Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016654.1 Corchorus olitorius cultivar O-4 contig16687, 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: 69821
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3365 original size:19 final size:19
Alignment explanation
Indices: 3341--3378 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3331 ACTAAAATTC
3341 ATGAACACCATATATATAA
1 ATGAACACCATATATATAA
3360 ATGAACACCATATATATAA
1 ATGAACACCATATATATAA
3379 TATTAATAAT
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:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (19 bp):
ATGAACACCATATATATAA
Found at i:4092 original size:42 final size:44
Alignment explanation
Indices: 4041--4134 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
4031 AGTGCATTAC
* *
4041 CTAA-ATTCTA-T-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAA
*
4082 CTAATATTCTACTCCTGCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAA
4127 CTAATATT
1 CTAATATT
4135 AATTATTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
43 1 0.02
45 35 0.76
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:5798 original size:2 final size:2
Alignment explanation
Indices: 5786--5815 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5776 TGAGATAAGT
*
5786 TA TA TA CA 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
5816 ATAAAGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5905 original size:20 final size:20
Alignment explanation
Indices: 5880--5919 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5870 TTAGGTTCAA
5880 CTCTCACAGAATGTGAGTTT
1 CTCTCACAGAATGTGAGTTT
*
5900 CTCTCACGGAATGTGAGTTT
1 CTCTCACAGAATGTGAGTTT
5920 GTTTGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CTCTCACAGAATGTGAGTTT
Found at i:6687 original size:54 final size:54
Alignment explanation
Indices: 6605--6715 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
6595 TGTATGTAAT
6605 TTACGCATTCATAAAAGATCTCTATATACGGAAATTTTAAATGTAAAAAAAAAA
1 TTACGCATTCATAAAAGATCTCTATATACGGAAATTTTAAATGTAAAAAAAAAA
*
6659 TTACGCATTCATAAAAGATCTCTATATACGGAAATTTTAAATGTAAAAAACAAA
1 TTACGCATTCATAAAAGATCTCTATATACGGAAATTTTAAATGTAAAAAAAAAA
6713 TTA
1 TTA
6716 GAAACGATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.31
Consensus pattern (54 bp):
TTACGCATTCATAAAAGATCTCTATATACGGAAATTTTAAATGTAAAAAAAAAA
Found at i:7215 original size:35 final size:35
Alignment explanation
Indices: 7169--7238 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
7159 ATTTACTTGC
7169 CCATAAGATAAAGGGGAACTTATTGGCATCACAGT
1 CCATAAGATAAAGGGGAACTTATTGGCATCACAGT
7204 CCATAAGATAAAGGGGAACTTATTGGCATCACAGT
1 CCATAAGATAAAGGGGAACTTATTGGCATCACAGT
7239 ACACGCTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (35 bp):
CCATAAGATAAAGGGGAACTTATTGGCATCACAGT
Found at i:14827 original size:28 final size:28
Alignment explanation
Indices: 14795--14881 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
14785 TCGGGTCAAG
14795 TATGACAAGCAAGATACATGAGTGCTCA
1 TATGACAAGCAAGATACATGAGTGCTCA
*
14823 TATGAC-A-CTAAGAT--ATG-GTACTTCGA
1 TATGACAAGC-AAGATACATGAGTGC-TC-A
* *
14849 GTATGACAAGTAAGATACATGAGTGCTCC
1 -TATGACAAGCAAGATACATGAGTGCTCA
14878 TATG
1 TATG
14882 GCACTAAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
24 3 0.07
25 5 0.11
26 2 0.04
27 12 0.26
28 16 0.35
30 5 0.11
31 3 0.07
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (28 bp):
TATGACAAGCAAGATACATGAGTGCTCA
Found at i:14887 original size:55 final size:55
Alignment explanation
Indices: 14793--14901 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
14783 TGTCGGGTCA
*
14793 AGTATGACAAGCAAGATACATGAGTGCTCATATGACACTAAGATATGGTACTTCG
1 AGTATGACAAGCAAGATACATGAGTGCTCATATGACACTAAGATATGATACTTCG
* * *
14848 AGTATGACAAGTAAGATACATGAGTGCTCCTATGGCACTAAGATATGATACTTC
