Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 104 of 318
Found at i:33759304 original size:21 final size:21
Alignment explanation
Indices: 33759278--33759327 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
33759268 ATTTTGATAT
* *
33759278 ACATGATTTGACATGATATGC
1 ACATGATATGACATGAGATGC
**
33759299 ACATGATATGTTATGAGATGC
1 ACATGATATGACATGAGATGC
33759320 ACATGATA
1 ACATGATA
33759328 CACTCATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (21 bp):
ACATGATATGACATGAGATGC
Found at i:33759429 original size:25 final size:24
Alignment explanation
Indices: 33759374--33759445 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
33759364 GGAGGAAGTG
*
33759374 CAAAAAGGGCTTTGCCCGAGTTTAC
1 CAAAAA-GGCTTTGCCCCAGTTTAC
* *
33759399 CGAAAAGGCCTTTGCCCCAGTTTAT
1 CAAAAAGG-CTTTGCCCCAGTTTAC
*
33759424 CAAAAAGAGCTTTACCCCAGTT
1 CAAAAAG-GCTTTGCCCCAGTT
33759446 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 2 0.05
25 37 0.93
26 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (24 bp):
CAAAAAGGCTTTGCCCCAGTTTAC
Found at i:33763946 original size:44 final size:44
Alignment explanation
Indices: 33763898--33763998 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
33763888 GTGGCCTTAC
* * * *
33763898 AGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTACAGTGG
1 AGCAGATTAAAGCAACAAATCCTATCTCCCTGAAATTACAGTGG
* * *
33763942 AGCAGATTGAAGCAACAAATCCTATCTCTCTGAAATTGCAGTGG
1 AGCAGATTAAAGCAACAAATCCTATCTCCCTGAAATTACAGTGG
33763986 AGCAGATTAAAGC
1 AGCAGATTAAAGC
33763999 GAGCTAATCC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (44 bp):
AGCAGATTAAAGCAACAAATCCTATCTCCCTGAAATTACAGTGG
Found at i:33764026 original size:45 final size:44
Alignment explanation
Indices: 33763898--33764028 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 44
33763888 GTGGCCTTAC
* * ** * *
33763898 AGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTACAGTGG
1 AGCAGATTAAAGCAACAAATCCAATCTCTCTGAAGTTGCAGTGG
* * *
33763942 AGCAGATTGAAGCAACAAATCCTATCTCTCTGAAATTGCAGTGG
1 AGCAGATTAAAGCAACAAATCCAATCTCTCTGAAGTTGCAGTGG
* *
33763986 AGCAGATTAAAGCGAGCTAATCCAATAC-CTCTGAAGTTGCAGT
1 AGCAGATTAAAGC-AACAAATCCAAT-CTCTCTGAAGTTGCAGT
33764029 AGGTCGGATT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 49 0.67
45 23 0.32
46 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (44 bp):
AGCAGATTAAAGCAACAAATCCAATCTCTCTGAAGTTGCAGTGG
Found at i:33764413 original size:13 final size:13
Alignment explanation
Indices: 33764395--33764422 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33764385 CTTTTTTTAC
33764395 AACTTTAAACCCA
1 AACTTTAAACCCA
33764408 AACTTTAAACCCA
1 AACTTTAAACCCA
33764421 AA
1 AA
33764423 AACAAATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (13 bp):
AACTTTAAACCCA
Found at i:33765881 original size:22 final size:22
Alignment explanation
Indices: 33765855--33765906 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
33765845 TACATACCAT
*
33765855 TTATTTTTGAATTTGTTTATTA
1 TTATTTTTGAATTTGCTTATTA
*
33765877 TTATTTTTTAATTTGCTTATTA
1 TTATTTTTGAATTTGCTTATTA
*
33765899 TTCTTTTT
1 TTATTTTT
33765907 CTTATTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.71
Consensus pattern (22 bp):
TTATTTTTGAATTTGCTTATTA
Found at i:33766947 original size:23 final size:23
Alignment explanation
Indices: 33766882--33766954 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
33766872 CTATCTCCTA
33766882 CCAAACACAACC-AATTTACCCT
1 CCAAACACAACCAAATTTACCCT
* **
33766904 CCAAACAGAACCAAACATACCCT
1 CCAAACACAACCAAATTTACCCT
* *
33766927 CCAAGCACAACCAAATTTACCCC
1 CCAAACACAACCAAATTTACCCT
33766950 CCAAA
1 CCAAA
33766955 TGCATCCACT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 11 0.27
23 30 0.73
ACGTcount: A:0.44, C:0.41, G:0.03, T:0.12
Consensus pattern (23 bp):
CCAAACACAACCAAATTTACCCT
Found at i:33769637 original size:77 final size:77
Alignment explanation
Indices: 33769510--33769664 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
33769500 TTTTGAAACC
33769510 AGCTTTATAATCCAATTCTGGAAATTTGTTCGGATTCTTTGCTACTTCATTTTGGATTTTAATCT
1 AGCTTTATAATCCAATTCTGGAAATTTGTTCGGATTCTTTGCTACTTCATTTTGGATTTTAATCT
33769575 TGATTTAATTAA
66 TGATTTAATTAA
33769587 AGCTTTATAATCCAATTCTGGAAATTTGTTCGGATTCTTTGCTACTTCATTTTGGATTTTAATCT
1 AGCTTTATAATCCAATTCTGGAAATTTGTTCGGATTCTTTGCTACTTCATTTTGGATTTTAATCT
33769652 TGATTTAATTAA
66 TGATTTAATTAA
33769664 A
1 A
33769665 TCTGTTTCAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (77 bp):
AGCTTTATAATCCAATTCTGGAAATTTGTTCGGATTCTTTGCTACTTCATTTTGGATTTTAATCT
TGATTTAATTAA
Found at i:33776451 original size:12 final size:12
Alignment explanation
Indices: 33776434--33776459 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33776424 CTTTTTAGCC
33776434 AAAAAAAAAAAG
1 AAAAAAAAAAAG
33776446 AAAAAAAAAAAG
1 AAAAAAAAAAAG
33776458 AA
1 AA
33776460 CAAATTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:33778525 original size:15 final size:16
Alignment explanation
Indices: 33778494--33778532 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
33778484 TGACTCAAAT
33778494 AAAATATTTTATGTTA
1 AAAATATTTTATGTTA
*
33778510 AAAATATTTT-TTTTA
1 AAAATATTTTATGTTA
*
33778525 AAATTATT
1 AAAATATT
33778533 GACTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
AAAATATTTTATGTTA
Found at i:33781900 original size:30 final size:30
Alignment explanation
Indices: 33781866--33781941 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
33781856 GTCACCACTA
33781866 ACCATTTTTCATTACAAACATAACAGAGCT
1 ACCATTTTTCATTACAAACATAACAGAGCT
* * ** *
33781896 ACCA-TTTTCTGTTACAAACGTAATGGAGGT
1 ACCATTTTTC-ATTACAAACATAACAGAGCT
33781926 ACCATTTTTCATTACA
1 ACCATTTTTCATTACA
33781942 GTTTCACTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 5 0.13
30 28 0.74
31 5 0.13
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (30 bp):
ACCATTTTTCATTACAAACATAACAGAGCT
Found at i:33789651 original size:22 final size:23
Alignment explanation
Indices: 33789621--33789669 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
33789611 AAAAAAGATT
33789621 TTTCGAAAAAATAAATAAAAAAC
1 TTTCGAAAAAATAAATAAAAAAC
*
33789644 TTTC-AAAAAATCAATAAAAAAC
1 TTTCGAAAAAATAAATAAAAAAC
33789666 TTTC
1 TTTC
33789670 CTTTCGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
TTTCGAAAAAATAAATAAAAAAC
Found at i:33793922 original size:3 final size:3
Alignment explanation
Indices: 33793914--33794034 Score: 81
Period size: 3 Copynumber: 40.7 Consensus size: 3
33793904 CATAAAAGAC
* * * *
33793914 AAT AAT AAT AAT AAT AAT -AT AAT ACCT -AT GAT ACT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* * * *
33793958 AAT AAT AAG AA- AATT AAT ATT AGT ATT AAT AAT AAT GGAA- AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT
* *
33794004 AAT AAC AAT AAT AAT -AT AGT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
33794035 AAGTGAAATT
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
2 9 0.10
3 79 0.85
4 3 0.03
5 2 0.02
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33794135 original size:24 final size:24
Alignment explanation
Indices: 33794082--33794138 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
33794072 TATGTTAATA
*
33794082 ACAATAATAATATATAAAGGATAGG
1 ACAATAATAATATATAAA-GAAAGG
*
33794107 A-AATAATAATATGATAAA-AAATG
1 ACAATAATAATAT-ATAAAGAAAGG
33794130 ACAATAATA
1 ACAATAATA
33794139 TGATAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 18 0.64
25 6 0.21
ACGTcount: A:0.61, C:0.04, G:0.11, T:0.25
Consensus pattern (24 bp):
ACAATAATAATATATAAAGAAAGG
Found at i:33794141 original size:11 final size:11
Alignment explanation
Indices: 33794109--33794147 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
33794099 AGGATAGGAA
33794109 ATAATAATATG
1 ATAATAATATG
*
33794120 ATAA-AAAATG
1 ATAATAATATG
*
33794130 ACAATAATATG
1 ATAATAATATG
33794141 ATAATAA
1 ATAATAA
33794148 AAATAATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (11 bp):
ATAATAATATG
Found at i:33795734 original size:10 final size:9
Alignment explanation
Indices: 33795705--33795762 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
33795695 TTTCTTTTTC
33795705 ATATTAT-T
1 ATATTATAT
*
33795713 ATTTTA-AT
1 ATATTATAT
33795721 ATATGTATAT
1 ATAT-TATAT
33795731 ATATTATAT
1 ATATTATAT
* *
33795740 TTGTGTATAT
1 ATAT-TATAT
33795750 -TATTATAT
1 ATATTATAT
33795758 ATATT
1 ATATT
33795763 TTTAATGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 14 0.35
9 15 0.38
10 11 0.28
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (9 bp):
ATATTATAT
Found at i:33795880 original size:25 final size:24
Alignment explanation
Indices: 33795814--33795880 Score: 57
Period size: 25 Copynumber: 2.7 Consensus size: 24
33795804 TTTATGTCGT
* *
33795814 TGTATGTATATTTTATTATTAGTTA
1 TGTATGTATTTTTTA-TACTAGTTA
*
33795839 TGTAT-T-TTTTATATATACTATTTCA
1 TGTATGTATTTT-T-TATACTAGTT-A
33795864 TGTATGTATTTTTTATA
1 TGTATGTATTTTTTATA
33795881 TGTTATCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
23 3 0.09
24 8 0.24
25 17 0.50
26 2 0.06
27 4 0.12
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (24 bp):
TGTATGTATTTTTTATACTAGTTA
Found at i:33817962 original size:22 final size:23
Alignment explanation
Indices: 33817937--33817982 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
33817927 CAACCAAACC
33817937 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
33817959 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
33817982 A
1 A
33817983 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:33817988 original size:23 final size:23
Alignment explanation
Indices: 33817944--33817988 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33817934 ACCAATTCAA
*
33817944 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
33817967 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
33817989 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:33830038 original size:17 final size:18
Alignment explanation
Indices: 33830013--33830050 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
33830003 AAAGTGGACA
33830013 AAAAAAAATATAA-TACC
1 AAAAAAAATATAATTACC
* *
33830030 AAAATAAATCTAATTACC
1 AAAAAAAATATAATTACC
33830048 AAA
1 AAA
33830051 TTCAAGGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAAAATATAATTACC
Found at i:33833687 original size:27 final size:27
Alignment explanation
Indices: 33833650--33833747 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
33833640 TACAGGTTGC
* * *
33833650 GCCTATGTCAGAGGCGCGACTAGTTGA
1 GCCTATCTCAGAGGCGCGACTAATCGA
* * *
