Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009771.1 Corchorus capsularis cultivar CVL-1 contig09792, 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: 37044
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1758 original size:76 final size:74
Alignment explanation
Indices: 1677--1822 Score: 274
Period size: 76 Copynumber: 1.9 Consensus size: 74
1667 TTTCTTGGGA
1677 ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAGAATATACAAAAAAAATTGTTGTATATATAT
1 ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAGAATATAC-AAAAAAA-TGTTGTATATATAT
1742 AAAAAAAGATT
64 AAAAAAAGATT
1753 ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAGAATATACAAAAAAATGTTGTATATATATAA
1 ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAGAATATACAAAAAAATGTTGTATATATATAA
1818 AAAAA
66 AAAAA
1823 TTATATATAT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 21 0.30
75 7 0.10
76 42 0.60
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.29
Consensus pattern (74 bp):
ATTTCCAAAATTTTAGTAAGTCAGAAAATACGAAGAATATACAAAAAAATGTTGTATATATATAA
AAAAAGATT
Found at i:1798 original size:36 final size:36
Alignment explanation
Indices: 1682--1798 Score: 82
Period size: 36 Copynumber: 3.1 Consensus size: 36
1672 TGGGAATTTC
1682 CAAAATTTTAGTAAGTCAGAAAATACGAAGAATATA
1 CAAAATTTTAGTAAGTCAGAAAATACGAAGAATATA
* * * *
1718 CAAAAAAAATTGTT-GTATA-T-ATATAAA-A-AAAGATTATTTC
1 C----AAAATT-TTAGTA-AGTCAGA-AAATACGAAGA--ATATA
1758 CAAAATTTTAGTAAGTCAGAAAATACGAAGAATATA
1 CAAAATTTTAGTAAGTCAGAAAATACGAAGAATATA
1794 CAAAA
1 CAAAA
1799 AAATGTTGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 28
0.62 0.08 0.29
Matches are distributed among these distances:
35 3 0.05
36 22 0.37
37 3 0.05
38 8 0.14
39 3 0.05
40 17 0.29
41 3 0.05
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (36 bp):
CAAAATTTTAGTAAGTCAGAAAATACGAAGAATATA
Found at i:1831 original size:21 final size:21
Alignment explanation
Indices: 1789--1839 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1779 AATACGAAGA
* *
1789 ATATACAAAAAAATGTTGTAT
1 ATATATAAAAAAATGTTATAT
1810 ATATATAAAAAAAT-TATATAT
1 ATATATAAAAAAATGT-TATAT
1831 ATATATAAA
1 ATATATAAA
1840 GTTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
ATATATAAAAAAATGTTATAT
Found at i:6607 original size:132 final size:132
Alignment explanation
Indices: 6369--6625 Score: 401
Period size: 132 Copynumber: 1.9 Consensus size: 132
6359 TGAAAAAAGT
6369 TTTTAACTAATTTGTTTCTCCTCAAGCTTGAAGATTATGCACCAAAACAATCTTCAAAAACAACA
1 TTTTAACTAATTTGTTTCTCCTCAAGCTTGAAGATTATGCACCAAAACAATCTTCAAAAACAACA
* * *
6434 TATGCATGCTAAGCCCAGCATCTTTATGGCAGGTGGTGGTAGAGTCTGCCTTAGTTGAACATGTA
66 TATGCATGCTAAGCCCAGCATCTTTATGGCAGCTGGTGGTAGAGTCGGCCTT-GTTCAACATGTA
6499 AGC
130 AGC
* * *
6502 TTTTAACTAATTTGTTTCTCCT-AAGTTTGAAGATTATGCACCAAAACCATTTTCAAAAACAACA
1 TTTTAACTAATTTGTTTCTCCTCAAGCTTGAAGATTATGCACCAAAACAATCTTCAAAAACAACA
** *
6566 TATGCATGCTAAG-CCATGTGTCTTTATGGCAGCTTGTGGTAGAGTCGGCCTTGTTCAACA
66 TATGCATGCTAAGCCCA-GCATCTTTATGGCAGCTGGTGGTAGAGTCGGCCTTGTTCAACA
6626 CCAAAACGCA
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 10 0.09
132 82 0.72
133 22 0.19
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (132 bp):
TTTTAACTAATTTGTTTCTCCTCAAGCTTGAAGATTATGCACCAAAACAATCTTCAAAAACAACA
TATGCATGCTAAGCCCAGCATCTTTATGGCAGCTGGTGGTAGAGTCGGCCTTGTTCAACATGTAA
GC
Found at i:14429 original size:21 final size:21
Alignment explanation
Indices: 14405--14448 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
14395 CTCAAAAAAT
14405 ATGTCTAATCTTAATCACCCA
1 ATGTCTAATCTTAATCACCCA
14426 ATGTCTAATCTTAATCACCCA
1 ATGTCTAATCTTAATCACCCA
14447 AT
1 AT
14449 CATCTCGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (21 bp):
ATGTCTAATCTTAATCACCCA
Found at i:17065 original size:61 final size:61
Alignment explanation
Indices: 16992--17110 Score: 220
Period size: 61 Copynumber: 2.0 Consensus size: 61
16982 CAAATTTTCA
*
