Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012320.1 Corchorus olitorius cultivar O-4 contig12353, 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: 18424
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:5263 original size:26 final size:23
Alignment explanation
Indices: 5233--5279 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
5223 CTTGAAAATT
5233 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
5259 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
5280 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:7957 original size:15 final size:16
Alignment explanation
Indices: 7933--7972 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7923 AGAGGTTGAA
*
7933 AGAAAGCAATTACA-T
1 AGAAAACAATTACACT
*
7948 AGAAAACAATTATACT
1 AGAAAACAATTACACT
7964 AGAAAACAA
1 AGAAAACAA
7973 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTACACT
Found at i:11896 original size:21 final size:21
Alignment explanation
Indices: 11872--11913 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11862 TCTTGAAGAG
*
11872 TTGAAGGCCATCAGAGTTCAT
1 TTGAAGGCCATCAGAGATCAT
* *
11893 TTGAAGGGCATTAGAGATCAT
1 TTGAAGGCCATCAGAGATCAT
11914 AAGCAAAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (21 bp):
TTGAAGGCCATCAGAGATCAT
Found at i:12935 original size:32 final size:32
Alignment explanation
Indices: 12870--12966 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 32
12860 AAAATACTGG
*
12870 CAAAATAGTGGCGTT-T-T-ATACATAAATAGCCC
1 CAAAATAGTGGCGTTCTCTGA-ACA-AAACA-CCC
12902 CAAAATAGTGGCGTTCTCTGAACAAAACACCC
1 CAAAATAGTGGCGTTCTCTGAACAAAACACCC
* * *
12934 CAAAATAGTGGCGTTCTCAGAAGAAAACGCCC
1 CAAAATAGTGGCGTTCTCTGAACAAAACACCC
12966 C
1 C
12967 TATTTTGGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
32 48 0.83
33 5 0.09
34 4 0.07
35 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (32 bp):
CAAAATAGTGGCGTTCTCTGAACAAAACACCC
Found at i:15062 original size:26 final size:27
Alignment explanation
Indices: 14991--15062 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 27
14981 AGACTCTGAG
14991 TCGAGTTTTCCAATTTTTTAATTTTCTTTT
1 TCGA-TTTTCC-A-TTTTTAATTTTCTTTT
*
15021 TCGATTTTAC-TCTTTT-ATTTTCTTTT
1 TCGATTTTCCAT-TTTTAATTTTCTTTT
15047 TC-ATTTTTCCATTTTT
1 TCGA-TTTTCCATTTTT
15063 TCTTTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 1 0.03
26 22 0.59
27 5 0.14
29 5 0.14
30 4 0.11
ACGTcount: A:0.14, C:0.15, G:0.04, T:0.67
Consensus pattern (27 bp):
TCGATTTTCCATTTTTAATTTTCTTTT
Found at i:15709 original size:25 final size:24
Alignment explanation
Indices: 15680--15743 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
15670 ATATTATCAT
15680 AAAATAATTTACAAATACATCTCAC
1 AAAATAATTTACAAATA-ATCTCAC
* * *
15705 AAAAT-CTTTCTCAAATAATTTCAC
1 AAAATAATTT-ACAAATAATCTCAC
*
15729 AAAATATATTCACAA
1 AAAATA-ATTTACAA
15744 TATAGTTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
24 14 0.47
25 14 0.47
26 2 0.07
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATAATTTACAAATAATCTCAC
Found at i:16048 original size:42 final size:45
Alignment explanation
Indices: 15997--16090 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
15987 AGTGCATTAC
*
15997 CTAA-ATTCTAC-TC-C-ATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTTCTCTATCTCTAGATAATTCATCAAAATAAAA
* *
16038 CTAATATTCTACTTCTCTATCTCTAGATAATTCATCTAAATAAAG
1 CTAATATTCTACTTCTCTATCTCTAGATAATTCATCAAAATAAAA
16083 CTAATATT
1 CTAATATT
16091 AATTGTTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 7 0.15
43 2 0.04
44 1 0.02
45 32 0.70
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.37
Consensus pattern (45 bp):
CTAATATTCTACTTCTCTATCTCTAGATAATTCATCAAAATAAAA
Found at i:17278 original size:135 final size:132
Alignment explanation
Indices: 17049--17296 Score: 322
Period size: 135 Copynumber: 1.9 Consensus size: 132
17039 CGCCACTAAA
* *
17049 TTAGAATAATTGGTGGGAAAATTCCCCCAAAATAATTCAACATAAAGTTAAAAGATAAACTAAAC
1 TTAGAAAAATTGGTGGGAAAATTCCCCCAAAATAATTAAACATAAAGTTAAAAGATAAACTAAAC
*
17114 CATTTAGCGGCGTTTTGGTATTGGAAACGCCACTAAATAGTGGCGTTTCGTATAAAGACGCCGCT
66 CATTTAGCGGCGTTTTGGTATTAGAAACGCCACTAAATAGTGGCGTTTCGTATAAAGACGCCGCT
17179 AT
131 AT
* * *
17181 TTAGAAAAATTGGTGGGAAAAATATTCCCCCCAAAATAATTAAAGGA-AAAGTTAGAAG-TAAAG
1 TTAGAAAAATTGGTGGG--AAA-ATT-CCCCCAAAATAATTAAA-CATAAAGTTAAAAGATAAAC
* ** * *
17244 TAAGA-TATTTAGCGGCGTTTTTTTGTTAGAAACGCCACTAATTAGTGGCGTTT
61 TAA-ACCATTTAGCGGCGTTTTGGTATTAGAAACGCCACTAAATAGTGGCGTTT
17297 ACTTGAGAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
132 16 0.16
134 3 0.03
135 52 0.53
136 27 0.27
137 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (132 bp):
TTAGAAAAATTGGTGGGAAAATTCCCCCAAAATAATTAAACATAAAGTTAAAAGATAAACTAAAC
CATTTAGCGGCGTTTTGGTATTAGAAACGCCACTAAATAGTGGCGTTTCGTATAAAGACGCCGCT
AT
Found at i:17296 original size:33 final size:31
Alignment explanation
Indices: 17252--17345 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
17242 AGTAAGATAT
* *
17252 TTAGCGGCGTTTTTTTGTTAGAAACGCCACTAA
1 TTAGTGGCGTTTTCTTG--AGAAACGCCACTAA
* *
17285 TTAGTGGCGTTTACTTGAGAAATGCCACTAA
1 TTAGTGGCGTTTTCTTGAGAAACGCCACTAA
* * *
17316 TTAGTGGTGTTTTACTTTAAAAACG-CACTA
1 TTAGTGGCGTTTT-CTTGAGAAACGCCACTA
17346 TTATATTAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 29 0.57
32 8 0.16
33 14 0.27
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (31 bp):
TTAGTGGCGTTTTCTTGAGAAACGCCACTAA
Found at i:17312 original size:31 final size:32
Alignment explanation
Indices: 17271--17345 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
17261 TTTTTTTGTT
17271 AGAAACGCCACTAATTAGTGGCG-TTTACTTG
1 AGAAACGCCACTAATTAGTGGCGTTTTACTTG
* * *
17302 AGAAATGCCACTAATTAGTGGTGTTTTACTTT
1 AGAAACGCCACTAATTAGTGGCGTTTTACTTG
*
17334 AAAAACG-CACTA
1 AGAAACGCCACTA
17346 TTATATTAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 26 0.68
32 12 0.32
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (32 bp):
AGAAACGCCACTAATTAGTGGCGTTTTACTTG
Done.