Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 11 of 16
Found at i:1404219 original size:266 final size:266
Alignment explanation
Indices: 1403745--1405007 Score: 2132
Period size: 266 Copynumber: 4.8 Consensus size: 266
1403735 GCACAACCAA
*
1403745 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTCG
1 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTTG
*
1403810 ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGCTGAAAATTTGATTTATGAAT
66 ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGTTGAAAATTTGATTTATGAAT
1403875 TTTTTTAATTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTCAAATA
131 TTTTTTAATTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTCAAATA
1403940 ATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAACAA
196 ATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAACAA
1404005 AACCGG
261 AACCGG
1404011 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTTG
1 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTTG
*
1404076 ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGCTGAAAATTTGATTTATGAAT
66 ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGTTGAAAATTTGATTTATGAAT
1404141 TTTTTTAATTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTCAAATA
131 TTTTTTAATTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTCAAATA
1404206 ATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAACAA
196 ATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAACAA
1404271 AACCGG
261 AACCGG
1404277 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTTG
1 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTTG
*
1404342 ACATCGTTTGAAGCCATTACCTGGACAAAAGCATATGAAACTTGTTGAAAATTTGATTTATGAAT
66 ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGTTGAAAATTTGATTTATGAAT
1404407 TTTTTTAATTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTCAAATA
131 TTTTTTAATTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTCAAATA
1404472 ATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAACAA
196 ATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAACAA
1404537 AACCGG
261 AACCGG
* *
1404543 TGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTCG
1 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTTG
1404608 ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGTTGAAAATTTGATTTATGAAT
66 ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGTTGAAAATTTGATTTATGAAT
**
1404673 TTTTTTAATTTTATTTACGAGTAATCAATCTATTAACATTTGTCCC--CTTTTTTTTGAAATCAA
131 TTTTTTAA-TTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTT--TTTCAA
1404736 ATAATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAA
193 ATAATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAA
*
1404801 CAAAGCCGG
258 CAAAACCGG
* * ** * ** *
1404810 TGGTGGAATCATTCTCAGGACTAGATGACGGCGAATGCTTAGAGCCAGTGCTTATCATAA-TCTT
1 CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGT-TT
* * ** * * * *
1404874 GACGTTGTTTGAA-CCTATTACCTACACAAAAACATACGAAACTTATTGGAGATTTGATTTATGA
65 GACATCGTTTGAAGCC-ATTACCTGGACAAAAACATATGAAACTTGTTGAAAATTTGATTTATG-
* * *
1404938 AATTTTTTTAAATTT-TTTAACGAATAATCAATCAATTAACATTTGT---TAC--TTTTTTTTTC
128 AATTTTTTT-AATTTATTT-ACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTC
1404997 AAATAATAATA
191 AAATAATAATA
1405008 AAAAGAAGGT
Statistics
Matches: 958, Mismatches: 29, Indels: 23
0.95 0.03 0.02
Matches are distributed among these distances:
263 13 0.01
265 15 0.02
266 667 0.70
267 224 0.23
268 37 0.04
269 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (266 bp):
CGGTGGAATCATTCTCAGGACTAGACGACAACGAATGCTCAGAGCCACCGCTTATCGTAAGTTTG
ACATCGTTTGAAGCCATTACCTGGACAAAAACATATGAAACTTGTTGAAAATTTGATTTATGAAT
TTTTTTAATTTATTTACGAGTAATCAATCTATTAACATTTGTCCCTTCTTTTTTTTTTTCAAATA
ATAATATACCTCAGGCAGAGGCAGAGGCTGAGTTGGAGTTCGAGGTTGAGGTGGATGGACAACAA
AACCGG
Found at i:1405489 original size:17 final size:17
Alignment explanation
Indices: 1405467--1405500 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1405457 CCTATAATGA
1405467 AAAATATTAATTA-AAAT
1 AAAATA-TAATTATAAAT
1405484 AAAATATAATTATAAAT
1 AAAATATAATTATAAAT
1405501 TTTAATACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATATAATTATAAAT
Found at i:1407321 original size:19 final size:18
Alignment explanation
Indices: 1407298--1407343 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
1407288 CATCAAAATA
1407298 TTTTTAATTTTATTTTAT
1 TTTTTAATTTTATTTTAT
**
1407316 TATTTTAAAATTATTTTAT
1 T-TTTTAATTTTATTTTAT
1407335 TTTTTAATT
1 TTTTTAATT
1407344 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTAATTTTATTTTAT
Found at i:1407333 original size:30 final size:28
Alignment explanation
Indices: 1407293--1407361 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
1407283 TAAAACATCA
*
1407293 AAATATTTTTAATTTTATT-TTATTATTTT
1 AAATAATTTTAATTTT-TTATTATT-TTTT
*
1407322 AAAATTATTTT-ATTTTTTAATTATTTTTT
1 -AAATAATTTTAATTTTTT-ATTATTTTTT
1407351 AAATAATTTTA
1 AAATAATTTTA
1407362 TATCACTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 11 0.33
29 9 0.27
30 13 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
AAATAATTTTAATTTTTTATTATTTTTT
Found at i:1407336 original size:16 final size:16
Alignment explanation
Indices: 1407315--1407348 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1407305 TTTTATTTTA
1407315 TTATTTTAAAATTATT
1 TTATTTTAAAATTATT
**
1407331 TTATTTTTTAATTATT
1 TTATTTTAAAATTATT
1407347 TT
1 TT
1407349 TTAAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTAAAATTATT
Found at i:1407781 original size:2 final size:2
Alignment explanation
Indices: 1407776--1407800 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1407766 AGCAAGTGAT
1407776 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1407801 GCATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1408660 original size:25 final size:26
Alignment explanation
Indices: 1408632--1408694 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 26
1408622 AAATTAATGT
1408632 AAATAGTTTAATTT-AT-T-AATAATAA
1 AAATA-TTTAATTTAATGTAAATAAT-A
*
1408657 AAATATAATAATTTAATGTAAATAATA
1 AAATAT-TTAATTTAATGTAAATAATA
1408684 AAATATTTAAT
1 AAATATTTAAT
1408695 AATTTATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 1 0.03
25 11 0.34
26 6 0.19
27 8 0.25
28 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
AAATATTTAATTTAATGTAAATAATA
Found at i:1408672 original size:22 final size:22
Alignment explanation
Indices: 1408647--1408697 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1408637 GTTTAATTTA
*
1408647 TTAATAATAAA-AATATAATAAT
1 TTAATAATAAATAATAAAAT-AT
*
1408669 TTAAT-GTAAATAATAAAATAT
1 TTAATAATAAATAATAAAATAT
1408690 TTAATAAT
1 TTAATAAT
1408698 TTATATATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTAATAATAAATAATAAAATAT
Found at i:1408691 original size:21 final size:21
Alignment explanation
Indices: 1408654--1408694 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1408644 TTATTAATAA
*
1408654 TAAAAATATAATAATTTAATG
1 TAAAAATAAAATAATTTAATG
1408675 TAAATAATAAAAT-ATTTAAT
1 TAAA-AATAAAATAATTTAAT
1408695 AATTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAATAAAATAATTTAATG
Found at i:1408740 original size:24 final size:25
Alignment explanation
Indices: 1408713--1408765 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
1408703 TATTCATATC
1408713 ATATTTATATTATT-TTTTATAATT
1 ATATTTATATTATTATTTTATAATT
* *
1408737 ATATTTTTATTATTATTTTATATTT
1 ATATTTATATTATTATTTTATAATT
1408762 ATAT
1 ATAT
1408766 AAATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
ATATTTATATTATTATTTTATAATT
Found at i:1408745 original size:14 final size:12
Alignment explanation
Indices: 1408716--1408760 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
1408706 TCATATCATA
1408716 TTTATATTATTT
1 TTTATATTATTT
*
1408728 TTTATAATTATAT
1 TTTAT-ATTATTT
1408741 TTT-TATTATTAT
1 TTTATATTATT-T
1408753 TTTATATT
1 TTTATATT
1408761 TATATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 5 0.18
12 10 0.36
13 13 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:1408762 original size:17 final size:17
Alignment explanation
Indices: 1408693--1408856 Score: 55
Period size: 17 Copynumber: 9.8 Consensus size: 17
1408683 AAAATATTTA
*
1408693 ATAATTTATATATTCATATC
1 ATAA-TTATATATT--TATT
* *
1408713 ATATTTATATTATTTTTT
1 ATAATTATA-TATTTATT
*
1408731 ATAATTATATTTTTATT
1 ATAATTATATATTTATT
* *
1408748 ATTATTTTATATTTA-T
1 ATAATTATATATTTATT
* *
1408764 ATAAATTTTA-ATATATT
1 AT-AATTATATATTTATT
1408781 AATAATT-TAT-TTTA-T
1 -ATAATTATATATTTATT
* *
1408796 ATAAATTTTA-ATATATT
1 AT-AATTATATATTTATT
*
1408813 A-AA-TAT-T-TATATT
1 ATAATTATATATTTATT
*
1408826 ATATTTATATGATTT-TT
1 ATAATTATAT-ATTTATT
1408843 ATAA-TATTATATTT
1 ATAATTA-TATATTT
1408857 CGTCAGTAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
13 7 0.06
14 5 0.05
15 10 0.09
16 24 0.22
17 39 0.35
18 14 0.13
19 5 0.05
20 7 0.06
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (17 bp):
ATAATTATATATTTATT
Found at i:1408763 original size:14 final size:13
Alignment explanation
Indices: 1408716--1408760 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
1408706 TCATATCATA
1408716 TTTATATTATT-T
1 TTTATATTATTAT
1408728 TTTATAATTA-TAT
1 TTTAT-ATTATTAT
1408741 TTT-TATTATTAT
1 TTTATATTATTAT
1408753 TTTATATT
1 TTTATATT
1408761 TATATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.14
12 13 0.45
13 12 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATATTATTAT
Found at i:1408780 original size:20 final size:20
Alignment explanation
Indices: 1408755--1408812 Score: 60
Period size: 13 Copynumber: 3.3 Consensus size: 20
1408745 ATTATTATTT
1408755 TATATTTATATAAATTTTAA
1 TATATTTATATAAATTTTAA