33833677 GCCTTTTTCAGAGGCGCGACTAATCGT
1 GCCTATCTCAGAGGCGCGACTAATCGA
*
33833704 GCCTATCTCAGAGGCGCGACTAATCGT
1 GCCTATCTCAGAGGCGCGACTAATCGA
33833731 GCCTATCTCAGAGGCGC
1 GCCTATCTCAGAGGCGC
33833748 AAATGGTAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.20, C:0.28, G:0.29, T:0.23
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCGACTAATCGA
Found at i:33833761 original size:27 final size:27
Alignment explanation
Indices: 33833684--33833762 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
33833674 TGAGCCTTTT
* * * *
33833684 TCAGAGGCGCGACTAATCGTGCCTATC
1 TCAGAGGCGCAAATAATAGGGCCTATC
* * * *
33833711 TCAGAGGCGCGACTAATCGTGCCTATC
1 TCAGAGGCGCAAATAATAGGGCCTATC
**
33833738 TCAGAGGCGCAAATGGTAGGGCCTA
1 TCAGAGGCGCAAATAATAGGGCCTA
33833763 CAAGAACTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (27 bp):
TCAGAGGCGCAAATAATAGGGCCTATC
Found at i:33833762 original size:54 final size:54
Alignment explanation
Indices: 33833650--33833762 Score: 118
Period size: 54 Copynumber: 2.1 Consensus size: 54
33833640 TACAGGTTGC
* * * * * * * * *
33833650 GCCTATGTCAGAGGCGCGACTAGTTGAGCCTTTTTCAGAGGCGCGACTAATCGT
1 GCCTATCTCAGAGGCGCGACTAATCGAGCCTATCTCAGAGGCGCAAATAATAGG
* **
33833704 GCCTATCTCAGAGGCGCGACTAATCGTGCCTATCTCAGAGGCGCAAATGGTAGG
1 GCCTATCTCAGAGGCGCGACTAATCGAGCCTATCTCAGAGGCGCAAATAATAGG
33833758 GCCTA
1 GCCTA
33833763 CAAGAACTTC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (54 bp):
GCCTATCTCAGAGGCGCGACTAATCGAGCCTATCTCAGAGGCGCAAATAATAGG
Found at i:33838913 original size:3 final size:3
Alignment explanation
Indices: 33838905--33839111 Score: 201
Period size: 3 Copynumber: 69.3 Consensus size: 3
33838895 TTAATTAATT
* *
33838905 TTA TTA TTA TTA TTT TTA CTA TTA TT- TATA TTCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT-A TTA TTA TTA TTA
* * * *
33838951 TTA TTTA TTA TCA TCA TTA TTA TTA ATA TTA TTA TT- TT- TTA CTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
33838995 TTA TTA TTTA TTA TCA TTA TTA TTA TTA CTA CTA TTA CTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
33839041 TTA TTA TTA TTAA TTA TTA TCA TTA TTA TCA TTA TTA TTA CTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
33839087 TT- TTA TT- TT- TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
33839112 CATTTTTTAT
Statistics
Matches: 171, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
2 11 0.06
3 147 0.86
4 13 0.08
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:33838941 original size:25 final size:26
Alignment explanation
Indices: 33838904--33839088 Score: 138
Period size: 25 Copynumber: 7.3 Consensus size: 26
33838894 ATTAATTAAT
* *
33838904 TTTATTATT-ATTATTTTTACTATTA
1 TTTATTATTCATTATTATTAATATTA
*
33838929 TTTA-TATTCATTATTATTATTATTA
1 TTTATTATTCATTATTATTAATATTA
33838954 TTTATTATCATCATTATTATTAATATTA
1 TTTATTAT--TCATTATTATTAATATTA
* * *
33838982 -TTATTTTTTACTATTATT-AT-TTA
1 TTTATTATTCATTATTATTAATATTA
* * *
33839005 -TTATCATT-ATTATTATTACTACTA
1 TTTATTATTCATTATTATTAATATTA
* *
33839029 -TTACTATT-ATTATTATTATTATTA
1 TTTATTATTCATTATTATTAATATTA
* * *
33839053 ATTATTA-TCATTATTATCATTATTA
1 TTTATTATTCATTATTATTAATATTA
33839078 TTACTATTATT
1 TT--TATTATT
33839089 TTATTTTTTA
Statistics
Matches: 131, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
22 8 0.06
23 10 0.08
24 29 0.22
25 52 0.40
26 3 0.02
27 11 0.08
28 18 0.14
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATTATTCATTATTATTAATATTA
Found at i:33840848 original size:38 final size:38
Alignment explanation
Indices: 33840797--33840871 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
33840787 ACATGCCAGA
*
33840797 GTTGTAGGATTTCACTCGTATCAGCATAAGCCAAAATC
1 GTTGTAAGATTTCACTCGTATCAGCATAAGCCAAAATC
**
33840835 GTTGTAAGATTTCACTCGTATTGGCATAAGCCAAAAT
1 GTTGTAAGATTTCACTCGTATCAGCATAAGCCAAAAT
33840872 AATCTTCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (38 bp):
GTTGTAAGATTTCACTCGTATCAGCATAAGCCAAAATC
Found at i:33843250 original size:16 final size:16
Alignment explanation
Indices: 33843229--33843261 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33843219 TAAAAGATTA
33843229 AAAGTAA-ATAATACAC
1 AAAGTAATAT-ATACAC
33843245 AAAGTAATATATACAC
1 AAAGTAATATATACAC
33843261 A
1 A
33843262 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:33844516 original size:15 final size:16
Alignment explanation
Indices: 33844498--33844527 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33844488 GGTTTTGGGC
33844498 TGTTGGG-TTTTTAGA
1 TGTTGGGCTTTTTAGA
33844513 TGTTGGGCTTTTTAG
1 TGTTGGGCTTTTTAG
33844528 CCCGGGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.53
Consensus pattern (16 bp):
TGTTGGGCTTTTTAGA
Found at i:33845299 original size:205 final size:205
Alignment explanation
Indices: 33844899--33845854 Score: 1473
Period size: 205 Copynumber: 4.7 Consensus size: 205
33844889 AAATCTGCTT
* * * *
33844899 CTTCGATTTGTTCCCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * *
33844964 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * *
33845029 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTA-CTGCTCTCCATCGAAATG
131 GGATC-TACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATG
33845093 GAGATGCCAGA
195 GAGATGCCAGA
33845104 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * * * *
33845169 GCGGAAACCAAATTAGCTATGTCTTTGATTTGCTCTTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
** * * * * *
33845234 GGATCTACTTCAGTAAAAACATCTGAAGTTTGGATCTGCTATGTGTCTGCCCTCCGTCAAAATGG
131 GGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATGG
*
33845299 AGATGCCAGG
196 AGATGCCAGA
* *
33845309 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAATTCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * *
33845374 ACAAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTATAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * *
33845439 AGATCTACTTCAGTGAAATCATCTGAAGGCTAAATCTGCTATGTATCTGCTCTCCATCGAAATGG
131 GGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATGG
33845504 AGATGCCAGA
196 AGATGCCAGA
*
33845514 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
*
33845579 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAATGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * * *
33845644 AGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTACTATGCATCTGCTCTCCATCGAAATGG
131 GGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATGG
33845709 AGATGCCAGA
196 AGATGCCAGA
* * * * * *
33845719 CTTCGACTTGTTCTCTAAAAATACAGAGTTGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* *
33845784 GCGAAAATCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
33845849 GGATCT
131 GGATCT
33845855 GCTTTAGCCA
Statistics
Matches: 686, Mismatches: 64, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
204 33 0.05
205 653 0.95
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATGG
AGATGCCAGA
Found at i:33850352 original size:23 final size:24
Alignment explanation
Indices: 33850277--33850443 Score: 241
Period size: 24 Copynumber: 7.0 Consensus size: 24
33850267 GCTTTATCAT
*
33850277 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
33850302 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
33850326 ATAACTGGGGCATAAGTCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
33850349 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
33850372 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
33850396 ATAACTGGGGCGTAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
33850421 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
33850444 GCACTTCCTC
Statistics
Matches: 130, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
23 45 0.35
24 51 0.39
25 34 0.26
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:33850352 original size:47 final size:47
Alignment explanation
Indices: 33850298--33850442 Score: 229
Period size: 47 Copynumber: 3.1 Consensus size: 47
33850288 CCTAGCCTCT
* *
33850298 TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGTCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
33850345 TTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
* *
33850391 TTTTGATAACTGGGGCGTAAGCCCTTTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
33850440 TTT
1 TTT
33850443 TGCACTTCCT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
46 22 0.24
47 43 0.47
48 3 0.03
49 23 0.25
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:33850518 original size:20 final size:20
Alignment explanation
Indices: 33850493--33850559 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
33850483 TTATGAATGC
33850493 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
33850513 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* **
33850533 GTCATGTGCATATTGTACAT
1 ATCATGTGCATATCATACAT
*
33850553 ACCATGT
1 ATCATGT
33850560 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:33850524 original size:11 final size:11
Alignment explanation
Indices: 33850493--33850545 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
33850483 TTATGAATGC
33850493 ATCATGTGCAT
1 ATCATGTGCAT
*
33850504 ATCA--TACAT
1 ATCATGTGCAT
33850513 ATCATGTGCAT
1 ATCATGTGCAT
*
33850524 ATCA--TACAT
1 ATCATGTGCAT
*
33850533 GTCATGTGCAT
1 ATCATGTGCAT
33850544 AT
1 AT
33850546 TGTACATACC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.47
11 17 0.53
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:33850642 original size:25 final size:25
Alignment explanation
Indices: 33850596--33850643 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
33850586 ATATTTAAGC
* * * *
33850596 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
33850621 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
33850644 CATTTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:33858471 original size:23 final size:24
Alignment explanation
Indices: 33858396--33858562 Score: 223
Period size: 24 Copynumber: 7.0 Consensus size: 24
33858386 GCTTTATCAT
*
33858396 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
33858421 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
33858445 ATAACTGGGGCATAAGTCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
33858468 ATAACTGGGGCATAAG-TCTTTTC
1 ATAACTGGGGCATAAGCCCTTTTA
*
33858491 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
33858515 ATAACTGGGGCGTAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
33858540 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
33858563 GCACTTCCTC
Statistics
Matches: 127, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
