Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold181
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: 968729
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 5 of 7
Found at i:507284 original size:13 final size:14
Alignment explanation
Indices: 507261--507289 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
507251 ATGTTCAACA
507261 AATTCTCCAGCTTG
1 AATTCTCCAGCTTG
507275 AATT-TCCAGCTTG
1 AATTCTCCAGCTTG
507288 AA
1 AA
507290 AGCAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (14 bp):
AATTCTCCAGCTTG
Found at i:507775 original size:22 final size:24
Alignment explanation
Indices: 507750--507796 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
507740 CATAAAATCA
507750 TATAATA-C-GATGCATAT-AATTC
1 TATAATACCAGATGCAT-TGAATTC
507772 TATAATACCAGATGCATTGAATTC
1 TATAATACCAGATGCATTGAATTC
507796 T
1 T
507797 CAAAGACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 2 0.09
24 13 0.59
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (24 bp):
TATAATACCAGATGCATTGAATTC
Found at i:508343 original size:18 final size:18
Alignment explanation
Indices: 508286--508349 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
508276 ATTACTTAAG
508286 TAAATATTAATT-TAATAA
1 TAAA-ATTAATTATAATAA
* * *
508304 -AAAATTTA-CATAAAAA
1 TAAAATTAATTATAATAA
*
508320 TTAAATTAATTATAATAA
1 TAAAATTAATTATAATAA
*
508338 TAAAATAAATTA
1 TAAAATTAATTA
508350 AAATTTTTTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
16 9 0.26
17 9 0.26
18 16 0.47
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTAATTATAATAA
Found at i:508353 original size:33 final size:32
Alignment explanation
Indices: 508291--508380 Score: 76
Period size: 33 Copynumber: 2.8 Consensus size: 32
508281 TTAAGTAAAT
*
508291 ATTAATTTAATAAAAAATTTACATAAAAATTAA
1 ATTAATTTAATAAAAAA-TTAAATAAAAATTAA
* *
508324 ATTAATTATAATAATAAAA-TAAATTAAAATT-T
1 ATTAATT-TAATAA-AAAATTAAATAAAAATTAA
* **
508356 TTTAATTTTTTTAAAAAATTAAATA
1 ATTAA-TTTAATAAAAAATTAAATA
508381 TCTACTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
31 4 0.09
32 13 0.28
33 19 0.41
34 6 0.13
35 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
ATTAATTTAATAAAAAATTAAATAAAAATTAA
Found at i:508965 original size:21 final size:24
Alignment explanation
Indices: 508921--508974 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
508911 ATATAATGAG
508921 ATATTATAA--TTTTTATTTAATA
1 ATATTATAATTTTTTTATTTAATA
*
508943 AT-TT-TAATTTTTTTA-TTATTA
1 ATATTATAATTTTTTTATTTAATA
508964 ATATTATAATT
1 ATATTATAATT
508975 GATAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 9 0.33
22 10 0.37
23 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATTATAATTTTTTTATTTAATA
Found at i:510770 original size:3 final size:3
Alignment explanation
Indices: 510764--510792 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
510754 TTAAACAACA
510764 GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
510793 GGGTTGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:511521 original size:2 final size:2
Alignment explanation
Indices: 511514--511551 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
511504 TAGAGATACA
511514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
511552 CTCCTTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:511700 original size:23 final size:23
Alignment explanation
Indices: 511670--511715 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
511660 CTCCATACGA
511670 TCTCAATTCCTCCATTTTTGTGG
1 TCTCAATTCCTCCATTTTTGTGG
511693 TCTCAATTCCTCCATTTTTGTGG
1 TCTCAATTCCTCCATTTTTGTGG
511716 ATGGCTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (23 bp):
TCTCAATTCCTCCATTTTTGTGG
Found at i:511786 original size:22 final size:20
Alignment explanation
Indices: 511747--511847 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 20
511737 AGTCTGATAA
511747 TTTATATATTTATATTATAT
1 TTTATATATTTATATTATAT
*
511767 TTTATATATTT-TAATTTTAT
1 TTTATATATTTAT-ATTATAT
* * *
511787 TTAAAATATTATATATAAT-T
1 TTTATATATT-TATATTATAT
*
511807 ATTTAT-TATATATATTAATAT
1 -TTTATATATTTATATT-ATAT
* *
511828 TTTAAATATATAT-TTATAT
1 TTTATATATTTATATTATAT
511847 T
1 T
511848 GTGTTTATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
19 11 0.17
20 37 0.58
21 15 0.23
22 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATATATTTATATTATAT
Found at i:511866 original size:23 final size:24
Alignment explanation
Indices: 511840--511884 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
511830 TAAATATATA
*
511840 TTTATATTGTGTT-TATTTTATTT
1 TTTATATTATGTTATATTTTATTT
511863 TTTATATTATGTTATATTTTAT
1 TTTATATTATGTTATATTTTAT
511885 ATATTATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (24 bp):
TTTATATTATGTTATATTTTATTT
Found at i:513058 original size:2 final size:2
Alignment explanation
Indices: 513053--513091 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
513043 TATCCTTTTG
* *
513053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
513092 GCAAAGTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:514918 original size:18 final size:18
Alignment explanation
Indices: 514895--514931 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
514885 TATTTGTAAA
514895 CCTTATTGATTTGCACTT
1 CCTTATTGATTTGCACTT
514913 CCTTATTGATTTGCACTT
1 CCTTATTGATTTGCACTT
514931 C
1 C
514932 GCAAATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.49
Consensus pattern (18 bp):
CCTTATTGATTTGCACTT
Found at i:518595 original size:21 final size:21
Alignment explanation
Indices: 518582--518623 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
518572 TAACTAGATG
518582 TATCGATACATTAAAAAAATA
1 TATCGATACATTAAAAAAATA
518603 TATCGATACATCTGAAAAAAA
1 TATCGATACAT-T-AAAAAAA
518624 AGATAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (21 bp):
TATCGATACATTAAAAAAATA
Found at i:518655 original size:20 final size:20
Alignment explanation
Indices: 518630--518795 Score: 116
Period size: 20 Copynumber: 7.8 Consensus size: 20
518620 AAAAAGATAG
518630 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* * *
518650 AATGTATCGATCCATTCATA
1 AATGTATCGATACATTGAAA
* * *
518670 CATGTATTGATACATTAAAA
1 AATGTATCGATACATTGAAA
*
518690 AATGTATCGGTACATCTAGGTAAAAAGACAA
1 AATGTATCGATACA--T---T-----GA-AA
*
518721 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* *
518741 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* * *
518761 CATATATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
518781 AATGTATCGATACAT
1 AATGTATCGATACAT
518796 CTGGGTAAAA
Statistics
Matches: 111, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
20 89 0.80
21 2 0.02
22 1 0.01
25 1 0.01
26 1 0.01
29 1 0.01
30 1 0.01
31 15 0.14
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:518715 original size:91 final size:90
Alignment explanation
Indices: 518579--518806 Score: 312
Period size: 91 Copynumber: 2.5 Consensus size: 90
518569 TTTTAACTAG
* ** * *
518579 ATGTATCGATACATTAAAAAAATATATCGATACATCTGAAAAAAAAGATAGAATGTATCGATACA
1 ATGTATCGATACATT-AAAAAATGTATCGATACATCTG-GTAAAAAGACAAAATGTATCGATACA
*
518644 TTGAAAAATGTATCGATCCATTCATAC
64 TTGAAAAATGTATCGATACATTCATAC
* *
518671 ATGTATTGATACATTAAAAAATGTATCGGTACATCTAGGTAAAAAGACAAAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATGTATCGATACATCT-GGTAAAAAGACAAAATGTATCGATACAT
*
518736 TGAAGAATGTATCGATACATTCATAC
65 TGAAAAATGTATCGATACATTCATAC
* * *
