Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015529.1 Corchorus capsularis cultivar CVL-1 contig15550, 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: 60570
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:106 original size:20 final size:20
Alignment explanation
Indices: 77--120 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
67 CCAATAACAA
77 ATTTAAATTT-TATTACATAT
1 ATTTAAATTTATATT-CATAT
* *
97 ATTTATATTTATATTTATAT
1 ATTTAAATTTATATTCATAT
117 ATTT
1 ATTT
121 CTAATTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAAATTTATATTCATAT
Found at i:1018 original size:23 final size:23
Alignment explanation
Indices: 988--1031 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
978 CCGCCCTTTT
* *
988 TCTTTTTTCTTTTCTTTCTTCTC
1 TCTTTTTTCTTCTCCTTCTTCTC
1011 TCTTTTTTCTTCTCCTTCTTC
1 TCTTTTTTCTTCTCCTTCTTC
1032 CCGACCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TCTTTTTTCTTCTCCTTCTTCTC
Found at i:3239 original size:23 final size:23
Alignment explanation
Indices: 3213--3258 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3203 AACGAGGCAG
3213 TTAATAAGTCCATTTAAAGTGGT
1 TTAATAAGTCCATTTAAAGTGGT
3236 TTAATAAGTCCATTTAAAGTGGT
1 TTAATAAGTCCATTTAAAGTGGT
3259 GTTCTGTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (23 bp):
TTAATAAGTCCATTTAAAGTGGT
Found at i:4954 original size:45 final size:44
Alignment explanation
Indices: 4902--5009 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 44
4892 ATATGGAATT
* *
4902 TTGATAACTTCCCA-ATGAAATTTTGATAACCAACACTATGAGATG
1 TTGATAACCT-CCATATGAAATATTGATAACC-ACACTATGAGATG
* * *
4947 TTGATAACCTCCATATGATATATTGATAACCACATTATGAAAAT-
1 TTGATAACCTCCATATGAAATATTGATAACCACACTATG-AGATG
* *
4991 TTAAAAACCTCCATATGAA
1 TTGATAACCTCCATATGAA
5010 TTGTTAGTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 26 0.49
45 27 0.51
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (44 bp):
TTGATAACCTCCATATGAAATATTGATAACCACACTATGAGATG
Found at i:5085 original size:22 final size:21
Alignment explanation
Indices: 4849--5281 Score: 203
Period size: 22 Copynumber: 19.7 Consensus size: 21
4839 TTTTTAACCT
*
4849 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
4871 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTC-C
* *
4893 TATGGAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCT-CC
* *
4915 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* *
4938 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
4959 ATATGATATATTGATAACCACAT
1 -TATGAAATTTTGATAACCTC-C
* * *
4982 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
5003 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTC-C
* * *
5026 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTC-C
* * *
5048 TATGAAATTGTAATAACCTCGT
1 TATGAAATTTTGATAACCTC-C
*
5070 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
*
5093 TATAAAATTTTGATAAACCTCTC
1 TATGAAATTTTGAT-AACCTC-C
*
5116 TATAAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
** * *
5138 TATGATTTTTTGATAATCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
5160 TATGAAATTTTGTTAATCTCTC
1 TATGAAATTTTGATAACCTC-C
* * *
5182 TATGAAATTTTGATCTACATAC
1 TATGAAATTTTGAT-AACCTCC
* *
5204 TATGAAATTTTGATAATCATCT
1 TATGAAATTTTGATAA-CCTCC
* * *
5226 TATGAAAATTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
*
5248 TATGAAATTTTGATATCCTTCC
1 TATGAAATTTTGATAACC-TCC
5270 --TGAAATTTTGAT
1 TATGAAATTTTGAT
5282 TACTCCATAA
Statistics
Matches: 315, Mismatches: 71, Indels: 52
