Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022847.1 Corchorus olitorius cultivar O-4 contig22880, 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: 17413
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8673 original size:16 final size:16
Alignment explanation
Indices: 8652--8685 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
8642 TTTTTACTTT
8652 TTATATAATTATTCAA
1 TTATATAATTATTCAA
8668 TTATATAATTATTCAA
1 TTATATAATTATTCAA
8684 TT
1 TT
8686 CATTGTGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATAATTATTCAA
Found at i:9174 original size:123 final size:125
Alignment explanation
Indices: 9021--9273 Score: 438
Period size: 123 Copynumber: 2.0 Consensus size: 125
9011 AATTGGAAGC
* * *
9021 AATAATTTTTTTTGTTGTTGTTATTTGATTTCTTTACTCTCAGTTTTTTCACTCCTATTATCTTC
1 AATAATTTTTTTTGTTGTTGTTATTCGATTTCTTTACTCTCAGTTTTTTCAATCCTATTATCCTC
9086 TTTGCTTACAATAGTATCTTCTCATTCACATCAATGGGAGCTACAATAGACCCCATAG-T
66 TTTGCTTACAATAGTATCTTCTCATTCACATCAATGGGAGCTACAATAGACCCCATAGTT
* *
9145 AATAATTTTTTTT-TTTTTGTTATTCGATTTCTTTACTTTCAGTTTTTTCAATCCTATTATCCTC
1 AATAATTTTTTTTGTTGTTGTTATTCGATTTCTTTACTCTCAGTTTTTTCAATCCTATTATCCTC
*
9209 TTTGCTTACAATAGTATCTTCTCATTCACATCAATGGGAGCTACGATAGACCCCATAGTT
66 TTTGCTTACAATAGTATCTTCTCATTCACATCAATGGGAGCTACAATAGACCCCATAGTT
9269 AATAA
1 AATAA
9274 AAGAGGCAAA
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
123 103 0.84
124 19 0.16
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.47
Consensus pattern (125 bp):
AATAATTTTTTTTGTTGTTGTTATTCGATTTCTTTACTCTCAGTTTTTTCAATCCTATTATCCTC
TTTGCTTACAATAGTATCTTCTCATTCACATCAATGGGAGCTACAATAGACCCCATAGTT
Found at i:11489 original size:55 final size:55
Alignment explanation
Indices: 11390--11501 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 55
11380 ACAACCAAGA
* *
11390 CAAATGCCCAATGGCTTTAATCCAAGATTCAATGTTCCGTTTCTATACTTTTTTT
1 CAAACGCCCAATGGCTTTAATCCAAGATTCAATGTTCCGTTTCTACACTTTTTTT
* * *
11445 CAAACGCCCGATGGCTTTAATCGAAGATTCAATGTTCCAG-TTCTACGCTTTTTTT
1 CAAACGCCCAATGGCTTTAATCCAAGATTCAATGTTCC-GTTTCTACACTTTTTTT
11500 CA
1 CA
11502 TCCAAAATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 50 0.98
56 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (55 bp):
CAAACGCCCAATGGCTTTAATCCAAGATTCAATGTTCCGTTTCTACACTTTTTTT
Found at i:11600 original size:2 final size:2
Alignment explanation
Indices: 11595--11626 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11585 TATATTATGC
11595 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
11627 TCTATTACTT
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
Found at i:14728 original size:68 final size:66
Alignment explanation
Indices: 14617--14755 Score: 158
Period size: 68 Copynumber: 2.1 Consensus size: 66
14607 AAAATTTCAA
* ***
14617 TAACCGTCGTATGAAATTTTGATAATCTCCATAAGAGAATTTGATAACCTTTTTTTATGAAATTT
1 TAACCGTCGTATGAAATTTTGATAATCACCATAAGAGAATTTGATAACC--TCCATATGAAATTT
14682 TGG
64 TGG
* *
14685 TAACC-TCTGTATGAAATTTTGATAATCA-CACTACGA-AGTTTTGATAACCTCCATATGAAATT
