Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010796.1 Corchorus olitorius cultivar O-4 contig10828, 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: 29950
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:50 original size:14 final size:14
Alignment explanation
Indices: 31--57 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21 CAAAATTTTA
31 AACTTAAATAAAAG
1 AACTTAAATAAAAG
45 AACTTAAATAAAA
1 AACTTAAATAAAA
58 AAATTTCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTAAATAAAAG
Found at i:738 original size:28 final size:28
Alignment explanation
Indices: 706--770 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
696 TTTTTAGTCT
* *
706 TTTCGACAGAGTTCCCCGGACTTGAATG
1 TTTCGACAGAGTTCCCCGGACTCGAACG
734 TTTCGACAGAGTTCCCCGGACTCGAACG
1 TTTCGACAGAGTTCCCCGGACTCGAACG
*
762 TTTCAACAG
1 TTTCGACAG
771 TTTGTTGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (28 bp):
TTTCGACAGAGTTCCCCGGACTCGAACG
Found at i:2687 original size:22 final size:22
Alignment explanation
Indices: 2482--2740 Score: 131
Period size: 22 Copynumber: 12.0 Consensus size: 22
2472 CATCTGAAAT
* * *
2482 ACCACACTCTAAAATTTTGATG
1 ACCACACTATGAAATTTTGATA
* *
2504 ATCGCACTATGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
*
2526 ACCTC-CTTATGAAATTTTGAT-
1 ACCACAC-TATGAAATTTTGATA
* * * * *
2547 TCTGA-TCTATAAAATTTTGTTA
1 AC-CACACTATGAAATTTTGATA
* * * *
2569 ACCTCTCTATTTAATTTTTGATA
1 ACCACACTA-TGAAATTTTGATA
* *
2592 ATCACACTATAAAATTTTG-TA
1 ACCACACTATGAAATTTTGATA
* *
2613 A-C-CTCTATGAAATTTTTATA
1 ACCACACTATGAAATTTTGATA
* * * * *
2633 ACCACACCATAAAACTGTGATG
1 ACCACACTATGAAATTTTGATA
* * *
2655 ACCTCATTATGAGATTTTGATA
1 ACCACACTATGAAATTTTGATA
2677 ACCACACTATGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
* * *
2699 A-C-CTC-ATGAAATTTCGAGA
1 ACCACACTATGAAATTTTGATA
** *
2718 AGTACAATATGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
2740 A
1 A
2741 TCTGATCTTT
Statistics
Matches: 173, Mismatches: 52, Indels: 24
0.69 0.21 0.10
Matches are distributed among these distances:
19 25 0.14
20 6 0.03
21 20 0.12
22 106 0.61
23 16 0.09
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
ACCACACTATGAAATTTTGATA
Found at i:2704 original size:44 final size:43
Alignment explanation
Indices: 2493--2846 Score: 216
Period size: 44 Copynumber: 8.1 Consensus size: 43
2483 CCACACTCTA
* * * *
2493 AAATTTTGATGATCGCACTATGAAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCACACTATAAAATTTTGATAACCT-CTTATG
* * * * *
2537 AAATTTTGAT-TCTGA-TCTATAAAATTTTGTTAACCTCTCTATTT
1 AAATTTTGATAAC-CACACTATAAAATTTTGATAACCTCT-TA-TG
* *
2581 AATTTTTGATAATCACACTATAAAATTTTG-TAACCTC-TATG
1 AAATTTTGATAACCACACTATAAAATTTTGATAACCTCTTATG
* * * * *
2622 AAATTTTTATAACCACACCATAAAACTGTGATGACCTCATTATG
1 AAATTTTGATAACCACACTATAAAATTTTGATAACCTC-TTATG
* *
2666 AGATTTTGATAACCACACTATGAAATTTTGATAACCTC--ATG
1 AAATTTTGATAACCACACTATAAAATTTTGATAACCTCTTATG
* * ** * * * *
2707 AAATTTCGAGAAGTACAATATGAAATTTTGATAATCTGATCTTTGTG
1 AAATTTTGATAACCACACTATAAAATTTTGATAA-C--CTC-TTATG
* * * * * * * * * *
2754 ATAGTTAGATGATCACTCTATGAGATTTTGATGACTTTCTTATG
1 AAATTTTGATAACCACACTATAAAATTTTGATAAC-CTCTTATG
* * *
