Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 2 of 199
Found at i:455518 original size:36 final size:36
Alignment explanation
Indices: 455471--455541 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
455461 CTCCGAAACC
455471 TTGGAGATCCTCACAGG-AAGGTCGCAACATCATGTT
1 TTGGAGATCCTCAC-GGTAAGGTCGCAACATCATGTT
*
455507 TTGGAGATCCTCACGGTAAGGTGGCAACATCATGT
1 TTGGAGATCCTCACGGTAAGGTCGCAACATCATGT
455542 CTGTTCCGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (36 bp):
TTGGAGATCCTCACGGTAAGGTCGCAACATCATGTT
Found at i:460982 original size:358 final size:358
Alignment explanation
Indices: 460325--461058 Score: 1441
Period size: 358 Copynumber: 2.0 Consensus size: 358
460315 ATTGTTATCC
460325 TGGTCCCACTACTGGTTTTACTATGTTTAGTCCTCAAGTTGGACATCCTGGTTTTACTGGGTTGA
1 TGGTCCCACTACTGGTTTTACTATGTTTAGTCCTCAAGTTGGACATCCTGGTTTTACTGGGTTGA
460390 ATACTCAAAGTAATCTTGCTGGTTCTGGAGGACTTAATGTGTCTGCACATATACCTTCTACTGGA
66 ATACTCAAAGTAATCTTGCTGGTTCTGGAGGACTTAATGTGTCTGCACATATACCTTCTACTGGA
460455 ATGCCTCCTACCCATGCTGGTACTTCACATTTTGCTGCATATAACTGCAGTATGCCGATAGTCAG
131 ATGCCTCCTACCCATGCTGGTACTTCACATTTTGCTGCATATAACTGCAGTATGCCGATAGTCAG
460520 CAATCTCAGTCCTGCAAACCCTTATGTTATGTCCTGTAACAATGGTAATCCTTTTGTTAGTGGTG
196 CAATCTCAGTCCTGCAAACCCTTATGTTATGTCCTGTAACAATGGTAATCCTTTTGTTAGTGGTG
460585 CTGGCTCTTTGTGTTCAGGTTCTACTCAAGCTAGTTCAGAAGGTAATCGAATCTCTAAGTGTTTG
261 CTGGCTCTTTGTGTTCAGGTTCTACTCAAGCTAGTTCAGAAGGTAATCGAATCTCTAAGTGTTTG
460650 CAAGCTACACCAGCAGTGGTTGCAGATCCGGCT
326 CAAGCTACACCAGCAGTGGTTGCAGATCCGGCT
460683 TGGTCCCACTACTGGTTTTACTATGTTTAGTCCTCAAGTTGGACATCCTGGTTTTACTGGGTTGA
1 TGGTCCCACTACTGGTTTTACTATGTTTAGTCCTCAAGTTGGACATCCTGGTTTTACTGGGTTGA
460748 ATACTCAAAGTAATCTTGCTGGTTCTGGAGGACTTAATGTGTCTGCACATATACCTTCTACTGGA
66 ATACTCAAAGTAATCTTGCTGGTTCTGGAGGACTTAATGTGTCTGCACATATACCTTCTACTGGA
460813 ATGCCTCCTACCCATGCTGGTACTTCACATTTTGCTGCATATAACTGCAGTATGCCGATAGTCAG
131 ATGCCTCCTACCCATGCTGGTACTTCACATTTTGCTGCATATAACTGCAGTATGCCGATAGTCAG
460878 CAATCTCAGTCCTGCAAACCCTTATGTTATGTCCTGTAACAATGGTAATCCTTTTGTTAGTGGTG
196 CAATCTCAGTCCTGCAAACCCTTATGTTATGTCCTGTAACAATGGTAATCCTTTTGTTAGTGGTG
460943 CTGGCTCTTTGTGTTCAGGTTCTACTCAAGCTAGTTCAGAAGGTAATCGAATCTCTAAGTGTTTG
261 CTGGCTCTTTGTGTTCAGGTTCTACTCAAGCTAGTTCAGAAGGTAATCGAATCTCTAAGTGTTTG
461008 CAAGCTACACCAGCAGTGGTTGCAGATCCGGCT
326 CAAGCTACACCAGCAGTGGTTGCAGATCCGGCT
*
461041 TGGTACCCAGATACTGGT
1 TGGT-CCCA-CTACTGGT
461059 GCAACTGGGC
Statistics
Matches: 373, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
358 362 0.97
359 4 0.01
360 7 0.02
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (358 bp):
TGGTCCCACTACTGGTTTTACTATGTTTAGTCCTCAAGTTGGACATCCTGGTTTTACTGGGTTGA
ATACTCAAAGTAATCTTGCTGGTTCTGGAGGACTTAATGTGTCTGCACATATACCTTCTACTGGA
ATGCCTCCTACCCATGCTGGTACTTCACATTTTGCTGCATATAACTGCAGTATGCCGATAGTCAG
CAATCTCAGTCCTGCAAACCCTTATGTTATGTCCTGTAACAATGGTAATCCTTTTGTTAGTGGTG
CTGGCTCTTTGTGTTCAGGTTCTACTCAAGCTAGTTCAGAAGGTAATCGAATCTCTAAGTGTTTG
CAAGCTACACCAGCAGTGGTTGCAGATCCGGCT
Found at i:465532 original size:18 final size:19
Alignment explanation
Indices: 465504--465539 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
465494 TTATTTTTCA
465504 ATTTTTAGTGTAAATATTG
1 ATTTTTAGTGTAAATATTG
*
465523 ATTTTT-GTGTAATTATT
1 ATTTTTAGTGTAAATATT
465540 TGTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (19 bp):
ATTTTTAGTGTAAATATTG
Found at i:469480 original size:94 final size:94
Alignment explanation
Indices: 469381--469575 Score: 372
Period size: 94 Copynumber: 2.1 Consensus size: 94
469371 ACTGGTTAAA
469381 AAAAAAGTTAATTAAACCAACAAAAATCAATACAAATATAATCATTAATCATCTTCCTAAACCTT
1 AAAAAAGTTAATTAAACCAACAAAAATCAATACAAATATAATCATTAATCATCTTCCTAAACCTT
*
469446 TCTAGTTTGGGGTTGACACTTTTTTAGAG
66 TCTAGTATGGGGTTGACACTTTTTTAGAG
*
469475 AAAAAAGTTAATTAAACCAACAAAAATCAATGCAAATATAATCATTAATCATCTTCCTAAACCTT
1 AAAAAAGTTAATTAAACCAACAAAAATCAATACAAATATAATCATTAATCATCTTCCTAAACCTT
469540 TCTAGTATGGGGTTGACACTTTTTTAGAG
66 TCTAGTATGGGGTTGACACTTTTTTAGAG
469569 AAAAAAG
1 AAAAAAG
469576 CGATGGATTC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 99 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (94 bp):
AAAAAAGTTAATTAAACCAACAAAAATCAATACAAATATAATCATTAATCATCTTCCTAAACCTT
TCTAGTATGGGGTTGACACTTTTTTAGAG
Found at i:471799 original size:18 final size:18
Alignment explanation
Indices: 471773--471845 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 18
471763 ATGATGATCC
* *
471773 TAACGAAAATAATATTAG
1 TAACAAAAATAATAATAG
* *
471791 TAACAAAAATCATAATAT
1 TAACAAAAATAATAATAG
* * * *
471809 TAATATAAATAATCATAT
1 TAACAAAAATAATAATAG
*
471827 TAATAAAAATAATAATAG
1 TAACAAAAATAATAATAG
471845 T
1 T
471846 GTAAACGAGA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (18 bp):
TAACAAAAATAATAATAG
Found at i:479303 original size:28 final size:30
Alignment explanation
Indices: 479271--479349 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
479261 CTATTAAAAA
479271 AATAAAAA-TTT-AATAA-TCAAGTGGCTTG
1 AATAAAAACTTTAAATAATTC-AGTGGCTTG
479299 AATAAAAACTTTAGAATAATTCAGTGGCTT-
1 AATAAAAACTTTA-AATAATTCAGTGGCTTG
*
479329 AA-AAATAATATTTAAATAATT
1 AATAAA-AA-CTTTAAATAATT
479350 TAATTACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
28 8 0.18
29 6 0.14
30 11 0.25
31 17 0.39
32 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (30 bp):
AATAAAAACTTTAAATAATTCAGTGGCTTG
Found at i:487585 original size:6 final size:6
Alignment explanation
Indices: 487574--487600 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
487564 ACTCAAAATT
487574 TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTA
487601 ATTGAAACGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:497554 original size:11 final size:12
Alignment explanation
Indices: 497528--497553 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
497518 TAATTAATAA
497528 TTTATTAAATTT
1 TTTATTAAATTT
497540 TTTATTAAATTT
1 TTTATTAAATTT
497552 TT
1 TT
497554 AGTGCGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATTAAATTT
Found at i:498174 original size:22 final size:21
Alignment explanation
Indices: 498132--498173 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
498122 AATCGTACCT
498132 ACACTTTTTGTAAAATAAAAG
1 ACACTTTTTGTAAAATAAAAG
*
498153 ACACATTTTTGATAAATTAAA
1 ACAC-TTTTTG-TAAAATAAA
498174 GTAAAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 6 0.33
23 8 0.44
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (21 bp):
ACACTTTTTGTAAAATAAAAG
Found at i:507608 original size:21 final size:20
Alignment explanation
Indices: 507575--507614 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
507565 TTAAATTATT
507575 TATAACATTTTCTCTAAATA
1 TATAACATTTTCTCTAAATA
* *
507595 TATAATATGTTTCTTTAAAT
1 TATAACAT-TTTCTCTAAAT
507615 TTTTACTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (20 bp):
TATAACATTTTCTCTAAATA
Found at i:515718 original size:13 final size:13
Alignment explanation
Indices: 515700--515725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
515690 TTGGTAATTG
515700 TTTATACCAGACA
1 TTTATACCAGACA
515713 TTTATACCAGACA
1 TTTATACCAGACA
515726 ATAAGGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTATACCAGACA
