Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014902.1 Corchorus olitorius cultivar O-4 contig14935, 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: 37279
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1865 original size:19 final size:19
Alignment explanation
Indices: 1841--1881 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1831 CTTGACTGCA
1841 TATATTAAAAGGGCAATAC
1 TATATTAAAAGGGCAATAC
1860 TATATTAAAAGGGCAATAC
1 TATATTAAAAGGGCAATAC
1879 TAT
1 TAT
1882 TACATGACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (19 bp):
TATATTAAAAGGGCAATAC
Found at i:5091 original size:15 final size:15
Alignment explanation
Indices: 5073--5111 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5063 TTATTTTTTA
* *
5073 AAAATAAATTTTAAT
1 AAAATAAAATATAAT
*
5088 AAAATAAAATATACT
1 AAAATAAAATATAAT
5103 AAAATAAAA
1 AAAATAAAA
5112 ATATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAAAATATAAT
Found at i:12101 original size:19 final size:18
Alignment explanation
Indices: 12061--12101 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
12051 TCCCTGAAAT
*
12061 AATTCTTCAATGATCTTT
1 AATTCTTCAATGATCTTC
*
12079 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
12098 AATT
1 AATT
12102 AATCTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:12606 original size:15 final size:15
Alignment explanation
Indices: 12586--12615 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12576 CAGTCCGGTC
12586 CGGTTTCAAAAACAA
1 CGGTTTCAAAAACAA
12601 CGGTTTCAAAAACAA
1 CGGTTTCAAAAACAA
12616 TGGGAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
CGGTTTCAAAAACAA
Found at i:14322 original size:14 final size:14
Alignment explanation
Indices: 14303--14330 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14293 TTTTCAACTT
14303 TAATATATGTTATA
1 TAATATATGTTATA
14317 TAATATATGTTATA
1 TAATATATGTTATA
14331 GATTTACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TAATATATGTTATA
Found at i:17151 original size:20 final size:20
Alignment explanation
Indices: 17115--17152 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17105 ATTTCTATTC
*
17115 TTTCTTTTTTCTTTTTTCCT
1 TTTCTTTTTTCTATTTTCCT
17135 TTTCTTATTTT-TATTTTC
1 TTTCTT-TTTTCTATTTTC
17153 TTCTTTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTTCTATTTTCCT
Found at i:17172 original size:17 final size:17
Alignment explanation
Indices: 17152--17197 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
17142 TTTTTATTTT
17152 CTTCTTTCTTCCCAACG
1 CTTCTTTCTTCCCAACG
*
17169 CTTCTTT-TTCTCCAGCG
1 CTTCTTTCTTC-CCAACG
*
17186 CTGC-TTCTTCCC
1 CTTCTTTCTTCCC
17198 CAAACACCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.07, C:0.41, G:0.09, T:0.43
Consensus pattern (17 bp):
CTTCTTTCTTCCCAACG
Found at i:18606 original size:8 final size:8
Alignment explanation
Indices: 18593--18639 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
18583 CATTATTTTT
18593 TATCTTAC
1 TATCTTAC
18601 TATCTTAC
1 TATCTTAC
18609 TATCTTA-
1 TATCTTAC
18616 T-T-TTAC
1 TATCTTAC
18622 TATCTTAC
1 TATCTTAC
18630 TATCTTAC
1 TATCTTAC
18638 TA
1 TA
18640 CTATATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 3 0.08
6 2 0.06
7 2 0.06
8 29 0.81
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (8 bp):
TATCTTAC
Found at i:18621 original size:21 final size:21
Alignment explanation
Indices: 18592--18643 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
18582 GCATTATTTT
18592 TTATCTTACTATCTTACTATC
1 TTATCTTACTATCTTACTATC
*
18613 TTATTTTACTATCTTACTATC
1 TTATCTTACTATCTTACTATC
18634 TTA-C-TACTAT
1 TTATCTTACTAT
18644 ATAAAAGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.21
21 23 0.79
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATCTTACTATCTTACTATC
Found at i:18628 original size:29 final size:28
Alignment explanation
Indices: 18585--18639 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
18575 CTAAGCGGCA
*
18585 TTATTTTTTATCTTACTATCTTACTATC
1 TTATTTTCTATCTTACTATCTTACTATC
18613 TTATTTTACTATCTTACTATCTTACTA
1 TTATTTT-CTATCTTACTATCTTACTA
18640 CTATATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (28 bp):
TTATTTTCTATCTTACTATCTTACTATC
Found at i:20253 original size:17 final size:18
