Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022968.1 Corchorus olitorius cultivar O-4 contig23001, 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: 34911
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:1328 original size:2 final size:2
Alignment explanation
Indices: 1321--1351 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1311 CCTCCCTGGG
1321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1352 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1462 original size:22 final size:22
Alignment explanation
Indices: 1424--1593 Score: 102
Period size: 22 Copynumber: 7.8 Consensus size: 22
1414 TAAATAATTT
*
1424 TATGAAATTTTTAATAACTACCC
1 TATGAAA-TTTTGATAACTACCC
* * **
1447 TATTAAATTTTGATAACCACGT
1 TATGAAATTTTGATAACTACCC
*
1469 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAACTACCC
* *
1490 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCC
* * *
1512 TATGAAACTTTGATGACCTA-AC
1 TATGAAATTTTGAT-AACTACCC
* *
1534 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTACCC
*
1557 TATGAAATTTTG-TAACCT-TCC
1 TATGAAATTTTGATAA-CTACCC
*
1578 TATG-ATTTTTGATAAC
1 TATGAAATTTTGATAAC
1594 CTCTCTGTGA
Statistics
Matches: 115, Mismatches: 26, Indels: 15
0.74 0.17 0.10
Matches are distributed among these distances:
20 7 0.06
21 28 0.24
22 60 0.52
23 20 0.17
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:1559 original size:23 final size:21
Alignment explanation
Indices: 1469--1595 Score: 82
Period size: 21 Copynumber: 5.9 Consensus size: 21
1459 ATAACCACGT
1469 TATGAAATTTTGATAA--TTACC
1 TATGAAATTTT-ATAACCTT-CC
* *
1490 TATGAAATTGTGATAAAC-TCC
1 TATGAAATT-TTATAACCTTCC
* * **
1511 ATATGAAACTTTGATGACCTAAC
1 -TATGAAA-TTTTATAACCTTCC
1534 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-AT-AACCTTCC
*
1557 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTATAACCTTCC
*
1578 TATG-ATTTTTGATAACCT
1 TATGAAATTTT-ATAACCT
1596 CTCTGTGAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
20 5 0.06
21 36 0.42
22 25 0.29
23 19 0.22
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCC
Found at i:1581 original size:44 final size:44
Alignment explanation
Indices: 1469--1582 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
1459 ATAACCACGT
*
1469 TATGAAATTTTGATAA--TTACCTATGAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACCTT-CCTATGAAATTGTAATAAACTCCA
* * ** *
1512 TATGAAACTTTGATGACCTAACTATGAAATTTTAATAAACCTTCC-
1 TATGAAATTTTGATAACCTTCCTATGAAATTGTAATAAA-C-TCCA
1557 TATGAAATTTTG-TAACCTTCCTATGA
1 TATGAAATTTTGATAACCTTCCTATGA
1583 TTTTTGATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
43 14 0.25
44 27 0.47
45 13 0.23
46 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTTCCTATGAAATTGTAATAAACTCCA
Found at i:1593 original size:21 final size:20
Alignment explanation
Indices: 1549--1629 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 20
1539 AATTTTAATA
1549 AACCTTCCTATGAAATTTTGT
1 AACCTTCCTATG-AATTTTGT
*
1570 AACCTTCCTATGATTTTTGAT
1 AACCTTCCTATGAATTTTG-T
*
1591 AACC-TCTCTGTGAGATTTTGTT
1 AACCTTC-CTATGA-ATTTTG-T
*
1613 AATCTTCCTAT-AATTTT
1 AACCTTCCTATGAATTTT
1630 TTTATACCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 13 0.26
21 23 0.46
22 12 0.24
23 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.47
Consensus pattern (20 bp):
AACCTTCCTATGAATTTTGT
Found at i:1957 original size:42 final size:42
Alignment explanation
Indices: 1883--1966 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1873 CACTGAGTTC
* * * *
1883 CTCCATTCAACATTCCTTCACATAGCATATTATCAATTTGAG
1 CTCCATTCAACATTACTCCAAATAGCACATTATCAATTTGAG
* * *
1925 CTCCATTCAACATTACTCCAAATGGTACATTATCAGTTTGAG
1 CTCCATTCAACATTACTCCAAATAGCACATTATCAATTTGAG
1967 TGCTCTCATG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.35
Consensus pattern (42 bp):
CTCCATTCAACATTACTCCAAATAGCACATTATCAATTTGAG
Found at i:6913 original size:2 final size:2
Alignment explanation
Indices: 6906--6938 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6896 AAAAATACAC
