Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_pilon, 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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 25
Found at i:5086806 original size:12 final size:12
Alignment explanation
Indices: 5086789--5086821 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5086779 ATACCTTATT
5086789 TATAAATATATA
1 TATAAATATATA
5086801 TATAAATATATA
1 TATAAATATATA
5086813 T-T-AATATAT
1 TATAAATATAT
5086822 TTTCTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 1 0.05
12 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATAAATATATA
Found at i:5094504 original size:14 final size:12
Alignment explanation
Indices: 5094459--5094508 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 12
5094449 TTATGCTTAA
5094459 AGAAAAAAAAAG
1 AGAAAAAAAAAG
*
5094471 AGAAAAAAGAAAA
1 AGAAAAAA-AAAG
5094484 AGAAAATAAAAAG
1 AGAAAA-AAAAAG
5094497 TAGAAAATAAAA
1 -AGAAAA-AAAA
5094509 CGGAGGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 8 0.24
13 12 0.36
14 13 0.39
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:5094883 original size:18 final size:18
Alignment explanation
Indices: 5094857--5094894 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5094847 CAAGTTTATC
*
5094857 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
5094875 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
5094893 TT
1 TT
5094895 CTTTCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:5095598 original size:22 final size:22
Alignment explanation
Indices: 5095570--5095623 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
5095560 CATTCTACAT
5095570 TCTTCAAAGATGATAGATGCTC
1 TCTTCAAAGATGATAGATGCTC
* *
5095592 TCTTCAAAAATGATAGATTCTC
1 TCTTCAAAGATGATAGATGCTC
*
5095614 TTTTCAAAGA
1 TCTTCAAAGA
5095624 AGAAAGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATGCTC
Found at i:5095631 original size:22 final size:22
Alignment explanation
Indices: 5095570--5095632 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
5095560 CATTCTACAT
* *
5095570 TCTTCAAAGATGATAGATGCTC
1 TCTTCAAAGAAGATAGATTCTC
5095592 TCTTCAAA-AATGATAGATTCTC
1 TCTTCAAAGAA-GATAGATTCTC
* *
5095614 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGAAGATAGATT
5095633 TATTGGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
TCTTCAAAGAAGATAGATTCTC
Found at i:5096257 original size:123 final size:122
Alignment explanation
Indices: 5096020--5096474 Score: 682
Period size: 123 Copynumber: 3.7 Consensus size: 122
5096010 CACTCGATGG
* *
5096020 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
* * * * *
5096085 TGAGAAGAGCTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGAAGATATATCAAC
66 TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
*
5096142 ATCAACATTTTCAGAAGGAGTTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAA-GAGTTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* * *
5096207 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTTTCATAGAAGGAGATAGATCATC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
* * * *
5096265 AT-ACACTTTTCCAGAGAAAGTTCATAAT-AAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCA
1 ATCA-ACATTTCCAGA-AGAGTTCATAATGAA-AAGAACTCATCTGAAGAAGAAGAAGAAGTTCA
*
5096328 TAATGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAGAAGGAGATAGATCAAC
63 TAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
*
5096388 ATCAACATTTCCAGAAGAGTTCATAATGAGAAA-AACTCATCTGAAGAAGGAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGA-AAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
*
5096452 ATGAGAAGAATTTGTTCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
5096475 GCCTTAATTT
Statistics
Matches: 300, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
122 79 0.26
123 218 0.73
124 3 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:5096853 original size:3 final size:3
Alignment explanation
Indices: 5096830--5096895 Score: 59
Period size: 3 Copynumber: 22.0 Consensus size: 3
5096820 TTTTTTCATT
5096830 TTA TT- TTA TT- TTA TTA TTTA TTA TT- TATA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA -TTA TTA TTA TTA TTA
*
5096875 TTA TTAA TTA -AA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA
5096896 CAGGCCCAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
2 6 0.11
3 38 0.72
4 8 0.15
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5096889 original size:15 final size:13
Alignment explanation
Indices: 5096835--5096895 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
5096825 TCATTTTATT
*
5096835 TTATT-TTATTAT
1 TTATTATTATTAA
*
5096847 TTATTATT-TATAT
1 TTATTATTAT-TAA
5096860 TTATTATTATT-A
1 TTATTATTATTAA
5096872 TTATTATTAATTAAA
1 TTATTATT-ATT-AA
5096887 TTATTATTA
1 TTATTATTA
5096896 CAGGCCCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
12 14 0.33
13 17 0.40
14 2 0.05
15 9 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:5098363 original size:15 final size:16
Alignment explanation
Indices: 5098332--5098364 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5098322 AAATCCTATT
*
5098332 TATAAATTTATTTTTA
1 TATAAATTTAATTTTA
5098348 TATAAA-TTAATTTTA
1 TATAAATTTAATTTTA
5098363 TA
1 TA
5098365 AACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATAAATTTAATTTTA
Found at i:5098615 original size:23 final size:23
Alignment explanation
Indices: 5098588--5098633 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5098578 ATTTTTCTGA
* *
5098588 TATTTCTAAGTAAATAAATATAT
1 TATTTATAAATAAATAAATATAT
* *
5098611 TATTTATAAATATATATATATAT
1 TATTTATAAATAAATAAATATAT
5098634 ATATATATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATAT
Found at i:5099944 original size:20 final size:20
Alignment explanation
Indices: 5099890--5099937 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
5099880 TTAGAATGTT
5099890 AGAGTGTGGATGTATGTATG
1 AGAGTGTGGATGTATGTATG
5099910 AGAGTGTGGATGTATGTATG
1 AGAGTGTGGATGTATGTATG
5099930 AGAGTGTG
1 AGAGTGTG
5099938 ATTGTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (20 bp):
AGAGTGTGGATGTATGTATG
Found at i:5105453 original size:20 final size:20
Alignment explanation
Indices: 5105416--5105452 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
5105406 GTTTGATCAC
5105416 TTATTTAATTTTTAAAAATA
1 TTATTTAATTTTTAAAAATA
5105436 TTATTT-ATTTTTAAAAA
1 TTATTTAATTTTTAAAAA
5105453 AATCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTAATTTTTAAAAATA
Found at i:5117612 original size:24 final size:24
Alignment explanation
Indices: 5117580--5117630 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
5117570 CTTTGAGCTC
5117580 GATCAATTTCACTTTAAAACTCTA
1 GATCAATTTCACTTTAAAACTCTA
*
5117604 GATCGATTTCACTTTAAAACTCTA
1 GATCAATTTCACTTTAAAACTCTA
5117628 GAT
1 GAT
5117631 TACTTTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (24 bp):
GATCAATTTCACTTTAAAACTCTA
Found at i:5121596 original size:2 final size:2
Alignment explanation
Indices: 5121585--5121642 Score: 54
Period size: 2 Copynumber: 31.5 Consensus size: 2
5121575 AAAATATAAA
* * *
5121585 AT AT -T AT AT AT AT A- AT -T AT AA AA AT A- AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5121622 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
5121643 ATCGGGGCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5121596 original size:22 final size:21
Alignment explanation
Indices: 5121566--5121607 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5121556 GTATTATATA
5121566 ATTAATATAAAAATATAAAAT
1 ATTAATATAAAAATATAAAAT
* *
5121587 ATTATATATATAATTATAAAA
1 ATTA-ATATAAAAATATAAAA
5121608 ATAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAATATAAAAATATAAAAT
Found at i:5121620 original size:28 final size:29
Alignment explanation
Indices: 5121557--5121632 Score: 104
Period size: 28 Copynumber: 2.6 Consensus size: 29
5121547 TTAGGGTTTG
5121557 TATTATATA-ATTAATATAAAAATATAAAA
1 TATTATATATA-TAATATAAAAATATAAAA
5121586 TATTATATATATAAT-TATAAAA-ATAAAA
1 TATTATATATATAATATA-AAAATATAAAA
5121614 TATTATATATATATATATA
1 TATTATATATATA-ATATA
5121633 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
28 21 0.49
29 19 0.44
30 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TATTATATATATAATATAAAAATATAAAA
Found at i:5125464 original size:20 final size:20
Alignment explanation
Indices: 5125439--5125576 Score: 181
Period size: 20 Copynumber: 6.8 Consensus size: 20
5125429 TGCGATTTTC
*
5125439 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
5125459 CAAATTCTCGCGAA-GCGATAGT
1 CAAA-T-TCGC-AACGCGAAAGT
5125481 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
5125501 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
5125521 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
5125541 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
5125560 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
5125577 TTTAATTTCG
Statistics
Matches: 106, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
19 18 0.17
20 68 0.64
21 2 0.02
22 16 0.15
23 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:5125579 original size:20 final size:20
Alignment explanation
Indices: 5125357--5125590 Score: 133