1408775 TATA-TTA-AT-AA--TT--
1 TATATTTATATAAATTTTAA
1408788 TAT-TTTATATAAATTTTAA
1 TATATTTATATAAATTTTAA
1408807 TATATT
1 TATATT
1408813 AAATATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
13 6 0.20
14 2 0.07
15 4 0.13
17 4 0.13
18 2 0.07
19 6 0.20
20 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATTTATATAAATTTTAA
Found at i:1408780 original size:27 final size:27
Alignment explanation
Indices: 1408684--1408824 Score: 83
Period size: 32 Copynumber: 5.0 Consensus size: 27
1408674 GTAAATAATA
*
1408684 AAATATTTAATA-ATTTATATATTCATAT
1 AAAT-TTTAATATATTT-TATATTTATAT
* * * *
1408712 CATATTTATATTATTTTTTATAATTATAT
1 -AAATTT-TAATATATTTTATATTTATAT
*
1408741 ---TTTTATTATTATTTTATATTTATAT
1 AAATTTTAATA-TATTTTATATTTATAT
*
1408766 AAATTTTAATATATTAATAATTTATTTTATAT
1 AAATTTTAATATATT--T--TATA-TTTATAT
**
1408798 AAATTTTAATATATTAAATATTTATAT
1 AAATTTTAATATATTTTATATTTATAT
1408825 TATATTTATA
Statistics
Matches: 89, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
24 5 0.06
25 17 0.19
27 11 0.12
28 11 0.12
29 17 0.19
30 3 0.03
31 3 0.03
32 22 0.25
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
AAATTTTAATATATTTTATATTTATAT
Found at i:1408785 original size:18 final size:17
Alignment explanation
Indices: 1408751--1408829 Score: 73
Period size: 16 Copynumber: 4.9 Consensus size: 17
1408741 TTTTATTATT
1408751 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1408768 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
1408785 A-TTTAT-TTTATATAA
1 ATTTTATATTTATATAA
*
1408800 ATTTTA-ATATAT-TAA
1 ATTTTATATTTATATAA
1408815 ATATTTATA-TTATAT
1 AT-TTTATATTTATAT
1408830 TTATATGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 9 0.18
16 18 0.35
17 9 0.18
18 6 0.12
19 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1408800 original size:32 final size:32
Alignment explanation
Indices: 1408744--1408829 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
1408734 ATTATATTTT
* *
1408744 TATTATTATTTTATATTTATATAAATTTTAATA
1 TATTAATAATTTAT-TTTATATAAATTTTAATA
1408777 TATTAATAATTTATTTTATATAAATTTTAATA
1 TATTAATAATTTATTTTATATAAATTTTAATA
*
1408809 TATTAA-ATATTTATATTATAT
1 TATTAATA-ATTTATTTTATAT
1408830 TTATATGATT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 1 0.02
32 36 0.73
33 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTAATAATTTATTTTATATAAATTTTAATA
Found at i:1408830 original size:18 final size:18
Alignment explanation
Indices: 1408713--1408830 Score: 67
Period size: 18 Copynumber: 6.9 Consensus size: 18
1408703 TATTCATATC
* **
1408713 ATATTTATATTATTTTTT
1 ATATTTATATTATATTAA
* *
1408731 ATAATTATATTTTTATT-A
1 ATATTTATA-TTATATTAA
*
1408749 TTATTTTATATT-TATATAA
1 ATA-TTTATATTATAT-TAA
1408768 AT-TTTA-A-TATATT-A
1 ATATTTATATTATATTAA
*
1408782 ATAATTTATTTTATA-TAA
1 AT-ATTTATATTATATTAA
1408800 AT-TTTA-A-TATATTAA
1 ATATTTATATTATATTAA
1408815 ATATTTATATTATATT
1 ATATTTATATTATATT
1408831 TATATGATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 28
0.68 0.08 0.25
Matches are distributed among these distances:
14 7 0.09
15 7 0.09
16 16 0.21
17 9 0.12
18 26 0.34
19 12 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTATATTATATTAA
Found at i:1408834 original size:11 final size:11
Alignment explanation
Indices: 1408701--1408845 Score: 62
Period size: 11 Copynumber: 13.9 Consensus size: 11
1408691 TAATAATTTA
*
1408701 TATATTCATAT
1 TATATTTATAT
*
1408712 CATATTTATAT
1 TATATTTATAT
*
1408723 TATTTTTTATAAT
1 TA-TATTTAT-AT
*
1408736 TATATTTTTA-
1 TATATTTATAT
*
1408746 T-TA-TTATTT
1 TATATTTATAT
1408755 TATATTTATA-
1 TATATTTATAT
* *
1408765 TAAATTT-TAA
1 TATATTTATAT
*
1408775 TATATTAATAAT
1 TATATTTAT-AT
1408787 T-TATTT-TAT
1 TATATTTATAT
* *
1408796 ATAAATTT-TAA
1 -TATATTTATAT
1408807 TATA-TTA-A-
1 TATATTTATAT
1408815 -ATATTTATAT
1 TATATTTATAT
1408825 TATATTTATAT
1 TATATTTATAT
* *
1408836 GATTTTTATA
1 TATATTTATA
1408846 ATATTATATT
Statistics
Matches: 100, Mismatches: 19, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
7 3 0.03
8 6 0.06
9 11 0.11
10 19 0.19
11 44 0.44
12 13 0.13
13 4 0.04
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1409822 original size:2 final size:2
Alignment explanation
Indices: 1409815--1409846 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1409805 ATAAGGAATA
*
1409815 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1409847 GTCATAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1410138 original size:16 final size:16
Alignment explanation
Indices: 1410119--1410169 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1410109 TATATGTACG
1410119 TAATAATTATTTATAA
1 TAATAATTATTTATAA
*
1410135 TAATATTTATTTAT--
1 TAATAATTATTTATAA
* **
1410149 TTATAATTAGATATAA
1 TAATAATTATTTATAA
1410165 TAATA
1 TAATA
1410170 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 10 0.37
16 17 0.63
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TAATAATTATTTATAA
Found at i:1412050 original size:5 final size:5
Alignment explanation
Indices: 1412042--1412215 Score: 63
Period size: 5 Copynumber: 33.6 Consensus size: 5
1412032 ATTTAATTTT
* * * * * *
1412042 TTATA TTATA TTATA TTTTAA TTAT- TTTTA TAAATA ATATA ATATA TAATAA
1 TTATA TTATA TTATA TTAT-A TTATA TTATA T-TATA TTATA TTATA TTAT-A
*
1412094 TTTATA TT-TA TTTTTA TTATAA TTATA TT-TAA TTATTA TTAT- TTATA
1 -TTATA TTATA -TTATA TTAT-A TTATA TTAT-A TTA-TA TTATA TTATA
* * * * * * * *
1412141 -TATA TTTTA TTTTA TTAATA ATATA TTTTA CATAAA TTTTA ATAT- TTATA
1 TTATA TTATA TTATA TT-ATA TTATA TTATA -TTATA TTATA TTATA TTATA
1412191 TTATA TTTATA TTAATA TTATA TTA
1 TTATA -TTATA TT-ATA TTATA TTA
1412216 CCTCACATTT
Statistics
Matches: 126, Mismatches: 25, Indels: 36
0.67 0.13 0.19
Matches are distributed among these distances:
4 17 0.13
5 71 0.56
6 34 0.27
7 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:1412104 original size:6 final size:6
Alignment explanation
Indices: 1412093--1412214 Score: 52
Period size: 6 Copynumber: 21.5 Consensus size: 6
1412083 ATATATAATA
*
1412093 ATTTAT ATTTAT -TTT-T A-TTAT AATTAT ATTTA- ATTATTATT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT A-T-TTA-T ATTTAT
* * ** *
1412140 A--TAT ATTT-T ATTT-T ATTAAT A-ATAT ATTT-T ACATAA ATTTTAAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT A-TTT-AT
*
1412184 ATTTAT A-TTAT ATTTAT ATTAAT A-TTAT ATT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
1412215 ACCTCACATT
Statistics
Matches: 87, Mismatches: 13, Indels: 32
0.66 0.10 0.24
Matches are distributed among these distances:
4 7 0.08
5 30 0.34
6 36 0.41
7 10 0.11
8 3 0.03
9 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (6 bp):
ATTTAT
Found at i:1412114 original size:41 final size:39
Alignment explanation
Indices: 1412052--1412165 Score: 102
Period size: 41 Copynumber: 2.7 Consensus size: 39
1412042 TTATATTATA
1412052 TTATATTTTAATTATTTTTATAAATAATATAATATATAATAAT
1 TTATA-TTT-ATT-TTTTTATAAATAATATAAT-TATAATAAT
* * * *
1412095 TTATATTTATTTTTATTATAATTATATTTAATTATTATTAT
1 TTATATTTATTTTT-TTATAAATA-ATATAATTATAATAAT
* *
1412136 TTATATATATTTTATTTTATTAATAATATA
1 TTATATTTA-TTT-TTTTATAAATAATATA
1412166 TTTTACATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
40 3 0.05
41 30 0.51
42 19 0.32
43 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (39 bp):
TTATATTTATTTTTTTATAAATAATATAATTATAATAAT
Found at i:1414291 original size:34 final size:34
Alignment explanation
Indices: 1414253--1414335 Score: 166
Period size: 34 Copynumber: 2.4 Consensus size: 34
1414243 CTAACATATT
1414253 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
1414287 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
1414321 ACCTAACACACCTAA
1 ACCTAACACACCTAA
1414336 TATGCTTCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:1414337 original size:21 final size:22
Alignment explanation
Indices: 1414308--1414360 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1414298 CTAACATTCT
*
1414308 CACCAAATA-CATCACCTAACA
1 CACCTAATAGCATCACCTAACA
*
1414329 CACCTAATATGCTTCACCTAACA
1 CACCTAATA-GCATCACCTAACA
*
1414352 CACTTAATA
1 CACCTAATA
1414361 AAAAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 8 0.30
23 19 0.70
ACGTcount: A:0.42, C:0.34, G:0.02, T:0.23
Consensus pattern (22 bp):
CACCTAATAGCATCACCTAACA
Found at i:1419116 original size:34 final size:34
Alignment explanation
Indices: 1419078--1419160 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
1419068 CTAACATATT
*
1419078 ACCTAACACACTTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
1419112 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
* *
1419146 ACCTAATACATCTAA
1 ACCTAACACACCTAA
1419161 TATGCTTCAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:1421666 original size:34 final size:34
Alignment explanation
Indices: 1421611--1421827 Score: 276
Period size: 34 Copynumber: 6.4 Consensus size: 34
1421601 ATTAATATTA
*
1421611 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
1421644 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
1421678 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* ** *
1421712 TGTTGATTAAATGAGAAATTTGGTAACTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
1421746 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
1421780 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
1421814 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1421828 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 15 0.09
34 142 0.90
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:1421803 original size:102 final size:101
Alignment explanation
Indices: 1421611--1421827 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
1421601 ATTAATATTA
