Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012353.1 Corchorus olitorius cultivar O-4 contig12386, 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: 68006
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:634 original size:17 final size:17
Alignment explanation
Indices: 612--645 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
602 AATTCTTTTT
*
612 TTTTTTTGAGTTTTGAA
1 TTTTTTGGAGTTTTGAA
*
629 TTTTTTGGATTTTTGAA
1 TTTTTTGGAGTTTTGAA
646 AACCTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (17 bp):
TTTTTTGGAGTTTTGAA
Found at i:5170 original size:2 final size:2
Alignment explanation
Indices: 5137--5161 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5127 TTAACCTTAG
5137 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 A
5162 ACTTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5291 original size:18 final size:18
Alignment explanation
Indices: 5268--5312 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
5258 TAAAGAGTCT
5268 ACAGAAGCAGATGATGAA
1 ACAGAAGCAGATGATGAA
5286 ACAGAAGCAGATGATGAA
1 ACAGAAGCAGATGATGAA
5304 ACAGAAGCA
1 ACAGAAGCA
5313 AAGGTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.13, G:0.27, T:0.09
Consensus pattern (18 bp):
ACAGAAGCAGATGATGAA
Found at i:5486 original size:31 final size:31
Alignment explanation
Indices: 5415--5486 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
5405 GTCTATCAGC
*
5415 TTTTAATTTGTTTAATTTAAGACATTCATTT
1 TTTTAATTTGTTTAATTTAAGACATTAATTT
*
5446 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACATTAATTT
5476 GTTTTAATTTG
1 -TTTTAATTTG
5487 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACATTAATTT
Found at i:5776 original size:13 final size:12
Alignment explanation
Indices: 5740--5786 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
5730 TCAATCTTTA
*
5740 TATATATTGATAA
1 TATATATT-ATAT
*
5753 TA-ATGTTATAT
1 TATATATTATAT
5764 TATATTATTATAT
1 TATA-TATTATAT
5777 TATATATTAT
1 TATATATTAT
5787 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5935 original size:17 final size:17
Alignment explanation
Indices: 5915--5963 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
5905 AAATAAAACT
5915 CGAGCCCGAACCCGACC
1 CGAGCCCGAACCCGACC
*
5932 CGAGCCCGAACCCTACC
1 CGAGCCCGAACCCGACC
*
5949 CGAGACCGAACCCGA
1 CGAGCCCGAACCCGA
5964 AAATACCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.27, C:0.49, G:0.22, T:0.02
Consensus pattern (17 bp):
CGAGCCCGAACCCGACC
Found at i:5975 original size:16 final size:16
Alignment explanation
Indices: 5954--6073 Score: 90
Period size: 16 Copynumber: 7.6 Consensus size: 16
5944 CTACCCGAGA
5954 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
* *
5970 CCGAACTCG-ACATAAC
1 CCGAACCCGAAAAT-AC
5986 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
* *
6002 CCGAGCCCGACTTAAT--
1 CCGAACCCGA--AAATAC
6018 CC-AATCCCGAAAATAC
1 CCGAA-CCCGAAAATAC
6034 CCGAACCCGAAAA-AGC
1 CCGAACCCGAAAATA-C
* *
6050 CCGAACTCG-AAGTAC
1 CCGAACCCGAAAATAC
*
6065 CCTAACCCG
1 CCGAACCCG
6074 CCCGAGCCCG
Statistics
Matches: 82, Mismatches: 12, Indels: 21
0.71 0.10 0.18
Matches are distributed among these distances:
14 3 0.04
15 15 0.18
16 56 0.68
17 5 0.06
18 3 0.04
ACGTcount: A:0.38, C:0.38, G:0.14, T:0.10
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:5995 original size:32 final size:32
Alignment explanation
Indices: 5954--6073 Score: 129
Period size: 32 Copynumber: 3.8 Consensus size: 32
5944 CTACCCGAGA
*
5954 CCGAACCCGAAAATACCCGAACTCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* * *
5986 CCGAACCCGAAAATACCCGAGCCCGACTTAAT
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
6018 CC-AATCCCGAAAATACCCGAACCCGA-AAAAGC
1 CCGAA-CCCGAAAATACCCGAACCCGACATAA-C
* * *
6050 CCGAACTCG-AAGTACCCTAACCCG
1 CCGAACCCGAAAATACCCGAACCCG
6074 CCCGAGCCCG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
31 17 0.23
32 55 0.74
33 2 0.03
ACGTcount: A:0.38, C:0.38, G:0.14, T:0.10