1 AGTATGACAAGCAAGATACATGAGTGCTCATATGACACTAAGATATGATACTTC
14902 ATGACCAAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (55 bp):
AGTATGACAAGCAAGATACATGAGTGCTCATATGACACTAAGATATGATACTTCG
Found at i:16223 original size:17 final size:18
Alignment explanation
Indices: 16195--16239 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
16185 TATAAAAGGG
16195 CACTATTTCATTAAAA-CC
1 CACTA-TTCATTAAAAGCC
16213 CACTATTCATTAAAAGCC
1 CACTATTCATTAAAAGCC
*
16231 CATTATTCA
1 CACTATTCA
16240 CAAATGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (18 bp):
CACTATTCATTAAAAGCC
Found at i:16586 original size:28 final size:28
Alignment explanation
Indices: 16551--16614 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
16541 TGTTGCTTAA
*
16551 TTGG-CATTAGGATCATCTAGGGGG-ATT
1 TTGGTCATTAGGA-CACCTAGGGGGCATT
***
16578 TTGGTCATTTTTACACCTAGGGGGCATT
1 TTGGTCATTAGGACACCTAGGGGGCATT
16606 TTGGTCATT
1 TTGGTCATT
16615 TGTACTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 14 0.45
28 17 0.55
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (28 bp):
TTGGTCATTAGGACACCTAGGGGGCATT
Found at i:16636 original size:26 final size:27
Alignment explanation
Indices: 16598--16668 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 27
16588 TTACACCTAG
*
16598 GGGGCATTTTGGTCATTTGTAC-TTCA
1 GGGGCATTTTGGTCATTTGCACATTCA
* *
16624 GGGGTATTCTGGTCATTTGCACATTCA
1 GGGGCATTTTGGTCATTTGCACATTCA
*
16651 GGGGCATTTTGATCATTT
1 GGGGCATTTTGGTCATTT
16669 TAAGTTCACA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.41
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACATTCA
Found at i:19455 original size:41 final size:41
Alignment explanation
Indices: 19393--19486 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
19383 TTTTCATATA
* * * *
19393 GTCCCTAATTTAGGTTTATGTTTGTTAATTGATTCAATTTT
1 GTCCCTGATTTAGGTTAATGTTTATTAATTGATTCAATTTC
*
19434 GTCCCTGATTTAGAG-TAATGTTTATTTATTGATTCAATTTC
1 GTCCCTGATTTAG-GTTAATGTTTATTAATTGATTCAATTTC
*
19475 GCCCCTGATTTA
1 GTCCCTGATTTA
19487 AGATTTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.98
42 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (41 bp):
GTCCCTGATTTAGGTTAATGTTTATTAATTGATTCAATTTC
Found at i:20652 original size:17 final size:18
Alignment explanation
Indices: 20630--20664 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20620 TCCTAATTTG
*
20630 GAGAAAAATAAA-CAAAA
1 GAGAAAAAAAAATCAAAA
20647 GAGAAAAAAAAATCAAAA
1 GAGAAAAAAAAATCAAAA
20665 AGTGTTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.77, C:0.06, G:0.11, T:0.06
Consensus pattern (18 bp):
GAGAAAAAAAAATCAAAA
Found at i:28454 original size:72 final size:73
Alignment explanation
Indices: 28304--28438 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 73
28294 TGTAGCGAGG
* *
28304 CATCATCAAGCCGACGGTGAAGAAGTAGTGCACGACACTCACCTAGTCTTCCTTGTTATGATAAT
1 CATCATCAAGCCGACGGGGAAGAAGTAGTGCACGACACTCACCTAGTCTTCCTTGTTATGACAAT
28369 TTCCTCAT
66 TTCCTCAT
* * * * * *
28377 CATCATCAAGCCGCCGGGGAAG-TGTAGTGCGCGGCTCTGACCTAGTCTTCCTTGTTATGACA
1 CATCATCAAGCCGACGGGGAAGAAGTAGTGCACGACACTCACCTAGTCTTCCTTGTTATGACA
28439 TTTTACCCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
72 34 0.63
73 20 0.37
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (73 bp):
CATCATCAAGCCGACGGGGAAGAAGTAGTGCACGACACTCACCTAGTCTTCCTTGTTATGACAAT
TTCCTCAT
Found at i:28666 original size:95 final size:95
Alignment explanation
Indices: 28377--28675 Score: 380
Period size: 95 Copynumber: 3.2 Consensus size: 95
28367 ATTTCCTCAT
* * * * * *
28377 CATCATCAAGCCGCCGGGGAAGTGTAGTGCGCGGCTCTGACCTAGTCTTCCTTGTTATGACATTT
1 CATCATCAAGCCGCCGGTGAAGAGTAGTGCACGGCTCTCACCTAGTCTTCCTTGTTATGGCTTTT
28442 TACCCATTATCATTACAAGATGTGGCGAGG
66 TACCCATTATCATTACAAGATGTGGCGAGG
* * * *
