Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold95
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: 582947
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Warning! 25 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:531945 original size:3 final size:3
Alignment explanation
Indices: 531939--531970 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
531929 ATTATAAAAA
*
531939 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
531971 ATAAGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:532428 original size:2 final size:2
Alignment explanation
Indices: 532421--532460 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
532411 TATATCTTGA
532421 AT 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 AT
532461 GAGATAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533840 original size:19 final size:20
Alignment explanation
Indices: 533818--533861 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
533808 ATTTGATCCC
*
533818 TTTTAAGAAAAATT-AATTT
1 TTTTAAAAAAAATTCAATTT
*
533837 TTTTAAAAAAAATTCGATTT
1 TTTTAAAAAAAATTCAATTT
533857 TTTTA
1 TTTTA
533862 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTAAAAAAAATTCAATTT
Found at i:534267 original size:21 final size:20
Alignment explanation
Indices: 534242--534301 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
534232 GTAATCTGAC
534242 TTTATTTAATTTAAATTATT
1 TTTATTTAATTTAAATTATT
* ** *
534262 ATTTATATAATAAAAAATATT
1 -TTTATTTAATTTAAATTATT
534283 TTTATTTAAATTT-AATTAT
1 TTTATTT-AATTTAAATTAT
534302 AAAAATATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTTAATTTAAATTATT
Found at i:536104 original size:22 final size:22
Alignment explanation
Indices: 536079--536121 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
536069 TATTTTTATT
*
536079 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TACAAAAATATA
536101 TAAATATTAATACAAAAATAT
1 TAAATATTAATACAAAAATAT
536122 TATTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATTAATACAAAAATATA
Found at i:537035 original size:22 final size:22
Alignment explanation
Indices: 537010--537054 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
537000 ATTTATTTCT
*
537010 TTTAAAAAT-TTAATTATGAAAA
1 TTTAAAAATGTTAA-TATAAAAA
537032 TTTAAAAATGTTAATATAAAAA
1 TTTAAAAATGTTAATATAAAAA
537054 T
1 T
537055 AATATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTAAAAATGTTAATATAAAAA
Found at i:537588 original size:18 final size:17
Alignment explanation
Indices: 537567--537600 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
537557 TTAACAGTAT
*
537567 ATTTTATATTATAATTTA
1 ATTTAATATTA-AATTTA
537585 ATTTAATATTAAATTT
1 ATTTAATATTAAATTT
537601 TTTCATGTTA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:538040 original size:15 final size:15
Alignment explanation
Indices: 537985--538041 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
537975 TAATTTTTTT
*
537985 ATTATTTTTAAAAAA
1 ATTATATTTAAAAAA
**
538000 ATT-TATATTAAATCA
1 ATTATAT-TTAAAAAA
* *
538015 ATTCTAATTAAAAAA
1 ATTATATTTAAAAAA
538030 ATTATATTTAAA
1 ATTATATTTAAA
538042 TTTAACTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 2 0.06
15 28 0.88
16 2 0.06
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTATATTTAAAAAA
Found at i:538392 original size:5 final size:5
Alignment explanation
Indices: 538359--538400 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
538349 AAATAATTAA
*
538359 AATAT AATAT AATAT AAAAT -ATAT AAATAT AATAT AAATAT A
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT -AATAT A
538401 TTAATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.62
6 9 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:538399 original size:11 final size:11
Alignment explanation
Indices: 538333--538400 Score: 68
