Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012849.1 Corchorus capsularis cultivar CVL-1 contig12870, 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: 29903
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:88 original size:5 final size:5
Alignment explanation
Indices: 78--106 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
68 CCCTTAATAC
78 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
107 CTTTGTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:2007 original size:15 final size:15
Alignment explanation
Indices: 1989--2038 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
1979 AGATATTGGA
1989 AATTGATCAAAATCT
1 AATTGATCAAAATCT
*
2004 AATTAATTCAAAATCT
1 AATTGA-TCAAAATCT
2020 AATTGATCAAAATCT
1 AATTGATCAAAATCT
2035 AATT
1 AATT
2039 AATTGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 18 0.56
16 14 0.44
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (15 bp):
AATTGATCAAAATCT
Found at i:2016 original size:16 final size:16
Alignment explanation
Indices: 1995--2042 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
1985 TGGAAATTGA
1995 TCAAAATCTAATTAAT
1 TCAAAATCTAATTAAT
*
2011 TCAAAATCTAATTGA-
1 TCAAAATCTAATTAAT
2026 TCAAAATCTAATTAAT
1 TCAAAATCTAATTAAT
2042 T
1 T
2043 GATTAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (16 bp):
TCAAAATCTAATTAAT
Found at i:2056 original size:2 final size:2
Alignment explanation
Indices: 2049--2079 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2039 AATTGATTAA
*
2049 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2080 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2080 original size:10 final size:10
Alignment explanation
Indices: 2046--2082 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
2036 ATTAATTGAT
2046 TAAATATATA
1 TAAATATATA
2056 TATATATATATA
1 TA-A-ATATATA
2068 TAAATATATA
1 TAAATATATA
2078 TAAAT
1 TAAAT
2083 GAATTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 14 0.56
11 2 0.08
12 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TAAATATATA
Found at i:3202 original size:11 final size:11
Alignment explanation
Indices: 3159--3196 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3149 TTCGTATATA
*
3159 AAATAAATTAT
1 AAATTAATTAT
3170 CAAA-TAATTAT
1 -AAATTAATTAT
3181 AAATTAATTAT
1 AAATTAATTAT
3192 AAATT
1 AAATT
3197 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:7723 original size:2 final size:2
Alignment explanation
Indices: 7716--7740 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7706 CAATAAAGAT
7716 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7741 CTCAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10177 original size:21 final size:21
Alignment explanation
Indices: 10151--10190 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
10141 TTTAGCTAGG
10151 GGTCTTACAAGGTCAAGAAAA
1 GGTCTTACAAGGTCAAGAAAA