518762 ATATATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCT-GGTAAAAA
518807 TGTGACTTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
91 105 0.88
92 15 0.12
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (90 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATCTGGTAAAAAGACAAAATGTATCGATACATT
GAAAAATGTATCGATACATTCATAC
Found at i:522444 original size:22 final size:22
Alignment explanation
Indices: 522428--522469 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
522418 TAAATTTAAT
522428 TATAAAAATATATAAATATTAG
1 TATAAAAATATATAAATATTAG
* *
522450 TATAAAAATATTTTAATATT
1 TATAAAAATATATAAATATT
522470 TTAATATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATAAAAATATATAAATATTAG
Found at i:523120 original size:34 final size:35
Alignment explanation
Indices: 523082--523172 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 35
523072 TCTTACAATA
* *
523082 TTATCTTTTCGAATGCTAAGATAGAACTTTTTC-C
1 TTATCTTTTCGAATGCTAAGATAGAACTTCTACAC
*
523116 TTATCTTTTCAAATGCTAAGATAGAACTTCTACAC
1 TTATCTTTTCGAATGCTAAGATAGAACTTCTACAC
* *
523151 -TATCTTTTTGAAAGCTAAGATA
1 TTATCTTTTCGAATGCTAAGATA
523173 TAACCTCTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
34 49 0.98
35 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (35 bp):
TTATCTTTTCGAATGCTAAGATAGAACTTCTACAC
Found at i:523785 original size:20 final size:20
Alignment explanation
Indices: 523740--523832 Score: 77
Period size: 20 Copynumber: 4.6 Consensus size: 20
523730 GCCAATTGCA
*
523740 TGTATTGATATATTTTC-ATAG
1 TGTATTGATATA-TTGCAAT-G
523761 TGTATTGATATATTGCAATG
1 TGTATTGATATATTGCAATG
*
523781 TGTATCGATATATTGCAACT-
1 TGTATTGATATATTGCAA-TG
* *
523801 TGTATCGATACA-T-CTATATG
1 TGTATTGATATATTGC-A-ATG
523821 TGTATTGATATA
1 TGTATTGATATA
523833 AATAAGGGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
18 1 0.02
19 3 0.05
20 43 0.69
21 15 0.24
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATTGATATATTGCAATG
Found at i:524228 original size:22 final size:22
Alignment explanation
Indices: 524202--524244 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
524192 ATGATGATAA
*
524202 TATGATGTTATGATTATTTATT
1 TATGATGTTATCATTATTTATT
* *
524224 TATGATTTTATCATTTTTTAT
1 TATGATGTTATCATTATTTAT
524245 CATTGATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.63
Consensus pattern (22 bp):
TATGATGTTATCATTATTTATT
Found at i:525418 original size:20 final size:21
Alignment explanation
Indices: 525395--525445 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 21
525385 TTTAAAATAT
*
525395 TTTATATTATATTTATAT-TA
1 TTTATATTATAATTATATCTA
525415 TTTA-A-TATAATTATATCGTA
1 TTTATATTATAATTATATC-TA
525435 TTTAATATTAT
1 TTT-ATATTAT
525446 CAGATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 9 0.36
21 1 0.04
22 1 0.04
23 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTATATTATAATTATATCTA
Found at i:525423 original size:18 final size:19
Alignment explanation
Indices: 525402--525442 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
525392 TATTTTATAT
*
525402 TATATTTATAT-TATTTAA
1 TATAATTATATCTATTTAA
525420 TATAATTATATCGTATTTAA
1 TATAATTATATC-TATTTAA
525440 TAT
1 TAT
525443 TATCAGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TATAATTATATCTATTTAA
Found at i:527792 original size:29 final size:30
Alignment explanation
Indices: 527729--527797 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 30
527719 CGTATTTTTA
* ** *
527729 AATATA-ATATAAAAATTTTAAATTTTTTT
1 AATATATATATAAAAAATTTAAAAATATTT
527758 AA-ATATATA-AAAAAATTTAAAAATATTT
1 AATATATATATAAAAAATTTAAAAATATTT
*
527786 AATATATCTATA
1 AATATATATATA
527798 TAAATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 20 0.62
29 11 0.34
30 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (30 bp):
AATATATATATAAAAAATTTAAAAATATTT
Found at i:528627 original size:13 final size:13
Alignment explanation
Indices: 528611--528644 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
528601 TTGTAATTTT
*
528611 ATTATTTTTAATA
1 ATTATTTATAATA
528624 ATTATTTATAATA
1 ATTATTTATAATA
528637 A-TATTTAT
1 ATTATTTAT
528645 TATTGTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATTTATAATA
Found at i:531536 original size:14 final size:14
Alignment explanation
Indices: 531517--531563 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
531507 CTCCTCCTTA
531517 AATATAAAAAATAT
1 AATATAAAAAATAT
531531 AATAT--AAAATAT
1 AATATAAAAAATAT
* *
531543 AACACAAAAAATAT
1 AATATAAAAAATAT
531557 ATATATA
1 A-ATATA
531564 TAAATACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
12 10 0.38
14 13 0.50
15 3 0.12
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (14 bp):
AATATAAAAAATAT
Found at i:531684 original size:3 final size:3
Alignment explanation
Indices: 531678--531702 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
531668 ATAATAATAA
531678 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
531703 GTTGTGGTGA
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):
TAT
Found at i:531800 original size:23 final size:21
Alignment explanation
Indices: 531743--531808 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
531733 TAAAATACAT
*
531743 AAATTTTTATAATAATTTTTA
1 AAATTTTTAAAATAATTTTTA
* **
531764 ATATTTTTGCAATAATTTTTA
1 AAATTTTTAAAATAATTTTTA
531785 AAAGTTTTTAAAAATAATTTTTA
1 AAA-TTTTT-AAAATAATTTTTA
531808 A
1 A
531809 TTTCTTAGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 20 0.54
22 5 0.14
23 12 0.32
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (21 bp):
AAATTTTTAAAATAATTTTTA
Found at i:532340 original size:35 final size:32
Alignment explanation
Indices: 532289--532353 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
532279 TCTGTCTAAT
* **
532289 AATATTTTTTAATATTATTATTATATTAAATAA
1 AATATATTTTAATATTAAAATT-TATTAAATAA
532322 AATATATTTTAATCTATTAAAATTTATTAAAT
1 AATATATTTTAA--TATTAAAATTTATTAAAT
532354 TAATTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.41
34 8 0.30
35 8 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
AATATATTTTAATATTAAAATTTATTAAATAA
Found at i:533110 original size:14 final size:14
Alignment explanation
Indices: 533087--533120 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
533077 CATATGAAAT
*
533087 ATAAAAATAATATA
1 ATAAATATAATATA
533101 ATAAATATAATATA
1 ATAAATATAATATA
533115 ATAAAT
1 ATAAAT
533121 TTAAATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAAATATAATATA
Found at i:533211 original size:8 final size:9
Alignment explanation
Indices: 533164--533213 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 9
533154 ATATCATATC
*
533164 TATATTTAA
1 TATATTTAT
*
533173 TAT-TTTAA
1 TATATTTAT
533181 TATATTTAT
1 TATATTTAT
533190 TA-ATTTAT
1 TATATTTAT
*
533198 TTTATTT-T
1 TATATTTAT
533206 TATATTTA
1 TATATTTA
533214 CATGATGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 22 0.63
9 13 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATATTTAT
Found at i:533632 original size:24 final size:26
Alignment explanation
Indices: 533579--533632 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
533569 ATGGAGTTAG
*
533579 ATATATTACAATTATAGATATAATAG
1 ATATATTACAATTATAGATATAATAA
* *
533605 ATATGTTACAATTA-A-TTATAATAA
1 ATATATTACAATTATAGATATAATAA
533629 ATAT
1 ATAT
533633 TAATAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
26 13 0.52
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41
Consensus pattern (26 bp):
