Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012663.1 Corchorus capsularis cultivar CVL-1 contig12684, whole genome shotgun sequence
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: 58070
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:375 original size:16 final size:16
Alignment explanation
Indices: 350--380 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
340 TCTACAAATT
350 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
366 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
381 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:1824 original size:53 final size:53
Alignment explanation
Indices: 1765--1867 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
1755 CGGTTTTTTT
* *
1765 ATTTTATAAATTCTTTTAAGAAAATTGAGTTAAGAAATCAAATTTTGTTGCGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGCGA
1818 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTG
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTG
1868 TGAAATGATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (53 bp):
ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGCGA
Found at i:2622 original size:16 final size:16
Alignment explanation
Indices: 2601--2733 Score: 144
Period size: 16 Copynumber: 8.4 Consensus size: 16
2591 CAGACAGTTT
2601 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
2617 TTTCGGGTCA-TCTGGG
1 TTTCGGGTCATTC-GGG
* *
2633 -TTCGCGTTATTCGGG
1 TTTCGGGTCATTCGGG
*
2648 TTTCGTGTCATTCGGG
1 TTTCGGGTCATTCGGG
* *
2664 TCTCGGGTCATACGGG
1 TTTCGGGTCATTCGGG
*
2680 TTTCGGGTCATTTGGG
1 TTTCGGGTCATTCGGG
* * * *
2696 TCTCGAGTCATTTGTG
1 TTTCGGGTCATTCGGG
*
2712 TTCCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
2728 TTTCGG
1 TTTCGG
2734 ATCTACCGGG
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
15 12 0.13
16 83 0.87
ACGTcount: A:0.08, C:0.20, G:0.35, T:0.38
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:3023 original size:42 final size:42
Alignment explanation
Indices: 2977--3058 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
2967 TAGATATTAA
*
2977 TTTTGAATAATAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATAATAAATACATAATTAATTATCAGGTGAGGTAGG
* *
3019 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATAATAAATACATAATTAATTATCAGGTGAGGTA
3059 TGTGTCCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (42 bp):
TTTTGAATAATAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:3657 original size:16 final size:16
Alignment explanation
Indices: 3577--3664 Score: 97
Period size: 16 Copynumber: 5.4 Consensus size: 16
3567 GGTTAACTTC
*
3577 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
3593 TTGGAGTCATTCGGGTC
1 TCGG-GTCATTCGGGTT
3610 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
3626 TCGGGTCA-TCTAGGTT
1 TCGGGTCATTC-GGGTT
*
3642 ACGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
3658 TCAGGTC
1 TCGGGTC
3665 GGGCGGGTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
15 2 0.03
16 42 0.71
17 15 0.25
ACGTcount: A:0.10, C:0.18, G:0.35, T:0.36
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:5401 original size:49 final size:49
Alignment explanation
Indices: 5344--5441 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
5334 TGACATGTGT
5344 CGCGAATCTGGGTTTGATGGATGAGTCTACAGATAGAATATCATATATA
1 CGCGAATCTGGGTTTGATGGATGAGTCTACAGATAGAATATCATATATA
5393 CGCGAATCTGGGTTTGATGGATGAGTCTACAGATAGAATATCATATATA
1 CGCGAATCTGGGTTTGATGGATGAGTCTACAGATAGAATATCATATATA
5442 GACATAGACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (49 bp):
CGCGAATCTGGGTTTGATGGATGAGTCTACAGATAGAATATCATATATA
Found at i:5589 original size:5 final size:5
Alignment explanation
Indices: 5579--5604 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5569 GGAATTCATT
5579 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
5605 TTACCTGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:16380 original size:29 final size:30
Alignment explanation
Indices: 16334--16391 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
16324 ATTGTTCTTA
* *
16334 ATTTGGAAATTCAGGGGACAAAATGTCCTG
