Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018795.1 Corchorus olitorius cultivar O-4 contig18828, 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: 23162
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:709 original size:29 final size:29
Alignment explanation
Indices: 667--816 Score: 191
Period size: 29 Copynumber: 5.2 Consensus size: 29
657 CTTAAAGTAA
*
667 AAATGACCAAAATGCCCCTGGATGTGCAG
1 AAATGACCATAATGCCCCTGGATGTGCAG
* *
696 AAATGACCAAAATGCCCCTGGAGGTGCCAG
1 AAATGACCATAATGCCCCTGGATGTG-CAG
* *
726 -AATGACCATAATGCCCCTGTAGGTGC-G
1 AAATGACCATAATGCCCCTGGATGTGCAG
753 AAAATGACCATAATGCCCCTGGATGTGCA-
1 -AAATGACCATAATGCCCCTGGATGTGCAG
*
782 AGAATGACCATAATGCCCCTGAATGTGCA-
1 A-AATGACCATAATGCCCCTGGATGTGCAG
811 AAATGA
1 AAATGA
817 TCACTTAAGA
Statistics
Matches: 110, Mismatches: 6, Indels: 11
0.87 0.05 0.09
Matches are distributed among these distances:
27 1 0.01
28 7 0.06
29 99 0.90
30 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (29 bp):
AAATGACCATAATGCCCCTGGATGTGCAG
Found at i:739 original size:58 final size:58
Alignment explanation
Indices: 668--816 Score: 212
Period size: 58 Copynumber: 2.6 Consensus size: 58
658 TTAAAGTAAA
* * *
668 AATGACCAAAATGCCCCTGGATGTGCAGAAATGACCAAAATGCCCCTGGAGGTGCCAG
1 AATGACCATAATGCCCCTGAATGTGCAGAAATGACCAAAATGCCCCTGGAGGTGCAAG
* * * *
726 AATGACCATAATGCCCCTGTAGGTGC-GAAAATGACCATAATGCCCCTGGATGTGCAAG
1 AATGACCATAATGCCCCTGAATGTGCAG-AAATGACCAAAATGCCCCTGGAGGTGCAAG
784 AATGACCATAATGCCCCTGAATGTGCA-AAATGA
1 AATGACCATAATGCCCCTGAATGTGCAGAAATGA
817 TCACTTAAGA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
57 7 0.09
58 74 0.91
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (58 bp):
AATGACCATAATGCCCCTGAATGTGCAGAAATGACCAAAATGCCCCTGGAGGTGCAAG
Found at i:4312 original size:39 final size:39
Alignment explanation
Indices: 4267--4350 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
4257 CAACAGCAGC
4267 CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCT
1 CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCT
* *
4306 CTCCCTCTCCCTATACATCCGAGCAGGCTCAGCCTCTCT
1 CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCT
4345 CTCCCT
1 CTCCCT
4351 TTGCAACTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.14, C:0.50, G:0.11, T:0.25
Consensus pattern (39 bp):
CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCT
Found at i:4792 original size:33 final size:33
Alignment explanation
Indices: 4748--4831 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
4738 ACTTTTCGGC
* *
4748 GGTGCCACCCCAACAGGGTGACGCCGCCATGGT
1 GGTGCCGCCCCAACAGGGAGACGCCGCCATGGT
4781 GGTGCCGCCCCAACAGGGAGACGCCGCCATGGT
1 GGTGCCGCCCCAACAGGGAGACGCCGCCATGGT
* *
4814 GGTGTCGCCCCAAAAGGG
1 GGTGCCGCCCCAACAGGG
4832 CGATTATTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.19, C:0.35, G:0.36, T:0.11
Consensus pattern (33 bp):
GGTGCCGCCCCAACAGGGAGACGCCGCCATGGT
Found at i:8715 original size:50 final size:50
Alignment explanation
Indices: 8630--9198 Score: 913
Period size: 50 Copynumber: 11.4 Consensus size: 50
8620 TCCAGAAGCC
* * *
8630 AATTCGAAGGCAGTTTAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
*
8680 AATTGGAAGACAGTTCAAAGGACAAGCGGGAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
8730 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* * *
8780 AGTTGGAAGACAGTTCGAAGGATAAGCAGGAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
**
8830 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTCCAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* *
8880 AATTGGAAGACAGTTGAAAGGATAAGCGGGAGACGATCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* * *
