Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017583.1 Corchorus olitorius cultivar O-4 contig17616, 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: 46069
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:414 original size:156 final size:155
Alignment explanation
Indices: 82--384 Score: 457
Period size: 156 Copynumber: 1.9 Consensus size: 155
72 TTTTGGCCAC
82 AATACTCATAAAAAATATATAATTCAACACAACAAACATTGAAGGGCTTTTCACGCTTCGAATAT
1 AATACTCATAAAAAATATATAATTCAACACAACAAACATTGAAGGGCTTTTCACGCTTCGAATAT
* * * * *
147 CGTTTTTCATGTTTTTTTCCAAATTAATTTTTATTAAATCGAAACAAGATTCAGATGCTCGTAAA
66 CGTTTTTCA-CTATTTTTCCAAATAAATTTTGATTAAATCGAAACAAGATTCAGATGCTAGTAAA
212 AACAAATCCTTAAATCCAATGCGGCT
130 AACAAATCCTTAAATCCAATGCGGCT
* *
238 AATACTCATAAAAAATATATAATTCAACTCCAA-AAACATTGAAGGGCTTTTCACGCTTCTAATA
1 AATACTCATAAAAAATATATAATTCAAC-ACAACAAACATTGAAGGGCTTTTCACGCTTCGAATA
** **
302 TCGTTTTTC-CTATTTTTCCAAACTAAATTTTGATTAAATCGAAACTGGATTTGGATGCTAGTAA
65 TCGTTTTTCACTATTTTTCCAAA-TAAATTTTGATTAAATCGAAACAAGATTCAGATGCTAGTAA
*
366 AAACATATCCTTAAATCCA
129 AAACAAATCCTTAAATCCA
385 GTGTGGCTGA
Statistics
Matches: 133, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
154 11 0.08
155 52 0.39
156 67 0.50
157 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (155 bp):
AATACTCATAAAAAATATATAATTCAACACAACAAACATTGAAGGGCTTTTCACGCTTCGAATAT
CGTTTTTCACTATTTTTCCAAATAAATTTTGATTAAATCGAAACAAGATTCAGATGCTAGTAAAA
ACAAATCCTTAAATCCAATGCGGCT
Found at i:1378 original size:20 final size:20
Alignment explanation
Indices: 1349--1386 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1339 ATATCGTTTT
1349 TCCCCAACTGAATATGCATG
1 TCCCCAACTGAATATGCATG
*
1369 TCCCCTACTGAATATGCA
1 TCCCCAACTGAATATGCA
1387 ACTACATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (20 bp):
TCCCCAACTGAATATGCATG
Found at i:1400 original size:25 final size:25
Alignment explanation
Indices: 1371--1486 Score: 131
Period size: 25 Copynumber: 5.0 Consensus size: 25
1361 TATGCATGTC
*
1371 CCCTACTGAATATGCAACTACATGA
1 CCCTACTAAATATGCAACTACATGA
* *
1396 CCCTACTGAATATGCAACGACATGA
1 CCCTACTAAATATGCAACTACATGA
1421 CCCTACTAAATATGCAACTACATG-
1 CCCTACTAAATATGCAACTACATGA
* *
1445 TCC--C-----ATGCAACTACAAGA
1 CCCTACTAAATATGCAACTACATGA
1463 CCCTACTAAATATGCAACTACATG
1 CCCTACTAAATATGCAACTACATG
1487 TCCCATGCAA
Statistics
Matches: 76, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
17 12 0.16
18 2 0.03
20 1 0.01
22 1 0.01
24 2 0.03
25 58 0.76
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.22
Consensus pattern (25 bp):
CCCTACTAAATATGCAACTACATGA
Found at i:1466 original size:42 final size:42
Alignment explanation
Indices: 1407--1621 Score: 211
Period size: 42 Copynumber: 5.0 Consensus size: 42
1397 CCTACTGAAT
*
1407 ATGCAACGACATGACCCTACTAAATATGCAACTACATGTCCC
1 ATGCAACTACATGACCCTACTAAATATGCAACTACATGTCCC
*
1449 ATGCAACTACAAGACCCTACTAAATATGCAACTACATGTCCC
1 ATGCAACTACATGACCCTACTAAATATGCAACTACATGTCCC
* * * ** ***
1491 ATGCAACTACAAGACCCTACTACATGT-CCCCTAC-TG-AAT
1 ATGCAACTACATGACCCTACTAAATATGCAACTACATGTCCC
* *
1530 ATGCAACTACATGACCCTACTGAATATGCAACTACATGACCCTAC
1 ATGCAACTACATGACCCTACTAAATATGCAACTACATG-TCC--C
* *
1575 TGAATATGCAACTACATGTCCCTACTGAATATGCAACTACATGTCCC
1 -----ATGCAACTACATGACCCTACTAAATATGCAACTACATGTCCC
1622 CTACAGAATA
Statistics
Matches: 142, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
39 23 0.16
40 7 0.05
41 7 0.05
42 65 0.46
47 1 0.01
49 2 0.01
50 37 0.26
ACGTcount: A:0.35, C:0.31, G:0.11, T:0.23
Consensus pattern (42 bp):
ATGCAACTACATGACCCTACTAAATATGCAACTACATGTCCC
Found at i:1538 original size:26 final size:26
Alignment explanation
Indices: 1509--1985 Score: 765
Period size: 26 Copynumber: 18.7 Consensus size: 26
1499 ACAAGACCCT
1509 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
*
1535 ACTACATG-ACCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
*
1560 ACTACATG-ACCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1585 ACTACATGT-CCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
*
1610 ACTACATGTCCCCTACAGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
