Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007144.1 Corchorus capsularis cultivar CVL-1 contig07165, 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: 6331
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:728 original size:33 final size:32
Alignment explanation
Indices: 691--754 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
681 GATTTTCACA
*
691 ATTTTCTTTT-CTTTTATTTTTTGTGATTTTTTG
1 ATTTT-TTTTACTTTTACTTTTTGT-ATTTTTTG
*
724 ATTTTTTTTATTTTTACTTTTTGTATTTTTT
1 ATTTTTTTTACTTTTACTTTTTGTATTTTTT
755 TGCAAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.11, C:0.05, G:0.06, T:0.78
Consensus pattern (32 bp):
ATTTTTTTTACTTTTACTTTTTGTATTTTTTG
Found at i:1353 original size:8 final size:8
Alignment explanation
Indices: 1340--1402 Score: 65
Period size: 8 Copynumber: 7.9 Consensus size: 8
1330 GGTACTAAAG
1340 AATTGAAT
1 AATTGAAT
*
1348 AATTGAAG
1 AATTGAAT
*
1356 CATTGAAT
1 AATTGAAT
**
1364 AATTGAGG
1 AATTGAAT
1372 AATTGAA-
1 AATTGAAT
*
1379 ACATGGAAT
1 A-ATTGAAT
1388 AATTGAAT
1 AATTGAAT
1396 AATTGAA
1 AATTGAA
1403 GAAAGACCAC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
7 1 0.02
8 42 0.95
9 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.30
Consensus pattern (8 bp):
AATTGAAT
Found at i:1360 original size:16 final size:16
Alignment explanation
Indices: 1337--1405 Score: 86
Period size: 16 Copynumber: 4.3 Consensus size: 16
1327 TGAGGTACTA
1337 AAGAATTGAATAATTG
1 AAGAATTGAATAATTG
*
1353 AAGCATTGAATAATTG
1 AAGAATTGAATAATTG
* *
1369 AGGAATTGAA-ACATGG
1 AAGAATTGAATA-ATTG
*
1385 AATAATTGAATAATTG
1 AAGAATTGAATAATTG
1401 AAGAA
1 AAGAA
1406 AGACCACCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
15 1 0.02
16 41 0.95
17 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.28
Consensus pattern (16 bp):
AAGAATTGAATAATTG
Found at i:1367 original size:24 final size:24
Alignment explanation
Indices: 1340--1403 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
1330 GGTACTAAAG
*
1340 AATTGAATAATTGAAGCATTGAAT
1 AATTGAATAATTGAAGCATGGAAT
** *
1364 AATTGAGGAATTGAAACATGGAAT
1 AATTGAATAATTGAAGCATGGAAT
1388 AATTGAATAATTGAAG
1 AATTGAATAATTGAAG
1404 AAAGACCACC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (24 bp):
AATTGAATAATTGAAGCATGGAAT
Found at i:1509 original size:58 final size:56
Alignment explanation
Indices: 1384--1517 Score: 171
Period size: 58 Copynumber: 2.3 Consensus size: 56
1374 TTGAAACATG
* *
1384 GAATAATTGAATAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTAAAGCTTT
1 GAATAATTG-A-AATTGAAGAAAGACCACCCTGGATCAGTGAAGTAAATTAAAGATTT
* * *
1442 GAATGATTGAAGATTTGAAGAAAGACCATCCTGGATCAGTGAAGTAAATTGAAGAATTT
1 GAATAATTGAA-A-TTGAAGAAAGACCACCCTGGATCAGTGAAGTAAATTAAAG-ATTT
1501 -AATAATTGAAATTGAAG
1 GAATAATTGAAATTGAAG
1518 CATTGACATA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