22 1 0.01
23 39 0.31
24 53 0.42
25 34 0.27
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:33858497 original size:70 final size:71
Alignment explanation
Indices: 33858414--33858555 Score: 223
Period size: 70 Copynumber: 2.0 Consensus size: 71
33858404 AGGCCTAGCC
*
33858414 TCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGTCC-TTTAATAACTGGGG
1 TCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGG
33858478 CATAAG
66 CATAAG
* * * *
33858484 TCTTTTCATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCGTAAGCCCTTTTTAATAACTGGG
1 TCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGG
33858549 GCATAAG
65 GCATAAG
33858556 CCCTTTTGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 45 0.69
72 20 0.31
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (71 bp):
TCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGG
CATAAG
Found at i:33858637 original size:20 final size:20
Alignment explanation
Indices: 33858612--33858678 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
33858602 TTATGAATGC
33858612 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
33858632 ATCATGTCCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
33858652 GTCATGTGCATATCGTACAT
1 ATCATGTGCATATCATACAT
*
33858672 ACCATGT
1 ATCATGT
33858679 TTGTCAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:33858761 original size:25 final size:25
Alignment explanation
Indices: 33858715--33858762 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
33858705 ATATTTAAGC
* * * *
33858715 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
33858740 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
33858763 CATTTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:33865299 original size:16 final size:16
Alignment explanation
Indices: 33865278--33865310 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33865268 TAAAAGATTA
33865278 AAAGTAA-ATAATACAC
1 AAAGTAATAT-ATACAC
33865294 AAAGTAATATATACAC
1 AAAGTAATATATACAC
33865310 A
1 A
33865311 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:33870305 original size:45 final size:43
Alignment explanation
Indices: 33870208--33870324 Score: 119
Period size: 45 Copynumber: 2.7 Consensus size: 43
33870198 ATCTCATCCC
* * *
33870208 CCTGAAGTAGTAGTGGA-ACAGATTGAAGTTGTAGATCTTATCT
1 CCTGAAGTTGTAGTGGAGA-AGATTGAAGTGGCAGATCTTATCT
* * *
33870251 CCTTAAAGTTGTAGTGGAGTAGATCGAAGATGGCAGATCTTATCTT
1 CC-TGAAGTTGTAGTGGAGAAGATTGAAG-TGGCAGATCTTATC-T
* *
33870297 CCTGAAGTTGCAGTAGAGAAGATTGAAG
1 CCTGAAGTTGTAGTGGAGAAGATTGAAG
33870325 CCACTAGCCT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 2 0.03
44 21 0.36
45 33 0.56
46 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (43 bp):
CCTGAAGTTGTAGTGGAGAAGATTGAAGTGGCAGATCTTATCT
Found at i:33870409 original size:89 final size:89
Alignment explanation
Indices: 33870244--33870414 Score: 197
Period size: 89 Copynumber: 1.9 Consensus size: 89
33870234 AGTTGTAGAT
* * * ** *
33870244 CTTATCTCCTTAAAGTTGTAGTGGAGTAGATCGAAGATGGCAGATCTTATCTTCCTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGATCAAAGACAGCAGATCTTATCTTCCCGAAGTTGCA
*
33870309 GTAGAGAAGATTGAAGCCACTAGC
66 GTAGAGAAGATTAAAGCCACTAGC
*
33870333 CTTATCTCCCTAAAGTTGTAGTGGAGCAGA-CTAAAGACAGC-GAATCTTAT-TTCCACGACGTT
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGATC-AAAGACAGCAG-ATCTTATCTTCC-CGAAGTT
*
33870395 GCAGTGGA-ATAGATTAAAGC
63 GCAGTAGAGA-AGATTAAAGC
33870415 TATAAATTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
88 7 0.10
89 62 0.90
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (89 bp):
CTTATCTCCCTAAAGTTGTAGTGGAGCAGATCAAAGACAGCAGATCTTATCTTCCCGAAGTTGCA
GTAGAGAAGATTAAAGCCACTAGC
Found at i:33870501 original size:44 final size:44
Alignment explanation
Indices: 33870432--33870789 Score: 158
Period size: 44 Copynumber: 7.6 Consensus size: 44
33870422 TATGGCGAAT
* *
33870432 CTTATCTTCCTGAAGTTACAGTGGAGCAAATTGAAGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGC
* * * * * * **
33870476 CTTATCTCCCTGAAGTTGTAATGGAGCAGACTGAAGACAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCA-CCAGC
* * * * **
33870521 CTTATTTCCCTGATGTTGCAGTGGAACAAATTGAAGTTACAAATTATGGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAG---C-CACCA--GC
* * * *
33870571 GAATCTTATCTTCCTGAAGTTGCATTGGAACAGATTGAAGCCACCAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGC
* * * * * **
33870619 CTTATCTCCCTGAAGTTGTAGTGGAGCAAACTAAAGACAACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAG-CCACCAGC
* * * * * ** *
33870664 CTTATTTCTCTGATGTTGCAGTGGAACAGATTGAAGCTACAAATTATGATAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGC--C--ACCA-G-----C
* ** *
33870718 TTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGC
*
33870762 CTTATCTCCCTGAAGTTGCAGCGGAGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA
33870790 GACTGAAAAC
Statistics
Matches: 226, Mismatches: 66, Indels: 44
0.67 0.20 0.13
Matches are distributed among these distances:
44 86 0.38
45 63 0.28
48 5 0.02
49 2 0.01
50 4 0.02
51 1 0.00
52 1 0.00
54 64 0.28
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGC
Found at i:33870539 original size:143 final size:143
Alignment explanation
Indices: 33870287--33870981 Score: 942
Period size: 143 Copynumber: 4.9 Consensus size: 143
33870277 AAGATGGCAG
* * * *
33870287 ATCTTATCTTCCTGAAGTTGCAGTAGAGAAGATTGAAGCCACTAGCCTTATCTCCCTAAAGTTGT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * * *
33870352 AGTGGAGCAGACTAAAGACAGCGAATCTTATTTCCAC-GACGTTGCAGTGGAATAGATTAAAGCT
66 AGTGGAGCAGACTGAAGACAGCAAATCTTATTTCC-CTGATGTTGCAGTGGAACAGATTGAAGCT
*
33870416 ATAAATTATGGCGA
130 ACAAATTATGGCGA
* *
33870430 ATCTTATCTTCCTGAAGTTACAGTGGAGCAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * *
33870495 AATGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGATGTTGCAGTGGAACAAATTGAAGTTA
66 AGTGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
33870560 CAAATTATGGCGA
131 CAAATTATGGCGA
* *
33870573 ATCTTATCTTCCTGAAGTTGCATTGGAACAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * *
33870638 AGTGGAGCAAACTAAAGACAACAAATCTTATTTCTCTGATGTTGCAGTGGAACAGATTGAAGCTA
66 AGTGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
***
33870703 CAAATTATGATAA
131 CAAATTATGGCGA
* * *
33870716 ATTTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * * * *
33870781 AGCGGAGCAGACTGAAAACATCAAATCTTATTTCCTTGATGATGCAATGGAACAGATTGAAGCTA
66 AGTGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
*
33870846 AAAATTATGGCGA
131 CAAATTATGGCGA
* ** * *
33870859 ATCTTATATTCCTGAAGTTGCAGTAAAGCAGATTGAAGCCACCAGCCTTATCTCTCTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * * * * * * *
33870924 AGCGTAGCAGACTGAAGATAGTAGATTTTATTTCCTTGAAGTTGCAGTGGAGCAGATT
66 AGTGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATT
33870982 AAAACTATGA
Statistics
Matches: 487, Mismatches: 64, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
142 1 0.00
143 486 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (143 bp):
ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
AGTGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
CAAATTATGGCGA
Found at i:33871400 original size:8 final size:8
Alignment explanation
Indices: 33871387--33871415 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
33871377 TTATGTTTAG
33871387 TATATTAT
1 TATATTAT
33871395 TATATTAT
1 TATATTAT
33871403 TATATTAT
1 TATATTAT
33871411 TATAT
1 TATAT
33871416 AATAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:33872544 original size:15 final size:15
Alignment explanation
Indices: 33872518--33872574 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
33872508 CATATATATT
33872518 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
33872532 ATATAATTTCAATCA
1 ATATAATTTCAATCA
*
33872547 AAATAATTTCAATCA
1 ATATAATTTCAATCA
*
33872562 ATATAAATTCAAT
1 ATATAATTTCAAT
33872575 AAATTCATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 6 0.15
15 33 0.85
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:33873802 original size:5 final size:5
Alignment explanation
Indices: 33873794--33873830 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
33873784 TCTTTAGTTT
33873794 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
33873831 TAAAACATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:33874401 original size:44 final size:43
Alignment explanation
Indices: 33874281--33874401 Score: 125
Period size: 44 Copynumber: 2.7 Consensus size: 43
33874271 TCATAGTTTT
* ** *
33874281 AATCTGCTCCACTGCAACTTCAAGGAAATAAAATCTGCTATCTTC
1 AATCTGCTCTACTGCAACTTC-AGGAAAT-AAGGCTGCTAGCTTC
* * * * *
33874326 AGTCTGCTCTGCTGCAACTTCAGAGAGATAAGGCTGGTGGCTTC
1 AATCTGCTCTACTGCAACTTCAG-GAAATAAGGCTGCTAGCTTC
33874370 AATCTGCTCTACTGCAACTTCAGGAATATAAG
1 AATCTGCTCTACTGCAACTTCAGGAA-ATAAG
33874402 ATTCGCCATA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
43 2 0.03
44 38 0.61
45 22 0.35
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
AATCTGCTCTACTGCAACTTCAGGAAATAAGGCTGCTAGCTTC
Found at i:33874470 original size:143 final size:143
Alignment explanation
Indices: 33874281--33874975 Score: 917
Period size: 143 Copynumber: 4.9 Consensus size: 143
33874271 TCATAGTTTT
* * * * * * **
33874281 AATCTGCTCCACTGCAACTTCAAGGAAATAAAATCTGCTATCTTCAGTCTGCTCTGCTGCAACTT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGCTGTTTTCAGTCTGCTCCACTGCAACTT
* *
33874346 CAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCTACTGCAACTTCAGGAATATAAGATTCGCCAT
66 CAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
*
33874411 AATTTTTAGCTTC
131 AATTTGTAGCTTC
* * * * *
33874424 AATCTGTTCCATTGCATCATCAAGGAAATAAAATTTGATGTTTTCAGTCTGCTCCGCTGCAACTT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGCTGTTTTCAGTCTGCTCCACTGCAACTT
* * * *
33874489 CAGAGAGATAAGGGTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAAATTCGTCAT
66 CAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
33874554 AATTTGTAGCTTC
131 AATTTGTAGCTTC
* * * * * *
33874567 AATCTGTTCCACTGCAACATCAGGGAAATAAGATTTGTTGTCTTT-AGTTTACTCCATTACAACT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGCTGT-TTTCAGTCTGCTCCACTGCAACT
* * * *
33874631 TCAGGGAGATAAGGCTAGTGGCTTCAATCTGTTCCAATGCAACTTCAGGAAGATAAGATTCGCCA
65 TCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCA
* *
33874696 TAATTTGTAACTTT
130 TAATTTGTAGCTTC
* * * *
33874710 AATTTGTTCCACTGCAACATCAGGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCATTGCAACTT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGCTGTTTTCAGTCTGCTCCACTGCAACTT
