Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011913.1 Corchorus olitorius cultivar O-4 contig11946, 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: 31330
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:536 original size:29 final size:29
Alignment explanation
Indices: 492--558 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
482 ACAAATAATA
492 TTTTCAATTTGATCCTTACATTTTTCAAT
1 TTTTCAATTTGATCCTTACATTTTTCAAT
*
521 TTTTCAATTTGGTCCTTACATTTTTCAAT
1 TTTTCAATTTGATCCTTACATTTTTCAAT
550 TTTTCAATT
1 TTTTCAATT
559 ACATCCCCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTCAATTTGATCCTTACATTTTTCAAT
Found at i:3337 original size:2 final size:2
Alignment explanation
Indices: 3330--3357 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3320 AAAGCAGCTA
3330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3358 TTTTTAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4174 original size:5 final size:5
Alignment explanation
Indices: 4164--4189 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4154 CCTTTTTTAG
4164 ACCCA ACCCA ACCCA ACCCA ACCCA A
1 ACCCA ACCCA ACCCA ACCCA ACCCA A
4190 GGTACTCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:7088 original size:24 final size:24
Alignment explanation
Indices: 7043--7089 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
7033 GAACTAGTGT
* *
7043 TTTTGGAAGCAAAGACTTTTGGTC
1 TTTTGAAAGCAAAGACTATTGGTC
7067 TTTTGAAAGCAAATGA-TATTGGT
1 TTTTGAAAGCAAA-GACTATTGGT
7090 TAATCTTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (24 bp):
TTTTGAAAGCAAAGACTATTGGTC
Found at i:12089 original size:17 final size:17
Alignment explanation
Indices: 12067--12100 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12057 TGTTCATGTT
*
12067 AGCATTTAGTTTTAGTA
1 AGCATTTAGTTTCAGTA
12084 AGCATTTAGTTTCAGTA
1 AGCATTTAGTTTCAGTA
12101 GATTACCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (17 bp):
AGCATTTAGTTTCAGTA
Found at i:12355 original size:13 final size:13
Alignment explanation
Indices: 12337--12361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12327 CACCAAAAAG
12337 TAGAAATTAGAAC
1 TAGAAATTAGAAC
12350 TAGAAATTAGAA
1 TAGAAATTAGAA
12362 GATACAGCGG
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:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (13 bp):
TAGAAATTAGAAC
Found at i:15644 original size:19 final size:19
Alignment explanation
Indices: 15596--15641 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
15586 ACAATCACAA
*
15596 TTCTAGATTTA-TTTTCTC
1 TTCTAGTTTTAGTTTTCTC
15614 TTCTAGTTTTAGTTTT-TC
1 TTCTAGTTTTAGTTTTCTC
15632 TTCTAGTTTT
1 TTCTAGTTTT
15642 TAGGCAAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.65
Consensus pattern (19 bp):
TTCTAGTTTTAGTTTTCTC
Found at i:17164 original size:29 final size:29
Alignment explanation
Indices: 17131--17497 Score: 381
Period size: 29 Copynumber: 12.9 Consensus size: 29
17121 TTCGCACGCT
*
17131 CAGGGGAATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
17160 CAGGGGCATTTTGGTCATTTTCGCACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
17189 CAGGGGTATTTTGGTCATTTTAGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
17218 C-GGGGCA-TTTGATCA-TTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
17244 CA-TGGTA-TTTGGTCA-TTTTGCATAT-
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
17269 CTGGGGCGTTTTGGTCA-TTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
17297 CAGGGGCATTTTGGTCATTTTCGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
17326 CGGGGGCATTTTGATCATTTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
17355 CAGGGGCATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
17384 CGGGGGCAATTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
17413 CGGGGGCATTTTGGTCATTTTTACACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* ** * * * * *
17442 CAAGGGCATTTCAGCCATCTTTACACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
17471 CTGGCGCAGTTTGGTCATTTTTGCATA
1 CAGGGGCATTTTGGTCATTTTTGCATA
17498 CTCTAGGTTC
Statistics
Matches: 279, Mismatches: 54, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
25 1 0.00
26 31 0.11
27 24 0.09
28 20 0.07
29 203 0.73
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTTTGCATATC
Found at i:25483 original size:25 final size:25
Alignment explanation
Indices: 25455--25503 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
25445 AATATTATAT
25455 GGCAAC-TTAAGCATTGCATTACATA
1 GGCAACATT-AGCATTGCATTACATA
**
25480 GGCAACATTTTCATTGCATTACAT
1 GGCAACATTAGCATTGCATTACAT
25504 GATCCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (25 bp):
GGCAACATTAGCATTGCATTACATA
Done.