Period size: 11 Copynumber: 6.1 Consensus size: 11
538323 AATTATTTAA
*
538333 AATATAAATAA
1 AATATAAATAT
*
538344 AATAAAAATAATT
1 AATATAAAT-A-T
*
538357 AAAATATAATAT
1 AATATA-AATAT
538369 AATATAAA-AT
1 AATATAAATAT
538379 -ATATAAATAT
1 AATATAAATAT
538389 AATATAAATAT
1 AATATAAATAT
538400 A
1 A
538401 TTAATTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 7 0.15
10 4 0.09
11 21 0.45
12 7 0.15
13 5 0.11
14 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATATAAATAT
Found at i:538721 original size:24 final size:22
Alignment explanation
Indices: 538652--538728 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 22
538642 TAGTATAATT
*
538652 ATATAA-ATAAAATAAAGTTAAA
1 ATATAATATAGAATAAA-TTAAA
* *
538674 ATATAATATATAAAATAATATAAA
1 ATATAATATAGAATA-AAT-TAAA
538698 ATATTAATATACGAATAAATT-AA
1 ATA-TAATATA-GAATAAATTAAA
538721 AT-TAATAT
1 ATATAATAT
538729 TGTATAAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 6 0.13
22 6 0.13
23 11 0.24
24 10 0.22
25 10 0.22
26 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (22 bp):
ATATAATATAGAATAAATTAAA
Found at i:540673 original size:24 final size:24
Alignment explanation
Indices: 540643--540692 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
540633 TTTAAACTTC
540643 AAATTTATTAAATATTATCTTTTT
1 AAATTTATTAAATATTATCTTTTT
*
540667 AAATTTATTAAATATTATTTTTTT
1 AAATTTATTAAATATTATCTTTTT
540691 AA
1 AA
540693 TATAATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATTTATTAAATATTATCTTTTT
Found at i:540700 original size:24 final size:24
Alignment explanation
Indices: 540643--540700 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
540633 TTTAAACTTC
*
540643 AAATTTATTAAATATTATCTTTTT
1 AAATTAATTAAATATTATCTTTTT
*
540667 AAATTTATTAAATATTAT-TTTTT
1 AAATTAATTAAATATTATCTTTTT
*
540690 TAATATAATTA
1 AAAT-TAATTA
540701 TATCAAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATTAATTAAATATTATCTTTTT
Found at i:542166 original size:16 final size:16
Alignment explanation
Indices: 542106--542171 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
542096 AATACGAATG
*
542106 TTAAAT-ATAAATATTT
1 TTAAATAATAAA-AATT
*
542122 TTAAAAAATAAAAATT
1 TTAAATAATAAAAATT
542138 TTAAATAATAAAAATT
1 TTAAATAATAAAAATT
* *
542154 TTAACTTAAAAAAAATT
1 TTAA-ATAATAAAAATT
542171 T
1 T
542172 AATTATATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
16 27 0.63
17 16 0.37
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAATAATAAAAATT
Found at i:543474 original size:20 final size:19
Alignment explanation
Indices: 543449--543506 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
543439 TGTCAAAAAA
*
543449 TATTATAATTTATGTATTAG
1 TATTAT-ATTTATATATTAG
*
543469 TATTATATTTATATATT-T
1 TATTATATTTATATATTAG
543487 TATTAT-TTTATA-ATTA-
1 TATTATATTTATATATTAG
543503 TATT
1 TATT
543507 TAACGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.20
17 6 0.17
18 6 0.17
19 10 0.29
20 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTATATTTATATATTAG
Found at i:543507 original size:29 final size:29
Alignment explanation
Indices: 543470--543529 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
543460 ATGTATTAGT
543470 ATTATATTTATA-TATTTTATTATTT-TATA
1 ATTATATTTA-ACTATTTTA-TATTTATATA
543499 ATTATATTTAACGTATTTTATATTTATATA
1 ATTATATTTAAC-TATTTTATATTTATATA
543529 A
1 A
543530 ATTTTGATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 1 0.04
29 15 0.54
30 12 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTATATTTAACTATTTTATATTTATATA
Found at i:544421 original size:27 final size:27
Alignment explanation
Indices: 544386--544438 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
544376 AAAGTAGCAT
* *
544386 ATACGGTGCATTTGCTTTATATGTTTC
1 ATACAGTGCATCTGCTTTATATGTTTC
*
544413 ATACAGTGCGTCTGCTTTATATGTTT
1 ATACAGTGCATCTGCTTTATATGTTT
