Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014874.1 Corchorus capsularis cultivar CVL-1 contig14895, 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: 25169
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:325 original size:2 final size:2
Alignment explanation
Indices: 318--342 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
308 TATACTATCA
318 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
343 GATTAGGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2033 original size:12 final size:10
Alignment explanation
Indices: 2008--2042 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
1998 CAAAAAGTAT
2008 TTTTTTTTTG
1 TTTTTTTTTG
2018 TTTTTTTTTG
1 TTTTTTTTTG
2028 AATTTTTTTTTG
1 --TTTTTTTTTG
2040 TTT
1 TTT
2043 GCTGCATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3149 original size:2 final size:2
Alignment explanation
Indices: 3144--3182 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
3134 AAGATTGGAT
* *
3144 TA TA TA GTA TC TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3183 AGGATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:6329 original size:22 final size:21
Alignment explanation
Indices: 6296--6341 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
6286 CGAAATCTTT
*
6296 TTATAAATTTTTTTTAACCTTC
1 TTATAAATTTTTGTTAACC-TC
6318 TTATGAAA-TTTTGTTAACCTC
1 TTAT-AAATTTTTGTTAACCTC
6339 TTA
1 TTA
6342 AAGGAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 14 0.64
23 3 0.14
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (21 bp):
TTATAAATTTTTGTTAACCTC
Found at i:6531 original size:22 final size:22
Alignment explanation
Indices: 6473--6533 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
6463 AAAACCTCCA
*
6473 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* * *
6495 TCGTAAAATTTTGATAATCACAC
1 T-ATGAAATTGTGATAATCACAC
6518 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
6534 CCTCGCTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 13 0.43
23 11 0.37
24 6 0.20
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:6572 original size:23 final size:23
Alignment explanation
Indices: 6544--6623 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
6534 CCTCGCTTTG
6544 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
6567 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
6590 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
6612 AAATCTTGATAA
1 AAATTTTGATAA
6624 CTACAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:6622 original size:45 final size:45
Alignment explanation
Indices: 6498--6623 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 45
6488 ATCACACTCG
* * *
6498 TAAAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTT
1 TAAAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTA
* *
6542 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTA
1 TAAAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTA
* *
6588 TAAAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 TAAAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
6624 CTACAAATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
44 12 0.18
45 31 0.46
46 25 0.37
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (45 bp):
TAAAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTA
Found at i:6657 original size:22 final size:22
Alignment explanation
Indices: 6500--6863 Score: 182
Period size: 22 Copynumber: 16.8 Consensus size: 22
6490 CACACTCGTA
* * *
6500 AAATTTTGATAATCACACTATG
1 AAATTTTGATAAACTCCCTATG
* * * *
6522 AAATTGTGATAACCTCGCTTTG
1 AAATTTTGATAAACTCCCTATG
* *
6544 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAA-CTCCCTATG
*
6567 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAA-CTCCCTATG
* *
6590 AAATTTTGAT-AACTTTCTTATG
1 AAATTTTGATAAAC-TCCCTATG
* *
6612 AAATCTTGAT-AA----CTA-C
1 AAATTTTGATAAACTCCCTATG
6628 AAATTTTGATAAACTCCCTATG
1 AAATTTTGATAAACTCCCTATG
