Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020014.1 Corchorus olitorius cultivar O-4 contig20047, 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: 9226
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:200 original size:20 final size:19
Alignment explanation
Indices: 177--251 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 19
167 AAAAATATTA
177 AAATAAAAAAAGTAATAGAT
1 AAATAAAAAAA-TAATAGAT
*
197 AAATAAATAAATAAATAGAT
1 AAATAAAAAAAT-AATAGAT
217 AAATAAGTAAAAATAATAGAT
1 AAATAA--AAAAATAATAGAT
*
238 AAATAAAAAGATAA
1 AAATAAAAAAATAA
252 ATAGGTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.16
20 23 0.47
21 13 0.27
22 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAAAAAAATAATAGAT
Found at i:204 original size:4 final size:4
Alignment explanation
Indices: 177--254 Score: 61
Period size: 4 Copynumber: 19.2 Consensus size: 4
167 AAAAATATTA
* * * *
177 AAAT AAAA AAAGT -AAT AGAT AAAT AAAT AAAT AAAT AGAT AAAT AAGT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
225 AAAA ATAAT AGAT AAAT AAA- AAGAT AAAT A
1 AAAT A-AAT AAAT AAAT AAAT AA-AT AAAT A
255 GGTATATAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
3 3 0.05
4 49 0.86
5 5 0.09
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:205 original size:12 final size:12
Alignment explanation
Indices: 195--364 Score: 85
Period size: 12 Copynumber: 15.0 Consensus size: 12
185 AAAGTAATAG
*
195 ATAAATAAATAA
1 ATAAATAGATAA
207 ATAAATAGATAA
1 ATAAATAGATAA
*
219 ATAAGTA-A-AA
1 ATAAATAGATAA
229 AT-AATAGATAA
1 ATAAATAGATAA
*
240 ATAAAAAGATAA
1 ATAAATAGATAA
** * *
252 ATAGGTATATAG
1 ATAAATAGATAA
*
264 ATAATTAGATAA
1 ATAAATAGATAA
** *
276 ATAGGTAGGTAA
1 ATAAATAGATAA
*
288 A-AAA-A-ATAG
1 ATAAATAGATAA
297 AT-AATAG-TAA
1 ATAAATAGATAA
307 ATAAATAGAT-A
1 ATAAATAGATAA
** * *
318 ATAGCTAAATTA
1 ATAAATAGATAA
*
330 ATGAATA-A-AA
1 ATAAATAGATAA
340 GGATAAATAG-TAA
1 --ATAAATAGATAA
353 ATAAATAGATAA
1 ATAAATAGATAA
365 TAGTTAAATT
Statistics
Matches: 115, Mismatches: 29, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
9 8 0.07
10 12 0.10
11 28 0.24
12 65 0.57
13 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (12 bp):
ATAAATAGATAA
Found at i:337 original size:19 final size:18
Alignment explanation
Indices: 190--383 Score: 75
Period size: 16 Copynumber: 10.5 Consensus size: 18
180 TAAAAAAAGT
*
190 AATAGATAAATAAATAAATA
1 AATAGAT-AAT-AGTAAATA
*
210 AATAGATAA-A-TAAGTA
1 AATAGATAATAGTAAATA
226 AA-A-ATAATAGATAAATA
1 AATAGATAATAG-TAAATA
* **
243 AAAAGATAA-A-TAGGTA
1 AATAGATAATAGTAAATA
* *
259 TATAGATAAT--TAGATA
1 AATAGATAATAGTAAATA
* * *
275 AATAGGT-A-GGTAAAAAA
1 AATAGATAATAGT-AAATA
292 AATAGATAATAGTAAATA
1 AATAGATAATAGTAAATA
310 AATAGATAATAGCTAAATTAA
1 AATAGATAATAG-TAAA-T-A
331 TGAATAAAAGGATAAATAGTAAATA
1 --AAT---A-GAT-AATAGTAAATA
*
356 AATAGATAATAGTTAAATT
1 AATAGATAATAG-TAAATA
*
375 AATAAATAA
1 AATAGATAA
384 AAAAATCGTT
Statistics
Matches: 136, Mismatches: 16, Indels: 45
0.69 0.08 0.23
Matches are distributed among these distances:
14 4 0.03
15 3 0.02
16 29 0.21
17 17 0.12
18 24 0.18
19 28 0.21
20 9 0.07
21 1 0.01
23 6 0.04
25 1 0.01
26 2 0.01
27 7 0.05
28 5 0.04
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (18 bp):
AATAGATAATAGTAAATA
Found at i:754 original size:12 final size:12
Alignment explanation
Indices: 737--762 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
727 CTAAATTATT
737 AAAAAAAAATTA
1 AAAAAAAAATTA
749 AAAAAAAAATTA
1 AAAAAAAAATTA
761 AA
1 AA
763 CTCTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:1786 original size:35 final size:35
Alignment explanation
Indices: 1745--2654 Score: 1208