28472 CATCATCAAGCCGACGGTGAAGAAGTAGTGCACGTCTCTCA-CTAG---T-CTTGTTAT-GATAA
1 CATCATCAAGCCGCCGGTGAAG-AGTAGTGCACGGCTCTCACCTAGTCTTCCTTGTTATGGCT-T
* * *
28531 TTTACTCATCATCA-T-CAAGATGTGGCAAGG
64 TTTACCCATTATCATTACAAGATGTGGCGAGG
*
28561 CATCATCAAGCCGCTGGTGAAGAGTAGTGCACGGCTCTCACCTAGTCTTCCTTGTTATGGCTTTT
1 CATCATCAAGCCGCCGGTGAAGAGTAGTGCACGGCTCTCACCTAGTCTTCCTTGTTATGGCTTTT
**
28626 TACCCATTATCATTACAAGACATGGCGAGG
66 TACCCATTATCATTACAAGATGTGGCGAGG
28656 CATCATCAAGCCGCCGGTGA
1 CATCATCAAGCCGCCGGTGA
28676 TTGAGCGGTC
Statistics
Matches: 170, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
88 17 0.10
89 38 0.22
90 1 0.01
91 20 0.12
92 2 0.01
93 20 0.12
94 3 0.02
95 55 0.32
96 14 0.08
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (95 bp):
CATCATCAAGCCGCCGGTGAAGAGTAGTGCACGGCTCTCACCTAGTCTTCCTTGTTATGGCTTTT
TACCCATTATCATTACAAGATGTGGCGAGG
Found at i:29387 original size:147 final size:147
Alignment explanation
Indices: 29142--29444 Score: 471
Period size: 147 Copynumber: 2.1 Consensus size: 147
29132 ATTTTAGAGG
* * *
29142 TCTGTTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTGTCGGGTACTGTTGG
1 TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTATCGGGTACTGTTGC
** * * *
29207 GACCCACAGTAGGCTGACGTGGTAGCACATGAGGCATACTGTCCTTGGGGATTACTAATAGGTGA
66 GACCCACAACAGGCTGACGTGGTAGCACATGAGGCATAATGTCCCTGGGGATTACGAATAGGTGA
* **
29272 ATTTATTGTTCATGGCC
131 ATTTACTGTTCACAGCC
*
29289 TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGGGCCCACTATCGGGTACTGTTGC
1 TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTATCGGGTACTGTTGC
* *
29354 GACCCACAACAGGCTGACGTGGTAGCACATGAGGCATAATGTCCCTGGGGCTTACGGATAGGTGA
66 GACCCACAACAGGCTGACGTGGTAGCACATGAGGCATAATGTCCCTGGGGATTACGAATAGGTGA
*
29419 ATTTACTGTTCACAGTC
131 ATTTACTGTTCACAGCC
29436 TCTGCTGGA
1 TCTGCTGGA
29445 GTATCGGGCC
Statistics
Matches: 141, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
147 141 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.28
Consensus pattern (147 bp):
TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTATCGGGTACTGTTGC
GACCCACAACAGGCTGACGTGGTAGCACATGAGGCATAATGTCCCTGGGGATTACGAATAGGTGA
ATTTACTGTTCACAGCC
Found at i:29906 original size:20 final size:21
Alignment explanation
Indices: 29881--29921 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29871 TGAAGGGAAT
29881 CTTGT-CATAAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
* *
29901 CTTGTCCTTGAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
29922 TTGATGGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
CTTGTCCATAAGCATTAAATG
Found at i:30662 original size:15 final size:16
Alignment explanation
Indices: 30642--30680 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
30632 GAGGTTGAAC
30642 GAAAACAATTAAAC-A
1 GAAAACAATTAAACTA
*
30657 GAAAACAATTATACTA
1 GAAAACAATTAAACTA
30673 GAAAACAA
1 GAAAACAA
30681 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (16 bp):
GAAAACAATTAAACTA
Found at i:35499 original size:37 final size:39
Alignment explanation
Indices: 35403--35704 Score: 274
Period size: 40 Copynumber: 7.9 Consensus size: 39
35393 TAAAATCTTG
*
35403 GATGGGATCTTTCCCCT-AATTGAAAGCTTGAAAAAGACTA
1 GATGGGATCTTT-CCCTAAATTGAAAACTTG-AAAAGACTA
* * * *
35443 AATGGGATCTTTTCTTAAATTGAAAACTTG-AAA-ACTC
1 GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
* * *
35480 GACGGGATCTTTCCCTAAATTTAAAAATTTTGAAGAAGACTA
1 GATGGGATCTTTCCCTAAA-TTGAAAA-CTTGAA-AAGACTA
35522 GATGGGATCTTTCCCTAAATT-AAAACTCTGAAAAAGAC-A
1 GATGGGATCTTTCCCTAAATTGAAAACT-TG-AAAAGACTA
*
35561 GGATGGGATCTTTCCCTAAATT----ACTT--AAATACTA
1 -GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
* * *
35595 GATGTGATCTTTCCCTAAATTGAAATCTTG--AATACTA
1 GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
* *
35632 GATGGGATCTTTCCCTAATTTTGAAATCTTGAAAA-ACTA
