Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006703.1 Corchorus capsularis cultivar CVL-1 contig06724, 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: 19457
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Found at i:754 original size:39 final size:39
Alignment explanation
Indices: 705--781 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
695 CGATGCCAAT
*
705 GTCTCTTTTAGTTTCTTTTTGTGGCTGGCCGCTGGTGTA
1 GTCTCTTTTAGGTTCTTTTTGTGGCTGGCCGCTGGTGTA
*
744 GTCTTTTTTAGGTTCTTTTTGTGGCTGGCCGCTGGTGT
1 GTCTCTTTTAGGTTCTTTTTGTGGCTGGCCGCTGGTGT
782 TTGGATAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.04, C:0.17, G:0.30, T:0.49
Consensus pattern (39 bp):
GTCTCTTTTAGGTTCTTTTTGTGGCTGGCCGCTGGTGTA
Found at i:1340 original size:42 final size:43
Alignment explanation
Indices: 1280--1362 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 43
1270 TTGTAGTGGT
1280 GAGATGATGCATGATGAAGACAATGCTCGGAAATCAGATGATC
1 GAGATGATGCATGATGAAGACAATGCTCGGAAATCAGATGATC
1323 GAGAT-ATGCATGATGAAGACAATGCTCGGAAATCAGATGA
1 GAGATGATGCATGATGAAGACAATGCTCGGAAATCAGATGA
1363 ACGGGATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 35 0.88
43 5 0.12
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (43 bp):
GAGATGATGCATGATGAAGACAATGCTCGGAAATCAGATGATC
Found at i:1593 original size:30 final size:32
Alignment explanation
Indices: 1544--1608 Score: 116
Period size: 30 Copynumber: 2.1 Consensus size: 32
1534 AACATACTAT
1544 TGGACAAATTTTGAATTCTATGATATGGAAGG
1 TGGACAAATTTTGAATTCTATGATATGGAAGG
1576 TGGACAAA-TTT-AATTCTATGATATGGAAGG
1 TGGACAAATTTTGAATTCTATGATATGGAAGG
1606 TGG
1 TGG
1609 TTCATATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 22 0.67
31 3 0.09
32 8 0.24
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (32 bp):
TGGACAAATTTTGAATTCTATGATATGGAAGG
Found at i:1823 original size:25 final size:27
Alignment explanation
Indices: 1791--1848 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
1781 AAATTTTTTC
1791 CAGTTTC-TTTGTTGCCAGGTTG-TTT
1 CAGTTTCTTTTGTTGCCAGGTTGATTT
1816 CAGTTTCTTTTGTTGCCAGGTTGATTT
1 CAGTTTCTTTTGTTGCCAGGTTGATTT
*
1843 GAGTTT
1 CAGTTT
1849 GTGGCAGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 7 0.23
26 15 0.50
27 8 0.27
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (27 bp):
CAGTTTCTTTTGTTGCCAGGTTGATTT
Found at i:8897 original size:44 final size:43
Alignment explanation
Indices: 8843--8989 Score: 145
Period size: 44 Copynumber: 3.4 Consensus size: 43
8833 ATAGCCCCAC
* * *
8843 TGAAAATTTGATAATCTCATTATAGAATTTCGATAACCTCCCTA
1 TGAAATTTTGATAATCTCAATAT-GAATTTTGATAACCTCCCTA
* * *
8887 TGAAAGTTTGATAA-CAACAATATGACATTTTGATAACC-CACTA
1 TGAAATTTTGATAATC-TCAATATGA-ATTTTGATAACCTCCCTA
* * * *
8930 TGAAATTTTGATAATCTCAGTGTGAAATTTTGATAATCTCCATA
1 TGAAATTTTGATAATCTCAATATG-AATTTTGATAACCTCCCTA
*
8974 TCAAATTTTGATAATC
1 TGAAATTTTGATAATC
8990 ACACTATAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
43 36 0.42
44 49 0.58
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (43 bp):
TGAAATTTTGATAATCTCAATATGAATTTTGATAACCTCCCTA
Found at i:8942 original size:43 final size:43
Alignment explanation
Indices: 8843--9062 Score: 144
Period size: 44 Copynumber: 5.1 Consensus size: 43
8833 ATAGCCCCAC
* * * * *
8843 TGAAAATTTGATAATCTCATTAT-AGAATTTCGATAACCTCCCTA
1 TGAAATTTTGATAATCACAATATGA-AATTTTGATAACC-CACTA
* *
8887 TGAAAGTTTGATAA-CAACAATATGACATTTTGATAACCCACTA
1 TGAAATTTTGATAATC-ACAATATGAAATTTTGATAACCCACTA
* * *
8930 TGAAATTTTGATAATCTCAGTGTGAAATTTTGATAATCTCCA-TA
1 TGAAATTTTGATAATCACAATATGAAATTTTGATAA-C-CCACTA
* * * * ** *
8974 TCAAATTTTGATAATCACACTAT-AAA-ATTGGTAATGCATTA
1 TGAAATTTTGATAATCACAATATGAAATTTTGATAACCCACTA
*** * *
9015 TGAAAATTTTGATAATCACGCCATGAAATTTCGATAACCTCCCTA
