Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024412.1 Corchorus olitorius cultivar O-4 contig24445, 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: 18265
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:3344 original size:11 final size:11
Alignment explanation
Indices: 3328--3363 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
3318 GGTCAATCCA
3328 TAGTTCATTTT
1 TAGTTCATTTT
3339 TAGTTCATTTT
1 TAGTTCATTTT
3350 TAGTTCATTTT
1 TAGTTCATTTT
3361 TAG
1 TAG
3364 GATTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.61
Consensus pattern (11 bp):
TAGTTCATTTT
Found at i:6963 original size:20 final size:19
Alignment explanation
Indices: 6930--6977 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
6920 GATAATTCAA
*
6930 AATTCCAAACTTAAGTAAAAG
1 AATT-CAAAATTAAG-AAAAG
*
6951 AATTCAAAATTAAGAAGAG
1 AATTCAAAATTAAGAAAAG
*
6970 ATTTCAAA
1 AATTCAAA
6978 TCTGAGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
21 4 0.17
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (19 bp):
AATTCAAAATTAAGAAAAG
Found at i:8101 original size:38 final size:37
Alignment explanation
Indices: 8023--8102 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
8013 TTGGGCCAAG
* * * * * *
8023 GCTGGGCCGCCGCTGGCCTGCGTGCTTGGCCTGGCGC
1 GCTGGGCCGCCGCAGGCCCGCGCGCCTGGCCTAGCAC
*
8060 GCTGGGCCGCTTGCAGGCCCGCGCGCCTGGCCTAGCAC
1 GCTGGGCCGC-CGCAGGCCCGCGCGCCTGGCCTAGCAC
8098 GCTGG
1 GCTGG
8103 CCTGGCTGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
37 10 0.29
38 25 0.71
ACGTcount: A:0.04, C:0.39, G:0.41, T:0.16
Consensus pattern (37 bp):
GCTGGGCCGCCGCAGGCCCGCGCGCCTGGCCTAGCAC
Found at i:8145 original size:5 final size:5
Alignment explanation
Indices: 8127--8186 Score: 56
Period size: 5 Copynumber: 12.2 Consensus size: 5
8117 CAAGTTGGCC
*
8127 TCTTT TCTTCT T-TTT T-TTT TC-CT TCTTT TCTTT TCTTT T-TTT TCTTCT
1 TCTTT TCTT-T TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTT-T
8175 TCTTCT TCTTT T
1 TCTT-T TCTTT T
8187 GGCTTCCGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
4 13 0.27
5 22 0.46
6 13 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:8157 original size:23 final size:22
Alignment explanation
Indices: 8127--8186 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 22
8117 CAAGTTGGCC
8127 TCTTTTCTTCTTTTTTTTTTCCT
1 TCTTTTCTTCTTTTTTTTTT-CT
8150 TCTTTTCTT-TTCTTTTTTTTCT
1 TCTTTTCTTCTT-TTTTTTTTCT
8172 TCTTCTTCTTCTTTT
1 TCTT-TTCTTCTTTT
8187 GGCTTCCGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.24
23 24 0.71
24 2 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TCTTTTCTTCTTTTTTTTTTCT
Found at i:8179 original size:28 final size:28
Alignment explanation
Indices: 8127--8186 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
8117 CAAGTTGGCC
8127 TCTTTTCTTCTTTTTTTTTTCCTTCTTT
1 TCTTTTCTTCTTTTTTTTTTCCTTCTTT
*
8155 TCTTTTC-T-TTTTTTTCTT-CTTCTTCT
1 TCTTTTCTTCTTTTTTTTTTCCTTCTT-T
8181 TCTTTT
1 TCTTTT
8187 GGCTTCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 6 0.20
26 16 0.53
27 1 0.03
28 7 0.23
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (28 bp):
TCTTTTCTTCTTTTTTTTTTCCTTCTTT
Found at i:9855 original size:21 final size:21
Alignment explanation
Indices: 9816--9856 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9806 GTCTTTGACC
*
9816 TAACCTTATTAAGAGTTTTAG
1 TAACCTTATTAAGAATTTTAG
**
9837 TAACCTTATTGTGAATTTTA
1 TAACCTTATTAAGAATTTTA
9857 AAAGACTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (21 bp):
TAACCTTATTAAGAATTTTAG
Found at i:12344 original size:57 final size:57