1 GATGGGATCTTTCCCTAA-ATTGAAAACTTGAAAAGACTA
*
35671 GGTGGGATCTTTCCCTAAATT-AAAACTTTGAAAA
1 GATGGGATCTTTCCCTAAATTGAAAAC-TTGAAAA
35705 ATACTTTGGT
Statistics
Matches: 221, Mismatches: 22, Indels: 40
0.78 0.08 0.14
Matches are distributed among these distances:
33 25 0.11
34 1 0.00
36 1 0.00
37 52 0.24
38 29 0.13
39 28 0.13
40 58 0.26
41 6 0.03
42 21 0.10
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (39 bp):
GATGGGATCTTTCCCTAAATTGAAAACTTGAAAAGACTA
Found at i:35680 original size:39 final size:37
Alignment explanation
Indices: 35403--35704 Score: 244
Period size: 37 Copynumber: 7.9 Consensus size: 37
35393 TAAAATCTTG
*
35403 GATGGGATCTTTCCCCT-AATTGAAAGCTTGAAAAAGACTA
1 GATGGGATCTTT-CCCTAAATTGAAATCTTG--AAA-ACTA
* * * * *
35443 AATGGGATCTTTTCTTAAATTGAAAACTTGAAAACTC
1 GATGGGATCTTTCCCTAAATTGAAATCTTGAAAACTA
* * *
35480 GACGGGATCTTTCCCTAAATTTAAAAATTTTGAAGAAGACTA
1 GATGGGATCTTTCCCTAAA-TT-GAAATCTTG-A-AA-ACTA
*
35522 GATGGGATCTTTCCCTAAATT-AAAACTCTGAAAAAGAC-A
1 GATGGGATCTTTCCCTAAATTGAAATCT-TG--AAA-ACTA
35561 GGATGGGATCTTTCCCTAAATT---A-CTT-AAATACTA
1 -GATGGGATCTTTCCCTAAATTGAAATCTTGAAA-ACTA
* *
35595 GATGTGATCTTTCCCTAAATTGAAATCTTGAATACTA
1 GATGGGATCTTTCCCTAAATTGAAATCTTGAAAACTA
*
35632 GATGGGATCTTTCCCTAATTTTGAAATCTTGAAAAACTA
1 GATGGGATCTTTCCCTAA-ATTGAAATCTTG-AAAACTA
* *
35671 GGTGGGATCTTTCCCTAAATT-AAAACTTTGAAAA
1 GATGGGATCTTTCCCTAAATTGAAATC-TTGAAAA
35705 ATACTTTGGT
Statistics
Matches: 219, Mismatches: 25, Indels: 39
0.77 0.09 0.14
Matches are distributed among these distances:
33 25 0.11
34 1 0.00
36 2 0.01
37 52 0.24
38 24 0.11
39 36 0.16
40 52 0.24
41 6 0.03
42 21 0.10
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (37 bp):
GATGGGATCTTTCCCTAAATTGAAATCTTGAAAACTA
Found at i:39320 original size:20 final size:20
Alignment explanation
Indices: 39295--39341 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
39285 ACAATGCCAT
*
39295 AATGAATTTAATTACTAGCA
1 AATGAAATTAATTACTAGCA
39315 AATGAAATTAATTACTAGCA
1 AATGAAATTAATTACTAGCA
39335 AATGAAA
1 AATGAAA
39342 AATGGAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (20 bp):
AATGAAATTAATTACTAGCA
Found at i:39973 original size:11 final size:11
Alignment explanation
Indices: 39957--39982 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39947 CTGTTGAGCA
39957 TATTATTATGT
1 TATTATTATGT
39968 TATTATTATGT
1 TATTATTATGT
39979 TATT
1 TATT
39983 TCAATTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
TATTATTATGT
Found at i:42765 original size:23 final size:29
Alignment explanation
Indices: 42707--42815 Score: 157
Period size: 29 Copynumber: 3.8 Consensus size: 29
42697 AACAGCAACG
* * * *
42707 CTACAACATGTTGCT-TATACCAGCAACAA
1 CTACAACATGTTGCTCT-CAGCAACATCAA
42736 CTACAACATGTTGCTCTCAGCAACATCAA
1 CTACAACATGTTGCTCTCAGCAACATCAA
42765 CTACAACATGTTGCTCTCAGCAACATCAA
1 CTACAACATGTTGCTCTCAGCAACATCAA
*
42794 CTACAACATGTTGCGCTCAGCA
1 CTACAACATGTTGCTCTCAGCA
42816 GCAACAATAT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
29 73 0.99
30 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.24
Consensus pattern (29 bp):
CTACAACATGTTGCTCTCAGCAACATCAA
Found at i:42955 original size:42 final size:41
Alignment explanation
Indices: 42909--43092 Score: 111
Period size: 42 Copynumber: 4.4 Consensus size: 41
42899 AAGCGCTAAT
*
42909 TGCTGCTACATATTCAGCAGCGATTTTTCTACAAGCATCGAC
1 TGCTGTTACAT-TTCAGCAGCGATTTTTCTACAAGCATCGAC
* ** * * * **
42951 TGCTGTTTCATTCTCAGCAATGATCTTTC-AAAAGGC-GCTGGT
1 TGCTGTTACATT-TCAGCAGCGATTTTTCTACAA-GCATC-GAC
*
42993 TGCTGTTGCATCTTCAGCAGCGATTTTTCTACAAGCATCGAC
1 TGCTGTTACAT-TTCAGCAGCGATTTTTCTACAAGCATCGAC
* * * ** * * *
43035 TTCTGTTTCATTCTCATCAATGATATTTCTACAAACATCGGC
1 TGCTGTTACATT-TCAGCAGCGATTTTTCTACAAGCATCGAC
* *
43077 TACTGCTACATCTTCA
1 TGCTGTTACAT-TTCA
43093 TCAAGGATCT
Statistics
