Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017181.1 Corchorus olitorius cultivar O-4 contig17214, 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: 35365
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5144 original size:12 final size:13
Alignment explanation
Indices: 5126--5155 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5116 GTTTTCTTTA
5126 ATTTTCTTGATTG
1 ATTTTCTTGATTG
5139 -TTTTCTTGATTG
1 ATTTTCTTGATTG
5151 ATTTT
1 ATTTT
5156 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:5387 original size:16 final size:17
Alignment explanation
Indices: 5366--5397 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5356 GAGATTGCGT
5366 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
5382 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
5398 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:11205 original size:68 final size:69
Alignment explanation
Indices: 11059--11222 Score: 303
Period size: 69 Copynumber: 2.4 Consensus size: 69
11049 TCGATAAGTC
* *
11059 GACAATTTTTTGGAAGAAAATT-TCGACAAAATTGCAAGCAAACCGACGCCACCCTTAGTCGACT
1 GACAATTTTTTGGAGGAAAATTGCCGACAAAATTGCAAGCAAACCGACGCCACCCTTAGTCGACT
11123 AGAA
66 AGAA
11127 GACAATTTTTTGGAGGAAAATTGCCGACAAAATTGCAAGCAAACCGACGCCACCCTTAGTCGACT
1 GACAATTTTTTGGAGGAAAATTGCCGACAAAATTGCAAGCAAACCGACGCCACCCTTAGTCGACT
11192 AGAA
66 AGAA
11196 GACAATTTTTTGGAGGAAAATTGCCGA
1 GACAATTTTTTGGAGGAAAATTGCCGA
11223 TAAGAAGCAA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
68 21 0.23
69 72 0.77
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (69 bp):
GACAATTTTTTGGAGGAAAATTGCCGACAAAATTGCAAGCAAACCGACGCCACCCTTAGTCGACT
AGAA
Found at i:15097 original size:12 final size:13
Alignment explanation
Indices: 15079--15108 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
15069 GTTTTCTTTA
15079 ATTTTCTTGATTG
1 ATTTTCTTGATTG
15092 -TTTTCTTGATTG
1 ATTTTCTTGATTG
15104 ATTTT
1 ATTTT
15109 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:17199 original size:24 final size:24
Alignment explanation
Indices: 17171--17216 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17161 CTTTTTAAAA
17171 ATTTGTTTGAACACAATAGCTAAT
1 ATTTGTTTGAACACAATAGCTAAT
*
17195 ATTTGTTTGAACAGAATAGCTA
1 ATTTGTTTGAACACAATAGCTA
17217 CTGAAGGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (24 bp):
ATTTGTTTGAACACAATAGCTAAT
Found at i:18559 original size:22 final size:22
Alignment explanation
Indices: 18535--18616 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
18525 ATTAAATTTT
* *
18535 TATGAAATCTTGATAATTACTT
1 TATGAAATTTTGATAATTACTC
** *
18557 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAATTACTC
*
18579 TATGAAATTTTGATAATTACCC
1 TATGAAATTTTGATAATTACTC
*
18601 AATGAAATTTTGATAA
1 TATGAAATTTTGATAA
18617 ACTTCCTATG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAATTACTC
Found at i:18627 original size:22 final size:21
Alignment explanation
Indices: 18535--18714 Score: 83
Period size: 22 Copynumber: 8.5 Consensus size: 21
18525 ATTAAATTTT
* *
18535 TATGAAATCTTGATAA-TTACTT
1 TATGAAATTTTGATAACTT-C-C
**
18557 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACTTC-C
18579 TATGAAATTTTGATAA-TTACCC
1 TATGAAATTTTGATAACTT--CC
*
18601 AATGAAATTTTGATAAACTTCC
1 TATGAAATTTTGAT-AACTTCC
*
18623 TATGAAGTTTTG---A----C
1 TATGAAATTTTGATAACTTCC
* *
18637 TATGAAATATTAATAAAGCTTCC
1 TATGAAATTTTGAT-AA-CTTCC
* *
18660 TATAAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAA-CTTCC
* *
18682 TATG-ATTCTTTGATAACCTCCC
1 TATGAAAT-TTTGATAA-CTTCC
18704 TATGAAATTTT
1 TATGAAATTTT
18715 TTTTAATCTC
Statistics
Matches: 120, Mismatches: 22, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
14 10 0.08
18 2 0.02
21 2 0.02
22 87 0.73
23 17 0.14
24 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTCC
Found at i:18653 original size:36 final size:37
Alignment explanation
Indices: 18602--18672 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
18592 TAATTACCCA
* * * *
18602 ATGAAATTTTGATAAA-CTTCCTATGAAGTTTTGACT
1 ATGAAATATTAATAAAGCTTCCTATAAAATTTTGACT
