Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 16 of 26
Found at i:2598871 original size:23 final size:22
Alignment explanation
Indices: 2598800--2598871 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
2598790 TAAATTTTTT
* *
2598800 TATATTATA-TATATATTATATGT
1 TATATTATATTATATA-AATAT-A
*
2598823 TATATTATA-TATATATATTATA
1 TATATTATATTATATA-AATATA
2598845 TATATTATATTAATATAAATATA
1 TATATTATATT-ATATAAATATA
2598868 TATA
1 TATA
2598872 AAAAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.21
23 29 0.67
24 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TATATTATATTATATAAATATA
Found at i:2598880 original size:45 final size:46
Alignment explanation
Indices: 2598831--2598917 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
2598821 GTTATATTAT
* *
2598831 ATATATATATTAT-ATATATTATATTAATATAAATAT-ATATAAAAA
1 ATATATATATGATAATATATAATA-TAATATAAATATAATATAAAAA
*
2598876 ATATATATATGATAATATATAATATAATATACATATAATATA
1 ATATATATATGATAATATATAATATAATATAAATATAATATA
2598918 TTGTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 23 0.62
46 14 0.38
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (46 bp):
ATATATATATGATAATATATAATATAATATAAATATAATATAAAAA
Found at i:2598883 original size:23 final size:25
Alignment explanation
Indices: 2598805--2598918 Score: 90
Period size: 25 Copynumber: 4.6 Consensus size: 25
2598795 TTTTTTATAT
* * * **
2598805 TATATATATATTATATGTTATATTA
1 TATATATATAATATATATAATAAAA
* * * *
2598830 TATATATATATTATATATATTATAT
1 TATATATATAATATATATAATAAAA
2598855 TA-ATATA-AATATATATAA-AAAA
1 TATATATATAATATATATAATAAAA
* *
2598877 TATATATATGATAATATATAATATAA
1 TATATATATAAT-ATATATAATAAAA
*
2598903 TATACATATAATATAT
1 TATATATATAATATAT
2598919 TGTTTATTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.06
23 14 0.19
24 7 0.10
25 34 0.47
26 13 0.18
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (25 bp):
TATATATATAATATATATAATAAAA
Found at i:2598895 original size:12 final size:11
Alignment explanation
Indices: 2598800--2598918 Score: 90
Period size: 11 Copynumber: 11.1 Consensus size: 11
2598790 TAAATTTTTT
*
2598800 TATATTATATA
1 TATATAATATA
* *
2598811 TATATTATATGT
1 TATATAATAT-A
*
2598823 TATATTATATA
1 TATATAATATA
*
2598834 TATATATTATA
1 TATATAATATA
*
2598845 TATATTATAT-
1 TATATAATATA
2598855 TAATATAA-ATA
1 T-ATATAATATA
2598866 TATATAA-A-A
1 TATATAATATA
2598875 -A-AT-ATATA
1 TATATAATATA
2598883 TATGATAATATA
1 TAT-ATAATATA
2598895 TAATATAATATA
1 T-ATATAATATA
*
2598907 CATATAATATA
1 TATATAATATA
2598918 T
1 T
2598919 TGTTTATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
6 1 0.01
7 3 0.03
8 2 0.02
9 2 0.02
10 10 0.11
11 45 0.51
12 24 0.27
13 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (11 bp):
TATATAATATA
Found at i:2599022 original size:20 final size:18
Alignment explanation
Indices: 2598991--2599035 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2598981 ATTTTGTAAT
2598991 TTTTTTTATTTTCACT-TTA
1 TTTTTTTATTTT-A-TATTA
2599010 TTTTTTTAGTTTTATATTA
1 TTTTTTTA-TTTTATATTA
2599029 TTTTTTT
1 TTTTTTT
2599036 CGTTAAGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTTATTTTATATTA
Found at i:2602496 original size:89 final size:89
Alignment explanation
Indices: 2602340--2603259 Score: 999
Period size: 89 Copynumber: 10.3 Consensus size: 89
2602330 TCTGTCGTAT
* **
2602340 CATTAGTCAAATATTTTTCAT-T-GTGTCAGAAGGAATCTGATACCCACATGCATCTGTCACATC
1 CATTAGTCAAATA-TTTTC-TGTCGTGTCAGAAAGAATCTGATACCTGCATGCATCTGTCACATC
2602403 TTTCGGGTTTCAAGAAATTTATTAGG
64 TTTCGGGTTTCAAGAAATTTATTAGG
* * * *
2602429 CATTAGTCAAATATTTTCTATCGTGTCAGAATGAATCTGATACCTGCATGCATCTGTCATATTTT
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCTGCATGCATCTGTCACATCTT
2602494 TCGGGTTTCAAGAAATTTATTA-G
66 TCGGGTTTCAAGAAATTTATTAGG
* * * * * *
2602517 CATTAGTTAAATATTTTATGTCGTGTCAGAAGGAATCTGATATCC-ACATGCATATGTCATATCT
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATA-CCTGCATGCATCTGTCACATCT
2602581 TTCGGG-TTCTAAGAAATTTATTAGG
65 TTCGGGTTTC-AAGAAATTTATTAGG
* * * * *
2602606 CATTAGTTAAATATTTTCTGTCATGTCAG-AAGAAACCTGACACCTGCATGTATCTGTCACATCT
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAG-AATCTGATACCTGCATGCATCTGTCACATCT
2602670 TTCGGGTTTCAAGAAATTTATTAGG
65 TTCGGGTTTCAAGAAATTTATTAGG
* * * * *
2602695 CATTAATCAAATATTTT-TCGTCGTGTCAGAAAAAATCTGATATCC-GCATGCATTTATCACATA
1 CATTAGTCAAATATTTTCT-GTCGTGTCAGAAAGAATCTGATA-CCTGCATGCATCTGTCACATC
*
2602758 TTTCAGG-TTCTAAGAAATTTATTAGG
64 TTTCGGGTTTC-AAGAAATTTATTAGG
* * *
2602784 TATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCTGCATGCATCTGTCACATCTT
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCTGCATGCATCTGTCACATCTT
** * *
2602849 TCGAATTCCAAGAAATTTATTAAG
66 TCGGGTTTCAAGAAATTTATTAGG
* * * * * * *
2602873 TATTAGTCAAATATTTTATGTCATGTCAGAAAGAATCTGATA-CTCACATTCATTTGTCACATAT
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCT-GCATGCATCTGTCACATCT
* * *
2602937 TTTGAGTTTCAAGAAATTTATTAAG
65 TTCGGGTTTCAAGAAATTTATTAGG
* * *
2602962 TATTAGTCAAATATTTTATGTCGTGTCAGAAAGAATCTGATA-CTCGCATACATCTGTCACATCT
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCT-GCATGCATCTGTCACATCT
* *
2603026 TTCGAG-TTCAAAAAAATTTATTAGG
65 TTCGGGTTTC-AAGAAATTTATTAGG
* * * * * *
2603051 TATTAATCAAATATTTTCTATCATGTCA-AAAGAAATCTGATGCCTGCATGCATCTGTCACATAT
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAAAG-AATCTGATACCTGCATGCATCTGTCACATCT
* ** *
2603115 TT-TGAATTCAAGAAATTTATTAAG
65 TTCGGGTTTCAAGAAATTTATTAGG
** * *
2603139 CATTAGTCAAATATTTAT-TGTCTGTGTCA-AAAGGTTTCTGATACCCGCATACATCTGTCACAT
1 CATTAGTCAAATATTT-TCTGTC-GTGTCAGAAA-GAATCTGATACCTGCATGCATCTGTCACAT
* * *
2603202 CTTTTGAGTTCCAAGAAATTTATTAGG
63 CTTTCGGGTTTCAAGAAATTTATTAGG
* * *
2603229 CATTAGTTAAATATTTTCTGTCATATCAGAA
1 CATTAGTCAAATATTTTCTGTCGTGTCAGAA
2603260 GAAATTTAAT
Statistics
Matches: 712, Mismatches: 93, Indels: 51
0.83 0.11 0.06
Matches are distributed among these distances:
87 4 0.01
88 129 0.18
89 529 0.74
90 50 0.07
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (89 bp):
CATTAGTCAAATATTTTCTGTCGTGTCAGAAAGAATCTGATACCTGCATGCATCTGTCACATCTT
TCGGGTTTCAAGAAATTTATTAGG
Found at i:2603279 original size:89 final size:89
Alignment explanation
Indices: 2602340--2603384 Score: 995
Period size: 89 Copynumber: 11.8 Consensus size: 89
2602330 TCTGTCGTAT
* * *
2602340 CATTAGTCAAATATTTTTCAT-T-GTGTCAGAAGGAATCTGATACCCACATGCATCTGTCACATC
1 CATTAGTCAAATA-TTTTC-TGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATC
* * *
2602403 TTTCGGGTTTCAAGAAATTTATTAGG
64 TTTTGAGTTCCAAGAAATTTATTAGG
* * * *
2602429 CATTAGTCAAATATTTTCTATCGTGTCAGAATG-AATCTGATACCTGCATGCATCTGTCATAT-T
1 CATTAGTCAAATATTTTCTGTCATGTCAGAA-GAAATCTGATACCCGCATGCATCTGTCACATCT
* *
2602492 TTTCGGGTTTCAAGAAATTTATTA-G
65 TTT-GAGTTCCAAGAAATTTATTAGG
* * * * * * * *
2602517 CATTAGTTAAATATTTTATGTCGTGTCAGAAGGAATCTGATATCCACATGCATATGTCATATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCTT
* * *
2602582 TCGGGTTCTAAGAAATTTATTAGG
66 TTGAGTTCCAAGAAATTTATTAGG
* * * * *
2602606 CATTAGTTAAATATTTTCTGTCATGTCAGAAGAAACCTGACACCTGCATGTATCTGTCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCTT
* * *
2602671 TCGGGTTTCAAGAAATTTATTAGG
66 TTGAGTTCCAAGAAATTTATTAGG
* * * * * * *
2602695 CATTAATCAAATATTTT-TCGTCGTGTCAGAAAAAATCTGATATCCGCATGCATTTATCACAT-A
1 CATTAGTCAAATATTTTCT-GTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCT
* *
2602758 TTTCAGGTTCTAAGAAATTTATTAGG
65 TTTGA-GTTCCAAGAAATTTATTAGG
* * *
2602784 TATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCTGCATGCATCTGTCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCTT
* * *
2602849 TCGAATTCCAAGAAATTTATTAAG
66 TTGAGTTCCAAGAAATTTATTAGG
* * * * * * *
2602873 TATTAGTCAAATATTTTATGTCATGTCAGAA-AGAATCTGATACTCACATTCATTTGTCACATAT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGA-AATCTGATACCCGCATGCATCTGTCACATCT
* *
2602937 TTTGAGTTTCAAGAAATTTATTAAG
65 TTTGAGTTCCAAGAAATTTATTAGG
* * * * *
2602962 TATTAGTCAAATATTTTATGTCGTGTCAGAA-AGAATCTGATACTCGCATACATCTGTCACATCT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGA-AATCTGATACCCGCATGCATCTGTCACATCT
* * *
2603026 TTCGAGTTCAAAAAAATTTATTAGG
65 TTTGAGTTCCAAGAAATTTATTAGG
* * * * * * *
2603051 TATTAATCAAATATTTTCTATCATGTCAAAAGAAATCTGATGCCTGCATGCATCTGTCACATATT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCTT
* *
2603116 TTGAATT-CAAGAAATTTATTAAG
66 TTGAGTTCCAAGAAATTTATTAGG
* * *** *
2603139 CATTAGTCAAATATTTAT-TGTCTGTGTCAAAAGGTTTCTGATACCCGCATACATCTGTCACATC
1 CATTAGTCAAATATTT-TCTGTC-ATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATC
2603203 TTTTGAGTTCCAAGAAATTTATTAGG
64 TTTTGAGTTCCAAGAAATTTATTAGG
* * * * * *
2603229 CATTAGTTAAATATTTTCTGTCATATCAGAAGAAATTTAATACCCGCATACA--TATCACATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCTT
* ***
2603292 TTG-GATTTCAA-AAATTTTATTTTA
66 TTGAG-TTCCAAGAAA-TTTATTAGG
* * * * * * * * * *
