Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007446.1 Hibiscus syriacus cultivar Beakdansim tig00020348_pilon, 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: 85899
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:325 original size:40 final size:41
Alignment explanation
Indices: 281--369 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 41
271 CCAGATTCGT
* * * *
281 AACGCGATTTTGACTATCGCAATGCG--AATATGTAAATCGC
1 AACGCGATTCTGACCATCGCAACGCGATAATATAT-AATCGC
*
321 AACGCGATTCTGACCATTGCAACGCGATAATATATAATCGC
1 AACGCGATTCTGACCATCGCAACGCGATAATATATAATCGC
362 AACGCGAT
1 AACGCGAT
370 AATACATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 22 0.52
41 14 0.33
42 6 0.14
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (41 bp):
AACGCGATTCTGACCATCGCAACGCGATAATATATAATCGC
Found at i:407 original size:21 final size:21
Alignment explanation
Indices: 339--405 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
329 TCTGACCATT
*
339 GCAACGCGATAATATATAATC
1 GCAACGCGATAATACATAATC
360 GCAACGCGATAATACATAATC
1 GCAACGCGATAATACATAATC
* *
381 ACAATGCGATAATACATAATC
1 GCAACGCGATAATACATAATC
402 GCAA
1 GCAA
406 TGTGATTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (21 bp):
GCAACGCGATAATACATAATC
Found at i:431 original size:19 final size:19
Alignment explanation
Indices: 403--439 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
393 TACATAATCG
*
403 CAATGTGATTTTCAAAGCA
1 CAATGCGATTTTCAAAGCA
422 CAATGCGATTTTCAAAGC
1 CAATGCGATTTTCAAAGC
440 GCCATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (19 bp):
CAATGCGATTTTCAAAGCA
Found at i:1077 original size:20 final size:19
Alignment explanation
Indices: 1009--1093 Score: 73
Period size: 20 Copynumber: 4.4 Consensus size: 19
999 ATCGTAACGT
*
1009 GATTTTAGTTTCGCGTTGC
1 GATTTTATTTTCGCGTTGC
1028 GATTTTCA-TTTCGCGTTGC
1 GATTTT-ATTTTCGCGTTGC
* * * *
1047 AATAGTTATTTTCGTGTTGT
1 GAT-TTTATTTTCGCGTTGC
*
1067 GATTTTCATTTTCGTGTTGC
1 GATTTT-ATTTTCGCGTTGC
*
1087 GGTTTTA
1 GATTTTA
1094 AGTTTCAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
19 23 0.43
20 31 0.57
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.52
Consensus pattern (19 bp):
GATTTTATTTTCGCGTTGC
Found at i:3034 original size:20 final size:20
Alignment explanation
Indices: 3011--3078 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
3001 GAAACTTAAA
3011 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
3031 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
3051 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3071 ATCGCAAC
1 ATCGCAAC
3079 TGGATAATCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3124 original size:20 final size:20
Alignment explanation
Indices: 3084--3136 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
3074 GCAACTGGAT
*
3084 AATCGCAATGTG-AAATAAA
1 AATCGCAATGCGAAAATAAA
*
3103 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATAAA
*
3123 AATCGCAACGCGAA
1 AATCGCAATGCGAA
3137 TTTAGTTTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATAAA
Found at i:3154 original size:19 final size:19
Alignment explanation
Indices: 3132--3169 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3122 AAATCGCAAC
3132 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
3151 GCGATTTTGGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
3170 ATGATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.45
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:3194 original size:19 final size:19
Alignment explanation
Indices: 3137--3194 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
3127 GCAACGCGAA
3137 TTTAGTTTCGCGTTGCGATT
1 TTTA-TTTCGCGTTGCGATT
** **
3157 TTGGTTTCGCGTTATGATT
1 TTTATTTCGCGTTGCGATT
*
3176 TTTATTTCGCATTGCGATT
1 TTTATTTCGCGTTGCGATT
3195 ATCGTGTTGC
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 27 0.93
20 2 0.07
ACGTcount: A:0.12, C:0.14, G:0.22, T:0.52
Consensus pattern (19 bp):
TTTATTTCGCGTTGCGATT
Found at i:3257 original size:20 final size:20
Alignment explanation
Indices: 3234--3277 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3224 AGATAGTCAT
3234 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
* *
3254 TTTCGTGTTGTGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
3274 TTTC
1 TTTC
3278 AAAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:3847 original size:21 final size:21
Alignment explanation
Indices: 3753--3852 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
3743 GCCCGACTCA
3753 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
3774 TCT-CCTATCGTTCAAGAGG-C
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
3794 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
3815 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
*
3836 CCTGTCATCGTTGAAGA
1 CCTGTCATCGTTCAAGA