1 ATTTGGAAATTCAAGGGACAAAACGTCCTG
*
16364 ATTT-GAAGTTCAAGGGACAAAACGTCCT
1 ATTTGGAAATTCAAGGGACAAAACGTCCT
16392 TGACGCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (30 bp):
ATTTGGAAATTCAAGGGACAAAACGTCCTG
Found at i:18273 original size:15 final size:15
Alignment explanation
Indices: 18253--18293 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
18243 AATTTAATTG
18253 TTACTTTCCCTATAA
1 TTACTTTCCCTATAA
*
18268 TTACTTTCCCCATAA
1 TTACTTTCCCTATAA
18283 TTACTTTCCCT
1 TTACTTTCCCT
18294 GGAATCACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (15 bp):
TTACTTTCCCTATAA
Found at i:18315 original size:30 final size:30
Alignment explanation
Indices: 18253--18317 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
18243 AATTTAATTG
* * * * *
18253 TTACTTTCCCTATAATTACTTTCCCCATAA
1 TTACTTTCCCTAGAATCACTATCCCAAGAA
*
18283 TTACTTTCCCTGGAATCACTATCCCAAGAA
1 TTACTTTCCCTAGAATCACTATCCCAAGAA
18313 TTACT
1 TTACT
18318 CTCCTATGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.29, G:0.05, T:0.38
Consensus pattern (30 bp):
TTACTTTCCCTAGAATCACTATCCCAAGAA
Found at i:18493 original size:31 final size:30
Alignment explanation
Indices: 18392--18494 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 30
18382 GCCGGCTAAT
*
18392 TGCTCAAATAAGGGCCTAACGTTTTCCAAAA
1 TGCTCAAATAAGGCCCTAACG-TTTCCAAAA
* * *
18423 TGCTC-AATAAGGGCCCCATC-TTT--AAATT
1 TGCTCAAATAA-GGCCCTAACGTTTCCAAA-A
*
18451 TGGC-CAAATAAGGTCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGCCCTAACGTTT-CCAAAA
18482 TGCTCAAATAAGG
1 TGCTCAAATAAGG
18495 GCCTGTCTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
27 3 0.05
28 8 0.15
29 13 0.24
30 7 0.13
31 21 0.38
32 3 0.05
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGCCCTAACGTTTCCAAAA
Found at i:18565 original size:31 final size:29
Alignment explanation
Indices: 18529--18693 Score: 113
Period size: 31 Copynumber: 5.5 Consensus size: 29
18519 TGACACCGGC
18529 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTT-GA-AACGTTAGG
** * **
18560 CCCTTATTTG-GTCAAATT-AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTGAAACG-TTAGG
*
18589 CCCTTATTTGAGCATTTTCGATAACGTTAGA
1 CCCTTATTTGAGCATTTT-GA-AACGTTAGG
** * * *
18620 CCCTTATTTG-GCCAAATT-AAAAGATCGG
1 CCCTTATTTGAG-CATTTTGAAACGTTAGG
18648 ACCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 -CCCTTATTTGAGCATTTT-G-AAACGTTAGG
18680 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
18694 ATTAGCCATT
Statistics
Matches: 100, Mismatches: 22, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
28 8 0.08
29 33 0.33
30 4 0.04
31 45 0.45
32 10 0.10
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAACGTTAGG
Found at i:18624 original size:60 final size:60
Alignment explanation
Indices: 18529--18689 Score: 270
Period size: 60 Copynumber: 2.7 Consensus size: 60
18519 TGACACCGGC
* *
18529 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
*
18589 CCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
*
18649 CCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
18690 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:18656 original size:29 final size:28
Alignment explanation
Indices: 18560--18658 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
18550 TAACGTTAGG
*
18560 CCCTTATTTGGTCAAATTAAAAGATCGGG
1 CCCTTATTTGG-CAAATTAAAAGATCGGA
** * **
18589 CCCTTATTTGAGCATTTTCGATAACG-TTAGA
1 CCCTTATTTG-GCAAATT--A-AAAGATCGGA
18620 CCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGG-CAAATTAAAAGATCGGA
18649 CCCTTATTTG
1 CCCTTATTTG
18659 AGCATTTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.06
29 28 0.53
30 2 0.04
31 17 0.32
32 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (28 bp):
CCCTTATTTGGCAAATTAAAAGATCGGA
Found at i:20334 original size:18 final size:18
Alignment explanation
Indices: 20311--20356 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
20301 GAAAATCTGA
*
20311 TCCGAACCCGATAACCTG
1 TCCGAACCCGATAACCCG
20329 TCCGAACCCG-TAACCCG
1 TCCGAACCCGATAACCCG
*
20346 -CCCAACCCGAT
1 TCCGAACCCGAT
20357 TTGACCAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 10 0.40