2603316 TATTAGTCAAATATCTTCTATTATGTCAAAAGAAATCTAATATCCGTATGTATCTGTCAAATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCTT
2603381 TTGA
66 TTGA
2603385 ATTATAAATA
Statistics
Matches: 798, Mismatches: 136, Indels: 43
0.82 0.14 0.04
Matches are distributed among these distances:
86 4 0.01
87 66 0.08
88 114 0.14
89 574 0.72
90 40 0.05
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (89 bp):
CATTAGTCAAATATTTTCTGTCATGTCAGAAGAAATCTGATACCCGCATGCATCTGTCACATCTT
TTGAGTTCCAAGAAATTTATTAGG
Found at i:2603279 original size:267 final size:265
Alignment explanation
Indices: 2602340--2603387 Score: 1096
Period size: 267 Copynumber: 3.9 Consensus size: 265
2602330 TCTGTCGTAT
* *
2602340 CATTAGTCAAATATTTTTCAT-T-GTGTCAGAAGGAATCTGATACCCACATGCATCTGTCACATC
1 CATTAGTCAAATA-TTTT-ATGTCATGTCAAAAGGAATCTGATACCCACATGCATCTGTCACATC
* *
2602403 TTTCGGGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCGTGTCAGAATG-AATCT
64 TTTCGAGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCAGAA-GAAATCT
* * * * * * * * *
2602467 GATACCTGCATGCATCTGTCATATTTTTCGGGTTTCAAGAAATTTATTA-GCATTAGTTAAATAT
128 GATACCCGCATACATCTATCACATCTTTCGAG-TTCAAAAAATTTATTAGGTATTAGTCAAATAT
* * * * * * * * **
2602531 TTTATGTCGTGTCAGAAGGAATCTGATATCC-ACATGCATATGTCATATCTTTCGGGTTCTAAGA
192 TTTCTATCATGTCAAAAGAAATCTGATA-CCTGCATGCATCTGTCACATCTTTCGAATTC-AAGA
*
2602595 AATTTATTAGG
255 AATTTATTAAG
* * * * * * ** *
2602606 CATTAGTTAAATATTTTCTGTCATGTCAGAAGAAACCTGACACCTGCATGTATCTGTCACATCTT
1 CATTAGTCAAATATTTTATGTCATGTCAAAAGGAATCTGATACCCACATGCATCTGTCACATCTT
* * *
2602671 TCGGGTTTCAAGAAATTTATTAGGCATTAATCAAATATTTT-TCGTCGTGTCAGAAAAAATCTGA
66 TCGAGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCT-GTCGTGTCAGAAGAAATCTGA
* * * * *
2602735 TATCCGCATGCATTTATCACATATTTC-AGGTTCTAAGAAATTTATTAGGTATTAGTCAAATATT
130 TACCCGCATACATCTATCACATCTTTCGA-GTTC-AAAAAATTTATTAGGTATTAGTCAAATATT
* * *
2602799 TTCTGTCATGTCAGAAGGAATCTGATACCTGCATGCATCTGTCACATCTTTCGAATTCCAAGAAA
193 TTCTATCATGTCAAAAGAAATCTGATACCTGCATGCATCTGTCACATCTTTCGAATT-CAAGAAA
2602864 TTTATTAAG
257 TTTATTAAG
* * * * *
2602873 TATTAGTCAAATATTTTATGTCATGTCAGAAA-GAATCTGATACTCACATTCATTTGTCACATAT
1 CATTAGTCAAATATTTTATGTCATGTCA-AAAGGAATCTGATACCCACATGCATCTGTCACATCT
* * * *
2602937 TTTGAGTTTCAAGAAATTTATTAAGTATTAGTCAAATATTTTATGTCGTGTCAGAA-AGAATCTG
65 TTCGAGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCAGAAGA-AATCTG
* * *
2603001 ATACTCGCATACATCTGTCACATCTTTCGAGTTCAAAAAAATTTATTAGGTATTAATCAAATATT
129 ATACCCGCATACATCTATCACATCTTTCGAGTTC-AAAAAATTTATTAGGTATTAGTCAAATATT
* * *
2603066 TTCTATCATGTCAAAAGAAATCTGATGCCTGCATGCATCTGTCACATATTTTGAATTCAAGAAAT
193 TTCTATCATGTCAAAAGAAATCTGATACCTGCATGCATCTGTCACATCTTTCGAATTCAAGAAAT
2603131 TTATTAAG
258 TTATTAAG
* ** * *
2603139 CATTAGTCAAATA-TTTATTGTCTGTGTCAAAAGGTTTCTGATACCCGCATACATCTGTCACATC
1 CATTAGTCAAATATTTTA-TGTC-ATGTCAAAAGGAATCTGATACCCACATGCATCTGTCACATC
* * * * * * *
2603203 TTTTGAGTTCCAAGAAATTTATTAGGCATTAGTTAAATATTTTCTGTCATATCAGAAGAAATTTA
64 TTTCGAGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCAGAAGAAATCTG
* * * *** *
2603268 ATACCCGCATACA--TATCACATCTTTTGGATTTCAAAAATTTTATTTTATATTAGTCAAATATC
129 ATACCCGCATACATCTATCACATC-TTTCGAGTTCAAAAAATTTATTAGGTATTAGTCAAATATT
* * * * * *
2603331 TTCTATTATGTCAAAAGAAATCTAATATCC-GTATGTATCTGTCAAATCTTTTGAATT
193 TTCTATCATGTCAAAAGAAATCTGATA-CCTGCATGCATCTGTCACATCTTTCGAATT
2603388 ATAAATATTT
Statistics
Matches: 665, Mismatches: 98, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
264 1 0.00
265 92 0.14
266 189 0.28
267 377 0.57
268 6 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (265 bp):
CATTAGTCAAATATTTTATGTCATGTCAAAAGGAATCTGATACCCACATGCATCTGTCACATCTT
TCGAGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTCAGAAGAAATCTGAT
ACCCGCATACATCTATCACATCTTTCGAGTTCAAAAAATTTATTAGGTATTAGTCAAATATTTTC
TATCATGTCAAAAGAAATCTGATACCTGCATGCATCTGTCACATCTTTCGAATTCAAGAAATTTA
TTAAG
Found at i:2603321 original size:87 final size:88
Alignment explanation
Indices: 2603230--2603421 Score: 210
Period size: 89 Copynumber: 2.2 Consensus size: 88
2603220 TTTATTAGGC
* * * * *
2603230 ATTAGTTAAATATTTTCTGTCATATCAGAAGAAATTTAATACCCGCA-TA-CATATCACATCTTT
1 ATTAGTCAAATATTTTCTATCATATCAAAAGAAATCTAATACCCGCAGTATC-TATCAAATCTTT
*
2603293 TGGATT-TCAAAAATTTTATTTTAT
65 TGAATTAT-AAAAATTTTATTTTAT
* * * * * *
2603317 ATTAGTCAAATATCTTCTATTATGTCAAAAGAAATCTAATATCCGTATGTATCTGTCAAATCTTT
1 ATTAGTCAAATATTTTCTATCATATCAAAAGAAATCTAATACCCGCA-GTATCTATCAAATCTTT
*
2603382 TGAATTATAAATATTTTATTTTAT
65 TGAATTATAAAAATTTTATTTTAT
*
2603406 ATTAATCAAATATTTT
1 ATTAGTCAAATATTTT
2603422 TTTATCAGAA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
87 38 0.44
89 46 0.53
90 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (88 bp):
ATTAGTCAAATATTTTCTATCATATCAAAAGAAATCTAATACCCGCAGTATCTATCAAATCTTTT
GAATTATAAAAATTTTATTTTAT
Found at i:2603519 original size:2 final size:2
Alignment explanation
Indices: 2603510--2603599 Score: 69
Period size: 2 Copynumber: 50.5 Consensus size: 2
2603500 AATAAATAAA
2603510 AT AT -T AT AT AT -T AT AT AT AT -T AT -T AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2603546 -T AT -T AT AT AT -T A- AT AT AA AT AT AT AT AT AT AT A- ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
2603584 -T AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
2603600 GTAACAATTG
Statistics
Matches: 71, Mismatches: 4, Indels: 26
0.70 0.04 0.26
Matches are distributed among these distances:
1 12 0.17
2 58 0.82
3 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2603531 original size:16 final size:16
Alignment explanation
Indices: 2603510--2603598 Score: 83
Period size: 16 Copynumber: 5.2 Consensus size: 16
2603500 AATAAATAAA
2603510 ATATTATATATTATAT
1 ATATTATATATTATAT
2603526 ATATTATTATATTATTAT
1 ATATTA-TATATTA-TAT
2603544 ATTATTATATATTA-AT
1 A-TATTATATATTATAT
*
2603560 ATAAATATATATATATAT
1 AT-ATTATATAT-TATAT
*
2603578 AACTATTATAT-GTATAT
1 -A-TATTATATATTATAT
2603595 ATAT
1 ATAT
2603599 AGTAACAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
15 4 0.06
16 18 0.29
17 14 0.23
18 13 0.21
19 12 0.19
20 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (16 bp):
ATATTATATATTATAT
Found at i:2603691 original size:35 final size:31
Alignment explanation
Indices: 2603644--2603726 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 31
2603634 TTGTATTCTC
* *
2603644 TTTTTTATTTTTTTAATATTTTAATTTATTTAA
1 TTTTTTAATTTTTTAATATTTTAA--TATATAA
*
2603677 TTTTTTTTAATTTTTTAAAATTTTAATATATAA
1 --TTTTTTAATTTTTTAATATTTTAATATATAA
*
2603710 TTTTTAAATTTTTTAAT
1 TTTTTTAATTTTTTAAT
2603727 TTATTTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 15 0.35
33 6 0.14
35 22 0.51
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (31 bp):
TTTTTTAATTTTTTAATATTTTAATATATAA
Found at i:2603694 original size:8 final size:8
Alignment explanation
Indices: 2603644--2603734 Score: 76
Period size: 8 Copynumber: 11.0 Consensus size: 8
2603634 TTGTATTCTC
*
2603644 TTTTTTAT
1 TTTTTTAA
2603652 TTTTTTAA
1 TTTTTTAA
*
2603660 TATTTTAA
1 TTTTTTAA
2603668 TTTATTTAA
1 TTT-TTTAA
2603677 TTTTTTTTAA
1 --TTTTTTAA
2603687 TTTTTTAA
1 TTTTTTAA
**
2603695 AATTTTAA
1 TTTTTTAA
* *
2603703 -TATATAA
1 TTTTTTAA
*
2603710 TTTTTAAA
1 TTTTTTAA
2603718 TTTTTTAA
1 TTTTTTAA
2603726 TTTATTTAA
1 TTT-TTTAA
2603735 ATAAATTATA
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
7 4 0.06
8 44 0.67
9 10 0.15
10 5 0.08
11 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTTTAA
Found at i:2603724 original size:9 final size:9
Alignment explanation
Indices: 2603650--2603736 Score: 54
Period size: 9 Copynumber: 9.2 Consensus size: 9
2603640 TCTCTTTTTT
*
2603650 ATTTTTTTA
1 ATTTTTTAA
*
2603659 ATATTTT-A
1 ATTTTTTAA
2603667 ATTTATTTAA
1 ATTT-TTTAA
* *
2603677 TTTTTTTTA
1 ATTTTTTAA
2603686 ATTTTTTAAA
1 ATTTTTT-AA
2603696 ATTTTAATATATA
1 ATTTT--T-TA-A
2603709 A-TTTTTAA
1 ATTTTTTAA
2603717 ATTTTTT-A
1 ATTTTTTAA
2603725 ATTTATTTAA
1 ATTT-TTTAA
2603735 AT
1 AT
2603737 AAATTATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
8 11 0.18
9 29 0.47
10 14 0.23
12 5 0.08
13 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:2609816 original size:25 final size:25
Alignment explanation
Indices: 2609771--2609818 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2609761 TTTAATTAAC
* *
2609771 TATTATATAATTATATAAATTTATT
1 TATTATATAAATAAATAAATTTATT
2609796 TATTATATTAAATAAAT-AATTTA
1 TATTATA-TAAATAAATAAATTTA
2609819 AAAGATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTATATAAATAAATAAATTTATT
Found at i:2614328 original size:11 final size:11
Alignment explanation
Indices: 2614295--2614343 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
2614285 ATTTATTTGG
**
2614295 TTTAATTTTTA
1 TTTAATTTAAA
*
2614306 TTGAATTT-AA
1 TTTAATTTAAA
2614316 TTTAATTTAAA
1 TTTAATTTAAA
2614327 TTTAAATTTAAA
1 TTT-AATTTAAA
2614339 TTTAA
1 TTTAA