544439 AAAAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (27 bp):
ATACAGTGCATCTGCTTTATATGTTTC
Found at i:546852 original size:25 final size:25
Alignment explanation
Indices: 546792--546852 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
546782 TAAATAAATA
546792 AATTAAATAATTTAACTAAAATTTTAT
1 AATTAAA-AATTTAAC-AAAATTTTAT
*
546819 AATATAAAATTTTAA-AAAATTTTAT
1 AAT-TAAAAATTTAACAAAATTTTAT
546844 AATTAAAAA
1 AATTAAAAA
546853 GAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 5 0.16
25 13 0.42
27 9 0.29
28 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AATTAAAAATTTAACAAAATTTTAT
Found at i:547407 original size:29 final size:30
Alignment explanation
Indices: 547343--547409 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
547333 TTAAAATTTA
*
547343 TATAA-AT-ATAAAATACTTTAAATATAAT
1 TATAATATAATAAAATACTATAAATATAAT
*
547371 TATTATATAATAAAATA-TATAAATATAA-
1 TATAATATAATAAAATACTATAAATATAAT
547399 TATGAATATAA
1 TAT-AATATAA
547410 AATTTATAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 7 0.21
29 18 0.55
30 8 0.24
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (30 bp):
TATAATATAATAAAATACTATAAATATAAT
Found at i:550766 original size:17 final size:17
Alignment explanation
Indices: 550744--550776 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
550734 TTAAAAATGT
550744 TAAAAATCA-AATAAATA
1 TAAAAAT-ATAATAAATA
550761 TAAAAATATAATAAAT
1 TAAAAATATAATAAAT
550777 TATTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAATATAATAAATA
Found at i:552487 original size:20 final size:22
Alignment explanation
Indices: 552434--552488 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
552424 TTTTTTAATT
552434 TAAA-TTTAATTATAAAAATATA
1 TAAATTTTAA-TATAAAAATATA
*
552456 TAAATATTAATATAAAAA-ATA
1 TAAATTTTAATATAAAAATATA
*
552477 -AATTTTTAATAT
1 TAAATTTTAATAT
552489 TTAATTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.34
21 3 0.10
22 12 0.41
23 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTTAATATAAAAATATA
Found at i:554745 original size:20 final size:20
Alignment explanation
Indices: 554706--554749 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
554696 TGTATCTTTC
554706 TTTTCTTTAGCTTGTAATTT
1 TTTTCTTTAGCTTGTAATTT
* *
554726 ATTTTTTTTAG-TTTTAATTT
1 -TTTTCTTTAGCTTGTAATTT
554746 TTTT
1 TTTT
554750 AATTTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTCTTTAGCTTGTAATTT
Found at i:554746 original size:15 final size:15
Alignment explanation
Indices: 554723--554756 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
554713 TAGCTTGTAA
* *
554723 TTTATTTTTTTTAGT
1 TTTAATTTTTTTAAT
554738 TTTAATTTTTTTAAT
1 TTTAATTTTTTTAAT
554753 TTTA
1 TTTA
554757 TTCAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTAATTTTTTTAAT
Found at i:555443 original size:79 final size:74
Alignment explanation
Indices: 555341--555482 Score: 187
Period size: 79 Copynumber: 1.9 Consensus size: 74
555331 AGAAAATAAA
* *
555341 TGGAAATGAGGACATGAGTTTTATAGAGAATTGAGTAATAAGTTTGTTTTTTTTTTTGTTATAAG
1 TGGAAATGAGGACATGAGTTTTATACACAATTGAGTAATAA-----TTTTTTTTTTTGTTATAAG
555406 TAACAACTGCCTCG
61 TAACAACTGCCTCG
* *
555420 TGGAAATTG-GGATATGAGTTTTATACACACTTGAGTAATAATTTTTTTTTTTGTTATAAGTAA
1 TGGAAA-TGAGGACATGAGTTTTATACACAATTGAGTAATAATTTTTTTTTTTGTTATAAGTAA
555483 TAATTGACAT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
74 22 0.38
79 34 0.59
80 2 0.03
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (74 bp):
TGGAAATGAGGACATGAGTTTTATACACAATTGAGTAATAATTTTTTTTTTTGTTATAAGTAACA
ACTGCCTCG
Found at i:556281 original size:26 final size:24
Alignment explanation
Indices: 556239--556293 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
556229 TTGTATAAGA
*
556239 TTTTGATTTTTTTTAATTTC-ATT
1 TTTTGATTTTTTCTAATTTCTATT
556262 TATTTGATTTTTTAACTAATTTCTATT
1 T-TTTGATTTTTT--CTAATTTCTATT