Period size: 35 Copynumber: 26.0 Consensus size: 35
1735 ATCTTTTGGG
* * * * *
1745 GATCAACTCTGACCATTGAAAACTTGTTGGAATGT
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* ** * *
1780 GATCAACTTTGATCATAAAAAAAAAGTTTCTTG-AATAA
1 GATCAACTCTGATCAT---CGAAAA-CTTCTTGAAATGA
*
1818 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1853 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
1888 -ATCAACTCTGATCAT-GAAGAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAA-AACTTCTTGAAATGA
* ** *
1922 GATCAACTCTGATAATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
1957 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1992 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2027 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** *
2062 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
2097 GATCAACTCTGATCATCGAAAACTTCTTAAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
2132 GGTCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2167 GATCAACTCTAATCAACGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * * *
2202 GATCAATTCTGATCAACGAAAACTTCTTGGAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** *
2237 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-CGAAAACTTCTTGAAATGA
*
2273 GATCAACTCTGATCATCAAAAACTTC-TGAAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTG-AAATGA
2308 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2343 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2378 GATCAACTCTGATCAT-AAAAACTT-TTGGAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2411 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
2446 GATCAACTCTGATCATCAAAAACTTCTTG-AATGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAT-GA
* *
2481 GATCAACTCTGATCAT-AAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2515 GATCAAATCTGATCATCGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
2550 -ATTCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GA-TCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2585 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** *
2620 GATCAACTCTGATCATAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
2655 CCGCACTGGG
Statistics
Matches: 784, Mismatches: 73, Indels: 36
0.88 0.08 0.04
Matches are distributed among these distances:
33 25 0.03
34 84 0.11
35 612 0.78
36 36 0.05
38 22 0.03
39 5 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
Found at i:2764 original size:22 final size:22
Alignment explanation
Indices: 2736--2783 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2726 AACACCTGTA
*
2736 CTTGAC-TCTTCATCTACCCTTT
1 CTTGACTTCTTC-TCTACCCATT
*
2758 CTTGACTTCTTCTTTACCCATT
1 CTTGACTTCTTCTCTACCCATT
2780 CTTG
1 CTTG
2784 GCTATTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.48
Consensus pattern (22 bp):
CTTGACTTCTTCTCTACCCATT
Found at i:3869 original size:37 final size:39
Alignment explanation
Indices: 3792--3871 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 39
3782 ATCTTTTTGA
** * *
3792 AAAACATTTTTTTCTTTTTTGAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTTC-TTTTTGAAAAGATCACACCTAGAGG
3832 AAAACA-TTTTTTC-TTTTGAAAAGATCACACCTAGAGG
1 AAAACATTTTTTTCTTTTTGAAAAGATCACACCTAGAGG
3869 AAA
1 AAA
3872 GTTTCATTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 23 0.64
39 7 0.19
40 6 0.17
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (39 bp):
AAAACATTTTTTTCTTTTTGAAAAGATCACACCTAGAGG
Found at i:4111 original size:16 final size:16
Alignment explanation
Indices: 4077--4117 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4067 CTTCTTTCTT
**
4077 TTCTTTTC-TTTTCTT
1 TTCTTTTCTTTTTCAA
4092 TTCTTTTCTTTTTCAA
