Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023276.1 Corchorus olitorius cultivar O-4 contig23309, 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: 31035
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:781 original size:16 final size:16
Alignment explanation
Indices: 762--798 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
752 AATATTTAAA
762 AAAAAACAAAAAAAAC
1 AAAAAACAAAAAAAAC
* *
778 AAAAAATAAAAAAAAT
1 AAAAAACAAAAAAAAC
794 AAAAA
1 AAAAA
799 CGTGGCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (16 bp):
AAAAAACAAAAAAAAC
Found at i:793 original size:9 final size:9
Alignment explanation
Indices: 738--798 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
728 TAAAATTCGA
738 AAAAAAAATT
1 AAAAAAAA-T
*
748 AAAAAATATTT
1 AAAAAA-A-AT
759 AAAAAAAA-
1 AAAAAAAAT
767 ACAAAAAAA-
1 A-AAAAAAAT
*
776 ACAAAAAAT
1 AAAAAAAAT
785 AAAAAAAAT
1 AAAAAAAAT
794 AAAAA
1 AAAAA
799 CGTGGCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 7 0.16
9 21 0.49
10 7 0.16
11 8 0.19
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1901 original size:19 final size:19
Alignment explanation
Indices: 1877--1923 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1867 CTTGATTAAA
1877 TTAAATAAAATCCACCTGG
1 TTAAATAAAATCCACCTGG
*
1896 TTAAATAAAATCCACGTGG
1 TTAAATAAAATCCACCTGG
*
1915 CT-AATAAAA
1 TTAAATAAAA
1924 AGGGTTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (19 bp):
TTAAATAAAATCCACCTGG
Found at i:2387 original size:16 final size:15
Alignment explanation
Indices: 2353--2472 Score: 91
Period size: 16 Copynumber: 7.7 Consensus size: 15
2343 TCGGGTGGGA
* *
2353 TCGGATTCGGGTCTT
1 TCGGGTTCGGGTTTT
2368 TCGGGTTCGGGATTTT
1 TCGGGTTCGGG-TTTT
*
2384 TCGGGTTCGGATATTT
1 TCGGGTTCGGGT-TTT
*
2400 TCGGGTTCGGGTTAAGT
1 TCGGGTTCGGGTT--TT
*
2417 T-AGGTTCGGGATTTT
1 TCGGGTTCGGG-TTTT
** *
2432 T-GGACTCGGGTTATG
1 TCGGGTTCGGGTT-TT
2447 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGT-TTT
2463 TCGGGTTCGG
1 TCGGGTTCGG
2473 TCTCGGGTAG
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
14 2 0.02
15 22 0.27
16 54 0.65
17 5 0.06
ACGTcount: A:0.09, C:0.13, G:0.38, T:0.40
Consensus pattern (15 bp):
TCGGGTTCGGGTTTT
Found at i:2470 original size:47 final size:48
Alignment explanation
Indices: 2353--2472 Score: 113
Period size: 47 Copynumber: 2.5 Consensus size: 48
2343 TCGGGTGGGA
* * ** *
2353 TCGGATTCGGGT-CTTTCGGGTTCGGGATTTTTCGGGTTCGGATATTT
1 TCGGGTTCGGGTAATTTCGGGTTCGGGATTTTTCGGACTCGGATATTG
* * *
2400 TCGGGTTCGGGTTAAGTT-AGGTTCGGGATTTTT-GGACTCGGGT-TATG
1 TCGGGTTCGGG-TAATTTCGGGTTCGGGATTTTTCGGACTCGGATAT-TG
*
2447 TCGGGTTCGGGTATTTTCGGGTTCGG
1 TCGGGTTCGGGTAATTTCGGGTTCGG
2473 TCTCGGGTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
46 5 0.09
47 36 0.62
48 15 0.26
49 2 0.03
ACGTcount: A:0.09, C:0.13, G:0.38, T:0.40
Consensus pattern (48 bp):
TCGGGTTCGGGTAATTTCGGGTTCGGGATTTTTCGGACTCGGATATTG
Found at i:2493 original size:23 final size:23
Alignment explanation
Indices: 2462--2517 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2452 TTCGGGTATT
* *
2462 TTCGGGTTCGGTCTCGGGTAGGG
1 TTCGGGTTCGGGCTCAGGTAGGG
* *
2485 TTCGAGTTCGGGCTCAGGTCGGG
1 TTCGGGTTCGGGCTCAGGTAGGG
2508 TTCGGGTTCG
1 TTCGGGTTCG
2518 AGTTTGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.05, C:0.20, G:0.45, T:0.30
