Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold415
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: 1242643
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 7 of 8
Found at i:1007743 original size:14 final size:15
Alignment explanation
Indices: 1007719--1007748 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1007709 TTGATTTATT
1007719 ATATAATAATAAAAA
1 ATATAATAATAAAAA
1007734 ATAT-ATAATAAAAA
1 ATATAATAATAAAAA
1007748 A
1 A
1007749 AACAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATATAATAATAAAAA
Found at i:1011781 original size:17 final size:17
Alignment explanation
Indices: 1011761--1011804 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1011751 ATAAAATATA
1011761 TATATATATAATATTAG
1 TATATATATAATATTAG
* * *
1011778 TATATGTATGATTTTAG
1 TATATATATAATATTAG
*
1011795 TAAATATATA
1 TATATATATA
1011805 TTTAATAGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
TATATATATAATATTAG
Found at i:1013636 original size:21 final size:22
Alignment explanation
Indices: 1013592--1013636 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1013582 TCCCTAAAAC
* * *
1013592 TTTGAAAGATAATTTTCTATCA
1 TTTGAAAGATAATTATCAAGCA
1013614 TTTGAAA-ATAATTATCAAGCA
1 TTTGAAAGATAATTATCAAGCA
1013635 TT
1 TT
1013637 GTCAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (22 bp):
TTTGAAAGATAATTATCAAGCA
Found at i:1015158 original size:20 final size:20
Alignment explanation
Indices: 1015133--1015181 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1015123 AAAATTTGAC
*
1015133 AATATAAAGATTAAATTAAA
1 AATATAAAGATTAAAATAAA
**
1015153 AATATAAATCTTAAAATAAA
1 AATATAAAGATTAAAATAAA
1015173 AATACTAAA
1 AATA-TAAA
1015182 CACATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AATATAAAGATTAAAATAAA
Found at i:1015563 original size:2 final size:2
Alignment explanation
Indices: 1015556--1015580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1015546 AAAAGCCATC
1015556 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 A
1015581 ACAAGGTACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1015800 original size:128 final size:130
Alignment explanation
Indices: 1015655--1015890 Score: 440
Period size: 128 Copynumber: 1.8 Consensus size: 130
1015645 TTATTTGACG
* *
1015655 TGTATGTTTGTAAAATTTATATAATTTATTATTTCTATATAA-TTTTTTTAAAAATAAATCTGGC
1 TGTATGTTTGTAAAATTTATATAATTTATTATTTCTATATAATTTTTTTTAAAAACAAATCTGGA
1015719 AAAAAA-TTAACATTTGATTAAGTACCAAATTTTAAAAATTAAATCTTTATATTGTCAAATTTTA
66 AAAAAATTTAACATTTGATTAAGTACCAAATTTTAAAAATTAAATCTTTATATTGTCAAATTTTA
1015783 TGTATGTTTGTAAAATTTATATAATTTATTATTTCTATATAATTTTTTTTAAAAACAAATCTGGA
1 TGTATGTTTGTAAAATTTATATAATTTATTATTTCTATATAATTTTTTTTAAAAACAAATCTGGA
1015848 AAAAAATTTAACATTTGATTAAGTACCAAATTTTAAAAATTAA
66 AAAAAATTTAACATTTGATTAAGTACCAAATTTTAAAAATTAA
1015891 TTAAAACCAT
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
128 42 0.40
129 26 0.25
130 36 0.35
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (130 bp):
TGTATGTTTGTAAAATTTATATAATTTATTATTTCTATATAATTTTTTTTAAAAACAAATCTGGA
AAAAAATTTAACATTTGATTAAGTACCAAATTTTAAAAATTAAATCTTTATATTGTCAAATTTTA
Found at i:1019814 original size:3 final size:3
Alignment explanation
Indices: 1019801--1019840 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1019791 TCCACCTCTT
*
1019801 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1019841 GAAGTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1022299 original size:2 final size:2
Alignment explanation
Indices: 1022286--1022325 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1022276 GTCACCATAC
*
1022286 AT AT AA 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 AT
1022326 CATGGTATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1023166 original size:14 final size:14
Alignment explanation
Indices: 1023149--1023181 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1023139 AAAATGACAG
*
1023149 ATTTATAATGATAA
1 ATTTATAAAGATAA
1023163 ATTTATAAAGATAA
1 ATTTATAAAGATAA
1023177 ATTTA
1 ATTTA
1023182 AATAATGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATTTATAAAGATAA
Found at i:1024810 original size:22 final size:22
Alignment explanation
Indices: 1024763--1024814 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1024753 GAATATAATT
* * *
1024763 TAATTAAAATTTAATTTTATAG
1 TAATTAAAATATAATTTTAAAC
1024785 TAATTAAAA-ATAATTTTAAAAC
1 TAATTAAAATATAATTTT-AAAC
1024807 TAATTAAA
1 TAATTAAA
1024815 TTATCATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TAATTAAAATATAATTTTAAAC
Found at i:1025256 original size:2 final size:2
Alignment explanation
Indices: 1025251--1025299 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
1025241 TAACACACAC
* *
1025251 AT AT AT AT AT AT AT AT AT AT AT AT CT -T GT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1025290 AT AT AT AT AT
1 AT AT AT AT AT
1025300 GATGACTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1027050 original size:6 final size:6
Alignment explanation
Indices: 1027033--1027067 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1027023 ATCTGCATAG
*
1027033 CTCAGC CACAGC CTCAGC CTCAGC CTCAGC CTCAG
1 CTCAGC CTCAGC CTCAGC CTCAGC CTCAGC CTCAG
1027068 ATCATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.49, G:0.17, T:0.14
Consensus pattern (6 bp):
CTCAGC
Found at i:1027844 original size:34 final size:35
Alignment explanation
Indices: 1027753--1027845 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 35
1027743 AGTAATTCAT
* *
1027753 ATTA-ATTATATAATAAT-AAAA-TTTATATATTT
1 ATTATATTATATCATAATAAAAATTTTATATATTA
* *
1027785 ATTATATTATTATGCAATAAAAAAAATTTTATGTATTA
1 ATTATATTA-TAT-C-ATAATAAAAATTTTATATATTA
*
1027823 ATT-TGTTATATCATAATAAAAAT
1 ATTATATTATATCATAATAAAAAT
1027846 ATAAAGCACA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
32 4 0.08
33 4 0.08
34 13 0.27
35 1 0.02
36 7 0.14
37 8 0.16
38 12 0.24
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (35 bp):
ATTATATTATATCATAATAAAAATTTTATATATTA
Found at i:1028442 original size:34 final size:34
Alignment explanation
Indices: 1028378--1028560 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
1028368 ATCAATTATA
* *
1028378 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1028411 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1028445 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1028479 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1028513 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1028547 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1028561 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1033037 original size:34 final size:34
Alignment explanation
Indices: 1032971--1033155 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
1032961 AAGTGGGAGA
* *
1032971 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1033004 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1033038 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1033072 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1033106 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1033140 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1033156 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1034700 original size:22 final size:23
Alignment explanation
Indices: 1034666--1034710 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1034656 TCGAAAAAAA
1034666 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
1034688 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
1034711 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:1035094 original size:17 final size:17
Alignment explanation
Indices: 1035074--1035109 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1035064 AAGGAAGATG
* *
1035074 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1035091 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1035108 AA
1 AA
1035110 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1035488 original size:2 final size:2
Alignment explanation
Indices: 1035475--1035515 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1035465 TTATTTTATT
*
1035475 TA TA TG TA 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 TA T
1035516 TTTGAAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1042971 original size:27 final size:27
Alignment explanation
Indices: 1042928--1043719 Score: 1190
Period size: 27 Copynumber: 28.9 Consensus size: 27
1042918 GTGGCATTTT
* *
1042928 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1042956 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1042983 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1043011 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1043038 CTTTTAAAATCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1043066 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1043093 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1043120 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1043147 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** *
1043174 CTTTTAAGTCCACAACTCTATGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1043202 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1043229 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1043256 CTTTTAAGTCCACAACTCTGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1043284 CTTTTAA-TACCACAACTCCGTGGCACC
1 CTTTTAAGT-CCACAACTCCGTGGCACC
1043311 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1043338 CTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1043365 CTTTTAAGTCCATAACTCCATGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1043393 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1043420 CTTTTAAGACCACAACTCCGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1043447 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1043474 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1043502 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1043529 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1043557 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1043584 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1043612 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1043640 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1043667 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
1043695 CTTTTAAATTCACAAGTCGGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA
1043720 ACCCATTCCA
Statistics
Matches: 703, Mismatches: 50, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
27 449 0.64
28 254 0.36
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1042996 original size:55 final size:54
Alignment explanation
Indices: 1042928--1043719 Score: 1190
Period size: 55 Copynumber: 14.5 Consensus size: 54
1042918 GTGGCATTTT
* * *
1042928 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1042983 CTTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * * *
1043038 CTTTTAAAATCCACAACTCCGTGGTACCCTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
1043093 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
** *
1043147 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTATGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
1043202 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1043256 CTTTTAAGTCCACAACTCTGTGGCATTCCTTTTAA-TACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT-CCACAACTCCGTGGCACC
*
1043311 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1043365 CTTTTAAGTCCATAACTCCATGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1043420 CTTTTAAGACCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * ** *
1043474 CTTTTAAGTCCATAACTCTGTGGCATCTTTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1043529 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1043584 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA-CC
1043640 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
