Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023827.1 Corchorus olitorius cultivar O-4 contig23860, 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: 26475
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:32 original size:16 final size:15
Alignment explanation
Indices: 11--53 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1 GATTATTGTT
11 TTTGTTGTTTCTTCCC
1 TTTGTT-TTTCTTCCC
* *
27 TTTGTTTGTTCTTGCT
1 TTTGTTT-TTCTTCCC
43 TTTGTTTTTCT
1 TTTGTTTTTCT
54 ATTTCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.00, C:0.16, G:0.14, T:0.70
Consensus pattern (15 bp):
TTTGTTTTTCTTCCC
Found at i:6282 original size:2 final size:2
Alignment explanation
Indices: 6277--6310 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6267 TATATAAACC
6277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6311 AGAGTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8392 original size:86 final size:86
Alignment explanation
Indices: 8247--8413 Score: 316
Period size: 86 Copynumber: 1.9 Consensus size: 86
8237 ACACAATGGA
* *
8247 TAATCAAATTACCCAGTATGGCATAATTTCCATGTTTATAATAAATCTAGAACACTCTGCAACAG
1 TAATCAAACTACCCAGTATGGCATAATGTCCATGTTTATAATAAATCTAGAACACTCTGCAACAG
8312 ATACAAATGAGATACAGCAAC
66 ATACAAATGAGATACAGCAAC
8333 TAATCAAACTACCCAGTATGGCATAATGTCCATGTTTATAATAAATCTAGAACACTCTGCAACAG
1 TAATCAAACTACCCAGTATGGCATAATGTCCATGTTTATAATAAATCTAGAACACTCTGCAACAG
8398 ATACAAATGAGATACA
66 ATACAAATGAGATACA
8414 AACGGCAGTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (86 bp):
TAATCAAACTACCCAGTATGGCATAATGTCCATGTTTATAATAAATCTAGAACACTCTGCAACAG
ATACAAATGAGATACAGCAAC
Found at i:13254 original size:13 final size:13
Alignment explanation
Indices: 13236--13260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13226 AGGGAATATA
13236 AGCAAAGAGTTTG
1 AGCAAAGAGTTTG
13249 AGCAAAGAGTTT
1 AGCAAAGAGTTT
13261 TCTAATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (13 bp):
AGCAAAGAGTTTG
Found at i:15704 original size:132 final size:134
Alignment explanation
Indices: 15506--15777 Score: 426
Period size: 132 Copynumber: 2.0 Consensus size: 134
15496 CCTAAGCAAT
* * * *
15506 CGCCACCATTTGAATATATGGAGGAGATAATTTTTCTTTTTCTTTTTTTTTGGAGGGAAAAGTTC
1 CGCCGCCATTTGAATATATGGAGGAGATAATTTCTCTTTTTCTTTTTTTTTGGAGAGAAAAATTC
* * *
15571 CCTCCCTAGTAAAACA-AAAAAGGTTTCCAAGTATACGCTTATAATATATAGCGGCGTTTATTTA
66 CCTCCCCAATAAAACAGAAAAA-GTTTCCAAGTATACGCTTATAATATATAGCGGCGTTTATCTA
15635 GTAAA
130 GTAAA
15640 CGCCGCCATTTGAATATATGGAGGGAGATAA-TTCT-TTTTTC-TTTTTTTTGGAGAGAAAAATT
1 CGCCGCCATTTGAATATATGGA-GGAGATAATTTCTCTTTTTCTTTTTTTTTGGAGAGAAAAATT
*
15702 CCCTCCCCAATAAAACAGAAAAAGTTTCCAAGTATACGCTTATAATATATAGCGGCGTTTATCTG
65 CCCTCCCCAATAAAACAGAAAAAGTTTCCAAGTATACGCTTATAATATATAGCGGCGTTTATCTA
15767 GTAAA
130 GTAAA
15772 CGCCGC
1 CGCCGC
15778 TAATTGGTGG
Statistics
Matches: 128, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
132 85 0.66
133 11 0.09
134 24 0.19
135 8 0.06
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (134 bp):
CGCCGCCATTTGAATATATGGAGGAGATAATTTCTCTTTTTCTTTTTTTTTGGAGAGAAAAATTC
CCTCCCCAATAAAACAGAAAAAGTTTCCAAGTATACGCTTATAATATATAGCGGCGTTTATCTAG
TAAA
Found at i:15916 original size:166 final size:164
Alignment explanation
Indices: 15623--15959 Score: 541
Period size: 166 Copynumber: 2.0 Consensus size: 164
15613 AATATATAGC
* * *
15623 GGCGTTT-ATTTAGTAAACGCCGCCATTTGAATATATGGAGGGAGATAATTCTTTTTTCTTTTTT