ATATATTACAATTATAGATATAATAA
Found at i:533650 original size:16 final size:18
Alignment explanation
Indices: 533617--533661 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
533607 ATGTTACAAT
533617 TAATTATAATAAATATTAA
1 TAATTATAA-AAATATTAA
533636 TAATTA-AAAAA-ATTAA
1 TAATTATAAAAATATTAA
533652 -AATTATAAAA
1 TAATTATAAAA
533662 TAGTGACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.20
16 9 0.36
17 3 0.12
18 2 0.08
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATTATAAAAATATTAA
Found at i:534650 original size:17 final size:17
Alignment explanation
Indices: 534630--534672 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
534620 TTGAATGTGA
* * *
534630 ATATTGAATATATGTAT
1 ATATTAAATAAATATAT
534647 ATATTAAATAAATATAT
1 ATATTAAATAAATATAT
534664 ATATTAAAT
1 ATATTAAAT
534673 TTTTTTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (17 bp):
ATATTAAATAAATATAT
Found at i:542047 original size:18 final size:18
Alignment explanation
Indices: 542008--542048 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
541998 AAATAATTTT
**
542008 TTATTAAATAAATATATT
1 TTATTAAATAAATATAAA
*
542026 TTATTAAATAAATTTAAA
1 TTATTAAATAAATATAAA
542044 TTATT
1 TTATT
542049 TAATTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTAAATAAATATAAA
Found at i:542079 original size:23 final size:22
Alignment explanation
Indices: 542038--542080 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
542028 ATTAAATAAA
* *
542038 TTTAAATTATTTAATTTTTATC
1 TTTAAATAATTTAAATTTTATC
542060 TTTAAATAAATTTAAATTTTA
1 TTTAAAT-AATTTAAATTTTA
542081 AAAATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAATAATTTAAATTTTATC
Found at i:542865 original size:14 final size:14
Alignment explanation
Indices: 542843--542875 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
542833 CTGTAAACTC
*
542843 GTTCAAGTTTCAGT
1 GTTCTAGTTTCAGT
542857 GTTCTAGTTTCAGT
1 GTTCTAGTTTCAGT
542871 GTTCT
1 GTTCT
542876 TCTTCTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (14 bp):
GTTCTAGTTTCAGT
Found at i:543676 original size:27 final size:27
Alignment explanation
Indices: 543638--543690 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
543628 GTGTAAGAAA
*
543638 CTGAGTCAGTTTTCTAATGAATGAATT
1 CTGAGTCAGTTTCCTAATGAATGAATT
*
543665 CTGATTCAGTTTCCTAATGAATGAAT
1 CTGAGTCAGTTTCCTAATGAATGAAT
543691 GGAAGCTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (27 bp):
CTGAGTCAGTTTCCTAATGAATGAATT
Found at i:545653 original size:13 final size:13
Alignment explanation
Indices: 545637--545663 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
545627 TTTATTCAGC
545637 ATAGATTTTCACT
1 ATAGATTTTCACT
545650 ATAGATTTTCACT
1 ATAGATTTTCACT
545663 A
1 A
545664 GACCAACAAA
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:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
ATAGATTTTCACT
Found at i:550315 original size:2 final size:2
Alignment explanation
Indices: 550308--550354 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
550298 TCATCTCCAA
*
550308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
550350 AT AT A
1 AT AT A
550355 ATTGATGCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:551901 original size:23 final size:23
Alignment explanation
Indices: 551864--551907 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
551854 TTTTTTATAA
*
551864 AAAAAAATTATAA-TTTAAAAGT
1 AAAAAAATTAAAATTTTAAAAGT
551886 AAAAAAATTAAAAATTTTAAAA
1 AAAAAAATT-AAAATTTTAAAA
551908 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
24 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAATTAAAATTTTAAAAGT
Found at i:551907 original size:15 final size:14
Alignment explanation
Indices: 551889--551924 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
551879 TAAAAGTAAA
551889 AAAATTAAAAATTTT
1 AAAATTAAAAA-TTT
*
551904 AAAATTTAAAATTT
1 AAAATTAAAAATTT
551918 AAAATTA
1 AAAATTA
551925 CTTAAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATTAAAAATTT
Found at i:554989 original size:15 final size:14
Alignment explanation
Indices: 554970--555018 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
554960 ATTTTTATTT
554970 TATAAATTTTAATA
1 TATAAATTTTAATA
554984 TAATAATAATTTATAATA
1 T-AT-A-AATTT-TAATA
*
555002 TATAAATTTTAAAA
1 TATAAATTTTAATA
555016 TAT
1 TAT
555019 TTATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 2 0.07
17 7 0.23
18 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAAATTTTAATA
Found at i:559150 original size:22 final size:22
Alignment explanation
Indices: 559125--559169 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
559115 ATTCTTTATT
559125 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
*
559147 TAAATATTTATATAAAAATATA
1 TAAATATTAATATAAAAATATA
559169 T
1 T
559170 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:559401 original size:23 final size:24
Alignment explanation
Indices: 559375--559419 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
559365 AAATTATATA
559375 TATTAAA-ATTAAAATTTTAAATT
1 TATTAAATATTAAAATTTTAAATT
* *
559398 TATTAAATATTATATTTTTAAA
1 TATTAAATATTAAAATTTTAAA
559420 ATATTAACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAAATATTAAAATTTTAAATT
Found at i:559414 original size:16 final size:16
Alignment explanation
Indices: 559383--559425 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
559373 TATATTAAAA
* *
559383 TTAAAATTTTAAATTT
1 TTAAAATATTATATTT
559399 ATT-AAATATTATATTT
1 -TTAAAATATTATATTT
559415 TTAAAATATTA
1 TTAAAATATTA
559426 ACGCGTCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAATATTATATTT
Found at i:559424 original size:23 final size:23
Alignment explanation
Indices: 559372--559426 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
559362 AAAAAATTAT
559372 ATATATTAAAATTAAAATTTTAA
1 ATATATTAAAATTAAAATTTTAA
* * *
559395 ATTTATTAAATATTATATTTTTAA
1 ATATATTAAA-ATTAAAATTTTAA
559419 A-ATATTAA
1 ATATATTAA
559427 CGCGTCATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATTAAAATTAAAATTTTAA
Found at i:560980 original size:34 final size:33
Alignment explanation
Indices: 560859--561014 Score: 195
Period size: 34 Copynumber: 4.7 Consensus size: 33
560849 GGTTTGGTAA
* * *
560859 AAATCACCATTTAATCAATAATGGTAAGCTATC
1 AAATCACCATTTAATCAACAATGGTAAACTACC
** *
560892 AAATTTCTCATTTAATCAACAATGGTAAGCTACC
1 AAATCAC-CATTTAATCAACAATGGTAAACTACC
* * ** *
560926 AAATCACCATTTAGTTAACAATGACAAACCACC
1 AAATCACCATTTAATCAACAATGGTAAACTACC
560959 AAATCACCCATTTAATCAACAATGGTAAACTACC
1 AAATCA-CCATTTAATCAACAATGGTAAACTACC
560993 AAATCACCATTTAATCAACAAT
1 AAATCACCATTTAATCAACAAT
561015 TCTCCCACTT
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
33 47 0.45
34 57 0.55
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (33 bp):
AAATCACCATTTAATCAACAATGGTAAACTACC
Found at i:565463 original size:34 final size:34
Alignment explanation
Indices: 565420--565534 Score: 151
Period size: 34 Copynumber: 3.4 Consensus size: 34
565410 TAAAAACCAC
* * **
565420 CATTTAATCAATAATGGTAAGCTACCAAATTTCT
1 CATTTAATCAACAATGGTAAACTACCAAATCACT
* *
565454 CATTTAATCAACAATGGTAAACCACTAAATCACT
1 CATTTAATCAACAATGGTAAACTACCAAATCACT
*
565488 CATTTAATCAACAATGATAAACTACCAAATCAC-
1 CATTTAATCAACAATGGTAAACTACCAAATCACT
*
565521 CATTTAATTAACAA
1 CATTTAATCAACAA
565535 ACAGACGTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.18
34 58 0.82
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (34 bp):
