Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003331.1 Corchorus capsularis cultivar CVL-1 contig03339, 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, 723
Length: 1205
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Found at i:199 original size:37 final size:37
Alignment explanation
Indices: 159--504 Score: 282
Period size: 37 Copynumber: 9.4 Consensus size: 37
149 ATTTAAGGTT
*
159 CCTGTTTAGGTGTTTCATCAAAATCTTGTTCAAGATT
1 CCTGTTTAGGTGTTTCATCAAAATCTTGTTCAAGATC
* * * *
196 CCTGTTTAGAT-TTCTTATC-AAATCCTTGTTTAAGGTC
1 CCTGTTTAGGTGTT-TCATCAAAAT-CTTGTTCAAGATC
* *
233 CCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATT
1 CCTGTTTAGGTGTTTCATCAAAATCTTGTTCAAGATC
* * * *
270 CCTGTTTAGGT-TTCTTAT-TAAATCCTTGTTTAAGGTC
1 CCTGTTTAGGTGTT-TCATCAAAAT-CTTGTTCAAGATC
*
307 CCTGTTTAGGTG--TCATCAAAATCTTGTTCAAGATT
1 CCTGTTTAGGTGTTTCATCAAAATCTTGTTCAAGATC
* * * * *
342 CCTATTTAGGT-TTCTTATCAAAATCTTTATTTAAGATA
1 CCTGTTTAGGTGTT-TCATCAAAATC-TTGTTCAAGATC
* * * *
380 CCTGTTTAGGTGTGTCATCAAAACCTTCTTCAAGATG
1 CCTGTTTAGGTGTTTCATCAAAATCTTGTTCAAGATC
* * *
417 CCTGTTTAGGT-TTCTTATC-AAATCCTTATTTAA-AGTC
1 CCTGTTTAGGTGTT-TCATCAAAAT-CTTGTTCAAGA-TC
* *
454 CCTATTTAGGTGTCTCATCAAAATCTTGTT-AATGATC
1 CCTGTTTAGGTGTTTCATCAAAATCTTGTTCAA-GATC
*
491 CCTATTTAGGTGTT
1 CCTGTTTAGGTGTT
505 CGAAAACCAA
Statistics
Matches: 244, Mismatches: 45, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
35 23 0.09
36 22 0.09
37 159 0.65
38 39 0.16
39 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (37 bp):
CCTGTTTAGGTGTTTCATCAAAATCTTGTTCAAGATC
Found at i:261 original size:74 final size:74
Alignment explanation
Indices: 140--501 Score: 523
Period size: 74 Copynumber: 4.9 Consensus size: 74
130 TTTTTCATGA
* *
140 CAAATCCTTATTTAAGGTTCCTGTTTAGGTGTTTCATCAAAATCTTGTTCAAGATTCCTGTTTAG
1 CAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAG
*
205 ATTTCTTAT
66 GTTTCTTAT
*
214 CAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAG
1 CAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAG
279 GTTTCTTAT
66 GTTTCTTAT
* * *
288 TAAATCCTTGTTTAAGGTCCCTGTTTAGGTG--TCATCAAAATCTTGTTCAAGATTCCTATTTAG
1 CAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAG
351 GTTTCTTAT
66 GTTTCTTAT
* * * * * * *
360 CAAAATCTTTATTTAAGATACCTGTTTAGGTGTGTCATCAAAACCTTCTTCAAGATGCCTGTTTA
1 C-AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTA
425 GGTTTCTTAT
65 GGTTTCTTAT
* * * *
435 CAAATCCTTATTTAAAGTCCCTATTTAGGTGTCTCATCAAAATCTTGTT-AATGATCCCTATTTA
1 CAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAA-GATTCCTGTTTA
499 GGT
65 GGT
502 GTTCGAAAAC
Statistics
Matches: 259, Mismatches: 25, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
72 40 0.15
73 28 0.11
74 153 0.59
75 38 0.15
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (74 bp):
CAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAG
GTTTCTTAT
Found at i:744 original size:43 final size:43
Alignment explanation
Indices: 653--768 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
643 TTCTTGGCTC
* * *
653 AAAAATCAAATTTCAAAACCTGCA-TTCATGGTTTATTCTTCAA
1 AAAAATCAAAATTCAAAACTTGCATTTCATGATTTATTCTTC-A
696 AAAAATCAAAATTCAAAACTTGCATTTCA-GCATTCTATTCTTC-
1 AAAAATCAAAATTCAAAACTTGCATTTCATG-ATT-TATTCTTCA
* * *
739 GAAAATCAAAGTTCAAAATTTGCATTTCAT
1 AAAAATCAAAATTCAAAACTTGCATTTCAT
769 TATTCAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
43 49 0.78
44 6 0.10
45 8 0.13
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (43 bp):
AAAAATCAAAATTCAAAACTTGCATTTCATGATTTATTCTTCA
Found at i:791 original size:150 final size:147
Alignment explanation
Indices: 658--1064 Score: 590
