Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020070.1 Corchorus olitorius cultivar O-4 contig20103, 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: 38052
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Found at i:12584 original size:17 final size:16
Alignment explanation
Indices: 12555--12588 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12545 CTCCTCTGTT
12555 TTTTTCAATTTTTCTC
1 TTTTTCAATTTTTCTC
*
12571 TTTTTCCATCTTTTCTC
1 TTTTTCAAT-TTTTCTC
12588 T
1 T
12589 ATTAGTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTCAATTTTTCTC
Found at i:15052 original size:38 final size:39
Alignment explanation
Indices: 15008--15085 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
14998 TAAGCAGGTT
*
15008 TGAGGCTTTAAGCAGA-GACCTAAGCAGGTTTGATTAAA
1 TGAGGCTCTAAGCAGAGGACCTAAGCAGGTTTGATTAAA
15046 TGAGGCTCTAAGCAGAGGGACCTAAGCAGGTTTGATTAAA
1 TGAGGCTCTAAGCAGA-GGACCTAAGCAGGTTTGATTAAA
15086 CACGAATTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 15 0.41
40 22 0.59
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.24
Consensus pattern (39 bp):
TGAGGCTCTAAGCAGAGGACCTAAGCAGGTTTGATTAAA
Found at i:15079 original size:40 final size:38
Alignment explanation
Indices: 15008--15266 Score: 131
Period size: 38 Copynumber: 6.8 Consensus size: 38
14998 TAAGCAGGTT
*
15008 TGAGGCTTTAAGCAGAGACCTAAGCAGGTTTGATTAAA
1 TGAGGCTCTAAGCAGAGACCTAAGCAGGTTTGATTAAA
15046 TGAGGCTCTAAGCAGAGGGACCTAAGCAGGTTTGATTAAA
1 TGAGGCTCTAAGCAGA--GACCTAAGCAGGTTTGATTAAA
* ** * *
15086 -CACGAATTCTAAACA-AGAACCTAAGCAGGTTTGAGTAAA
1 TGA-G-GCTCTAAGCAGAG-ACCTAAGCAGGTTTGATTAAA
** * *
15125 TGAAACT-T---CAAAGACCTAAGTAGGTTT-ACTTAAA
1 TGAGGCTCTAAGCAGAGACCTAAGCAGGTTTGA-TTAAA
* * * * **
15159 CGGAAGTTCTAAACA-AGGACCTAAGCAGG-TTCCTTAAA
1 -TGAGGCTCTAAGCAGA-GACCTAAGCAGGTTTGATTAAA
* *** **
15197 CAGAAATTCTAAGCAGAGACCTAAGCAGGTTTTCTTAAA
1 -TGAGGCTCTAAGCAGAGACCTAAGCAGGTTTGATTAAA
*** * *
15236 TGAAATTCTAAACATAGACCTAAGCAGGTTT
1 TGAGGCTCTAAGCAGAGACCTAAGCAGGTTT
15267 ACTTAAACAG
Statistics
Matches: 181, Mismatches: 23, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
33 1 0.01
34 19 0.10
35 6 0.03
36 1 0.01
37 1 0.01
38 78 0.43
39 43 0.24
40 25 0.14
41 7 0.04
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (38 bp):
TGAGGCTCTAAGCAGAGACCTAAGCAGGTTTGATTAAA
Found at i:15207 original size:38 final size:39
Alignment explanation
Indices: 15063--15532 Score: 310
Period size: 39 Copynumber: 12.6 Consensus size: 39
15053 CTAAGCAGAG
15063 GGACCTAAGCAGGTTTGA-TTAAACACG-AATTCTAAACAA
1 GGACCTAAGCAGGTTT-ACTTAAACA-GAAATTCTAAACAA
* * *
15102 GAACCTAAGCAGGTTTGA-GTAAA-TGAAACTTC---A-AA
1 GGACCTAAGCAGGTTT-ACTTAAACAGAAA-TTCTAAACAA