CATTTAATCAACAATGGTAAACTACCAAATCACT
Found at i:571539 original size:2 final size:2
Alignment explanation
Indices: 571532--571558 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
571522 CTCATGTGTT
571532 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
571559 TCTAATTCAA
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:571978 original size:2 final size:2
Alignment explanation
Indices: 571971--572009 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
571961 ATCATGTCTT
571971 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
572010 TTGTCTGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:576466 original size:2 final size:2
Alignment explanation
Indices: 576449--576482 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
576439 TTTCATAAAA
* *
576449 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
576483 TTTGTTGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:579278 original size:15 final size:13
Alignment explanation
Indices: 579244--579284 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
579234 ATTTAAATAT
*
579244 ATATTAAATATAA
1 ATATCAAATATAA
579257 ATATCAAATATAA
1 ATATCAAATATAA
579270 ATATTTCAAATATAA
1 ATA--TCAAATATAA
579285 TAAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.60
15 10 0.40
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:579466 original size:2 final size:2
Alignment explanation
Indices: 579461--579485 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
579451 CATATGTGTG
579461 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 T
579486 TAACATCTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:581290 original size:20 final size:21
Alignment explanation
Indices: 581250--581306 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
581240 AGATTTGATA
*
581250 ATAAATACATACTATATTTTA-T
1 ATAAATATATA-TA-ATTTTAGT
581272 ATAAATATATATAATTTTATGT
1 ATAAATATATATAATTTTA-GT
581294 ATAAATATA-ATAA
1 ATAAATATATATAA
581307 AAATATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
22 20 0.62
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAATATATATAATTTTAGT
Found at i:581321 original size:20 final size:19
Alignment explanation
Indices: 581298--581342 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
581288 TTATGTATAA
581298 ATATAATAAAAATATTAAAT
1 ATATAATAAAAAT-TTAAAT
581318 ATATAA-AAAAATTTAAAT
1 ATATAATAAAAATTTAAAT
581336 ATA-AATA
1 ATATAATA
581343 TAATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 6 0.25
20 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAATAAAAATTTAAAT
Found at i:582755 original size:29 final size:29
Alignment explanation
Indices: 582718--582773 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
582708 TTTTAAAAAT
**
582718 TAATAATTAATTAAATAAATTATATTTTA
1 TAATAATTAAAAAAATAAATTATATTTTA
* *
582747 TAATTATTAAAAAAATTAATTATATTT
1 TAATAATTAAAAAAATAAATTATATTT
582774 AATTAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAATAATTAAAAAAATAAATTATATTTTA
Found at i:583797 original size:2 final size:2
Alignment explanation
Indices: 583790--583818 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
583780 TTGTCATCCC
583790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
583819 TTGTACAGGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:585075 original size:22 final size:22
Alignment explanation
Indices: 585050--585091 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
585040 ATTAAAATAT
585050 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
585072 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
585092 AATTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:585096 original size:28 final size:29
Alignment explanation
Indices: 585060--585116 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
585050 TATTTTTATA
*
585060 TTAATATTT-ATATATTTTTATAATTAAAT
1 TTAATATTTAAAATA-TTTTATAATTAAAT
*
585089 TTAA-ATTTAAAATATTTTATTATTAAAT
1 TTAATATTTAAAATATTTTATAATTAAAT
585117 AATAATTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAATATTTAAAATATTTTATAATTAAAT
Found at i:585123 original size:28 final size:28
Alignment explanation
Indices: 585012--585124 Score: 67
Period size: 28 Copynumber: 4.1 Consensus size: 28
585002 GTTGAGTTAA
* * *
585012 TTAAAATATATTTTTTATT-TATAATATT
1 TTAAAATAT-TTTATTATTAAATAATAAT
* *
585040 ATTAAAATA--TTATTTTTATATTAAT-AT
1 -TTAAAATATTTTATTATTA-AATAATAAT
* * *
585067 TT-ATATATTTTTATAATTAAAT-TTAAAT
1 TTAAAATA-TTTTATTATTAAATAAT-AAT
585095 TTAAAATATTTTATTATTAAATAATAAT
1 TTAAAATATTTTATTATTAAATAATAAT
585123 TT
1 TT
585125 GGTTTGAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 19
0.66 0.14 0.20
Matches are distributed among these distances:
25 4 0.06
26 9 0.15
27 3 0.05
28 33 0.53
29 13 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAAAATATTTTATTATTAAATAATAAT
Found at i:585800 original size:4 final size:4
Alignment explanation
Indices: 585791--585817 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
585781 TGAGTTTTGC
585791 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
585818 TAACAAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:588723 original size:2 final size:2
Alignment explanation
Indices: 588716--588753 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
588706 ATCTAACATC
*
588716 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
588754 TCATAGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:602158 original size:29 final size:29
Alignment explanation
Indices: 602126--602189 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
602116 ATTAATTTTA
602126 ATTTTAAAATAAATTATCAAAATAATATT
1 ATTTTAAAATAAATTATCAAAATAATATT
* * * * *
602155 ATTTTAAAATTATTTATTAAAATACTGTT
1 ATTTTAAAATAAATTATCAAAATAATATT
602184 ATTTTA
1 ATTTTA
602190 CTTTTGATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTTTAAAATAAATTATCAAAATAATATT
Found at i:602849 original size:16 final size:17
Alignment explanation
Indices: 602816--602855 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
602806 CAAATATTTA
*
602816 TATTTTTAGATTCGTAT
1 TATTTTTAGATTCATAT
602833 TATTTTTAGATT-ATAT
1 TATTTTTAGATTCATAT
602849 T-TTTTTA
1 TATTTTTA
602856 TATAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 4 0.18
17 12 0.55
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (17 bp):
TATTTTTAGATTCATAT
Found at i:603351 original size:22 final size:24
Alignment explanation
Indices: 603326--603377 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
603316 TTTTTATTTT
603326 TTTAAAAATATA-TTTT-TTAAAA
1 TTTAAAAATATACTTTTATTAAAA
* * *
603348 TTTAATAATTTACTTTTATTAAAT
1 TTTAAAAATATACTTTTATTAAAA
603372 TTTAAA
1 TTTAAA
603378 GTGTAGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 4 0.17
24 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTAAAAATATACTTTTATTAAAA
Found at i:603615 original size:18 final size:18
Alignment explanation
Indices: 603573--603608 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
603563 GTTTTCTGAT
603573 TATATATCCCTATATATA
1 TATATATCCCTATATATA
*
603591 TATATATTCCTATATATA
1 TATATATCCCTATATATA
603609 ATCATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATATCCCTATATATA
Found at i:605789 original size:43 final size:44
Alignment explanation
Indices: 605704--605790 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
605694 TTTGAGGCAA
* * *
605704 AACTCAAAACTAACTACAATATTTTTCTCAAAATCGAACCAATT
