Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018940.1 Corchorus olitorius cultivar O-4 contig18973, 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: 18965
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:2385 original size:14 final size:15
Alignment explanation
Indices: 2358--2390 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2348 AAGTATTGTC
2358 ATATCAATTATATCA
1 ATATCAATTATATCA
2373 ATATCAA-TATATCA
1 ATATCAATTATATCA
2387 ATAT
1 ATAT
2391 AAAAGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATCAATTATATCA
Found at i:2680 original size:18 final size:18
Alignment explanation
Indices: 2602--2680 Score: 60
Period size: 18 Copynumber: 4.5 Consensus size: 18
2592 TCACAACTTT
2602 TTAT-TTATCTTACTATC
1 TTATCTTATCTTACTATC
* *
2619 TTATTATTACTATTACTA--
1 TTA-TCTTA-TCTTACTATC
2637 TTA-C-TATTCTTACTATC
1 TTATCTTA-TCTTACTATC
* *
2654 ATATTTTATCTTACTATC
1 TTATCTTATCTTACTATC
2672 TTATCTTAT
1 TTATCTTAT
2681 TACTATTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
15 9 0.19
17 5 0.11
18 21 0.45
19 5 0.11
20 7 0.15
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATCTTATCTTACTATC
Found at i:4454 original size:22 final size:22
Alignment explanation
Indices: 4415--4577 Score: 61
Period size: 22 Copynumber: 7.4 Consensus size: 22
4405 CCTTATAAAC
*
4415 TTTTGATAAGATTCCTATGAAA
1 TTTTGATAAAATTCCTATGAAA
*
4437 TTTTGATAACAATT-CTATGCAA
1 TTTTGATAA-AATTCCTATGAAA
* * * *
4459 TTTCGA-AAACCTTCCAATCAAA
1 TTTTGATAAA-ATTCCTATGAAA
* *
4481 -TTTCA-AGAACTTCCCTATGAAA
1 TTTTGATA-AAATT-CCTATGAAA
* ** *
4503 TTTTGTTAACCTCCCTAT-AGAA
1 TTTTGATAAAATTCCTATGA-AA
* *
4525 TTTTGA-AAACATTACTATAAAA
1 TTTTGATAAA-ATTCCTATGAAA
* **
4547 TTTTGAT-GACCTCCTAATGAAA
1 TTTTGATAAAATTCCT-ATGAAA
4569 TTTTGATAA
1 TTTTGATAA
4578 CCATCCACTT
Statistics
Matches: 102, Mismatches: 26, Indels: 25
0.67 0.17 0.16
Matches are distributed among these distances:
20 1 0.01
21 17 0.17
22 73 0.72
23 10 0.10
24 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTTGATAAAATTCCTATGAAA
Found at i:4591 original size:22 final size:22
Alignment explanation
Indices: 4497--4626 Score: 81
Period size: 22 Copynumber: 5.9 Consensus size: 22
4487 GAACTTCCCT
*
4497 ATGAAATTTTGTTAACCTCCCT-
1 ATGAAATTTTGATAACCT-CCTA
* * *
4519 AT-AGAATTTTGAAAACATTACT-
1 ATGA-AATTTTGATAAC-CTCCTA
* *
4541 ATAAAATTTTGATGACCTCCTA
1 ATGAAATTTTGATAACCTCCTA
4563 ATGAAATTTTGATAACCATCC-A
1 ATGAAATTTTGATAACC-TCCTA
* * *
4585 CTTAAATTTTGATAACCGCACT-
1 ATGAAATTTTGATAACCTC-CTA
* *
4607 ATAAAATTTTGATAATCTCC
1 ATGAAATTTTGATAACCTCC
4627 ATGTAAAATG
Statistics
Matches: 84, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
21 6 0.07
22 73 0.87
23 5 0.06
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCTA
Found at i:4633 original size:22 final size:21
Alignment explanation
Indices: 4566--4635 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
4556 CCTCCTAATG
4566 AAATTTTGATAACCATCCACTT-
1 AAATTTTGATAA-C-TCCACTTA
4588 AAATTTTGATAAC-CGCACTATA
1 AAATTTTGATAACTC-CACT-TA
4610 AAATTTTGATAATCTCCA-TGTA
1 AAATTTTGATAA-CTCCACT-TA
4632 AAAT
1 AAAT
4636 GTTTTCTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.02
20 4 0.10
21 2 0.05
22 31 0.74
23 3 0.07
24 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
AAATTTTGATAACTCCACTTA
Found at i:4737 original size:23 final size:23
Alignment explanation
Indices: 4707--4764 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
4697 GCTTGGTATG
*
4707 AAATTTTGATAAACATTCATATA
1 AAATTTTGATAAACATCCATATA
* *
4730 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACATCCATATA
4753 AAATTTTGATAA
1 AAATTTTGATAA
4765 CCTCCTCGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACATCCATATA
Found at i:4769 original size:22 final size:22
Alignment explanation
Indices: 4707--4937 Score: 115
Period size: 22 Copynumber: 10.7 Consensus size: 22
4697 GCTTGGTATG
* * *
4707 AAATTTTGATAAACATTCATATA
1 AAATTTTGAT-AACCTCCCTATA
4730 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCCCTATA
* *
4753 AAATTTTGATAACCT-CCTCGTG
1 AAATTTTGATAACCTCCCT-ATA
*
4775 AAATTTTGATAA--T--C-A-C
1 AAATTTTGATAACCTCCCTATA
4791 AAATTTTGATAACCTCTCCCTAT-
1 AAATTTTGATAA-C-CTCCCTATA
* * * ** *
4814 GATTTTTCGATAACTTCATTATG
1 AAATTTT-GATAACCTCCCTATA
* * *
4837 AAATTTTGTTAACGTCCCTATG
1 AAATTTTGATAACCTCCCTATA
4859 AAATTTTGATAA-C-CCCTATA
1 AAATTTTGATAACCTCCCTATA
* * *** *
4879 AAATTTTGAAAAACAAACTATG
1 AAATTTTGATAACCTCCCTATA
*
4901 AAATTTTGATAATCC-CCCTTTA
1 AAATTTTGATAA-CCTCCCTATA
*
4923 AAATTTTAATAACCT
1 AAATTTTGATAACCT
4938 TCATATATGA
Statistics
Matches: 161, Mismatches: 32, Indels: 31
0.72 0.14 0.14
Matches are distributed among these distances:
16 12 0.07
19 1 0.01
20 19 0.12
21 6 0.04
22 75 0.47
23 43 0.27
24 5 0.03
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATA
Found at i:5151 original size:43 final size:43
Alignment explanation
Indices: 5054--5174 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 43
5044 TCCATGAAAT
* * * * *
5054 GTTATCAGAATTTCATAATTTGGTTACCAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAATATGGTTACAAAATTTCATAGGAAG
* * *
5097 GTTATAAAAAATTT-ATACTATGGTTACAAAAATTTCATATGAAG
1 GTTAT-CAAAATTTCATAATATGGTTAC-AAAATTTCATAGGAAG
*
5141 GTTATCAAAATTTCATAGA-GTGGTTATCAAAATT
1 GTTATCAAAATTTCATA-ATATGGTTA-CAAAATT
5175 ATAGGGATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
43 23 0.37
44 38 0.61
45 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (43 bp):
GTTATCAAAATTTCATAATATGGTTACAAAATTTCATAGGAAG
Found at i:5165 original size:22 final size:22
Alignment explanation
Indices: 5104--5174 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
5094 GAGGTTATAA
5104 AAAATTT-ATACT-ATGGTTA-C
1 AAAATTTCATA-TGATGGTTATC
*
5124 AAAAATTTCATATGAAGGTTATC
1 -AAAATTTCATATGATGGTTATC
5147 AAAATTTCATA-GAGTGGTTATC
1 AAAATTTCATATGA-TGGTTATC
5169 AAAATT
1 AAAATT
5175 ATAGGGATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.23
22 33 0.75
23 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (22 bp):
AAAATTTCATATGATGGTTATC
Found at i:10965 original size:19 final size:18
Alignment explanation
Indices: 10941--10976 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10931 TGAAGACCAT
10941 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
10960 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
10977 TCTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:18051 original size:12 final size:12
Alignment explanation
Indices: 18031--18060 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
18021 AAAAAGGGAA
18031 AAAAGTAAATAAG
1 AAAA-TAAATAAG
18044 AAAATAAATAAG
1 AAAATAAATAAG
18056 AAAAT
1 AAAAT
18061 TCCGGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (12 bp):
AAAATAAATAAG
Found at i:18677 original size:21 final size:19
Alignment explanation
Indices: 18652--18709 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
18642 GCTGCTCTAA
18652 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
18673 TAATCTAATTTGTACAGTG
1 TAATCTCATCTGTACAGTC
18692 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
18710 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Done.