1 TTCTTTTCTTTTTCAA
4108 TTCTTTTCTT
1 TTCTTTTCTT
4118 CATTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTCTTTTTCAA
Found at i:4129 original size:5 final size:5
Alignment explanation
Indices: 4071--4117 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
4061 TTTCAACTTC
* *
4071 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCTT TTTCA ATTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTTCT T
4118 CATTTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 32 0.86
6 5 0.14
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:7100 original size:20 final size:19
Alignment explanation
Indices: 7077--7151 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 19
7067 AAAAATATTA
7077 AAATAAAAAAAGTAATAGAT
1 AAATAAAAAAA-TAATAGAT
*
7097 AAATAAATAAATAAATAGAT
1 AAATAAAAAAAT-AATAGAT
7117 AAATAAGTAAAAATAATAGAT
1 AAATAA--AAAAATAATAGAT
*
7138 AAATAAAAAGATAA
1 AAATAAAAAAATAA
7152 ATAGGTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.16
20 23 0.47
21 13 0.27
22 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAAAAAAATAATAGAT
Found at i:7104 original size:4 final size:4
Alignment explanation
Indices: 7077--7154 Score: 61
Period size: 4 Copynumber: 19.2 Consensus size: 4
7067 AAAAATATTA
* * * *
7077 AAAT AAAA AAAGT -AAT AGAT AAAT AAAT AAAT AAAT AGAT AAAT AAGT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
7125 AAAA ATAAT AGAT AAAT AAA- AAGAT AAAT A
1 AAAT A-AAT AAAT AAAT AAAT AA-AT AAAT A
7155 GGTATATAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
3 3 0.05
4 49 0.86
5 5 0.09
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:7105 original size:12 final size:12
Alignment explanation
Indices: 7095--7264 Score: 85
Period size: 12 Copynumber: 15.0 Consensus size: 12
7085 AAAGTAATAG
*
7095 ATAAATAAATAA
1 ATAAATAGATAA
7107 ATAAATAGATAA
1 ATAAATAGATAA
*
7119 ATAAGTA-A-AA
1 ATAAATAGATAA
7129 AT-AATAGATAA
1 ATAAATAGATAA
*
7140 ATAAAAAGATAA
1 ATAAATAGATAA
** * *
7152 ATAGGTATATAG
1 ATAAATAGATAA
*
7164 ATAATTAGATAA
1 ATAAATAGATAA
** *
7176 ATAGGTAGGTAA
1 ATAAATAGATAA
*
7188 A-AAA-A-ATAG
1 ATAAATAGATAA
7197 AT-AATAG-TAA
1 ATAAATAGATAA
7207 ATAAATAGAT-A
1 ATAAATAGATAA
** * *
7218 ATAGCTAAATTA
1 ATAAATAGATAA
*
7230 ATGAATA-A-AA
1 ATAAATAGATAA
7240 GGATAAATAG-TAA
1 --ATAAATAGATAA
7253 ATAAATAGATAA
1 ATAAATAGATAA
7265 TAGTTAAATT
Statistics
Matches: 115, Mismatches: 29, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
9 8 0.07
10 12 0.10
11 28 0.24
12 65 0.57
13 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (12 bp):
ATAAATAGATAA
Found at i:7237 original size:19 final size:18
Alignment explanation
Indices: 7090--7283 Score: 75
Period size: 16 Copynumber: 10.5 Consensus size: 18
7080 TAAAAAAAGT
*
7090 AATAGATAAATAAATAAATA
1 AATAGAT-AAT-AGTAAATA
*
7110 AATAGATAA-A-TAAGTA
1 AATAGATAATAGTAAATA
7126 AA-A-ATAATAGATAAATA
1 AATAGATAATAG-TAAATA
* **
7143 AAAAGATAA-A-TAGGTA
1 AATAGATAATAGTAAATA
* *
7159 TATAGATAAT--TAGATA
1 AATAGATAATAGTAAATA
* * *
7175 AATAGGT-A-GGTAAAAAA
1 AATAGATAATAGT-AAATA
7192 AATAGATAATAGTAAATA
1 AATAGATAATAGTAAATA
7210 AATAGATAATAGCTAAATTAA
1 AATAGATAATAG-TAAA-T-A
7231 TGAATAAAAGGATAAATAGTAAATA
1 --AAT---A-GAT-AATAGTAAATA
*
7256 AATAGATAATAGTTAAATT
1 AATAGATAATAG-TAAATA
*
7275 AATAAATAA
1 AATAGATAA
7284 AAAAATCGTT
Statistics
Matches: 136, Mismatches: 16, Indels: 45
0.69 0.08 0.23
Matches are distributed among these distances:
14 4 0.03
15 3 0.02
16 29 0.21
17 17 0.12
18 24 0.18
19 28 0.21
20 9 0.07
21 1 0.01
23 6 0.04
25 1 0.01
26 2 0.01
27 7 0.05
28 5 0.04
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (18 bp):
AATAGATAATAGTAAATA
Done.