56 7 0.10
57 3 0.04
58 54 0.81
59 3 0.04
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (56 bp):
GAATAATTGAAATTGAAGAAAGACCACCCTGGATCAGTGAAGTAAATTAAAGATTT
Found at i:1515 original size:22 final size:22
Alignment explanation
Indices: 1487--1793 Score: 148
Period size: 22 Copynumber: 14.0 Consensus size: 22
1477 TCAGTGAAGT
* *
1487 AAATTGAAGAATTTAATAATTG
1 AAATTGAAGAATTGAAGAATTG
* *
1509 AAATTGAAGCATTGACA-TATTG
1 AAATTGAAGAATTGA-AGAATTG
1531 AAATTGAA-ACATTGAAGAATTG
1 AAATTGAAGA-ATTGAAGAATTG
*
1553 AAATTGAA-ACATTGAAGGATTG
1 AAATTGAAGA-ATTGAAGAATTG
* *
1575 AATTTGAAGAATAG-A-AATTG
1 AAATTGAAGAATTGAAGAATTG
* *
1595 AAGCACTGAAGGATTG-A-AATTG
1 AA--ATTGAAGAATTGAAGAATTG
*
1617 AAACATTGAATAATTG-A-AATTG
1 -AA-ATTGAAGAATTGAAGAATTG
* *
1639 AAACATTGAAGGATTG-A-ATTTG
1 -AA-ATTGAAGAATTGAAGAATTG
*
1661 AAGAATTG-A-AATTGAAGCATTG
1 -A-AATTGAAGAATTGAAGAATTG
*
1683 AAGGATTG-A-ATTTGAAGAATTG
1 AA--ATTGAAGAATTGAAGAATTG
*
1705 AAATTGAAGCATTGAAGGAA-TG
1 AAATTGAAGAATTGAA-GAATTG
**
1727 AAATTGAA-ACAGCGAATG-ATTG
1 AAATTGAAGA-ATTGAA-GAATTG
* *
1749 AATTTGAAGAATTGAAGATTTG
1 AAATTGAAGAATTGAAGAATTG
*
1771 AAATTG-AGACATTGAATAATTG
1 AAATTGAAGA-ATTGAAGAATTG
1793 A
1 A
1794 GTAATGGAAG
Statistics
Matches: 228, Mismatches: 37, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
20 15 0.07
21 11 0.05
22 193 0.85
23 9 0.04
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.29
Consensus pattern (22 bp):
AAATTGAAGAATTGAAGAATTG
Found at i:1546 original size:36 final size:36
Alignment explanation
Indices: 1541--1734 Score: 244
Period size: 36 Copynumber: 5.2 Consensus size: 36
1531 AAATTGAAAC
*
1541 ATTGAAGAATTGAAATTGAAACATTGAAGGATTGAA
1 ATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAA
* * *
1577 TTTGAAGAATAGAAATTGAAGCACTGAAGGATTGAA
1 ATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAA
*
1613 ATTGAAACATTGAATAATTGAAATTGAAACATTGAAGGATTGAA
1 ATTG--A-A--G---AATTGAAATTGAAGCATTGAAGGATTGAA
*
1657 TTTGAAGAATTGAAATTGAAGCATTGAAGGATTGAA
1 ATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAA
* *
1693 TTTGAAGAATTGAAATTGAAGCATTGAAGGAATGAA
1 ATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAA
1729 ATTGAA
1 ATTGAA
1735 ACAGCGAATG
Statistics
Matches: 138, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
36 103 0.75
38 1 0.01
39 2 0.01
41 2 0.01
42 1 0.01
44 29 0.21
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (36 bp):
ATTGAAGAATTGAAATTGAAGCATTGAAGGATTGAA
Found at i:1592 original size:80 final size:78
Alignment explanation
Indices: 1495--1734 Score: 314
Period size: 80 Copynumber: 3.1 Consensus size: 78
1485 GTAAATTGAA
*
1495 GAATTT-AATAATTGAAATTGAAGCATTGACATATTGAAATTGAAACATTGAAGAATTGAAATTG
1 GAATTTGAAGAATTGAAATTGAAGCATTGA-A-ATTGAAATTGAAACATTGAAGAATTGAAATTG
1559 AAACATTGAAGGATT
