCCCCACTCTCC-TT
1 TCCCC-TCTCCCCACTC-CCATT
*
25432528 TCCCCTCTCCCCTCTCCCATT
1 TCCCCTCTCCCCACTCCCATT
*
25432549 TCCTCTCT
1 TCCCCTCT
25432557 TCTTTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.04, C:0.59, G:0.00, T:0.37
Consensus pattern (21 bp):
TCCCCTCTCCCCACTCCCATT
Found at i:25433369 original size:20 final size:19
Alignment explanation
Indices: 25433346--25433542 Score: 86
Period size: 20 Copynumber: 10.6 Consensus size: 19
25433336 ATTTTAATAT
25433346 TATATTATATATATTTTTCA
1 TATATTATATATATTTTT-A
25433366 TATATTATATATATGTTTT-
1 TATATTATATATAT-TTTTA
25433385 TA-A-TAT-TATATTTTATA
1 TATATTATATATATTTT-TA
*
25433402 TATCATTATGTATATTTTTA
1 TAT-ATTATATATATTTTTA
* *
25433422 -ATA-TATATAT-TTGTGA
1 TATATTATATATATTTTTA
*
25433438 -AGTATTATCA-ATAGTTTT-
1 TA-TATTAT-ATATATTTTTA
25433456 T-TATTAT-TATTATTTTTA
1 TATATTATATA-TATTTTTA
* *
25433474 -ATATGTATATAT-TGTGTA
1 TATAT-TATATATATTTTTA
* **
25433492 TATATTTTA-ATACTACATTA
1 TATATTATATATA-T-TTTTA
25433512 TATA-TATATAT-TTTTTA
1 TATATTATATATATTTTTA
25433529 TATTATGTATATAT
1 TA-TAT-TATATAT
25433543 TTCAAGTATT
Statistics
Matches: 135, Mismatches: 16, Indels: 52
0.67 0.08 0.26
Matches are distributed among these distances:
15 3 0.02
16 12 0.09
17 32 0.24
18 20 0.15
19 20 0.15
20 36 0.27
21 12 0.09
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TATATTATATATATTTTTA
Found at i:25433374 original size:25 final size:23
Alignment explanation
Indices: 25433322--25433404 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 23
25433312 CTAATATGTA
* *
25433322 TATATTATGTAAATATTTTAATAT
1 TATATTATATATAT-TTTTAATAT
*
25433346 TATATTATATATATTTTTCATA-
1 TATATTATATATATTTTTAATAT
*
25433368 TAT-TATATATATGTTTTTAATAT
1 TATAT-TATATATATTTTTAATAT
*
25433391 TATATTTTATATAT
1 TATATTATATATAT
25433405 CATTATGTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 18 0.37
23 17 0.35
24 13 0.27
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (23 bp):
TATATTATATATATTTTTAATAT
Found at i:25433425 original size:35 final size:36
Alignment explanation
Indices: 25433351--25433433 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
25433341 AATATTATAT
25433351 TATATATATTTTTCATATATTATATATATGTTTTTAA
1 TATATATATTTTTCATATATTATATATA-GTTTTTAA
*
25433388 TAT-TATATTTTAT-ATATCATTATGTATA-TTTTTAA
1 TATATATATTTT-TCATAT-ATTATATATAGTTTTTAA
25433423 TATATATATTT
1 TATATATATTT
25433434 GTGAAGTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
35 10 0.24
36 19 0.45
37 13 0.31
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (36 bp):
TATATATATTTTTCATATATTATATATAGTTTTTAA
Found at i:25433486 original size:26 final size:27
Alignment explanation
Indices: 25433457--25433543 Score: 63
Period size: 27 Copynumber: 3.1 Consensus size: 27
25433447 AATAGTTTTT
25433457 TATTAT-TATTATTTTTAATATGTATA
1 TATTATATATTATTTTTAATATGTATA
* * **
25433483 TATTGTGTA-TATATTTTAATACTACATTA
1 TATTATATATTAT-TTTTAATA-TGTA-TA
*
25433512 TATATATATATT-TTTTATATTATGTATA
1 TAT-TATATATTATTTT-TAATATGTATA
25433540 TATT
1 TATT
25433544 TCAAGTATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
26 8 0.17
27 11 0.24
28 7 0.15
29 10 0.22
30 9 0.20
31 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (27 bp):
TATTATATATTATTTTTAATATGTATA
Found at i:25434347 original size:21 final size:19
Alignment explanation
Indices: 25434323--25434374 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
25434313 TAATATGTAT
25434323 TGTATATATTTATTTATACTA
1 TGTATATATTTA-TT-TACTA
* *
25434344 TGTATATATATATTTAGTA
1 TGTATATATTTATTTACTA
25434363 TGTATATATTTA
1 TGTATATATTTA
25434375 GTATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 15 0.54
20 2 0.07
21 11 0.39
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (19 bp):
TGTATATATTTATTTACTA
Found at i:25434363 original size:15 final size:15
Alignment explanation
Indices: 25434345--25434378 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
25434335 TTTATACTAT
25434345 GTATATATATATTTA
1 GTATATATATATTTA
*
25434360 GTATGTATATATTTA
1 GTATATATATATTTA
25434375 GTAT
1 GTAT
25434379 TATTATGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
GTATATATATATTTA
Found at i:25434385 original size:21 final size:19
Alignment explanation
Indices: 25434323--25434385 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 19
25434313 TAATATGTAT
25434323 TGTATATATTTATTTATACTA
1 TGTATATATTTATTTAT--TA
* *
25434344 TGTATATATATATTTAGTA
1 TGTATATATTTATTTATTA
25434363 TGTATATATTTAGTATTATTA
1 TGTATATATTTA-T-TTATTA
25434384 TG
1 TG
25434386 CGTGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.36
20 1 0.03
21 22 0.61
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TGTATATATTTATTTATTA
Found at i:25434632 original size:34 final size:34
Alignment explanation
Indices: 25434579--25434644 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
25434569 TACTATCGCA
**
25434579 CGTATATTGTTAATGTTTTA-TATATTGTCTATTT
1 CGTATATTGTTAACCTTTTATTAT-TTGTCTATTT
*
25434613 CGTATATTTTTAACCTTTTATTATTTGTCTAT