* *
33874775 CAGAGAGATAAGGCTGGTGGCTTCAATTTGCTCGACTGCAACTTCAGGAAGATAAGATTCGCCAT
66 CAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
* *
33874840 AATTTATAGCTTT
131 AATTTGTAGCTTC
* ** * *
33874853 AATCTGTTCCACTGCAACGTCGTGGAAATAAGATTCGCTGTCTTT-AGTCTGCTCCACTACAACT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGCTGT-TTTCAGTCTGCTCCACTGCAACT
* * * *
33874917 TTAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCTACTGCAACTTCAGGAAGATAAGAT
65 TCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT
33874976 CTGCCATCTT
Statistics
Matches: 486, Mismatches: 63, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
142 2 0.00
143 479 0.99
144 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (143 bp):
AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGCTGTTTTCAGTCTGCTCCACTGCAACTT
CAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
AATTTGTAGCTTC
Found at i:33874929 original size:45 final size:45
Alignment explanation
Indices: 33874849--33875020 Score: 118
Period size: 45 Copynumber: 3.8 Consensus size: 45
33874839 TAATTTATAG
* * * * *
33874849 CTTTAATCTGTTCCACTGCAAC-GTCGTGGAAATAAGATTCGCTGT
1 CTTTAGTCTGCTCCACTGCAACTTTAG-GGAGATAAGATTCGCTGT
* ** * *
33874894 CTTTAGTCTGCTCCACTACAACTTTAGGGAGATAAGGCTAG-TGG
1 CTTTAGTCTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTGT
* * * * * **
33874938 CTTCAATCTGCTCTACTGCAACTTCAGGAAGATAAGA-TCTGCCAT
1 CTTTAGTCTGCTCCACTGCAACTTTAGGGAGATAAGATTC-GCTGT
* *
33874983 CTTT-GATCTACTCCACTGCAACTTTAAGGAGATAAGAT
1 CTTTAG-TCTGCTCCACTGCAACTTTAGGGAGATAAGAT
33875021 CTACAACTTC
Statistics
Matches: 94, Mismatches: 28, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
43 1 0.01
44 33 0.35
45 58 0.62
46 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
CTTTAGTCTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTGT
Found at i:33880416 original size:16 final size:16
Alignment explanation
Indices: 33880395--33880427 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33880385 AAGCTTTTCC
33880395 TGTGTA-TATATTACTT
1 TGTGTATTAT-TTACTT
33880411 TGTGTATTATTTACTT
1 TGTGTATTATTTACTT
33880427 T
1 T
33880428 TAATCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.61
Consensus pattern (16 bp):
TGTGTATTATTTACTT
Found at i:33882370 original size:21 final size:21
Alignment explanation
Indices: 33882344--33882384 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
33882334 CCTATTTGCT
33882344 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
*
33882365 AGGCACCTCGTGTGTTGTAT
1 AGGCACCTCGTGTGTCGTAT
33882385 ACTGATCAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:33883819 original size:27 final size:27
Alignment explanation
Indices: 33883786--33883845 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
33883776 AAAAACCATC
*
33883786 AACCCAAACTAAACCCAATCCCAACCA
1 AACCCAAACTAAACCCAATCCCAAACA
33883813 AACCCAAACTAAACCCAATCCCAAACA
1 AACCCAAACTAAACCCAATCCCAAACA
33883840 AACCCA
1 AACCCA
33883846 CTTAACCCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (27 bp):
AACCCAAACTAAACCCAATCCCAAACA
Found at i:33883844 original size:16 final size:17
Alignment explanation
Indices: 33883810--33883845 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
33883800 CCAATCCCAA
33883810 CCAAACCCAAACTAAAC
1 CCAAACCCAAACTAAAC
*
33883827 CCAATCCCAAAC-AAAC
1 CCAAACCCAAACTAAAC
33883843 CCA
1 CCA
33883846 CTTAACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (17 bp):
CCAAACCCAAACTAAAC
Found at i:33884402 original size:13 final size:13
Alignment explanation
Indices: 33884386--33884411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33884376 TATATCTTTG
33884386 CTCATATTACTGT
1 CTCATATTACTGT
33884399 CTCATATTACTGT
1 CTCATATTACTGT
33884412 TGTTAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
CTCATATTACTGT
Found at i:33894019 original size:10 final size:10
Alignment explanation
Indices: 33894000--33894038 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
33893990 TTAAATTCTA
33894000 AAAGATAAAT
1 AAAGATAAAT
33894010 ACAA-ATAAAT
1 A-AAGATAAAT
33894020 AAAGATAAAT
1 AAAGATAAAT
*
33894030 GAAGATAAA
1 AAAGATAAA
33894039 AACTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:33896431 original size:23 final size:23
Alignment explanation
Indices: 33896403--33896451 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33896393 TCAAATAGAG
*
33896403 TAAAAAGTGAAATGAAAATGAAAT
1 TAAAATGTGAAATG-AAATGAAAT
* *
33896427 TAAAATTTGGAATGAAATGAAAT
1 TAAAATGTGAAATGAAATGAAAT
33896450 TA
1 TA
33896452 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (23 bp):
TAAAATGTGAAATGAAATGAAAT
Found at i:33896540 original size:22 final size:21
Alignment explanation
Indices: 33896515--33896570 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
33896505 GAAATGAAGT
33896515 TGAAATTAAATTAAAATTGGAA
1 TGAAATTAAATTAAAATT-GAA
* *
33896537 TGAAATGAAATTCAAATTGAA
1 TGAAATTAAATTAAAATTGAA
33896558 TAGAAATTGAAAT
1 T-GAAATT-AAAT
33896571 GAATATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (21 bp):
TGAAATTAAATTAAAATTGAA
Found at i:33896542 original size:33 final size:33
Alignment explanation
Indices: 33896504--33896573 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
33896494 ACTTTTTAAT
* * *
33896504 TGAAATGAAGTTGAAATTAAATTA-AAATTGGAA
1 TGAAATGAAATTCAAATTAAA-TAGAAATTGAAA
*
33896537 TGAAATGAAATTCAAATTGAATAGAAATTGAAA
1 TGAAATGAAATTCAAATTAAATAGAAATTGAAA
33896570 TGAA
1 TGAA
33896574 TATATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.53, C:0.01, G:0.17, T:0.29
Consensus pattern (33 bp):
TGAAATGAAATTCAAATTAAATAGAAATTGAAA
Found at i:33896557 original size:17 final size:17
Alignment explanation
Indices: 33896501--33896570 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
33896491 TGAACTTTTT
*
33896501 AATTGAAATGAAGTTGA
1 AATTGAAATGAAATTGA
* *
33896518 AATT-AAATTAAAATTGG
1 AATTGAAA-TGAAATTGA
*
33896535 AA-TGAAATGAAATTCA
1 AATTGAAATGAAATTGA
33896551 AATTG-AATAGAAATTGA
1 AATTGAAAT-GAAATTGA
33896568 AAT
1 AAT
33896571 GAATATATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
16 15 0.36
17 27 0.64
ACGTcount: A:0.53, C:0.01, G:0.16, T:0.30
Consensus pattern (17 bp):
AATTGAAATGAAATTGA
Found at i:33896822 original size:28 final size:28
Alignment explanation
Indices: 33896763--33896821 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
33896753 AAAAAAGGTG
* *
33896763 AAATGAATATGGAATGAAATGAAATTTA
1 AAATGAATATGGAATGAAATAAAATATA
33896791 AAATGAATAT-GAGATGAAATTAAAATATA
1 AAATGAATATGGA-ATGAAA-TAAAATATA
33896820 AA
1 AA
33896822 TTTAAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 16 0.59
29 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (28 bp):
AAATGAATATGGAATGAAATAAAATATA
Found at i:33896868 original size:21 final size:21
Alignment explanation
Indices: 33896812--33896981 Score: 88
Period size: 21 Copynumber: 7.9 Consensus size: 21
33896802 AGATGAAATT
* *
33896812 AAAATATAAATTTAAATGAGA
1 AAAAAATAAATTGAAATGAGA
*
33896833 AAAAAATGAA-T---ATGA-A
1 AAAAAATAAATTGAAATGAGA
*
33896849 AAAAGAATAAATTGGAATGAGA
1 AAAA-AATAAATTGAAATGAGA
*
33896871 GAAAAATAAATTGAAATGAGATTA
1 AAAAAATAAATTGAAATGAG---A
* *
33896895 AAATGTGAAATGAATATGAAATTA-A
1 AAA----AAATAAAT-TGAAATGAGA
33896920 ATTAAAATATAAATTGAAATGA-A
1 A--AAAA-ATAAATTGAAATGAGA
33896943 AAAATAATAAATTGAAAT--GA
1 AAAA-AATAAATTGAAATGAGA
*
33896963 AAAAAATAAATTTAAATGA
1 AAAAAATAAATTGAAATGA
33896982 AATGAAATGA
Statistics
Matches: 117, Mismatches: 11, Indels: 42
0.69 0.06 0.25
Matches are distributed among these distances:
16 5 0.04
17 9 0.08
18 1 0.01
19 12 0.10
20 6 0.05
21 42 0.36
22 5 0.04
23 11 0.09
24 8 0.07
25 2 0.02
27 2 0.02
28 7 0.06
29 7 0.06
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (21 bp):
AAAAAATAAATTGAAATGAGA
Found at i:33896915 original size:29 final size:28
Alignment explanation
Indices: 33896874--33896943 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
33896864 AATGAGAGAA
* * *
33896874 AAATAAAT-TGAAATGAGATTAAAATGT
1 AAATGAATATGAAATGAAATTAAAATAT
*
33896901 GAAATGAATATGAAATTAAATTAAAATAT
1 -AAATGAATATGAAATGAAATTAAAATAT
33896930 AAATTGAA-ATGAAA
1 AAA-TGAATATGAAA
33896944 AAATAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 16 0.44
29 20 0.56
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.29
Consensus pattern (28 bp):
AAATGAATATGAAATGAAATTAAAATAT
Found at i:33896917 original size:94 final size:91
Alignment explanation
Indices: 33896814--33896981 Score: 225
Period size: 94 Copynumber: 1.8 Consensus size: 91
33896804 ATGAAATTAA
*
33896814 AATATAAATTTAAATGAGAAA-A-AAA-TGAATATGAAAAAAGAATAAATTGGAATGAGAGAAAA
1 AATATAAA-TTAAATGA-AAATATAAATTGAA-ATGAAAAAAGAATAAATTGAAATGA-A-AAAA
33896876 ATAAATTGAAATGAGATTAAAATGTGAAATG
61 ATAAATTGAAATGAGATTAAAATGTGAAATG
* *
33896907 AATATGAAATTAAATTAAAATATAAATTGAAATGAAAAAATAATAAATTGAAATGAAAAAAATAA
1 AATAT-AAATTAAATGAAAATATAAATTGAAATGAAAAAAGAATAAATTGAAATGAAAAAAATAA
*
33896972 ATTTAAATGA
65 ATTGAAATGA
33896982 AATGAAATGA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
92 20 0.30
93 14 0.21
94 29 0.43
95 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (91 bp):
AATATAAATTAAATGAAAATATAAATTGAAATGAAAAAAGAATAAATTGAAATGAAAAAAATAAA
TTGAAATGAGATTAAAATGTGAAATG
Found at i:33896928 original size:18 final size:18
Alignment explanation
Indices: 33896805--33897063 Score: 113
Period size: 18 Copynumber: 13.6 Consensus size: 18
33896795 GAATATGAGA
*
33896805 TGAAATTAAAATATAAAT
1 TGAAATGAAAATATAAAT
*
33896823 TTAAATGAGAAA-A-AAA-
1 TGAAATGA-AAATATAAAT
*
33896839 TGAATATGAAAAAAGAATAAAT
1 TGAA-ATG--AAAA-TATAAAT
* *
33896861 TGGAATGAGAGAAAAATAAAT
1 TGAAAT--GA-AAATATAAAT
* *
33896882 TGAAATGAGATTA-AAAT
1 TGAAATGAAAATATAAAT
33896899 GTGAAATG--AATATGAAAT
1 -TGAAATGAAAATAT-AAAT
*
33896917 T-AAATTAAAATATAAAT
1 TGAAATGAAAATATAAAT
33896934 TGAAATGAAAAAATAATAAAT
1 TGAAATG--AAAAT-ATAAAT
*
33896955 TGAAATGAAAAAAATAAAT
1 TGAAATG-AAAATATAAAT
* * *
33896974 TTAAATGAAATGAAATGAATTT
1 TGAAATGAAA--ATAT-AA-AT
33896996 TGAAATGAAAATGAAATGAAATT
1 TGAAATGAAAAT---AT-AAA-T
* *
33897019 TGAAATGAAAAT-GACA-
1 TGAAATGAAAATATAAAT
*
33897035 TGAAATTAAAATATAAAT
1 TGAAATGAAAATATAAAT
33897053 TGAAATGAAAA
1 TGAAATGAAAA
33897064 AAAAATAACA
Statistics
Matches: 188, Mismatches: 23, Indels: 60
0.69 0.08 0.22
Matches are distributed among these distances:
16 21 0.11
17 18 0.10
18 47 0.25
19 18 0.10
20 16 0.09
21 33 0.18
22 16 0.09
23 19 0.10
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