Consensus pattern (23 bp):
TTCGGGTTCGGGCTCAGGTAGGG
Found at i:3505 original size:23 final size:23
Alignment explanation
Indices: 3475--3524 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3465 TATTTTGGGT
3475 TCGGTCTCAGGTCGGGATCGGGC
1 TCGGTCTCAGGTCGGGATCGGGC
* *
3498 TCGGTCTCGGGTCGGGTTCGGGC
1 TCGGTCTCAGGTCGGGATCGGGC
3521 TCGG
1 TCGG
3525 GCTGCCTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.26, G:0.46, T:0.24
Consensus pattern (23 bp):
TCGGTCTCAGGTCGGGATCGGGC
Found at i:3541 original size:6 final size:6
Alignment explanation
Indices: 3486--3527 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
3476 CGGTCTCAGG
* * *
3486 TCGGGA TCGGGC TCGGTC TCGGG- TCGGGT TCGGGC TCGGGC T
1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC T
3528 GCCTCGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.02, C:0.26, G:0.48, T:0.24
Consensus pattern (6 bp):
TCGGGC
Found at i:4034 original size:44 final size:44
Alignment explanation
Indices: 3986--4075 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
3976 AAGTAGATTA
* * * *
3986 TTTAAACTAGTTTTCTAGTTTGGGTTGAATTGTCATTTAGATGT
1 TTTAAACTAGTTTCCTAATTTGCGTTGAATTCTCATTTAGATGT
*
4030 TTTAAACTAGTTTCCTAATTTGCTTTGAATTCTCATTTAGATGT
1 TTTAAACTAGTTTCCTAATTTGCGTTGAATTCTCATTTAGATGT
4074 TT
1 TT
4076 GAACATACGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (44 bp):
TTTAAACTAGTTTCCTAATTTGCGTTGAATTCTCATTTAGATGT
Found at i:6678 original size:51 final size:51
Alignment explanation
Indices: 6576--6679 Score: 131
Period size: 51 Copynumber: 2.0 Consensus size: 51
6566 GTTCTTCATA
* *
6576 TTTTCCTTGTTTAGATCTTGTCTCAGGACATTCAAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACATTAAAAACACTCTATTAGTGT
* * *
6627 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACA-TAAAAACACTGTATTCGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACATTAAAAACACTCTATTAGTGT
6678 TT
1 TT
6680 CTCTTTCAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 23 0.50
52 22 0.48
53 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.45
Consensus pattern (51 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACATTAAAAACACTCTATTAGTGT
Found at i:11304 original size:22 final size:21
Alignment explanation
Indices: 11262--11304 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11252 TTGGAATGGC
*
11262 GATGGCACGGGCATGGCCGGT
1 GATGGCACGGGAATGGCCGGT
*
11283 GATGGCACGGTGAATGGGCGGT
1 GATGGCACGG-GAATGGCCGGT
11305 AATGACTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.16, C:0.19, G:0.49, T:0.16
Consensus pattern (21 bp):
GATGGCACGGGAATGGCCGGT
Found at i:11420 original size:42 final size:42
Alignment explanation
Indices: 11373--11466 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
11363 GCCGGTCCTA
* * * *
11373 GCCGGGCATGTGGCTCGGATGAGGCTTGAGATGGCGGGCATG
1 GCCGGGCATGAGGCGCAGATGAGGCTTGAGATGCCGGGCATG
* * *
11415 GCCGGGCATGAGGCGCAGCTGAGGCTTGTGGTGCCGGGCATG
1 GCCGGGCATGAGGCGCAGATGAGGCTTGAGATGCCGGGCATG
11457 GCCGGGCATG
1 GCCGGGCATG
11467 GCCGGGCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.13, C:0.22, G:0.48, T:0.17
Consensus pattern (42 bp):
GCCGGGCATGAGGCGCAGATGAGGCTTGAGATGCCGGGCATG
Found at i:11462 original size:10 final size:10
Alignment explanation
Indices: 11447--11483 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