3853 TGTCCCTCAC
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
20 14 0.24
21 45 0.76
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:5408 original size:20 final size:20
Alignment explanation
Indices: 5383--5460 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
5373 AGGTATTCTT
*
5383 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
5403 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
5423 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
* *
5443 TCGCAACACGAAAGTCAA
1 TCGCAACGCGAAACTCAA
5461 TTCATGTTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:5427 original size:40 final size:40
Alignment explanation
Indices: 5383--5460 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
5373 AGGTATTCTT
* **
5383 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGCAACACGAAAGTCAAAA
*
5423 TCGCAATGCGAAAGCCAAAATCGCAACACGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGCAACACGAAAGTCAA
5461 TTCATGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGCAACACGAAAGTCAAAA
Found at i:5484 original size:20 final size:20
Alignment explanation
Indices: 5466--5697 Score: 188
Period size: 20 Copynumber: 12.8 Consensus size: 20
5456 GTCAATTCAT
*
5466 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCAAATTCGC
5486 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
* *
5506 ATTGCGATAGTCAAATTTGC
1 GTTGCGATAGTCAAATTCGC
5526 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
5546 GTTGCGAT--T----TTTGC
1 GTTGCGATAGTCAAATTCGC
5560 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
5580 GTTGCGAT--T----TTTGC
1 GTTGCGATAGTCAAATTCGC
* *
5594 GTTGCGATAGTCAAATTTGA
1 GTTGCGATAGTCAAATTCGC
*
5614 GTTGCGAT--T----TTTGC
1 GTTGCGATAGTCAAATTCGC
5628 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
5648 GTTGCGAT--T----TTTGC
1 GTTGCGATAGTCAAATTCGC
* *
5662 GTTGTGATAGTCATATTCGC
1 GTTGCGATAGTCAAATTCGC
*
5682 GTTGCGATATTCAAAT
1 GTTGCGATAGTCAAAT
5698 GAATGTGTAA
Statistics
Matches: 171, Mismatches: 17, Indels: 48
0.72 0.07 0.20
Matches are distributed among these distances:
14 47 0.27
16 4 0.02
18 4 0.02
20 116 0.68
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:5559 original size:34 final size:34
Alignment explanation
Indices: 5485--5689 Score: 311
Period size: 34 Copynumber: 5.9 Consensus size: 34
5475 GTCAAATTCA
*
5485 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTTG
5525 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
5559 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* *
5593 CGTTGCGATAGTCAAATTTGAGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
5627 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* *
5661 CGTTGTGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
5690 ATTCAAATGA
Statistics
Matches: 158, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
34 129 0.82
38 1 0.01
40 28 0.18
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:5563 original size:14 final size:14
Alignment explanation
Indices: 5544--5635 Score: 58
Period size: 14 Copynumber: 5.7 Consensus size: 14
5534 AGTCAAATTC
5544 GCGTTGCGATTTTT
1 GCGTTGCGATTTTT
*
5558 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGAT--T----TTT
5578 GCGTTGCGATTTTT
1 GCGTTGCGATTTTT
5592 GCGTTGCGATAGTCAAATTT
1 GCGTTGCGAT--T----TTT
*
5612 GAGTTGCGATTTTT
1 GCGTTGCGATTTTT
5626 GCGTTGCGAT
1 GCGTTGCGAT
5636 AGTCAAATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
14 34 0.55
16 2 0.03
18 2 0.03
20 24 0.39
ACGTcount: A:0.16, C:0.15, G:0.28, T:0.40
Consensus pattern (14 bp):
GCGTTGCGATTTTT
Found at i:5920 original size:140 final size:140
Alignment explanation
Indices: 5668--5950 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
5658 TTGCGTTGTG
*
5668 ATAGTCATATTCGCGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTTAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTTAACAGATCA
5733 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
5798 AATACACATA
131 AATACACATA
* *
5808 ATAGTCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTTAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTTAACAGATCA
5873 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
5938 AATACACATA
131 AATACACATA
5948 ATA
1 ATA
5951 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTTAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:9170 original size:20 final size:20
Alignment explanation
Indices: 9145--9315 Score: 177
Period size: 20 Copynumber: 8.4 Consensus size: 20
9135 GAAATTCAGT
*
9145 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
9165 GTTGCGATAGTCAGAATCGA
1 GTTGCGATAGTCAGAATCGC
** *
9185 GTTGCGATTATGT-ATTATCAC
1 GTTGCGA-TA-GTCAGAATCGC
9206 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
9226 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
