Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021016.1 Corchorus olitorius cultivar O-4 contig21049, 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: 13362
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:6466 original size:27 final size:28
Alignment explanation
Indices: 6436--6525 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 28
6426 AAATGATCAC
6436 AATGCCCCCT-GAAGTACAAATGACTAA
1 AATGCCCCCTAGAAGTACAAATGACTAA
** *
6463 AATGCCCCCTAGGTGTA-AAGATGACCAA
1 AATGCCCCCTAGAAGTACAA-ATGACTAA
* * * *
6491 AATG-CCCTTGGACGTGCAAATGACTAA
1 AATGCCCCCTAGAAGTACAAATGACTAA
*
6518 AACGCCCC
1 AATGCCCC
6526 TGGATTTTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
27 29 0.59
28 20 0.41
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.18
Consensus pattern (28 bp):
AATGCCCCCTAGAAGTACAAATGACTAA
Found at i:6712 original size:90 final size:87
Alignment explanation
Indices: 6551--6715 Score: 224
Period size: 90 Copynumber: 1.9 Consensus size: 87
6541 ACCCAAAATT
*
6551 CCCCTAGATGACCCTAATGCCAATTAAGCAACAAATTGATTTAAATAAAGGATATGGGACAAAAA
1 CCCCTAGATGACCCTAATGCCAATTAAGAAACAAATTGATTTAAATAAAGGATATGGGACAAAAA
*
6616 TGGGTGTCTACAGCAAAAATGC
66 TAGGTGTCTACAGCAAAAATGC
* * * * *
6638 CCCCTAGGTGATCTTAATGCCTGATTAAGAAATAAATTGATTTAAATTGAAAGGATAT-GGACAA
1 CCCCTAGATGACCCTAATGCC-AATTAAGAAACAAATTGATTTAAA-T-AAAGGATATGGGAC-A
6702 AAAATAGGTGTCTA
62 AAAATAGGTGTCTA
6716 TAGCTGCCCC
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
87 18 0.27
88 21 0.31
89 5 0.07
90 23 0.34
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (87 bp):
CCCCTAGATGACCCTAATGCCAATTAAGAAACAAATTGATTTAAATAAAGGATATGGGACAAAAA
TAGGTGTCTACAGCAAAAATGC
Found at i:6960 original size:50 final size:50
Alignment explanation
Indices: 6885--7365 Score: 755
Period size: 50 Copynumber: 9.5 Consensus size: 50
6875 CGGTCAACTT
*
6885 CTTTGAACTGTCTTCCAATTTAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
6935 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGCACCTTCTTCCGTTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * * *
6985 CTTTGAACTGCCTTCCAATTGAATCTTAAAAAGGACCGCCTTCTGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
* * *
7036 CTTTGAACTGTCTTCTAATTCAATCTTAAAAAGAACCATCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
*
7087 CTTTGAACTGTCTTCCAATTCTATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
7137 CTTTGAACTGCCTTCCAATTCAATCTTAAAAAGGAGCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
* * *
7188 CTTTGAACTGTTTTCTAATTCAATCTTAAAAAGGACTGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
* *
7239 CTTTCAACTGCCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
7289 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
7339 CTTTGAACTGTCTTCCAATTCAATCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT
7366 TAGAAAATCA
Statistics
Matches: 392, Mismatches: 37, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
50 214 0.55
51 178 0.45
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:7059 original size:101 final size:101
Alignment explanation
Indices: 6885--7365 Score: 759
Period size: 101 Copynumber: 4.8 Consensus size: 101
6875 CGGTCAACTT
*
6885 CTTTGAACTGTCTTCCAATTTAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
* * *
6950 CAATTCAATCTT-AAAAGCACCTTCTTCCGTTTATC
66 CAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* * * *
6985 CTTTGAACTGCCTTCCAATTGAATCTTAAAAAGGACCGCCTTCTGCTTATCCTTTGAACTGTCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
* * *
7050 CTAATTCAATCTTAAAAAGAACCATCTTCCGCTTATC
65 CCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* *
7087 CTTTGAACTGTCTTCCAATTCTATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGCCTTC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
*
7152 CAATTCAATCTTAAAAAGGAGCGTCTTCCGCTTATC
66 CAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
* * * * *
7188 CTTTGAACTGTTTTCTAATTCAATCTTAAAAAGGACTGTCTTCCGCTTATCCTTTCAACTGCCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
7253 CCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
65 CCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
7289 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
7354 CAATTCAATCTT
66 CAATTCAATCTT
7366 TAGAAAATCA
Statistics
Matches: 349, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
100 72 0.21
101 185 0.53
102 92 0.26
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (101 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
CAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
Found at i:7162 original size:152 final size:152
Alignment explanation
Indices: 6885--7365 Score: 786
Period size: 152 Copynumber: 3.2 Consensus size: 152
6875 CGGTCAACTT
*
6885 CTTTGAACTGTCTTCCAATTTAATCTT-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
* * * *
6949 CCAATTCAATCTTAAAAGCACCTTCTTCCGTTTATCCTTTGAACTGCCTTCCAATTGAATCTTAA
66 CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGCCTTCCAATTCAATCTTAA
* *
7014 AAAGGACCGCCTTCTGCTTATC
131 AAAGGACCGTCTTCCGCTTATC
* * *
