Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012619.1 Corchorus capsularis cultivar CVL-1 contig12640, 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: 33824
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9815 original size:21 final size:21
Alignment explanation
Indices: 9752--9815 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
9742 TCTCTGTAAT
*
9752 TTAAGAAATACTCAACTCAAA
1 TTAAGAAATACTCAACTGAAA
****
9773 TTATAGAAAT--TTTTTTGTAAA
1 TTA-AGAAATACTCAACTG-AAA
9794 TTAAGAAATACTCAACTGAAA
1 TTAAGAAATACTCAACTGAAA
9815 T
1 T
9816 CCTGATCCTT
Statistics
Matches: 30, Mismatches: 9, Indels: 8
0.64 0.19 0.17
Matches are distributed among these distances:
20 8 0.27
21 13 0.43
22 9 0.30
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (21 bp):
TTAAGAAATACTCAACTGAAA
Found at i:16974 original size:19 final size:19
Alignment explanation
Indices: 16950--16987 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16940 GCAAACCCCT
16950 TTTTCATTTCACAAAACTC
1 TTTTCATTTCACAAAACTC
16969 TTTTCATTTCACAAAACTC
1 TTTTCATTTCACAAAACTC
16988 GAACTTGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTCATTTCACAAAACTC
Found at i:17087 original size:50 final size:49
Alignment explanation
Indices: 17008--17104 Score: 167
Period size: 50 Copynumber: 2.0 Consensus size: 49
16998 CCTAAATCTA
*
17008 AGAATTACTTGAGATATCAATTCCTTTCATTTAACCTAACATGTATAGT
1 AGAATTACTTGAGATATCAATTCCTTTCATTTAACCCAACATGTATAGT
*
17057 AGAACTTACTTGAGATATCAGTTCCTTTCATTTAACCCAACATGTATA
1 AGAA-TTACTTGAGATATCAATTCCTTTCATTTAACCCAACATGTATA
17105 AGTCGATGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 4 0.09
50 41 0.91
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (49 bp):
AGAATTACTTGAGATATCAATTCCTTTCATTTAACCCAACATGTATAGT
Found at i:22910 original size:22 final size:22
Alignment explanation
Indices: 22885--23489 Score: 233
Period size: 22 Copynumber: 28.0 Consensus size: 22
22875 ATAATCCCAT
22885 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
22907 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* **
22929 TATGAAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* * ** * *
22951 TAT-CATTTTTTTTAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
22972 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
22994 TAAGGAATTTTGA-AGACC-TCAG
1 TATGAAATTTTGATA-ACCTTC-C
23016 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
23038 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
*
23061 TATGAGATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
23082 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
23105 TATGAAAATTTAAAAACC--CC
1 TATGAAATTTTGATAACCTTCC
* * *
23125 ATATG-AATTGTT-AGTAATCATAC
1 -TATGAAATT-TTGA-TAACCTTCC
* *
23148 TCTGAAATTTTGATAATCACAT--
1 TATGAAATTTTGATAA-C-CTTCC
23170 TATGAAATTTTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
23192 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
23215 TATAAAATTTTGATAA-ATCTCC
1 TATGAAATTTTGATAACCT-TCC
* * *
23237 TTATAAAATTTTGATAACTTTCT
1 -TATGAAATTTTGATAACCTTCC
* *
23260 TATTAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
*
23277 TAT-AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
23298 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*** * *
23320 TATGAAATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
* *
23342 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
23364 TATGAAATTTAGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
23386 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
23407 -CTGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
23427 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
23451 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
*
23468 TATGAAATTTTGATTACCTTCC
1 TATGAAATTTTGATAACCTTCC
23490 CAGAAATACC
Statistics
Matches: 434, Mismatches: 105, Indels: 88