1043695 CTTTTAAATTCACAAGTCGGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA
1043720 ACCCATTCCA
Statistics
Matches: 681, Mismatches: 47, Indels: 18
0.91 0.06 0.02
Matches are distributed among these distances:
54 237 0.35
55 399 0.59
56 45 0.07
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1043028 original size:82 final size:81
Alignment explanation
Indices: 1042928--1043719 Score: 1192
Period size: 82 Copynumber: 9.6 Consensus size: 81
1042918 GTGGCATTTT
*
1042928 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
*
1042993 CCACAACTCCGTGGTACC
64 CCACAACTCCGTGGCACC
* * * *
1043011 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAATCCACAACTCCGTGGTACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCTGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1043076 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
*
1043093 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1043158 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
*
1043174 CTTTTAAGTCCACAACTCTATGGCATTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCTGTGGCA-TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1043239 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
1043256 CTTTTAAGTCCACAACTCTGTGGCATTCCTTTTAA-TACCACAACTCCGTGGCACCCTTTTAAGT
1 CTTTTAAGTCCACAACTCTGTGGCA-TCCTTTTAAGT-CCACAACTCCGTGGCACCCTTTTAAGT
1043320 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * *
1043338 CTTTTAAGTCCACAACTCCGTGGCA-CTCTTTTAAGTCCATAACTCCATGGCATCCCTTTTAAGT
1 CTTTTAAGTCCACAACTCTGTGGCATC-CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
1043402 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * * *
1043420 CTTTTAAGACCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
1043485 ATAACTCTGTGGCATCT
66 ACAACTCCGTGGCA-CC
* * *
1043502 TTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCTGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1043567 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
*
1043584 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGT
1 CTTTTAAGTCCACAACTCTGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
1043649 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * * * *
1043667 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAATTCACAAGTCGGTGGCA
1 CTTTTAAGTCCACAACTCTGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCA
1043720 ACCCATTCCA
Statistics
Matches: 658, Mismatches: 40, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
80 1 0.00
81 116 0.18
82 384 0.58
83 157 0.24
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:1043742 original size:32 final size:32
Alignment explanation
Indices: 1043705--1044115 Score: 662
Period size: 32 Copynumber: 12.8 Consensus size: 32
1043695 CTTTTAAATT
*
1043705 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1043737 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1043769 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1043801 CACAGGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1043833 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1043865 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1043897 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1043929 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
1043961 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
1043993 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1044025 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1044057 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* ** *
1044089 CGCAAGTTAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
1044116 TCACCATTTT
Statistics
Matches: 356, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
31 3 0.01
32 350 0.98
33 3 0.01
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1044861 original size:22 final size:23
Alignment explanation
Indices: 1044827--1044871 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1044817 GATCGAAAAA
1044827 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
1044849 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
1044872 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:1045254 original size:17 final size:17
Alignment explanation
Indices: 1045234--1045269 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1045224 AAGGAAGATG
* *
1045234 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1045251 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1045268 AA
1 AA
1045270 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1048728 original size:16 final size:16
Alignment explanation
Indices: 1048707--1048738 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1048697 TTTATATATT
1048707 TTATAATTAAATTTAA
1 TTATAATTAAATTTAA
1048723 TTATAATTAAATTTAA
1 TTATAATTAAATTTAA
1048739 ATCAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAATTAAATTTAA
Found at i:1050192 original size:32 final size:32
Alignment explanation
Indices: 1050154--1050220 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1050144 CAAAATAAAT
1050154 AATTATTAAAATATGCATCCAAGTAGAGGTGC
1 AATTATTAAAATATGCATCCAAGTAGAGGTGC
1050186 AATTATTAAAATATGCATCCAAGTAGAGGTGC
1 AATTATTAAAATATGCATCCAAGTAGAGGTGC
1050218 AAT
1 AAT
1050221 GTCAATGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (32 bp):
AATTATTAAAATATGCATCCAAGTAGAGGTGC
Found at i:1050439 original size:2 final size:2
Alignment explanation
Indices: 1050432--1050457 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1050422 TGTTTAACGG
1050432 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1050458 GTTATTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1051179 original size:16 final size:17
Alignment explanation
Indices: 1051158--1051192 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1051148 TTTGTACATA
1051158 TTTAGGTT-AATTCATT
1 TTTAGGTTCAATTCATT
*
1051174 TTTAGGTTCAATTTATT
1 TTTAGGTTCAATTCATT
1051191 TT
1 TT
1051193 AAATTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TTTAGGTTCAATTCATT
Found at i:1052440 original size:17 final size:17
Alignment explanation
Indices: 1052420--1052463 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1052410 ATAAAAAAAA
1052420 TATATATATAATATTAG
1 TATATATATAATATTAG
* * *
1052437 TATATGTATGATTTTAG
1 TATATATATAATATTAG
*
1052454 TAAATATATA
1 TATATATATA
1052464 TTTAATAGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
TATATATATAATATTAG
Found at i:1057420 original size:28 final size:28
Alignment explanation
Indices: 1057364--1057447 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
1057354 TAATTAGAAT
* * *
1057364 TTAATTTTATACTAAAATAAATTCTTAT-A
1 TTAATTTTA-AAT-AAATATATTTTTATAA
*
1057393 TTAATTTTAATATTAATATATTTTTATAA
1 TTAATTTTAA-ATAAATATATTTTTATAA
*
1057422 TTAATTTTAAATAAAAATATTTTTAT
1 TTAATTTTAAATAAATATATTTTTAT
1057448 TAAATAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
28 26 0.55
29 21 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAATTTTAAATAAATATATTTTTATAA
Found at i:1057455 original size:29 final size:29
Alignment explanation
Indices: 1057394--1057455 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1057384 ATTCTTATAT
* * *
1057394 TAATTTTAATATTAATATATTTTTATAAT
1 TAATTTTAATATAAAAATATTTTTATAAA
1057423 TAATTTTAA-ATAAAAATATTTTTATTAAA
1 TAATTTTAATATAAAAATATTTTTA-TAAA
1057452 TAAT
1 TAAT
1057456 AATTATGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATTTTAATATAAAAATATTTTTATAAA
Found at i:1059581 original size:21 final size:21
Alignment explanation
Indices: 1059557--1059597 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1059547 ACTATTAATA
1059557 ATTATTATAATGATGAGATTT
1 ATTATTATAATGATGAGATTT
*
1059578 ATTATTCTAATGATGAGATT
1 ATTATTATAATGATGAGATT
1059598 AAAATCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (21 bp):
ATTATTATAATGATGAGATTT
Found at i:1063278 original size:79 final size:79
Alignment explanation
Indices: 1063185--1063335 Score: 198
Period size: 79 Copynumber: 1.9 Consensus size: 79
1063175 CATGCCATCG
** * *
1063185 TTATTTTTAATCTCACTTGAGCTAATCTCAACACCTATT-CAAATAGATCC-TATGTCTCAATAA
1 TTATTTTTAATCTCACCAGAGATAATCTCAACACCT-TTCCAAATAGA-CCATATGTCTCAAGAA
1063248 GTATAAAAAGTTACTA
64 GTATAAAAAGTTACTA
** * *
1063264 TTATTTTTAATCTCACCAGAGATAATCTCATTATCTTTCCAAATGGACCATATGTCTCAAGAAGT
1 TTATTTTTAATCTCACCAGAGATAATCTCAACACCTTTCCAAATAGACCATATGTCTCAAGAAGT
1063329 ATAAAAA
66 ATAAAAA
1063336 CATTTTAGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 4 0.06
79 58 0.94
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (79 bp):
TTATTTTTAATCTCACCAGAGATAATCTCAACACCTTTCCAAATAGACCATATGTCTCAAGAAGT
ATAAAAAGTTACTA
Found at i:1064114 original size:2 final size:2
Alignment explanation
Indices: 1064107--1064133 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1064097 GTTTTTATTC
1064107 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 A
1064134 CACGATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1064636 original size:2 final size:2
Alignment explanation
Indices: 1064629--1064657 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1064619 ATGGCTTTAT
1064629 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
1064658 GTATGTATTT
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:1071207 original size:20 final size:20
Alignment explanation
Indices: 1071182--1071257 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1071172 AAAAAGATAG
1071182 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* *
1071202 AATGTATCGTTACATTCAAA
1 AATGTATCGATACATTGAAA
*
1071222 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
*
1071242 ATTGTATCGATACATT
1 AATGTATCGATACATT
1071258 TGGGTAAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1072085 original size:3 final size:3
Alignment explanation
Indices: 1072077--1072108 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1072067 TATATCTTAA
1072077 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1072109 AAATAAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1072429 original size:21 final size:21
Alignment explanation
Indices: 1072392--1072446 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1072382 AATACTTTTC
1072392 TTTTAATTTTATAATT-A-TTT
1 TTTTAATTTT-TAATTAAGTTT
1072412 TTTTATATATTTTAATTAAGTTT
1 TTTTA-AT-TTTTAATTAAGTTT
1072435 TTTTAATTTTTA
1 TTTTAATTTTTA
1072447 CAAGACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.16
21 12 0.39
22 6 0.19
23 8 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTAATTTTTAATTAAGTTT
Found at i:1073861 original size:19 final size:17
Alignment explanation
Indices: 1073830--1073865 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
1073820 GCAAGCAATT
1073830 TATTTTTTAAAATTTTA
1 TATTTTTTAAAATTTTA
1073847 TATTTTTTATTAAATTTTA
1 TATTTTTTA--AAATTTTA
1073866 AAATATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTTAAAATTTTA
Found at i:1074558 original size:18 final size:17
Alignment explanation
Indices: 1074527--1074567 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1074517 TTTAGGTTCG
*
1074527 ATTTATTTTAAATTTGA
1 ATTTATTTTAAATTTAA
*
1074544 ATTTCATTTTGAATTTAA
1 ATTT-ATTTTAAATTTAA
1074562 ATTTAT
1 ATTTAT
1074568 ATTATTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:1074898 original size:3 final size:3
Alignment explanation
Indices: 1074890--1074917 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1074880 TTTCCAAATT
1074890 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1074918 CATCATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1077338 original size:91 final size:93
Alignment explanation
Indices: 1077167--1077373 Score: 283
Period size: 91 Copynumber: 2.2 Consensus size: 93
1077157 CACCTCTGCT
* * * *
1077167 ACACATTAATACTATTTAATCTTGACGGCCTAACCACCGAAATGTAAGATAAATGGTGCAACCAA
1 ACACATTATTACTATTTAATTTTGACGGCCTAACCACCGAAATGTAAGATAAATGGAGCAACAAA
* *
