Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004956.1 Corchorus capsularis cultivar CVL-1 contig04974, 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, 790
Length: 1318
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Found at i:128 original size:21 final size:21
Alignment explanation
Indices: 104--147 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
94 AAAAAGTGTA
*
104 AAAAATGGGGCGATATTTAGC
1 AAAAATAGGGCGATATTTAGC
* *
125 AAAACTAGGGCGGTATTTAGC
1 AAAAATAGGGCGATATTTAGC
146 AA
1 AA
148 CCCCTCTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCGATATTTAGC
Found at i:305 original size:2 final size:2
Alignment explanation
Indices: 298--325 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
288 CTTTCATTGC
298 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
326 CTTTATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:679 original size:45 final size:45
Alignment explanation
Indices: 621--706 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
611 AAGATCTCAA
* * *
621 TATGAAATTTTGATAACTTTCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAAC-CTCCATATGAAATATTGATAACCAACAC
* *
666 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
707 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 4 0.11
45 31 0.89
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:700 original size:22 final size:22
Alignment explanation
Indices: 590--1068 Score: 174
Period size: 22 Copynumber: 22.0 Consensus size: 22
580 GAAATTCGGT
* *
590 TAACCTCCTTATGGAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* *
612 -AGATCTCAATATGAAATTTTGA
1 TA-ACCTCCATATGAAATTTTGA
*
634 TAACTTTCCA-ATGAAATTTTGA
1 TAAC-CTCCATATGAAATTTTGA
** * *
656 TAACCAACACTATGAGATGTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
679 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
* ** * *
701 TAACCACGTTATGAAAATTTAA
1 TAACCTCCATATGAAATTTTGA
* * *
723 AAACCTTCATATG-ACTTGTT-A
1 TAACCTCCATATGAAATT-TTGA
* * *
744 GTAA-TTACACTCTGAAATTTTGA
1 -TAACCTCCA-TATGAAATTTTGA
*
767 TAA--TCACACTATGAAATTGTGA
1 TAACCTC-CA-TATGAAATTTTGA
*
789 TAACCTCGC-TACGAAATTTTGA
1 TAACCTC-CATATGAAATTTTGA
* *
811 TAAATCTTCC-TATAAAATTTTGA
1 T-AA-CCTCCATATGAAATTTTGA
* *
834 TAAACCTCCCTATAAAATTTTGA
1 T-AACCTCCATATGAAATTTTGA
** * * * *
857 TAAATTTCTTATGAAATCTTAA
1 TAACCTCCATATGAAATTTTGA
*
879 TAA----C-TA-CAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* **
895 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCATATGAAATTTTGA
** *
917 TAA-CTTAATTATGAAATTTTGT
1 TAACCTCCA-TATGAAATTTTGA
* *
939 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * *
961 TCTACATAC-TATGAAA-TTTGA
1 T-AACCTCCATATGAAATTTTGA
* *
982 TAACC-CTCTTGTGAAATTTTGA
1 TAACCTC-CATATGAAATTTTGA
* **
1004 -AAACTAAACTATGAAATTTTGA
1 TAACCTCCA-TATGAAATTTTGA
*
1026 TAACCTTCATATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* *
1048 TATCCTCC--CTGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
1068 T
1 T
1069 TACTCCAAAA
Statistics
Matches: 339, Mismatches: 87, Indels: 64
0.69 0.18 0.13
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 16 0.05
21 29 0.09
22 208 0.61
23 67 0.20
24 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:830 original size:23 final size:23
Alignment explanation
Indices: 758--861 Score: 104
Period size: 23 Copynumber: 4.6 Consensus size: 23
748 TTACACTCTG
* * *
758 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAATCTCCCTATA
* * * **
780 AAATTGTGAT-AACCTCGCTACG
1 AAATTTTGATAAATCTCCCTATA
*
802 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTCCCTATA
*
825 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTCCCTATA
848 AAATTTTGATAAAT
1 AAATTTTGATAAAT
862 TTCTTATGAA
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
22 26 0.39
23 41 0.61
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAATCTCCCTATA
Found at i:854 original size:46 final size:45
Alignment explanation
Indices: 758--861 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 45
748 TTACACTCTG
* * *
758 AAATTTTGAT-AATCACACTATGAAATTGTGATAACCTCGCTACG
1 AAATTTTGATAAATCACACTATAAAATTGTGATAACCTCCCTACA
* * *
802 AAATTTTGATAAATCTTC-CTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATC-ACACTATAAAATTGTGAT-AACCTCCCTACA
848 AAATTTTGATAAAT
1 AAATTTTGATAAAT
862 TTCTTATGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 10 0.20
45 17 0.33
46 24 0.47
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (45 bp):
AAATTTTGATAAATCACACTATAAAATTGTGATAACCTCCCTACA
Found at i:1198 original size:22 final size:22
Alignment explanation
Indices: 1173--1305 Score: 83
Period size: 22 Copynumber: 5.8 Consensus size: 22
1163 TAATCACATT
1173 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
1195 TGAAATTTTCATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
1217 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
1239 TGAAATAAATTTTGATAATCCTATCTTTA
1 TG--A-AAA-TTTGATAA-CC--TCTTTA
* *
1268 TG-AAATTTCGATAATCACTTTA
1 TGAAAATTT-GATAACCTCTTTA
*
1290 TG-AGATTTGATAACCT
1 TGAAAATTTGATAACCT
1306 TCTATCAAAT
Statistics
Matches: 85, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
21 9 0.11
22 45 0.53
24 4 0.05
25 9 0.11
26 10 0.12
27 2 0.02
29 6 0.07
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Done.