Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007517.1 Corchorus capsularis cultivar CVL-1 contig07538, 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: 16249
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:925 original size:55 final size:55
Alignment explanation
Indices: 864--1054 Score: 286
Period size: 55 Copynumber: 3.6 Consensus size: 55
854 AAAAAGGGTC
* *
864 AATCAGTAATTAAGTAAAAAGGGATTAATCAGAGTCAAGGTAATAGTAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
919 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA-G-----GTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
968 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * * *
1023 AATCAGTAATCAGGTAAAAAGATAATAATCAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAG
1055 TAAACTGATA
Statistics
Matches: 124, Mismatches: 6, Indels: 12
0.87 0.04 0.08
Matches are distributed among these distances:
49 47 0.38
50 1 0.01
54 1 0.01
55 75 0.60
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.25
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:962 original size:49 final size:49
Alignment explanation
Indices: 864--1023 Score: 234
Period size: 49 Copynumber: 3.2 Consensus size: 49
854 AAAAAGGGTC
* *
864 AATCAGTAATTAAGTAAAAAGGGATTAATCAGAGTCAAGGTAATAGTAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA-G-----GTAATCAGTA
919 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATCAGTA
968 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT-AGT-
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATCAGTA
1015 AATCAGTAA
1 AATCAGTAA
1024 ATCAGTAATC
Statistics
Matches: 103, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
47 9 0.09
48 3 0.03
49 53 0.51
54 1 0.01
55 37 0.36
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (49 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATCAGTA
Found at i:1044 original size:104 final size:104
Alignment explanation
Indices: 864--1054 Score: 328
Period size: 104 Copynumber: 1.8 Consensus size: 104
854 AAAAAGGGTC
*
864 AATCAGTAATTAAGTAAAAAGGGATTAATCAGAGTCAAGGTAATAGTAATCAATAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAATAAATCAGTAAT
* *
929 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATCAGTA
66 CAAGTAAAAAGAGAATAATCAGAGTCAAGGTAATCAGTA
*
968 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAATAAATCAGTAAT
* *
1033 CAGGTAAAAAGATAATAATCAG
66 CAAGTAAAAAGAGAATAATCAG
1055 TAAACTGATA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 81 1.00
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.25
Consensus pattern (104 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAATAAATCAGTAAT
CAAGTAAAAAGAGAATAATCAGAGTCAAGGTAATCAGTA
Found at i:1083 original size:71 final size:71
Alignment explanation
Indices: 998--1144 Score: 222
Period size: 71 Copynumber: 2.1 Consensus size: 71
988 GAGATTAATC
* *
998 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAATAATCAGTAAACTGA
1 AGAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAACTGA
*
1063 TAATTA
66 TAATAA
* * * * *
1069 AGAGTCCAGATAATAGTAATCAGTAAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGA
1 AGAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAACTGA
1134 TAATAA
66 TAATAA
1140 AGAGT
1 AGAGT
1145 TAGAGTGATC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (71 bp):
AGAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAACTGA
TAATAA
Found at i:1131 original size:34 final size:34
Alignment explanation
Indices: 1010--1131 Score: 122