Period size: 20 Copynumber: 11.6 Consensus size: 20
5125347 AAATGACCAA
*
5125357 CAAATTCGCAGCGCGAA-TT
1 CAAATTCGCAACGCGAATTT
* * *
5125376 CTAATTTCGCAAC-CCAGTTT
1 C-AAATTCGCAACGCGAATTT
* *
5125396 CCAATTTCGCAACACGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
*** *
5125419 -AAATTCGCGTTGCGATTTT
1 CAAATTCGCAACGCGAATTT
*
5125438 CCAAATTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
*
5125459 CAAATTCTCGCGAA-GCG-ATAGT
1 CAAA-T-TCGC-AACGCGAAT-TT
**
5125481 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
* **
5125501 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
**
5125521 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
*
5125541 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
5125560 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
5125580 -AATTTCGCAAC
1 CAAATTCGCAAC
5125591 AGGTTTTAGT
Statistics
Matches: 175, Mismatches: 25, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
19 32 0.18
20 93 0.53
21 30 0.17
22 17 0.10
23 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:5126536 original size:24 final size:24
Alignment explanation
Indices: 5126478--5126524 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5126468 AGTCAGTATT
* *
5126478 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGATCAATACC
5126502 CGAACTTTGATCTTGATCAATAC
1 CGAACTTTGATCTTGATCAATAC
5126525 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGATCAATACC
Found at i:5129255 original size:25 final size:25
Alignment explanation
Indices: 5129217--5129266 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5129207 AAATCAATTA
*
5129217 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
5129242 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
5129267 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:5129688 original size:24 final size:24
Alignment explanation
Indices: 5129636--5129688 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5129626 TTTCATATGT
* *
5129636 AATTGGAGTTTGAATTTAAATTTA
1 AATTTGAGTTTGAATTTAAATATA
*
5129660 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
5129684 AATTT
1 AATTT
5129689 TGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:5129991 original size:39 final size:39
Alignment explanation
Indices: 5129948--5130034 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
5129938 TCCGATGCTC
5129948 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
5129987 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
5130026 ATCAAAATC
1 ATCAAAATC
5130035 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:5130301 original size:20 final size:20
Alignment explanation
Indices: 5130276--5130313 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5130266 GCAAAGCTTA
5130276 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
5130296 TTTCGCGTTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
5130314 TACCTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:5132044 original size:4 final size:4
Alignment explanation
Indices: 5132014--5132057 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
5132004 GGGCCGCTGA
* *
5132014 AAAT AAATT AATAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAA-T AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
5132058 TGCCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 27 0.79
5 6 0.18
6 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:5132912 original size:18 final size:18
Alignment explanation
Indices: 5132891--5132926 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5132881 AGAATGTCCA
5132891 GGGGGTA-CAGATTCCCCT
1 GGGGGTATC-GATTCCCCT
5132909 GGGGGTATCGATTCCCCT
1 GGGGGTATCGATTCCCCT
5132927 AAATTCCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:5132940 original size:27 final size:27
Alignment explanation
Indices: 5132905--5132957 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5132895 GTACAGATTC
5132905 CCCTGGGGGTATCGATTCCCCTAAATT
1 CCCTGGGGGTATCGATTCCCCTAAATT
5132932 CCCTGGGGGTATCGATTCCCCTAAAT
1 CCCTGGGGGTATCGATTCCCCTAAAT
5132958 AAAAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (27 bp):
CCCTGGGGGTATCGATTCCCCTAAATT
Found at i:5133932 original size:31 final size:31
Alignment explanation
Indices: 5133890--5134093 Score: 345
Period size: 31 Copynumber: 6.6 Consensus size: 31
5133880 AGGATCGAGG
5133890 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
5133921 ATTTACTTATGTTCTTCGGGACAAATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5133952 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5133983 GTTTACCTATGTTCTTCGGGGCATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5134014 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5134045 GTTTACCTATGTTCTTCGGGACATGTGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
5134076 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
5134094 AATCTATGGA
Statistics
Matches: 162, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 162 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5137112 original size:18 final size:18
Alignment explanation
Indices: 5137091--5137159 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
5137081 AGAATGTCTA
5137091 GGGGGTA-CAGATTCCCCT
1 GGGGGTATC-GATTCCCCT
5137109 GGGGGTATCGATTCCCC-
1 GGGGGTATCGATTCCCCT
*
5137126 --GGG-AACAGATTCCCCT
1 GGGGGTATC-GATTCCCCT
5137142 GGGGGGTATCGATTCCCC
1 -GGGGGTATCGATTCCCC
5137160 CCTAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
14 2 0.05
15 11 0.26
18 15 0.36
19 12 0.29
20 2 0.05
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:5138143 original size:31 final size:31
Alignment explanation
Indices: 5138105--5138287 Score: 284
Period size: 31 Copynumber: 6.0 Consensus size: 31
5138095 GGGTCGAGGA
5138105 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
5138136 TTTACCTATGTTC-TCGGGACATA--GACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
*
5138164 TTTACCTATGTTCTTCGGGGCATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
*
5138195 TTTACCTATGTTCTTCGGGGCATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
5138226 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
* * *
5138257 ATTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTTACCTATGTTCTTCGGGA-CATATGGACTG
5138288 GTTCTTCGGG
Statistics
Matches: 143, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
28 18 0.13
29 9 0.06
30 10 0.07
31 105 0.73
32 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTG
Found at i:5138219 original size:90 final size:92
Alignment explanation
Indices: 5138105--5138274 Score: 290
Period size: 90 Copynumber: 1.9 Consensus size: 92
5138095 GGGTCGAGGA
*
5138105 TTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTC-TCGGGACATA-GACTGTTTA
1 TTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATAGGACTGATTA
*
5138168 CCTATGTTCTTCGGGGCATATGGACTG
66 CCTAGGTTCTTCGGGGCATATGGACTG
*
5138195 TTTACCTATGTTCTTCGGGGCATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGATT
1 TTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATA-GGACTGATT
5138260 ACCTAGGTTCTTCGG
65 ACCTAGGTTCTTCGG
5138275 AATCTATGGA
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
90 43 0.58
91 10 0.14
93 21 0.28
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (92 bp):
TTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATAGGACTGATTA
CCTAGGTTCTTCGGGGCATATGGACTG
Found at i:5139094 original size:21 final size:21
Alignment explanation
Indices: 5139070--5139127 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
5139060 ATCTTCACGT
*
5139070 AAAGTACCAACCTCATGACGC
1 AAAGCACCAACCTCATGACGC
5139091 AAAGCACCAACCTCATGACGC
1 AAAGCACCAACCTCATGACGC
*
5139112 AAAGCACCGACCTCAT
1 AAAGCACCAACCTCAT
5139128 CACGTAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.36, G:0.14, T:0.12
Consensus pattern (21 bp):
AAAGCACCAACCTCATGACGC
Found at i:5140942 original size:110 final size:107
Alignment explanation
Indices: 5140755--5140972 Score: 391
Period size: 110 Copynumber: 2.0 Consensus size: 107
5140745 GAGATGTCAC
5140755 ATTGACATTTCAAACCTTTATTTTGTAAAATAACTGAACATTTGAATATATTAAAAAATACAATC
1 ATTGACATTTCAAACCTTTATTTTGTAAAATAACTGAACATTTGAATATATTAAAAAATACAATC
5140820 AGTATTATTCAATTATGTTTGGTAGAAAAATTTGAGATAAAA
66 AGTATTATTCAATTATGTTTGGTAGAAAAATTTGAGATAAAA
*
5140862 ATTGACATTTCAAACCTTTATTCTTGTAAAATAACTGAACATTTGAATTTATATTAAGAAATACA
1 ATTGACATTTCAAACCTTTATT-TTGTAAAATAACTGAACATTTGAA--TATATTAAAAAATACA
*
5140927 ATCTGTATTATTCAATTATGTTTGGTAGAAAAATTTGAGATAAAA
63 ATCAGTATTATTCAATTATGTTTGGTAGAAAAATTTGAGATAAAA
5140972 A
1 A
5140973 AAAAACGTGT
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
107 22 0.21
108 24 0.23
110 60 0.57
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (107 bp):
ATTGACATTTCAAACCTTTATTTTGTAAAATAACTGAACATTTGAATATATTAAAAAATACAATC
AGTATTATTCAATTATGTTTGGTAGAAAAATTTGAGATAAAA
Found at i:5141710 original size:30 final size:31
Alignment explanation
Indices: 5141653--5141774 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
5141643 CCCGAAGGAC
* * *
5141653 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