1 GGCGTTTCATTTAGGAAACGCCGCCATTTGAATATATGGAGGGAGAGAATTATTTTTTCTTTTTT
*
15687 TTGGAGAGAAAAATTCCCTCCCCAATAAAACAGAAAAAGTTTCCAAGTATACGCTTATAATATAT
66 TTGGAGAGAAAAATTCCCTCCCCAATAAAACAAAAAAAGTTTCCAAGTATACGCTTATAATATAT
* * * *
15752 AGCGGCGTTTATCTGGTAAACGCCGCTAATTGGT
131 AGCGACGTTTATCTGGCAAACGCCGCTAAGTAGT
*
15786 GGCGTTTCTTTTAGGAAACGCCGCCATTTGAATATATGGAGGGAGAGAATTATTTTTTCCTTTTT
1 GGCGTTTCATTTAGGAAACGCCGCCATTTGAATATATGGAGGGAGAGAATTATTTTTT-CTTTTT
* *
15851 TTTGGAGGGAAAAATTCCCTCCCCCAGTAAAACAAAAAAAGTTTCCAAGTATACGCTTATAATAT
65 TTTGGAGAGAAAAATTCCCT-CCCCAATAAAACAAAAAAAGTTTCCAAGTATACGCTTATAATAT
*
15916 ATAGCGACGTTTATTTGGCAAACGCCGCTAAGTAGT
129 ATAGCGACGTTTATCTGGCAAACGCCGCTAAGTAGT
15952 GGCGTTTC
1 GGCGTTTC
15960 CCTCTGTAAA
Statistics
Matches: 159, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
163 7 0.04
164 46 0.29
165 25 0.16
166 81 0.51
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (164 bp):
GGCGTTTCATTTAGGAAACGCCGCCATTTGAATATATGGAGGGAGAGAATTATTTTTTCTTTTTT
TTGGAGAGAAAAATTCCCTCCCCAATAAAACAAAAAAAGTTTCCAAGTATACGCTTATAATATAT
AGCGACGTTTATCTGGCAAACGCCGCTAAGTAGT
Found at i:16694 original size:21 final size:21
Alignment explanation
Indices: 16670--16739 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
16660 ATATTTGGCA
16670 TGAATATTTGTGTTGATATAT
1 TGAATATTTGTGTTGATATAT
16691 TGAATATTTG-G-T-ATGA-A-
1 TGAATATTTGTGTTGAT-ATAT
16708 T--AT-T-TGTGTTGATATAT
1 TGAATATTTGTGTTGATATAT
16725 TGAATATTTGTGTTG
1 TGAATATTTGTGTTG
16740 TTATGTCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 20
0.66 0.00 0.34
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 4 0.10
16 3 0.08
17 2 0.05
18 3 0.08
19 4 0.10
20 2 0.05
21 17 0.44
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.51
Consensus pattern (21 bp):
TGAATATTTGTGTTGATATAT
Found at i:16707 original size:34 final size:34
Alignment explanation
Indices: 16659--16734 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
16649 TAAAGATTTA
16659 AATATTTGGCATGAATATTTGTGTTGATATATTG
1 AATATTTGGCATGAATATTTGTGTTGATATATTG
*
16693 AATATTTGGTATGAATATTTGTGTTGATATATTG
1 AATATTTGGCATGAATATTTGTGTTGATATATTG
16727 AATATTTG
1 AATATTTG
16735 TGTTGTTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.30, C:0.01, G:0.20, T:0.49
Consensus pattern (34 bp):
AATATTTGGCATGAATATTTGTGTTGATATATTG
Found at i:20770 original size:22 final size:21
Alignment explanation
Indices: 20743--20792 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
20733 TTAGTGCCCT
*
20743 AAAAAATTATGGTGATTATTGC
1 AAAAAATTATGGTGAATA-TGC
*
20765 AAAAAATTCTGGTGAATATGC
1 AAAAAATTATGGTGAATATGC
*
20786 AGAAAAT
1 AAAAAAT
20793 GCTGCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (21 bp):
AAAAAATTATGGTGAATATGC
Found at i:21061 original size:44 final size:44
Alignment explanation
Indices: 20992--21138 Score: 206
Period size: 44 Copynumber: 3.3 Consensus size: 44
20982 TGATTTTAAT
* * * * *
20992 TTCTTAATATTATTTTCTAATTATAATATCATTGCATTTATAAA
1 TTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAAA
*
21036 TTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAAT
1 TTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAAA
*
21080 TTCTAAGTATTATTTTCTAAATATAATTTCATTACATATAT-AA
1 TTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAAA
*
21123 TTCCTAAATATAATTT
1 TT-CTAAATATTATTT
21139 CATTACATAT
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 3 0.03
