Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold379
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: 674618
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.31
Warning! 39194 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:599425 original size:350 final size:346
Alignment explanation
Indices: 598788--599487 Score: 1231
Period size: 350 Copynumber: 2.0 Consensus size: 346
598778 AATATAAACC
* * *
598788 CTAACATGAATTAGCGGTAGAATAAGCTAAAACGAGCTACGAGGACTCCAAAAACGTAAAAAAAT
1 CTAACATGAATTAACGGTAGAATAAGCTAAAACGAGCTACGAGGACTCCAAAAACATAAAAAAAA
*
598853 AAAAAAACGAGGCTTGGATCACTTACTATGAGCTTGAGAAAATGAAGAAACCATAGCTATGGAGT
66 AAAAAAACGAGGCTTGGATCACTTACTATGAGCTTGAGAAAATGAAAAAACCATAGCTATGGAGT
* *
598918 CCCTTGAAGTTTCGGCCCTTATCGAAGAAGATGAGCACATTTTGTCATCTTTTACCCTTTAATTC
131 CCCTTGAAGTTTCGGCCCTTATCGAAGAAGATGAGCACATTTTGCCATATTTTACCCTTTAATTC
598983 TTTTTATTACCAAAGGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGCATGCC
196 TTTTTATTACCAAAGGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGCATGCC
*
599048 CATTTTTGTCAATGAAAATCTAATGGTCTAATTACCATTTAAGGACCTCTACTTCAATTATGCAC
261 CATTTTTGTCAATGAAAATCTAATGGTCTAATTACCATTTAAGGACCTCTACTTCAATAATGCAC
599113 TTCTATTAAATCCTTTATCAT
326 TTCTATTAAATCCTTTATCAT
* *
599134 CTAACATGAATTAATGGTAGAATAAGCTAAACCGAGCTACGAGGACTCCAAAAACATAAAAAAAA
1 CTAACATGAATTAACGGTAGAATAAGCTAAAACGAGCTACGAGGACTCCAAAAACATAAAAAAAA
*
599199 ACATTAAAAAC-AGGGCTTGGATGCACTTACTATGAGCTTGAGAAAATGAAAAAACCCTAGCTAT
66 A-A--AAAAACGA-GGCTTGGAT-CACTTACTATGAGCTTGAGAAAATGAAAAAACCATAGCTAT
*
599263 GGAGTCCCTTGAAGTTTCGGCCCTTATCGAAGAAGATGAGCACATTTTGCCATATTTTTCCCTTT
126 GGAGTCCCTTGAAGTTTCGGCCCTTATCGAAGAAGATGAGCACATTTTGCCATATTTTACCCTTT
*
599328 AATTCTTTTTATTACCAAATGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGC
191 AATTCTTTTTATTACCAAAGGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGC
*
599393 ATGCCCATTTTTGTCCATGAAAATCTAATGGTCTAATTACCATTTAAGGACCTCTACTTCAATAA
256 ATGCCCATTTTTGTCAATGAAAATCTAATGGTCTAATTACCATTTAAGGACCTCTACTTCAATAA
599458 TGCACTTCTATTAAATCCTTTATCAT
321 TGCACTTCTATTAAATCCTTTATCAT
599484 CTAA
1 CTAA
599488 AGCTCATATT
Statistics
Matches: 336, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
346 61 0.18
347 1 0.00
348 1 0.00
349 15 0.04
350 258 0.77
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (346 bp):
CTAACATGAATTAACGGTAGAATAAGCTAAAACGAGCTACGAGGACTCCAAAAACATAAAAAAAA
AAAAAAACGAGGCTTGGATCACTTACTATGAGCTTGAGAAAATGAAAAAACCATAGCTATGGAGT
CCCTTGAAGTTTCGGCCCTTATCGAAGAAGATGAGCACATTTTGCCATATTTTACCCTTTAATTC
TTTTTATTACCAAAGGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGCATGCC
CATTTTTGTCAATGAAAATCTAATGGTCTAATTACCATTTAAGGACCTCTACTTCAATAATGCAC
TTCTATTAAATCCTTTATCAT
Found at i:605686 original size:20 final size:20
Alignment explanation
Indices: 605661--605699 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
605651 TACTTTATTC
605661 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
605681 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
605700 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:610151 original size:15 final size:15
Alignment explanation
Indices: 610133--610161 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
610123 GATGTTTTAT
610133 TTGACCATGTTAAAC
1 TTGACCATGTTAAAC
610148 TTGACCATGTTAAA
1 TTGACCATGTTAAA
610162 GAGGGCGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTGACCATGTTAAAC
Found at i:613321 original size:3 final size:3
Alignment explanation
Indices: 613313--613343 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
613303 CATAAATTTA