2614344 ATAGTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 8 0.24
11 14 0.42
12 11 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:2614330 original size:6 final size:6
Alignment explanation
Indices: 2614309--2614345 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2614299 ATTTTTATTG
2614309 AATTT- AATTT- AATTTA AATTTA AATTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
2614346 AGTAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:2614901 original size:23 final size:22
Alignment explanation
Indices: 2614874--2614916 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2614864 TAGTGCGTTT
*
2614874 AATTCATATATATTCATAAATAA
1 AATTCATATATAAT-ATAAATAA
*
2614897 AATTCATTTATAATATAAAT
1 AATTCATATATAATATAAAT
2614917 TCATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTCATATATAATATAAATAA
Found at i:2614916 original size:17 final size:16
Alignment explanation
Indices: 2614892--2614923 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2614882 TATATTCATA
2614892 AATAAAATTCATTTAT
1 AATAAAATTCATTTAT
2614908 AATATAAATTCATTTA
1 AATA-AAATTCATTTA
2614924 AAAGTTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAAATTCATTTAT
Found at i:2615795 original size:16 final size:17
Alignment explanation
Indices: 2615738--2615796 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
2615728 TCATATTTAA
*
2615738 AAATATTTATATTTATAT
1 AAAT-TTTATACTTATAT
*
2615756 TAATTTTAATACGTTA-AT
1 AAATTTT-ATAC-TTATAT
2615774 -AATTTTATA-TTATAT
1 AAATTTTATACTTATAT
2615789 AAATTTTA
1 AAATTTTA
2615797 AATCAAGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 3 0.09
15 2 0.06
16 10 0.29
17 9 0.26
18 8 0.23
19 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
AAATTTTATACTTATAT
Found at i:2622248 original size:2 final size:2
Alignment explanation
Indices: 2622241--2622278 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2622231 GGAACTTATA
2622241 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2622279 GAACGTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2622584 original size:20 final size:21
Alignment explanation
Indices: 2622559--2622612 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
2622549 TTTATATTAA
2622559 ATATTATATTATTAA-ATAAT
1 ATATTATATTATTAATATAAT
* *
2622579 ATATTATTATTGTTAATTTAAT
1 ATATTA-TATTATTAATATAAT
*
2622601 AAATT-TATTATT
1 ATATTATATTATT
2622613 TATTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.43
21 8 0.29
22 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTATATTATTAATATAAT
Found at i:2622589 original size:18 final size:15
Alignment explanation
Indices: 2622553--2622587 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2622543 TTTAATTTTA
2622553 TATTAAATATTATAT
1 TATTAAATATTATAT
*
2622568 TATTAAATAATATAT
1 TATTAAATATTATAT
2622583 TATTA
1 TATTA
2622588 TTGTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTAAATATTATAT
Found at i:2622633 original size:28 final size:27
Alignment explanation
Indices: 2622570--2622642 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
2622560 TATTATATTA
* *
2622570 TTAAATAATATATTA-TTATTGTTAAT
1 TTAAATAATTTATTATTTATTGTAAAT
2622596 TT-AATAAATTTATTATTTATT-TAAATAT
1 TTAAAT-AATTTATTATTTATTGT-AA-AT
*
2622624 TTAAATAATTTTTTATTTA
1 TTAAATAATTTATTATTTA
2622643 AATTAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 3 0.08
26 11 0.28
27 6 0.15
28 16 0.41
29 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TTAAATAATTTATTATTTATTGTAAAT
Found at i:2623088 original size:11 final size:11
Alignment explanation
Indices: 2623046--2623088 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
2623036 TTATATTTTA
2623046 AATAT-AATCAT
1 AATATAAAT-AT
*
2623057 AATATAAAAAT
1 AATATAAATAT
*
2623068 AATATTAATAT
1 AATATAAATAT
2623079 AATATAAATA
1 AATATAAATA
2623089 CATAAGTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 25 0.93
12 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAAATAT
Found at i:2624603 original size:22 final size:22
Alignment explanation
Indices: 2624567--2624630 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
2624557 AATTTAATTT
2624567 AATTAAT-TTTATAATTTTTTAA
1 AATTAATATTT-TAATTTTTTAA
*
2624589 AATATAATA-TTTAATAATTTTAA
1 AAT-TAATATTTTAAT-TTTTTAA
*
2624612 AATTTATATTTTAATTTTT
1 AATTAATATTTTAATTTTT
2624631 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTAATATTTTAATTTTTTAA
Found at i:2626695 original size:7 final size:7
Alignment explanation
Indices: 2626683--2626721 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
2626673 AAAATTATTA
2626683 TAAATAT
1 TAAATAT
2626690 TAAATAT
1 TAAATAT
*
2626697 TAAATTT
1 TAAATAT
2626704 TAAATTTAT
1 TAAA--TAT
2626713 TAAATAT
1 TAAATAT
2626720 TA
1 TA
2626722 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 22 0.79
9 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TAAATAT
Found at i:2626713 original size:16 final size:16
Alignment explanation
Indices: 2626683--2626731 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2626673 AAAATTATTA
2626683 TAAATATTAAA--TAT
1 TAAATATTAAATTTAT
*
2626697 TAAATTTTAAATTTAT
1 TAAATATTAAATTTAT
*
2626713 TAAATATTATATTT-T
1 TAAATATTAAATTTAT
2626728 TAAA
1 TAAA
2626732 ATAATTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 10 0.33
15 5 0.17
16 15 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATATTAAATTTAT
Found at i:2627235 original size:28 final size:31
Alignment explanation
Indices: 2627200--2627260 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
2627190 TATAATGAAG
2627200 TATTTTAA-TTTTATATTATT-AAA-TATAA
1 TATTTTAATTTTTATATTATTAAAATTATAA
*
2627228 TATTTTAATTTTTATATTTTTAAAATTATAA
1 TATTTTAATTTTTATATTATTAAAATTATAA
2627259 TA
1 TA
2627261 AGTAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 8 0.28
29 11 0.38
30 3 0.10
31 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TATTTTAATTTTTATATTATTAAAATTATAA
Found at i:2627289 original size:17 final size:19
Alignment explanation
Indices: 2627247--2627289 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
2627237 TTTTATATTT
2627247 TTAAAATTATAATAAGTAAA
1 TTAAAATTAT-ATAAGTAAA
*
2627267 TAAAAATTAT-TAA-TAAA
1 TTAAAATTATATAAGTAAA
2627284 TTAAAA
1 TTAAAA
2627290 AATATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
20 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAATTATATAAGTAAA
Found at i:2627290 original size:18 final size:19
Alignment explanation
Indices: 2627249--2627295 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
2627239 TTATATTTTT
2627249 AAAATTATAATAAGTAAATA
1 AAAATTAT-ATAAGTAAATA
2627269 AAAATTAT-TAA-TAAATTA
1 AAAATTATATAAGTAAA-TA
*
2627287 AAAAATATA
1 AAAATTATA
2627296 AATATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
20 8 0.33
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATTATATAAGTAAATA
Found at i:2627621 original size:24 final size:24
Alignment explanation
Indices: 2627572--2627622 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2627562 TATAATTATA
*
2627572 TATTAATTTAATAATTGATTTGTT
1 TATTAATTTAATAATTGAATTGTT
* *
2627596 TATTTATTTAATTATTGTAATT-TT
1 TATTAATTTAATAATTG-AATTGTT
2627620 TAT
1 TAT
2627623 CTTTTTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
TATTAATTTAATAATTGAATTGTT
Found at i:2628544 original size:20 final size:21
Alignment explanation
Indices: 2628507--2628554 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2628497 TATCAAAATA
2628507 TATATTTTATTAATTATTTAT
1 TATATTTTATTAATTATTTAT
2628528 TATA-TTTATT-ATGTATTTA-
1 TATATTTTATTAAT-TATTTAT
2628547 -ATATTTTA
1 TATATTTTA
2628555 AATATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 6 0.24
20 12 0.48
21 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TATATTTTATTAATTATTTAT
Found at i:2628810 original size:28 final size:27
Alignment explanation
Indices: 2628778--2628836 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
2628768 TTATTTATAT
*
2628778 TAAATTAAAT-TATTTAATTATTAATTAA
1 TAAATAAAATATATTTAATT-TTAATT-A
*
2628806 TAAATAAAATATTTTTAATTTTAATTA
1 TAAATAAAATATATTTAATTTTAATTA
2628833 TAAA
1 TAAA
2628837 ATATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.18
28 15 0.54
29 8 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAAATAAAATATATTTAATTTTAATTA
Found at i:2628825 original size:22 final size:22
Alignment explanation
Indices: 2628794--2628863 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
2628784 AAATTATTTA
2628794 ATTATTAATTAATAAATAAAAT
1 ATTATTAATTAATAAATAAAAT
* *
2628816 ATTTTTAATTTTAAT-TATAAAAT
1 ATTATTAA--TTAATAAATAAAAT
2628839 ATTATT-ATTAATATAA-AAAA-
1 ATTATTAATTAATA-AATAAAAT
2628859 ATTAT
1 ATTAT
2628864 AATATATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
20 10 0.25
21 4 0.10
22 9 0.22
23 12 0.30
24 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTATTAATTAATAAATAAAAT
Found at i:2628875 original size:35 final size:33
Alignment explanation