64 AAACATTGAAGGATT
* * *
1574 GAATTTGAAGAATAGAAATTGAAGCACTGAAGGATTGAAATTGAAACATTGAATAATTGAAATTG
1 GAATTTGAAGAATTGAAATTGAAGCATTGAA--ATTGAAATTGAAACATTGAAGAATTGAAATTG
1639 AAACATTGAAGGATT
64 AAACATTGAAGGATT
* *
1654 GAATTTGAAGAATTGAAATTGAAGCATTG-AA--G-GATTG-AA-TTTGAAGAATTGAAATTGAA
1 GAATTTGAAGAATTGAAATTGAAGCATTGAAATTGAAATTGAAACATTGAAGAATTGAAATTGAA
* *
1713 GCATTGAAGGAAT
66 ACATTGAAGGATT
*
1726 GAAATTGAA
1 GAATTTGAA
1735 ACAGCGAATG
Statistics
Matches: 146, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
72 37 0.25
73 2 0.01
74 4 0.03
75 1 0.01
77 1 0.01
79 8 0.05
80 93 0.64
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.29
Consensus pattern (78 bp):
GAATTTGAAGAATTGAAATTGAAGCATTGAAATTGAAATTGAAACATTGAAGAATTGAAATTGAA
ACATTGAAGGATT
Found at i:1748 original size:58 final size:58
Alignment explanation
Indices: 1527--1764 Score: 304
Period size: 58 Copynumber: 4.1 Consensus size: 58
1517 GCATTGACAT
*
1527 ATTGAAATTGAAACATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTTGAAGA
1 ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTTGAAGA
* * * ** *
1585 ATAGAAATTGAAGCACTGAAGGATTGAAATTGAAACATTGAATAATTGAAATTGAA-A
1 ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTTGAAGA
* *
1642 CATTGAAGGATTGAA--TTTGAAGAATTGAAATTGAAGCATTGAAGGATTGAATTTGAAGA
1 -ATTGAA--ATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTTGAAGA
** *
1701 ATTGAAATTGAAGCATTGAAGGAA-TGAAATTGAAACAGCGAATGATTGAATTTGAAGA
1 ATTGAAATTGAAGCATTGAA-GAATTGAAATTGAAACATTGAAGGATTGAATTTGAAGA
1759 ATTGAA
1 ATTGAA
1765 GATTTGAAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
56 6 0.04
57 1 0.01
58 136 0.89
59 4 0.03
60 6 0.04
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.28
Consensus pattern (58 bp):
ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTTGAAGA
Found at i:1843 original size:8 final size:8
Alignment explanation
Indices: 1830--1939 Score: 63
Period size: 8 Copynumber: 14.1 Consensus size: 8
1820 CATCGAAGTA
1830 AATTGAAG
1 AATTGAAG
1838 AATTGAAG
1 AATTGAAG
*
1846 CATTG-AG
1 AATTGAAG
*
1853 TAAGTGAAG
1 -AATTGAAG
1862 AATTGAAG
1 AATTGAAG
1870 CAA-T-AAG
1 -AATTGAAG
1877 TAATCT-AAG
1 -AAT-TGAAG
*
1886 AATTGAGG
1 AATTGAAG
*
1894 AAAT--A-
1 AATTGAAG
1899 AATTGAAG
1 AATTGAAG
*
1907 TATTGAAG
1 AATTGAAG
*
1915 AATTGTAG
1 AATTGAAG
*
1923 AATTGAAT
1 AATTGAAG
*
1931 AATTAAAG
1 AATTGAAG
1939 A
1 A
1940 GCCGAAGAGA
Statistics
Matches: 77, Mismatches: 16, Indels: 18
0.69 0.14 0.16
Matches are distributed among these distances:
5 3 0.04
7 9 0.12
8 57 0.74
9 8 0.10
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.27
Consensus pattern (8 bp):
AATTGAAG
Found at i:1891 original size:24 final size:24
Alignment explanation
Indices: 1833--1879 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1823 CGAAGTAAAT
* *
