Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022544.1 Corchorus olitorius cultivar O-4 contig22577, 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: 17349
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:69 original size:4 final size:4
Alignment explanation
Indices: 49--271 Score: 105
Period size: 4 Copynumber: 56.5 Consensus size: 4
39 AATAGGTAGC
* *
49 TAAA -AAA T-AA T-AA TAAA TAAA TAAA TAGA T-AA TAAC TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA
* * *
94 -AAGA TAAA T-AG TAAA TAAA TAGA TGATAA TTAA -AAA TAAA TAAA -AAGA
1 TAA-A TAAA TAAA TAAA TAAA TAAA T-A-AA TAAA TAAA TAAA TAAA TAA-A
* * * *
142 TAAA T-AG TAAA TAAA TATA TAATA GTTAA -AAA TAAA TAAA TAGA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
190 T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA TAGA TAAA T-AG
1 TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* *
237 TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA TA
1 TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TA
272 GAAAAAAATA
Statistics
Matches: 163, Mismatches: 32, Indels: 48
0.67 0.13 0.20
Matches are distributed among these distances:
3 31 0.19
4 110 0.67
5 14 0.09
6 8 0.05
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:171 original size:44 final size:44
Alignment explanation
Indices: 60--296 Score: 323
Period size: 44 Copynumber: 5.3 Consensus size: 44
50 AAAAAATAAT
* * *
60 AATAAATAAATAAATAGATAATAACTAAAATAAAAAGATAAATAGTA
1 AATAAATAGAT-AATAGTTAA-AAAT-AAATAAAAAGATAAATAGTA
* *
107 AATAAATAGATGATAATTAAAAATAAATAAAAAGATAAATAGTA
1 AATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTA
* *
151 AATAAATATATAATAGTTAAAAATAAATAAATAGATAAATAGTA
1 AATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTA
*
195 AATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTA
1 AATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTA
* * *
239 AATAAATAGATAATAGTTAAAAATAAATAAATAGAAAAAAATAGTG
1 AATAAATAGATAATAGTTAAAAATAAATAAA-A-AGATAAATAGTA
285 AATAAATA-ATAA
1 AATAAATAGATAA
297 AAAATCTTTT
Statistics
Matches: 174, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
44 134 0.77
45 7 0.04
46 23 0.13
47 10 0.06
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (44 bp):
AATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTA
Found at i:198 original size:7 final size:8
Alignment explanation
Indices: 10--242 Score: 82
Period size: 8 Copynumber: 30.1 Consensus size: 8
1 TAGGTATAG
10 AGATAAAT
1 AGATAAAT
* *
18 AGATACAG
1 AGATAAAT
26 AGA-ATAAT
1 AGATA-AAT
34 AGATAAAT
1 AGATAAAT
* **
42 AGGTAGCT
1 AGATAAAT
*
50 A-AAAAAT
1 AGATAAAT
57 A-AT-AAT
1 AGATAAAT
*
63 AAATAAAT
1 AGATAAAT
* *
71 AAATAGAT
1 AGATAAAT
*
79 A-ATAACT
1 AGATAAAT
* *
86 AAAATAAAA
1 -AGATAAAT
95 AGATAAAT
1 AGATAAAT
103 AG-TAAAT
1 AGATAAAT
* *
110 AAATAGAT
1 AGATAAAT
*
118 -GATAATT
1 AGATAAAT
125 A-A-AAAT
1 AGATAAAT
* *
131 AAATAAAA
1 AGATAAAT
139 AGATAAAT
1 AGATAAAT
147 AG-TAAAT
1 AGATAAAT
* *
154 AAATATAT
1 AGATAAAT
**
162 A-ATAGTT
1 AGATAAAT
169 A-A-AAAT
1 AGATAAAT
*
175 AAATAAAT
1 AGATAAAT
183 AGATAAAT
1 AGATAAAT
191 AGTAAATAAAT
1 AG---ATAAAT
202 AGAT-AAT
1 AGATAAAT
*
209 AGTTAAAAAT
1 AG--ATAAAT
*
219 AAATAAAT
1 AGATAAAT
227 AGATAAAT
1 AGATAAAT
235 AG-TAAAT
1 AGATAAAT
242 A
1 A
243 AATAGATAAT
Statistics
Matches: 167, Mismatches: 39, Indels: 39
0.68 0.16 0.16
Matches are distributed among these distances:
6 11 0.07
7 47 0.28
8 91 0.54
9 6 0.04
10 4 0.02
11 8 0.05
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Found at i:1110 original size:2 final size:2
Alignment explanation
Indices: 1103--1130 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1093 TAATACATAC
1103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1131 GAAAAAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2344 original size:55 final size:55
Alignment explanation
Indices: 2278--2388 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
2268 TGTGTTTCCT
