Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015829.1 Corchorus capsularis cultivar CVL-1 contig15850, 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: 19207
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:970 original size:32 final size:32
Alignment explanation
Indices: 934--1002 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
924 TCTCCCTTGC
* *
934 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
1 TCGGGTCAAATTTGGGTCAGGTTAATTCGGGT
*
966 TCGGGTCAATTTTGGGTCAGGTTAATTCGGGT
1 TCGGGTCAAATTTGGGTCAGGTTAATTCGGGT
998 TCGGG
1 TCGGG
1003 CTCGGATTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.14, C:0.12, G:0.38, T:0.36
Consensus pattern (32 bp):
TCGGGTCAAATTTGGGTCAGGTTAATTCGGGT
Found at i:1169 original size:20 final size:20
Alignment explanation
Indices: 1144--1184 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1134 CATAAATGAA
*
1144 ATTTTCAGAA-ATTATTATTT
1 ATTTTCA-AATATTAGTATTT
1164 ATTTTCAAATATTAGTATTT
1 ATTTTCAAATATTAGTATTT
1184 A
1 A
1185 ATTCAGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAAATATTAGTATTT
Found at i:1221 original size:16 final size:16
Alignment explanation
Indices: 1202--1274 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
1192 TTTTTTCAGG
* *
1202 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGAGATTT
1218 TTCGGGTTTC-AGATTT
1 TTCGGG-TTCGAGATTT
* *
1234 TACGGGTTC-TGATTT
1 TTCGGGTTCGAGATTT
*
1249 TTCGGGTTTGAGATTT
1 TTCGGGTTCGAGATTT
1265 TTCGGGTTCG
1 TTCGGGTTCG
1275 GGCGAGTTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
15 15 0.32
16 29 0.62
17 3 0.06
ACGTcount: A:0.08, C:0.12, G:0.32, T:0.48
Consensus pattern (16 bp):
TTCGGGTTCGAGATTT
Found at i:1253 original size:31 final size:31
Alignment explanation
Indices: 1215--1273 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1205 GGGTTCGGGT
1215 TTTTTCGGGTTTCAGATTTTACGGGTTCTGA
1 TTTTTCGGGTTTCAGATTTTACGGGTTCTGA
* *
1246 TTTTTCGGGTTTGAGATTTTTCGGGTTC
1 TTTTTCGGGTTTCAGATTTTACGGGTTC
1274 GGGCGAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.10, C:0.12, G:0.27, T:0.51
Consensus pattern (31 bp):
TTTTTCGGGTTTCAGATTTTACGGGTTCTGA
Found at i:1431 original size:33 final size:33
Alignment explanation
Indices: 1382--1457 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
1372 GCCACCTCTA
* * *
1382 CTCATCGTATGGTGAGATGCCTCCTGGCGACAC
1 CTCACCGTATGATGAGACGCCTCCTGGCGACAC
* *
1415 CTCACCGTATGATGAGACGCCTCCTGGGGACGC
1 CTCACCGTATGATGAGACGCCTCCTGGCGACAC
*
1448 CTCCCCGTAT
1 CTCACCGTAT
1458 TGATTACAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.17, C:0.34, G:0.26, T:0.22
Consensus pattern (33 bp):
CTCACCGTATGATGAGACGCCTCCTGGCGACAC
Found at i:1605 original size:7 final size:7
Alignment explanation
Indices: 1582--1620 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1572 CATATGGACT
1582 CTAAACC
1 CTAAACC
*
1589 CT-AACA
1 CTAAACC
1595 CTAAACC
1 CTAAACC
1602 CTAAACC
1 CTAAACC
1609 CTAAACC
1 CTAAACC
1616 CTAAA
1 CTAAA
1621 TGTGATTGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:2057 original size:7 final size:7
Alignment explanation
Indices: 2037--2118 Score: 73
Period size: 7 Copynumber: 12.1 Consensus size: 7
2027 CAATAACTAG
2037 GGGTTTA
1 GGGTTTA
*
2044 AGG-TTA
1 GGGTTTA
2050 GGGTTTA
1 GGGTTTA
2057 GGGTTT-
1 GGGTTTA
***
2063 TCATTTA
1 GGGTTTA
2070 GGGTTTA
1 GGGTTTA
2077 GGGTTTA
1 GGGTTTA
*
2084 TGG-TTA
1 GGGTTTA
2090 GGGGTTTA
1 -GGGTTTA
2098 GGGTTTA
1 GGGTTTA
*
2105 -GGATTA
1 GGGTTTA
2111 GGGTTTA
1 GGGTTTA
2118 G
1 G
2119 AGTTCATATG
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
6 16 0.28
7 39 0.67
8 3 0.05
ACGTcount: A:0.17, C:0.01, G:0.39, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:2062 original size:20 final size:20
Alignment explanation
Indices: 2037--2118 Score: 96
Period size: 20 Copynumber: 4.0 Consensus size: 20
2027 CAATAACTAG
2037 GGGTTTAAGGTTAGGGTTTA
1 GGGTTTAAGGTTAGGGTTTA
* *
2057 GGGTTTTCA-TTTAGGGTTTA
1 GGG-TTTAAGGTTAGGGTTTA
*
2077 GGGTTTATGGTTAGGGGTTTA
1 GGGTTTAAGGTTA-GGGTTTA
2098 GGGTTT-AGGATTAGGGTTTA
1 GGGTTTAAGG-TTAGGGTTTA
2118 G
1 G
