Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012466.1 Corchorus olitorius cultivar O-4 contig12499, 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: 17034
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:228 original size:51 final size:50
Alignment explanation
Indices: 127--228 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
117 GTTCTTCATA
* **
127 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
177 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
228 T
1 T
229 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:4082 original size:17 final size:17
Alignment explanation
Indices: 4062--4114 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
4052 CCATAAAAAT
4062 AAAAA-GAAAAATGAATGA
1 AAAAATGAAAAA--AATGA
4080 AAAAATGAAAAAAATG-
1 AAAAATGAAAAAAATGA
4096 AAAAATGAAAAAAA-GA
1 AAAAATGAAAAAAATGA
4112 AAA
1 AAA
4115 TAAAGGCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.03
16 17 0.52
17 4 0.12
18 5 0.15
19 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (17 bp):
AAAAATGAAAAAAATGA
Found at i:4088 original size:8 final size:8
Alignment explanation
Indices: 4075--4114 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
4065 AAGAAAAATG
4075 AATGAAAA
1 AATGAAAA
4083 AATGAAAAA
1 AATG-AAAA
4092 AATG-AAA
1 AATGAAAA
4099 AATGAAAA
1 AATGAAAA
*
4107 AAAGAAAA
1 AATGAAAA
4115 TAAAGGCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.24
8 14 0.48
9 8 0.28
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (8 bp):
AATGAAAA
Found at i:4529 original size:7 final size:7
Alignment explanation
Indices: 4517--4569 Score: 74
Period size: 7 Copynumber: 7.6 Consensus size: 7
4507 ACAAAATAAT
4517 AAAATCA
1 AAAATCA
4524 AAAATCA
1 AAAATCA
4531 AAAATC-
1 AAAATCA
4537 AAAATACAA
1 AAAAT-C-A
4546 AAAATCA
1 AAAATCA
4553 AAAATCA
1 AAAATCA
4560 AAAAT-A
1 AAAATCA
4566 AAAA
1 AAAA
4570 AAAAGAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.23
7 27 0.63
8 1 0.02
9 5 0.12
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATCA
Found at i:4534 original size:22 final size:20
Alignment explanation
Indices: 4517--4569 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
4507 ACAAAATAAT
4517 AAAATCAAAAATCAAAAATCA
1 AAAAT-AAAAATCAAAAATCA
*
4538 AAATACAAAAAATCAAAAATCA
1 AAA-A-TAAAAATCAAAAATCA
4560 AAAATAAAAA
1 AAAATAAAAA
4570 AAAAGAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 5 0.18
21 4 0.14
22 19 0.68
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAATAAAAATCAAAAATCA
Found at i:4549 original size:29 final size:28
Alignment explanation
Indices: 4508--4573 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 28
4498 ATAATAATAA
*
4508 CAAAATAATAAAATCAAAAATCAAAAAT
1 CAAAATAAAAAAATCAAAAATCAAAAAT
4536 CAAAATACAAAAAATCAAAAATCAAAAAT
1 CAAAATA-AAAAAATCAAAAATCAAAAAT
4565 -AAAA-AAAAA
1 CAAAATAAAAA
4574 GAATTGATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 4 0.11
27 1 0.03
28 11 0.31
29 20 0.56
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.14
Consensus pattern (28 bp):
CAAAATAAAAAAATCAAAAATCAAAAAT
Found at i:4570 original size:22 final size:22
Alignment explanation
Indices: 4523--4572 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
4513 TAATAAAATC
4523 AAAAATCAAAAATCAAAATACA
1 AAAAATCAAAAATCAAAATACA
*
4545 AAAAATCAAAAATCAAAAATAAA
1 AAAAATCAAAAATC-AAAATACA
4568 AAAAA
1 AAAAA
4573 AGAATTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (22 bp):
AAAAATCAAAAATCAAAATACA
Found at i:4571 original size:8 final size:7
Alignment explanation
Indices: 4492--4570 Score: 61
Period size: 7 Copynumber: 11.0 Consensus size: 7
4482 TCAAGAAATT
4492 TAAAAAA
1 TAAAAAA
*
4499 T-AATAA
1 TAAAAAA
4505 TAACAAAA
1 TAA-AAAA
4513 TAATAAAA
1 TAA-AAAA
*
4521 TCAAAAA
1 TAAAAAA
*
4528 TCAAAAA
1 TAAAAAA
*
4535 TCAAAATA
1 T-AAAAAA
*
4543 CAAAAAA
1 TAAAAAA
*
4550 TCAAAAA
1 TAAAAAA
*
4557 TCAAAAA
1 TAAAAAA
4564 TAAAAAA
1 TAAAAAA