0.72 0.16 0.12
Matches are distributed among these distances:
20 13 0.04
21 12 0.04
22 223 0.71
23 63 0.20
24 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:5141 original size:90 final size:89
Alignment explanation
Indices: 5030--5195 Score: 201
Period size: 90 Copynumber: 1.9 Consensus size: 89
5020 TCACACTCTG
* *
5030 AAATTTTGATAATCACACTATGAAATTGTAATAACCTCGTTATGAAATTTTGATAAATCT-TCCT
1 AAATTTTGATAACCACACTATGAAATTGTAATAACCTCATTATGAAATTTTG-TAAATCTCT-CT
5094 ATAAAATTTTGATAAACCTCTCTATA
64 ATAAAATTTTGATAAACCTCTCTATA
* ** * * * *
5120 AAATTTTGATAACCTTC-CTATGATTTTTTGATAATCTCATTATGAAATTTTGTTAATCTCTCTA
1 AAATTTTGATAACC-ACACTATGAAATTGTAATAACCTCATTATGAAATTTTGTAAATCTCTCTA
*
5184 TGAAATTTTGAT
65 TAAAATTTTGAT
5196 CTACATACTA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
89 20 0.31
90 43 0.67
91 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.43
Consensus pattern (89 bp):
AAATTTTGATAACCACACTATGAAATTGTAATAACCTCATTATGAAATTTTGTAAATCTCTCTAT
AAAATTTTGATAAACCTCTCTATA
Found at i:5193 original size:44 final size:45
Alignment explanation
Indices: 4849--5577 Score: 216
Period size: 44 Copynumber: 16.8 Consensus size: 45
4839 TTTTTAACCT
* * * * * *
4849 TATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA-AGACCTCA-A
1 TATGAAATTTTGATAATCTCTCTATGAAATTTTGATA-ACCTCATC
* * * *
4893 TATGGAATTTTGATAA-CTTCCCAATGAAATTTTGATAACCAACA-C
1 TATGAAATTTTGATAATC-TCTCTATGAAATTTTGATAACC-TCATC
* * * * * *
4938 TATGAGATGTTGATAACCTC-CATATGATATATTGATAACCACAT-
1 TATGAAATTTTGATAATCTCTC-TATGAAATTTTGATAACCTCATC
* * * * * *
4982 TATGAAAATTTAAAAACCTC-CATATG-AATTGTT-AGTAATCACA-C
1 TATGAAATTTTGATAATCTCTC-TATGAAATT-TTGA-TAACCTCATC
* * * * * *
5026 TCTGAAATTTTGATAATCACACTATGAAATTGTAATAACCTCGT-
1 TATGAAATTTTGATAATCTCTCTATGAAATTTTGATAACCTCATC
*
5070 TATGAAATTTTGATAAATCT-TCCTATAAAATTTTGATAAACCTC-TC
1 TATGAAATTTTGAT-AATCTCT-CTATGAAATTTTGAT-AACCTCATC
* * ** *
5116 TATAAAATTTTGATAACCT-TCCTATGATTTTTTGATAATCTCAT-
1 TATGAAATTTTGATAATCTCT-CTATGAAATTTTGATAACCTCATC
*
5160 TATGAAATTTTGTTAATCTCTCTATGAAATTTTGAT---CTACATAC
1 TATGAAATTTTGATAATCTCTCTATGAAATTTTGATAACCT-CAT-C
* * * *
5204 TATGAAATTTTGATAATCATCT-TATGAAAATTTGA-AAACTAAAC
1 TATGAAATTTTGATAATC-TCTCTATGAAATTTTGATAACCTCATC
* *
5248 TATGAAATTTTGAT-ATC-CT-TCCTGAAATTTTGATTA-CTCCAT-
1 TATGAAATTTTGATAATCTCTCT-ATGAAATTTTGATAACCT-CATC
* * * * * * *
5290 AATAAAAGTTTAATAACCT-TC-CT--AA-TTTGGTAA-C-CATAC
1 TATGAAATTTTGATAATCTCTCTATGAAATTTTGATAACCTCAT-C
* * * *
5329 TATGAAATTTTAATAACCTCCCCA-G-AA-----AT-A-C-CA-C
1 TATGAAATTTTGATAATCTCTCTATGAAATTTTGATAACCTCATC
* * * *
5363 TATGAAATTTTTG-TAATCACAT-TTTGAAAATTTGATAACCTCTTC
1 TATGAAA-TTTTGATAATCTC-TCTATGAAATTTTGATAACCTCATC
* * * * * * *
5408 -ATAAAATTTTGTTGATCCCTCTATGAAATTCTGATAATCACAT-
1 TATGAAATTTTGATAATCTCTCTATGAAATTTTGATAACCTCATC
* * **
5451 TATGTAATTTTGATAA-C-CTCGATTAGAAATTTTGATAACAACA-C
1 TATGAAATTTTGATAATCTCTCTA-T-GAAATTTTGATAACCTCATC
*
5495 TATGAAATTTTGATAATCT-TCCTAT-AAATTTTGATAATCCGAT-TTC
1 TATGAAATTTTGATAATCTCT-CTATGAAATTTTGATAA-CC--TCATC
* * *
5541 TATGAAATTTCGATAATCACTCTATGAGA-TTTGATAA
1 TATGAAATTTTGATAATCTCTCTATGAAATTTTGATAA
5578 TCTATCAAAT
Statistics
Matches: 518, Mismatches: 102, Indels: 128
0.69 0.14 0.17
Matches are distributed among these distances:
34 13 0.03
35 5 0.01
36 6 0.01
37 4 0.01
39 23 0.04
40 3 0.01
41 9 0.02
42 32 0.06
43 33 0.06
44 249 0.48
45 84 0.16
46 54 0.10
47 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (45 bp):
