Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018969.1 Corchorus olitorius cultivar O-4 contig19002, 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: 87205
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3483 original size:50 final size:50
Alignment explanation
Indices: 3408--3507 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
3398 GGCATCTGGG
3408 CCTAAGCACAAGAGGGATGGATTAGGCTTCTGGGAAGCTTAGTGAACCTA
1 CCTAAGCACAAGAGGGATGGATTAGGCTTCTGGGAAGCTTAGTGAACCTA
3458 CCTAAGCACAAGAGGGATGGATTAGGCTTCTGGGAAGCTTAGTGAACCTA
1 CCTAAGCACAAGAGGGATGGATTAGGCTTCTGGGAAGCTTAGTGAACCTA
3508 TGCCGAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (50 bp):
CCTAAGCACAAGAGGGATGGATTAGGCTTCTGGGAAGCTTAGTGAACCTA
Found at i:14152 original size:11 final size:11
Alignment explanation
Indices: 14136--14160 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14126 AGAAAATTGT
14136 TTGTTTTTGGA
1 TTGTTTTTGGA
14147 TTGTTTTTGGA
1 TTGTTTTTGGA
14158 TTG
1 TTG
14161 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:16707 original size:22 final size:22
Alignment explanation
Indices: 16662--16714 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
16652 TGCTTTCTAA
**
16662 TTAATTGTTTTCTTTAATTTTC
1 TTAATTGTTTTCTTTAATAGTC
* *
16684 TTGATTGTTTTCTTTGATAGTC
1 TTAATTGTTTTCTTTAATAGTC
16706 TTAATTGTT
1 TTAATTGTT
16715 AGTTTGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (22 bp):
TTAATTGTTTTCTTTAATAGTC
Found at i:41662 original size:24 final size:24
Alignment explanation
Indices: 41630--41679 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
41620 AAAATTGAAC
*
41630 AAAAAAAAAAAACAAACA-AGTCA
1 AAAAAAAAAAAACAAACACAGCCA
41653 AAAAAAAAAAAACAAACACAGCCA
1 AAAAAAAAAAAACAAACACAGCCA
41677 AAA
1 AAA
41680 TCACCATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.78, C:0.16, G:0.04, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAAACAAACACAGCCA
Found at i:41926 original size:92 final size:90
Alignment explanation
Indices: 41757--41929 Score: 215
Period size: 92 Copynumber: 1.9 Consensus size: 90
41747 CCCGAAAAAA
* * ***
41757 TGCTTCCACCTCCAAGTATTTGACCAAATAAAAAAAGATTTACTTTTTCCACTTAAACTTTCCAG
1 TGCTTCCACCTCCAAGCATTTGA-CAAATAAAAAAAGATTTACCTTTTCCAAAAAAACTTTCCAG
41822 AAACCCAAAAAAAAAAGGAAATGAAAT
65 AAACCC-AAAAAAAAAGGAAATGAAAT
*
41849 TGCTTCCACCTCCAAGCATTTGA-AAATAAAAAAAAGGATTTCCCTTTTCCAAAAAAAAGACTTT
1 TGCTTCCACCTCCAAGCATTTGACAAAT-AAAAAAA-GATTTACCTTTTCC--AAAAAA-ACTTT
41913 CCAGAAA-CCAAAAAAAA
61 CCAGAAACCCAAAAAAAA
41930 TGTCAATTAG
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
90 4 0.06
91 7 0.10
92 34 0.49
93 8 0.11
94 5 0.07
95 12 0.17
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.24
Consensus pattern (90 bp):
TGCTTCCACCTCCAAGCATTTGACAAATAAAAAAAGATTTACCTTTTCCAAAAAAACTTTCCAGA
AACCCAAAAAAAAAGGAAATGAAAT
Found at i:41962 original size:9 final size:8
Alignment explanation
Indices: 41948--41977 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
41938 AGTTTCCTTT
41948 AAAAAAAC
1 AAAAAAAC
41956 GAAAAAAAC
1 -AAAAAAAC
41965 AAAAAAAC
1 AAAAAAAC
41973 AAAAA
1 AAAAA
41978 CAAAAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:42605 original size:15 final size:16
Alignment explanation
Indices: 42585--42614 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42575 GTTTTGTAAG
42585 TATTTA-TTTAGTTTA
1 TATTTATTTTAGTTTA
42600 TATTTATTTTAGTTT
1 TATTTATTTTAGTTT
42615 TTAAATATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TATTTATTTTAGTTTA
Found at i:45724 original size:31 final size:28
Alignment explanation
Indices: 45661--45728 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
45651 GGGACAAAAA
* **
45661 TTTTTTCTTTTTTTTTATGACGCAAATT
1 TTTTTTTTTTTTTTTTATGACGCAAACG