1 CGTATATTGTTAACCTTTTATTATTTGTCTAT
25434645 CCCGAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (34 bp):
CGTATATTGTTAACCTTTTATTATTTGTCTATTT
Found at i:25438931 original size:3 final size:3
Alignment explanation
Indices: 25438923--25439291 Score: 134
Period size: 3 Copynumber: 121.7 Consensus size: 3
25438913 TAATTTAATA
* * *
25438923 TAT TAT TAT TACT TAT TAT T-T TAC TAT TAT TGT CTAA TA- TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * * *
25438968 TAT CAC TAT TAT TAT TAC T-T TAC TAT TGT AATT TAT GGTAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT --TAT TAT TAT
* *
25439015 TAC TCT TAT T-T TCAT TAT TAT TAT TAT TAT TAT TAT TATT TAT T-T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * * * * * *
25439060 TCT T-T T-T TAC TAT TGT TAT TAGT GACC TAT TAC TAT TCT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT
* * * * * *
25439105 CA- TAC TAT TAT T-T CCTAT T-T TA- TAT TAT TAT TGT TAT CAA CAT
1 TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * **
25439148 ATAT TAT TAT CAT TAAT GTAT TGT TAT TCCC TAT TAT TAT TAT TAT TAT
1 -TAT TAT TAT TAT T-AT -TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * *
25439197 TAT TAT TAT TCCT T-T TAT TATT TAT TAT CAA TA- TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * ** *
25439242 TAT TGT TAT TAT TGT TAT TGT TGT TAT TGT TAT TGC TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25439290 TA
1 TA
25439292 CCACCTTATT
Statistics
Matches: 268, Mismatches: 70, Indels: 56
0.68 0.18 0.14
Matches are distributed among these distances:
2 23 0.09
3 213 0.79
4 27 0.10
5 5 0.02
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:25439404 original size:17 final size:17
Alignment explanation
Indices: 25439382--25439415 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25439372 TTTTATTATC
25439382 ATTATTACTATCATATT
1 ATTATTACTATCATATT
*
25439399 ATTATTACTATTATATT
1 ATTATTACTATCATATT
25439416 TTCATCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATTACTATCATATT
Found at i:25439643 original size:13 final size:14
Alignment explanation
Indices: 25439627--25439691 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 14
25439617 TTTAATTTCA
25439627 ATTT-TTTTAGCTT
1 ATTTATTTTAGCTT
*
25439640 ATTTATTATT-TCTTT
1 ATTTATT-TTAGC-TT
*
25439655 TTTTATTTTAGCTT
1 ATTTATTTTAGCTT
*
25439669 ATTCATTTTA-CTT
1 ATTTATTTTAGCTT
*
25439682 ATTTGTTTTA
1 ATTTATTTTA
25439692 TCTTTTCTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
13 15 0.37
14 15 0.37
15 11 0.27
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69
Consensus pattern (14 bp):
ATTTATTTTAGCTT
Found at i:25442431 original size:15 final size:15
Alignment explanation
Indices: 25442413--25442443 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25442403 TTTTAATAAA
25442413 TTTTTTAAAAAAAAT
1 TTTTTTAAAAAAAAT
*
25442428 TTTTTTAAAAATAAT
1 TTTTTTAAAAAAAAT
25442443 T
1 T
25442444 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTTTAAAAAAAAT
Found at i:25442562 original size:16 final size:16
Alignment explanation
Indices: 25442541--25442571 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25442531 GATGAGTTCA
25442541 AAATTAAAAAAAATAG
1 AAATTAAAAAAAATAG
*
25442557 AAATTATAAAAAATA
1 AAATTAAAAAAAATA
25442572 TTAATAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATTAAAAAAAATAG
Found at i:25446411 original size:28 final size:29
Alignment explanation
Indices: 25446379--25446458 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
25446369 GTTGAGAGAT
25446379 GAAGAGCCTTGATGAAAGA-ATGAAAGAC
1 GAAGAGCCTTGATGAAAGAGATGAAAGAC
* * *
25446407 GAAGAGCTTTGATAAAAGAGATGAGAGAC
1 GAAGAGCCTTGATGAAAGAGATGAAAGAC
* * *
25446436 GAAGAGTCTAGATGAAAGGGATG
1 GAAGAGCCTTGATGAAAGAGATG
25446459 TGAGAGGGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 17 0.40
29 26 0.60
ACGTcount: A:0.44, C:0.07, G:0.33, T:0.16
Consensus pattern (29 bp):
GAAGAGCCTTGATGAAAGAGATGAAAGAC
Found at i:25446440 original size:29 final size:28
Alignment explanation
Indices: 25446371--25446441 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
25446361 GCAGCCAAGT
* *
25446371 TGAGAGATGAAGAGCCTTGATGAAAGAA
1 TGAGAGACGAAGAGCCTTGATAAAAGAA
* *
25446399 TGAAAGACGAAGAGCTTTGATAAAAGAGA
1 TGAGAGACGAAGAGCCTTGATAAAAGA-A
25446428 TGAGAGACGAAGAG
1 TGAGAGACGAAGAG
25446442 TCTAGATGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 23 0.62
29 14 0.38
ACGTcount: A:0.45, C:0.07, G:0.32, T:0.15
Consensus pattern (28 bp):
TGAGAGACGAAGAGCCTTGATAAAAGAA
Found at i:25446453 original size:29 final size:28
Alignment explanation
Indices: 25446371--25446463 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
25446361 GCAGCCAAGT
*
25446371 TGAGAGATGAAGAGCCTTGATGAAAGA-A
1 TGAGAGACGAAGAG-CTTGATGAAAGAGA
* *
25446399 TGAAAGACGAAGAGCTTTGATAAAAGAGA
1 TGAGAGACGAAGAGC-TTGATGAAAGAGA
* *
25446428 TGAGAGACGAAGAGTCTAGATGAAAGGGA
1 TGAGAGACGAAGAG-CTTGATGAAAGAGA
*
25446457 TGTGAGA
1 TGAGAGA
25446464 GGGATTTTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 1 0.02