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 13 0.03
18 2 0.00
19 2 0.00
20 25 0.06
21 40 0.09
22 257 0.59
23 75 0.17
24 9 0.02
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:23222 original size:23 final size:23
Alignment explanation
Indices: 23174--23275 Score: 104
Period size: 23 Copynumber: 4.5 Consensus size: 23
23164 TCACATTATG
* *
23174 AAATTTTGAT-AA-CCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATA
23196 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
23219 AAATTTTGATAAATC-TCCTTATA
1 AAATTTTGATAAATCTTCC-TATA
* * *
23242 AAATTTTGATAACT-TTCTTATT
1 AAATTTTGATAAATCTTCCTATA
*
23264 AAATCTTGATAA
1 AAATTTTGATAA
23276 CTATAAATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
22 27 0.39
23 40 0.57
24 3 0.04
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:23331 original size:44 final size:44
Alignment explanation
Indices: 22885--24157 Score: 359
Period size: 44 Copynumber: 29.4 Consensus size: 44
22875 ATAATCCCAT
* * **
22885 TATGAAATTTTGATAACCTTCCTATGAAATTTTAATAATGAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CCTCAC
* *** * * ** * *
22929 TATGAAATTTTGAGAACCTTTTTAT-CATTTTTTTTAACTTTC-T
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAC-CTCAC
* * * *
22972 TATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA-AGACCTCAG
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATA-ACCTCAC
* * *
23016 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCAC
* * * * * **
23061 TATGAGATTTTGATAACCTCCATATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * *
23105 TATGAAAATTTAAAAACC-CCATATG-AATTGTT-AGTAATCAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAA-CCTCAC
* * * ** *
23148 TCTGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * *
23192 TATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAATCTC-C
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACCTCAC
* * * * * *
23237 TTATAAAATTTTGATAACTTTCTTATTAAATCTTGAT-A----AC
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * *
23277 TAT-AAATTTTGATAACCTCCCTATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
** * * *
23320 TATGAAATTTTGATCTGCAT-ACTATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGATAA-CCTCAC
* * ** *
23364 TATGAAATTTAGA-AAACTAAACTATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCT-CCCTATGAAATTTTGATAACCTCAC
* * * * * *
23407 -CTGAAATTTTGATATCCTCCATAATAAAAGTTTAATAACCTTC-C
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACC-TCAC
* * *
23451 --T--AA-TTTGGTAACCAT-ACTATGAAATTTTGATTACCTTC-C
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACC-TCAC
* * * * *
23490 CA-G-AA-----AT-A-C-CACTATGAAATTTTTG-TAATCACAT
1 TATGAAATTTTGATAACCTCCCTATGAAA-TTTTGATAACCTCAC
* * * ** * **
23524 TCTGAAAATTTGATAGCCTCTTTCTGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * * * * *
23568 TATAAAATTTTGTTGACC-CCTCTATCAAATTCTGATAATCACAT
1 TATGAAATTTTGATAACCTCC-CTATGAAATTTTGATAACCTCAC
* * * * * ** *
23612 TATGTAATTTTGATAATCTCGCTTTGGAATTTTGATAACAACAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * *
23656 TATGAAATTTTGATAATCTTCCTAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-C--CTCAC
* * * * *
23702 TATGAAATTTCGATAATCACTCTATGAGA-TTTGATAACCTTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCAC
* * * * *
23745 -ATCAAATTTTGGT-A-CTCCTTATGAAATTGAGAATTTTATAACCTTTA-
1 TATGAAATTTTGATAACCTCCCTATGAAA-T-----TTTGATAACC-TCAC
* * * * *
23792 GATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * *
23836 CATGAAATATTGGTAACCT-CCTAATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACCTCAC
* *
23880 TATGAAATTCTT-ATAACCTCGCTATGACATTTTGATAA--T--C
1 TATGAAATT-TTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* ** * * * *
23920 --T----CTTTGATAACCTTTCTATAAAATTGTGAAAATTAACCACCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTG---A-TAACCTCAC
