Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011125.1 Corchorus capsularis cultivar CVL-1 contig11146, 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: 59602
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:863 original size:29 final size:29
Alignment explanation
Indices: 812--892 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 29
802 GCTCATTTAA
* * *
812 CTCCACTTCAGGGACTAAATTGCATAT-TT
1 CTCCACTTGAGGGACCAATTTGC-TATGTT
841 -TCACACTTGAGGGACCAATTTGCTATGTT
1 CTC-CACTTGAGGGACCAATTTGCTATGTT
870 CGCTCCACTTGAGGGACCAATTT
1 --CTCCACTTGAGGGACCAATTT
893 TGTACTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 5 0.11
29 19 0.43
31 18 0.41
32 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (29 bp):
CTCCACTTGAGGGACCAATTTGCTATGTT
Found at i:13624 original size:129 final size:129
Alignment explanation
Indices: 13394--13650 Score: 334
Period size: 129 Copynumber: 2.0 Consensus size: 129
13384 GTTCAATGCC
* * *
13394 CTCCCAATCAGGATCTGACACGATTCGATTCCGGATTAGTCGATACTCAATGTGATAGACTTTAA
1 CTCCCAATCAGGATCTAACACGATTCAATTCCGGATTAGTCGATACTCAATGTGATAAACTTTAA
* * * * * *
13459 GAGAACTTACTCTCAATCAGTACCTGACATGGTTCGACTCCAGATTAGTCGATACTCAATGTGT
66 GAGAACTTACTCCCAATCAGGACCTAACACGATTCGACTCCAGATTAGTCGAGACTCAATGTGT
* * * * *
13523 CTCCCAATCGGGGTCTAATACGGTTCAATTCCGGATTAGTTGATACTCAATGTGATAAACTTTAA
1 CTCCCAATCAGGATCTAACACGATTCAATTCCGGATTAGTCGATACTCAATGTGATAAACTTTAA
* * ** * *
13588 GAGAACTTCCTCCCAATCGGGGTCTAACACGATTCGATTCCGGATTAGTCGAGACTCAATGTG
66 GAGAACTTACTCCCAATCAGGACCTAACACGATTCGACTCCAGATTAGTCGAGACTCAATGTG
13651 GCCACTGGAT
Statistics
Matches: 108, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
129 108 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (129 bp):
CTCCCAATCAGGATCTAACACGATTCAATTCCGGATTAGTCGATACTCAATGTGATAAACTTTAA
GAGAACTTACTCCCAATCAGGACCTAACACGATTCGACTCCAGATTAGTCGAGACTCAATGTGT
Found at i:15902 original size:12 final size:11
Alignment explanation
Indices: 15880--15915 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
15870 CAGATGAACC
15880 TCTTTTTTCTT
1 TCTTTTTTCTT
15891 TCTTTCTTTCTT
1 TCTTT-TTTCTT
*
15903 TCTTTTTTTTT
1 TCTTTTTTCTT
15914 TC
1 TC
15916 ATGTGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:24604 original size:20 final size:21
Alignment explanation
Indices: 24566--24604 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
24556 ATTTTTGTGC
24566 TTTTCTTTTCCTGACTGCAAA
1 TTTTCTTTTCCTGACTGCAAA
* *
24587 TTTT-TTTTCTTGATTGCA
1 TTTTCTTTTCCTGACTGCA
24605 GGTTACAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.56
Consensus pattern (21 bp):
TTTTCTTTTCCTGACTGCAAA
Found at i:25897 original size:12 final size:12
Alignment explanation
Indices: 25880--25904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25870 AGAAGACGCA
25880 TGCTTTTCTTTT
1 TGCTTTTCTTTT
25892 TGCTTTTCTTTT
1 TGCTTTTCTTTT
25904 T
1 T
25905 ACTACTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (12 bp):
TGCTTTTCTTTT
Found at i:36824 original size:15 final size:16
Alignment explanation
Indices: 36794--36826 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
36784 AACAACAACA
36794 ATTTTCTTTCTCTTTT
1 ATTTTCTTTCTCTTTT
*
36810 ATTTT-TTTTTCTTTT
1 ATTTTCTTTCTCTTTT
36825 AT
1 AT
36827 CATTTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTCTTTCTCTTTT
Found at i:40451 original size:3 final size:3
Alignment explanation
Indices: 40443--40499 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
40433 ACAATAATGC
*
40443 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40491 ATT ATT ATT
