Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018699.1 Corchorus olitorius cultivar O-4 contig18732, 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: 19877
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1716 original size:25 final size:23
Alignment explanation
Indices: 1670--1717 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1660 CTATCCTTCT
1670 ATTCATCTATCATCAAGTTTTTC
1 ATTCATCTATCATCAAGTTTTTC
1693 ATTCATCTCATCGATCAAAGTTTTT
1 ATTCATCT-ATC-ATC-AAGTTTTT
1718 TCAATTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
24 3 0.14
25 3 0.14
26 8 0.36
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (23 bp):
ATTCATCTATCATCAAGTTTTTC
Found at i:6292 original size:16 final size:16
Alignment explanation
Indices: 6271--6302 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6261 TTAGCGATGA
*
6271 ATAATAAAGATGATCC
1 ATAATAAAAATGATCC
6287 ATAATAAAAATGATCC
1 ATAATAAAAATGATCC
6303 CAATTCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25
Consensus pattern (16 bp):
ATAATAAAAATGATCC
Found at i:7966 original size:43 final size:42
Alignment explanation
Indices: 7902--7988 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 42
7892 TAAAACTCTC
** *
7902 TTGACCCTATGGACTGGTTTGGAATGTAACTATTTACTTTGT
1 TTGACCCTATGGACTGGTTTGGAATACAACCATTTACTTTGT
7944 TTGACCCTATGTGACTGGTTTGGAATACAACCATTTACTTTGT
1 TTGACCCTATG-GACTGGTTTGGAATACAACCATTTACTTTGT
7987 TT
1 TT
7989 ACTGTGAGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 11 0.27
43 30 0.73
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (42 bp):
TTGACCCTATGGACTGGTTTGGAATACAACCATTTACTTTGT
Found at i:9562 original size:20 final size:21
Alignment explanation
Indices: 9523--9567 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
9513 GTGCAAAAAT
* *
9523 TCAAGCTCCGTGCTTTTTCTC
1 TCAAGCCCCGCGCTTTTTCTC
9544 TCAAGCCCCGCGC-TTTTCTC
1 TCAAGCCCCGCGCTTTTTCTC
9564 TCAA
1 TCAA
9568 TTTTCTCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.13, C:0.38, G:0.13, T:0.36
Consensus pattern (21 bp):
TCAAGCCCCGCGCTTTTTCTC
Found at i:10746 original size:58 final size:56
Alignment explanation
Indices: 10596--10747 Score: 163
Period size: 58 Copynumber: 2.7 Consensus size: 56
10586 GACTTCTTAA
*
10596 TTAACTTAATTACTCTGAATTAAGCC-A--ATTACTGATTACCCTTCTTTTACTTT
1 TTAACTTAATTACTCTGAATTAAGCCTATTATTACTGATTACCCATCTTTTACTTT
* * *
10649 TTAACTTAATTTCTCTGAATTAAG-TTAATTATTATTGATTA-CCAT-TTTTACTTTT
1 TTAACTTAATTACTCTGAATTAAGCCT-ATTATTACTGATTACCCATCTTTTAC-TTT
* *
10704 TAGCTAACTTAATTACTTTGAATTAAGCCTATTACTACTGATTA
1 T---TAACTTAATTACTCTGAATTAAGCCTATTATTACTGATTA
10748 TCTTTCTACT
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
53 23 0.28
54 7 0.09
55 7 0.09
56 10 0.12
58 33 0.41
59 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (56 bp):