TATGAAATTTTGATAATCTCTCTATGAAATTTTGATAACCTCATC
Found at i:5454 original size:22 final size:22
Alignment explanation
Indices: 5363--5579 Score: 112
Period size: 22 Copynumber: 9.8 Consensus size: 22
5353 GAAATACCAC
5363 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAATCACAT
* * * *
5385 TTTGAAAATTTGATAACCTC-T
1 TATGAAATTTTGATAATCACAT
* * * *
5406 TCATAAAATTTTGTTGATC-CCT
1 T-ATGAAATTTTGATAATCACAT
*
5428 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* * *
5451 TATGTAATTTTGATAACCTCGAT
1 TATGAAATTTTGATAATCAC-AT
*
5474 TA-GAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-ACAT
* *
5495 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAATC-ACAT
5517 TAT-AAATTTTGATAATC-CGATTT
1 TATGAAATTTTGATAATCAC-A--T
*
5540 CTATGAAATTTCGATAATCAC-T
1 -TATGAAATTTTGATAATCACAT
*
5562 CTATGAGA-TTTGATAATC
1 -TATGAAATTTTGATAATC
5580 TATCAAATTT
Statistics
Matches: 151, Mismatches: 28, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.01
21 34 0.23
22 90 0.60
23 9 0.06
24 3 0.02
25 13 0.09
26 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:5549 original size:25 final size:23
Alignment explanation
Indices: 5494--5579 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 23
5484 GATAACAACA
5494 CTATGAAATTTTGATAAT-CTTC
1 CTATGAAATTTTGATAATCCTTC
*
5516 CTAT-AAATTTTGATAATCCGATTT
1 CTATGAAATTTTGATAATCC--TTC
*
5540 CTATGAAATTTCGATAATCAC-T-
1 CTATGAAATTTTGATAATC-CTTC
*
5562 CTATGAGA-TTTGATAATC
1 CTATGAAATTTTGATAATC
5580 TATCAAATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
21 22 0.40
22 12 0.22
23 1 0.02
24 6 0.11
25 13 0.24
26 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCCTTC
Found at i:5654 original size:22 final size:22
Alignment explanation
Indices: 5628--5730 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
5618 ATAACATTCA
5628 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* *
5650 CATGAAATATT-AGTAACCT-CC
1 TATGAAATTTTGA-TAACCTCCC
* * *
5671 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCTCCC
* *
5694 TATGAAATTCTT-ATAAACTCGC
1 TATGAAATT-TTGATAACCTCCC
*
5716 TATGACATTTTGATA
1 TATGAAATTTTGATA
5731 TAATCTCTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
21 5 0.08
22 54 0.86
23 4 0.06
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:5883 original size:21 final size:21
Alignment explanation
Indices: 5823--5919 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 21
5813 TAACCTGATC
5823 CTATGAAATTTCGGTAACCACA
1 CTATGAAATTT-GGTAACCACA
*
5845 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAA-TTTGGTAAC--CACA
5868 -TATGAAATTTGGTAACCACA
1 CTATGAAATTTGGTAACCACA
* *
5888 CTATGGAAATTTGATAACCTC-
1 CTAT-GAAATTTGGTAACCACA
5909 CTCATGAAATT
1 CT-ATGAAATT
5920 ATAATAATCA
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 19 0.30
22 36 0.56
23 5 0.08
24 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (21 bp):
CTATGAAATTTGGTAACCACA
Found at i:5889 original size:43 final size:43
Alignment explanation
Indices: 5821--5919 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
5811 AATAACCTGA
*
5821 TCCTATGAAATTTCGGTAACCACACTAT-GAAATTTTGATAACT
1 TCCTATGAAATTTCGGTAACCACACTATGGAAA-TTTGATAACC
5864 TCCATATGAAATTT-GGTAACCACACTATGGAAATTTGATAACC
1 TCC-TATGAAATTTCGGTAACCACACTATGGAAATTTGATAACC
5907 TCCTCATGAAATT
1 TCCT-ATGAAATT
5920 ATAATAATCA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
42 1 0.02
43 37 0.71
44 14 0.27
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (43 bp):