1 ATT ATT ATT
40500 CAAAAGGGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:41247 original size:10 final size:10
Alignment explanation
Indices: 41232--41270 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
41222 AGGCAAACTA
41232 GAAAACAGAG
1 GAAAACAGAG
41242 GAAAACAGAG
1 GAAAACAGAG
*
41252 GAGAAAAATGAG
1 GA-AAACA-GAG
41264 GAAAACA
1 GAAAACA
41271 AGAGAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 12 0.48
11 8 0.32
12 5 0.20
ACGTcount: A:0.62, C:0.08, G:0.28, T:0.03
Consensus pattern (10 bp):
GAAAACAGAG
Found at i:52807 original size:75 final size:75
Alignment explanation
Indices: 52722--52916 Score: 311
Period size: 75 Copynumber: 2.6 Consensus size: 75
52712 TTTAATCATG
* *
52722 GTAAGTAGAAATGTTGGGCCTTGGTTCAAAATCATTAGCAAATGATTTCTTCTCCCCCTTAAGAT
1 GTAAGCAGAAATGTTGGGCCTTGGTTCAAAATCATTAGCAAATGATTTCTTCTCCCCCTTAACAT
52787 CACCATCACC
66 CACCATCACC
* *
52797 GTAAGCAGAAATGTTGGGCCTTGGTTCAAAATC-TTCAACAAATGATTTCTTCTCCCCTTTAACA
1 GTAAGCAGAAATGTTGGGCCTTGGTTCAAAATCATT-AGCAAATGATTTCTTCTCCCCCTTAACA
52861 TCACCATCACC
65 TCACCATCACC
* * *
52872 ATAAGCAGAAATATTGGGCCTTGGTTCAAAATCATCAGCAAATGA
1 GTAAGCAGAAATGTTGGGCCTTGGTTCAAAATCATTAGCAAATGA
52917 CTTCCCTCCT
Statistics
Matches: 110, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
74 2 0.02
75 107 0.97
76 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (75 bp):
GTAAGCAGAAATGTTGGGCCTTGGTTCAAAATCATTAGCAAATGATTTCTTCTCCCCCTTAACAT
CACCATCACC
Found at i:58041 original size:66 final size:66
Alignment explanation
Indices: 57935--58259 Score: 456
Period size: 66 Copynumber: 4.9 Consensus size: 66
57925 TCATCATTCA
* * * * *
57935 TCAGTATACACTGAAGCGCTTGGTCTGGGCTCGAAATCTTTCA-CAAATGATTTAAGACCAGCAT
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTT-AGCAAATGATTTAAGACCAACAT
57999 CG
65 CG
58001 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATC
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATC
58066 G
66 G
*
58067 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATC
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATC
58132 G
66 G
*
58133 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATC
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATC
58198 G
66 G
* * * ** *** * **
58199 T-TGCTATATGCCGTTGGGTTTGGCCTCGGCTCGAAATCTTTCGTGAATGATTTAAGACCAA
1 TCAG-TATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAA
58260 TACTATCGGT
Statistics
Matches: 239, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
65 2 0.01
66 237 0.99
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (66 bp):
TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATC
G
Found at i:58120 original size:132 final size:132
Alignment explanation
Indices: 57876--58199 Score: 470
Period size: 132 Copynumber: 2.4 Consensus size: 132
57866 TCTATATTGT
* * * *
57876 AGCACTTGGTCTCGGCTCAAAATCTTTCGCAAATGATTTAAGATCAATATCATCATTCATCAGTA
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGA-C-----CAACA-TCGTCAGTA
* * * * *
57941 TACACTGAAGCGCTTGGTCTGGGCTCGAAATCTTTCACAAATGATTTAAGACCAGCATCGTCAGT
59 TACACTGAAGCACTTGGCCTCGGCTCAAAATCTTTCACAAATGATTTAAGACCAACATCGTCAGT
58006 ATACGCTGA
124 ATACGCTGA
* *
58015 AGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACGCTG
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACACTG
58080 AAGCACTTGGCCTCGGCTCAAAATCTTT-AGCAAATGATTTAAGACCAACATCGTCAGTATACGC
66 AAGCACTTGGCCTCGGCTCAAAATCTTTCA-CAAATGATTTAAGACCAACATCGTCAGTATACGC
58144 TGA
130 TGA