Matches: 106, Mismatches: 28, Indels: 16
0.71 0.19 0.11
Matches are distributed among these distances:
41 6 0.06
42 94 0.89
43 6 0.06
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (41 bp):
TGCTGTTACATTTCAGCAGCGATTTTTCTACAAGCATCGAC
Found at i:43106 original size:84 final size:83
Alignment explanation
Indices: 42911--43092 Score: 233
Period size: 84 Copynumber: 2.2 Consensus size: 83
42901 GCGCTAATTG
* *
42911 CTGCTACATATTCAGCAGCGATTTTTCTACAAGCATCGACTGCTGTTTCATTCTCAGCAATGATC
1 CTGCTACATCTTCAGCAGCGATTTTTCTACAAGCATCGACTGCTGTTTCATTCTCAGCAATGATA
* *
42976 TTTCAAAAGGCGCTGGTTG
66 TTTCAAAA-GCGCTGGCTA
* * * *
42995 CTGTTGCATCTTCAGCAGCGATTTTTCTACAAGCATCGACTTCTGTTTCATTCTCATCAATGATA
1 CTGCTACATCTTCAGCAGCGATTTTTCTACAAGCATCGACTGCTGTTTCATTCTCAGCAATGATA
*
43060 TTTCTACAAA-C-ATCGGCTA
66 TTTC-A-AAAGCGCT-GGCTA
43079 CTGCTACATCTTCA
1 CTGCTACATCTTCA
43093 TCAAGGATCT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 1 0.01
84 79 0.94
85 1 0.01
86 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (83 bp):
CTGCTACATCTTCAGCAGCGATTTTTCTACAAGCATCGACTGCTGTTTCATTCTCAGCAATGATA
TTTCAAAAGCGCTGGCTA
Found at i:44075 original size:14 final size:14
Alignment explanation
Indices: 44056--44085 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
44046 GCAGAGGTTG
44056 AAAGAAAACAATTA
1 AAAGAAAACAATTA
44070 AAAGAAAACAATTA
1 AAAGAAAACAATTA
44084 AA
1 AA
44086 CTAGAGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAGAAAACAATTA
Found at i:50855 original size:32 final size:30
Alignment explanation
Indices: 50809--50877 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
50799 AGGAAAAAAA
*
50809 TTTTTTTTTCTGACGCAGAAATAAA-ATTTTT
1 TTTTTTTTTATGACGCA-AAA-AAACATTTTT
*
50840 TTTTATTTTTATGACGCAAAAAAACCTTTTT
1 TTTT-TTTTTATGACGCAAAAAAACATTTTT
50871 TTTTTTT
1 TTTTTTT
50878 ACACAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 6 0.18
31 16 0.47
32 12 0.35
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (30 bp):
TTTTTTTTTATGACGCAAAAAAACATTTTT
Found at i:51262 original size:16 final size:15
Alignment explanation
Indices: 51224--51265 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
51214 GCATAGGTTG
*
51224 AAAGAAAGCAATTAA
1 AAAGAAAACAATTAA
51239 AAAGAAAACAATTAA
1 AAAGAAAACAATTAA
*
51254 ACTAGAAAACAA
1 A-AAGAAAACAA
51266 AGCAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.12
Consensus pattern (15 bp):
AAAGAAAACAATTAA
Found at i:52671 original size:29 final size:30
Alignment explanation
Indices: 52634--52694 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
52624 AATTCTTTCC
* *
52634 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
52663 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
52694 T
1 T
52695 ACGAACTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.64
31 10 0.36
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:52680 original size:12 final size:12
Alignment explanation
Indices: 52663--52695 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
52653 TGTCTTCAAA
52663 TCTTCAAATAAG
1 TCTTCAAATAAG
*
52675 TCTTC-AATGAG
1 TCTTCAAATAAG
52686 TCTTCAAATA
1 TCTTCAAATA
52696 CGAACTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (12 bp):
TCTTCAAATAAG
Found at i:54719 original size:15 final size:15
Alignment explanation
Indices: 54691--54730 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
54681 ACTTTGTTTC
54691 GTTTTCTAGTTTAATT
1 GTTTTCT-GTTTAATT
54707 GTTTTCTGTTTAATT
1 GTTTTCTGTTTAATT
54722 GTTTTCTGT
1 GTTTTCTGT
54731 CAACCTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.12, C:0.07, G:0.15, T:0.65
Consensus pattern (15 bp):
GTTTTCTGTTTAATT
Found at i:55931 original size:18 final size:19
Alignment explanation
Indices: 55910--55953 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
55900 TATAAAAGGG