9247 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* **
9267 TTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
9288 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
9308 GTTGCGAT
1 GTTGCGAT
9316 TTACATATTC
Statistics
Matches: 123, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
19 6 0.05
20 69 0.56
21 42 0.34
22 6 0.05
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:9209 original size:41 final size:41
Alignment explanation
Indices: 9160--9316 Score: 287
Period size: 41 Copynumber: 3.8 Consensus size: 41
9150 GACAGTCAGA
*
9160 ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
9201 ATCACGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
9242 ATCGCGTTGCGATAGTCAGAATCGCTTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
9283 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT
9317 TACATATTCG
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
Found at i:9272 original size:61 final size:61
Alignment explanation
Indices: 9145--9316 Score: 172
Period size: 61 Copynumber: 2.8 Consensus size: 61
9135 GAAATTCAGT
* **
9145 GTTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATTATCAC
1 GTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTAGAATCAC
** * *
9206 GTTGCGATAGTCAGAATCGCGTTGCGATTATGT-ATTATCGCGTTGCGA-TA-GTCAGAATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGA-TA-GTCAGAATCGAGTTGCGATTATGT-AGAATCAC
* ** *
9267 TTTGCGATTATGT-ATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT
1 GTTGCGA-TA-GTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATT
9317 TACATATTCG
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
60 4 0.04
61 54 0.59
62 30 0.33
63 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (61 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTAGAATCAC
Found at i:9426 original size:20 final size:19
Alignment explanation
Indices: 9403--9448 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
9393 GGAAACTGAT
* *
9403 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
9423 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
9442 TTGCGAT
1 TTGCGAT
9449 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:9438 original size:19 final size:19
Alignment explanation
Indices: 9414--9450 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9404 TGCGATACTG
*
9414 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
9433 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
9451 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:9808 original size:22 final size:20
Alignment explanation
Indices: 9770--9809 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
9760 AAATAATTAA
*
9770 AATTTATATAATTAAAAACT
1 AATTTATATAATAAAAAACT
9790 AATTTATACTTAATAAAAAA
1 AATTTATA--TAATAAAAAA
9810 TTTCATCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTATATAATAAAAAACT
Found at i:19444 original size:21 final size:22
Alignment explanation
Indices: 19397--19456 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
19387 ACCCCCATGA
**
19397 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCCT-AAG
19420 GGGAACCGATTCCCCCCCT-AG
1 GGGAACCGATTCCCCCCCTAAG
* *
19441 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
19457 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.48
23 17 0.52
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCCTAAG
Found at i:21675 original size:13 final size:13
Alignment explanation
Indices: 21657--21682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21647 GGAGAAGTGT
21657 TAAGTGTTTTAAA
1 TAAGTGTTTTAAA
21670 TAAGTGTTTTAAA
1 TAAGTGTTTTAAA
21683 GGGAGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TAAGTGTTTTAAA
Found at i:24373 original size:84 final size:84
Alignment explanation
Indices: 24222--24385 Score: 206
Period size: 84 Copynumber: 2.0 Consensus size: 84
24212 AGTATATAGT
** * * * *
24222 TTCCTAAAGGGCTCATTGCTATAAAAAAACATGGATAATCTATATCCATGTATCCAAGGGGACTA
1 TTCCTAAAGGAATCATTGCAATAAAAAAACATGGATAATCTATATCCATATACCCAAGGGAACTA
*
24287 AATTGTTTGAAACTATGAG
66 AATTATTTGAAACTATGAG
* * *
24306 TTCCTAAAGGAATCATTGCAATAAAACAAATATGGAT-ATCCTATCTCCATATACCCAA-GGAAT
1 TTCCTAAAGGAATCATTGCAATAAAA-AAACATGGATAAT-CTATATCCATATACCCAAGGGAAC
24369 TAAATTATTTGAAACTA
64 TAAATTATTTGAAACTA
24386 ACAACAATGG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 44 0.65
85 24 0.35
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (84 bp):
TTCCTAAAGGAATCATTGCAATAAAAAAACATGGATAATCTATATCCATATACCCAAGGGAACTA
AATTATTTGAAACTATGAG
Found at i:25248 original size:13 final size:14
Alignment explanation
Indices: 25224--25261 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
25214 TCTTATCTTA
25224 TTTTTATA-TTA-T
1 TTTTTATATTTAGT
25236 TTTTTATATTTATGT
1 TTTTTATATTTA-GT
25251 TTTTTATATTT
