Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014934.1 Corchorus olitorius cultivar O-4 contig14967, 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: 156235
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5618 original size:34 final size:34
Alignment explanation
Indices: 5575--5643 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
5565 AAACCTTCGA
5575 AGTGGGAAAGCAGGTGCATCATGCACATGATCAT
1 AGTGGGAAAGCAGGTGCATCATGCACATGATCAT
*
5609 AGTGGGAAAGCAGGTGCATCATGCGCATGATCAT
1 AGTGGGAAAGCAGGTGCATCATGCACATGATCAT
5643 A
1 A
5644 TGCATGGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.20
Consensus pattern (34 bp):
AGTGGGAAAGCAGGTGCATCATGCACATGATCAT
Found at i:10921 original size:2 final size:2
Alignment explanation
Indices: 10914--10958 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
10904 TCTCATTTTG
*
10914 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10956 CT C
1 CT C
10959 ATATCGGCGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:11903 original size:38 final size:39
Alignment explanation
Indices: 11837--11916 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
11827 ATTTGGCCAT
11837 AATGGATAAAGGAGTGATTATAAGATTGAAATATCAATGA
1 AATGGATAAAGGAG-GATTATAAGATTGAAATATCAATGA
11877 AATGGATAAAGGA-GATTATAAGATTGAAATATCAATGA
1 AATGGATAAAGGAGGATTATAAGATTGAAATATCAATGA
11915 AA
1 AA
11917 AGATGAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 27 0.68
40 13 0.32
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGGATAAAGGAGGATTATAAGATTGAAATATCAATGA
Found at i:15423 original size:16 final size:17
Alignment explanation
Indices: 15402--15437 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
15392 GATCACCCCT
*
15402 TTAA-GGGTGATCTGGA
1 TTAAGGGGTGATCAGGA
15418 TTAAGGGGTGATCAGGA
1 TTAAGGGGTGATCAGGA
15435 TTA
1 TTA
15438 CCACCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.28, C:0.06, G:0.36, T:0.31
Consensus pattern (17 bp):
TTAAGGGGTGATCAGGA
Found at i:15475 original size:17 final size:17
Alignment explanation
Indices: 15453--15501 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
15443 ATAAACCCAT
15453 GTAATCTTTGATCACCG
1 GTAATCTTTGATCACCG
*
15470 GTAATC-TTGCATCACTG
1 GTAATCTTTG-ATCACCG
* *
15487 GTGATCTTAGATCAC
1 GTAATCTTTGATCAC
15502 TAGTGATCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.11
17 22 0.81
18 2 0.07
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (17 bp):
GTAATCTTTGATCACCG
Found at i:15502 original size:17 final size:16
Alignment explanation
Indices: 15460--15510 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
15450 CATGTAATCT
* *
15460 TTGATCACCGGTAATC
1 TTGATCACTGGTGATC
15476 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
15493 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
15510 T
1 T
15511 GGGGGGTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:16264 original size:49 final size:50
Alignment explanation
Indices: 16121--16265 Score: 175
Period size: 53 Copynumber: 2.8 Consensus size: 50
16111 ATGCTCTATT
* *
16121 TGTATTGAGTTTTATCATCGATAATATGAGTTGCTTAATAGTACAATATCATA
1 TGTATTGAGTTTTATCAT-GATAATATGAGTTGCTTAACACTAC-A-ATCATA
* * * * *
16174 GGTTTTGAGCTTTATCATTGATAATATGAATTACTTAACACTAC-ATCATA
1 TGTATTGAGTTTTATCA-TGATAATATGAGTTGCTTAACACTACAATCATA
*
16224 TGTATTGAGTTTTATCATGATAATATGAGTTGTTTAACACTA
1 TGTATTGAGTTTTATCATGATAATATGAGTTGCTTAACACTA
16266 GAGCATAAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
49 22 0.28
50 20 0.26
53 35 0.45
54 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (50 bp):
TGTATTGAGTTTTATCATGATAATATGAGTTGCTTAACACTACAATCATA