44 89 0.97
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (44 bp):
TTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAAA
Found at i:21083 original size:30 final size:28
Alignment explanation
Indices: 21030--21281 Score: 117
Period size: 30 Copynumber: 8.6 Consensus size: 28
21020 TCATTGCATT
* * *
21030 TATAAATTCTAAATAT-TATTTTCTAAA
1 TATAATTTCTTAATATATAATTTCTAAA
*
21057 TATAATTTCATTACATATATAATTTCTAAG
1 TATAATTTC-TTA-ATATATAATTTCTAAA
*
21087 TATTATTT-TCTAA-ATATAATTTCATTACATA
1 TATAATTTCT-TAATATATAATTTC--TA-A-A
*
21118 TATAA-TTCCTAA-ATATAATTTCATTACATA
1 TATAATTTCTTAATATATAATTTC--TA-A-A
* * *
21148 TATAATTTCTAAATAT-TATTTTCTAAT
1 TATAATTTCTTAATATATAATTTCTAAA
* *
21175 TATAA-TTCATTACATTTATAATTTATAAA
1 TATAATTTC-TTA-ATATATAATTTCTAAA
* *
21204 TATTATTTCCTAAT-TATAATTTCATTACATA
1 TATAATTTCTTAATATATAATTTC--TA-A-A
* * * *
21235 TATAATTTCTAAATACTATTATTTTCTCAT
1 TATAATTTCTTAATA-TA-TAATTTCTAAA
21265 TATAATTTCTT-ATATAT
1 TATAATTTCTTAATATAT
21282 GGCGGCTTTT
Statistics
Matches: 176, Mismatches: 27, Indels: 44
0.71 0.11 0.18
Matches are distributed among these distances:
26 3 0.02
27 34 0.19
28 12 0.07
29 29 0.16
30 59 0.34
31 28 0.16
32 3 0.02
33 2 0.01
34 6 0.03
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.50
Consensus pattern (28 bp):
TATAATTTCTTAATATATAATTTCTAAA
Found at i:21130 original size:74 final size:73
Alignment explanation
Indices: 21052--21212 Score: 259
Period size: 74 Copynumber: 2.2 Consensus size: 73
21042 ATATTATTTT
*
21052 CTAAATATAATTTCATTACATATATAATTTCTAAGTATTATTTTCTAAATATAATTTCATTACAT
1 CTAAATATAATTTCATTACATATATAATTTCTAAATATTATTTTCTAAATATAA-TTCATTACAT
21117 ATATAATTC
65 ATATAATTC
* *
21126 CTAAATATAATTTCATTACATATATAATTTCTAAATATTATTTTCTAATTATAATTCATTACATT
1 CTAAATATAATTTCATTACATATATAATTTCTAAATATTATTTTCTAAATATAATTCATTACATA
*
21191 TATAATTT
66 TATAATTC
* *
21199 ATAAATATTATTTC
1 CTAAATATAATTTC
21213 CTAATTATAA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 29 0.36
74 52 0.64
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (73 bp):
CTAAATATAATTTCATTACATATATAATTTCTAAATATTATTTTCTAAATATAATTCATTACATA
TATAATTC
Found at i:21189 original size:43 final size:44
Alignment explanation
Indices: 21126--21281 Score: 217
Period size: 43 Copynumber: 3.5 Consensus size: 44
21116 TATATAATTC
*
21126 CTAAATATAATTTCATTACATATATAATTTCTAAATATTATTTT
1 CTAATTATAATTTCATTACATATATAATTTCTAAATATTATTTT
* * *
21170 CTAATTATAA-TTCATTACATTTATAATTTATAAATATTATTTC
1 CTAATTATAATTTCATTACATATATAATTTCTAAATATTATTTT
21213 CTAATTATAATTTCATTACATATATAATTTCTAAATACTATTATTTT
1 CTAATTATAATTTCATTACATATATAATTTCT-AA-A-TATTATTTT
* *
21260 CTCATTATAATTTC-TTATATAT
1 CTAATTATAATTTCATTACATAT
21282 GGCGGCTTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
43 40 0.40
44 28 0.28
45 2 0.02
46 8 0.08
47 21 0.21
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (44 bp):
CTAATTATAATTTCATTACATATATAATTTCTAAATATTATTTT
Found at i:21234 original size:117 final size:118
Alignment explanation
Indices: 20988--21249 Score: 379
Period size: 117 Copynumber: 2.3 Consensus size: 118
20978 GGCCTGATTT
* * * *
20988 TAATTTC-TTA-ATAT-TATTTTCTAATTATAATATCATTGCATTTATAAATTCTAAATATTATT
1 TAATTTCATTACATATATAATTTCTAAATATAATATCATTACATATATAAATTCTAAATATTATT
* * *
21050 TTCTAAATATAATTTCATTACATATATAATTTCTAAGTATTATTTTCTAAATA
66 TTCTAAATATAATTTCATTACATATATAATTTATAAATATTATTTCCTAAATA
* * *