2278 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
2333 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
2388 T
1 T
2389 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (55 bp):
TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
Found at i:2531 original size:43 final size:42
Alignment explanation
Indices: 2453--2534 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 42
2443 TAAGGATCAG
2453 GATTTGAGTTGAGTATTGCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTGCTTAATTTACAAAGAATTTTCTAT
**
2495 GATTTGAGTTGAGTATTTTTTTAATTTACAAAGAATTTTC
1 GATTTGAGTTGAGTA-TTGCTTAATTTACAAAGAATTTTC
2535 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 15 0.41
43 22 0.59
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTGCTTAATTTACAAAGAATTTTCTAT
Found at i:8733 original size:37 final size:37
Alignment explanation
Indices: 8622--8752 Score: 136
Period size: 37 Copynumber: 3.5 Consensus size: 37
8612 AAAATATTGT
* * * *
8622 TGATGGGAACTTTCCCACTTTGAAAACTAAAACCAAAAC
1 TGATGGGAACTTTCCCAATTTGAAAACTTAGA--AAACC
** ***
8661 TGATGGGAACTTTCCCTAAAATGAACGGTTAGAAAACC
1 TGATGGGAACTTTCCC-AATTTGAAAACTTAGAAAACC
* *
8699 TGATGGGAACTTTCCCAATTTGAAAACTTTGAAAACT
1 TGATGGGAACTTTCCCAATTTGAAAACTTAGAAAACC
8736 TGATGGGAACTTTCCCA
1 TGATGGGAACTTTCCCA
8753 CTTTTGATTT
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
37 31 0.41
38 20 0.27
39 16 0.21
40 8 0.11
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (37 bp):
TGATGGGAACTTTCCCAATTTGAAAACTTAGAAAACC
Found at i:8808 original size:58 final size:58
Alignment explanation
Indices: 8718--8874 Score: 271
Period size: 58 Copynumber: 2.7 Consensus size: 58
8708 CTTTCCCAAT
8718 TTGAAAACTTTGAAAACTTGATGGGAACTTTCCCACTTTTGATTTGAAAAGACCTAAA
1 TTGAAAACTTTGAAAACTTGATGGGAACTTTCCCACTTTTGATTTGAAAAGACCTAAA
* *
8776 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTTGATTTGAAAAGATCTAAA
1 TTGAAAACTTTGAAAACTTGATGGGAACTTTCCCACTTTTGATTTGAAAAGACCTAAA
* *
8834 TTGAACACTTTGAAAACTTGAAGGGAACTTTCCCA-TTTTGA
1 TTGAAAACTTTGAAAACTTGATGGGAACTTTCCCACTTTTGA
8875 AAACTTGAAG
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 6 0.06
58 89 0.94
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (58 bp):
TTGAAAACTTTGAAAACTTGATGGGAACTTTCCCACTTTTGATTTGAAAAGACCTAAA
Found at i:8874 original size:28 final size:28
Alignment explanation
Indices: 8842--8958 Score: 120
Period size: 28 Copynumber: 4.4 Consensus size: 28
8832 AATTGAACAC
8842 TTTGAAAACTTGAAGGGAACTTTCCCAT
1 TTTGAAAACTTGAAGGGAACTTTCCCAT
* *
8870 TTTGAAAACTTGAAGGGAACTTTTCAAT
1 TTTGAAAACTTGAAGGGAACTTTCCCAT
* ** *
8898 TTTGAAAACTTAAATCGAA---T---AG
1 TTTGAAAACTTGAAGGGAACTTTCCCAT
* *
8920 TTTGAAAACTTGATGGGAACTTTCCCAC
1 TTTGAAAACTTGAAGGGAACTTTCCCAT
8948 TTTGAAAACTT
1 TTTGAAAACTT
8959 AAGTTGAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
22 16 0.22
25 2 0.03
28 54 0.75
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (28 bp):
TTTGAAAACTTGAAGGGAACTTTCCCAT
Found at i:8929 original size:50 final size:50
Alignment explanation
Indices: 8870--8986 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 50
8860 ACTTTCCCAT
* * *
8870 TTTGAAAACTTGAAGGGAACTTTTCAATTTTGAAAACTTAAATCGAATAG
1 TTTGAAAACTTGAAGGGAACTTTCCAACTTTGAAAACTTAAATCGAATAC
* * * *
8920 TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAACTTAAGTTGAATAC
1 TTTGAAAACTTGAAGGGAACTTTCCAACTTTGAAAACTTAAATCGAATAC
8970 TTTGAAAACTTTGAAGG
1 TTTGAAAAC-TTGAAGG
8987 AAATGCTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 52 0.90
51 6 0.10
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (50 bp):
TTTGAAAACTTGAAGGGAACTTTCCAACTTTGAAAACTTAAATCGAATAC
Found at i:12166 original size:20 final size:21
Alignment explanation
Indices: 12128--12167 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12118 TAAAACTAAG
12128 TCTGATTTGAATTTGAAAACT
1 TCTGATTTGAATTTGAAAACT
12149 TCTG-TTTGAATCTT-AAAAC
1 TCTGATTTGAAT-TTGAAAAC
12168 ACTTGATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTGATTTGAATTTGAAAACT
Done.