Found at i:531655 original size:18 final size:18
Alignment explanation
Indices: 531631--531673 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
531621 AATTGATTTT
531631 TTAATTAAATAACTTTAAA
1 TTAATTAAA-AACTTTAAA
*
531650 -TAATTAAAAATTTTAAA
1 TTAATTAAAAACTTTAAA
531667 TTAATTA
1 TTAATTA
531674 TAGGAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAACTTTAAA
Found at i:548692 original size:21 final size:21
Alignment explanation
Indices: 548668--548708 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
548658 TAAATATCAC
548668 AATTTATATGTATTT-TATATT
1 AATTTATATG-ATTTATATATT
*
548689 AATTTTTATGATTTATATAT
1 AATTTATATGATTTATATAT
548709 ATATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
AATTTATATGATTTATATATT
Found at i:549153 original size:103 final size:105
Alignment explanation
Indices: 548885--549153 Score: 379
Period size: 103 Copynumber: 2.6 Consensus size: 105
548875 TTACTTCAAC
* * * * *
548885 TTTGTCTTTTCC-TTTTCATGTCCT-TTTTAGTTTTCTGATCTA-TGCTTATCTACTTCTATTTC
1 TTTGTCTTTGCCTTTTTCATCT-CTGTTTTAGTTTTCAGATC-ACTGCTTCTTTAC-TCTATTTC
*
548947 AGTGGGTTTTTTTTTGTTTTTTGGGTTTTCAACTTTAGAACAAG
63 AGCGGG-TTTTTTTTGTTTTTTGGGTTTTCAACTTTAGAACAAG
* * *
548991 TTTATCTTTGCTTTTTTCATCTCTGTTTTAGTTTTCAGATCACTGCTTCTTT-TTCTATTTCAGC
1 TTTGTCTTTGCCTTTTTCATCTCTGTTTTAGTTTTCAGATCACTGCTTCTTTACTCTATTTCAGC
549055 GGG-TTTTTTTGTTTTTTGGGTTTTCAACTTTAGAACAAG
66 GGGTTTTTTTTGTTTTTTGGGTTTTCAACTTTAGAACAAG
549094 TTTGTCTTTGCCTTTTTCATCTCTGTTTTAGTTTTCAGATCACTGCTTCTTTACT-TATTT
1 TTTGTCTTTGCCTTTTTCATCTCTGTTTTAGTTTTCAGATCACTGCTTCTTTACTCTATTT
549154 TTCAGTGGGG
Statistics
Matches: 147, Mismatches: 12, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
103 91 0.62
104 1 0.01
105 13 0.09
106 12 0.08
107 30 0.20
ACGTcount: A:0.14, C:0.16, G:0.13, T:0.57
Consensus pattern (105 bp):
TTTGTCTTTGCCTTTTTCATCTCTGTTTTAGTTTTCAGATCACTGCTTCTTTACTCTATTTCAGC
GGGTTTTTTTTGTTTTTTGGGTTTTCAACTTTAGAACAAG
Found at i:550967 original size:33 final size:33
Alignment explanation
Indices: 550925--550989 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
550915 GAAGTCATTA
*
550925 AACTTCCATTGTTAACCAAATAGGGTTTTATTG
1 AACTTCCATTGTTAACCAAACAGGGTTTTATTG
*
550958 AACTTCCATTGTTAACTAAACAGGGTTTTATT
1 AACTTCCATTGTTAACCAAACAGGGTTTTATT
550990 ATATACACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (33 bp):
AACTTCCATTGTTAACCAAACAGGGTTTTATTG
Found at i:553049 original size:1 final size:1
Alignment explanation
Indices: 553043--553076 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
553033 ACACAATCTC
553043 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
553077 GGAAAGTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:554160 original size:42 final size:42
Alignment explanation
Indices: 554089--554169 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
554079 CATTGCAGGC
* *
554089 AGACTTGTATTGATACAACTCATAAGATGTATGGGTAGACGT
1 AGACTTGTATTGATACAACTCACAAGATGTATAGGTAGACGT
* *
554131 AGACTTGTATTGATAC-ATTGCACATGATGTATAGGTAGA
1 AGACTTGTATTGATACAACT-CACAAGATGTATAGGTAGA
554170 GGTCCCCCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.32
Consensus pattern (42 bp):
AGACTTGTATTGATACAACTCACAAGATGTATAGGTAGACGT
Found at i:557794 original size:13 final size:13
Alignment explanation
Indices: 557776--557800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
557766 CTAAATAGAT
557776 AATTTTTTTAATC
1 AATTTTTTTAATC
557789 AATTTTTTTAAT
1 AATTTTTTTAAT
557801 TATATGTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTTTAATC
Found at i:560375 original size:15 final size:17
Alignment explanation
Indices: 560357--560402 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
560347 TTTTTAAGAG
560357 AATTATTTATAAA-AA-
1 AATTATTTATAAATAAT
560372 AATTA-TTA-AAATAAT
1 AATTATTTATAAATAAT
560387 AATTATTTAT-AATAAT
1 AATTATTTATAAATAAT
560403 TAGTAATTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.11
14 5 0.19
15 10 0.37
16 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTATTTATAAATAAT
Found at i:565815 original size:8 final size:8
Alignment explanation
Indices: 565802--565832 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
565792 CGGAATTATC
565802 ATATTTAA
1 ATATTTAA
565810 ATATTTAA
1 ATATTTAA
565818 ATATTTAA
1 ATATTTAA
565826 ATATTTA
1 ATATTTA
565833 CTTGACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATATTTAA
Found at i:571943 original size:38 final size:38
Alignment explanation
Indices: 571899--571974 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
571889 ATCTACTCTT
*
571899 TTTTGAAATATCAAATTTAAACATTTTTACCCTGTCGA
1 TTTTGAAATATCAAATTTAAACATTTGTACCCTGTCGA
* *
571937 TTTTGAAATATTAAATTTAAATATTTGTACCCTGTCGA
1 TTTTGAAATATCAAATTTAAACATTTGTACCCTGTCGA
571975 AGTAAGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (38 bp):
TTTTGAAATATCAAATTTAAACATTTGTACCCTGTCGA
Found at i:575259 original size:43 final size:43
Alignment explanation
Indices: 575211--575294 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
575201 CAAAAAATGC
* * *
575211 ACACACTAGCAGTCACACGGTCATGTGATCTTAA-TTTGAATAT
1 ACACACGAGCAGACACACGGTCATGTG-TCTCAACTTTGAATAT
* *
575254 ACACACGGGCAGACACACGGTCGTGTGTCTCAACTTTGAAT
1 ACACACGAGCAGACACACGGTCATGTGTCTCAACTTTGAAT
575295 GTCTACACGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 5 0.14
43 30 0.86
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
ACACACGAGCAGACACACGGTCATGTGTCTCAACTTTGAATAT
Found at i:575472 original size:11 final size:11
Alignment explanation
Indices: 575456--575480 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
575446 GTGTATGTTT
575456 ATTGTGAATTG
1 ATTGTGAATTG
575467 ATTGTGAATTG
1 ATTGTGAATTG
575478 ATT
1 ATT
575481 AATTGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (11 bp):
ATTGTGAATTG
Found at i:577722 original size:3 final size:3
Alignment explanation
Indices: 577714--577754 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
577704 ATAAATTTCA
* *
577714 TAT TAT TAT TGT TAT TAT TAT TAT ATAT TTT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT T
577755 GCTTTTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:577747 original size:19 final size:18
Alignment explanation
Indices: 577714--577754 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
577704 ATAAATTTCA
577714 TATTATTATTGTTATTAT
1 TATTATTATTGTTATTAT
*
577732 TATTATATATTTTTATTAT
1 TATTAT-TATTGTTATTAT
577751 TATT
1 TATT
577755 GCTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TATTATTATTGTTATTAT
Found at i:577869 original size:2 final size:2
Alignment explanation
Indices: 577864--577889 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
577854 TTTTATTTTC
577864 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
577890 TTACATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577988 original size:37 final size:38
Alignment explanation
Indices: 577945--578036 Score: 109
Period size: 37 Copynumber: 2.4 Consensus size: 38
577935 TTATTTTATG
577945 ATTCATATATATATATACATACCTATATGTATATACTT
1 ATTCATATATATATATACATACCTATATGTATATACTT
* * *
577983 -TTCATAT-TTTAATTTACATACGTATATGTATATACTT
1 ATTCATATATAT-ATATACATACCTATATGTATATACTT