Indices: 2628822--2628896 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 33
2628812 AAATATTTTT
* *
2628822 AATTTTAATTATAAAATATTATTATTAATATAAAAA
1 AATTATAATTATAAAATA-TATT-TTAAAAT-AAAA
* *
2628858 AATTATAA-TATATAATATATTTTAAAATATAA
1 AATTATAATTATAAAATATATTTTAAAATAAAA
2628890 AATTATA
1 AATTATA
2628897 TTTTTAAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 10 0.29
33 6 0.17
34 4 0.11
35 8 0.23
36 7 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
AATTATAATTATAAAATATATTTTAAAATAAAA
Found at i:2628934 original size:2 final size:2
Alignment explanation
Indices: 2628927--2628955 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2628917 AACTAAACCT
2628927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2628956 TTGGGGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2629402 original size:15 final size:16
Alignment explanation
Indices: 2629376--2629405 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2629366 TGAAATTTTT
2629376 TTTATATAAATAATTA
1 TTTATATAAATAATTA
2629392 TTTATAT-AATAATT
1 TTTATATAAATAATT
2629406 TTATTAAATA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATATAAATAATTA
Found at i:2629464 original size:12 final size:12
Alignment explanation
Indices: 2629418--2629469 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
2629408 ATTAAATACG
*
2629418 TAAATATTTTATA
1 TAAATA-TTAATA
*
2629431 TTAATATTAATAAA
1 TAAATATTAAT--A
2629445 TAAATATTAATA
1 TAAATATTAATA
*
2629457 TAATTATTAATA
1 TAAATATTAATA
2629469 T
1 T
2629470 TTAATTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 17 0.52
13 5 0.15
14 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTAATA
Found at i:2629464 original size:26 final size:27
Alignment explanation
Indices: 2629418--2629468 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2629408 ATTAAATACG
*
2629418 TAAATATTTTATATTAATATTAATAAA
1 TAAATATTTAATATTAATATTAATAAA
2629445 TAAATA-TTAATA-TAATTATTAATA
1 TAAATATTTAATATTAA-TATTAATA
2629469 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 13 0.59
27 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAATATTTAATATTAATATTAATAAA
Found at i:2629473 original size:19 final size:18
Alignment explanation
Indices: 2629429--2629482 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 18
2629419 AAATATTTTA
2629429 TATTAATATTAATA-AA-
1 TATTAATATTAATATAAT
2629445 TA--AATATTAATATAAT
1 TATTAATATTAATATAAT
*
2629461 TATTAATATTTAATTTAAT
1 TATTAATA-TTAATATAAT
2629480 TAT
1 TAT
2629483 GATCCGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.31
15 2 0.06
16 4 0.12
18 4 0.12
19 12 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAATATTAATATAAT
Found at i:2629555 original size:14 final size:13
Alignment explanation
Indices: 2629536--2629598 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 13
2629526 TATTATAATT
*
2629536 ATATTAAATTTTAA
1 ATATT-AATATTAA
2629550 ATATT-ATATTAA
1 ATATTAATATTAA
*
2629562 ATATTTAT-TTAAAA
1 ATATTAATATT--AA
2629576 ATATTAATATTAA
1 ATATTAATATTAA
*
2629589 ATATTTATAT
1 ATATTAATAT
2629599 ATTTGATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
12 13 0.31
13 13 0.31
14 14 0.33
15 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTAATATTAA
Found at i:2629563 original size:12 final size:12
Alignment explanation
Indices: 2629546--2629598 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
2629536 ATATTAAATT
2629546 TTAAATATTATA
1 TTAAATATTATA
2629558 TTAAATATT-TA
1 TTAAATATTATA
2629569 TTTAAAAATATTAATA
1 -TT--AAATATT-ATA
2629585 TTAAATATTTATA
1 TTAAATA-TTATA
2629598 T
1 T
2629599 ATTTGATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
11 2 0.06
12 11 0.31
13 9 0.26
14 9 0.26
15 2 0.06
16 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:2629649 original size:26 final size:26
Alignment explanation
Indices: 2629595--2629664 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
2629585 TTAAATATTT
**
2629595 ATATATTTG-ATAAAAAATAATAATG
1 ATATATTTGTATAAAAAATAATAAAA
**
2629620 ATATATTTGTATAAAAAATTTTAAAA
1 ATATATTTGTATAAAAAATAATAAAA
2629646 ATAT-TTT-TATTAAAAAATA
1 ATATATTTGTA-TAAAAAATA
2629665 TATAGTACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 2 0.05
25 20 0.53
26 16 0.42
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATATTTGTATAAAAAATAATAAAA
Found at i:2631831 original size:2 final size:2
Alignment explanation
Indices: 2631824--2631852 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2631814 GGAAAGAAGA
2631824 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2631853 GTAGACATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2639775 original size:9 final size:10
Alignment explanation
Indices: 2639752--2639784 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2639742 TTTCCTCCTT
2639752 TTTTTTATTA
1 TTTTTTATTA
2639762 TTTTTTATTA
1 TTTTTTATTA
2639772 TTTTTTATT-
1 TTTTTTATTA
2639781 TTTT
1 TTTT
2639785 ATGAAAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:2649340 original size:3 final size:3
Alignment explanation
Indices: 2649332--2649372 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2649322 GGAAACTGTT
2649332 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2649373 TACCGTTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2650409 original size:172 final size:176
Alignment explanation
Indices: 2650216--2650548 Score: 514
Period size: 172 Copynumber: 1.9 Consensus size: 176
2650206 ATATGAAAAA
*
2650216 TTTTTGTCACACATTCAAATAAAATATAAATCAATAATAAATAACATGAAGATTTTTA-T-TAT-
1 TTTTTGTCACACATTCAAATAAAATATAAATCAATAATAAATAACATGAAGATTTTGATTATATA
* * *
2650278 TTTTATCAAATTTATTAAGAATTTTATTATAAAATGTAATTATGATAT-AATAAAAAAATTTTAA
66 TTTTATAAAATTTATTAAGAATTTTATTATAAAATATAATTATGAAATGAATAAAAAAATTTTAA
* *
2650342 TACGCATCCAAAT-AACGTTATCTTTAATAATTACGATATAAAATTT
131 TACCCATCCAAATGAA-ATTATCTTTAATAATTACGATATAAAATTT
* * *
2650388 TTTTTGTCACACATTCAAATAAAGTATAAATCAATAATAAATAATATGATGATTTTGATTATATA
1 TTTTTGTCACACATTCAAATAAAATATAAATCAATAATAAATAACATGAAGATTTTGATTATATA
*
2650453 TTTTATAAAATTTATTAAGAATTTTATTATAAAATATAATTATGAAATGATTAAAAAAATTTTAA
66 TTTTATAAAATTTATTAAGAATTTTATTATAAAATATAATTATGAAATGAATAAAAAAATTTTAA
* *
2650518 TACCCATCTAAATGAAATTATTTTTAATAAT
131 TACCCATCCAAATGAAATTATCTTTAATAAT
2650549 AATCTCAACA
Statistics
Matches: 144, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
172 54 0.38
173 1 0.01
174 3 0.02
175 45 0.31
176 39 0.27
177 2 0.01
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (176 bp):
TTTTTGTCACACATTCAAATAAAATATAAATCAATAATAAATAACATGAAGATTTTGATTATATA
TTTTATAAAATTTATTAAGAATTTTATTATAAAATATAATTATGAAATGAATAAAAAAATTTTAA
TACCCATCCAAATGAAATTATCTTTAATAATTACGATATAAAATTT
Found at i:2650798 original size:15 final size:16
Alignment explanation
Indices: 2650775--2650812 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2650765 ATATTATTTT
2650775 TTAATATTAATATATA
1 TTAATATTAATATATA
*
2650791 TTAA-ATTAATATATT
1 TTAATATTAATATATA
2650806 TTAATAT
1 TTAATAT
2650813 ATCGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATATTAATATATA
Found at i:2651084 original size:32 final size:32
Alignment explanation
Indices: 2651012--2651072 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
2651002 TAATGAATGT
*
2651012 TAAATTTATGAGTAATTATATATAATATTCAA
1 TAAATTTATGAGAAATTATATATAATATTCAA
*
2651044 TAAATTTATGAGAAATTATATTTAATATT
1 TAAATTTATGAGAAATTATATATAATATT
2651073 TATCAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (32 bp):
TAAATTTATGAGAAATTATATATAATATTCAA
Found at i:2656768 original size:58 final size:58
Alignment explanation
Indices: 2656702--2656909 Score: 299
Period size: 58 Copynumber: 3.6 Consensus size: 58
2656692 CCTTGGCGGA
* *
2656702 GATCTAAGTTTGGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGGTGAC
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGGTGGC
* *
2656760 GATCTAAGTTCCGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCTTGGTGGC
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGGTGGC
* * * * * * *
2656818 AATCTAAGTTCGGGTGACTTGGCATCACTTGGTGCGTGAATTGGGTCGCCCTAGTGGC
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGGTGGC
* *
2656876 GATCTAAGTTCGGGTGACTCGGCGTCACCCAGTG
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTG
2656910 CGCGGATCTA
Statistics
Matches: 131, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 131 1.00
ACGTcount: A:0.16, C:0.22, G:0.34, T:0.28
Consensus pattern (58 bp):
GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGGTGGC
Found at i:2656827 original size:116 final size:117
Alignment explanation
Indices: 2656656--2656909 Score: 318
Period size: 116 Copynumber: 2.2 Consensus size: 117
2656646 CCGAGTCTGA
* * *
2656656 GTGACTTGGTGTCACGT-GATGTGGTAATCTGGGTCACCTTGGCGGAGATCTAAGTTTGGGTGAC
1 GTGACTTGGCGTCACCTAG-TGTGGTAATCTGGGTCACCTTGGCGGAGATCTAAGTTCGGGTGAC
* * *
2656720 TTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGGTGACGATCTAAGTTCCG
65 TTGGCATCACCTAGTGCGTGAATCGGGTCGCCCTAGTGACGATCTAAGTTCCG
* *
2656773 GTGACTTGGCGTCACCTAGTGT-GTGAATC-GGGTCGCCTTGGTGGCA-ATCTAAGTTCGGGTGA
1 GTGACTTGGCGTCACCTAGTGTGGT-AATCTGGGTCACCTTGGCGG-AGATCTAAGTTCGGGTGA
* * * * *
2656835 CTTGGCATCACTTGGTGCGTGAATTGGGTCGCCCTAGTGGCGATCTAAGTTCGG
64 CTTGGCATCACCTAGTGCGTGAATCGGGTCGCCCTAGTGACGATCTAAGTTCCG
* *
2656889 GTGACTCGGCGTCACCCAGTG
1 GTGACTTGGCGTCACCTAGTG
2656910 CGCGGATCTA
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
116 95 0.80
117 23 0.19
118 1 0.01
ACGTcount: A:0.16, C:0.21, G:0.34, T:0.29
Consensus pattern (117 bp):
GTGACTTGGCGTCACCTAGTGTGGTAATCTGGGTCACCTTGGCGGAGATCTAAGTTCGGGTGACT
TGGCATCACCTAGTGCGTGAATCGGGTCGCCCTAGTGACGATCTAAGTTCCG
Found at i:2656924 original size:58 final size:58
Alignment explanation
Indices: 2656702--2656943 Score: 286
Period size: 58 Copynumber: 4.2 Consensus size: 58
2656692 CCTTGGCGGA
* * * *
2656702 GATCTAAGTTTGGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGGTGAC
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGCGTGAATCGGGTCGCCCTAGTGGC
* * * *
2656760 GATCTAAGTTCCGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCTTGGTGGC
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGCGTGAATCGGGTCGCCCTAGTGGC
* * * * *
2656818 AATCTAAGTTCGGGTGACTTGGCATCACTTGGTGCGTGAATTGGGTCGCCCTAGTGGC
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGCGTGAATCGGGTCGCCCTAGTGGC
* * * * ** * * *
2656876 GATCTAAGTTCGGGTGACTCGGCGTCACCCAGTGCGCGGATCTAGTCGCCTTAGTAGT
1 GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGCGTGAATCGGGTCGCCCTAGTGGC
2656934 GATCTAAGTT
1 GATCTAAGTT
2656944 TGTAGTGTGA
Statistics
Matches: 157, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 157 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.29
Consensus pattern (58 bp):
GATCTAAGTTCGGGTGACTTGGCGTCACCTAGTGCGTGAATCGGGTCGCCCTAGTGGC
Found at i:2665023 original size:13 final size:13
Alignment explanation
Indices: 2665005--2665042 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
2664995 CAAAGATCAG
2665005 TGTATCGATACAA
1 TGTATCGATACAA
2665018 TGTATCGATACAA
1 TGTATCGATACAA
2665031 TGTATCGATACA
1 TGTATCGATACA
2665043 TTTTCTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2665107 original size:32 final size:32
Alignment explanation
Indices: 2665066--2665151 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
2665056 AGCTTCGTAG
*
2665066 CGATACATTGTATTGATATAAAACTTATGTAT
1 CGATACATTGTATCGATATAAAACTTATGTAT
* *
2665098 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATATAAAACTTATGTAT
2665130 CGATACATTGTATCGATATAAA
1 CGATACATTGTATCGATATAAA
2665152 TCGTTGAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATATAAAACTTATGTAT
Found at i:2665111 original size:13 final size:13
Alignment explanation
Indices: 2665093--2665147 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
2665083 ATAAAACTTA
2665093 TGTATCGATACAT
1 TGTATCGATACAT
2665106 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
2665124 ATGTATCGATACAT
1 -TGTATCGATACAT
2665138 TGTATCGATA
1 TGTATCGATA
2665148 TAAATCGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 19 0.53
14 1 0.03
16 6 0.17
18 1 0.03
19 9 0.25
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2667904 original size:14 final size:14
Alignment explanation
Indices: 2667864--2667904 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2667854 TCTAATTTAA
* *
2667864 AAATAAAAAATTAT
1 AAATAATAAATTTT
*
2667878 AAATATTAAATTTT
1 AAATAATAAATTTT
2667892 AAATAATAAATTT
1 AAATAATAAATTT
2667905 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATAATAAATTTT
Found at i:2667924 original size:29 final size:29
Alignment explanation
Indices: 2667891--2667950 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2667881 TATTAAATTT
**
2667891 TAAATAATAAATTTATTT-TTTATTAAAAA
1 TAAATAA-AAATTTATTTGAATATTAAAAA
*
2667920 TAAATTAAAATTTATTTGAATATTAAAAA
1 TAAATAAAAATTTATTTGAATATTAAAAA
2667949 TA
1 TA
2667951 TCGAGTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATAAAAATTTATTTGAATATTAAAAA
Found at i:2669069 original size:31 final size:31
Alignment explanation
Indices: 2669020--2669082 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
2669010 TTATAATTAA
2669020 TTTATTATTTTATATTTTAAGTTTTTAAAAT
1 TTTATTATTTTATATTTTAAGTTTTTAAAAT
*
2669051 TTTATTTATTTTAT-TTTTAATTTTTTAAAAT
1 TTTA-TTATTTTATATTTTAAGTTTTTAAAAT
2669082 T
1 T
2669083 GAAAAGCCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTATTATTTTATATTTTAAGTTTTTAAAAT
Found at i:2669779 original size:17 final size:16
Alignment explanation
Indices: 2669755--2669788 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2669745 ATATAAAAAA
2669755 TAAAAAATAATAATAT
1 TAAAAAATAATAATAT
*
2669771 TAAACAAATAATCATAT
1 TAAA-AAATAATAATAT
2669788 T
1 T
2669789 TATCCATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAAATAATAATAT
Found at i:2669914 original size:40 final size:40
Alignment explanation
Indices: 2669823--2669914 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 40
2669813 ATTTTATAAT
* * * *
2669823 AAAAATAATAATAATATTATATTATATAATTCTAAAATTA
1 AAAAATAATTATAATATTATATAATATAAATATAAAATTA
** *
2669863 AATTATGAATTAT-ATATTATATAATATAAATATATAATTTA
1 AAAAAT-AATTATAATATTATATAATATAAATATA-AAATTA
2669904 AAAAATAATTA
1 AAAAATAATTA
2669915 ACATGATATA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
40 27 0.66
41 14 0.34
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (40 bp):
AAAAATAATTATAATATTATATAATATAAATATAAAATTA
Found at i:2670151 original size:29 final size:30
Alignment explanation
Indices: 2670100--2670171 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
2670090 TTCATCCAAA
* * *
2670100 TATATTAATGTAATTTCATAATAAA-AATAT
1 TATATT-ATATAATTTAAAAATAAATAATAT
*
2670130 TATATTATATAATTTAAAAATAAATTATAT
1 TATATTATATAATTTAAAAATAAATAATAT
*
2670160 AATATATATATA
1 TATAT-TATATA
2670172 TATAATTCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 15 0.43
30 14 0.40
31 6 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TATATTATATAATTTAAAAATAAATAATAT
Found at i:2670191 original size:35 final size:37
Alignment explanation
Indices: 2670125--2670201 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 37
2670115 TCATAATAAA
*
2670125 AATAT-TATATTATATAATTTAAAAATAAATT-ATAT
1 AATATATATATTATATAATTGAAAAATAAATTAATAT
*
2670160 AATATATATA-TATATAATTCGAAAGAT-AATTAATAT
1 AATATATATATTATATAATT-GAAAAATAAATTAATAT
*
2670196 GATATA
1 AATATA
2670202 AAAAATCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 18 0.50
36 18 0.50
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (37 bp):
AATATATATATTATATAATTGAAAAATAAATTAATAT
Found at i:2671506 original size:40 final size:40
Alignment explanation
Indices: 2671449--2671528 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
2671439 AGCTTTGAAT
*
2671449 TGGTAATGACAGGGGCATATGCATTTCAAGGGAGTAGTAG
1 TGGTAATGACAGAGGCATATGCATTTCAAGGGAGTAGTAG
2671489 TGGTAATGACAGAGGCATATGCATTTCAAGGGAGTAGTAG
1 TGGTAATGACAGAGGCATATGCATTTCAAGGGAGTAGTAG
2671529 AAGCAAAGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.34, T:0.25
Consensus pattern (40 bp):
TGGTAATGACAGAGGCATATGCATTTCAAGGGAGTAGTAG
Found at i:2674046 original size:2 final size:2
Alignment explanation
Indices: 2674039--2674071 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2674029 GTCATCTATG
2674039 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2674072 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2674076 original size:2 final size:2
Alignment explanation
Indices: 2674071--2674119 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2674061 TCTCTCTCTC
*
2674071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2674113 AA TA TA T
1 TA TA TA T
2674120 CACATTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2675296 original size:16 final size:16
Alignment explanation
Indices: 2675275--2675307 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2675265 TATCATAATT
*
2675275 TATCCATTATGTAACA
1 TATCCATCATGTAACA
2675291 TATCCATCATGTAACA
1 TATCCATCATGTAACA
2675307 T
1 T
2675308 GTATGATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (16 bp):
TATCCATCATGTAACA
Found at i:2677403 original size:31 final size:31
Alignment explanation
Indices: 2677367--2677448 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
2677357 TAACAATTCA
* *
2677367 AAATTTTTATTGTTTTAATTTATTAAAAATT
1 AAATTTTAATTATTTTAATTTATTAAAAATT
2677398 AAATTTTAATTATTTTAATTTATTAAAAATT
1 AAATTTTAATTATTTTAATTTATTAAAAATT
*
2677429 AAATTTTAATTATTTAAATT
1 AAATTTTAATTATTTTAATT
2677449 AAAAATTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
AAATTTTAATTATTTTAATTTATTAAAAATT
Found at i:2677437 original size:22 final size:20
Alignment explanation
Indices: 2677409--2677451 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
2677399 AATTTTAATT
2677409 ATTTTAATTTATTAAAAATTAA