1 TTTTTATATTT
25262 TTTATTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
15 12 0.52
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTATATTTAGT
Found at i:26355 original size:32 final size:32
Alignment explanation
Indices: 26314--26377 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
26304 AAAATCTAAA
*
26314 GTAAGATTAGTAATCTCCTCCCATATAGCTTT
1 GTAAGATTAGTAATCTCCTCCCATATAACTTT
26346 GTAAGATTAGTAATCTCCTCCCATATAACTTT
1 GTAAGATTAGTAATCTCCTCCCATATAACTTT
26378 CTTTTGAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (32 bp):
GTAAGATTAGTAATCTCCTCCCATATAACTTT
Found at i:27772 original size:18 final size:18
Alignment explanation
Indices: 27749--27812 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
27739 ACCGGTTCTA
*
27749 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
* *
27767 ACCCGACTCGACCAGTTG
1 ACCCGACCCGACCCGTTG
* *
27785 ACCCAATCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
27803 ACCCGACCCG
1 ACCCGACCCG
27813 TTGACTGTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.20, C:0.47, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:27810 original size:13 final size:13
Alignment explanation
Indices: 27792--27817 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27782 TTGACCCAAT
27792 CCGACCCGTTGAC
1 CCGACCCGTTGAC
27805 CCGACCCGTTGAC
1 CCGACCCGTTGAC
27818 TGTTAACCGG
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:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:31432 original size:21 final size:20
Alignment explanation
Indices: 31406--31447 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
31396 TTATCATTCA
31406 TTTTAAAATTTTAAATTATTT
1 TTTTAAAATTTTAAATT-TTT
*
31427 TTTTAATATTTTAAATTTTT
1 TTTTAAAATTTTAAATTTTT
31447 T
1 T
31448 AATAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAAAATTTTAAATTTTT
Found at i:31456 original size:16 final size:16
Alignment explanation
Indices: 31420--31461 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
31410 AAAATTTTAA
*
31420 ATTATTTTTTTAATAT
1 ATTAATTTTTTAATAT
*
31436 TTTAAATTTTTTAATA-
1 ATT-AATTTTTTAATAT
31452 ATTAATTTTT
1 ATTAATTTTT
31462 ATTTTTAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTAATTTTTTAATAT
Found at i:31467 original size:38 final size:39
Alignment explanation
Indices: 31420--31506 Score: 92
Period size: 38 Copynumber: 2.3 Consensus size: 39
31410 AAAATTTTAA
31420 ATTATTTTTTTAATAT-TTTAAATTT-TT-TAATAATTAATT
1 ATTA-TTTTTTAATATCTTTAAATTTATTATAA-AATT-ATT
* * *
31459 TTTA-TTTTTAGTATCTTTATATTTATTATAAAATTATT
1 ATTATTTTTTAATATCTTTAAATTTATTATAAAATTATT
31497 ATTATTTTTT
1 ATTATTTTTT
31507 CTTTAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
37 9 0.22
38 14 0.35
39 14 0.35
40 3 0.08
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (39 bp):
ATTATTTTTTAATATCTTTAAATTTATTATAAAATTATT
Found at i:31985 original size:76 final size:76
Alignment explanation
Indices: 31857--32018 Score: 261
Period size: 76 Copynumber: 2.1 Consensus size: 76
31847 TGTGTCTTCA
* * *
31857 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAATTCATGGG
1 ACGTGGGGACCAACTTTGTTATATTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
31922 AAGAATAATGC
66 AAGAATAATGC
* * * *
31933 ATGTGGGGACCAACTTTGTTATATTTGGTAGCATGATGTTTGCAGGAAAATAAGGAAATCATGGG
1 ACGTGGGGACCAACTTTGTTATATTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
31998 AAGAATAATGC
66 AAGAATAATGC
32009 ACGTGGGGAC
1 ACGTGGGGAC
32019 GGGAATGAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (76 bp):
ACGTGGGGACCAACTTTGTTATATTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
AAGAATAATGC
Found at i:35290 original size:8 final size:7
Alignment explanation
Indices: 35255--35418 Score: 69
Period size: 8 Copynumber: 23.4 Consensus size: 7
35245 ACTCGAGTAT
35255 ATATTTA
1 ATATTTA
*
35262 ATA-ATA
1 ATATTTA
35268 ATTATTTA
1 A-TATTTA
35276 A-ATTTA
1 ATATTTA
35282 ATCATTTA
1 AT-ATTTA
35290 A-ATTTA
1 ATATTTA
35296 ATGATTTA
1 AT-ATTTA
*
35304 ATA-ATA
1 ATATTTA
35310 ATTATTTA
1 A-TATTTA
*
35318 A-CTTTA
1 ATATTTA
*
35324 ATGATTTC
1 AT-ATTTA
*
35332 ATA-ATA
1 ATATTTA
35338 ATTATTTA
1 A-TATTTA
*
35346 A-CTTTA
1 ATATTTA
35352 ATGATTTA
1 AT-ATTTA
*
35360 A-ATTAA
1 ATATTTA
35366 ATACTTTA
1 ATA-TTTA
*
35374 ATAATTA
1 ATATTTA
*
35381 TTATTTA
1 ATATTTA
*
35388 A-CTTTA
1 ATATTTA
35394 ATGATTTA
1 AT-ATTTA
*
35402 A-ATTAA
1 ATATTTA
35408 ATACTTTA
1 ATA-TTTA
35416 ATA
1 ATA
35419 ATAATTACTT
Statistics
Matches: 115, Mismatches: 22, Indels: 39
0.65 0.12 0.22
Matches are distributed among these distances:
6 45 0.39
7 21 0.18
8 49 0.43
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (7 bp):
ATATTTA
Found at i:35297 original size:28 final size:28
Alignment explanation
Indices: 35266--35598 Score: 138
Period size: 28 Copynumber: 11.9 Consensus size: 28