*
6906 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6939 CTAAATGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10067 original size:30 final size:31
Alignment explanation
Indices: 10025--10105 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
10015 TTGAGAAGTT
10025 TGGTAAGG-TTGTGAAAGTTGA-GAAAAAGAA
1 TGGTAAGGTTTGTGAAAGTTGAGGAAAAAG-A
* *
10055 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATGA
1 TGGTAAGGTTTGTGA-AAGTTGAGGAAAAAGA
10085 TGGTAAGGTTTG-GAAAGTTGA
1 TGGTAAGGTTTGTGAAAGTTGA
10106 AAAGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 5 0.11
30 25 0.57
31 14 0.32
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (31 bp):
TGGTAAGGTTTGTGAAAGTTGAGGAAAAAGA
Found at i:15256 original size:108 final size:109
Alignment explanation
Indices: 15066--15261 Score: 322
Period size: 108 Copynumber: 1.8 Consensus size: 109
15056 ATTTGCTAAA
*
15066 CACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAACTCTATAACTAAAATGATTTGTTA
1 CACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAACTCTAAAACTAAAATGATTTGTTA
* *
15131 GCCACACATCACGAATGCTCGACGCGCCAGTGCGACCCGATAAC
66 GCCACAAATCAAGAATGCTCGACGCGCCAGTGCGACCCGATAAC
* *
15175 CACCTATTCACATATATGATAAGAACTGAGAG-AAAAAAAACTCTAAAACTAAAATGATTTGTTA
1 CACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAACTCTAAAACTAAAATGATTTGTTA
* *
15239 GCTATAAATCAAGAATGCTCGAC
66 GCCACAAATCAAGAATGCTCGAC
15262 ACACCAACGT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 50 0.62
109 30 0.38
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.22
Consensus pattern (109 bp):
CACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAACTCTAAAACTAAAATGATTTGTTA
GCCACAAATCAAGAATGCTCGACGCGCCAGTGCGACCCGATAAC
Found at i:23301 original size:2 final size:2
Alignment explanation
Indices: 23294--23322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23284 ACATCACAAC
23294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23323 AACCCATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30522 original size:11 final size:11
Alignment explanation
Indices: 30498--30532 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
30488 TTAACAGCGT
30498 AACAAAAACAA
1 AACAAAAACAA
* *
30509 AACGAAAACGA
1 AACAAAAACAA
30520 AACAAAAACAA
1 AACAAAAACAA
30531 AA
1 AA
30533 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:33558 original size:107 final size:107
Alignment explanation
Indices: 33407--33680 Score: 408
Period size: 107 Copynumber: 2.6 Consensus size: 107
33397 AGGTTTTTTA
* * *
33407 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCACCAAATTAAGATTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCACCAAATTAAAACTTT
* * *
33472 ATGTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTG
66 ATGTTTATTGTAAGGGTAAATTCCAAAATCAATAATTTATTG
* * *
33514 TTATAGGGTTTTAGAAATAAAATACAAAACCAATTTCACTAAGTTTAGCGCCAAATTAAAACTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCACCAAATTAAAACTTT
* * *
33579 ATTTTTATTGTAAGGGTAAATTCCATAATCAATAATTTATTT
66 ATGTTTATTGTAAGGGTAAATTCCAAAATCAATAATTTATTG
*
33621 TTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAAGCA-CAAATTAAAA
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTT-AGCACCAAATTAAAA
33681 TTAAAATTTT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
106 22 0.15
107 128 0.85
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (107 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCACCAAATTAAAACTTT
ATGTTTATTGTAAGGGTAAATTCCAAAATCAATAATTTATTG
Found at i:34717 original size:29 final size:29
Alignment explanation
Indices: 34642--34719 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
34632 CGTTAGACTG
*
34642 AGGGGACAAAACGTCCCAAAATTAAAATTT
1 AGGGGACAAAACGT-CCAAAATTAAAATTC
* * * *
34672 AGAGAACAAAATGTCCAAAATTGAAATTC
1 AGGGGACAAAACGTCCAAAATTAAAATTC
*
34701 AGGGGACAAAACATCCAAA
1 AGGGGACAAAACGTCCAAA
34720 CGCTACAAGT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (29 bp):
AGGGGACAAAACGTCCAAAATTAAAATTC
Done.