556289 TTTTG
1 TTTTG
556294 TCCTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 11 0.41
26 11 0.41
27 4 0.15
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.69
Consensus pattern (24 bp):
TTTTGATTTTTTCTAATTTCTATT
Found at i:559080 original size:23 final size:21
Alignment explanation
Indices: 559041--559085 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
559031 TATATATATA
559041 TATAAATATAAATTTTAAAAT
1 TATAAATATAAATTTTAAAAT
*
559062 TATAAATATTTAATATTTAAAAT
1 TATAAATA-TAAAT-TTTAAAAT
559085 T
1 T
559086 CTTAATCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 4 0.19
23 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAATATAAATTTTAAAAT
Found at i:561521 original size:117 final size:117
Alignment explanation
Indices: 561311--561544 Score: 450
Period size: 117 Copynumber: 2.0 Consensus size: 117
561301 GACTTATGGG
*
561311 TGATGACGGAATATGGTGTAGCTGACTCTTGGGTTAAACAATTCACCATTGAAGTAATGTCCAAG
1 TGATGAAGGAATATGGTGTAGCTGACTCTTGGGTTAAACAATTCACCATTGAAGTAATGTCCAAG
*
561376 GTAGCGATTGGAGCATGACAAAGTCCAAGCAAATTGAGGAGCAACCAAAACC
66 GTAGCGATTGGAGCATGACAAAGACCAAGCAAATTGAGGAGCAACCAAAACC
561428 TGATGAAGGAATATGGTGTAGCTGACTCTTGGGTTAAACAATTCACCATTGAAGTAATGTCCAAG
1 TGATGAAGGAATATGGTGTAGCTGACTCTTGGGTTAAACAATTCACCATTGAAGTAATGTCCAAG
561493 GTAGCGATTGGAGCATGACAAAGACCAAGCAAATTGAGGAGCAACCAAAACC
66 GTAGCGATTGGAGCATGACAAAGACCAAGCAAATTGAGGAGCAACCAAAACC
561545 AAAGTTATTA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (117 bp):
TGATGAAGGAATATGGTGTAGCTGACTCTTGGGTTAAACAATTCACCATTGAAGTAATGTCCAAG
GTAGCGATTGGAGCATGACAAAGACCAAGCAAATTGAGGAGCAACCAAAACC
Found at i:561839 original size:39 final size:39
Alignment explanation
Indices: 561785--561906 Score: 199
Period size: 39 Copynumber: 3.1 Consensus size: 39
561775 GCTTGGTTTC
561785 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGA
1 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGA
561824 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGAAGA
1 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTC---AGAAGA
* *
561866 ATTGCCCGGGGAAAGTAAAAGTACGATGCTTTCAGAAGA
1 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGA
561905 AT
1 AT
561907 GAAATTGAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
39 41 0.53
42 37 0.47
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (39 bp):
ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGA
Found at i:561877 original size:42 final size:42
Alignment explanation
Indices: 561785--561905 Score: 203
Period size: 42 Copynumber: 3.0 Consensus size: 42
561775 GCTTGGTTTC
561785 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTC---AGAAGA
1 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGAAGA
561824 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGAAGA
1 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGAAGA
* *
561866 ATTGCCCGGGGAAAGTAAAAGTACGATGCTTTCAGAAGAA
1 ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGAA
561906 TGAAATTGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
39 33 0.43
42 44 0.57
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (42 bp):
ATTGCCTGGGGAAAGTACAAGTACGATGCTTTCAGAAGAAGA
Found at i:562550 original size:28 final size:27
Alignment explanation
Indices: 562494--562551 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
562484 ATTTATTTAT
* *
562494 ATTTTAATTAATTTTTACTAATGATTA
1 ATTTTAATTAAATTTTACTAATGAATA
*
562521 ATTTTAAATTAAATTTTATTAAAT-AATA
1 ATTTT-AATTAAATTTTACT-AATGAATA
562549 ATT
1 ATT
562552 ATTTATAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 18 0.69
29 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTTAATTAAATTTTACTAATGAATA
Found at i:563275 original size:2 final size:2
Alignment explanation
Indices: 563258--563293 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