TCCTATGAAATTTCGGTAACCACACTATGGAAATTTGATAACC
Found at i:7395 original size:38 final size:37
Alignment explanation
Indices: 7331--7421 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 37
7321 CCCAAATAGG
* * * *
7331 ACGTTGGAGACAAAGATAAAAAGCAAAATTAGATACA
1 ACGTTGGAAACAAAAACAAAAAGCAAAATTAAATACA
* * **
7368 ACGATTGGAAACCAAAACAAAAGGCAAAATTAAATAGG
1 ACG-TTGGAAACAAAAACAAAAAGCAAAATTAAATACA
7406 ACGTTGGAAACAAAAA
1 ACGTTGGAAACAAAAA
7422 GCCAAATTGA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 15 0.34
38 29 0.66
ACGTcount: A:0.55, C:0.12, G:0.19, T:0.14
Consensus pattern (37 bp):
ACGTTGGAAACAAAAACAAAAAGCAAAATTAAATACA
Found at i:7582 original size:31 final size:31
Alignment explanation
Indices: 7547--7611 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
7537 GGTAATTTAG
* *
7547 AAATATGTTTTAAAAAAAAAGGTACAATTGA
1 AAATATATTTTAAAAAAAAAGGTACAATCGA
* *
7578 AAATATATTTTAAAAATAAGGGTACAATCGA
1 AAATATATTTTAAAAAAAAAGGTACAATCGA
7609 AAA
1 AAA
7612 CATAAAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (31 bp):
AAATATATTTTAAAAAAAAAGGTACAATCGA
Found at i:7686 original size:157 final size:160
Alignment explanation
Indices: 7478--7782 Score: 501
Period size: 159 Copynumber: 1.9 Consensus size: 160
7468 ATAGTAATTA
* *
7478 ATAATGGAATAATTTATGATTAAAAAAATAATGGAATAATAATAATATTATTTAGTAATGGTAAT
1 ATAATGGAATAATTTATGATTAAAAAAATAATGGAATAATAATAATATTATTTACTAATGGCAAT
7543 TTAGAAATATG-TTTTAAAAAAAAAGGTACAATTGAAAATATATTTTAAAAATAAGGGTACAATC
66 TTAGAAATATGTTTTTAAAAAAAAAGGTACAATTGAAAATATATTTTAAAAATAAGGGTACAATC
7607 G-AAAACATAAAGTTTCCCTAATAATTAAT
131 GAAAAACATAAAGTTTCCCTAATAATTAAT
7636 ATAATGGAATAATTTATGATT-AAAAAATAATGGAATAATTAA-AATATTATTTACTAATGGCAA
1 ATAATGGAATAATTTATGATTAAAAAAATAATGGAATAA-TAATAATATTATTTACTAATGGCAA
* * * *
7699 TTTAGAAATATGTTTTTTAAATAAAATGGTACAATTGGAAATATGTTTTAAAAATAAGGGTACAA
65 TTTAGAAATATG-TTTTTAAAAAAAAAGGTACAATTGAAAATATATTTTAAAAATAAGGGTACAA
*
7764 TCGAAAAATATAAAGTTTC
129 TCGAAAAACATAAAGTTTC
7783 TCCTTATTTG
Statistics
Matches: 136, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
157 48 0.35
158 24 0.18
159 50 0.37
160 14 0.10
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.34
Consensus pattern (160 bp):
ATAATGGAATAATTTATGATTAAAAAAATAATGGAATAATAATAATATTATTTACTAATGGCAAT
TTAGAAATATGTTTTTAAAAAAAAAGGTACAATTGAAAATATATTTTAAAAATAAGGGTACAATC
GAAAAACATAAAGTTTCCCTAATAATTAAT
Found at i:7761 original size:31 final size:32
Alignment explanation
Indices: 7703--7764 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
7693 TGGCAATTTA
*
7703 GAAATATGTTTTTTAAATAAAATGGTACAATTG
1 GAAATATG-TTTTTAAATAAAAGGGTACAATTG
7736 GAAATATG-TTTTAAA-AATAAGGGTACAAT
1 GAAATATGTTTTTAAATAA-AAGGGTACAAT
7765 CGAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 17 0.63
33 8 0.30
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.35
Consensus pattern (32 bp):
GAAATATGTTTTTAAATAAAAGGGTACAATTG
Found at i:8139 original size:12 final size:12
Alignment explanation
Indices: 8122--8146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8112 ATGGTCAGAT
8122 GATGAAGAGAAC
1 GATGAAGAGAAC
8134 GATGAAGAGAAC
1 GATGAAGAGAAC
8146 G
1 G
8147 GGAACCAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.36, T:0.08
Consensus pattern (12 bp):
GATGAAGAGAAC
Found at i:12798 original size:31 final size:29
Alignment explanation
Indices: 12726--12799 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
12716 TGCCGCCACA