Alignment explanation
Indices: 12280--12396 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
12270 TAAAGTAAGT
12280 CATATTGAAGTTCAACGGTTATATTGAGAAGGAATTATTCTTGTAACTAAATTCCAA
1 CATATTGAAGTTCAACGGTTATATTGAGAAGGAATTATTCTTGTAACTAAATTCCAA
*
12337 CATATTGAAGTTCAACGGTTATATTGAGAAGGAATTATTCTTGTAATTAAATTCCAA
1 CATATTGAAGTTCAACGGTTATATTGAGAAGGAATTATTCTTGTAACTAAATTCCAA
12394 CAT
1 CAT
12397 TTTTGTATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (57 bp):
CATATTGAAGTTCAACGGTTATATTGAGAAGGAATTATTCTTGTAACTAAATTCCAA
Found at i:13292 original size:76 final size:76
Alignment explanation
Indices: 13166--13315 Score: 257
Period size: 76 Copynumber: 2.0 Consensus size: 76
13156 TTTAATCAAA
*
13166 CTTGGATTTTCTCAAAGATGGGAGATTTGACTTAGTACATAATTATCATATGAATTCATGACATG
1 CTTGGATTTTCTCAAAGATGAGAGATTTGACTTAGTACATAATTATCATATGAATTCATGACATG
13231 AGTAAGACAAG
66 AGTAAGACAAG
* *
13242 CTTGGATTTTCTCAAAGATTAGAGATTTGACTTAGTA-AGTAATTGTCATATGAATTCATGACAT
1 CTTGGATTTTCTCAAAGATGAGAGATTTGACTTAGTACA-TAATTATCATATGAATTCATGACAT
13306 GAGTAAGACA
65 GAGTAAGACA
13316 TTATTTTGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
75 1 0.01
76 69 0.99
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (76 bp):
CTTGGATTTTCTCAAAGATGAGAGATTTGACTTAGTACATAATTATCATATGAATTCATGACATG
AGTAAGACAAG
Found at i:14195 original size:49 final size:49
Alignment explanation
Indices: 14120--14216 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
14110 AAAAGAAATA
* * *
14120 ATTAGCCATATTAATCCCACCCTTTAAAGGATTTAACTTAAATCATATT
1 ATTAGACATATTAATCCCACCATTTAAAAGATTTAACTTAAATCATATT
*
14169 ATTAGACATATTAATCCTACCATTTAAAAGATTTAACTTAAATCATAT
1 ATTAGACATATTAATCCCACCATTTAAAAGATTTAACTTAAATCATAT
14217 ATATACCCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (49 bp):
ATTAGACATATTAATCCCACCATTTAAAAGATTTAACTTAAATCATATT
Found at i:17355 original size:22 final size:22
Alignment explanation
Indices: 17324--17517 Score: 124
Period size: 22 Copynumber: 8.6 Consensus size: 22
17314 ATTTTGTAAA
17324 GGTTATCAAAATTACAAAAGAT
1 GGTTATCAAAATTACAAAAGAT
* * **
17346 GGTTACCAAAATTTGAAAATTTTAATGGA
1 GGTTATCAAAA-TT-ACAA----AA-GAT
17375 GGTTATCAAAATTACAAAAGAT
1 GGTTATCAAAATTACAAAAGAT
* * * *
17397 GGTTACCAAAATTTCATATGA-
1 GGTTATCAAAATTACAAAAGAT
* * *
17418 GGTTATCAAAATTATAAAGGGT
1 GGTTATCAAAATTACAAAAGAT
* *** *
17440 CGTTATCAAAATTACATGTGGT
1 GGTTATCAAAATTACAAAAGAT
* **
17462 GGTTATCAAAATTTCAATCGA-
1 GGTTATCAAAATTACAAAAGAT
17483 GGTTATCAAAATTACAAATAG-T
1 GGTTATCAAAATTACAAA-AGAT
17505 GGTTATCAAAATT
1 GGTTATCAAAATT
17518 TCGAATGGTG
Statistics
Matches: 130, Mismatches: 32, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
21 31 0.24
22 74 0.57
23 4 0.03
24 3 0.02
27 3 0.02
28 4 0.03
29 11 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (22 bp):
GGTTATCAAAATTACAAAAGAT
Found at i:17450 original size:43 final size:44
Alignment explanation
Indices: 17370--17517 Score: 138
Period size: 43 Copynumber: 3.4 Consensus size: 44
17360 GAAAATTTTA
* *
17370 ATGGAGGTTATCAAAATTACAAAAGATGGTTACCAAAATTTCAT
1 ATGGAGGTTATCAAAATTACAAAAGATCGTTACCAAAATTACAT
* * * *
17414 AT-GAGGTTATCAAAATTATAAAGGGTCGTTATCAAAATTACAT
1 ATGGAGGTTATCAAAATTACAAAAGATCGTTACCAAAATTACAT
* * * ** * * *
17457 GTGGTGGTTATCAAAATTTCAATCGA-GGTTATCAAAATTACAA
1 ATGGAGGTTATCAAAATTACAAAAGATCGTTACCAAAATTACAT
* *
17500 ATAGTGGTTATCAAAATT
1 ATGGAGGTTATCAAAATT
17518 TCGAATGGTG
Statistics
Matches: 86, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 67 0.78
44 19 0.22
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (44 bp):
