Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018997.1 Corchorus olitorius cultivar O-4 contig19030, 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: 28589
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:526 original size:13 final size:13
Alignment explanation
Indices: 510--538 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
500 TGGTTTTCCC
510 TTTTT-TTCTTTT
1 TTTTTCTTCTTTT
522 TTTTTCTTCTTTT
1 TTTTTCTTCTTTT
535 TTTT
1 TTTT
539 CTGCTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTCTTTT
Found at i:2138 original size:40 final size:38
Alignment explanation
Indices: 2094--2889 Score: 171
Period size: 40 Copynumber: 20.4 Consensus size: 38
2084 AAGTCACTGG
*
2094 TCCTGAATAGGATTTTTGAAATTGACTGATAAAGCAAGAA
1 TCCTGAATAGGA-TTCTGAAATTGACTGATAAAGCAAG-A
* *
2134 TCCTGAATAGGATTCTGAAAAAGTGTCTTGATAAAGCAATGA
1 TCCTGAATAGGATTCTG--AAATTGAC-TGATAAAGCAA-GA
* * * *
2176 TCCTGAGTAGGATTCTGAAATTAATTCGATAAAGCTATGA
1 TCCTGAATAGGATTCTGAAATTGACT-GATAAAGC-AAGA
*
2216 TCCTGAATAGGATTCTG-AA-T---T--T--A--ATGA
1 TCCTGAATAGGATTCTGAAATTGACTGATAAAGCAAGA
** *
2243 TCCT-AAGTAGGATTCTGAAATTGACCAATAAAGAAATGA
1 TCCTGAA-TAGGATTCTGAAATTGACTGATAAAGCAA-GA
* * *
2282 TCCTGAATAGGATTTTGAAAAGTGGCTCGATAAAGCAATGA
1 TCCTGAATAGGATTCTG-AAATTGACT-GATAAAGCAA-GA
* *
2323 TCCT-AAGTAGGATTCTGAAATTAATTTGATAAAGCAATGA
1 TCCTGAA-TAGGATTCTGAAATTGA-CTGATAAAGCAA-GA
** * * * * *
2363 TCCTGAGCAGGGTT-TGAAAACTAATTTGATAAAACAATGA
1 TCCTGAATAGGATTCTG-AAATTGA-CTGATAAAGCAA-GA
** * * * *
2403 TCCTGAGCAGGGTTTTGAAATTAATTTGATAAA--AAGATTA
1 TCCTGAATAGGATTCTGAAATTGA-CTGATAAAGCAAG---A
** * * * * *
2443 TCCTGAGCAAGATTTTAAAATTAATTTGATAAAGCAATGA
1 TCCTGAATAGGATTCTGAAATTGA-CTGATAAAGCAA-GA
** ** * *
2483 TCCTGAGCAGGA-T-TGAAATCAACTGGTAAAGAAATGA
1 TCCTGAATAGGATTCTGAAATTGACTGATAAAGCAA-GA
** * * * * *
2520 T-CTCGAGCAGGGTTTTGAAATTAATTTGATAAAAAG-ATGA
1 TCCT-GAATAGGATTCTGAAATTGA-CTGAT--AAAGCAAGA
** * * *
2560 TCCTGAGCAGGATTCTGAAATTGATTTGACAATGCAATGA
1 TCCTGAATAGGATTCTGAAATTGA-CTGATAAAGCAA-GA
** * * * * *
2600 TCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGA
1 TCCTGAATAGGATTCTGAAATTGA-CTGATAAAGCAA-GA
** * * * * *
2640 TCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAG-ATGA
1 TCCTGAATAGGATTCTGAAATTGA-CTGAT--AAAGCAAGA
** * *
2680 TCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGA
1 TCCTGAATAGGATTCTGAAATTGA-CTGATAAAGCAA-GA
** * * * *
2720 TCCTGAGCAGGATTTTGAAATTAATTTGATAAAACAATGA
1 TCCTGAATAGGATTCTGAAATTGA-CTGATAAAGCAA-GA
** * * * *
2760 TCCTGAGCAGGGTTCTGAAATTAATTTAATAAAGCAATGA
1 TCCTGAATAGGATTCTGAAATTGA-CTGATAAAGCAA-GA
* * * *
2800 TCCTGAGTAGGATTGTG--ATTGACTGGTAAAGAAATGA
1 TCCTGAATAGGATTCTGAAATTGACTGATAAAGCAA-GA
* ** * * *
2837 TCCTCAGCAGGATTCTGGAATCGACTAATAAAGCAATGA
1 TCCTGAATAGGATTCTGAAATTGACTGATAAAGCAA-GA
*
2876 TCATGAATAGGATT
1 TCCTGAATAGGATT
2890 AAAACACATA
Statistics
Matches: 619, Mismatches: 89, Indels: 97
0.77 0.11 0.12
Matches are distributed among these distances:
26 2 0.00
27 18 0.03
28 2 0.00
29 1 0.00
30 1 0.00
