Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016903.1 Corchorus olitorius cultivar O-4 contig16936, 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: 25530
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:558 original size:51 final size:51
Alignment explanation
Indices: 461--559 Score: 114
Period size: 51 Copynumber: 1.9 Consensus size: 51
451 CTTCATATTT
* *
461 TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGTTTTTC
1 TCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGTTTTTC
* *
512 TCTTGTTTCA-ATCTTGTCTTC-GGAC-ATAAAAACACTGTATTCGTGTTT
1 TCTTGTTT-AGATCTTGTC-TCAGGACAAT-AAAACACTCTATTAGTGTTT
560 CTCTTTTAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
50 2 0.05
51 36 0.88
52 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.44
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGTTTTTC
Found at i:961 original size:22 final size:23
Alignment explanation
Indices: 936--986 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
926 CTACAGTATA
*
936 AAAAAT-TTATAGGGAGATTAAC
1 AAAAATCTCATAGGGAGATTAAC
* *
958 -AAAATCTCATAGGGAGGTTATC
1 AAAAATCTCATAGGGAGATTAAC
980 AAAAATC
1 AAAAATC
987 ATAGGAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 13 0.54
23 6 0.25
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (23 bp):
AAAAATCTCATAGGGAGATTAAC
Found at i:990 original size:21 final size:22
Alignment explanation
Indices: 944--997 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
934 TAAAAAATTT
* *
944 ATAGGGAGATTAACAAAATCTC
1 ATAGGGAGGTTAACAAAATATC
*
966 ATAGGGAGGTTATCAAAA-ATC
1 ATAGGGAGGTTAACAAAATATC
*
987 ATAGGAAGGTT
1 ATAGGGAGGTT
998 GCGAAATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (22 bp):
ATAGGGAGGTTAACAAAATATC
Found at i:1048 original size:22 final size:21
Alignment explanation
Indices: 1018--1142 Score: 110
Period size: 22 Copynumber: 5.8 Consensus size: 21
1008 ATAGGAATGT
* * *
1018 TTATTAAAATTTCATTGTTAGG
1 TTATCAAAATTTCATAG-TAGA
*
1040 TTATCAAAATTTCATATGGAGA
1 TTATCAAAATTTCATA-GTAGA
*
1062 TTATCACAATTTCATAGGTA-A
1 TTATCAAAATTTCATA-GTAGA
* *
1083 TTATCAGAATTTCATAGCATGA
1 TTATCAAAATTTCATAGTA-GA
*
1105 TTATCAAAATTTAATAGGGTAG-
1 TTATCAAAATTTCATA--GTAGA
1127 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
1143 AAAATATTCA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.02
21 16 0.19
22 63 0.74
23 2 0.02
24 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
TTATCAAAATTTCATAGTAGA
Found at i:1094 original size:43 final size:44
Alignment explanation
Indices: 1040--1142 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 44
1030 CATTGTTAGG
* * *
1040 TTATCAAAATTTCATATGGA-GATTATCACAATTTCATA-GGTAA
1 TTATCAAAATTTCATA-GCATGATTATCAAAATTTAATAGGGTAA
* *
1083 TTATCAGAATTTCATAGCATGATTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATAGCATGATTATCAAAATTTAATAGGGTAA
1127 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
1143 AAAATATTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.04
43 31 0.60
44 19 0.37
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAGCATGATTATCAAAATTTAATAGGGTAA
Found at i:9430 original size:2 final size:2
Alignment explanation
Indices: 9425--9454 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9415 CTTTTTTTTA
*
9425 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9455 TTCCAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10148 original size:178 final size:178
Alignment explanation
Indices: 9836--10172 Score: 473
Period size: 178 Copynumber: 1.9 Consensus size: 178
9826 TTCCACCATA
* *
9836 AGCACAAATTATGTAATATTAAGCAGACCGTCTATTTCCGTTAACCAAAAAAACTAATTCTTTGG
1 AGCACAAATTATATAATATTAAGCAGACCGTCTATTCCCGTTAACCAAAAAAACTAATTCTTTGG
* * *
9901 AAGCATTTTTTATACCTTGAATATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGATCAT
66 AAACATTTTTTATAACTTGAACATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGATCAT
*
9966 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTAG
131 GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAG
** * * * *
10014 AGCA-AAAGTTATATAATATTAAGTGGATCGTCTATTCCCGTTAACCGAAACAA-TAAATTTTTT
1 AGCACAAA-TTATATAATATTAAGCAGACCGTCTATTCCCGTTAACCAAAAAAACT-AATTCTTT
* *
10077 GGAAACATTTTTTA-AACTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