** ** * * *
1421611 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1421676 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1421712 TGTTGATTAAATGAGAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * *
1421777 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1421814 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1421828 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1426147 original size:34 final size:34
Alignment explanation
Indices: 1426090--1426303 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 34
1426080 AAGTGGGAGA
*
1426090 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
1426123 ATTGTTGATTAAATGGGTGATTTGGT-GGTT---
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1426153 ATTGTTGACTAAATGGGAGA-TTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1426186 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1426220 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
1426254 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1426288 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1426304 TGGTTTTTAC
Statistics
Matches: 154, Mismatches: 19, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
29 5 0.03
30 21 0.14
33 37 0.24
34 90 0.58
35 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1426189 original size:63 final size:65
Alignment explanation
Indices: 1426090--1426303 Score: 238
Period size: 63 Copynumber: 3.2 Consensus size: 65
1426080 AAGTGGGAGA
* *
1426090 ATTGTTGATTAAATGGTGA-TTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGT-GGTT
1 ATTGTTGATTAAATGG-GAGATTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGGTT
1426153 -
65 C
* * ** *
1426153 ATTGTTGACTAAATGGGAGATTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGGAGATTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGGTT-
1426218 CC
65 -C
* * * *
1426220 ATTATTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAAT-GGTAGATTTGGTAGGT
1 ATTGTTGATTAAATGGGAGA-TTGGTAGCTTACCATTGTTGATTAAATGGGT-GATTTGGTAGG-
1426284 TGTC
63 T-TC
1426288 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1426304 TGGTTTTTAC
Statistics
Matches: 125, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
62 2 0.02
63 50 0.40
64 3 0.02
67 18 0.14
68 50 0.40
69 1 0.01
70 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.41
Consensus pattern (65 bp):
ATTGTTGATTAAATGGGAGATTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGGTTC
Found at i:1428324 original size:18 final size:17
Alignment explanation
Indices: 1428301--1428339 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
1428291 AATTATTTAG
1428301 AAATAGCAAATAAAGATA-
1 AAATAGC-AAT-AAGATAT
1428319 AAATAGCAATAAGATAT
1 AAATAGCAATAAGATAT
1428336 AAAT
1 AAAT
1428340 TAACTACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 7 0.35
18 7 0.35
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
AAATAGCAATAAGATAT
Found at i:1428986 original size:20 final size:20
Alignment explanation
Indices: 1428961--1429001 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1428951 AGGATTAGGT
1428961 ATTCAATGCTAAATGAAATA
1 ATTCAATGCTAAATGAAATA
1428981 ATTCAATGCTAAATGAAATA
1 ATTCAATGCTAAATGAAATA
1429001 A
1 A
1429002 AAAAAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (20 bp):
ATTCAATGCTAAATGAAATA
Found at i:1430024 original size:2 final size:2
Alignment explanation
Indices: 1430017--1430041 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1430007 TAGCAAGTGT
1430017 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1430042 TCTAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1431361 original size:20 final size:20
Alignment explanation
Indices: 1431337--1431385 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1431327 ATAATTTCAT
1431337 AAATTATTTGA-TAAAAATA
1 AAATTATTTGAGTAAAAATA
* **
1431356 ATAATTATATGAGTAATTATA
1 A-AATTATTTGAGTAAAAATA
1431377 AAATTATTT
1 AAATTATTT
1431386 AAAAGCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.67
21 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
AAATTATTTGAGTAAAAATA
Found at i:1432423 original size:27 final size:27
Alignment explanation
Indices: 1432388--1432460 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
1432378 ACAAGCCACA
* *
1432388 ATTTTTGACAAACAAAAAGGAACTACC
1 ATTTTTGACAAACAAAAAGGAACCAAC
* * *
1432415 ATTTTTGACAAATACAAAGTAACCAAC
1 ATTTTTGACAAACAAAAAGGAACCAAC
* *
1432442 ATTTTTGAAAAACATAAAG
1 ATTTTTGACAAACAAAAAG
1432461 AGTGGTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCAAC
Found at i:1438472 original size:17 final size:16
Alignment explanation
Indices: 1438434--1438506 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 16
1438424 TAAAGTATTA
1438434 TATATTTATATAAATT
1 TATATTTATATAAATT
*
1438450 TTTATTTAT-TAATAATT
1 TATATTTATAT-A-AATT
1438467 TATA-TTATATAAATTT
1 TATATTTATATAAA-TT
*
1438483 TAATAATTTATATTATATT
1 T-AT-ATTTATA-TAAATT
1438502 TATAT
1 TATAT
1438507 ATTGTATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
15 3 0.07
16 17 0.37
17 12 0.26
18 3 0.07
19 8 0.17
20 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTTATATAAATT
Found at i:1438508 original size:32 final size:32
Alignment explanation
Indices: 1438429--1438508 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
1438419 TAATTTAAAG
* *
1438429 TATTATATATTTATATAAATTTTTATTTATTAA
1 TATTATAT-TTTATATAAATTTTTAATAATTAA
* *
1438462 TAATT-TATATTATATAAA-TTTTAATAATTTA
1 T-ATTATATTTTATATAAATTTTTAATAATTAA
1438493 TATTATATTTATATAT
1 TATTATATTT-TATAT
1438509 TGTATATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 3 0.08
31 15 0.38
32 14 0.36
33 4 0.10
34 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTATATTTTATATAAATTTTTAATAATTAA
Found at i:1440227 original size:13 final size:13
Alignment explanation
Indices: 1440209--1440241 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1440199 AAAGAATTGA
1440209 AGAGGGATACAAG
1 AGAGGGATACAAG
*
1440222 AGAGGGATACATG
1 AGAGGGATACAAG
1440235 AGAGGGA
1 AGAGGGA
1440242 GGAGGGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.42, T:0.09
Consensus pattern (13 bp):
AGAGGGATACAAG
Found at i:1440396 original size:27 final size:27
Alignment explanation
Indices: 1440321--1440397 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
1440311 AAACAACAAG
* *
1440321 CCACAATTTTTTACAAACAAAAAGGAA
1 CCACCATTTTTTACAAACACAAAGGAA
* * *
1440348 CTACCATTTTTTACAAATACAAAGTAA
1 CCACCATTTTTTACAAACACAAAGGAA
*
1440375 CCACCATTTTTGACAAACACAAA
1 CCACCATTTTTTACAAACACAAA
1440398 TGGTGGCTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.26
Consensus pattern (27 bp):
CCACCATTTTTTACAAACACAAAGGAA
Found at i:1444792 original size:13 final size:13
Alignment explanation
Indices: 1444774--1444806 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1444764 AAAGAATTGA
1444774 AGAGGGATACAAG
1 AGAGGGATACAAG
*
1444787 AGAGGGATACATG
1 AGAGGGATACAAG
1444800 AGAGGGA
1 AGAGGGA
1444807 GGATGGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.42, T:0.09
Consensus pattern (13 bp):
AGAGGGATACAAG
Found at i:1444929 original size:27 final size:27
Alignment explanation
Indices: 1444891--1444958 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
1444881 ACAAGCCATA
*
1444891 ATTTTTGACAAACAAAAAGAAACTACC
1 ATTTTTGACAAACAAAAAGAAACCACC
* * *
1444918 ATTTTTGACAAATATAAAGTAACCACC
1 ATTTTTGACAAACAAAAAGAAACCACC
*
1444945 ATTTTTAACAAACA
1 ATTTTTGACAAACA
1444959 CAAATGGTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.28
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGAAACCACC
Found at i:1446596 original size:12 final size:12
Alignment explanation
Indices: 1446579--1446626 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
1446569 TTTAAAGTAA
1446579 GTCTTCGTCTTT
1 GTCTTCGTCTTT
*
1446591 GTCTTCATCTTT
1 GTCTTCGTCTTT
*
1446603 GTCTTTGTC-TT
1 GTCTTCGTCTTT
1446614 GTC-TCGTCTTT
1 GTCTTCGTCTTT
1446625 GT
1 GT
1446627 TTTCATCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 4 0.13
11 9 0.29
12 18 0.58
ACGTcount: A:0.02, C:0.23, G:0.17, T:0.58
Consensus pattern (12 bp):
GTCTTCGTCTTT
Found at i:1446678 original size:11 final size:11
Alignment explanation
Indices: 1446662--1446704 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1446652 TTTTATTTTA
1446662 TATATTTATAT
1 TATATTTATAT
1446673 TATATTTATA-
1 TATATTTATAT
*
1446683 TATTTTTCATAT
1 TATATTT-ATAT
1446695 TCATATTTAT
1 T-ATATTTAT
1446705 TGTGTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 6 0.22
11 13 0.48
12 3 0.11
13 5 0.19
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1446936 original size:16 final size:16
Alignment explanation
Indices: 1446917--1446980 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
1446907 ATTATTATAT
1446917 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
*
1446933 ATTTAT-TAAAAATTT-
1 ATTTATAT-AAATTTTA
*
1446948 ATTTTTATAAATTTTA
1 ATTTATATAAATTTTA
* *
1446964 ATATATTTAAATATTTA
1 ATTTATATAAAT-TTTA
1446981 TATTATATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 12 0.32
16 22 0.58
17 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:1446957 original size:31 final size:32
Alignment explanation
Indices: 1446916--1446988 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
1446906 TATTATTATA
*
1446916 TATTTATATAAATTTTAATTTA-TTAAAAATT
1 TATTTATATAAATTTTAATATATTTAAAAATT
* *
1446947 TATTTTTATAAATTTTAATATATTTAAATATT
1 TATTTATATAAATTTTAATATATTTAAAAATT
1446979 TATATTATAT
1 TAT-TTATAT
1446989 TCATATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 20 0.56
32 11 0.31
33 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTTATATAAATTTTAATATATTTAAAAATT
Found at i:1446963 original size:15 final size:15