5141684 CAGTCCATATGT-CCGAGGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5141714 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5141745 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
5141775 CCCTCGACCC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
30 27 0.32
31 57 0.67
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5141749 original size:61 final size:62
Alignment explanation
Indices: 5141653--5141774 Score: 185
Period size: 61 Copynumber: 2.0 Consensus size: 62
5141643 CCCGAAGGAC
* * * *
5141653 CAGTCCATAGATTCCGAAGAACCTAGGTAATCAGTCCATATGT-CCGAGGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
5141714 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
5141775 CCCTCGACCC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 38 0.69
62 17 0.31
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (62 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5146035 original size:31 final size:31
Alignment explanation
Indices: 5145997--5146181 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
5145987 TCCGAAGGAC
* * *
5145997 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
5146028 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5146059 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5146090 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5146121 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5146152 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
5146182 CCCTCGACCC
Statistics
Matches: 150, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5147674 original size:19 final size:20
Alignment explanation
Indices: 5147652--5147694 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5147642 AATTCGCAAC
5147652 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
5147671 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
5147691 GCGA
1 GCGA
5147695 ATTTGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:5147983 original size:22 final size:22
Alignment explanation
Indices: 5147955--5148005 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5147945 GATGGAGATA
5147955 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
5147977 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
5147999 GACGGAT
1 GACGGAT
5148006 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:5148180 original size:21 final size:21
Alignment explanation
Indices: 5148154--5148194 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5148144 CGTTGCGATT
5148154 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
5148175 GCGAATTTGGAAAATCGCAA
1 GCGAATTTGGAAAATCGCAA
5148195 TACGATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:5148256 original size:20 final size:19
Alignment explanation
Indices: 5148211--5148275 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
5148201 TTACATATTT
5148211 GCGTTGCGAAATTAGAAA-C
1 GCGTTGCGAAATT-GAAATC
* *
5148230 TGAGTTGCGAAATTGTAATTC
1 -GCGTTGCGAAATTG-AAATC
*
5148251 GCGTTGCGAATTTGAAATC
1 GCGTTGCGAAATTGAAATC
5148270 GCGTTG
1 GCGTTG
5148276 TGAATTTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
19 11 0.29
20 26 0.68
21 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (19 bp):
GCGTTGCGAAATTGAAATC
Found at i:5148271 original size:19 final size:19
Alignment explanation
Indices: 5148211--5148283 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
5148201 TTACATATTT
*
5148211 GCGTTGCGAAATTAGAAA-C
1 GCGTTGCG-AATTTGAAATC
* * *
5148230 TGAGTTGCGAAATTGTAATTC
1 -GCGTTGCGAATTTG-AAATC
5148251 GCGTTGCGAATTTGAAATC
1 GCGTTGCGAATTTGAAATC
*
5148270 GCGTTGTGAATTTG
1 GCGTTGCGAATTTG
5148284 TTGGTCATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 21 0.49
20 21 0.49
21 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (19 bp):
GCGTTGCGAATTTGAAATC
Found at i:5152188 original size:21 final size:21
Alignment explanation
Indices: 5152137--5152233 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
5152127 ATTATGACTA
5152137 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
**
5152158 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
** ** *
5152179 TCGCAATGCGATACTGACTA-
1 TCGCAATGCGATTTTCCCAAT
* *
5152199 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCCCAAT
*
5152220 TCGCATTGCGATTT
1 TCGCAATGCGATTT
5152234 ACGTATTCGC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 13 0.23
21 39 0.70
22 4 0.07
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:5152190 original size:62 final size:62
Alignment explanation
Indices: 5152115--5152233 Score: 179
Period size: 62 Copynumber: 1.9 Consensus size: 62
5152105 CAGTTTCTAG
* *
5152115 ATTCGCAACGCGATTA-TGACTATCGCAATGCGATTTTCC-AATTTCGCGTTGCGATTTTCCCA
1 ATTCGCAACGCGA-TACTGACTATCGCAATGCAATTTTCCTAA-TTCGCATTGCGATTTTCCCA
*
5152177 ATTCGCAATGCGATACTGACTATCGCAATGCAATTTTCCTAATTCGCATTGCGATTT
1 ATTCGCAACGCGATACTGACTATCGCAATGCAATTTTCCTAATTCGCATTGCGATTT
5152234 ACGTATTCGC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
61 2 0.04
62 48 0.92
63 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (62 bp):
ATTCGCAACGCGATACTGACTATCGCAATGCAATTTTCCTAATTCGCATTGCGATTTTCCCA
Found at i:5152254 original size:41 final size:41
Alignment explanation
Indices: 5152157--5152272 Score: 128
Period size: 41 Copynumber: 2.8 Consensus size: 41
5152147 ATTTTCCAAT
*
5152157 TTCGCGTTGCGATTTTCCCAATTCGCAATGCGATACTGACTA
1 TTCGCGTTGCGATTTTCCTAATTCGCAATGCGATA-TGACTA
** * * *
5152199 -TCGCAATGCAATTTTCCTAATTCGCATTGCGAT-TTACGTA
1 TTCGCGTTGCGATTTTCCTAATTCGCAATGCGATATGAC-TA
*
5152239 TTCGCGTTGCGATTTTCATAATTCGCAAATGCGA
1 TTCGCGTTGCGATTTTCCTAATTCGC-AATGCGA
5152273 ATTATGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
39 3 0.05
40 2 0.03
41 49 0.82
42 6 0.10
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (41 bp):
TTCGCGTTGCGATTTTCCTAATTCGCAATGCGATATGACTA
Found at i:5152264 original size:21 final size:21
Alignment explanation
Indices: 5152137--5152265 Score: 77
Period size: 21 Copynumber: 6.2 Consensus size: 21
5152127 ATTATGACTA
* *
5152137 TCGCAATGCGATTTTCCA-ATT
1 TCGCATTGCGATTTT-CATAAT
* **
5152158 TCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCATAAT
* ** *
5152179 TCGCAATGCGATACTGACT-A-
1 TCGCATTGCGATTTTCA-TAAT
* * *
5152199 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
5152220 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
5152240 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
5152261 TCGCA
1 TCGCA
5152266 AATGCGAATT
Statistics
Matches: 79, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
19 1 0.01
20 31 0.39
21 47 0.59
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:5152305 original size:20 final size:20
Alignment explanation
Indices: 5152261--5152333 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
5152251 TTTTCATAAT
* *
5152261 TCGCAAATGCGAATTATGAAAA
1 TCGC-AATGCGAA-TACGTAAA
5152283 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
5152303 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
5152323 TCGCAATGCGA
1 TCGCAATGCGA
5152334 TTTACATAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.07
20 31 0.67
21 8 0.17
22 4 0.09
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:5152911 original size:19 final size:19
Alignment explanation
Indices: 5152887--5152931 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
5152877 GCAATGAGAG
*
5152887 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
5152906 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
5152925 AATCGCA
1 AATCGCA
5152932 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:5152949 original size:19 final size:19
Alignment explanation
Indices: 5152927--5153087 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
5152917 GAAACCAAAA
*
5152927 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5152946 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5152960 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5152979 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
5152998 TCGCGTTGCGATAGTCA-T
1 TCGCGTTGCGATTTTCATT
5153016 T-GCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
5153029 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
5153046 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
5153066 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5153086 TC
1 TC
5153088 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
12 8 0.07
13 1 0.01
14 12 0.10
15 2 0.02
16 3 0.03
17 13 0.11
18 2 0.02
19 45 0.38
20 30 0.26
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5152974 original size:33 final size:33
Alignment explanation
Indices: 5152932--5153062 Score: 135
Period size: 33 Copynumber: 3.9 Consensus size: 33
5152922 CAAAATCGCA
**
5152932 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
** *
5152965 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATAGTCATTTCGCGTTGCGA--TTC---TCTCG
5153003 TTGCGATAGTCA-TT-GCGTTGCGA-T-TCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
5153032 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
5153063 ATTATCTCGT
Statistics
Matches: 84, Mismatches: 4, Indels: 19
0.79 0.04 0.18
Matches are distributed among these distances:
29 16 0.19
30 2 0.02
32 9 0.11
33 27 0.32
34 2 0.02
35 3 0.04
36 9 0.11
37 2 0.02
38 14 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:5153034 original size:29 final size:31
Alignment explanation
Indices: 5153001--5153062 Score: 101
Period size: 29 Copynumber: 2.0 Consensus size: 31
5152991 TTTCATTTCG
5153001 CGTTGCGATAGTCA-TT-GCGTTGCGATTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCT
5153030 CGTTGCGATAGTCATTTCCGCGTTGCGATTCT
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCT
5153062 C
1 C
5153063 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 14 0.47
30 2 0.07
32 14 0.47
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (31 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCT
Found at i:5153064 original size:20 final size:20
Alignment explanation
Indices: 5153030--5153087 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
5153020 TTGCGATTCT
**
5153030 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
5153050 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
5153070 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
5153088 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:5153074 original size:69 final size:69
Alignment explanation
Indices: 5152948--5153078 Score: 194
Period size: 69 Copynumber: 1.9 Consensus size: 69
5152938 TTTTCATTTC
** *
5152948 GCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGT
1 GCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATTCTCATTTCGCGTTGCGATAGT
5153013 CATT
66 CATT
*
5153017 GCGTTGCGA-T-TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATTATCTCGTTGCGAT
1 GCGTTGCGATTCTCTCGTTGCGATAGTCATTT-CGCGTTGCGATTCTCATT-TCGCGTTGCGAT
5153079 TTTCATTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
67 18 0.32
68 18 0.32
69 20 0.36
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (69 bp):
GCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATTCTCATTTCGCGTTGCGATAGT
CATT
Found at i:5156573 original size:14 final size:14
Alignment explanation
Indices: 5156554--5156589 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5156544 ATTGTTTAAT
5156554 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
5156568 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
5156582 TGATTTGT
1 TGATTTGT
5156590 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:5156733 original size:14 final size:14
Alignment explanation
Indices: 5156714--5156768 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5156704 GCGAAATGAA
5156714 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5156728 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5156747 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5156761 AATCGCAA
1 AATCGCAA
5156769 TGCGATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5156741 original size:33 final size:33
Alignment explanation
Indices: 5156696--5156773 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
5156686 AAAAAGTACT
5156696 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5156729 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
5156762 ATCGCAATGCGA
1 ATCGCAATGCGA
5156774 TATTAAATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5156755 original size:19 final size:19
Alignment explanation
Indices: 5156696--5156756 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
5156686 AAAAAGTACT
*
5156696 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
5156715 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
5156729 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
5156748 ATCGCAACG
1 ATCGCAACG
5156757 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:5156885 original size:65 final size:65
Alignment explanation
Indices: 5156778--5156906 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
5156768 ATGCGATATT
*
5156778 AAATTCGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCA-TTCACATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGA-TTTCATTTCACATTGC
5156842 A
65 A
* *
5156843 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTCATTTCACATTGC
5156907 GATAGTAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 5 0.08
65 55 0.92
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.41
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTCATTTCACATTGCA
Found at i:5156895 original size:32 final size:33
Alignment explanation
Indices: 5156785--5156909 Score: 148
Period size: 32 Copynumber: 3.8 Consensus size: 33
5156775 ATTAAATTCG
*
5156785 CGTTGCGATTTTCATTTCGCATTACGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
* * * * **
5156818 CGTTGCGATTTTCA-TTCACATTGCAAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTAC-GATTCTCT
5156850 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
*
5156883 CGTTGCGA-TTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTACGAT
5156910 AGTAATTTCC
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
32 42 0.56
33 33 0.44
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTACGATTCTCT
Found at i:5159412 original size:24 final size:24
Alignment explanation
Indices: 5159378--5159431 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5159368 CTGAAACATC
*
5159378 ATCAAAATCCGAGTATTAACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
* * *
5159402 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
5159426 ATCAAA
1 ATCAAA
5159432 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:5160235 original size:20 final size:21
Alignment explanation
Indices: 5160210--5160261 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5160200 TTTTCCTAAT
*
5160210 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
5160230 TCGCAATGAGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
5160251 TCGCAATGCGA
1 TCGCAATGCGA
5160262 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:5160335 original size:20 final size:20
Alignment explanation
Indices: 5160227--5160337 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
5160217 GCGAATAAGT
*
5160227 AAATCGCAATGAGAATT-TGGA
1 AAATCGCAACGAG-ATTCT-GA
* * *
5160248 AAATCGCAATGCGATACTGA
1 AAATCGCAACGAGATTCTGA
** ** *
5160268 CTATCGCAACGAGATAATACA
1 AAATCGCAACGAGATTCT-GA
*
5160289 AAATCGCAACGAGATTCTGC
1 AAATCGCAACGAGATTCTGA
***
5160309 CTTTCGCAACGAGATTCTGA
1 AAATCGCAACGAGATTCTGA
5160329 AAATCGCAA
1 AAATCGCAA
5160338 TCATCTTCAA
Statistics
Matches: 67, Mismatches: 21, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
20 39 0.58
21 28 0.42
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGAGATTCTGA
Found at i:5160576 original size:20 final size:20
Alignment explanation
Indices: 5160551--5160618 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
5160541 CAACGGGGAA
5160551 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ****
5160571 ATCGCAATTCG-AAATAAAAA
1 ATCGCAACGCGAAAAT-GGCT
5160591 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
5160611 ATCGCAAC
1 ATCGCAAC
5160619 TAGAAAATCG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 4 0.12
20 26 0.76
21 4 0.12
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:5160631 original size:34 final size:34
Alignment explanation
Indices: 5160535--5160638 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
5160525 ATTCATTTGA
** *
5160535 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACTAGAAAATCGCAACGCGAAAATGG
*
5160569 CTATCGCAATTCGAAATAAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C----TAGAAAATCGCAACGCGAAAATGG
*
5160609 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACTAGAAAATCGCAACGCGAAA
5160639 TGAAAATCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 27 0.47
36 1 0.02
38 1 0.02
40 29 0.50
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.15
Consensus pattern (34 bp):
CTATCGCAACTAGAAAATCGCAACGCGAAAATGG
Found at i:5160686 original size:19 final size:19
Alignment explanation
Indices: 5160645--5160712 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
5160635 GAAATGAAAA
5160645 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
5160661 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5160678 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5160697 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
5160713 TCGTTACGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5162785 original size:19 final size:18
Alignment explanation
Indices: 5162741--5162860 Score: 94
Period size: 19 Copynumber: 6.9 Consensus size: 18
5162731 ACGAAACTTA
5162741 AAATCGCAACGCGAAAATGG
1 AAATCGCAACGCG-AAAT-G
** *
5162761 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
5162779 CAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
*
5162794 AAATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
5162812 AAAATCGCAACGCGAAATG
1 -AAATCGCAACGCGAAATG
*
5162831 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
5162845 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
5162861 CACAGATCGC
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.22
16 12 0.15
17 4 0.05
18 10 0.12
19 28 0.34
20 10 0.12
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:5162790 original size:39 final size:34