**
12726 ATCAATTTGGGATATAACGTTTCAAAACG
1 ATCAATTAAGGATATAACGTTTCAAAACG
* * **
12755 ATCATTTCAGGATATAACGTTATCCAATCCG
1 ATCAATTAAGGATATAACGTT-T-CAAAACG
12786 ATCAATTAAGGATA
1 ATCAATTAAGGATA
12800 AAATTGGACG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 18 0.50
30 1 0.03
31 17 0.47
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (29 bp):
ATCAATTAAGGATATAACGTTTCAAAACG
Found at i:12868 original size:20 final size:20
Alignment explanation
Indices: 12843--12881 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12833 CGCGGTTAAT
*
12843 TGTGCCACGTGGATGCCACG
1 TGTGCCACATGGATGCCACG
*
12863 TGTGCCACATTGATGCCAC
1 TGTGCCACATGGATGCCAC
12882 ATGTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (20 bp):
TGTGCCACATGGATGCCACG
Found at i:32796 original size:29 final size:28
Alignment explanation
Indices: 32763--32846 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
32753 TAGGTAAGAG
32763 AGGAAGAGAGGGTATCAAGTTACATGGGA
1 AGGAA-AGAGGGTATCAAGTTACATGGGA
*
32792 AGG-AATA-GGTAAAATCAAGTTACATGGGA
1 AGGAAAGAGGGT---ATCAAGTTACATGGGA
*
32821 AGG-AATA-GGTAATCAAGTTACATGGG
1 AGGAAAGAGGGT-ATCAAGTTACATGGG
32847 GTATCAAGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
26 3 0.06
27 18 0.35
28 1 0.02
29 29 0.57
ACGTcount: A:0.40, C:0.07, G:0.32, T:0.20
Consensus pattern (28 bp):
AGGAAAGAGGGTATCAAGTTACATGGGA
Found at i:32842 original size:27 final size:28
Alignment explanation
Indices: 32776--32846 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 28
32766 AAGAGAGGGT
32776 ATCAAGTTACATGGGAAGGAATAGGTAAA
1 ATCAAGTTACATGGGAAGGAATAGGT-AA
32805 ATCAAGTTACATGGGAAGGAATAGGT-A
1 ATCAAGTTACATGGGAAGGAATAGGTAA
32832 ATCAAGTTACATGGG
1 ATCAAGTTACATGGG
32847 GTATCAAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 16 0.38
29 26 0.62
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.23
Consensus pattern (28 bp):
ATCAAGTTACATGGGAAGGAATAGGTAA
Found at i:33033 original size:16 final size:16
Alignment explanation
Indices: 33012--33043 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33002 GGAAGTGTAC
33012 TTCGTTATTAATGTGA
1 TTCGTTATTAATGTGA
33028 TTCGTTATTAATGTGA
1 TTCGTTATTAATGTGA
33044 GTAATTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
TTCGTTATTAATGTGA
Found at i:33989 original size:3 final size:3
Alignment explanation
Indices: 33981--34008 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
33971 TTCGAGACTA
33981 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
34009 CCCTCCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:41200 original size:13 final size:13
Alignment explanation
Indices: 41182--41206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41172 AGTTGAGACC
41182 TAATGTAATTAAT
1 TAATGTAATTAAT
41195 TAATGTAATTAA
1 TAATGTAATTAA
41207 CGAATATCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TAATGTAATTAAT
Found at i:41468 original size:2 final size:2
Alignment explanation
Indices: 41461--41489 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41451 AGAGCAAGAA
41461 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41490 ATGGCCACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60114 original size:13 final size:13
Alignment explanation
Indices: 60096--60120 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60086 GGGTAGTAAA
60096 AATGGATTAGTTG
1 AATGGATTAGTTG
60109 AATGGATTAGTT
1 AATGGATTAGTT
60121 TTAATAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (13 bp):
AATGGATTAGTTG
Done.