Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017169.1 Corchorus olitorius cultivar O-4 contig17202, 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: 108228
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--44 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42 TA T
1 TA T
45 TATTACATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48 original size:10 final size:11
Alignment explanation
Indices: 1--58 Score: 72
Period size: 10 Copynumber: 5.7 Consensus size: 11
1 TATATA-TATA
1 TATATATTATA
11 TATATA-TATA
1 TATATATTATA
21 TATATA-TATA
1 TATATATTATA
31 TATATATTATA
1 TATATATTATA
*
42 TAT-TATTACA
1 TATATATTATA
52 TAT-TATT
1 TATATATT
59 TGAAACACCC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
10 39 0.85
11 7 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATATTATA
Found at i:323 original size:57 final size:57
Alignment explanation
Indices: 233--347 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
223 ATCCGTTTCT
* *
233 TTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTCATAATAAATCATATCCCCCCTATCTATACTTAATTATTC
* *
290 TTTCACACAATAAATGTCATAATAAATCTTATCCCCCTTATCTATACTTAATTATTC
1 TTTCACACAATAAATGTCATAATAAATCATATCCCCCCTATCTATACTTAATTATTC
347 T
1 T
348 ATAAAATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (57 bp):
TTTCACACAATAAATGTCATAATAAATCATATCCCCCCTATCTATACTTAATTATTC
Found at i:480 original size:21 final size:21
Alignment explanation
Indices: 414--481 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
404 AAGAATCAGG
*
414 ATTTGAGTTGAGTATTTCTTA
1 ATTTAAGTTGAGTATTTCTTA
** * *
435 ATTTACA-AAGAAT-TTTCTATG
1 ATTTA-AGTTGAGTATTTCT-TA
456 ATTTAAGTTGAGTATTTCTTA
1 ATTTAAGTTGAGTATTTCTTA
477 ATTTA
1 ATTTA
482 CAGAGAATTT
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
20 6 0.18
21 22 0.65
22 6 0.18
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (21 bp):
ATTTAAGTTGAGTATTTCTTA
Found at i:1658 original size:56 final size:57
Alignment explanation
Indices: 1572--1686 Score: 205
Period size: 56 Copynumber: 2.0 Consensus size: 57
1562 TATCCATTTC
*
1572 CTTTCACACAATAAATGTTATAATAAATCCTATC-CCCCTATCTTTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATT
*
1628 CTTTCATACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATT
1685 CT
1 CT
1687 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 33 0.59
57 23 0.41
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (57 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATT
Found at i:1816 original size:42 final size:42
Alignment explanation
Indices: 1752--1832 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
1742 TAAGGATCCG
*
1752 GATTTGAGTTCAGTATTTCTTAATTTACAAAAAATTTTCTTT
1 GATTTGAGTTCAGTATTCCTTAATTTACAAAAAATTTTCTTT
* * *
1794 GATTTGAGTTGAGTATTCCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTCAGTATTCCTTAATTTACAAAAAATTTTC
1833 AAGACTTAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTCAGTATTCCTTAATTTACAAAAAATTTTCTTT
Found at i:4870 original size:12 final size:12
Alignment explanation
Indices: 4833--4878 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
4823 AATTATTAAG
4833 TATATATATTACA
1 TATATAT-TTACA
* *
4846 TATATAGTAACA
1 TATATATTTACA
4858 TATATATTTACA
1 TATATATTTACA
4870 TAGTATATT
1 TA-TATATT
4879 GTATATTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (12 bp):
TATATATTTACA
Found at i:9970 original size:21 final size:20
Alignment explanation
Indices: 9909--9971 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
9899 TTGACACTGT
9909 TTAGCAACTGTACAAATGAGA
1 TTAG-AACTGTACAAATGAGA
* * *
9930 TTA-CACTGTACAGATTAGA
1 TTAGAACTGTACAAATGAGA
*
9949 TTAGGAACCGTACAAATGAGA
1 TTA-GAACTGTACAAATGAGA
9970 TT
1 TT
9972 GCTAGAGCAG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (20 bp):
TTAGAACTGTACAAATGAGA
Found at i:17998 original size:23 final size:23
Alignment explanation
Indices: 17972--18017 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17962 GGGAGGAAAA
17972 TAAATATATT-TACACAAGATTTT
1 TAAATATATTGTA-ACAAGATTTT
* *
17995 TAAATGTATTGTAAGAAGATTTT
1 TAAATATATTGTAACAAGATTTT