32 1 0.00
34 1 0.00
35 1 0.00
36 3 0.00
37 46 0.07
38 23 0.04
39 61 0.10
40 381 0.62
41 39 0.06
42 37 0.06
43 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (38 bp):
TCCTGAATAGGATTCTGAAATTGACTGATAAAGCAAGA
Found at i:2281 original size:39 final size:40
Alignment explanation
Indices: 2238--2344 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 40
2228 TTCTGAATTT
2238 AATGATCCTAAGTAGGATTCTGAAATTGAC-CAATAAAGA
1 AATGATCCTAAGTAGGATTCTGAAATTGACTCAATAAAGA
* * * * *
2277 AATGATCCTGAA-TAGGATTTTGAAAAGTGGCTCGATAAAGC
1 AATGATCCT-AAGTAGGATTCTG-AAATTGACTCAATAAAGA
2318 AATGATCCTAAGTAGGATTCTGAAATT
1 AATGATCCTAAGTAGGATTCTGAAATT
2345 AATTTGATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 18 0.32
40 14 0.25
41 25 0.44
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (40 bp):
AATGATCCTAAGTAGGATTCTGAAATTGACTCAATAAAGA
Found at i:2324 original size:41 final size:41
Alignment explanation
Indices: 2238--2813 Score: 194
Period size: 40 Copynumber: 14.5 Consensus size: 41
2228 TTCTGAATTT
* * * *
2238 AATGATCCT-AAGTAGGATTCTGAAATTGAC-CAATAAAGA
1 AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* **
2277 AATGATCCTGAA-TAGGATTTTGAAAAGTGGCTCGATAAAGC
1 AATGATCCTGAAGTAGGATTCTG-AAAGTAACTCGATAAAGC
* * *
2318 AATGATCCT-AAGTAGGATTCTGAAATTAATTTGATAAAGC
1 AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * * *
2358 AATGATCCTG-AGCAGGGTT-TGAAAACTAATTTGATAAAAC
1 AATGATCCTGAAGTAGGATTCTG-AAAGTAACTCGATAAAGC
* * * * * * *
2398 AATGATCCTG-AGCAGGGTTTTGAAATTAATTTGATAAA-A
1 AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * * * * *
2437 AGATTATCCTG-AGCAAGATTTTAAAATTAATTTGATAAAGC
1 A-ATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * *
2478 AATGATCCTG-AGCAGGA-T-TGAAA-TCAACT-GGTAAAGA
1 AATGATCCTGAAGTAGGATTCTGAAAGT-AACTCGATAAAGC
* * * * * * *
2515 AATGAT-CTCG-AGCAGGGTTTTGAAATTAATTTGATAAA-A
1 AATGATCCT-GAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * * * *
2554 AGATGATCCTG-AGCAGGATTCTGAAATTGATTTGACAATGC
1 A-ATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * * * *
2595 AATGATCCTG-AGCAGGGTTTTGAAATTAATTTGATAAAAC
1 AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * * * *
2635 AATGATCCTG-AGCAGGGTTTTGAAATTAATTTGATAAA-A
1 AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * * *
2674 AGATGATCCTG-AGCAGGATTCTGAAATTGATTTGACAAAGC
1 A-ATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * * *
2715 AATGATCCTG-AGCAGGATTTTGAAATTAATTTGATAAAAC
1 AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
* * * * **
2755 AATGATCCTG-AGCAGGGTTCTGAAATTAATTTAATAAAGC
1 AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
2795 AATGATCCTG-AGTAGGATT
1 AATGATCCTGAAGTAGGATT
2814 GTGATTGACT
Statistics
Matches: 458, Mismatches: 59, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
36 2 0.00
37 20 0.04
38 8 0.02
39 33 0.07
40 363 0.79
41 32 0.07
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (41 bp):
AATGATCCTGAAGTAGGATTCTGAAAGTAACTCGATAAAGC
Found at i:2340 original size:147 final size:149
