Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015988.1 Corchorus capsularis cultivar CVL-1 contig16009, 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: 64887
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:2049 original size:31 final size:29
Alignment explanation
Indices: 2003--2079 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
1993 GCTTAATATC
* *
2003 CAAATTAGCCACTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T-CATTTTGGGA
**
2034 CAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTCATTTTGGGA
2063 CAAATTGGCCCCTTAAC
1 CAAATTGGCCCCTTAAC
2080 CCTTAAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.60
30 1 0.02
31 16 0.38
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTCATTTTGGGA
Found at i:2832 original size:27 final size:28
Alignment explanation
Indices: 2776--2832 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2766 TCTCGTTTTT
2776 AAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
*
2804 AAAAGTTAAGGGGTCAATTTGTCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
2832 A
1 A
2833 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (28 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAA
Found at i:6784 original size:33 final size:34
Alignment explanation
Indices: 6738--6802 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
6728 TAGTTTTTGT
*
6738 TTTTTCCGTTTTTTCTAAAAAAAAAAG-TTTTCC
1 TTTTTCCGATTTTTCTAAAAAAAAAAGATTTTCC
6771 TTTTTCCGATTTTTCTAAAAAAAAAAGATTTT
1 TTTTTCCGATTTTTCTAAAAAAAAAAGATTTT
6803 TGCGATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (34 bp):
TTTTTCCGATTTTTCTAAAAAAAAAAGATTTTCC
Found at i:6802 original size:19 final size:21
Alignment explanation
Indices: 6778--6817 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6768 TCCTTTTTCC
6778 GATTTTT-C-TAAAAAAAAAA
1 GATTTTTGCATAAAAAAAAAA
6797 GATTTTTGCGATAAAAAAAAA
1 GATTTTTGC-ATAAAAAAAAA
6818 TAATTAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
22 10 0.56
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (21 bp):
GATTTTTGCATAAAAAAAAAA
Found at i:14477 original size:36 final size:36
Alignment explanation
Indices: 14428--14500 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
14418 TCTTGACTCC
* **
14428 TTCACTTATTTGAATTCCTTT-TGCCCTGTTATGATT
1 TTCACTTAATTGAATT-CTTTCTGCCCTAATATGATT
14464 TTCACTTAATTGAATTCTTTCTGCCCTAATATGATT
1 TTCACTTAATTGAATTCTTTCTGCCCTAATATGATT
14500 T
1 T
14501 GTGATTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 4 0.12
36 29 0.88
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.51
Consensus pattern (36 bp):
TTCACTTAATTGAATTCTTTCTGCCCTAATATGATT
Found at i:24751 original size:22 final size:22
Alignment explanation
Indices: 24709--24752 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24699 TATTCATATG
* * *
24709 AAATTATGATAATTTCTCTATT
1 AAATTATAATAATTACACTATT
24731 AAATTATAATAATTACACTATT
1 AAATTATAATAATTACACTATT
24753 TTTTATGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATTATAATAATTACACTATT
Found at i:25047 original size:22 final size:22
Alignment explanation
Indices: 24879--25305 Score: 131
Period size: 22 Copynumber: 19.5 Consensus size: 22
24869 ACCTCCTTAA
* *
24879 GAAATTTTGA-AGATCTCAATAT
1 GAAATTTTGATA-ATCACACTAT
