Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017359.1 Corchorus olitorius cultivar O-4 contig17392, 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: 29141
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1658 original size:30 final size:30
Alignment explanation
Indices: 1622--1688 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
1612 AAAATTTTTC
1622 TTTTATTTC-TTTT-ATTTTCTTTTTCCCTTT
1 TTTTATTTCTTTTTCATTTTC-TTTT-CCTTT
*
1652 TTTTA-TTCTTTTTCCTTTTCTTTTCCTTT
1 TTTTATTTCTTTTTCATTTTCTTTTCCTTT
1681 TCTTTATT
1 T-TTTATT
1689 CCAAAATGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
29 9 0.28
30 17 0.53
31 6 0.19
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTATTTCTTTTTCATTTTCTTTTCCTTT
Found at i:1675 original size:11 final size:11
Alignment explanation
Indices: 1661--1685 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1651 TTTTTATTCT
1661 TTTTCCTTTTC
1 TTTTCCTTTTC
1672 TTTTCCTTTTC
1 TTTTCCTTTTC
1683 TTT
1 TTT
1686 ATTCCAAAAT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCCTTTTC
Found at i:1680 original size:18 final size:17
Alignment explanation
Indices: 1616--1682 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 17
1606 TATTCTAAAA
**
1616 TTTTTCTTTTATTTCTTT
1 TTTTTCTTTT-TCCCTTT
1634 TATTTTCTTTTTCCCTTTT
1 T-TTTTCTTTTTCCC-TTT
1653 TTTATTCTTTTT-CCTTT
1 TTT-TTCTTTTTCCCTTT
*
1670 TCTTTTCCTTTTC
1 T-TTTTCTTTTTC
1683 TTTATTCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
17 11 0.27
18 9 0.22
19 21 0.51
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTTCCCTTT
Found at i:5970 original size:2 final size:2
Alignment explanation
Indices: 5963--5989 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5953 GAGAAACAAA
5963 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5990 GGAAAAGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6775 original size:17 final size:18
Alignment explanation
Indices: 6730--6777 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
6720 TTAACATTTT
6730 TTTTATATTATATATATAA
1 TTTTATA-TATATATATAA
* *
6749 -TTTATGTATATTTATAAA
1 TTTTATATATATATAT-AA
6767 TTTTATATATA
1 TTTTATATATA
6778 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.33
18 7 0.29
19 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTATATATATATATAA
Found at i:6870 original size:22 final size:22
Alignment explanation
Indices: 6839--6887 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
6829 TCGATATAAT
*
6839 TTTCTCTCTCTCGTCTTCTCCC
1 TTTCTCTCTCTCATCTTCTCCC
*
6861 TTTCTGTCTCTCATCTTCTCCC
1 TTTCTCTCTCTCATCTTCTCCC
6883 TTTCT
1 TTTCT
6888 AATCTCAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.02, C:0.41, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTCTCTCTCTCATCTTCTCCC
Found at i:6898 original size:22 final size:22
Alignment explanation
Indices: 6852--6898 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
6842 CTCTCTCTCG
* *
6852 TCTTCTCCCTTTCTGTCTCTCA
1 TCTTCTCCCTTTCTATCTCTAA
6874 TCTTCTCCCTTTCTAATCTC-AA
1 TCTTCTCCCTTTCT-ATCTCTAA
6896 TCT
1 TCT
6899 CAAAGCCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.11, C:0.38, G:0.02, T:0.49
Consensus pattern (22 bp):
TCTTCTCCCTTTCTATCTCTAA
Found at i:7840 original size:12 final size:12
Alignment explanation
Indices: 7784--7840 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
7774 TTTATAATTA
7784 AATATATATAA-
1 AATATATATAAT
7795 AATA-ATAT--T
1 AATATATATAAT
7804 AGATATATATAAT
1 A-ATATATATAAT
* *
7817 TACATATATAAT
1 AATATATATAAT
7829 AATATATATAAT
1 AATATATATAAT
7841 TATTAAACGG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
9 1 0.03
10 7 0.19
11 8 0.22
12 20 0.54
13 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (12 bp):