Period size: 150 Copynumber: 2.7 Consensus size: 147
648 GGCTCAAAAA
658 TCAAATTTCAAAACCTGCATTCATGGTTTATTCTTCAAAAAAATCAAAATTCAAAACTTGCATTT
1 TCAAA-TTCAAAACCTGCATTCATGGTTTATTCTTCAAAAAAATCAAAATTCAAAACTTGCATTT
*
723 CAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAAATCAAAATT
65 CAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATGATTC-AAAAATCAAAATT
788 CAAAATCAGCATCTCAAGGT
129 CAAAATCAG-ATCTCAAGGT
*
808 TCAAAATTCAAAACCTGCATTCATGGTTTATTCTTCAAAAAAATCAAAATTCAAAACTTACATTT
1 TC-AAATTCAAAACCTGCATTCATGGTTTATTCTTCAAAAAAATCAAAATTCAAAACTTGCATTT
* *
873 CAGTATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATGATTCAATAATCAAAATTC
65 CAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATGATTCAAAAATCAAAATTC
*
938 AAAATCAGCATCTCATGGT
130 AAAATCAG-ATCTCAAGGT
* * *
957 TCGAAATTCAAAACCTGCATTTCACGGTTCATTCTTC--AAAAGTCAAAATTCAAAACTTGCATT
1 TC-AAATTCAAAACCTGCA-TTCATGGTTTATTCTTCAAAAAAATCAAAATTCAAAACTTGCATT
* * **
1020 TCA-CGGTTC-ATTCTTC-AAAACTCAAAATTCAAAACCTGCATTTCA
64 TCAGC-ATTCTATTCTTCGAAAA-TCAAAGTTCAAAATTTGCATTTCA
1065 CGGTTCATTC
Statistics
Matches: 238, Mismatches: 15, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
146 4 0.02
147 28 0.12
148 30 0.13
149 49 0.21
150 124 0.52
151 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (147 bp):
TCAAATTCAAAACCTGCATTCATGGTTTATTCTTCAAAAAAATCAAAATTCAAAACTTGCATTTC
AGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATGATTCAAAAATCAAAATTCA
AAATCAGATCTCAAGGT
Found at i:827 original size:28 final size:27
Alignment explanation
Indices: 780--835 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
770 ATTCAAAAAA
*
780 TCAAAATTCAAAATCAGCATCTCAAGGT
1 TCAAAATTCAAAACCAGCAT-TCAAGGT
* *
808 TCAAAATTCAAAACCTGCATTCATGGT
1 TCAAAATTCAAAACCAGCATTCAAGGT
835 T
1 T
836 TATTCTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (27 bp):
TCAAAATTCAAAACCAGCATTCAAGGT
Found at i:968 original size:35 final size:35
Alignment explanation
Indices: 886--969 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
876 TATTCTATTC
* ** *
886 TTCGAAAATCAAAGTTCAAAATTTGCATTTCATGA
1 TTCGAAAATCAAAATTCAAAATCAGCATCTCATGA
*
921 TTC-AATAATCAAAATTCAAAATCAGCATCTCATGG
1 TTCGAA-AATCAAAATTCAAAATCAGCATCTCATGA
*
956 TTCGAAATTCAAAA
1 TTCGAAAATCAAAA
970 CCTGCATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 2 0.05
35 37 0.90
36 2 0.05
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (35 bp):
TTCGAAAATCAAAATTCAAAATCAGCATCTCATGA
Found at i:976 original size:28 final size:28
Alignment explanation
Indices: 932--986 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
922 TCAATAATCA
* *
932 AAATTCAAAATCAGCATCTCATGGTTCG
1 AAATTCAAAACCAGCATCTCACGGTTCG
* *
960 AAATTCAAAACCTGCATTTCACGGTTC
1 AAATTCAAAACCAGCATCTCACGGTTC
987 ATTCTTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (28 bp):
AAATTCAAAACCAGCATCTCACGGTTCG
Found at i:1006 original size:42 final size:42
Alignment explanation
Indices: 960--1105 Score: 249
Period size: 42 Copynumber: 3.5 Consensus size: 42
950 TCATGGTTCG
960 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA
1 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA
* *
1002 AAATTCAAAACTTGCATTTCACGGTTCATTCTTCAAAACTCA
1 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA
1044 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTC-
1 AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA
* *
1085 AAATTTAAAACTTGCATTTCA
1 AAATTCAAAACCTGCATTTCA
1106 GCATTCCTTT
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 19 0.19
42 79 0.81
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (42 bp):
AAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCA
Done.