Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014010.1 Corchorus capsularis cultivar CVL-1 contig14031, 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: 35739
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:17286 original size:31 final size:31
Alignment explanation
Indices: 17251--17377 Score: 128
Period size: 31 Copynumber: 4.4 Consensus size: 31
17241 TTTGAAACAT
* *
17251 GTGGCATGCCACATGTCACTTTTTGGTATAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
* **
17282 GTGGCGTGACATGTGTCACTTTTTGGTACA-
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
* *
17312 -T---GTGGCAC--G--ACTTTTTGGTACAT
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
17335 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
17366 GTGGCGTGCCAC
1 GTGGCGTGCCAC
17378 GTCGGACACC
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
22 13 0.17
24 2 0.03
26 5 0.06
27 6 0.08
29 2 0.03
31 50 0.64
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.34
Consensus pattern (31 bp):
GTGGCGTGCCACATGTCACTTTTTGGTACAC
Found at i:17326 original size:53 final size:53
Alignment explanation
Indices: 17268--17370 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
17258 GCCACATGTC
* ** *
17268 ACTTTTTGGTATACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
17321 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
17371 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:19879 original size:34 final size:35
Alignment explanation
Indices: 19810--19900 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 35
19800 AGAATGGTTT
19810 AATCAATACGGCCTTCTTCAGTCAAAAAAAAAAAAA
1 AATCAATACGGCCTTCTTCAGTC-AAAAAAAAAAAA
*
19846 AATCAATACGGCCTTCTTCAGTC-GAAAAAAAAAA
1 AATCAATACGGCCTTCTTCAGTCAAAAAAAAAAAA
19880 AATCAATACGGCCCTTCTTCA
1 AATCAATACGG-CCTTCTTCA
19901 TTAGCTCTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
34 21 0.40
35 9 0.17
36 23 0.43
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.22
Consensus pattern (35 bp):
AATCAATACGGCCTTCTTCAGTCAAAAAAAAAAAA
Found at i:24018 original size:2 final size:2
Alignment explanation
Indices: 24002--24038 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
23992 ATAGGAAACA
24002 AT AT AGT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24039 GATAATAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24194 original size:2 final size:2
Alignment explanation
Indices: 24189--24263 Score: 77
Period size: 2 Copynumber: 38.5 Consensus size: 2
24179 AAAAGAACAA
* *
24189 AT AT AT AT AT AT AT AT AGT GT AT AT AGG AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT
*
24232 AT A- AT AT AT AT AT GT A- AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24264 AGGTGGGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
1 4 0.07
2 55 0.90
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Found at i:24223 original size:11 final size:10
Alignment explanation
Indices: 24189--24243 Score: 53
Period size: 9 Copynumber: 5.7 Consensus size: 10
24179 AAAAGAACAA
*
24189 ATATATATAT
1 ATATATAGAT
24199 ATATATAG-T
1 ATATATAGAT
*
24208 GTATATAGGAT
1 ATATATA-GAT
*
24219 ATATATATAT
1 ATATATAGAT
24229 A-ATATA-AT
1 ATATATAGAT
24237 ATATATA
1 ATATATA
24244 TGTAATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 3 0.08
9 17 0.45
10 11 0.29
11 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (10 bp):
ATATATAGAT
Found at i:31821 original size:2 final size:2
Alignment explanation
Indices: 31814--31849 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31804 TTATGATTGC
31814 TA TA TA TA TA 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 TA TA TA TA TA
31850 ATTATAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32045 original size:31 final size:31
Alignment explanation
Indices: 31987--32046 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
31977 CTCTCCCAAA
*
31987 GGCTCAAACTCTCTTCCTCCCAGAGATTTAT
1 GGCTCAAACTCTCTTCCTCCCACAGATTTAT
* *
32018 GGCTCAAACTCTCTTCCTCTCTCAGATTT
1 GGCTCAAACTCTCTTCCTCCCACAGATTT
32047 CTAGTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (31 bp):
GGCTCAAACTCTCTTCCTCCCACAGATTTAT
Found at i:33578 original size:2 final size:2
Alignment explanation
Indices: 33567--33597 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
33557 TATCCATCCG
33567 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33598 TTAATAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34517 original size:1 final size:1
Alignment explanation
Indices: 34511--34537 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
34501 TCGAAATCAC
34511 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
34538 CCCAAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.