*
24901 GAAATTTTGATAA-CTTC-CTAAT
1 GAAATTTTGATAATC-ACACT-AT
24923 GAAATTTTGATAATCAACACTAT
1 GAAATTTTGATAATC-ACACTAT
* *
24946 GAGATGTTGATAACCTC-CA-TAT
1 GAAATTTTGATAA--TCACACTAT
* * * **
24968 GATATATTGATAACCACGTTAT
1 GAAATTTTGATAATCACACTAT
* * *
24990 GAAAATTTAAAAACCTC-CA-TAT
1 GAAATTTTGATAA--TCACACTAT
*
25012 G-AATTGTT-AGTAATCACACTCT
1 GAAATT-TTGA-TAATCACACTAT
25034 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAATCACACTAT
* * * * *
25056 GTAATTGTGATAACCTCGCTAT
1 GAAATTTTGATAATCACACTAT
***
25078 GAAATTTTGATAAATCTTTCTAT
1 GAAATTTTGAT-AATCACACTAT
* * *
25101 AAAATTTTGATAAAC-CTGCCTAT
1 GAAATTTTGATAATCAC--ACTAT
* *
25124 AAAATTTTGATAACTTC-C-TTAT
1 GAAATTTTGATAA--TCACACTAT
*
25146 GAAATCTTGATAA-C-CAC---
1 GAAATTTTGATAATCACACTAT
* * *
25163 -AAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAATCACACTAT
** * * *
25184 GACTTTTTGATAACCTCATTAT
1 GAAATTTTGATAATCACACTAT
* * *
25206 GAAATTTTGTTAATCTCCCTAT
1 GAAATTTTGATAATCACACTAT
* *
25228 GAAATTTTGAT-CTACATACTAT
1 GAAATTTTGATAAT-CACACTAT
* * *
25250 GAAATTTTGATAA-CCCTCTTGT
1 GAAATTTTGATAATCACAC-TAT
* *
25272 GAAATTTTGA-AAACTAAACTAT
1 GAAATTTTGATAATC-ACACTAT
25294 GAAATTTTGATA
1 GAAATTTTGATA
25306 TCCTCCCTGA
Statistics
Matches: 305, Mismatches: 65, Indels: 69
0.69 0.15 0.16
Matches are distributed among these distances:
16 11 0.04
17 1 0.00
18 2 0.01
19 2 0.01
20 3 0.01
21 14 0.05
22 204 0.67
23 61 0.20
24 3 0.01
25 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAATCACACTAT
Found at i:25105 original size:23 final size:23
Alignment explanation
Indices: 25058--25136 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
25048 CACACTATGT
* *
25058 AATTGTGAT-AACCT-CGCTATGA
1 AATTTTGATAAACCTGC-CTATAA
* **
25080 AATTTTGATAAATCTTTCTATAA
1 AATTTTGATAAACCTGCCTATAA
25103 AATTTTGATAAACCTGCCTATAA
1 AATTTTGATAAACCTGCCTATAA
25126 AATTTTGATAA
1 AATTTTGATAA
25137 CTTCCTTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 8 0.17
23 40 0.83
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (23 bp):
AATTTTGATAAACCTGCCTATAA
Found at i:25251 original size:44 final size:44
Alignment explanation
Indices: 24854--25764 Score: 277
Period size: 44 Copynumber: 21.2 Consensus size: 44
24844 TTAATCTTCT
* * * * *
24854 TATGAAATTTAGTTAACCTCCTTAAGAAATTTTGA-AGATC-TCAA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATA-A-CATCAC
* *
24898 TATGAAATTTTGATAA-CTTCCTAATGAAATTTTGATAATCAACAC
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAA-CATCAC
* * * * *
24943 TATGAGATGTTGATAACCTCCATATGATATATTGATAAC--CAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * *
24985 GTTATGAAAATTTAAAAACCTCCATATG-AATTGTT-AGTAATCA-CAC
1 --TATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAA-CATCAC
* * * * * * * *
25031 TCTGAAATTTTGATAATCACACTATGTAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* ** * *
25075 TATGAAATTTTGATAAATCTTTCTATAAAATTTTGATAAACCTGC-C
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACAT-CAC
* * * *
25121 TATAAAATTTTGATAACTTCCTTATGAAATCTTGATAAC--CAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
** * *
25163 ----AAATTTTGATAACCTCCCTATGACTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * *
25203 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACATCAC
* * * *
25247 TATGAAATTTTGATAACC-CTCTTGTGAAATTTTGAAAAC-TAAAC
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACAT-CAC
* * *
25291 TATGAAATTTTGATATCCTCCC--TG-AATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * * * *
25331 T-TGAAATTTTGATTA-CTCCATAATAAAAGTTTAATAACCTTC-C
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAA-CATCAC
* * * *
25374 --T--AATTTAG-TAACCAT-ACTATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACATCAC
* * ** *
25413 CA-G-AA-----AT-A-C-CACTATGGATTTTTTG-TAATCA-CAT
1 TATGAAATTTTGATAACCTCCCTAT-GAAATTTTGATAA-CATCAC
* * ** * **
25447 TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * * * *
25491 TATAAAATTTTGTTGACC-CCTGTATGAAATTCTGATAATCA-CAT
1 TATGAAATTTTGATAACCTCC-CTATGAAATTTTGATAA-CATCAC
* * * * * *
25535 TATGTAATTTTCATAACCTCGCTTTGAAATTTTGATAACAACAG
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* ** *
25579 TATGAAATTTTGATAATCTTTCTAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA--C-ATCAC
* * * * * * *
25625 TATGAAATTTCGATAATCACTCTATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * * *
25667 TATCAAATTTTGGT-A-CTCCTTATGAAATTGACTTTTATAACCTTCA-
1 TATGAAATTTTGATAACCTCCCTATGAAA-T---TTTGATAA-CATCAC
* * * * *
25713 TATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
25757 TATGAAAT
1 TATGAAAT
25765 ATTTAATGAT
Statistics
Matches: 641, Mismatches: 152, Indels: 148
0.68 0.16 0.16
Matches are distributed among these distances:
34 9 0.01
35 10 0.02
36 3 0.00
37 1 0.00
38 37 0.06
39 27 0.04
40 20 0.03
41 18 0.03
42 31 0.05
43 43 0.07
44 276 0.43
45 81 0.13
46 72 0.11
47 5 0.01
48 8 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
Found at i:25349 original size:19 final size:20
Alignment explanation
Indices: 25293--25343 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
25283 AACTAAACTA
25293 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
25313 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
25332 TGAAATTTTGAT
1 TGAAATTTTGAT
25344 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:25501 original size:22 final size:22
Alignment explanation
Indices: 25449--25764 Score: 162
Period size: 22 Copynumber: 14.3 Consensus size: 22
25439 AATCACATTT
*
25449 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
25471 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
25493 TAAAATTTTGTTGACCCCTGTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
25515 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* * *
25537 TGTAATTTTCATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
25559 TGAAATTTTGATAACAACAGTA
1 TGAAATTTTGATAACCTCTTTA
*
25581 TGAAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
25603 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
25627 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
25649 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
25669 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
* *
25689 TGAAATTGACTTTTATAACCT-TCATA
1 TGAAA-T---TTTGATAACCTCT-TTA
* **
25715 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTTTA
* **
25737 TAAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCTTTA
25759 TGAAAT
1 TGAAAT
25765 ATTTAATGAT
Statistics