35256 TATTTAATAA
* *
35266 TAATTATTTAAATTTAATCATTTAAATT
1 TAATGATTTAAATTTAATTATTTAAATT
* *
35294 TAATGATTT-AATAATAATTATTTAACTT
1 TAATGATTTAAAT-TTAATTATTTAAATT
*
35322 TAATGATTTCATAA--TAATTATTTAACTT
1 TAATGATTT-A-AATTTAATTATTTAAATT
* *
35350 TAATGATTTAAA-TTAAATACTTTAATAAT
1 TAATGATTTAAATTTAATTA-TTTAA-ATT
* * *
35379 T-ATTATTTAACTTTAATGATTTAAATT
1 TAATGATTTAAATTTAATTATTTAAATT
* * * *
35406 AAAT-ACTTT-AATAATAATTACTTAACTT
1 TAATGA-TTTAAAT-TTAATTATTTAAATT
* * * *
35434 TAATGATTT-AATAATAATTACTTCACTT
1 TAATGATTTAAAT-TTAATTATTTAAATT
* * *
35462 TAATAATTTAACTTTAATGATTT--ATT
1 TAATGATTTAAATTTAATTATTTAAATT
* * * *
35488 AATAATTATTTAACTTTAATGATTT-AATAA
1 --TAATGATTTAAATTTAATTATTTAAAT-T
* * * * *
35518 TAATTAATTCACTTTAA-TAATTAAACTT
1 TAATGATTTAAATTTAATTATTTAAA-TT
*
35546 TAATGATTT--ATTAATAATTATTTAACTT
1 TAATGATTTAAATT--TAATTATTTAAATT
*
35574 TAATGA-TTAAAGTTTAATAATTTAA
1 TAATGATTTAAA-TTTAATTATTTAA
35599 TAATAGTAAT
Statistics
Matches: 241, Mismatches: 39, Indels: 50
0.73 0.12 0.15
Matches are distributed among these distances:
26 6 0.02
27 19 0.08
28 192 0.80
29 20 0.08
30 2 0.01
31 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (28 bp):
TAATGATTTAAATTTAATTATTTAAATT
Found at i:35304 original size:42 final size:41
Alignment explanation
Indices: 35257--35603 Score: 160
Period size: 42 Copynumber: 8.3 Consensus size: 41
35247 TCGAGTATAT
*
35257 ATTTAATAATAATTATTTAAATTTAATCATTTAAATTTAATG
1 ATTTAATAATAATGATTTAAATTTAAT-ATTTAAATTTAATG
* * *
35299 ATTTAATAATAATTATTTAACTTTAATGATTTCATAA--TAATT
1 ATTTAATAATAATGATTTAAATTTAAT-ATTT-A-AATTTAATG
* * * *
35341 ATTTAACT-TTAATGATTTAAATTAAATACTTTAATAATT-ATT
1 ATTTAA-TAATAATGATTTAAATTTAATA-TTTAA-ATTTAATG
* * * *
35383 ATTTAACT-TTAATGATTTAAATTAAATACTTT-AATAATAATT
1 ATTTAA-TAATAATGATTTAAATTTAATA-TTTAAAT-TTAATG
* * * * * * *
35425 ACTTAACT-TTAATGATTT-AATAATAATTACTTCACTTTAATA
1 ATTTAA-TAATAATGATTTAAAT-TTAA-TATTTAAATTTAATG
* *
35467 ATTTAACT-TTAATGATTT--ATTAATAATTATTTAACTTTAATG
1 ATTTAA-TAATAATGATTTAAATT--TAA-TATTTAAATTTAATG
* * * * *
35509 ATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATG
1 ATTTAATAATAATGATTTAAATTTAATATTTAAA-TTTAATG
* * * *
35551 ATTTATTAATAATTATTTAACTTTAATGA-TTAAAGTTTAATA
1 ATTTAATAATAATGATTTAAATTTAAT-ATTTAAA-TTTAATG
35593 ATTTAATAATA
1 ATTTAATAATA
35604 GTAATGATAT
Statistics
Matches: 253, Mismatches: 33, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
40 2 0.01
41 17 0.07
42 222 0.88
43 8 0.03
44 4 0.02
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (41 bp):
ATTTAATAATAATGATTTAAATTTAATATTTAAATTTAATG
Found at i:35338 original size:70 final size:69
Alignment explanation
Indices: 35257--35581 Score: 302
Period size: 70 Copynumber: 4.6 Consensus size: 69
35247 TCGAGTATAT
*
35257 ATTTAATAATAATTATTTAAATTTAATCATTTAAATTTAATGATTTAATAATAATTATTTAACTT
1 ATTTAATAATAATTATTT-AATTTAATTATTTAAATTTAATGATTTAATAATAATTATTTAACTT
35322 TAATG
65 TAATG
* * * *
35327 ATTTCATAATAATTATTTAACTTTAATGATTTAAATTAAAT-ACTTTAATAATTATTATTTAACT
1 ATTTAATAATAATTATTTAA-TTTAATTATTTAAATTTAATGA-TTTAATAATAATTATTTAACT
35391 TTAATG
64 TTAATG
* * * * * * *
35397 ATTTAA-ATTAAATACTTTAATAATAATTACTTAACTTTAATGATTTAATAATAATTACTTCACT
1 ATTTAATAATAATTA-TTTAAT-TTAATTATTTAAATTTAATGATTTAATAATAATTATTTAACT
*
35461 TTAATA
64 TTAATG
* * * * *
35467 ATTTAACT-TTAATGATTT-ATTAATAATTATTTAACTTTAATGATTTAATAATAATTAATTCAC
1 ATTTAA-TAATAATTATTTAATT--TAATTATTTAAATTTAATGATTTAATAATAATTATTTAAC
*
35530 TTTAATA
63 TTTAATG
* * * *
35537 ATTAAACT-TTAATGATTT-ATTAATAATTATTTAACTTTAATGATT
1 ATTTAA-TAATAATTATTTAATT--TAATTATTTAAATTTAATGATT
35582 AAAGTTTAAT
Statistics
Matches: 224, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
69 12 0.05
70 206 0.92
71 6 0.03
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (69 bp):
ATTTAATAATAATTATTTAATTTAATTATTTAAATTTAATGATTTAATAATAATTATTTAACTTT
AATG
Found at i:35372 original size:22 final size:22
Alignment explanation
Indices: 35346--35417 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
35336 TAATTATTTA
35346 ACTTTAATGATTTAAATTAAAT
1 ACTTTAATGATTTAAATTAAAT
* **
35368 ACTTTAAT-AATT--ATTATTT
1 ACTTTAATGATTTAAATTAAAT
35387 AACTTTAATGATTTAAATTAAAT
1 -ACTTTAATGATTTAAATTAAAT
35410 ACTTTAAT
1 ACTTTAAT
35418 AATAATTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 5 0.12
20 8 0.20
21 6 0.15
22 16 0.40
23 5 0.12
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (22 bp):
ACTTTAATGATTTAAATTAAAT
Found at i:36534 original size:16 final size:16
Alignment explanation
Indices: 36478--36535 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
36468 AAATAATTAT
* *
36478 AAAAATCAACAAAATA
1 AAAAATAAACATAATA
* *
36494 AATAAATAAAAATATTA
1 AA-AAATAAACATAATA
* *
36511 TAATATAAACATAATA
1 AAAAATAAACATAATA
36527 AAAAATAAA
1 AAAAATAAA