ACGTcount: A:0.26, C:0.46, G:0.15, T:0.13
Consensus pattern (18 bp):
TCCGAACCCGATAACCCG
Found at i:20483 original size:16 final size:16
Alignment explanation
Indices: 20458--20507 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
20448 TAACCCAGAA
*
20458 ACCCGAATGACCCGAG
1 ACCCGTATGACCCGAG
*
20474 ACCCGTATGACCCGAA
1 ACCCGTATGACCCGAG
*
20490 ACCCGTATAACCCGAG
1 ACCCGTATGACCCGAG
20506 AC
1 AC
20508 ATTAACCCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.32, C:0.38, G:0.20, T:0.10
Consensus pattern (16 bp):
ACCCGTATGACCCGAG
Found at i:20494 original size:32 final size:31
Alignment explanation
Indices: 20442--20507 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
20432 AGACTCGAAT
*
20442 GACCCGTAACCCAGAAACCCGAATGACCCGA
1 GACCCGTAACCCAGAAACCCGAATAACCCGA
*
20473 GACCCGTATGACCC-GAAACCCGTATAACCCGA
1 GACCCGTA--ACCCAGAAACCCGAATAACCCGA
20505 GAC
1 GAC
20508 ATTAACCCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 8 0.26
32 19 0.61
33 4 0.13
ACGTcount: A:0.33, C:0.38, G:0.20, T:0.09
Consensus pattern (31 bp):
GACCCGTAACCCAGAAACCCGAATAACCCGA
Found at i:20659 original size:21 final size:21
Alignment explanation
Indices: 20612--20659 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
20602 ATATAATTTA
20612 TATTATTGTTATAATTTTACC
1 TATTATTGTTATAATTTTACC
*
20633 -AGTTATTGTTATGATTTTACC
1 TA-TTATTGTTATAATTTTACC
20654 TATTAT
1 TATTAT
20660 AAATTGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (21 bp):
TATTATTGTTATAATTTTACC
Found at i:21138 original size:16 final size:15
Alignment explanation
Indices: 21104--21252 Score: 95
Period size: 16 Copynumber: 9.4 Consensus size: 15
21094 GAACCCGCCA
* *
21104 ACCCGAGACCCAGTAG
1 ACCCGAGACCGAAT-G
*
21120 ACCTGAGACCTGAATG
1 ACCCGAGACC-GAATG
21136 ACCCG-GAATCCGAATG
1 ACCCGAG-A-CCGAATG
21152 ACCCGAGACCCGAATG
1 ACCCGAGA-CCGAATG
* * * *
21168 AACCGAAACCCGTATA
1 ACCCGAGA-CCGAATG
*
21184 ACCCGAGACCCGAACG
1 ACCCGAGA-CCGAATG
*
21200 ACCCGAGACCCGAATA
1 ACCCGAGA-CCGAATG
*
21216 ACCCGA-ACCCAGATG
1 ACCCGAGACCGA-ATG
*
21231 ACCCGAAACCCGAATG
1 ACCCGAGA-CCGAATG
21247 ACCCGA
1 ACCCGA
21253 AAAAACTGAT
Statistics
Matches: 107, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
14 3 0.03
15 10 0.09
16 86 0.80
17 8 0.07
ACGTcount: A:0.34, C:0.36, G:0.21, T:0.08
Consensus pattern (15 bp):
ACCCGAGACCGAATG
Found at i:21157 original size:9 final size:8
Alignment explanation
Indices: 21145--21253 Score: 63
Period size: 9 Copynumber: 13.6 Consensus size: 8
21135 GACCCGGAAT
21145 CCGAATGAC
1 CCGAA-GAC
21154 CCG-AGAC
1 CCGAAGAC
*
21161 CCGAATGAA
1 CCGAA-GAC
21170 CCGAA-AC
1 CCGAAGAC
21177 CCGTATA-AC
1 CCG-A-AGAC
21186 CCG-AGAC
1 CCGAAGAC
21193 CCGAACGAC
1 CCGAA-GAC
21202 CCG-AGAC
1 CCGAAGAC
*
21209 CCGAATAAC
1 CCGAA-GAC
21218 CCG-A-AC
1 CCGAAGAC
*
21224 CCAGATGAC
1 CC-GAAGAC
21233 CCGAA-AC
1 CCGAAGAC
21240 CCGAATGAC
1 CCGAA-GAC
21249 CCGAA
1 CCGAA
21254 AAAACTGATG
Statistics
Matches: 81, Mismatches: 5, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
6 5 0.06
7 29 0.36
8 9 0.11
9 38 0.47
ACGTcount: A:0.36, C:0.38, G:0.20, T:0.06
Consensus pattern (8 bp):
CCGAAGAC
Found at i:21160 original size:32 final size:32
Alignment explanation
Indices: 21119--21252 Score: 155
Period size: 32 Copynumber: 4.2 Consensus size: 32
21109 AGACCCAGTA
* * * *
21119 GACCTGAGACCTGAATGACCCGGAATCCGAAT
1 GACCCGAGACCCGAATGACCCGAAACCCGAAT
* *
21151 GACCCGAGACCCGAATGAACCGAAACCCGTAT
1 GACCCGAGACCCGAATGACCCGAAACCCGAAT
* * *
21183 AACCCGAGACCCGAACGACCCGAGACCCGAAT
1 GACCCGAGACCCGAATGACCCGAAACCCGAAT
*
21215 AACCCGA-ACCC-AGATGACCCGAAACCCGAAT
1 GACCCGAGACCCGA-ATGACCCGAAACCCGAAT
21246 GACCCGA
1 GACCCGA
21253 AAAAACTGAT
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
30 1 0.01
31 26 0.30
32 60 0.69
ACGTcount: A:0.34, C:0.36, G:0.22, T:0.08
Consensus pattern (32 bp):
GACCCGAGACCCGAATGACCCGAAACCCGAAT
Found at i:21253 original size:16 final size:16
Alignment explanation
Indices: 21131--21254 Score: 135
Period size: 16 Copynumber: 7.8 Consensus size: 16
21121 CCTGAGACCT
* *
21131 GAATGACCCGGAATCC