Matches: 218, Mismatches: 58, Indels: 36
0.70 0.19 0.12
Matches are distributed among these distances:
19 2 0.01
20 14 0.06
21 27 0.12
22 141 0.65
23 2 0.01
24 9 0.04
25 14 0.06
26 9 0.04
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:25815 original size:22 final size:22
Alignment explanation
Indices: 25790--25831 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25780 GTTAACCACA
25790 CTATGAAATTCTT-ATAATCTCG
1 CTATGAAATT-TTGATAATCTCG
*
25812 CTATGACATTTTGATAATCT
1 CTATGAAATTTTGATAATCT
25832 TTTTGATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCG
Found at i:25836 original size:56 final size:56
Alignment explanation
Indices: 25720--25842 Score: 142
Period size: 56 Copynumber: 2.2 Consensus size: 56
25710 TCATATGAAA
*
25720 TTTTGATAACCACACTATAAAATTTTGATAACCTCCCTATGAAATATTTAATGATG
1 TTTTGATAACCACACTATAAAATTTTGATAACCTCCCTATGAAATATTTAATAATG
* * * * * * *
25776 TTTTGTTAACCACACTATGAAATTCTT-ATAATCTCGCTATGACAT-TTTGATAATCT
1 TTTTGATAACCACACTATAAAATT-TTGATAACCTCCCTATGAAATATTTAATAAT-G
25832 TTTTGATAACC
1 TTTTGATAACC
25843 TTTCTGTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 7 0.12
56 47 0.84
57 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (56 bp):
TTTTGATAACCACACTATAAAATTTTGATAACCTCCCTATGAAATATTTAATAATG
Found at i:25889 original size:22 final size:22
Alignment explanation
Indices: 25864--26022 Score: 99
Period size: 22 Copynumber: 7.1 Consensus size: 22
25854 TTGTGACAAT
*
25864 TAACCACCTTATGAAATTTCAA
1 TAACCACCTTATGAAATTTTAA
* * *
25886 TAACCAACC-AAAGAGATTTTAA
1 TAACC-ACCTTATGAAATTTTAA
* **
25908 TAACCTGATCTTATGAAATTTTGG
1 TAACC--ACCTTATGAAATTTTAA
**
25932 TAACCACAC-TATGAAATTTTGG
1 TAACCAC-CTTATGAAATTTTAA
* *
25954 TAACCACAC-TATGGAATTTTGA
1 TAACCAC-CTTATGAAATTTTAA
* * *
25976 TAACCTCCTCATGAAATTGTAA
1 TAACCACCTTATGAAATTTTAA
* * *
25998 TAACCATCTTATAAAATTTTGA
1 TAACCACCTTATGAAATTTTAA
26020 TAA
1 TAA
26023 TCACATAGAG
Statistics
Matches: 107, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.01
22 87 0.81
23 6 0.06
24 13 0.12
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCACCTTATGAAATTTTAA
Found at i:25935 original size:24 final size:22
Alignment explanation
Indices: 25919--25993 Score: 107
Period size: 22 Copynumber: 3.4 Consensus size: 22
25909 AACCTGATCT
25919 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
25941 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
* * *
25963 TATGGAATTTTGATAACCTC-C
1 TATGAAATTTTGGTAACCACAC
25984 TCATGAAATT
1 T-ATGAAATT
25994 GTAATAACCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 2 0.04
22 46 0.96
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCACAC
Found at i:26222 original size:19 final size:20
Alignment explanation
Indices: 26191--26228 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
26181 TATTGACATT
26191 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
26210 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
26229 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:26605 original size:31 final size:31
Alignment explanation
Indices: 26540--26598 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
26530 TGGCAATTTA
26540 GAAATATGTTTTAAAGAAAAGGGTACAACTG
1 GAAATATGTTTTAAAGAAAAGGGTACAACTG