1 TAACCGTC-GTATGAAATTTTGATAATCACCA-TAAGAGA-ATTTGATAACCTCCATATGAAATT
14747 TTGG
63 TTGG
14751 TAACC
1 TAACC
14756 ACACTATGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
66 19 0.31
67 5 0.08
68 38 0.61
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (66 bp):
TAACCGTCGTATGAAATTTTGATAATCACCATAAGAGAATTTGATAACCTCCATATGAAATTTTG
G
Found at i:14777 original size:23 final size:22
Alignment explanation
Indices: 14210--14794 Score: 186
Period size: 22 Copynumber: 26.4 Consensus size: 22
14200 CTCCAACGTA
* *
14210 GAAATATTGATAACCATAC--T
1 GAAATTTTGATAACCACACTAT
* * * *
14230 GAAAAATTTGATAACCTCATTGT
1 G-AAATTTTGATAACCACACTAT
* * *
14253 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* * *
14275 GAAAGTTTGATAACCACAATGT
1 GAAATTTTGATAACCACACTAT
*
14297 GAAATTTTGATAACCACACTCT
1 GAAATTTTGATAACCACACTAT
* *
14319 GAAATTCTGATAACCACACAAT
1 GAAATTTTGATAACCACACTAT
* *
14341 GAAGTTTTGATAACCTCATATTCTAT
1 GAAATTTTGATAA-C-CACA--CTAT
* *
14367 GAAATTTTGATAATCACATTAT
1 GAAATTTTGATAACCACACTAT
* * * *
14389 -AAA-ATTGGTAATCGCACTAT
1 GAAATTTTGATAACCACACTAT
*
14409 GAAAATTTTGATAACCACACCAT
1 G-AAATTTTGATAACCACACTAT
*
14432 GAAATTTTGATAACTTCCCTA-TAAGAAT
1 GAAATTTTGATAAC--CAC-ACT----AT
* ** *
14460 GAAATTGTGATATTCTCTA-TAT
1 GAAATTTTGATAACCAC-ACTAT
* * * *
14482 GTAATTTTGATAACCTCTCCAT
1 GAAATTTTGATAACCACACTAT
* * * *
14504 -AATATTTTCATAAGCTCCCTAT
1 GAA-ATTTTGATAACCACACTAT
* *
14526 GAAATTTTGTTAACCATC-CTAG
1 GAAATTTTGATAACCA-CACTAT
*
14548 GAAATTTTGATAA-GA-AC---
1 GAAATTTTGATAACCACACTAT
***
14565 -AAATTTTGATAA-CGTTCTAAT
1 GAAATTTTGATAACCACACT-AT
* *
14586 -TAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCACACTAT
* ** * *
14607 AAAATTTCAATAACCGTC-GTAT
1 GAAATTTTGATAACC-ACACTAT
*
14629 GAAATTTTGATAATCTC-CA-TAA
1 GAAATTTTGATAA-C-CACACTAT
****
14651 GAGAA-TTTGATAACCTTTTTTTAT
1 GA-AATTTTGATAACC--ACACTAT
* * **
14675 GAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCACACTAT
* *
14697 GAAATTTTGATAATCACACTAC
1 GAAATTTTGATAACCACACTAT
* *
14719 GAAGTTTTGATAACCTC-CATAT
1 GAAATTTTGATAACCACAC-TAT
*
14741 GAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* **
14763 GAAAATTTTAATAACCTTACTAT
1 G-AAATTTTGATAACCACACTAT
*
14786 GTAATTTTG
1 GAAATTTTG
14795 GTTTGATTGT
Statistics
Matches: 418, Mismatches: 105, Indels: 82
0.69 0.17 0.14
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
20 16 0.04
21 33 0.08
22 256 0.61
23 44 0.11
24 22 0.05
25 1 0.00
26 20 0.05
28 13 0.03
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:14792 original size:45 final size:44
Alignment explanation
Indices: 14694--14796 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 44
14684 GTAACCTCTG
* * * * *
14694 TATGAAATTTTGATAATCACACTACGAAGTTTTGATAACCTCCA
1 TATGAAATTTTGGTAACCACACTACGAAATTTTAATAACCTACA
*
14738 TATGAAATTTTGGTAACCACACTATGAAAATTTTAATAACCTTAC-
1 TATGAAATTTTGGTAACCACACTACG-AAATTTTAATAACC-TACA
*
14783 TATGTAATTTTGGT
1 TATGAAATTTTGGT
14797 TTGATTGTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 23 0.46
45 25 0.50