1 GAATGACCCGAAACCC
*
21147 GAATGACCCGAGACCC
1 GAATGACCCGAAACCC
*
21163 GAATGAACCGAAACCC
1 GAATGACCCGAAACCC
* * *
21179 GTATAACCCGAGACCC
1 GAATGACCCGAAACCC
* *
21195 GAACGACCCGAGACCC
1 GAATGACCCGAAACCC
*
21211 GAATAACCCG-AACCC
1 GAATGACCCGAAACCC
21226 -AGATGACCCGAAACCC
1 GA-ATGACCCGAAACCC
21242 GAATGACCCGAAA
1 GAATGACCCGAAA
21255 AAACTGATGA
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
14 1 0.01
15 11 0.12
16 76 0.85
17 1 0.01
ACGTcount: A:0.36, C:0.35, G:0.21, T:0.07
Consensus pattern (16 bp):
GAATGACCCGAAACCC
Found at i:22449 original size:2 final size:2
Alignment explanation
Indices: 22442--22476 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22432 ACTAACAAGA
22442 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 A
22477 ATGGATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24648 original size:2 final size:2
Alignment explanation
Indices: 24641--24677 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
24631 CGAATATTTC
24641 AT AT AT AT AT AT AT AT A- 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
24678 GGACTTAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24661 original size:17 final size:17
Alignment explanation
Indices: 24641--24674 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24631 CGAATATTTC
24641 ATATATATATATATATA
1 ATATATATATATATATA
24658 ATATATATATATATATA
1 ATATATATATATATATA
24675 TATGGACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:25551 original size:11 final size:11
Alignment explanation
Indices: 25535--25565 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
25525 CTTGTTTTTT
25535 GTTTTTGTTTC
1 GTTTTTGTTTC
*
25546 GTTTTTGTTTT
1 GTTTTTGTTTC
25557 GTTTTTGTT
1 GTTTTTGTT
25566 ACGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:31735 original size:14 final size:14
Alignment explanation
Indices: 31716--31745 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
31706 TGATAAACCA
31716 TTGAAAATTTTCAT
1 TTGAAAATTTTCAT
31730 TTGAAAATTTTCAT
1 TTGAAAATTTTCAT
31744 TT
1 TT
31746 CATTGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (14 bp):
TTGAAAATTTTCAT
Found at i:31765 original size:19 final size:20
Alignment explanation
Indices: 31719--31766 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
31709 TAAACCATTG
31719 AAAATTTTCATTTGAAAATT
1 AAAATTTTCATTTGAAAATT
***
31739 TTCA-TTTCA-TTGAAAATT
1 AAAATTTTCATTTGAAAATT
31757 AAAATTTTCA
1 AAAATTTTCA
31767 ATGGTTTTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 3
0.70 0.20 0.10
Matches are distributed among these distances:
18 10 0.48
19 10 0.48
20 1 0.05
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
AAAATTTTCATTTGAAAATT
Found at i:32697 original size:14 final size:16
Alignment explanation
Indices: 32662--32703 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
32652 TAAAGTTTGG
*
32662 ATTCAGTACTTATAAT
1 ATTCAGTACTTATAAA
32678 ATTCAGTA-TTA-AAA
1 ATTCAGTACTTATAAA
*
32692 ATTCAGTGCTTA
1 ATTCAGTACTTA
32704 ATCTTTCAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 6 0.26
16 8 0.35
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (16 bp):
ATTCAGTACTTATAAA
Found at i:33258 original size:16 final size:16
Alignment explanation
Indices: 33239--33321 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
33229 AACCGACTTG
*
33239 AACCTGAACCCGAAAA
1 AACCTAAACCCGAAAA
*
33255 AACCCAAACCCG-AAA
1 AACCTAAACCCGAAAA
* *
33270 GAGCTCAAACCCGAAAA
1 AACCT-AAACCCGAAAA
**
33287 ATTC-ATAACCCGAAAA
1 AACCTA-AACCCGAAAA
**
33303 AACCCGAACCCGAATAA
1 AACCTAAACCCGAA-AA
33320 AA
1 AA
33322 AAATGTATGA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
15 6 0.12
16 37 0.73
17 8 0.16
ACGTcount: A:0.51, C:0.31, G:0.11, T:0.07
Consensus pattern (16 bp):
AACCTAAACCCGAAAA
Found at i:33968 original size:22 final size:22
Alignment explanation
Indices: 33910--33968 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
33900 ATTTCTATGC
* * *
33910 TTATCAAAATTTAATATTGATG
1 TTATCAAAATTTCATATGGAGG
**
33932 TTAT-AAGTTTTCATATGGAGG
1 TTATCAAAATTTCATATGGAGG
33953 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