* * *
15137 -GACCTAAGTAGGTTTACTTAAACGGAAGTTCTAAACAA
1 GGACCTAAGCAGGTTTACTTAAACAGAAATTCTAAACAA
* *
15175 GGACCTAAGCAGG-TTCCTTAAACAGAAATTCTAAGC-A
1 GGACCTAAGCAGGTTTACTTAAACAGAAATTCTAAACAA
* *
15212 GAGACCTAAGCAGGTTTTCTTAAA-TGAAATTCTAAACATA
1 G-GACCTAAGCAGGTTTACTTAAACAGAAATTCTAAACA-A
15252 -GACCTAAGCAGGTTTACTTAAACAGAAATTCT----AA
1 GGACCTAAGCAGGTTTACTTAAACAGAAATTCTAAACAA
* * *
15286 -G--C--AG-A--TTTGA-TTAAACGA-AACTCCTAAACGTA
1 GGACCTAAGCAGGTTT-ACTTAAAC-AGAAATTCTAAAC-AA
* ** *
15318 -GACCTAAGCAGGTTTACTTGAATGGAAGTTCTAAACAA
1 GGACCTAAGCAGGTTTACTTAAACAGAAATTCTAAACAA
15356 GGACCTAAGCAGGTTTACTTAAAC-GAAAATTCTAAAC-A
1 GGACCTAAGCAGGTTTACTTAAACAG-AAATTCTAAACAA
* * * **
15394 GAGACCTAAGCAGGTTTAATCAAAC-GAGAATT-TAACCGT
1 G-GACCTAAGCAGGTTTACTTAAACAGA-AATTCTAAACAA
* *
15433 GGACCTAAGCAGGTTT-TTCTAAACAGAAATTCTAAGC-A
1 GGACCTAAGCAGGTTTACT-TAAACAGAAATTCTAAACAA
* * *
15471 GAGACCTAAGCAGGTTTTCTTAAA-TGAGATTCTAAACATA
1 G-GACCTAAGCAGGTTTACTTAAACAGAAATTCTAAACA-A
15511 -GACCTAAGCAGGTTTACTTAAA
1 GGACCTAAGCAGGTTTACTTAAA
15533 TGGCAACTCT
Statistics
Matches: 346, Mismatches: 43, Indels: 85
0.73 0.09 0.18
Matches are distributed among these distances:
27 14 0.04
28 2 0.01
29 1 0.00
30 2 0.01
32 3 0.01
33 1 0.00
34 23 0.07
35 6 0.02
36 3 0.01
37 6 0.02
38 132 0.38
39 150 0.43
40 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (39 bp):
GGACCTAAGCAGGTTTACTTAAACAGAAATTCTAAACAA
Found at i:15272 original size:77 final size:75
Alignment explanation
Indices: 15064--15532 Score: 351
Period size: 77 Copynumber: 6.3 Consensus size: 75
15054 TAAGCAGAGG
*
15064 GACCTAAGCAGGTTTGA-TTAAAC-ACGAATTCTAAACA-AGAACCTAAGCAGGTTTGA-GTAAA
1 GACCTAAGCAGGTTT-ACTTAAACGA--AATTCTAAACAGAG-ACCTAAGCAGGTTT-ACTTAAA
*
15125 -TGAAACTTC--A-AA
61 CAGAAA-TTCTAACAA
* * *
15137 GACCTAAGTAGGTTTACTTAAACGGAAGTTCTAAACA-AGGACCTAAGCAGG-TTCCTTAAACAG
1 GACCTAAGCAGGTTTACTTAAAC-GAAATTCTAAACAGA-GACCTAAGCAGGTTTACTTAAACAG
15200 AAATTCTAAGCAGA
64 AAATTCTAA-CA-A
* * *
15214 GACCTAAGCAGGTTTTCTTAAATGAAATTCTAAACATAGACCTAAGCAGGTTTACTTAAACAGAA
1 GACCTAAGCAGGTTTACTTAAACGAAATTCTAAACAGAGACCTAAGCAGGTTTACTTAAACAGAA
15279 ATTCT---AA
66 ATTCTAACAA
* * **
15286 G--C--AG-A--TTTGA-TTAAACGAAACTCCTAAAC-GTAGACCTAAGCAGGTTTACTTGAATG
1 GACCTAAGCAGGTTT-ACTTAAACGAAA-TTCTAAACAG-AGACCTAAGCAGGTTTACTTAAACA
*
15342 GAAGTTCTAAACAA
63 GAAATTCT-AACAA
* *
15356 GGACCTAAGCAGGTTTACTTAAACGAAAATTCTAAACAGAGACCTAAGCAGGTTTAATCAAAC-G
1 -GACCTAAGCAGGTTTACTTAAACG-AAATTCTAAACAGAGACCTAAGCAGGTTTACTTAAACAG
**
15420 AGAATT-TAACCGTG
64 A-AATTCTAA-C-AA
* * * *
15434 GACCTAAGCAGGTTT-TTCTAAACAGAAATTCTAAGCAGAGACCTAAGCAGGTTTTCTTAAA-TG
1 GACCTAAGCAGGTTTACT-TAAAC-GAAATTCTAAACAGAGACCTAAGCAGGTTTACTTAAACAG