28 22 0.41
29 30 0.56
30 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.33, T:0.17
Consensus pattern (28 bp):
TGAGAGACGAAGAGCTTGATGAAAGAGA
Found at i:25448067 original size:25 final size:26
Alignment explanation
Indices: 25448039--25448094 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
25448029 TTGAAACTTG
* *
25448039 ATTTTTTT-TAGTTTTTAAATTTTTA
1 ATTTTTTTATAATTTCTAAATTTTTA
*
25448064 ATTTTTTTATAATTTCTAATTTTTTA
1 ATTTTTTTATAATTTCTAAATTTTTA
*
25448090 GTTTT
1 ATTTT
25448095 GAACTCATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (26 bp):
ATTTTTTTATAATTTCTAAATTTTTA
Found at i:25448071 original size:18 final size:18
Alignment explanation
Indices: 25448050--25448088 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
25448040 TTTTTTTTAG
*
25448050 TTTTTA-AATTTTTAATT
1 TTTTTATAATTTCTAATT
25448067 TTTTTATAATTTCTAATT
1 TTTTTATAATTTCTAATT
25448085 TTTT
1 TTTT
25448089 AGTTTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATAATTTCTAATT
Found at i:25450934 original size:19 final size:19
Alignment explanation
Indices: 25450899--25450940 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
25450889 AATTAAACTT
* *
25450899 GAAAATTAGACCTAAGATG
1 GAAAATTAGACCCAAGATC
25450918 GAAAATT-GAACCCAAGATC
1 GAAAATTAG-ACCCAAGATC
25450937 GAAA
1 GAAA
25450941 CCCAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (19 bp):
GAAAATTAGACCCAAGATC
Found at i:25451463 original size:32 final size:32
Alignment explanation
Indices: 25451426--25451497 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
25451416 CGATGGTTGT
25451426 GACGACAACGATCCGGCGACCGACAGATGGTC
1 GACGACAACGATCCGGCGACCGACAGATGGTC
* * ****
25451458 GACGACAATGGTTTTTCGACCGACAGATGGTC
1 GACGACAACGATCCGGCGACCGACAGATGGTC
*
25451490 GGCGACAA
1 GACGACAA
25451498 TAATTCTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.31, T:0.15
Consensus pattern (32 bp):
GACGACAACGATCCGGCGACCGACAGATGGTC
Found at i:25452098 original size:12 final size:12
Alignment explanation
Indices: 25452077--25452127 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
25452067 TGACGTGGCA
*
25452077 GAGGAGGACGAT
1 GAGGATGACGAT
* *
25452089 GAGGAAGACGAA
1 GAGGATGACGAT
*
25452101 GATGATGACGAT
1 GAGGATGACGAT
*
25452113 GACGATGACGAT
1 GAGGATGACGAT
25452125 GAG
1 GAG
25452128 CTATATGGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.41, T:0.12
Consensus pattern (12 bp):
GAGGATGACGAT
Found at i:25452113 original size:6 final size:6
Alignment explanation
Indices: 25452083--25452126 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
25452073 GGCAGAGGAG
* * * *
25452083 GACGAT GAGGAA GACGAA GATGAT GACGAT GACGAT GACGAT GA
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GA
25452127 GCTATATGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.36, T:0.14
Consensus pattern (6 bp):
GACGAT
Found at i:25461335 original size:2 final size:2
Alignment explanation
Indices: 25461328--25461364 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25461318 GACCAATTAT
25461328 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
25461365 TATAATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25468385 original size:15 final size:15
Alignment explanation
Indices: 25468363--25468410 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
25468353 TTTTTTAAGA
25468363 TTACATTTTAATCAC
1 TTACATTTTAATCAC
* *
25468378 TTATATTTGAAAT-A-
1 TTACATTT-TAATCAC
25468392 TTACATTTTAATCAC
1 TTACATTTTAATCAC
25468407 TTAC
1 TTAC
25468411 GTTATCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 12 0.46
16 3 0.12
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (15 bp):
TTACATTTTAATCAC
Found at i:25472633 original size:35 final size:37
Alignment explanation
Indices: 25472588--25472658 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
25472578 AGAACAACTA
*
25472588 AATTATACAAAAC-ATAAAGAAATCATGACACTGGTT
1 AATTATACAAAACTAAAAAGAAATCATGACACTGGTT
25472624 AATT-TACAAAACTTAAAAAGAAATCATGACACTGG
1 AATTATACAAAAC-TAAAAAGAAATCATGACACTGG
25472659 AAGCTATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 8 0.25
36 4 0.12
37 20 0.62
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (37 bp):
AATTATACAAAACTAAAAAGAAATCATGACACTGGTT
Found at i:25480472 original size:39 final size:39
Alignment explanation
Indices: 25480429--25480529 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
25480419 ATCGTGATCT
* *
25480429 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAAGCTAACTAAAGCACATAAGTGCTAAACG
* *
25480468 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAAGCTAACTAAAGCACATAAGTGCTAAACG
* * *
25480507 GAAGCCCGGAGGCTAACTGAAGC
1 GAAGCCCGAAAGCTAACTAAAGC
25480530 TCATCAGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAAGCTAACTAAAGCACATAAGTGCTAAACG
Found at i:25480511 original size:21 final size:21
Alignment explanation
Indices: 25480448--25480511 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
25480438 AATCTAGCTA
25480448 AAGCACATAAGTGCTAAACGG
1 AAGCACATAAGTGCTAAACGG