33969 GTATGGTGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGAGG
Found at i:34150 original size:22 final size:22
Alignment explanation
Indices: 34125--34231 Score: 105
Period size: 22 Copynumber: 4.9 Consensus size: 22
34115 TTCATATGGA
*
34125 GGTTATCAAATTTTTATAGTGT
1 GGTTATCAAAATTTTATAGTGT
* * *
34147 GGTTACCAAAATTTCATAAGT-A
1 GGTTATCAAAATTTTAT-AGTGT
34169 GGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAATTTTATAGTGT
*
34191 GATTATC-AAATTTTCATAG-GCAT
1 GGTTATCAAAATTTT-ATAGTG--T
34214 -GTTATCAAAATTTTATAG
1 GGTTATCAAAATTTTATAG
34232 GGAATACCAA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
21 11 0.16
22 48 0.69
23 11 0.16
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGTGT
Found at i:34176 original size:44 final size:44
Alignment explanation
Indices: 34113--34250 Score: 172
Period size: 44 Copynumber: 3.2 Consensus size: 44
34103 TGATGTGGTT
* * * *
34113 ATTTCATATGGAGGTTATCAAATTTTTATAGTGTGGTTACCAAA
1 ATTTCATAAGCAGGTTATCAAAATTTTATAGTGTGATTACCAAA
* *
34157 ATTTCATAAGTAGGTTATCAAAATTTTATAGTGTGATTATCAAA
1 ATTTCATAAGCAGGTTATCAAAATTTTATAGTGTGATTACCAAA
* * * *
34201 TTTTCATAGGCATGTTATCAAAATTTTATAG-G-GAATACCAAA
1 ATTTCATAAGCAGGTTATCAAAATTTTATAGTGTGATTACCAAA
34243 ATTTCATA
1 ATTTCATA
34251 GTATGATTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 15 0.18
43 1 0.01
44 66 0.80
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40
Consensus pattern (44 bp):
ATTTCATAAGCAGGTTATCAAAATTTTATAGTGTGATTACCAAA
Found at i:34260 original size:64 final size:65
Alignment explanation
Indices: 34175--34295 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 65
34165 AGTAGGTTAT
* * *
34175 CAAAATTTTATAGTGTGATTATCAAATTTTCATAGGCATG-TTATCAAAATTTTATAGGGAATAC
1 CAAAATTTCATAGTATGATTATCAAATTTTCATAGGCAGGTTTATCAAAATTTTATAGGGAATAC
** * *
34239 CAAAATTTCATAGTATGATTATTGAATTTTCATAGGGAGGTTTATCGAAATTTTATA
1 CAAAATTTCATAGTATGATTATCAAATTTTCATAGGCAGGTTTATCAAAATTTTATA
34296 TGAAAGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 34 0.69
65 15 0.31
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (65 bp):
CAAAATTTCATAGTATGATTATCAAATTTTCATAGGCAGGTTTATCAAAATTTTATAGGGAATAC
Found at i:34349 original size:22 final size:22
Alignment explanation
Indices: 34113--34402 Score: 75
Period size: 22 Copynumber: 13.2 Consensus size: 22
34103 TGATGTGGTT
34113 ATTTCATATGGAGG-TTATCAAA
1 ATTTCATATGG-GGATTATCAAA
* * * *
34135 TTTTTATAGTGTGG-TTACCAAA
1 ATTTCATA-TGGGGATTATCAAA
* *
34157 ATTTCATAAGTAGG-TTATCAAA
1 ATTTCATATG-GGGATTATCAAA
* *
34179 ATTTTATA-GTGTGATTATCAAA
1 ATTTCATATG-GGGATTATCAAA
* *
34201 TTTTCATA--GGCATGTTATCAAA
1 ATTTCATATGGGGA--TTATCAAA
* * *
34223 ATTT--TATAGGGAATACCAAA
1 ATTTCATATGGGGATTATCAAA
** **
34243 ATTTCATA-GTATGATTATTGAA
1 ATTTCATATG-GGGATTATCAAA
* * * *
34265 TTTTCATAGGGAGGTTTATCGAA
1 ATTTCATATGG-GGATTATCAAA
* ** *
34288 ATTTTATAT-GAAAGTTTTCAAA
1 ATTTCATATGGGGA-TTATCAAA
* **
34310 ATATCATTATGTTG-TTATCAAA
1 ATTTCA-TATGGGGATTATCAAA
*
34332 ATTTCATATGGGGATTATCGAA
1 ATTTCATATGGGGATTATCAAA
* *
34354 ATTTCATAATGAGG-CTATC-AA
1 ATTTCAT-ATGGGGATTATCAAA
* *
34375 ATATTCATATTGTGGTTTATCAAA
1 AT-TTCATA-TGGGGATTATCAAA
34399 ATTT
1 ATTT
34403 GTTTGGGATA
Statistics
Matches: 193, Mismatches: 54, Indels: 41
0.67 0.19 0.14
Matches are distributed among these distances:
20 14 0.07
21 14 0.07
22 130 0.67
23 31 0.16
24 4 0.02
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (22 bp):
ATTTCATATGGGGATTATCAAA
Found at i:34470 original size:34 final size:34
Alignment explanation
Indices: 34414--34480 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
34404 TTTGGGATAT
*
34414 ACCGAAATTCCATAGTGTGGTTATCGAAATTTTG
1 ACCGAAATTCCATAGTGAGGTTATCGAAATTTTG
*
34448 ACCGAAATTTCATAAG-GAGGTTATCGAAATTTT
1 ACCGAAATTCCAT-AGTGAGGTTATCGAAATTTT
34481 AGGGAAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (34 bp):
ACCGAAATTCCATAGTGAGGTTATCGAAATTTTG
Found at i:34478 original size:22 final size:22
Alignment explanation
Indices: 34452--34817 Score: 115
Period size: 22 Copynumber: 16.6 Consensus size: 22
34442 ATTTTGACCG
*