18018 GGTTTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
TAAATATATTGTAACAAGATTTT
Found at i:29760 original size:14 final size:16
Alignment explanation
Indices: 29731--29765 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29721 GCAACCTCCC
29731 CACCCCACCCACCCCA
1 CACCCCACCCACCCCA
29747 CACCCC-CCCACCCACA
1 CACCCCACCCACCC-CA
29763 CAC
1 CAC
29766 ACAAATCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.26, C:0.74, G:0.00, T:0.00
Consensus pattern (16 bp):
CACCCCACCCACCCCA
Found at i:36094 original size:17 final size:18
Alignment explanation
Indices: 36067--36101 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
36057 GTGAAAAATC
36067 ATATATATAGAATTAATA
1 ATATATATAGAATTAATA
*
36085 ATAT-TATAGATTTAATA
1 ATATATATAGAATTAATA
36102 CTCATGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
ATATATATAGAATTAATA
Found at i:43599 original size:5 final size:5
Alignment explanation
Indices: 43589--43622 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
43579 CTGTCTTCTA
* *
43589 TTTTC TTTTC TTTTC CTTTC TTTCC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
43623 TCTCTTCCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:68576 original size:21 final size:21
Alignment explanation
Indices: 68550--68589 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
68540 CGCTGCTCTA
*
68550 ATAATCTCATCTGTACAGTAC
1 ATAATCTAATCTGTACAGTAC
68571 ATAATCTAATCTGTACAGT
1 ATAATCTAATCTGTACAGT
68590 GTAATTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
ATAATCTAATCTGTACAGTAC
Found at i:69408 original size:6 final size:6
Alignment explanation
Indices: 69399--69436 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
69389 GAATTAAATT
69399 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
69437 TTCTAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:72522 original size:60 final size:59
Alignment explanation
Indices: 72430--72545 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 59
72420 ATATTGTATG
* * **
72430 ATCCACCAATAGTGTGAAGCACCCAACAATCTGAAAGTAGTGGCATATCCTATCCAATA
1 ATCCACCAAAAGTGTGAAGCACCCAACAATCTGAAAGCAGTGGCATAGACTATCCAATA
*
72489 ATCCACCAAAAGGTGTGGAGCACCCAACAATCTGAAAGCAGTGGCATAGACTATCCA
1 ATCCACCAAAA-GTGTGAAGCACCCAACAATCTGAAAGCAGTGGCATAGACTATCCA
72546 CAAACACAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 10 0.20
60 41 0.80
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (59 bp):
ATCCACCAAAAGTGTGAAGCACCCAACAATCTGAAAGCAGTGGCATAGACTATCCAATA
Found at i:76846 original size:43 final size:45
Alignment explanation
Indices: 76799--76890 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 45
76789 TTGAGACTTG
*
76799 AATCCAGGACCTCACAG-G-CACAGTAAACCTACCAGTTGAGCTA
1 AATCCAGGACCTCACAGAGCCACAGTAAACCTACCAATTGAGCTA
*
76842 AATCCAGGACCTCACAGTACAGCCACGGTAAACCTACCAATTGAGCTA
1 AATCCAGGACCTCACAG---AGCCACAGTAAACCTACCAATTGAGCTA
76890 A
1 A
76891 TAACTTGAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 17 0.40
47 1 0.02
48 24 0.57
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.16
Consensus pattern (45 bp):
AATCCAGGACCTCACAGAGCCACAGTAAACCTACCAATTGAGCTA
Found at i:78260 original size:30 final size:30
Alignment explanation
Indices: 78203--78260 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
78193 ACACCATTTT
* *
78203 TTTCTTCTTTTTTGTTAATTTTTCTCTTGC
1 TTTCTTCTTTTTTCTTAATTTTCCTCTTGC
*
78233 TTTCTTCTTTTCTTCTT-CTTTTCCTCTT
1 TTTCTTCTTTT-TTCTTAATTTTCCTCTT
78261 TTTGCAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.71
Consensus pattern (30 bp):
TTTCTTCTTTTTTCTTAATTTTCCTCTTGC
Found at i:79195 original size:13 final size:13
Alignment explanation
Indices: 79173--79208 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
79163 AAAATTCTAT
79173 TTGACCCTCCAAA
1 TTGACCCTCCAAA
* *
79186 TTGTCCCTCCAAC
1 TTGACCCTCCAAA
79199 TTGACCCTCC
1 TTGACCCTCC
79209 TAATAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.44, G:0.08, T:0.28
Consensus pattern (13 bp):
TTGACCCTCCAAA
Found at i:79253 original size:41 final size:41
Alignment explanation
Indices: 79207--79288 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
