Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013311.1 Corchorus olitorius cultivar O-4 contig13344, 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: 30536
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:5438 original size:17 final size:17
Alignment explanation
Indices: 5416--5449 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5406 AATTTTCCTA
*
5416 TGACAACTATACATGCT
1 TGACAACTATAAATGCT
5433 TGACAACTATAAATGCT
1 TGACAACTATAAATGCT
5450 CCTTGACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (17 bp):
TGACAACTATAAATGCT
Found at i:5456 original size:20 final size:19
Alignment explanation
Indices: 5411--5456 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 19
5401 AATTCAATTT
*
5411 TCCTATGACAACTATACATG
1 TCCT-TGACAACTATAAATG
5431 --CTTGACAACTATAAATG
1 TCCTTGACAACTATAAATG
5448 CTCCTTGAC
1 -TCCTTGAC
5457 TACAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 14 0.64
18 2 0.09
20 6 0.27
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (19 bp):
TCCTTGACAACTATAAATG
Found at i:6836 original size:29 final size:31
Alignment explanation
Indices: 6802--6872 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
6792 GACTCGGCCT
*
6802 AATTTGGGGCAGAA-GCTTT-CAATTTG-GTC
1 AATTTGGGGCAAAACG-TTTCCAATTTGTGTC
*
6831 TATTTGGGGCAAAACGTTTCCAATTTGTGTC
1 AATTTGGGGCAAAACGTTTCCAATTTGTGTC
*
6862 AATTAGGGGCA
1 AATTTGGGGCA
6873 TACCGTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 15 0.43
30 8 0.23
31 12 0.34
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (31 bp):
AATTTGGGGCAAAACGTTTCCAATTTGTGTC
Found at i:8762 original size:10 final size:10
Alignment explanation
Indices: 8747--8791 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
8737 GCCTAAACAG
*
8747 AAAACATAAC
1 AAAACAGAAC
8757 AAAACAAGAAC
1 AAAAC-AGAAC
*
8768 AGAACAGAAC
1 AAAACAGAAC
*
8778 AGAACAGAAC
1 AAAACAGAAC
8788 AAAA
1 AAAA
8792 GTTCCGTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.69, C:0.18, G:0.11, T:0.02
Consensus pattern (10 bp):
AAAACAGAAC
Found at i:10337 original size:38 final size:38
Alignment explanation
Indices: 10286--10362 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
10276 TTAGAAGTAA
*
10286 AAACCAAAGGAGGATTTCGCTACAAGTCTTCAAACACT
1 AAACCAAAGGAGGATTTCGCTACAAGTCTTAAAACACT
10324 AAACCAAAGGAGGATTTCGCTACAAGTCTTAAAACACT
1 AAACCAAAGGAGGATTTCGCTACAAGTCTTAAAACACT
10362 A
1 A
10363 TGTAGAACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.21
Consensus pattern (38 bp):
AAACCAAAGGAGGATTTCGCTACAAGTCTTAAAACACT
Found at i:10723 original size:16 final size:16
Alignment explanation
Indices: 10698--10732 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10688 ACAATTCAGA
10698 AAGCAAAAAAGCTCTG
1 AAGCAAAAAAGCTCTG
* *
10714 AAGCAGAAAAGGTCTG
1 AAGCAAAAAAGCTCTG
10730 AAG
1 AAG
10733 TATTTTCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAAAAAAGCTCTG
Found at i:10885 original size:41 final size:41
Alignment explanation
Indices: 10828--11028 Score: 226
Period size: 41 Copynumber: 4.9 Consensus size: 41
10818 TTTTCGTTTG
10828 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
10869 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATTAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * *
10910 TTCAAGAACAAGTCATCGAGACTCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * * *
10954 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTTAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
10995 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
11029 CAAATCAAAC
Statistics
Matches: 136, Mismatches: 20, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
40 14 0.10
41 84 0.62
42 4 0.03
43 1 0.01
44 33 0.24
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:10995 original size:85 final size:82
Alignment explanation
Indices: 10828--11028 Score: 244
Period size: 85 Copynumber: 2.4 Consensus size: 82
10818 TTTTCGTTTG
* * *** *
10828 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACCC
1 TTCAAGAACAAGTCATCGAGACCCTTGAATGAAATTATCAATTCAAGACCAAGTCATCAAGACCC
10893 TTGAATTAAATTATTAA
66 TTGAATTAAATTATTAA
* *
10910 TTCAAGAACAAGTCATCGAGACTCTTGAATCGAATTATTATCAATTCAAGACCAAGTCGTCAAGA
1 TTCAAGAACAAGTCATCGAGACCCTTGAAT-GAA--ATTATCAATTCAAGACCAAGTCATCAAGA
* *
10975 CCCTTGAATTAGATTGTTAA
63 CCCTTGAATTAAATTATTAA
* *
10995 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGAACAAGTCA-TCGAGACCCTTGAATGAAAT
11029 CAAATCAAAC
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
81 2 0.02
82 28 0.27
83 4 0.04
84 10 0.10
85 56 0.55
86 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (82 bp):
TTCAAGAACAAGTCATCGAGACCCTTGAATGAAATTATCAATTCAAGACCAAGTCATCAAGACCC
TTGAATTAAATTATTAA
Found at i:16170 original size:19 final size:18
Alignment explanation
Indices: 16146--16181 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16136 TGAAGACTTA
16146 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
16165 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
16182 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:22996 original size:11 final size:12