34452 AAATTTCATAAGGAGGTTATCG
1 AAATTTCATAAGGAGGTTATCA
* * *
34474 AAATTT--TAGGGAAGTTATTA
1 AAATTTCATAAGGAGGTTATCA
**
34494 AAATTTCATTGGGAGGTTA-CTA
1 AAATTTCATAAGGAGGTTATC-A
* *
34516 AAATTTCAT-AGATAGCTTATCA
1 AAATTTCATAAG-GAGGTTATCA
** * *
34538 AAATTTCATAATAAGGCTATGA
1 AAATTTCATAAGGAGGTTATCA
* * *
34560 AAAGTTCATAAAGAGATTATCA
1 AAATTTCATAAGGAGGTTATCA
* * *
34582 ACATTTTAT-AGAAAGGTTTATCA
1 AAATTTCATAAG-GAGG-TTATCA
* **
34605 AAATTACATTTGTGAGGGTTATCA
1 AAATTTCATAAG-GA-GGTTATCA
*
34629 AAA-TTCTATAAAGAGGTTATCA
1 AAATTTC-ATAAGGAGGTTATCA
* * ** *
34651 TAATTTCATATACTGTTGTTACCA
1 AAATTTCATA-A-GGAGGTTATCA
* * * *
34675 AAATTTCAT-ATGTGTTTACCA
1 AAATTTCATAAGGAGGTTATCA
* ** *
34696 ACATTTCATTGGGAGGTTATCG
1 AAATTTCATAAGGAGGTTATCA
* *
34718 AAATTTCAT-AGTATAGTTATCA
1 AAATTTCATAAGGA-GGTTATCA
**
34740 AAATTT-AT--GGTATAATTATCA
1 AAATTTCATAAGG-A-GGTTATCA
* *
34761 AAATTTCATAATGAAGTTATCA
1 AAATTTCATAAGGAGGTTATCA
* ** * * *
34783 AACTTTTGTTATGTGGTTATCA
1 AAATTTCATAAGGAGGTTATCA
*
34805 AAATTTTATAAGG
1 AAATTTCATAAGG
34818 CAATTAATTA
Statistics
Matches: 253, Mismatches: 71, Indels: 40
0.70 0.20 0.11
Matches are distributed among these distances:
20 17 0.07
21 38 0.15
22 144 0.57
23 23 0.09
24 29 0.11
25 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
AAATTTCATAAGGAGGTTATCA
Found at i:34758 original size:21 final size:22
Alignment explanation
Indices: 34712--34770 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
34702 CATTGGGAGG
* *
34712 TTATCGAAATTTCATAGTATAG
1 TTATCAAAATTTCATAGTATAA
*
34734 TTATCAAAATTT-ATGGTATAA
1 TTATCAAAATTTCATAGTATAA
34755 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
34771 ATGAAGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTATAA
Found at i:37222 original size:12 final size:12
Alignment explanation
Indices: 37205--37230 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37195 TTTTAGCAAT
37205 GCTACTTGTCCA
1 GCTACTTGTCCA
37217 GCTACTTGTCCA
1 GCTACTTGTCCA
37229 GC
1 GC
37231 CTAATTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.19, T:0.31
Consensus pattern (12 bp):
GCTACTTGTCCA
Found at i:37777 original size:18 final size:18
Alignment explanation
Indices: 37754--37789 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
37744 TTTGATAAAC
37754 CATTGAAAATTTTAATTT
1 CATTGAAAATTTTAATTT
37772 CATTGAAAATTTTAATTT
1 CATTGAAAATTTTAATTT
37790 TCAATAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
CATTGAAAATTTTAATTT
Found at i:38601 original size:15 final size:15
Alignment explanation
Indices: 38570--38620 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
38560 ACTTATGAGA
38570 TTCAGTA-TTAAAAT
1 TTCAGTACTTAAAAT
**
38584 TTCAGTACTTAATCT
1 TTCAGTACTTAAAAT
*
38599 TTCAGCACTTAAAATT
1 TTCAGTACTTAAAA-T
38615 TTCAGT
1 TTCAGT
38621 TTATTAAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 7 0.24
15 16 0.55
16 6 0.21
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (15 bp):
TTCAGTACTTAAAAT
Found at i:41689 original size:32 final size:32
Alignment explanation
Indices: 41647--41709 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
41637 TTTAGGTGCT
41647 GGCAACTGTATGAACATGGA-ATTTTAATTTTC
1 GGCAACTGTATGAACAT-GACATTTTAATTTTC
* *
41679 GGCAATTGTATGAACATGACTTTTTAATTTT
1 GGCAACTGTATGAACATGACATTTTAATTTT
41710 AAGAAATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (32 bp):
GGCAACTGTATGAACATGACATTTTAATTTTC
Found at i:43446 original size:16 final size:14
Alignment explanation
Indices: 43414--43454 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
43404 AGAGAAAAAG
43414 AAAAGGAAAAAGGA
1 AAAAGGAAAAAGGA
43428 AAAAGGAAATAAGGGA
1 AAAAGGAAA-AA-GGA
*
43444 AAATGGAAAAA
1 AAAAGGAAAAA
43455 TTGGGATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 9 0.38
15 4 0.17
16 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (14 bp):
AAAAGGAAAAAGGA
Found at i:43455 original size:8 final size:7
Alignment explanation
Indices: 43414--43454 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
43404 AGAGAAAAAG
43414 AAAAGGA
1 AAAAGGA
43421 AAAAGGA
1 AAAAGGA
43428 AAAAGGA
1 AAAAGGA
