Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015941.1 Corchorus capsularis cultivar CVL-1 contig15962, 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: 18880
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:47 original size:22 final size:22
Alignment explanation
Indices: 22--374 Score: 218
Period size: 22 Copynumber: 16.0 Consensus size: 22
12 AAGGTATCTG
* * *
22 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATAGTAATCAGT
44 AAAGAGTAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
66 AAAAAGTAAGAA-GGTAATCA--
1 AAAGAGTAA-AATAGTAATCAGT
* *
86 ACAAGAGTAAAATAATAGTCAGT
1 A-AAGAGTAAAATAGTAATCAGT
*
109 AAAAAGT-AAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
130 -AAGAGTAAAAAAGTAATAAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
151 -AAGAAGTAAAA-GGAAATCAGT
1 AAAG-AGTAAAATAGTAATCAGT
*
172 -AAGAGTAAAA-AGGTGATCAGT
1 AAAGAGTAAAATA-GTAATCAGT
193 AAAGAGTAAAA-AGCTAATCA--
1 AAAGAGTAAAATAG-TAATCAGT
213 ACAAGAAGTAAAA-AGGTAATCAGT
1 A-AAG-AGTAAAATA-GTAATCAGT
* * * *
237 AAAAAGCAAAA-GGCAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
258 AAAAAGTAAAAGAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
*
280 AAAAAAGGAGCAGAAAATAGTAATCAGT
1 ---AAA-GAG--TAAAATAGTAATCAGT
*
308 AAAAGAGTAAAATGGTAATCAGT
1 -AAAGAGTAAAATAGTAATCAGT
* *
331 AAAAAGTAAGAA-GGTAATCA--
1 AAAGAGTAA-AATAGTAATCAGT
*
351 ACAAGAGTAGAATAGTAATCAGT
1 A-AAGAGTAAAATAGTAATCAGT
374 A
1 A
375 CAAAATAAAG
Statistics
Matches: 266, Mismatches: 38, Indels: 53
0.75 0.11 0.15
Matches are distributed among these distances:
20 19 0.07
21 91 0.34
22 106 0.40
23 23 0.09
24 1 0.00
25 6 0.02
26 6 0.02
28 14 0.05
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (22 bp):
AAAGAGTAAAATAGTAATCAGT
Found at i:92 original size:43 final size:42
Alignment explanation
Indices: 45--383 Score: 274
Period size: 43 Copynumber: 7.7 Consensus size: 42
35 GTAATTAGTA
45 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
* * **
88 AAGAGTAAAATAATAGTCAGTAAAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * * * **
130 AAGAGTAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
* * *
172 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAAC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
* *
215 AAGAAGTAAAA-AGGTAATCAGTAAAAAGCAAAAGGCAATCAGTA-
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * * * *
259 AAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT--AAAA--AG--TAAAA-GGTAATCA--AC
*
310 AAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
353 AAGAGTAGAATAGTAATCAGTACAAAA-TAAA
1 AAGAGTAAAATAGTAATCAGTA-AAAAGTAAA
384 GAACAATCAG
Statistics
Matches: 243, Mismatches: 35, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
41 2 0.01
42 65 0.27
43 92 0.38
44 29 0.12
45 14 0.06
46 2 0.01
47 4 0.02
49 8 0.03
50 9 0.04
51 18 0.07
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:128 original size:21 final size:21
Alignment explanation
Indices: 30--417 Score: 170
Period size: 21 Copynumber: 17.8 Consensus size: 21
20 TGAAAGGGTA
* * *
30 AAATGGTAATTAGTAAAGAGT
1 AAATAGTAATCAGTAAAAAGT
51 AAAATAGTAATCAGTAAAAAGT
1 -AAATAGTAATCAGTAAAAAGT
*
73 AAGA-AGGTAATCA--ACAAGAGT
1 AA-ATA-GTAATCAGTA-AAAAGT
* *
94 AAAATAATAGTCAGTAAAAAGT
1 -AAATAGTAATCAGTAAAAAGT
*
116 AAATAGTAATCAGT-AAGAGT
1 AAATAGTAATCAGTAAAAAGT
* * *
136 AAAAAAGTAATAAGTAAGAAGT
1 -AAATAGTAATCAGTAAAAAGT
* *
158 AAA-AGGAAATCAGT-AAGAGT
1 AAATA-GTAATCAGTAAAAAGT
* * *
178 AAAAAGGTGATCAGTAAAGAGT
1 AAATA-GTAATCAGTAAAAAGT
* ** *
200 AAAAAGCTAATCAACAAGAAGT
1 AAATAG-TAATCAGTAAAAAGT
* *
222 AAAAAGGTAATCAGTAAAAAGC
1 AAATA-GTAATCAGTAAAAAGT
*
244 AAA-AGGCAATCAGTAAAAAGT
1 AAATA-GTAATCAGTAAAAAGT
* *
265 AAAAGAGTAATCAGTAAAAAAGGAGCAGA
1 -AAATAGTAATCAGT---AAA--A--AGT
294 AAATAGTAATCAGTAAAAGAGT
1 AAATAGTAATCAGTAAAA-AGT
*
316 AAAATGGTAATCAGTAAAAAGT
1 -AAATAGTAATCAGTAAAAAGT
*
338 AAGA-AGGTAATCA--ACAAGAGT
1 AA-ATA-GTAATCAGTA-AAAAGT
359 AGAATAGTAATCAGTACAAAA-T
1 A-AATAGTAATCAGTA-AAAAGT
* **
381 AAAGAACAATCAGTAAAATAGT
1 AAATAGTAATCAGTAAAA-AGT
* *
403 -GATGGTAATCAGTAA
1 AAATAGTAATCAGTAA
418 TTCAGTAAAA
Statistics
Matches: 285, Mismatches: 48, Indels: 67
0.71 0.12 0.17
Matches are distributed among these distances:
20 18 0.06
21 112 0.39
22 107 0.38
23 26 0.09
25 6 0.02
27 1 0.00
28 13 0.05
29 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (21 bp):
AAATAGTAATCAGTAAAAAGT
Found at i:280 original size:15 final size:15
Alignment explanation
Indices: 262--317 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
252 ATCAGTAAAA
262 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
277 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
291 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
305 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
318 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:14888 original size:2 final size:2
Alignment explanation
Indices: 14877--14921 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
14867 CTAGTTTTCT
14877 TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14915 TA GTA TA
1 TA -TA TA
14922 CAAGATAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 4 0.11
2 32 0.84
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16141 original size:24 final size:25
Alignment explanation
Indices: 16081--16141 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
16071 TTCAAACCCT
*
16081 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
16106 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
16130 AAA-TTCAGTTTC
1 AAACTTCA-TTTC
16142 CTTCATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 4 0.12
24 12 0.35
25 18 0.53
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:16178 original size:26 final size:26
Alignment explanation
Indices: 16149--16216 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
16139 TTCCTTCATT
16149 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
16175 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
16201 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
16217 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:17418 original size:2 final size:2
Alignment explanation
Indices: 17411--17437 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17401 ATTTTGTAGA
17411 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17438 GTTCAACGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17828 original size:18 final size:18
Alignment explanation
Indices: 17796--17831 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17786 CTTATGAAAT
**
17796 TCCAAAAAATTTTCAAAA
1 TCCAAAAAAACTTCAAAA
17814 TCCAAAAAAACTTCAAAA
1 TCCAAAAAAACTTCAAAA
17832 AACATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.22
Consensus pattern (18 bp):
TCCAAAAAAACTTCAAAA
Done.