1077232 ATGCAATATATTAGATTTAATAA-TATA
66 ATGCAATAAATTAGATTTAATAAGTACA
* * * * * *
1077259 ACACATTATTACTATTTAATTTTGACGGTCTGA-CACTGAAATGTAATATACATGGAGCAAGAAA
1 ACACATTATTACTATTTAATTTTGACGGCCTAACCACCGAAATGTAAGATAAATGGAGCAACAAA
1077323 ATGCAATAAATTAGATTTAATAATGTACA
66 ATGCAATAAATTAGATTTAATAA-GTACA
1077352 ACACATTATTACTATTTAATTT
1 ACACATTATTACTATTTAATTT
1077374 CACATAAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 47 0.47
92 29 0.29
93 25 0.25
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (93 bp):
ACACATTATTACTATTTAATTTTGACGGCCTAACCACCGAAATGTAAGATAAATGGAGCAACAAA
ATGCAATAAATTAGATTTAATAAGTACA
Found at i:1078835 original size:134 final size:134
Alignment explanation
Indices: 1078678--1078949 Score: 544
Period size: 134 Copynumber: 2.0 Consensus size: 134
1078668 CTAAAATATA
1078678 TTATATAAAATGGATCTCATTTTTTTGTCTAAGCCCTTTTTTCAAATCTAATATTTTTACTAAAA
1 TTATATAAAATGGATCTCATTTTTTTGTCTAAGCCCTTTTTTCAAATCTAATATTTTTACTAAAA
1078743 CTCTCCAAAATATTTAATAGAAGTTCAAGTTTGAACGAATAACCAAACCTATGAACACTTTTATT
66 CTCTCCAAAATATTTAATAGAAGTTCAAGTTTGAACGAATAACCAAACCTATGAACACTTTTATT
1078808 ATTT
131 ATTT
1078812 TTATATAAAATGGATCTCATTTTTTTGTCTAAGCCCTTTTTTCAAATCTAATATTTTTACTAAAA
1 TTATATAAAATGGATCTCATTTTTTTGTCTAAGCCCTTTTTTCAAATCTAATATTTTTACTAAAA
1078877 CTCTCCAAAATATTTAATAGAAGTTCAAGTTTGAACGAATAACCAAACCTATGAACACTTTTATT
66 CTCTCCAAAATATTTAATAGAAGTTCAAGTTTGAACGAATAACCAAACCTATGAACACTTTTATT
1078942 ATTT
131 ATTT
1078946 TTAT
1 TTAT
1078950 TTATAAATAT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 138 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (134 bp):
TTATATAAAATGGATCTCATTTTTTTGTCTAAGCCCTTTTTTCAAATCTAATATTTTTACTAAAA
CTCTCCAAAATATTTAATAGAAGTTCAAGTTTGAACGAATAACCAAACCTATGAACACTTTTATT
ATTT
Found at i:1082695 original size:13 final size:13
Alignment explanation
Indices: 1082677--1082711 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1082667 CCAAGCCACA
1082677 TTTTTTCTCTTTT
1 TTTTTTCTCTTTT
1082690 TTTTTTCT-TTTT
1 TTTTTTCTCTTTT
*
1082702 TTTCTTCTCT
1 TTTTTTCTCT
1082712 CATTCCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTCTTTT
Found at i:1082709 original size:12 final size:12
Alignment explanation
Indices: 1082677--1082709 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1082667 CCAAGCCACA
1082677 TTTTTTC-TCTT
1 TTTTTTCTTCTT
1082688 TTTTTT-TTCTT
1 TTTTTTCTTCTT
1082699 TTTTTTCTTCT
1 TTTTTTCTTCT
1082710 CTCATTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTCTT
Found at i:1084898 original size:19 final size:18
Alignment explanation
Indices: 1084851--1084898 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1084841 GAATCAATAT
*
1084851 AATAAATAATTTTTCTTA
1 AATAAATTATTTTTCTTA
*
1084869 AATAAAATATTTTT-TTAA
1 AATAAATTATTTTTCTT-A
1084887 AATCAAATTATT
1 AAT-AAATTATT
1084899 CATGGACATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 7 0.28
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (18 bp):
AATAAATTATTTTTCTTA
Found at i:1085686 original size:21 final size:21
Alignment explanation
Indices: 1085662--1085702 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1085652 TACTAATTTT
*
1085662 AATCTCATTATTATAATAATA
1 AATCTCATCATTATAATAATA
* *
1085683 AATCTTATCATTATAGTAAT
1 AATCTCATCATTATAATAAT
1085703 TATTAAAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
AATCTCATCATTATAATAATA
Found at i:1085790 original size:24 final size:24
Alignment explanation
Indices: 1085767--1085825 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 24
1085757 TAATAAAAAT
1085767 TATTAATATATAAATAC-TTTAAA
1 TATTAATATATAAATACATTTAAA
*
1085790 TA-TAAT-TATTAATTACATTTAAAA
1 TATTAATATA-TAAATACATTT-AAA
1085814 TATTAA-ATATAA
1 TATTAATATATAA
1085826 CATGAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
21 2 0.07
22 10 0.33
23 5 0.17
24 8 0.27
25 5 0.17
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTAATATATAAATACATTTAAA
Found at i:1087007 original size:21 final size:22
Alignment explanation
Indices: 1086944--1087007 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 22
1086934 AAAATTATAT
*
1086944 ACACATAATAAATTATATAAATTTT
1 ACACAT-ATAAA-TAT-TAAATTTG
*
1086969 ACACATATACATA--AAATTTG
1 ACACATATAAATATTAAATTTG
1086989 ACA-ATATAAATATTAAATT
1 ACACATATAAATATTAAATT
1087008 GATAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 8 0.24
20 9 0.26
21 5 0.15
23 2 0.06
24 4 0.12
25 6 0.18
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (22 bp):
ACACATATAAATATTAAATTTG
Found at i:1087392 original size:15 final size:15
Alignment explanation
Indices: 1087372--1087404 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1087362 ATACATATAC
1087372 ATATA-AATATAA-T
1 ATATATAATATAAGT
1087385 ATATATAATATAAGT
1 ATATATAATATAAGT
1087400 ATATA
1 ATATA
1087405 AAACTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 7 0.39
15 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
ATATATAATATAAGT
Found at i:1089537 original size:2 final size:2
Alignment explanation
Indices: 1089530--1089556 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1089520 TGTACCTTGT
1089530 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 T
1089557 GATGGCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1089969 original size:20 final size:19
Alignment explanation
Indices: 1089923--1089973 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1089913 AATTATATAT
1089923 ATCTTTAGTATTTTTATTTA
1 ATCTTTA-TATTTTTATTTA
** *
1089943 AGATTTATTTTTTTAATTTA
1 ATCTTTATATTTTT-ATTTA
1089963 ATCTTTATATT
1 ATCTTTATATT
1089974 GTCAAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
ATCTTTATATTTTTATTTA
Found at i:1094789 original size:13 final size:13
Alignment explanation
Indices: 1094747--1094789 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1094737 TATTTTCTAT
*
1094747 TTTTTCACTTTTC
1 TTTTTCAATTTTC
** *
1094760 TCCTTCAATTTTT
1 TTTTTCAATTTTC
1094773 TTTTTCAATTTTC
1 TTTTTCAATTTTC
1094786 TTTT
1 TTTT
1094790 CACTTTATCA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTCAATTTTC
Found at i:1095474 original size:11 final size:11
Alignment explanation
Indices: 1095458--1095495 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1095448 ACTATTTTCT
1095458 AATAAAAATTA
1 AATAAAAATTA
1095469 AATAAAAA-TA
1 AATAAAAATTA
1095479 AATAGAAAATTA
1 AATA-AAAATTA
*
1095491 GATAA
1 AATAA
1095496 CTAATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 6 0.25
11 13 0.54
12 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAAAAATTA
Found at i:1096509 original size:2 final size:2
Alignment explanation
Indices: 1096497--1096525 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1096487 GTACCCTTGT
1096497 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1096526 ATGATTTTTT
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):
TA
Found at i:1097304 original size:5 final size:5
Alignment explanation
Indices: 1097291--1097324 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1097281 CTAGATACGG
* *
1097291 TCCCT TCCCA TCCCA TCCCA TCCCA TCCTA TCCC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCC
1097325 TGTTTCCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.15, C:0.59, G:0.00, T:0.26
Consensus pattern (5 bp):
TCCCA
Found at i:1097655 original size:16 final size:14
Alignment explanation
Indices: 1097623--1097651 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1097613 CTTCTTTGAT
1097623 AATTA-ATTTTTAA
1 AATTATATTTTTAA
1097636 AATTATATTTTTAA
1 AATTATATTTTTAA
1097650 AA
1 AA
1097652 AATTTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTATATTTTTAA
Found at i:1098505 original size:25 final size:25
Alignment explanation
Indices: 1098477--1098525 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1098467 TTTTAAATAT
*
1098477 TAATTCATA-TATTCATATCATATTG
1 TAATT-ATATTATTAATATCATATTG
*
1098502 TAATTATATTTTTAATATCATATT
1 TAATTATATTATTAATATCATATT
1098526 CACGTAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (25 bp):
TAATTATATTATTAATATCATATTG
Found at i:1099586 original size:32 final size:31
Alignment explanation
Indices: 1099550--1099677 Score: 89
Period size: 32 Copynumber: 4.0 Consensus size: 31
1099540 TTTGAGTTGT
1099550 TTTTGGGTTCGGATCATTTTAGGTTCAGGG-CA
1 TTTTGGGTTCGG-TCATTTTAGGTTC-GGGTCA
* * *
1099582 TTTTGTGTTTGGGTCACTTT-GGATTCGGGTCA
1 TTTTG-GGTTCGGTCATTTTAGG-TTCGGGTCA
* * * **
1099614 TTTCGGGTTCAGGTCATTTCAGGTTCGAGTTG
1 TTTTGGGTTC-GGTCATTTTAGGTTCGGGTCA
* * *
1099646 TTTCGGGTTTGGGTCATTTCAGGTTCGGGTCA
1 TTTTGGG-TTCGGTCATTTTAGGTTCGGGTCA
1099678 ATCAATTTTA
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
31 8 0.11
32 58 0.77
33 9 0.12
ACGTcount: A:0.12, C:0.14, G:0.32, T:0.42
Consensus pattern (31 bp):
TTTTGGGTTCGGTCATTTTAGGTTCGGGTCA
Found at i:1099628 original size:16 final size:16
Alignment explanation
Indices: 1099605--1099677 Score: 83
Period size: 16 Copynumber: 4.6 Consensus size: 16
1099595 TCACTTTGGA
*
1099605 TTCGGGTCATTTCGGG
1 TTCGGGTCATTTCAGG
*
1099621 TTCAGGTCATTTCAGG
1 TTCGGGTCATTTCAGG
* ** *
1099637 TTCGAGTTGTTTCGGG
1 TTCGGGTCATTTCAGG
*
1099653 TTTGGGTCATTTCAGG
1 TTCGGGTCATTTCAGG
1099669 TTCGGGTCA
1 TTCGGGTCA
1099678 ATCAATTTTA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.11, C:0.16, G:0.33, T:0.40
Consensus pattern (16 bp):
TTCGGGTCATTTCAGG
Found at i:1100746 original size:16 final size:16
Alignment explanation
Indices: 1100725--1100819 Score: 75
Period size: 16 Copynumber: 5.9 Consensus size: 16
1100715 GGGTTAATTA
1100725 TTCGGGTCATTTCGAG
1 TTCGGGTCATTTCGAG
*
1100741 TTCGGGTCATTTCGGG
1 TTCGGGTCATTTCGAG
* *
1100757 TTTGGGTCATTCTGGA-
1 TTCGGGTCATT-TCGAG
* ** *
1100773 TTCGGATCATTTTAAA
1 TTCGGGTCATTTCGAG
**
1100789 TTCAAGTCATTTCGAG
1 TTCGGGTCATTTCGAG
* *
1100805 TTCGAGTCAGTTCGA
1 TTCGGGTCATTTCGA
1100820 ATTTGAGTTG
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
15 2 0.03
16 57 0.93
17 2 0.03
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (16 bp):
TTCGGGTCATTTCGAG
Found at i:1101172 original size:36 final size:36
Alignment explanation
Indices: 1101116--1101210 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
1101106 TTTTTAATTA
* *
1101116 ATTATATTAATTATATAAT-AATGAAATTTATATATTT
1 ATTATATT-ATTATATAATAAAAG-AATTTATATATCT
*
1101153 ATTATATTATTATACAATAAAAGAATTTATATATCT
1 ATTATATTATTATATAATAAAAGAATTTATATATCT
1101189 ATTA-ATTTATTATATAATAAAA
1 ATTATA-TTATTATATAATAAAA
1101211 TATAAAAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
35 1 0.02
36 40 0.77
37 11 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (36 bp):
ATTATATTATTATATAATAAAAGAATTTATATATCT
Found at i:1107000 original size:16 final size:17
Alignment explanation
Indices: 1106979--1107012 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1106969 AATCGAAATA
1106979 TTATTT-AATTAAATTT
1 TTATTTAAATTAAATTT
*
1106995 TTATTTAAATTTAATTT
1 TTATTTAAATTAAATTT
1107012 T
1 T
1107013 AAAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTAAATTAAATTT
Found at i:1110958 original size:21 final size:21
Alignment explanation
Indices: 1110911--1110960 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1110901 TATTTAATAT
*
1110911 TTTTATGTTAAGTTATTTTTA
1 TTTTATTTTAAGTTATTTTTA
1110932 TTTTATTTTAA-TTAGTTTTT-
1 TTTTATTTTAAGTTA-TTTTTA
1110952 TTATTATTT
1 TT-TTATTT
1110961 ATATCACCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (21 bp):
TTTTATTTTAAGTTATTTTTA
Found at i:1111337 original size:20 final size:18
Alignment explanation
Indices: 1111301--1111339 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1111291 ATATAAGGTG
*
1111301 TATATAATAATTTATTAA
1 TATATAATAATTAATTAA
1111319 TATATAATAATATGAATTAA
1 TATATAATAAT-T-AATTAA
1111339 T
1 T
1111340 TAAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 1 0.06
20 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATATAATAATTAATTAA
Found at i:1111466 original size:19 final size:19
Alignment explanation