11437 GGCTTGTGGT
11447 GCCGGGCATG
1 GCCGGGCATG
11457 GCCGGGCATG
1 GCCGGGCATG
11467 GCCGGGCATG
1 GCCGGGCATG
11477 GCCGGGC
1 GCCGGGC
11484 GTGATACTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.08, C:0.32, G:0.51, T:0.08
Consensus pattern (10 bp):
GCCGGGCATG
Found at i:15706 original size:19 final size:18
Alignment explanation
Indices: 15673--15708 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15663 TTGAAATAAA
15673 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
15691 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
15709 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:15707 original size:11 final size:11
Alignment explanation
Indices: 15672--15720 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
15662 CTTGAAATAA
15672 ATCTTC-AATG
1 ATCTTCAAATG
15682 ATCTTC-AA-G
1 ATCTTCAAATG
*
15691 -TCTTCAAATT
1 ATCTTCAAATG
15701 ATCTTCAAATG
1 ATCTTCAAATG
*
15712 GTCTTCAAA
1 ATCTTCAAA
15721 CACGAACTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
8 5 0.15
9 3 0.09
10 8 0.24
11 17 0.52
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (11 bp):
ATCTTCAAATG
Found at i:16791 original size:9 final size:9
Alignment explanation
Indices: 16777--16805 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
16767 GTATTGTATC
16777 ATTTTATTT
1 ATTTTATTT
16786 ATTTTATTT
1 ATTTTATTT
16795 ATTTTATTT
1 ATTTTATTT
16804 AT
1 AT
16806 ATAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTATTT
Found at i:18245 original size:19 final size:17
Alignment explanation
Indices: 18231--18289 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 17
18221 AAAAAAATGA
18231 ATAAATAAAATAAAAATCT
1 ATAAATAAAATAAAAA--T
* * *
18250 ATTAATAATATAAATAT
1 ATAAATAAAATAAAAAT
*
18267 ATAAATATAAATAAAAAA
1 ATAAATA-AAATAAAAAT
18285 ATAAA
1 ATAAA
18290 AGTAGAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 7 0.22
18 12 0.38
19 13 0.41
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAATAAAATAAAAAT
Found at i:19168 original size:63 final size:63
Alignment explanation
Indices: 19062--19189 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
19052 TTTTTTCCTC
* *
19062 TAGAAATAGCACACCATGTTTTTTTTAGTACAGCCGCCTGTTCTTTTTGGGCTTGTTCACACT
1 TAGAAATACCACACCATGTTTTTTTTAGTACAGCCGCCCGTTCTTTTTGGGCTTGTTCACACT
* *
19125 TAGAAATACCACACCATGTTTTTTTTAGTACAGTCGCCCGTTCTTTTTGGGTTTGTTCACACT
1 TAGAAATACCACACCATGTTTTTTTTAGTACAGCCGCCCGTTCTTTTTGGGCTTGTTCACACT
19188 TA
1 TA
19190 ACCACACCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (63 bp):
TAGAAATACCACACCATGTTTTTTTTAGTACAGCCGCCCGTTCTTTTTGGGCTTGTTCACACT
Found at i:20559 original size:1 final size:1
Alignment explanation
Indices: 20553--20578 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
20543 CTCCGCTTTC
20553 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
20579 AAATTTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22795 original size:17 final size:16
Alignment explanation
Indices: 22741--22791 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
22731 ATCACCCCCC
22741 AGATCACTAGTGATCTA
1 AGATCACTAGTGATC-A
*
22758 AGATCACCAGTGATGCA
1 AGATCACTAGTGAT-CA
*
22775 AGATCACTGGTGATCA
1 AGATCACTAGTGATCA
22791 A
1 A
22792 AGATTACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (16 bp):
AGATCACTAGTGATCA
Done.