Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019152.1 Corchorus olitorius cultivar O-4 contig19185, 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: 30464
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:64 original size:22 final size:21
Alignment explanation
Indices: 21--75 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
11 TGATTACCTT
21 CTATGAAATTTTTGTAACCACA
1 CTATGAAA-TTTTGTAACCACA
* **
43 TTATGAAATTTTGATAGTCACA
1 CTATGAAATTTTG-TAACCACA
65 CTATGAAATTT
1 CTATGAAATTT
76 CAATAATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
CTATGAAATTTTGTAACCACA
Found at i:2573 original size:24 final size:25
Alignment explanation
Indices: 2539--2589 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2529 ATTGGAGTAT
* *
2539 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
*
2564 TTATTT-TCTTGCTTATTTATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
2588 TT
1 TT
2590 GTAAGTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGCTTATTAATTTTA
Found at i:4431 original size:205 final size:205
Alignment explanation
Indices: 4037--4434 Score: 719
Period size: 206 Copynumber: 1.9 Consensus size: 205
4027 CTTAATAACT
* *
4037 TTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACCCATTATTA
1 TTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTACTA
4102 TTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTAA
66 TTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTAA
*
4167 ATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCTGATTTATTTATCA
131 ATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTATCA
4232 ATGGTGAATG
196 ATGGTGAATG
4242 TTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGATCATAAGATACAACACATTAC
1 TTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGA--ATAAGATACAACACATTAC
* *
4307 TATTA-TATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATT
64 TATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATT
4371 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCGATTTATTTAT
129 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTAT
4435 TATTAAGGAA
Statistics
Matches: 186, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
205 61 0.33
206 103 0.55
207 22 0.12
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (205 bp):
TTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTACTA
TTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTAA
ATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTATCA
ATGGTGAATG
Found at i:4600 original size:42 final size:40
Alignment explanation
Indices: 4541--4624 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 40
4531 CTACCTAAGA
4541 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-TA-TATTAC
*
4583 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
4623 AT
1 AT
4625 AGGAATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 8 0.20
41 2 0.05
42 31 0.76
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:8415 original size:27 final size:27
Alignment explanation
Indices: 8368--8420 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
8358 TTTTAACTTT
8368 TTTTTAAAAAATTAATAATTAGTTATTA
1 TTTTTAAAAAATTAATAATTA-TTATTA
* *
8396 TTTTT-AAAAATTAGTTATTATTATT
1 TTTTTAAAAAATTAATAATTATTATT
8421 TTATATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 13 0.57
28 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTTAAAAAATTAATAATTATTATTA
Found at i:8431 original size:23 final size:20
Alignment explanation
Indices: 8379--8417 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8369 TTTTAAAAAA
*
8379 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
8399 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
8418 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:12717 original size:18 final size:19
Alignment explanation
Indices: 12676--12723 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
12666 GATGAAAGTC
*
12676 ATCATAGAATTGCTCCTCG
1 ATCATAGAATTTCTCCTCG
*
12695 A-CATAGAATTTCTCCT-T
1 ATCATAGAATTTCTCCTCG
12712 ATCATAGAATTT
1 ATCATAGAATTT
12724 GATGAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATAGAATTTCTCCTCG
Found at i:21062 original size:11 final size:11
Alignment explanation
Indices: 21046--21071 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21036 GTTTGGAATG
21046 AGACAAATAAT
1 AGACAAATAAT
21057 AGACAAATAAT
1 AGACAAATAAT
21068 AGAC
1 AGAC
21072 TATATGGAAA
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:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (11 bp):
AGACAAATAAT
Found at i:21253 original size:23 final size:23
Alignment explanation
Indices: 21219--21262 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
21209 TGAATAAAAA
*
21219 ACAACATTTCATCT-GAAAATTG
1 ACAACATATCATCTAGAAAATTG
*
21241 ACAACAATATCATTTAGAAAAT
1 ACAAC-ATATCATCTAGAAAAT
21263 GAAGATGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 7 0.39
24 6 0.33
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (23 bp):
ACAACATATCATCTAGAAAATTG
Found at i:24040 original size:15 final size:15
Alignment explanation
Indices: 24020--24048 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24010 CTAAGATTCT
24020 AAAGAAAAGAAAAAA
1 AAAGAAAAGAAAAAA
24035 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
24049 GGATTAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAA
Found at i:27886 original size:12 final size:12
Alignment explanation
Indices: 27869--27894 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27859 AGGTTGTTGT
27869 ACACATTCATAA
1 ACACATTCATAA
27881 ACACATTCATAA
1 ACACATTCATAA
27893 AC
1 AC
27895 CAACGAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (12 bp):
ACACATTCATAA
Found at i:29405 original size:31 final size:32
Alignment explanation
Indices: 29354--29413 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
29344 TTTTGAATCA
* *
29354 TCTATTATATCCTTATTTTTCGTATATATCTG
1 TCTATTATATCCCTATTTTTCGAATATATCTG
29386 TCTATTATA-CCCTATTTTTCGAATATAT
1 TCTATTATATCCCTATTTTTCGAATATAT
29414 TTCTTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (32 bp):
TCTATTATATCCCTATTTTTCGAATATATCTG
Found at i:30411 original size:25 final size:24
Alignment explanation
Indices: 30360--30416 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
30350 GTCAGTCTTG
*
30360 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
30383 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
30408 AATTTATTT
1 AATTTATTT
30417 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Done.