*
578020 ACTT-ATATATATCTATA
1 A-TTCATATATATATATA
578037 TAATAATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
36 2 0.05
37 31 0.70
38 7 0.16
39 4 0.09
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (38 bp):
ATTCATATATATATATACATACCTATATGTATATACTT
Found at i:584188 original size:11 final size:11
Alignment explanation
Indices: 584172--584196 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
584162 GTGTATGTTA
584172 ATTGTGAATTG
1 ATTGTGAATTG
584183 ATTGTGAATTG
1 ATTGTGAATTG
584194 ATT
1 ATT
584197 AATTGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (11 bp):
ATTGTGAATTG
Found at i:588576 original size:52 final size:52
Alignment explanation
Indices: 588518--588617 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
588508 AGAAATTATA
588518 AATTAATAAATAGTAAAATTTCTCTTTAGCCCCTTAAAAATGAAAAAATAAT
1 AATTAATAAATAGTAAAATTTCTCTTTAGCCCCTTAAAAATGAAAAAATAAT
*
588570 AATTAATATATAGTAAAATTTCTCTTTAGCCCCTTAAAAATGAAAAAA
1 AATTAATAAATAGTAAAATTTCTCTTTAGCCCCTTAAAAATGAAAAAA
588618 ATTATGTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AATTAATAAATAGTAAAATTTCTCTTTAGCCCCTTAAAAATGAAAAAATAAT
Found at i:610985 original size:11 final size:11
Alignment explanation
Indices: 610969--610993 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
610959 GTGTATGTTT
610969 ATTGTGAATTG
1 ATTGTGAATTG
610980 ATTGTGAATTG
1 ATTGTGAATTG
610991 ATT
1 ATT
610994 AATTGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (11 bp):
ATTGTGAATTG
Found at i:617754 original size:17 final size:17
Alignment explanation
Indices: 617732--617765 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
617722 TATTCTTTGC
*
617732 TTTGTGGATTAGCTAAT
1 TTTGTGGATTAGATAAT
617749 TTTGTGGATTAGATAAT
1 TTTGTGGATTAGATAAT
617766 GAATATTCTG
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:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTGTGGATTAGATAAT
Found at i:622640 original size:19 final size:19
Alignment explanation
Indices: 622616--622663 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
622606 GTGTCCCTTA
622616 TTTTTCAAAATTTT-CATCT
1 TTTTTCAAAATTTTCCAT-T
* *
622635 TTTTTCTAACTTTTCCATT
1 TTTTTCAAAATTTTCCATT
622654 TTGTTTCAAA
1 TT-TTTCAAA
622664 TTGACCTCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTCAAAATTTTCCATT
Found at i:636269 original size:136 final size:125
Alignment explanation
Indices: 636077--636516 Score: 508
Period size: 125 Copynumber: 3.4 Consensus size: 125
636067 AATAAGAGAG
* * * * * * *
636077 TAAAATCAAAATAACAACGAAAATAAAAAATCGAGCACACTCCTTAGCATCGCACCTTAAATGCA
1 TAAAAACAAAAGAAGAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
* * * *
636142 AGATCATACCTTAACGTAGACAACATAGAAACTCCGAAACATTATAGCAAGAATACTCCG
66 AGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGAATACTCCA
* *
636202 TAAAAACAACCAAGCTCAATAATAGAGTAAA-AACAAAATAACAA-CGAGCACTCCTTAGCATCA
1 TAAAAACAA--AAG---AAGAACA-A--AAATAA-AAAAT--CAAGC-A-CACTCCTTAGCATCA
* *
636265 CACCTTAAATGTAAGATCATCCCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAAA
53 CACCTTAAATGTAAGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGA
636330 ATACTCCA
118 ATACTCCA
* * *
636338 TGAAAACAAAAGAAGAACAAAAATTAGAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
1 TAAAAACAAAAGAAGAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
* * *
636403 AGATCATACCTTAACATAGACAACCTAAAAACTCCAAAAAATTGTAGCAAGAATACTCCA
66 AGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGAATACTCCA
* * * *
636463 TAAAAACAAAAGAACG-ACGAAAATTAAAAATCGAGCACACTCGTTAGCATCACA
1 TAAAAACAAAAGAA-GAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACA
636517 AAACATCAGA
Statistics
Matches: 270, Mismatches: 29, Indels: 32
0.82 0.09 0.10
Matches are distributed among these distances:
125 138 0.51
126 5 0.02
127 3 0.01
128 7 0.03
129 1 0.00
130 5 0.02
131 6 0.02
132 2 0.01
133 8 0.03
134 4 0.01
135 3 0.01
136 88 0.33
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (125 bp):
TAAAAACAAAAGAAGAACAAAAATAAAAAATCAAGCACACTCCTTAGCATCACACCTTAAATGTA
AGATCATACCTTAACATAGACAACCTAGAAACTCCGAAACATTGTAGCAAGAATACTCCA
Found at i:637290 original size:24 final size:24
Alignment explanation
Indices: 637254--637300 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
637244 GCGAGTTTGG
** * *
637254 ACTTTTCTTATTTTCCTTTTCTTC
1 ACTTTTCAAATTTCCCTCTTCTTC
637278 ACTTTTCAAATTTCCCTCTTCTT
1 ACTTTTCAAATTTCCCTCTTCTT
637301 TTCCTTTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.60
Consensus pattern (24 bp):
ACTTTTCAAATTTCCCTCTTCTTC
Found at i:639564 original size:37 final size:37
Alignment explanation
Indices: 639461--639775 Score: 465
Period size: 37 Copynumber: 8.4 Consensus size: 37
639451 TACGTATGAT
* *
639461 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
639496 CACCTATCACTTTGTTTC-TGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
639532 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
639569 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
639606 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
639643 TAAAGCTATTACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 -----C----ACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
639689 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
639726 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
639763 CACTTATCACTTT
1 CACTTATCACTTT
639776 TCACTTTCCA
Statistics
Matches: 260, Mismatches: 8, Indels: 22
0.90 0.03 0.08
Matches are distributed among these distances:
35 9 0.03
36 38 0.15
37 175 0.67
41 1 0.00
42 1 0.00
46 36 0.14
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:639746 original size:120 final size:120
Alignment explanation
Indices: 639533--639762 Score: 442
Period size: 120 Copynumber: 1.9 Consensus size: 120
639523 AAGTGTAGCC
* *
639533 ACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCTTGATCAGATA
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATA
639598 AGTGTAGCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATT
66 AGTGTAGCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATT
639653 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATA
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATA
639718 AGTGTAGCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
66 AGTGTAGCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
639763 CACTTATCAC
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (120 bp):
ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATA
AGTGTAGCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATT
Found at i:643485 original size:13 final size:13
Alignment explanation
Indices: 643467--643493 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
643457 TTAATTTCAA
643467 AATTAAACAAATT
1 AATTAAACAAATT
643480 AATTAAACAAATT
1 AATTAAACAAATT
643493 A
1 A
643494 TCCCCTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AATTAAACAAATT
Found at i:646835 original size:31 final size:31
Alignment explanation
Indices: 646800--646858 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
646790 AATGCCATGT
*
646800 TATCAAGTTTAGGGACTAA-ATTGAAAAAGGA
1 TATCAAATTTAGGGACTAATA-TGAAAAAGGA