16992 AAAAATAAGATTTACCTAGTATGCCATGAAATTTAGAAATGATTGTGGTTTAAATAAGTTG
1 AAAAATAAGATTTACCAAGTATGCCATGAAATTTAGAAATGATTGTGGTTTAAATAAGTTG
*
17053 AAAATTAAGATTTACCAAGTATGCCATGAAATTTAGAAATGATTGTGGTTTAAATAAG
1 AAAAATAAGATTTACCAAGTATGCCATGAAATTTAGAAATGATTGTGGTTTAAATAAG
17111 GGGCAAGTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.34
Consensus pattern (61 bp):
AAAAATAAGATTTACCAAGTATGCCATGAAATTTAGAAATGATTGTGGTTTAAATAAGTTG
Found at i:29067 original size:21 final size:21
Alignment explanation
Indices: 29042--29083 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29032 GATATCTTCA
*
29042 CAAGCTTTCGGCTCTTCTAGC
1 CAAGCTGTCGGCTCTTCTAGC
*
29063 CAAGCTGTGGGCTCTTCTAGC
1 CAAGCTGTCGGCTCTTCTAGC
29084 AAGACCCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.31, G:0.24, T:0.31
Consensus pattern (21 bp):
CAAGCTGTCGGCTCTTCTAGC
Found at i:31633 original size:23 final size:22
Alignment explanation
Indices: 31600--31649 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
31590 TGGAATGGCC
31600 TTGC-GATATCTCAT-TTATTTT
1 TTGCAGATATCTCATGTTA-TTT
31621 TTGCAGATGATCTCATGTTATTT
1 TTGCAGAT-ATCTCATGTTATTT
31644 TTGCAG
1 TTGCAG
31650 GCTTCGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.15
22 3 0.12
23 16 0.62
24 3 0.12
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (22 bp):
TTGCAGATATCTCATGTTATTT
Found at i:33993 original size:26 final size:26
Alignment explanation
Indices: 33951--34015 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 26
33941 ATAAATTATT
*
33951 AAAAAAACATATTTATTTTTTTGACAGTAA
1 AAAAAAACATATTTA--TTTATG--AGTAA
*
33981 AAAAAAACATATTTATTTATGATTAA
1 AAAAAAACATATTTATTTATGAGTAA
34007 AAAAAAACA
1 AAAAAAACA
34016 CACTAACTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 13 0.39
28 5 0.15
30 15 0.45
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (26 bp):
AAAAAAACATATTTATTTATGAGTAA
Found at i:34411 original size:161 final size:161
Alignment explanation
Indices: 34144--34480 Score: 626
Period size: 161 Copynumber: 2.1 Consensus size: 161
34134 GTCTATACCA
34144 TATA-TATAAATATAAAATTAAATTATGGCTTTTATTTTTTTTAATTAGAGGCACTAATTTAGGA
1 TATACTATAAATATAAAATTAAATTATGGCTTTTATTTTTTTTAATTAGAGGCACTAATTTAGGA
34208 GTTTAGGTCATCTATCTCATTTGAAAATATAACACT-AAAAAA-AGGGGAAGGGCATGAAAATGA
66 GTTTAGGTCATCTATCTCATTTGAAAATATAACACTAAAAAAAGAGGGGAAGGGCATGAAAATGA
34271 CTTATCTTTACTCCAAAAGATGGACTACTAT
131 CTTATCTTTACTCCAAAAGATGGACTACTAT
34302 TATACTATAAATATAAAATTAAATTATGGCTTTTATTTATTTTTTAATTAGAGGCACTAATTTAG
1 TATACTATAAATATAAAATTAAATTATGGCTTTTA-TT-TTTTTTAATTAGAGGCACTAATTTAG
34367 GAGTTTAGGTCATCTATCTCATTTGAAAATATAACACTAAAAAAAGAGGGGAAGGGCATGAAAAT
64 GAGTTTAGGTCATCTATCTCATTTGAAAATATAACACTAAAAAAAGAGGGGAAGGGCATGAAAAT
34432 GACTTATCTTTACTCCAAAAGATGGACTACTAT
129 GACTTATCTTTACTCCAAAAGATGGACTACTAT
34465 TATACTATAATATATA
1 TATACTATAA-ATATA
34481 TATATTCTCT
Statistics
Matches: 173, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
158 4 0.02
159 30 0.17
160 2 0.01
161 64 0.37
162 6 0.03
163 62 0.36
164 5 0.03
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (161 bp):
TATACTATAAATATAAAATTAAATTATGGCTTTTATTTTTTTTAATTAGAGGCACTAATTTAGGA
GTTTAGGTCATCTATCTCATTTGAAAATATAACACTAAAAAAAGAGGGGAAGGGCATGAAAATGA
CTTATCTTTACTCCAAAAGATGGACTACTAT
Found at i:35912 original size:28 final size:28
Alignment explanation
Indices: 35877--35952 Score: 152
Period size: 28 Copynumber: 2.7 Consensus size: 28
35867 AAAAAAATTT
35877 AAGACTCGTATCTTAATTTCATCAAAAA
1 AAGACTCGTATCTTAATTTCATCAAAAA
35905 AAGACTCGTATCTTAATTTCATCAAAAA
1 AAGACTCGTATCTTAATTTCATCAAAAA
35933 AAGACTCGTATCTTAATTTC
1 AAGACTCGTATCTTAATTTC
35953 TAGATTTAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (28 bp):
AAGACTCGTATCTTAATTTCATCAAAAA
Found at i:37027 original size:2 final size:2
Alignment explanation
Indices: 37020--37044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37010 AATCATTTTC
37020 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.