26571 GAAATATGTTTTAAA-AATAAGGGTACAA
1 GAAATATGTTTTAAAGAA-AAGGGTACAA
26599 TCGGAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAGAAAAGGGTACAACTG
Found at i:27566 original size:55 final size:55
Alignment explanation
Indices: 27483--27642 Score: 220
Period size: 55 Copynumber: 3.0 Consensus size: 55
27473 GGAATCTTTC
*
27483 TTCAAGGAACACTGGGAGATCA-TGAAGATTTCAAGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCACT-AAGATCTCAAGCGAGTGTCAGCATTGAAGCT
*
27538 TTCAAGGAACACTGGGAGATCACTAAGATCTCAAGCAAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCACTAAGATCTCAAGCGAGTGTCAGCATTGAAGCT
* ** * *
27593 TTTAAGGAACACT--GA-ATCACGGAGATCTCAGGCGAGCGTCAGCATTGAAG
1 TTCAAGGAACACTGGGAGATCACTAAGATCTCAAGCGAGTGTCAGCATTGAAG
27643 ATTGATAAGA
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
52 30 0.31
53 2 0.02
55 63 0.66
56 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (55 bp):
TTCAAGGAACACTGGGAGATCACTAAGATCTCAAGCGAGTGTCAGCATTGAAGCT
Found at i:27886 original size:21 final size:21
Alignment explanation
Indices: 27860--27899 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
27850 ACTGGCGGGC
27860 TTTACTTGCTGAGGAAGGCTT
1 TTTACTTGCTGAGGAAGGCTT
27881 TTTACTTGCTGAGGAAGGC
1 TTTACTTGCTGAGGAAGGC
27900 GAACTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (21 bp):
TTTACTTGCTGAGGAAGGCTT
Found at i:28086 original size:17 final size:17
Alignment explanation
Indices: 28048--28080 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28038 CTCATAGTAC
*
28048 CTAGGTAGTATGAGGTA
1 CTAGGTAGCATGAGGTA
28065 CTAGGTAGCATGAGGT
1 CTAGGTAGCATGAGGT
28081 GATAGGCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (17 bp):
CTAGGTAGCATGAGGTA
Found at i:28754 original size:156 final size:155
Alignment explanation
Indices: 28426--28781 Score: 366
Period size: 156 Copynumber: 2.3 Consensus size: 155
28416 TAAACCGAGC
* * * * * *
28426 TTCTCACCTCAAAATGTCCTTAAATGAAAAATTGGCATAAGTTTTTCATTCTAAGTCTGAATGAG
1 TTCTCACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTACATTCTAAGTCTCAACGAG
* * *
28491 CTAAAATTTGCCAAGGGACTTAGAATATCGACATAAGACTATGGAAAAATTTCTAAGTAAAACCG
66 CTAAAATTTACCAAGAGACTTAGAATATCGACATAAGACTATGGAAAAATATCTAAGTAAAACCG
* * *
28556 AACTCCCTTTGATGGTGAACTAGGT
131 AACTCCCTTAGATAGAGAACTAGGT
* * *
28581 TTCTCTCC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTACATTCTAAGTC-CAACGA
1 TTCTCACCTC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTACATTCTAAGTCTCAACG-
* * * *
28644 AGCT-GATTTTCCACCAATAGACTTAGATTAT-GACCATAA-AGCTATGGGAAAAA-ATCTAAGT
64 AGCTAAAATTT--ACCAAGAGACTTAGAATATCGA-CATAAGA-CTAT-GGAAAAATATCTAAGT
* * *
28705 AAAACCGAACTCTC-TAGCATAGAGAAGTTGGT
124 AAAACCGAACTCCCTTAG-ATAGAGAACTAGGT
* * *
28737 TTGTCACCTCAAATTGTCCTCAACTGAAAAACTAGCATAAGTTTT
1 TTCTCACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTT
28782 TTATACTAAG
Statistics
Matches: 164, Mismatches: 28, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
154 8 0.05
155 57 0.35
156 91 0.55
157 8 0.05
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (155 bp):
TTCTCACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTACATTCTAAGTCTCAACGAG
CTAAAATTTACCAAGAGACTTAGAATATCGACATAAGACTATGGAAAAATATCTAAGTAAAACCG
AACTCCCTTAGATAGAGAACTAGGT