TGAAATGAAAATATAAAT
Found at i:33896986 original size:5 final size:5
Alignment explanation
Indices: 33896900--33897040 Score: 63
Period size: 5 Copynumber: 26.2 Consensus size: 5
33896890 GATTAAAATG
* * * **
33896900 TGAAA TGAATA TGAAA TTAAA TTAAAA TATAAA TTGAAA TGAAA AAATAA
1 TGAAA TGAA-A TGAAA TGAAA -TGAAA T-GAAA -TGAAA TGAAA TGA-AA
* * *
33896950 T-AAA TTGAAA TGAAA -AAAA T-AAA TTTAAA TGAAA TGAAA TGAATTT
1 TGAAA -TGAAA TGAAA TGAAA TGAAA -TGAAA TGAAA TGAAA TGAA--A
*
33896996 TGAAA TGAAAA TGAAA TGAAA TTTGAAA TGAAAA TGACA TGAAA T
1 TGAAA TG-AAA TGAAA TGAAA --TGAAA TG-AAA TGAAA TGAAA T
33897041 TAAAATATAA
Statistics
Matches: 107, Mismatches: 13, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
4 8 0.07
5 56 0.52
6 33 0.31
7 10 0.09
ACGTcount: A:0.59, C:0.01, G:0.13, T:0.28
Consensus pattern (5 bp):
TGAAA
Found at i:33897001 original size:12 final size:11
Alignment explanation
Indices: 33896966--33897027 Score: 56
Period size: 12 Copynumber: 5.6 Consensus size: 11
33896956 GAAATGAAAA
*
33896966 AAATAAATTT-
1 AAATGAATTTG
*
33896976 AAATGAA-ATG
1 AAATGAATTTG
33896986 AAATGAATTTTG
1 AAATGAA-TTTG
**
33896998 AAATGAAAATG
1 AAATGAATTTG
33897009 AAATGAAATTTG
1 AAATG-AATTTG
33897021 AAATGAA
1 AAATGAA
33897028 AATGACATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 1 0.02
10 13 0.32
11 9 0.22
12 18 0.44
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (11 bp):
AAATGAATTTG
Found at i:33897011 original size:23 final size:23
Alignment explanation
Indices: 33896933--33897062 Score: 127
Period size: 23 Copynumber: 6.0 Consensus size: 23
33896923 AAAATATAAA
*
33896933 TTGAAATGAAAA-AATAAT-AAA-
1 TTGAAATGAAAATGA-AATGAAAT
33896954 TTGAAATGAAAA--AAAT-AAAT
1 TTGAAATGAAAATGAAATGAAAT
*
33896974 TT-AAATG-AAATGAAATGAATT
1 TTGAAATGAAAATGAAATGAAAT
33896995 TTGAAATGAAAATGAAATGAAAT
1 TTGAAATGAAAATGAAATGAAAT
*
33897018 TTGAAATGAAAATGACATGAAA-
1 TTGAAATGAAAATGAAATGAAAT
*
33897040 TTAAAAT-ATAAATTGAAATGAAA
1 TTGAAATGA-AAA-TGAAATGAAA
33897063 AAAAAATAAC
Statistics
Matches: 96, Mismatches: 5, Indels: 14
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.03
19 11 0.11
20 7 0.07
21 18 0.19
22 14 0.15
23 43 0.45
ACGTcount: A:0.59, C:0.01, G:0.13, T:0.27
Consensus pattern (23 bp):
TTGAAATGAAAATGAAATGAAAT
Found at i:33897321 original size:23 final size:21
Alignment explanation
Indices: 33897286--33897350 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
33897276 ACTTGAAATG
33897286 AATATGAAA-TGAAATGAAATTAA
1 AATAT-AAATTGAAATGAAA--AA
33897309 AATATAAATTGAAAT-AAAAA
1 AATATAAATTGAAATGAAAAA
33897329 AAT-T-AATTGAAATGAGAAAA
1 AATATAAATTGAAATGA-AAAA
33897349 AA
1 AA
33897351 ATTGAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.23
19 2 0.05
20 11 0.28
22 6 0.15
23 11 0.28
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.25
Consensus pattern (21 bp):
AATATAAATTGAAATGAAAAA
Found at i:33897326 original size:17 final size:17
Alignment explanation
Indices: 33897300--33897359 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
33897290 TGAAATGAAA
*
33897300 TGAAATTAAAATATAAAT
1 TGAAA-TAAAAAATAAAT
*
33897318 TGAAATAAAAAAATTAAT
1 TGAAAT-AAAAAATAAAT
*
33897336 TGAAATGAGAAAA-AAAT
1 TGAAAT-AAAAAATAAAT
33897353 TGAAATA
1 TGAAATA
33897360 TTAAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.03
17 10 0.28
18 25 0.69
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (17 bp):
TGAAATAAAAAATAAAT
Found at i:33897342 original size:41 final size:42
Alignment explanation
Indices: 33897314--33897687 Score: 141
Period size: 41 Copynumber: 9.3 Consensus size: 42
33897304 ATTAAAATAT
33897314 AAAT-TGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
1 AAATATGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
* * * * * **
33897355 AAATATTAAATAAAAAAATT-GTTAAAAAGTTGAAATGCAA-TG
1 AAATATGAAATAAAAAAATTAATTGAAATG-AGAAA-AAAATTG
** *
33897397 AAATATGAAAT---GTAATGTAATTTGAAATGA-ATATAAAATT-
1 AAATATGAAATAAAAAAAT-TAA-TTGAAATGAGA-AAAAAATTG
*
33897437 -AA-ATGAAAGTTGAAATAAA-T-A-TGAAATGA-AAATAAAATAT-
1 AAATATGAAA--T-AAAAAAATTAATTGAAATGAGAAA-AAAAT-TG
* * *
33897477 AAAT-TGCAAT--TAAAA--AATTGAAATCAGACAAAAAA-T-
1 AAATATGAAATAAAAAAATTAATTGAAATGAGA-AAAAAATTG
* *
33897513 -AATATG-AA-AAAAGAATAAATTGAAATGAGAAAAAAATTG
1 AAATATGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
33897552 AAATATGAAAT---AAAATGTAATTTGAAATGA-AAATAAAATAT-
1 AAATATGAAATAAAAAAAT-TAA-TTGAAATGAGAAA-AAAAT-TG
* * *
33897593 AAAT-TGAAATGAAAAACACTAAATTGAAATGGGACAAAAAATT-
1 AAATATGAAAT-AAAAA-AATTAATTGAAATGAGA-AAAAAATTG
* * *
33897636 -AATAT-AAAAAAAAAGAATAAATTGAAATGAGAAAAAATTTG
1 AAATATGAAATAAAAA-AATTAATTGAAATGAGAAAAAAATTG
33897677 AAATATGAAAT
1 AAATATGAAAT
33897688 GAAATGAAAA
Statistics
Matches: 248, Mismatches: 38, Indels: 92
0.66 0.10 0.24
Matches are distributed among these distances:
35 5 0.02
36 10 0.04
37 13 0.05
38 25 0.10
39 26 0.10
40 30 0.12
41 59 0.24
42 49 0.20
43 15 0.06
44 12 0.05
45 4 0.02
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (42 bp):
AAATATGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
Found at i:33897405 original size:17 final size:17
Alignment explanation
Indices: 33897385--33897425 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
33897375 GTTAAAAAGT
33897385 TGAAATGCAATGAAATA
1 TGAAATGCAATGAAATA
* * *
33897402 TGAAATGTAATGTAATT
1 TGAAATGCAATGAAATA
33897419 TGAAATG
1 TGAAATG
33897426 AATATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (17 bp):
TGAAATGCAATGAAATA
Found at i:33897435 original size:28 final size:29
Alignment explanation
Indices: 33897393--33897469 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
33897383 GTTGAAATGC
* *
33897393 AATGAAATATGAAATGT-AATGTAATTTGA
1 AATG-AATATGAAATGTAAATGAAAGTTGA
*
33897422 AATGAATATAAAAT-TAAATGAAAGTTGA
1 AATGAATATGAAATGTAAATGAAAGTTGA
* *
33897450 AATAAATATGAAATGAAAAT
1 AATGAATATGAAATGTAAAT
33897470 AAAATATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.03
28 31 0.77
29 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (29 bp):
AATGAATATGAAATGTAAATGAAAGTTGA
Found at i:33897463 original size:23 final size:23
Alignment explanation
Indices: 33897424--33897467 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
33897414 TAATTTGAAA
*
33897424 TGAATATAAAATTAAATGAAAGT
1 TGAATATAAAATGAAATGAAAGT
33897447 TGAA-ATAAATATGAAATGAAA
1 TGAATATAAA-ATGAAATGAAA
33897468 ATAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (23 bp):
TGAATATAAAATGAAATGAAAGT
Found at i:33897561 original size:17 final size:18
Alignment explanation
Indices: 33897529--33897567 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
33897519 AAAAAAGAAT
33897529 AAATTGAAATGAGAAA-A
1 AAATTGAAATGAGAAATA
33897546 AAATTGAAAT-ATGAAATA
1 AAATTGAAATGA-GAAATA
33897564 AAAT
1 AAAT
33897568 GTAATTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (18 bp):
AAATTGAAATGAGAAATA
Found at i:33897578 original size:155 final size:155
Alignment explanation
Indices: 33897395--33897944 Score: 413
Period size: 155 Copynumber: 3.5 Consensus size: 155
33897385 TGAAATGCAA
** * *
33897395 TGAAAT-ATGAAATGTAATGTAATTTGAAATGAATATAAAATTAAATGAAAGTTGAAATAAATAT
1 TGAAATAATGAAATAAAATGTAATATGAAATGAATATAAAATGAAATGAAAGTTGAAATAAATAT
* *
33897459 GAAATGAAAATAAAATATAAATTGCAATTAAAAAATTGAAATCAGACAAAAAATAATATGAAAAA
66 GAAATGAAAATAAAATATAAATTGAAATAAAAAAATTGAAAT-AGACAAAAAATAATATGAAAAA
33897524 AGAATAAATTGAAATGAGAAAAAAAT
130 AGAATAAATTGAAATGAGAAAAAAAT
* * * ***
33897550 TGAAAT-ATGAAATAAAATGTAATTTGAAATGAAAATAAAATATAAATTGAAATGAAAAACACTA
1 TGAAATAATGAAATAAAATGTAATATGAAATGAATATAAAAT-GAAA-TGAAA-GTTGAA-A-TA
* * *
33897614 AAT-TGAAATGGGACAAAAAATTAATATAAA---AAAAAAGAATAAATTGAAAT-GAGAAAAAAT
61 AATATGAAAT--GA-AAATAA--AATATAAATTGAAATAA-AA-AAATTGAAATAGACAAAAAAT
* *
33897674 --T-TGAAATATG---AAA-TGAAAT--GAAAAAAAT
119 AATATGAAAAAAGAATAAATTGAAATGAGAAAAAAAT
* *
33897702 TGAAATGCAATGAAATATGAAT-TGAATATGGAATGGAATATAATTTGAAATGAAATGAAAGTTG
1 TGAAAT--AATGAAATA-AAATGT-AATATGAAAT-GAATAT-A----AAATGAAATGAAAGTTG
* *
33897766 AAATGAATATGAAATGAAAATAAAACATAAATTGAAATAAAAAAACTTGAAATGAGACAAAAAAT
56 AAATAAATATGAAATGAAAATAAAATATAAATTGAAATAAAAAAA-TTGAAAT-AGACAAAAAA-
33897831 TAATATGAAAAAA-AACGTAAATTGAAATGAGAAAAAAA-
118 TAATATGAAAAAAGAA--TAAATTGAAATGAGAAAAAAAT
* * * * * * *
33897869 T-AAATTGAAATGAAAAAAAATTTAA-ATGTAATGAAATATGAAATGAAATGTAATTTGAAATGA
1 TGAAA-T--AATGAAATAAAATGTAATATGAAATG-AATATAAAATGAAATGAAAGTTGAAATAA
33897932 ATATGAAATGAAA
62 ATATGAAATGAAA
33897945 GCTGAAATGA
Statistics
Matches: 315, Mismatches: 35, Indels: 85
0.72 0.08 0.20
Matches are distributed among these distances:
152 15 0.05
153 7 0.02
154 9 0.03
155 64 0.20
156 22 0.07
157 22 0.07
158 19 0.06
159 11 0.03
160 45 0.14
161 23 0.07
162 11 0.03
163 10 0.03
164 9 0.03
165 14 0.04
166 14 0.04
167 12 0.04
168 8 0.03
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (155 bp):
TGAAATAATGAAATAAAATGTAATATGAAATGAATATAAAATGAAATGAAAGTTGAAATAAATAT
GAAATGAAAATAAAATATAAATTGAAATAAAAAAATTGAAATAGACAAAAAATAATATGAAAAAA
GAATAAATTGAAATGAGAAAAAAAT
Found at i:33897618 original size:84 final size:84
Alignment explanation
Indices: 33897528--33897691 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 84
33897518 GAAAAAAGAA
* * *
33897528 TAAATTGAAATGAGA-AAAAAATTGAAATATGAAATAAAATG-TAATTTGAAATGAAAATAAAAT
1 TAAATTGAAATGAGACAAAAAATT--AATAT-AAAAAAAAAGATAAATTGAAATGAAAA-AAAAT
33897591 AT-AAAT-TGAAATGAAAAACAC
62 ATGAAATATGAAATGAAAAACAC
* * *
33897612 TAAATTGAAATGGGACAAAAAATTAATATAAAAAAAAAGAATAAATTGAAATGAGAAAAAATTTG
1 TAAATTGAAATGAGACAAAAAATTAATATAAAAAAAAAG-ATAAATTGAAATGAAAAAAAATATG
33897677 AAATATGAAATGAAA
65 AAATATGAAATGAAA
33897692 TGAAAAAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
82 8 0.12
83 11 0.16
84 32 0.46
85 18 0.26
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.24
Consensus pattern (84 bp):
TAAATTGAAATGAGACAAAAAATTAATATAAAAAAAAAGATAAATTGAAATGAAAAAAAATATGA
AATATGAAATGAAAAACAC
Found at i:33897669 original size:125 final size:116
Alignment explanation
Indices: 33897458--33897693 Score: 328
Period size: 125 Copynumber: 2.0 Consensus size: 116
33897448 GAAATAAATA
* * *
33897458 TGAAATGAAAATAAAATATAAATTGCAATTAAAAAATTGAAATCAGACAAAAAATAATATGAAAA
1 TGAAATGAAAATAAAATATAAATTGAAATAAAAAAATTGAAATCAGACAAAAAATAATATAAAAA
33897523 AAGAATAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATGTAATT
66 AAGAATAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATGTAATT
**
33897574 TGAAATGAAAATAAAATATAAATTGAAATGAAAAACACTAAATTGAAATGGGACAAAAAATTAAT
