Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018942.1 Corchorus olitorius cultivar O-4 contig18975, 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: 65713
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1079 original size:13 final size:12
Alignment explanation
Indices: 1058--1092 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
1048 AATAAAGTAA
1058 TAATACTATTAT
1 TAATACTATTAT
1070 TAATTACTATTAT
1 TAA-TACTATTAT
1083 TAATACTATT
1 TAATACTATT
1093 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Found at i:15930 original size:33 final size:30
Alignment explanation
Indices: 15888--16005 Score: 127
Period size: 30 Copynumber: 3.9 Consensus size: 30
15878 GGCACCTCTA
*
15888 CTGGTGGTTGCTGCTGCTGCTGCGCCGCC-CCTT
1 CTGGTGGTTGCTGCTGCTGC-GC-CC-CCTCC-C
15921 CTGGTGGTTGCTGCTGCTGCGCCCCCTCCC
1 CTGGTGGTTGCTGCTGCTGCGCCCCCTCCC
*
15951 CTGGTGGTTGCTGCTGCTCCGCCCCCT---
1 CTGGTGGTTGCTGCTGCTGCGCCCCCTCCC
* * *
15978 CTGGTGGTAGCAGCTGCTCCGCCCCCTC
1 CTGGTGGTTGCTGCTGCTGCGCCCCCTC
16006 TGGTGGTAGC
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
27 25 0.32
30 28 0.35
31 4 0.05
32 2 0.03
33 20 0.25
ACGTcount: A:0.02, C:0.41, G:0.31, T:0.27
Consensus pattern (30 bp):
CTGGTGGTTGCTGCTGCTGCGCCCCCTCCC
Found at i:15943 original size:27 final size:27
Alignment explanation
Indices: 15902--16105 Score: 185
Period size: 27 Copynumber: 7.4 Consensus size: 27
15892 TGGTTGCTGC
* *
15902 TGCTGCTGCGCCGCCCCTTCTGGTGGT
1 TGCTGCTGCTCCGCCCCCTCTGGTGGT
*
15929 TGCTGCTGCTGCGCCCCCTCCCCTGGTGGT
1 TGCTGCTGCTCCGCCCCCT---CTGGTGGT
15959 TGCTGCTGCTCCGCCCCCTCTGGTGGT
1 TGCTGCTGCTCCGCCCCCTCTGGTGGT
* *
15986 AGCAGCTGCTCCGCCCCCTCTGGTGGT
1 TGCTGCTGCTCCGCCCCCTCTGGTGGT
* * * * **
16013 AGCAGCGGCTCCACATCCTCTGGTGGT
1 TGCTGCTGCTCCGCCCCCTCTGGTGGT
* * *
16040 TGCTGCTGCGCCGCCGCCTCTGTTGGAT
1 TGCTGCTGCTCCGCCCCCTCTGGTGG-T
* * * * *
16068 T-TTGCAGCCCCGCCGCCTCTGTTGGT
1 TGCTGCTGCTCCGCCCCCTCTGGTGGT
*
16094 TGCTGCGGCTCC
1 TGCTGCTGCTCC
16106 ACCTTCGTCA
Statistics
Matches: 148, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
26 2 0.01
27 118 0.80
28 2 0.01
30 26 0.18
ACGTcount: A:0.04, C:0.39, G:0.30, T:0.27
Consensus pattern (27 bp):
TGCTGCTGCTCCGCCCCCTCTGGTGGT
Found at i:19818 original size:14 final size:14
Alignment explanation
Indices: 19785--19826 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
19775 TTTATTACTG
19785 TTTTATTAAAT--T
1 TTTTATTAAATGAT
*
19797 GTTT-TTAAATGAT
1 TTTTATTAAATGAT
19810 TTTTATTAAATGAT
1 TTTTATTAAATGAT
19824 TTT
1 TTT
19827 GGGTGCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 3 0.12
13 4 0.16
14 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (14 bp):
TTTTATTAAATGAT
Found at i:24703 original size:14 final size:14
Alignment explanation
Indices: 24670--24711 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
24660 TTTATTACTG
24670 TTTTATTAAAT--T
1 TTTTATTAAATGAT
*
24682 GTTT-TTAAATGAT
1 TTTTATTAAATGAT
24695 TTTTATTAAATGAT
1 TTTTATTAAATGAT
24709 TTT
1 TTT
24712 GGATGCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 3 0.12
13 4 0.16
14 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (14 bp):
TTTTATTAAATGAT
Found at i:26528 original size:21 final size:22
Alignment explanation
Indices: 26498--26539 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
26488 CCCGAAGGTA
26498 ATTATATATAT-TTATATAAAT
1 ATTATATATATATTATATAAAT
*
26519 ATTATCTATATAATTATATAA
1 ATTATATATAT-ATTATATAA
26540 TTTGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTATATATATATTATATAAAT
Found at i:28655 original size:11 final size:11
Alignment explanation
Indices: 28621--28655 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28611 CACTTTACTG
*
28621 TTGATTTGCTG
1 TTGATTTGCTA
*
28632 TTGATTTGTTA
1 TTGATTTGCTA
28643 TTGATTTGCTA
1 TTGATTTGCTA
28654 TT
1 TT
28656 AAGCTTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.14, C:0.06, G:0.20, T:0.60
Consensus pattern (11 bp):
TTGATTTGCTA
Found at i:31080 original size:91 final size:87
Alignment explanation
Indices: 30932--31109 Score: 302