** ** * *
23962 TATGAAATTTCAATAACCAACCTAAGAAATTTTAATAACC-CGATCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTC-A--C
* * * *
24008 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* ** * * *
24051 ATATGAAATTTTGATAACTTCCAAATGAAATTTTGGTAACCACTC
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * *
24096 TATGAAATTTTGATAACCT-CCTCATGAAATTATAATAACCATC-T
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACC-TCAC
24140 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
24158 ACATAGAGAC
Statistics
Matches: 895, Mismatches: 240, Indels: 188
0.68 0.18 0.14
Matches are distributed among these distances:
33 3 0.00
34 30 0.03
35 7 0.01
36 3 0.00
37 2 0.00
38 30 0.03
39 21 0.02
40 19 0.02
41 8 0.01
42 26 0.03
43 109 0.12
44 412 0.46
45 91 0.10
46 82 0.09
47 14 0.02
48 28 0.03
49 2 0.00
50 8 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
Found at i:23355 original size:82 final size:85
Alignment explanation
Indices: 23191--23358 Score: 191
Period size: 82 Copynumber: 2.0 Consensus size: 85
23181 GATAACCTCG
* * * *
23191 CTATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAATCTCCTTATAAAATTTTGATAACT
1 CTATGAAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAACA
* *
23256 TTCTTATTAAATCTTGATAA
66 TACTTATGAAATCTTGATAA
* * * **
23276 CTAT-AAATTTTGAT-AACCTCCCTATGAAATTTTG-TTAATCTCCCTATGAAATTTTGATCTGC
1 CTATGAAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGAT-AAC
*
23338 ATAC-TATGAAATTTTGATAA
65 ATACTTATGAAATCTTGATAA
23358 C
1 C
23359 CCTCTTATGA
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
82 36 0.51
83 20 0.29
84 10 0.14
85 4 0.06
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (85 bp):
CTATGAAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAACA
TACTTATGAAATCTTGATAA
Found at i:23413 original size:20 final size:20
Alignment explanation
Indices: 23388--23426 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
23378 AACTAAACTA
23388 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
23408 TGAAATTTTGATATCCTCC
1 TGAAATTTTGATATCCTCC
23427 ATAATAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:23578 original size:22 final size:22
Alignment explanation
Indices: 23526--24157 Score: 140
Period size: 22 Copynumber: 28.7 Consensus size: 22
23516 AATCACATTC
* * *
23526 TGAAAATTTGATAGCCTCTTTC
1 TGAAATTTTGATAACCTCTTTA
23548 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
23570 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
23592 TCAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* * *
23614 TGTAATTTTGATAATCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
* ** *
23636 TGGAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTCTTTA
23658 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
* *
23680 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTTTA
* * * *
23704 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* **
23726 TGAGA-TTTGATAACCT-TCCA
1 TGAAATTTTGATAACCTCTTTA
* *
23746 TCAAATTTTGGT-A-CTCCTTATGAAA
1 TGAAATTTTGATAACCT-CTT-T---A
*
23771 TTGAGAATTTT-ATAACCT-TTAGA
1 -TGA-AATTTTGATAACCTCTT-TA
* **
23794 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTTTA
* ***
23816 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTTTA
* * * *
23838 TGAAATATTGGTAACCTCCTAA
1 TGAAATTTTGATAACCTCTTTA
* * **
23860 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTTTA
**
23882 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTTTA
* *
23904 TGACATTTTGATAATCTCTTTGA
1 TGAAATTTTGATAACCTCTTT-A
* ** *
23927 T-AACCTTTCT-ATAA---AATTG
1 TGAA-ATTT-TGATAACCTCTTTA
* * **
23946 TGAAA--AT--TAACCACCCTA
1 TGAAATTTTGATAACCTCTTTA
** * *
23964 TGAAATTTCAATAACCAAC-CTA
1 TGAAATTTTGATAACC-TCTTTA
* * *
23986 AGAAATTTTAATAACC-CGATCCTA
1 TGAAATTTTGATAACCTC--T-TTA
* * **