Alignment explanation
Indices: 5162740--5162828 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 34
5162730 CACGAAACTT
5162740 AAAATCGCAACGCGAAAATGGCTATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAAA-----ATCGCAATGCGAAATG
*
5162779 CAAATCGCAA--CGACAAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGA-AAAATCGCAATGCGAAATG
5162812 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
5162829 TGAAATCGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
33 25 0.56
34 2 0.04
35 3 0.07
37 3 0.07
38 3 0.07
39 9 0.20
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (34 bp):
AAAATCGCAACGCGAAAAATCGCAATGCGAAATG
Found at i:5162799 original size:14 final size:14
Alignment explanation
Indices: 5162780--5162855 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 14
5162770 TGCGAAATGC
5162780 AAATCGCAACGACA
1 AAATCGCAACGACA
*
5162794 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
*
5162813 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
5162829 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
5162845 AAATCGCAACG
1 AAATCGCAACG
5162856 CGAAACACAG
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
14 20 0.39
16 7 0.14
17 1 0.02
18 10 0.20
19 13 0.25
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:5162850 original size:51 final size:52
Alignment explanation
Indices: 5162740--5162860 Score: 181
Period size: 51 Copynumber: 2.3 Consensus size: 52
5162730 CACGAAACTT
*** *
5162740 AAAATCGCAACGCGAAAATGGCTATCGCAATGCGAAATGCAAATCGCAACGAC
1 AAAATCGCAACGCG-AAATGAAAATCGCAACGCGAAATGCAAATCGCAACGAC
*
5162793 AAAATCGCAATGCGAAATGAAAATCGCAACGCGAAATG-AAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGCAAATCGCAACGAC
5162844 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
5162861 CACAGATCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
51 29 0.47
52 20 0.32
53 13 0.21
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (52 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGCAAATCGCAACGAC
Found at i:5162910 original size:14 final size:14
Alignment explanation
Indices: 5162891--5162994 Score: 100
Period size: 14 Copynumber: 6.7 Consensus size: 14
5162881 TCATTTCACA
5162891 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
5162905 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
5162922 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
5162938 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
5162952 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
5162969 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
5162985 TTGCGATTTT
1 TTGCGATTTT
5162995 CATTTCGCAT
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
14 36 0.47
15 6 0.08
16 8 0.11
17 8 0.11
18 6 0.08
19 12 0.16
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:5162916 original size:33 final size:33
Alignment explanation
Indices: 5162872--5162947 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
5162862 ACAGATCGCA
*
5162872 TTGCGACTTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
*
5162905 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
5162938 TTGCGATTTT
1 TTGCGATTTT
5162948 GTCGTTGCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACATTGCGATTTTGTCG
Found at i:5162960 original size:47 final size:47
Alignment explanation
Indices: 5162891--5162994 Score: 208
Period size: 47 Copynumber: 2.2 Consensus size: 47
5162881 TCATTTCACA
5162891 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5162938 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5162985 TTGCGATTTT
1 TTGCGATTTT
5162995 CATTTCGCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (47 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:5162975 original size:33 final size:33
Alignment explanation
Indices: 5162938--5163007 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
5162928 GATTTTGTCG
5162938 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
5162971 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
5163004 TTGC
1 TTGC
5163008 AATAGCCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:5163017 original size:19 final size:20
Alignment explanation
Indices: 5162995--5163038 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5162985 TTGCGATTTT
5162995 CATTT-CGCATTGCAATAGC
1 CATTTCCGCATTGCAATAGC
* * *
5163014 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCAATAGC
5163034 CATTT
1 CATTT
5163039 TCATGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCAATAGC
Found at i:5163551 original size:18 final size:18
Alignment explanation
Indices: 5163525--5163569 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5163515 GTCGATCAGA
*
5163525 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
5163543 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
5163561 TGATGGCTC
1 TGATGGCTC
5163570 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:5164937 original size:20 final size:20
Alignment explanation
Indices: 5164889--5164947 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
5164879 AATAGTTTCT
** *
5164889 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
5164909 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
5164929 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
5164948 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:5165167 original size:22 final size:22
Alignment explanation
Indices: 5165141--5165184 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5165131 GATGGAGAAA
5165141 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
5165163 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
5165185 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:5165459 original size:20 final size:20
Alignment explanation
Indices: 5165353--5165484 Score: 115
Period size: 20 Copynumber: 6.5 Consensus size: 20
5165343 CGCTTTGAAA
*
5165353 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
5165374 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
5165394 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
5165414 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
5165435 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
5165455 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5165475 ATCGCATTGC
1 ATCGCATTGC
5165485 AATTTTCCCA
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 63 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5165490 original size:61 final size:61
Alignment explanation
Indices: 5165353--5165490 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
5165343 CGCTTTGAAA
* * * *
5165353 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
5165414 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
*
5165475 ATCGCATTGCAATTTT
1 ATCGCATTGCGATTTT
5165491 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:5165506 original size:61 final size:61
Alignment explanation
Indices: 5165373--5165508 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
5165363 GATTATGTAT
* * * * * * ** *
5165373 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAA
* * *
5165434 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTT-CCAA
5165496 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
5165509 TTACTTATTC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAA
Found at i:5181023 original size:21 final size:20
Alignment explanation
Indices: 5180971--5181037 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
5180961 TAATTCAAAG
*
5180971 TCCCTTAGAAAAAGAATCGA
1 TCCCTTACAAAAAGAATCGA
*
5180991 TCCCTTAAAAAAAGAATCGA
1 TCCCTTACAAAAAGAATCGA
**
5181011 TCCCTTTACAAAAAGGTTCGA
1 TCCC-TTACAAAAAGAATCGA
5181032 TCCCTT
1 TCCCTT
5181038 CACCAAAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 25 0.60
21 17 0.40
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (20 bp):
TCCCTTACAAAAAGAATCGA
Found at i:5181054 original size:21 final size:21
Alignment explanation
Indices: 5180971--5181055 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
5180961 TAATTCAAAG
* *
5180971 TCCCTT-AGAAAAAGAATCGA
1 TCCCTTCACAAAAAGGATCGA
* *
5180991 TCCCTT-AAAAAAAGAATCGA
1 TCCCTTCACAAAAAGGATCGA
* *
5181011 TCCCTTTACAAAAAGGTTCGA
1 TCCCTTCACAAAAAGGATCGA
* *
5181032 TCCCTTCACCAAAAGGATAGA
1 TCCCTTCACAAAAAGGATCGA
5181053 TCC
1 TCC
5181056 TTCGATGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 25 0.45
21 31 0.55
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (21 bp):
TCCCTTCACAAAAAGGATCGA
Found at i:5185936 original size:218 final size:218
Alignment explanation
Indices: 5185320--5185974 Score: 1294
Period size: 218 Copynumber: 3.0 Consensus size: 218
5185310 ATTCTTGTAT
5185320 AATGTTTATATTAATAATAGAAAAAGAGGCAAAAAGCCTTTGCTACTTAATGCATTAAACGAGAT
1 AATGTTTATATTAATAATAGAAAAAGAGGCAAAAAGCCTTTGCTACTTAATGCATTAAACGAGAT
5185385 GATTCACAGTGACCAACACTAACAGCTACTGAATTAACTACAGATACCATTAAAGAAACTAATCT
66 GATTCACAGTGACCAACACTAACAGCTACTGAATTAACTACAGATACCATTAAAGAAACTAATCT
5185450 TTGAATCGTGAAGTCGAAATGCTCATAAAACTTAATTGATTTGCCCTTTGATCTTCTGCATTCAA
131 TTGAATCGTGAAGTCGAAATGCTCATAAAACTTAATTGATTTGCCCTTTGATCTTCTGCATTCAA
5185515 TACGCTAAAAGTAAACGAAACTG
196 TACGCTAAAAGTAAACGAAACTG