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:7165 original size:25 final size:24
Alignment explanation
Indices: 7129--7175 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
7119 TCCTTCTATT
7129 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
7152 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
7176 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:13312 original size:227 final size:227
Alignment explanation
Indices: 12917--13358 Score: 767
Period size: 227 Copynumber: 1.9 Consensus size: 227
12907 CTGGGGGCGG
*
12917 GTAGGGGTACCCGGGGCTGGGCACCATAAGAAACGGCCTTAACACAAGTATGAGGCTACACGGGG
1 GTAGGGGTACCCGGGGCCGGGCACCATAAGAAACGGCCTTAACACAAGTATGAGGCTACACGGGG
* *
12982 GCGGGTAGGGCTACCCGGAGCCGGGTGACCCCCGGATTTATTTTTATTATTGCGTTTTTTTTTAT
66 GCGGGAAGGGCTACCCGGAGCCGGGTCACCCCCGGATTTATTTTTATTATTGCGTTTTTTTTTAT
*
13047 TTATTTTTCCTAGTTGGACTTGGAATTAGGTTATGTTTTGCCTATATAAAGGCATCAACCCCCTC
131 TTATTTTTCCTAGTTGGACTTGGAATTAGGTTATGTTTTGCCTATATAAAGGCATCAAACCCCTC
13112 TTTTGTATTCAAGTTGAGTTACCCGGGGGTGT
196 TTTTGTATTCAAGTTGAGTTACCCGGGGGTGT
* ** * *
13144 GTAGGGGTACCCGGGGCCGGGCACCATCATTAACGGCCTTAACACAAGTCTGAGGCTACCCGGGG
1 GTAGGGGTACCCGGGGCCGGGCACCATAAGAAACGGCCTTAACACAAGTATGAGGCTACACGGGG
* *
13209 GCGGGAAGGGGTACCCGGGGCCGGGTCACCCCCGGATTTATTTTTATTATTGCGTTTTTTTTTAT
66 GCGGGAAGGGCTACCCGGAGCCGGGTCACCCCCGGATTTATTTTTATTATTGCGTTTTTTTTTAT
* *
13274 TTATTTTTCCTAGTTGGACTTGGAATTAGGTTATGTTTTGTCTATATAAAGGGATCAAACCCCTC
131 TTATTTTTCCTAGTTGGACTTGGAATTAGGTTATGTTTTGCCTATATAAAGGCATCAAACCCCTC
13339 TTTTGTATTCAAGTTGAGTT
196 TTTTGTATTCAAGTTGAGTT
13359 GATTAATAAA
Statistics
Matches: 202, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
227 202 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (227 bp):
GTAGGGGTACCCGGGGCCGGGCACCATAAGAAACGGCCTTAACACAAGTATGAGGCTACACGGGG
GCGGGAAGGGCTACCCGGAGCCGGGTCACCCCCGGATTTATTTTTATTATTGCGTTTTTTTTTAT
TTATTTTTCCTAGTTGGACTTGGAATTAGGTTATGTTTTGCCTATATAAAGGCATCAAACCCCTC
TTTTGTATTCAAGTTGAGTTACCCGGGGGTGT
Found at i:22458 original size:2 final size:2
Alignment explanation
Indices: 22451--22525 Score: 52
Period size: 2 Copynumber: 40.0 Consensus size: 2
22441 CTGACCATCC
* * * *
22451 AT AT AT AT AT AT AT AT AT AT A- AT TT TT GT AT CT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
22491 AT AT A- AT AT AT AT AA AT A- AA AT TT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22526 TAACTTAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
1 5 0.09
2 53 0.91
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22593 original size:24 final size:24
Alignment explanation
Indices: 22556--22615 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
22546 AAACGTCAAT
*
22556 TATAA-TAGATATTTTGTTATATA
1 TATAATTACATATTTTGTTATATA
*
22579 TATAATTACATATTTTGTTTTATA
1 TATAATTACATATTTTGTTATATA
22603 -ATATATTACATAT
1 TATA-ATTACATAT
22616 ATAATATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (24 bp):
TATAATTACATATTTTGTTATATA
Found at i:22637 original size:22 final size:20
Alignment explanation
Indices: 22599--22656 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
22589 TATTTTGTTT
* *
22599 TATAATATATTACATATATAA
1 TATAATATAATATATATA-AA
22620 TATAATTATAATATATATAAA
1 TATAA-TATAATATATATAAA
*
22641 TTTAA-ATTAATATATA
1 TATAATA-TAATATATA
22657 AATCCATTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 9 0.28
21 11 0.34
22 11 0.34
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATATAATATATATAAA
Found at i:22656 original size:27 final size:27
Alignment explanation
Indices: 22598--22657 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
22588 ATATTTTGTT
*
22598 TTATAATATATTACATATATAATATAA
1 TTATAATATATTAAATATATAATATAA
*
22625 TTATAATATATATAAATTTA-AAT-TAA
1 TTATAATATAT-TAAATATATAATATAA
22651 TATATAA
1 T-TATAA
22658 ATCCATTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 19 0.66
28 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TTATAATATATTAAATATATAATATAA
