Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020977.1 Corchorus olitorius cultivar O-4 contig21010, 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: 7234
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1376 original size:65 final size:62
Alignment explanation
Indices: 1302--1514 Score: 234
Period size: 65 Copynumber: 3.4 Consensus size: 62
1292 GAAAGGTAAA
* * *
1302 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATT-GAAA--G
* *
1367 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
* * * * * ** * * *
1429 ATCATGACAACTTATGGTGTCAATTG--CAAGATCATGACAACTT-ATGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCA-AATATCAATTGAAAG
1489 ATCATGACAACTTCTGGTGTCAATTG
1 ATCATGACAACTTCTGGTGTCAATTG
1515 CAACATCATG
Statistics
Matches: 133, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
59 1 0.01
60 50 0.38
62 25 0.19
64 3 0.02
65 54 0.41
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (62 bp):
ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATATCAATTGAAAG
Found at i:1452 original size:30 final size:30
Alignment explanation
Indices: 1367--1567 Score: 253
Period size: 30 Copynumber: 6.7 Consensus size: 30
1357 TTGGAAATTT
* * *
1367 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTATGGTGTCAATTG--CAAC
* * * * *
1399 ATTATGACATCTTCA-AGTATCAATTGCAAG
1 ATCATGACAACTT-ATGGTGTCAATTGCAAC
*
1429 ATCATGACAACTTATGGTGTCAATTGCAAG
1 ATCATGACAACTTATGGTGTCAATTGCAAC
1459 ATCATGACAACTTATGGTGTCAATTGCAAC
1 ATCATGACAACTTATGGTGTCAATTGCAAC
*
1489 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTATGGTGTCAATTGCAAC
*
1519 ATCATGACAACTTTTGGTGTCAATTGCAA-
1 ATCATGACAACTTATGGTGTCAATTGCAAC
*
1548 ATCATGACAACTTCTGGTGT
1 ATCATGACAACTTATGGTGT
1568 AATGACAACT
Statistics
Matches: 152, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
29 20 0.13
30 112 0.74
32 20 0.13
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (30 bp):
ATCATGACAACTTATGGTGTCAATTGCAAC
Found at i:1495 original size:60 final size:60
Alignment explanation
Indices: 1367--1746 Score: 428
Period size: 60 Copynumber: 6.5 Consensus size: 60
1357 TTGGAAATTT
* * * * * *
1367 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCA-AGTATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTT-ATGGTGTCAATTGCAAG
* *
1429 ATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAG
* *
1489 ATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTTTGGTGTCAATTGCAA-
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAG
*
1548 ATCATGACAACTTCTGGTG-----T-----A--ATGACAACTTTTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAG
* * *
1596 ATTATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAG
* * * * * *
1656 ATTATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAG
* * *
1716 ACCATGACAACTTCTGGTGTCATTTGTAAGA
1 ATCATGACAACTTCTGGTGTCAATTGCAAGA
1747 AAAAAAAGTT
Statistics
Matches: 285, Mismatches: 19, Indels: 30
0.85 0.06 0.09
Matches are distributed among these distances:
47 26 0.09
48 18 0.06
49 1 0.00
53 1 0.00
54 1 0.00
58 1 0.00
59 20 0.07
60 192 0.67
62 25 0.09
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (60 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAG
Found at i:1574 original size:18 final size:18
Alignment explanation
Indices: 1551--1585 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1541 ATTGCAAATC
1551 ATGACAACTTCTGGTGTA
1 ATGACAACTTCTGGTGTA
*
1569 ATGACAACTTTTGGTGT
1 ATGACAACTTCTGGTGT
1586 CAATTGCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (18 bp):
ATGACAACTTCTGGTGTA
Found at i:1591 original size:47 final size:48
Alignment explanation
Indices: 1522--1615 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 48
1512 TTGCAACATC
1522 ATGACAACTTTTGGTGTCAATTGCAA-ATCATGACAACTTCTGGTGTA
1 ATGACAACTTTTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTA
*
1569 ATGACAACTTTTGGTGTCAATTGCAAGATTATGACAACTTCTGGTGT
1 ATGACAACTTTTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGT
1616 CAATTGCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 26 0.58
48 19 0.42
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (48 bp):
ATGACAACTTTTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTA
Found at i:1605 original size:30 final size:30
Alignment explanation
Indices: 1569--1746 Score: 257
Period size: 30 Copynumber: 5.9 Consensus size: 30
1559 TTCTGGTGTA
* **
1569 ATGACAACTTTTGGTGTCAATTGCAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAGACC
*
1599 ATGACAACTTCTGGTGTCAATTGCAAGAGC
1 ATGACAACTTCTGGTGTCAATTGCAAGACC
**
1629 ATGACAACTTCTGGTGTCAATTGCAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAGACC
* *
1659 ATGACAACTTCTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGACC
*
1689 ATGACAACTTCTGGTGTCAATTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGACC
* *
1719 ATGACAACTTCTGGTGTCATTTGTAAGA
1 ATGACAACTTCTGGTGTCAATTGCAAGA
1747 AAAAAAAGTT
Statistics