Alignment explanation
Indices: 22965--22996 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
22955 ATAAGATTAT
22965 TTTTAAAAAAGA
1 TTTTAAAAAAGA
*
22977 TTTTAAAAAAGG
1 TTTTAAAAAAGA
22989 TTTTAAAA
1 TTTTAAAA
22997 TTTCTATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (12 bp):
TTTTAAAAAAGA
Found at i:24582 original size:28 final size:29
Alignment explanation
Indices: 24549--24622 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 29
24539 CTAAATTGGG
24549 AGTTTAGGGGGCAAACGTCCAAAAT-TA-A
1 AGTTTAGGGGGCAAACGT-CAAAATCTAGA
*
24577 AGTTTAGGGGGCAAAATGTCAAAATCGTAGA
1 AGTTTAGGGGGC-AAACGTCAAAATC-TAGA
*
24608 AGTTCAGGGGGCAAA
1 AGTTTAGGGGGCAAA
24623 AAGGGCATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 18 0.45
29 5 0.12
30 5 0.12
31 12 0.30
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (29 bp):
AGTTTAGGGGGCAAACGTCAAAATCTAGA
Found at i:26430 original size:16 final size:16
Alignment explanation
Indices: 26405--26435 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26395 ATCTATCAGT
*
26405 CTTTTTTTTTCTTTTG
1 CTTTTCTTTTCTTTTG
26421 CTTTTCTTTTCTTTT
1 CTTTTCTTTTCTTTT
26436 AAGTTCTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
CTTTTCTTTTCTTTTG
Found at i:28222 original size:2 final size:2
Alignment explanation
Indices: 28206--28255 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
28196 TTTTTGGCGC
* * *
28206 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28247 TA CTA TA TA
1 TA -TA TA TA
28256 AGTCTAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28568 original size:116 final size:115
Alignment explanation
Indices: 28366--28684 Score: 488
Period size: 116 Copynumber: 2.8 Consensus size: 115
28356 CAGGATTTTA
* *
28366 TTTCCATATTAAGAAAGTC-T-AA-AATAATAACAATTATTTTTACATTAAACAACTTATTATTA
1 TTTCCATATTAA-AAAGTCTTAAATAATACTAACAATT-TTTTTACGTTAAACAACTTATTATTA
28428 TAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTCTTC
64 TAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTCTTC
28480 TTTCCATATTATAAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTAT
1 TTTCCATATTA-AAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTAT
*
28545 AATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTC
65 AATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTCTTC
** *
28596 TTTCCATATTAAAAAAGT-TTAAAATAATACTAACAA-TTTTTTACGTTAAACATTTTCTTATTA
1 TTTCCATATT-AAAAAGTCTT-AAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTA
*
28659 TAATTATTAAACTTATTATTA-TTATA
64 TAATTATTAAAATTATTATTAGTTATA
28685 ACAATTATTA
Statistics
Matches: 192, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
114 22 0.11
115 48 0.25
116 109 0.57
117 13 0.07
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (115 bp):
TTTCCATATTAAAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTATA
ATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTCTTC
Found at i:28675 original size:18 final size:19
Alignment explanation
Indices: 28652--28702 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
28642 TAAACATTTT
28652 CTTATTATAATTATTAA-A
1 CTTATTATAATTATTAACA
*
28670 CTTATTATTATTA-TAACA
1 CTTATTATAATTATTAACA
*
28688 ATTATTATTAATTAT
1 CTTATTA-TAATTAT
28703 ATGATCACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.11
18 19 0.70
19 5 0.19
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
CTTATTATAATTATTAACA
Found at i:28679 original size:15 final size:15
Alignment explanation
Indices: 28656--28698 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28646 CATTTTCTTA
*
28656 TTATAATTATTAAAC
1 TTATTATTATTAAAC
28671 TTATTATTATTATAAC
1 TTATTATTATTA-AAC
*
28687 -AATTATTATTAA
1 TTATTATTATTAA
28699 TTATATGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.84
16 3 0.12
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATTATTATTAAAC
Found at i:29707 original size:154 final size:154
Alignment explanation
Indices: 29417--29724 Score: 517
Period size: 154 Copynumber: 2.0 Consensus size: 154
29407 AATAATTTTT
**** *
29417 TAAACAGTAACAGAAACAATAAATATTAATTATTAAAAGTTTTGATTTTTTTTTTGAAAAATTTA
1 TAAACAGTAACAGAAACAATAAATATTAATTATTAAAAGTTTTGATTTTTTTAAAAAAAAAATTA
* * *
29482 ATAGATCATTCATTCACTACTTTTATTTTGCTCTGTTAGCTTAAATCACTTTATTCCATTCCTTA
66 ATAGATCATTCATTCACTACTTTTATTTTGCTCGGTTAACTTAAATCACTTTATTCCATTCATTA
29547 TGATGCATAAAATTGGTAGTGTAA
131 TGATGCATAAAATTGGTAGTGTAA
*
29571 TAAACGGTAACAGAAACAATAAATATTAATTATTAAAAGTTTTGATTTTTTTAAAAAAAAAATTA
1 TAAACAGTAACAGAAACAATAAATATTAATTATTAAAAGTTTTGATTTTTTTAAAAAAAAAATTA
*
29636 ATAGATCATTCATTCACTACTTTTATTTTGCTCGGTTAACTTAAATCACTTTATTTCATTCATTA
66 ATAGATCATTCATTCACTACTTTTATTTTGCTCGGTTAACTTAAATCACTTTATTCCATTCATTA
*
29701 TTATGCATAAAATTGGTAGTGTAA
131 TGATGCATAAAATTGGTAGTGTAA
29725 AAATAAAAAA
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 143 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (154 bp):
TAAACAGTAACAGAAACAATAAATATTAATTATTAAAAGTTTTGATTTTTTTAAAAAAAAAATTA
ATAGATCATTCATTCACTACTTTTATTTTGCTCGGTTAACTTAAATCACTTTATTCCATTCATTA
TGATGCATAAAATTGGTAGTGTAA
Done.