4571 AAAGAATTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
6 5 0.09
7 37 0.64
8 16 0.28
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:6368 original size:169 final size:169
Alignment explanation
Indices: 5929--6622 Score: 1041
Period size: 169 Copynumber: 4.1 Consensus size: 169
5919 CATCAAATTC
* *
5929 AGATTCATATTTAAGTTAAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCC
1 AGATTCATGTTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCC
*
5994 TCCGGGCACAAATTCAGAAACCT-TCGGGTGTTAATTCTGATAAGTCCTCCGGGCAATCGGTAAA
66 TCCGGGCACAAATTCAGAAACCTCT-GGGTATTAATTCTGATAAGTCCTCCGGGCAATCGGTAAA
*
6058 ACCTCCGGGTACCATTTCATTTCATCAATTTTTTTTTTCATCAA
130 ACCTCCGGGTACCATTTCATTTCATCAA----GTTTTTCATCAA
* * * *
6102 AGATTCATATTCAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCC
1 AGATTCATGTTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCC
* *
6167 TCCGGGCACAAATTCAGAAACCTCTGGGTATTAATTCTGGTAAGTCCTCCGGGCAATTGGTAAAA
66 TCCGGGCACAAATTCAGAAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAATCGGTAAAA
** * * * *
6232 CCTCCAAGTATCATTTCATTTTATCGAGTTTTTCAT-TA
131 CCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAA
* *
6270 AGAATTCATGTTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACAATGGTAAGTC
1 AG-ATTCATGTTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTC
* * * * *
6335 CTCTGGGCACAATTTCATAAACCTCTAGGTATTAATTCTGATAAGTCCTCCGGGCAACCGGTAAA
65 CTCCGGGCACAAATTCAGAAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAATCGGTAAA
* *
6400 ACCTCCGGGTACCATTTCATTTTATCAAGTTTTTCATTAA
130 ACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAA
* *
6440 AGATCCGTGTTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCC
1 AGATTCATGTTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCC
* **
6505 TCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCTAGGCAATCGGTAAAA
66 TCCGGGCACAAATTCAGAAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAATCGGTAAAA
6570 CCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAA
131 CCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAA
*
6609 AAATTCATGTTTAA
1 AGATTCATGTTTAA
6623 AATCCTTGGT
Statistics
Matches: 471, Mismatches: 47, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
168 3 0.01
169 321 0.68
170 3 0.01
173 143 0.30
174 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (169 bp):
AGATTCATGTTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCC
TCCGGGCACAAATTCAGAAACCTCTGGGTATTAATTCTGATAAGTCCTCCGGGCAATCGGTAAAA
CCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAA
Found at i:6761 original size:38 final size:36
Alignment explanation
Indices: 6711--7133 Score: 308
Period size: 30 Copynumber: 13.1 Consensus size: 36
6701 ACTTAATCTG
6711 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
6747 AGTTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
1 --TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
*
6785 AGTTTATTTTAATCCTGGTTTAGGATTATTGCTTTATC
1 --TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
*
6823 ------TTAATCCTAGTTTAGGATCATTG------C
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
*
6847 TTTATTTTAATCCTGGTTGAGGATCATTGC--T-TC
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
* *
6880 ---ATCTTAATCCTGGTTTAGGATCATTGCTTTATTAG
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTA-T-C
*
6915 TTTATTTTAATCCTGGTTTAGGATTATTGCTTTATC
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
6951 ------TTAATCCTGGTTTAGGATCATTG------C
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
*
6975 TTTATTTTAATCCTGGTTGAGGATCATTGC--T-TC
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
*
7008 ---ATCTTAATCCTGGTTTAGGATCATTG------C
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
*
7035 TTTATTTTAATCCTGGTTGAGGATCATTG------C
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
7065 TTTATTTTAATCCTGGTTTAGGATCATTG------C
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
* *