Matches: 137, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 137 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAGACC
Found at i:1634 original size:197 final size:198
Alignment explanation
Indices: 1370--1737 Score: 549
Period size: 197 Copynumber: 1.9 Consensus size: 198
1360 GAAATTTATC
* * *
1370 ATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTATCAATTGCAAGATCATG
1 ATGACAACTTCTGGTGTCAATTG-ACAAAATTATGACAACTTCAAGTATCAATTGCAAGAGCATG
*
1435 ACAACTTATGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAACATCATGACAAC
65 ACAACTTATGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAACACCATGACAAC
* *
1500 TTCTGGTGTCAATTGCAACATCATGACAACTTTTGGTGTCAATTGCAAATCATGACAACTTCTGG
130 TTCTGGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAAATCATGACAACTTCTGG
1565 TGTA
195 TGTA
* * ** *
1569 ATGACAACTTTTGGTGTCAATTG-CAAGATTATGACAACTTCTGGTGTCAATTGCAAGAGCATGA
1 ATGACAACTTCTGGTGTCAATTGACAAAATTATGACAACTTCAAGTATCAATTGCAAGAGCATGA
* * * * * *
1633 CAACTTCTGGTGTCAATTGCAAGATTATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACT
66 CAACTTATGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAACACCATGACAACT
* *
1698 TCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCA
131 TCTGGTGTCAATTGCAACACCATGACAACTTCTGGTGTCA
1738 TTTGTAAGAA
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
197 128 0.85
199 22 0.15
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (198 bp):
ATGACAACTTCTGGTGTCAATTGACAAAATTATGACAACTTCAAGTATCAATTGCAAGAGCATGA
CAACTTATGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAACACCATGACAACT
TCTGGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAAATCATGACAACTTCTGGT
GTA
Found at i:1648 original size:107 final size:108
Alignment explanation
Indices: 1462--1675 Score: 358
Period size: 107 Copynumber: 2.0 Consensus size: 108
1452 TTGCAAGATC
*
1462 ATGACAACTTATGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAACATCATGAC
1 ATGACAACTTATGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAACAGCATGAC
*
1527 AACTTTTGGTGTCAATTGCAA-ATCATGACAACTTCTGGTGTA
66 AACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTA
* * * *
1569 ATGACAACTTTTGGTGTCAATTGCAAGATTATGACAACTTCTGGTGTCAATTGCAAGAGCATGAC
1 ATGACAACTTATGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAACAGCATGAC
*
1634 AACTTCTGGTGTCAATTGCAAGATTATGACAACTTCTGGTGT
66 AACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGT
1676 CATTTGTAAG
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
107 80 0.81
108 19 0.19
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (108 bp):
ATGACAACTTATGGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAACAGCATGAC
AACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTA
Found at i:1694 original size:167 final size:168
Alignment explanation
Indices: 1418--1735 Score: 512
Period size: 167 Copynumber: 1.9 Consensus size: 168
1408 TCTTCAAGTA
*
1418 TCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAACTTATGGTGTCAAT
1 TCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAGAGCATGACAACTTATGGTGTCAAT
* *
1483 TGCAACATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAACTTTTGGTGTCAATTGCAA
66 TGCAACATCATGACAACTTCTGGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAA
*
1548 -ATCATGACAACTTCTGGTGTAATGACAACTTTTGGTG
131 GACCATGACAACTTCTGGTGTAATGACAACTTTTGGTG
* * *
1585 TCAATTGCAAGATTATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAACTTCTGGTGTCAAT
1 TCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAGAGCATGACAACTTATGGTGTCAAT
* * * * * *
1650 TGCAAGATTATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCAATTGTAA
66 TGCAACATCATGACAACTTCTGGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAA
1715 GACCATGACAACTTCTGGTGT
131 GACCATGACAACTTCTGGTGT
1736 CATTTGTAAG
Statistics
Matches: 137, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
167 118 0.86
168 19 0.14
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (168 bp):
TCAATTGCAAGATCATGACAACTTATGGTGTCAATTGCAAGAGCATGACAACTTATGGTGTCAAT
TGCAACATCATGACAACTTCTGGTGTCAATTGCAACACCATGACAACTTCTGGTGTCAATTGCAA
GACCATGACAACTTCTGGTGTAATGACAACTTTTGGTG
Found at i:3683 original size:2 final size:2
Alignment explanation
Indices: 3678--3712 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3668 TATATGTGTG
3678 TA TA TA TA TA 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 TA TA TA TA TA T
3713 CTCTCCGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7130 original size:35 final size:35
Alignment explanation
Indices: 7073--7142 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
7063 CTGATTCAGT
7073 TCCTGTGAGGGTACTAGAACTGTGAGAACAAATGG
1 TCCTGTGAGGGTACTAGAACTGTGAGAACAAATGG
* *
7108 TCCTTTGAGGTTACTA-ATACTGTGAGAACAAATGG
1 TCCTGTGAGGGTACTAGA-ACTGTGAGAACAAATGG
7143 GGAAAGATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (35 bp):
TCCTGTGAGGGTACTAGAACTGTGAGAACAAATGG
Done.