Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011966.1 Corchorus olitorius cultivar O-4 contig11999, 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: 18968
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Found at i:893 original size:30 final size:30
Alignment explanation
Indices: 857--955 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 30
847 CTGATCAAAT
857 AGTTAATCATGAGATGGCAGTCGAACTTAA
1 AGTTAATCATGAGATGGCAGTCGAACTTAA
* * * *
887 AGTTAATCATGAGAATCGGATATTTCTGATC-AAA
1 AGTTAATCATGAG-AT-GG-CA-GTC-GAACTTAA
*
921 TAGTTAATCAAGAGATGGCAGTCGAACTTAA
1 -AGTTAATCATGAGATGGCAGTCGAACTTAA
952 AGTT
1 AGTT
956 GTCACTCTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
30 20 0.38
31 6 0.11
32 3 0.06
33 3 0.06
34 6 0.11
35 15 0.28
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (30 bp):
AGTTAATCATGAGATGGCAGTCGAACTTAA
Found at i:915 original size:65 final size:65
Alignment explanation
Indices: 834--955 Score: 235
Period size: 65 Copynumber: 1.9 Consensus size: 65
824 TCACCTGTGG
*
834 GAATCGGATATTTCTGATCAAATAGTTAATCATGAGATGGCAGTCGAACTTAAAGTTAATCATGA
1 GAATCGGATATTTCTGATCAAATAGTTAATCAAGAGATGGCAGTCGAACTTAAAGTTAATCATGA
899 GAATCGGATATTTCTGATCAAATAGTTAATCAAGAGATGGCAGTCGAACTTAAAGTT
1 GAATCGGATATTTCTGATCAAATAGTTAATCAAGAGATGGCAGTCGAACTTAAAGTT
956 GTCACTCTTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (65 bp):
GAATCGGATATTTCTGATCAAATAGTTAATCAAGAGATGGCAGTCGAACTTAAAGTTAATCATGA
Found at i:4854 original size:31 final size:31
Alignment explanation
Indices: 4819--4890 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
4809 TAAATTATTG
*
4819 CAAATTAAAACAAAT-TAAGCATTAAATTAAA
1 CAAATTAAAA-AAATGCAAGCATTAAATTAAA
* ** *
4850 CAAATCATTAAAATGCAAGCTTTAAATTAAA
1 CAAATTAAAAAAATGCAAGCATTAAATTAAA
4881 CAAATTAAAA
1 CAAATTAAAA
4891 GCTGATAGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGCAAGCATTAAATTAAA
Found at i:5049 original size:15 final size:15
Alignment explanation
Indices: 5029--5058 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5019 AATTTCATAT
5029 ATTTAATTAATTATA
1 ATTTAATTAATTATA
*
5044 ATTTAATTAGTTATA
1 ATTTAATTAATTATA
5059 CTACATGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTAATTAATTATA
Found at i:6676 original size:41 final size:42
Alignment explanation
Indices: 6573--6679 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 42
6563 TCATTTGATT
*
6573 ATTTGATTAGTGTTAGTGATTAAGTATTGATTAGTAATATTAGA
1 ATTTGATTAATGTTAGTGA-TAAGTATTGATTAG-AATATTAGA
** * * **
6617 AAGTGA-TAA-GTTAATGATAAGTATTGATTA-ACTATTATC
1 ATTTGATTAATGTTAGTGATAAGTATTGATTAGAATATTAGA
6656 ATTTGATTAATGTTAGTGATAAGT
1 ATTTGATTAATGTTAGTGATAAGT
6680 TAATATTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
39 10 0.20
40 3 0.06
41 25 0.49
42 7 0.14
43 2 0.04
44 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (42 bp):
ATTTGATTAATGTTAGTGATAAGTATTGATTAGAATATTAGA
Found at i:7247 original size:21 final size:21
Alignment explanation
Indices: 7186--7239 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