1 ATTTTAA-TTATT-AAAATTAA
*
2677431 ATTTTAATTATTTAAATTAA
1 ATTTTAATTATTAAAATTAA
2677451 A
1 A
2677452 AATTCAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 5 0.25
22 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTAATTATTAAAATTAA
Found at i:2677445 original size:15 final size:15
Alignment explanation
Indices: 2677396--2677448 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2677386 TTATTAAAAA
2677396 TTAAATTTTAATTATT
1 TTAAATTTTAATTA-T
* * *
2677412 TTAATTTATTAA-AAA
1 TTAAATT-TTAATTAT
2677427 TTAAATTTTAATTAT
1 TTAAATTTTAATTAT
2677442 TTAAATT
1 TTAAATT
2677449 AAAAATTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.48
16 7 0.24
17 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAAATTTTAATTAT
Found at i:2677568 original size:21 final size:21
Alignment explanation
Indices: 2677542--2677586 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2677532 CGATGATATC
2677542 ATTTTAATA-AATATTTTTTTA
1 ATTTTAATACAATA-TTTTTTA
*
2677563 ATTTTAATACACTATTTTTTA
1 ATTTTAATACAATATTTTTTA
2677584 ATT
1 ATT
2677587 AAATTCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTAATACAATATTTTTTA
Found at i:2682170 original size:9 final size:9
Alignment explanation
Indices: 2682156--2682190 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2682146 GTTCGAGGGC
2682156 ATGGGTGGT
1 ATGGGTGGT
*
2682165 ATGGGTGGC
1 ATGGGTGGT
*
2682174 ATGGGCGGT
1 ATGGGTGGT
2682183 ATGGGTGG
1 ATGGGTGG
2682191 CCGAAGTTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.11, C:0.06, G:0.57, T:0.26
Consensus pattern (9 bp):
ATGGGTGGT
Found at i:2682176 original size:18 final size:18
Alignment explanation
Indices: 2682153--2682191 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2682143 ACTGTTCGAG
*
2682153 GGCATGGGTGGTATGGGT
1 GGCATGGGCGGTATGGGT
2682171 GGCATGGGCGGTATGGGT
1 GGCATGGGCGGTATGGGT
2682189 GGC
1 GGC
2682192 CGAAGTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.56, T:0.23
Consensus pattern (18 bp):
GGCATGGGCGGTATGGGT
Found at i:2683424 original size:2 final size:2
Alignment explanation
Indices: 2683414--2683452 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2683404 AAAAAAAGTT
*
2683414 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2683453 TTGGTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2687870 original size:75 final size:75
Alignment explanation
Indices: 2687747--2687899 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
2687737 TCCAGAAGGA
2687747 AACTAAAGCTTGTCAAAGTTGGGAATTAACATCAGAAAATGCATTGAACATCTATATGTACTGAA
1 AACTAAAGCTTGTCAAAGTTGGGAATTAACATCAGAAAATGCATTGAACATCTATATGTACTGAA
2687812 AGGAATTTAC
66 AGGAATTTAC
2687822 AACTAAAGCTTGTCAAAGTTGGGAATTAACATCAGAAAATGCATTGAACATCTATATGTACTGAA
1 AACTAAAGCTTGTCAAAGTTGGGAATTAACATCAGAAAATGCATTGAACATCTATATGTACTGAA
2687887 AGGAATTTAC
66 AGGAATTTAC
2687897 AAC
1 AAC
2687900 CAAGTACTCT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (75 bp):
AACTAAAGCTTGTCAAAGTTGGGAATTAACATCAGAAAATGCATTGAACATCTATATGTACTGAA
AGGAATTTAC
Found at i:2689387 original size:187 final size:187
Alignment explanation
Indices: 2689072--2689438 Score: 535
Period size: 187 Copynumber: 2.0 Consensus size: 187
2689062 ACTTCCTACC
* * * * *
2689072 AGTCTTATTCTATCCTTGTCCTGCTTGAGCTAAACCCCAAAGCATCTCCATTTTTCTGTAGATAA
1 AGTCTTATTCTATCCTTGTCCTGCTTGAGCTAAAACCCAAAGCATCTCCATATTTCTATAAAGAA
** * * *
2689137 AGTTTTCAATAAACTAGGACTGTTACCAAGTTAGTGGAGTCCAACCATAAAAGACTCCATGGCGT
66 AAATTTCAATAAAATAGGACTATTACCAAGTTAGTGGAGTCCAACCATAAAAGAATCCATGGCGT
*
2689202 CTTAGAGCTTCTCCATCTGAAGACTTA-ACGGTACTAGCCAGTAAGCACAATCCATGG
131 CTGAGAGCTTCTCCATCTGAAGACTTAGA-GGTACTAGCCAGTAAGCACAATCCATGG
*
2689259 AGTCTTATTCTATCCTT-TGCTGCTTGAGCTAAAACCCAAGAGCATC-CTCA-ATTTCTATAAAG
1 AGTCTTATTCTATCCTTGTCCTGCTTGAGCTAAAACCCAA-AGCATCTC-CATATTTCTATAAAG
2689321 AAAAATTTCAATAAAATAGGACTATTACCAAAGTTAGTGGAGTCCAACCATAAAAGAATCCATGG
64 AAAAATTTCAATAAAATAGGACTATTACC-AAGTTAGTGGAGTCCAACCATAAAAGAATCCATGG
* * *
2689386 CGTCTGATAGCTTCTCCATCTGGAGACTTAGAGGTACTGGCCAGTAAGCACAA
128 CGTCTGAGAGCTTCTCCATCTGAAGACTTAGAGGTACTAGCCAGTAAGCACAA
2689439 GCTTCCAACA
Statistics
Matches: 161, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
186 54 0.34
187 106 0.66
188 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (187 bp):
AGTCTTATTCTATCCTTGTCCTGCTTGAGCTAAAACCCAAAGCATCTCCATATTTCTATAAAGAA
AAATTTCAATAAAATAGGACTATTACCAAGTTAGTGGAGTCCAACCATAAAAGAATCCATGGCGT
CTGAGAGCTTCTCCATCTGAAGACTTAGAGGTACTAGCCAGTAAGCACAATCCATGG
Found at i:2691740 original size:21 final size:21
Alignment explanation
Indices: 2691716--2691769 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
2691706 TTTTTATAAA
2691716 TATTA-ATTAAAATAATTATAT
1 TATTATATTAAAA-AATTATAT
* *
2691737 TATTATTTTAAAAATTTATATT
1 TATTATATTAAAAAATTATA-T
*
2691759 TAATATATTAA
1 TATTATATTAA
2691770 TTTTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTATATTAAAAAATTATAT
Found at i:2692967 original size:16 final size:17
Alignment explanation
Indices: 2692936--2692968 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2692926 GCTTGTGTTA
2692936 TTTTATGTCATGTCGTG
1 TTTTATGTCATGTCGTG
*
2692953 TTTTGTGTC-TGTCGTG
1 TTTTATGTCATGTCGTG
2692969 CTCTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (17 bp):
TTTTATGTCATGTCGTG
Found at i:2701310 original size:2 final size:2
Alignment explanation
Indices: 2701303--2701338 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2701293 TTGTGGAATG
2701303 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2701339 ATAGGGCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2706408 original size:271 final size:270
Alignment explanation
Indices: 2705926--2706468 Score: 1077
Period size: 271 Copynumber: 2.0 Consensus size: 270
2705916 ATTTCAGCAA
2705926 TTTGAGTTTTGGAACGAAACGTGGTAAGAAACCCAACTAACCAGAAAAAAAGAAAAAAACAGAGG
1 TTTGAGTTTTGGAACGAAACGTGGTAAGAAACCCAACTAACCAGAAAAAAAGAAAAAAACAGAGG
2705991 GTTAGCTACTGCCAGCATCATCAGTGATGAGAATCCTCGCGGGAGGAAGCAAAAAATTTAATGTT
66 GTTAGCTACTGCCAGCATCATCAGTGATGAGAATCCTCGCGGGAGGAAGCAAAAAATTTAATGTT
2706056 GGGATTGAAATAAAAGAAAATTAAATTATAAAATATTGGGGGGCGAAAATAGTTTTTTTTCAAAT
131 GGGATTGAAATAAAAGAAAATTAAATTATAAAATATTGGGGGGCGAAAATAGTTTTTTTTCAAAT
2706121 AATTTTTTGAGCAATTGTTAAGAACTTTAAGGAGTTTGGGGTAGTTTGGAAAGGGCTAAGGCTCC
196 AATTTTTTGAGCAATTGTTAAGAACTTTAAGGAGTTTGGGGTAGTTTGGAAAGGGCTAAGGCTCC
2706186 TGCGGGCTCC
261 TGCGGGCTCC
2706196 TTTGAGTTTTGGAACGAAACGTGGTAAGAAACCCAACTAACCAGAAAAAAAGAAAAAAAACAGAG
1 TTTGAGTTTTGGAACGAAACGTGGTAAGAAACCCAACTAACCAGAAAAAAAG-AAAAAAACAGAG
2706261 GGTTAGCTACTGCCAGCATCATCAGTGATGAGAATCCTCGCGGGAGGAAGCAAAAAATTTAATGT
65 GGTTAGCTACTGCCAGCATCATCAGTGATGAGAATCCTCGCGGGAGGAAGCAAAAAATTTAATGT
2706326 TGGGATTGAAATAAAAGAAAATTAAATTATAAAATATTGGGGGGCGAAAATAGTTTTTTTTCAAA
130 TGGGATTGAAATAAAAGAAAATTAAATTATAAAATATTGGGGGGCGAAAATAGTTTTTTTTCAAA
2706391 TAATTTTTTGAGCAATTGTTAAGAACTTTAAGGAGTTTGGGGTAGTTTGGAAAGGGCTAAGGCTC
195 TAATTTTTTGAGCAATTGTTAAGAACTTTAAGGAGTTTGGGGTAGTTTGGAAAGGGCTAAGGCTC
2706456 CTGCGGGCTCC
260 CTGCGGGCTCC
2706467 TT
1 TT
2706469 GGATACACCC
Statistics
Matches: 272, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
270 52 0.19
271 220 0.81
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (270 bp):
TTTGAGTTTTGGAACGAAACGTGGTAAGAAACCCAACTAACCAGAAAAAAAGAAAAAAACAGAGG
GTTAGCTACTGCCAGCATCATCAGTGATGAGAATCCTCGCGGGAGGAAGCAAAAAATTTAATGTT
GGGATTGAAATAAAAGAAAATTAAATTATAAAATATTGGGGGGCGAAAATAGTTTTTTTTCAAAT
AATTTTTTGAGCAATTGTTAAGAACTTTAAGGAGTTTGGGGTAGTTTGGAAAGGGCTAAGGCTCC
TGCGGGCTCC
Found at i:2708060 original size:3 final size:3
Alignment explanation
Indices: 2708054--2708116 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
2708044 TTCATCATCA
* * * * * *
2708054 TCT TCT TCT TCT TCT TCT TTT TCT TTT TCT TTT TCT TCA CCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2708102 TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT
2708117 GTTAAGTAAC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2708779 original size:30 final size:28
Alignment explanation
Indices: 2708737--2708813 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 28
2708727 ATATAATTTG
2708737 AATTAATT-TAAAATTTTATTTTATTATT
1 AATTAATTATAAAATTTTATTTTA-TATT
2708765 AATTATATTATAAAAATATTT-TTTTATATT
1 AATTA-ATTAT-AAAAT-TTTATTTTATATT
* *
2708795 AA-TAGTTATATAATTTTAT
1 AATTAATTATAAAATTTTAT
2708814 AATTAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
26 3 0.07
27 5 0.12
28 9 0.21
29 5 0.12
30 7 0.17
31 10 0.24
32 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
AATTAATTATAAAATTTTATTTTATATT
Found at i:2710152 original size:25 final size:24
Alignment explanation
Indices: 2710110--2710165 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
2710100 ATTTAATACG
* *
2710110 AATAATAAATAAATTTAAATTTTAA
1 AATATTAAATAAATTTAAAATTT-A
2710135 AATATTAATATAAA-TTAAAATTTA
1 AATATTAA-ATAAATTTAAAATTTA
2710159 AATATTA
1 AATATTA
