Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010332.1 Corchorus capsularis cultivar CVL-1 contig10353, 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: 100279
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:1493 original size:21 final size:21
Alignment explanation
Indices: 1463--1502 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1453 TAAGAAAGAG
1463 GATATAAAAAATGAAGGGGGA
1 GATATAAAAAATGAAGGGGGA
* *
1484 GATATTAAAACTGAAGGGG
1 GATATAAAAAATGAAGGGG
1503 ATTTTGTAGG
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:0.47, C:0.03, G:0.33, T:0.17
Consensus pattern (21 bp):
GATATAAAAAATGAAGGGGGA
Found at i:1563 original size:42 final size:42
Alignment explanation
Indices: 1497--1588 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
1487 ATTAAAACTG
* * *
1497 AAGGGGATTTTGTAGGCATCCCAACTTTCCGGGATCATAAGA
1 AAGGGGATTTTGTACGCAACCCAACTTTCCGGGACCATAAGA
* * *
1539 AAGGGGATTTTGTACGCAAGCCAACTTTTCGGGACCATAGGA
1 AAGGGGATTTTGTACGCAACCCAACTTTCCGGGACCATAAGA
*
1581 AAGAGGAT
1 AAGGGGAT
1589 ATTAAAACTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (42 bp):
AAGGGGATTTTGTACGCAACCCAACTTTCCGGGACCATAAGA
Found at i:6168 original size:13 final size:12
Alignment explanation
Indices: 6150--6176 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6140 AAAAACCCCA
6150 AATTTTTCAACC
1 AATTTTTCAACC
6162 AATTTTTCAACC
1 AATTTTTCAACC
6174 AAT
1 AAT
6177 GATTTCGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (12 bp):
AATTTTTCAACC
Found at i:6385 original size:27 final size:27
Alignment explanation
Indices: 6347--6402 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
6337 CCGCCGCCCT
*
6347 CAATCCTTTCGCTGCCGTTAACTTCAC
1 CAATCCCTTCGCTGCCGTTAACTTCAC
6374 CAATCCCTTCGCTGCCGTTAACTTCAC
1 CAATCCCTTCGCTGCCGTTAACTTCAC
6401 CA
1 CA
6403 CCAAGATCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.39, G:0.11, T:0.30
Consensus pattern (27 bp):
CAATCCCTTCGCTGCCGTTAACTTCAC
Found at i:6700 original size:25 final size:26
Alignment explanation
Indices: 6666--6715 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
6656 ATTGCCGGTT
6666 TCAGATTGTGTAT-CTATGCTCAATG
1 TCAGATTGTGTATCCTATGCTCAATG
6691 TCAGATTGTGTATCCTATGCTCAAT
1 TCAGATTGTGTATCCTATGCTCAAT
6716 TCGGTTCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (26 bp):
TCAGATTGTGTATCCTATGCTCAATG
Found at i:8146 original size:12 final size:12
Alignment explanation
Indices: 8129--8160 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
8119 CCCAAAAGGA
8129 TCAGAGGCAGCT
1 TCAGAGGCAGCT
*
8141 TCAGAGGGAGCT
1 TCAGAGGCAGCT
8153 TCAGAGGC
1 TCAGAGGC
8161 TTCTCAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.38, T:0.16
Consensus pattern (12 bp):
TCAGAGGCAGCT
Found at i:8220 original size:34 final size:34
Alignment explanation
Indices: 8177--8246 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
8167 AGCAATCTTG
8177 TGATTGTAGAAAATAGTTGAAAGACTTGGGTTTT
1 TGATTGTAGAAAATAGTTGAAAGACTTGGGTTTT
8211 TGATTGTAGAAAATAGTTGAAAGACTTGGGTTTT
1 TGATTGTAGAAAATAGTTGAAAGACTTGGGTTTT
8245 TG
1 TG
8247 GTATGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39
Consensus pattern (34 bp):
TGATTGTAGAAAATAGTTGAAAGACTTGGGTTTT
Found at i:18683 original size:17 final size:17
Alignment explanation
Indices: 18661--18697 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18651 CAGTTATTTG
18661 ACATTGAAGCATAAAGA
1 ACATTGAAGCATAAAGA
*
18678 ACATTGAAGCATAAGGA
1 ACATTGAAGCATAAAGA
18695 ACA
1 ACA
18698 CTCAATCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (17 bp):
ACATTGAAGCATAAAGA
Found at i:38465 original size:18 final size:16
Alignment explanation
Indices: 38442--38486 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 16
38432 AATCTCATAC
38442 TTTCTAATTTCATTAAA
1 TTTCTAATTTCATT-AA
38459 TTTTCTAATTTCATTAA
1 -TTTCTAATTTCATTAA
38476 TTTCTAATTTC
1 TTTCTAATTTC
38487 CATTGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 14 0.52
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTCTAATTTCATTAA
Found at i:60645 original size:1 final size:1
Alignment explanation