1 AACTCAAAACTAACCAAAATATATTTCTCAAAATCGAACCAATT
*
605748 AACTCAAAATTAACCAAAATATATTT-TCAAAA-CTGAACCAATT
1 AACTCAAAACTAACCAAAATATATTTCTCAAAATC-GAACCAATT
605791 CAAATCGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.03
43 15 0.39
44 22 0.58
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (44 bp):
AACTCAAAACTAACCAAAATATATTTCTCAAAATCGAACCAATT
Found at i:612263 original size:3 final size:3
Alignment explanation
Indices: 612255--612292 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
612245 GAACAACGTT
*
612255 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
612293 CAAATTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:616094 original size:2 final size:2
Alignment explanation
Indices: 616087--616121 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
616077 TCTATAGATG
*
616087 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
616122 CTTTGCATTG
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:617573 original size:2 final size:2
Alignment explanation
Indices: 617566--617598 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
617556 ATGCATCTGA
617566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
617599 GAGTCATCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:617824 original size:26 final size:25
Alignment explanation
Indices: 617782--617831 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
617772 TTTGTTTGTT
617782 TTATTGTTTAAAAATATTAAAAATA
1 TTATTGTTTAAAAATATTAAAAATA
* *
617807 TTATTTTTATAAAAATATTTAAAAT
1 TTATTGTT-TAAAAATATTAAAAAT
617832 TTTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TTATTGTTTAAAAATATTAAAAATA
Found at i:620669 original size:12 final size:12
Alignment explanation
Indices: 620650--620680 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
620640 TATAGCCCCC
620650 CAGCTTCTGCTT
1 CAGCTTCTGCTT
*
620662 CTGCTTCTGCTT
1 CAGCTTCTGCTT
620674 CAGCTTC
1 CAGCTTC
620681 CCCTGTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.06, C:0.35, G:0.16, T:0.42
Consensus pattern (12 bp):
CAGCTTCTGCTT
Found at i:621354 original size:25 final size:23
Alignment explanation
Indices: 621326--621399 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 23
621316 TACATAAATA
621326 TAATTTAAAATAATTAATATATAAT
1 TAATTT-AAATAATTAATATAT-AT
* * *
621351 TAATATAAATAAATTAAAAAATAT
1 TAATTTAAAT-AATTAATATATAT
621375 GTAATTT-AAT-ATTAATATATAT
1 -TAATTTAAATAATTAATATATAT
621397 TAA
1 TAA
621400 AATTTATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 3 0.07
22 10 0.24
24 9 0.22
25 19 0.46
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATTTAAATAATTAATATATAT
Found at i:621359 original size:36 final size:36
Alignment explanation
Indices: 621319--621430 Score: 89
Period size: 30 Copynumber: 3.2 Consensus size: 36
621309 AAAATTATAC
621319 ATAAATATAATTTAAAATAATTAATATATAATTAAT
1 ATAAATATAATTTAAAATAATTAATATATAATTAAT
* *
621355 ATAAATA-AA-TTAAAA-AA-T-ATGTA-ATTTAAT
1 ATAAATATAATTTAAAATAATTAATATATAATTAAT
*
621385 ATTAATAT-ATATTAAAAT--TTATATATATATATATAAAT
1 ATAAATATAAT-TTAAAATAATTA-ATATATA-AT-T-AAT
621423 ATAAATAT
1 ATAAATAT
621431 GATATAAAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
30 13 0.22
31 4 0.07
32 8 0.14
33 2 0.03
34 10 0.17
35 3 0.05
36 8 0.14
37 1 0.02
38 10 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
ATAAATATAATTTAAAATAATTAATATATAATTAAT
Found at i:621384 original size:30 final size:31
Alignment explanation
Indices: 621352--621428 Score: 61
Period size: 32 Copynumber: 2.5 Consensus size: 31
621342 ATATATAATT
*
621352 AATA-TAA-ATAAATTAAAAAATATGTAATTT
1 AATATTAATATAAATTAAAAAATATATAA-TT
* **
621382 AATATTAATATATATTAAAATTTATAT-ATAT
1 AATATTAATATAAATTAAAAAATATATAAT-T
*
621413 ATATATAAATATAAAT
1 A-ATATTAATATAAAT
621429 ATGATATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
30 5 0.14
31 6 0.16
32 26 0.70
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
AATATTAATATAAATTAAAAAATATATAATT
Found at i:624160 original size:15 final size:16
Alignment explanation
Indices: 624124--624163 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
624114 TTTAATATTT
*
624124 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
624141 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
624156 ATAAAATT
1 ATAAAATT
624164 TATTTAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:624166 original size:16 final size:17
Alignment explanation
Indices: 624124--624166 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
624114 TTTAATATTT
*
624124 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
624141 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
624156 ATAAAATTTAT
1 ATAAAATTTAT
624167 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:626096 original size:2 final size:2
Alignment explanation
Indices: 626048--626077 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
626038 ATGTAGTTCA
626048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
626078 TAGATACTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:631019 original size:17 final size:17
Alignment explanation
Indices: 630993--631029 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
630983 AAAAAAATTG
*
630993 ATTTAATAAATTTATAT
1 ATTTAATAAATTTAGAT
*
631010 ATTTAGTAAATTTAGAT
1 ATTTAATAAATTTAGAT
631027 ATT
1 ATT
631030 GAATGGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
ATTTAATAAATTTAGAT
Found at i:634574 original size:50 final size:49
Alignment explanation
Indices: 634485--634855 Score: 352
Period size: 50 Copynumber: 7.4 Consensus size: 49
634475 TCATCAACCT
* * * * *
634485 AAGTGGTCGTAATTATTAACAATTATTT-ACTAACCTTTGACAATAGAGA
1 AAGTGGTCATAATTGTTGACGATT-TTTCACCAACCTTTGACAATAGAGA
** * * *
634534 AAGATAATCATAATTGTTGACGATTTTTCACTAACATTTGATAATAGAGA
1 AAG-TGGTCATAATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGA
* * * * * *
634584 GAGGTGGTTATAATTGTTGATGATTCTTCACCGACCTTTGACAATAAAGA
1 -AAGTGGTCATAATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGA
* * *
634634 GAAGTGGTCATAATTGTTGACGATTCTTCATCAACTTTTGACAATAGAGA
1 -AAGTGGTCATAATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGA
* * * *
634684 GATGTAGCCATAATTGTTGACGATTCTTT-ACCAACCTTTGATAATAGAGA
1 -AAGTGGTCATAATTGTTGACGATT-TTTCACCAACCTTTGACAATAGAGA
* * *
634734 GAGGTGGCCGTAATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGA
1 -AAGTGGTCATAATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGA
* * *
634784 GAAGTAGGTCATAATAGTTGACGATTCTTT-ACCAACCTTTGATAATAAAGA
1 -AAGT-GGTCATAATTGTTGACGATT-TTTCACCAACCTTTGACAATAGAGA
*
634835 AAGGTGGTCGTAATTGTTGAC
1 AA-GTGGTCATAATTGTTGAC
634856 TCTAAGTATA
Statistics
Matches: 269, Mismatches: 45, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
49 9 0.03
50 215 0.80
51 42 0.16
52 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (49 bp):
AAGTGGTCATAATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGA
Found at i:634674 original size:100 final size:98
Alignment explanation
Indices: 634485--634855 Score: 409
Period size: 100 Copynumber: 3.7 Consensus size: 98
634475 TCATCAACCT
* * * * * * * **
634485 AAGTGGTCGTAATTATTAACAATTATTTACTAACCTTTGACAATAGAGAAAGATAATCATAATTG
1 AAGTGGTCATAATTGTTGACGATTCTTTACCAACCTTTGACAATAAAGAAAG-TGGTCATAATTG
*
634550 TTGACGATTTTTCACTAACATTTGATAATAGAGAG
65 TTGACGATTTTTCAC-AACATTTGACAATAGAGAG
* * * * *
634585 AGGTGGTTATAATTGTTGATGATTCTTCACCGACCTTTGACAATAAAGAGAAGTGGTCATAATTG