Found at i:23818 original size:18 final size:17
Alignment explanation
Indices: 23789--23822 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
23779 AAATTTTTTA
23789 TTTATTTATAATTTAAT
1 TTTATTTATAATTTAAT
23806 TTTATTTACTAATTTAA
1 TTTATTTA-TAATTTAA
23823 CTTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATTTATAATTTAAT
Found at i:24309 original size:18 final size:18
Alignment explanation
Indices: 24283--24341 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
24273 GTTCTCAAAC
24283 AATGAATTTGTGAGAGAG
1 AATGAATTTGTGAGAGAG
* * *
24301 AATGCA-TT-T-A-CGAC
1 AATGAATTTGTGAGAGAG
24315 AATGAATTTGTGAGAGAG
1 AATGAATTTGTGAGAGAG
*
24333 AATGCATTT
1 AATGAATTT
24342 ACGAATAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 2 0.07
17 3 0.10
18 15 0.50
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (18 bp):
AATGAATTTGTGAGAGAG
Found at i:24322 original size:32 final size:32
Alignment explanation
Indices: 24281--24345 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
24271 ACGTTCTCAA
24281 ACAATGAATTTGTGAGAGAGAATGCATTTACG
1 ACAATGAATTTGTGAGAGAGAATGCATTTACG
24313 ACAATGAATTTGTGAGAGAGAATGCATTTACG
1 ACAATGAATTTGTGAGAGAGAATGCATTTACG
24345 A
1 A
24346 ATAAAACTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (32 bp):
ACAATGAATTTGTGAGAGAGAATGCATTTACG
Found at i:26612 original size:20 final size:20
Alignment explanation
Indices: 26587--26624 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26577 AATTCAACTC
26587 GATCTAAGATAACATTGATT
1 GATCTAAGATAACATTGATT
*
26607 GATCTAAGATAACGTTGA
1 GATCTAAGATAACATTGA
26625 GCGCAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
GATCTAAGATAACATTGATT
Found at i:27489 original size:14 final size:15
Alignment explanation
Indices: 27470--27513 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
27460 ATAAAACAAA
27470 TTGTTATATATAT-T
1 TTGTTATATATATAT
27484 TTGTTATATATATAAT
1 TTGTTATATATAT-AT
*
27500 ATGTTATATATATA
1 TTGTTATATATATA
27514 ATATATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.48
15 1 0.04
16 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTGTTATATATATAT
Found at i:27519 original size:18 final size:16
Alignment explanation
Indices: 27441--27548 Score: 82
Period size: 16 Copynumber: 6.8 Consensus size: 16
27431 AAAACGTTAA
*
27441 TTATAATATATAATATA
1 TTAT-ATATATAATATG
* *
27458 TTATA-AAACAA-ATTG
1 TTATATATATAATA-TG
*
27473 TTATATATAT--TTTG
1 TTATATATATAATATG
27487 TTATATATATAATATG
1 TTATATATATAATATG
27503 TTATATATATAATAT-
1 TTATATATATAATATG
* *
27518 ATATTATATATAATATAA
1 TTA-TATATATAATAT-G
27536 TTATAATATATAA
1 TTAT-ATATATAA
27549 ATTTAAATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
14 13 0.18
15 12 0.16
16 33 0.45
17 5 0.07
18 10 0.14
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATATATATAATATG
Found at i:27565 original size:2 final size:2
Alignment explanation
Indices: 27488--27547 Score: 55
Period size: 2 Copynumber: 34.0 Consensus size: 2
27478 TATATTTTGT
*
27488 TA TA TA TA TA -A TA TG T- TA TA TA TA TA -A TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27526 TA TA -A TA TA -A T- TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
27548 AATTTAAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
1 8 0.16
2 41 0.84
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:39676 original size:21 final size:21
Alignment explanation
Indices: 39663--39719 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
39653 ATGGCATCTT
39663 AACCTTCTCCAATGAGCTTGG
1 AACCTTCTCCAATGAGCTTGG
39684 AACCTTCTCCAATGAGCTTGG
1 AACCTTCTCCAATGAGCTTGG
* *
39705 AACATGCTCCAATGA
1 AACCTTCTCCAATGA
39720 ACTCCTTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (21 bp):
AACCTTCTCCAATGAGCTTGG
Found at i:44717 original size:21 final size:21
Alignment explanation
Indices: 44679--44719 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44669 TTATAAACCC
*
44679 TAGTACCACTTAGGTCCAATT