Indices: 60639--60669 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
60629 TCAGCCTCAC
60639 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60670 GAACAAACCA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:63609 original size:11 final size:11
Alignment explanation
Indices: 63593--63617 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
63583 TTTTTTTGTT
63593 TTTCGTTTTTG
1 TTTCGTTTTTG
63604 TTTCGTTTTTG
1 TTTCGTTTTTG
63615 TTT
1 TTT
63618 TTCTGTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (11 bp):
TTTCGTTTTTG
Found at i:70682 original size:3 final size:3
Alignment explanation
Indices: 70676--70717 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
70666 CGTTGTTGAG
* *
70676 GTT GTT GTT GTT GTT GTT GCT GTT ATT GTT G-T GTTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G-TT GTT GTT
70718 TGAATCATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.02, C:0.02, G:0.31, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:71295 original size:17 final size:17
Alignment explanation
Indices: 71269--71306 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
71259 TGATTTTATT
71269 TCAG-CTTCGTAATTTC
1 TCAGTCTTCGTAATTTC
71285 TCAGTCTTCGTAATTTC
1 TCAGTCTTCGTAATTTC
71302 TCAGT
1 TCAGT
71307 TACACAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (17 bp):
TCAGTCTTCGTAATTTC
Found at i:81282 original size:33 final size:32
Alignment explanation
Indices: 81213--81278 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
81203 GGCCGGTTAC
*
81213 AATTTTACAGCTTCTTTTTTGAGGTAAGTGAT
1 AATTTTACAGCTTCTTTTTTGAGGTAAGTAAT
* *
81245 AATTTTACAGATTTTTTTTTTG-GGTAAGTAAT
1 AATTTTACAG-CTTCTTTTTTGAGGTAAGTAAT
81277 AA
1 AA
81279 ATTTGCAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (32 bp):
AATTTTACAGCTTCTTTTTTGAGGTAAGTAAT
Found at i:83700 original size:42 final size:43
Alignment explanation
Indices: 83654--83751 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 43
83644 TTTTATTTAA
83654 ATTATATATATTATAAAGTAAAATCTGAGCAAAAT-TATATAT
1 ATTATATATATTATAAAGTAAAATCTGAGCAAAATATATATAT
83696 A-T-TATATATTATAAAGTAAAATCTGAGCAAAATAATATATAT
1 ATTATATATATTATAAAGTAAAATCTGAGCAAAAT-ATATATAT
83738 ATTATATATATTAT
1 ATTATATATATTAT
83752 TTTTATTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
40 31 0.60
41 1 0.02
42 9 0.17
43 1 0.02
44 10 0.19
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (43 bp):
ATTATATATATTATAAAGTAAAATCTGAGCAAAATATATATAT
Found at i:83745 original size:9 final size:9
Alignment explanation
Indices: 83731--83779 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
83721 AGCAAAATAA
83731 TATATATAT
1 TATATATAT
83740 TATATATAT
1 TATATATAT
83749 TAT-T-T-T
1 TATATATAT
* *
83755 TATTTAAAT
1 TATATATAT
83764 TATATATAT
1 TATATATAT
83773 TATATAT
1 TATATAT
83780 TATAAAGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
6 4 0.12
7 2 0.06
8 1 0.03
9 27 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATATAT
Found at i:83794 original size:33 final size:33
Alignment explanation
Indices: 83731--83799 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
83721 AGCAAAATAA
* ** *
83731 TATATATATTATATATATTATTTTTATTTAAAT
1 TATATATATTATATATATAAAGTATATTTAAAT
83764 TATATATATTATATATTATAAAGTAT-TTTAAAT
1 TATATATATTATATA-TATAAAGTATATTTAAAT
83797 TAT
1 TAT
83800 TTTCTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TATATATATTATATATATAAAGTATATTTAAAT
Found at i:90576 original size:6 final size:6
Alignment explanation
Indices: 90565--90599 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
90555 GCTCTCCACG
90565 CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCC
1 CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCC
90600 CATCCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.69, G:0.00, T:0.17
Consensus pattern (6 bp):
CTCCCA
Found at i:100253 original size:2 final size:2
Alignment explanation
Indices: 100246--100277 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
100236 TAGCTCCTAC
100246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100278 GA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.