563248 GGATTTCTTT
563258 TA TA T- TA TA T- 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 TA
563294 ATTTGTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:566405 original size:21 final size:21
Alignment explanation
Indices: 566381--566422 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
566371 AACAATTACC
566381 TAATATATAA-AAATATAAAAT
1 TAATATA-AATAAATATAAAAT
*
566402 TAATATAAATAATTATAAAAT
1 TAATATAAATAAATATAAAAT
566423 GATCACACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATATAAATAAATATAAAAT
Found at i:568275 original size:36 final size:33
Alignment explanation
Indices: 568210--568275 Score: 80
Period size: 36 Copynumber: 1.9 Consensus size: 33
568200 TACTATTTAA
*
568210 AATAATATAAAAATTAAAAAATATTTTTATATT
1 AATAATATAAAAATTAAAAAATATATTTATATT
568243 AATAATATAATTAAATTTAAATAAA-ATATTTAT
1 AATAATATAA--AAA-TTAAA-AAATATATTTAT
568276 TGTCATGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 10 0.36
35 3 0.11
36 12 0.43
37 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATAATATAAAAATTAAAAAATATATTTATATT
Found at i:572302 original size:27 final size:27
Alignment explanation
Indices: 572253--572310 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
572243 CCATTGGTCT
* *
572253 TAAATTTGAAAAATTAAATAAATTAAA
1 TAAATTTAAAAAATTAAATAAATAAAA
*
572280 TAAATTTAAAAAATT-GATCAAATAAAA
1 TAAATTTAAAAAATTAAAT-AAATAAAA
572307 TAAA
1 TAAA
572311 ATATGAGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
TAAATTTAAAAAATTAAATAAATAAAA
Found at i:572852 original size:17 final size:16
Alignment explanation
Indices: 572831--572870 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
572821 AAATATAAGT
572831 TTTTAAAAATTAAAAA
1 TTTTAAAAATTAAAAA
* *
572847 TATTTAACATTTAAAAA
1 T-TTTAAAAATTAAAAA
572864 TTTTAAA
1 TTTTAAA
572871 TATCAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTAAAAATTAAAAA
Found at i:573266 original size:132 final size:133
Alignment explanation
Indices: 573113--573374 Score: 481
Period size: 134 Copynumber: 2.0 Consensus size: 133
573103 GCTGCTTTGG
** *
573113 TTTATTGCCCTTCATTTTATAGTGTATAGTTTTA-CATGGTAAGTATATAAAAATATTTATTTTG
1 TTTATTGCCCTTCATTTTATAGCATATAGTTTTAGAATGGTAAGTATATAAAAATATTTATTTTG
573177 TGTAAAATGACTATAAATTCTAAGTTTAAGAGGATTTTATAATTAATATAATTTTTATGGAGTTA
66 TGTAAAATGACTATAAATTCTAAGTTTAAGAGGATTTTATAATTAATATAATTTTTATGGAGTTA
573242 ATA
131 ATA
573245 TTTATTGCCCTTCATTTTATAGCATATAGTTTTATGAATGGTAAGTATATAAAAATATTTATTTT
1 TTTATTGCCCTTCATTTTATAGCATATAGTTTTA-GAATGGTAAGTATATAAAAATATTTATTTT
573310 GTGTAAAATGACTATAAATTCTAAGTTTAAGAGGATTTTATAATTAATATAATTTTTATGGAGTT
65 GTGTAAAATGACTATAAATTCTAAGTTTAAGAGGATTTTATAATTAATATAATTTTTATGGAGTT
573375 TTTCAAAAAT
Statistics
Matches: 125, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
132 32 0.26
134 93 0.74
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.46
Consensus pattern (133 bp):
TTTATTGCCCTTCATTTTATAGCATATAGTTTTAGAATGGTAAGTATATAAAAATATTTATTTTG
TGTAAAATGACTATAAATTCTAAGTTTAAGAGGATTTTATAATTAATATAATTTTTATGGAGTTA
ATA
Found at i:576383 original size:106 final size:105
Alignment explanation
Indices: 576199--576392 Score: 289
Period size: 106 Copynumber: 1.8 Consensus size: 105
576189 TGTCAATATG
* * *
576199 CAATATTTAATGAATTAAAAGACCTTACAACTTCATATATGTCATGTATGTTGGCAACATGTCAT
1 CAATATTTAATGAATTAAAAGACCTTACAACTTCATAAATGTCATGTATGTTGACAACATGTCAC
576264 ACTTAATTTACCATATAATAATTAGGTGGTAGATTTTTTT
66 ACTTAATTTACCATATAATAATTAGGTGGTAGATTTTTTT
* * * ** * *
576304 CAATATTTAATGAAATTGAAAGACGTTACAATTTCATAAATGTCATGTATGTTGATGACGTGTTA
1 CAATATTTAATG-AATTAAAAGACCTTACAACTTCATAAATGTCATGTATGTTGACAACATGTCA
576369 CACTTAATTTACCATATAATAATT
65 CACTTAATTTACCATATAATAATT
576393 GAAAGATTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
105 12 0.15
106 66 0.85