TTAACTTAATTACTCTGAATTAAGCCTATTATTACTGATTACCCATCTTTTACTTT
Found at i:10843 original size:60 final size:56
Alignment explanation
Indices: 10707--10846 Score: 131
Period size: 57 Copynumber: 2.4 Consensus size: 56
10697 TACTTTTTAG
* * *
10707 CTAACTTAATTACTTTGAATTAAGCCTATTACTACTGATTATCTTTCTACTTCTTGT
1 CTAACTTAATTAC-CTGAATTAAACCTATTACTACTGATTATCTTTCTACTCCTTGT
* ** *
10764 CTGACTCGATTACCTTGAATTAAACC-AGTTATTACTGATTATCCTTTTCTAACTCCTTGAT
1 CTAACTTAATTACC-TGAATTAAACCTA-TTACTACTGATTAT-C-TTTCT-ACTCCTTG-T
10825 -TAACTTAATTACGCTGAATTAA
1 CTAACTTAATTAC-CTGAATTAA
10847 GTCAAAAACT
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
56 1 0.02
57 33 0.50
58 1 0.02
59 5 0.08
60 24 0.36
61 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (56 bp):
CTAACTTAATTACCTGAATTAAACCTATTACTACTGATTATCTTTCTACTCCTTGT
Found at i:10903 original size:119 final size:117
Alignment explanation
Indices: 10708--10924 Score: 276
Period size: 119 Copynumber: 1.8 Consensus size: 117
10698 ACTTTTTAGC
** * ** ** *
10708 TAACTTAATTACTTTGAATTAAGCCTATTACTACTGATTATCTTTCTACTTCTTGTCTGACTCGA
1 TAACTTAATTACGCTGAATTAAGCCAAAAACTACTGATTATCTTTCTACTTCTTAACTGACTCAA
* *
10773 TTACCTTGAATTAAACCAGTTATTACTGATTATCCTTTTCTAACTCCTTGAT
66 TTACCTTGAATTAAACCACTCATTACTGATTATCCTTTTCTAACTCCTTGAT
*
10825 TAACTTAATTACGCTGAATTAAGTCAAAAACTACTGATTGCATCTCTT-TACTTCTTAACTGACT
1 TAACTTAATTACGCTGAATTAAGCCAAAAACTACTGATT--ATCT-TTCTACTTCTTAACTGACT
*
10889 CAATTA-CTCTGAATTAAGCCACTCATTACTGATTAT
63 CAATTACCT-TGAATTAAACCACTCATTACTGATTAT
10925 TTTTCTTTGA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
117 33 0.39
118 2 0.02
119 47 0.56
120 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (117 bp):
TAACTTAATTACGCTGAATTAAGCCAAAAACTACTGATTATCTTTCTACTTCTTAACTGACTCAA
TTACCTTGAATTAAACCACTCATTACTGATTATCCTTTTCTAACTCCTTGAT
Found at i:10984 original size:59 final size:59
Alignment explanation
Indices: 10587--10970 Score: 168
Period size: 59 Copynumber: 6.6 Consensus size: 59
10577 TACTTCGTTG
* * * ***
10587 ACTTCTTAATTAACTTAATTACTCTGAATTAAGCCA---ATTACTGATTACCCTTCTTTT
1 ACTTCTTAACTGACTCAATTACTCTGAATTAAGCCACTCATTACTGATTATTTTTC-TTT
* * ** * * * ***
10644 ACTTTTTAACT---T-AATTTCTCTGAATTAAGTTAATTATTATTGATTACCATT-TTT
1 ACTTCTTAACTGACTCAATTACTCTGAATTAAGCCACTCATTACTGATTATTTTTCTTT
* * * * * * * *
10698 ACTTTTTAGCTAACTTAATTACTTTGAATTAAGCCTA-TTACTACTGATTATCTTTC--T
1 ACTTCTTAACTGACTCAATTACTCTGAATTAAGCC-ACTCATTACTGATTATTTTTCTTT
** * * * * *
10755 ACTTCTTGTCTGACTCGATTAC-CTTGAATTAAACCAGTTATTACTGATTATCCTTTTC-TA
1 ACTTCTTAACTGACTCAATTACTC-TGAATTAAGCCACTCATTACTGATTAT--TTTTCTTT
* * * * * * * *** * *** *
10815 ACTCCTTGATTAACTTAATTACGCTGAATTAAGTCAAAAACTACTGATTGCATCTCTTT
1 ACTTCTTAACTGACTCAATTACTCTGAATTAAGCCACTCATTACTGATTATTTTTCTTT