1 AAGTGGTCATAATTGTTGACGATTCTTTACCAACCTTTGACAATAAAGA-AAGTGGTCATAATTG
* *
634650 TTGACGATTCTTCATCAACTTTTGACAATAGAGAG
65 TTGACGATTTTTCA-CAACATTTGACAATAGAGAG
* * * * * * * *
634685 ATGTAGCCATAATTGTTGACGATTCTTTACCAACCTTTGATAATAGAGAGAGGTGGCCGTAATTG
1 AAGTGGTCATAATTGTTGACGATTCTTTACCAACCTTTGACAATAAAGA-AAGTGGTCATAATTG
*
634750 TTGACGATTTTTCACCAACCTTTGACAATAGAGAG
65 TTGACGATTTTTCA-CAACATTTGACAATAGAGAG
* * *
634785 AAGTAGGTCATAATAGTTGACGATTCTTTACCAACCTTTGATAATAAAGAAAGGTGGTCGTAATT
1 AAGT-GGTCATAATTGTTGACGATTCTTTACCAACCTTTGACAATAAAGAAA-GTGGTCATAATT
634850 GTTGAC
64 GTTGAC
634856 TCTAAGTATA
Statistics
Matches: 228, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
100 166 0.73
101 62 0.27
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (98 bp):
AAGTGGTCATAATTGTTGACGATTCTTTACCAACCTTTGACAATAAAGAAAGTGGTCATAATTGT
TGACGATTTTTCACAACATTTGACAATAGAGAG
Found at i:634764 original size:150 final size:151
Alignment explanation
Indices: 634516--634837 Score: 443
Period size: 150 Copynumber: 2.1 Consensus size: 151
634506 ATTATTTACT
* *
634516 AACCTTTGACAATAGAGAAAGATAATCATAATTGTTGACGATTTTTCACTAACATTTGATAATAG
1 AACCTTTGACAATAGAGAAAGATAACCATAATTGTTGACGATTTTTCACCAACATTTGATAATAG
** * *
634581 AGAGAGGTGGTTATAATTGTTGATGATTCTTCACCGACCTTTGACAATAAAGAGAAGT-GGTCAT
66 AGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGAGAAGTAGGTCAT
* *
634645 AATTGTTGACGATTCTTCATC
131 AATAGTTGACGATTCTTCACC
* * * *
634666 AACTTTTGACAATAGAGAGATG-TAGCCATAATTGTTGACGATTCTTT-ACCAACCTTTGATAAT
1 AACCTTTGACAATAGAGA-AAGATAACCATAATTGTTGACGATT-TTTCACCAACATTTGATAAT
* * *
634729 AGAGAGAGGTGGCCGTAATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGAGAAGTAGGTC
64 AGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGAGAAGTAGGTC
*
634794 ATAATAGTTGACGATTCTTTACC
129 ATAATAGTTGACGATTCTTCACC
* *
634817 AACCTTTGATAATAAAGAAAG
1 AACCTTTGACAATAGAGAAAG
634838 GTGGTCGTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
150 105 0.70
151 44 0.30
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (151 bp):
AACCTTTGACAATAGAGAAAGATAACCATAATTGTTGACGATTTTTCACCAACATTTGATAATAG
AGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGAGAAGTAGGTCAT
AATAGTTGACGATTCTTCACC
Found at i:636126 original size:13 final size:13
Alignment explanation
Indices: 636104--636137 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
636094 TGTTATGGAG
*
636104 GATCAAAGTTTTC
1 GATCAGAGTTTTC
636117 GATCAGAGTTTTC
1 GATCAGAGTTTTC
*
636130 AATCAGAG
1 GATCAGAG
636138 ATTATGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (13 bp):
GATCAGAGTTTTC
Found at i:636806 original size:51 final size:51
Alignment explanation
Indices: 636696--636857 Score: 222
Period size: 51 Copynumber: 3.2 Consensus size: 51
636686 ATGGAAAGTA
* ** * *
636696 CTTTTGACAATAGAGAGAGGTTGTTACAATTGTTGACGATTATTCA-CAAC
1 CTTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
*
636746 C-TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGTTTCTTCACCAAC
1 CTTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
* *
636796 CTTTTGACAATAGAAAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAA-
1 CTTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
*
636846 CTTTTGATAATA
1 CTTTTGACAATA
636858 AAGAAAGATG
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
49 38 0.38
50 17 0.17
51 45 0.45
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (51 bp):
CTTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
Found at i:636876 original size:50 final size:49
Alignment explanation
Indices: 636723--636879 Score: 183
Period size: 51 Copynumber: 3.1 Consensus size: 49
636713 AGGTTGTTAC
* * * * *
636723 AATTGTTGACGATTATTCA-CAACCTTTGACAATAGAGAGAGGTGGCCAT
1 AATTGTTGACGATTCTTCACCAACTTTTGACAATA-AGAAAGATGGCCGT
*
636772 AATTGTTGACGTTTCTTCACCAACCTTTTGACAAT-AGAAAGAGGTGGCCGT
1 AATTGTTGACGATTCTTCACCAA-CTTTTGACAATAAGAAAGA--TGGCCGT
* *
636823 AATTGTTGACGATTCTTCACCAACTTTTGATAATAAAGAAAGATGACCGT
1 AATTGTTGACGATTCTTCACCAACTTTTGACAAT-AAGAAAGATGGCCGT
636873 AATTGTT
1 AATTGTT
636880 AACTCTAAGT
Statistics
Matches: 93, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
49 22 0.24
50 26 0.28
51 38 0.41
52 7 0.08
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (49 bp):
AATTGTTGACGATTCTTCACCAACTTTTGACAATAAGAAAGATGGCCGT
Found at i:641749 original size:18 final size:18
Alignment explanation
Indices: 641702--641761 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
641692 TTTTATATTT
641702 AATATTTATATAAGATAAA
1 AATATTTATATAAGA-AAA
* *
641721 GATATAATATATAA-AAAA
1 AATAT-TTATATAAGAAAA
*
641739 TAATATTTATATAATAAAA
1 -AATATTTATATAAGAAAA
641758 AATA
1 AATA
641762 AATTGAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 14 0.41
19 13 0.38
20 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATATTTATATAAGAAAA
Found at i:643540 original size:15 final size:15
Alignment explanation
Indices: 643520--643552 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
643510 ATAATATTTG
643520 TATTTGAATATGAGT
1 TATTTGAATATGAGT
643535 TATTTGAATATGAGT
1 TATTTGAATATGAGT
643550 TAT
1 TAT
643553 AATCTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
TATTTGAATATGAGT
Found at i:644741 original size:34 final size:34
Alignment explanation
Indices: 644686--644834 Score: 156
Period size: 34 Copynumber: 4.4 Consensus size: 34
644676 CCTTTTAGCT
* **
644686 ATTTAGTCAA-AATGACAAACCACTAAATCACTT
1 ATTTAGTCAACAATGACAAACCACCAAATCACCC
* ** * *
644719 ATTTAATCAACAATGGTAAACCACCAAATCATCA
1 ATTTAGTCAACAATGACAAACCACCAAATCACCC
644753 ATTTAGTCAACAATGACAAACCACCAAATCACCC
1 ATTTAGTCAACAATGACAAACCACCAAATCACCC
* **** *
644787 ATTTAGTCAATAATGGTGGACCACTAAATCACCC
1 ATTTAGTCAACAATGACAAACCACCAAATCACCC
*
644821 ATTTAATCAACAAT
1 ATTTAGTCAACAAT
644835 TCTTCTACTT
Statistics
Matches: 95, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
33 9 0.09
34 86 0.91
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (34 bp):
ATTTAGTCAACAATGACAAACCACCAAATCACCC
Found at i:644773 original size:68 final size:68
Alignment explanation
Indices: 644686--644834 Score: 192
Period size: 68 Copynumber: 2.2 Consensus size: 68
644676 CCTTTTAGCT
* **
644686 ATTTAGTCAA-AATGACAAACCACTAAATCACTTATTTAATCAACAATGGTAAACCACCAAATCA
1 ATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAATCA
*
644750 TCA
66 CCA
* * ** *
644753 ATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAGTCAATAATGGTGGACCACTAAATCA
1 ATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAATCA
*
644818 CCC
66 CCA
*
644821 ATTTAATCAACAAT
1 ATTTAGTCAACAAT
644835 TCTTCTACTT
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
67 10 0.14
68 60 0.86
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (68 bp):
ATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAATCA
CCA
Found at i:648613 original size:179 final size:179
Alignment explanation
Indices: 648313--648672 Score: 711
Period size: 179 Copynumber: 2.0 Consensus size: 179
648303 AGAAGCTCCG
*
648313 CACATTCATTTTCCTCTATCTTGTGTCTCAACATTGTTAGCTGAGAAAATAGAGTCTTCAATGTG
1 CACATTCATTTTCCTCTATCTTGTGTCCCAACATTGTTAGCTGAGAAAATAGAGTCTTCAATGTG
648378 TTAATGCGGTAAGTCACCGATGTAGATTTCGCCATGTGAAGAGTGTAAAGTTTTCTTTTTAAGAA
66 TTAATGCGGTAAGTCACCGATGTAGATTTCGCCATGTGAAGAGTGTAAAGTTTTCTTTTTAAGAA
648443 AATTTTGTTGTGTAGTGACTTGGTCTCGTACAGTTTTGTAAGAGTATCC
131 AATTTTGTTGTGTAGTGACTTGGTCTCGTACAGTTTTGTAAGAGTATCC
648492 CACATTCATTTTCCTCTATCTTGTGTCCCAACATTGTTAGCTGAGAAAATAGAGTCTTCAATGTG