1 TGAAATGAAAATAAAATATAAATTGAAAT---AAA-A--AAATTGAAATCAGACAAAAAA-TAAT
* *
33897639 ATAAAAAAAAAGAATAAATTGAAATGAGAAAAAATTTGAAATATGAAATGAAATG
59 AT--AAAAAAAGAATAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATG
33897694 AAAAAAATTG
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
116 28 0.27
119 2 0.02
120 1 0.01
122 19 0.18
123 6 0.06
125 48 0.46
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (116 bp):
TGAAATGAAAATAAAATATAAATTGAAATAAAAAAATTGAAATCAGACAAAAAATAATATAAAAA
AAGAATAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATGTAATT
Found at i:33897681 original size:27 final size:26
Alignment explanation
Indices: 33897658--33897717 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 26
33897648 AAGAATAAAT
33897658 TGAAATGAGAAAAAATTTGAAATATGAAA
1 TGAAATGA-AAAAAA-TTGAAATA-GAAA
*
33897687 TGAAATGAAAAAAATTGAAAT-GCAA
1 TGAAATGAAAAAAATTGAAATAGAAA
33897712 TGAAAT
1 TGAAAT
33897718 ATGAATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 9 0.30
27 7 0.23
28 6 0.20
29 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (26 bp):
TGAAATGAAAAAAATTGAAATAGAAA
Found at i:33897691 original size:5 final size:5
Alignment explanation
Indices: 33897681--33898058 Score: 75
Period size: 5 Copynumber: 68.2 Consensus size: 5
33897671 AATTTGAAAT
* * *
33897681 ATGAA ATGAA ATGAA A-AAA ATTGAA ATGCA ATGAAA TATGAA TTGAA
1 ATGAA ATGAA ATGAA ATGAA A-TGAA ATGAA ATG-AA -ATGAA ATGAA
* *
33897728 TATGGA ATGGAA TAT-AA TTTGAA ATGAA ATGAA AGTTGAA ATGAA TATGAA
1 -ATGAA AT-GAA -ATGAA -ATGAA ATGAA ATGAA A--TGAA ATGAA -ATGAA
* * **
33897779 ATGAAA ATAAAA CAT-AA ATTGAA AT-AA A-AAA ACTTGAA ATGAGA CAAAAA
1 ATG-AA AT-GAA -ATGAA A-TGAA ATGAA ATGAA A--TGAA ATGA-A -ATGAA
* ** * **
33897829 ATTAA TATGAA AAAAA ACGTAA ATTGAA ATGAGA AAAAA AT-AA ATTGAA
1 ATGAA -ATGAA ATGAA ATG-AA A-TGAA ATGA-A ATGAA ATGAA A-TGAA
** * * *
33897878 ATGAA AAAAA ATTTAA ATGTA ATGAAA TATGAA ATGAA ATGTAA TTTGAA
1 ATGAA ATGAA A-TGAA ATGAA ATG-AA -ATGAA ATGAA ATG-AA -ATGAA
* * *
33897928 ATGAA TATGAA ATGAA AGCTGAA ATGAA TACGAA ATGAAA ATAAA ATATAA
1 ATGAA -ATGAA ATGAA A--TGAA ATGAA -ATGAA ATG-AA ATGAA AT-GAA
* * * *
33897979 ATTAAA ATGTGGA ATGAAA ATGAA ATTAA GTGAA ATTTGAA ATGAAA ATGAA
1 A-TGAA A--TGAA ATG-AA ATGAA ATGAA ATGAA A--TGAA ATG-AA ATGAA
*
33898031 ATTAA ATGAA ATGAAA TATGAA ATGAA A
1 ATGAA ATGAA ATG-AA -ATGAA ATGAA A
33898059 AAAAAAATGA
Statistics
Matches: 277, Mismatches: 49, Indels: 94
0.66 0.12 0.22
Matches are distributed among these distances:
4 13 0.05
5 137 0.49
6 87 0.31
7 40 0.14
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.25
Consensus pattern (5 bp):
ATGAA
Found at i:33897692 original size:12 final size:12
Alignment explanation
Indices: 33897675--33897784 Score: 56
Period size: 11 Copynumber: 9.4 Consensus size: 12
33897665 AGAAAAAATT
33897675 TGAAATATGAAA
1 TGAAATATGAAA
**
33897687 TGAAATGAAAAAAA
1 TGAAAT--ATGAAA
*
33897701 TTG-AA-ATGCAA
1 -TGAAATATGAAA
*
33897712 TGAAATATGAAT
1 TGAAATATGAAA
*
33897724 TG-AATATGGAA
1 TGAAATATGAAA
* *
33897735 TGGAATAT-AATT
1 TGAAATATGAA-A
33897747 TG-AA-ATGAAA
1 TGAAATATGAAA
33897757 TGAAAGT-TGAAA
1 TGAAA-TATGAAA
33897769 TG-AATATGAAA
1 TGAAATATGAAA
33897780 TGAAA
1 TGAAA
33897785 ATAAAACATA
Statistics
Matches: 73, Mismatches: 12, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
10 7 0.10
11 30 0.41
12 28 0.38
14 6 0.08
15 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.19, T:0.26
Consensus pattern (12 bp):
TGAAATATGAAA
Found at i:33897721 original size:27 final size:29
Alignment explanation
Indices: 33897658--33897722 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 29
33897648 AAGAATAAAT
*
33897658 TGAAATGA-GAAAAAATTTGAAATATGAAA
1 TGAAAT-ATGAAAAAAATTGAAATATGAAA
*
33897687 TG-AA-ATGAAAAAAATTG-AA-ATGCAA
1 TGAAATATGAAAAAAATTGAAATATGAAA
33897712 TGAAATATGAA
1 TGAAATATGAA
33897723 TTGAATATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
25 7 0.23
26 5 0.16
27 15 0.48
28 2 0.06
29 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (29 bp):
TGAAATATGAAAAAAATTGAAATATGAAA
Found at i:33897786 original size:17 final size:15
Alignment explanation
Indices: 33897681--33898058 Score: 75
Period size: 17 Copynumber: 22.7 Consensus size: 15
33897671 AATTTGAAAT
33897681 ATGAAATGAAATGAA
1 ATGAAATGAAATGAA
* *
33897696 A-AAAATTGAAATGCA
1 ATGAAA-TGAAATGAA
*
33897711 ATGAAATATGAATTGAA
1 ATG-AA-ATGAAATGAA
*
33897728 TATGGAATGGAATAT-AA
1 -ATGAAAT-GAA-ATGAA
*
33897745 TTTGAAATGAAATGAA
1 -ATGAAATGAAATGAA
33897761 AGTTGAAATGAATATGAA
1 A--TGAAATGAA-ATGAA
*
33897779 ATGAAAATAAAACAT-AA
1 ATG-AAAT-GAA-ATGAA
*
33897796 ATTGAAAT-AAA-AAA
1 A-TGAAATGAAATGAA
**
33897810 ACTTGAAATGAGACAAAAA
1 A--TGAAATGA-A-ATGAA
* **
33897829 ATTAATATGAAAAAAA
1 ATGAA-ATGAAATGAA
*
33897845 ACGTAAATTGAAATGAGA
1 ATG-AAA-TGAAATGA-A
**
33897863 AAAAAAT-AAATTGAA
1 ATGAAATGAAA-TGAA
** *
33897878 ATGAAAAAAAATTTAA
1 ATGAAATGAAA-TGAA
*
33897894 ATGTAATGAAATATGAA
1 ATGAAATG-AA-ATGAA
*
33897911 ATGAAATGTAATTTGAA
1 ATGAAATG-AA-ATGAA
33897928 ATGAATATGAAATGAA
1 ATGAA-ATGAAATGAA
*
33897944 AGCTGAAATGAATACGAA
1 A--TGAAATGAA-ATGAA
* *
33897962 ATGAAAATAAAATATAA
1 ATG-AAATGAAAT-GAA
* *
33897979 ATTAAAATGTGGAATGAAA
1 A-TGAAA--TGAAATG-AA
* *
33897998 ATGAAATTAAGTGAA
1 ATGAAATGAAATGAA
33898013 ATTTGAAATGAAAATGAA
1 A--TGAAATG-AAATGAA
*
33898031 ATTAAATGAAATGAAA
1 ATGAAATGAAATG-AA
33898047 TATGAAATGAAA
1 -ATGAAATGAAA
33898059 AAAAAAATGA
Statistics
Matches: 273, Mismatches: 47, Indels: 84
0.68 0.12 0.21
Matches are distributed among these distances:
14 7 0.03
15 37 0.14
16 53 0.19
17 116 0.42
18 49 0.18
19 11 0.04
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.25
Consensus pattern (15 bp):
ATGAAATGAAATGAA
Found at i:33897819 original size:38 final size:36
Alignment explanation
Indices: 33897775--33897896 Score: 120
Period size: 38 Copynumber: 3.2 Consensus size: 36
33897765 GAAATGAATA
*
33897775 TGAAATGAAAATAAAACATAAATTGAAATAAAAAAACT
1 TGAAATGAAAA-AAAA-ATAAATTGAAATAAAAAAAAT
* *
33897813 TGAAATGAGACAAAAAATTAATATGAAA-AAAAACGTAAAT
1 TGAAATGA-AAAAAAAATAAAT-TGAAATAAAAA---AAAT
*
33897853 TGAAATGAGAAAAAAATAAATTGAAATGAAAAAAAAT
1 TGAAATGAAAAAAAAATAAATTGAAAT-AAAAAAAAT
*
33897890 TTAAATG
1 TGAAATG
33897897 TAATGAAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
37 20 0.29
38 22 0.31
39 12 0.17
40 16 0.23
ACGTcount: A:0.64, C:0.03, G:0.11, T:0.21
Consensus pattern (36 bp):
TGAAATGAAAAAAAAATAAATTGAAATAAAAAAAAT
Found at i:33897853 original size:22 final size:20
Alignment explanation
Indices: 33897798--33897889 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 20
33897788 AAACATAAAT
*
33897798 TGAAATAAAAA-AACTTGAAA
1 TGAAA-AAAAATAAATTGAAA
* *
33897818 TG-AGACAAA-AAATT-AATA
1 TGAAAAAAAATAAATTGAA-A
33897836 TGAAAAAAAACGTAAATTGAAA
1 TGAAAAAAAA--TAAATTGAAA
33897858 TGAGAAAAAAATAAATTGAAA
1 TGA-AAAAAAATAAATTGAAA
33897879 TGAAAAAAAAT
1 TGAAAAAAAAT
33897890 TTAAATGTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.03
18 11 0.18
19 6 0.10
20 10 0.17
21 13 0.22
22 9 0.15
23 9 0.15
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (20 bp):
TGAAAAAAAATAAATTGAAA
Found at i:33897904 original size:21 final size:20
Alignment explanation
Indices: 33897516--33897889 Score: 135
Period size: 23 Copynumber: 17.6 Consensus size: 20
33897506 AAAAAATAAT
33897516 ATGAAAAAAGAATAAATTGAA
1 ATGAAAAAA-AATAAATTGAA
33897537 ATGAGAAAAAAATTGAAATATGAA
1 ATGA-AAAAAAA-T-AAAT-TGAA
** *
33897561 AT---AAAATGTAATTTGAA
1 ATGAAAAAAAATAAATTGAA
33897578 ATGAAAATAAAATATAAATTGAA
1 ATG-AAA-AAAA-ATAAATTGAA
* *
33897601 ATGAAAAACACTAAATTGAA
1 ATGAAAAAAAATAAATTGAA
* *
33897621 ATGGGACAAAAAATTAATAT-AA
1 AT--GAAAAAAAATAAAT-TGAA
33897643 A--AAAAAAGAATAAATTGAA
1 ATGAAAAAA-AATAAATTGAA
*
33897662 ATGAGAAAAAATTTGAAATATGAA
1 ATGA-AAAAAA-AT-AAAT-TGAA
*
33897686 ATGAAATGAAAA-AAATTGAA
1 ATGAAA-AAAAATAAATTGAA
* * *
33897706 ATGCAATGAAATATGAATTGAA
1 ATG-AA-AAAAAATAAATTGAA
** * *
33897728 TATGGAATGGAATATAATTTGAA
1 -AT-GAA-AAAAAATAAATTGAA
**
33897751 ATGAAATGAAAGTTGAAA-TGAA
1 ATGAAA--AAAAAT-AAATTGAA
* *
33897773 TATGAAATGAAAATAAAACAT-AA
1 -ATGAAA-AAAAAT-AAA-TTGAA
*
33897796 ATTGAAATAAAAA-AACTTGAA
1 A-TGAAA-AAAAATAAATTGAA
* *
33897817 ATG-AGACAAA-AAATT-AA
1 ATGAAAAAAAATAAATTGAA
33897834 TATGAAAAAAAACGTAAATTGAA
1 -ATGAAAAAAAA--TAAATTGAA
33897857 ATGAGAAAAAAATAAATTGAA
1 ATGA-AAAAAAATAAATTGAA
33897878 ATGAAAAAAAAT
1 ATGAAAAAAAAT
33897890 TTAAATGTAA
Statistics
Matches: 269, Mismatches: 42, Indels: 85
0.68 0.11 0.21
Matches are distributed among these distances:
17 8 0.03
18 20 0.07
19 16 0.06
20 33 0.12
21 42 0.16
22 63 0.23
23 68 0.25
24 19 0.07
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.23
Consensus pattern (20 bp):
ATGAAAAAAAATAAATTGAA
Found at i:33897941 original size:23 final size:23
Alignment explanation
Indices: 33897906--33897967 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
33897896 GTAATGAAAT
* **
33897906 ATGAA-ATGAAATGTAATTTGAA
1 ATGAATATGAAATGAAAGCTGAA
33897928 ATGAATATGAAATGAAAGCTGAA
1 ATGAATATGAAATGAAAGCTGAA
*
33897951 ATGAATACGAAATGAAA
1 ATGAATATGAAATGAAA
33897968 ATAAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.24
Consensus pattern (23 bp):
ATGAATATGAAATGAAAGCTGAA
Found at i:33898023 original size:28 final size:28
Alignment explanation
Indices: 33897959--33898042 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
33897949 AAATGAATAC
* * *
33897959 GAAATGAAAATAAAATATAAATTAAAATGT
1 GAAATGAAAATGAAAT-TAAA-TGAAATTT
* *
33897989 GGAATGAAAATGAAATTAAGTGAAATTT
1 GAAATGAAAATGAAATTAAATGAAATTT
33898017 GAAATGAAAATGAAATTAAATGAAAT
1 GAAATGAAAATGAAATTAAATGAAAT
33898043 GAAATATGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 30 0.64
29 3 0.06
30 14 0.30
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.26
Consensus pattern (28 bp):
GAAATGAAAATGAAATTAAATGAAATTT
Found at i:33898051 original size:28 final size:25
Alignment explanation
Indices: 33897866--33898058 Score: 100
Period size: 28 Copynumber: 6.9 Consensus size: 25
33897856 AATGAGAAAA
**
33897866 AAAT-AAATTGAAATGAAAAAAAATTT
1 AAATGAAA-TGAAATGAAATGAAA-TT
*
33897892 AAATGTAATGAAATATGAAATGAAATGT
1 AAATGAAATG-AA-ATGAAATGAAAT-T
* *
33897920 AATTTGAAATGAATATGAAATGAAAGCTG
1 AA-ATGAAATGAA-ATGAAATGAAA--TT
* *
33897949 AAATGAATACGAAATGAAAATAAAATAT
1 AAATGAA-ATGAAATG-AAATGAAAT-T
* *
33897977 AAATTAAAATGTGGAATGAAAATGAAATT
1 AAA-TGAAA--TGAAATG-AAATGAAATT
*
33898006 AAGTGAAATTTGAAATGAAAATGAAATT