2710166 TAAAAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 8 0.29
25 15 0.54
26 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATATTAAATAAATTTAAAATTTA
Found at i:2710370 original size:12 final size:12
Alignment explanation
Indices: 2710355--2710380 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2710345 TTAGTTTATT
2710355 TTTTATAATTAA
1 TTTTATAATTAA
2710367 TTTTATAATTAA
1 TTTTATAATTAA
2710379 TT
1 TT
2710381 AAATAAAATT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTATAATTAA
Found at i:2710420 original size:24 final size:24
Alignment explanation
Indices: 2710392--2710443 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2710382 AATAAAATTT
*
2710392 TTAAA-AAAACATTTTAAACTAAAC
1 TTAAATAAAA-ATTTAAAACTAAAC
* *
2710416 TTAAATAAAAATTTAAAATTTAAC
1 TTAAATAAAAATTTAAAACTAAAC
2710440 TTAA
1 TTAA
2710444 CTATTACGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAATAAAAATTTAAAACTAAAC
Found at i:2710834 original size:31 final size:30
Alignment explanation
Indices: 2710799--2710867 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
2710789 TTTAATTTAA
* *
2710799 TTTAAATTATTATATTATAATAAAATAATAT
1 TTTAAATTATAATA-TATAATAAAATAAGAT
* * *
2710830 TTTAATAATATAATATATAATAATATTAGAT
1 TTTAA-ATTATAATATATAATAAAATAAGAT
2710861 TTTAAAT
1 TTTAAAT
2710868 CAATCCAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
30 1 0.03
31 23 0.74
32 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TTTAAATTATAATATATAATAAAATAAGAT
Found at i:2710835 original size:16 final size:16
Alignment explanation
Indices: 2710810--2710852 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2710800 TTAAATTATT
2710810 ATATTATAATAAAATA
1 ATATTATAATAAAATA
* *
2710826 ATATTTTAATAATATA
1 ATATTATAATAAAATA
2710842 ATA-TATAATAA
1 ATATTATAATAA
2710853 TATTAGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTATAATAAAATA
Found at i:2710843 original size:8 final size:8
Alignment explanation
Indices: 2710814--2710855 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
2710804 ATTATTATAT
2710814 TATAATAA
1 TATAATAA
* *
2710822 AATAATAT
1 TATAATAA
*
2710830 TTTAATAA
1 TATAATAA
2710838 TATAAT-A
1 TATAATAA
2710845 TATAATAA
1 TATAATAA
2710853 TAT
1 TAT
2710856 TAGATTTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TATAATAA
Found at i:2721751 original size:2 final size:2
Alignment explanation
Indices: 2721738--2721775 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2721728 TGCAGATTTC
*
2721738 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2721776 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2721780 original size:2 final size:2
Alignment explanation
Indices: 2721775--2721807 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2721765 TATATATATA
2721775 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2721808 AAAATAGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2725368 original size:2 final size:2
Alignment explanation
Indices: 2725361--2725389 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2725351 GTACTTTCAG
2725361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2725390 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2725394 original size:2 final size:2
Alignment explanation
Indices: 2725389--2725422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2725379 ATATATATAT
2725389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2725423 GATGGTGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2726563 original size:8 final size:8
Alignment explanation
Indices: 2726550--2726588 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
2726540 TGAGAAGTGT
2726550 AGATTTCC
1 AGATTTCC
*
2726558 AGATTTTC
1 AGATTTCC
2726566 AGATTTCC
1 AGATTTCC
2726574 AGATTTCC
1 AGATTTCC
*
2726582 TGATTTC
1 AGATTTC
2726589 TAGCAGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (8 bp):
AGATTTCC
Found at i:2726586 original size:16 final size:16
Alignment explanation
Indices: 2726551--2726656 Score: 59
Period size: 16 Copynumber: 6.3 Consensus size: 16
2726541 GAGAAGTGTA
* *
2726551 GATTTCCAGATTTTCA
1 GATTTCCAGATTTCCT
2726567 GATTTCCAGATTTCCT
1 GATTTCCAGATTTCCT
* *
2726583 GATTTCTAGCAGTTTTTCT
1 GATTTC---CAGATTTCCT
*
2726602 GATTTCTGCAGATTTCCA
1 GATTTC--CAGATTTCCT
*** * *
2726620 GATCAGCAAATTTACT
1 GATTTCCAGATTTCCT
**
2726636 GATTTTGAGATTTCCT
1 GATTTCCAGATTTCCT
2726652 GATTT
1 GATTT
2726657 TCTAGATATC
Statistics
Matches: 67, Mismatches: 20, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
16 42 0.63
18 11 0.16
19 14 0.21
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (16 bp):
GATTTCCAGATTTCCT
Found at i:2726846 original size:15 final size:15
Alignment explanation
Indices: 2726826--2726857 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2726816 AAGAAAGCTA
2726826 TTCTCTCCAATCTGT
1 TTCTCTCCAATCTGT
*
2726841 TTCTCTCCTATCTGT
1 TTCTCTCCAATCTGT
2726856 TT
1 TT
2726858 TTACCTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.31, G:0.06, T:0.53
Consensus pattern (15 bp):
TTCTCTCCAATCTGT
Found at i:2726909 original size:13 final size:13
Alignment explanation
Indices: 2726891--2726918 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2726881 TTCTACCTAG
2726891 ATTTCAACATGGT
1 ATTTCAACATGGT
2726904 ATTTCAACATGGT
1 ATTTCAACATGGT
2726917 AT
1 AT
2726919 CAGAGCCATA
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:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTTCAACATGGT
Found at i:2729868 original size:86 final size:86
Alignment explanation
Indices: 2729723--2729894 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
2729713 CTGGAGTTGG
2729723 GGGTACATATTATTGCTAAACCTATCATAGGTACCAGTATGATATCAATTTCTCTATCGGGGGTT
1 GGGTACATATTATTGCTAAACCTATCATAGGTACCAGTATGATATCAATTTCTCTATCGGGGGTT
2729788 TCGAAGTACACTCCAGTCGCA
66 TCGAAGTACACTCCAGTCGCA
2729809 GGGTACATATTATTGCTAAACCTATCATAGGTACCAGTATGATATCAATTTCTCTATCGGGGGTT
1 GGGTACATATTATTGCTAAACCTATCATAGGTACCAGTATGATATCAATTTCTCTATCGGGGGTT
2729874 TCGAAGTACACTCCAGTCGCA
66 TCGAAGTACACTCCAGTCGCA
2729895 CAAAATCAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (86 bp):
GGGTACATATTATTGCTAAACCTATCATAGGTACCAGTATGATATCAATTTCTCTATCGGGGGTT
TCGAAGTACACTCCAGTCGCA
Found at i:2732464 original size:8 final size:8
Alignment explanation
Indices: 2732451--2732489 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2732441 ATAATATTGT
2732451 AGATTTCC
1 AGATTTCC
*
2732459 AGATTTTC
1 AGATTTCC
*
2732467 AGATTTCT
1 AGATTTCC
2732475 AGATTTCC
1 AGATTTCC
*
2732483 TGATTTC
1 AGATTTC
2732490 TAGCAGACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (8 bp):
AGATTTCC
Found at i:2732487 original size:16 final size:16
Alignment explanation
Indices: 2732452--2732569 Score: 62
Period size: 16 Copynumber: 7.0 Consensus size: 16
2732442 TAATATTGTA
* * *
2732452 GATTTCCAGATTTTCA
1 GATTTCTAGATTTCCT
2732468 GATTTCTAGATTTCCT
1 GATTTCTAGATTTCCT
2732484 GATTTCTAGCAGACTTT-CT
1 GATTTCT---AGA-TTTCCT
*
2732503 GATTTCTGCAGATTTCCA
1 GATTTCT--AGATTTCCT
* * *
2732521 GATCTGC-AAATTTACT
1 GAT-TTCTAGATTTCCT
2732537 GATTT-TGAGATTTCCT
1 GATTTCT-AGATTTCCT
*
2732553 GATTTTCTAGATATCCT
1 GA-TTTCTAGATTTCCT
2732570 TGAATTATGG
Statistics
Matches: 80, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.01
16 38 0.47
17 14 0.17
18 10 0.12
19 14 0.17
20 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (16 bp):
GATTTCTAGATTTCCT
Found at i:2732506 original size:19 final size:17
Alignment explanation
Indices: 2732458--2732557 Score: 68
Period size: 16 Copynumber: 5.8 Consensus size: 17
2732448 TGTAGATTTC
*
2732458 CAGATTTTCAGATTTCT-
1 CAGA-TTTCTGATTTCTG
2732475 -AGATTTCCTGATTTCTAG
1 CAGATTT-CTGATTTCT-G
2732493 CAGACTTTCTGATTTCTG
1 CAGA-TTTCTGATTTCTG
*
2732511 CAGATTTCCAGA--TCTG
1 CAGATTT-CTGATTTCTG
*
2732527 CAAATTTACTGATTT-TG
1 CAGATTT-CTGATTTCTG
2732544 -AGATTTCCTGATTT
1 CAGATTT-CTGATTT
2732558 TCTAGATATC
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.04
16 36 0.53
17 5 0.07
18 9 0.13
19 12 0.18
20 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (17 bp):
CAGATTTCTGATTTCTG
Found at i:2732747 original size:15 final size:15
Alignment explanation
Indices: 2732727--2732758 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2732717 AAGAAAGTTG
2732727 TTCTCTCCAATCTGT
1 TTCTCTCCAATCTGT
*
2732742 TTCTCTCCTATCTGT
1 TTCTCTCCAATCTGT
2732757 TT
1 TT
2732759 TTACCTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.31, G:0.06, T:0.53
Consensus pattern (15 bp):
TTCTCTCCAATCTGT
Found at i:2736305 original size:8 final size:8
Alignment explanation
Indices: 2736292--2736330 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2736282 AGGGTAGTGT
2736292 AGATTTCC
1 AGATTTCC
*
2736300 AGATTTTC
1 AGATTTCC
*
2736308 AGATTTCT
1 AGATTTCC
2736316 AGATTTCC
1 AGATTTCC
*
2736324 TGATTTC
1 AGATTTC
2736331 TAGCAAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (8 bp):