46 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCACACTACGAAATTTTAATAACCTACA
Found at i:16763 original size:22 final size:22
Alignment explanation
Indices: 16520--16763 Score: 142
Period size: 22 Copynumber: 11.1 Consensus size: 22
16510 CTCCAATGTA
* *
16520 GAAATATT-GATAACCTCATTTT
1 GAAAT-TTCGATAACCTCACTAT
*
16542 GCAAATTT-GATAACCT-AATAT
1 G-AAATTTCGATAACCTCACTAT
*
16563 GAAATTTCGATAACCTCCCTAT
1 GAAATTTCGATAACCTCACTAT
* *
16585 GAAAATTCGATAACCACACTAT
1 GAAATTTCGATAACCTCACTAT
* * *
16607 GAAATTTGGGTAA-TTACACTAT
1 GAAATTTCGATAACCT-CACTAT
* * *
16629 GAAATTTCGATAATCTCAGTGT
1 GAAATTTCGATAACCTCACTAT
* *
16651 GAAATTTTGATAATCTGC-CTAT
1 GAAATTTCGATAACCT-CACTAT
* ** * *
16673 AAAATTTTAATAATCACACTAAAT
1 GAAATTTCGATAACCTCACT--AT
* * *
16697 -AAAATT-GGTAACCGCACTAT
1 GAAATTTCGATAACCTCACTAT
* * *
16717 GAAAATTTTGATAACCACACCAT
1 G-AAATTTCGATAACCTCACTAT
*
16740 GAAATTTCGATAACCTCCCTAT
1 GAAATTTCGATAACCTCACTAT
16762 GA
1 GA
16764 GAATGAAACT
Statistics
Matches: 174, Mismatches: 36, Indels: 24
0.74 0.15 0.10
Matches are distributed among these distances:
20 8 0.05
21 13 0.07
22 128 0.74
23 23 0.13
24 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (22 bp):
GAAATTTCGATAACCTCACTAT
Found at i:16824 original size:22 final size:23
Alignment explanation
Indices: 16792--16852 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
16782 CTCTCTATGT
*
16792 ATTTTCGATAACCTCTCC-ATAAA
1 ATTTTC-ATAACCTCTCCTACAAA
16815 ATTTTCATAACCTC-CCTACAAA
1 ATTTTCATAACCTCTCCTACAAA
**
16837 ATTTTGTTAACCTCTC
1 ATTTTCATAACCTCTC
16853 TAGGAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 24 0.73
23 7 0.21
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (23 bp):
ATTTTCATAACCTCTCCTACAAA
Found at i:16920 original size:22 final size:22
Alignment explanation
Indices: 16895--17016 Score: 88
Period size: 22 Copynumber: 5.5 Consensus size: 22
16885 CCTCCCTCCC
* *
16895 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACCTCTA
*
16917 TATGAAATTTTGACAA-CTAC-A
1 TATGAAATTTTGATAACCT-CTA
* *
16938 CTATGAAGTTTTGATAATCTCTA
1 -TATGAAATTTTGATAACCTCTA
* *
16961 TATGAAATTTTGGTAACCAC-A
1 TATGAAATTTTGATAACCTCTA
* * * *
16982 CTACGAAATTTTGATAATCTTTC
1 -TATGAAATTTTGATAACCTCTA
*
17005 TATGTAATTTTG
1 TATGAAATTTTG
17017 GTTTGATTGT
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
21 3 0.04
22 71 0.92
23 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTA
Found at i:16983 original size:44 final size:44
Alignment explanation
Indices: 16894--17018 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
16884 ACCTCCCTCC
* * * ** *
16894 CTATGAAATTTTGGTAACCTCTGTATGAAATTTTGACAACTACA
1 CTATGAAATTTTGATAATCTCTATATGAAATTTTGGTAACCACA
*
16938 CTATGAAGTTTTGATAATCTCTATATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAATCTCTATATGAAATTTTGGTAACCACA
* * * *
16982 CTACGAAATTTTGATAATCTTTCTATGTAATTTTGGT
1 CTATGAAATTTTGATAATCTCTATATGAAATTTTGGT
17019 TTGATTGTCA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCTCTATATGAAATTTTGGTAACCACA
Done.