Period size: 91 Copynumber: 2.0 Consensus size: 87
30922 TGGCAATTAT
*
30932 GATATTAATTTTATTTTTTAATACTTCATTTATAATAGTAATAATAATATTACTATTTTAATGTT
1 GATATTAATTTTATTTTCTAATACTTCATTTATAATAGTAATAATAATATTACTATTTTAATGTT
30997 AACTAATGAATTCTAATACTTC
66 AACTAATGAATTCTAATACTTC
*
31019 GATATTAATTTTATTTTCTAATACTTCATTTATTTATAATAGTAATAATAATATTATTATTTTAA
1 GATATTAATTTTATTTTCTAATACTTC----ATTTATAATAGTAATAATAATATTACTATTTTAA
31084 TGTTAACTAATGAATTCTAATACTTC
62 TGTTAACTAATGAATTCTAATACTTC
31110 ATTTATAATA
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
87 26 0.31
91 59 0.69
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (87 bp):
GATATTAATTTTATTTTCTAATACTTCATTTATAATAGTAATAATAATATTACTATTTTAATGTT
AACTAATGAATTCTAATACTTC
Found at i:33678 original size:2 final size:2
Alignment explanation
Indices: 33665--33705 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
33655 ACTAAAAATA
33665 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33706 TTGTGGTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34931 original size:15 final size:15
Alignment explanation
Indices: 34913--34951 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
34903 TTCTCTCTTC
* *
34913 CTTTCTTTTTTTTTT
1 CTTTCTATTTTTATT
34928 CTTTCTATTTTTATT
1 CTTTCTATTTTTATT
*
34943 CTTTTTATT
1 CTTTCTATT
34952 AAGTTTAGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTCTATTTTTATT
Found at i:35204 original size:104 final size:105
Alignment explanation
Indices: 34963--35223 Score: 409
Period size: 106 Copynumber: 2.5 Consensus size: 105
34953 AGTTTAGCCT
*
34963 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
35028 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* *
35070 TAATTTCACTAAGTTTAGCCCAAATTAAATTTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
35135 ATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
35174 TAA-TTCACTAAGTTTAGTCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
35224 TAGAAAAATT
Statistics
Matches: 144, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 42 0.29
104 36 0.25
106 48 0.33
107 18 0.12
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:35695 original size:57 final size:56
Alignment explanation
Indices: 35607--35721 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 56
35597 TATCTGTTTC
35607 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTAT-CCCCCTATCTCTACTTAATTATT
35664 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
35720 CT
1 CT
35722 ACAAAAATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 25 0.43
57 33 0.57
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:36240 original size:25 final size:24
Alignment explanation
Indices: 36208--36259 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 24
36198 ACTTAGCTAA
36208 AGATGCAATTTGTGAATTCTTAAG
1 AGATGCAATTTGTGAATTCTTAAG
36232 AGATCGCAATTTGTGAATTCTTAAG
1 AGAT-GCAATTTGTGAATTCTTAAG
36257 AGA
1 AGA
36260 CCACAAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (24 bp):
AGATGCAATTTGTGAATTCTTAAG
Found at i:46583 original size:17 final size:17
Alignment explanation
Indices: 46561--46606 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 17
46551 CAACAATTGC
46561 TGATACAAAAAAAAAGA
1 TGATACAAAAAAAAAGA
46578 TGATACAAAAAAAAAAAGA
1 TGATAC--AAAAAAAAAGA
46597 TGATACAAAA
1 TGATACAAAA
46607 GAAACATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.37
19 17 0.63
ACGTcount: A:0.70, C:0.07, G:0.11, T:0.13
Consensus pattern (17 bp):
TGATACAAAAAAAAAGA
Found at i:46591 original size:19 final size:19
Alignment explanation
Indices: 46567--46606 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
46557 TTGCTGATAC
46567 AAAAAAAAAGATGATACAA
1 AAAAAAAAAGATGATACAA
46586 AAAAAAAAAGATGATACAA
1 AAAAAAAAAGATGATACAA
46605 AA
1 AA
46607 GAAACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAAAAAAAGATGATACAA
Found at i:48771 original size:11 final size:11
Alignment explanation
Indices: 48749--48790 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
48739 ACAAAATGAA
48749 AGCTCG-GCCG
1 AGCTCGAGCCG
48759 AGCTCGAGCCG
1 AGCTCGAGCCG