AGATTTCC
Found at i:2736328 original size:16 final size:16
Alignment explanation
Indices: 2736292--2736333 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2736282 AGGGTAGTGT
* *
2736292 AGATTTCCAGATTTTC
1 AGATTTCTAGATTTCC
2736308 AGATTTCTAGATTTCC
1 AGATTTCTAGATTTCC
*
2736324 TGATTTCTAG
1 AGATTTCTAG
2736334 CAAACTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (16 bp):
AGATTTCTAGATTTCC
Found at i:2736576 original size:15 final size:15
Alignment explanation
Indices: 2736556--2736587 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2736546 AAGAAAGCTG
2736556 TTCTCTCCAATCTGT
1 TTCTCTCCAATCTGT
*
2736571 TTCTCTCCTATCTGT
1 TTCTCTCCAATCTGT
2736586 TT
1 TT
2736588 TTACCTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.31, G:0.06, T:0.53
Consensus pattern (15 bp):
TTCTCTCCAATCTGT
Found at i:2740137 original size:30 final size:30
Alignment explanation
Indices: 2740103--2740161 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
2740093 CCCACGTCTG
2740103 AACCTGTGTCTAAACCCGTTTCTACACCTA
1 AACCTGTGTCTAAACCCGTTTCTACACCTA
*
2740133 AACCTGTGTCTAAACGCGTTTCTACACCT
1 AACCTGTGTCTAAACCCGTTTCTACACCT
2740162 GTAACCAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (30 bp):
AACCTGTGTCTAAACCCGTTTCTACACCTA
Found at i:2748779 original size:2 final size:2
Alignment explanation
Indices: 2748772--2748815 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2748762 GTTGGAAATG
**
2748772 CA CA CA CA CA TG CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2748814 CA
1 CA
2748816 ACCAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.48, G:0.02, T:0.02
Consensus pattern (2 bp):
CA
Found at i:2751094 original size:34 final size:34
Alignment explanation
Indices: 2751055--2751119 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
2751045 TAATATAAAA
*
2751055 ACTTCTAAGCAGTGAATATGCATTGTAATATGAC
1 ACTTCTAAACAGTGAATATGCATTGTAATATGAC
*
2751089 ACTTCTAAACAGTGAATATGCCTTGTAATAT
1 ACTTCTAAACAGTGAATATGCATTGTAATAT
2751120 TGGTTCTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (34 bp):
ACTTCTAAACAGTGAATATGCATTGTAATATGAC
Found at i:2752423 original size:2 final size:2
Alignment explanation
Indices: 2752416--2752444 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2752406 TTTGCAATCA
2752416 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2752445 AATTGTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2753104 original size:15 final size:14
Alignment explanation
Indices: 2753086--2753141 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2753076 TGATAAAAGT
2753086 TATTTTAAAAATATA
1 TATTTT-AAAATATA
2753101 TATTTTAAAATATAA
1 TATTTTAAAATAT-A
*
2753116 AAGTATTTAAAAT-TA
1 TA-T-TTTAAAATATA
2753131 TATTTTCAAAA
1 TATTTT-AAAA
2753142 CAAAATAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 3 0.09
14 12 0.34
15 10 0.29
16 2 0.06
17 8 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
TATTTTAAAATATA
Found at i:2753133 original size:32 final size:33
Alignment explanation
Indices: 2753078--2753141 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
2753068 TTGAATTTTG
*
2753078 ATAAAAGTTATTTTAAAAATATATATTTTAAAAT
1 ATAAAAGTTATTTTAAAAATATAT-TTTCAAAAT
*
2753112 ATAAAAG-TA-TTTAAAATTATATTTTCAAAA
1 ATAAAAGTTATTTTAAAAATATATTTTCAAAA
2753142 CAAAATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.25
32 12 0.43
33 2 0.07
34 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (33 bp):
ATAAAAGTTATTTTAAAAATATATTTTCAAAAT
Found at i:2753161 original size:20 final size:20
Alignment explanation
Indices: 2753133--2753180 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2753123 TAAAATTATA
* *
2753133 TTTTCAAAACAAA-ATAACAT
1 TTTTTAAAA-AAACATAAAAT
2753153 TTTTTAAAAAAACATAAAAT
1 TTTTTAAAAAAACATAAAAT
*
2753173 TTCTTAAA
1 TTTTTAAA
2753181 TGATATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (20 bp):
TTTTTAAAAAAACATAAAAT
Found at i:2753525 original size:144 final size:144
Alignment explanation
Indices: 2753258--2753525 Score: 339
Period size: 144 Copynumber: 1.9 Consensus size: 144
2753248 TATTTTTAAA
* *
2753258 TATAAAAATTTTTAAAATTATGTTAAAAAAATTTACAATATCTAAAATTTTTTGAAAAAATAAAA
1 TATAAAAATTTTTAAAATTATGTTAAAAAAATTTACAAAATATAAAATTTTTTGAAAAAATAAAA
* *** *
2753323 ATAAAAAACTAGCTTATTTTAGTATTTAATTTTTTTAAAAAATAATATATTTATTAAAAAACGAA
66 ATAAAAAACTAGCTTATTTTAATATTTAATTTTTTTAAAAAATAATATAAAGAATAAAAAACGAA
2753388 AAGGAATGGAACCC
131 AAGGAATGGAACCC
* * *
2753402 TATAAAAA-TTTTAAAATTATCTGTT-AAAAATTTTACAAAATATGAAAA-TTTTTGCAAGAATA
1 TATAAAAATTTTTAAAATTA--TGTTAAAAAAATTTACAAAATAT-AAAATTTTTTGAAAAAATA
* * *
2753464 AAAATTAAAAAATTAGTTTATTTTAATATTTAA-TTTTTTAAAAAAT-TTATGAAAGAATAAAA
63 AAAA-TAAAAAACTAGCTTATTTTAATATTTAATTTTTTTAAAAAATAATAT-AAAGAATAAAA
2753526 TGAAAATGTC
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
143 14 0.13
144 59 0.56
145 33 0.31
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.38
Consensus pattern (144 bp):
TATAAAAATTTTTAAAATTATGTTAAAAAAATTTACAAAATATAAAATTTTTTGAAAAAATAAAA
ATAAAAAACTAGCTTATTTTAATATTTAATTTTTTTAAAAAATAATATAAAGAATAAAAAACGAA
AAGGAATGGAACCC
Found at i:2754758 original size:36 final size:39
Alignment explanation
Indices: 2754689--2754760 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
2754679 TTCGTCTATA
* *
2754689 TAAAATATTAATATATTATATATTTATTTAAATTTAATT
1 TAAAATATGAATATATTATATATTTATATAAATTTAATT
2754728 TAAAATATGAATATATT-T-T-TTTATATAAATTTA
1 TAAAATATGAATATATTATATATTTATATAAATTTA
2754761 TTTTTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 13 0.42
37 1 0.03
38 1 0.03
39 16 0.52
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (39 bp):
TAAAATATGAATATATTATATATTTATATAAATTTAATT
Found at i:2754762 original size:18 final size:18
Alignment explanation
Indices: 2754741--2754775 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2754731 AATATGAATA
2754741 TATTTTT-TTATATAAATT
1 TATTTTTATT-TATAAATT
2754759 TATTTTTATTTATAAAT
1 TATTTTTATTTATAAAT
2754776 AAGTAGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTTATTTATAAATT
Found at i:2755772 original size:22 final size:21
Alignment explanation
Indices: 2755746--2755798 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
2755736 TTAGTACTCA
*
2755746 TTATATTATTATAATATAATTT
1 TTATATTAATAT-ATATAATTT
* *
2755768 TTATATTAATATTTATATTTT
1 TTATATTAATATATATAATTT
2755789 TTATAATTAA
1 TTAT-ATTAA
2755799 ATTTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTAATATATATAATTT
Found at i:2755789 original size:21 final size:21
Alignment explanation
Indices: 2755746--2755803 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
2755736 TTAGTACTCA
* *
2755746 TTATATTATTATAATATAATTT
1 TTATATTAATAT-TTATAATTT
*
2755768 TTATATTAATATTTATATTTT
1 TTATATTAATATTTATAATTT
2755789 TTATAATTAA-ATTTA
1 TTAT-ATTAATATTTA
2755804 AATAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTAATATTTATAATTT
Found at i:2757127 original size:20 final size:19
Alignment explanation
Indices: 2757069--2757137 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 19
2757059 AATAATTAAA
2757069 TATTATTT-TATTAAATTT
1 TATTATTTATATTAAATTT
*
2757087 TA--ATTTGT-TTAAATATAT
1 TATTATTTATATTAAAT-T-T
2757105 TATTATTTATATATAAATTT
1 TATTATTTATAT-TAAATTT
2757125 TATT-TTT-TATTAA
1 TATTATTTATATTAA
2757138 TGATTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
16 10 0.23
17 5 0.12
18 8 0.19
19 3 0.07
20 10 0.23
21 2 0.05
22 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (19 bp):
TATTATTTATATTAAATTT
Found at i:2758176 original size:28 final size:27
Alignment explanation
Indices: 2758131--2758191 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
2758121 TTTTATTATT
*
2758131 TAAAAATATATATATTTTTAATATAAATA
1 TAAAAACATATA-ATTTTTAA-ATAAATA
* *
2758160 TAAAAACATA-ATTTTTTAAATATATA
1 TAAAAACATATAATTTTTAAATAAATA
2758186 TAAAAA
1 TAAAAA
2758192 TTTAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 12 0.41
27 7 0.24
28 1 0.03
29 9 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAAAACATATAATTTTTAAATAAATA
Found at i:2758574 original size:14 final size:14
Alignment explanation
Indices: 2758555--2758600 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
2758545 TTTATATTTA
2758555 AAATATATTAAAAT
1 AAATATATTAAAAT
2758569 -AA-ATATTAAATAT
1 AAATATATTAAA-AT
* *
2758582 AAATATTTTAAAAA
1 AAATATATTAAAAT
2758596 AAATA
1 AAATA
2758601 AAGTGCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 8 0.30
13 4 0.15
14 8 0.30
15 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATATTAAAAT
Found at i:2758576 original size:12 final size:13
Alignment explanation
Indices: 2758559--2758588 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2758549 TATTTAAAAT
2758559 ATATTAAA-ATAA
1 ATATTAAATATAA
2758571 ATATTAAATATAA
1 ATATTAAATATAA
2758584 ATATT
1 ATATT
2758589 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTAAATATAA
Done.