*
55910 CACTATTTCATT-AAAGCC
1 CACTATTCCATTAAAAGCC
55928 CACTA-TCCATTAAAAGCC
1 CACTATTCCATTAAAAGCC
*
55946 CATTATTC
1 CACTATTC
55954 ACAAATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 15 0.68
19 2 0.09
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (19 bp):
CACTATTCCATTAAAAGCC
Found at i:56527 original size:93 final size:96
Alignment explanation
Indices: 56312--56734 Score: 544
Period size: 93 Copynumber: 4.5 Consensus size: 96
56302 ATGACTTAGT
* *
56312 CCATCGTCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGAAGAAGTAGTGCACGGCTC
1 CCATCATCATTACAAGATGTGGCGAGGCATCATCAAGCCGCCGGTGAAGAAGTAGTGCACGGCTC
* *
56377 TCACCTAGTCTTCCTAGTTATGAT-AATTTTC
66 TCA-CTAGTCTTCCTTGTTATGATCAATTTAC
* * * * *
56408 TCATCATCA-T-CAAGATGTGGCAAGGCATCAACAAGCCGCCAGTGAAG-AGTACTGCACGGCTC
1 CCATCATCATTACAAGATGTGGCGAGGCATCATCAAGCCGCCGGTGAAGAAGTAGTGCACGGCTC
*
56470 TCA-TAGTCTTCCTTGTTATG-TCATTTTAC
66 TCACTAGTCTTCCTTGTTATGATCAATTTAC
* * * *
56499 CCATTATCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGAAGAAGTAGTGCAAGACTC
1 CCATCATCATTACAAGATGTGGCGAGGCATCATCAAGCCGCCGGTGAAGAAGTAGTGCACGGCTC
56564 TCACCTAGTCTTCCTTGTTATGAT-AATTTAC
66 TCA-CTAGTCTTCCTTGTTATGATCAATTTAC
* * * * * *
56595 TCATCATCA-T-CAAGATGTGCCAAGGCTTCATCAAGCCGCCGGTGAAG-AGTAGTGCACGGTTG
1 CCATCATCATTACAAGATGTGGCGAGGCATCATCAAGCCGCCGGTGAAGAAGTAGTGCACGGCTC
56657 TCACCTAGTCTTCCTTGTTATGA-CAATTTAC
66 TCA-CTAGTCTTCCTTGTTATGATCAATTTAC
* *
56688 CCATTATCATTACAAGACGTGGCGAGGCATCATCAAGCCGCCGGTGA
1 CCATCATCATTACAAGATGTGGCGAGGCATCATCAAGCCGCCGGTGA
56735 TTGAGTGGTA
Statistics
Matches: 281, Mismatches: 36, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
90 1 0.00
91 28 0.10
92 1 0.00
93 98 0.35
94 82 0.29
95 33 0.12
96 37 0.13
97 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (96 bp):
CCATCATCATTACAAGATGTGGCGAGGCATCATCAAGCCGCCGGTGAAGAAGTAGTGCACGGCTC
TCACTAGTCTTCCTTGTTATGATCAATTTAC
Found at i:56633 original size:187 final size:188
Alignment explanation
Indices: 56318--56797 Score: 703
Period size: 187 Copynumber: 2.6 Consensus size: 188
56308 TAGTCCATCG
*
56318 TCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGAAGAAGTAGTGCACGGCTCTCACCT
1 TCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGAAGAAGTAGTGCAAGGCTCTCACCT
* *
56383 AGTCTTCCTAGTTATGATAATTTTCTCATCATCATCAAGATGTGGCAAGGCATCAACAAGCCGCC
66 AGTCTTCCTAGTTATGATAATTTACTCATCATCATCAAGATGTGCCAAGGCATCAACAAGCCGCC
* *
56448 AGTGAAGAGTACTGCACGGCTCTCA-TAGTCTTCCTTGTTATGTCATTTTACCCATTA
131 AGTGAAGAGTACTGCACGGCTCTCACTAGTCTTCCTTGTTATGACAATTTACCCATTA
*
56505 TCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGAAGAAGTAGTGCAAGACTCTCACCT
1 TCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGAAGAAGTAGTGCAAGGCTCTCACCT
* * *
56570 AGTCTTCCTTGTTATGATAATTTACTCATCATCATCAAGATGTGCCAAGGCTTCATCAAGCCGCC
66 AGTCTTCCTAGTTATGATAATTTACTCATCATCATCAAGATGTGCCAAGGCATCAACAAGCCGCC
* * * *
56635 GGTGAAGAGTAGTGCACGGTTGTCACCTAGTCTTCCTTGTTATGACAATTTACCCATTA
131 AGTGAAGAGTACTGCACGGCTCTCA-CTAGTCTTCCTTGTTATGACAATTTACCCATTA
* * * * ** * *
56694 TCATTACAAGACGTGGCGAGGCATCATCAAGCCGCCGGTGATTG-AGTGGTATATGGCTCTCACA
1 TCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGA-AGAAGTAGTGCAAGGCTCTCACC
* * * *
56758 TAGTCTTCCTAGTAATGATATTTTGCTCACCATCATCAAG
65 TAGTCTTCCTAGTTATGATAATTTACTCATCATCATCAAG
56798 GCATGGCAAG
Statistics
Matches: 263, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
187 144 0.55
189 118 0.45
190 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (188 bp):
TCATTACAAGATGTGGCGAGGCATCATCAAGCCGACGGTGAAGAAGTAGTGCAAGGCTCTCACCT
AGTCTTCCTAGTTATGATAATTTACTCATCATCATCAAGATGTGCCAAGGCATCAACAAGCCGCC
AGTGAAGAGTACTGCACGGCTCTCACTAGTCTTCCTTGTTATGACAATTTACCCATTA
Found at i:56839 original size:94 final size:94
Alignment explanation
Indices: 56561--56890 Score: 279