2119 AGTTCATATG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.06
20 29 0.56
21 20 0.38
ACGTcount: A:0.17, C:0.01, G:0.39, T:0.43
Consensus pattern (20 bp):
GGGTTTAAGGTTAGGGTTTA
Found at i:2088 original size:14 final size:14
Alignment explanation
Indices: 2037--2118 Score: 73
Period size: 13 Copynumber: 6.1 Consensus size: 14
2027 CAATAACTAG
*
2037 GGGTTTAAGG-TTA
1 GGGTTTAGGGTTTA
2050 GGGTTTAGGGTTT-
1 GGGTTTAGGGTTTA
***
2063 TCATTTAGGGTTTA
1 GGGTTTAGGGTTTA
*
2077 GGGTTTATGG-TTA
1 GGGTTTAGGGTTTA
2090 GGGGTTTAGGGTTTA
1 -GGGTTTAGGGTTTA
*
2105 -GGATTAGGGTTTA
1 GGGTTTAGGGTTTA
2118 G
1 G
2119 AGTTCATATG
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
13 34 0.63
14 17 0.31
15 3 0.06
ACGTcount: A:0.17, C:0.01, G:0.39, T:0.43
Consensus pattern (14 bp):
GGGTTTAGGGTTTA
Found at i:3914 original size:33 final size:33
Alignment explanation
Indices: 3862--4071 Score: 189
Period size: 33 Copynumber: 6.5 Consensus size: 33
3852 GTCCAGGCAT
* *
3862 CCCAGGAGGTGCCTCACCATACGGGGAGGCATC
1 CCCAGGAGGCGCCTCACCATACGGGGAGGCGTC
* * * *
3895 CCAAGGAGGCGCTTGACCATATGGGGAGGCGTC
1 CCCAGGAGGCGCCTCACCATACGGGGAGGCGTC
* *
3928 CCCAGGAGGGGCCTCACCATACGGGGAGACGTC
1 CCCAGGAGGCGCCTCACCATACGGGGAGGCGTC
* *
3961 CCTAGGAGGCGCCT----GTACGGGGAGGCGTC
1 CCCAGGAGGCGCCTCACCATACGGGGAGGCGTC
** ** * *
3990 CCCAGGAGGCGCCTCACGGTACGATGAGAC-TT
1 CCCAGGAGGCGCCTCACCATACGGGGAGGCGTC
* ** * *
4022 CCCAGGAGGCACCTCACCATACGATGAGAC-TT
1 CCCAGGAGGCGCCTCACCATACGGGGAGGCGTC
4054 CCCAGGAGGCGCCTCACC
1 CCCAGGAGGCGCCTCACC
4072 GTATCATGAG
Statistics
Matches: 148, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
29 26 0.18
32 47 0.32
33 75 0.51
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (33 bp):
CCCAGGAGGCGCCTCACCATACGGGGAGGCGTC
Found at i:3989 original size:29 final size:29
Alignment explanation
Indices: 3947--4003 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3937 GGCCTCACCA
*
3947 TACGGGGAGACGTCCCTAGGAGGCGCCTG
1 TACGGGGAGACGTCCCCAGGAGGCGCCTG
*
3976 TACGGGGAGGCGTCCCCAGGAGGCGCCT
1 TACGGGGAGACGTCCCCAGGAGGCGCCT
4004 CACGGTACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.30, G:0.42, T:0.12
Consensus pattern (29 bp):
TACGGGGAGACGTCCCCAGGAGGCGCCTG
Found at i:4081 original size:32 final size:32
Alignment explanation
Indices: 3990--4104 Score: 169
Period size: 32 Copynumber: 3.6 Consensus size: 32
3980 GGGAGGCGTC
*
3990 CCCAGGAGGCGCCTCACGGTACGATGAGACTT
1 CCCAGGAGGCGCCTCACCGTACGATGAGACTT
* *
4022 CCCAGGAGGCACCTCACCATACGATGAGACTT
1 CCCAGGAGGCGCCTCACCGTACGATGAGACTT
4054 CCCAGGAGGCGCCTCACCGTATC-ATGAGACTT
1 CCCAGGAGGCGCCTCACCGTA-CGATGAGACTT
* *
4086 CTCAAGAGGCGCCTCACCG
1 CCCAGGAGGCGCCTCACCG
4105 GAATTGTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
32 74 0.99
33 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (32 bp):
CCCAGGAGGCGCCTCACCGTACGATGAGACTT
Found at i:14850 original size:26 final size:23
Alignment explanation
Indices: 14796--14850 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 23
14786 CACATTTCTC
*
14796 ATTTTCCTTATCTTTTCTTTATT
1 ATTTTCCTCATCTTTTCTTTATT
*
14819 AGTTTTCACTCATCTTTTATTTTATTT
1 A-TTTTC-CTCATCTTTT-CTTTA-TT
14846 ATTTT
1 ATTTT
14851 GTTTCTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 5 0.19
25 9 0.35
26 8 0.31
27 3 0.12
ACGTcount: A:0.16, C:0.15, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTTCCTCATCTTTTCTTTATT
Found at i:18023 original size:21 final size:21
Alignment explanation
Indices: 17997--18042 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
17987 CTATGTTATT
*
17997 TTAGATCACATTGATCATTCA
1 TTAGATCACATAGATCATTCA
18018 TTAGATCACATAGATCATTCA
1 TTAGATCACATAGATCATTCA
18039 TTAG
1 TTAG
18043 TTTGGTAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (21 bp):
TTAGATCACATAGATCATTCA
Found at i:18328 original size:3 final size:3
Alignment explanation
Indices: 18320--18371 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
18310 ATATCAAAAT
*
18320 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18368 ATA A
1 ATA A
18372 AATTTGTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Done.