36536 TTCGCTTATT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAACATAATA
Found at i:38514 original size:76 final size:75
Alignment explanation
Indices: 38387--38541 Score: 247
Period size: 76 Copynumber: 2.1 Consensus size: 75
38377 TCCCGTCCTA
* *
38387 ACGTGCATTATTCTTCCTATGATTTCCTTATTTTCCTGCAAACATCATGCTACCAAACATAACAA
1 ACGTGCATTATTCTTCCCATGAATTCCTTATTTTCCTGCAAACATCATGCTACCAAACATAACAA
38452 AGCTAGTCCCC
66 AGCTAGT-CCC
* * *
38463 ACGTGCATTATTCTTCCCATGAATTCCTTATTTTGCTGCAAACTTCCTGCTACCAAACATAACAA
1 ACGTGCATTATTCTTCCCATGAATTCCTTATTTTCCTGCAAACATCATGCTACCAAACATAACAA
*
38528 AGCTGGTCCC
66 AGCTAGTCCC
38538 ACGT
1 ACGT
38542 TTAAGACACA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 7 0.10
76 66 0.90
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (75 bp):
ACGTGCATTATTCTTCCCATGAATTCCTTATTTTCCTGCAAACATCATGCTACCAAACATAACAA
AGCTAGTCCC
Found at i:43443 original size:135 final size:135
Alignment explanation
Indices: 43176--43433 Score: 389
Period size: 135 Copynumber: 1.9 Consensus size: 135
43166 TATAGGGAGA
* *
43176 GAGGAAAATGAGTTGAGCAAAACTAGACATCTTGGAGAGGAACCTACGTATATGCCGGAAAGATC
1 GAGGAAAATGAGTCGAGCAAAACTAGACATCATGGAGAGGAACCTACGTATATGCCGGAAAGATC
*
43241 AGCAGCACCAGAAAAGTCCATTGAAACTCTTTCAAATTTATCTTTTCCACATTATAATATGAGTT
66 AGCAGCACCAGAAAAGTCCATTGAAACTCTTTCAAATTTATCATTTCCACATTATAATATGAGTT
43306 TGCAT
131 TGCAT
* * *
43311 GAGGAAAATGAGTCGA-CTAAAA-TGAGATATCATGGAGAGGAACCTGC-TCATATGCTGGAAAG
1 GAGGAAAATGAGTCGAGC-AAAACT-AGACATCATGGAGAGGAACCTACGT-ATATGCCGGAAAG
*
43373 ATCAGCAGCACCAGAAAAGTCCATTGAAACT-TGTTCAGATTTATCATTTCCACATTATAAT
63 ATCAGCAGCACCAGAAAAGTCCATTGAAACTCT-TTCAAATTTATCATTTCCACATTATAAT
43434 CTGGATTTGC
Statistics
Matches: 112, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
134 4 0.04
135 108 0.96
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (135 bp):
GAGGAAAATGAGTCGAGCAAAACTAGACATCATGGAGAGGAACCTACGTATATGCCGGAAAGATC
AGCAGCACCAGAAAAGTCCATTGAAACTCTTTCAAATTTATCATTTCCACATTATAATATGAGTT
TGCAT
Found at i:44211 original size:39 final size:39
Alignment explanation
Indices: 44157--44271 Score: 178
Period size: 39 Copynumber: 2.9 Consensus size: 39
44147 TTCTAGCCAT
*
44157 AATGTTGATTCTGGTGAAAGGAGGTACTCCAGTTTGCGA
1 AATGTTGATTCTGGTGAAAGGAGGTACTCTAGTTTGCGA
* *
44196 AATGTTGATTCTGGTGGAAA-GAGTTACTCTAGTTTGCGT
1 AATGTTGATTCTGGT-GAAAGGAGGTACTCTAGTTTGCGA
*
44235 AGTGTTGATTCTGGTGAAAGGAGGTACTCTAGTTTGC
1 AATGTTGATTCTGGTGAAAGGAGGTACTCTAGTTTGC
44272 ATGCTGCACC
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
38 4 0.06
39 61 0.88
40 4 0.06
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.35
Consensus pattern (39 bp):
AATGTTGATTCTGGTGAAAGGAGGTACTCTAGTTTGCGA
Found at i:47117 original size:314 final size:318
Alignment explanation
Indices: 46714--47350 Score: 977
Period size: 315 Copynumber: 2.0 Consensus size: 318
46704 GAATTATTTT
* * * *
46714 AATTAATATTAAATAACTTTTTATGTTTAAAAGTATTTGATTAATTTTTTACAAAAAAAAGGGTC
1 AATTAATATTAAATAACTATTTATGTTTAAAAGTATTTAATTAATTTTCTACAAAAAAAAGGGTA
* * * *
46779 AGTTATTACCCTACTTCTCCTTACCCCATCACATATGAGAATAGAGTCTCACGGT-GGACAATTC
66 AGTTACTACCCTACTCCCCCTTACCCCATCACATATGAGAATAGAGTCCCACGGTAGG-CAATTC
* * * *
46843 ATAATTGTTGGAGGTCTT-CACGGAAGTTGCTCTCAATCTAGCATTGGGGGCAG-TCTACTATCA
130 ATAATTGCTGGAGGTCTTCCACGGAAGTTGCTCTCAACCTAGCATTAGAGGCAGCT-TACTA-CA
*
46906 -TACC-TCTCCCTTACCCCATTACATATGAGAATATGGTCAGCTAATTTTTAA-TTTTTTCCTAC
193 CTACCTTC-CCCTTACCCCATTACATATGAGAATAGGGTCAGCTAATTTTTAATTTTTTTCCTAC
*
46968 TCACAGTTTCTCTAGGTTGAAG-AAAGAAGACCAATTTAATAGCTAGCTTATTTAAGCGGTG
257 TCACAGTTTCTCTAGGTTGAAGAAAAGAAGACCAATTTAATAACTAGCTTATTTAAGCGGTG
47029 AATTAATATTAAATAAC-ATTTATGTTTAAAAGTATTTAATTAATTTTCTAC-AAAAAAAGGGTA
1 AATTAATATTAAATAACTATTTATGTTTAAAAGTATTTAATTAATTTTCTACAAAAAAAAGGGTA
* * *
47092 AGTTACTACCCTACCTCCCCCTTACCCCATTACATATGGGAATCGAGTCCCACGGTAGGCAATTC
66 AGTTACTACCCTA-CTCCCCCTTACCCCATCACATATGAGAATAGAGTCCCACGGTAGGCAATTC
* *
47157 ATAATTGCTGGATGTCTTCCACGGAAGTTGCTCTCAACCTAGCGTTAGAGGCAGCTTACTACACT
130 ATAATTGCTGGAGGTCTTCCACGGAAGTTGCTCTCAACCTAGCATTAGAGGCAGCTTACTACACT
*
47222 ACCTTCCCCTTACCCCATTACATATGGGAATAGGGTCAGCTAATTTTTAATTTTTTTCCTACTCA
195 ACCTTCCCCTTACCCCATTACATATGAGAATAGGGTCAGCTAATTTTTAATTTTTTTCCTACTCA
*
47287 CAGTTTCTCTAGGTTGAAGAAAAGAAGACCAATTTAATAACTAGCTTATTTAAGTGGTG
260 CAGTTTCTCTAGGTTGAAGAAAAGAAGACCAATTTAATAACTAGCTTATTTAAGCGGTG
47346 AATTA
1 AATTA
47351 CATGTACATA
Statistics
Matches: 293, Mismatches: 21, Indels: 14
0.89 0.06 0.04
Matches are distributed among these distances:
313 23 0.08
314 91 0.31
315 101 0.34
316 36 0.12
317 42 0.14
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (318 bp):
AATTAATATTAAATAACTATTTATGTTTAAAAGTATTTAATTAATTTTCTACAAAAAAAAGGGTA
AGTTACTACCCTACTCCCCCTTACCCCATCACATATGAGAATAGAGTCCCACGGTAGGCAATTCA