Indices: 1111442--1111479 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1111432 TTTATAATTT
* *
1111442 TAAATATTTATTAATTTAA
1 TAAATATTAAATAATTTAA
1111461 TAAATATTAAATAATTTAA
1 TAAATATTAAATAATTTAA
1111480 AATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATATTAAATAATTTAA
Found at i:1111973 original size:21 final size:22
Alignment explanation
Indices: 1111934--1111974 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1111924 AAATCAATCG
1111934 ATAACTTTAAATATAAAATAAA
1 ATAACTTTAAATATAAAATAAA
* *
1111956 ATAA-TTTTAATATTAAATA
1 ATAACTTTAAATATAAAATA
1111975 GAGCAATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAACTTTAAATATAAAATAAA
Found at i:1112856 original size:15 final size:15
Alignment explanation
Indices: 1112817--1112857 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1112807 TTTTATATTT
1112817 TTTTAAAATTTAATA
1 TTTTAAAATTTAATA
*
1112832 -TTTAGTAATTTAATA
1 TTTTA-AAATTTAATA
1112847 TTTTAAAATTT
1 TTTTAAAATTT
1112858 TAAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTTAAAATTTAATA
Found at i:1114652 original size:30 final size:30
Alignment explanation
Indices: 1114618--1114706 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
1114608 TTTTTTAATG
* *
1114618 TTTAATTTATACTTATATAGATGCT-TAACT
1 TTTAATTTATACTTAAATAAAT-CTCTAACT
*
1114648 TTTAATTTATATTTAAATAAATCTCTAACT
1 TTTAATTTATACTTAAATAAATCTCTAACT
*
1114678 TTTAATTTATACTTAAATAAATCTTTAAC
1 TTTAATTTATACTTAAATAAATCTCTAAC
1114707 ATAAATTAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
29 2 0.04
30 51 0.96
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.49
Consensus pattern (30 bp):
TTTAATTTATACTTAAATAAATCTCTAACT
Found at i:1117204 original size:17 final size:18
Alignment explanation
Indices: 1117184--1117263 Score: 73
Period size: 17 Copynumber: 4.7 Consensus size: 18
1117174 AATTCTTTAG
1117184 TATATATAATATATA-TA
1 TATATATAATATATAGTA
*
1117201 TATATAT-ATA-A-AGTG
1 TATATATAATATATAGTA
1117216 TATATATAATAT-TAGTA
1 TATATATAATATATAGTA
* *
1117233 TATATATGATTTA-AGTAAA
1 TATATATAATATATAGT--A
1117252 TATATATAATAT
1 TATATATAATAT
1117264 GTACATTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
14 1 0.02
15 9 0.18
16 6 0.12
17 23 0.46
19 11 0.22
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
TATATATAATATATAGTA
Found at i:1117233 original size:15 final size:15
Alignment explanation
Indices: 1117155--1117238 Score: 64
Period size: 15 Copynumber: 5.3 Consensus size: 15
1117145 TTATTCAAGA
* *
1117155 ATATAATTTTAGTGT
1 ATATAATATTAGTAT
*
1117170 ATATAATTCTTTAGTAT
1 ATATAA-T-ATTAGTAT
1117187 ATATAATA-TA-TAT
1 ATATAATATTAGTAT
*
1117200 ATATATATATAAAGTGTAT
1 ATATA-ATAT-TA--GTAT
1117219 ATATAATATTAGTAT
1 ATATAATATTAGTAT
1117234 ATATA
1 ATATA
1117239 TGATTTAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.14
14 5 0.09
15 15 0.26
16 3 0.05
17 14 0.25
18 4 0.07
19 8 0.14
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (15 bp):
ATATAATATTAGTAT
Found at i:1117255 original size:32 final size:31
Alignment explanation
Indices: 1117154--1117255 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 31
1117144 TTTATTCAAG
* * *
1117154 AATATAATTTTAGTGTATATA-ATTCTTTAGTA
1 AATATAATATTAGTATATATATA-T-TTAAGTA
* *
1117186 TATATAATA-TA-TATATATATATATAAAGTGTA
1 AATATAATATTAGTATATATATAT-TTAA--GTA
*
1117218 TATATAATATTAGTATATATATGATTTAAGTA
1 AATATAATATTAGTATATATAT-ATTTAAGTA
1117250 AATATA
1 AATATA
1117256 TATAATATGT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
30 10 0.18
31 3 0.05
32 27 0.48
33 2 0.04
34 12 0.21
35 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (31 bp):
AATATAATATTAGTATATATATATTTAAGTA
Found at i:1117259 original size:2 final size:2
Alignment explanation
Indices: 1117184--1117239 Score: 55
Period size: 2 Copynumber: 28.5 Consensus size: 2
1117174 AATTCTTTAG
* *
1117184 TA TA TA TA -A TA TA TA TA TA TA TA TA TA AA GTG TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
1117225 TA T- TA GTA TA TA TA T
1 TA TA TA -TA TA TA TA T
1117240 GATTTAAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
1 3 0.07
2 40 0.89
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1119913 original size:17 final size:17
Alignment explanation
Indices: 1119891--1119924 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1119881 GATAAACCTA
1119891 ATTTTGTAAA-TAATATG
1 ATTTTG-AAAGTAATATG
1119908 ATTTTGAAAGTAATATG
1 ATTTTGAAAGTAATATG
1119925 TTTATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (17 bp):
ATTTTGAAAGTAATATG
Found at i:1128534 original size:11 final size:11
Alignment explanation
Indices: 1128518--1128547 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1128508 CCTTTGCTTG
1128518 GCTGGAAACAA
1 GCTGGAAACAA
*
1128529 GCTGGAAATAA
1 GCTGGAAACAA
1128540 GCTGGAAA
1 GCTGGAAA
1128548 AGTGGATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.13
Consensus pattern (11 bp):
GCTGGAAACAA
Found at i:1129165 original size:20 final size:20
Alignment explanation
Indices: 1129140--1129216 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
1129130 GTAAAAAGAC
*
1129140 AGAATGTATCGATATATTGA
1 AGAATGTATCGATACATTGA
*
1129160 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
1129180 TA-CATATATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
1129200 AAAATGTATCAATACAT
1 AGAATGTATCGATACAT
1129217 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1130848 original size:165 final size:162
Alignment explanation
Indices: 1130572--1130874 Score: 356
Period size: 165 Copynumber: 1.8 Consensus size: 162
1130562 AAAAATTTAC
* ** * *
1130572 AGATATTTATTGGTAGGAAATTAAAAGTTAGGATGTGGCATTGGGGGTTTTGGCAACATGGAACA
1 AGATATTTATTGGTAGGAAATTAAAAGTTAAGACAT-GAATTGGGGGTTTTAGCAACATGGAACA
** * * * *
1130637 CAAAGTTGATTGGCTAGCTCTTAATAAGGGAACTAGCATCGACTCTTAGGACGATTAGGATACTA
65 CAAAGTTGATCAGCTAGCTCTTAATAAGGGAACTAACATCGACTCTTAGGACAATAAAGATACTA
1130702 AATAGTGACAAATCATTTATACCAATTGGTTGTT
130 AA-AGTGACAAATCATTTATACCAATTGGTTGTT
* *
1130736 AGATATTTATTGGTAGGAAATTCAAGGTTAAGACAT-AATATGGGGGTGTTTCAGCAACATGGAA
1 AGATATTTATTGGTAGGAAATTAAAAGTTAAGACATGAAT-TGGGGGT-TTT-AGCAACATGGAA
** * * * * * * *
1130800 TGCAAGGTTGATCAGCTGGCTTTTGATAAGGGAACTAACATTGACTCTTGGGCCAATAAAGATAC
63 CACAAAGTTGATCAGCTAGCTCTTAATAAGGGAACTAACATCGACTCTTAGGACAATAAAGATAC
1130865 TAAAAGTGAC
128 TAAAAGTGAC
1130875 TCATGAGAAG
Statistics
Matches: 114, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
162 2 0.02
163 7 0.06
164 40 0.35
165 65 0.57
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (162 bp):
AGATATTTATTGGTAGGAAATTAAAAGTTAAGACATGAATTGGGGGTTTTAGCAACATGGAACAC
AAAGTTGATCAGCTAGCTCTTAATAAGGGAACTAACATCGACTCTTAGGACAATAAAGATACTAA
AAGTGACAAATCATTTATACCAATTGGTTGTT
Found at i:1131567 original size:84 final size:84
Alignment explanation
Indices: 1131426--1131594 Score: 259
Period size: 84 Copynumber: 2.0 Consensus size: 84
1131416 TACAAGTGTC
* *
1131426 TGGCTACATTTATACCACGATGATTGTCTATCTGCACATATTGTCTCAATCAATAGTGATAAATC
1 TGGCTACATTTATACCACGATGATTATCTATCTGCACATATTATCTCAATCAATAGTGATAAATC
*
1131491 ATTTATAACAATTAGTTGT
66 ATTTATAACAATAAGTTGT
* * *
1131510 TGGCTGCATTTATACCAC-ATTGATTATCTATCTGCACGTATTATCTTAATCAATAGTGATAAAT
1 TGGCTACATTTATACCACGA-TGATTATCTATCTGCACATATTATCTCAATCAATAGTGATAAAT
*
1131574 CATTTATACCAATAAGTTGT
65 CATTTATAACAATAAGTTGT
1131594 T
1 T
1131595 AGATATTTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
83 1 0.01
84 76 0.99
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (84 bp):
TGGCTACATTTATACCACGATGATTATCTATCTGCACATATTATCTCAATCAATAGTGATAAATC
ATTTATAACAATAAGTTGT
Found at i:1132774 original size:392 final size:393
Alignment explanation
Indices: 1131541--1134140 Score: 1361
Period size: 406 Copynumber: 6.7 Consensus size: 393
1131531 GATTATCTAT
* * * * *
1131541 CTGCACGTATTATCTTAATCAATAGTGATAAATCATTTATACCAA-TAAGTTGTTAGATATTT-T
1 CTGCACTTATTGTCTCAATCAATAGTGACAAATCATTCATACCAACT-AGTTGTTAGATATTTAT
* ** * * * *
1131604 GTGGTA-GAACATTGAAACTT--G-GCT--CA-AAGGGTTTTGGCAACATGGAACACAA-AGTTG
65 -TGGTAGGAA-ATTGAAAGTTAAGATATGGCATGAGGGTTTAGGCAACATAGAACACAAGA-CTG
* *** * **** * * *
1131661 ATTGGCTAGCTCTTGATAAAAGAACTAGCATCAACCATTCGAATGAGAAGGATACTAAACGTGAC
127 ATTGGCTAGCTCTTGATAAAGGAACTAGCATCAATTTTTAGGGCAACAAAGATACTAAACATGAC
*** * * *
1131726 TCACGTTGAGGAAGTTGAATTATTAATGGAATGAATAATCAAACACTAAAAGCCAAGCTAAGCTT
192 TCAC-AAAAGGAAATTGAATTATTAATGGAATG-A-AATTAAACACTAAAAGCCAAGCTAAGCCT
** * * * * *
1131791 ATTAATGATAACAATAACATTTATTTTAACTTTAAAAGTGGTTAAAAAGCTTCGCATCTTTGCCA
254 ATTAACAACAATAATAACATTTATTTTAAGTTTAAAAGTGGTTAAAAAGCTTTGCATCTTTGGCA
* * * * * * * * *
1131856 TGTTTGGGTTAGATTTTGTCCAAATCAGGCAAAATGCAGTTGTTTCCCTAAATTCATTCCACAAT
319 TGTTTGGATTAGATTTTGTCCAAATCATGCTAAATGCAATTGTCTACCTACATTTATTCCACGAT
* **
1131921 GATCGCATGG
384 GATTGTGTGG
* *
1131931 CTACA-TGTATTGTCTCAATCAATAGCGACAAATCATTCATACCAACTAGTTGTTAGATATTTAT
1 CTGCACT-TATTGTCTCAATCAATAGTGACAAATCATTCATACCAACTAGTTGTTAGATATTTAT
* * *
1131995 TGGTAGGAAATTGAAATTTAAGATGTGGCATGAAGGCGCATAAAGGTTTTGGCAACATAGAACAC
65 TGGTAGGAAATTGAAAGTTAAGATATGGCATG-A---G------GGTTTAGGCAACATAGAACAC
* ** ** * * * * * * *
1132060 AAGGCCAATTGTTTAGCTTTTGATAAAAGAGCTAACATCAACTTTTAGGACAACAGAGATACTAA
120 AAGACTGATTGGCTAGCTCTTGATAAAGGAACTAGCATCAATTTTTAGGGCAACAAAGATACTAA
* * ** * * * *
1132125 ACATGACTTATGAGCAGGAAATTGAACTATTAATTGAATCATTAATTAAATACTAAAAGCCAAGC
185 ACATGACTCA-CAAAAGGAAATTGAATTATTAATGGAATGA--AATTAAACACTAAAAGCCAAGC
* * *** * *
1132190 TAAGCCTATTAATAACAACT-ATAACATTTATTTTAAGCTTAAAAGTAAATAAAAAGCATTGTAT
247 TAAGCCTATTAACAACAA-TAATAACATTTATTTTAAGTTTAAAAGTGGTTAAAAAGCTTTGCAT
** * * * * * *
1132254 CTTTGGCACATTTGGATTAGATTTTATCCAAATCATGCTAAACGCAACTATCTACCTACATGTCT
311 CTTTGGCATGTTTGGATTAGATTTTGTCCAAATCATGCTAAATGCAATTGTCTACCTACATTTAT
* * **
1132319 TCTATGATGATTGTGTAC
376 TCCACGATGATTGTGTGG
* * * ** ** *
1132337 CTGCACATATTGTCTCTATCAACAGTGACAAATCATTTGTACCAACTAGTTGAAAGATGTTTATT
1 CTGCACTTATTGTCTCAATCAATAGTGACAAATCATTCATACCAACTAGTTGTTAGATATTTATT
* * *
1132402 GGTAGGAAATTGAAAGTTAAGATATGGCATGAGGGTTTAGGCGACATAAAACACAAGATTGATTG
66 GGTAGGAAATTGAAAGTTAAGATATGGCATGAGGGTTTAGGCAACATAGAACACAAGACTGATTG
* * * * *
1132467 GCTGGCTCTTGATAAAGGAACTAGCATCAATTTTTGGGGCAACAAAAATATTAAAAATGACTCAC
131 GCTAGCTCTTGATAAAGGAACTAGCATCAATTTTTAGGGCAACAAAGATACTAAACATGACTCAC
* *
1132532 AATAAGGAAATTGAATTATTAATGGAATG-AA-TAAACATTAAAAGCCAAG-TGAAGCCTATTGA
196 AA-AAGGAAATTGAATTATTAATGGAATGAAATTAAACACTAAAAGCCAAGCT-AAGCCTATTAA
* * *
1132594 CAACAATAATAACATTTATTTTAAGTTTAAAGGTGGTTAAAAGGCTTTGCATCCTTGGCATGTTT
259 CAACAATAATAACATTTATTTTAAGTTTAAAAGTGGTTAAAAAGCTTTGCATCTTTGGCATGTTT
* * * * * * *** *
1132659 AGATTAAATCTTGTCAAAATCTTACTAAATGCAATTGTCTGTTTACATTTGTTCCACGATGATTG
324 GGATTAGATTTTGTCCAAATCATGCTAAATGCAATTGTCTACCTACATTTATTCCACGATGATTG
1132724 TGTGG
389 TGTGG
* * * *
1132729 CTGCACTTATTATCTCAATCAATAATGATAAATCATTCATACCAACTAGTTGTTGGATATTTATT
1 CTGCACTTATTGTCTCAATCAATAGTGACAAATCATTCATACCAACTAGTTGTTAGATATTTATT
* * * * *
1132794 GGTAGGAAATTGAAAGTTAAGACATGGCATAGGAGGTTTTA-GCAATATTGAACACAAAACTGAT
66 GGTAGGAAATTGAAAGTTAAGATATGGCAT--GAGGGTTTAGGCAACATAGAACACAAGACTGAT
* * * * * ** * * *
1132858 CGGCTAGCTCTTGATAAGGGAAGTAGCATCACTTTTCAAATG--ACAAGGATACTAAACGTGATT
129 TGGCTAGCTCTTGATAAAGGAACTAGCATCAATTTT-TAGGGCAACAAAGATACTAAACATGACT
* * * * *
1132921 CACAAAGAGGAAATTGAATTATTATTAGAATGAGTAATTAAACAGTAAAAGCCAAGCCAAGCTTA
193 CACAAA-AGGAAATTGAATTATTAATGGAATGA--AATTAAACACTAAAAGCCAAGCTAAGCCTA
* * *** *
1132986 TTAACGACAATAATAACATTTATTTTAAGTTTAAAAGTGGTTAAAAGGCTTTGCAT-TTCAACAC
255 TTAACAACAATAATAACATTTATTTTAAGTTTAAAAGTGGTTAAAAAGCTTTGCATCTTTGGCAT
* * * * * * * **
1133050 ATTTGGATTAGATTTTGTCTAAATCATGCAAAATGCAACT-ACTTATCTACATTCATTCCATAAT
320 GTTTGGATTAGATTTTGTCCAAATCATGCTAAATGCAATTGTC-TACCTACATTTATTCCACGAT
* **
1133114 GATCGCATGG
384 GATTGTGTGG
* * * * * * *
1133124 CTACA-TGTATTATCTTAATCAACAATGACAAATCATTCATACGAACTAGTTGTTGGATATTTAT
1 CTGCACT-TATTGTCTCAATCAATAGTGACAAATCATTCATACCAACTAGTTGTTAGATATTTAT