646831 TATCAAATTTAGGGACTAATATGAAAAA
1 TATCAAATTTAGGGACTAATATGAAAAA
646859 ATAGGACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (31 bp):
TATCAAATTTAGGGACTAATATGAAAAAGGA
Found at i:650927 original size:14 final size:14
Alignment explanation
Indices: 650908--650935 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
650898 TGTTGGTATG
650908 AAATAAATTTAACA
1 AAATAAATTTAACA
650922 AAATAAATTTAACA
1 AAATAAATTTAACA
650936 GTATTAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAAATTTAACA
Found at i:651881 original size:15 final size:17
Alignment explanation
Indices: 651851--651884 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
651841 ATCGGAACAC
651851 CTTATATATATAATGAA
1 CTTATATATATAATGAA
*
651868 CTTATAATATATGATGA
1 CTTAT-ATATATAATGA
651885 CAACAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (17 bp):
CTTATATATATAATGAA
Found at i:663247 original size:24 final size:24
Alignment explanation
Indices: 663211--663259 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
663201 AATTATATGA
*
663211 AGAAAAATGAAAGAGAGAAAAATT
1 AGAAAAATAAAAGAGAGAAAAATT
663235 AGAAAAATAAAAGAGAGAAAAATT
1 AGAAAAATAAAAGAGAGAAAAATT
663259 A
1 A
663260 ATACAAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.12
Consensus pattern (24 bp):
AGAAAAATAAAAGAGAGAAAAATT
Found at i:668612 original size:3 final size:3
Alignment explanation
Indices: 668604--668641 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
668594 ATTGATCAAT
668604 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
668642 TTTTGTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:670080 original size:7 final size:7
Alignment explanation
Indices: 670068--670097 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
670058 TTCCACTTCA
670068 AAAGCTG
1 AAAGCTG
670075 AAAGCTG
1 AAAGCTG
670082 AAAGCTG
1 AAAGCTG
670089 AAAGCTG
1 AAAGCTG
670096 AA
1 AA
670098 GGTGTGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (7 bp):
AAAGCTG
Found at i:676138 original size:21 final size:20
Alignment explanation
Indices: 676105--676143 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
676095 TGACCTCACA
676105 TTTTAATATTAGAATTTTTC
1 TTTTAATATTAGAATTTTTC
*
676125 TTTTAGATTTTAG-ATTTTT
1 TTTTA-ATATTAGAATTTTT
676144 TGAACCGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTAATATTAGAATTTTTC
Found at i:678378 original size:2 final size:2
Alignment explanation
Indices: 678371--678398 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
678361 GAGTGAGTGT
678371 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
678399 TACCTGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:683486 original size:2 final size:2
Alignment explanation
Indices: 683479--683513 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
683469 ATGAGAAATC
*
683479 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
683514 CTCACGTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:688901 original size:31 final size:30
Alignment explanation
Indices: 688865--688938 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
688855 CACTATCAAC
* *
688865 TTAATTTAATTACATTATATAACATTTTAAT
1 TTAATTTAATTACATTACATAACA-ATTAAT
* * *
688896 TTAATTTAATCACATTACGTAATAATTAAT
1 TTAATTTAATTACATTACATAACAATTAAT
688926 TTAATTTAATTAC
1 TTAATTTAATTAC
688939 GATATTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (30 bp):
TTAATTTAATTACATTACATAACAATTAAT
Found at i:689117 original size:5 final size:5
Alignment explanation
Indices: 689107--689146 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
689097 CATCCGTACA
689107 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
689147 ATGTAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CATAT
Found at i:694741 original size:27 final size:27
Alignment explanation
Indices: 694690--694740 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
694680 TTTTTCAATG
*
694690 AATTAAAAAATTGAAGTATAAAAAAGA
1 AATTAAAAAATGGAAGTATAAAAAAGA
694717 AATTAAAAAA-GGAAGTATAAAAAA
1 AATTAAAAAATGGAAGTATAAAAAA
694741 ATCAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.20
Consensus pattern (27 bp):
AATTAAAAAATGGAAGTATAAAAAAGA
Found at i:715049 original size:2 final size:2
Alignment explanation
Indices: 715042--715071 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
715032 AAGTTAAAGC
*
715042 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
715072 GTATGTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:715805 original size:22 final size:22
Alignment explanation
Indices: 715769--715834 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 22
715759 ATATTAAAAC
* * **
715769 CCTAAACTCTTAACCCTACTAT
1 CCTAAACACTAAACCCTAAGAT
715791 CCTAAACACTAAA-CCTAAGAT
1 CCTAAACACTAAACCCTAAGAT
* *
715812 CATAAACACTAACCCCTAA-AT
1 CCTAAACACTAAACCCTAAGAT
715833 CC
1 CC
715835 GAGAGTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.41, C:0.35, G:0.02, T:0.23
Consensus pattern (22 bp):
CCTAAACACTAAACCCTAAGAT
Found at i:717190 original size:30 final size:31
Alignment explanation
Indices: 717120--717190 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
717110 GGTAAGTTTG
* *
717120 AGGACCAAATTGATAGAATTTGTAAATGTGA
1 AGGACTAAATTGATAGAATATGTAAATGTGA
*
717151 AGGATTAAATTGATAGAATATGTAATAT-T-A
1 AGGACTAAATTGATAGAATATGTAA-ATGTGA
717181 AGGACTAAAT
1 AGGACTAAAT
717191 GTGTTATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 23 0.66
32 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (31 bp):
AGGACTAAATTGATAGAATATGTAAATGTGA
Found at i:726895 original size:12 final size:12
Alignment explanation
Indices: 726878--726904 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
726868 AAGAGAAGGA
726878 TGATGATGATGG
1 TGATGATGATGG
726890 TGATGATGATGG
1 TGATGATGATGG
726902 TGA
1 TGA
726905 GGACCTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (12 bp):
TGATGATGATGG
Found at i:727314 original size:2 final size:2
Alignment explanation
Indices: 727307--727333 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
727297 CCTCAAGCTT
727307 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
727334 GAGAAGGAGG
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:739241 original size:3 final size:3
Alignment explanation
Indices: 739227--739270 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
739217 TCTTCCTCCG
* *
739227 CCA CCG CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCT CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
739271 TCCGTTTCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.27, C:0.68, G:0.02, T:0.02
Consensus pattern (3 bp):
CCA
Found at i:739431 original size:9 final size:9
Alignment explanation
Indices: 739392--739434 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
739382 AACTTCTCCA
739392 CTACTACTC
1 CTACTACTC
* *
739401 CTACTCCTA
1 CTACTACTC
*
739410 CTCCTACTC
1 CTACTACTC
*
739419 CTACTACTT
1 CTACTACTC
739428 CTACTAC
1 CTACTAC
739435 CAACAACAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (9 bp):
CTACTACTC
Found at i:739432 original size:6 final size:6
Alignment explanation
Indices: 739395--739423 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