8930 AATTGGAAGACAGTTCGAAGGATAAGCGGGACACGATCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* *
8980 AATTGGAAGACAGTTCGAAGGATAAGCGGCAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
*
9030 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCGTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* * * * *
9080 AATTGGAAGACAGCTCAAAGGGTAAGTGGGAGACGATCCCTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* *
9130 AATTGGAACACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
*
9180 AATTGGAACACAGTTCAAA
1 AATTGGAAGACAGTTCAAA
9199 AAAAAATGTT
Statistics
Matches: 480, Mismatches: 39, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 480 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (50 bp):
AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
Found at i:9461 original size:27 final size:27
Alignment explanation
Indices: 9438--9526 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
9428 TTAGCATTGG
*
9438 GGTCATTTGCACGTCCAGTGGCATTTT
1 GGTCATTTGCACGTCCAGAGGCATTTT
*
9465 GGTCATTTGCACGTCTAGAGGCATTTT
1 GGTCATTTGCACGTCCAGAGGCATTTT
* *
9492 GGTCATTTACACGTCTA-AGGGCATTTT
1 GGTCATTTGCACGTCCAGA-GGCATTTT
*
9519 AGTCATTT
1 GGTCATTT
9527 CAAGTACATT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
26 1 0.02
27 56 0.98
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (27 bp):
GGTCATTTGCACGTCCAGAGGCATTTT
Found at i:12713 original size:15 final size:17
Alignment explanation
Indices: 12693--12725 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
12683 AGTTTGATAA
12693 GCCTTTGA-AT-GAATT
1 GCCTTTGACATGGAATT
12708 GCCTTTGACATGGAATT
1 GCCTTTGACATGGAATT
12725 G
1 G
12726 GATATCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (17 bp):
GCCTTTGACATGGAATT
Found at i:22517 original size:48 final size:48
Alignment explanation
Indices: 22446--22560 Score: 176
Period size: 48 Copynumber: 2.4 Consensus size: 48
22436 AACATTGAAG
22446 ACAGGAATGAAATATTGAAAACAACAACTTCCGACCGGGAAGGACAAA
1 ACAGGAATGAAATATTGAAAACAACAACTTCCGACCGGGAAGGACAAA
* * *
22494 ACAGGAATGAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAA
1 ACAGGAATGAAATATTGAAAACAACAACTTCCGACCGGGAAGGACAAA
* * *
22542 ACGGGAATAAAACATTGAA
1 ACAGGAATGAAATATTGAA
22561 GACAGGAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (48 bp):
ACAGGAATGAAATATTGAAAACAACAACTTCCGACCGGGAAGGACAAA
Found at i:22601 original size:116 final size:116
Alignment explanation
Indices: 22397--22676 Score: 382
Period size: 116 Copynumber: 2.4 Consensus size: 116
22387 AGAGAATAGG
* * * *
22397 AACAACTCCTTCCGATGGAGAAGGGCAAAATGGGAATATAACATTGAAGACAGGAATGAAATATT
1 AACAACACCTTCCGACGG-GAAGGGCAAAACGGGAATAAAACATTGAAGACAGGAATGAAATATT
* **
22462 GAAAACAACAACTTCCGACCGGGAAGGACAAAACAGGAATG-AAATGTTGAA
65 AAAAACAACAACTTCCGACCGGGAAGGACAAAACAGGAATGAAAACATTGAA
22513 AACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACATTGAAGACAGGAATGAAATATT
1 AACAACACCTTCCGA-CGGGAAGGGCAAAACGGGAATAAAACATTGAAGACAGGAATGAAATATT
* * * * *
22578 AAAAACAACACCTTCCGACCGGGAGGGGCAAAACGGGACTGAAAACATTGAA
65 AAAAACAACAACTTCCGACCGGGAAGGACAAAACAGGAATGAAAACATTGAA
* * * * *
22630 AACAACACCTTCTGACTGGAAGGGCAAAACAGGAATGAAATATTGAA
1 AACAACACCTTCCGACGGGAAGGGCAAAACGGGAATAAAACATTGAA
22677 ATCAACACCT
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
116 121 0.83
117 24 0.17
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (116 bp):
AACAACACCTTCCGACGGGAAGGGCAAAACGGGAATAAAACATTGAAGACAGGAATGAAATATTA
AAAACAACAACTTCCGACCGGGAAGGACAAAACAGGAATGAAAACATTGAA
Found at i:22607 original size:68 final size:69