2798 AAATTTTTATAACCATACTATAAAATTTTGATAAGCTCCTTATG
1 AAATTTTGATAACCACACTATAAAATTTTGATAACCT-CTTATG
2842 AAATT
1 AAATT
2847 GAGATTTTTA
Statistics
Matches: 232, Mismatches: 63, Indels: 30
0.71 0.19 0.09
Matches are distributed among these distances:
41 56 0.24
42 11 0.05
43 21 0.09
44 103 0.44
45 15 0.06
46 1 0.00
47 25 0.11
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (43 bp):
AAATTTTGATAACCACACTATAAAATTTTGATAACCTCTTATG
Found at i:2845 original size:22 final size:23
Alignment explanation
Indices: 2792--2846 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
2782 TGATGACTTT
*
2792 CTTATGAAATTTTTATAACCATA
1 CTTATGAAATTTTGATAACCATA
* * *
2815 C-TATAAAATTTTGATAAGC-TC
1 CTTATGAAATTTTGATAACCATA
2836 CTTATGAAATT
1 CTTATGAAATT
2847 GAGATTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.08
22 23 0.88
23 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (23 bp):
CTTATGAAATTTTGATAACCATA
Found at i:2896 original size:50 final size:50
Alignment explanation
Indices: 2800--2896 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
2790 TTCTTATGAA
* *
2800 ATTTTTATAACCATACTATAAAATTTTGATAAGCTCCTTATGAAATTGAG
1 ATTTTTATAACCATACTATAAAATTTTGATAAGCTCCCTATAAAATTGAG
* * **
2850 ATTTTTATAACC-TTCTAATGAAATTTTGATATTCTCCCTATAAAATT
1 ATTTTTATAACCATACT-ATAAAATTTTGATAAGCTCCCTATAAAATT
2897 TTAGTAACCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
49 3 0.08
50 37 0.93
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (50 bp):
ATTTTTATAACCATACTATAAAATTTTGATAAGCTCCCTATAAAATTGAG
Found at i:2990 original size:22 final size:22
Alignment explanation
Indices: 2953--3142 Score: 118
Period size: 22 Copynumber: 8.4 Consensus size: 22
2943 GATAACTATG
2953 TTGATAACC-TCTCTATGAAATT
1 TTGATAACCAT-TCTATGAAATT
* *
2975 TTGATTACCATACTATGAAATT
1 TTGATAACCATTCTATGAAATT
2997 TTGATAACC-TTCTCATGAAATT
1 TTGATAACCATTCT-ATGAAATT
* ** *
3019 TTAATCTCCCGATTCTATGAAGTT
1 TTGAT-AACC-ATTCTATGAAATT
* *
3043 TTGATAACCACTGTATGAAATT
1 TTGATAACCATTCTATGAAATT
* * *
3065 TTGGTAATC-TTATTATGAAATT
1 TTGATAACCATT-CTATGAAATT
* **
3087 TTGGTAACCAACCTCACCGTGAAATT
1 TTGATAACCATTCT-A---TGAAATT
* *
3113 TTGATAATC-TCCTTATGAAATT
1 TTGATAACCATTC-TATGAAATT
3135 TTGATAAC
1 TTGATAAC
3143 GTTAGTATAA
Statistics
Matches: 130, Mismatches: 26, Indels: 24
0.72 0.14 0.13
Matches are distributed among these distances:
21 4 0.03
22 87 0.67
23 6 0.05
24 11 0.08
25 7 0.05
26 15 0.12
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (22 bp):
TTGATAACCATTCTATGAAATT
Found at i:3050 original size:46 final size:44
Alignment explanation
Indices: 2953--3066 Score: 140
Period size: 46 Copynumber: 2.5 Consensus size: 44
2943 GATAACTATG
*
2953 TTGATAACCTCTCTATGAAATTTTGATTACCATACTATGAAATT
1 TTGATAACCTCTCTATGAAATTTTAATTACCATACTATGAAATT
* * *
2997 TTGATAACCT-TCTCATGAAATTTTAATCTCCCGATTCTATGAAGTT
1 TTGATAACCTCTCT-ATGAAATTTTAAT-TACC-ATACTATGAAATT
* *
3043 TTGATAACCACTGTATGAAATTTT
1 TTGATAACCTCTCTATGAAATTTT
3067 GGTAATCTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
43 3 0.05
44 22 0.37
45 3 0.05
46 30 0.50
47 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (44 bp):
TTGATAACCTCTCTATGAAATTTTAATTACCATACTATGAAATT