Period size: 94 Copynumber: 3.5 Consensus size: 94
56551 TAGTGCAAGA
* * * * * *
56561 CTCTCACCTAGTCTTCCTTGTTATGATAATTTACTCATCATCATCAA-G-ATGTGCCAAGGCTTC
1 CTCTCACATAGTCTTCCTAGTAATGATATTTTACTCACCATCATCAAGGCATG-G-CAAGGCATC
* ** ** **
56624 ATCAAGCCGCCGGTGA-AGAGTAGTGCACGG
64 ATCAAGCCGCCGGTGATTGAGCGGTATATAG
* * * * * * * * ** * * *
56654 TTGTCACCTAGTCTTCCTTGTTATGACAATTTACCCATTATCATTACAAGACGTGGCGAGGCATC
1 CTCTCACATAGTCTTCCTAGTAATGATATTTTACTCACCATCA-T-CAAGGCATGGCAAGGCATC
* *
56719 ATCAAGCCGCCGGTGATTGAGTGGTATATGG
64 ATCAAGCCGCCGGTGATTGAGCGGTATATAG
* *
56750 CTCTCACATAGTCTTCCTAGTAATGATATTTTGCTCACCATCATCAAGGCATGGCAAGGCATCGT
1 CTCTCACATAGTCTTCCTAGTAATGATATTTTACTCACCATCATCAAGGCATGGCAAGGCATCAT
* *
56815 CATGCTGCCGGTGATTGAGCGGTATATAG
66 CAAGCCGCCGGTGATTGAGCGGTATATAG
* * * *
56844 CTCTCACCTAGTCTTCCTTGTTATGATGTTTTACTCACCATCATCAA
1 CTCTCACATAGTCTTCCTAGTAATGATATTTTACTCACCATCATCAA
56891 TGTATTATTA
Statistics
Matches: 194, Mismatches: 38, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
93 38 0.20
94 85 0.44
95 27 0.14
96 42 0.22
97 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (94 bp):
CTCTCACATAGTCTTCCTAGTAATGATATTTTACTCACCATCATCAAGGCATGGCAAGGCATCAT
CAAGCCGCCGGTGATTGAGCGGTATATAG
Found at i:57280 original size:147 final size:148
Alignment explanation
Indices: 57035--57338 Score: 457
Period size: 147 Copynumber: 2.1 Consensus size: 148
57025 ATTTCAGAGG
*
57035 TCTGTTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTATCGGGTACTGTTAA
1 TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTATCGGGTACTGTTAA
* * *
57100 GATCCACAGAAGGCTAACGTGGTAGCACATGAGGCATACTATCCGTGGGGCTTACTAATAGGTGA
66 GACCCACAGAAGGCTAACGTGGTAGCACATGAGGCATACTATCCGTGGGGCTTACGAAAAGGTGA
57165 ATTTACTATTCA-CAGCC
131 ATTTACTATTCATCAGCC
* * **
57182 TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGGGTCCACTATCGGGTACTGTTGG
1 TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTATCGGGTACTGTTAA
* * * * *
57247 GACCCACAGCAGGTTGACGTGGTAGCACATGAGGCATATTGTCCGTGGGGCTTACGAAAAGGTGA
66 GACCCACAGAAGGCTAACGTGGTAGCACATGAGGCATACTATCCGTGGGGCTTACGAAAAGGTGA
* * *
57312 ATTTACTGTTCATCGGCT
131 ATTTACTATTCATCAGCC
57330 TCTGCTGGA
1 TCTGCTGGA
57339 GTATCGGGCC
Statistics
Matches: 140, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
147 128 0.91
148 12 0.09
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (148 bp):
TCTGCTGGAAAGTTACTGTTCATGACCTCTGCTGGGATGTCGAGCCCACTATCGGGTACTGTTAA
GACCCACAGAAGGCTAACGTGGTAGCACATGAGGCATACTATCCGTGGGGCTTACGAAAAGGTGA
ATTTACTATTCATCAGCC
Found at i:57793 original size:20 final size:21
Alignment explanation
Indices: 57768--57807 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
57758 TGAAGGGAAT
57768 CTTGT-CATAAGCATTAAATA
1 CTTGTCCATAAGCATTAAATA
* *
57788 CTTGTCCTTGAGCATTAAAT
1 CTTGTCCATAAGCATTAAAT
57808 GATGATGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
CTTGTCCATAAGCATTAAATA
Found at i:59814 original size:30 final size:30
Alignment explanation
Indices: 59780--59873 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
59770 TTTGGCGCCG
59780 TTGCCGGGGAAGGGTAACTTTTTCTGGTTT
1 TTGCCGGGGAAGGGTAACTTTTTCTGGTTT
59810 TTGCCGGGGAAGGGTAACTTTTTCTGGTTT
1 TTGCCGGGGAAGGGTAACTTTTTCTGGTTT
*
59840 TTGCCAGGGAAGGG-AACTTTTTCTGGTTT
1 TTGCCGGGGAAGGGTAACTTTTTCTGGTTT
59869 TTGCC
1 TTGCC
59874 ATGGGAAGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
29 20 0.32
30 43 0.68
ACGTcount: A:0.14, C:0.15, G:0.32, T:0.39
Consensus pattern (30 bp):
TTGCCGGGGAAGGGTAACTTTTTCTGGTTT
Found at i:60062 original size:27 final size:27
Alignment explanation
Indices: 59999--60052 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
59989 TTTTTGATCT
59999 GAAAAAAAAACATTTGTGTTTTGCGTC
1 GAAAAAAAAACATTTGTGTTTTGCGTC
*
60026 GAAAAAAAAATATTT-TGTTTCTGCGTC