613313 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
613344 GTAAGAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:616144 original size:20 final size:22
Alignment explanation
Indices: 616119--616158 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
616109 ATCCCTATAC
*
616119 TTTTTAGATT-TATA-AACCTG
1 TTTTTAAATTATATATAACCTG
616139 TTTTTAAATTATATATAACC
1 TTTTTAAATTATATATAACC
616159 GCGCAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTTAAATTATATATAACCTG
Found at i:619750 original size:22 final size:22
Alignment explanation
Indices: 619722--619765 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
619712 TTTTGAACCA
619722 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
619744 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
619766 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:625162 original size:18 final size:17
Alignment explanation
Indices: 625141--625184 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
625131 ACTAAATATC
625141 ATAAATAAAAAAATAAA
1 ATAAATAAAAAAATAAA
* *
625158 GATAAAGCATAAAAATAAA
1 -ATAAA-TAAAAAAATAAA
625177 ATAAATAA
1 ATAAATAA
625185 CCATATGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
17 1 0.05
18 10 0.48
19 10 0.48
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (17 bp):
ATAAATAAAAAAATAAA
Found at i:632695 original size:62 final size:57
Alignment explanation
Indices: 632619--632761 Score: 162
Period size: 57 Copynumber: 2.4 Consensus size: 57
632609 AATTGACGGT
* *
632619 AAAAAGGATCTAGCCCGAATGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAAGGATCTAGCCCGAACGGGTGAT-C--T--TGATATAGCCCTCCCAAAGAATATGTG-G
*
632682 AAAAA-GATCTAGCCCGGACGGGTGATCTTGATATAGCCCTCCCAAAGAATATGTGG
1 AAAAAGGATCTAGCCCGAACGGGTGATCTTGATATAGCCCTCCCAAAGAATATGTGG
* * * *
632738 AAAATGGATTTAGCCTGGACGGGT
1 AAAAAGGATCTAGCCCGAACGGGT
632762 AATCCGACTT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
56 5 0.07
57 42 0.58
59 1 0.01
61 1 0.01
62 19 0.26
63 5 0.07
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (57 bp):
AAAAAGGATCTAGCCCGAACGGGTGATCTTGATATAGCCCTCCCAAAGAATATGTGG
Found at i:632730 original size:57 final size:57
Alignment explanation
Indices: 632653--632761 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
632643 GATCCTATCC
*
632653 TGATATAGCCCTCCCGAAGAATATGTGTGAAAA-AGATCTAGCCCGGACGGGTGATCT
1 TGATATAGCCCTCCCAAAGAATATGTG-GAAAATAGATCTAGCCCGGACGGGTGATCT
* * *
632710 TGATATAGCCCTCCCAAAGAATATGTGGAAAATGGATTTAGCCTGGACGGGT
1 TGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGT
632762 AATCCGACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
56 5 0.11
57 42 0.89
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (57 bp):
TGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGTGATCT
Found at i:636522 original size:33 final size:33
Alignment explanation
Indices: 636484--636549 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
636474 TTTAAATATC
636484 TTTCCTATTTATCATGAACTATCATTATAATTT
1 TTTCCTATTTATCATGAACTATCATTATAATTT
*
636517 TTTCCTATTTATCATGATCTATCATTATAATTT
1 TTTCCTATTTATCATGAACTATCATTATAATTT
636550 ATGCATGTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (33 bp):
TTTCCTATTTATCATGAACTATCATTATAATTT
Found at i:640837 original size:9 final size:11
Alignment explanation
Indices: 640804--640834 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
640794 TTATTTCTTT
640804 AAATTTCTCTC
1 AAATTTCTCTC
640815 AAATTTCTCTC
1 AAATTTCTCTC
640826 AAATTTCTC
1 AAATTTCTC
640835 AAAGCTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATTTCTCTC
Found at i:642625 original size:18 final size:18