** * **
6650 ATTTTTTGATAACCTCAATATG
1 AAATTTTGATAAACTCCCTATG
* *
6672 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAAACTCCCTATG
** *
6694 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGATAAAC-TCCCTATG
*
6716 AAATTTTGAT-GAC-CCTCTTATG
1 AAATTTTGATAAACTCC-C-TATG
**
6738 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAAACT-CCCTATG
* * * *
6760 AAATTTTAATAACCTTCATATG
1 AAATTTTGATAAACTCCCTATG
**
6782 AAATTTTGATATCCTCCC--TG
1 AAATTTTGATAAACTCCCTATG
* * *
6802 AAATTTTGAT-TACTCCATAATA
1 AAATTTTGATAAACTCCCT-ATG
* * *
6824 AAAGTTT-ATATACCTTCCTATG
1 AAATTTTGATA-AACTCCCTATG
*
6846 AAATTTTGATAACCTCCC
1 AAATTTTGATAAACTCCC
6864 CAGAACTACC
Statistics
Matches: 258, Mismatches: 62, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.03
17 4 0.02
19 5 0.02
20 12 0.05
21 9 0.03
22 170 0.66
23 49 0.19
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAAACTCCCTATG
Found at i:6989 original size:22 final size:22
Alignment explanation
Indices: 6876--7112 Score: 121
Period size: 22 Copynumber: 10.7 Consensus size: 22
6866 GAACTACCAC
6876 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAATCACAT
* * * * * *
6898 TTTGAAAATGTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* * *
6920 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
** * * *
6942 TACAAAATTTTGTTGA-CCCAT
1 TATGAAATTTTGATAATCACAT
6963 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* * * *
6986 TATGTAATTTTGATAACCTCGT
1 TATGAAATTTTGATAATCACAT
*
7008 TTTGAAATTTTGATAA-CA-AT
1 TATGAAATTTTGATAATCACAT
*
7028 ACTATGAAATTTTGATAATCTTCA-
1 --TATGAAATTTTGATAATC-ACAT
*
7052 TAT-AAATTTTGATAATCTGATCTT
1 TATGAAATTTTGATAATC--A-CAT
* *
7076 TATGAAATTTCGATATTCAC-T
1 TATGAAATTTTGATAATCACAT
*
7097 CTATGAGA-TTTGATAA
1 -TATGAAATTTTGATAA
7113 CCTTCTATCA
Statistics
Matches: 164, Mismatches: 38, Indels: 27
0.72 0.17 0.12
Matches are distributed among these distances:
20 1 0.01
21 28 0.17
22 112 0.68
23 7 0.04
24 3 0.02
25 13 0.08
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:6989 original size:66 final size:67
Alignment explanation
Indices: 6919--7066 Score: 180
Period size: 66 Copynumber: 2.3 Consensus size: 67
6909 GATAACCTCT
* * *
6919 TTATGAAATTTTGATAACCTC-TTTACAAAATTTTGTTGACCCAT-CTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTCGTTT-CAAAATTTTGAT-AACAATACTATGAAATTTTGATAATC
6982 -ACA
64 TACA
* ** *
6985 TTATGTAATTTTGATAACCTCGTTTTGAAATTTTGATAACAATACTATGAAATTTTGATAATCTT
1 TTATGAAATTTTGATAACCTCGTTTCAAAATTTTGATAACAATACTATGAAATTTTGATAATCTA
7050 CA
66 CA
7052 -TAT-AAATTTTGATAA
1 TTATGAAATTTTGATAA
7067 TCTGATCTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
65 15 0.21
66 51 0.72
67 5 0.07
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (67 bp):
TTATGAAATTTTGATAACCTCGTTTCAAAATTTTGATAACAATACTATGAAATTTTGATAATCTA
CA
Found at i:7181 original size:22 final size:22
Alignment explanation
Indices: 6964--7181 Score: 96
Period size: 22 Copynumber: 9.7 Consensus size: 22
6954 TTGACCCATC
*
6964 TATGAAATTTTGATAATC-ACA
1 TATGAAATTTTGATAATCTTCA
* * *
6985 TTATGTAATTTTGATAA-CCTCGT
1 -TATGAAATTTTGATAATCTTC-A
* *
7008 TTTGAAATTTTGATAA-CAAT-A
1 TATGAAATTTTGATAATC-TTCA
7029 CTATGAAATTTTGATAATCTTCA
1 -TATGAAATTTTGATAATCTTCA
*
7052 TAT-AAATTTTGATAATCTGATCTT
1 TATGAAATTTTGATAATCT--TC-A
* * *
7076 TATGAAATTTCGATATTCACTC-
1 TATGAAATTTTGATAATC-TTCA
* *
7098 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAATCTTCA
* * *
7118 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATAAT-CTTCA
*
7140 TGAAATTGAGACTTTT-ATAATCTTCA
1 T---A-TGA-AATTTTGATAATCTTCA
7166 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
7182 CCACACTATA
Statistics
Matches: 147, Mismatches: 28, Indels: 42
0.68 0.13 0.19
Matches are distributed among these distances:
20 7 0.05
21 34 0.23
22 67 0.46
23 6 0.04
24 5 0.03
25 16 0.11
26 7 0.05
27 5 0.03
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCA
Found at i:7195 original size:22 final size:21
Alignment explanation
Indices: 7170--7271 Score: 62
Period size: 22 Copynumber: 4.6 Consensus size: 21
7160 TCTTCATATG
7170 AAATTTTGATAACCACACTATA
1 AAATTTT-ATAACCACACTATA
* * * *
7192 AAATTTTAATAACCTCCCCATG
1 AAATTTT-ATAACCACACTATA
* * *
7214 AAATATTAGTAACCTCA-TAATG
1 AAATTTTA-TAACCACACT-ATA
* *
7236 AAATTTTGTTAACCATACTATA
1 AAATTTT-ATAACCACACTATA
7258 AAATTCTTATAACC
1 AAATT-TTATAACC
7272 TCGCTACGAC
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
21 1 0.02
22 57 0.93
23 3 0.05
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATTTTATAACCACACTATA
Found at i:7434 original size:22 final size:21
Alignment explanation
Indices: 7334--7464 Score: 91
Period size: 22 Copynumber: 5.9 Consensus size: 21
7324 AATTAACCAC
** *
7334 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTGATAACC-T
* *
7356 CCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGATAACC---T
* * *
7380 CCAATGAAATTTTGGTAACCA
1 CCTATGAAATTTTGATAACCT
*
7401 CACTATGGAATTTTGATAACCT
1 C-CTATGAAATTTTGATAACCT
* *
7423 CCTCATGAAATTATAATAACCTT
1 CCT-ATGAAATTTTGATAACC-T
*
7446 CTTATGAAATTTTGATAAC
1 CCTATGAAATTTTGATAAC
7465 TATATAGAGA
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.03
22 63 0.73
23 3 0.03
24 17 0.20
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACCT
Found at i:7773 original size:26 final size:25
Alignment explanation
Indices: 7741--7800 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
7731 CGGTTTAAAT
* *
7741 TGAAAATTTTAATTAATTTTTGAATAA
1 TGAAAATTTT-ACTAAATTTT-AATAA
*
7768 T-AAAATTATACTAAATTTTAATAA
1 TGAAAATTTTACTAAATTTTAATAA
7792 TGAAAATTT
1 TGAAAATTT
7801 AGAAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 6 0.21
25 14 0.50
26 7 0.25
27 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (25 bp):
TGAAAATTTTACTAAATTTTAATAA
Found at i:9760 original size:11 final size:11
Alignment explanation
Indices: 9736--9770 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
9726 TTGACAGCGC
9736 AACAAAAACAA
1 AACAAAAACAA
* *
9747 AACGAAAACGA
1 AACAAAAACAA
9758 AACAAAAACAA
1 AACAAAAACAA
9769 AA
1 AA
9771 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:9907 original size:2 final size:2
Alignment explanation
Indices: 9900--9937 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
9890 TTCGTACTTT
*
9900 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9938 TAATTGAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11209 original size:17 final size:17
Alignment explanation
Indices: 11187--11221 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11177 ATCAGCAGCC
11187 TAGGATATTTTCAATAT
1 TAGGATATTTTCAATAT
11204 TAGGATATTTTCAATAT
1 TAGGATATTTTCAATAT
11221 T
1 T
11222 TAAATGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (17 bp):
TAGGATATTTTCAATAT
Found at i:24374 original size:15 final size:15
Alignment explanation
Indices: 24354--24403 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
24344 TTTCTTCAAG
24354 AATTAAAATAATATT
1 AATTAAAATAATATT
*
24369 AATT---A-AATATC
1 AATTAAAATAATATT
*
24380 AATAAAAATAATATT
1 AATTAAAATAATATT
24395 AATTAAAAT
1 AATTAAAAT
24404 CCTCAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
11 8 0.30
12 1 0.04
14 1 0.04
15 17 0.63
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTAAAATAATATT
Found at i:24439 original size:12 final size:12
Alignment explanation
Indices: 24408--24432 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24398 TAAAATCCTC
24408 AAATTATTAATT
1 AAATTATTAATT
24420 AAATTATTAATT
1 AAATTATTAATT
24432 A
1 A
24433 GTTTATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTATTAATT
Found at i:24966 original size:2 final size:2
Alignment explanation
Indices: 24961--24991 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24951 ATATAGTTAT
24961 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24992 ATTTATGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.