Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000295.1 Corchorus capsularis cultivar CVL-1 contig00295, 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, 838
Length: 1398
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Found at i:443 original size:26 final size:24
Alignment explanation
Indices: 413--467 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
403 AAATTTAACT
413 TTGGACCATTTCATTAAGAGTTAATC
1 TTGGACCATTTC--TAAGAGTTAATC
* *
439 TTGGA-CTTTTCTCAGAGTTAATC
1 TTGGACCATTTCTAAGAGTTAATC
462 TTGGAC
1 TTGGAC
468 TTTTCTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 16 0.62
25 5 0.19
26 5 0.19
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
TTGGACCATTTCTAAGAGTTAATC
Found at i:459 original size:23 final size:23
Alignment explanation
Indices: 429--474 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
419 CATTTCATTA
429 AGAGTTAATCTTGGACTTTTCTC
1 AGAGTTAATCTTGGACTTTTCTC
452 AGAGTTAATCTTGGACTTTTCTC
1 AGAGTTAATCTTGGACTTTTCTC
475 CTTTTGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (23 bp):
AGAGTTAATCTTGGACTTTTCTC
Found at i:695 original size:26 final size:26
Alignment explanation
Indices: 666--752 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 26
656 GTAATCAGTA
666 AATCAGTAATTAAGTGAAAAGAGATT
1 AATCAGTAATTAAGTGAAAAGAGATT
* * *
692 AATCAG-AGTCAAAGT-AATAGTA-ATCTGT
1 AATCAGTAAT-TAAGTGAAAAG-AGA--T-T
720 AAATCAGTAATTAAGTGAAAAGAGATT
1 -AATCAGTAATTAAGTGAAAAGAGATT
747 AATCAG
1 AATCAG
753 AGTTAAAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 18
0.66 0.09 0.26
Matches are distributed among these distances:
25 7 0.15
26 17 0.37
27 2 0.04
28 2 0.04
29 11 0.24
30 7 0.15
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.26
Consensus pattern (26 bp):
AATCAGTAATTAAGTGAAAAGAGATT
Found at i:712 original size:55 final size:55
Alignment explanation
Indices: 650--1025 Score: 612
Period size: 55 Copynumber: 6.8 Consensus size: 55
640 CTTTCTTAAA
* * *
650 GTAATAGTAATCAGTAAATCAGTAATTAAGTGAA-AAGAGATTAATCAGAGTCAAA
1 GTAATAGTAATCAGTAAATCAGTAGTCAAGT-AAGAAGAGATTAATCAGAGTCAAG
* * * * *
705 GTAATAGTAATCTGTAAATCAGTAATTAAGTGAA-AAGAGATTAATCAGAGTTAAA
1 GTAATAGTAATCAGTAAATCAGTAGTCAAGT-AAGAAGAGATTAATCAGAGTCAAG
*
760 GTAATAGTAATCAGTAAATAAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
1 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
815 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
1 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
870 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
1 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
925 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
1 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
* * *
980 GTAATAGTAATCAGTAAATCAATAGTTAAGTAAAAAGAGATTAATC
1 GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATC
1026 GGTAAATTGA
Statistics
Matches: 308, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
54 2 0.01
55 306 0.99
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (55 bp):
GTAATAGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAG
Found at i:1050 original size:71 final size:72
Alignment explanation
Indices: 975--1111 Score: 213
Period size: 71 Copynumber: 1.9 Consensus size: 72
965 TTAATCAGAG
* * * *
975 TCAAGGTAATAGTAATCAGTAAATCAATAGTTAAGTAAAAAGAGATTAATCGGTAAATTGA-TAA
1 TCAAGGTAATAGTAATCAGTAAATCAATAATCAAGTAAAAAGAGAGTAATCAGTAAATTGAGTAA
1039 TTAAGAA
66 TTAAGAA
* *
1046 TCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAGTAATCAGTAAATTGAGTAA
1 TCAAGGTAATAGTAATCAGTAAATCAATAATCAAGTAAAAAGAGAGTAATCAGTAAATTGAGTAA
1111 T
66 T
1112 CAGTAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
71 55 0.93
72 4 0.07
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.28
Consensus pattern (72 bp):
TCAAGGTAATAGTAATCAGTAAATCAATAATCAAGTAAAAAGAGAGTAATCAGTAAATTGAGTAA
TTAAGAA
Found at i:1097 original size:34 final size:34
Alignment explanation
Indices: 983--1117 Score: 105
Period size: 34 Copynumber: 3.9 Consensus size: 34
973 AGTCAAGGTA
* * *
983 ATAGTAATCAGTAAATCAATAGTTAAGTAAAAAG
1 ATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
* * * * * *
1017 AGATTAATCGGTAAAT-TGATAATTAAG-AATCAAGG
1 ATAGTAATCAGTAAATCAG-TAATCAAGTAA--AAAG
1052 TAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
1 --ATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
*
1088 ATAGTAATCAGTAAATTGAGTAATC-AGTAA
1 ATAGTAATCAGTAAA-TCAGTAATCAAGTAA
1118 TTAAAGAGCC
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
33 2 0.03
34 40 0.51
35 11 0.14
36 3 0.04
37 20 0.25
38 3 0.04
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (34 bp):
ATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
Found at i:1111 original size:16 final size:15
Alignment explanation
Indices: 1056--1117 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 15
1046 TCAAGGTAAT
*
1056 AGTAATCAGTAAATC
1 AGTAATCAGTAAATG
*
1071 AGTAATCAAGTAAAAAG
1 AGTAATC-AGT-AAATG
1088 ATAGTAATCAGTAAATTG
1 --AGTAATCAGTAAA-TG
1106 AGTAATCAGTAA
1 AGTAATCAGTAA
1118 TTAAAGAGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.18
16 15 0.38
17 6 0.15
18 4 0.10
19 7 0.18
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (15 bp):
AGTAATCAGTAAATG
Done.