Found at i:16953 original size:26 final size:26
Alignment explanation
Indices: 16921--16973 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
16911 GATCCGCATG
16921 TATAGTCTACTAAACTCTACGGTGTA
1 TATAGTCTACTAAACTCTACGGTGTA
16947 TATAGTCTACTAAACTCTACGGTGTA
1 TATAGTCTACTAAACTCTACGGTGTA
16973 T
1 T
16974 TGAATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (26 bp):
TATAGTCTACTAAACTCTACGGTGTA
Found at i:22040 original size:33 final size:33
Alignment explanation
Indices: 21998--22078 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
21988 TGTCTAAACA
*
21998 CTAGCACGTGTACAGTTGCTCGAATATGTTTGT
1 CTAGCACGTGTACAGTTGATCGAATATGTTTGT
22031 CTAGCACGTGTACAGTTGATCGAATATGTTTGT
1 CTAGCACGTGTACAGTTGATCGAATATGTTTGT
22064 CTAGCACGTGTACAG
1 CTAGCACGTGTACAG
22079 ATTAAGATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (33 bp):
CTAGCACGTGTACAGTTGATCGAATATGTTTGT
Found at i:23969 original size:33 final size:33
Alignment explanation
Indices: 23927--23994 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
23917 ACCTTAGCTC
23927 TTCAAATAATTATTGACTCCTTATTTTTGTTTG
1 TTCAAATAATTATTGACTCCTTATTTTTGTTTG
*
23960 TTCAAATAATTATTGACTCCTTGTTTTTGTTTG
1 TTCAAATAATTATTGACTCCTTATTTTTGTTTG
23993 TT
1 TT
23995 TAGGTCATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (33 bp):
TTCAAATAATTATTGACTCCTTATTTTTGTTTG
Found at i:24676 original size:17 final size:18
Alignment explanation
Indices: 24649--24682 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
24639 TTTAATGCTG
*
24649 ATTATTCAGAAGGAGAAA
1 ATTATTCAGAAAGAGAAA
24667 ATTA-TCAGAAAGAGAA
1 ATTATTCAGAAAGAGAA
24683 GAGTTCAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21
Consensus pattern (18 bp):
ATTATTCAGAAAGAGAAA
Found at i:28079 original size:8 final size:8
Alignment explanation
Indices: 28066--28091 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28056 TTCTCGGCCG
28066 AAGGCCCA
1 AAGGCCCA
28074 AAGGCCCA
1 AAGGCCCA
28082 AAGGCCCA
1 AAGGCCCA
28090 AA
1 AA
28092 AATCTAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.35, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGGCCCA
Found at i:39187 original size:85 final size:85
Alignment explanation
Indices: 39084--39253 Score: 261
Period size: 85 Copynumber: 2.0 Consensus size: 85
39074 TGGGTGAATT
*** *
39084 TACCAACATGGATGGCTGCGTATGTAAGGT-CTCGAATCTGAGACCTACTTAAACTGGAACAAGT
1 TACCAACATGGATGGCTGCGTACACAA-GTCCTCGAATCTGAGACCTACTTAAACTGAAACAAGT
* *
39148 CGTTTACTACTTGATTTAATC
65 CGCTTACTACTTGATTCAATC
*
39169 TACCAACATGGATGGCTGCGTACACAAGTCCTCGAATCTGAGACCTACTTAAACTGAAATAAGTC
1 TACCAACATGGATGGCTGCGTACACAAGTCCTCGAATCTGAGACCTACTTAAACTGAAACAAGTC
39234 GCTTACTACTTGATTCAATC
66 GCTTACTACTTGATTCAATC
39254 CCTGATAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 2 0.03
85 75 0.97
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (85 bp):
TACCAACATGGATGGCTGCGTACACAAGTCCTCGAATCTGAGACCTACTTAAACTGAAACAAGTC
GCTTACTACTTGATTCAATC
Found at i:43748 original size:30 final size:30
Alignment explanation
Indices: 43714--43772 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
43704 TTCCTTTTTT
43714 TTTTTGCCAATTATTTGTACTTTTATTTCC
1 TTTTTGCCAATTATTTGTACTTTTATTTCC
*
43744 TTTTTTCCAATTATTTGTACTTTTATTTC
1 TTTTTGCCAATTATTTGTACTTTTATTTC
43773 ATTCTCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTTTGCCAATTATTTGTACTTTTATTTCC
Found at i:46051 original size:18 final size:19
Alignment explanation
Indices: 46028--46065 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
46018 GAGGTGGACG
46028 ACGGAGGAGGCGA-CGGCT