1 GAAAAAAAAACATTTGTGTTT-TGCGTC
60053 ATATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (27 bp):
GAAAAAAAAACATTTGTGTTTTGCGTC
Found at i:62490 original size:173 final size:173
Alignment explanation
Indices: 62201--62534 Score: 650
Period size: 173 Copynumber: 1.9 Consensus size: 173
62191 TGGATCTTTG
*
62201 GTTCATCCCAAAGGTGTTCTAGAGAATGTTTTAATTCAAGTTGAACACTTGGTTTTTCCTATTGA
1 GTTCATCCCAAAGGTGTTCTAGAGAATGTCTTAATTCAAGTTGAACACTTGGTTTTTCCTATTGA
62266 CATCTTCGTTATGGAGATGGAACATTCGAAAGATCAATGTCCGCTTTTATTAGGAAGACCCTTCT
66 CATCTTCGTTATGGAGATGGAACATTCGAAAGATCAATGTCCGCTTTTATTAGGAAGACCCTTCT
*
62331 TAAGAACTTCCCATACTAAGATTGATGTATTAATTCCAAAGGT
131 TAAGAACATCCCATACTAAGATTGATGTATTAATTCCAAAGGT
62374 GTTCATCCCAAAGGTGTTCTAGAGAATGTCTTAATTCAAGTTGAACACTTGGTTTTTCCTATTGA
1 GTTCATCCCAAAGGTGTTCTAGAGAATGTCTTAATTCAAGTTGAACACTTGGTTTTTCCTATTGA
62439 CATCTTCGTTATGGAGATGGAACATTCGAAAGATCAATGTCCGCTTTTATTAGGAAGACCCTTCT
66 CATCTTCGTTATGGAGATGGAACATTCGAAAGATCAATGTCCGCTTTTATTAGGAAGACCCTTCT
62504 TAAGAACATCCCATACTAAGATTGATGTATT
131 TAAGAACATCCCATACTAAGATTGATGTATT
62535 CGATGGTTCA
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 159 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (173 bp):
GTTCATCCCAAAGGTGTTCTAGAGAATGTCTTAATTCAAGTTGAACACTTGGTTTTTCCTATTGA
CATCTTCGTTATGGAGATGGAACATTCGAAAGATCAATGTCCGCTTTTATTAGGAAGACCCTTCT
TAAGAACATCCCATACTAAGATTGATGTATTAATTCCAAAGGT
Found at i:68176 original size:124 final size:124
Alignment explanation
Indices: 68000--68276 Score: 369
Period size: 124 Copynumber: 2.2 Consensus size: 124
67990 TGTAGGACTG
* * * ** *
68000 CCTTGCTGACATGTCACTCTACCGAGGAGGAGGTTCTGCTGCTGCAAAGTGCTGCTAAGCACTTT
1 CCTTTCTGACATGTCACTCTGCCGAGAAGGAGGTTCCACTGCTGCAAAGTGCTACTAAGCACTTT
* * * * * *
68065 CACCGAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAA
66 AACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCAA
* *
68124 CCTTTCTGACATGTCACTCTGCCGAGAAGGAGGTTCCACTGCTAG-AAAGTGCTATTAGGCACTT
1 CCTTTCTGACATGTCACTCTGCCGAGAAGGAGGTTCCACTGCT-GCAAAGTGCTACTAAGCACTT
*
68188 TAACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCTA
65 TAACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCAA
* *
68248 CCTTGT-TGGCATGTCGCTCTGCCGAGAAG
1 CCTT-TCTGACATGTCACTCTGCCGAGAAG
68277 AAGGCCCCGC
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
124 132 0.99
125 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (124 bp):
CCTTTCTGACATGTCACTCTGCCGAGAAGGAGGTTCCACTGCTGCAAAGTGCTACTAAGCACTTT
AACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCAA
Found at i:68300 original size:124 final size:124
Alignment explanation
Indices: 68000--68311 Score: 342
Period size: 124 Copynumber: 2.5 Consensus size: 124
67990 TGTAGGACTG
* * * * ** ** * *
68000 CCTTGCTGACATGTCACTCTACCGAGGAGGAGGTTCTGCTGCT-GCAAAGTGCTGCTAAGCACTT
1 CCTTTCTGACATGTCACTCTGCCGAGAAGAAGGCCCCACTGCTAG-AAAGTGCTTCTAGGCACTT
* * * * * *
68064 TCACCGAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAA
65 TAACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCAA
* **
68124 CCTTTCTGACATGTCACTCTGCCGAGAAGGAGGTTCCACTGCTAGAAAGTGCTAT-TAGGCACTT
1 CCTTTCTGACATGTCACTCTGCCGAGAAGAAGGCCCCACTGCTAGAAAGTGCT-TCTAGGCACTT
*
68188 TAACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCTA
65 TAACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCAA
* * * * * *
68248 CCTTGT-TGGCATGTCGCTCTGCCGAGAAGAAGGCCCCGCTGCTGGGAGGTGCTTCTAGGCACTT
1 CCTT-TCTGACATGTCACTCTGCCGAGAAGAAGGCCCCACTGCTAGAAAGTGCTTCTAGGCACTT
68312 CAATCGAAGT
Statistics
Matches: 161, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
123 1 0.01
124 158 0.98
125 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (124 bp):
CCTTTCTGACATGTCACTCTGCCGAGAAGAAGGCCCCACTGCTAGAAAGTGCTTCTAGGCACTTT
AACCAAAGTCTTATCCTCCATCAACAAAAGAGGCCAGCAGCATGGCTAACCTGGGGCAA
Done.