Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015826.1 Corchorus capsularis cultivar CVL-1 contig15847, 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: 23740
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:1501 original size:18 final size:18
Alignment explanation
Indices: 1480--1529 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1470 TTTTTGCTTG
1480 TTCTTTAACGTTTTTTTT
1 TTCTTTAACGTTTTTTTT
** *
1498 TTCTTTTTC-TTCGTTTTT
1 TTCTTTAACGTT-TTTTTT
1516 TTC-TTAACGTTTTT
1 TTCTTTAACGTTTTT
1530 AGATTTTCCT
Statistics
Matches: 24, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (18 bp):
TTCTTTAACGTTTTTTTT
Found at i:1976 original size:17 final size:17
Alignment explanation
Indices: 1927--1976 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
1917 TTTCCTCTTG
* *
1927 TTCTTTAACGTCTTTTT
1 TTCTTTAACTTTTTTTT
**
1944 TTCTTTTTCTTCTTTTTT
1 TTCTTTAACTT-TTTTTT
1962 TTCTTTAACTTTTTT
1 TTCTTTAACTTTTTT
1977 AGATTTTCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.74
Consensus pattern (17 bp):
TTCTTTAACTTTTTTTT
Found at i:2377 original size:32 final size:32
Alignment explanation
Indices: 2336--2400 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2326 TCAGATCCTA
* *
2336 CCCCTTACTGAGTTCTTGGAATCGCCACTAAT
1 CCCCTTACTGAGTTCTTAGAATCGCCAATAAT
*
2368 CCCCTTACTGAGTTCTTAGAGTCGCCAATAAT
1 CCCCTTACTGAGTTCTTAGAATCGCCAATAAT
2400 C
1 C
2401 TTTTTTGCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (32 bp):
CCCCTTACTGAGTTCTTAGAATCGCCAATAAT
Found at i:3178 original size:35 final size:35
Alignment explanation
Indices: 3132--3404 Score: 365
Period size: 35 Copynumber: 7.7 Consensus size: 35
3122 TTCTTACTAA
*
3132 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGAACT
3167 ACTTAATTACCCTGAATTAAGGTTGATTACT-AACTT
1 ACTTAATTACCCTGAATTAA-GTTGATTACTGAAC-T
* *
3203 ACTCAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
*
3238 CCTTAATTACCCTGAATTAAGTTGATTACTG-ACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
*
3272 CACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
* *
3308 ACTTAATTACCATGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
3343 ACTTAATTACCCTGAATTAAGTTACTGACTTACT-AACCT
1 ACTTAATTACCCTGAATTAAG-T--TGA-TTACTGAA-CT
*
3382 ACTTAATTACCCTAAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
3405 ACTTATTACT
Statistics
Matches: 215, Mismatches: 12, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
34 2 0.01
35 147 0.68
36 33 0.15
37 1 0.00
38 6 0.03
39 26 0.12
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGAACT
Found at i:8973 original size:23 final size:21
Alignment explanation
Indices: 8939--8980 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
8929 ATAGATTCAA
*
8939 TTAGTCATGTTCATGAACACG
1 TTAGTCATGTTCACGAACACG
8960 TTAGTTCATTGTTCACGAACA
1 TTAG-TCA-TGTTCACGAACA
8981 AGTCCATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (21 bp):
TTAGTCATGTTCACGAACACG
Found at i:9700 original size:77 final size:77
Alignment explanation
Indices: 9619--9772 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
9609 GTCGTTTACC
*
9619 TTGAAAAAATCAAAGTGGGGTTGGATTTTAACAAGTCTCAACTCCATTCTTAATTCTACTAACCA
1 TTGAAAAAATCAAAGTGGGGTTGGATTCTAACAAGTCTCAACTCCATTCTTAATTCTACTAACCA
9684 AGATTAAATACT
66 AGATTAAATACT
9696 TTGAAAAAATCAAAGTGGGGTTGGATTCTAACAAGTCTCAACTCCATTCTTAATTCTACTAACCA
1 TTGAAAAAATCAAAGTGGGGTTGGATTCTAACAAGTCTCAACTCCATTCTTAATTCTACTAACCA
9761 AGATTAAATACT
66 AGATTAAATACT
9773 AACAAGCTTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (77 bp):
TTGAAAAAATCAAAGTGGGGTTGGATTCTAACAAGTCTCAACTCCATTCTTAATTCTACTAACCA
AGATTAAATACT
Found at i:12215 original size:13 final size:13
Alignment explanation
Indices: 12173--12206 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
12163 TTAACCTTAG
12173 TTAAAAATTAGGA
1 TTAAAAATTAGGA
*
12186 TTAACAATTAGGA
1 TTAAAAATTAGGA
12199 TTAAAAAT
1 TTAAAAAT
12207 CAGAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (13 bp):