Alignment explanation
Indices: 1446916--1446963 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1446906 TATTATTATA
*
1446916 TATTTATATAAATTT
1 TATTTTTATAAATTT
*
1446931 TAATTTATTA-AAAATT
1 T-ATTT-TTATAAATTT
1446947 TATTTTTATAAATTT
1 TATTTTTATAAATTT
1446962 TA
1 TA
1446964 ATATATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.11
15 12 0.44
16 10 0.37
17 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTTTATAAATTT
Found at i:1447729 original size:18 final size:17
Alignment explanation
Indices: 1447706--1447751 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
1447696 GTTGCTTAAT
1447706 TTTATTTATTGTGCTTTA
1 TTTATTTATT-TGCTTTA
*
1447724 TTTATTATATTTTCTTTA
1 TTTATT-TATTTGCTTTA
1447742 TTTAATTTAT
1 TTT-ATTTAT
1447752 AATCTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (17 bp):
TTTATTTATTTGCTTTA
Found at i:1452006 original size:24 final size:26
Alignment explanation
Indices: 1451963--1452038 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 26
1451953 ATTTTCTAAT
* *
1451963 AAAAATTAGCCACCAATTTTGACAAAC
1 AAAAA-TAGCCACTATTTTTGACAAAC
* * *
1451990 -AACA-AGCCACTATTTTTTACATAC
1 AAAAATAGCCACTATTTTTGACAAAC
* *
1452014 AAAAATAACCACTATATTTGACAAA
1 AAAAATAGCCACTATTTTTGACAAA
1452039 TACAAAGGGT
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
24 16 0.43
25 3 0.08
26 18 0.49
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (26 bp):
AAAAATAGCCACTATTTTTGACAAAC
Found at i:1453583 original size:21 final size:21
Alignment explanation
Indices: 1453557--1453608 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1453547 TTGTAGCGAA
1453557 CATCTTTCTTGCTAGGAAATC
1 CATCTTTCTTGCTAGGAAATC
1453578 CATCTTTCTTGCTAGGAAATC
1 CATCTTTCTTGCTAGGAAATC
1453599 CATCTTTCTT
1 CATCTTTCTT
1453609 TGCAAATACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (21 bp):
CATCTTTCTTGCTAGGAAATC
Found at i:1454008 original size:21 final size:22
Alignment explanation
Indices: 1453970--1454015 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1453960 ATCTGTTGAA
* **
1453970 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1453991 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1454013 ACT
1 ACT
1454016 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1456609 original size:28 final size:28
Alignment explanation
Indices: 1456578--1456641 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1456568 TATTTTTTAC
1456578 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
*
1456606 ATACAAAGGAAACCACCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
1456634 ATACAAAG
1 ATACAAAG
1456642 GGTGGCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:1456642 original size:28 final size:28
Alignment explanation
Indices: 1456588--1456642 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1456578 ATACAAAAAT
1456588 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
1456616 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
1456643 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:1457851 original size:18 final size:20
Alignment explanation
Indices: 1457815--1457851 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
1457805 GTTACAATCA
*
1457815 TATATAAAATATTTTATATT
1 TATATAAAATATTTGATATT
1457835 TATAT-AAAT-TTTGATAT
1 TATATAAAATATTTGATAT
1457852 GTTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TATATAAAATATTTGATATT
Found at i:1458150 original size:17 final size:16
Alignment explanation
Indices: 1458116--1458154 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1458106 TATTTTTTGA
*
1458116 AAAATAATAATTTAAT
1 AAAATAATAATATAAT
*
1458132 AAAATAATAAATATGAT
1 AAAATAAT-AATATAAT
1458149 AAAATA
1 AAAATA
1458155 TTTGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATAATAATATAAT
Found at i:1458595 original size:20 final size:20
Alignment explanation
Indices: 1458572--1458609 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1458562 AACAAAAAAT
*
1458572 AAAAAAATAATATAATATAA
1 AAAAAAATAACATAATATAA
*
1458592 AAAAATATAACATAATAT
1 AAAAAAATAACATAATAT
1458610 GAATACATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAAATAACATAATATAA
Found at i:1458598 original size:15 final size:16
Alignment explanation
Indices: 1458569--1458606 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1458559 TGTAACAAAA
*
1458569 AATAAAAAAATAATAT
1 AATATAAAAATAATAT
1458585 AATATAAAAA-AATAT
1 AATATAAAAATAATAT
*
1458600 AACATAA
1 AATATAA
1458607 TATGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATAAAAATAATAT
Found at i:1458675 original size:18 final size:18
Alignment explanation
Indices: 1458625--1458675 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1458615 CATAAATATG
1458625 TCAAAATTTATAT-AATA
1 TCAAAATTTATATAAATA
1458642 T--AAA-TTAT-TAATATA
1 TCAAAATTTATATAA-ATA
1458657 TCAAAATTTATATAAATA
1 TCAAAATTTATATAAATA
1458675 T
1 T
1458676 GTCATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
13 1 0.04
14 5 0.18
15 7 0.25
17 4 0.14
18 8 0.29
19 3 0.11
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
TCAAAATTTATATAAATA
Found at i:1459059 original size:24 final size:24
Alignment explanation
Indices: 1459010--1459059 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1459000 CTTATATTTT
* * *
1459010 TTCCATTTTTTCTTCAATGTTACG
1 TTCCATTTTTCCTGCAATGATACG
1459034 TTCCATTTGTTCCTGCAATGAT-CG
1 TTCCATTT-TTCCTGCAATGATACG
1459058 TT
1 TT
1459060 TAACCTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (24 bp):
TTCCATTTTTCCTGCAATGATACG
Found at i:1460931 original size:31 final size:32
Alignment explanation
Indices: 1460893--1460954 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
1460883 TCATTTAAGA
* *
1460893 TTTAAACTCTTTCGA-TTTAAATTATTTTAGG
1 TTTAAACTCTTTCAAGTTCAAATTATTTTAGG
*
1460924 TTTAAACTCTTTCAAGTTCGAATTATTTTAG
1 TTTAAACTCTTTCAAGTTCAAATTATTTTAG
1460955 ATTTCGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (32 bp):
TTTAAACTCTTTCAAGTTCAAATTATTTTAGG
Found at i:1461902 original size:10 final size:10
Alignment explanation
Indices: 1461887--1461918 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1461877 AAATTCAAAC
1461887 AACAAAATAA
1 AACAAAATAA
1461897 AACAAAATAA
1 AACAAAATAA
*
1461907 AATAAAATAA
1 AACAAAATAA
1461917 AA
1 AA
1461919 ATTTAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (10 bp):
AACAAAATAA
Found at i:1463799 original size:165 final size:165
Alignment explanation
Indices: 1463480--1463881 Score: 596
Period size: 165 Copynumber: 2.4 Consensus size: 165
1463470 AAAAAATAAT
*
1463480 AATTAAATTGATAATTAAATTTTAATTTTTATAAAAAATTAATAATTAAAATTTAATCATTTTTA
1 AATTAAATTGATAATTAAATTTTAATTTTTATAAAAAATTAATAATTAAAATTTGATCATTTTTA
* * *
1463545 TTTTTAATGTGAAAATCCTATTATTAGAAATTAATAATTAGATAGTCCTTTTTTTCTATCATTTC
66 TTTTTAATGTGAAAATCCTATTATTAGAAATTAATAATTAGATAATCCTTTGTTTCAATCATTTC
* * *
1463610 ACATCCAAATTATTACAGGCTTGAA-TTATTAAAA
131 ACAGCCAAATTATTAAAAGCTTGAATTTATTAAAA
*
1463644 AATTAAATTTATAATTAAATTTTAATTTTTATAAAAAATTAATAATTAAAATTTGATCATTTTGT
1 AATTAAATTGATAATTAAATTTTAATTTTTATAAAAAATTAATAATTAAAATTTGATCATTTT-T
* *
1463709 ATTTTTAGTGTGAAAATCCTATTATTATG-AATTAATAATTAGGTAAT-CTTTGGTTTCAATCAT
65 ATTTTTAATGTGAAAATCCTATTATTA-GAAATTAATAATTAGATAATCCTTT-GTTTCAATCAT
* * *
1463772 TTCACGGCTAAATTATTAAAAGCTTGAATTTTTTTTAAAA
128 TTCACAGCCAAATTATTAAAAGCTTGAA--TTTATTAAAA
*
1463812 AATAAAATTGATAATTAAATTTTAATTTTTATAAAAAAATTAATAATTAAAATTTGAT-ATTTTT
1 AATTAAATTGATAATTAAATTTTAATTTTTAT-AAAAAATTAATAATTAAAATTTGATCATTTTT
1463876 ATTTTT
65 ATTTTT
1463882 CGATTATTTC
Statistics
Matches: 216, Mismatches: 15, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
164 65 0.30
165 75 0.35
166 1 0.00
167 7 0.03
168 43 0.20
169 25 0.12
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (165 bp):
AATTAAATTGATAATTAAATTTTAATTTTTATAAAAAATTAATAATTAAAATTTGATCATTTTTA
TTTTTAATGTGAAAATCCTATTATTAGAAATTAATAATTAGATAATCCTTTGTTTCAATCATTTC
ACAGCCAAATTATTAAAAGCTTGAATTTATTAAAA
Found at i:1463858 original size:32 final size:34
Alignment explanation
Indices: 1463815--1463877 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 34
1463805 TTTAAAAAAT
* *
1463815 AAAATTGATAATT-AAATTTTA-ATTTTTATAAA
1 AAAATTAATAATTAAAATTTGATATTTTTATAAA
1463847 AAAATTAATAATTAAAATTTGATATTTTTAT
1 AAAATTAATAATTAAAATTTGATATTTTTAT
1463878 TTTTCGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 12 0.44
33 7 0.26
34 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (34 bp):
AAAATTAATAATTAAAATTTGATATTTTTATAAA
Found at i:1464086 original size:129 final size:130
Alignment explanation
Indices: 1463952--1464206 Score: 374
Period size: 130 Copynumber: 2.0 Consensus size: 130
1463942 AGCTAAAATA
* * *
1463952 ATTTCAAATTTAAATTATTTTATATTTTACTTTTT-ATTTTTTATCAAATTAAATTT-ATACCTA
1 ATTTCAAATTCAAATTATTTTATATTTTACTTTTTAAATTTTCATCAAATTAAATTTCA-ACCT-
* * * *
1464015 TTT-AATTTTAATTT-TTTGAATAAATTTTTATATTCAAATTTATATTATTTAAAAAATAACATT
64 TTTCAAGTTTAATTTGTTT-AACAAATTTTCATATTCAAATATATATTATTTAAAAAATAACATT
1464078 TTC
128 TTC
*
1464081 ATTTCAAATTCAAATTATTTTATATTTTACTTTTTAAATTTTCGTCAAATTAAATTTCAACCTTT
1 ATTTCAAATTCAAATTATTTTATATTTTACTTTTTAAATTTTCATCAAATTAAATTTCAACCTTT
*
1464146 TCAAGTTTAATTTGTTTAACAAATTTTCATATTTAAATATATATTATTTAAAAAATAACAT
66 TCAAGTTTAATTTGTTTAACAAATTTTCATATTCAAATATATATTATTTAAAAAATAACAT
1464207 ATTTTAAAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
129 37 0.33
130 72 0.64
131 4 0.04
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.53
Consensus pattern (130 bp):
ATTTCAAATTCAAATTATTTTATATTTTACTTTTTAAATTTTCATCAAATTAAATTTCAACCTTT
TCAAGTTTAATTTGTTTAACAAATTTTCATATTCAAATATATATTATTTAAAAAATAACATTTTC
Found at i:1465846 original size:22 final size:23
Alignment explanation