* * * * * * * * * *
1133188 TAGTAGGAAATCGAAGGTTAAAATGTGGCATAAAGGTTTTA-GCAACATGGAACACAAG-GTTAC
65 TGGTAGGAAATTGAAAGTTAAGATATGGCAT-GAGGGTTTAGGCAACATAGAACACAAGACTGA-
* * * * * * * * **
1133251 TTGGCTGGCCCTTGAT-ATGTGAACTAACATTAACTCTTAGGACAACAAAGATACTAAATGTGAC
128 TTGGCTAGCTCTTGATAAAG-GAACTAGCATCAATTTTTAGGGCAACAAAGATACTAAACATGAC
* * * * * * ** **
1133315 TTAGAAAGAGTAAATCGAATTATTAAT----T-AAATGTGAGC-CT-ATTG--AAAATAA--C-A
192 TCACAAA-AGGAAATTGAATTATTAATGGAATGAAAT-TAAACACTAAAAGCCAAGCTAAGCCTA
* *** ** * * * * ** * *
1133368 ATAACATTTATTTTAA-GTTTAGATGT-AG-TTAAAAG-GCCTT--GTATCTTCGGCA-CATTTG
255 TTAACAACAATAATAACATTTA-TTTTAAGTTTAAAAGTG-GTTAAAAAGCTT-TGCATC-TTTG
* ** * * * *
1133426 G-A-------A-T--A----G----AATCATTCTAAATTTAACTGCCTAGCTACATTTATTCCAT
316 GCATGTTTGGATTAGATTTTGTCCAAATCATGCTAAATGCAATTGTCTACCTACATTTATTCCAC
*
1133472 GATGATTGTGTGT
381 GATGATTGTGTGG
* * * * * * * * *
1133485 TTACA-TGTATTGTCAC-ATTAACAATGACAAATCGTTCATACTAACTAGTTGTTGGATATTTAT
1 CTGCACT-TATTGTCTCAATCAATAGTGACAAATCATTCATACCAACTAGTTGTTAGATATTTAT
* * ** * * * ***
1133548 TGGTAGAAAATTG-AAGTTTAAGACATGATATGAGGGATTTTGGCAACATGGAATACAATTTTGA
65 TGGTAGGAAATTGAAAG-TTAAGATATGGCATGAGGG-TTTAGGCAACATAGAACACAAGACTGA
* * * * * * * *** * * * **
1133612 TTAGCTGGCTCTTAATGAGGGAACTAGCATCGATTCTTAGGATGATAAGGATACTGAAGGTGACT
128 TTGGCTAGCTCTTGATAAAGGAACTAGCATCAATTTTTAGGGCAACAAAGATACTAAACATGACT
* * * * * * * * *
1133677 TATGAAAAAGAAATTGGATTATTAATGAAATGAGTAATTAAACACTAAAAGCCAAGCCAATCTTG
193 CA-CAAAAGGAAATTGAATTATTAATGGAATGA--AATTAAACACTAAAAGCCAAGCTAAGCCTA
* * ** * ** * * * * *
1133742 TTGACGATGATAGA-AACATTTGTTTTTGGATTAAAATTGGTTAAAAGGCTTTGCATCTTCGGTA
255 TTAACAACAATA-ATAACATTTATTTTAAGTTTAAAAGTGGTTAAAAAGCTTTGCATCTTTGGCA
** * * * * *
1133806 CATTTGGATTAGATTTTGTCCAAATCATGCCAAATGCAACTGGCTGCCTACATTTATTCCACTAT
319 TGTTTGGATTAGATTTTGTCCAAATCATGCTAAATGCAATTGTCTACCTACATTTATTCCACGAT
1133871 GATTGTGTGG
384 GATTGTGTGG
* * * * * *
1133881 CT--ATCTATAATGTCTCAACCGATAGTGAGAAATCATTCATACCAATTGGTTGTT-GA-ATTTT
1 CTGCA-CT-TATTGTCTCAATCAATAGTGACAAATCATTCATACCAACTAGTTGTTAGATA-TTT
* * * * * * * **
1133942 TTTGGTAGGAAACT-AAATATTAAGACATGGCAAGGAGGTTTTA-GCAACATAAAACACAAGGTT
63 ATTGGTAGGAAATTGAAA-GTTAAGATATGGC-ATGAGGGTTTAGGCAACATAGAACACAAGACT
* * * ** *
1134005 GATTGGCTGGCTCTTGATAAAGGAACTAGTATCAACTTTTAAAGCAACAAGGATACTAAACATGA
126 GATTGGCTAGCTCTTGATAAAGGAACTAGCATCAATTTTTAGGGCAACAAAGATACTAAACATGA
* * * *
1134070 CTCATGAAGAA-AAAATTGAATTATTAATGTAATGAGTAATTAAACACTAAAA-CCAAGCCAAGC
191 CTCA-CAA-AAGGAAATTGAATTATTAATGGAATGA--AATTAAACACTAAAAGCCAAGCTAAGC
1134133 CTATTAAC
252 CTATTAAC
1134141 GATAGCCACT
Statistics
Matches: 1672, Mismatches: 433, Indels: 206
0.72 0.19 0.09
Matches are distributed among these distances:
359 5 0.00
360 66 0.04
361 131 0.08
362 9 0.01
365 2 0.00
366 1 0.00
367 3 0.00
368 5 0.00
369 3 0.00
371 5 0.00
372 1 0.00
374 10 0.01
375 4 0.00
376 8 0.00
377 8 0.00
378 8 0.00
379 5 0.00
380 11 0.01
381 6 0.00
382 12 0.01
385 5 0.00
386 1 0.00
387 2 0.00
388 5 0.00
389 3 0.00
390 67 0.04
391 9 0.01
392 255 0.15
393 56 0.03
394 73 0.04
395 291 0.17
396 257 0.15
397 33 0.02
400 1 0.00
402 1 0.00
405 2 0.00
406 308 0.18
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (393 bp):
CTGCACTTATTGTCTCAATCAATAGTGACAAATCATTCATACCAACTAGTTGTTAGATATTTATT
GGTAGGAAATTGAAAGTTAAGATATGGCATGAGGGTTTAGGCAACATAGAACACAAGACTGATTG
GCTAGCTCTTGATAAAGGAACTAGCATCAATTTTTAGGGCAACAAAGATACTAAACATGACTCAC
AAAAGGAAATTGAATTATTAATGGAATGAAATTAAACACTAAAAGCCAAGCTAAGCCTATTAACA
ACAATAATAACATTTATTTTAAGTTTAAAAGTGGTTAAAAAGCTTTGCATCTTTGGCATGTTTGG
ATTAGATTTTGTCCAAATCATGCTAAATGCAATTGTCTACCTACATTTATTCCACGATGATTGTG
TGG
Found at i:1137490 original size:20 final size:20
Alignment explanation
Indices: 1137464--1137518 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1137454 AAAACGACGG
* *
1137464 AATGTATCGATACATTTATA
1 AATGTATCGATACATTGAAA
* * *
1137484 CATGTATCAATATATTGAAA
1 AATGTATCGATACATTGAAA
1137504 AATGTATCGATACAT
1 AATGTATCGATACAT
1137519 CTGGGTACTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1138527 original size:28 final size:28
Alignment explanation
Indices: 1138465--1139567 Score: 1292
Period size: 28 Copynumber: 38.7 Consensus size: 28
1138455 AGAGTTACCC
*
1138465 CTGACTTGTGGGCTTTGAAAAGAGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCA
* * *
1138494 CTGACTTATGGGTTTTGAAAGGGTGTCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* * *
1138522 TTGACTTGTGCGCTTTGAAAAGAGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCA
* **
1138551 CTGATTTGTGGGCTTTGAAAAAGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
*
1138579 CTGACTT-TGGGCTTTGAAAAGAGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCA
* * *
1138607 CTGACTTATAGGCTTTGAAAAGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* * *
1138635 TTGACTTGCGTGTGCTTTGAAAGGGTGCGA
1 CTGACTT--GTGGGCTTTGAAAGGGTGCCA
*
1138665 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* * **
1138693 TTGACTTATGGGCTTTGAAAATAGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCA
1138722 CTGACTTGTGGGCTTTGAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
1138750 CTGACTTACGTGGGCTTTGAAAGGGTGCCA
1 CTGACTT--GTGGGCTTTGAAAGGGTGCCA
* *
1138780 CTGACTTGTGGGCTTTAAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
1138808 CTGACTTGTGGGCTTTGAAAGGGTACTA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* **
1138836 TTGACTTGCAAAGGCTTTGAAAGGGTGCCA
1 CTGACTTG--TGGGCTTTGAAAGGGTGCCA
**
1138866 CTGACTTGTGGGCTTTGAAAATGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
*
1138894 TTGACTTGCGTGGGCTTTGAAAGGGTGCCA
1 CTGACTT--GTGGGCTTTGAAAGGGTGCCA
* * **
1138924 CTGACTTTTGGGCTTTGAAAGGATGTGA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
1138952 CTAACTTGTGGGCTTTGAAAAGAGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCA
* *
1138981 CTAACTTGTGGGCTTTTAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* * *
1139009 CTAACTTGTGGGCTTTGAAAGGATGCTA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
*
1139037 CTAACTTGTGGGCTTTGAAAGGAGTTGCCA
1 CTGACTTGTGGGCTTTGAAAGG-G-TGCCA
* * *
1139067 CTAACTTGTGGGCTTTGAAAGGATGTCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
1139095 CTGACTTGTGGGCTTTGAAAGGGTACGA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
*
1139123 CTAACTTGTGGGCTTTGAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
1139151 CTGACTTGTGGGCTTTGAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
1139179 CTGACTTGCGTGGGCTTTGAAAGGGTGCCA
1 CTGACTT--GTGGGCTTTGAAAGGGTGCCA
* * * *
1139209 CTAACTTATAGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* * *
1139237 CTAACTTGTGGG-TTTAAAAAGAGTGCCA
1 CTGACTTGTGGGCTTT-GAAAGGGTGCCA
*
1139265 CTGACTTATGGGCTTTGAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
1139293 CTGACCTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* * *
1139321 CTAACTTGTGGGTTTTGAAAAGAGTTGCCA
1 CTGACTTGTGGGCTTTG-AAAG-GGTGCCA
* *
1139351 CTGACTTGTGGGCTTTGAAAGGATACCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* * *
1139379 CTAACTTATGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
*
1139407 CTGACTTGTTGGCTTTGAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
1139435 CTGACTTGTGGGCTTTGAAAGGAGTGCCA
1 CTGACTTGTGGGCTTTGAAAGG-GTGCCA
* * *
1139464 CTAACTTATGGGCTTTAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
1139492 CTAACTTGTGGGCTTTGAAAAGAGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCA
* * * *
1139521 CTGACTTGTAGGCTTTAAAAAGGTACCA
1 CTGACTTGTGGGCTTTGAAAGGGTGCCA
1139549 CTGACTTGTGGGCTTTGAA
1 CTGACTTGTGGGCTTTGAA
1139568 GAGATAAATG
Statistics
Matches: 919, Mismatches: 132, Indels: 47
0.84 0.12 0.04
Matches are distributed among these distances:
27 12 0.01
28 583 0.63
29 152 0.17
30 172 0.19
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
CTGACTTGTGGGCTTTGAAAGGGTGCCA
Found at i:1138567 original size:86 final size:85
Alignment explanation
Indices: 1138441--1139567 Score: 1304
Period size: 86 Copynumber: 13.2 Consensus size: 85
1138431 CACCGACTCA
* * * * *
1138441 TGTGGGGTTTGAAAAGAGTTACCCCTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTATGGG
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGG
* * * *
1138506 TTTTGAAAGGGTGTCATTGACT
64 CTTTGAAAGGGTGCCACTAACT
* * **
1138528 TGTGCGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAAGTGCCACTGACTT-TGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
1138592 TTGAAAAGAGTGCCACTGACT
66 TTG-AAAGGGTGCCACTAACT
* * * * *
1138613 TATAGGCTTTGAAAAG-GTGCCATTGACTTGCGTGTGCTTTGAAAGGGTGCGACTGACTTGTGGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
* * *
1138677 CTTTGAAAGGATGCCATTGACT
64 CTTTGAAAGGGTGCCACTAACT
* *
1138699 TATGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTACGTGGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGG
*
1138764 CTTTGAAAGGGTGCCACTGACT
64 CTTTGAAAGGGTGCCACTAACT
* * * **
1138786 TGTGGGCTTT-AAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGGGTACTATTGACTTGCAAAG
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG--TGG
*
1138849 GCTTTGAAAGGGTGCCACTGACT
63 GCTTTGAAAGGGTGCCACTAACT
* * *
1138872 TGTGGGCTTTGAAAA-TGTGCCATTGACTTGCGTGGGCTTTGAAAGGGTGCCACTGACTTTTGGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
* **
1138936 CTTTGAAAGGATGTGACTAACT
64 CTTTGAAAGGGTGCCACTAACT
* * *
1138958 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTTAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
1139023 TTGAAAGGATGCTACTAACT
66 TTGAAAGGGTGCCACTAACT
* * * *
1139043 TGTGGGCTTTGAAAGGAGTTGCCACTAACTTGTGGGCTTTGAAAGGATGTCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* *
1139108 TTTGAAAGGGTACGACTAACT
65 TTTGAAAGGGTGCCACTAACT
*
1139129 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGG
1139193 CTTTGAAAGGGTGCCACTAACT
64 CTTTGAAAGGGTGCCACTAACT
* * * * * * *
1139215 TATAGGCTTTGAAAGGA-TGCCACTAACTTGTGGG-TTTAAAAAGAGTGCCACTGACTTATGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGC
* *
1139278 TTTGAAAGGGTGCCACTGACC
65 TTTGAAAGGGTGCCACTAACT
* * * *
1139299 TGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGTTTTGAAAAGAGTTGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGG
* *
1139363 CTTTGAAAGGATACCACTAACT
64 CTTTGAAAGGGTGCCACTAACT
* * *
1139385 TATGGGCTTTGAAAGGA-TGCCACTGACTTGTTGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1139449 TTGAAAGGAGTGCCACTAACT
66 TTGAAAGG-GTGCCACTAACT
* * * * *
1139470 TATGGGCTTT-AAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
* * * *
1139534 TTTAAAAAGGTACCACTGACT
65 TTTGAAAGGGTGCCACTAACT
1139555 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
1139568 GAGATAAATG
Statistics
Matches: 905, Mismatches: 108, Indels: 55
0.85 0.10 0.05
Matches are distributed among these distances:
84 145 0.16
85 215 0.24
86 430 0.48
87 90 0.10
88 25 0.03
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
TTGAAAGGGTGCCACTAACT
Found at i:1139192 original size:114 final size:112
Alignment explanation
Indices: 1138465--1139567 Score: 1292
Period size: 114 Copynumber: 9.7 Consensus size: 112
1138455 AGAGTTACCC
* * * * *
1138465 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTATGGGTTTTGAAAGGGTGTCATTGACTTG
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * **
1138530 TGCGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAAGTGCCA
65 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * * *
1138579 CTGACTT-TGGGCTTTGAAAAGAGTGCCACTGACTTATAGGCTTTGAAAAGGTGCCATTGACTTG
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT-
* * *
1138643 CGTGTGCTTTGAAAGGGTGCGACTGACTTGTGGGCTTTGAAAGGATGCCA
64 -GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * **
1138693 TTGACTTATGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTA
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT-
* *
1138758 CGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGATGCCA
64 -GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * **
1138808 CTGACTTGTGGGCTTTGAAAGGGTACTATTGACTTGCAAAGGCTTTGAAAGGGTGCCACTGACTT
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGACTT
** *
1138873 GTGGGCTTTGAAAATGTGCCATTGACTTGCGTGGGCTTTGAAAGGGTGCCA
64 GTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCA
* * ** * * *
1138924 CTGACTTTTGGGCTTTGAAAGGATGTGACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTG
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
* * * *
1138989 TGGGCTTTTAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATGCTA
65 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * *
1139037 CTAACTTGTGGGCTTTGAAAGGAGTTGCCACTAACTTGTGGGCTTTGAAAGGATGTCACTGACTT
1 CTGACTTGTGGGCTTTGAAAGG-G-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT
* * *
1139102 GTGGGCTTTGAAAGGGTACGACTAACTTGTGGGCTTTGAAAGGGTGCCA
64 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
*
1139151 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTAACTT
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTT
* * * * * *
1139216 ATAGGCTTTGAAAGGATGCCACTAACTTGTGGG-TTTAAAAAGAGTGCCA
64 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCA
* * * *
1139265 CTGACTTATGGGCTTTGAAAGGGTGCCACTGACCTGTGGGCTTTGAAAGGATGCCACTAACTTGT
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * * *
1139330 GGGTTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAGGATACCA
66 GGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * *
1139379 CTAACTTATGGGCTTTGAAAGGATGCCACTGACTTGTTGGCTTTGAAAGGGTGCCACTGACTTGT
1 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * *
1139444 GGGCTTTGAAAGGAGTGCCACTAACTTATGGGCTTTAAAAGGGTGCCA
66 GGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * * * *
1139492 CTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGGCTTTAAAAAGGTACCACTGACTTG
1 CTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
1139557 TGGGCTTTGAA
65 TGGGCTTTGAA
1139568 GAGATAAATG
Statistics
Matches: 860, Mismatches: 111, Indels: 36
0.85 0.11 0.04
Matches are distributed among these distances:
112 46 0.05
113 147 0.17
114 410 0.48
115 184 0.21
116 73 0.08
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (112 bp):
CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
GGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
Found at i:1140804 original size:12 final size:11
Alignment explanation
Indices: 1140789--1140828 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1140779 CCCCTTTCTG
*
1140789 TTTTTTGTTAT
1 TTTTTTGTTTT
*
1140800 TTTTTTCTTTGT
1 TTTTTTGTTT-T
1140812 TTTTTTGTTTT
1 TTTTTTGTTTT
1140823 TTTTTT
1 TTTTTT
1140829 TGGGTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.88
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:1140829 original size:12 final size:12
Alignment explanation
Indices: 1140789--1140830 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1140779 CCCCTTTCTG
1140789 TTTTTTG-TTAT
1 TTTTTTGTTTAT
* *
1140800 TTTTTTCTTTGT
1 TTTTTTGTTTAT
*
1140812 TTTTTTGTTTTT
1 TTTTTTGTTTAT
1140824 TTTTTTG
1 TTTTTTG
1140831 GGTATGAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (12 bp):
TTTTTTGTTTAT
Found at i:1153285 original size:20 final size:20
Alignment explanation
Indices: 1153259--1153334 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
1153249 TAAAAAGATG
1153259 AAATGTATCGATAC-TTTAA
1 AAATGTATCGATACATTTAA
*
1153278 AGAATGTATCGATACATTTAT
1 A-AATGTATCGATACATTTAA
* * *
1153299 ACATGTATCGATGCATTGAA
1 AAATGTATCGATACATTTAA
* *
1153319 AAATATATCAATACAT
1 AAATGTATCGATACAT
1153335 CTGGGTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.02
20 40 0.87
21 5 0.11
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTTAA
Found at i:1154821 original size:395 final size:394
Alignment explanation
Indices: 1154026--1154870 Score: 941
Period size: 395 Copynumber: 2.1 Consensus size: 394
1154016 GAACAGTAAT
* * ** * * **
1154026 ATTTATTTTAAGTTT-AAAGTGGCTAAAAGGCTCTACATTTTTAGCATGTTTGGATTAGATTTTG
1 ATTTATTTTAAGTTTGAAAGTGGTTAAAACGCTCTGTATCTTTGGCACATTTGGATTAGATTTTG
* * * * ***** *
1154090 TTCAAATCATGCTAAATGCAACTATCTATCTACATTCATTCCATGATGATTGTGTGGTTGTACGT
66 TCCAAATCATGCTAAATGCAACTACCTACCTACATTCATTCCATGATGATTATGTGCCCACACAT
* * * ** **
1154155 ATTGTCTCAATCAACAATGATAGATCATCATACCAACTAATTGTTGGATATTTATTGGTAGGATG
131 ATTGTCTCAATCAACAATGACAAATCATCATACCAACTAATTATTGGATATTTATTGGTAAAAAA
** * * * *
1154220 TTGAAAGTTAAGACATGGCATAGAGGTTTTGGCAACATGGAACACAAGGTTGGTTGGCTGGCTCT
196 TTGAAAGTTAAGACATAACATAGAGGTTTTAGCAACATGGAACACAAGATTGATTGGCTAGCTCT
* * * * *
1154285 TAATAAGGGAACTACCATCAGCTGTTGGGATGACGAGGATACTAAATGTGACTCACAATGAGGAA
261 TAATAAAGGAACTACCATCAGCTCTTAGGATGACAAGGATACTAAATGTGACTCACAA-GAGCAA
* * * * * *
1154350 ATTAAATTATTAATTGAATGAGTAATTACACACTAGAAGCCAAGCCAAGCCTGTTGGCAACAACA
325 ATTAAATTATTAATAGAATGAGCAATTAAACACTAAAAGCCAAGCCAAGCCTATTGACAACAACA
* *
1154415 ATAAT
390 AAAAC
* * *
1154420 ATTTATTTTAAGTTT-AGAAGTTGTTAAAACGCTTTGTATCTTTGGTACATTTGGATTAGATTTT
1 ATTTATTTTAAGTTTGA-AAGTGGTTAAAACGCTCTGTATCTTTGGCACATTTGGATTAGATTTT
* *
1154484 GTCCAAATCATGTTAAATGCAACTGCCTACCTACATTCATTCCATGATGATTATGTGCCCACACA
65 GTCCAAATCATGCTAAATGCAACTACCTACCTACATTCATTCCATGATGATTATGTGCCCACACA
* *
1154549 TATTGTCTCAATCAACAGTGACAAATCATTCATACCAACTAGTTATTGGATATTTATTGGTAAAA
130 TATTGTCTCAATCAACAATGACAAATCA-TCATACCAACTAATTATTGGATATTTATTGGTAAAA
* * *
1154614 AATTGAAGGTTAAAGACATAACATTGGGGTTTTAGCAACATGGAACACAAGATTGATTGGCTAGC
194 AATTGAAAGTT-AAGACATAACATAGAGGTTTTAGCAACATGGAACACAAGATTGATTGGCTAGC
* * * * *
1154679 TCTTGATAAAGGAATTAGCATC-GATTCTTAGGATGA-AAGGATACTAAAATGTTTTA-TGCA-A
258 TCTTAATAAAGGAACTACCATCAG-CTCTTAGGATGACAAGGATACT-AAATG--TGACT-CACA
** * * *
1154740 A-A-CAAATTGGATTTTTAATAGAATGAGCAATTAAACACTAAAAGTCGAGCCAAGCCTATTGAC
318 AGAGCAAATTAAATTATTAATAGAATGAGCAATTAAACACTAAAAGCCAAGCCAAGCCTATTGAC
**
1154803 AATGACAAAAAC
383 AACAACAAAAAC
* *
1154815 ATTTATTTTTAGTTTGAAAGTGGTTAAAAGGCTCTGTATCTTTGGCACATTTGGAT
1 ATTTATTTTAAGTTTGAAAGTGGTTAAAACGCTCTGTATCTTTGGCACATTTGGAT
1154871 GAGTAATTAA
Statistics
Matches: 371, Mismatches: 71, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
394 16 0.04
395 220 0.59
396 51 0.14
397 77 0.21
398 3 0.01
399 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (394 bp):
ATTTATTTTAAGTTTGAAAGTGGTTAAAACGCTCTGTATCTTTGGCACATTTGGATTAGATTTTG
TCCAAATCATGCTAAATGCAACTACCTACCTACATTCATTCCATGATGATTATGTGCCCACACAT
ATTGTCTCAATCAACAATGACAAATCATCATACCAACTAATTATTGGATATTTATTGGTAAAAAA
TTGAAAGTTAAGACATAACATAGAGGTTTTAGCAACATGGAACACAAGATTGATTGGCTAGCTCT
TAATAAAGGAACTACCATCAGCTCTTAGGATGACAAGGATACTAAATGTGACTCACAAGAGCAAA
TTAAATTATTAATAGAATGAGCAATTAAACACTAAAAGCCAAGCCAAGCCTATTGACAACAACAA
AAAC
Found at i:1155001 original size:107 final size:107
Alignment explanation
Indices: 1154762--1154977 Score: 378
Period size: 107 Copynumber: 2.0 Consensus size: 107
1154752 TTTTAATAGA
* * *
1154762 ATGAGCAATTAAACACTAAAAGTCGAGCCAAGCCTATTGACAATGACAAAAACATTTATTTTTAG
1 ATGAGTAATTAAACACTAAAAGCCAAGCCAAGCCTATTGACAATGACAAAAACATTTATTTTTAG
* *
1154827 TTTGAAAGTGGTTAAAAGGCTCTGTATCTTTGGCACATTTGG
66 TTTGAAAGTGGTTAAAAAGCTCTGTATCTTTGGCACACTTGG
1154869 ATGAGTAATTAAACACTAAAAGCCAAGCCAAGCCTATTGACAATGACAAAAACATTTATTTTTAG
1 ATGAGTAATTAAACACTAAAAGCCAAGCCAAGCCTATTGACAATGACAAAAACATTTATTTTTAG
*
1154934 TTTGAAAGTGGTTAAAAAGCTTTGTATCTTTGGCACACTTGG
66 TTTGAAAGTGGTTAAAAAGCTCTGTATCTTTGGCACACTTGG
1154976 AT
1 AT
1154978 TAGATTTTGT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (107 bp):
ATGAGTAATTAAACACTAAAAGCCAAGCCAAGCCTATTGACAATGACAAAAACATTTATTTTTAG
TTTGAAAGTGGTTAAAAAGCTCTGTATCTTTGGCACACTTGG
Found at i:1156663 original size:20 final size:20
Alignment explanation
Indices: 1156635--1156709 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1156625 TCATACCCTG
* *
1156635 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTACA
* *
1156655 ATATATCGATACA-TGTACGA
1 ATGTATCGATACATTCTAC-A
*
1156675 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTCTACA
1156695 ATGTATCGATACATT
1 ATGTATCGATACATT
1156710 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.07
20 39 0.85
21 4 0.09
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTACA
Found at i:1159288 original size:12 final size:12
Alignment explanation
Indices: 1159271--1159295 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1159261 AAATTTCTTT
1159271 TACTTGTCATTA
1 TACTTGTCATTA
1159283 TACTTGTCATTA
1 TACTTGTCATTA
1159295 T
1 T
1159296 GATGATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTGTCATTA
Found at i:1160997 original size:16 final size:19
Alignment explanation
Indices: 1160951--1160997 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 19
1160941 GGCCACTCTT
1160951 TTTTTTTTTATTGATGTTCA
1 TTTTTTTTT-TTGATGTTCA
*
1160971 TTTTTATTTTT-AT-TT-A
1 TTTTTTTTTTTGATGTTCA
1160987 TTTTTTTTTTT
1 TTTTTTTTTTT
1160998 TGCTATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 11 0.44
17 2 0.08
18 2 0.08
19 2 0.08
20 8 0.32
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTTTGATGTTCA
Found at i:1170695 original size:6 final size:6
Alignment explanation
Indices: 1170684--1170738 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
1170674 CTTTGCACCC
1170684 AAAACA AAAACA AAAA-A AAAAC- AAAAC- AAAA-A AAAACAA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAAC-A AAAACA
*
1170729 AAAAGA AAAA
1 AAAACA AAAA
1170739 AATAGCAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 18 0.41
6 20 0.45
7 6 0.14
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:1170706 original size:17 final size:17
Alignment explanation
Indices: 1170684--1170738 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 17
1170674 CTTTGCACCC
1170684 AAAACAAAAACAAAAAA
1 AAAACAAAAACAAAAAA
1170701 AAAAC-AAAAC-AAAAA
1 AAAACAAAAACAAAAAA
1170716 AAAACAAAAAACAAAAAGA
1 AAAAC-AAAAACAAAAA-A
1170735 AAAA
1 AAAA
1170739 AATAGCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.29
16 5 0.15
17 10 0.29
18 4 0.12
19 5 0.15
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAACAAAAACAAAAAA
Found at i:1170711 original size:22 final size:22
Alignment explanation
Indices: 1170683--1170750 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 22
1170673 CCTTTGCACC
1170683 CAAAACAAAAACAAAA-AAAAAA
1 CAAAACAAAAA-AAAACAAAAAA
1170705 CAAAACAAAAAAAAACAAAAAA
1 CAAAACAAAAAAAAACAAAAAA
1170727 CAAAA-AGAAAAAAATAGCAAAAAA
1 CAAAACA-AAAAAAA-A-CAAAAAA
1170751 TAGAAGGGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.12
22 29 0.69
23 1 0.02
24 7 0.17
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (22 bp):
CAAAACAAAAAAAAACAAAAAA
Found at i:1170714 original size:15 final size:16
Alignment explanation
Indices: 1170684--1170738 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 16
1170674 CTTTGCACCC
1170684 AAAACAAAAACAAAAAA
1 AAAAC-AAAACAAAAAA
1170701 AAAACAAAACAAAAAA
1 AAAACAAAACAAAAAA
*
1170717 AAACAAAAAACAAAAAGA
1 AAA-ACAAAACAAAAA-A
1170735 AAAA
1 AAAA
1170739 AATAGCAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 14 0.40
17 17 0.49
18 4 0.11
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAACAAAACAAAAAA
Found at i:1170750 original size:1 final size:1
Alignment explanation
Indices: 1170684--1170740 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
1170674 CTTTGCACCC
* * * * * * *
1170684 AAAACAAAAACAAAAAAAAAACAAAACAAAAAAAAACAAAAAACAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1170741 TAGCAAAAAA
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1172011 original size:29 final size:29
Alignment explanation
Indices: 1171969--1172740 Score: 1147
Period size: 29 Copynumber: 26.9 Consensus size: 29
1171959 AATGTTCATC