AATATATATAAT
Found at i:7923 original size:14 final size:14
Alignment explanation
Indices: 7904--7930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7894 ACCGCATAGT
7904 CGGTTTAGGCGGTG
1 CGGTTTAGGCGGTG
7918 CGGTTTAGGCGGT
1 CGGTTTAGGCGGT
7931 TAAATGGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.48, T:0.30
Consensus pattern (14 bp):
CGGTTTAGGCGGTG
Found at i:9219 original size:10 final size:10
Alignment explanation
Indices: 9204--9233 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
9194 AAATACAACA
*
9204 AAAAAATCAT
1 AAAAAATCAC
9214 AAAAAATCAC
1 AAAAAATCAC
9224 AAAAAATCAC
1 AAAAAATCAC
9234 GAGGAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.70, C:0.17, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAATCAC
Found at i:12938 original size:193 final size:193
Alignment explanation
Indices: 12609--12970 Score: 643
Period size: 193 Copynumber: 1.9 Consensus size: 193
12599 TATAGTATTA
* *
12609 AAATATGAAACTTTTAAAGTTTAAATAATGCCCATGAGCATTTAAGCCAAGTATTGCAAAGCTAA
1 AAATATGAAACTTTTAAAGTTCAAATAATGCCCATGAGCATTCAAGCCAAGTATTGCAAAGCTAA
*
12674 AACACGGTTTGAATTGTTACTCAATTAGCATGTAGAGTTTGGTTTAACAATGAACTAGTCGTATA
66 AACACGGTTTGAATTGTTACTCAATTAGCATGAAGAGTTTGGTTTAACAATGAACTAGTCGTATA
12739 TCAGTATTTATGGAGTAAAGCCTAGTAGACTTGGTTATGATTGTCAAACTTCCCAAACAACTT
131 TCAGTATTTATGGAGTAAAGCCTAGTAGACTTGGTTATGATTGTCAAACTTCCCAAACAACTT
* * *
12802 AAATATGAAATTTTTTAAGTTCAAATAATGCCTATGAGCATTCAAGCCAAGTATTGCAAAGCTAA
1 AAATATGAAACTTTTAAAGTTCAAATAATGCCCATGAGCATTCAAGCCAAGTATTGCAAAGCTAA
* * *
12867 AACACGGTTTGAATTGTTACTCAATTAGCTTGAAGAGTTTGGTTTAACAGTGAACTAGTTGTATA
66 AACACGGTTTGAATTGTTACTCAATTAGCATGAAGAGTTTGGTTTAACAATGAACTAGTCGTATA
12932 TCAGTATTTATGGAGTAAAGCCTAGTAGACTTGGTTATG
131 TCAGTATTTATGGAGTAAAGCCTAGTAGACTTGGTTATG
12971 CCCCTAGTTT
Statistics
Matches: 160, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
193 160 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (193 bp):
AAATATGAAACTTTTAAAGTTCAAATAATGCCCATGAGCATTCAAGCCAAGTATTGCAAAGCTAA
AACACGGTTTGAATTGTTACTCAATTAGCATGAAGAGTTTGGTTTAACAATGAACTAGTCGTATA
TCAGTATTTATGGAGTAAAGCCTAGTAGACTTGGTTATGATTGTCAAACTTCCCAAACAACTT
Found at i:17361 original size:52 final size:53
Alignment explanation
Indices: 17296--17410 Score: 171
Period size: 53 Copynumber: 2.2 Consensus size: 53
17286 CTAAGATCAC
* *
17296 AAACTT-AATTACGTC-AAATTGTCGTGGAGAATTTTCTATGAAATAAATTATG
1 AAACTTGAA-TACGTCAAAATTGTCGTGGAGAATTTCCAATGAAATAAATTATG
* *
17348 AAACTTGAATACGTCAAAATTGTTGTGGAGGATTTCCAATGAAATAAATTATG
1 AAACTTGAATACGTCAAAATTGTCGTGGAGAATTTCCAATGAAATAAATTATG
17401 AAACTTGAAT
1 AAACTTGAAT
17411 TAGAGGATAC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
52 12 0.21
53 45 0.79
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (53 bp):
AAACTTGAATACGTCAAAATTGTCGTGGAGAATTTCCAATGAAATAAATTATG
Found at i:21745 original size:27 final size:27
Alignment explanation
Indices: 21709--21764 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
21699 CCTACATAAA
21709 TTTAATAACCTCACATTCTTAGA-ATT
1 TTTAATAACCTCACATTCTTAGACATT
***
21735 TTTAAGTAACCTTGTATTCTTAGACATT
1 TTTAA-TAACCTCACATTCTTAGACATT
21763 TT
1 TT
21765 AGTATAGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 15 0.60
28 5 0.20
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (27 bp):
TTTAATAACCTCACATTCTTAGACATT
Found at i:22716 original size:7 final size:7
Alignment explanation
Indices: 22679--22712 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
22669 TTGATAGTAT
22679 AAATTAA
1 AAATTAA
22686 AAATTAA
1 AAATTAA
22693 AAATTAA
1 AAATTAA
*
22700 AACATTCA
1 AA-ATTAA
22708 AAATT
1 AAATT
22713 CAAATACTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATTAA
Done.