1833 TGAAGAATTGAAGCATTGAGTAAG
1 TGAAGAATTGAAGCAATAAGTAAG
1857 TGAAGAATTGAAGCAATAAGTAA
1 TGAAGAATTGAAGCAATAAGTAA
1880 TCTAAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.26, T:0.23
Consensus pattern (24 bp):
TGAAGAATTGAAGCAATAAGTAAG
Found at i:1971 original size:16 final size:16
Alignment explanation
Indices: 1952--1984 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1942 CGAAGAGATA
1952 AATTGAA-ATATTGAAT
1 AATTGAAGA-ATTGAAT
1968 AATTGAAGAATTGAAT
1 AATTGAAGAATTGAAT
1984 A
1 A
1985 GTTAAAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (16 bp):
AATTGAAGAATTGAAT
Found at i:2020 original size:53 final size:53
Alignment explanation
Indices: 1896--2023 Score: 195
Period size: 53 Copynumber: 2.4 Consensus size: 53
1886 AATTGAGGAA
* * *
1896 ATAAATTGAAGTATTGAAGAATTGTAGAATTGAATAATTAAAGAGCCGAAGAG
1 ATAAATTGAAGAATTGAATAATTGAAGAATTGAATAATTAAAGAGCCGAAGAG
* *
1949 ATAAATTGAA-ATATTGAATAATTGAAGAATTGAATAGTTAAAGAGTCGAAGAG
1 ATAAATTGAAGA-ATTGAATAATTGAAGAATTGAATAATTAAAGAGCCGAAGAG
2002 ATAAATTGAAGAATTGAATAAT
1 ATAAATTGAAGAATTGAATAAT
2024 GGAGAGTTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
53 67 0.99
54 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.28
Consensus pattern (53 bp):
ATAAATTGAAGAATTGAATAATTGAAGAATTGAATAATTAAAGAGCCGAAGAG
Found at i:3845 original size:15 final size:15
Alignment explanation
Indices: 3799--3850 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 15
3789 CATGACTCTC
*
3799 TTTTGAAAAACAT-T
1 TTTTGAAAAAAATAT
* *
3813 TTTTGAAGAAAACA-
1 TTTTGAAAAAAATAT
3827 TTTTGAAAAAAATAT
1 TTTTGAAAAAAATAT
3842 TTTTGAAAA
1 TTTTGAAAA
3851 CCATGACTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 22 0.71
15 9 0.29
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (15 bp):
TTTTGAAAAAAATAT
Found at i:3877 original size:33 final size:33
Alignment explanation
Indices: 3778--3893 Score: 125
Period size: 33 Copynumber: 3.6 Consensus size: 33
3768 AAACATTTTT
*
3778 TTTTTGAAAACCATGACTCTCTTTTGAAAAACA
1 TTTTTGAAAACCATGACTCTTTTTTGAAAAACA
* *** *
3811 TTTTTTGAAGAA--A--AC-ATTTTGAAAAAAATA
1 -TTTTTGAA-AACCATGACTCTTTTTTGAAAAACA
3841 TTTTTGAAAACCATGACTCTTTTTTGAAAAACA
1 TTTTTGAAAACCATGACTCTTTTTTGAAAAACA
3874 TTTTTGAAAACCATGACTCT
1 TTTTTGAAAACCATGACTCT
3894 CTAATATTCC
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.03
29 8 0.12
30 10 0.15
31 2 0.03
32 2 0.03
33 31 0.48
34 8 0.12
35 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (33 bp):
TTTTTGAAAACCATGACTCTTTTTTGAAAAACA
Found at i:3941 original size:14 final size:13
Alignment explanation
Indices: 3922--3951 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3912 TCATTCATTC
3922 TTTTATTATTTCTT
1 TTTTATTATTT-TT
3936 TTTTATTATTTTT
1 TTTTATTATTTTT
3949 TTT
1 TTT
3952 AGAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTATTTTT
Done.