Period size: 34 Copynumber: 3.5 Consensus size: 34
1000 AGTCAAGGTA
* * *
1010 ATAGTAATCAGTAAATCAGTAATCAGGTAAAAAG
1 ATAGTAATCAGTAAATTAGTAATTAAGTAAAAAG
* * * *
1044 ATAATAATCAGTAAACT-GATAATTAAGAGTCCAGATA-
1 ATAGTAATCAGTAAATTAG-TAATT-A-AGT--AAAAAG
1081 ATAGTAATCAGTAAATTAGTAATTAAGTAAAAAG
1 ATAGTAATCAGTAAATTAGTAATTAAGTAAAAAG
1115 ATAGTAATCAGTAAATT
1 ATAGTAATCAGTAAATT
1132 GATAATAAAG
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
33 4 0.06
34 35 0.50
35 4 0.06
36 3 0.04
37 20 0.29
38 4 0.06
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (34 bp):
ATAGTAATCAGTAAATTAGTAATTAAGTAAAAAG
Found at i:1481 original size:17 final size:17
Alignment explanation
Indices: 1459--1491 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1449 AGGTAAAAAA
1459 TAGTAA-AAGAGAGTAAT
1 TAGTAATAA-AGAGTAAT
1476 TAGTAATAAAGAGTAA
1 TAGTAATAAAGAGTAA
1492 GAAATGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (17 bp):
TAGTAATAAAGAGTAAT
Found at i:1585 original size:30 final size:31
Alignment explanation
Indices: 1551--1613 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
1541 GATAAAAATG
1551 GTAAAAAAAAAAGAGT-AAAAATGGTATTAA
1 GTAAAAAAAAAAGAGTAAAAAATGGTATTAA
*** *
1581 GT-AAAAAGGGAGAGTAAAAAATGGTATTCA
1 GTAAAAAAAAAAGAGTAAAAAATGGTATTAA
1611 GTA
1 GTA
1614 GAAGCAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.21
Consensus pattern (31 bp):
GTAAAAAAAAAAGAGTAAAAAATGGTATTAA
Found at i:1662 original size:26 final size:26
Alignment explanation
Indices: 1451--1694 Score: 155
Period size: 27 Copynumber: 9.2 Consensus size: 26
1441 GGCAAGTAAG
* *
1451 GTAAAAAATAGTAAAAGA-GAGTAATTA
1 GTAAAAAAGAGTAAAA-ATG-GTAATCA
* *
1478 GTAATAAAGAGTAAGAAATGGTGATCA
1 GTAAAAAAGAGTAA-AAATGGTAATCA
*
1505 GTAAAAAAGAGTAAAAAGTGGTATTCA
1 GTAAAAAAGAGTAAAAA-TGGTAATCA
*
1532 G-AAAAAAGGGATAAAAATGGTAA--A
1 GTAAAAAAGAG-TAAAAATGGTAATCA
* * *
1556 -AAAAAAAGAGTAAAAATGGTATTAA
1 GTAAAAAAGAGTAAAAATGGTAATCA
*
1581 GTAAAAAGGGAGAGTAAAAAATGGTATTCA
1 GTAAAAA---AGAGT-AAAAATGGTAATCA
* *
1611 GTAGAAGCAGAA-AGGAAAGA-GGTAATCA
1 GTA-AA--A-AAGAGTAAAAATGGTAATCA
1639 GTAAAAAAG-GTAAAACATGGTAATCA
1 GTAAAAAAGAGTAAAA-ATGGTAATCA
* * *
1665 GTACAAAA-AGTAAAAAATGATAATTA
1 GTAAAAAAGAGT-AAAAATGGTAATCA
1691 GTAA
1 GTAA
1695 TCAAGAAATA
Statistics
Matches: 174, Mismatches: 22, Indels: 43
0.73 0.09 0.18
Matches are distributed among these distances:
23 11 0.06
24 15 0.09
25 3 0.02
26 49 0.28
27 51 0.29
28 13 0.07
29 9 0.05
30 18 0.10
31 3 0.02
33 1 0.01
34 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.19
Consensus pattern (26 bp):
GTAAAAAAGAGTAAAAATGGTAATCA
Found at i:5176 original size:19 final size:18
Alignment explanation
Indices: 5152--5188 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5142 TTGAAGATTT
5152 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
5171 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
5189 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:14978 original size:22 final size:23
Alignment explanation
Indices: 14953--15017 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
14943 TTTTTAATTA
14953 ATTGTTTTCTTTAATTTT-CTTG
1 ATTGTTTTCTTTAATTTTGCTTG
*
14975 ATTGCTTTCTTAGTTAATTTTGCTTG
1 ATTGTTTTC-T--TTAATTTTGCTTG
* **
15001 TTTGTTTGATTTAATTT
1 ATTGTTTTCTTTAATTT
15018 AACTCTACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 8 0.24
23 8 0.24
25 9 0.26
26 9 0.26
ACGTcount: A:0.15, C:0.08, G:0.12, T:0.65
Consensus pattern (23 bp):
ATTGTTTTCTTTAATTTTGCTTG
Done.