7095 TTTATTTTAATCCTGGTTGAGGGTCATTGCTTTAT-
1 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
7130 TTTA
1 TTTA
7134 ATCCTGGTTT
Statistics
Matches: 330, Mismatches: 20, Indels: 73
0.78 0.05 0.17
Matches are distributed among these distances:
24 2 0.01
27 1 0.00
30 216 0.65
32 1 0.00
33 2 0.01
34 1 0.00
35 4 0.01
37 1 0.00
38 102 0.31
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (36 bp):
TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATC
Found at i:6821 original size:30 final size:30
Alignment explanation
Indices: 6787--7307 Score: 695
Period size: 30 Copynumber: 17.1 Consensus size: 30
6777 GCTTTATCAG
*
6787 TTTATTTTAATCCTGGTTTAGGATTATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
6817 TTTATCTTAATCCTAGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
6847 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
6877 TTCATCTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
6907 TTTATTAGTTTATTTTAATCCTGGTTTAGGATTATTGC
1 --------TTTATTTTAATCCTGGTTTAGGATCATTGC
*
6945 TTTATCTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
6975 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
7005 TTCATCTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
7035 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
7065 TTTATTTTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
7095 TTTATTTTAATCCTGGTTGAGGGTCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * *
7125 TTTATTTTAATCCTGGTTTAGAATCGTCGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
7155 TTTATTTTAATCCTGGTTGAGCG-TCATCGC
1 TTTATTTTAATCCTGGTTTAG-GATCATTGC
* *
7185 TTTATTTTAATCCTGGTTTAGGATCGTCGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
7215 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
7245 TTCATTTTAATCCTGGTTTAGGGTCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
7275 TTTATTTCAAAATTCT-GTTTAGGATCATTGC
1 TTTATTT--TAATCCTGGTTTAGGATCATTGC
7306 TT
1 TT
7308 CATCAGTTTG
Statistics
Matches: 434, Mismatches: 45, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
29 1 0.00
30 385 0.89
31 16 0.04
32 5 0.01
38 27 0.06
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.48
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTTAGGATCATTGC
Found at i:7443 original size:39 final size:39
Alignment explanation
Indices: 7400--7501 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
7390 TTGATTTCAG
7400 AATCCTGATTTAGGATTATTGCTTTATAAGTTTTATTCC
1 AATCCTGATTTAGGATTATTGCTTTATAAGTTTTATTCC
* * *
7439 AATCCTGATTTAGGATTATTGCTTTGTCAGTTTTATTTC
1 AATCCTGATTTAGGATTATTGCTTTATAAGTTTTATTCC
* *
7478 GATCCTGATTTAGGATCATTGCTT
1 AATCCTGATTTAGGATTATTGCTT
7502 ATCAGTTGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.48
Consensus pattern (39 bp):
AATCCTGATTTAGGATTATTGCTTTATAAGTTTTATTCC
Found at i:7547 original size:78 final size:78
Alignment explanation
Indices: 7401--7548 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 78
7391 TGATTTCAGA
* * *
7401 ATCCTGATTTAGGATTATTGCTTTATAAGTTTTATTCCAATCCTGATTTAGGATTATTGCTTTGT
1 ATCCTGATTTAGGATCATTGCTTTATAAGTTATATTCCAATCCTGATTTAGGATTATTGCTTTAT
7466 CAGTTTTATTTCG
66 CAGTTTTATTTCG
* * * *
7479 ATCCTGATTTAGGATCATTGC-TTATCAGTTGAT-TTCATAATCGT-ATTTAGGATTTTTGCTTT
1 ATCCTGATTTAGGATCATTGCTTTATAAGTT-ATATTC-CAATCCTGATTTAGGATTATTGC-TT
7541 TATCAGTT
63 TATCAGTT
7549 AGTTTCAGGA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
77 25 0.42
78 35 0.58
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (78 bp):
ATCCTGATTTAGGATCATTGCTTTATAAGTTATATTCCAATCCTGATTTAGGATTATTGCTTTAT
CAGTTTTATTTCG
Found at i:16611 original size:15 final size:15
Alignment explanation
Indices: 16581--16622 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
16571 TTACCCCGCT
16581 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
16597 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
16612 TTGCTTTCTGT
1 TTGTTTTCTGT
16623 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.