739385 TTCTCCACTA
739395 CTACTC CTACTC CTACTC CTACTC CTACT
1 CTACTC CTACTC CTACTC CTACTC CTACT
739424 ACTTCTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (6 bp):
CTACTC
Found at i:739434 original size:12 final size:12
Alignment explanation
Indices: 739387--739434 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
739377 TCAAAAACTT
739387 CTCC-ACTACTA
1 CTCCTACTACTA
*
739398 CTCCTACTCCTA
1 CTCCTACTACTA
*
739410 CTCCTACTCCTA
1 CTCCTACTACTA
* *
739422 CTACTTCTACTA
1 CTCCTACTACTA
739434 C
1 C
739435 CAACAACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.21, C:0.46, G:0.00, T:0.33
Consensus pattern (12 bp):
CTCCTACTACTA
Found at i:750392 original size:3 final size:3
Alignment explanation
Indices: 750384--750428 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
750374 GGTTTTATAG
750384 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
750429 GGGGTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:752827 original size:3 final size:3
Alignment explanation
Indices: 752819--752872 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
752809 AATGAGTAGG
752819 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
752867 TAA TAA
1 TAA TAA
752873 GGGTAATTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:759194 original size:31 final size:32
Alignment explanation
Indices: 759159--759218 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
759149 ACACATCAGC
759159 AAAAATAAAAGAAA-ATTCAATTTTTTTTGTA
1 AAAAATAAAAGAAATATTCAATTTTTTTTGTA
*
759190 AAAAATAAAAGAAATATTTAATTTTTTTT
1 AAAAATAAAAGAAATATTCAATTTTTTTT
759219 ACTAGAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (32 bp):
AAAAATAAAAGAAATATTCAATTTTTTTTGTA
Found at i:759906 original size:6 final size:6
Alignment explanation
Indices: 759895--759919 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
759885 AGAGAACAAC
759895 ATTAAA ATTAAA ATTAAA ATTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA A
759920 CATACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTAAA
Found at i:764216 original size:45 final size:45
Alignment explanation
Indices: 764165--764251 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
764155 CTTTTTTTTT
764165 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTATCTA
1 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTATCTA
764210 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTAT
1 ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTAT
764252 AAAACTCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.43
Consensus pattern (45 bp):
ACTAAAGTTGGGGTTGTTGAGTTGTAACAAGTTTGTTGTTATCTA
Found at i:764939 original size:25 final size:25
Alignment explanation
Indices: 764910--764961 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
764900 TATATAATTT
764910 AAGTTTA-AGAAAATAATTTTTATAC
1 AAGTTTATA-AAAATAATTTTTATAC
* *
764935 AAGTTTATAAAAGTTATTTTTATAC
1 AAGTTTATAAAAATAATTTTTATAC
764960 AA
1 AA
764962 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
AAGTTTATAAAAATAATTTTTATAC
Found at i:766963 original size:22 final size:22
Alignment explanation
Indices: 766892--766964 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 22
766882 AAAAATGGAG
*
766892 AAAATTATGTTTAACCCCTT-A
1 AAAATTATGTTTAATCCCTTAA
* ** ***
766913 AAAATGATGAATAATAAATTAA
1 AAAATTATGTTTAATCCCTTAA
* *
766935 TACATTATGTTTAATCCCTTAA
1 AAAATTATGTTTAATCCCTTAA
766957 AAAATTAT
1 AAAATTAT
766965 TATTCAATTC
Statistics
Matches: 34, Mismatches: 17, Indels: 1
0.65 0.33 0.02
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAATTATGTTTAATCCCTTAA
Found at i:769444 original size:13 final size:13
Alignment explanation
Indices: 769426--769450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
769416 AACTGCAGAT
769426 CGTTACAATATCA
1 CGTTACAATATCA
769439 CGTTACAATATC
1 CGTTACAATATC
769451 TATTTAGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
CGTTACAATATCA
Found at i:772146 original size:16 final size:17
Alignment explanation
Indices: 772125--772164 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
772115 TTAATTTAAT
772125 TTAAATTATTTT-TCAA
1 TTAAATTATTTTCTCAA
*
772141 TTAAATAATTTTCTCAA
1 TTAAATTATTTTCTCAA
*
772158 TTCAATT
1 TTAAATT
772165 CTAATCACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTATTTTCTCAA
Found at i:773439 original size:46 final size:46
Alignment explanation
Indices: 773388--773482 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
773378 ATTAAAATTA
* *
773388 AAACTTAGAAACCAAA-CATTAA-ATATATAGTTTGGAGAACAACATT
1 AAACTT-GAAACCAAAGC-CTAACATATATAGTTAGGAGAACAACATT
* * *
773434 AAACTTTAAATCAAAGCCTAACCTATATAGTTAGGAGAACAACATT
1 AAACTTGAAACCAAAGCCTAACATATATAGTTAGGAGAACAACATT
773480 AAA
1 AAA
773483 ATTAAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 10 0.24
46 32 0.76
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (46 bp):
AAACTTGAAACCAAAGCCTAACATATATAGTTAGGAGAACAACATT
Found at i:783265 original size:3 final size:3
Alignment explanation
Indices: 783259--783306 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
783249 ATCATCATCG
* * * *
783259 GAA GAA GAA GAA GAG GAG GAA GAA GAA GAA GAG GAA GAA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
783307 CCTGGAGTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:783279 original size:18 final size:18
Alignment explanation
Indices: 783258--783306 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
783248 AATCATCATC
783258 GGAAGAAGAAGAAGAGGA
1 GGAAGAAGAAGAAGAGGA
783276 GGAAGAAGAAGAAGAGGA
1 GGAAGAAGAAGAAGAGGA
* *
783294 AGAAGAAGGAGAA
1 GGAAGAAGAAGAA
783307 CCTGGAGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (18 bp):
GGAAGAAGAAGAAGAGGA
Found at i:783280 original size:15 final size:15
Alignment explanation
Indices: 783262--783301 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
783252 ATCATCGGAA
*
783262 GAAGAAGAAGAGGAG
1 GAAGAAGAAGAAGAG
783277 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
783292 GAAGAAGAAG
1 GAAGAAGAAG
783302 GAGAACCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:783588 original size:21 final size:19
Alignment explanation
Indices: 783564--783613 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
783554 AAAAAAAGCA
*
783564 ATTATATTATAATTTTATTAC
1 ATTATATTA-AATTATATT-C
783585 ATTATAATTAAATTATATTC
1 ATTAT-ATTAAATTATATTC
783605 ATT-TATTAA
1 ATTATATTAA
783614 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 4 0.15
21 13 0.48
22 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTATATTAAATTATATTC
Found at i:795114 original size:10 final size:10
Alignment explanation
Indices: 795035--795117 Score: 112
Period size: 10 Copynumber: 8.3 Consensus size: 10
795025 TGGGCTATGT
*
795035 CATCAGTGAT
1 CATCAGTGAA
795045 CATCAGTGAA
1 CATCAGTGAA
* *
795055 CATCAATGAT
1 CATCAGTGAA
*
795065 CATCAGTGAT
1 CATCAGTGAA
795075 CATCAGTGAA
1 CATCAGTGAA
*
795085 TATCAGTGAA
1 CATCAGTGAA
*
795095 CTTCAGTGAA
1 CATCAGTGAA
795105 CATCAGTGAA
1 CATCAGTGAA
795115 CAT
1 CAT
795118 AAGACCATGG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 64 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (10 bp):