Found at i:42792 original size:34 final size:35
Alignment explanation
Indices: 42713--42801 Score: 108
Period size: 34 Copynumber: 2.5 Consensus size: 35
42703 AATACTTTTT
* * * * *
42713 ACTGATTAGTACTTTACCCTTTACCATTTTTCCTTT
1 ACTGATTACT-CTTTACTCTGTACCATTCTTCCTTA
42749 ACTGATTACTCTTTACTCTGTACCATTCTT-CTTA
1 ACTGATTACTCTTTACTCTGTACCATTCTTCCTTA
*
42783 ACTGATTACTTTTTACTCT
1 ACTGATTACTCTTTACTCT
42802 TTACTCTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 21 0.45
35 17 0.36
36 9 0.19
ACGTcount: A:0.20, C:0.25, G:0.06, T:0.49
Consensus pattern (35 bp):
ACTGATTACTCTTTACTCTGTACCATTCTTCCTTA
Found at i:42897 original size:36 final size:35
Alignment explanation
Indices: 42857--42931 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 35
42847 TGATTACTCT
42857 TTACTCTTTACTCGTTACCATTTTTTTATTTACTGA
1 TTACTCTTTACTCGTTACCA-TTTTTTATTTACTGA
* *
42893 TTACTCTTTACTCTTTACCATTTTTTCTTTACTGA
1 TTACTCTTTACTCGTTACCATTTTTTATTTACTGA
42928 TTAC
1 TTAC
42932 CATGTCCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 18 0.49
36 19 0.51
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (35 bp):
TTACTCTTTACTCGTTACCATTTTTTATTTACTGA
Found at i:42957 original size:54 final size:55
Alignment explanation
Indices: 42889--43019 Score: 255
Period size: 55 Copynumber: 2.4 Consensus size: 55
42879 TTTTTATTTA
42889 CTGATTACTCTTTACTCTTTACCA-TTTTTTCTTTACTGATTACCATGTCCTTTG
1 CTGATTACTCTTTACTCTTTACCATTTTTTTCTTTACTGATTACCATGTCCTTTG
42943 CTGATTACTCTTTACTCTTTACCATTTTTTTCTTTACTGATTACCATGTCCTTTG
1 CTGATTACTCTTTACTCTTTACCATTTTTTTCTTTACTGATTACCATGTCCTTTG
42998 CTGATTACTCTTTACTCTTTAC
1 CTGATTACTCTTTACTCTTTAC
43020 ACTTTACCAT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
54 24 0.32
55 52 0.68
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.52
Consensus pattern (55 bp):
CTGATTACTCTTTACTCTTTACCATTTTTTTCTTTACTGATTACCATGTCCTTTG
Found at i:43064 original size:22 final size:22
Alignment explanation
Indices: 43036--43225 Score: 178
Period size: 22 Copynumber: 8.8 Consensus size: 22
43026 CCATTTTTTC
43036 TTTACTGATTACTCTTTTACTT
1 TTTACTGATTACTCTTTTACTT
*
43058 TTTACTGATTACTATTTTTACTCT
1 TTTACTGATTACT-CTTTTACT-T
* *
43082 TTT-CTAATTACTATTTTACTT
1 TTTACTGATTACTCTTTTACTT
* *
43103 TTTACTGGTTAC-CTTTTTGCTT
1 TTTACTGATTACTC-TTTTACTT
* *
43125 TTTACTGATTAC-C-ATTGCTT
1 TTTACTGATTACTCTTTTACTT
* *
43145 CTTACTGATTA--CTATTACTT
1 TTTACTGATTACTCTTTTACTT
* * *
43165 TCTACTGATTAGTCTTTTAATT
1 TTTACTGATTACTCTTTTACTT
43187 TTTACTGATTAC-CATTTTACTT
1 TTTACTGATTACTC-TTTTACTT
*
43209 TTTACTAATTACTCTTT
1 TTTACTGATTACTCTTT
43226 ACTGATTGCC
Statistics
Matches: 140, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
19 1 0.01
20 31 0.22
21 5 0.04
22 83 0.59
23 16 0.11
24 4 0.03
ACGTcount: A:0.21, C:0.17, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTACTGATTACTCTTTTACTT
Found at i:43107 original size:7 final size:7
Alignment explanation
Indices: 43044--43130 Score: 50
Period size: 7 Copynumber: 11.7 Consensus size: 7
43034 TCTTTACTGA
43044 TTACTCTT
1 TTACT-TT
43052 TTACTTT
1 TTACTTT
**
43059 TTACTGA
1 TTACTTT
43066 TTACTATTT
1 TTAC--TTT
43075 TTACTCTT
1 TTACT-TT
**
43083 TT-CTAA
1 TTACTTT
43089 TTACTATT
1 TTACT-TT
43097 TTACTTT
1 TTACTTT