** *
25480469 AAGC-CCGAAG-GCT-AACTG
1 AAGCACATAAGTGCTAAACGG
25480487 AAGCACATAAGTGCTAAACGG
1 AAGCACATAAGTGCTAAACGG
25480508 AAGC
1 AAGC
25480512 CCGGAGGCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.24
19 7 0.21
20 7 0.21
21 12 0.35
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (21 bp):
AAGCACATAAGTGCTAAACGG
Found at i:25484334 original size:25 final size:25
Alignment explanation
Indices: 25484300--25484389 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
25484290 ATATTATTAT
*
25484300 TATTTTTTATTTTAAGTTTTTCTTA
1 TATTATTTATTTTAAGTTTTTCTTA
* *
25484325 TATTATTTATTTTAAATTGTT-TTA
1 TATTATTTATTTTAAGTTTTTCTTA
* ***
25484349 TTATTTTTTATTTTAAGTTTTTCACG
1 -TATTATTTATTTTAAGTTTTTCTTA
*
25484375 TATTATGTATTTTAA
1 TATTATTTATTTTAA
25484390 ACTATTATCC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 3 0.06
25 49 0.94
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (25 bp):
TATTATTTATTTTAAGTTTTTCTTA
Found at i:25484350 original size:50 final size:50
Alignment explanation
Indices: 25484296--25484390 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
25484286 AACTATATTA
** *
25484296 TTATTATTTTTTATTTTAAGTTTTTCTTATATTATTTATTTTAAATTGTT
1 TTATTATTTTTTATTTTAAGTTTTTCACATATTATGTATTTTAAATTGTT
*
25484346 TTATTATTTTTTATTTTAAGTTTTTCACGTATTATGTATTTTAAA
1 TTATTATTTTTTATTTTAAGTTTTTCACATATTATGTATTTTAAA
25484391 CTATTATCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.66
Consensus pattern (50 bp):
TTATTATTTTTTATTTTAAGTTTTTCACATATTATGTATTTTAAATTGTT
Found at i:25484472 original size:27 final size:28
Alignment explanation
Indices: 25484419--25484545 Score: 102
Period size: 28 Copynumber: 4.5 Consensus size: 28
25484409 ATTTTAAAGG
25484419 TTATTTATTTTAAA--ATTTTTATATATA
1 TTATTTATTTTAAATTATTTTT-TATATA
*
25484446 TTATTTATTTTGAATTATTTTTTTATATA
1 TTATTTATTTTAAATTA-TTTTTTATATA
* * * *
25484475 TATCTTTTATTTTTAAACTA--TTTTGTACA
1 T-T-ATTTA-TTTTAAATTATTTTTTATATA
*
25484504 TTATTTATTTTAAATT-TCTTTTTACATA
1 TTATTTATTTTAAATTAT-TTTTTATATA
*
25484532 TTATTTATCTTAAA
1 TTATTTATTTTAAA
25484546 CTCTTTTATA
Statistics
Matches: 79, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
26 8 0.10
27 17 0.22
28 20 0.25
29 16 0.20
30 6 0.08
31 4 0.05
32 8 0.10
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (28 bp):
TTATTTATTTTAAATTATTTTTTATATA
Found at i:25484529 original size:26 final size:26
Alignment explanation
Indices: 25484419--25484686 Score: 162
Period size: 26 Copynumber: 10.2 Consensus size: 26
25484409 ATTTTAAAGG
25484419 TTATTTATTTTAAAATTT-TTATATATA
1 TTATTTATTTT-AAATTTCTT-TATATA
*
25484446 TTATTTATTTTGAATTATTTTTTTATATA
1 TTATTTATTTT-AA--ATTTCTTTATATA
* * * *
25484475 TATCTTTTATTTTTAAACTAT-TTTGTACA
1 T-T-ATTTA-TTTTAAA-TTTCTTTATATA
*
25484504 TTATTTATTTTAAATTTCTTTTTACATA
1 TTATTTATTTTAAATTTC--TTTATATA
* *
25484532 TTATTTATCTTAAA-CTCTTT-TATA
1 TTATTTATTTTAAATTTCTTTATATA
* *
25484556 -T-GTTATTTTAAAGTGTC-TTATATA
1 TTATTTATTTTAAA-TTTCTTTATATA
* * *
25484580 TTATCTATTTTAAATTGCTTTGTATA
1 TTATTTATTTTAAATTTCTTTATATA
* *
25484606 TTATCTATTTT-AATTTGTTTATATA
1 TTATTTATTTTAAATTTCTTTATATA
* * *
25484631 TTATTTATTTTAAA-ATGTTT-TATG
1 TTATTTATTTTAAATTTCTTTATATA
* *
25484655 GTATTTACTTTAAATTGT-TTTATATA
1 TTATTTATTTTAAATT-TCTTTATATA
25484681 TTATTT
1 TTATTT
25484687 TGTTTTGTTT
Statistics
Matches: 189, Mismatches: 32, Indels: 41
0.72 0.12 0.16
Matches are distributed among these distances:
22 9 0.05
23 3 0.02
24 24 0.13
25 37 0.20
26 44 0.23
27 19 0.10
28 19 0.10
29 19 0.10
30 5 0.03
31 6 0.03
32 4 0.02
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (26 bp):
TTATTTATTTTAAATTTCTTTATATA
Found at i:25484685 original size:50 final size:48
Alignment explanation
Indices: 25484503--25484686 Score: 165
Period size: 50 Copynumber: 3.7 Consensus size: 48
25484493 TATTTTGTAC
* * * * *
25484503 ATTATTTATTTTAAATTTCTTTTTACATATTATTTATCTTAAACTCTTTT
1 ATTATTTATTTTAAA-TT-GTTTTATATATTATTTATTTTAAAATGTTTT
* * * *
25484553 A-TATGTTATTTTAAAGTGTCTTATATATTATCTATTTTAAATTGCTTTGTAT
1 ATTAT-TTATTTTAAATTGTTTTATATATTATTTATTTTAAAATG--TT-T-T
* *
25484605 ATTATCTATTTTAATTTG-TTTATATATTATTTATTTTAAAATGTTTT
1 ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT
*
25484652 ATGGTATTTACTTTAAATTGTTTTATATATTATTT
1 AT--TATTTATTTTAAATTGTTTTATATATTATTT
25484687 TGTTTTGTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
47 3 0.03
48 21 0.19
49 19 0.18
50 27 0.25
51 23 0.21
52 12 0.11
53 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (48 bp):
ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT
Found at i:25488476 original size:15 final size:17
Alignment explanation
Indices: 25488445--25488479 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
25488435 CTACACGTGG
25488445 TAATTTTATTTTAGTTT
1 TAATTTTATTTTAGTTT
25488462 TAATTTT-TTTT-GTTT
1 TAATTTTATTTTAGTTT
25488477 TAA
1 TAA
25488480 AATATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 4 0.22
17 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TAATTTTATTTTAGTTT