Indices: 1465818--1465871 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 23
1465808 ACATTTTTTC
1465818 TTTTTTAA-AAAAAACTACTCAA
1 TTTTTTAATAAAAAACTACTCAA
1465840 TTTTTTAAATTAAAAAACTACTCAA
1 TTTTTT-AA-TAAAAAACTACTCAA
1465865 TTTTTTA
1 TTTTTTA
1465872 GACACTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.21
23 2 0.07
24 1 0.03
25 20 0.69
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTTTTAATAAAAAACTACTCAA
Found at i:1466790 original size:10 final size:10
Alignment explanation
Indices: 1466772--1466818 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1466762 AACATTTAAT
1466772 AATAAAAATA
1 AATAAAAATA
*
1466782 AATAGAAATA
1 AATAAAAATA
* *
1466792 TATAAAAAGA
1 AATAAAAATA
1466802 AAT-AAAATAA
1 AATAAAAAT-A
1466812 AATAAAA
1 AATAAAA
1466819 TATCTAATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
9 4 0.14
10 22 0.76
11 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AATAAAAATA
Found at i:1466816 original size:20 final size:20
Alignment explanation
Indices: 1466772--1466818 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1466762 AACATTTAAT
*
1466772 AATAAAAATAAATAGAAATA
1 AATAAAAAGAAATAGAAATA
*
1466792 TATAAAAAGAAATA-AAATAA
1 AATAAAAAGAAATAGAAAT-A
1466812 AATAAAA
1 AATAAAA
1466819 TATCTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (20 bp):
AATAAAAAGAAATAGAAATA
Found at i:1467601 original size:28 final size:27
Alignment explanation
Indices: 1467570--1467704 Score: 98
Period size: 28 Copynumber: 4.8 Consensus size: 27
1467560 TAATTCTATG
* * *
1467570 TATTTATATTATATTTATGTTAATTTTT
1 TATTTATATTATATTTATATT-ATTATA
1467598 TA-TTATAATTATATTTATATTATTATA
1 TATTTAT-ATTATATTTATATTATTATA
*
1467625 TATTTATA-TAAATTT-TAATTTATTAATAAA
1 TATTTATATTATATTTAT-A-TTATT-AT--A
* *
1467655 TTATTTATATAAAATTTA-ATATATTTATA
1 -TATTTATATTATATTTATAT-TA-TTATA
1467684 TATTTATATTATATTTATATT
1 TATTTATATTATATTTATATT
1467705 GTTTTTATAA
Statistics
Matches: 87, Mismatches: 7, Indels: 26
0.73 0.06 0.22
Matches are distributed among these distances:
25 1 0.01
26 7 0.08
27 16 0.18
28 37 0.43
29 3 0.03
30 2 0.02
31 13 0.15
32 8 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TATTTATATTATATTTATATTATTATA
Found at i:1467660 original size:31 final size:32
Alignment explanation
Indices: 1467613--1467697 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
1467603 TAATTATATT
* *
1467613 TATATTATTAT-A-TATTTATATAAATTTTAA
1 TATATTAATATAATTATTTATATAAAATTTAA
*
1467643 TTTATTAATA-AATTATTTATATAAAATTTAA
1 TATATTAATATAATTATTTATATAAAATTTAA
* *
1467674 TATATTTATATATTTATATTATAT
1 TATATTAATATAATTAT-TTATAT
1467698 TTATATTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 9 0.20
31 25 0.56
32 5 0.11
33 6 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATATTAATATAATTATTTATATAAAATTTAA
Found at i:1467713 original size:11 final size:11
Alignment explanation
Indices: 1467570--1467704 Score: 69
Period size: 11 Copynumber: 12.9 Consensus size: 11
1467560 TAATTCTATG
1467570 TATTTATATTA
1 TATTTATATTA
*
1467581 TATTTATGTTA
1 TATTTATATTA
*
1467592 -ATTTTTTATTA
1 TA-TTTATATTA
*
1467603 TAATTATATT-
1 TATTTATATTA
1467613 TATATTAT-TATA
1 TAT-TTATAT-TA
1467625 TATTTATA-TA
1 TATTTATATTA
*
1467635 AATTT-TAATT-
1 TATTTAT-ATTA
* *
1467645 TATTAATA-AA
1 TATTTATATTA
*
1467655 TTATTTATATAA
1 -TATTTATATTA
*
1467667 AATTTA-A-TA
1 TATTTATATTA
1467676 TA-TT-TA-TA
1 TATTTATATTA
1467684 TATTTATATTA
1 TATTTATATTA
1467695 TATTTATATT
1 TATTTATATT
1467705 GTTTTTATAA
Statistics
Matches: 94, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
8 7 0.07
9 5 0.05
10 18 0.19
11 58 0.62
12 6 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1468462 original size:7 final size:7
Alignment explanation
Indices: 1468440--1468482 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
1468430 TTATATTTTC
1468440 TTTAATT
1 TTTAATT
1468447 ATTTAATT
1 -TTTAATT
*
1468455 TATAA--
1 TTTAATT
1468460 TTTAATT
1 TTTAATT
1468467 TTTAATT
1 TTTAATT
1468474 TTTAATT
1 TTTAATT
1468481 TT
1 TT
1468483 ATTTAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.13
7 20 0.65
8 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTAATT
Found at i:1468472 original size:19 final size:19
Alignment explanation
Indices: 1468440--1468486 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
1468430 TTATATTTTC
1468440 TTTAATTATTTAATTTATAA
1 TTTAATT-TTTAATTTATAA
*
1468460 TTTAATTTTTAATTTTTAA
1 TTTAATTTTTAATTTATAA
*
1468479 TTTTATTT
1 TTTAATTT
1468487 AATTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTTAATTTATAA
Found at i:1468835 original size:31 final size:31
Alignment explanation
Indices: 1468800--1468892 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 31
1468790 TTCAGCCCTA
* *
1468800 TTTTAAA-ACAAA-ATTTATTTTTTAATTAATT
1 TTTTAAATA-AAATATTTATATTTAAATT-ATT
1468831 TTTTAAATAAAATATTTATATTTAAATTATT
1 TTTTAAATAAAATATTTATATTTAAATTATT
1468862 TTAAATATAAAATAAAAT-TTTATATTTAAAT
1 TT---T-T-AAATAAAATATTTATATTTAAAT
1468893 AAATAATCTG
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
31 15 0.28
32 14 0.26
34 1 0.02
35 14 0.26
36 9 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTTAAATAAAATATTTATATTTAAATTATT
Found at i:1469485 original size:15 final size:18
Alignment explanation
Indices: 1469451--1469487 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
1469441 ATGTTATCAA
1469451 ATTTAAATATATATTTTT
1 ATTTAAATATATATTTTT
1469469 ATTTAAA-AT-TA-TTTT
1 ATTTAAATATATATTTTT
1469484 ATTT
1 ATTT
1469488 TAATTAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 2 0.11
18 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTAAATATATATTTTT
Found at i:1469552 original size:27 final size:30
Alignment explanation
Indices: 1469513--1469572 Score: 90
Period size: 27 Copynumber: 2.1 Consensus size: 30
1469503 ATCAATTCAA
*
1469513 TAAATTATTTATTATTTT-ATAA-TATTTT
1 TAAATTATTTATTATTTTGATAAGTAATTT
1469541 TAAA-TATTTATTATTTTGATAAGTAATTT
1 TAAATTATTTATTATTTTGATAAGTAATTT
1469570 TAA
1 TAA
1469573 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 13 0.45
28 8 0.28
29 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TAAATTATTTATTATTTTGATAAGTAATTT
Found at i:1470257 original size:259 final size:260
Alignment explanation
Indices: 1469536--1470316 Score: 1384
Period size: 260 Copynumber: 3.0 Consensus size: 260
1469526 ATTTTATAAT
1469536 ATTTTTAAATATTTATTATTTTGATAAGTAATTTTAATAAAAAAATTGATTTAGTAAATATACCT
1 ATTTTTAAATATTTATTATTTTGATAAGTAATTTTAATAAAAAAATTGATTTAGTAAATATACCT
* *
1469601 TACTTATTTTTTAAGATAATTTTAACATATGTAAATATCTAATTTTATCCAATTAATAAAATATG
66 GACTTATTTTTTAAGATAATTTTAACATATGTAGATATCTAATTTTATCCAATTAATAAAATATG
1469666 AAATTTTAAGATAATTCGAAATAAAGTCACAAATTAGATCTAGTTGTATAGATATTTTGATTCGT
131 AAATTTTAAGATAATTCGAAATAAAGTCACAAATTAGATCTAGTTGTATAGATATTTTGATTCGT
1469731 TACTTAAATATATTAAATTAAATTTTACTTGAAGTCATTTTTTACTTAAGCTTTAATTAAATTAA
196 TACTTAAATATATTAAATTAAATTTTACTTGAAGTCATTTTTTACTTAAGCTTTAATTAAATTAA
* *
1469796 ATTTTTAAATATTTATTATTTTGATAAGTAATTTTAATAAAAAAATTCATCTAGTAAATATACCT
1 ATTTTTAAATATTTATTATTTTGATAAGTAATTTTAATAAAAAAATTGATTTAGTAAATATACCT
*
1469861 GACTTATTTTTTAAGATAATTTTAACATATGTAGATATCTAATTTTATCCAATTAATAAAATATA
66 GACTTATTTTTTAAGATAATTTTAACATATGTAGATATCTAATTTTATCCAATTAATAAAATATG
* *
1469926 AAATTTTAAGGTAATTCGAAATAAAGTCACAAATTAGATCTAGTTGTATAGATATTTTGACTCGT
131 AAATTTTAAGATAATTCGAAATAAAGTCACAAATTAGATCTAGTTGTATAGATATTTTGATTCGT
1469991 TACTTAAATATATTAAATTAAATTTTACTTGAAGTCATTTTTTACTTAAGCTTTAATTAAATTAA
196 TACTTAAATATATTAAATTAAATTTTACTTGAAGTCATTTTTTACTTAAGCTTTAATTAAATTAA
* * *
1470056 ATTTTTAAATATTTTTTATTTTGATAAGTAATTTTAAT-AAAAAATTGATTTAATAAATATACAT
1 ATTTTTAAATATTTATTATTTTGATAAGTAATTTTAATAAAAAAATTGATTTAGTAAATATACCT
**
1470120 GACTTATTTTTTAAGATAATTTTAACATACATAGATATCTAATTTTATCCAATTAATAAAATATG
66 GACTTATTTTTTAAGATAATTTTAACATATGTAGATATCTAATTTTATCCAATTAATAAAATATG
* * * * *
1470185 AAATTTTAAGATAATTCAAAATGAAGTCACAAATTAAATTTAATTGTATAGATATTTTGATTCGT
131 AAATTTTAAGATAATTCGAAATAAAGTCACAAATTAGATCTAGTTGTATAGATATTTTGATTCGT
* *
1470250 AACTTAAATATATTAAATTAAATTTTACTTGAAGTCATTTTTTACTCAAGCTTTAATTAAATTAA
196 TACTTAAATATATTAAATTAAATTTTACTTGAAGTCATTTTTTACTTAAGCTTTAATTAAATTAA
1470315 AT
1 AT
1470317 CAAATTATTA
Statistics
Matches: 497, Mismatches: 24, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
259 207 0.42
260 290 0.58
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (260 bp):
ATTTTTAAATATTTATTATTTTGATAAGTAATTTTAATAAAAAAATTGATTTAGTAAATATACCT
GACTTATTTTTTAAGATAATTTTAACATATGTAGATATCTAATTTTATCCAATTAATAAAATATG
AAATTTTAAGATAATTCGAAATAAAGTCACAAATTAGATCTAGTTGTATAGATATTTTGATTCGT
TACTTAAATATATTAAATTAAATTTTACTTGAAGTCATTTTTTACTTAAGCTTTAATTAAATTAA
Found at i:1470424 original size:22 final size:20
Alignment explanation
Indices: 1470393--1470433 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1470383 TTAATGCATA
1470393 TAAAAATAAATAATAAAAAAAT
1 TAAAAAT-AA-AATAAAAAAAT
*
1470415 TAAAATTAAAATAAAAAAA
1 TAAAAATAAAATAAAAAAA
1470434 GGGAGGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAAATAAAATAAAAAAAT
Found at i:1471153 original size:82 final size:82
Alignment explanation
Indices: 1471058--1471219 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 82
1471048 ACTTAGATGC
* *
1471058 ATTTATGAACTTCACGTGAATGGATAAACCC-CAGCATGGGTTTTGGGGTTTCAAGGACTAATCA
1 ATTTATGAACTTCACATGAATGGAT-AACCCACAGCATGGGTTTTGGGATTTCAAGGACTAATCA
* *
1471122 CGCTACTTATAGATTAGG
65 AGCTACCTATAGATTAGG
* *
1471140 ATTTATGAACTTCACATGAGTTGATAACCCACAGCATGGGTTTTGGGATTTCAAGGACTAATCAA
1 ATTTATGAACTTCACATGAATGGATAACCCACAGCATGGGTTTTGGGATTTCAAGGACTAATCAA
*
1471205 GTTACCTATAGATTA
66 GCTACCTATAGATTA
1471220 AGTAAGAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 5 0.07