CATCAGTGAA
Found at i:796903 original size:20 final size:20
Alignment explanation
Indices: 796878--796927 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
796868 TTGATTAAGG
796878 TATCGATACCTTGGATGTGA
1 TATCGATACCTTGGATGTGA
*
796898 TATCGATACCTTGGATGTGG
1 TATCGATACCTTGGATGTGA
796918 TATCGATACC
1 TATCGATACC
796928 AAAATTACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACCTTGGATGTGA
Found at i:809867 original size:22 final size:22
Alignment explanation
Indices: 809812--809854 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
809802 TTTATTGTTC
809812 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
809834 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
809855 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:815877 original size:2 final size:2
Alignment explanation
Indices: 815872--815900 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
815862 AATATATATT
815872 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
815901 AACTTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:817649 original size:3 final size:3
Alignment explanation
Indices: 817641--817667 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
817631 AACCGTATGT
817641 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
817668 GCAGAGCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:819215 original size:20 final size:20
Alignment explanation
Indices: 819177--819221 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
819167 AATATATTAC
*
819177 TAATATTTTATTAAATAAAAA
1 TAATATTTTAATAAAT-AAAA
*
819198 TAAT-TTTTAATAATTAAAA
1 TAATATTTTAATAAATAAAA
819217 TAATA
1 TAATA
819222 AACTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATTTTAATAAATAAAA
Found at i:822802 original size:109 final size:108
Alignment explanation
Indices: 822598--823008 Score: 623
Period size: 108 Copynumber: 3.8 Consensus size: 108
822588 CTAAATGAGA
*
822598 CAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATTTTTTTCGT
1 CAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTTTTCGT
*
822663 TCTACCAAATAGCTAAATATCCTTTT-AAAATTTCAAAAATAAGG
65 TCGACCAAATAGCTAAATATCCTTTTAAAAATTTC-AAAATAAGG
822707 CAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCGTT
1 CAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCGTT
**
822772 CGACCAAATAGCTAAATATCCTTTTAAAAATTTTGAAATAAGG
66 CGACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATAAGG
*
822815 CAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATTTTTTCGTT
1 CAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCGTT
* *
822880 TGACCAAATAGCTAAATATCCTTTCAAAAAATTTCAAAATAAGG
66 CGACCAAATAGCTAAATATCCTTT-TAAAAATTTCAAAATAAGG
* * * * *
822924 CAATGTTTTA-CGTTTAGAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTTCG-GTTTCTCGT
1 CAAT-ATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCGT
** *
822986 TTAACCAAATAGCCAAATATCCT
65 TCGACCAAATAGCTAAATATCCT
823009 CTTGAATCTT
Statistics
Matches: 282, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
107 28 0.10
108 154 0.55
109 96 0.34
110 4 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (108 bp):
CAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTTCGTT
CGACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATAAGG
Found at i:832767 original size:24 final size:25
Alignment explanation
Indices: 832722--832785 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
832712 TTTGACTTTT
* *
832722 TAAAAAAGTTAAGGATCAAAATTAAC
1 TAAAAAAATTAA-AATCAAAATTAAC
832748 TAAAAAAATTAAAATC-AAATTAAC
1 TAAAAAAATTAAAATCAAAATTAAC
*
832772 AAAAAAAATATAAA
1 TAAAAAAAT-TAAA
832786 TGCTGAAGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.47
25 7 0.21
26 11 0.32
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.22
Consensus pattern (25 bp):
TAAAAAAATTAAAATCAAAATTAAC
Found at i:834325 original size:20 final size:20
Alignment explanation
Indices: 834302--834342 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
834292 ACCCCAAACT
*
834302 TAAACCCATAATCCTAAATC
1 TAAACCCATAATCCCAAATC
* *
834322 TAAACTCGTAATCCCAAATC
1 TAAACCCATAATCCCAAATC
834342 T
1 T
834343 TTGAACCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAACCCATAATCCCAAATC
Found at i:834636 original size:5 final size:5
Alignment explanation
Indices: 834614--834650 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
834604 ATTTAAAAAA
*
834614 TTAA- TTAAT TTAA- GTAAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
834651 GTTGGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:834650 original size:10 final size:9
Alignment explanation
Indices: 834614--834647 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
834604 ATTTAAAAAA
834614 TTAATTAAT
1 TTAATTAAT
*
834623 TTAAGTAAT
1 TTAATTAAT
834632 TTAATTTAAT
1 TTAA-TTAAT
834642 TTAATT
1 TTAATT
834648 TAAGTTGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (9 bp):
TTAATTAAT
Found at i:837947 original size:26 final size:24
Alignment explanation
Indices: 837918--837973 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 24
837908 TTTGACTTTT
*
837918 TAAAAAAATTAAGGATCAAAATTAAC
1 TAAAAAAATTAA-AATC-AAATTAAC
837944 TAAAAAAATTAAAATCAAATTAAC
1 TAAAAAAATTAAAATCAAATTAAC
837968 -AAAAAA
1 TAAAAAA
837974 TATAAATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 6 0.21
24 8 0.28
25 3 0.10
26 12 0.41
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.21
Consensus pattern (24 bp):
TAAAAAAATTAAAATCAAATTAAC
Found at i:842359 original size:16 final size:16
Alignment explanation
Indices: 842315--842362 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
842305 AACTATAATT
842315 TATTAAATAAAA-ATTA
1 TATT-AATAAAATATTA
842331 TATTAATTAAAATATTA
1 TATTAA-TAAAATATTA
*
842348 TTTTAATAAAATATT
1 TATTAATAAAATATT
842363 TAATTTTACG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.62
17 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAATAAAATATTA
Found at i:842427 original size:20 final size:20
Alignment explanation
Indices: 842387--842433 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
842377 AAAATATATT
*
842387 AATAATATTTTATTAAATAAA
1 AATAATATTTTAATAAAT-AA
*
842408 AATAAT-TTTTAATAATTAA
1 AATAATATTTTAATAAATAA
842427 AATAATA
1 AATAATA
842434 AACTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 8 0.35
20 9 0.39
21 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATAATATTTTAATAAATAA
Found at i:842428 original size:19 final size:21
Alignment explanation
Indices: 842387--842433 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
842377 AAAATATATT
*
842387 AATAATATTTTATTAAATAAA
1 AATAATATTTTAATAAATAAA
*
842408 AATAAT-TTTTAAT-AATTAA
1 AATAATATTTTAATAAATAAA
842427 AATAATA
1 AATAATA
842434 AACTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.48
20 6 0.26
21 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAATATTTTAATAAATAAA
Found at i:843557 original size:2 final size:2
Alignment explanation
Indices: 843546--843592 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
843536 TTAAAACATT
*
843546 TA TA -A TA TA TA TG TA TA T- TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