ATGGAGGTTATCAAAATTACAAAAGATCGTTACCAAAATTACAT
Found at i:17518 original size:43 final size:43
Alignment explanation
Indices: 17441--17565 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
17431 ATAAAGGGTC
** *
17441 GTTATCAAAATTACATGTGGTGGTTATCAAAATTTCAATCGAG
1 GTTATCAAAATTACAAATAGTGGTTATCAAAATTTCAATCGAG
* *
17484 GTTATCAAAATTACAAATAGTGGTTATCAAAATTTCGAATGGTG
1 GTTATCAAAATTACAAATAGTGGTTATCAAAATTTC-AATCGAG
* * * ***
17528 GTTTTCAAAAATTTCAAACAGCAATTATCAAAATTTCA
1 GTTATC-AAAATTACAAATAGTGGTTATCAAAATTTCA
17566 TAGGACAGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
43 33 0.48
44 11 0.16
45 25 0.36
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (43 bp):
GTTATCAAAATTACAAATAGTGGTTATCAAAATTTCAATCGAG
Found at i:17527 original size:65 final size:63
Alignment explanation
Indices: 17375--17544 Score: 196
Period size: 65 Copynumber: 2.6 Consensus size: 63
17365 TTTTAATGGA
* * * * *
17375 GGTTATCAAAATTACAAAAGATGGTTACCAAAATTTCATATGAGGTTATCAAAATTATAAAGGGT
1 GGTTATCAAAATTAC-AATGGTGGTTATCAAAATTTCA-ATGAGGTTATCAAAATTACAAAGAGT
* * *
17440 CGTTATCAAAATTACATGTGGTGGTTATCAAAATTTCAATCGAGGTTATCAAAATTACAAATAGT
1 GGTTATCAAAATTACA-ATGGTGGTTATCAAAATTTCAAT-GAGGTTATCAAAATTACAAAGAGT
* *
17505 GGTTATCAAAATTTCGAATGGTGGTTTTCAAAAATTTCAA
1 GGTTATCAAAATTAC-AATGGTGGTTATC-AAAATTTCAA
17545 ACAGCAATTA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
64 3 0.03
65 75 0.84
66 11 0.12
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (63 bp):
GGTTATCAAAATTACAATGGTGGTTATCAAAATTTCAATGAGGTTATCAAAATTACAAAGAGT
Found at i:17528 original size:22 final size:21
Alignment explanation
Indices: 17361--17544 Score: 145
Period size: 22 Copynumber: 8.5 Consensus size: 21
17351 CCAAAATTTG
* *
17361 AAAATTTTAATGGAGGTTATC
1 AAAATTTCAATGGTGGTTATC
* * * *
17382 AAAATTACAAAAGATGGTTACC
1 AAAATTTC-AATGGTGGTTATC
*
17404 AAAATTTCATAT-GAGGTTATC
1 AAAATTTCA-ATGGTGGTTATC
* * *
17425 AAAATTATAAAGGGTCGTTATC
1 AAAATT-TCAATGGTGGTTATC
* *
17447 AAAATTACATGTGGTGGTTATC
1 AAAATTTCA-ATGGTGGTTATC
* *
17469 AAAATTTCAATCGAGGTTATC
1 AAAATTTCAATGGTGGTTATC
* *
17490 AAAATTACAAATAGTGGTTATC
1 AAAATTTC-AATGGTGGTTATC
*
17512 AAAATTTCGAATGGTGGTTTTC
1 AAAATTTC-AATGGTGGTTATC
17534 AAAAATTTCAA
1 -AAAATTTCAA
17545 ACAGCAATTA
Statistics
Matches: 125, Mismatches: 31, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
21 37 0.30
22 80 0.64
23 8 0.06
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
AAAATTTCAATGGTGGTTATC
Found at i:17557 original size:45 final size:43
Alignment explanation
Indices: 17464--17565 Score: 114
Period size: 45 Copynumber: 2.3 Consensus size: 43
17454 CATGTGGTGG
* ***
17464 TTATCAAAATTTCAATCGAGGTTATCAAAATTACAAATAGTGG
1 TTATCAAAATTTCAATCGAGGTTATCAAAATTACAAACAGCAA
* * * *
17507 TTATCAAAATTTCGAATGGTGGTTTTCAAAAATTTCAAACAGCAA
1 TTATCAAAATTTC-AATCGAGGTTATC-AAAATTACAAACAGCAA
17552 TTATCAAAATTTCA
1 TTATCAAAATTTCA
17566 TAGGACAGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 13 0.27
44 11 0.22
45 25 0.51
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (43 bp):
TTATCAAAATTTCAATCGAGGTTATCAAAATTACAAACAGCAA
Found at i:17709 original size:22 final size:21
Alignment explanation
Indices: 17683--17735 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
17673 ATTATAAGTG
* *
17683 GTTATCAAATTTTCAAAGGACC
1 GTTATCAAATTATAAAAGG-CC
*
17705 GTTATCAACATTATAAAAGGCG
1 GTTATCAA-ATTATAAAAGGCC
17727 GTTATCAAA
1 GTTATCAAA
17736 ATTTGATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 17 0.63
23 9 0.33
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
GTTATCAAATTATAAAAGGCC
Done.