82 67 0.93
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (82 bp):
ATTTATGAACTTCACATGAATGGATAACCCACAGCATGGGTTTTGGGATTTCAAGGACTAATCAA
GCTACCTATAGATTAGG
Found at i:1472339 original size:3 final size:3
Alignment explanation
Indices: 1472331--1472355 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1472321 CTCTAGAAAA
1472331 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1472356 CTAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1475722 original size:42 final size:45
Alignment explanation
Indices: 1475676--1475764 Score: 105
Period size: 47 Copynumber: 2.0 Consensus size: 45
1475666 AAACATAAAT
1475676 AATAAAA-AC-AT-GAGTATTATTAATTATATTATAAAT-AAATAA
1 AATAAAATACAATAGAGTATTATTAATTATATTAT-AATCAAATAA
* *
1475718 AATAAAATACAAATAATATTATTATTAATTATATTATAATCAAATAA
1 AATAAAATAC-AAT-AGAGTATTATTAATTATATTATAATCAAATAA
1475765 CAAATGAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
42 7 0.18
43 2 0.05
45 2 0.05
46 3 0.08
47 25 0.64
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (45 bp):
AATAAAATACAATAGAGTATTATTAATTATATTATAATCAAATAA
Found at i:1477625 original size:2 final size:2
Alignment explanation
Indices: 1477618--1477652 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1477608 TGAAAAAGAA
1477618 AT AT AT 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 AT AT AT A
1477653 AAGATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1478768 original size:16 final size:16
Alignment explanation
Indices: 1478701--1478760 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
1478691 AGTCTTTGGT
**
1478701 TTTG-ATTATTTCGAG
1 TTTGAATTATTTTAAG
* *
1478716 TTTAAATTATTATAAG
1 TTTGAATTATTTTAAG
*
1478732 ATTGAATTATTTTAAG
1 TTTGAATTATTTTAAG
1478748 TTTGAATTATTTT
1 TTTGAATTATTTT
1478761 GGATTTGATT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
15 3 0.08
16 33 0.92
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.55
Consensus pattern (16 bp):
TTTGAATTATTTTAAG
Found at i:1484753 original size:17 final size:16
Alignment explanation
Indices: 1484727--1484763 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1484717 GTAACAAAAA
*
1484727 ATAATTAAAATATAAT
1 ATAATTAAAAAATAAT
1484743 ATAATTTAAAAAATAAT
1 ATAA-TTAAAAAATAAT
1484760 ATAA
1 ATAA
1484764 ATATAATACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATTAAAAAATAAT
Found at i:1487028 original size:32 final size:32
Alignment explanation
Indices: 1486992--1487071 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1486982 TCGGATTTAT
** *
1486992 ATCATTTAAGATTTGAACTTTTTCAAA-TTCGA
1 ATCATTTAAGATTCAAACTTTTT-AAAGTTCAA
1487024 ATCATTTTAAG-TTCAAACTTTTTAAAGTTCAA
1 ATCA-TTTAAGATTCAAACTTTTTAAAGTTCAA
*
1487056 ATCATTTTAGATTCAA
1 ATCATTTAAGATTCAA
1487072 GTTAAGTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 8 0.20
32 27 0.66
33 6 0.15
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (32 bp):
ATCATTTAAGATTCAAACTTTTTAAAGTTCAA
Found at i:1487071 original size:16 final size:16
Alignment explanation
Indices: 1487023--1487064 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1487013 TTCAAATTCG
1487023 AATCATTTTAAGTTCA
1 AATCATTTTAAGTTCA
*
1487039 AA-CTTTTTAAAGTTCA
1 AATCATTTT-AAGTTCA
1487055 AATCATTTTA
1 AATCATTTTA
1487065 GATTCAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (16 bp):
AATCATTTTAAGTTCA
Found at i:1489813 original size:2 final size:2
Alignment explanation
Indices: 1489806--1489838 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1489796 AAATTTGTTC
*
1489806 AT AT AT AT AC AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1489839 TTTAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1490255 original size:2 final size:2
Alignment explanation
Indices: 1490237--1490281 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1490227 AGAATAATTA
* *
1490237 AT AT -T AT AT AC AC 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 AT AT
1490278 AT AT
1 AT AT
1490282 GCAATTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1490792 original size:11 final size:11
Alignment explanation
Indices: 1490775--1490813 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1490765 TTATGATAAG
1490775 AAATTAAAAAT
1 AAATTAAAAAT
*
1490786 TAATTAAAATAT
1 AAATTAAAA-AT
*
1490798 AAATAAAAAAT
1 AAATTAAAAAT
1490809 AAATT
1 AAATT
1490814 TTAATTATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATTAAAAAT
Found at i:1490914 original size:37 final size:37
Alignment explanation
Indices: 1490838--1490915 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
1490828 TTAATCTATA
* * ** *
1490838 AAATAAAAATTAAATTAAATATAATTAATTATTATTC
1 AAATAAAAATTAAACTAAATATAATAAAAAATTAATC
*
1490875 AAATTAAAATTAAACTAAAT-TAATAAAAAATTAAATC
1 AAATAAAAATTAAACTAAATATAATAAAAAATT-AATC
1490912 AAAT
1 AAAT
1490916 CAAATATCAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 9 0.26
37 25 0.74
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (37 bp):
AAATAAAAATTAAACTAAATATAATAAAAAATTAATC
Found at i:1491078 original size:6 final size:6
Alignment explanation
Indices: 1491064--1491097 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1491054 GGAAATTCGA
* *
1491064 TTTTGC TTTTAC TTTTGC TTTTAC TTTTGC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1491098 TGCCTCATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.06, C:0.15, G:0.09, T:0.71
Consensus pattern (6 bp):
TTTTGC
Found at i:1491081 original size:12 final size:12
Alignment explanation
Indices: 1491064--1491097 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1491054 GGAAATTCGA
1491064 TTTTGCTTTTAC
1 TTTTGCTTTTAC
1491076 TTTTGCTTTTAC
1 TTTTGCTTTTAC
1491088 TTTTGCTTTT
1 TTTTGCTTTT
1491098 TGCCTCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.15, G:0.09, T:0.71
Consensus pattern (12 bp):
TTTTGCTTTTAC
Found at i:1491168 original size:22 final size:22
Alignment explanation
Indices: 1491140--1491211 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
1491130 TCATTATTTT
1491140 TAAATATAATTTTTATAATTAA
1 TAAATATAATTTTTATAATTAA
*
1491162 TAAATAT-A-TTTTACTCA-T-A
1 TAAATATAATTTTTA-TAATTAA
*
1491181 TGAATAATAATTTTTATAATTAA
1 TAAAT-ATAATTTTTATAATTAA
1491204 TAAATATA
1 TAAATATA
1491212 TCTTATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
19 5 0.12
20 8 0.20
21 6 0.15
22 16 0.40
23 5 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (22 bp):
TAAATATAATTTTTATAATTAA
Found at i:1491201 original size:42 final size:42
Alignment explanation
Indices: 1491145--1491229 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
1491135 ATTTTTAAAT
* *
1491145 ATAATTTTTATAATTAATAAATATATTTTACT-CATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTA-TAAATATGAATA
1491187 ATAATTTTTATAATTAATAAATATATCTTATAAATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTATAAATATGAATA
1491229 A
1 A
1491230 AAATAGTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (42 bp):
ATAATTTTTATAATTAATAAATATATCTTATAAATATGAATA
Found at i:1491217 original size:20 final size:20
Alignment explanation
Indices: 1491140--1491219 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 20
1491130 TCATTATTTT
1491140 TAAATATAATTTTTATAATTAA
1 TAAATAT-A-TTTTATAATTAA
*
1491162 TAAATATATTTTACTCATATGAA
1 TAAATATATTTTA-T-A-ATTAA
1491185 T-AATA-ATTTTTATAATTAA
1 TAAATATA-TTTTATAATTAA
*
1491204 TAAATATATCTTATAA
1 TAAATATATTTTATAA
1491220 ATATGAATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
19 5 0.10
20 17 0.35
21 5 0.10
22 17 0.35
23 5 0.10
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (20 bp):
TAAATATATTTTATAATTAA
Found at i:1492323 original size:17 final size:17
Alignment explanation
Indices: 1492301--1492334 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1492291 ATAAATTTTA
1492301 ATTTTTTACTTAAATCT
1 ATTTTTTACTTAAATCT
*
1492318 ATTTTTTATTTAAATCT
1 ATTTTTTACTTAAATCT
1492335 TAATATCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTTACTTAAATCT
Found at i:1496454 original size:2 final size:2
Alignment explanation
Indices: 1496447--1496484 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1496437 ATGATTCTTC
1496447 AT AT AT 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
1496485 TTCTAGGTCT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1497090 original size:20 final size:20
Alignment explanation
Indices: 1497065--1497107 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1497055 GCTACCCAAA
1497065 AACTTCAAGTTCTTCGAGGT
1 AACTTCAAGTTCTTCGAGGT
1497085 AACTTCAAGTTCTTCGAGGT
1 AACTTCAAGTTCTTCGAGGT
1497105 AAC
1 AAC
1497108 CTATAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AACTTCAAGTTCTTCGAGGT
Found at i:1497698 original size:38 final size:38
Alignment explanation
Indices: 1497656--1497780 Score: 110
Period size: 38 Copynumber: 3.3 Consensus size: 38
1497646 ATTCACGTTG
*
1497656 GAATTCCCTAGTCACCAGCCATCGGCCAATTCCAAATT
1 GAATTCTCTAGTCACCAGCCATCGGCCAATTCCAAATT
* ** * * * *
1497694 GAATTCTCTAATCGTCAGTCGTCGGCTAATTTCAAATT
1 GAATTCTCTAGTCACCAGCCATCGGCCAATTCCAAATT
** * *
1497732 GAATTCTCTAG-CTGTCAGCC-GCTGGCCAATTTCAAATT
1 GAATTCTCTAGTC-ACCAGCCATC-GGCCAATTCCAAATT
1497770 GAATTCTCTAG
1 GAATTCTCTAG
1497781 CCGTCAGCCG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
37 2 0.03
38 71 0.97
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (38 bp):
GAATTCTCTAGTCACCAGCCATCGGCCAATTCCAAATT
Found at i:1497781 original size:38 final size:38
Alignment explanation
Indices: 1497671--1497824 Score: 159
Period size: 38 Copynumber: 3.9 Consensus size: 38
1497661 CCCTAGTCAC
* * *
1497671 CAGCCATCGGCCAATTCCAAATTGAATTCTCTA-ATCGT
1 CAGCCGTCGGCCAATTTCAAATTGAATTCTCTAGCT-GT
* *
1497709 CAGTCGTCGGCTAATTTCAAATTGAATTCTCTAGCTGT