7176 TGAGTCCATC
*
7186 TATTTTT-G-TGAGCCCAGAT
1 TATTTTTAGTTGAGCCCAAAT
* *
7205 TGTTTTTGGTTGAGCCCAAAT
1 TATTTTTAGTTGAGCCCAAAT
7226 TATTTTTAGTTGAG
1 TATTTTTAGTTGAG
7240 TCTAAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 6 0.21
20 1 0.03
21 22 0.76
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.46
Consensus pattern (21 bp):
TATTTTTAGTTGAGCCCAAAT
Found at i:7586 original size:16 final size:17
Alignment explanation
Indices: 7567--7605 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
7557 TTGGTTTTTT
7567 TTTCTCAT-TTTTTCTC
1 TTTCTCATATTTTTCTC
*
7583 TTTCTTATCATTTTTCTC
1 TTTCTCAT-ATTTTTCTC
7601 TTTCT
1 TTTCT
7606 TTCTTCCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
18 13 0.65
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCTCATATTTTTCTC
Found at i:7597 original size:32 final size:31
Alignment explanation
Indices: 7537--7597 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
7527 TTTGCATGCA
* **
7537 TTCTATTTTCTCTCTTTCTTTTGGTTTTTTT
1 TTCTATTTTCTCTCTTTCTTATCATTTTTTT
*
7568 TTCTCATTTTTTCTCTTTCTTATCATTTTT
1 TTCT-ATTTTCTCTCTTTCTTATCATTTTT
7598 CTCTTTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (31 bp):
TTCTATTTTCTCTCTTTCTTATCATTTTTTT
Found at i:10643 original size:104 final size:105
Alignment explanation
Indices: 10518--10727 Score: 404
Period size: 104 Copynumber: 2.0 Consensus size: 105
10508 AATTTCATCT
10518 AATTACACCCGAAAGCCATCAAAACCTCTCAAAATCAACAAAAAACAGAATAACCCAACCAATCA
1 AATTACACCCGAAAGCCATCAAAACCTCTCAAAATCAACAAAAAACAGAATAACCCAACCAATCA
*
10583 ACAT-AAAAACCCACAAATATTCAACAAAAATCCACAAAC
66 ACATAAAAAACCCACAAACATTCAACAAAAATCCACAAAC
10622 AATTACACCCGAAAGCCATCAAAACCTCTCAAAATCAACAAAAAACAGAATAACCCAACCAATCA
1 AATTACACCCGAAAGCCATCAAAACCTCTCAAAATCAACAAAAAACAGAATAACCCAACCAATCA
10687 ACATAAAAAACCCACAAACATTCAACAAAAATCCACAAAC
66 ACATAAAAAACCCACAAACATTCAACAAAAATCCACAAAC
10727 A
1 A
10728 TTCAACAAAA
Statistics
Matches: 104, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 69 0.66
105 35 0.34
ACGTcount: A:0.55, C:0.30, G:0.03, T:0.12
Consensus pattern (105 bp):
AATTACACCCGAAAGCCATCAAAACCTCTCAAAATCAACAAAAAACAGAATAACCCAACCAATCA
ACATAAAAAACCCACAAACATTCAACAAAAATCCACAAAC
Found at i:10722 original size:21 final size:21
Alignment explanation
Indices: 10692--10777 Score: 127
Period size: 21 Copynumber: 4.0 Consensus size: 21
10682 AATCAACATA
*
10692 AAAAACCCACAAACATTCAAC
1 AAAAATCCACAAACATTCAAC
10713 AAAAATCCACAAACATTCAAC
1 AAAAATCCACAAACATTCAAC
*
10734 AAAAATCCACAAACATTCCAAG
1 AAAAATCCACAAACATT-CAAC
* *
10756 ATAAATCCACAAACAATCAAC
1 AAAAATCCACAAACATTCAAC
10777 A
1 A
10778 TTAAAAATCA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 41 0.69
22 18 0.31
ACGTcount: A:0.57, C:0.29, G:0.01, T:0.13
Consensus pattern (21 bp):
AAAAATCCACAAACATTCAAC
Found at i:10753 original size:11 final size:11
Alignment explanation
Indices: 10698--10753 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
10688 CATAAAAAAC
10698 CCACAAACATT
1 CCACAAACATT
* *
10709 CAACAAA-AAT
1 CCACAAACATT
10719 CCACAAACATT