10874 ACTTCTTAACTGACTCAATTACTCTGAATTAAGCCACTCATTACTGATTATTTTTCTTT
1 ACTTCTTAACTGACTCAATTACTCTGAATTAAGCCACTCATTACTGATTATTTTTCTTT
* *
10933 GAC-TCTTATCTGACTTAATTAC-CTTGAATTAAGCCACT
1 -ACTTCTTAACTGACTCAATTACTC-TGAATTAAGCCACT
10971 TATATTGACT
Statistics
Matches: 248, Mismatches: 61, Indels: 34
0.72 0.18 0.10
Matches are distributed among these distances:
53 17 0.07
54 14 0.06
56 15 0.06
57 50 0.20
58 33 0.13
59 81 0.33
60 37 0.15
61 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.44
Consensus pattern (59 bp):
ACTTCTTAACTGACTCAATTACTCTGAATTAAGCCACTCATTACTGATTATTTTTCTTT
Found at i:11172 original size:36 final size:36
Alignment explanation
Indices: 11071--11353 Score: 249
Period size: 36 Copynumber: 7.9 Consensus size: 36
11061 AAGCCATTTA
* *
11071 TTACTGAC-GTACTTAATTACCCTAAATTAAGTTAT
1 TTACTGACTTTACTTAATTACCCTGAATTAAGTTAT
*
11106 TTACTGAC-TTACTTAATT-GCCTGAATTAAGTTAT
1 TTACTGACTTTACTTAATTACCCTGAATTAAGTTAT
* * **
11140 TTACTAACTTTACTTAATTATCCTGAATTAAGTTGC
1 TTACTGACTTTACTTAATTACCCTGAATTAAGTTAT
* **
11176 TTACTGACTTTACTCAATTACCCTGAATTAAGTTGC
1 TTACTGACTTTACTTAATTACCCTGAATTAAGTTAT
** * * * * *
11212 AAACTGATTTTAATTAATTGCCCCGAATTAA-ATAT
1 TTACTGACTTTACTTAATTACCCTGAATTAAGTTAT
* *
11247 TTACTGA-TTTACTTAATTACCCTGAAATAAGATGATT
1 TTACTGACTTTACTTAATTACCCTGAATTAAG-TTA-T
* * *
11284 ATTACTGATTTTACTTAATTATCCT-AAATAAGTTGA-
1 -TTACTGACTTTACTTAATTACCCTGAATTAAGTT-AT
* *
11320 TTACT-ATCTTTACTTAATTTCCCTGAATAAAGTT
1 TTACTGA-CTTTACTTAATTACCCTGAATTAAGTT
11354 GATCATTACT
Statistics
Matches: 203, Mismatches: 35, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
34 41 0.20
35 52 0.26
36 78 0.38
37 2 0.01
38 15 0.07
39 15 0.07
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (36 bp):
TTACTGACTTTACTTAATTACCCTGAATTAAGTTAT
Found at i:11218 original size:106 final size:105
Alignment explanation
Indices: 11071--11277 Score: 247
Period size: 106 Copynumber: 2.0 Consensus size: 105
11061 AAGCCATTTA
* *** * *
11071 TTACTGACGTACTTAATTACCCTAAATTAAGTTATTTACTGA-CTTACTTAATTG-CCTGAATTA
1 TTACTGACGTACTCAATTACCCTAAATTAAGTTACAAACTGATCTTAATTAATTGCCCCGAATTA
* * *
11134 AGTTATTTACTAACTTTACTTAATTATCCTGAATTAAGTTGC
66 A-ATATTTACTAA-TTTACTTAATTACCCTGAAATAAGTTGC
* * * *
11176 TTACTGACTTTACTCAATTACCCTGAATTAAGTTGCAAACTGATTTTAATTAATTGCCCCGAATT
1 TTACTGAC-GTACTCAATTACCCTAAATTAAGTTACAAACTGATCTTAATTAATTGCCCCGAATT
*
11241 AAATATTTACTGATTTACTTAATTACCCTGAAATAAG
65 AAATATTTACTAATTTACTTAATTACCCTGAAATAAG
11278 ATGATTATTA
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
105 8 0.09
106 49 0.58
107 19 0.22
108 9 0.11
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (105 bp):
TTACTGACGTACTCAATTACCCTAAATTAAGTTACAAACTGATCTTAATTAATTGCCCCGAATTA
AATATTTACTAATTTACTTAATTACCCTGAAATAAGTTGC
Done.