Alignment explanation
Indices: 2101--2368 Score: 416
Period size: 147 Copynumber: 1.8 Consensus size: 149
2091 TGGTCCTGAA
* ** * * *
2101 TAGGATTTTTGAAATTGACTGATAAAGCAAGAATCCTGAATAGGATTCTGAAAAAGTGTCTTGAT
1 TAGGATTTCTGAAATTGACCAATAAAGAAAGAATCCTGAATAGGATTCTGAAAAAGTGGCTCGAT
* *
2166 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAATTCGATAAAGCTATGATCCTGAATAGGATTC
66 AAAGCAATGATCCTAAGTAGGATTCTGAAATTAATTCGATAAAGCAATGATCCTGAATAGGATTC
2231 TGAATTTAATGATCCTAAG
131 TGAATTTAATGATCCTAAG
*
2250 TAGGA-TTCTGAAATTGACCAATAAAGAAATG-ATCCTGAATAGGATTTTG-AAAAGTGGCTCGA
1 TAGGATTTCTGAAATTGACCAATAAAGAAA-GAATCCTGAATAGGATTCTGAAAAAGTGGCTCGA
*
2312 TAAAGCAATGATCCTAAGTAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGA
65 TAAAGCAATGATCCTAAGTAGGATTCTGAAATTAATTCGATAAAGCAATGATCCTGA
2369 GCAGGGTTTG
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
147 65 0.60
148 37 0.34
149 6 0.06
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (149 bp):
TAGGATTTCTGAAATTGACCAATAAAGAAAGAATCCTGAATAGGATTCTGAAAAAGTGGCTCGAT
AAAGCAATGATCCTAAGTAGGATTCTGAAATTAATTCGATAAAGCAATGATCCTGAATAGGATTC
TGAATTTAATGATCCTAAG
Found at i:2379 original size:80 final size:80
Alignment explanation
Indices: 2238--2847 Score: 595
Period size: 80 Copynumber: 7.7 Consensus size: 80
2228 TTCTGAATTT
* * * *** ** *
2238 AATGATCCTAAGTAGGATTCTGAAATTGA-CCAATAAAGAAATGATCCTGAATAGGATTTTGAAA
1 AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAAATGATCCTGAGCAGG-GTTTGAAA
* *** *
2302 AGTGGCTCGATAAAGC
65 ATTAATTTGATAAAGC
* * *
2318 AATGATCCTAAGTAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTGAAAA
1 AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAAATGATCCTGAGCAGGGTTTGAAAA
* *
2383 CTAATTTGATAAAAC
66 TTAATTTGATAAAGC
* * * * * *
2398 AATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAA-AAGATTATCCTGAGCAAGATTTTAAA
1 AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAA-ATGATCCTGAGCAGGGTTTGAAA
2462 ATTAATTTGATAAAGC
65 ATTAATTTGATAAAGC
* * *
2478 AATGATCCTGAGCAGGA-T-TGAAATCAA-CTGGTAAAGAAATGAT-CTCGAGCAGGGTTTTG-A
1 AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAAATGATCCT-GAGCAGGG-TTTGAA
*
2538 AATTAATTTGATAAA-A
64 AATTAATTTGATAAAGC
* * * *
2554 AGATGATCCTGAGCAGGATTCTGAAATTGATTTGACAATGCAATGATCCTGAGCAGGGTTTTG-A
1 A-ATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAAATGATCCTGAGCAGGG-TTTGAA
*
2618 AATTAATTTGATAAAAC
64 AATTAATTTGATAAAGC
* * *
2635 AATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAA-AAGATGATCCTGAGCAGGATTCTG-A
1 AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAA-ATGATCCTGAGCAGGGTT-TGAA
* *
2698 AATTGATTTGACAAAGC
64 AATTAATTTGATAAAGC
*
2715 AATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA-ACAATGATCCTGAGCAGGGTTCTG-A
1 AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGA-AATGATCCTGAGCAGGGTT-TGAA
*
2778 AATTAATTTAATAAAGC
64 AATTAATTTGATAAAGC
* * * * * *
2795 AATGATCCTGAGTAGGATTGTG--ATTGA-CTGGTAAAGAAATGATCCTCAGCAGG
1 AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAAATGATCCTGAGCAGG
2848 ATTCTGGAAT
Statistics
Matches: 452, Mismatches: 63, Indels: 33
0.82 0.11 0.06
Matches are distributed among these distances:
76 3 0.01
77 69 0.15
78 19 0.04
79 12 0.03
80 325 0.72
81 24 0.05
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (80 bp):
AATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGAAATGATCCTGAGCAGGGTTTGAAAA
TTAATTTGATAAAGC
Found at i:2464 original size:120 final size:119
Alignment explanation
Indices: 2319--2813 Score: 696
Period size: 120 Copynumber: 4.2 Consensus size: 119
2309 CGATAAAGCA
* * *
2319 ATGATCCTAAGTAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTGAAAAC
1 ATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCTGAGCAGGGTTTG-AAAC
2384 TAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAG
65 TAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAG
* * * * * *
2439 ATTATCCTGAGCAAGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAGCA-GGATTGAAA-T
1 ATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCTGAGCAGGGTTTGAAACT
* *
2502 CAA-CTGGTAAAGA-AATGAT-CTCGAGCAGGGTTTTGAAATTAATTTGATAAAAAG
66 -AATTTGATAAA-ACAATGATCCT-GAGCAGGGTTTTGAAATTAATTTGATAAAAAG
* * *
2556 ATGATCCTGAGCAGGATTCTGAAATTGATTTGACAATGCAATGATCCTGAGCAGGGTTTTGAAAT
1 ATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCTGAGCAGGG-TTTGAAAC
2621 TAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAG
65 TAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAG
* * *
2676 ATGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGATCCTGAGCAGGATTTTGAAAT
1 ATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCTGAGCAGG-GTTTGAAAC
* * *
2741 TAATTTGATAAAACAATGATCCTGAGCAGGGTTCTGAAATTAATTTAATAAAGCA-
65 TAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAA-AAG
*
2796 ATGATCCTGAGTAGGATT
1 ATGATCCTGAGCAGGATT
2814 GTGATTGACT
Statistics
Matches: 339, Mismatches: 25, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
116 2 0.01
117 91 0.27
118 8 0.02
119 14 0.04
120 221 0.65
121 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (119 bp):
ATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCTGAGCAGGGTTTGAAACT
AATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAG
Found at i:2888 original size:39 final size:37
Alignment explanation
Indices: 2786--2889 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 37
2776 GAAATTAATT
* *
2786 TAATAAAGCAATGATCCTGAGTAGGATTGTGATTGAC
1 TAATAAAGCAATGATCCTGAGTAGGATTCTGATCGAC
** * * *
2823 TGGTAAAGAAATGATCCTCAGCAGGATTCTGGAATCGAC
1 TAATAAAGCAATGATCCTGAGTAGGATTCT-G-ATCGAC
* *
2862 TAATAAAGCAATGATCATGAATAGGATT
1 TAATAAAGCAATGATCCTGAGTAGGATT
2890 AAAACACATA
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
37 24 0.47
38 1 0.02
39 26 0.51
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (37 bp):
TAATAAAGCAATGATCCTGAGTAGGATTCTGATCGAC
Found at i:3243 original size:140 final size:142
Alignment explanation
Indices: 2952--3265 Score: 508
Period size: 140 Copynumber: 2.2 Consensus size: 142
2942 GGTGGACAAG
* * * *