58147 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGT
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGT
58200 TGCTATATGC
Statistics
Matches: 172, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
131 1 0.01
132 126 0.73
133 4 0.02
138 1 0.01
139 40 0.23
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (132 bp):
AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACACTG
AAGCACTTGGCCTCGGCTCAAAATCTTTCACAAATGATTTAAGACCAACATCGTCAGTATACGCT
GA
Found at i:58222 original size:132 final size:132
Alignment explanation
Indices: 57876--58259 Score: 466
Period size: 132 Copynumber: 2.9 Consensus size: 132
57866 TCTATATTGT
* * * *
57876 AGCACTTGGTCTCGGCTCAAAATCTTTCGCAAATGATTTAAGATCAATATCATCATTCATCAGTA
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGA-C-----CAACA-TCGTCAGTA
* * * * * *
57941 TACACTGAAGCGCTTGGTCTGGGCTCGAAATCTTTCA-CAAATGATTTAAGACCAGCATCGTCAG
59 TACGCCGAAGCACTTGGCCTCGGCTCGAAATCTTT-AGCAAATGATTTAAGACCAACATCGTCAG
58005 TATACGCTGA
123 TATACGCTGA
* *
58015 AGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACGCTG
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACGCCG
*
58080 AAGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACGCT
66 AAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACGCT
58145 GA
131 GA
* *
58147 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGT-TGCTATATGCC
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAG-TATACGCC
** *** * **
58211 GTTGGGTTTGGCCTCGGCTCGAAATCTTTCGTGAATGATTTAAGACCAA
65 GAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAA
58260 TACTATCGGT
Statistics
Matches: 219, Mismatches: 24, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
131 2 0.01
132 172 0.79
133 4 0.02
138 1 0.00
139 40 0.18
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (132 bp):
AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACGCCG
AAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATACGCT
GA
Found at i:58224 original size:198 final size:201
Alignment explanation
Indices: 57876--58259 Score: 490
Period size: 198 Copynumber: 1.9 Consensus size: 201
57866 TCTATATTGT
* * *
57876 AGCACTTGGTCTCGGCTCAAAATCTTTCGCAAATGATTTAAGATCAATATCATCATTCATCAGTA
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGATC---A-CAACATTCATCAGTA
* * * * *
57941 TACACTGAAGCGCTTGGTCTGGGCTCGAAATCTTTCACAAATGATTTAAGACCAGCATCGTCAGT
62 TACACTGAAGCACTTGGCCTCGGCTCAAAATCTTTCACAAATGATTTAAGACCAACATCGTCAGT
*
58006 ATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAG
127 ATACGCCGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAG
58071 TATACGCTGA
192 TATACGCTGA
* *
58081 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGA-C-CAACA-TCGTCAGTATACG
1 AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGATCACAACATTCATCAGTATACA
*
58143 CTGAAGCACTTGGCCTCGGCTCAAAATCTTT-AGCAAATGATTTAAGACCAACATCGT-TGCTAT
66 CTGAAGCACTTGGCCTCGGCTCAAAATCTTTCA-CAAATGATTTAAGACCAACATCGTCAG-TAT
* ** *** * **
58206 ATGCCGTTGGGTTTGGCCTCGGCTCGAAATCTTTCGTGAATGATTTAAGACCAA
129 ACGCCGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAA
58260 TACTATCGGT
Statistics
Matches: 156, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
197 2 0.01
198 108 0.69
199 4 0.03
204 1 0.01
205 41 0.26
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (201 bp):
AGCACTTGGCCTCGGCTCAAAATCTTTAGCAAATGATTTAAGATCACAACATTCATCAGTATACA
CTGAAGCACTTGGCCTCGGCTCAAAATCTTTCACAAATGATTTAAGACCAACATCGTCAGTATAC
GCCGAAGCACTTGGCCTCGGCTCGAAATCTTTAGCAAATGATTTAAGACCAACATCGTCAGTATA
CGCTGA
Done.