21103 TAATTTCATTACATATATAATTCCTAAATATAATTTCATTACATATATAATTTCTAAATATTATT
1 TAATTTCATTACATATATAATTTCTAAATATAATATCATTACATATATAAATTCTAAATATTATT
* * *
21168 TTCTAATTATAA-TTCATTACATTTATAATTTATAAATATTATTTCCTAATTA
66 TTCTAAATATAATTTCATTACATATATAATTTATAAATATTATTTCCTAAATA
21220 TAATTTCATTACATATATAATTTCTAAATA
1 TAATTTCATTACATATATAATTTCTAAATA
21250 CTATTATTTT
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
115 7 0.05
116 3 0.02
117 68 0.52
118 52 0.40
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.50
Consensus pattern (118 bp):
TAATTTCATTACATATATAATTTCTAAATATAATATCATTACATATATAAATTCTAAATATTATT
TTCTAAATATAATTTCATTACATATATAATTTATAAATATTATTTCCTAAATA
Found at i:21269 original size:117 final size:116
Alignment explanation
Indices: 21029--21274 Score: 345
Period size: 117 Copynumber: 2.1 Consensus size: 116
21019 ATCATTGCAT
* * *
21029 TTATAAATTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAATTTCTAAGTATTATT
1 TTATAATTTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAATTTATAAATATTATT
*
21094 TTCTAAATATAATTTCATTACATATATAATTCCTAAATATAATTTCATTACA
66 TCCTAAATATAATTTCATTACATATATAATTCCTAAATATAATTTCA-TACA
* *
21146 TATATAATTTCTAAATATTATTTTCTAATTATAA-TTCATTACATTTATAATTTATAAATATTAT
1 T-TATAATTTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAATTTATAAATATTAT
* *
21210 TTCCTAATTATAATTTCATTACATATATAATTTCTAAATACTATTATTTTC-T-CA
65 TTCCTAAATATAATTTCATTACATATATAATTCCTAAATA-TA--A-TTTCATACA
21264 TTATAATTTCT
1 TTATAATTTCT
21275 TATATATGGC
Statistics
Matches: 116, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
117 75 0.65
118 35 0.30
119 1 0.01
120 1 0.01
121 4 0.03
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.50
Consensus pattern (116 bp):
TTATAATTTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAATTTATAAATATTATT
TCCTAAATATAATTTCATTACATATATAATTCCTAAATATAATTTCATACA
Found at i:21889 original size:20 final size:21
Alignment explanation
Indices: 21856--21902 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
21846 AAAACAAAAG
* *
21856 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
21877 AAAAAAATA-AAATCTTC-AC
1 AAAAAAATAGAAATCTTCAAC
*
21896 AAGAAAA
1 AAAAAAA
21903 GAGATGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:22414 original size:20 final size:21
Alignment explanation
Indices: 22375--22414 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22365 CGTTAAAGTA
* *
22375 TCGATTTGTTGTTCTAGGTCT
1 TCGATTTATGGTTCTAGGTCT
22396 TCGATTTATGGTT-TAGGTC
1 TCGATTTATGGTTCTAGGTC
22415 AAAAATCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (21 bp):
TCGATTTATGGTTCTAGGTCT
Found at i:23756 original size:1 final size:1
Alignment explanation
Indices: 23709--23739 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
23699 CCTCTCCTTC
23709 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23740 CTTTCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26212 original size:32 final size:32
Alignment explanation
Indices: 26176--26268 Score: 141
Period size: 32 Copynumber: 2.9 Consensus size: 32
26166 AAAGCCCCAG
26176 ATTTAGCGGCGTCTATTGAAGAAAACGCCCCT
1 ATTTAGCGGCGTCTATTGAAGAAAACGCCCCT
* *
26208 ATTTAGCGGCATCTATTGAAGAAAACACCCCT
1 ATTTAGCGGCGTCTATTGAAGAAAACGCCCCT
* **
26240 ATTTAGCGGCGTCTAGTGAATCAAACGCC
1 ATTTAGCGGCGTCTATTGAAGAAAACGCC
26269 GTAAAATAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (32 bp):
ATTTAGCGGCGTCTATTGAAGAAAACGCCCCT
Done.