Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012558.1 Corchorus olitorius cultivar O-4 contig12591, 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: 5030
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Found at i:1029 original size:23 final size:23
Alignment explanation
Indices: 1018--1060 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1008 TATAAACTTT
1018 TGATAA-GATTCCTATGAAATTG
1 TGATAACGATTCCTATGAAATTG
*
1040 TGATAACGATT-CTATGCAATT
1 TGATAACGATTCCTATGAAATT
1061 TCGAAAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (23 bp):
TGATAACGATTCCTATGAAATTG
Found at i:1234 original size:22 final size:22
Alignment explanation
Indices: 1138--1220 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
1128 TAAAAACATT
* *
1138 ACTATAAAATTTTGATGACCTC
1 ACTATAAAATTTTGATAACCGC
*
1160 -CTAATGAAATTTTGATAA-C-C
1 ACT-ATAAAATTTTGATAACCGC
* *
1180 ATCGACAAAATTTTGATAACCGC
1 A-CTATAAAATTTTGATAACCGC
1203 ACTATAAAATTTTGATAA
1 ACTATAAAATTTTGATAA
1221 TCTCCATGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 16 0.33
22 30 0.61
23 2 0.04
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (22 bp):
ACTATAAAATTTTGATAACCGC
Found at i:1359 original size:23 final size:23
Alignment explanation
Indices: 1329--1386 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1319 GCTTGGTATG
*
1329 AAATTTTGATAAACATTCATATA
1 AAATTTTGATAAACATCCATATA
* *
1352 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACATCCATATA
1375 AAATTTTGATAA
1 AAATTTTGATAA
1387 CCTCCTCGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACATCCATATA
Found at i:1391 original size:22 final size:22
Alignment explanation
Indices: 1329--1559 Score: 108
Period size: 22 Copynumber: 10.7 Consensus size: 22
1319 GCTTGGTATG
* * *
1329 AAATTTTGATAAACATTCATATA
1 AAATTTTGAT-AACCTCCCTATA
1352 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCCCTATA
* *
1375 AAATTTTGATAACCT-CCTCGTG
1 AAATTTTGATAACCTCCCT-ATA
*
1397 AAATTTTGATAA--T--C-A-C
1 AAATTTTGATAACCTCCCTATA
1413 AAATTTTGATAACCTCTCCCTAT-
1 AAATTTTGATAA-C-CTCCCTATA
* * * ** *
1436 GATTTTTCGATAACTTCATTATG
1 AAATTTT-GATAACCTCCCTATA
* * *
1459 AAATTTTGTTAACGTCCCTATG
1 AAATTTTGATAACCTCCCTATA
1481 AAATTTTGATAA-C-CCCTATA
1 AAATTTTGATAACCTCCCTATA
*** *
1501 AAATTTTGAATAA-CAAACTATG
1 AAATTTTG-ATAACCTCCCTATA
* *
1523 AAATCTTGATAATCC-CCCTTTA
1 AAATTTTGATAA-CCTCCCTATA
*
1545 AAATTTTAATAACCT
1 AAATTTTGATAACCT
1560 TCATATATGA
Statistics
Matches: 161, Mismatches: 31, Indels: 33
0.72 0.14 0.15
Matches are distributed among these distances:
16 12 0.07
19 1 0.01
20 16 0.10
21 14 0.09
22 70 0.43
23 43 0.27
24 5 0.03
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATA
Found at i:1522 original size:42 final size:42
Alignment explanation
Indices: 1476--1557 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 42
1466 GTTAACGTCC
*
1476 CTATGAAATTTTGATAA-CCCCTATAAAATTTTGAATAACAAA
1 CTATGAAATCTTGATAACCCCCTATAAAATTTT-AATAACAAA
*
1518 CTATGAAATCTTGATAATCCCCCTTTAAAATTTTAATAAC
1 CTATGAAATCTTGATAA-CCCCCTATAAAATTTTAATAAC
1558 CTTCATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 16 0.44
43 6 0.17
44 14 0.39
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.35
Consensus pattern (42 bp):
CTATGAAATCTTGATAACCCCCTATAAAATTTTAATAACAAA