843585 TA TA TA TA
1 TA TA TA TA
843593 GGCGCACACA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:843620 original size:3 final size:3
Alignment explanation
Indices: 843612--843645 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
843602 ATATAAATAC
*
843612 AAT AAT AAT AAT -AT AAT AAT AAT TAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
843646 ACAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:849320 original size:24 final size:24
Alignment explanation
Indices: 849292--849345 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
849282 CTGAAGAAAG
* *
849292 ATGAACTGTTAAATACATGCAGAA
1 ATGAACTGTTAAACACATACAGAA
*
849316 ATGAACTGTTCAACACATACAGAA
1 ATGAACTGTTAAACACATACAGAA
849340 A-GAACT
1 ATGAACT
849346 TACTTTTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (24 bp):
ATGAACTGTTAAACACATACAGAA
Found at i:854321 original size:3 final size:3
Alignment explanation
Indices: 854313--854358 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
854303 TTCTCCGTCA
* *
854313 CTC CTC CT- CTC CT- CTG CTC CTC CTC CTC CTC CTC CTC TTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
854359 AGCATCCACG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.37
Consensus pattern (3 bp):
CTC
Found at i:862186 original size:21 final size:20
Alignment explanation
Indices: 862149--862187 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
862139 ATATATAATT
* *
862149 TCGAAAAATTAATAATTAAA
1 TCGAAAAATCAACAATTAAA
862169 TCGAAAAAGTCAACAATTA
1 TCGAAAAA-TCAACAATTA
862188 GGTGACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (20 bp):
TCGAAAAATCAACAATTAAA
Found at i:868499 original size:13 final size:13
Alignment explanation
Indices: 868481--868505 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
868471 GGTCAAGGCT
868481 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
868494 TTTTCTTTTTTT
1 TTTTCTTTTTTT
868506 TAAATTTGCA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:869865 original size:27 final size:28
Alignment explanation
Indices: 869836--869901 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
869826 TAGTAATGAT
*
869836 AAAAATTAAACTTAAATTT-TGAAATTTA
1 AAAAATAAAAC-TAAATTTCTGAAATTTA
*
869864 AAAAATAAAACTAAATTTCTGAAA-ATA
1 AAAAATAAAACTAAATTTCTGAAATTTA
869891 AAAAA-AAAACT
1 AAAAATAAAACT
869902 GTGGCTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 6 0.17
27 14 0.40
28 15 0.43
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAAATAAAACTAAATTTCTGAAATTTA
Found at i:872101 original size:20 final size:20
Alignment explanation
Indices: 872076--872113 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
872066 TTAAATTTCA
*
872076 AAATTTTTAAAAATAAAACT
1 AAATTTCTAAAAATAAAACT
872096 AAATTTCTAAAAATAAAA
1 AAATTTCTAAAAATAAAA
872114 ATACAGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTTCTAAAAATAAAACT
Found at i:872478 original size:21 final size:21
Alignment explanation
Indices: 872454--872497 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
872444 ACATAAAAAG
* *
872454 ATAAAAATACCTTTAAATAAT
1 ATAAAAATACCCTCAAATAAT
872475 ATAAAAATACCCTCAAATAAT
1 ATAAAAATACCCTCAAATAAT
872496 AT
1 AT
872498 TTAACCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAAATACCCTCAAATAAT
Found at i:876220 original size:17 final size:18
Alignment explanation
Indices: 876209--876241 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
876199 TTTATATATG
876209 GATATT-AATTATA-AAA
1 GATATTGAATTATATAAA
876225 GATATTGAATTATATAA
1 GATATTGAATTATATAA
876242 TTTTACATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 7 0.47
18 2 0.13
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (18 bp):
GATATTGAATTATATAAA
Found at i:880184 original size:13 final size:13
Alignment explanation
Indices: 880166--880190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
880156 TAGAGGGGTT
880166 TTAAAATTAAAAA
1 TTAAAATTAAAAA
880179 TTAAAATTAAAA
1 TTAAAATTAAAA
880191 CCATGTAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:890097 original size:66 final size:66
Alignment explanation
Indices: 889991--890123 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
889981 TGGATGTGAG
889991 GATGGTTATAGGTTACTTGCAAGATGTTGTAGATTTCATTCATAGGCAAGATGTTTATTTTTCAT
1 GATGGTTATAGGTTACTTGCAAGATGTTGTAGATTTCATTCATAGGCAAGATGTTTATTTTTCAT
890056 T
66 T
890057 GATGGTTATAGGTTACTTGCAAGATGTTGTAGATTTCATTCATAGGCAAGATGTTTATTTTTCAT
1 GATGGTTATAGGTTACTTGCAAGATGTTGTAGATTTCATTCATAGGCAAGATGTTTATTTTTCAT
890122 T
66 T
890123 G
1 G
890124 GATTATTATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.44
Consensus pattern (66 bp):
GATGGTTATAGGTTACTTGCAAGATGTTGTAGATTTCATTCATAGGCAAGATGTTTATTTTTCAT
T
Found at i:893104 original size:31 final size:31
Alignment explanation
Indices: 893069--893134 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
893059 TTAATATGCC
* * *
893069 ATTTGGTACTTGCATTTGACTTTAATGTTTA
1 ATTTGGTACTTGAATTTAACTTTAATGTTAA
893100 ATTTGGTACTTGAATTTAACTTTAATGTTAA
1 ATTTGGTACTTGAATTTAACTTTAATGTTAA
893131 ATTT
1 ATTT
893135 AATACCCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.52
Consensus pattern (31 bp):
ATTTGGTACTTGAATTTAACTTTAATGTTAA
Found at i:896121 original size:16 final size:14
Alignment explanation
Indices: 896086--896113 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
896076 TATTGATCCT
896086 TATTGATCCTTATA
1 TATTGATCCTTATA
896100 TATTGATCCTTATA
1 TATTGATCCTTATA
896114 AATATTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TATTGATCCTTATA
Found at i:903602 original size:40 final size:40
Alignment explanation
Indices: 903532--903654 Score: 158
Period size: 39 Copynumber: 3.0 Consensus size: 40
903522 ACCAAAAATT
903532 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
903576 TATTTTAAAATTAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
* * * *
903615 AAATTTAAAATTTAAAAAATTAAAAAAAAGGATTTTAAAA
1 TATTTTAAAATTAAAAAAATT-AAAAAAAGTATTTTAAAA
903655 GTAAAAATAT
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
39 36 0.49
40 7 0.10
41 18 0.25
43 6 0.08
44 6 0.08
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:913744 original size:27 final size:27
Alignment explanation
Indices: 913701--913754 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
913691 TAGGCCCACC
*
913701 TTTATTATTATTATTTAAAATATTTTAT
1 TTTATTATTAATATTTAAAA-ATTTTAT
*
913729 TTTATT-TTAATATTTAATAATTTTAT
1 TTTATTATTAATATTTAAAAATTTTAT
913755 ATATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 11 0.46
28 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTATTAATATTTAAAAATTTTAT
Found at i:915186 original size:30 final size:29
Alignment explanation
Indices: 915152--915208 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
915142 AACATAATTT
915152 AATAATATAAAAT-TATTAAAAATATATCAC
1 AATAA-ATAAAATATATTAAAAA-ATATCAC
*
915182 AATAACTAAAATATATTAAAAAATATC
1 AATAAATAAAATATATTAAAAAATATC
915209 TTATTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (29 bp):
AATAAATAAAATATATTAAAAAATATCAC
Found at i:917449 original size:4 final size:4
Alignment explanation
Indices: 917442--917508 Score: 62
Period size: 4 Copynumber: 16.8 Consensus size: 4