1 CCACAAACATT
* *
10730 CAACAAA-AAT
1 CCACAAACATT
10740 CCACAAACATT
1 CCACAAACATT
10751 CCA
1 CCA
10754 AGATAAATCC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 16 0.46
11 19 0.54
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (11 bp):
CCACAAACATT
Found at i:10763 original size:43 final size:42
Alignment explanation
Indices: 10692--10777 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
10682 AATCAACATA
*
10692 AAAAACCCACAAACATTCAACAAAAATCCACAAACATTCAAC
1 AAAAACCCACAAACATTCAACAAAAATCCACAAACAATCAAC
* * *
10734 AAAAATCCACAAACATTCCAAGATAAATCCACAAACAATCAAC
1 AAAAACCCACAAACATT-CAACAAAAATCCACAAACAATCAAC
10777 A
1 A
10778 TTAAAAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.57, C:0.29, G:0.01, T:0.13
Consensus pattern (42 bp):
AAAAACCCACAAACATTCAACAAAAATCCACAAACAATCAAC
Found at i:10773 original size:11 final size:11
Alignment explanation
Indices: 10698--10773 Score: 61
Period size: 11 Copynumber: 7.1 Consensus size: 11
10688 CATAAAAAAC
*
10698 CCACAAACATT
1 CCACAAACAAT
*
10709 CAACAAA-AAT
1 CCACAAACAAT
*
10719 CCACAAACATT
1 CCACAAACAAT
*
10730 CAACAAA-AAT
1 CCACAAACAAT
*
10740 CCACAAACATT
1 CCACAAACAAT
10751 CCA-AGATA-AAT
1 CCACA-A-ACAAT
10762 CCACAAACAAT
1 CCACAAACAAT
10773 C
1 C
10774 AACATTAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
10 18 0.36
11 30 0.60
12 2 0.04
ACGTcount: A:0.54, C:0.30, G:0.01, T:0.14
Consensus pattern (11 bp):
CCACAAACAAT
Found at i:14114 original size:42 final size:42
Alignment explanation
Indices: 14067--14151 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
14057 CTCGATGAAA
* *
14067 TGGATTTGAGAGGAATGGCCGAAGGCTTGTTATTCCTCGTTG
1 TGGATTTGAGAGAAATGGCCAAAGGCTTGTTATTCCTCGTTG
14109 TGGATTTGAGAGAAATGGCCAAAGGCTTGTTATTCCTCGTTG
1 TGGATTTGAGAGAAATGGCCAAAGGCTTGTTATTCCTCGTTG
14151 T
1 T
14152 CAGATTTGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (42 bp):
TGGATTTGAGAGAAATGGCCAAAGGCTTGTTATTCCTCGTTG
Found at i:14352 original size:18 final size:18
Alignment explanation
Indices: 14326--14363 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
14316 GCTTTGTTGA
14326 TGGAAAAGAACTTTGCTT
1 TGGAAAAGAACTTTGCTT
*
14344 TGGAGAAGAACTTTGCTT
1 TGGAAAAGAACTTTGCTT
14362 TG
1 TG
14364 TTGTTGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (18 bp):
TGGAAAAGAACTTTGCTT
Found at i:14405 original size:34 final size:36
Alignment explanation
Indices: 14336--14415 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 36
14326 TGGAAAAGAA
* *
14336 CTTTGCTT--TGGAGAAGAACTTTGCTTTGTTGTTG
1 CTTTGCTTGATGGAGAAGAACTTTGCTTAGATGTTG
14370 CTTTG-TTGATGGAGAA-AACTTTGCTTCAGAT-TTG
1 CTTTGCTTGATGGAGAAGAACTTTGCTT-AGATGTTG
14404 CTTTGCTTGATG
1 CTTTGCTTGATG
14416 CTTGCCTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 2 0.05
34 23 0.57
35 15 0.38
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.45
Consensus pattern (36 bp):
CTTTGCTTGATGGAGAAGAACTTTGCTTAGATGTTG
Found at i:15805 original size:1 final size:1
Alignment explanation
Indices: 15799--15824 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