24010 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTCTTTA
* **
24032 TGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAACCTCTTTA
* ***
24054 TGAAATTTTGATAACTTCCAAA
1 TGAAATTTTGATAACCTCTTTA
* * *
24076 TGAAATTTTGGTAACCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
24098 TGAAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACCTCTTTA
* *
24120 TGAAATTATAATAACCATC-TTA
1 TGAAATTTTGATAACC-TCTTTA
24142 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
24158 ACATAGAGAC
Statistics
Matches: 453, Mismatches: 114, Indels: 86
0.69 0.17 0.13
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
18 6 0.01
19 3 0.01
20 14 0.03
21 36 0.08
22 321 0.71
23 18 0.04
24 20 0.04
25 13 0.03
26 9 0.02
27 7 0.02
28 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:24158 original size:22 final size:22
Alignment explanation
Indices: 23953--24158 Score: 188
Period size: 22 Copynumber: 9.3 Consensus size: 22
23943 TTGTGAAAAT
* **
23953 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
23975 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
*
23997 TAACCCGATCCTATGAAATTTTGG
1 TAA-CC-ATCCTATGAAATTTTGA
24021 TAACCA-CACTATGAAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
*
24043 TAA-CTTCCATATGAAATTTTGA
1 TAACCATCC-TATGAAATTTTGA
* * *
24065 TAA-CTTCCAAATGAAATTTTGG
1 TAACCATCC-TATGAAATTTTGA
24087 TAACCA-CTCTATGAAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* *
24109 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTGA
*
24131 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
24153 TAACCA
1 TAACCA
24159 CATAGAGACA
Statistics
Matches: 155, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.03
22 125 0.81
23 9 0.06
24 16 0.10
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:24355 original size:19 final size:19
Alignment explanation
Indices: 24324--24360 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
24314 TATTGACATT
24324 TAAAAATTGAAATTAAAAG
1 TAAAAATTGAAATTAAAAG
24343 TAAAATATT-AAATTAAAA
1 TAAAA-ATTGAAATTAAAA
24361 AACTAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAAATTGAAATTAAAAG
Found at i:24508 original size:15 final size:15
Alignment explanation
Indices: 24490--24538 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
24480 ATCTAATATT
24490 ATAATTAATAATGGA
1 ATAATTAATAATGGA
* *
24505 ATAATTTATAAT-TA
1 ATAATTAATAATGGA
24519 A-AA--AATAATGGA
1 ATAATTAATAATGGA
24531 ATAATTAA
1 ATAATTAA
24539 AATATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 5 0.19
12 2 0.08
13 4 0.15
14 2 0.08
15 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (15 bp):
ATAATTAATAATGGA
Found at i:24609 original size:30 final size:33
Alignment explanation
Indices: 24557--24624 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 33
24547 TTAGTAATGG
*
24557 CAATCTAGAAATATGGTTTTAAAAA-AAGGGTA
1 CAATCTAGAAATATGATTTTAAAAATAAGGGTA
24589 CAAT-TAGAAATAT-ATTTTAAAAATAAGGGTA
1 CAATCTAGAAATATGATTTTAAAAATAAGGGTA
24620 CAATC
1 CAATC
24625 GGAAAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 9 0.27
31 20 0.61
32 4 0.12
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (33 bp):
CAATCTAGAAATATGATTTTAAAAATAAGGGTA
Found at i:25943 original size:9 final size:9
Alignment explanation
Indices: 25925--25955 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25915 TTTTTCTCTG
25925 TTCACCTGT
1 TTCACCTGT
*
25934 TTCACTTGT
1 TTCACCTGT
25943 TTCACCTGT
1 TTCACCTGT
25952 TTCA
1 TTCA
25956 AACCTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.29, G:0.10, T:0.48
Consensus pattern (9 bp):
TTCACCTGT
Found at i:33420 original size:2 final size:2
Alignment explanation
Indices: 33413--33448 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33403 AGGCTAAGAC
33413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33449 AATGCACTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.