5185538 AATGTTTATATTAATAATAG-AAAAGAGGCAAAAAGCCTTTGCTACTTAATGCATTAAACGAGAT
1 AATGTTTATATTAATAATAGAAAAAGAGGCAAAAAGCCTTTGCTACTTAATGCATTAAACGAGAT
5185602 GATTCACAGTGACCAACACTAACAGCTACTGAATTAACTACAGATACCATTAAAGAAACTAATCT
66 GATTCACAGTGACCAACACTAACAGCTACTGAATTAACTACAGATACCATTAAAGAAACTAATCT
5185667 TTGAATCGTGAAGTCGAAATGCTCATAAAACTTAATTGATTTGCCCTTTGATCTTCTGCATTCAA
131 TTGAATCGTGAAGTCGAAATGCTCATAAAACTTAATTGATTTGCCCTTTGATCTTCTGCATTCAA
5185732 TACGCTAAAAGTAAACGAAACTG
196 TACGCTAAAAGTAAACGAAACTG
5185755 AATGTTTATATTAATAATAGAAAAAGAGGCAAAAAGCCTTTGCTACTTAATGCATTAAACGAGAT
1 AATGTTTATATTAATAATAGAAAAAGAGGCAAAAAGCCTTTGCTACTTAATGCATTAAACGAGAT
*
5185820 GATTCACAGTGACCAACACTAACAGCTACTTAATTAACTACAGATACCATTAAAGAAACTAATCT
66 GATTCACAGTGACCAACACTAACAGCTACTGAATTAACTACAGATACCATTAAAGAAACTAATCT
5185885 TTGAATCGTGAAGTCGAAATGCTCATAAAACTTAATTGATTTGCCCTTTGATCTTCTGCATTCAA
131 TTGAATCGTGAAGTCGAAATGCTCATAAAACTTAATTGATTTGCCCTTTGATCTTCTGCATTCAA
5185950 TACGCTAAAAGTAAACGAAACTG
196 TACGCTAAAAGTAAACGAAACTG
5185973 AA
1 AA
5185975 GCATCGGATT
Statistics
Matches: 435, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
217 217 0.50
218 218 0.50
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (218 bp):
AATGTTTATATTAATAATAGAAAAAGAGGCAAAAAGCCTTTGCTACTTAATGCATTAAACGAGAT
GATTCACAGTGACCAACACTAACAGCTACTGAATTAACTACAGATACCATTAAAGAAACTAATCT
TTGAATCGTGAAGTCGAAATGCTCATAAAACTTAATTGATTTGCCCTTTGATCTTCTGCATTCAA
TACGCTAAAAGTAAACGAAACTG
Found at i:5189524 original size:24 final size:27
Alignment explanation
Indices: 5189497--5189560 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 27
5189487 TATTTTATGC
*
5189497 ATTTTCTTTTTTA-ATT-TA-ATATAT
1 ATTTTATTTTTTAGATTATATATATAT
5189521 ATTTTTATTTTTTAGATTATATATATAT
1 A-TTTTATTTTTTAGATTATATATATAT
5189549 ATATATTATTTT
1 AT-T-TTATTTT
5189561 CTTATTATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 1 0.03
25 11 0.33
26 3 0.09
27 3 0.09
28 8 0.24
29 7 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (27 bp):
ATTTTATTTTTTAGATTATATATATAT
Found at i:5189567 original size:28 final size:27
Alignment explanation
Indices: 5189503--5189685 Score: 75
Period size: 29 Copynumber: 6.7 Consensus size: 27
5189493 ATGCATTTTC
*
5189503 TTTTTTAATT-TA-ATATATATTTTTA
1 TTTTTTAATTATATATATATATTATTA
5189528 TTTTTTAGATTATATATATATATATATTA
1 TTTTTTA-ATTATATATATATAT-TATTA
5189557 TTTTCTT-ATTATCAGT-T-T-TATTA--A
1 TTTT-TTAATTAT-A-TATATATATTATTA
*
5189581 TTTATATATATATATATATATATATATTACTA
1 TTT-T-T-TA-AT-TATATATATATATTATTA
* * *
5189613 TTTTTTATTTTTTATTTATTATATATATATA
1 TTTTTTA-ATTATATATA-TATAT-TAT-TA
* *
5189644 TTATTT-ATTTTAT-TAT-TATTATTA
1 TTTTTTAATTATATATATATATTATTA
*
5189668 TTTGTTTTATT-TATATAT
1 TTT-TTTAATTATATATAT
5189686 TTTTTTTCTT
Statistics
Matches: 126, Mismatches: 9, Indels: 45
0.70 0.05 0.25
Matches are distributed among these distances:
24 8 0.06
25 18 0.14
26 15 0.12
27 7 0.06
28 26 0.21
29 29 0.23
30 11 0.09
31 8 0.06
32 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTTTAATTATATATATATATTATTA
Found at i:5189590 original size:2 final size:2
Alignment explanation
Indices: 5189583--5189607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5189573 TTTATTAATT
5189583 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5189608 TACTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5189635 original size:49 final size:50
Alignment explanation
Indices: 5189522--5189685 Score: 148
Period size: 49 Copynumber: 3.3 Consensus size: 50
5189512 TTAATATATA
* * *
5189522 TTTTTATTT-TT-TAGAT-TATATATATATATATATTATTTTCTTATTAT
1 TTTTTATTTATTATATATATATATATATATATATATTATATTATTATTAT
* *
5189569 CAGTTTTATTAATTTATATATATATATATATATATATATTACTATT-TT-TTAT
1 --TTTTTATTTA-TTATATATATATATATATATATATATTA-TATTATTATTAT
*
5189621 TTTTTATTTATTATATATATATAT-TAT-T-TATTTTATTATTATTATTATT
1 TTTTTATTTATTATATATATATATATATATATATATTA-TATTATTATTA-T
5189670 TGTTTTATTTA-TATAT
1 T-TTTTATTTATTATAT
5189686 TTTTTTTCTT
Statistics
Matches: 98, Mismatches: 8, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
46 10 0.10
47 3 0.03
48 6 0.06
49 28 0.29
50 17 0.17
51 2 0.02
52 8 0.08
53 21 0.21
54 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (50 bp):
TTTTTATTTATTATATATATATATATATATATATATTATATTATTATTAT
Found at i:5189636 original size:31 final size:30
Alignment explanation
Indices: 5189518--5189669 Score: 97
Period size: 31 Copynumber: 5.0 Consensus size: 30
5189508 TAATTTAATA
*
5189518 TATATT-TTTATTTT-TTA-GATTATATA-
1 TATATTATTTATTTTATTATTATTATATAT
* *
5189544 TATATATATATTATTTTCTTATTATCAGT-T-T
1 TATAT-TAT-TTATTTTATTATTATTA-TATAT
* *
5189575 TAT-TAATTTATATATATATATATATATATATAT
1 TATATTATTTAT-TTTAT-TAT-TAT-TATATAT
*
5189608 TACTATTTTTTATTTT-TTATTTATTATATAT
1 TA-TATTATTTATTTTATTA-TTATTATATAT
5189639 ATATATTATTTATTTTATTATTATTAT-TAT
1 -TATATTATTTATTTTATTATTATTATATAT
5189669 T
1 T
5189670 TGTTTTATTT
Statistics
Matches: 98, Mismatches: 10, Indels: 33
0.70 0.07 0.23
Matches are distributed among these distances:
26 5 0.05
27 1 0.01
28 5 0.05
29 13 0.13
30 10 0.10
31 37 0.38
32 13 0.13
33 5 0.05
34 3 0.03
35 6 0.06
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (30 bp):
TATATTATTTATTTTATTATTATTATATAT
Found at i:5189668 original size:21 final size:20
Alignment explanation
Indices: 5189611--5189729 Score: 90
Period size: 21 Copynumber: 6.0 Consensus size: 20
5189601 TATATATTAC
5189611 TATTTT-TTATT-TTTTATT
1 TATTTTATTATTATTTTATT
* *
5189629 TATTATA-TATATATATTATT
1 TATTTTATTAT-TATTTTATT
5189649 TATTTTATTATTATTATTATT
1 TATTTTATTATTATT-TTATT
*
5189670 TGTTTTATTTATATATTTT-TT
1 TATTTTA-TTAT-TATTTTATT
5189691 T-TCTTTATT-TT-TTTATATT
1 TAT-TTTATTATTATTT-TATT
*
5189710 TATTTTACTTACTATTTTAT
1 TATTTTA-TTATTATTTTAT
5189730 CTTTACTTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 25
0.72 0.05 0.22
Matches are distributed among these distances:
17 3 0.04
18 10 0.12
19 9 0.11
20 21 0.26
21 25 0.31
22 9 0.11
23 4 0.05
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (20 bp):
TATTTTATTATTATTTTATT
Found at i:5189686 original size:17 final size:16
Alignment explanation
Indices: 5189662--5189713 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 16
5189652 TTTATTATTA
5189662 TTATTATTTGTTTTAT
1 TTATTATTTGTTTTAT
* *
5189678 TTATATATTTTTTTTCT
1 TTAT-TATTTGTTTTAT
*
5189695 TTATT-TTT-TTATAT
1 TTATTATTTGTTTTAT
5189709 TTATT
1 TTATT
5189714 TTACTTACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 3 0.10
16 5 0.16
17 14 0.45
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTATTATTTGTTTTAT
Found at i:5189727 original size:23 final size:24
Alignment explanation
Indices: 5189675--5189743 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 24
5189665 TTATTTGTTT
* *
5189675 TATTTATATATTT-TTTTTCTTTAT
1 TATTT-TATATTTATTTTACTTTAC
*
5189699 TTTTTTATATTTATTTTAC-TTAC
1 TATTTTATATTTATTTTACTTTAC
* *
5189722 TATTTTATCTTTACTTT-CTTTA
1 TATTTTATATTTATTTTACTTTA
5189744 TCTTATCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 27 0.73
24 9 0.24
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTTATATTTATTTTACTTTAC
Found at i:5192841 original size:11 final size:11
Alignment explanation
Indices: 5192825--5192886 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
5192815 AGATTCAATC
5192825 AGAACAAAAAG
1 AGAACAAAAAG
5192836 AGAACAAAAAG
1 AGAACAAAAAG
5192847 AGAA-AAAAA-
1 AGAACAAAAAG
* *
5192856 AAAAGCAAAGAG
1 AGAA-CAAAAAG
* *
5192868 AAAATAAAAAG
1 AGAACAAAAAG
5192879 AGAA-AAAA
1 AGAACAAAA
5192887 CAAAGGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 3 0.07
10 9 0.21
11 27 0.63
12 4 0.09
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (11 bp):
AGAACAAAAAG
Found at i:5193028 original size:69 final size:69
Alignment explanation
Indices: 5192950--5193087 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
5192940 GATTCAAACT
* * * *
5192950 ATGAGATTGATCAAGCAAAATCATTTCTAAATCTCTGAACCACTTCACTCGAAGATCATAGATCA
1 ATGAGATTGATCAAGCAAAATCATTTCTAAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
5193015 TCAA
66 TCAA
* * *
5193019 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCAAAGATCATAGAGCA
1 ATGAGATTGATCAAGCAAAATCATTTCTAAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
5193084 TCAA
66 TCAA
5193088 GAGAGAGACA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCAAAATCATTTCTAAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
TCAA
Found at i:5194075 original size:32 final size:31
Alignment explanation
Indices: 5194002--5194087 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 31
5193992 GCATCTTTAA
*
5194002 AGATTCAACATCAAATGTTGGGGTATTTTTT
1 AGATTCAACATCAAATGTTGGGGAATTTTTT
* * *
5194033 ATATTTAACATTAAATGTTGGGGAATTTTTTT
1 AGATTCAACATCAAATGTTGGGGAA-TTTTTT
* *
5194065 AGATTCAACATCGAATATTGGGG
1 AGATTCAACATCAAATGTTGGGG
5194088 CATCTTTGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (31 bp):
AGATTCAACATCAAATGTTGGGGAATTTTTT
Found at i:5195258 original size:30 final size:30
Alignment explanation
Indices: 5195186--5195247 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
5195176 TCCGAATGAC
* *
5195186 CTATCCAGAAGCCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