TTAAAAATTAGGA
Found at i:12298 original size:15 final size:18
Alignment explanation
Indices: 12276--12320 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
12266 CCAAAAAAAA
12276 TATTTTTA-TT-TTCTTT
1 TATTTTTACTTCTTCTTT
12292 T-TTTTTACTTGCTTCTTT
1 TATTTTTACTT-CTTCTTT
12310 TATTTTTACTT
1 TATTTTTACTT
12321 GCTCCGTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.24
16 3 0.12
18 7 0.28
19 9 0.36
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.76
Consensus pattern (18 bp):
TATTTTTACTTCTTCTTT
Found at i:12309 original size:18 final size:19
Alignment explanation
Indices: 12286--12323 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12276 TATTTTTATT
12286 TTCTTTT-TTTTTACTTGC
1 TTCTTTTATTTTTACTTGC
12304 TTCTTTTATTTTTACTTGC
1 TTCTTTTATTTTTACTTGC
12323 T
1 T
12324 CCGTGACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (19 bp):
TTCTTTTATTTTTACTTGC
Found at i:16274 original size:32 final size:33
Alignment explanation
Indices: 16193--16290 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 33
16183 ATCATTCGGA
* * *
16193 TTACGGATC-ATTCGGGTTCGGATTATCTC-AG
1 TTACAGATCAATTCGGGTTCGGATAATTTCGAG
* *
16224 ATT-CAGATCAATTCGGGTTTGGATAATTTTGAG
1 -TTACAGATCAATTCGGGTTCGGATAATTTCGAG
* *
16257 TTACAGAT-AATTTGGGTTCGGATCATTTCGAG
1 TTACAGATCAATTCGGGTTCGGATAATTTCGAG
16289 TT
1 TT
16291 TCAGGTCATT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
31 5 0.09
32 42 0.78
33 7 0.13
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.39
Consensus pattern (33 bp):
TTACAGATCAATTCGGGTTCGGATAATTTCGAG
Found at i:23153 original size:170 final size:166
Alignment explanation
Indices: 22782--23219 Score: 524
Period size: 170 Copynumber: 2.6 Consensus size: 166
22772 TGAGTCATTT
*
22782 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGA-CAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** * ** * *
22847 TTAAGTAACCTGCCAAGTAGGTAAAGA-TG-AAAAAGATTAGTTCTCAAGCTCATCATCAATCCT
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGGAAAAAAAAAAAGCTCTCAAGCTCAAAAGCAAGCCT
* * *
22910 TGATGAGGATCTTTTATTAATTCCACTAGTCTATTCAA
129 TGATGAGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * * * *
22948 GTCCATTAAGAAATGAACAAAAAGATTACTTATTTAATCCACTCAATAATCAAAAGTTATGACAT
1 GTCAATTGAGAAATG-ACAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
23013 TTAAGTAATCTGCCAAGTAGGAAAAGACGGAAAATAAAAAAAGCTCTCTAA-CTCTAAAAGCAAG
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGGAAAA-AAAAAAAGCTCTC-AAGCTC-AAAAGCAAG
*
23077 CCTTGGT-AGAGATCTTTTAGTAATTCCACTACTCTATTAAA
126 CCTTGATGAG-GATCTTTTAGTAATTCCACTACTCTATTAAA
* *
23118 GTTAATTGAGAAATGACTGAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGAC-AAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
23183 TTAAGTAATCTGTCAAGTGGGAAAAGACGGAAAAAAA
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGGAAAAAAA
23220 TTAGTTTTCT
Statistics
Matches: 230, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
166 80 0.35
167 2 0.01
168 3 0.01
169 20 0.09
170 125 0.54
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (166 bp):
GTCAATTGAGAAATGACAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGGAAAAAAAAAAAGCTCTCAAGCTCAAAAGCAAGCCTTG
ATGAGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:23371 original size:19 final size:17
Alignment explanation
Indices: 23330--23370 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
23320 AATAATAATA
23330 ATATATACTAATTCTTC
1 ATATATACTAATTCTTC
23347 ATATATACTAATTCTTC
1 ATATATACTAATTCTTC
*
23364 ATTTATA
1 ATATATA
23371 TTATATATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATACTAATTCTTC
Found at i:23537 original size:2 final size:2
Alignment explanation
Indices: 23530--23565 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
23520 ATTCTTCATC
23530 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23566 TCAATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.