Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024832.1 Corchorus olitorius cultivar O-4 contig24865, 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: 37442
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:388 original size:15 final size:16
Alignment explanation
Indices: 358--390 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
348 TTAATTTGCT
358 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
374 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
389 TT
1 TT
391 ACTTTCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:8166 original size:13 final size:13
Alignment explanation
Indices: 8148--8172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8138 TTGGGGTGAT
8148 TTATCCTTGTTAC
1 TTATCCTTGTTAC
8161 TTATCCTTGTTA
1 TTATCCTTGTTA
8173 AACGTTGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (13 bp):
TTATCCTTGTTAC
Found at i:8697 original size:16 final size:16
Alignment explanation
Indices: 8672--8710 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
8662 AGTGTTGTTC
8672 TAGGAATCTGTAGGAG
1 TAGGAATCTGTAGGAG
*
8688 TAGGACTCTGTAGGAG
1 TAGGAATCTGTAGGAG
8704 TAGGAAT
1 TAGGAAT
8711 GCGACTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.26
Consensus pattern (16 bp):
TAGGAATCTGTAGGAG
Found at i:13107 original size:39 final size:39
Alignment explanation
Indices: 13053--13131 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
13043 GCCGTTGGAA
13053 TTTGGAACTAAAATCCAACAAACAACATTAATTAAGATG
1 TTTGGAACTAAAATCCAACAAACAACATTAATTAAGATG
*
13092 TTTGGAACTAAAATCCAACAAACAGCATTAATTAAGATG
1 TTTGGAACTAAAATCCAACAAACAACATTAATTAAGATG
13131 T
1 T
13132 GATCAAGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (39 bp):
TTTGGAACTAAAATCCAACAAACAACATTAATTAAGATG
Found at i:20051 original size:2 final size:2
Alignment explanation
Indices: 20044--20081 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20034 CAATTTAAAC
20044 TA TA 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 TA TA
20082 CTATTAGGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22353 original size:54 final size:54
Alignment explanation
Indices: 22271--22375 Score: 194
Period size: 54 Copynumber: 1.9 Consensus size: 54
22261 AAAGTTTGTT
22271 CTAAAATTTGTATTGTGGTTGGCTTTTAATAATTGTAGTAGGGTTTATATACAA
1 CTAAAATTTGTATTGTGGTTGGCTTTTAATAATTGTAGTAGGGTTTATATACAA
22325 CTAAAATTTGTATTGTGGTTGAG-TTTTAATAATTGTAGTAGGGTTTATATA
1 CTAAAATTTGTATTGTGGTTG-GCTTTTAATAATTGTAGTAGGGTTTATATA
22376 TAATAAATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 49 0.98
55 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.46
Consensus pattern (54 bp):
CTAAAATTTGTATTGTGGTTGGCTTTTAATAATTGTAGTAGGGTTTATATACAA
Found at i:22379 original size:25 final size:26
Alignment explanation
Indices: 22351--22408 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
22341 GGTTGAGTTT
22351 TAATAATTGTAGTAG-GGTTTATATA
1 TAATAATTGTAGTAGAGGTTTATATA
*
22376 TAATAAATTGTTAGT-GAAGTTTATATA
1 TAAT-AATTG-TAGTAGAGGTTTATATA
22403 TAATAA
1 TAATAA
22409 ACTGTTAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.14
26 8 0.28
27 17 0.59
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (26 bp):
TAATAATTGTAGTAGAGGTTTATATA
Found at i:22397 original size:27 final size:27
Alignment explanation
Indices: 22367--22425 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
22357 TTGTAGTAGG
*
22367 GTTTATATATAATAAATTGTTAGTGAA
1 GTTTATATATAATAAACTGTTAGTGAA
22394 GTTTATATATAATAAACTGTTAGTGAA
1 GTTTATATATAATAAACTGTTAGTGAA
22421 GTTTA
1 GTTTA
22426 GCAGACTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (27 bp):
GTTTATATATAATAAACTGTTAGTGAA
Found at i:23066 original size:12 final size:12
Alignment explanation
Indices: 23049--23073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23039 AGTGTATCAA
23049 AATCAAATAATT
1 AATCAAATAATT
23061 AATCAAATAATT
1 AATCAAATAATT
23073 A
1 A
23074 GCCATTGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AATCAAATAATT
Found at i:29561 original size:30 final size:29
Alignment explanation
Indices: 29498--29562 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
29488 CACATTATGT
*
29498 AAAAAGCTTATACGATTGATGCCAAAAAG
1 AAAAAGCTTATACGATTGATGCCAAAAAA
*
29527 AAAAAGCTTATACGATT-ATTCAACAAAAAA
1 AAAAAGCTTATACGATTGATGC--CAAAAAA
29557 AAAAAG
1 AAAAAG
29563 AAAAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 3 0.09
29 17 0.53
30 12 0.38
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (29 bp):
AAAAAGCTTATACGATTGATGCCAAAAAA
Found at i:33195 original size:51 final size:50
Alignment explanation
Indices: 33094--33196 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
33084 GTTCTTCATA
* *
33094 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
* * *
33144 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGT
33195 TT
1 TT
33197 CTCTTTCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
Found at i:33771 original size:23 final size:21
Alignment explanation
Indices: 33741--33785 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
33731 CCAGGGTATA
**
33741 ATTTCTTTACTTTTTTTCATTT
1 ATTTCTTTAAGTTTTTTC-TTT
33763 ATTTACTTTAAGTTTTTTCTTT
1 ATTT-CTTTAAGTTTTTTCTTT
33785 A
1 A
33786 ATACACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTCTTTAAGTTTTTTCTTT
Done.