Found at i:25511564 original size:18 final size:18
Alignment explanation
Indices: 25511541--25511609 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
25511531 GCACATAAGT
25511541 GCTAACGGAAGCCCGAAG
1 GCTAACGGAAGCCCGAAG
* **
25511559 GCTAACTGAAGCACATAAG
1 GCTAACGGAAGC-CCGAAG
*
25511578 TGCTAAACGGAAGCCCGGAG
1 -GCT-AACGGAAGCCCGAAG
*
25511598 GCTAACTGAAGC
1 GCTAACGGAAGC
25511610 TCATCAGAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 19 0.47
19 7 0.17
20 6 0.15
21 8 0.20
ACGTcount: A:0.35, C:0.25, G:0.29, T:0.12
Consensus pattern (18 bp):
GCTAACGGAAGCCCGAAG
Found at i:25511600 original size:39 final size:38
Alignment explanation
Indices: 25511510--25511609 Score: 146
Period size: 38 Copynumber: 2.6 Consensus size: 38
25511500 ATCGTGATCT
** * *
25511510 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAACG
25511548 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCT-AACG
*
25511587 GAAGCCCGGAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
25511610 TCATCAGAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 30 0.54
39 26 0.46
ACGTcount: A:0.37, C:0.24, G:0.26, T:0.13
Consensus pattern (38 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAACG
Found at i:25515145 original size:24 final size:24
Alignment explanation
Indices: 25515117--25515198 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
25515107 TTATTATTTT
25515117 TTATTTTAAGTTTTTCTTATATTA
1 TTATTTTAAGTTTTTCTTATATTA
* * *
25515141 TTATTTTAAATTGTT-TTATTATTT
1 TTATTTTAAGTTTTTCTTA-TATTA
***
25515165 TTATTTTAAGTTTTTCACGTATTA
1 TTATTTTAAGTTTTTCTTATATTA
25515189 TGTATTTTAA
1 T-TATTTTAA
25515199 ACTATTATCC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
23 3 0.07
24 35 0.76
25 8 0.17
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.65
Consensus pattern (24 bp):
TTATTTTAAGTTTTTCTTATATTA
Found at i:25515213 original size:48 final size:47
Alignment explanation
Indices: 25515105--25515213 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 47
25515095 AAAACTATAT
* ** *
25515105 TATTATTATTTTTTATTTTAAGTTTTTCTTATATTATTATTTTAAATTG
1 TATTATCA-TTTTTATTTTAAGTTTTTCACATATTATTATTTTAAA-TC
* * *
25515154 TTTTATTATTTTTATTTTAAGTTTTTCACGTATTATGTATTTTAAA-C
1 TATTATCATTTTTATTTTAAGTTTTTCACATATTAT-TATTTTAAATC
25515201 TATTATCCATTTT
1 TATTAT-CATTTT
25515214 AAATATTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
47 5 0.10
48 30 0.59
49 16 0.31
ACGTcount: A:0.26, C:0.06, G:0.05, T:0.64
Consensus pattern (47 bp):
TATTATCATTTTTATTTTAAGTTTTTCACATATTATTATTTTAAATC
Found at i:25515279 original size:26 final size:26
Alignment explanation
Indices: 25515191--25515493 Score: 162
Period size: 26 Copynumber: 11.7 Consensus size: 26
25515181 ACGTATTATG
* **
25515191 TATTTTAAACTATTATCCATTTTAAA-
1 TATTTTATA-TATTATTTATTTTAAAT
**
25515217 TATTTTA-AGGTTATTTATTTTAAAAT
1 TATTTTATATATTATTTATTTT-AAAT
*
25515243 T-TTTATATATATTATTTATTTTGAAT
1 TATTT-TATATATTATTTATTTTAAAT
* *
25515269 TATTTTTTATATATATCTTTTATTTTTAAAC
1 TA--TTTTATATAT-T-ATTTA-TTTTAAAT
* *
25515300 TATTTTGTACATTATTTATTTTAAATT
1 TATTTTATATATTATTTATTTTAAA-T
* * * *
25515327 TCTTTTTACATATTATTTATCTTAAAC
1 T-ATTTTATATATTATTTATTTTAAAT
* * *
25515354 T-CTTT-TATA-T-GTTATTTTAAAG
1 TATTTTATATATTATTTATTTTAAAT
* * *
25515376 TGTCTTATATATTATCTATTTTAAAT
1 TATTTTATATATTATTTATTTTAAAT
** * *
25515402 TGCTTTGTATATTATCTATTTT-AAT
1 TATTTTATATATTATTTATTTTAAAT
25515427 T-TGTTTATATATTATTTATTTTAAA-
1 TAT-TTTATATATTATTTATTTTAAAT
** *
25515452 -ATGTTT-TATGGTATTTACTTTAAAT
1 TAT-TTTATATATTATTTATTTTAAAT
*
25515477 TGTTTTATATATTATTT
1 TATTTTATATATTATTT
25515494 TGTTTTGTTT
Statistics
Matches: 213, Mismatches: 42, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
22 10 0.05
23 3 0.01
24 31 0.15
25 40 0.19
26 60 0.28
27 18 0.08
28 27 0.13
29 12 0.06
30 4 0.02
31 8 0.04
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (26 bp):
TATTTTATATATTATTTATTTTAAAT
Found at i:25515492 original size:50 final size:48
Alignment explanation
Indices: 25515310--25515493 Score: 165
Period size: 50 Copynumber: 3.7 Consensus size: 48
25515300 TATTTTGTAC
* * * * *
25515310 ATTATTTATTTTAAATTTCTTTTTACATATTATTTATCTTAAACTCTTTT
1 ATTATTTATTTTAAA-TT-GTTTTATATATTATTTATTTTAAAATGTTTT
* * * *
25515360 A-TATGTTATTTTAAAGTGTCTTATATATTATCTATTTTAAATTGCTTTGTAT
1 ATTAT-TTATTTTAAATTGTTTTATATATTATTTATTTTAAAATG--TT-T-T
* *
25515412 ATTATCTATTTTAATTTG-TTTATATATTATTTATTTTAAAATGTTTT
1 ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT
*
25515459 ATGGTATTTACTTTAAATTGTTTTATATATTATTT
1 AT--TATTTATTTTAAATTGTTTTATATATTATTT
25515494 TGTTTTGTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
47 3 0.03
48 21 0.19
49 19 0.18
50 27 0.25
51 23 0.21
52 12 0.11
53 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (48 bp):
ATTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAAATGTTTT
Found at i:25519253 original size:15 final size:17
Alignment explanation
Indices: 25519222--25519256 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