Alignment explanation
Indices: 22494--22629 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 69
22484 GAAGGACAAA
* *
22494 ACAGGAATGAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAAT-AAAACATT
1 ACAGGAATGAAATATTAAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATGAAAACATT
22558 GAAG
66 GAAG
* *
22562 ACAGGAATGAAATATTAAAAACAACACCTTCCGACCGGGAGGGGCAAAACGGGACTGAAAACATT
1 ACAGGAATGAAATATTAAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATGAAAACATT
22627 GAA
66 GAA
22630 AACAACACCT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 52 0.83
69 11 0.17
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (69 bp):
ACAGGAATGAAATATTAAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATGAAAACATT
GAAG
Found at i:23001 original size:48 final size:48
Alignment explanation
Indices: 22565--22989 Score: 663
Period size: 48 Copynumber: 8.9 Consensus size: 48
22555 ATTGAAGACA
* *
22565 GGAATGAAATATTAAAAACAACACCTTCCGACCGGGAGGGGCAAAACG
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
* * * * *
22613 GGACTGAAAACATTGAAAACAACACCTTCTGA-CTGGAAGGGCAAAACA
1 GGAATG-AAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
22661 GGAATGAAATATTGAAATCAACACCTTCTGACCGGGAAGGGCAAAACG
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
22709 GGAAAGAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
22757 GGAATGAAACATTGAAAACAACACCTTCCGACCGTGAAGGGCAAAACG
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
* * * *
22805 GGAATGACATATTGAAAACAACACCTTCCGACTGGGAAGGGCATAACA
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
**
22853 GGAATTCAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
22901 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
22949 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGG
1 GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGG
22990 TAAACTGGGA
Statistics
Matches: 343, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
47 23 0.07
48 298 0.87
49 22 0.06
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (48 bp):
GGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
Found at i:23028 original size:41 final size:41
Alignment explanation
Indices: 22867--23043 Score: 138
Period size: 48 Copynumber: 4.0 Consensus size: 41
22857 TTCAATATTG
** *
22867 AAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATGAAATATT
1 AAAACAACACCTTCCGACAAGGAAGGG-AAAACTGG---G-AAT-TT
** *
22914 GAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATGAAATATT
1 -AAAACAACACCTTCCGACAAGGAAGGG-AAAACTGG---G-AAT-TT
** *
22962 GAAAACAACACCTTCCGACCGGGAAGGGTAAACTGGGAATTT
1 -AAAACAACACCTTCCGACAAGGAAGGGAAAACTGGGAATTT
*
23004 AAAACAACACCTTCCGATAAGGAAGGGAAAACTGGGAATT
1 AAAACAACACCTTCCGACAAGGAAGGGAAAACTGGGAATT
23044 ATCGAAGGAA
Statistics
Matches: 123, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
41 36 0.29
42 2 0.02
43 3 0.02
44 1 0.01
47 6 0.05
48 75 0.61
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.14
Consensus pattern (41 bp):
AAAACAACACCTTCCGACAAGGAAGGGAAAACTGGGAATTT
Found at i:23122 original size:43 final size:43
Alignment explanation
Indices: 23075--23156 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
23065 TCCGACCGAC
23075 AAGGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGG
1 AAGGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGG
23118 AAGGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAAC
1 AAGGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAAC
23157 TATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (43 bp):
AAGGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGG
Done.