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (105 bp):
CAATATTTAATGAATTAAAAGACCTTACAACTTCATAAATGTCATGTATGTTGACAACATGTCAC
ACTTAATTTACCATATAATAATTAGGTGGTAGATTTTTTT
Found at i:576546 original size:22 final size:20
Alignment explanation
Indices: 576518--576571 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
576508 TTTGTTCTTT
576518 TATATAAATATAAACACATTAA
1 TATATAAATATAAA-ACA-TAA
576540 TATATAAATAT-AAACATAA
1 TATATAAATATAAAACATAA
576559 -ATATAAATATAAA
1 TATATAAATATAAA
576572 TGTATAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
20 3 0.10
21 2 0.06
22 11 0.35
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
TATATAAATATAAAACATAA
Found at i:576560 original size:12 final size:12
Alignment explanation
Indices: 576543--576572 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
576533 ACATTAATAT
576543 ATAAATATAAAC
1 ATAAATATAAAC
*
576555 ATAAATATAAAT
1 ATAAATATAAAC
576567 ATAAAT
1 ATAAAT
576573 GTATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAAATATAAAC
Found at i:577711 original size:11 final size:11
Alignment explanation
Indices: 577697--577721 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
577687 ATGCATTTAA
577697 AAATTAAAATT
1 AAATTAAAATT
577708 AAATTAAAATT
1 AAATTAAAATT
577719 AAA
1 AAA
577722 ATTATATTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:577713 original size:5 final size:6
Alignment explanation
Indices: 577696--577725 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
577686 AATGCATTTA
577696 AAAATT AAAATT -AAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT AAAATT A
577726 TATTTTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:580560 original size:17 final size:17
Alignment explanation
Indices: 580540--580595 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
580530 ATTTTATATT
580540 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
* *
580557 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTTTTTTTTC
** * *
580574 TTCATCTTTTTTCTTTA
1 TTTTTCTTTTTTTTTTC
580591 TTTTT
1 TTTTT
580596 TACCTAACTC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:580587 original size:13 final size:11
Alignment explanation
Indices: 580538--580596 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
580528 CCATTTTATA
580538 TTTT-TTTCTT
1 TTTTCTTTCTT
*
580548 TTTTTTTTC-T
1 TTTTCTTTCTT
580558 TTTTCTTTCTT
1 TTTTCTTTCTT
*
580569 TCTTCTTCATCTT
1 TTTTCTT--TCTT
*
580582 TTTTCTTTATT
1 TTTTCTTTCTT
580593 TTTT
1 TTTT
580597 ACCTAACTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 13 0.32
11 18 0.44
13 10 0.24
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:580594 original size:11 final size:10
Alignment explanation
Indices: 580538--580596 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
580528 CCATTTTATA
580538 TTTTTTTCTTT
1 TTTTTTTC-TT
580549 TTTTTTTCTT
1 TTTTTTTCTT
*
580559 TTTCTTTCTT
1 TTTTTTTCTT
* * *
580569 TCTTCTTCAT
1 TTTTTTTCTT
*
580579 CTTTTTTCTT
1 TTTTTTTCTT
580589 TATTTTTT
1 T-TTTTTT
580597 ACCTAACTCT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 23 0.62
11 14 0.38
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:581889 original size:13 final size:13
Alignment explanation
Indices: 581871--581896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
581861 CAATTTTTGG
581871 TGTATCGATACAT
1 TGTATCGATACAT
581884 TGTATCGATACAT
1 TGTATCGATACAT
581897 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:581908 original size:32 final size:33
Alignment explanation
Indices: 581851--581915 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
581841 TACAAGCCAA
**
581851 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
581884 TGTATCGATAC-ATACTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
581916 CTTTTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Done.