Alignment explanation
Indices: 20228--20274 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
20218 ATTGAGGTTT
*
20228 GAAAGTTTGAA-AATTGA
1 GAAAATTTGAAGAATTGA
20245 GAAAATTTGAGAGAATTGA
1 GAAAATTTGA-AGAATTGA
*
20264 -AAATTTTGAAG
1 GAAAATTTGAAG
20275 TTTGAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAAATTTGAAGAATTGA
Found at i:21126 original size:131 final size:134
Alignment explanation
Indices: 20896--21164 Score: 454
Period size: 131 Copynumber: 2.0 Consensus size: 134
20886 ATAACTATAA
*
20896 AAAGAAAAATCTCTTCTAAGTGAACTTAAGGAAAAGTACTATATAGACTTCTACATCAGTAGGCG
1 AAAGAAAAATCTCTTCCAAGTGAACTTAAGGAAAAGTACTATATAGACTTCT--ATCAGTAGGCG
*
20961 ATAAAATCTACATAGCAAGCATGGTAAAGTATGAAGTAGAAGATATAACCAGTTGGCACACCATA
64 ATAAAATCTACATAGCAAGCATGGTAAAGTATGAAGTAGAAGATATAACCAGTTGGCACAACATA
21026 AAGACC
129 AAGACC
21032 AAAGAAAAATCTCTTCCAAGTGAACTTAAGGAAAAGTACTATATAGA-TT-T-TCAGTAGGCGAT
1 AAAGAAAAATCTCTTCCAAGTGAACTTAAGGAAAAGTACTATATAGACTTCTATCAGTAGGCGAT
* * *
21094 AAAGTCTACATAGCAAGCATGGTAAAGTATGAAGTGGAAGATATACCCAGTTGGCACAACATAAA
66 AAAATCTACATAGCAAGCATGGTAAAGTATGAAGTAGAAGATATAACCAGTTGGCACAACATAAA
21159 GACC
131 GACC
21163 AA
1 AA
21165 TTTGAAGCCA
Statistics
Matches: 128, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
131 79 0.62
134 1 0.01
135 2 0.02
136 46 0.36
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (134 bp):
AAAGAAAAATCTCTTCCAAGTGAACTTAAGGAAAAGTACTATATAGACTTCTATCAGTAGGCGAT
AAAATCTACATAGCAAGCATGGTAAAGTATGAAGTAGAAGATATAACCAGTTGGCACAACATAAA
GACC
Found at i:22045 original size:30 final size:30
Alignment explanation
Indices: 21961--22050 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
21951 AAAATCACCA
* * *
21961 ATTGACCCCATTAAATTGAAATTTTTGTAGT
1 ATTGACCCCATTAAATT-AAAATTTTATAAT
* * **
21992 ATAGACCCTATTTAAATGGAAATTTTATAAT
1 ATTGACCCCA-TTAAATTAAAATTTTATAAT
*
22023 ATTGACCCCACTAAATTAAAATTTTATA
1 ATTGACCCCATTAAATTAAAATTTTATA
22051 GCGTTACCCC
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 15 0.33
31 25 0.54
32 6 0.13
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (30 bp):
ATTGACCCCATTAAATTAAAATTTTATAAT
Found at i:22404 original size:12 final size:12
Alignment explanation
Indices: 22387--22417 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
22377 TTTTGCTATT
22387 ATTGAAAAAGTA
1 ATTGAAAAAGTA
22399 ATTGAAAAAGTA
1 ATTGAAAAAGTA
*
22411 ATAGAAA
1 ATTGAAA
22418 GTTTGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (12 bp):
ATTGAAAAAGTA
Found at i:30081 original size:27 final size:26
Alignment explanation
Indices: 30019--30086 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
30009 ACTAAAGCCT
*
30019 AAATGCAAACCCAAAGTCAAAATGTC
1 AAATGCAAGCCCAAAGTCAAAATGTC
* * * *
30045 AACTTTCAAGGCCAAAGTTAAAATGTCC
1 AA-ATGCAAGCCCAAAGTCAAAATGT-C
30073 AAATGCAAGCCCAA
1 AAATGCAAGCCCAA
30087 CATGAACCCA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
26 2 0.06
27 27 0.84
28 3 0.09
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.18
Consensus pattern (26 bp):
AAATGCAAGCCCAAAGTCAAAATGTC
Found at i:31803 original size:11 final size:11
Alignment explanation
Indices: 31787--31811 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31777 AGGTAGCAGT
31787 AACTTAAACAC
1 AACTTAAACAC
31798 AACTTAAACAC
1 AACTTAAACAC
31809 AAC
1 AAC
31812 AACATAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (11 bp):
AACTTAAACAC
Found at i:33959 original size:28 final size:28
Alignment explanation
Indices: 33919--34006 Score: 176
Period size: 28 Copynumber: 3.1 Consensus size: 28
33909 TAGTTCTGCA
33919 CAAACTTACGATAATATCCAGTAAGTCC
1 CAAACTTACGATAATATCCAGTAAGTCC
33947 CAAACTTACGATAATATCCAGTAAGTCC
1 CAAACTTACGATAATATCCAGTAAGTCC
33975 CAAACTTACGATAATATCCAGTAAGTCC
1 CAAACTTACGATAATATCCAGTAAGTCC
34003 CAAA
1 CAAA
34007 AAACCCCTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (28 bp):
CAAACTTACGATAATATCCAGTAAGTCC
Found at i:36647 original size:11 final size:11
Alignment explanation
Indices: 36631--36655 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36621 AGGTTGCAGT
36631 AACTTAAACAC
1 AACTTAAACAC
36642 AACTTAAACAC
1 AACTTAAACAC
36653 AAC
1 AAC
36656 AACATAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (11 bp):
AACTTAAACAC
Done.