1 TG-AAATTTTGATAATCACAATATGAAATTTTGATAACC-CACTA
9060 TGA
1 TGA
9063 GAATGAAATT
Statistics
Matches: 137, Mismatches: 29, Indels: 20
0.74 0.16 0.11
Matches are distributed among these distances:
40 2 0.01
41 3 0.02
42 25 0.18
43 40 0.29
44 58 0.42
45 9 0.07
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (43 bp):
TGAAATTTTGATAATCACAATATGAAATTTTGATAACCCACTA
Found at i:8959 original size:87 final size:85
Alignment explanation
Indices: 8843--9062 Score: 212
Period size: 87 Copynumber: 2.6 Consensus size: 85
8833 ATAGCCCCAC
* *
8843 TGAAAATTTGATAATCTCATTAT-AGAATTTCGATAACCTCCCTATGAAAGTTTGATAA-CAACA
1 TGAAATTTTGATAATCTCAGTATGA-AATTTCGATAACCTCCCTATGAAAGTTTGATAATC-ACA
**
8906 ATATGACATTTTGATAACCCACTA
64 ATAT-A-AAATTGATAACCCACTA
* * * * * * *
8930 TGAAATTTTGATAATCTCAGTGTGAAATTTTGATAATCTCCATATCAAATTTTGATAATCACACT
1 TGAAATTTTGATAATCTCAGTATGAAATTTCGATAACCTCCCTATGAAAGTTTGATAATCACAAT
* ** *
8995 ATAAAATTGGTAATGCATTA
66 ATAAAATTGATAACCCACTA
* *
9015 TGAAAATTTTGATAATCAC-GCCATGAAATTTCGATAACCTCCCTATGA
1 TG-AAATTTTGATAATCTCAG-TATGAAATTTCGATAACCTCCCTATGA
9063 GAATGAAATT
Statistics
Matches: 107, Mismatches: 22, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
85 14 0.13
86 37 0.35
87 54 0.50
88 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (85 bp):
TGAAATTTTGATAATCTCAGTATGAAATTTCGATAACCTCCCTATGAAAGTTTGATAATCACAAT
ATAAAATTGATAACCCACTA
Found at i:8988 original size:22 final size:23
Alignment explanation
Indices: 8843--9151 Score: 125
Period size: 22 Copynumber: 13.9 Consensus size: 23
8833 ATAGCCCCAC
* *
8843 TGAAAATTTGATAATCT-CATTA
1 TGAAATTTTGATAATCTCCACTA
* *
8865 T-AGAATTTCGATAACCTCC-CTA
1 TGA-AATTTTGATAATCTCCACTA
* ** *
8887 TGAAAGTTTGATAA-CAACAATA
1 TGAAATTTTGATAATCTCCACTA
*
8909 TGACATTTTGATAA-C-CCACTA
1 TGAAATTTTGATAATCTCCACTA
* *
8930 TGAAATTTTGATAATCT-CAGTG
1 TGAAATTTTGATAATCTCCACTA
8952 TGAAATTTTGATAATCTCCA-TA
1 TGAAATTTTGATAATCTCCACTA
* *
8974 TCAAATTTTGATAATC-ACACTA
1 TGAAATTTTGATAATCTCCACTA
* * * *
8996 T-AAA-ATTGGTAA--TGCATTA
1 TGAAATTTTGATAATCTCCACTA
*
9015 TGAAAATTTTGATAATCACGC-C-A
1 TG-AAATTTTGATAATCTC-CACTA
* *
9038 TGAAATTTCGATAACCTCC-CTA
1 TGAAATTTTGATAATCTCCACTA
** *
9060 TGAGAATGAAATTGTGATGTTCT-CTCTA
1 TGA-AAT----TT-TGATAATCTCCACTA
* * * *
9088 TGTAATTTTGATAA-CTTCTCCA
1 TGAAATTTTGATAATCTCCACTA
* *
9110 TGAAATTTTCATAACCTCC-CTA
1 TGAAATTTTGATAATCTCCACTA
* *
9132 TGAAATTTTGTTAACCTCCA
1 TGAAATTTTGATAATCTCCA
9152 GGAAATTTTG
Statistics
Matches: 216, Mismatches: 45, Indels: 51
0.69 0.14 0.16
Matches are distributed among these distances:
19 5 0.02
20 6 0.03
21 32 0.15
22 141 0.65
23 15 0.07
25 1 0.00
27 6 0.03
28 10 0.05
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (23 bp):
TGAAATTTTGATAATCTCCACTA
Found at i:9158 original size:20 final size:20
Alignment explanation
Indices: 9091--9165 Score: 87
Period size: 22 Copynumber: 3.5 Consensus size: 20
9081 CTCTCTATGT
9091 AATTTTGATAACTTCTCCATGA
1 AATTTTGATAAC--CTCCATGA
*
9113 AATTTTCATAACCTCCCTATGA
1 AATTTTGATAACCT-CC-ATGA
* *
9135 AATTTTGTTAACCTCCAGGA
1 AATTTTGATAACCTCCATGA
9155 AATTTTGATAA
1 AATTTTGATAA
9166 GCACGAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
20 15 0.33
21 4 0.09
22 27 0.59
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
AATTTTGATAACCTCCATGA
Found at i:9529 original size:22 final size:22
Alignment explanation
Indices: 9501--9552 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
9491 TTTTTTTATT
9501 AAATTTTGATAACTATAC-TATG
1 AAATTTTGATAAC-ATACATATG
* *
9523 AAATTTTGATAACCTCCATATG
1 AAATTTTGATAACATACATATG
9545 AAATTTTG
1 AAATTTTG
9553 GGAACCACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACATACATATG
Done.