**
43104 TTACTGG
1 TTACTTT
43111 TTACCTTT
1 TTA-CTTT
*
43119 TTGCTTT
1 TTACTTT
43126 TTACT
1 TTACT
43131 GATTACCATT
Statistics
Matches: 59, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
6 2 0.03
7 34 0.58
8 18 0.31
9 5 0.08
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.61
Consensus pattern (7 bp):
TTACTTT
Found at i:46481 original size:20 final size:20
Alignment explanation
Indices: 46456--46495 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46446 TGCAACTAAC
46456 TACTTCTAGTATTTTGTAAT
1 TACTTCTAGTATTTTGTAAT
46476 TACTTCTAGTATTTTGTAAT
1 TACTTCTAGTATTTTGTAAT
46496 GGGATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
TACTTCTAGTATTTTGTAAT
Found at i:46649 original size:15 final size:15
Alignment explanation
Indices: 46629--46657 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46619 AACCACCACT
46629 AATGCAAATTAATGA
1 AATGCAAATTAATGA
46644 AATGCAAATTAATG
1 AATGCAAATTAATG
46658 GAATATATGA
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:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (15 bp):
AATGCAAATTAATGA
Found at i:52448 original size:19 final size:18
Alignment explanation
Indices: 52424--52459 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52414 GAAGACTTAT
52424 TTGAAGATAATTTGAAGAG
1 TTGAAGATAA-TTGAAGAG
*
52443 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
52460 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAG
Found at i:61684 original size:55 final size:55
Alignment explanation
Indices: 61595--61757 Score: 220
Period size: 55 Copynumber: 3.0 Consensus size: 55
61585 GGAATCTTTC
* * *
61595 TTCAAGGAACACTGGGAGATCA-CGAAGATTTCAAGCGAGTGTCAGCATTTAAGCT
1 TTCAAGGAACACTGGGAGATCATAG-AGATCTCAAGCGAGTGTCAGCATTGAAGCT
* *
61650 TTCAAGGAACACTGGGAGATCATTGAGATCTCAAGCAAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCATAGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
* * * * *
61705 TTCAAGGAACATTGGAAAATCATAGAGATCTCAGGCGAGCGTCAGCATTGAAG
1 TTCAAGGAACACTGGGAGATCATAGAGATCTCAAGCGAGTGTCAGCATTGAAG
61758 ATTGATAAGA
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 95 0.99
56 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (55 bp):
TTCAAGGAACACTGGGAGATCATAGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
Found at i:63592 original size:26 final size:26
Alignment explanation
Indices: 63558--63608 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
63548 TATTTTTTAT
63558 TACTAATTACCAT-TATTTACTCTTTG
1 TACTAATTACCATAT-TTTACTCTTTG
*
63584 TACTGATTACCATATTTTACTCTTT
1 TACTAATTACCATATTTTACTCTTT
63609 TTTATTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51
Consensus pattern (26 bp):
TACTAATTACCATATTTTACTCTTTG
Found at i:64064 original size:22 final size:22
Alignment explanation
Indices: 63992--64056 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
63982 CTATTACTTC
*
63992 TTACTGATTAGCA--TTACTCT
1 TTACTGATTACCACTTTACTCT
*
64012 TTACTGATTATCACTTTACTCT
1 TTACTGATTACCACTTTACTCT
*
64034 TTACTGATTACCATTTTAC-CT
1 TTACTGATTACCACTTTACTCT
64055 TT
1 TT
64057 TATTGATTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.30
21 4 0.10
22 24 0.60
ACGTcount: A:0.23, C:0.22, G:0.06, T:0.49
Consensus pattern (22 bp):
TTACTGATTACCACTTTACTCT
Done.