25519212 CTACACGTGG
25519222 TAATTTTATTTTAGTTT
1 TAATTTTATTTTAGTTT
25519239 TAATTTT-TTTT-GTTT
1 TAATTTTATTTTAGTTT
25519254 TAA
1 TAA
25519257 AATATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 4 0.22
17 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TAATTTTATTTTAGTTT
Found at i:25532502 original size:22 final size:21
Alignment explanation
Indices: 25532462--25532515 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
25532452 GTGTTTGAGG
* * *
25532462 TCTCGAAACAATTGTTCTTAGA
1 TCTCGAGACAAGTGGTCTT-GA
*
25532484 TCTCGAGACAAGTGGTCTTTA
1 TCTCGAGACAAGTGGTCTTGA
25532505 TCTCGAGACAA
1 TCTCGAGACAA
25532516 AAGAACATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (21 bp):
TCTCGAGACAAGTGGTCTTGA
Found at i:25537948 original size:13 final size:13
Alignment explanation
Indices: 25537930--25537977 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
25537920 TTCTTCCTTC
25537930 TCTTCTCTTCTCT
1 TCTTCTCTTCTCT
* *
25537943 TCTTCTATTTTCT
1 TCTTCTCTTCTCT
* *
25537956 TTTTCTCATTCTTT
1 TCTTCTC-TTCTCT
25537970 TCTTCTCT
1 TCTTCTCT
25537978 AGCCGAAACA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (13 bp):
TCTTCTCTTCTCT
Found at i:25539441 original size:46 final size:45
Alignment explanation
Indices: 25539388--25539563 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
25539378 TATTTGGGCA
25539388 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
** * *
25539434 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATAT-AACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC---ACTTATGGA-T-GCGAAG
*
25539481 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
25539527 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25539564 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 7 0.06
45 1 0.01
46 65 0.59
47 28 0.25
48 1 0.01
49 7 0.06
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:25539543 original size:93 final size:93
Alignment explanation
Indices: 25539384--25539555 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
25539374 AGGATATTTG
* *
25539384 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
25539449 TTGAGTCCGAGTTCGAGAGATATAACTA
66 TTGAGTCCGAGTTCGAGAGATATAACTA
* *
25539477 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
25539542 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
25539556 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATATAACTA
Found at i:25550502 original size:19 final size:20
Alignment explanation
Indices: 25550475--25550521 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
25550465 CGAATACGCC
*
25550475 AACAAAAGCTCG-AAAGCTG
1 AACAGAAGCTCGAAAAGCTG
25550494 AACAGAAGCTCGTAAAAGCTG
1 AACAGAAGCTCG-AAAAGCTG
25550515 AACAGAA
1 AACAGAA
25550522 AGTAAAACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.44
21 14 0.56
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (20 bp):
AACAGAAGCTCGAAAAGCTG
Found at i:25554655 original size:22 final size:21
Alignment explanation
Indices: 25554616--25554660 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
25554606 ATTTAAAAAT
25554616 TATTTTATACTAACATTTTATA
1 TATTTTATACTAACA-TTTATA
*
25554638 TATTTTATAATTAA-ATTTATA
1 TATTTTAT-ACTAACATTTATA
25554659 TA
1 TA
25554661 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 9 0.43
23 4 0.19
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTATACTAACATTTATA
Found at i:25554808 original size:20 final size:21
Alignment explanation
Indices: 25554783--25554833 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
25554773 GCAAATTAAT
*
25554783 AGACCTATCCATGGGTTGGG-
1 AGACCTATCCATGGGTCGGGC
25554803 AGACCTATCCATGGGTCGGGC
1 AGACCTATCCATGGGTCGGGC
25554824 AG-CCTATCCA
1 AGACCTATCCA
25554834 GCTAGACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (21 bp):
AGACCTATCCATGGGTCGGGC
Found at i:25555597 original size:25 final size:25
Alignment explanation
Indices: 25555569--25555620 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
25555559 ATCAAGTGAG
*
25555569 TATTTTTTATTTTAAAATATTACAT
1 TATTTTTTATTTCAAAATATTACAT
*
25555594 TATTTTTTATTTCAAAATGTTACAT
1 TATTTTTTATTTCAAAATATTACAT
25555619 TA
1 TA
25555621 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (25 bp):
TATTTTTTATTTCAAAATATTACAT
Found at i:25558374 original size:22 final size:22
Alignment explanation
Indices: 25558316--25558374 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
25558306 TAAGTATAAA
25558316 AAAATAAATAAAA-AACATTTGT
1 AAAA-AAATAAAATAACATTTGT
* *
25558338 ATAAAAATATTAATAAC-TTTGT
1 AAAAAAATA-AAATAACATTTGT
25558360 AAAAAGAATAAAATA
1 AAAAA-AATAAAATA
25558375 TAGTTTTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 5 0.17
22 18 0.60
23 7 0.23
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAAAAATAAAATAACATTTGT
Found at i:25564241 original size:23 final size:23
Alignment explanation
Indices: 25564179--25564242 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
25564169 TCGGAATTTT
*
25564179 TCATAACATATAACATATCGAAA
1 TCATATCATATAACATATCGAAA
* *