1 CACATTCATTTTCCTCTATCTTGTGTCCCAACATTGTTAGCTGAGAAAATAGAGTCTTCAATGTG
648557 TTAATGCGGTAAGTCACCGATGTAGATTTCGCCATGTGAAGAGTGTAAAGTTTTCTTTTTAAGAA
66 TTAATGCGGTAAGTCACCGATGTAGATTTCGCCATGTGAAGAGTGTAAAGTTTTCTTTTTAAGAA
648622 AATTTTGTTGTGTAGTGACTTGGTCTCGTACAGTTTTGTAAGAGTATCC
131 AATTTTGTTGTGTAGTGACTTGGTCTCGTACAGTTTTGTAAGAGTATCC
648671 CA
1 CA
648673 AATTTCCTTT
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (179 bp):
CACATTCATTTTCCTCTATCTTGTGTCCCAACATTGTTAGCTGAGAAAATAGAGTCTTCAATGTG
TTAATGCGGTAAGTCACCGATGTAGATTTCGCCATGTGAAGAGTGTAAAGTTTTCTTTTTAAGAA
AATTTTGTTGTGTAGTGACTTGGTCTCGTACAGTTTTGTAAGAGTATCC
Found at i:649447 original size:34 final size:34
Alignment explanation
Indices: 649367--649513 Score: 159
Period size: 34 Copynumber: 4.3 Consensus size: 34
649357 TCTTTTAACT
* *
649367 ATTTAGTCAACAATGATAAACCACCAAATCACCC
1 ATTTAGTCAACAATGACAAATCACCAAATCACCC
* * * *
649401 ATTTAATTAACAATGACAAATTACCAAATCACCT
1 ATTTAGTCAACAATGACAAATCACCAAATCACCC
* * ***
649435 TTTTAGTCAACAATAACAAATCACCAAATCGTTC
1 ATTTAGTCAACAATGACAAATCACCAAATCACCC
* * *
649469 ATTTAGTCAAAAAATGACAAATCACTAAATCACTC
1 ATTTAGTC-AACAATGACAAATCACCAAATCACCC
649504 ATTTAGTCAA
1 ATTTAGTCAA
649514 TAAGTATAAC
Statistics
Matches: 91, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
34 62 0.68
35 29 0.32
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.27
Consensus pattern (34 bp):
ATTTAGTCAACAATGACAAATCACCAAATCACCC
Found at i:649831 original size:2 final size:2
Alignment explanation
Indices: 649819--649854 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
649809 TCACATAAGC
*
649819 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
649855 TATCTCAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:658160 original size:50 final size:50
Alignment explanation
Indices: 658101--658309 Score: 337
Period size: 50 Copynumber: 4.2 Consensus size: 50
658091 TATACTTAGA
* *
658101 GTCAACAATTATGGCCACCTCTTTCTATTGTTAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
658151 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
658201 GTCAACAATTATGACAACCTCTTTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
658251 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
658301 GTCAACAAT
1 GTCAACAAT
658310 GACAACAACT
Statistics
Matches: 145, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 145 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:662913 original size:50 final size:50
Alignment explanation
Indices: 662705--662899 Score: 320
Period size: 50 Copynumber: 3.9 Consensus size: 50
662695 TATACTTAGA
* *
662705 GTCAACAATTATGGCCACCTCTTTCTATTGTCAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
662755 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTAGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
662805 GTCAACAATTATAGCCATCTC-CTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
662855 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
662900 TGATAGTTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
49 1 0.01
50 132 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:665525 original size:16 final size:16
Alignment explanation
Indices: 665464--665527 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
665454 AATCTAATCA
* *
665464 AATTCAAATTCAAAAT
1 AATTTAAATTAAAAAT
*
665480 AATTTAAATTTAAAAT
1 AATTTAAATTAAAAAT
665496 AATTTAAAATTAAAAAT
1 AATTT-AAATTAAAAAT
665513 -ATTTAAATCTAAAAA
1 AATTTAAAT-TAAAAA
665528 ATACAAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
15 4 0.09
16 29 0.67
17 10 0.23
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTTAAATTAAAAAT
Found at i:665527 original size:17 final size:16
Alignment explanation
Indices: 665475--665530 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
665465 ATTCAAATTC
665475 AAAATAATTTAAATTTAA
1 AAAAT-ATTTAAA-TTAA
*
665493 AATAAT-TTAAAATT-A
1 AA-AATATTTAAATTAA
665508 AAAATATTTAAATCTAA
1 AAAATATTTAAAT-TAA
665525 AAAATA
1 AAAATA
665531 CAAGTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.09
15 9 0.28
16 3 0.09
17 12 0.38
18 2 0.06
19 3 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATTTAAATTAA
Found at i:665699 original size:3 final size:3
Alignment explanation
Indices: 665687--665730 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
665677 TCCAACGCCG
* * * *
665687 CCA CCT CCA CCA CCA CCA CCA CCA CCA CAA CCA GCA CCT CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
665731 TCCGCTAGGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.64, G:0.02, T:0.05
Consensus pattern (3 bp):
CCA
Found at i:665705 original size:15 final size:15
Alignment explanation
Indices: 665672--665719 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
665662 ACAACCAGCT
* * *
665672 CCACCTCCAACGCCG
1 CCACCTCCACCACCA
665687 CCACCTCCACCACCA
1 CCACCTCCACCACCA
* *
665702 CCACCACCACCACAA
1 CCACCTCCACCACCA
665717 CCA
1 CCA
665720 GCACCTCCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.29, C:0.62, G:0.04, T:0.04
Consensus pattern (15 bp):
CCACCTCCACCACCA
Found at i:666315 original size:32 final size:33
Alignment explanation
Indices: 666269--666335 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
666259 CGGCGTTTAA
* *
666269 GACTATTACAATTTCTTTTG-ACTTTAAACTAC
1 GACTATTACAATTTCGTTGGAACTTTAAACTAC
* *
666301 GACTCTTACAATTTCGTTGGAACTTTAAATTAC
1 GACTATTACAATTTCGTTGGAACTTTAAACTAC
666334 GA
1 GA
666336 TTGACTAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (33 bp):
GACTATTACAATTTCGTTGGAACTTTAAACTAC
Found at i:669217 original size:18 final size:19
Alignment explanation
Indices: 669194--669229 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
669184 TGAGTCGATT
669194 TATTTATTTAA-ATTTAAA
1 TATTTATTTAATATTTAAA
669212 TATTTATTTAATATTTAA
1 TATTTATTTAATATTTAA
669230 GAAAGTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTATTTAATATTTAAA
Found at i:669292 original size:22 final size:22
Alignment explanation
Indices: 669267--669308 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
669257 AAAAATGAGA
*
669267 TTAAATAAA-AAATTAGATTTAT
1 TTAAA-AAATAAATTAAATTTAT
669289 TTAAAAAATAAATTAAATTT
1 TTAAAAAATAAATTAAATTT
669309 TAACTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAAAATAAATTAAATTTAT
Found at i:669491 original size:37 final size:36
Alignment explanation
Indices: 669439--669522 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 36
669429 ATGTAAATAT
*
669439 TAAAAAAATAAATTAAATTATTAAATTTTAAAACTTAA
1 TAAAAAAATAAATTAAATTATTAAA-ATTAAAA-TTAA
*
669477 TAAAAAAAT-TATTAAATTATTAAAATTAAAATTAA
1 TAAAAAAATAAATTAAATTATTAAAATTAAAATTAA
*
669512 -AAAAAATTAAA
1 TAAAAAAATAAA
669523 AAATAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 7 0.17
35 5 0.12
36 6 0.15
37 14 0.34
38 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (36 bp):
TAAAAAAATAAATTAAATTATTAAAATTAAAATTAA
Found at i:669513 original size:29 final size:29
Alignment explanation
Indices: 669448--669513 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
669438 TTAAAAAAAT
669448 AAATT-AAATTATTAAATTTTAAAACTTA
1 AAATTAAAATTATTAAATTTTAAAACTTA
*
669476 ATAA-AAAAATTATTAAATTATTAAAA-TTA
1 A-AATTAAAATTATTAAATT-TTAAAACTTA
669505 AAATTAAAA
1 AAATTAAAA
669514 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 3 0.09
29 23 0.72
30 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATTAAAATTATTAAATTTTAAAACTTA
