Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015000.1 Corchorus olitorius cultivar O-4 contig15033, 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: 30146
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3239 original size:13 final size:13
Alignment explanation
Indices: 3221--3245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3211 CAGCTCCGGA
3221 CCCCCCCCCCCCG
1 CCCCCCCCCCCCG
3234 CCCCCCCCCCCC
1 CCCCCCCCCCCC
3246 CCGGTGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.96, G:0.04, T:0.00
Consensus pattern (13 bp):
CCCCCCCCCCCCG
Found at i:14444 original size:26 final size:26
Alignment explanation
Indices: 14408--14459 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
14398 CCCCTCCCCC
14408 CGGATGCGTTTTTTAGCTTATAAGCG
1 CGGATGCGTTTTTTAGCTTATAAGCG
14434 CGGATGCGTTTTTTAGCTTATAAGCG
1 CGGATGCGTTTTTTAGCTTATAAGCG
14460 ATCACAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (26 bp):
CGGATGCGTTTTTTAGCTTATAAGCG
Found at i:15838 original size:34 final size:36
Alignment explanation
Indices: 15795--15877 Score: 107
Period size: 34 Copynumber: 2.3 Consensus size: 36
15785 AGTTGTTGGC
* *
15795 TTCTTCTTTGCACATGATTCTGTTGAAAATT-TG-A
1 TTCTTCTTTGCACATAATTCAGTTGAAAATTCTGTA
*
15829 TTCTTCTTTGCTCATAATTCAGTTGAAAATTCTGTA
1 TTCTTCTTTGCACATAATTCAGTTGAAAATTCTGTA
*
15865 GTCTTCTTCTGCA
1 TTCTTCTT-TGCA
15878 GTGACAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 28 0.68
35 2 0.05
36 8 0.20
37 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (36 bp):
TTCTTCTTTGCACATAATTCAGTTGAAAATTCTGTA
Found at i:19847 original size:35 final size:35
Alignment explanation
Indices: 19801--19871 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
19791 GTAGATTACA
*
19801 CTACTTGCTTAATCTTTCACTCTTGTTATCATTCT
1 CTACTTGCTTAATCTTTCACTCTTGTTATCACTCT
*
19836 CTACTTGCTTAATTTTTCACTCTTGTTATCACTCT
1 CTACTTGCTTAATCTTTCACTCTTGTTATCACTCT
19871 C
1 C
19872 ATCAAGAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.27, G:0.06, T:0.51
Consensus pattern (35 bp):
CTACTTGCTTAATCTTTCACTCTTGTTATCACTCT
Found at i:21842 original size:25 final size:26
Alignment explanation
Indices: 21807--21858 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
21797 GAAATATCTA
21807 AAATATCCTTTTAATTTTAAAATTTT
1 AAATATCCTTTTAATTTTAAAATTTT
21833 AAATA-CCTTTTAATTTTAAAATTTT
1 AAATATCCTTTTAATTTTAAAATTTT
21858 A
1 A
21859 GTTTATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (26 bp):
AAATATCCTTTTAATTTTAAAATTTT
Found at i:23146 original size:30 final size:30
Alignment explanation
Indices: 23118--23346 Score: 350
Period size: 30 Copynumber: 7.6 Consensus size: 30
23108 TACATACAAA
* * *
23118 TGACACCAGAAGTTATCATGGTCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
23148 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
23178 TGACACCAGAAGTTGTCATAATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
23208 TGACACCAGAAGTTGTCATGCTCTTGCGAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
23238 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
23268 TGACACCAGAAGTTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
23298 TGACACCAGAAGTTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
23328 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
23347 ATTATATTAT
Statistics