48770 AGCTCGAGCCG
1 AGCTCGAGCCG
48781 AGCTTCGAGC
1 AGC-TCGAGC
48791 TCGGATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 6 0.20
11 18 0.60
12 6 0.20
ACGTcount: A:0.17, C:0.36, G:0.36, T:0.12
Consensus pattern (11 bp):
AGCTCGAGCCG
Found at i:48777 original size:6 final size:6
Alignment explanation
Indices: 48749--48793 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 6
48739 ACAAAATGAA
48749 AGCTCG -GC-CG AGCTCG AGC-CG AGCTCG AGC-CG AGCTTCG AGCTCG
1 AGCTCG AGCTCG AGCTCG AGCTCG AGCTCG AGCTCG AGC-TCG AGCTCG
48794 GATATATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
4 2 0.06
5 14 0.41
6 13 0.38
7 5 0.15
ACGTcount: A:0.16, C:0.36, G:0.36, T:0.13
Consensus pattern (6 bp):
AGCTCG
Found at i:49278 original size:50 final size:50
Alignment explanation
Indices: 49221--49383 Score: 238
Period size: 50 Copynumber: 3.3 Consensus size: 50
49211 GCAAGCAATA
* *
49221 ATGCATCCCAAATACCCTATTTAAGTTTAGCCAGTAATTACACACGTGAC
1 ATGCATCCCAAATACTCTATTTAAGTTTAGCCAATAATTACACACGTGAC
49271 ATGCATCCCAAATACTCTATTTAAGTTTA-CTCAATAATTACACACGTGAC
1 ATGCATCCCAAATACTCTATTTAAGTTTAGC-CAATAATTACACACGTGAC
* * * ** *
49321 ATGCATCCCAAATGCTCTATTTTAGTTTAGTCAATAAAAACACATGTGAC
1 ATGCATCCCAAATACTCTATTTAAGTTTAGCCAATAATTACACACGTGAC
49371 ATGCATCCCAAAT
1 ATGCATCCCAAAT
49384 TATAGAGTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
49 1 0.01
50 102 0.99
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (50 bp):
ATGCATCCCAAATACTCTATTTAAGTTTAGCCAATAATTACACACGTGAC
Found at i:52959 original size:2 final size:2
Alignment explanation
Indices: 52952--52977 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52942 CGGATTTAGC
52952 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
52978 TTTAAGGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53249 original size:211 final size:215
Alignment explanation
Indices: 52881--53324 Score: 659
Period size: 211 Copynumber: 2.1 Consensus size: 215
52871 TTTTTTTTAT
* *
52881 GTCTTAAATTTGAAATATTTATTTGTAGGGTTTAAGAATTTTAGTATAAACTTTAAGCAATCGGA
1 GTCTTAAATTTGAAATATATATTTGTAGGGTTTAAGAATTTTAGTATAAACTCTAAGCAATCGGA
* * * * * *
52946 TTTAGCATATATATATATATATATATATATATTTTAAGGGTATATCTTAAATTTGAGATATTTAT
66 TTTAACACATATATATATATATATAAAAATATTTTAAGGGTATATCTTAAATTTAAAATATTTAT
*
53011 TTGAAGGGTTTTAGAATTTTAGTTTAGACTCTAAGCAATCAGGTTTAGCCCCAAATTGTATATAT
131 TTGAAAGGTTTTAGAATTTTAGTTTAGACTCTAAGCAATCAGGTTTAGCCCCAAATTGTATATAT
*
53076 AAAAAATATTTTAAAGGTAC
196 AAAAAATATTTTAAAAGTAC
* *
53096 GTCTTAAATTTGAAATATATATTTGTAGGG-TTAA-AATTTTAGTTTAGACTCTAAGCAATCAGG
1 GTCTTAAATTTGAAATATATATTTGTAGGGTTTAAGAATTTTAGTATAAACTCTAAGCAATC-GG
* *
53159 -TTTAAACCCA-A-AT-TGTATATATAAAAATATTTTAAGGGTATATCTTAAATTTAAAATATTT
65 ATTT-AACACATATATATATATATATAAAAATATTTTAAGGGTATATCTTAAATTTAAAATATTT
*
53220 ATTT-ATAAGGTTTTAGAATTTTAGTTTAGACTCTAAGCAATCGGGTTTAGCCCCAAATTGTATA
129 ATTTGA-AAGGTTTTAGAATTTTAGTTTAGACTCTAAGCAATCAGGTTTAGCCCCAAATTGTATA
*
53284 TATAAAAAATATTTTAAAAGTAT
193 TATAAAAAATATTTTAAAAGTAC
*
53307 GTCTTAAATTTAAAATAT
1 GTCTTAAATTTGAAATAT
53325 TTATAAAGCT
Statistics
Matches: 209, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
210 1 0.00
211 141 0.67
212 2 0.01
213 27 0.13
214 9 0.04
215 29 0.14
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.41
Consensus pattern (215 bp):
GTCTTAAATTTGAAATATATATTTGTAGGGTTTAAGAATTTTAGTATAAACTCTAAGCAATCGGA
TTTAACACATATATATATATATATAAAAATATTTTAAGGGTATATCTTAAATTTAAAATATTTAT
TTGAAAGGTTTTAGAATTTTAGTTTAGACTCTAAGCAATCAGGTTTAGCCCCAAATTGTATATAT
AAAAAATATTTTAAAAGTAC
Found at i:61541 original size:128 final size:119
Alignment explanation
Indices: 61270--61585 Score: 343
Period size: 128 Copynumber: 2.6 Consensus size: 119
61260 ATGTAGCTAG
* *
61270 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG
1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAATGGGACAAAACCGA-TCATAAGGGAAAAAG
** * * * *
61333 AGTGCAGCATATCAAGTCCATTTGTCTTCTGGACAAATATTACATGTGCTCTTTAT
64 AGTGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGATCATTAT
** * *
61389 TGCCTCATTAAAAACCTTGTGTCGGAAAACCCAATGGGACAAAACCGAACAGAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
* *
61454 TGCTAGAGCA-ATTTAAGTCCATGTAAATGTCTTCAAGACAATTACATCTAAATGTGAT-ATTGT
66 TGC---AGCATA-TCAAGTCCAT-T---TGTCTTCAAGACAA--ACAT-TAAATGTGATCATTAT
**
61517 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
61582 TGCA
66 TGCA
61586 ACGCACTTTA
Statistics
Matches: 164, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
119 58 0.35
120 2 0.01
121 1 0.01
122 13 0.08
123 1 0.01
125 1 0.01
126 12 0.07
128 68 0.41
129 8 0.05
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (119 bp):
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
TGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGATCATTAT
Found at i:65430 original size:65 final size:62
Alignment explanation
Indices: 65351--65683 Score: 264
Period size: 60 Copynumber: 5.4 Consensus size: 62
65341 GATAGGTAAA
* * *
65351 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATT-GAAA--G
* *
65416 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * * * * * **** * * *
65478 ATCATGACAACTTATGGTGTCAATTG--CAAGATCATAACAACTTTTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * * *** * *
65538 ATCATGACAACTTCTGGTGTCAATTG--CAAAATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * ** * *** * *
65598 ATCATGACAACTTCTGGTGTCAATTG--CAAGAGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
*
65658 AGCATGACAACTTCTGGTGTCAATTG
1 ATCATGACAACTTCTGGTGTCAATTG
65684 CAAGATTATG
Statistics
Matches: 244, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
60 162 0.66
62 25 0.10
64 3 0.01
65 54 0.22
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (62 bp):
ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
Found at i:65501 original size:30 final size:30
Alignment explanation
Indices: 65416--65709 Score: 435
Period size: 30 Copynumber: 9.7 Consensus size: 30
65406 TTGGAAATTT
* *
65416 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * ** *
65448 ATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
65478 ATCATGACAACTTATGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
65508 ATCATAACAACTTTTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
65538 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
65568 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
65598 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
65628 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
65658 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
65688 ATTATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
65710 TTTG
Statistics
Matches: 239, Mismatches: 23, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
30 218 0.91
32 21 0.09
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:65575 original size:90 final size:90
Alignment explanation
Indices: 65348--65709 Score: 436
Period size: 90 Copynumber: 3.9 Consensus size: 90
65338 TTTGATAGGT
* * * * *** * *
65348 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAA
1 AAAATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATT-GCAA
* *
65413 TTTATCATGACAACTTCTGGTGTCAATTGAAT
63 --GATCATGACAACTTCTGGTGTCAATTG--C
* * ** * *
65445 AAAATTATGACATCTTCAAGTATCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAGAT
1 AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
* *
65510 CATAACAACTTTTGGTGTCAATTGC
66 CATGACAACTTCTGGTGTCAATTGC
* *
65535 AACATCATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAGAT
1 AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
65600 CATGACAACTTCTGGTGTCAATTGC
66 CATGACAACTTCTGGTGTCAATTGC
* * *
65625 AAGAGCATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGCAAGAT
1 AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
*
65690 TATGACAACTTCTGGTGTCA
66 CATGACAACTTCTGGTGTCA
65710 TTTG
Statistics
Matches: 231, Mismatches: 34, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
90 160 0.69
92 24 0.10
94 3 0.01
95 20 0.09
97 24 0.10
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (90 bp):
AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
CATGACAACTTCTGGTGTCAATTGC
Done.