2952 TCAGAATTGATACTCGGAGGTTTCTGAAATTGTGCCCGGTGGTCTCACAAATGCAAACTCGACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTCACAAATGCAAACTCAACCT
*
3017 TGAGCAAGGTTTATTTGAATTTTAAACGCAAATTTGATTAACAAAATGATGAAATGAGATGATAC
66 TGAGCAAGGTTTATTTGAATTTTAAACGCAAATTTGATTAACAAAATGATGAAATGAAATGATAC
3082 CCGGAGGATTTA
131 CCGGAGGATTTA
*
3094 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTCACAAATGCAAACTCAACCT
** *
3159 TGAGCAAGG-TT-TTTGAATTTTAAACGCAGCTTTGATTAA-AAACTTGATGAAATGAAATGATA
66 TGAGCAAGGTTTATTTGAATTTTAAACGCAAATTTGATTAACAAA-ATGATGAAATGAAATGATA
3221 CCCGGAGGATTTA
130 CCCGGAGGATTTA
*
3234 TCAGAATTAATACCCAGAGGTTTCTGAAATTG
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTG
3266 AAATTTAAAC
Statistics
Matches: 161, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
139 3 0.02
140 87 0.54
141 2 0.01
142 69 0.43
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (142 bp):
TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTCACAAATGCAAACTCAACCT
TGAGCAAGGTTTATTTGAATTTTAAACGCAAATTTGATTAACAAAATGATGAAATGAAATGATAC
CCGGAGGATTTA
Found at i:4277 original size:16 final size:16
Alignment explanation
Indices: 4253--4294 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
4243 TTACTTTCAA
4253 TTTTCGTTTTTTTTTG
1 TTTTCGTTTTTTTTTG
*
4269 TTTTTGTTTTTTTTTG
1 TTTTCGTTTTTTTTTG
4285 --TTCGTTTTTT
1 TTTTCGTTTTTT
4295 GAATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.38
16 15 0.62
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (16 bp):
TTTTCGTTTTTTTTTG
Found at i:10550 original size:12 final size:11
Alignment explanation
Indices: 10526--10590 Score: 57
Period size: 10 Copynumber: 6.1 Consensus size: 11
10516 CTATGTACCA
10526 TTTTTCTTTTC
1 TTTTTCTTTTC
10537 TTTTTCTTTGTC
1 TTTTTCTTT-TC
10549 TTTTTC--TTC
1 TTTTTCTTTTC
*
10558 TTTTTGTTTTTC
1 TTTTT-CTTTTC
**
10570 CCTTT-TTTTC
1 TTTTTCTTTTC
10580 TTTTT-TTTTC
1 TTTTTCTTTTC
10590 T
1 T
10591 GCTTATTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
9 7 0.16
10 15 0.33
11 9 0.20
12 14 0.31
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:10552 original size:17 final size:16
Alignment explanation
Indices: 10526--10588 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 16
10516 CTATGTACCA
10526 TTTT-TCTTTTCTTTT
1 TTTTGTCTTTTCTTTT
*
10541 TCTTTGTCTTTTTCTTCT
1 T-TTTGTC-TTTTCTTTT
**
10559 TTTTGT-TTTTCCCTT
1 TTTTGTCTTTTCTTTT
10574 TTTT-TCTTTT-TTTT
1 TTTTGTCTTTTCTTTT
10588 T
1 T
10589 CTGCTTATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.11
15 15 0.39
16 3 0.08
17 7 0.18
18 9 0.24
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTGTCTTTTCTTTT
Found at i:10560 original size:21 final size:21
Alignment explanation
Indices: 10532--10584 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
10522 ACCATTTTTC
10532 TTTTCTTTTTCTTTGT-CTTT
1 TTTTCTTTTTCTTTGTCCTTT
* *
10552 TTCTTCTTTTTGTTTTTCCCTTT
1 TT-TTCTTTTTCTTTGT-CCTTT
10575 TTTTCTTTTT
1 TTTTCTTTTT
10585 TTTTCTGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 12 0.43