25564202 TCATATTATTTAACATATC-AAA
1 TCATATCATATAACATATCGAAA
*
25564224 GTCATATCATATATCATAT
1 -TCATATCATATAACATAT
25564243 AATATATCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (23 bp):
TCATATCATATAACATATCGAAA
Found at i:25566182 original size:18 final size:18
Alignment explanation
Indices: 25566136--25566184 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
25566126 GAGAGGAAAG
25566136 AAAGAATAAAAAA-TAAA
1 AAAGAATAAAAAATTAAA
* * *
25566153 AGAGGA-ACAAAATTAAA
1 AAAGAATAAAAAATTAAA
25566170 AAAGAATAAAAAATT
1 AAAGAATAAAAAATT
25566185 GCGAGTGATT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
16 5 0.21
17 12 0.50
18 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.14
Consensus pattern (18 bp):
AAAGAATAAAAAATTAAA
Found at i:25571250 original size:14 final size:16
Alignment explanation
Indices: 25571221--25571250 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25571211 AAATCACTAA
25571221 TAATATTAATTTTTTT
1 TAATATTAATTTTTTT
25571237 TAAT-TTAATTTTTT
1 TAATATTAATTTTTT
25571251 CAATGAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TAATATTAATTTTTTT
Found at i:25573764 original size:40 final size:40
Alignment explanation
Indices: 25573709--25573829 Score: 181
Period size: 40 Copynumber: 3.0 Consensus size: 40
25573699 ATTTGATGTG
25573709 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
*
25573749 TATCCGGGCTTAAAGACCCGTAGGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
* * ** *
25573789 TACCCGGACTT-AAGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
25573828 TA
1 TA
25573830 ACCAGACTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 26 0.35
40 48 0.65
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
Found at i:25573824 original size:39 final size:39
Alignment explanation
Indices: 25573726--25573853 Score: 175
Period size: 39 Copynumber: 3.3 Consensus size: 39
25573716 GCTTAAAGAC
* * **
25573726 CCGCAGGCTATATGCTGGAATTATATCCGGGCTTAAAGAC
1 CCGCAGGCTATATGCTGGAATTATAACCGGACTT-AAGGT
* *
25573766 CCGTAGGCTATATGCTGGAATTATACCCGGACTTAAGGT
1 CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT
* *
25573805 CCGCAGGCTATGTGCTGGAATTATAACCAGACTTAAGGT
1 CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT
25573844 CCGCAGGCTA
1 CCGCAGGCTA
25573854 CGCGCTGGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 48 0.61
40 31 0.39
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (39 bp):
CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT
Found at i:25573861 original size:39 final size:39
Alignment explanation
Indices: 25573779--25573863 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 39
25573769 TAGGCTATAT
* * * *
25573779 GCTGGAATTATACCCGGACTTAAGGTCCGCAGGCTATGT
1 GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC
25573818 GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC
1 GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC
25573857 GCTGGAA
1 GCTGGAA
25573864 ATATGTCCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (39 bp):
GCTGGAATTATAACCAGACTTAAGGTCCGCAGGCTACGC
Found at i:25576323 original size:23 final size:21
Alignment explanation
Indices: 25576251--25576325 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
25576241 CCTGATCAGT
** *
25576251 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTA
* ** *
25576272 AAACGGTACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTA
25576293 ATACGACACACGAGGTGCCTAAA
1 ATACGACACACGAGGTGCCT--A
25576316 ATACGACACA
1 ATACGACACA
25576326 TAAAGTGCCT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 31 0.76
23 10 0.24
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTA
Found at i:25576650 original size:15 final size:15
Alignment explanation
Indices: 25576625--25576682 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
25576615 TCATATATAT
25576625 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
25576641 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
25576656 AATAATTTCAATCAA
1 TATAAATTCAATCAA
25576671 TATAAATTCAAT
1 TATAAATTCAAT
25576683 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:25577042 original size:8 final size:8
Alignment explanation
Indices: 25577029--25577067 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
25577019 TATCTTTATT
25577029 ATATAATA
1 ATATAATA
25577037 ATATAATA
1 ATATAATA
25577045 ATATAATA
1 ATATAATA
* *
25577053 ACATACTAA
1 ATATAAT-A
25577062 ATATAA
1 ATATAA
25577068 AAAAAAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 21 0.81
9 5 0.19
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (8 bp):
ATATAATA
Found at i:25582459 original size:24 final size:25
Alignment explanation
Indices: 25582430--25582479 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
25582420 TAAATTGTGT
25582430 TAGGTTTTTTTTTT-AAATTCTAGC
1 TAGGTTTTTTTTTTAAAATTCTAGC
25582454 TAGGTTTTTTTTTTAAAATTCTAGC
1 TAGGTTTTTTTTTTAAAATTCTAGC
25582479 T
1 T
25582480 TGTTTTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.58
Consensus pattern (25 bp):
