Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020482.1 Corchorus olitorius cultivar O-4 contig20515, 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: 26358
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:8239 original size:25 final size:24
Alignment explanation
Indices: 8202--8248 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
8192 CTAGAAAATT
8202 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
8228 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
8249 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 (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:9356 original size:18 final size:17
Alignment explanation
Indices: 9333--9370 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
9323 CCCAAATTAC
9333 TTATGGAAATTAGGGAAA
1 TTATGGAAATTA-GGAAA
9351 TTATGGAAATTAGGAAA
1 TTATGGAAATTAGGAAA
9368 TTA
1 TTA
9371 AATGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (17 bp):
TTATGGAAATTAGGAAA
Found at i:9368 original size:8 final size:9
Alignment explanation
Indices: 9337--9370 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
9327 AATTACTTAT
9337 GGAAATTAG
1 GGAAATTAG
*
9346 GGAAATTAT
1 GGAAATTAG
9355 GGAAATTA-
1 GGAAATTAG
9363 GGAAATTA
1 GGAAATTA
9371 AATGAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (9 bp):
GGAAATTAG
Found at i:11137 original size:22 final size:23
Alignment explanation
Indices: 11112--11160 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
11102 AGGAAATCAT
11112 GGAGATTTCAGAGAAAA-AA-CAC
1 GGAGATTT-AGAGAAAATAAGCAC
* *
11134 GGAGGTTTTGAGAAAATAAGCAC
1 GGAGATTTAGAGAAAATAAGCAC
11157 GGAG
1 GGAG
11161 CTTGGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 7 0.30
ACGTcount: A:0.43, C:0.10, G:0.31, T:0.16
Consensus pattern (23 bp):
GGAGATTTAGAGAAAATAAGCAC
Found at i:13849 original size:41 final size:41
Alignment explanation
Indices: 13792--13869 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
13782 CTATAACTTT
* *
13792 ATTTTATGAGTTCTTTTAAGAAAATTCAGTTAAGAAATGGA
1 ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAATGGA
*
13833 ATTTTATAAGTGCTTTTAAGAAAATTTAGTTAAGAAA
1 ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAA
13870 AGAAAGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (41 bp):
ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAATGGA
Found at i:22639 original size:221 final size:220
Alignment explanation
Indices: 22190--22813 Score: 950
Period size: 221 Copynumber: 2.8 Consensus size: 220
22180 TAAAAGGCTT
* * * * * *
22190 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGGGTAATTACAAAAAAGGGTAGTAGGAAAAG
1 AAACATTAATTAAAAGCAATTAAGGAAGTGAAATGAGTAATTACAAAAAAAGGTTGCAGGAAAAG
* * * * *
22255 GAAGGGGGGAAACTCATGGAGAGACTTTTTAGTCATCCGAAAATTGAGAAAAGACAAAAAAAAAA
66 GAAGGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAAATGAGAAAAGAC--CAAAAAAA
*
22320 GCCAAAAGGTGACACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAGGTACTGAGTT
129 G-CAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAGGTACTGAGTT
22385 GGTGAAAGGAAAAAAGAAAAGGGGGGAG
193 GGTGAAAGGAAAAAAGAAAAGGGGGGAG
* *
22413 AAACATTAATTAAAAGCAATTAAGGAAGTGAAATTAGTAAATACAAAAAAAGGTTGCAGGAAAAG
1 AAACATTAATTAAAAGCAATTAAGGAAGTGAAATGAGTAATTACAAAAAAAGGTTGCAGGAAAAG
* *
22478 GAAGGGGGGAAATTCATAGAGGGGCTTTTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAAAAGT
66 GAAGGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAAATGAGAAAAGACCAAAAAAAG-
* *
22543 CAAAAGATGGCACCACATTAATCCTCAATTTGGCCTTTTAGTGATTACCCTAGGTACTGAGTTGG
130 CAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAGGTACTGAGTTGG
*
22608 TGAGAGGAAAAAAGAAAAGGGGGGAG
195 TGAAAGGAAAAAAGAAAAGGGGGGAG
*
22634 AAACATTAATTAAAAGCAATTAAGGAAGTGAAATGAGTAATTACAAAAAAA-TTTAGCAGGAAAA
1 AAACATTAATTAAAAGCAATTAAGGAAGTGAAATGAGTAATTACAAAAAAAGGTT-GCAGGAAAA
* *
22698 -G--GGAGGGAAACTCATAGAGGGGCTTTTTAGTCATTCGAAAAATGAGAAAAGACCAAAAAAAG
65 GGAAGGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAAATGAGAAAAGACCAAAAAAAG
* *
22760 CTAAAAGGTGGCACCACATTAATTCTCAATTTGGCCTTTTAGTAATTTCCCTAG
130 C-AAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAG
22814 TAGCTAAAAA
Statistics
Matches: 369, Mismatches: 30, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
217 1 0.00
218 105 0.28
220 3 0.01
221 153 0.41
223 107 0.29
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.21
Consensus pattern (220 bp):
AAACATTAATTAAAAGCAATTAAGGAAGTGAAATGAGTAATTACAAAAAAAGGTTGCAGGAAAAG
GAAGGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAAATGAGAAAAGACCAAAAAAAGC
AAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAGGTACTGAGTTGGT
GAAAGGAAAAAAGAAAAGGGGGGAG
Found at i:23086 original size:40 final size:41
Alignment explanation
Indices: 23042--23127 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 41
23032 GCATTACCTA
*
23042 AATTCTA-CTCCATCTCTAGGCAATTCATCAAAATAAAGCT
1 AATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAGCT
* * *
23082 AATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAGTT
1 AATTCTA--CCTCCATCTCTAGACAATTCATCAAAATAAAGCT
23125 AAT
1 AAT
23128 ATTAATTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
40 7 0.18
43 32 0.82
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (41 bp):
AATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAGCT
Found at i:25508 original size:3 final size:3
Alignment explanation
Indices: 25500--25534 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
25490 GATTTAGTAA
25500 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
25535 ATACTCCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25551 original size:2 final size:2
Alignment explanation
Indices: 25546--25579 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25536 TACTCCTATC
25546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25580 CCAATAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.