18638 ATGAAATATTAATAAAGCTTCCTATAAAATTTTGA
1 ATGAAATATTAATAAAGCTTCCTATAAAATTTTGA
18673 TAATCTCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (37 bp):
ATGAAATATTAATAAAGCTTCCTATAAAATTTTGACT
Found at i:18736 original size:22 final size:22
Alignment explanation
Indices: 18658--18777 Score: 95
Period size: 22 Copynumber: 5.5 Consensus size: 22
18648 AATAAAGCTT
*
18658 CCTATAAAATTTTGATAATCTC
1 CCTATAAATTTTTGATAATCTC
* *
18680 CCTAT-GATTCTTTGATAACCTC
1 CCTATAAATT-TTTGATAATCTC
**
18702 CCTATGAAATTTTTTTTAATCTC
1 CCTAT-AAATTTTTGATAATCTC
*
18725 CCTATAAATTTTTTAT-ATCAT-
1 CCTATAAATTTTTGATAATC-TC
**
18746 AGTATGAAA-TTTTGATAATCTC
1 CCTAT-AAATTTTTGATAATCTC
*
18768 TCTATAAATT
1 CCTATAAATT
18778 ATATATCATT
Statistics
Matches: 77, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
21 18 0.23
22 42 0.55
23 14 0.18
24 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.46
Consensus pattern (22 bp):
CCTATAAATTTTTGATAATCTC
Found at i:29630 original size:2 final size:2
Alignment explanation
Indices: 29623--29647 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29613 GATTGGCAGT
29623 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29648 CTGTAAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31772 original size:25 final size:27
Alignment explanation
Indices: 31729--31786 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
31719 TTTTGAACTC
31729 ATTATTATTTATTATTTAA-AATATAT
1 ATTATTATTTATTATTTAATAATATAT
31755 -TTATTATTTATT-TATTAATTAATATAT
1 ATTATTATTTATTAT-TTAA-TAATATAT
31782 ATTAT
1 ATTAT
31787 ATCTAACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 1 0.04
25 16 0.57
27 7 0.25
28 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTATTATTTATTATTTAATAATATAT
Found at i:33111 original size:57 final size:55
Alignment explanation
Indices: 33041--33149 Score: 141
Period size: 55 Copynumber: 1.9 Consensus size: 55
33031 ATTAGAATAT
*
33041 TTTGAGTTGTTATTAACGAATACATATC-GTCATGTGATTTCA-TGTTCAAGTGTTTGA
1 TTTGAGTTATTATTAACG--TACATATCAG-CATGTGATTT-AGTGTTCAAGTGTTTGA
* *
33098 TTTGAGTTATTATTAACGTATATTTCAGCATGTGATTTAGTGTTCAAGTGTT
1 TTTGAGTTATTATTAACGTACATATCAGCATGTGATTTAGTGTTCAAGTGTT
33150 AGTGTGATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
54 1 0.02
55 28 0.60
56 1 0.02
57 17 0.36
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (55 bp):
TTTGAGTTATTATTAACGTACATATCAGCATGTGATTTAGTGTTCAAGTGTTTGA
Found at i:34462 original size:2 final size:2
Alignment explanation
Indices: 34455--34489 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34445 CTATTTGAGT
34455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34490 GCCATCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34637 original size:29 final size:29
Alignment explanation
Indices: 34588--34881 Score: 313
Period size: 29 Copynumber: 10.1 Consensus size: 29
34578 TTAATTGACC
*
34588 TTTTTGCATATCCAGGGGGCATTTTGGTCA
1 TTTTTGCACATCCA-GGGGCATTTTGGTCA
* * * *
34618 TTTTTACCCATCCAAGGGCATTATGGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* * * * * *
34647 TCTCTGCATATTCAGGGGAATTTTGGTTA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* * *
34676 TTTTTGCACATTCAGAGGCATTTTGGTTA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* * *
34705 TTTTTGCATATCCGGGGGCATTTTTGGTTA
1 TTTTTGCACATCCAGGGGCA-TTTTGGTCA
* * *
34735 TTTTTGCACATTCAGAGGCATTTTGGTTA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* * *
34764 -TTTTGCATATCCGGGGGCATTTTAGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* *
34792 TTTTTGCACATCTA-GGGCATTTTAGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* *
34820 TTTTTGCACATCTAGGGGCATTTTAGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
34849 TTTTTGCACATCCAGGGGCATTTTGGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
34878 TTTT
1 TTTT
34882 GGTTTTATTC
Statistics
Matches: 222, Mismatches: 39, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
28 50 0.23
29 136 0.61
30 36 0.16
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (29 bp):
TTTTTGCACATCCAGGGGCATTTTGGTCA
Done.