TAATTGCTGGAGGTCTTCCACGGAAGTTGCTCTCAACCTAGCATTAGAGGCAGCTTACTACACTA
CCTTCCCCTTACCCCATTACATATGAGAATAGGGTCAGCTAATTTTTAATTTTTTTCCTACTCAC
AGTTTCTCTAGGTTGAAGAAAAGAAGACCAATTTAATAACTAGCTTATTTAAGCGGTG
Found at i:47952 original size:18 final size:18
Alignment explanation
Indices: 47918--47951 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47908 TTTTCGAAAT
*
47918 ACTTTTAGGGATTTTTTG
1 ACTTTTAGCGATTTTTTG
47936 ACTTTTAGCG-TTTTTT
1 ACTTTTAGCGATTTTTT
47952 TTATGAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.09, G:0.18, T:0.59
Consensus pattern (18 bp):
ACTTTTAGCGATTTTTTG
Found at i:48745 original size:31 final size:31
Alignment explanation
Indices: 48710--48792 Score: 112
Period size: 33 Copynumber: 2.6 Consensus size: 31
48700 TATAGTTTGT
*
48710 GGTAATGATGCATGTTTTAGGGACTGGTTGA
1 GGTAATGATGCATGTTTTAGGGACTAGTTGA
*
48741 GGTAATGATGCATATTTTTTAGGGACTAGTTGA
1 GGTAATGATGC--ATGTTTTAGGGACTAGTTGA
* *
48774 GGCAATGATTCATGTTTTA
1 GGTAATGATGCATGTTTTA
48793 CCTAATGCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
31 18 0.40
33 27 0.60
ACGTcount: A:0.25, C:0.07, G:0.29, T:0.39
Consensus pattern (31 bp):
GGTAATGATGCATGTTTTAGGGACTAGTTGA
Found at i:50189 original size:30 final size:30
Alignment explanation
Indices: 50152--50223 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
50142 AACAAGGATT
* *
50152 ACACCATCATCA-AAGGCTATAACATCACAA
1 ACACCATCATCACAA-ACTACAACATCACAA
* *
50182 GCACCATCATCACAAACTGCAACATCACAA
1 ACACCATCATCACAAACTACAACATCACAA
50212 ACACCATCATCA
1 ACACCATCATCA
50224 TCACAAGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.44, C:0.35, G:0.06, T:0.15
Consensus pattern (30 bp):
ACACCATCATCACAAACTACAACATCACAA
Found at i:50192 original size:15 final size:15
Alignment explanation
Indices: 50174--50223 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
50164 AAGGCTATAA
*
50174 CATCACAAGCACCAT
1 CATCACAAACACCAT
** *
50189 CATCACAAACTGCAA
1 CATCACAAACACCAT
50204 CATCACAAACACCAT
1 CATCACAAACACCAT
50219 CATCA
1 CATCA
50224 TCACAAGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.44, C:0.38, G:0.04, T:0.14
Consensus pattern (15 bp):
CATCACAAACACCAT
Found at i:51324 original size:35 final size:35
Alignment explanation
Indices: 51283--51352 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
51273 CTTCCTATTT
*
51283 CTTCTGCTGCTGAAAAAAAGAGTAGAAATGAAGCA
1 CTTCTGCTGCTGAAAAAAAGAGGAGAAATGAAGCA
*
51318 CTTCTGCTGCTGGAAAAAAGAGGAGAAATGAAGCA
1 CTTCTGCTGCTGAAAAAAAGAGGAGAAATGAAGCA
51353 AATAGGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.19
Consensus pattern (35 bp):
CTTCTGCTGCTGAAAAAAAGAGGAGAAATGAAGCA
Found at i:72217 original size:24 final size:23
Alignment explanation
Indices: 72184--72232 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
72174 AAAAATTTAG
*
72184 GAACTAGATTGAAGCTCGAGACTC
1 GAACTAGATTGAAGCTC-AAACTC
* *
72208 GAACTCGATTTAAGCTCAAACTC
1 GAACTAGATTGAAGCTCAAACTC
72231 GA
1 GA
72233 TTCAAGTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
GAACTAGATTGAAGCTCAAACTC
Found at i:72231 original size:17 final size:17
Alignment explanation
Indices: 72209--72247 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
72199 TCGAGACTCG
*
72209 AACTCGATTTAAGCTCA
1 AACTCGATTCAAGCTCA
*
72226 AACTCGATTCAAGTTCA
1 AACTCGATTCAAGCTCA
72243 AACTC
1 AACTC
72248 AAACTCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (17 bp):
AACTCGATTCAAGCTCA
Found at i:72304 original size:14 final size:14
Alignment explanation
Indices: 72285--72351 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
72275 TTATATTATA
*
72285 TTTAAAAATATACT
1 TTTAAAAATATAAT
72299 TTTAAAAAATTATAAT
1 TTT-AAAAA-TATAAT
* * *
72315 TATCAATAATATATT
1 T-TTAAAAATATAAT
*
72330 TTTAATAATATAAT
1 TTTAAAAATATAAT
72344 TTTAAAAA
1 TTTAAAAA
72352 ATCTAAAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
14 21 0.49
15 11 0.26
16 10 0.23
17 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAAAATATAAT
Found at i:72376 original size:45 final size:45
Alignment explanation
Indices: 72285--72377 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
72275 TTATATTATA
* * * *
72285 TTTAAAAATATACTTTTAAAAAATTATAATTATCAATAATATATT
1 TTTAAAAATATAATTTTAAAAAATTAAAACTATCAATAATACATT
*
72330 TTTAATAATATAATTTTAAAAAATCTAAAACTAT-AAT-ATAACATT
1 TTTAAAAATATAATTTTAAAAAAT-TAAAACTATCAATAAT-ACATT
72375 TTT
1 TTT
72378 GTTTTAGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.05
45 32 0.78
46 7 0.17
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (45 bp):
TTTAAAAATATAATTTTAAAAAATTAAAACTATCAATAATACATT
Found at i:74239 original size:5 final size:5
Alignment explanation
Indices: 74225--74264 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
74215 AAAACAAGTC
*
74225 AAATA TAATA AAATA AAATA AAATA AAATA TATAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA -A-AATA AAA