Found at i:669709 original size:27 final size:27
Alignment explanation
Indices: 669678--669746 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
669668 AGCCACCCAT
*
669678 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* * *
669705 TGTTTGTAAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
669732 TATTTGTCAAAAATG
1 TGTTTGTCAAAAATG
669747 ATGTCATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:669846 original size:13 final size:13
Alignment explanation
Indices: 669828--669860 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
669818 GGCTCCCTCC
669828 TCCCTCTCAAGCA
1 TCCCTCTCAAGCA
*
669841 TCCCTCTTAAGCA
1 TCCCTCTCAAGCA
669854 T-CCTCTC
1 TCCCTCTC
669861 TTGTATTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.18, C:0.45, G:0.06, T:0.30
Consensus pattern (13 bp):
TCCCTCTCAAGCA
Found at i:674290 original size:27 final size:27
Alignment explanation
Indices: 674238--674305 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
674228 AGCCACCCAT
** *
674238 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATAATAGTTACTTTG
* *
674265 TGTTTGTCAAAAATAATAGTTTCTTTT
1 TGTTTGTCAAAAATAATAGTTACTTTG
* *
674292 TATTTATCAAAAAT
1 TGTTTGTCAAAAAT
674306 GGTGTCATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (27 bp):
TGTTTGTCAAAAATAATAGTTACTTTG
Found at i:678995 original size:2 final size:2
Alignment explanation
Indices: 678988--679014 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
678978 CCGAAGAAGC
678988 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
679015 CAAACAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:685608 original size:16 final size:18
Alignment explanation
Indices: 685594--685630 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
685584 GTAAATATAT
685594 AAATAATATAATATATTA
1 AAATAATATAATATATTA
*
685612 AAATAATATTAAAATATTA
1 AAATAATA-TAATATATTA
685631 TTTAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATATAATATATTA
Found at i:685709 original size:21 final size:19
Alignment explanation
Indices: 685677--685720 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
685667 TTTCTTTTTT
685677 ATATAAATATA-TATAAATA
1 ATATAAATATATTA-AAATA
685696 ATATAATATAATATTAAAATA
1 ATATAA-AT-ATATTAAAATA
685717 ATAT
1 ATAT
685721 TTATATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.27
20 2 0.09
21 12 0.55
22 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAATATATTAAAATA
Found at i:685762 original size:17 final size:17
Alignment explanation
Indices: 685729--685762 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
685719 ATTTATATAG
* *
685729 TATACTATAAGTTAAAT
1 TATACTATAAATAAAAT
685746 TATACTATAAATAAAAT
1 TATACTATAAATAAAAT
685763 AAATAATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
TATACTATAAATAAAAT
Found at i:698886 original size:16 final size:16
Alignment explanation
Indices: 698865--698895 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
698855 AAAGATATAA
698865 AAGTTATTCAACCAGT
1 AAGTTATTCAACCAGT
698881 AAGTTATTCAACCAG
1 AAGTTATTCAACCAG
698896 CGTAGTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (16 bp):
AAGTTATTCAACCAGT
Found at i:701445 original size:18 final size:19
Alignment explanation
Indices: 701416--701452 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
701406 AATAATATAT
*
701416 AAATATTTTTTTGATAAAA
1 AAATATTTTTTTAATAAAA
701435 AAATA-TTTTTTAATAAAA
1 AAATATTTTTTTAATAAAA
701453 TGATACATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAATATTTTTTTAATAAAA
Found at i:702164 original size:29 final size:28
Alignment explanation
Indices: 702120--702174 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
702110 TTCATATATT
* *
702120 ATTACGAATATACATGCTTAAATAAAATG
1 ATTAAGAATATACATGCAT-AATAAAATG
*
702149 ATTAAGAATATCCATGCATAATAAAA
1 ATTAAGAATATACATGCATAATAAAA
702175 GGTATAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (28 bp):
ATTAAGAATATACATGCATAATAAAATG
Found at i:704861 original size:21 final size:21
Alignment explanation
Indices: 704818--704861 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
704808 GATGCATTGG
* **
704818 TTGGATGAAAGAAGGTATTTT
1 TTGGATGAAAAAAGGTAACTT
*
704839 TTGGATGAAAAAATGTAACTT
1 TTGGATGAAAAAAGGTAACTT
704860 TT
1 TT
704862 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAAGGTAACTT
Found at i:706772 original size:24 final size:22
Alignment explanation
Indices: 706745--706801 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
706735 TTTATTTATT
706745 TATTTGATATTTAAAATTTTTAAA
1 TATTT-ATATTTAAAA-TTTTAAA
* *
706769 TATTAAATATTTATAATTTTAAA
1 TATT-TATATTTAAAATTTTAAA
706792 -ATTTATATTT
1 TATTTATATTT
706802 GCATATGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.21
22 3 0.10
23 7 0.24
24 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTATATTTAAAATTTTAAA
Found at i:706795 original size:15 final size:15
Alignment explanation
Indices: 706754--706798 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
706744 TTATTTGATA
*
706754 TTTAAAATTTTTAAAT
1 TTTAAAATTTAT-AAT
*
706770 ATTAAATATTTATAAT
1 TTTAAA-ATTTATAAT
706786 TTTAAAATTTATA
1 TTTAAAATTTATA
706799 TTTGCATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAAATTTATAAT
Found at i:707682 original size:36 final size:36
Alignment explanation
Indices: 707629--707705 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 36
707619 TATTATAATT
**
707629 TTTAATTTAATTTTTTAA-AATATAT-TTTT-TTAAAA
1 TTTAATTTAATGATTTAATAAT-TATCTTTTATT-AAA
707664 TTTAATCTTAATGATTTAATAATTATCTTTTATTAAA
1 TTTAAT-TTAATGATTTAATAATTATCTTTTATTAAA
707701 TTTAA
1 TTTAA
707706 AAATATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
35 6 0.17
36 13 0.36
37 15 0.42
38 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (36 bp):
TTTAATTTAATGATTTAATAATTATCTTTTATTAAA
Found at i:707744 original size:14 final size:15
Alignment explanation
Indices: 707724--707761 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
707714 ATAACTTAAA
707724 ATATATTTTAATATT
1 ATATATTTTAATATT
*
707739 -TATATTGTAATATT
1 ATATATTTTAATATT
707753 ATATATTTT
1 ATATATTTT
707762 TTAAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
ATATATTTTAATATT
Found at i:709281 original size:18 final size:18
Alignment explanation
Indices: 709258--709292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
709248 ATTGCAGTTT
* *
709258 CAGCTACTGAAGCAACAG
1 CAGCTAATGAAACAACAG
709276 CAGCTAATGAAACAACA
1 CAGCTAATGAAACAACA
709293 AAACTCGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (18 bp):
CAGCTAATGAAACAACAG
Found at i:710139 original size:2 final size:2
Alignment explanation
Indices: 710132--710168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
710122 TAGAATAGAC
710132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
710169 GGTTAAGAAG
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:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:717902 original size:20 final size:20
Alignment explanation
Indices: 717863--717919 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
717853 TAACAATCTT
*
717863 AAATATCCAAAAAT--AAAA
1 AAATATCTAAAAATAAAAAA
717881 AAATATCTAAAAATAAAAAA
1 AAATATCTAAAAATAAAAAA
* *
717901 AAATATCTGAGAATAAAAA
1 AAATATCTAAAAATAAAAA
717920 TGTGATGACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 13 0.38
20 21 0.62
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.19
Consensus pattern (20 bp):
AAATATCTAAAAATAAAAAA
Done.