45689 TTTTTTTTATTTTTTTTATGACGCAGAAACG
1 TTTTTTTT-TTTTTTTTATGACGC--AAACG
45720 TTTTTTTTT
1 TTTTTTTTT
45729 ATCGACGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.21
29 15 0.44
30 1 0.03
31 11 0.32
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (28 bp):
TTTTTTTTTTTTTTTTATGACGCAAACG
Found at i:45728 original size:23 final size:23
Alignment explanation
Indices: 45698--45741 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
45688 TTTTTTTTTA
45698 TTTTTTTTAT-GACGCAGAAACGT
1 TTTTTTTTATCGACGCA-AAACGT
45721 TTTTTTTTATCGACGCAAAAC
1 TTTTTTTTATCGACGCAAAAC
45742 TGAAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (23 bp):
TTTTTTTTATCGACGCAAAACGT
Found at i:46953 original size:11 final size:11
Alignment explanation
Indices: 46937--46962 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
46927 CCTTGCCTAA
46937 AAAACTAGAAG
1 AAAACTAGAAG
46948 AAAACTAGAAG
1 AAAACTAGAAG
46959 AAAA
1 AAAA
46963 TAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:49085 original size:29 final size:31
Alignment explanation
Indices: 49053--49119 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
49043 ACGCAATTTG
*
49053 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACATTACGAAAAGCAAGCAATTAA
*
49082 GGATATAACATTACGAAAAGCGAGCAATTAA
1 GGATATAACATTACGAAAAGCAAGCAATTAA
*
49113 GAATATA
1 GGATATA
49120 GTCAGTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (31 bp):
GGATATAACATTACGAAAAGCAAGCAATTAA
Found at i:52752 original size:13 final size:13
Alignment explanation
Indices: 52706--52752 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
52696 TCATGCACCC
*
52706 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
52720 AAAACCATTT-AT
1 AAAACAATTTAAT
*
52732 AAACCAATTTAAT
1 AAAACAATTTAAT
52745 AAAACAAT
1 AAAACAAT
52753 AATAAAATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
12 9 0.33
13 9 0.33
14 9 0.33
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:53184 original size:28 final size:28
Alignment explanation
Indices: 53131--53205 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
53121 TCCGGCGTTT
* * *
53131 AAGGGCAAAACTGCAA-TTTAGTCAACC
1 AAGGGCAAAACAGTAATTTTAGCCAACC
* * **
53158 AGGGGTAAAATGGTAATTTTAGCCAACC
1 AAGGGCAAAACAGTAATTTTAGCCAACC
53186 AAGGGCAAAACAGTAATTTT
1 AAGGGCAAAACAGTAATTTT
53206 GACATCTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 11 0.30
28 26 0.70
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (28 bp):
AAGGGCAAAACAGTAATTTTAGCCAACC
Found at i:54062 original size:28 final size:28
Alignment explanation
Indices: 54036--54090 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
54026 TGTAATTTAG
* *
54036 CATCACAAGGGTGATATAGTAATTTTACC
1 CATC-CAAGGGTAAAATAGTAATTTTACC
*
54065 CATCTAAGGGTAAAATAGTAATTTTA
1 CATCCAAGGGTAAAATAGTAATTTTA
54091 ACTCTTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (28 bp):
CATCCAAGGGTAAAATAGTAATTTTACC
Found at i:54169 original size:15 final size:16
Alignment explanation
Indices: 54145--54185 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
54135 TATATGTATA
54145 TTTTTTTTCTTA-TTC
1 TTTTTTTTCTTATTTC
*
54160 TTTTTCTTC-TATTTC
1 TTTTTTTTCTTATTTC
54175 TTTTTTTTCTT
1 TTTTTTTTCTT
54186 TTCCAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTTATTTC
Found at i:55889 original size:31 final size:29
Alignment explanation
Indices: 55834--55894 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 29
55824 CGATAAAAAG
*
55834 TTAAAATAACCCAGAAAAGTTCAACAAAT
1 TTAAAATAACCCAGAAAAGCTCAACAAAT
55863 TTAAAATAACCCAAGAAAAAGCTCAACAAAT
1 TTAAAATAACCC-AG-AAAAGCTCAACAAAT
55894 T
1 T
55895 ATGTTCTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 12 0.41
30 2 0.07
31 15 0.52