Matches: 186, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 186 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:23410 original size:62 final size:65
Alignment explanation
Indices: 23297--23600 Score: 368
Period size: 62 Copynumber: 4.8 Consensus size: 65
23287 GATGTTGCAA
* * * *
23297 TTGACACCAGAAGTTGTCATG--ATGTTGCA-ATTGACACCAGAAGTTGTCATATTATATTATTA
1 TTGACACCAGAAGTTGTCATGAAATATT--ATCTTGACACCAGAAGTTGTCATATCAAATTATTA
23359 TC
64 TC
23361 TTGACACCAGAAGTTGTCATGAAA-ATT-T-TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATGAAATATTATCTTGACACCAGAAGTTGTCATATCAAATTATTATC
*
23423 TTGACACCAGAAGTTGTCAT-AAAAATT-T-TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATGAAATATTATCTTGACACCAGAAGTTGTCATATCAAATTATTATC
* *
23485 TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTC--ATGAAA--ATT
1 TTGACACCAGAAGTTGTC--ATGAAA-TATTATCTTGACACCAGAAGTTGTCATATCAAATTATT
23546 A--
63 ATC
23547 TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT-G-AAA-TATTATCTTGACACCAGAAGTTGTCAT
23601 GCTGAGGAAA
Statistics
Matches: 220, Mismatches: 6, Indels: 28
0.87 0.02 0.11
Matches are distributed among these distances:
60 2 0.01
61 3 0.01
62 155 0.70
64 27 0.12
65 5 0.02
66 9 0.04
67 1 0.00
68 18 0.08
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (65 bp):
TTGACACCAGAAGTTGTCATGAAATATTATCTTGACACCAGAAGTTGTCATATCAAATTATTATC
Found at i:23489 original size:96 final size:96
Alignment explanation
Indices: 23327--23600 Score: 407
Period size: 96 Copynumber: 2.9 Consensus size: 96
23317 GATGTTGCAA
* *
23327 TTGACACCAGAAGTTGTCATATTATATTATTATCTTGACACCAGAAGTTGTC--ATGAAA--ATT
1 TTGACACCAGAAGTTGTCATA--A-A-AATT-T-TTGACACCAGAAGTTGTCATATCAAATTATT
23388 -T-TTGACACCAGAAGTTGTCATATCAAATTATTATC
60 ATCTTGACACCAGAAGTTGTCATATCAAATTATTATC
23423 TTGACACCAGAAGTTGTCATAAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTG
1 TTGACACCAGAAGTTGTCATAAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTG
23488 ACACCAGAAGTTGTCATATCAAATTATTATC
66 ACACCAGAAGTTGTCATATCAAATTATTATC
* * *
23519 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCTTG
1 TTGACACCAGAAGTTGTCATAAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTG
23584 ACACCAGAAGTTGTCAT
66 ACACCAGAAGTTGTCAT
23601 GCTGAGGAAA
Statistics
Matches: 167, Mismatches: 5, Indels: 12
0.91 0.03 0.07
Matches are distributed among these distances:
90 18 0.11
91 1 0.01
92 8 0.05
93 1 0.01
94 4 0.02
95 1 0.01
96 134 0.80
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (96 bp):
TTGACACCAGAAGTTGTCATAAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTG
ACACCAGAAGTTGTCATATCAAATTATTATC
Found at i:28908 original size:17 final size:17
Alignment explanation
Indices: 28871--28910 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
28861 ATTTTTTTGG
* *
28871 GTACTTGAGGTGGTTAG
1 GTACTTGAGGTGGTCAA
28888 GTACTTGAGGTGGTCAA
1 GTACTTGAGGTGGTCAA
28905 GTACTT
1 GTACTT
28911 TAGGGGTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (17 bp):
GTACTTGAGGTGGTCAA
Found at i:28932 original size:13 final size:13
Alignment explanation
Indices: 28914--28941 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28904 AGTACTTTAG
28914 GGGTACTTGAGGT
1 GGGTACTTGAGGT
28927 GGGTACTTGAGGT
1 GGGTACTTGAGGT
28940 GG
1 GG
28942 TTAGCCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.50, T:0.29
Consensus pattern (13 bp):
GGGTACTTGAGGT
Done.