Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014356.1 Corchorus olitorius cultivar O-4 contig14389, 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: 18068
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2278 original size:12 final size:11
Alignment explanation
Indices: 2235--2279 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2225 ATTCACGAAC
*
2235 ATGCTCGATTA
1 ATGCTCGTTTA
2246 ATGCTCGTTTA
1 ATGCTCGTTTA
* *
2257 TTGTTCGTTTA
1 ATGCTCGTTTA
2268 ATAGCTCGTTTA
1 AT-GCTCGTTTA
2280 TGTTCATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (11 bp):
ATGCTCGTTTA
Found at i:2283 original size:22 final size:22
Alignment explanation
Indices: 2243--2284 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2233 ACATGCTCGA
2243 TTAATGCTCGTTTATTGTTCGT
1 TTAATGCTCGTTTATTGTTCGT
2265 TTAATAGCTCGTTTA-TGTTC
1 TTAAT-GCTCGTTTATTGTTC
2285 ATTAATTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (22 bp):
TTAATGCTCGTTTATTGTTCGT
Found at i:3772 original size:23 final size:23
Alignment explanation
Indices: 3746--3790 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3736 ACTCAATTAG
* *
3746 TGTTCATGAACAAATTCGTTTAT
1 TGTTCACGAACAAATTCATTTAT
*
3769 TGTTCACGAACAAGTTCATTTA
1 TGTTCACGAACAAATTCATTTA
3791 AACGAGTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (23 bp):
TGTTCACGAACAAATTCATTTAT
Found at i:4595 original size:45 final size:47
Alignment explanation
Indices: 4513--4606 Score: 156
Period size: 45 Copynumber: 2.0 Consensus size: 47
4503 TCTTTTTTTC
4513 AATCAAACCAATCAATCAAAAAGCGTAACAGATCTCGATTACCG-CA
1 AATCAAACCAATCAATCAAAAAGCGTAACAGATCTCGATTACCGTCA
* *
4559 AATCAAATCAATCAATC-AAAAGTGTAACAGATCTCGATTACCGTCA
1 AATCAAACCAATCAATCAAAAAGCGTAACAGATCTCGATTACCGTCA
4605 AA
1 AA
4607 AACTGTAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 25 0.56
46 20 0.44
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (47 bp):
AATCAAACCAATCAATCAAAAAGCGTAACAGATCTCGATTACCGTCA
Found at i:6311 original size:13 final size:14
Alignment explanation
Indices: 6293--6321 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6283 AAACGGAAAA
6293 TCCAGAAGTG-TTT
1 TCCAGAAGTGCTTT
6306 TCCAGAAGTGCTTT
1 TCCAGAAGTGCTTT
6320 TC
1 TC
6322 AGTTGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (14 bp):
TCCAGAAGTGCTTT
Found at i:7612 original size:11 final size:11
Alignment explanation
Indices: 7596--7621 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7586 TTCTCGCCTT
7596 TTTTATTTATA
1 TTTTATTTATA
7607 TTTTATTTATA
1 TTTTATTTATA
7618 TTTT
1 TTTT
7622 CTATTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:8275 original size:21 final size:22
Alignment explanation
Indices: 8235--8275 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
8225 GACAAACTCG
*
8235 TAACCCGCATAACCCGAGAAGA
1 TAACCCGCATAACCCAAGAAGA
*
8257 TAACCCG-ATGACCCAAGAA
1 TAACCCGCATAACCCAAGAA
8276 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.32, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGCATAACCCAAGAAGA
Found at i:16067 original size:26 final size:26
Alignment explanation
Indices: 16038--16125 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 26
16028 CATTAGAAAT
16038 TAATTAGATAACAATTTCATCAACAA
1 TAATTAGATAACAATTTCATCAACAA
* * *
16064 TAATGAGAATTAAGTAAATTTTCATTAGA-AA
1 TAATTAG-A-TAA--CAA-TTTCATCA-ACAA
16095 TTAATTAGATAACAATTTCATCAACAA
1 -TAATTAGATAACAATTTCATCAACAA
16122 TAAT
1 TAAT
16126 GGACGCTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
26 11 0.23
27 10 0.21
28 5 0.10
30 5 0.10
31 10 0.21
32 7 0.15
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (26 bp):
TAATTAGATAACAATTTCATCAACAA
Found at i:16079 original size:58 final size:58
Alignment explanation
Indices: 16010--16126 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
16000 CATGAACTCG
16010 GAGAATTAAGTAAATTTTCATTAGAAATTAATTAGATAACAATTTCATCAACAATAAT
1 GAGAATTAAGTAAATTTTCATTAGAAATTAATTAGATAACAATTTCATCAACAATAAT
16068 GAGAATTAAGTAAATTTTCATTAGAAATTAATTAGATAACAATTTCATCAACAATAAT
1 GAGAATTAAGTAAATTTTCATTAGAAATTAATTAGATAACAATTTCATCAACAATAAT
16126 G
1 G
16127 GACGCTATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (58 bp):
GAGAATTAAGTAAATTTTCATTAGAAATTAATTAGATAACAATTTCATCAACAATAAT
Found at i:16320 original size:2 final size:2
Alignment explanation
Indices: 16315--16408 Score: 79
Period size: 2 Copynumber: 47.0 Consensus size: 2
16305 TGAAAAAAGT
* *
16315 TA TA TA TA TA TA TA TA TA TA TA TA CTA -A CA AA 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 TA TA
* * *
16357 TA TA TA TA TGA -A AA AA GT- TA TA TA T- TA TA TA TA TA TA TC TA
1 TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
16398 TA TA CTA TA TA
1 TA TA -TA TA TA
16409 AGTCTAAACT
Statistics
Matches: 79, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
1 4 0.05
2 70 0.89
3 5 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:16349 original size:26 final size:26
Alignment explanation
Indices: 16320--16394 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
16310 AAAGTTATAT
*
16320 ATATATATATATATATATACT-AACAA
1 ATATATATATATATATATA-TGAAAAA
16346 ATATATATATATATATATATGAAAAA
1 ATATATATATATATATATATGAAAAA
16372 AGTTATATATTATATATATATAT
1 A--TATATA-TATATATATATAT
16395 CTATATACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 24 0.55
28 6 0.14
29 13 0.30
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (26 bp):
ATATATATATATATATATATGAAAAA
Found at i:16680 original size:39 final size:40
Alignment explanation
Indices: 16624--16704 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
16614 TTTAATTCCT
16624 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
16664 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
16703 AT
1 AT
16705 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:16731 original size:25 final size:24
Alignment explanation
Indices: 16695--16741 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
16685 AATACTTACA
*
16695 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCATAGGTATTTTT
16719 TTAATTCAAATTCATAGGTATTT
1 TTAATT-AAATTCATAGGTATTT
16742 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTCATAGGTATTTTT
Found at i:17777 original size:36 final size:36
Alignment explanation
Indices: 17730--17799 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
17720 GAGATTTTGG
* *
17730 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
17766 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
17800 GGTTATCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.