1 CAGCCGTCGGCCAATTTCAAATTGAATTCTCTAGCTGT
*
1497747 CAGCCG-CTGGCCAATTTCAAATTGAATTCTCTAGCCGT
1 CAGCCGTC-GGCCAATTTCAAATTGAATTCTCTAGCTGT
1497785 CAGCCGTCAGCCGCCAGCCAATTTCAAATTGAATTCTCTA
1 CAGCCGT----CG---GCCAATTTCAAATTGAATTCTCTA
1497825 ACCGTCAACC
Statistics
Matches: 98, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
37 1 0.01
38 70 0.71
39 1 0.01
42 1 0.01
43 1 0.01
45 24 0.24
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (38 bp):
CAGCCGTCGGCCAATTTCAAATTGAATTCTCTAGCTGT
Found at i:1497809 original size:45 final size:45
Alignment explanation
Indices: 1497745--1497831 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
1497735 TTCTCTAGCT
** *
1497745 GTCAGCCGCTGGCCAATTTCAAATTGAATTCTCTAGCCGTCAGCC
1 GTCAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGTCAGCC
1497790 GTCAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGTCA
1 GTCAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGTCA
1497832 ACCAATTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (45 bp):
GTCAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGTCAGCC
Found at i:1501945 original size:38 final size:38
Alignment explanation
Indices: 1501903--1502049 Score: 186
Period size: 38 Copynumber: 3.9 Consensus size: 38
1501893 CCTTAGCCAC
* * *
1501903 CAGCCACCGGCCAATTCCAAATTGAATTCTCTAGTCGT
1 CAGCCACCGGTCAATTTCAAATTGAATTTTCTAGTCGT
*** *
1501941 CAGCCGTTGGTCAATTTCAAATTGAATTTTCTAGCCGT
1 CAGCCACCGGTCAATTTCAAATTGAATTTTCTAGTCGT
** * *
1501979 CAGCCGTCGGTCAATTTCAAATTAAATTTTTTAGTCGT
1 CAGCCACCGGTCAATTTCAAATTGAATTTTCTAGTCGT
*
1502017 CAGCCACCGGTCAATTTCAAATTGAATTATCTA
1 CAGCCACCGGTCAATTTCAAATTGAATTTTCTA
1502050 ACCGTCAACC
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 93 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (38 bp):
CAGCCACCGGTCAATTTCAAATTGAATTTTCTAGTCGT
Found at i:1502014 original size:76 final size:76
Alignment explanation
Indices: 1501914--1502056 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 76
1501904 AGCCACCGGC
* *** * *
1501914 CAATTCCAAATTGAATTCTCTAGTCGTCAGCCGTTGGTCAATTTCAAATTGAATTTTCTAGCCGT
1 CAATTCCAAATTAAATTCTCTAGTCGTCAGCCACCGGTCAATTTCAAATTGAATTATCTAACCGT
1501979 CAGCCGTCGGT
66 CAGCCGTCGGT
* * *
1501990 CAATTTCAAATTAAATTTTTTAGTCGTCAGCCACCGGTCAATTTCAAATTGAATTATCTAACCGT
1 CAATTCCAAATTAAATTCTCTAGTCGTCAGCCACCGGTCAATTTCAAATTGAATTATCTAACCGT
1502055 CA
66 CA
1502057 ACCAATTCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 58 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (76 bp):
CAATTCCAAATTAAATTCTCTAGTCGTCAGCCACCGGTCAATTTCAAATTGAATTATCTAACCGT
CAGCCGTCGGT
Found at i:1506026 original size:31 final size:33
Alignment explanation
Indices: 1505985--1506060 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
1505975 ATCAATTCTA
1505985 ATTTAAATCATATT-AG-TTT-AATTTTTTTCAT
1 ATTTAAATCAT-TTAAGATTTGAATTTTTTTCAT
* *
1506016 ATTTAGATCATTTAAGATTTGAATTTTTTTGA-
1 ATTTAAATCATTTAAGATTTGAATTTTTTTCAT
*
1506048 ATTTGAATCATTT
1 ATTTAAATCATTT
1506061 TAAATTCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 2 0.05
31 12 0.32
32 14 0.37
33 10 0.26
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (33 bp):
ATTTAAATCATTTAAGATTTGAATTTTTTTCAT
Found at i:1506700 original size:17 final size:17
Alignment explanation
Indices: 1506678--1506712 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1506668 GTAACACTTT
1506678 TGCTATATATCCCAATA
1 TGCTATATATCCCAATA
1506695 TGCTATATATCCCAATA
1 TGCTATATATCCCAATA
1506712 T
1 T
1506713 TAATTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (17 bp):
TGCTATATATCCCAATA
Found at i:1507659 original size:17 final size:17
Alignment explanation
Indices: 1507637--1507671 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1507627 GCAACACTTT
1507637 TGCTATATATCCCAATA
1 TGCTATATATCCCAATA
*
1507654 TGCTATATATCTCAATA
1 TGCTATATATCCCAATA
1507671 T
1 T
1507672 TAATTGACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (17 bp):
TGCTATATATCCCAATA
Found at i:1507798 original size:959 final size:954
Alignment explanation
Indices: 1505645--1508410 Score: 4106
Period size: 959 Copynumber: 2.9 Consensus size: 954
1505635 GTCTAAACAA
* * *
1505645 ATATATATATATATAAGAAGACCAAATTTAAATTAAATATTTAATTTTAAAATCAATTTAAACAT
1 ATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAATAT
* ** *
1505710 CTTTTTATATTAATTAATTCAGATAAAATTTTATAACACTTTTAGCTATAAAT-CC------C-A
66 CTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTT-GCTATATATCCCAATATGCTA
* * * *
1505767 T-TAT-T--A-ATT-A---ACCCTATTTTCTTAAATTAAAAATTTTCTATTCAACAAATGAATTA
130 TATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATTA
* * * * * * * * * *
1505823 ATTAAACATAATAGCTCTATATTTTTATATCAACTATATGTTGATTATAAAAAGTAACCTGTAAT
195 ATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAGT
* * *
1505888 TTTCAGACAAAAACTAATTAT-GCA-T--TT-T--A-----GTTACAAAACTTCCTTTTAAATAA
260 CTTCAGACAAGAATTAATTATAG-ATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAA
* *
1505941 AAGTGGTAGTTGGATGAATTTAGTGAGAAATCTGATCAATTCTAATTTAAATCATATT-AGTTTA
324 AAGTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGA-TTTA
* * * * *
1506005 ATTTTTTTCATATTTAGATCATTTAAGATTTGAATTTTTTTGAATTTGAATCATTTTAAATTCAT
388 ATTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCAT
* * * *
1506070 A-TTTTTTAAGTTTAAACCATTTTAGATTCAGATTAAGTATGAGTAAATTTTATTATATTTTTTT
453 ACTTTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTA-TATATATTTTT
* * * *
1506134 TAATTTTATGTTTTATATAATCATTTTTATATAATTTAATTATTAAAATTTTAAAATTCATTATT
517 TAATTTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCATTATT
1506199 ATGTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAA
582 ATGTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAA
* *
1506264 TGTCAACATTTGTTATCACAAATATTTTTTGGTTGCTAATTTCTTAATTAATTAAGGCCTTACTT
647 TGTCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTT
* *
1506329 CATTTAATTTAGGAAATACATTAGCAAAATGAAACTTACTTTCTGGTTCATATAGAGTAGCATTT
712 CATTTAATTTAGGAAATACATTAGCAAAATG-AA---ACTTGCT-GTTCATATAGAGTAGCACTT
* * * *
1506394 TTTTTTATAAAAAATTTCAACATTCAAAAATTCATTAAGCATCAATAAATTCAATTCAAGCTAAA
772 TTTTTTATAAAAAAATTCAACATTAAAAAATTCATTAAACATCAATTAATTCAATTCAAGCTAAA
* * ** ** *
1506459 ATAATTTATTATAAATATAAAACTTTTTTCAACAATGATTTTCGTATAGAGTAACGCTATTCAAT
837 ATAATTTATTATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCAAT
* ** *
1506524 TACCTTATCAAAAAGTCGTTTGATGGAGACCCGAACCTGCACAAAAGCAAGGG
902 TACCTTATCAAAAAGTCGTTCGATACAGACCCAAACCTGCACAAAAGCAAGGG
1506577 ------ATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAATAT
1 ATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAATAT
1506636 CTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAATATGCTAT
66 CTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAATATGCTAT
*
1506701 ATATCCCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATTAA
131 ATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATTAA
1506766 TTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAGTC
196 TTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAGTC
1506831 TTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAA
261 TTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAA
*
1506896 GTGGTAGTTGGATGAATTTAGTTAGAAATTTGATCAATTCTAATTCAAATCATATTGATTTAATT
326 GTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGATTTAATT
*
1506961 TTTTT-AGATTTAAATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACT
391 TTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACT
1507025 TTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTAAT
456 TTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTAAT
* *
1507090 TTTATGTTATATATAGTCATTTTTACATAATTTAAATATTAAAATTTAAAAATTCATTATTTTGT
521 TTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCATTATTATGT
1507155 CTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTC
586 CTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTC
* * *
1507220 AACATTTGTTGTCACTAATATTTTTGGGTTGCTAATTTTTTAATTAATTAAGACCTTACTTCATT
651 AACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTTCATT
* *
1507285 TAATTTAGGAAATACATTAGCAAAATGAAACTTGCT-TTCA-AAAAAGTAGCACTTTTTTTTATA
716 TAATTTAGGAAATACATTAGCAAAATGAAACTTGCTGTTCATATAGAGTAGCACTTTTTTTTATA
* * * ** * *
1507348 AAAAAATTCAGCATTTAAAAATTTATTAAATGTCAATTAATACAATTCGAGCTAAAATAACTTT-
781 AAAAAATTCAACATTAAAAAATTCATTAAACATCAATTAATTCAATTCAAGCTAAAATAA-TTTA
1507412 TTATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCAATTACCTGT-
845 TTATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCAATTACCT-TA
* * *** *
1507476 TGAAAAGGTCGTTCGATACCTTCCCAAATCTGCACAAAAGCAAGGG
909 TCAAAAAGTCGTTCGATACAGACCCAAACCTGCACAAAAGCAAGGG
1507522 ATATATATATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAAT
1 --------ATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAAT
* *
1507587 TTAAGTATCTATTTATATTAATTAATTCAGATAAAATTTGGCAACACTTTTGCTATATATCCCAA
58 TTAAATATCTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAA
1507652 TATGCTATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAA
123 TATGCTATATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAA
1507717 TGAATTAATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGC
188 TGAATTAATTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGC
1507782 TTATAGTCTTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTT
253 TTATAGTCTTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTT
*
1507847 AAATAAAAGTGGTAGTTAGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTG
318 AAATAAAAGTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTG
1507912 ATTTAATTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGA
383 ATTTAATTTTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGA
*
1507977 TTGATACTTTTTTTAA-TTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATA
448 TTCATAC-TTTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATA
* * *
1508041 TTTTTTTATTTTATGTTATATATAGTCATTTTTATATAATTTAAATGTTAAAATTCAAAAATTCA
512 TTTTTTAATTTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCA
1508106 TTATTATGTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATAT
577 TTATTATGTCTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATAT
1508171 ATTAATGTCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCT
642 ATTAATGTCAACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCT
** *
1508236 TACTTCATTTAATTTATAAAATACATTAGCAACATGAAACTTGCTTTCTTGTTCATATAGAGTAG
707 TACTTCATTTAATTTAGGAAATACATTAGCAAAATGAAACTTG----C-TGTTCATATAGAGTAG
* * * * * *
1508301 CACTTCTTTTTATAAAAAAATTTCAACATTCAAAAAATCCACTAAACATCAACTAATTTAATTTA
767 CACTTTTTTTTATAAAAAAA-TTCAACATT-AAAAAATTCATTAAACATCAATTAATTCAATTCA
*
1508366 AGCTAAAATAATTTATTATAAAAATAAAATTTCTTTCAACGCTGA
830 AGCTAAAATAATTTATTATAAAAATAAAATTTTTTTCAACGCTGA
1508411 GAGTAACGTT
Statistics
Matches: 1661, Mismatches: 114, Indels: 81
0.89 0.06 0.04
Matches are distributed among these distances:
925 8 0.00
926 98 0.06
932 1 0.00
933 2 0.00
934 3 0.00
937 1 0.00
938 3 0.00
939 1 0.00
942 116 0.07
943 2 0.00
945 163 0.10
946 9 0.01
948 7 0.00
951 2 0.00
952 276 0.17
953 139 0.08
954 1 0.00
959 384 0.23
960 331 0.20
961 8 0.00
964 1 0.00
965 1 0.00
966 4 0.00
967 26 0.02
968 11 0.01
969 63 0.04
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (954 bp):
ATATATATATATATAAGAATACCAAATTTAAATTAAATATTTAATTCTAAAATCAATTTAAATAT
CTATTTATATTAATTAATTCAGATAAAATTTGGTAACACTTTTGCTATATATCCCAATATGCTAT
ATATCTCAATATTAATTGACTCAATTCTCTTAAATTAAGAATTTTCTATTCAACAAATGAATTAA
TTAAACACAATAACTGTCTATTTTTATATCAACTAAATGTTGATTATAAAAGGTAGCTTATAGTC
TTCAGACAAGAATTAATTATAGATTAATTATGCATTCCGGTTACAAAACTTCCTTTTAAATAAAA
GTGGTAGTTGGATGAATTTAGTTAGAAATCTGATCAATTCTAATTCAAATCATATTGATTTAATT
TTTTTCAGATTTAGATCATTTAAGATTTGAACTCTTTTGAATTCGAATCATTTTAGATTCATACT
TTTTTAAGTTTAAATCATTTTAGATTCAGATTAAGTATGAATAGATTTTATATATATTTTTTAAT
TTTATGTTATATATAGTCATTTTTATATAATTTAAATATTAAAATTTAAAAATTCATTATTATGT
CTTTTAAAATAGGCTTTGGTATAATATAAAAATTTTAATTTTAATTATATTTATATATTAATGTC
AACATTTGTTATCACAAATATTTTTGGGTTGCTAATTTCTTAATTAATTAAGACCTTACTTCATT
TAATTTAGGAAATACATTAGCAAAATGAAACTTGCTGTTCATATAGAGTAGCACTTTTTTTTATA
AAAAAATTCAACATTAAAAAATTCATTAAACATCAATTAATTCAATTCAAGCTAAAATAATTTAT
TATAAAAATAAAATTTTTTTCAACGCTGATTTTAATATAAAGTAACGCTATTCAATTACCTTATC
AAAAAGTCGTTCGATACAGACCCAAACCTGCACAAAAGCAAGGG
Found at i:1507970 original size:32 final size:33
Alignment explanation
Indices: 1507934--1508010 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
1507924 TCAGATTTAG
* *
1507934 ATCATTTAAGATTTGA-ACTCTTTTGAATTCGA
1 ATCATTTTAGATTTGATACTCTTTTGAATTCAA
* * *
1507966 ATCATTTTAGA-TTGATACTTTTTTTAATTTAA
1 ATCATTTTAGATTTGATACTCTTTTGAATTCAA
1507998 ATCATTTTAGATT
1 ATCATTTTAGATT
1508011 CAGATTAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 4 0.11
32 33 0.87
33 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (33 bp):
ATCATTTTAGATTTGATACTCTTTTGAATTCAA
Found at i:1508467 original size:15 final size:15
Alignment explanation
Indices: 1508447--1508476 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1508437 ATGTTTTACA
1508447 TCAGACGCGGGGACG
1 TCAGACGCGGGGACG
1508462 TCAGACGCGGGGACG
1 TCAGACGCGGGGACG
1508477 GGAGGTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.47, T:0.07
Consensus pattern (15 bp):
TCAGACGCGGGGACG
Found at i:1509442 original size:22 final size:24
Alignment explanation
Indices: 1509390--1509445 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
1509380 CAAATTTTAA
*
1509390 TAATATTATATAATTTATTTATAT
1 TAATATTATAAAATTTATTTATAT
1509414 T-AT-TTATAAAATTT-TTTAT-T
1 TAATATTATAAAATTTATTTATAT
1509434 TAATATTATAAA
1 TAATATTATAAA
1509446 TTAAATGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
21 7 0.24
22 17 0.59
23 2 0.07
24 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATATTATAAAATTTATTTATAT
Found at i:1509451 original size:26 final size:25
Alignment explanation
Indices: 1509403--1509451 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1509393 TATTATATAA
**
1509403 TTTATTTATATTATTTATAAAATTT
1 TTTATTTATATTATAAATAAAATTT
*
1509428 TTTATTTAATATTATAAATTAAAT
1 TTTATTT-ATATTATAAATAAAAT
1509452 GATATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTATTTATATTATAAATAAAATTT
Found at i:1510066 original size:22 final size:22
Alignment explanation
Indices: 1510041--1510082 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1510031 TTTTTTTAAA
* *
1510041 ATTAAATGAAATTGAATCAAAT
1 ATTAAATAAAATTAAATCAAAT
*
1510063 ATTAAGTAAAATTAAATCAA
1 ATTAAATAAAATTAAATCAA
1510083 TTTGAACTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (22 bp):
ATTAAATAAAATTAAATCAAAT
Found at i:1510513 original size:6 final size:6
Alignment explanation
Indices: 1510502--1510535 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1510492 AGAAATTCGA
* *
1510502 TTTTGC TTTTGC TTTTGC TTTTAC TTTTTC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1510536 ACTTCGGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.74
Consensus pattern (6 bp):
TTTTGC
Found at i:1510519 original size:12 final size:12
Alignment explanation
Indices: 1510502--1510539 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1510492 AGAAATTCGA
*
1510502 TTTTGCTTTTGC
1 TTTTGCTTTTAC
1510514 TTTTGCTTTTAC
1 TTTTGCTTTTAC
*
1510526 TTTTTCTTTTAC
1 TTTTGCTTTTAC
1510538 TT
1 TT
1510540 CGGCTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.16, G:0.08, T:0.71
Consensus pattern (12 bp):
TTTTGCTTTTAC
Found at i:1510614 original size:22 final size:22
Alignment explanation
Indices: 1510589--1510661 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
1510579 ATCATTATTT
1510589 ATAAATATAATTTTTATAATTA
1 ATAAATATAATTTTTATAATTA
*
1510611 ATAAATAT-A-TTTTACTCA-T-
1 ATAAATATAATTTTTA-TAATTA
*
1510630 ATGAATAATAATTTTTATAATTA
1 ATAAAT-ATAATTTTTATAATTA
1510653 ATAAATATA
1 ATAAATATA
1510662 TCTTACAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 5 0.12
20 8 0.20
21 6 0.15
22 17 0.41
23 5 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (22 bp):
ATAAATATAATTTTTATAATTA
Found at i:1510651 original size:42 final size:42
Alignment explanation
Indices: 1510595--1510679 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
1510585 ATTTATAAAT
* **
1510595 ATAATTTTTATAATTAATAAATATATTTTACTCATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1510637 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1 ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
1510679 A
1 A
1510680 AAATAGTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (42 bp):
ATAATTTTTATAATTAATAAATATATCTTACAAATATGAATA
Found at i:1511543 original size:27 final size:29
Alignment explanation
Indices: 1511512--1511582 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 29
1511502 ATTTGTCCAT
*
1511512 ATTATATATTTTTAATTT-ATTTTTTA-A
1 ATTATATATTTTTAATTTAATTTTTAATA
1511539 ATTATATATTTTTAAATTTAATTTTTAATA
1 ATTATATATTTTT-AATTTAATTTTTAATA
1511569 ATT-TA-ATTTTTAAT
1 ATTATATATTTTTAAT
1511583 AATTTAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 16 0.40
28 11 0.28
29 9 0.22
30 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTATATATTTTTAATTTAATTTTTAATA
Found at i:1511556 original size:28 final size:27
Alignment explanation
Indices: 1511512--1511582 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
1511502 ATTTGTCCAT
*
1511512 ATTATATATTTTTAATTTATTTTTTAA
1 ATTATATATTTTTAATTTAATTTTTAA
1511539 ATTATATATTTTTAAATTTAATTTTTAATA
1 ATTATATATTTTT-AATTTAATTTTT-A-A
1511569 ATT-TA-ATTTTTAAT
1 ATTATATATTTTTAAT
1511583 AATTTAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 16 0.40
28 17 0.43
29 3 0.08
30 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTATATATTTTTAATTTAATTTTTAA
Found at i:1511598 original size:18 final size:15
Alignment explanation
Indices: 1511524--1511595 Score: 80
Period size: 15 Copynumber: 4.9 Consensus size: 15
1511514 TATATATTTT
*
1511524 TAATTT-ATTTTTTA
1 TAATTTAATTTTTAA
1511538 -AATTATATATTTTT-A
1 TAATT-TA-ATTTTTAA
1511553 -AATTTAATTTTTAA
1 TAATTTAATTTTTAA
1511567 TAATTTAATTTTTAA
1 TAATTTAATTTTTAA
1511582 TAATTTAATATTTT
1 TAATTTAAT-TTTT
1511596 TTATTAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.19
14 4 0.08
15 28 0.54
16 10 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTTAATTTTTAA
Found at i:1513509 original size:27 final size:27
Alignment explanation
Indices: 1513468--1513547 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
1513458 AAATAACAAG
*
1513468 CCACAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * * *
1513495 TCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
1513522 CCACCATTTTTTACAAACACAAAAGG
1 CCACCATTTTTGACAAACA-AAAAGG
1513548 TGGCTTTTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 38 0.90
28 4 0.10
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.24
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:1523313 original size:20 final size:19
Alignment explanation
Indices: 1523263--1523340 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
1523253 GGTAAAAAGA
1523263 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
1523282 ACAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
*
1523302 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* * *
1523322 GAAAAATGTATCAATACAT
1 -CATAATGTATCGATACAT
1523341 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.89
21 2 0.04
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Done.