1 AAATGAAA--TGAAATG-AAATGAAATT
33898034 AAATGAAATGAAATATGAAATGAAA
1 AAATGAAATG-AA-ATGAAATGAAA
33898059 AAAAAAATGA
Statistics
Matches: 133, Mismatches: 19, Indels: 29
0.73 0.10 0.16
Matches are distributed among these distances:
26 8 0.06
27 16 0.12
28 69 0.52
29 25 0.19
30 15 0.11
ACGTcount: A:0.58, C:0.01, G:0.16, T:0.26
Consensus pattern (25 bp):
AAATGAAATGAAATGAAATGAAATT
Found at i:33900477 original size:40 final size:40
Alignment explanation
Indices: 33900422--33900689 Score: 482
Period size: 40 Copynumber: 6.7 Consensus size: 40
33900412 GAGCATTGGA
33900422 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
33900462 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
33900502 ATATACCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
33900542 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
33900582 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
33900622 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
33900662 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
33900690 ATGTGTTTGC
Statistics
Matches: 219, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:33907746 original size:40 final size:40
Alignment explanation
Indices: 33907691--33907958 Score: 482
Period size: 40 Copynumber: 6.7 Consensus size: 40
33907681 GAGCATTGGA
33907691 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
33907731 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
33907771 ATATACCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
33907811 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
33907851 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
33907891 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
33907931 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
33907959 ATGTGTTTGC
Statistics
Matches: 219, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:33912025 original size:18 final size:17
Alignment explanation
Indices: 33911987--33912030 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
33911977 AGTCTAAATA
33911987 TTTTATTTATTCATTTAT
1 TTTTATTTATT-ATTTAT
33912005 TTTTATTTATT-TTTAGT
1 TTTTATTTATTATTTA-T
*
33912022 TTTTTTTTA
1 TTTTATTTA
33912031 AAGAGGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 9 0.38
18 11 0.46
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTATTTATTATTTAT
Found at i:33912028 original size:11 final size:10
Alignment explanation
Indices: 33911988--33912030 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
33911978 GTCTAAATAT
33911988 TTTATTTATTCA
1 TTTATTT-TT-A
33912000 TTTATTTTTA
1 TTTATTTTTA
33912010 TTTATTTTTA
1 TTTATTTTTA
*
33912020 GTTTTTTTTTA
1 -TTTATTTTTA
33912031 AAGAGGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 11 0.38
11 11 0.38
12 7 0.24
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:33913689 original size:27 final size:27
Alignment explanation
Indices: 33913659--33913727 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
33913649 AGTATAAAGA
*
33913659 GTATAACAGTCATTTCACCCTACAGGG
1 GTATTACAGTCATTTCACCCTACAGGG
33913686 GTATTACAGTCATTTCACCCTACAGGG
1 GTATTACAGTCATTTCACCCTACAGGG
33913713 GTATTACAGTCATTT
1 GTATTACAGTCATTT
33913728 TCGTCAGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (27 bp):
GTATTACAGTCATTTCACCCTACAGGG
Found at i:33920747 original size:29 final size:30
Alignment explanation
Indices: 33920715--33920780 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
33920705 ATATATAACG
**
33920715 AAATTTCTGTAATTAAAAGTAGA-ATGACT-
1 AAATTTCTAAAATTAAAAGTAGAGAT-ACTA
*
33920744 AAATTTTTAAAATTAAAAGTAGAGATACTA
1 AAATTTCTAAAATTAAAAGTAGAGATACTA
33920774 AAATTTC
1 AAATTTC
33920781 AATTGTGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (30 bp):
AAATTTCTAAAATTAAAAGTAGAGATACTA
Found at i:33925688 original size:48 final size:49
Alignment explanation
Indices: 33925631--33925736 Score: 196
Period size: 48 Copynumber: 2.2 Consensus size: 49
33925621 ACATTTGGTA
33925631 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTG-
1 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
33925679 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
1 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
33925728 CAAGATTTC
1 CAAG-TTTC
33925737 CAATTCCAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
48 48 0.86
49 4 0.07
50 4 0.07
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (49 bp):
CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
Found at i:33927504 original size:12 final size:12
Alignment explanation
Indices: 33927487--33927511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33927477 TAGTCAACAT
33927487 AGAAAGAGGAAG
1 AGAAAGAGGAAG
33927499 AGAAAGAGGAAG
1 AGAAAGAGGAAG
33927511 A
1 A
33927512 TGTTTTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AGAAAGAGGAAG
Found at i:33941409 original size:123 final size:124
Alignment explanation
Indices: 33941276--33941524 Score: 295
Period size: 124 Copynumber: 2.0 Consensus size: 124
33941266 ATTTCTTAAC
* * ** * * *
33941276 AAAAATTTCACTCAATGTTACTATCATGTTGTAGACATTAAAATAATA-TAAAATAATTATTTTG
1 AAAAAATTCACACAATCATACTATCATGCTATAAACATTAAAATAATATTAAAATAATTATTTTG
** *** *
33941340 A-CTTTGGATTTATAGTTTTGAAACCACTGTTATGATTTGACTAAAAACGGGCTGTTACA
66 ACCTCAGG-TTTATAGTCCCGAAACCACTGTTACGATTTGACTAAAAACGGGCTGTTACA
* *
33941399 AAAAAATTCACACAATCATATTATCATGCTATAAATATTAAAATAATATTAAAATAATTATTTTG
1 AAAAAATTCACACAATCATACTATCATGCTATAAACATTAAAATAATATTAAAATAATTATTTTG
* * * * *
33941464 ACCTCAGGTTTGTGGTCCCGAAACCACTGTTCCGGTTTGACTAAAAACGGGTTGTTACA
66 ACCTCAGGTTTATAGTCCCGAAACCACTGTTACGATTTGACTAAAAACGGGCTGTTACA
33941523 AA
1 AA
33941525 CATGTGACAA
Statistics
Matches: 104, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
123 39 0.38
124 61 0.59
125 4 0.04
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (124 bp):
AAAAAATTCACACAATCATACTATCATGCTATAAACATTAAAATAATATTAAAATAATTATTTTG
ACCTCAGGTTTATAGTCCCGAAACCACTGTTACGATTTGACTAAAAACGGGCTGTTACA
Found at i:33941460 original size:12 final size:11
Alignment explanation
Indices: 33941432--33941456 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33941422 TCATGCTATA
33941432 AATATTAAAAT
1 AATATTAAAAT
33941443 AATATTAAAAT
1 AATATTAAAAT
33941454 AAT
1 AAT
33941457 TATTTTGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:33944374 original size:3 final size:3
Alignment explanation
Indices: 33944366--33944412 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
33944356 TATGTAAATA
* *
33944366 AAT AAT AAT AGAT AA- AAT AAT AAT AAT GAT AGT AAT AAT AAAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
33944412 A
1 A
33944413 TATATAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:33944387 original size:18 final size:19
Alignment explanation
Indices: 33944361--33944412 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
33944351 AAACATATGT
33944361 AAATAAATAATAATAGATA-
1 AAAT-AATAATAATAGATAG
33944380 AAATAATAATAAT-GATAG
1 AAATAATAATAATAGATAG
*
33944398 TAATAATAAATAATA
1 AAATAAT-AATAATA
33944413 TATATAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.14
18 15 0.52
19 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (19 bp):
AAATAATAATAATAGATAG
Found at i:33944498 original size:12 final size:11
Alignment explanation
Indices: 33944470--33944516 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
33944460 GATTGAAGAA
*
33944470 ATAAATAAATAA
1 ATAAATAAA-AT
33944482 ATAAATAAAAT
1 ATAAATAAAAT
*
33944493 ATTAAATGAAAT
1 A-TAAATAAAAT
33944505 ATAAATAAAAT
1 ATAAATAAAAT
33944516 A
1 A
33944517 GTTTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 12 0.39
12 19 0.61
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:33946015 original size:45 final size:44
Alignment explanation
Indices: 33945854--33946336 Score: 150
Period size: 44 Copynumber: 10.6 Consensus size: 44
33945844 TCGTTCCAAC
* * * * * *
33945854 CCACTGCAACTTCAAGGG-TATAGGAATTGTCGATTCAATCTGCT
1 CCACTGCAACTTC-GGGGAGATAAGATTTGTAGATTTAATCTGCT
* * * *
33945898 CCACTGCATCTTCAGGGG-GATTAGACTTGTAGATTTAATCTACT
1 CCACTGCAACTTC-GGGGAGATAAGATTTGTAGATTTAATCTGCT
* * * * *
33945942 CCACTGCAACTTCGGGTAGTTGATATTTGTA-ACTTTTGATCTGCT
1 CCACTGCAACTTCGGGGAGATAAGATTTGTAGA--TTTAATCTGCT
* * * *
33945987 CCACCGCAACTTCGGGGAGATAAGATTTGCCATGATACCTTCAATCCGTT
1 CCACTGCAACTTCGGGGAGATAAGATTTG-TA-GAT---TT-AATCTGCT
* * * * *
33946037 CCATTGTAACTTCAGGGGTATGGGATTTATA-ATTTGTAGCTTAAATCTGTT
1 CCACTGCAACTTC-GGGG-A---GA--TA-AGATTTGTAGATTTAATCTGCT
* * ** ** * * *
33946088 CCACTGCAACTTCAGGGAAATAAGATCCGCTATCTTCAACCTACT
1 CCACTGCAACTTCGGGGAGATAAGATTTG-TAGATTTAATCTGCT
* ** * ** * *
33946133 CCATTGCAACTTTAGGGAGATAAGGTTAATGGCTTTAATCTGCT
1 CCACTGCAACTTCGGGGAGATAAGATTTGTAGATTTAATCTGCT
* * * *
33946177 CCACTGCAACTTCAGAGAGATAAGATTTGCCA-TTTTCAATCTGCT
1 CCACTGCAACTTCGGGGAGATAAGATTTG-TAGATTT-AATCTGCT
* * * * * * * *
33946222 CCACTGTAACTTCAGGGAGTTGAGGTTCGTA-ACTTCAATGTGCT
1 CCACTGCAACTTCGGGGAGATAAGATTTGTAGA-TTTAATCTGCT
** * * * * * **
33946266 CCACTGCAACTTTAGGGAGACAAGGTTTATGGCTTTAATCTAAT
1 CCACTGCAACTTCGGGGAGATAAGATTTGTAGATTTAATCTGCT
**
33946310 CCACTGCAACTTCAAGGAGATAAGATT
1 CCACTGCAACTTCGGGGAGATAAGATT
33946337 CATCATGGTA
Statistics
Matches: 323, Mismatches: 92, Indels: 48
0.70 0.20 0.10
Matches are distributed among these distances:
43 5 0.02
44 158 0.49
45 98 0.30
46 3 0.01
48 1 0.00
49 3 0.01
50 18 0.06
51 22 0.07
52 2 0.01
55 4 0.01
56 1 0.00
57 7 0.02
58 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCGGGGAGATAAGATTTGTAGATTTAATCTGCT
Found at i:33946197 original size:44 final size:43
Alignment explanation
Indices: 33946131--33946333 Score: 183
Period size: 44 Copynumber: 4.6 Consensus size: 43
33946121 CTTCAACCTA
* *
33946131 CTCCATTGCAACTTTAGGGAGATAAGGTTAATGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGTT-ATGGCTTTAATCTG
* * *
33946175 CTCCACTGCAACTTCAGAGAGATAAGATT-TGCCATTTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGTTATGGC--TTT-AATCTG
* * * * ** * *
33946220 CTCCACTGTAACTTCAGGGAGTTGAGGTTCGTAACTTCAATGTG
1 CTCCACTGCAACTTCAGGGAGATAAGGTT-ATGGCTTTAATCTG
* * *
33946264 CTCCACTGCAACTTTAGGGAGACAAGGTTTATGGCTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGG-TTATGGCTTTAATCTG
* *
33946308 ATCCACTGCAACTTCAAGGAGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
33946334 ATTCATCATG
Statistics
Matches: 124, Mismatches: 29, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
42 3 0.02
44 85 0.69
45 34 0.27
47 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGGTTATGGCTTTAATCTG
Found at i:33946233 original size:89 final size:89
Alignment explanation
Indices: 33946073--33946277 Score: 221
Period size: 89 Copynumber: 2.3 Consensus size: 89
33946063 TTATAATTTG
* * * *
33946073 TAGCTTAAATCTGTTCCACTGCAACTTCAGGGAAATAAGATCCGCTATCTTCAACCTACTCCATT
1 TAGCTTAAATCTGCTCCACTGCAACTTCAGAGAAATAAGATCCGCCATCTTCAACCTACTCCACT
*
33946138 GCAACTTTAGGGAGATAAGGTTAA
66 GCAACTTCAGGGAGATAAGGTTAA
* * * ** * * *
33946162 TGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCCATTTTCAATCTGCTCCACT
1 TAGCTTAAATCTGCTCCACTGCAACTTCAGAGAAATAAGATCCGCCATCTTCAACCTACTCCACT
* * * **
33946227 GTAACTTCAGGGAGTTGAGGTTCG
66 GCAACTTCAGGGAGATAAGGTTAA
* * *
33946251 TAACTTCAATGTGCTCCACTGCAACTT
1 TAGCTTAAATCTGCTCCACTGCAACTT
33946278 TAGGGAGACA
Statistics
Matches: 94, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
89 94 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (89 bp):
TAGCTTAAATCTGCTCCACTGCAACTTCAGAGAAATAAGATCCGCCATCTTCAACCTACTCCACT
GCAACTTCAGGGAGATAAGGTTAA
Found at i:33947210 original size:4 final size:4
Alignment explanation
Indices: 33947196--33947227 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
33947186 CCTTAGCCTC
33947196 TCTT T-TT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
33947228 TTTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TCTT
Found at i:33957010 original size:24 final size:24
Alignment explanation
Indices: 33956960--33957010 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
33956950 GTGTTATGTA
* * *
33956960 GAGGAAATCAATGAGAGGATTGGG
1 GAGGAAATCAAGGAGAAGATTAGG
*
33956984 GAGGAAATCAAGGAGAAGATTATG
1 GAGGAAATCAAGGAGAAGATTAGG
33957008 GAG
1 GAG
33957011 AGATTTTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.39, T:0.16
Consensus pattern (24 bp):
GAGGAAATCAAGGAGAAGATTAGG
Found at i:33958305 original size:18 final size:18
Alignment explanation
Indices: 33958264--33958306 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
33958254 CGTGGTATTT
33958264 ATGGGCTTGATGGGCCAC
1 ATGGGCTTGATGGGCCAC
*
33958282 ACGGGCTTG-TGGGCCTAC
1 ATGGGCTTGATGGGCC-AC
*
33958300 TTGGGCT
1 ATGGGCT
33958307 GCATAATGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.12, C:0.23, G:0.40, T:0.26
Consensus pattern (18 bp):
ATGGGCTTGATGGGCCAC
Found at i:33959939 original size:18 final size:18
Alignment explanation
Indices: 33959916--33959965 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
33959906 TCAATAATAT
*
33959916 TCATTTATTCAGTATCAG
1 TCATTTATTCAGTAACAG
*
33959934 TCATTTATTCTGTAACAG
1 TCATTTATTCAGTAACAG
*
33959952 TCAATTATTCAGTA
1 TCATTTATTCAGTA
33959966 GCAGACAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (18 bp):
TCATTTATTCAGTAACAG
Found at i:33960210 original size:16 final size:16
Alignment explanation
Indices: 33960189--33960219 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
33960179 GGTACGAAGT
33960189 ACCTGTAACACCCCTC
1 ACCTGTAACACCCCTC
33960205 ACCTGTAACACCCCT
1 ACCTGTAACACCCCT
33960220 AACCCGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.48, G:0.06, T:0.19
Consensus pattern (16 bp):
ACCTGTAACACCCCTC
Found at i:33960940 original size:46 final size:46
Alignment explanation
Indices: 33960880--33961229 Score: 446
Period size: 46 Copynumber: 8.0 Consensus size: 46
33960870 TTTGATGTGA
* * * * * *
33960880 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
33960926 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
33960972 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
33961018 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
33961064 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
33961102 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
33961148 TGCCATGGTATCTTTCAATCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
33961186 TGCCTTGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
33961230 AGAGCACACT
Statistics
Matches: 271, Mismatches: 16, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
38 64 0.24
39 2 0.01
40 6 0.02
41 2 0.01
43 2 0.01
44 6 0.02
45 6 0.02
46 183 0.68
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:33960996 original size:92 final size:88
Alignment explanation
Indices: 33960880--33961229 Score: 455
Period size: 84 Copynumber: 4.0 Consensus size: 88
33960870 TTTGATGTGA
* * * *
33960880 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CA--TTCT-TCAGGTTGCCATGGTATCTTTCAAC
** * * *
33960945 CATGGTCTTATTCTTTTCATGTCACGT
62 CATGGTCTTACACATTTCATATCAGGT
33960972 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CAT-TC-T-TCAGGTTGCCATGGTATCTTTCAAC
33961037 CATGGTCTTACACATTTCATATCAGGT
62 CATGGTCTTACACATTTCATATCAGGT
*
33961064 TGCCATGGTATCTTTCAACCATGGTCTTA-CA--C-ACAGGTTGCCATGGTATCTTTCAACCATG
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
33961125 GTCTTACACATTTCATATCAGGT
66 GTCTTACACATTTCATATCAGGT
* * *
33961148 TGCCATGGTATCTTTCAATCATGGTCTTA-CA--C-ACAGGTTGCCTTGGTATCTTTCAACCATG
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
33961209 GTCTTACACATTTCATATCAG
66 GTCTTACACATTTCATATCAG
33961230 AGAGCACACT
Statistics
Matches: 242, Mismatches: 14, Indels: 12
0.90 0.05 0.04
Matches are distributed among these distances:
84 131 0.54
87 1 0.00
90 3 0.01
91 2 0.01
92 105 0.43
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (88 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
GTCTTACACATTTCATATCAGGT
Found at i:33961110 original size:38 final size:38
Alignment explanation
Indices: 33961059--33961218 Score: 230
Period size: 38 Copynumber: 4.0 Consensus size: 38
33961049 CATTTCATAT
33961059 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
33961097 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
*
33961142 TCAGGTTGCCATGGTATCTTTCAATCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
*
33961181 CAGGTTGCCTTGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
33961219 TTTCATATCA
Statistics
Matches: 111, Mismatches: 3, Indels: 16
0.85 0.02 0.12
Matches are distributed among these distances:
38 69 0.62
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 32 0.29
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:33966392 original size:46 final size:46
Alignment explanation
Indices: 33966332--33966597 Score: 334
Period size: 46 Copynumber: 6.0 Consensus size: 46
33966322 TTTAACGTGA
* * * * * *
33966332 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
33966378 TGCCATGGTATCTTTCAACCATGGACTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
33966424 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
33966470 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
33966516 TGTCATGGTATCTTTCAACCATGGTCTTACACA---C--A--A-GT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
33966554 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
33966598 AGAGCACACT
Statistics
Matches: 194, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
38 34 0.18
39 1 0.01
41 2 0.01
43 2 0.01
45 5 0.03
46 150 0.77
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:33966570 original size:38 final size:38
Alignment explanation
Indices: 33966514--33966586 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
33966504 TTCATATCAG
*
33966514 GTTGTCATGGTATCTTTCAACCATGGTCTTACACACAA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAA
33966552 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
33966587 TTTCATATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (38 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAA
Found at i:33970280 original size:22 final size:21
Alignment explanation
Indices: 33970255--33970295 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
33970245 TCCCCTGTTC
*
33970255 TTCTCTGTTTCGTTTTCTTTGT
1 TTCTCTGTTTC-ATTTCTTTGT
*
33970277 TTCTCTTTTTCATTTCTTT
1 TTCTCTGTTTCATTTCTTT
33970296 TATTTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.71
Consensus pattern (21 bp):
TTCTCTGTTTCATTTCTTTGT
Found at i:33975340 original size:18 final size:18
Alignment explanation
Indices: 33975317--33975367 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
33975307 TCAATAATAT
33975317 TCATTTATTCAGTATCAG
1 TCATTTATTCAGTATCAG
** *
33975335 TCATTTATTTTGTAACAG
1 TCATTTATTCAGTATCAG
*
33975353 TCAATTATTCAGTAT
1 TCATTTATTCAGTAT
33975368 TAGACAATCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (18 bp):
TCATTTATTCAGTATCAG
Found at i:33975899 original size:37 final size:37
Alignment explanation
Indices: 33975850--33975922 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 37
33975840 TTCAATTTTC
*
33975850 CACTCAATATTCA-CATATTTTATTCAATATCAATAAT
1 CACTCAATATTCAGAATATTTTATTCAAT-TCAATAAT
*
33975887 CACT-AATAATTCATGAATTTTTTATTCAATTCAATA
1 CACTCAAT-ATTCA-GAATATTTTATTCAATTCAATA
33975923 TCGTAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 3 0.10
37 9 0.29
38 6 0.19
39 13 0.42
ACGTcount: A:0.40, C:0.16, G:0.01, T:0.42
Consensus pattern (37 bp):
CACTCAATATTCAGAATATTTTATTCAATTCAATAAT
Found at i:33976725 original size:22 final size:22
Alignment explanation
Indices: 33976683--33976734 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
33976673 ACTATTATAA
* *
33976683 TATTTATTATTTATACATGTAT
1 TATTTATTATATACACATGTAT
33976705 GTATTTATTA-ATACACATGTAT
1 -TATTTATTATATACACATGTAT
33976727 TCATTTAT
1 T-ATTTAT
33976735 CACATCACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 16 0.62
23 9 0.35
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.54
Consensus pattern (22 bp):
TATTTATTATATACACATGTAT
Found at i:33980233 original size:3 final size:3
Alignment explanation
Indices: 33980225--33980276 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
33980215 TATGTAAATA
* *
33980225 AAT AAT AAT AGAT AA- AAT AAT AAT AAT GAT AGT AAT AAT AAAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
33980271 ATAT AA
1 A-AT AA
33980277 GTAAAAGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 2 0.05
3 30 0.73
4 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:33984312 original size:9 final size:9
Alignment explanation
Indices: 33984280--33984328 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 9
33984270 TTTTTCAAAT
33984280 AATTATTAAA
1 AATTATT-AA
*
33984290 AATTATAGAA
1 AATTAT-TAA
*
33984300 AATTTTTAA
1 AATTATTAA
33984309 AATTATTAA
1 AATTATTAA
33984318 AATTAATTAA
1 AATT-ATTAA
33984328 A
1 A
33984329 GTTAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 14 0.42
10 19 0.58
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (9 bp):
AATTATTAA
Done.