43435 AATAAGGGA
1 AA-AA-GGA
*
43444 AAATGGA
1 AAAAGGA
43451 AAAA
1 AAAA
43455 TTGGGATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 22 0.73
8 3 0.10
9 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (7 bp):
AAAAGGA
Found at i:44791 original size:21 final size:22
Alignment explanation
Indices: 44761--44840 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 22
44751 GATTACCATC
*
44761 ACTTTTTACTGATTA-TTCTTT
1 ACTTTGTACTGATTACTTCTTT
44782 ACTTTGTACTGATTACTAT-TTT
1 ACTTTGTACTGATTACT-TCTTT
44804 ACTCTTGT--TGATTACCTTC-TT
1 ACT-TTGTACTGATTA-CTTCTTT
*
44825 ACTTTTTACTGATTAC
1 ACTTTGTACTGATTAC
44841 CATTTTACTC
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
20 3 0.06
21 27 0.54
22 15 0.30
23 5 0.10
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.55
Consensus pattern (22 bp):
ACTTTGTACTGATTACTTCTTT
Found at i:44835 original size:43 final size:42
Alignment explanation
Indices: 44779--45138 Score: 228
Period size: 42 Copynumber: 8.2 Consensus size: 42
44769 CTGATTATTC
* *
44779 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
* * * *
44821 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTAATTACTATT
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTATTGATTAC--CT
* * * * **
44868 TTCTGCACCTTTTTTAATGATTACTCTTTTACTTTTTACTGATTGTCT
1 TT-T--A-C-TTTTTACTGATTACTATTTTAC-TCTTATTGATTACCT
* * * *
44916 TTTGCTTTTTTACTGATTAC-CTTTTACTTCTTACTGATTAGCT
1 TTTAC-TTTTTACTGATTACTATTTTAC-TCTTATTGATTACCT
* * *
44959 TTTA-TTCTTTACTGATCACCT-TTTTACTCTTACTGATTTCCT
1 TTTACTT-TTTACTGATTA-CTATTTTACTCTTATTGATTACCT
* * *
45001 TTTACTTCTTACCT-ATTACTGTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTA-CTGATTACTATTTTACTCTTATTGATTACCT
* * * *
45042 ATTTACTTTTTACGGACTACTCTTTTACTC-TGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
* * *
45084 TCTTACTTTTTACTAATTACTATTTTACTCTTTACTAATTACCAT
1 T-TTACTTTTTACTGATTACTATTTTACTC-TTATTGATTACC-T
*
45129 TTTACCTTTT
1 TTTACTTTTT
45139 CAGATACCTT
Statistics
Matches: 254, Mismatches: 40, Indels: 46
0.75 0.12 0.14
Matches are distributed among these distances:
41 15 0.06
42 100 0.39
43 60 0.24
44 31 0.12
45 10 0.04
46 1 0.00
47 4 0.02
48 3 0.01
49 1 0.00
50 9 0.04
51 19 0.07
52 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTATTGATTACCT
Found at i:44916 original size:21 final size:22
Alignment explanation
Indices: 44878--45165 Score: 119
Period size: 22 Copynumber: 13.5 Consensus size: 22
44868 TTCTGCACCT
* *
44878 TTTTTAATGATTACTCTTTTAC
1 TTTTTACTGATTAGTCTTTTAC
*
44900 TTTTTACTGATT-GTCTTTTGC
1 TTTTTACTGATTAGTCTTTTAC
*
44921 TTTTTTACTGATTA-CCTTTTAC
1 -TTTTTACTGATTAGTCTTTTAC
*
44943 TTCTTACTGATTAG-CTTTTA-
1 TTTTTACTGATTAGTCTTTTAC
* *
44963 TTCTTTACTGATCA-CCTTTTTAC
1 TT-TTTACTGATTAGTC-TTTTAC
*
44986 -TCTTACTGATT--TCCTTTTAC
1 TTTTTACTGATTAGT-CTTTTAC
* * *
45006 TTCTTACCT-ATTACTGTTTTAC
1 TTTTTA-CTGATTAGTCTTTTAC
*
45028 -TCTTACTGATTA--CTATTTAC
1 TTTTTACTGATTAGTCT-TTTAC
* * *
45048 TTTTTACGGACTACTCTTTTAC
1 TTTTTACTGATTAGTCTTTTAC
* * *
45070 TCTGT--TGATTA-CCTTCTTAC
1 TTTTTACTGATTAGTCTT-TTAC
* * *
45090 TTTTTACTAATTACTATTTTAC
1 TTTTTACTGATTAGTCTTTTAC
* * *
45112 TCTTTACTAATTA-CCATTTTAC
1 TTTTTACTGATTAGTC-TTTTAC
* * *
45134 CTTTT-CAGA-TA-CCTTTTTAC
1 TTTTTACTGATTAGTC-TTTTAC
45154 TTTTTACTGATT
1 TTTTTACTGATT
45166 GCATGCTATT
Statistics
Matches: 206, Mismatches: 36, Indels: 48
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.02
20 40 0.19
21 75 0.36
22 82 0.40
23 5 0.02
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTTACTGATTAGTCTTTTAC
Found at i:45033 original size:14 final size:14
Alignment explanation
Indices: 44980--45035 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
44970 CTGATCACCT
44980 TTTTACTCTTACTG
1 TTTTACTCTTACTG
* * *
44994 ATTTCCTTTTACT-
1 TTTTACTCTTACTG
* *
45007 TCTTACCTATTACTG
1 TTTTA-CTCTTACTG
45022 TTTTACTCTTACTG
1 TTTTACTCTTACTG
45036 ATTACTATTT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
13 2 0.06
14 25 0.81
15 4 0.13
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.55
Consensus pattern (14 bp):
TTTTACTCTTACTG