1 TAGTACCACTTAGCTCCAATT
44700 TAGTACCACTT-GTCTCCAAT
1 TAGTACCACTTAG-CTCCAAT
44720 AGGGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (21 bp):
TAGTACCACTTAGCTCCAATT
Found at i:45214 original size:25 final size:24
Alignment explanation
Indices: 45177--45223 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
45167 CTAGAAAATT
45177 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
45203 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
45224 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:46087 original size:21 final size:21
Alignment explanation
Indices: 46074--46193 Score: 172
Period size: 21 Copynumber: 5.7 Consensus size: 21
46064 ATGGCATCTT
46074 AACCTTCTCCAATGAGCTTGG
1 AACCTTCTCCAATGAGCTTGG
46095 AACCTTCTCCAATGAGCTTGG
1 AACCTTCTCCAATGAGCTTGG
* *
46116 AACCTTCTCCAATAAACTTGG
1 AACCTTCTCCAATGAGCTTGG
*
46137 AACCTTCTCCAATGTGCTTGG
1 AACCTTCTCCAATGAGCTTGG
*
46158 -AGCTTGCTCCAATGAGCTTGG
1 AACCTT-CTCCAATGAGCTTGG
46179 AA-CTTGCTCCAATGA
1 AACCTT-CTCCAATGA
46194 ACTCCTAGCA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.04
21 85 0.94
22 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (21 bp):
AACCTTCTCCAATGAGCTTGG
Found at i:49849 original size:2 final size:2
Alignment explanation
Indices: 49842--49868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49832 AAATGTTCTT
49842 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
49869 TTACAAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50031 original size:2 final size:2
Alignment explanation
Indices: 50024--50048 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50014 ATAATTCAGT
50024 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
50049 TTCTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54175 original size:26 final size:27
Alignment explanation
Indices: 54123--54175 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
54113 ATTTTAGTTC
* *
54123 AAAAATTTGTTTTACTTTTTATCAAAA
1 AAAAAATTGTTTTACTTTTAATCAAAA
*
54150 AAAAAATTGTTTTAC-TTTAATTAAAA
1 AAAAAATTGTTTTACTTTTAATCAAAA
54176 TTGTAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (27 bp):
AAAAAATTGTTTTACTTTTAATCAAAA
Found at i:57262 original size:17 final size:17
Alignment explanation
Indices: 57240--57272 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
57230 TTATGTGATT
57240 AGTAT-ATATATACTAGG
1 AGTATAATAT-TACTAGG
57257 AGTATAATATTACTAG
1 AGTATAATATTACTAG
57273 TAACATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (17 bp):
AGTATAATATTACTAGG
Found at i:58443 original size:21 final size:19
Alignment explanation
Indices: 58403--58461 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
58393 GTGTAATTTT
*
58403 TCATTACACTCAAA-AGTGA
1 TCATTACAC-CAAATATTGA
58422 TGCCATTACACCAAATATTGA
1 T--CATTACACCAAATATTGA
* *
58443 TTATTACACTAAATATTGA
1 TCATTACACCAAATATTGA
58462 CAACTTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 17 0.50
20 4 0.12
21 13 0.38
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (19 bp):
TCATTACACCAAATATTGA
Found at i:66119 original size:24 final size:24
Alignment explanation
Indices: 66087--66135 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
66077 ATCTTTCCAC
66087 CTCAATGCAAAAATCAAATATGAA
1 CTCAATGCAAAAATCAAATATGAA
66111 CTCAATGCAAAAATCAAATATGAA
1 CTCAATGCAAAAATCAAATATGAA
66135 C
1 C
66136 AAAATCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.20
Consensus pattern (24 bp):
CTCAATGCAAAAATCAAATATGAA
Found at i:67232 original size:5 final size:6
Alignment explanation
Indices: 67210--67258 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
67200 AAAATTAACA
* *
67210 AAAACAC AAAAAC AAAAAC AAAAAC AAAATATG AAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAA-A-C AAAAAC AAAAAC AAAA
67259 CTAAAGGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
6 27 0.73
7 6 0.16
8 4 0.11
ACGTcount: A:0.80, C:0.12, G:0.02, T:0.06
Consensus pattern (6 bp):
AAAAAC
Done.