* * *
1636 ACAAAATGT-GCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
*
1661 ACTACATG-ACCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1686 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
*
1712 ACTACATGTCCCCTAATGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
* * *
1738 ACAAAATGT-GCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1763 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1789 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1815 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
* *
1841 ACTATATG-ACCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1866 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1892 ACTACATGT-CCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1917 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
1943 ACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCA
*
1969 ACTACATG-ACCCTACTG
1 ACTACATGTCCCCTACTG
1986 TATGAACTAC
Statistics
Matches: 421, Mismatches: 23, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
25 194 0.46
26 227 0.54
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (26 bp):
ACTACATGTCCCCTACTGAATATGCA
Found at i:1650 original size:51 final size:51
Alignment explanation
Indices: 1509--1985 Score: 780
Period size: 51 Copynumber: 9.4 Consensus size: 51
1499 ACAAGACCCT
*
1509 ACTACATGTCCCCTACTGAATATGCAACTACATGACCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
*
1560 ACTACATG-ACCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
* * * *
1610 ACTACATGTCCCCTACAGAATATGCAACAAAATGTGCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
*
1661 ACTACATG-ACCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGT-CCCTACTGAATATGCA
* * * *
1712 ACTACATGTCCCCTAATGAATATGCAACAAAATGTGCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
1763 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGT-CCCTACTGAATATGCA
* *
1815 ACTACATGTCCCCTACTGAATATGCAACTATATGACCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
1866 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
1917 ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCA
1 ACTACATGTCCCCTACTGAATATGCAACTACATGT-CCCTACTGAATATGCA
*
1969 ACTACATG-ACCCTACTG
1 ACTACATGTCCCCTACTG
1986 TATGAACTAC
Statistics
Matches: 395, Mismatches: 26, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
50 70 0.18
51 231 0.58
52 94 0.24
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (51 bp):
ACTACATGTCCCCTACTGAATATGCAACTACATGTCCCTACTGAATATGCA
Found at i:1777 original size:77 final size:77
Alignment explanation
Indices: 1509--1985 Score: 782
Period size: 77 Copynumber: 6.2 Consensus size: 77
1499 ACAAGACCCT
* *
1509 ACTACATGTCCCCTACTGAATATGCAACTACATG-ACCCTACTGAATATGCAACTACATG-ACCC
1 ACTACATGT-CCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCC
1572 TACTGAATATGCA
65 TACTGAATATGCA
* * * *
1585 ACTACATGTCCCTACTGAATATGCAACTACATGTCCCCTACAGAATATGCAACAAAATGT-GCCT
1 ACTACATGTCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
1649 ACTGAATATGCA
66 ACTGAATATGCA
*
1661 ACTACATGACCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
1 ACTACATGTCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
*
1726 AATGAATATGCA
66 ACTGAATATGCA
* * *
1738 ACAAAATGTGCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
1 ACTACATGTCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
1803 ACTGAATATGCA
66 ACTGAATATGCA
* *
1815 ACTACATGTCCCCTACTGAATATGCAACTATATG-ACCCTACTGAATATGCAACTACATGTCCCC
1 ACTACATGT-CCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCC
1879 TACTGAATATGCA
65 TACTGAATATGCA
1892 ACTACATGTCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
1 ACTACATGTCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
1957 ACTGAATATGCA
66 ACTGAATATGCA
*
1969 ACTACATGACCCTACTG
1 ACTACATGTCCCTACTG
1986 TATGAACTAC
Statistics
Matches: 372, Mismatches: 24, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
75 24 0.06
76 124 0.33
77 202 0.54
78 22 0.06
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (77 bp):