*
15497 AGATTCTAAACATA
64 AAATTCT-AACA-A
15511 GACCTAAGCAGGTTTACTTAAA
1 GACCTAAGCAGGTTTACTTAAA
15533 TGGCAACTCT
Statistics
Matches: 320, Mismatches: 35, Indels: 78
0.74 0.08 0.18
Matches are distributed among these distances:
65 12 0.04
66 36 0.11
67 1 0.00
68 2 0.01
70 3 0.01
71 1 0.00
72 12 0.04
73 48 0.15
74 2 0.01
75 3 0.01
76 32 0.10
77 120 0.38
78 44 0.14
79 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (75 bp):
GACCTAAGCAGGTTTACTTAAACGAAATTCTAAACAGAGACCTAAGCAGGTTTACTTAAACAGAA
ATTCTAACAA
Found at i:15312 original size:27 final size:27
Alignment explanation
Indices: 15254--15312 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
15244 TAAACATAGA
*
15254 CCTAAGCAGGTTTACTTAAACAGAAAT
1 CCTAAGCAGATTTACTTAAACAGAAAT
*
15281 TCTAAGCAGATTTGA-TTAAAC-GAAACT
1 CCTAAGCAGATTT-ACTTAAACAGAAA-T
15308 CCTAA
1 CCTAA
15313 ACGTAGACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 4 0.15
27 22 0.81
28 1 0.04
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (27 bp):
CCTAAGCAGATTTACTTAAACAGAAAT
Found at i:27187 original size:29 final size:30
Alignment explanation
Indices: 27131--27188 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
27121 AAACCGAAAA
*
27131 TGGGAACCTTCCCCTTAAAAACTGAAACTG
1 TGGGAACCTTCCCCTTAAAAACTAAAACTG
* *
27161 TGGGAACCTTCCCTTTGAAAA-TAAAACT
1 TGGGAACCTTCCCCTTAAAAACTAAAACT
27189 TAATTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (30 bp):
TGGGAACCTTCCCCTTAAAAACTAAAACTG
Found at i:37938 original size:15 final size:15
Alignment explanation
Indices: 37918--37993 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
37908 CTAATTGAAT
37918 AATATACAAAGTAAA
1 AATATACAAAGTAAA
* * *
37933 AATATA-TAATTGAAT
1 AATATACAAAGT-AAA
37948 AATATACAAA-TAAA
1 AATATACAAAGTAAA
* * *
37962 AATATA-TAATTGAAT
1 AATATACAAAGT-AAA
37977 AATATACAAAGTAAA
1 AATATACAAAGTAAA
37992 AA
1 AA
37994 AACACAATTA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
13 2 0.04
14 12 0.26
15 27 0.59
16 5 0.11
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (15 bp):
AATATACAAAGTAAA
Found at i:37971 original size:29 final size:30
Alignment explanation
Indices: 37909--37993 Score: 163
Period size: 29 Copynumber: 2.9 Consensus size: 30
37899 AAAGTTTGTC
37909 TAATTGAATAATATACAAAGTAAAAATATA
1 TAATTGAATAATATACAAAGTAAAAATATA
37939 TAATTGAATAATATACAAA-TAAAAATATA
1 TAATTGAATAATATACAAAGTAAAAATATA
37968 TAATTGAATAATATACAAAGTAAAAA
1 TAATTGAATAATATACAAAGTAAAAA
37994 AACACAATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 29 0.54
30 25 0.46
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (30 bp):
TAATTGAATAATATACAAAGTAAAAATATA
Done.