Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011174.1 Corchorus capsularis cultivar CVL-1 contig11195, 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: 5491
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Found at i:923 original size:197 final size:195
Alignment explanation
Indices: 687--1049 Score: 543
Period size: 194 Copynumber: 1.9 Consensus size: 195
677 TTTTTTTTTT
*
687 TTTTTTTTATTTCAAGGTATCAACTTTTTCATTATTGCATGTCACCTAAAAATCGTAGATCTTCA
1 TTTTTTTTATTCCAAGGTATCAACTTTTTCATTATTGCATGTCACCTAAAAATCGTAGATCTTCA
** ** *
752 AAAGGTTGTTGTAGGGAAGTAAAAAATGAACTCCAAAAGGAGATTTTAGTGGGAATCAAAGTAGA
66 AAACATTGTTGTAGGG--G-AAAAAATGAACTCCAAAAACAGATTTTAGTGGCAATCAAAGTAGA
*
817 TCTCTTTGATACATTTCTAGCTT-TAGAGGG-AAAATCAAACAGATTTGTCAACCGCTTGAGGGA
128 TCTCTTTGATACATGTCTAG-TTCTA-AGGGAAAAATCAAACAGATTTGTCAACCGCTTGAGGGA
880 TACCC
191 TACCC
* *
885 TTTTTTTTATTCCAAGTTATCAAC-TTTTCATTATTGCATGTCACTTAAAAATCGTAGATCTTCA
1 TTTTTTTTATTCCAAGGTATCAACTTTTTCATTATTGCATGTCACCTAAAAATCGTAGATCTTCA
* * * *
949 AAACATTGTTGTAGGGGAAAAAATGAACTCCAAAAACAGTTTTTAGTTGCAATTATAGTAGATCT
66 AAACATTGTTGTAGGGGAAAAAATGAACTCCAAAAACAGATTTTAGTGGCAATCAAAGTAGATCT
1014 CTTTGATACATGTCTAGTTCTAAGGGAAAAATCAAA
131 CTTTGATACATGTCTAGTTCTAAGGGAAAAATCAAA
1050 ATTAATTTGG
Statistics
Matches: 150, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
193 6 0.04
194 68 0.45
195 1 0.01
197 53 0.35
198 22 0.15
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (195 bp):
TTTTTTTTATTCCAAGGTATCAACTTTTTCATTATTGCATGTCACCTAAAAATCGTAGATCTTCA
AAACATTGTTGTAGGGGAAAAAATGAACTCCAAAAACAGATTTTAGTGGCAATCAAAGTAGATCT
CTTTGATACATGTCTAGTTCTAAGGGAAAAATCAAACAGATTTGTCAACCGCTTGAGGGATACCC
Found at i:2067 original size:31 final size:31
Alignment explanation
Indices: 2032--2202 Score: 151
Period size: 31 Copynumber: 5.6 Consensus size: 31
2022 TATGGCTAAT
*
2032 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* ** **
2063 TGCTCAAATAAGGGCCT--CCTCTT-TTAATT
1 TGCTCAAATAAGGGCCTAACGT-TTGCCAAAA
2092 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
2123 TACTCAAATAAGGGCTCGATC-TTTG--AATT
1 TGCTCAAATAAGGGC-CTAACGTTTGCCAAAA
2152 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
2183 TGCTCAAATAAGGGCCTAAC
1 TGCTCAAATAAGGGCCTAAC
2203 TGAAATCAGG
Statistics
Matches: 109, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.03
29 37 0.34
30 10 0.09
31 56 0.51
32 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:2129 original size:60 final size:61
Alignment explanation
Indices: 2036--2199 Score: 278
Period size: 60 Copynumber: 2.7 Consensus size: 61
2026 GCTAATTGCT
* * *
2036 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCTC-CTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTCGATCTTTGAATTTGGC
*
2096 CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGG-CTCGATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTCGATCTTTGAATTTGGC
2156 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCT
2200 AACTGAAATC
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
59 3 0.03
60 92 0.95
61 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (61 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTCGATCTTTGAATTTGGC
Found at i:2314 original size:60 final size:57
Alignment explanation
Indices: 2242--2403 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 57
2232 GATAACATTA
* *
2242 GACCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTCAAAGATCG
1 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATT-AAA-A-AG
*
2302 GACCCTTATTTGACCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAG
1 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAG
* **
2359 GCAAGTCCTTATTTGAGCATTTTAACAAACGTTAGGCCCTTATTT
1 G--A-CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
2404 AAGCAATTAG
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
57 2 0.02
58 1 0.01
59 4 0.04
60 85 0.92
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (57 bp):
GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAG
Found at i:2402 original size:31 final size:29
Alignment explanation
Indices: 2210--2408 Score: 125
Period size: 31 Copynumber: 6.6 Consensus size: 29
2200 AACTGAAATC
*
2210 AGGCCCTTATTTGAGCATTTTCGATAACATT
1 AGGCCCTTATTTGAGCATTTTC-A-AACGTT
* *
2241 AGACCCTTATTTGAGCATTTTGGCAAACATT
1 AGGCCCTTATTTGAGCATTTT--CAAACGTT
** *
2272 AGGCCCTTATTTG-GCCAAATTCAAA-GAT
1 AGGCCCTTATTTGAG-CATTTTCAAACGTT
* *
2300 CGGACCCTTATTTGACCATTTTGGCAAACGTT
1 AGG-CCCTTATTTGAGCATTTT--CAAACGTT
** * * **
2332 AGGCCCTTATTTG-GCCAAATTAAAAAGGC
1 AGGCCCTTATTTGAG-CATTTTCAAACGTT
* *
2361 AAGTCCTTATTTGAGCATTTTAACAAACGTT
1 AGGCCCTTATTTGAGCATTTT--CAAACGTT
*
2392 AGGCCCTTATTTAAGCA
1 AGGCCCTTATTTGAGCA
2409 ATTAGCCTTT
Statistics
Matches: 126, Mismatches: 30, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
28 3 0.02
29 37 0.29
30 2 0.02
31 78 0.62
32 5 0.04
33 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCATTTTCAAACGTT
Found at i:4372 original size:111 final size:109
Alignment explanation
Indices: 4256--4536 Score: 404
Period size: 111 Copynumber: 2.5 Consensus size: 109
4246 AAATAAAAAA
4256 AATTATATAA-ATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATAT
1 AATTATA-AAGATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATAT
** *
4320 TAGAAAATTTTTTTAATATATCCAATTTTTTTTGGTAAAAATAAAGT
65 TAGAAAA-AATTTTAATATATCCAA-ATTTTTTGGTAAAAATAAAGT
4367 AATTATAAAGATATT-AGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATAT
1 AATTATAAAGATATTGA-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATAT
*
4431 TAGAAAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGT
65 TAGAAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGT
* * *
4476 AATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 AATTATAAAGATATT-G----AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAA
4537 CTATAATAGT
Statistics
Matches: 155, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
109 35 0.23
110 17 0.11
111 66 0.43
114 36 0.23
115 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (109 bp):
AATTATAAAGATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATT
AGAAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGT
Done.