ACTACATGTCCCTACTGAATATGCAACTACATGTCCCCTACTGAATATGCAACTACATGTCCCCT
ACTGAATATGCA
Found at i:5637 original size:19 final size:19
Alignment explanation
Indices: 5613--5650 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5603 AAGTTGCTTT
5613 ATCGGCAATACAAGGCCAA
1 ATCGGCAATACAAGGCCAA
5632 ATCGGCAATACAAGGCCAA
1 ATCGGCAATACAAGGCCAA
5651 GCGCTACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGGCAATACAAGGCCAA
Found at i:6729 original size:19 final size:19
Alignment explanation
Indices: 6705--6743 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6695 TACTTTGGTT
6705 GCATTTTTTTTTTTGTGTG
1 GCATTTTTTTTTTTGTGTG
6724 GCATTTTTTTTTTTGTGTG
1 GCATTTTTTTTTTTGTGTG
6743 G
1 G
6744 GAATCTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.67
Consensus pattern (19 bp):
GCATTTTTTTTTTTGTGTG
Found at i:7003 original size:2 final size:2
Alignment explanation
Indices: 6996--7033 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6986 CTTGGTACCA
6996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7034 GCAATATGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14449 original size:31 final size:31
Alignment explanation
Indices: 14413--14494 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
14403 GGCCAAATAA
*
14413 GTTAGGCCCTTATTTGAGCATTTTGGCAAAC
1 GTTAGGCCCTTATTTGAGCATTTTGACAAAC
* *
14444 GTTAGGCCCCTATTTGAACATTTTGACAAAC
1 GTTAGGCCCTTATTTGAGCATTTTGACAAAC
*
14475 GTTAGGCCCTTATTTAAGCA
1 GTTAGGCCCTTATTTGAGCA
14495 ATTAGCCAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTAGGCCCTTATTTGAGCATTTTGACAAAC
Found at i:16465 original size:19 final size:19
Alignment explanation
Indices: 16412--16458 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
16402 GTTTGGTAAT
16412 TGTACAGATGAAATTACAC
1 TGTACAGATGAAATTACAC
16431 TGTACAGATGAAATTACAC
1 TGTACAGATGAAATTACAC
16450 TGTACAGAT
1 TGTACAGAT
16459 TAGATTAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (19 bp):
TGTACAGATGAAATTACAC
Found at i:16564 original size:19 final size:19
Alignment explanation
Indices: 16537--16573 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16527 ATTGATCCTA
*
16537 AAACGGTGATGAAACGGTC
1 AAACAGTGATGAAACGGTC
16556 AAACAGTGATGAAACGGT
1 AAACAGTGATGAAACGGT
16574 TACAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.30, T:0.16
Consensus pattern (19 bp):
AAACAGTGATGAAACGGTC
Found at i:18944 original size:21 final size:19
Alignment explanation
Indices: 18918--18975 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
18908 GCTGCTATAA
18918 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
18939 TAATCTAATCTGTATAGTG
1 TAATCTCATCTGTACAGTC
18958 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
18976 TACTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:21000 original size:3 final size:3
Alignment explanation
Indices: 20992--21034 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
20982 AAGTTAACTT
20992 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21035 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:26321 original size:19 final size:18
Alignment explanation
Indices: 26293--26328 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26283 AGGGATTTTT
26293 TTTGTTCTTTTTCCTTGC
1 TTTGTTCTTTTTCCTTGC
*
26311 TTTGCTTCTTTTTTCTTG
1 TTTG-TTCTTTTTCCTTG
26329 AGCTTCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.00, C:0.19, G:0.11, T:0.69
Consensus pattern (18 bp):
TTTGTTCTTTTTCCTTGC
Found at i:27333 original size:13 final size:13
Alignment explanation
Indices: 27315--27339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27305 CTCTGTTTTG
27315 GCTCTGTTTTTCT
1 GCTCTGTTTTTCT
27328 GCTCTGTTTTTC
1 GCTCTGTTTTTC
27340 AGTTGAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.16, T:0.60
Consensus pattern (13 bp):
GCTCTGTTTTTCT
Found at i:39104 original size:2 final size:2
Alignment explanation
Indices: 39097--39121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39087 CTGGTTCATT
39097 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
39122 AAAGCCAACC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.