22 8 0.29
23 6 0.21
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTTCTTTGTCCTTT
Found at i:15172 original size:61 final size:61
Alignment explanation
Indices: 15077--15199 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
15067 GAAGGCAATG
15077 TTTCATTCTATTGGCTAGGATTTTAGTGATGCATCTATAAATGATGGTGCAACATGAAATA
1 TTTCATTCTATTGGCTAGGATTTTAGTGATGCATCTATAAATGATGGTGCAACATGAAATA
*
15138 TTTCATTCTATTGGCTAGGATTTTAGTGATGCATCTATGAATGATGGTGCAACATGAAATA
1 TTTCATTCTATTGGCTAGGATTTTAGTGATGCATCTATAAATGATGGTGCAACATGAAATA
15199 T
1 T
15200 GCCTAAATTC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (61 bp):
TTTCATTCTATTGGCTAGGATTTTAGTGATGCATCTATAAATGATGGTGCAACATGAAATA
Found at i:17269 original size:5 final size:5
Alignment explanation
Indices: 17259--17327 Score: 92
Period size: 5 Copynumber: 14.4 Consensus size: 5
17249 TCATTTAGTT
17259 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG -TTT- TTTTG TTTTG -TTT-
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
*
17305 TTTTG TTTTT TTTTG TTGTTG TT
1 TTTTG TTTTG TTTTG TT-TTG TT
17328 GGGTGTTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
4 12 0.21
5 40 0.70
6 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:17297 original size:13 final size:13
Alignment explanation
Indices: 17264--17324 Score: 88
Period size: 13 Copynumber: 4.5 Consensus size: 13
17254 TAGTTTTTTG
17264 TTTTGTTTTGTTTT
1 TTTTGTTTTG-TTT
17278 GTTTTGTTTTGTTT
1 -TTTTGTTTTGTTT
17292 TTTTGTTTTGTTT
1 TTTTGTTTTGTTT
17305 TTTTGTTTT-TTT
1 TTTTGTTTTGTTT
17317 TTGTTGTT
1 TT-TTGTT
17325 GTTGGGTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.11
13 27 0.60
14 3 0.07
15 10 0.22
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTTTGTTTTGTTT
Found at i:22146 original size:2 final size:2
Alignment explanation
Indices: 22130--22168 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
22120 TCATGAGCTG
22130 AT AT A- AT AT -T 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 AT AT AT A
22169 CTAGTTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25121 original size:204 final size:201
Alignment explanation
Indices: 24751--25160 Score: 748
Period size: 204 Copynumber: 2.0 Consensus size: 201
24741 GCTTAATAAC
*
24751 TTTATGAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
24816 GATACAACAGATTATTATTATATATATAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATATAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGTTG
24881 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
24946 CGATTTA
195 CGATTTA
24953 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
25018 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATAT--AACTATAACAAAAAAAAGTAGTTGAACATTAGTGGT
25083 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
25148 CCGATTTA
194 CCGATTTA
25156 TTTAT
1 TTTAT
25161 TATTAAGGAA
Statistics
Matches: 201, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
202 89 0.44
203 18 0.09
204 94 0.47
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Done.