*
5195216 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
5195246 CT
1 CT
5195248 GTCTATAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:5195520 original size:4 final size:4
Alignment explanation
Indices: 5195511--5195555 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
5195501 ATATAACCAT
5195511 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
5195556 GTCATCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:5196518 original size:64 final size:63
Alignment explanation
Indices: 5196442--5196602 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
5196432 TCTTTAGCAT
* * * * *
5196442 ATGCATCGATGCAGTACCCGTGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAATGGG
1 ATGCATCGATGCACT-CCTGTGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAATAGG
* * **
5196506 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAGG
1 ATGCATCGATGCACTCC-TGTGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAATAGG
*
5196570 -TGCATCGATGCACTTCCTGTGCATCGATACACA
1 ATGCATCGATGCAC-TCCTGTGCATCGATGCACA
5196603 CTGAACAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 28 0.34
64 55 0.66
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTGTGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAATAGG
Found at i:5197617 original size:106 final size:105
Alignment explanation
Indices: 5197493--5197821 Score: 442
Period size: 106 Copynumber: 3.1 Consensus size: 105
5197483 ATATCGTGCC
* * * *
5197493 ACTCGAGACAACAAAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTACC
1 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
5197558 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
5197599 ACTCGAGAAAATACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTATCAACAAACAATTTCCC
1 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
5197664 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * * * *
5197705 ACTTGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAATAAACGATTTCTT
1 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTC-C
* * * *
5197770 AGTTCCAGAGCCAATTTTAACTTCACAGCGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
5197811 ACTCGAAAAAA
1 ACTCGAGAAAA
5197822 ATACAACTTA
Statistics
Matches: 195, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
105 1 0.01
106 194 0.99
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (105 bp):
ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:5198259 original size:37 final size:37
Alignment explanation
Indices: 5198184--5198270 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
5198174 ATTGAAAACA
* * **
5198184 TTTCCCTTGAAA-TAAATTTTATCTCGCTTAGGGTAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTAGGACAG
*
5198220 TTTCCCTTGAAACAAAATTTTGTCTCCCTT-GAGACAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTAG-GACAG
*
5198257 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
5198271 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTAGGACAG
Found at i:5198271 original size:87 final size:87
Alignment explanation
Indices: 5198073--5198251 Score: 306
Period size: 87 Copynumber: 2.1 Consensus size: 87
5198063 GACAATTTCT
*
5198073 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
*
5198138 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
* *
5198160 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTT-AGGGTAGTTTC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGA-GATAGTTTC
5198224 CCTTGAAACAAAATTTTGTCTCC
65 CCTTGAAACAAAATTTTGTCTCC
5198247 CTTGA
1 CTTGA
5198252 GACAGTTTCT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
86 1 0.01
87 86 0.99
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCC
Found at i:5198281 original size:87 final size:87
Alignment explanation
Indices: 5198073--5198310 Score: 248
Period size: 87 Copynumber: 2.7 Consensus size: 87
5198063 GACAATTTCT
*** * *
5198073 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATAAACATTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
*
5198138 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACAAAATTTTGTCTCC
*** * * *
5198160 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTT-AGGGTAGTTTC
1 CTTGAAACATAAACATTGAAAACATAAACATTGAAATAAATTTTATCTCGATTGA-GATAGTTTC
5198224 CCTTGAAACAAAATTTTGTCTCC
65 CCTTGAAACAAAATTTTGTCTCC
* ** * * * **
5198247 CTTGAGACAGT-TTCTCTTG-AAACATAAACATTGAAATTAATTTTGTCTCTCTTGAGATAGTTT
1 CTTGAAACA-TAAAC-ATTGAAAACATAAACATTGAAATAAATTTTATCTCGATTGAGATAGTTT
5198310 C
64 C
5198311 TGTAACACCC
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
86 1 0.01
87 125 0.95
88 5 0.04
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATAAACATTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCC
Found at i:5198912 original size:23 final size:23
Alignment explanation
Indices: 5198886--5198937 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5198876 CACCACAGCT
*
5198886 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
*
5198909 CGTAGAATTGCACCGAAGTG-CC
1 CGTAGAAATGCACCGAAGTGCCC
5198931 CGTAGAA
1 CGTAGAA
5198938 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:5198935 original size:22 final size:23
Alignment explanation
Indices: 5198894--5198939 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5198884 CTCGTATAAA
5198894 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
5198917 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
5198939 T
1 T
5198940 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:5199200 original size:30 final size:31
Alignment explanation
Indices: 5199159--5199218 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
5199149 TAGACATAGT
*
5199159 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
5199189 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
5199219 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:5199275 original size:29 final size:29
Alignment explanation
Indices: 5199233--5199304 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5199223 TTTTCTGCAT
* **
5199233 ATTCATGTCATGTAATACATATGATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
5199262 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
5199291 ATTCATGTCATGTA
1 ATTCATGTCATGTA
5199305 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:5199737 original size:65 final size:66
Alignment explanation
Indices: 5199605--5199774 Score: 193
Period size: 66 Copynumber: 2.6 Consensus size: 66
5199595 TCTTTCTCAT
* * *
5199605 GGGGGAATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGG-TCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
5199669 GA
65 GA
* * * *
5199671 -GGGGTATCGGTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
5199734 GA
65 GA
* * *
5199736 GGGGGTATCGGTTCCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTCCCCCCTG--GGGGTACCGATTCCCCT
5199775 AACCCAGAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
64 1 0.01
65 28 0.31
66 44 0.49
67 16 0.18
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
A
Found at i:5205857 original size:22 final size:22
Alignment explanation
Indices: 5205816--5205883 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
5205806 CTCGTATAAA
5205816 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
5205839 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5205861 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5205883 T
1 T
5205884 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:5206218 original size:29 final size:29
Alignment explanation
Indices: 5206176--5206247 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5206166 TTTTCTGCAT
* **
5206176 ATTCATGTCATGTAATACATATGATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
5206205 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
5206234 ATTCATGTCATGTA
1 ATTCATGTCATGTA
5206248 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:5206586 original size:18 final size:19
Alignment explanation
Indices: 5206549--5206585 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5206539 CTTTTTCTCA
*
5206549 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
5206568 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
5206586 TCAAGCAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:5206718 original size:67 final size:66
Alignment explanation
Indices: 5206550--5206721 Score: 211
Period size: 68 Copynumber: 2.6 Consensus size: 66
5206540 TTTTTCTCAT
* * *
5206550 GGGGGAATCGGTTCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATG
1 GGGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
5206615 A
66 A
* * * * *
5206616 GGGGGTATCGGTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGT--TCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
5206680 TGA
64 TGA
* *
5206683 GGGGGTATCGGTTCCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCTG--GGGGTACCGATTCCCCT
5206722 AACCCAGAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
65 6 0.07
66 11 0.12
67 34 0.37
68 40 0.44
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
A
Found at i:5207599 original size:37 final size:35
Alignment explanation
Indices: 5207544--5207777 Score: 207