1171969 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1171998 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172027 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1172055 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1172083 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172112 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172141 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1172169 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172198 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172226 CCTTTCAAAGCCCAAAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172255 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172283 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1172311 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1172340 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1172369 CTTTTCAAAGCCCACAAATCTGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172398 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172426 CCTTTCAAAGCCCACAAGTAAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172455 CCTTTCACAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172484 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172513 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172541 CCTTTCAAAGCTCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172569 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172597 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1172625 CATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1172654 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172681 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* *
1172712 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
1172741 ACCCTTTTCA
Statistics
Matches: 682, Mismatches: 49, Indels: 22
0.91 0.07 0.03
Matches are distributed among these distances:
28 317 0.46
29 325 0.48
30 18 0.03
31 22 0.03
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1172080 original size:57 final size:57
Alignment explanation
Indices: 1171969--1172752 Score: 1148
Period size: 57 Copynumber: 13.6 Consensus size: 57
1171959 AATGTTCATC
*
1171969 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172027 CTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172083 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172141 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1172198 CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCAAAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172255 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
1172311 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * *
1172369 CTTTTCAAAGCCCACAAATCTGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172426 CCTTTCAAAGCCCACAAGTAAGTGGCACTCCTTTCACAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1172484 CCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1172541 CCTTTCAAAGCTCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * *
1172597 CCTTTCGAAGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1172654 -CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* *
1172712 CCTTTTAAAGCCCATGCAAGTCAATGGCAACCCTTTTCAAA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGC-ACCC-TTTCAAA
1172753 TCACCACTGT
Statistics
Matches: 657, Mismatches: 56, Indels: 21
0.90 0.08 0.03
Matches are distributed among these distances:
56 159 0.24
57 291 0.44
58 174 0.26
59 12 0.02
61 11 0.02
62 4 0.01
63 6 0.01
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.22
Consensus pattern (57 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1173294 original size:20 final size:20
Alignment explanation
Indices: 1173266--1173340 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1173256 TCATACCCTG
1173266 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1173286 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1173306 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1173326 ATGTATCGATACATT
1 ATGTATCGATACATT
1173341 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1173333 original size:40 final size:39
Alignment explanation
Indices: 1173266--1173343 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1173256 TCATACCCTG
* *
1173266 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1173306 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1173344 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1175910 original size:12 final size:12
Alignment explanation
Indices: 1175893--1175917 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1175883 AATTTTCTTT
1175893 TACTTGTCATTA
1 TACTTGTCATTA
1175905 TACTTGTCATTA
1 TACTTGTCATTA
1175917 T
1 T
1175918 GATGATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTGTCATTA
Found at i:1177551 original size:15 final size:16
Alignment explanation
Indices: 1177526--1177567 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1177516 AATTTATTCA
1177526 ATAACATAAT-TTTAGT
1 ATAA-ATAATCTTTAGT
1177542 ATAAATAATTCTTTAGT
1 ATAAATAA-TCTTTAGT
*
1177559 ATATATAAT
1 ATAAATAAT
1177568 ACATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
16 6 0.26
17 13 0.57
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
ATAAATAATCTTTAGT
Found at i:1177565 original size:2 final size:2
Alignment explanation
Indices: 1177558--1177667 Score: 57
Period size: 2 Copynumber: 53.5 Consensus size: 2
1177548 AATTCTTTAG
* *
1177558 TA TA TA TA -A TA CA TA TA TA TA AA GTA TA TA TA TA -A TA CTA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA -TA
* * *
1177601 TA TA TGA T- TT TA GTA AA TA TA TA TT TCA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* * *
1177643 CTA AA AA TA TA -A AA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA T
1177668 TAACAGACAT
Statistics
Matches: 85, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
1 4 0.05
2 69 0.81
3 12 0.14
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1177576 original size:13 final size:13
Alignment explanation
Indices: 1177558--1177604 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
1177548 AATTCTTTAG
1177558 TATATATAATACA
1 TATATATAATACA
*
1177571 TATATATAA-AGTA
1 TATATATAATA-CA
1177584 TATATATAATAC-
1 TATATATAATACA
1177596 TAGTATATA
1 TA-TATATA
1177605 TGATTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 3 0.10
13 25 0.86
14 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (13 bp):
TATATATAATACA
Found at i:1180836 original size:19 final size:19
Alignment explanation
Indices: 1180812--1180849 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1180802 TTTATTTTTT
*
1180812 GTCTAA-ATTATTTTTTAAA
1 GTCTAACATT-TTTATTAAA
1180831 GTCTAACATTTTTATTAAA
1 GTCTAACATTTTTATTAAA
1180850 ACCCTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (19 bp):
GTCTAACATTTTTATTAAA
Found at i:1181593 original size:2 final size:2
Alignment explanation
Indices: 1181586--1181610 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1181576 TCGAGCCATT
1181586 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
1181611 GTATGTATGT
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:1182506 original size:30 final size:30
Alignment explanation
Indices: 1182472--1182562 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
1182462 GCATTTAACT
1182472 TTTAATTTATACCTAAATAAGCTCTTAATA
1 TTTAATTTATACCTAAATAAGCTCTTAATA
* * * * *
1182502 TTTAATCTATACTTAGATATG-TCCTTAATT
1 TTTAATTTATACCTAAATAAGCT-CTTAATA
* * * *
1182532 TTTAATTTATATCTAAAGAAACCCTTAATA
1 TTTAATTTATACCTAAATAAGCTCTTAATA
1182562 T
1 T
1182563 AAATCAATCT
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
29 1 0.02
30 44 0.98
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.45
Consensus pattern (30 bp):
TTTAATTTATACCTAAATAAGCTCTTAATA
Found at i:1184727 original size:2 final size:2
Alignment explanation
Indices: 1184720--1184747 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1184710 TAACTTAAGC
1184720 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
1184748 GTATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1185065 original size:15 final size:15
Alignment explanation
Indices: 1185033--1185066 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1185023 ATAATTTTAG
* *
1185033 TATATATATTTAATA
1 TATATATATTAAAAA
1185048 TATATATATTAAAAA
1 TATATATATTAAAAA
1185063 TATA
1 TATA
1185067 AAAGAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATTAAAAA
Found at i:1186380 original size:18 final size:16
Alignment explanation
Indices: 1186357--1186400 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
1186347 ATTTTGAATT
1186357 AATAAAATATTATTATAA
1 AATAAAATATT-TTA-AA
*
1186375 AATAAAAAAATTTTAAA
1 AAT-AAAATATTTTAAA
1186392 AATAAAATA
1 AATAAAATA
1186401 AGAGAGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 5 0.22
17 5 0.22
18 6 0.26
19 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAAATATTTTAAA
Found at i:1189956 original size:397 final size:396
Alignment explanation
Indices: 1188148--1192045 Score: 3313
Period size: 397 Copynumber: 10.0 Consensus size: 396
1188138 CAAGTAATTG
** * * * *
1188148 ATACCAACTAGTTGCTAGATATTTATTGGTAGGAAATTGAAAATTAAGACATGACTTGGTGGGTT
1 ATACCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCATGG-GGGTT
* * * *
1188213 TTGGCAACATGGAACACAAAGTTGGTTGGCTAG-TCCTTTG-T-AAGAGAACTAGCAACAGCTCT
65 TTGGCAACATGGAACACAAAGCTGGTTGGCTGGCT-C-TTGATAAAG-GAACTAGCATCAACTCT
* * **
1188275 T-GAGATGACAAGGATACTAAACGTGACTCACAACGAAGAAATTAAATTATTAAAGGAATGAGTA
127 TAG-GATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATTATTAATTGAATGAGTA
** ** **
1188339 ACCAAACACTAAAAAGCCAAGCCAAGCCTATTGACGATGACAATAACATTTATTTTAAGTTTAAA
191 ATTAAACACT-AAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTATTTTAAGTTTAAA
* * * * * * *
1188404 AGTAGTTAAAAAGCTTTGCATC-TTCGACACGTTTGGATTAAATTTTGTGCAAACCATGCCAAAT
255 AGTGGTTAAAAGGCTCTGCATCTTTAG-CACGTTTGGATTAGATTTTGTCCAAATCATGCCAAAT
* * * * * * * *
1188468 GCAAGTATCT-ACCTATATTCGTTCCATGATTATTACGTGGCTACACGTATTGTCTCAATCATCA
319 GCAACTACCTGA-CTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACA
* *
1188532 ATGACAAATAATTC
383 GTGACAAATCATTC
* * ** * **
1188546 ATACCAACTGGTTATTAGATATTTATTGAAAGGAAATTAAAAGTTAAGATTTGGCACTGGGGGTT
1 ATACCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCA-TGGGGGTT
* * * * * * ** *
1188611 TTGGCAACATAGAACACAAGGCTGATTGCCTGGCTCTTAAT-AAGGAAGTAGCATTGACTCTTGG
65 TTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTAG
** * * * *
1188675 GACAACAAGCATACTAAACGAGAATCACAA-GAAGGAAACTGAATTATTAA-TGAAATGAGTAAT
130 GATGACAAGGATACTAAACGTGACTCACAAGGAA-GAAATTGAATTATTAATTG-AATGAGTAAT
* * * *
1188738 TAAACATTAAAAGCCAAGCCAATCCTATTGATGACAATAATAACATTTATTTTAAGTTTAAAAGT
193 TAAACACTAAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTATTTTAAGTTTAAAAGT
* * * *
1188803 GGTTAAAAGGCTCTACATCTTT-GACACTTTTGGATTAGATTTTATCCAAATCATGCCAAATGCT
258 GGTTAAAAGGCTCTGCATCTTTAG-CACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGCA
* * * * * * *
1188867 ATTGCTTGCCTACACTT-GTTCCACGATGATTGCGTGGCTACATGTATTATTTCAATCAACAGTA
322 ACTACCTGACTACA-TTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACAGTG
1188931 ACAAATCATTC
386 ACAAATCATTC
* * **
1188942 ATACCAACTAGTTATTGGATATTTATTGGGAGGAAATTGAAAGTTAAGACATGGCATGAGGAATT
1 ATACCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCATGGGGGTTT
* * * * * ***
1189007 TAGTAACATGGAACATAAGGTTGGTTGGCAAACTCTTGATAAAGGAACTAGCAT-AAGCTCTTAG
66 TGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAA-CTCTTAG
* * * * * * * * *
1189071 AATGACAAAGATACTAAATGTGACTTACGATG-AGGAATTTAATTATTAATTGAATGAATAATTA
130 GATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATTATTAATTGAATGAGTAATTA
* * * * *
1189135 AATACTAGAAGCCAAGCTAAGTCC-ATTGA-CACAACAATAACATTTATTTTAGGTTTAAAAGTG
195 AACACTAAAAGCCAAGCCAAG-CCTATTGATAACAACAATAACATTTATTTTAAGTTTAAAAGTG
* * * * *
1189198 GTTACAAGTCTCTGCAT-TTCAGCACGTTTGGA-T---TTTTATCCAAATCATGCAAAATGCAAC
259 GTTAAAAGGCTCTGCATCTTTAGCACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGCAAC
* * * * * **
1189258 TGCCTGCCTACATTTGTTCCACGATAATTACGTGGCTACACCTATT-TCCTCAATCAACAGTGAC