Found at i:45485 original size:55 final size:55
Alignment explanation
Indices: 45416--45846 Score: 700
Period size: 55 Copynumber: 7.8 Consensus size: 55
45406 AATCAATTTA
* * * * *
45416 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
45471 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
45526 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
* **
45581 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
* * *
45636 CTGATTAATCTCTTTTTACTCAATTACTTATTTACTGATTGCTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
* **
45691 TTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
* *
45746 CTGATTAATCTCTTTTTACTTAATTACTGACTTACTGATTGCTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
* *
45801 TTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATT
45847 CGGACTGATC
Statistics
Matches: 347, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 347 1.00
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
Found at i:46913 original size:50 final size:49
Alignment explanation
Indices: 46808--46913 Score: 110
Period size: 50 Copynumber: 2.1 Consensus size: 49
46798 AGGTTAATCC
** *
46808 TTTATCAAAATGGAGTCTTTTAATCTAAAGGCTTAGCTTTTACTAATAA
1 TTTATCAAAATGGAGTCTTTTAATCTAAAGGCTTAGCCATTACTAACAA
* *
46857 TCTATCAAAATGAGAGTCTTTTAGAT-TAAAGG-TTAGTCCATTA-TCACCAA
1 TTTATCAAAATG-GAGTCTTTTA-ATCTAAAGGCTTAG-CCATTACT-AACAA
46907 TTTATCA
1 TTTATCA
46914 GAATTAGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
49 16 0.34
50 29 0.62
51 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (49 bp):
TTTATCAAAATGGAGTCTTTTAATCTAAAGGCTTAGCCATTACTAACAA
Found at i:49777 original size:13 final size:13
Alignment explanation
Indices: 49759--49815 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
49749 AATACCAAAT
49759 TACTAAATGAAAA
1 TACTAAATGAAAA
*
49772 TACTAATTGAAAA
1 TACTAAATGAAAA
* * *
49785 CACCATAATGCCAAA
1 TACTA-AATG-AAAA
49800 TCACTAAATGAAAA
1 T-ACTAAATGAAAA
49814 TA
1 TA
49816 TGCAAAAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 16 0.48
14 7 0.21
15 7 0.21
16 3 0.09
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.23
Consensus pattern (13 bp):
TACTAAATGAAAA
Found at i:49946 original size:27 final size:27
Alignment explanation
Indices: 49916--50020 Score: 156
Period size: 27 Copynumber: 3.9 Consensus size: 27
49906 AGGTGAACTT
* *
49916 AAAAATGACTAAAATGCCCCTGAGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
*
49943 AAAAATGACCAAAATGACCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
49970 AAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
* * *
49997 AAAAGTGACCAAAATACCCTTGGG
1 AAAAATGACCAAAATGCCCCTGGG
50021 CAACCCTAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGTGC
Found at i:53658 original size:13 final size:12
Alignment explanation
Indices: 53642--53674 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
53632 ATTAATTTGC
53642 TTTAGATTTAAGA
1 TTTAGATTT-AGA
53655 TTTAGATTTAGA
1 TTTAGATTTAGA
53667 TTT-GATTT
1 TTTAGATTT
53675 GCTTTGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
13 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (12 bp):
TTTAGATTTAGA
Found at i:53661 original size:6 final size:6
Alignment explanation
Indices: 53642--53674 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
53632 ATTAATTTGC
53642 TTTAGA TTTAAGA TTTAGA TTTAGA TTT-GA TTT
1 TTTAGA TTT-AGA TTTAGA TTTAGA TTTAGA TTT
53675 GCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:54064 original size:41 final size:39
Alignment explanation
Indices: 54005--54106 Score: 100
Period size: 40 Copynumber: 2.5 Consensus size: 39
53995 GGTTTTTCCG
*
54005 TTTTTCCGATTTTTCTTTTAAAAAAAATTAAT-TAT-TTTTT
1 TTTTTCTG-TTTTTCTTTTAAAAAAAA--AATATATATTTTT
*
54045 CTTTTTCTGTTTTTCCTTTTAAATAAAAAATATATATTTTT
1 -TTTTTCTGTTTTT-CTTTTAAAAAAAAAATATATATTTTT
* *
54086 ATTTTCTGTTTCTGCTTTTAA
1 TTTTTCTGTTT-TTCTTTTAA
54107 TTTTTTATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
39 3 0.06
40 25 0.47
41 25 0.47
ACGTcount: A:0.26, C:0.10, G:0.04, T:0.60
Consensus pattern (39 bp):
TTTTTCTGTTTTTCTTTTAAAAAAAAAATATATATTTTT
Done.