15789 ACAATGTAAG
15799 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
15825 GCATAAGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16445 original size:14 final size:14
Alignment explanation
Indices: 16426--16453 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16416 CCCTGCTTTC
16426 TTTTGAAGCTCCCT
1 TTTTGAAGCTCCCT
16440 TTTTGAAGCTCCCT
1 TTTTGAAGCTCCCT
16454 GCTTTGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (14 bp):
TTTTGAAGCTCCCT
Found at i:16691 original size:45 final size:43
Alignment explanation
Indices: 16583--16720 Score: 143
Period size: 45 Copynumber: 3.0 Consensus size: 43
16573 GCATCGATTA
*
16583 TTTATCGCCCTCT-TATCGGCATCTTGGCGGAGTTGATTTTTTT
1 TTTATCGCCCTCTGCATCGGCATCTTGGCGG-GTTGATTTTTTT
* *
16626 TTTATCGCCCTCTACCTCTGCATCGGCATTTTGGCAGGGCTGATTTTGTTT
1 TTTATCG----C--CCTCTGCATCGGCATCTTGGC-GGGTTGATTTT-TTT
*
16677 TTTATCGCCCTCTGCATCGGCATCTTGTCGGGGTTGATTTTTTT
1 TTTATCGCCCTCTGCATCGGCATCTTGGC-GGGTTGATTTTTTT
16721 ATCACCCTCT
Statistics
Matches: 79, Mismatches: 7, Indels: 17
0.77 0.07 0.17
Matches are distributed among these distances:
43 7 0.09
44 3 0.04
45 29 0.37
47 2 0.03
49 5 0.06
50 21 0.27
51 12 0.15
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (43 bp):
TTTATCGCCCTCTGCATCGGCATCTTGGCGGGTTGATTTTTTT
Found at i:16700 original size:51 final size:50
Alignment explanation
Indices: 16597--16700 Score: 138
Period size: 51 Copynumber: 2.1 Consensus size: 50
16587 TCGCCCTCTT
* * *
16597 ATCGGCATCTTGGCGGAGTTGATTTTTTTTTTATCGCCCTCTACCTCTGC
1 ATCGGCATCTTGGCGGAGCTGATTTTTTTTTTATCGCCCTCTACATCGGC
* *
16647 ATCGGCATTTTGGCAGG-GCTGATTTTGTTTTTTATCGCCCTCTGCATCGGC
1 ATCGGCATCTTGGC-GGAGCTGATTTT-TTTTTTATCGCCCTCTACATCGGC
16698 ATC
1 ATC
16701 TTGTCGGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
50 21 0.45
51 26 0.55
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (50 bp):
ATCGGCATCTTGGCGGAGCTGATTTTTTTTTTATCGCCCTCTACATCGGC
Found at i:16781 original size:46 final size:47
Alignment explanation
Indices: 16597--16827 Score: 229
Period size: 47 Copynumber: 4.9 Consensus size: 47
16587 TCGCCCTCTT
* * *
16597 ATCGGCATCTTGGCGGAGTTGATTTTTTTTTTATCGCCCTCTACCTCTGC
1 ATCGGCTTCTTGGCGGGGTTGA---TTTTTTTATCACCCTCTACCTCTGC
* * * * **
16647 ATCGGCATT-TTGGCAGGGCTGATTTTGTTTTTTA---TCGCCCTCTGC
1 ATCGGC-TTCTTGGCGGGGTTGATTTT-TTTATCACCCTCTACCTCTGC
* * *
16692 ATCGGCATCTTGTCGGGGTTGATTTTTTTATCACCCTCTACCTCTAC
1 ATCGGCTTCTTGGCGGGGTTGATTTTTTTATCACCCTCTACCTCTGC
* * *
16739 ATAGGCTTCTTGGCGGGGTTG-GTTATTTATCACCCTCTACCTCTGC
1 ATCGGCTTCTTGGCGGGGTTGATTTTTTTATCACCCTCTACCTCTGC
* *
16785 ATCGACTTCTTGGCGGGGTTGATTTTTTTATCGCCCTCTACCT
1 ATCGGCTTCTTGGCGGGGTTGATTTTTTTATCACCCTCTACCT
16828 TTTGCTTCAG
Statistics
Matches: 145, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
44 6 0.04
45 29 0.20
46 41 0.28
47 48 0.33
48 4 0.03
50 16 0.11
51 1 0.01
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.41
Consensus pattern (47 bp):
ATCGGCTTCTTGGCGGGGTTGATTTTTTTATCACCCTCTACCTCTGC
Done.