ACGTcount: A:0.56, C:0.18, G:0.07, T:0.20
Consensus pattern (29 bp):
TTAAAATAACCCAGAAAAGCTCAACAAAT
Found at i:68525 original size:31 final size:30
Alignment explanation
Indices: 68457--68541 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 30
68447 TTGAAATAAA
****
68457 AAACGTTATATCCTTAATTGCTTG-TTTTG
1 AAACGTTATATCCTTAATTGCTTGCGGCAG
*
68486 TAACGTTATATCCTTAATTGCTTGCGGCAG
1 AAACGTTATATCCTTAATTGCTTGCGGCAG
*
68516 CAAACGTTATATCCTAAATTGCTTGC
1 -AAACGTTATATCCTTAATTGCTTGC
68542 TTATCATCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.49
30 1 0.02
31 23 0.49
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (30 bp):
AAACGTTATATCCTTAATTGCTTGCGGCAG
Found at i:70966 original size:22 final size:22
Alignment explanation
Indices: 70941--70987 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
70931 GTGTTTTAGG
* *
70941 TTCTTCTTCGTCTCTTTCCTCT
1 TTCTTATTCGGCTCTTTCCTCT
*
70963 TTCTTATTCGGCTTTTTCCTCT
1 TTCTTATTCGGCTCTTTCCTCT
70985 TTC
1 TTC
70988 GTTGCTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.02, C:0.32, G:0.06, T:0.60
Consensus pattern (22 bp):
TTCTTATTCGGCTCTTTCCTCT
Found at i:71383 original size:87 final size:87
Alignment explanation
Indices: 71237--71413 Score: 327
Period size: 87 Copynumber: 2.0 Consensus size: 87
71227 AACTCGCTGG
71237 ATTTGCAAACAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATAATCTGAG
1 ATTTGCAAACAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATAATCTGAG
71302 TAAAACGTATTTGTGATGAAGT
66 TAAAACGTATTTGTGATGAAGT
* * *
71324 ATTTGCAAGCAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATAATTTGGG
1 ATTTGCAAACAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATAATCTGAG
71389 TAAAACGTATTTGTGATGAAGT
66 TAAAACGTATTTGTGATGAAGT
71411 ATT
1 ATT
71414 ACTAACTTAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.38
Consensus pattern (87 bp):
ATTTGCAAACAATTTGGGTATGATTTGCTTGCTAAGATCTAAACAATTAGTTTAAATAATCTGAG
TAAAACGTATTTGTGATGAAGT
Found at i:73799 original size:29 final size:27
Alignment explanation
Indices: 73740--73803 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
73730 AAAGCTCCAA
*
73740 TCTTCAATTCTTTCCTCTTCAAATAAT
1 TCTTCAATTCTTTCCTCTTCAAATAAG
*
73767 TCTTCAATGTC-TTCCAATCTTCAATTAAG
1 TCTTCAAT-TCTTTCC--TCTTCAAATAAG
73796 TCTTCAAT
1 TCTTCAAT
73804 AAGTCTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 12 0.38
28 2 0.06
29 18 0.56
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (27 bp):
TCTTCAATTCTTTCCTCTTCAAATAAG
Found at i:73808 original size:11 final size:12
Alignment explanation
Indices: 73784--73813 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
73774 TGTCTTCCAA
73784 TCTTCAATTAAG
1 TCTTCAATTAAG
73796 TCTTCAA-TAAG
1 TCTTCAATTAAG
73807 TCTTCAA
1 TCTTCAA
73814 ACACGAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (12 bp):
TCTTCAATTAAG
Found at i:77145 original size:29 final size:30
Alignment explanation
Indices: 77113--77174 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
77103 TTAAAGTTCC
*
77113 AATCTTCAAATAATTCTTCAAT-GTCTTCA
1 AATCTTCAAATAAGTCTTCAATAGTCTTCA
77142 AATCTTCAAATAAGTCTTCAATGAGTCTTCA
1 AATCTTCAAATAAGTCTTCAAT-AGTCTTCA
77173 AA
1 AA
77175 CACGAACTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 21 0.70
31 9 0.30
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (30 bp):
AATCTTCAAATAAGTCTTCAATAGTCTTCA
Found at i:83684 original size:29 final size:30
Alignment explanation
Indices: 83647--83706 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
83637 AATTCTTTCC
* *
83647 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
83676 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
83707 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Done.