Found at i:1747 original size:44 final size:46
Alignment explanation
Indices: 1683--1798 Score: 116
Period size: 44 Copynumber: 2.6 Consensus size: 46
1673 AAATGTTATC
* * * *
1683 AAAATTTCATAATTTGGTTACC-AAATTTTATAGGGAGGTTATGAA
1 AAAATTTCATAATATGGTTACCAAAATTTCATAGGAAGGTTATCAA
* *
1728 AAAATTT-ATACTATGGTTACCAAAATTTCATATGAAGGTTATC--
1 AAAATTTCATAATATGGTTACCAAAATTTCATAGGAAGGTTATCAA
* *
1771 AAAATTTCATAGA-GTGGTTATCAAAATT
1 AAAATTTCATA-ATATGGTTACCAAAATT
1799 ATAGGGATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 7 0.12
44 28 0.47
45 24 0.41
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (46 bp):
AAAATTTCATAATATGGTTACCAAAATTTCATAGGAAGGTTATCAA
Found at i:1754 original size:45 final size:45
Alignment explanation
Indices: 1683--1781 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
1673 AAATGTTATC
* * * *
1683 AAAATTTCATAATTTGGTTACCAAATTTTATAGGGAGGTTATGAA
1 AAAATTTCATAATATGGTTACCAAATTTCATAGGAAGGTTATCAA
* *
1728 AAAATTT-ATACTATGGTTACCAAAATTTCATATGAAGGTTATC--
1 AAAATTTCATAATATGGTTACC-AAATTTCATAGGAAGGTTATCAA
1771 AAAATTTCATA
1 AAAATTTCATA
1782 GAGTGGTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
43 7 0.15
44 15 0.33
45 24 0.52
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (45 bp):
AAAATTTCATAATATGGTTACCAAATTTCATAGGAAGGTTATCAA
Found at i:1767 original size:22 final size:22
Alignment explanation
Indices: 1742--1798 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1732 TTTATACTAT
*
1742 GGTTACCAAAATTTCATATGA-A
1 GGTTATCAAAATTTCATA-GAGA
*
1764 GGTTATCAAAATTTCATAGAGT
1 GGTTATCAAAATTTCATAGAGA
1786 GGTTATCAAAATT
1 GGTTATCAAAATT
1799 ATAGGGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGAGA
Found at i:1956 original size:22 final size:22
Alignment explanation
Indices: 1864--1966 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 22
1854 CAAAAGATTA
* *
1864 TGGTTATCAAAATTTCACAGTA
1 TGGTTATCAAATTTTCACAGTG
* * * *
1886 TGGTCATCAAATCTTCATAGAG
1 TGGTTATCAAATTTTCACAGTG
* * * * *
1908 AGGTTATCAAAGTTTGATAATG
1 TGGTTATCAAATTTTCACAGTG
* *
1930 AGGTTATCAAATTTTCGCAGTG
1 TGGTTATCAAATTTTCACAGTG
1952 TGGTTATCAATATTT
1 TGGTTATCAA-ATTT
1967 CTACGTTGGA
Statistics
Matches: 61, Mismatches: 19, Indels: 1
0.75 0.23 0.01
Matches are distributed among these distances:
22 57 0.93
23 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAATTTTCACAGTG
Found at i:4708 original size:47 final size:42
Alignment explanation
Indices: 4654--4747 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 42
4644 AGGTTGGGAG
4654 CAAAACATAAATAAACTATGACAAGGATATTATATAAGTCTAAACTT
1 CAAAACATAAAT-AA-TAT--C-AGGATATTATATAAGTCTAAACTT
***
4701 CAAAACATAAATAATATCTTTATATTATATAAGTCTAAACTT
1 CAAAACATAAATAATATCAGGATATTATATAAGTCTAAACTT
4743 CAAAA
1 CAAAA
4748 ATCATGACCT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
42 26 0.59
43 1 0.02
45 3 0.07
46 2 0.05
47 12 0.27
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (42 bp):
CAAAACATAAATAATATCAGGATATTATATAAGTCTAAACTT
Found at i:4860 original size:12 final size:12
Alignment explanation
Indices: 4843--4870 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4833 CATCAAAACC
4843 TATTAAAATAAA
1 TATTAAAATAAA
4855 TATTAAAATAAA
1 TATTAAAATAAA
4867 TATT
1 TATT
4871 TGCTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TATTAAAATAAA
Done.