10172 GGTCTTACAAGGTCAAGAA
1 GGTCTTACAAGGTCAAGAA
10191 GAGGGTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (21 bp):
GGTCTTACAAGGTCAAGAAAA
Found at i:25913 original size:21 final size:21
Alignment explanation
Indices: 25889--25928 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25879 AAGAGATTCG
*
25889 AAAGGAGACTACGGAGTTAGA
1 AAAGAAGACTACGGAGTTAGA
*
25910 AAAGAAGATTACGGAGTTA
1 AAAGAAGACTACGGAGTTA
25929 AAAGAACGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.30, T:0.17
Consensus pattern (21 bp):
AAAGAAGACTACGGAGTTAGA
Found at i:29240 original size:319 final size:315
Alignment explanation
Indices: 28527--29475 Score: 1017
Period size: 318 Copynumber: 3.0 Consensus size: 315
28517 TTTTGCAAAG
* * * *
28527 TTTTAGCCGAAATCGTGTACTAATAACCATCACGGTTTTTGACTAAAAACGC-CTTCT-AGGGCC
1 TTTTAG-CGAAATCATGTAC---TAACAATCACGG-TCTTGGCTAAAAACGCGCTT-TGA-GGCC
* * *
28590 CCGGCTCAATTTTGCATGATTTTTGTTGCCTAGAG-CCCTTGAAATATCTATATACATCTAAACA
59 CC-GCTCAGTTTTGCATGATTTTT-TTGCCTAAAGACCCTTGAAATATCTATATTCATCTAAACA
** *
28654 AATATCAGTAACGTTGGATTTAAGGATAAGTTTTTCGAGCATATGAATCTTGTTTCGATTTAATT
122 AATATCAGCCACGTTGGATTTAAGGATATGTTTTT-GAGCATATGAATCTTGTTTCGATTTAATT
* * *
28719 AGAAATTAATT-ACGAAAAAAAGGAAAAACGATATTAGAAGTGTGAAAAGCCCTTCATTAATCTT
186 AGAAATTAATTCA-GAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTC---AATGTT
** * * *
28783 TTTGGCGTTGAATTACCTATTTTTTCTGAGTATTGTGGCAAAAAGATGAGGAAAAATATTTCGGG
247 TTTGGCGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAA-TTGAGGAAAAATATTTCAGG
28848 TCAGT
311 TCAGT
* *
28853 TTTTAGCGAAATCATGTACTAACCATCACGGTCTTGGCTAAGAACGCGCTTTGAGGCCCCTGCTC
1 TTTTAGCGAAATCATGTACTAACAATCACGGTCTTGGCTAAAAACGCGCTTTGAGGCCCC-GCTC
* * * * * *
28918 AGTTTTGCAAGATTTTTTTGCCTAAAGACACATTGAAATATCGACATTCATCTAACCAAATGTCA
65 AGTTTTGCATGATTTTTTTGCCTAAAGAC-CCTTGAAATATCTATATTCATCTAAACAAATATCA
* * * * * *
28983 ACCACATTGGATTTAAGGATTTGATTTTATGAGAATCTGAATCTTGTTCCGATTTAATTAGAAAT
129 GCCACGTTGGATTTAAGGATATG-TTTT-TGAGCATATGAATCTTGTTTCGATTTAATTAGAAAT
* *
29048 TAATTCAGAAAAAATGG-AAAATGATATTAAAAGCGTGAAAAGCCCTTCAATGTTTTTGGCGTTG
192 TAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATGTTTTTGGCGTTG
29112 AATTATATATTTTTTCTGAGTATTATGGCAAGAAATTGAGGAAAAA-ATTTCCAGGTCAGT
257 AATTATATATTTTTTCTGAGTATTATGGCAA-AAATTGAGGAAAAATATTT-CAGGTCAGT
* * * * * * * *
29172 TATTT-G-GAAATCGTGTTCTAACGAAT-ACATGTTTTTGCTAAAAATGCGTTTTG-GATCCCCG
1 T-TTTAGCGAAATCATGTACTAAC-AATCAC-GGTCTTGGCTAAAAACGCGCTTTGAG-GCCCCG
* * * * * *
29233 ACTCAGTTTTG-ATTGA--TTTTTACGTAAATACTCCTTCAAATATCTATATTTATCTAATCAAA
62 -CTCAGTTTTGCA-TGATTTTTTTGCCTAAAGAC-CCTTGAAATATCTATATTCATCTAAACAAA
* * * *
29295 TTTCAGCCTCGTTGAATTGAAGGATATGTTTTTTTGAGCATATGAATCTTGTTTC-ATTTTAATT
124 TATCAGCCACGTTGGATTTAAGGATATG--TTTTTGAGCATATGAATCTTGTTTCGA-TTTAATT
*
29359 AGAAATTAAATCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATGTTTTTG
186 AGAAATTAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATGTTTTTG
* *
29424 GCGTTGAATTATATATTTTTCCTGAGTATTCTGGCAAAAAATTGAGGAAAAA
251 GCGTTGAATTATATATTTTTTCTGAGTATTATGGC-AAAAATTGAGGAAAAA
29476 CTTTTCGGCT
Statistics
Matches: 534, Mismatches: 70, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
316 1 0.00
317 104 0.19
318 113 0.21
319 101 0.19
320 15 0.03
321 40 0.07
322 90 0.17
323 50 0.09
324 2 0.00
325 12 0.02
326 6 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (315 bp):
TTTTAGCGAAATCATGTACTAACAATCACGGTCTTGGCTAAAAACGCGCTTTGAGGCCCCGCTCA
GTTTTGCATGATTTTTTTGCCTAAAGACCCTTGAAATATCTATATTCATCTAAACAAATATCAGC
CACGTTGGATTTAAGGATATGTTTTTGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTAAT
TCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATGTTTTTGGCGTTGAATT
ATATATTTTTTCTGAGTATTATGGCAAAAATTGAGGAAAAATATTTCAGGTCAGT
Found at i:29793 original size:287 final size:284
Alignment explanation
Indices: 29245--29781 Score: 746
Period size: 285 Copynumber: 1.9 Consensus size: 284
29235 TCAGTTTTGA
*
29245 TTGATTTTTACGTAAATACTCCTTCAAATATCTATATTTATCTAATCAAATTTCAGCCTCGTTGA
1 TTGATTTTTACGTAAATACTCCTTCAAATATCTATATTTATCTAATCAAATCTCAGCCTCGTTGA
* * *
29310 ATTGAAGGATATGTTTTTTTGAGCATATGAATCTTGTTTCATTTTAATTAGAAATTAAATCAGAA
66 ATTGAAGGATATGTTATTTCGAACATATGAATCTTGTTTCATTTTAATTAGAAATTAAATCAGAA
* * * *
29375 AAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATGTTTTTGGCGTTGAATTATATAT
131 AAAATGGAAAAACGATAATAGAAGCGTGAAAAGCCCTTCAATCTTTATGGCGTTAAATTATATAT
* * *
29440 TTTTCCTGAGTATTCTGGCAAAAAATTGAGGAAAAACTTTTCGGCTCAGTATTTACCAAAAATCG
196 TTTTCCTGAGTATTATGGAAAAAAATTGAGGAAAAACTTTTCGGATCAGTATTTACCAAAAATCG
29505 TGCACTAACGAACACGAGTTTGTC
261 TGCACTAACGAACACGAGTTTGTC
* * * *
29529 TTGATTTTTGACTTAAATAGTCCTTCAAATTTCTATATTTATCT-ATCCAAATCTC-GTCCTTGT
1 TTGATTTTT-ACGTAAATACTCCTTCAAATATCTATATTTATCTAAT-CAAATCTCAG-CCTCGT
* *
29592 TGGAA-TGAAGGATATGTTATTTCGAACATATTAATCTTGTTTCGA-TTTAATTAGAAATTAATT
63 T-GAATTGAAGGATATGTTATTTCGAACATATGAATCTTGTTTC-ATTTTAATTAGAAATTAAAT
* **
29655 CGGAAAATAAATGGAAAAACGATAATAGAA-CAAAGTGAAAAGCCCTTCAATCTTTATGGTTTTA
126 CAG-AAA-AAATGGAAAAACGATAATAGAAGC---GTGAAAAGCCCTTCAATCTTTATGGCGTTA
*
29719 AATTATAT-TTTTTCC-GAGTATTATGGAAAAAAATTGAGGAAAAACTTTTCGGATCAGTTTTTA
186 AATTATATATTTTTCCTGAGTATTATGGAAAAAAATTGAGGAAAAACTTTTCGGATCAGTATTTA
29782 GCCGAAATCG
Statistics
Matches: 222, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
284 12 0.05
285 97 0.44
286 8 0.04
287 65 0.29
288 7 0.03
289 33 0.15
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (284 bp):
TTGATTTTTACGTAAATACTCCTTCAAATATCTATATTTATCTAATCAAATCTCAGCCTCGTTGA
ATTGAAGGATATGTTATTTCGAACATATGAATCTTGTTTCATTTTAATTAGAAATTAAATCAGAA
AAAATGGAAAAACGATAATAGAAGCGTGAAAAGCCCTTCAATCTTTATGGCGTTAAATTATATAT
TTTTCCTGAGTATTATGGAAAAAAATTGAGGAAAAACTTTTCGGATCAGTATTTACCAAAAATCG
TGCACTAACGAACACGAGTTTGTC
Done.