64 GGAAACATTTTTTATAACTTG-AACATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGAT
* * *
10141 CATGGAACAATCTTTTAATAGACACTTAAATC
128 CATGGAACAACCTTTCAAGAGACACTTAAATC
10173 GCCTTAATCG
Statistics
Matches: 139, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
177 9 0.06
178 130 0.94
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (178 bp):
AGCACAAATTATATAATATTAAGCAGACCGTCTATTCCCGTTAACCAAAAAAACTAATTCTTTGG
AAACATTTTTTATAACTTGAACATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGATCAT
GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTAG
Found at i:10206 original size:178 final size:177
Alignment explanation
Indices: 9836--10213 Score: 456
Period size: 178 Copynumber: 2.1 Consensus size: 177
9826 TTCCACCATA
* *
9836 AGCACAAATTATGTAATATTAAGCAGACCGTCTATTTCCGTTAACCAAAAAAACTAATTCTTTGG
1 AGCA-AAATTATATAATATTAAGCAGACCGTCTATTCCCGTTAACCAAAAAAACTAATTCTTTGG
* * *
9901 AAGCATTTTTTATACCTTGAATATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGATCAT
65 AAACATTTTTTATAACTTGAACATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGATCAT
* * * * *
9966 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTAG
130 GGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGAAACCGAG
** * * * *
10014 AGCAAAAGTTATATAATATTAAGTGGATCGTCTATTCCCGTTAACCGAAACAA-TAAATTTTTTG
1 AGCAAAA-TTATATAATATTAAGCAGACCGTCTATTCCCGTTAACCAAAAAAACT-AATTCTTTG
* *
10078 GAAACATTTTTTA-AACTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC
64 GAAACATTTTTTATAACTTG-AACATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGATC
* * * * * *
10142 ATGGAACAATCTTTTAATAGACACTTAAATCGCCTTAATCGGATAACCGGAG
128 ATGGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGA-AACC-GAG
*
10194 AG-AAAATTATATAATGTTAA
1 AGCAAAATTATATAATATTAA
10214 ATAGACTGTT
Statistics
Matches: 170, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
177 9 0.05
178 151 0.89
179 6 0.04
180 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (177 bp):
AGCAAAATTATATAATATTAAGCAGACCGTCTATTCCCGTTAACCAAAAAAACTAATTCTTTGGA
AACATTTTTTATAACTTGAACATTAAATTTAGTTATCCAGTCCTTCATGAAAGTTGTAGATCATG
GAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGAAACCGAG
Found at i:10651 original size:131 final size:131
Alignment explanation
Indices: 10440--10702 Score: 508
Period size: 131 Copynumber: 2.0 Consensus size: 131
10430 ATTCTGATAA
10440 GAATTTAATTATAAGTTTAACTCTAATTAATTATGAAAAAGCAGAGTTTACAAGGTAAAATTCTT
1 GAATTTAATTATAAGTTTAACTCTAATTAATTATGAAAAAGCAGAGTTTACAAGGTAAAATTCTT
10505 AATTTTATGATATTATTGAATAAGGTTTTATAATTATAGTAACTTTTTCTAATAACATGTCAAAC
66 AATTTTATGATATTATTGAATAAGGTTTTATAATTATAGTAACTTTTTCTAATAACATGTCAAAC
10570 G
131 G
*
10571 GAATTTAATTATAAGTTTAACTCTAATTAATTATGAATAAGCAGAGTTTACAAGGTAAAATTCTT
1 GAATTTAATTATAAGTTTAACTCTAATTAATTATGAAAAAGCAGAGTTTACAAGGTAAAATTCTT
*
10636 ATTTTTATGATATTATTGAATAAGGTTTTATAATTATAGTAACTTTTTCTAATAACATGTCAAAC
66 AATTTTATGATATTATTGAATAAGGTTTTATAATTATAGTAACTTTTTCTAATAACATGTCAAAC
10701 G
131 G
10702 G
1 G
10703 GATATTAGAT
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 130 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41
Consensus pattern (131 bp):
GAATTTAATTATAAGTTTAACTCTAATTAATTATGAAAAAGCAGAGTTTACAAGGTAAAATTCTT
AATTTTATGATATTATTGAATAAGGTTTTATAATTATAGTAACTTTTTCTAATAACATGTCAAAC
G
Found at i:13109 original size:2 final size:2
Alignment explanation
Indices: 13102--13144 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
13092 ATTTGTGTTG
13102 TA TA TA 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 TA TA TA
13144 T
1 T
13145 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19242 original size:16 final size:15
Alignment explanation
Indices: 19204--19245 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
19194 ACAGAGATTG
19204 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
19219 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
19234 ACTAGAAAACAA
1 AC-AGAAAACAA
19246 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:21245 original size:12 final size:12
Alignment explanation
Indices: 21222--21255 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21212 TTGAAATAAT
21222 AATAATTA-TAA
1 AATAATTATTAA
*
21233 AATAGTTATTAA
1 AATAATTATTAA
21245 AATAATTATTA
1 AATAATTATTA
21256 TTTTCCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
AATAATTATTAA
Done.