7036 CTTTGAACTGTCTTCTAATTCAATCTTAAAAAGAACCATCTTCCGCTTATCCTTTGAACTGTCTT
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
*
7101 CCAATTCTATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGCCTTCCAATTCAATCTTAA
66 CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGCCTTCCAATTCAATCTTAA
*
7166 AAAGGAGCGTCTTCCGCTTATC
131 AAAGGACCGTCTTCCGCTTATC
* * * * *
7188 CTTTGAACTGTTTTCTAATTCAATCTTAAAAAGGACTGTCTTCCGCTTATCCTTTCAACTGCCTT
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
*
7253 CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTT-A
66 CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGCCTTCCAATTCAATCTTAA
7317 AAAGGACCGTCTTCCGCTTATC
131 AAAGGACCGTCTTCCGCTTATC
7339 CTTTGAACTGTCTTCCAATTCAATCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT
7366 TAGAAAATCA
Statistics
Matches: 306, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 72 0.24
152 234 0.76
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (152 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGCCTTCCAATTCAATCTTAA
AAAGGACCGTCTTCCGCTTATC
Found at i:7301 original size:23 final size:23
Alignment explanation
Indices: 7275--7354 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
7265 TAAAAGGACC
7275 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
** * * *
7298 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCGCTT--ATCCTT---TGAACT
7325 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
7348 GTCTTCC
1 GTCTTCC
7355 AATTCAATCT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 19 0.46
24 3 0.07
25 4 0.10
26 3 0.07
27 12 0.29
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACT
Found at i:7700 original size:64 final size:64
Alignment explanation
Indices: 7594--8237 Score: 903
Period size: 64 Copynumber: 10.1 Consensus size: 64
7584 CCGGTGCATC
* * * * * *
7594 TCTTAACAAGATCGTCTTCCGATCAACTTTTGAAGATTGTTGAGAAACCATTTTCTAGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * *
7658 TCTCGACAAGATCGTCTTCCAATTAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
*
7722 TCTTGACAAGATCGTCTTCTGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * * * *
7786 TTTTAACAAGATCATCTTCCGATCAATTTCTGAAAACTGTTGAGAAACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * *
7850 TCTTGACAAGATCGTCTTCCGCTCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * *
7914 TCTTGATAAGATCGTCTTTCGATTAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * * * * * * *
7978 TTTTAACATGATCATCTTCCAATAAATTTCTGAAAACTGTTGAGAAACCATCTTCTGGCGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * * *
8042 TCTTGACAAGATCTTCTTCCGCT-AATCTTCTGAAAATTATTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAA-CTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * * * *
8106 CCTTGACAAGATCGTCTTCCGATTAAATTCTGAAAATTGTTGAGAAACAATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
* * *
8170 TTTTGACAAGATCGTCTTCCGATCAATTTCTGAAAACTGTTGAGAACCCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
8234 TCTT
1 TCTT
8238 TAATGAGATT
Statistics
Matches: 511, Mismatches: 67, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
63 2 0.00
64 507 0.99
65 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT
Found at i:8314 original size:67 final size:67
Alignment explanation
Indices: 8220--8499 Score: 373
Period size: 67 Copynumber: 4.2 Consensus size: 67
8210 TGAGAACCCA
* * * * *
8220 TCTTCTGGTGTACTTCTTTAATGAGATTGCCTTCCAATCCATATTTGAAAATTCTTTCTAGCAAA
1 TCTTCCGGTGTA-TTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAA
8285 CAG
65 CAG
* * * **
8288 TCTTCTGATGTATTCCTTAATGAGATTGTCTTCTAATGGACATTTGAAAATTCTTTCTAGCAAA-
1 TCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAAC
8352 ACG
66 A-G
8355 TCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAAC
1 TCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAAC
*
8420 CG
66 AG
* * * * * *
8422 TCTTCCGGGGTACTCCTAAATGAGATTGTCTTCCAATCAACAGTGGAAAATCCTTTCTAGCAAAC
1 TCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAAC
*
8487 TG
66 AG
8489 TCTTCCGGTGT
1 TCTTCCGGTGT
8500 TCTTCTTAAA
Statistics
Matches: 189, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
66 1 0.01
67 177 0.94
68 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (67 bp):
TCTTCCGGTGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAAC
AG
Found at i:10729 original size:15 final size:14
Alignment explanation
Indices: 10693--10731 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
10683 ACCCAAAACC
10693 TTTTGAAAACCTAT
1 TTTTGAAAACCTAT
* *
10707 TTTTGAAAGCCTTT
1 TTTTGAAAACCTAT
10721 TTCTTGAAAAC
1 TT-TTGAAAAC
10732 AATTTCCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (14 bp):
TTTTGAAAACCTAT
Found at i:12553 original size:19 final size:18
Alignment explanation
Indices: 12520--12555 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12510 TGAAAATAAT
12520 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
12538 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
12556 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.