79197 ACTTGACCCT
* *
79207 CCTAATAATTAAGGAAACAAATTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGGAAACAAATTAAATCAAGATTTAGCCCC
** *
79248 CCTAATAATTAAGGTGAGAAATTAAATCAAGATTTAGCCCC
1 CCTAATAATTAAGGAAACAAATTAAATCAAGATTTAGCCCC
79289 TAGTTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (41 bp):
CCTAATAATTAAGGAAACAAATTAAATCAAGATTTAGCCCC
Found at i:79895 original size:15 final size:15
Alignment explanation
Indices: 79875--79904 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
79865 TCCAATTATA
79875 CATGAATTTAGCCAC
1 CATGAATTTAGCCAC
79890 CATGAATTTAGCCAC
1 CATGAATTTAGCCAC
79905 ACCCGAACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
CATGAATTTAGCCAC
Found at i:83442 original size:1 final size:1
Alignment explanation
Indices: 83436--83460 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
83426 TTGATATTGG
83436 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
83461 ACATTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:83898 original size:25 final size:25
Alignment explanation
Indices: 83864--83914 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
83854 CAGAATAAGA
83864 ACACTAAACTATTATTTACTCTCAT
1 ACACTAAACTATTATTTACTCTCAT
83889 ACACTAAACTATTATTTACTCTCAT
1 ACACTAAACTATTATTTACTCTCAT
83914 A
1 A
83915 TCATTTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (25 bp):
ACACTAAACTATTATTTACTCTCAT
Found at i:87327 original size:2 final size:2
Alignment explanation
Indices: 87287--87312 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
87277 TACGTGTGTC
87287 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
87313 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94685 original size:51 final size:50
Alignment explanation
Indices: 94584--94685 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 50
94574 GTTCTTCATA
* * **
94584 TTTTCCTTGTTTCAATCTTGTCTTAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTCAATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
94634 TTTTCTCTTGTTTCAATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTTCAATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
94685 T
1 T
94686 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 7 0.16
51 37 0.84
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTCAATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:98117 original size:27 final size:27
Alignment explanation
Indices: 98087--98139 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
98077 AGCCAAAAAC
* *
98087 TGAAAATGA-GATGAAGCTTCCAACAAT
1 TGAAAATGATG-TAAAGCCTCCAACAAT
98114 TGAAAATGATGTAAAGCCTCCAACAA
1 TGAAAATGATGTAAAGCCTCCAACAA
98140 AATCATCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (27 bp):
TGAAAATGATGTAAAGCCTCCAACAAT
Found at i:98173 original size:33 final size:33
Alignment explanation
Indices: 98131--98236 Score: 158
Period size: 33 Copynumber: 3.2 Consensus size: 33
98121 GATGTAAAGC
*
98131 CTCCAACAAAATCATCACCGGAGGATAAGCAAT
1 CTCCAACAAAACCATCACCGGAGGATAAGCAAT
*
98164 CTCCAACAAAACCATCACCGGAGGATAAACAAT
1 CTCCAACAAAACCATCACCGGAGGATAAGCAAT
* * * *
98197 CTCCAACAAAACCATCACCAGAGGAAAAGAAAC
1 CTCCAACAAAACCATCACCGGAGGATAAGCAAT
98230 CTCCAAC
1 CTCCAAC
98237 TCTGCCACTG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.11
Consensus pattern (33 bp):
CTCCAACAAAACCATCACCGGAGGATAAGCAAT
Found at i:100862 original size:22 final size:22
Alignment explanation
Indices: 100830--100871 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
100820 TGCGTCCGAG
*
100830 CCATGGTCAGGTCGCGATCGAA
1 CCATGGCCAGGTCGCGATCGAA
*
100852 CCATGGCCAGGTTGCGATCG
1 CCATGGCCAGGTCGCGATCG
100872 TCACGCGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (22 bp):
CCATGGCCAGGTCGCGATCGAA
Found at i:108134 original size:29 final size:28
Alignment explanation
Indices: 108090--108145 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
108080 TTCTTCAAAC
*
108090 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
108118 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
108146 GTGGAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Done.