917432 ACTTACATGC
* * * * * * *
917442 ATAT ATAT ATAC ATAT ATAT ACAT ACAT ACAT ATAC ATAC ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
917490 ATAT ATTT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATA
917509 AAGAAAAGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:917459 original size:10 final size:10
Alignment explanation
Indices: 917444--917508 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
917434 TTACATGCAT
917444 ATATATATAC
1 ATATATATAC
917454 ATATATATAC
1 ATATATATAC
*
917464 --ATACATAC
1 ATATATATAC
*
917472 ATATACATAC
1 ATATATATAC
* *
917482 ATACATATAT
1 ATATATATAC
* *
917492 ATATTTATAT
1 ATATATATAC
917502 ATATATA
1 ATATATA
917509 AAGAAAAGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
8 7 0.15
10 39 0.85
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATATAC
Found at i:917459 original size:14 final size:14
Alignment explanation
Indices: 917424--917508 Score: 82
Period size: 14 Copynumber: 5.9 Consensus size: 14
917414 AATGCCATTA
917424 ATATATATACT-TAC
1 ATATATATA-TATAC
917438 ATGCATATATATATAC
1 AT--ATATATATATAC
*
917454 ATATATATACATAC
1 ATATATATATATAC
* *
917468 ATACATATACATAC
1 ATATATATATATAC
* *
917482 ATACATATATATAT
1 ATATATATATATAC
*
917496 TTATATATATATA
1 ATATATATATATA
917509 AAGAAAAGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
14 49 0.79
15 1 0.02
16 12 0.19
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:917473 original size:18 final size:18
Alignment explanation
Indices: 917450--917495 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
917440 GCATATATAT
917450 ATACATATATATACATAC
1 ATACATATATATACATAC
*
917468 ATACATATACATACATAC
1 ATACATATATATACATAC
*
917486 ATATATATAT
1 ATACATATAT
917496 TTATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (18 bp):
ATACATATATATACATAC
Found at i:917500 original size:6 final size:6
Alignment explanation
Indices: 917442--917508 Score: 62
Period size: 6 Copynumber: 11.2 Consensus size: 6
917432 ACTTACATGC
* * * * * * *
917442 ATATAT ATATAC ATATAT ATACAT ACATAC ATATAC ATACAT ACATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
917490 ATATAT TTATAT ATATAT A
1 ATATAT ATATAT ATATAT A
917509 AAGAAAAGTG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAT
Found at i:920214 original size:6 final size:6
Alignment explanation
Indices: 920205--920237 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
920195 CTCCTCCTCT
*
920205 TCATGA TCATGA TCCTGA TCATGA TCATGA TCA
1 TCATGA TCATGA TCATGA TCATGA TCATGA TCA
920238 CTTTTCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (6 bp):
TCATGA
Found at i:924630 original size:19 final size:19
Alignment explanation
Indices: 924606--924644 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
924596 ACTGATAAGC
*
924606 TGAAGCTTAAT-TTAATATT
1 TGAAGCTCAATATT-ATATT
924625 TGAAGCTCAATATTATATT
1 TGAAGCTCAATATTATATT
924644 T
1 T
924645 AAACTTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (19 bp):
TGAAGCTCAATATTATATT
Found at i:925349 original size:2 final size:2
Alignment explanation
Indices: 925342--925377 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
925332 CTGCAAGATT
925342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
925378 ACCACTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:926341 original size:2 final size:2
Alignment explanation
Indices: 926334--926358 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
926324 AGGTTAATGC
926334 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 A
926359 ATAACTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:934386 original size:3 final size:3
Alignment explanation
Indices: 934378--934403 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
934368 TTTGACTTAC
934378 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
934404 TTCTACCATA
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:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:935243 original size:29 final size:28
Alignment explanation
Indices: 935181--935243 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
935171 TTGAGAGTTT
*
935181 AGTTTTTATTTTTATTTCATGAAATTTAG
1 AGTTTTTATTTTTATTTCA-GAAAATTAG
935210 AGTTTTTATTTTTCATATTTCA-AAAATTAG
1 AGTTTTTA-TTTT--TATTTCAGAAAATTAG
935240 -GTTT
1 AGTTT
935244 GATTATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
29 12 0.40
30 11 0.37
32 7 0.23
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (28 bp):
AGTTTTTATTTTTATTTCAGAAAATTAG
Found at i:945330 original size:37 final size:37
Alignment explanation
Indices: 945269--945414 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
945259 TACATATGAT
* *
945269 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
945304 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
945341 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
945378 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
945415 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:945431 original size:46 final size:46
Alignment explanation
Indices: 945378--945790 Score: 538
Period size: 46 Copynumber: 8.6 Consensus size: 46
945368 TAAGTGTAGC
* * **
945378 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
945424 CACTTATCACTTTGTCTCTTGATCAGATAAGCATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
945470 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
945522 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
945574 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
945620 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
945666 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
945712 TACTTATCACTTCTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCA---CT---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
945764 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
945791 AGTACTCAAA
Statistics
Matches: 338, Mismatches: 16, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
46 201 0.59
49 5 0.01
50 1 0.00
51 3 0.01
52 128 0.38
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:953089 original size:18 final size:18
Alignment explanation
Indices: 953066--953107 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
953056 TTCAAGGTGT
953066 AATTAATTTAAA-ATATTC
1 AATTAA-TTAAATATATTC
*
953084 AATTAATTAAATATATTT
1 AATTAATTAAATATATTC
953102 AATTAA
1 AATTAA
953108 AAATCTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAATTAAATATATTC
Found at i:954968 original size:2 final size:2
Alignment explanation
Indices: 954963--954987 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
954953 TGTTTTTTTA
954963 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 A
954988 CACACAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:960320 original size:20 final size:21
Alignment explanation
Indices: 960297--960339 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
960287 TTTAACTTTC
*
960297 TTTAT-ATATTTTTTAGAATT
1 TTTATAATATTTTTTAAAATT
960317 TTTATAAATATTTTTTAAAATT
1 TTTAT-AATATTTTTTAAAATT
960339 T
1 T
960340 AAAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTATAATATTTTTTAAAATT
Done.