Alignment explanation
Indices: 642602--642644 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
642592 TACCAGGTGC
*
642602 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
642620 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
642638 GTTTCCT
1 GTATCCT
642645 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:642909 original size:21 final size:21
Alignment explanation
Indices: 642885--642925 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
642875 CCAACACCTA
642885 CAACCACAACCCCCACCGGAG
1 CAACCACAACCCCCACCGGAG
*
642906 CAACCACAACCCCCGCCGGA
1 CAACCACAACCCCCACCGGA
642926 AGCTTAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.54, G:0.15, T:0.00
Consensus pattern (21 bp):
CAACCACAACCCCCACCGGAG
Found at i:643082 original size:24 final size:24
Alignment explanation
Indices: 643055--643110 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
643045 CATTTAATAA
*
643055 AATAAAAGTTGTTTTTA-ATATTTT
1 AATAAAAGTTATTTTTATAT-TTTT
* *
643079 AATAGTAATTTATTTTTATATTTTT
1 AATA-AAAGTTATTTTTATATTTTT
643104 AATAAAA
1 AATAAAA
643111 TAGAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 6 0.23
25 18 0.69
26 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (24 bp):
AATAAAAGTTATTTTTATATTTTT
Found at i:646568 original size:19 final size:20
Alignment explanation
Indices: 646544--646581 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
646534 ACTACAGTTA
646544 TTCAAA-AG-TGTAATGTTGT
1 TTCAAATAGTTGTAA-GTTGT
646563 TTCAAATAGTTGTAAGTTG
1 TTCAAATAGTTGTAAGTTG
646582 GATTCGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (20 bp):
TTCAAATAGTTGTAAGTTGT
Found at i:650089 original size:12 final size:12
Alignment explanation
Indices: 650061--650102 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
650051 CCATTTTTTT
650061 ATTTTTTATATA
1 ATTTTTTATATA
*
650073 A-TTTTAATATA
1 ATTTTTTATATA
650084 ATTTTTTATATA
1 ATTTTTTATATA
*
650096 AATTTTT
1 ATTTTTT
650103 CACCTATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTTTATATA
Found at i:650090 original size:13 final size:12
Alignment explanation
Indices: 650061--650102 Score: 59
Period size: 11 Copynumber: 3.5 Consensus size: 12
650051 CCATTTTTTT
650061 ATTTTTTATATA
1 ATTTTTTATATA
*
650073 A-TTTTAATATA
1 ATTTTTTATATA
650084 ATTTTTTATATAA
1 ATTTTTTATAT-A
650097 ATTTTT
1 ATTTTT
650103 CACCTATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 10 0.38
12 9 0.35
13 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTTTATATA
Found at i:650727 original size:25 final size:26
Alignment explanation
Indices: 650668--650728 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
650658 TGAAAACAGA
650668 GTGAACAAAACAAAACCACGAAAACT
1 GTGAACAAAACAAAACCACGAAAACT
* * *
650694 AT-AGGCAAAACAAAACCAC-AAAATT
1 GTGA-ACAAAACAAAACCACGAAAACT
650719 GTGAACAAAA
1 GTGAACAAAA
650729 TTGCGATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.10
Consensus pattern (26 bp):
GTGAACAAAACAAAACCACGAAAACT
Found at i:653028 original size:2 final size:2
Alignment explanation
Indices: 653023--653090 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
653013 TATATATGTA
* *
653023 TG TG TG TG TG CG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
653065 TG TG CG TG CG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
653091 CGTGGCTTAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.06, G:0.50, T:0.44
Consensus pattern (2 bp):
TG
Found at i:653046 original size:18 final size:18
Alignment explanation
Indices: 653023--653094 Score: 117
Period size: 18 Copynumber: 4.0 Consensus size: 18