324 TACCTGACTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGT-CTCAATCAACAGTGAC
*
1189322 AAAACATT-
388 AAATCATTC
1189330 -T----AC-A---A----ATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCATTGGGGGTT
1 ATACCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCA-TGGGGGTT
* * * * *
1189382 TTGGCAACACGAAACATAAAGTTGATTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTAG
65 TTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTAG
* * * * * * * * *
1189447 GATGACTAGGATACTATACCTAACTCATAATGAAGAAATTGAATTGA-TAATAGAATGAGCAATA
130 GATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATT-ATTAATTGAATGAGTAATT
* * *
1189511 AAACATTAAAAGCCAAGCTAAGCCTATTGACAACAACAATAACATTTATTTTAA-TCTTAAAAGT
194 AAACACTAAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTATTTTAAGT-TTAAAAGT
* * *
1189575 GGTTAAAAGTCTCTACATCTTTAGCACATTTGGATTAGATTTT-TACCAAATCATGCCAAATGCA
258 GGTTAAAAGGCTCTGCATCTTTAGCACGTTTGGATTAGATTTTGT-CCAAATCATGCCAAATGCA
* * * * *
1189639 ACTACCTGACTACATTCGTTCTACAATGATTGTGTGGTTACATGTATTGTCCCAATCAACAGTGA
322 ACTACCTGACTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACAGTGA
*
1189704 TAAATCATTC
387 CAAATCATTC
* * **
1189714 ACACCAACTGGTTATTGGATATTTATCAGTAGGAAATTGAAAGTTAA-AGCATGGCATGAGGGGT
1 ATACCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGA-CATGGCATG-GGGGT
* * * * ** * *
1189778 TTTGGCAACATGGAACACAAAGCTGGTTGGCTAGCTCTTGATAAAAGAATTAGTATCAGTTTTTG
64 TTTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTA
* * * *
1189843 GGATTACAAGGATACTAAACGTGACTCACAAGGAAAAAATTGAATTATTCATTGAATAAGTAATT
129 GGATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATTATTAATTGAATGAGTAATT
* * * *
1189908 AGACACTAAAAGCCAAGCCAAGCCCATTGATAAGAATAATAACATTTATTTTAAGTTTCAAAA-T
194 AAACACTAAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTATTTTAAGTTT-AAAAGT
* * * * * * * *
1189972 GGTTAAAAGGATTTGTATCTTTGGCACCTTTGGATTAGATTTTGTCTAAATCAGGCTAAATGCAA
258 GGTTAAAAGGCTCTGCATCTTTAGCACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGCAA
* * * * * * **
1190037 CTGCATGCCTACATTCGTTCCATGATGATTGGGTGCCTACACATATTGTCTCAATCAACAGTGAC
323 CTACCTGACTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACAGTGAC
*
1190102 AAATAATTC
388 AAATCATTC
* * * * * * * *
1190111 ATACTAACT-GATTGTTGGATATTTATTAGTAAGAAATTAAAAGTTAAGACACGACAAGGGGGGT
1 ATACCAACTAG-TTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGC-ATGGGGGT
** *
1190175 TTTGGCAACATGGAACACAAAGCTAATTGGCTGGCTCTTGATAAAGGAACTAACATCAACTCTTA
64 TTTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTA
* * * * * * * * * *
1190240 GGATGATAAAGTTACTTAACGTGACCCACAA-AAAGAAAATTAAATTATTAGTGGAATGAGTAGT
129 GGATGACAAGGATACTAAACGTGACTCACAAGGAAG-AAATTGAATTATTAATTGAATGAGTAAT
* * * * **
1190304 TATACACTAAAAGCCAAGCCAAGCCTACTGATGACAA-TATTTCATTTATTTTAAGTTTAAAAGT
193 TAAACACTAAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTATTTTAAGTTTAAAAGT
* * * * * *
1190368 GATTGAAAGGCTCTGCAT-TTTCG-ACGCATTGG----GA--TT-ACCAAATCATGCAAAATGCA
258 GGTTAAAAGGCTCTGCATCTTTAGCACG-TTTGGATTAGATTTTGTCCAAATCATGCCAAATGCA
* * * * **
1190424 A-TCCCT-ACCTATATTCATTCCACAATGAACG-GATGGCTACATGTATTGTCTCAATCAACAGT
322 ACTACCTGA-CTACATTCGTTCCACGATGATTGCG-TGGCTACATGTATTGTCTCAATCAACAGT
1190486 GACAAATCATTC
385 GACAAATCATTC
** * ** *
1190498 ATACCAACTAGTTGAAAGG-TATTTATTGGTAGGAAATT-AGAAGTTAAAATGTGGCATGAGGGT
1 ATACCAACTAGTT-ATTGGATATTTATTGGTAGGAAATTGA-AAGTTAAGACATGGCATGGGGGT
** * * * * * * * * * *
1190561 TTTGGCAACATAAAACCCAAGGCTAGTTGGCTGGCTCTTAATCAGGGAACTACCATCACCTTTTG
64 TTTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTA
* * * * * *
1190626 GGACGACAAGGATACTAAACGTGACTCACGATGAGGAAATTAAATTATTAATTGAATGACTAATT
129 GGATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATTATTAATTGAATGAGTAATT
* * *
1190691 AAACACT---AG--AAGCCAAGCCTATTAACAACAACAATAACATTTATTTTAAG-TTAAAAATG
194 AAACACTAAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTATTTTAAGTTTAAAAGTG
* * * * * * * * **
1190750 GTTAAAAGGCTTTGTATCTTTGGCACTTTTGGATTAGATTTTATCCAAGTCATGCTATATGCGGC
259 GTTAAAAGGCTCTGCATCTTTAGCACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGCAAC
* * *** ** * *
1190815 TACCTGCCTACATTCGTTCCACGAAGATTTTATACCTATATGTATTGTCTCAATCAATAGTGACA
324 TACCTGACTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACAGTGACA
1190880 AATCATTC
389 AATCATTC
* *
1190888 GTACCAA-TAGGTTGTTGGATATTTATTGGTA-GAAATT-AAAGGTTAAGACATGGCATGGGGGT
1 ATACCAACTA-GTTATTGGATATTTATTGGTAGGAAATTGAAA-GTTAAGACATGGCATGGGGGT
* *
1190950 TTTGGCAACATGGAACAC-AA-----TTGGTTGGCTCTTGATAAGGGAACTAGCATCAACTCTTA
64 TTTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTA
* * * ** ** * * *
1191009 GGATGAGAAGGATACTGAAGGTGACTCATGAGGGGGAAATTGGATTATTAATGGAATAAGTAATT
129 GGATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATTATTAATTGAATGAGTAATT
** * **
1191074 AAACACTAAAAGCCAAAG-CAAGCCTATTGATAATGACAA-AGACATTTATTTTTAGTTGGAAAG
194 AAACACTAAAAGCC-AAGCCAAGCCTATTGATAACAACAATA-ACATTTATTTTAAGTTTAAAAG
* * * * * *
1191137 TGGCTAAAAGGCTCTGCAT-TTTCAGCACGTTCGAATTATATTTTGTCCAAATCATGCCGAGTGC
257 TGGTTAAAAGGCTCTGCATCTTT-AGCACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGC
** ** * * * * *
1191201 AACTGGCT-ACCTACATTTATTCCACGATGATTGGGTGGCTACCTATATTGGCTCAATTAACAGT
321 AACTACCTGA-CTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACAGT
*
1191265 CG-CAAATTATTC
385 -GACAAATCATTC
1191277 A-AGCCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCAT-GGGG--
1 ATA-CCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCATGGGGGTT
* * * *** * *
1191338 CTAGCAACATGAAACACAAAGCCAATTGGCTGGC-CTTGATAAGGGAACTAGCATCAACTTTTAA
65 TTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTT-A
* * * * ** * * * *
1191402 GG-CGACAAGGGTACTAAGCATGACTCATGAGGAGGAAATTAAATTATTAA-TGAAATGAATAAC
129 GGATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATTATTAATTG-AATGAGTAAT
* * *
1191465 TAAGCACTAAAAGCCAAGCCAAGCCAATTGA-AGACAACAATAACATTTATTTTAAGCTTAAAAG
193 TAAACACTAAAAGCCAAGCCAAGCCTATTGATA-ACAACAATAACATTTATTTTAAGTTTAAAAG
* * * * * * *
1191529 TAGTTAAAAGGTTTTGCATCTTCAGCATGTTTGGATTAGATTTTGTCCAAATCATGCTAATTGCA
257 TGGTTAAAAGGCTCTGCATCTTTAGCACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGCA
* * * * * *
1191594 ACTATCTGGCTACATTTGTTCCACAATGATTGTGTGGCTACACGTATTG--TC--T---CA-TGA
322 ACTACCTGACTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACAGTGA
*
1191651 TAAATCATTC
387 CAAATCATTC
* * * * *
1191661 ATACCAATTACTTGTTGGATATTTATTGGTAAGAAATTGAAAGTTAAGACATGGCATGAGAGGTT
1 ATACCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCATG-GGGGTT
* * * * * * * *
1191726 TTGGCAACATGGAACATAATGTTAGTTGGCTGGCTCTTGATGAAGGAAGTAGCATCAACTATTGG
65 TTGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTAG
* * * * * * *
1191791 GATGACAAGGATACTAAATGTAACTCGCGAGG-GGAAAATTGAATCATTAATAGAATGAGTAATT
130 GATGACAAGGATACTAAACGTGACTCACAAGGAAG-AAATTGAATTATTAATTGAATGAGTAATT
* * * * * * *
1191855 AAA-AAT-TAA---AAGCTAAGCCTATTGATGAGAAGAATGACATTTATTTTTAAGTTTAAAAGT
194 AAACACTAAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTA-TTTTAAGTTTAAAAGT
* ** * *
1191915 GGTTAAAAGGCTTTGCATCTTCGGCATGTTTAGATTAGATTTTGTCCAAATCATGCCAAATGCAA
258 GGTTAAAAGGCTCTGCATCTTTAGCACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGCAA
* ** * * ** *
1191980 CTATCT-ACCTACATTTATT-C-CG-TAGATTGCATAGCTACATAAATTGTCTCAATCAATAGTG
323 CTACCTGA-CTACATTCGTTCCACGAT-GATTGCGTGGCTACATGTATTGTCTCAATCAACAGTG
1192041 ACAAA
386 ACAAA
1192046 GTTTGACATT
Statistics
Matches: 2806, Mismatches: 565, Indels: 265
0.77 0.16 0.07
Matches are distributed among these distances:
375 37 0.01
376 82 0.03
377 50 0.02
378 46 0.02
379 14 0.00
380 1 0.00
381 39 0.01
382 26 0.01
383 196 0.07
384 89 0.03
385 95 0.03
386 123 0.04
387 115 0.04
388 97 0.03
389 349 0.12
390 106 0.04
391 16 0.01
392 210 0.07
393 26 0.01
394 48 0.02
395 93 0.03
396 293 0.10
397 559 0.20
398 92 0.03
399 4 0.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (396 bp):
ATACCAACTAGTTATTGGATATTTATTGGTAGGAAATTGAAAGTTAAGACATGGCATGGGGGTTT
TGGCAACATGGAACACAAAGCTGGTTGGCTGGCTCTTGATAAAGGAACTAGCATCAACTCTTAGG
ATGACAAGGATACTAAACGTGACTCACAAGGAAGAAATTGAATTATTAATTGAATGAGTAATTAA
ACACTAAAAGCCAAGCCAAGCCTATTGATAACAACAATAACATTTATTTTAAGTTTAAAAGTGGT
TAAAAGGCTCTGCATCTTTAGCACGTTTGGATTAGATTTTGTCCAAATCATGCCAAATGCAACTA
CCTGACTACATTCGTTCCACGATGATTGCGTGGCTACATGTATTGTCTCAATCAACAGTGACAAA
TCATTC
Found at i:1192114 original size:3 final size:3
Alignment explanation
Indices: 1192101--1192155 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
1192091 TTAGGGGCAA
* *
1192101 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1192148 AAT AAT AA
1 AAT AAT AA
1192156 CTAAAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1192163 original size:15 final size:15
Alignment explanation
Indices: 1192106--1192165 Score: 77
Period size: 15 Copynumber: 4.0 Consensus size: 15
1192096 GGCAAAATAA
*
1192106 AATAATAATAATAAT
1 AATAATAATAAAAAT
**
1192121 AATAATAATAATGAT
1 AATAATAATAAAAAT
1192136 AATAATAATAAAAAT
1 AATAATAATAAAAAT
1192151 AATAACTAA-AAAAAT
1 AATAA-TAATAAAAAT
1192166 GTTGACAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
15 38 0.93
16 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAATAATAAAAAT
Found at i:1193286 original size:2 final size:2
Alignment explanation
Indices: 1193281--1193309 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1193271 TTAAAAAATC
1193281 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
1193310 CACACACAAT
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:1193688 original size:29 final size:29
Alignment explanation
Indices: 1193629--1193688 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1193619 TAGAATTACT
** *
1193629 ATTTAATAATAAAAATATTTTTTACTTAA
1 ATTTAATAATAAAAATATTTAATACTAAA
*
1193658 ATTTAATTATAAAAATATATTAATA-TAAA
1 ATTTAATAATAAAAATAT-TTAATACTAAA
1193687 AT
1 AT
1193689 AATATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTAATAATAAAAATATTTAATACTAAA
Found at i:1194235 original size:10 final size:10
Alignment explanation
Indices: 1194220--1194256 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
1194210 TAGTTATCTA
1194220 ATTTTTATTT
1 ATTTTTATTT
1194230 ATTTTTATTT
1 ATTTTTATTT
*
1194240 ATTTTTATTC
1 ATTTTTATTT
1194250 ATTTTTA
1 ATTTTTA
1194257 CACATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:1194263 original size:20 final size:20
Alignment explanation
Indices: 1194220--1194268 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1194210 TAGTTATCTA
* ***
1194220 ATTTTTATTTATTTTTATTT
1 ATTTTTATTCATTTTTACAC
1194240 ATTTTTATTCATTTTTACAC
1 ATTTTTATTCATTTTTACAC
1194260 ATTTTTATT
1 ATTTTTATT
1194269 AGAAAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTATTCATTTTTACAC
Found at i:1194819 original size:24 final size:24
Alignment explanation
Indices: 1194787--1194835 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1194777 ATGCGACACT
1194787 TGTCTAGTTAACATTTTTTAATGA
1 TGTCTAGTTAACATTTTTTAATGA
1194811 TGTCTAGTTAACATTTTTTAATGA
1 TGTCTAGTTAACATTTTTTAATGA
1194835 T
1 T
1194836 TTTATTAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (24 bp):
TGTCTAGTTAACATTTTTTAATGA
Found at i:1196589 original size:3 final size:3
Alignment explanation
Indices: 1196581--1196631 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1196571 AATTTGTAAA
1196581 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1196629 AAT
1 AAT
1196632 TTAAGATATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1196761 original size:15 final size:15
Alignment explanation
Indices: 1196741--1196781 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1196731 ACTCTTTTAA
1196741 TAATATTTTAAATAT
1 TAATATTTTAAATAT
1196756 TAATATTTTAAA-AT
1 TAATATTTTAAATAT
1196770 TAA-A-TTTAAATA
1 TAATATTTTAAATA
1196782 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.24
13 2 0.08
14 5 0.20
15 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATATTTTAAATAT
Done.