TAGGTTTTTTTTTTAAAATTCTAGC
Found at i:25583903 original size:40 final size:39
Alignment explanation
Indices: 25583848--25583980 Score: 176
Period size: 40 Copynumber: 3.4 Consensus size: 39
25583838 ATTTGATGTG
* *
25583848 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGACTT-AAGACCCACAGGCTATATGCTGGAATTA
*
25583888 TATCCGGGCTTAAAGACCCACAGGCTATATGCTGGAATTA
1 TATCCGGACTT-AAGACCCACAGGCTATATGCTGGAATTA
* ** *
25583928 TACCCGGACTTAAGGTCCACAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAAGACCCACAGGCTATATGCTGGAATTA
*
25583967 TAACCGGACTTAAG
1 TATCCGGACTTAAG
25583981 GTCCGCAGGC
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
39 38 0.44
40 48 0.56
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (39 bp):
TATCCGGACTTAAGACCCACAGGCTATATGCTGGAATTA
Found at i:25583960 original size:39 final size:39
Alignment explanation
Indices: 25583868--25583992 Score: 178
Period size: 39 Copynumber: 3.2 Consensus size: 39
25583858 TAAAGACCCG
* * **
25583868 CAGGCTATATGCTGGAATTATATCCGGGCTTAAAGACCCA
1 CAGGCTATATGCTGGAATTATAACCGGACTT-AAGGTCCA
*
25583908 CAGGCTATATGCTGGAATTATACCCGGACTTAAGGTCCA
1 CAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCCA
* *
25583947 CAGGCTATGTGCTGGAATTATAACCGGACTTAAGGTCCG
1 CAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCCA
25583986 CAGGCTA
1 CAGGCTA
25583993 CGCGCTGGAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 49 0.63
40 29 0.37
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (39 bp):
CAGGCTATATGCTGGAATTATAACCGGACTTAAGGTCCA
Found at i:25585553 original size:18 final size:18
Alignment explanation
Indices: 25585516--25585553 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25585506 GTTCACCTCT
*
25585516 TTTCTTAGTATTTATTAG
1 TTTCTTAGTATTTATGAG
25585534 TTTC-TAGTATTATATGAG
1 TTTCTTAGTATT-TATGAG
25585552 TT
1 TT
25585554 GTGGGTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (18 bp):
TTTCTTAGTATTTATGAG
Found at i:25586226 original size:6 final size:6
Alignment explanation
Indices: 25586203--25586240 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
25586193 TTTTTAACTA
25586203 ATAATT ATAAATT A-AATT ATAATT ATAATT ATAATT AT
1 ATAATT AT-AATT ATAATT ATAATT ATAATT ATAATT AT
25586241 CACAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 20 0.67
7 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:25590190 original size:18 final size:19
Alignment explanation
Indices: 25590154--25590192 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
25590144 ACTAAATAAT
25590154 AAAATATAATAATTATTTA
1 AAAATATAATAATTATTTA
25590173 AAAATAT-AT-ATTACTTTA
1 AAAATATAATAATTA-TTTA
25590191 AA
1 AA
25590193 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATATAATAATTATTTA
Found at i:25591301 original size:28 final size:28
Alignment explanation
Indices: 25591261--25591318 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
25591251 GTTTTGAGTA
*
25591261 TAAGTTTCCCTATTCATTCTATTATTAT
1 TAAGTTTCCCTATTCATTCTATTATCAT
*
25591289 TAAGTTTCCCTATTCGTTCTATTATCAT
1 TAAGTTTCCCTATTCATTCTATTATCAT
25591317 TA
1 TA
25591319 TGAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (28 bp):
TAAGTTTCCCTATTCATTCTATTATCAT
Found at i:25597003 original size:25 final size:24
Alignment explanation
Indices: 25596981--25597027 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25596971 TCGAAAAATG
25596981 AAAAAAAAATACATGCTACAAAAGC
1 AAAAAAAAAT-CATGCTACAAAAGC
* *
25597006 AAACAAAAATCGTGCTACAAAA
1 AAAAAAAAATCATGCTACAAAA
25597028 ATAGACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.62, C:0.17, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAAAAAAATCATGCTACAAAAGC
Found at i:25598377 original size:24 final size:28
Alignment explanation
Indices: 25598317--25598375 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
25598307 TGTCATAATG
*
25598317 ATATATACACATATGGTATTAAGAATAT
1 ATATATACACATATAGTATTAAGAATAT
*
25598345 ATATATACA-ATATAGTATTTAAAAATAT
1 ATATATACACATATAGTA-TTAAGAATAT
25598373 ATA
1 ATA
25598376 CATAAGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (28 bp):
ATATATACACATATAGTATTAAGAATAT
Found at i:25599172 original size:3 final size:3
Alignment explanation
Indices: 25599166--25599209 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
25599156 AAACATAAGC
* * *
25599166 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAC TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
25599210 TTATAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25599859 original size:13 final size:13
Alignment explanation
Indices: 25599812--25599863 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
25599802 AAAAAGGTAA
25599812 ATTTTTTT-TTAAT
1 ATTTTTTTATT-AT
*
25599825 ATTTGTTTTGTATAT
1 ATTT-TTTTAT-TAT
*
25599840 ATATTTTTATTAT
1 ATTTTTTTATTAT
25599853 ATTTTTTTATT
1 ATTTTTTTATT
25599864 TATGATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 17 0.52
14 9 0.27
15 6 0.18
16 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (13 bp):
ATTTTTTTATTAT
Done.