653013 TATATATGTA
653023 TGTGTGTGTGCGTGCGTG
1 TGTGTGTGTGCGTGCGTG
* *
653041 TGTGTGTGTGTGTGTGTG
1 TGTGTGTGTGCGTGCGTG
653059 TGTGTGTGTGCGTGCGTG
1 TGTGTGTGTGCGTGCGTG
*
653077 TGTGTGTGTGTGTGCGTG
1 TGTGTGTGTGCGTGCGTG
653095 GCTTAGCCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.00, C:0.07, G:0.50, T:0.43
Consensus pattern (18 bp):
TGTGTGTGTGCGTGCGTG
Found at i:661183 original size:29 final size:29
Alignment explanation
Indices: 661150--661215 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
661140 GTTACAAGAT
661150 ATATCAGATATAGATAAATGAT-ATATCAG
1 ATATCAGATATAGATAAA-GATCATATCAG
*
661179 ATATCAGATATAGATACAGATCATATCAG
1 ATATCAGATATAGATAAAGATCATATCAG
661208 ATA-CAGAT
1 ATATCAGAT
661216 GAAGATTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 8 0.23
29 27 0.77
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.29
Consensus pattern (29 bp):
ATATCAGATATAGATAAAGATCATATCAG
Found at i:661188 original size:16 final size:15
Alignment explanation
Indices: 661169--661215 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
661159 ATAGATAAAT
661169 GATATATCAGATATCA
1 GATATATCAGATA-CA
661185 G--ATAT-AGATACA
1 GATATATCAGATACA
661197 GATCATATCAGATACA
1 GAT-ATATCAGATACA
661213 GAT
1 GAT
661216 GAAGATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.11
13 5 0.19
14 4 0.15
15 4 0.15
16 11 0.41
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (15 bp):
GATATATCAGATACA
Found at i:661194 original size:22 final size:22
Alignment explanation
Indices: 661093--661188 Score: 122
Period size: 22 Copynumber: 4.3 Consensus size: 22
661083 GAATACATAA
* *
661093 ACAGAAACAAGATATATCATAT
1 ACAGATACAAGATATATCAGAT
*
661115 ACAGTTACAAGATATATCAGAT
1 ACAGATACAAGATATATCAGAT
*
661137 ACAGTTACAAGATATATCAGAT
1 ACAGATACAAGATATATCAGAT
*
661159 ATAGATA-AATGATATATCAGAT
1 ACAGATACAA-GATATATCAGAT
661181 ATCAGATA
1 A-CAGATA
661189 TAGATACAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
21 2 0.03
22 59 0.89
23 5 0.08
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.27
Consensus pattern (22 bp):
ACAGATACAAGATATATCAGAT
Found at i:662554 original size:108 final size:109
Alignment explanation
Indices: 662418--662636 Score: 431
Period size: 108 Copynumber: 2.0 Consensus size: 109
662408 TAGCATCACA
662418 ACGGAATGTAACGTAACAGATTCCGCAACCAATCGATGCGACCAAGAGGAAAAAGAAATTGATTC
1 ACGGAATGTAACGTAACAGATTCCGCAACCAATCGATGCGACCAAGAGGAAAAAGAAATTGATTC
662483 GAAGCAAAGAAGAGTAAAAAGAAAGGAACGATAGAAAAAAAAAG
66 GAAGCAAAGAAGAGTAAAAAGAAAGGAACGATAGAAAAAAAAAG
662527 ACGGAATGTAA-GTAACAGATTCCGCAACCAATCGATGCGACCAAGAGGAAAAAGAAATTGATTC
1 ACGGAATGTAACGTAACAGATTCCGCAACCAATCGATGCGACCAAGAGGAAAAAGAAATTGATTC
662591 GAAGCAAAGAAGAGTAAAAAGAAAGGAACGATAGAAAAAAAAAG
66 GAAGCAAAGAAGAGTAAAAAGAAAGGAACGATAGAAAAAAAAAG
662635 AC
1 AC
662637 ATGTTGAAAC
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 99 0.90
109 11 0.10
ACGTcount: A:0.52, C:0.14, G:0.23, T:0.12
Consensus pattern (109 bp):
ACGGAATGTAACGTAACAGATTCCGCAACCAATCGATGCGACCAAGAGGAAAAAGAAATTGATTC
GAAGCAAAGAAGAGTAAAAAGAAAGGAACGATAGAAAAAAAAAG
Found at i:666610 original size:4 final size:4
Alignment explanation
Indices: 666601--666648 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
666591 ATCTTAATTC
* * * * *
666601 TTTA TTTA TTCA TTTA TTTA TTTG TTTG CTTA TTTA TATA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
666649 AAACTTTGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:666766 original size:2 final size:2
Alignment explanation
Indices: 666759--666786 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
666749 TATAACTTTA