Found at i:6643 original size:16 final size:17
Alignment explanation
Indices: 6622--6663 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
6612 ATTGTTTGAC
6622 TAATTAGA-ATCAATTG
1 TAATTAGAGATCAATTG
*
6638 TAATTATTATGATCAATTG
1 TAATTA-GA-GATCAATTG
6657 TAATTAG
1 TAATTAG
6664 TTATTACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 6 0.29
17 1 0.05
19 14 0.67
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (17 bp):
TAATTAGAGATCAATTG
Found at i:6652 original size:19 final size:20
Alignment explanation
Indices: 6630--6667 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
6620 ACTAATTAGA
6630 ATCAATTGTAATTA-TTATG
1 ATCAATTGTAATTAGTTATG
6649 ATCAATTGTAATTAGTTAT
1 ATCAATTGTAATTAGTTAT
6668 TACCATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (20 bp):
ATCAATTGTAATTAGTTATG
Found at i:11414 original size:19 final size:18
Alignment explanation
Indices: 11381--11416 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11371 TTGAAATAAT
11381 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
11399 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
11417 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:19121 original size:19 final size:18
Alignment explanation
Indices: 19088--19123 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19078 TTGAAATAAT
19088 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
19106 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
19124 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:20994 original size:13 final size:12
Alignment explanation
Indices: 20976--21020 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
20966 ATTTTATTAC
20976 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
20989 TGTTTTATAAAT
1 TGTTTTATAAAT
*
21001 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
21015 TGTTTT
1 TGTTTT
21021 GGGTGCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:23824 original size:28 final size:28
Alignment explanation
Indices: 23766--23828 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
23756 TTAAGATGTC
* * **
23766 AAAATTACTATTTTACCCTTGGTCGGCT
1 AAAATTACCATTTTACCCCTGGTCGAAT
*
23794 AAAATTACCATTTTACCCCTGGTTGAAT
1 AAAATTACCATTTTACCCCTGGTCGAAT
23822 -AAATTAC
1 AAAATTAC
23829 AGTTTTGCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCTGGTCGAAT
Found at i:26148 original size:19 final size:19
Alignment explanation
Indices: 26120--26158 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
26110 TGTTTGACTA
26120 ATTAGAATCAATTGTAATT
1 ATTAGAATCAATTGTAATT
*
26139 ATTAGGATCAATTGTAATT
1 ATTAGAATCAATTGTAATT
26158 A
1 A
26159 GTTCTTACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (19 bp):
ATTAGAATCAATTGTAATT
Found at i:28088 original size:30 final size:31
Alignment explanation
Indices: 28031--28088 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
28021 CACCAACATA
28031 CTTCACACACACTAAAAAGTAGCCCAATATG
1 CTTCACACACACTAAAAAGTAGCCCAATATG
* * *
28062 CTTCACACCCACTCAAAAG-GGCCCAAT
1 CTTCACACACACTAAAAAGTAGCCCAAT
28089 GAAATGTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.17
Consensus pattern (31 bp):
CTTCACACACACTAAAAAGTAGCCCAATATG
Done.