74265 AGTAATGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 25 0.81
6 2 0.06
7 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
AAATA
Found at i:76716 original size:2 final size:2
Alignment explanation
Indices: 76638--76697 Score: 61
Period size: 2 Copynumber: 30.5 Consensus size: 2
76628 TTGTTTAAAC
* * * *
76638 TA TA TA -A TA TG TA TT TA TA TA TA TT TA -A AA CTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
76679 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
76698 TATTTTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.94
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76815 original size:2 final size:2
Alignment explanation
Indices: 76808--76836 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
76798 TTTAAAATTT
76808 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
76837 TAAAATTATA
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:77438 original size:112 final size:111
Alignment explanation
Indices: 77322--77658 Score: 266
Period size: 112 Copynumber: 3.1 Consensus size: 111
77312 TATGCCGTGG
77322 AATTGAAACCTAGCCTGAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAAT
1 AATTGAAACCT-GCCTGAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAAT
* *
77387 GTAGTCTATTTGGCTTTCGAACCCAATAACCTCCATCGTGGAGTTGA
65 GTAGTCTATTTGGATTTCGAACCCAATATCCTCCATCGTGGAGTTGA
* * * * ** * * *
77434 AATTG--ACCT--C-GAAAAGGTTTGACTAGAAGA-TTGCTCATCGATGCTAAGTTAAGCCAAAA
1 AATTGAAACCTGCCTGAAAA-CTTTAACTAGAA-ACTAGCTCCTCGCCGCTGAGTTAAGCTAGAA
* ** * * * ** * *
77493 TATAGTCGGTTTCGAATACGCTTATAGGTCAAGTATCCT--AT-GT-CA--TGG
64 TGTAGTCTATTTGGATTTCG---A-A-CCCAA-TATCCTCCATCGTGGAGTTGA
* * *
77541 AGTTGAAACCTGGCCTAAAAACTTTAATTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAAT
1 AATTGAAACCT-GCCTGAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAAT
* *
77606 GTAGTCTATTTGGATTTTGAACCCAATATCCTCCATCGCGGAGTTGA
65 GTAGTCTATTTGGATTTCGAACCCAATATCCTCCATCGTGGAGTTGA
77653 AATTGA
1 AATTGA
77659 CTTTGAAAAG
Statistics
Matches: 158, Mismatches: 46, Indels: 42
0.64 0.19 0.17
Matches are distributed among these distances:
106 11 0.07
107 55 0.35
108 4 0.03
109 7 0.04
110 8 0.05
111 4 0.03
112 60 0.38
113 9 0.06
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (111 bp):
AATTGAAACCTGCCTGAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAATG
TAGTCTATTTGGATTTCGAACCCAATATCCTCCATCGTGGAGTTGA
Found at i:77616 original size:219 final size:218
Alignment explanation
Indices: 77261--77930 Score: 740
Period size: 219 Copynumber: 3.1 Consensus size: 218
77251 CTTGACACTG
* * * * *
77261 AGTTAAGCCAAAATATAGTCGGTTTTGAATAAGCTTCTAAGTCAAGTATCATATGCCGTGGAATT
1 AGTTAAGCCAAAATATAGTCGGTTTTGAATAAGCTTATAGGTCAAGTATC-TATGTCATGGAGTT
* *
77326 GAAACCTAGCCTGAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAATGTAG
65 GAAACCTGGCCTAAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAATGTAG
* *
77391 TCTATTTGGCTTTCGAACCCAATAACCTCCATCGTGGAGTTGAAATTGACCTCGAAAAGGTTTGA
130 TCTATTTGGCTTTCGAACCCAATATCCTCCATCGTGGAGTTGAAATTGACTTCGAAAAGGTTTGA
*
77456 CTAGAAGAT-T-GCTCATCGATGCTA
195 CT-GAA-ATGTGGCTCATCGACGCTA
* *
77480 AGTTAAGCCAAAATATAGTCGGTTTCGAATACGCTTATAGGTCAAGTATCCTATGTCATGGAGTT
1 AGTTAAGCCAAAATATAGTCGGTTTTGAATAAGCTTATAGGTCAAGTAT-CTATGTCATGGAGTT
*
77545 GAAACCTGGCCTAAAAACTTTAATTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAATGTAG
65 GAAACCTGGCCTAAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAATGTAG
* * * *
77610 TCTATTTGGATTTTGAACCCAATATCCTCCATCGCGGAGTTGAAATTGACTTTGAAAAGGTTTGA
130 TCTATTTGGCTTTCGAACCCAATATCCTCCATCGTGGAGTTGAAATTGACTTCGAAAAGGTTTGA
* *** * *
77675 CTGAAATGTGGCTCTTTTCCGTTG
195 CTGAAATGTGGCTCATCGACGCTA
** * * ** * * * * *
77699 AGTTAAGCCAAAATGCAGTTGATTCTTG-ATTTGTTTTTGGGTCAAGTAT-T-TTTAATTGTGAA
1 AGTTAAGCCAAAATATAGTCGGTT-TTGAATAAGCTTATAGGTCAAGTATCTATGTCA-TG-G-A
* * * *
77761 GTTGAAA-CTGGCCTAGAAACTTTAACTAGAAACCAGCTCTTCGCCGCTGAGTTAAGCTAGAATA
62 GTTGAAACCTGGCCTAAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAATG
* * ** * * * *
77825 CAGTCAATTTGGCTTTCGAACTTAACATCCTCCGTCGTAGAGTTGAAATTGACTTCGAAAAAGTT
127 TAGTCTATTTGGCTTTCGAACCCAATATCCTCCATCGTGGAGTTGAAATTGACTTCGAAAAGGTT
* * * * * * * *
77890 TGATTGGAAGGTGGATCCTCGTCGTTG
192 TGACTGAAATGTGGCTCATCGACGCTA
77917 AGTTAAGCCAAAAT
1 AGTTAAGCCAAAAT
77931 GCAGTCAAAT
Statistics
Matches: 384, Mismatches: 60, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
216 3 0.01
217 5 0.01
218 143 0.37
219 230 0.60
220 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (218 bp):
AGTTAAGCCAAAATATAGTCGGTTTTGAATAAGCTTATAGGTCAAGTATCTATGTCATGGAGTTG
AAACCTGGCCTAAAAACTTTAACTAGAAACTAGCTCCTCGCCGCTGAGTTAAGCTAGAATGTAGT
CTATTTGGCTTTCGAACCCAATATCCTCCATCGTGGAGTTGAAATTGACTTCGAAAAGGTTTGAC
TGAAATGTGGCTCATCGACGCTA
Done.