666759 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
666787 GTACATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:668798 original size:9 final size:9
Alignment explanation
Indices: 668784--668808 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
668774 TGCAAATGCT
668784 ATAATAACA
1 ATAATAACA
668793 ATAATAACA
1 ATAATAACA
668802 ATAATAA
1 ATAATAA
668809 ATACATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:671203 original size:44 final size:43
Alignment explanation
Indices: 671034--671333 Score: 105
Period size: 44 Copynumber: 6.8 Consensus size: 43
671024 GGTAGATATG
* * *
671034 ATCTGAAATCTTCAATCTATTCCACTGTTGTCCAAGGA-AGTAGA
1 ATCTGAAATCTTCAATCTACTCCACTGTTGCCCAGGGAGA-TA-A
* * * ** *
671078 AT-T-ACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAA
1 ATCTGA-AATCTTCAATCTACTCCACTGTTGCC-CAGGGAGAT-AA
* ** * * * **
671122 ATCCGCCATCTTCGATCTACCCCACTATTGCTTAGGGAGATAA
1 ATCTGAAATCTTCAATCTACTCCACTGTTGCCCAGGGAGATAA
*
671165 TATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGA-AGTAGA
1 -ATCTGAAATCTTCAATCTACTCCACTGTTGCCCAGGGAGA-TA-A
* * * ** *
671210 AT-T--ATTGGCTTCAATGTACTCCACT-ATAACCAGAAGGAGGTAAA
1 ATCTGAAAT--CTTCAATCTACTCCACTGTTGCCCAG--GGAGAT-AA
* ** * * **
671254 ATCCGCCATCTTCGATCTGCTCCACT-TCTGCTTAGGGAGATAA
1 ATCTGAAATCTTCAATCTACTCCACTGT-TGCCCAGGGAGATAA
* *
671297 GATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGG
1 -ATCTGAAATCTTCAATCTACTCCACTGTTGCCCAGG
671334 AAAGTAGAAT
Statistics
Matches: 176, Mismatches: 59, Indels: 42
0.64 0.21 0.15
Matches are distributed among these distances:
41 2 0.01
42 6 0.03
43 41 0.23
44 88 0.50
45 35 0.20
46 3 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (43 bp):
ATCTGAAATCTTCAATCTACTCCACTGTTGCCCAGGGAGATAA
Found at i:671206 original size:132 final size:132
Alignment explanation
Indices: 670972--671543 Score: 948
Period size: 132 Copynumber: 4.3 Consensus size: 132
670962 NNNNNNNCTG
* * *
670972 TAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTATTGCTTAGGTAGATATGATC
1 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATC
* *
671037 TGAAATCTTCAATCTATTCCACTGTTGTCCAAGGAAGTAGAATTACTAGCTTCAATGTACTCCAC
66 TGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCAC
*
671102 TG
131 TA
* * *
671104 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACCCCACTATTGCTTAGGGAGATAATATC
1 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATC
* *
671169 TGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCAC
66 TGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCAC
671234 TA
131 TA
* *
671236 TAACCAGAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT-TCTGCTTAGGGAGATAAGAT
1 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAT-TGCTTAGGGAGATAAGAT
*
671300 CTGAAATCTTCAATCTATTCCACTGTTGTCCAGGAAAGTAGAATTACTGGCTTCAATGTACTCCA
65 CTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCA
671365 CTA
130 CTA
* * * * *
671368 TAACCAGAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGATTAAGGAGATAAGATC
1 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATC
671433 TGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCAC
66 TGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCAC
671498 TA
131 TA
*
671500 TAACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACT
1 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
671544 GTCAATGCAA
Statistics
Matches: 412, Mismatches: 26, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 411 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATC
TGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCAC
TA
Done.