1 ACGGAGGAGGCGATCGGCT
*
46046 ACGGAGGAGGTGATCGGCT
1 ACGGAGGAGGCGATCGGCT
46065 A
1 A
46066 TGGAATGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.24, C:0.18, G:0.47, T:0.11
Consensus pattern (19 bp):
ACGGAGGAGGCGATCGGCT
Found at i:50214 original size:87 final size:87
Alignment explanation
Indices: 50068--50234 Score: 291
Period size: 87 Copynumber: 1.9 Consensus size: 87
50058 AAATTTAAGT
*
50068 CCTTGCATGTTCTGGAAAATGACGGTGACGTAGTCCCTGAGAAGCGCCACCCAATTCTGCACCAA
1 CCTTGCATGTTCTGGAAAATGACGGTGACATAGTCCCTGAGAAGCGCCACCCAATTCTGCACCAA
50133 CCTTAGAATGAGTATTTCCACA
66 CCTTAGAATGAGTATTTCCACA
* *
50155 CCTTGCATGTTCTGGAATAA-GACGGTGACATAGTTCCTGAGACGCGCCACCCAATTCTGCACCA
1 CCTTGCATGTTCTGGAA-AATGACGGTGACATAGTCCCTGAGAAGCGCCACCCAATTCTGCACCA
50219 ACCTTAGAATGAGTAT
65 ACCTTAGAATGAGTAT
50235 ATATTTCCAC
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
87 74 0.97
88 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (87 bp):
CCTTGCATGTTCTGGAAAATGACGGTGACATAGTCCCTGAGAAGCGCCACCCAATTCTGCACCAA
CCTTAGAATGAGTATTTCCACA
Found at i:71592 original size:19 final size:19
Alignment explanation
Indices: 71568--71625 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
71558 CTGTTTAGCA
*
71568 ACTGTACATATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
71587 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATT--AC
*
71608 ATTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
71626 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:84732 original size:13 final size:13
Alignment explanation
Indices: 84711--84741 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
84701 AAGTTAAATT
*
84711 TATACTCATTATA
1 TATATTCATTATA
84724 TATATTCATTATA
1 TATATTCATTATA
84737 TATAT
1 TATAT
84742 CTTGATTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATTCATTATA
Found at i:100237 original size:13 final size:13
Alignment explanation
Indices: 100219--100244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100209 TTCAGTAGAC
100219 AAGCATTTTCTTT
1 AAGCATTTTCTTT
100232 AAGCATTTTCTTT
1 AAGCATTTTCTTT
100245 CTTTCTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
AAGCATTTTCTTT
Found at i:119236 original size:7 final size:7
Alignment explanation
Indices: 119224--119248 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
119214 TATGACGTGC
119224 TTGCAAA
1 TTGCAAA
119231 TTGCAAA
1 TTGCAAA
119238 TTGCAAA
1 TTGCAAA
119245 TTGC
1 TTGC
119249 CTTCGTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (7 bp):
TTGCAAA
Found at i:135710 original size:125 final size:126
Alignment explanation
Indices: 135487--135740 Score: 456
Period size: 125 Copynumber: 2.0 Consensus size: 126
135477 AATCTAAAGC
*
135487 TTCATTGGTTGGTCCTGGATCAGTTTTGAATAATCAGCATACAGAGCATTTAACTTATCAGTATC
1 TTCATTGGTTGGTCCTGGATCAGTTTTGAATAATCAGCATACAAAGCATTTAACTTATCAGTATC
** *
135552 AGGTTGCTCAGGAATATCATCACTCTCCATCAGGCAGCTGAGGGCCAACAAATGATCTGAA
66 AGGTTGCAAAGGAATATCATCACTCTCCATCAGGCAGCTGAGGGCCAAAAAATGATCTGAA
135613 TTCATTGGTTGGTCCTGGATCAGTTTTGAA-AATCAGCATACAAAGCATTTAACTTATCAGTATC
1 TTCATTGGTTGGTCCTGGATCAGTTTTGAATAATCAGCATACAAAGCATTTAACTTATCAGTATC
*
135677 AGGTTGCAAAGGAATATCATCACTCTCCATCAGGCGGCTGAGGGCCAAAAAATGATCTGAA
66 AGGTTGCAAAGGAATATCATCACTCTCCATCAGGCAGCTGAGGGCCAAAAAATGATCTGAA
135738 TTC
1 TTC
135741 TGTTCTAGTG
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
125 93 0.76
126 30 0.24
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (126 bp):
TTCATTGGTTGGTCCTGGATCAGTTTTGAATAATCAGCATACAAAGCATTTAACTTATCAGTATC
AGGTTGCAAAGGAATATCATCACTCTCCATCAGGCAGCTGAGGGCCAAAAAATGATCTGAA
Done.