Period size: 36 Copynumber: 6.6 Consensus size: 35
5207534 AAAATGAGTT
*
5207544 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCCCTC
1 TTGAGACAGTTT-CCTTGAAAC-AAATTTTGTCCCTC
*
5207581 TTGAGACAGTTTCACTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTC-CTTGAAACAAATTTTGTCCCTC
*
5207617 TTGAGACAGTTTCACTTGAAACAAA----AT--CT-
1 TTGAGACAGTTTC-CTTGAAACAAATTTTGTCCCTC
*
5207646 TTGA-ATATCGTTTCCTTGAAACAAATTTTGTCTCC-C
1 TTGAGACA--GTTTCCTTGAAACAAATTTTGTC-CCTC
* * *
5207682 TTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTC
1 TTGAGACAGTTTCCTTGA-AAC-AAATTTTGTCCCTC
* * *
5207719 TTGAGACAGTTTCTTTTGAAACAAATTTTATCCCCC
1 TTGAGACAGTTTC-CTTGAAACAAATTTTGTCCCTC
*
5207755 TTGAGACATTTTCTCTTGAAACA
1 TTGAGACAGTTTC-CTTGAAACA
5207778 CAAAAAAAAC
Statistics
Matches: 166, Mismatches: 15, Indels: 33
0.78 0.07 0.15
Matches are distributed among these distances:
28 2 0.01
29 15 0.09
30 7 0.04
32 1 0.01
33 1 0.01
35 8 0.05
36 79 0.48
37 49 0.30
38 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (35 bp):
TTGAGACAGTTTCCTTGAAACAAATTTTGTCCCTC
Found at i:5207663 original size:102 final size:103
Alignment explanation
Indices: 5207552--5207743 Score: 284
Period size: 102 Copynumber: 1.9 Consensus size: 103
5207542 TTTTGAGACA
5207552 GTTTCCCTTGAAACAAAATCTTGTC-CCTCTTGAGACAGTTTCACTTGA-AAC-AAATTTTGTCT
1 GTTTCCCTTGAAAC-AAATCTTGTCTCC-CTTGAGACAGTTTC-CTTGAGAACTAAATTTTGTCT
5207614 CTCTTGAGACAGTTTCACTTGAAACAAAATCTTTGAATATC
63 CTCTTGAGACAGTTTCACTTGAAACAAAATCTTTGAATATC
* * *
5207655 GTTT-CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTC
1 GTTTCCCTTGAAACAAATCTTGTCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTTGTCTCTC
**
5207719 TTGAGACAGTTTCTTTTGAAACAAA
66 TTGAGACAGTTTCACTTGAAACAAA
5207744 TTTTATCCCC
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
100 3 0.04
101 26 0.32
102 48 0.59
103 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (103 bp):
GTTTCCCTTGAAACAAATCTTGTCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTTGTCTCTC
TTGAGACAGTTTCACTTGAAACAAAATCTTTGAATATC
Found at i:5207842 original size:39 final size:36
Alignment explanation
Indices: 5207763--5207856 Score: 104
Period size: 39 Copynumber: 2.6 Consensus size: 36
5207753 CCTTGAGACA
5207763 TTTTCTCTTG-AA-ACACAAAAAAAACCCTCGAAAT
1 TTTTCTCTTGAAACACACAAAAAAAACCCTCGAAAT
* *
5207797 TGTTTCTCTTGAAACACACACACAAAAAACCTTTGAAAAT
1 T-TTTCTCTTGAAACACACA-A-AAAAAACCCTCG-AAAT
*
5207837 TTTTCTCCTGAAACAC-CAAA
1 TTTTCTCTTGAAACACACAAA
5207857 CCCTCGAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
34 1 0.02
35 9 0.18
36 3 0.06
37 6 0.12
38 3 0.06
39 24 0.47
40 5 0.10
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (36 bp):
TTTTCTCTTGAAACACACAAAAAAAACCCTCGAAAT
Found at i:5209201 original size:132 final size:132
Alignment explanation
Indices: 5209015--5209370 Score: 581
Period size: 132 Copynumber: 2.7 Consensus size: 132
5209005 GATTATATCT
* * *
5209015 ATATATATTATTT-TTATAAATAAGATATTTATTTACTT-AGAAATATCAGAAAATGACTTCTAG
1 ATATATATGATTTATGA-AAATAAGATATTTATTTATTTAAG-AATATCAGAAAATGACTTCTAG
5209078 GTGCTTTAAGACAGCCCATTTCTTAATATATTAATAAAACATTTTTCTAAAAATAATTAAAATAA
64 GTGCTTTAAGACAGCCCATTTCTTAATATATTAATAAAACATTTTTCTAAAAATAATTAAAATAA
5209143 ATTA
129 ATTA
5209147 ATATATATGATTTATGAAAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGGT
1 ATATATATGATTTATGAAAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGGT
* *
5209212 GCTTTAAGACAGCCCGTTTCTTAATATATTAATAAAACATTTTTTTAAAAATAATTAAAATAAAT
66 GCTTTAAGACAGCCCATTTCTTAATATATTAATAAAACATTTTTCTAAAAATAATTAAAATAAAT
5209277 TA
131 TA
* * * *
5209279 ATATATATGATTTATGAAAATAAGATATTTATTTCTTTAATAATATCATAAAAGGACTTCTAGGT
1 ATATATATGATTTATGAAAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGGT
* *
5209344 TCTTTAAGACAACCCATTTCTTAATAT
66 GCTTTAAGACAGCCCATTTCTTAATAT
5209371 TAAAAAAATA
Statistics
Matches: 210, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
132 206 0.98
133 4 0.02
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (132 bp):
ATATATATGATTTATGAAAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGGT
GCTTTAAGACAGCCCATTTCTTAATATATTAATAAAACATTTTTCTAAAAATAATTAAAATAAAT
TA
Found at i:5209560 original size:21 final size:22
Alignment explanation
Indices: 5209517--5209561 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5209507 TAGTAATAAG
5209517 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
5209539 AACATATAA-AATTAAA-ATATA
1 AACA-ATAATAATTAAATATATA
5209560 AA
1 AA
5209562 TAAACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:5209802 original size:2 final size:2
Alignment explanation
Indices: 5209795--5209831 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5209785 TTTATACTAA
*
5209795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5209832 AGAAGTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5210916 original size:26 final size:26
Alignment explanation
Indices: 5210878--5210929 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5210868 AATTTTTTAT
*
5210878 TAATAATAATAATAGTATAAATAAAA
1 TAATAATAATAATAGTAAAAATAAAA
* *
5210904 TAATAATATTAATATTAAAAATAAAA
1 TAATAATAATAATAGTAAAAATAAAA
5210930 ATAAAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
TAATAATAATAATAGTAAAAATAAAA
Found at i:5210922 original size:20 final size:22
Alignment explanation
Indices: 5210875--5210932 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
5210865 AATAATTTTT
5210875 TATTAATAATAATAATAGTATAA
1 TATTAA-AATAATAATAGTATAA
5210898 -A-TAAAATAATAATA-T-TAA
1 TATTAAAATAATAATAGTATAA
*
5210916 TATTAAAAATAAAAATA
1 TATT-AAAATAATAATA
5210933 AAAACAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 3 0.10
19 2 0.06
20 11 0.35
21 14 0.45
22 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TATTAAAATAATAATAGTATAA
Found at i:5211328 original size:138 final size:122
Alignment explanation
Indices: 5211283--5211620 Score: 352
Period size: 121 Copynumber: 2.9 Consensus size: 122
5211273 TTTCAATATG
** * *
5211283 TGAT-GAATCAAATTAAGGTTGAACAAGTTCTTCTCATTGTGAACTTCTTCTCCTTCTTCAGATG
1 TGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATG
*
5211347 AGTTCTTCTCATTATG-A-TCACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTA
66 AGTTCTTCTCATTATGAACTC-CTTCTGGAAATGTTGATCTTGATCTATCTCCTTCTA
*
5211403 TGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
1 TGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATG
* *
5211468 AGTTCTTCTCATTATGAACTTCC-TCTGGAAAAGTTGATC-----C-A------TCGA
66 AGTTCTTCTCATTATGAAC-TCCTTCTGGAAATGTTGATCTTGATCTATCTCCTTCTA
* * * * *
5211513 GTGAT-GAATTTAAGCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 -TGATAGAA-TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCA
* *
5211577 GATGAGTTCTTCTTATTATGAACT-CTACCTGGAAATGTTGATCT
62 GATGAGTTCTTCTCATTATGAACTCCT-TCTGGAAATGTTGATCT
5211621 ATCAAGCGAT
Statistics
Matches: 190, Mismatches: 17, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
110 6 0.03
111 9 0.05
112 37 0.19
113 43 0.23
116 1 0.01
117 1 0.01
120 4 0.02
121 71 0.37
122 15 0.08
123 1 0.01
124 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (122 bp):
TGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATG
AGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATCTTGATCTATCTCCTTCTA
Found at i:5211610 original size:113 final size:112
Alignment explanation
Indices: 5211417--5211681 Score: 406
Period size: 113 Copynumber: 2.4 Consensus size: 112
5211407 AGAATCAAAC
*
5211417 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* * * *
5211482 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTTAAGCA
66 TGAACTTACTCTGGAAAAGTTGATCCATCAAGCGATGAATTCAAGCA
* * *
5211529 AAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
* *
5211594 ATGAACTCTAC-CTGGAAATGTTGATCTATCAAGCGATGAATTCAAGCA
65 ATGAACT-TACTCTGGAAAAGTTGATCCATCAAGCGATGAATTCAAGCA
*
5211642 AAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
5211682 AAATGAGTTT
Statistics
Matches: 138, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
112 38 0.28
113 98 0.71
114 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
TGAACTTACTCTGGAAAAGTTGATCCATCAAGCGATGAATTCAAGCA
Found at i:5211678 original size:17 final size:17
Alignment explanation
Indices: 5211656--5211707 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
5211646 GTTAAACAAA
5211656 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
5211673 TTCTTCTTCA-AATG-AG
1 TTCTTC-TCATTATGAAC
*
5211689 TTTTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
5211706 TT
1 TT
5211708 TACCTAGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
15 3 0.11
16 9 0.33
17 12 0.44
18 3 0.11
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:5212113 original size:22 final size:22
Alignment explanation
Indices: 5212088--5212145 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
5212078 AATAAAGCTT
*
5212088 TCATCTTTGAAGAGATAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
5212110 TCATCTTTAAAGAAAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
5212132 TCACCTTTGAAGAG
1 TCATCTTTGAAGAG
5212146 TGTAGATGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Done.