Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 51
Found at i:970674 original size:39 final size:38
Alignment explanation
Indices: 970570--970677 Score: 127
Period size: 33 Copynumber: 2.9 Consensus size: 38
970560 CAAAATCGCA
* *
970570 TTGCGATTTTCATTTCGCGTTGCGA-T-TC---TCTCG
1 TTGCGATTCTCATTTCGCGTTGCGATTGTCATTTCACG
*
970603 TTGCGATTTTCATTTCGCGTTGCGATTGTCATTTCACG
1 TTGCGATTCTCATTTCGCGTTGCGATTGTCATTTCACG
* *
970641 TTGCGATTCTCATTATCTCGTTGCGATTTTCATTTCA
1 TTGCGATTCTCATT-TCGCGTTGCGATTGTCATTTCA
970678 ACCAAAAGAC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
33 25 0.38
34 1 0.02
35 2 0.03
38 17 0.26
39 20 0.31
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (38 bp):
TTGCGATTCTCATTTCGCGTTGCGATTGTCATTTCACG
Found at i:972337 original size:63 final size:63
Alignment explanation
Indices: 972113--972306 Score: 379
Period size: 63 Copynumber: 3.1 Consensus size: 63
972103 GTTACGTGAT
972113 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
*
972176 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTATGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
972239 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
972302 GAGGT
1 GAGGT
972307 GTTTACTTTA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 129 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:972955 original size:21 final size:21
Alignment explanation
Indices: 972931--972997 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
972921 TCATTCCTCG
972931 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
972952 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
972973 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
972994 AGAG
1 AGAG
972998 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:972955 original size:42 final size:42
Alignment explanation
Indices: 972875--972997 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
972865 GCCCGACTCG
* * * * * * *
972875 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
972917 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
972959 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
972998 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 62 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:974825 original size:20 final size:20
Alignment explanation
Indices: 974777--974835 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
974767 AATAGTTTCT
** *
974777 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
974797 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
974817 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
974836 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:975992 original size:13 final size:13
Alignment explanation
Indices: 975974--976022 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
975964 TCATAACCCG
975974 ACCCGACCCGTTT
1 ACCCGACCCGTTT
975987 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
976000 ACCCGACCAGTTG
1 ACCCGACCCGTTT
976013 ACCCGACCCG
1 ACCCGACCCG
976023 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:976023 original size:18 final size:18
Alignment explanation
Indices: 976000--976040 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
975990 CGACCCGTTT
976000 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
*
976018 ACCCGACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
976036 ACCCG
1 ACCCG
976041 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:976033 original size:13 final size:13
Alignment explanation
Indices: 975973--976046 Score: 76
Period size: 13 Copynumber: 5.3 Consensus size: 13
975963 GTCATAACCC
975973 GACCCGACCCGTT
1 GACCCGACCCGTT
*
975986 TACCCGACCCGTT
1 GACCCGACCCGTT
* *
975999 TACCCGACCAGTT
1 GACCCGACCCGTT
976012 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
976030 GACCCGACCCGTT
1 GACCCGACCCGTT
976043 GACC
1 GACC
976047 GTTGACCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.79
18 11 0.21
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:976044 original size:31 final size:31
Alignment explanation
Indices: 975987--976046 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
975977 CGACCCGTTT
*
975987 ACCCGACCCGTTTACCCGACCAGTTGACCCG
1 ACCCGACCCGTTGACCCGACCAGTTGACCCG
*
976018 ACCCGACCCGTTGACCCGACCCGTTGACC
1 ACCCGACCCGTTGACCCGACCAGTTGACC
976047 GTTGACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCAGTTGACCCG
Found at i:976050 original size:7 final size:7
Alignment explanation
Indices: 976038--976068 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
976028 TTGACCCGAC
976038 CCGTTGA
1 CCGTTGA
976045 CCGTTGA
1 CCGTTGA
*
976052 CCTTTGA
1 CCGTTGA
976059 CCGTTGA
1 CCGTTGA
976066 CCG
1 CCG
976069 GAGTTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.32, G:0.26, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:977389 original size:18 final size:18
Alignment explanation
Indices: 977363--977398 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
977353 TCGAAAGGAC
*
977363 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
977381 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
977399 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:978578 original size:23 final size:23
Alignment explanation
Indices: 978552--978625 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
978542 AATTCTATTA
*
978552 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
978575 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
978598 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
978622 TGAT
1 TGAT
978626 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:978613 original size:24 final size:24
Alignment explanation
Indices: 978558--978632 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
978548 ATTATGATCC
978558 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
978581 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
978605 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
978629 TGAC
1 TGAC
978633 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:980838 original size:13 final size:13
Alignment explanation
Indices: 980820--980868 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
980810 TCATAACCCG
980820 ACCCGACCCGTTT
1 ACCCGACCCGTTT
980833 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
980846 ACCCGACCAGTTG
1 ACCCGACCCGTTT
980859 ACCCGACCCG
1 ACCCGACCCG
980869 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:980869 original size:18 final size:18
Alignment explanation
Indices: 980846--980886 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
980836 CGACCCGTTT
980846 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
*
980864 ACCCGACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
980882 ACCCG
1 ACCCG
980887 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:980879 original size:13 final size:13
Alignment explanation
Indices: 980819--980892 Score: 76
Period size: 13 Copynumber: 5.3 Consensus size: 13
980809 GTCATAACCC
980819 GACCCGACCCGTT
1 GACCCGACCCGTT
*
980832 TACCCGACCCGTT
1 GACCCGACCCGTT
* *
980845 TACCCGACCAGTT
1 GACCCGACCCGTT
980858 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
980876 GACCCGACCCGTT
1 GACCCGACCCGTT
980889 GACC
1 GACC
980893 GTTGACCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.79
18 11 0.21
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:980890 original size:31 final size:31
Alignment explanation
Indices: 980833--980892 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
980823 CGACCCGTTT
*
980833 ACCCGACCCGTTTACCCGACCAGTTGACCCG
1 ACCCGACCCGTTGACCCGACCAGTTGACCCG
*
980864 ACCCGACCCGTTGACCCGACCCGTTGACC
1 ACCCGACCCGTTGACCCGACCAGTTGACC
980893 GTTGACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCAGTTGACCCG
Found at i:980896 original size:7 final size:7
Alignment explanation
Indices: 980884--980914 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
980874 TTGACCCGAC
980884 CCGTTGA
1 CCGTTGA
980891 CCGTTGA
1 CCGTTGA
*
980898 CCTTTGA
1 CCGTTGA
980905 CCGTTGA
1 CCGTTGA
980912 CCG
1 CCG
980915 GAGTTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.32, G:0.26, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:982235 original size:18 final size:18
Alignment explanation
Indices: 982209--982244 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
982199 TCGAAAGGAC
*
982209 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
982227 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
982245 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:983424 original size:23 final size:23
Alignment explanation
Indices: 983398--983471 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
983388 AATTCTATTA
*
983398 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
983421 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
983444 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
983468 TGAT
1 TGAT
983472 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:983459 original size:24 final size:24
Alignment explanation
Indices: 983404--983478 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
983394 ATTATGATCC
983404 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
983427 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
983451 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
983475 TGAC
1 TGAC
983479 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:984494 original size:20 final size:20
Alignment explanation
Indices: 984468--984540 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
984458 GATTATGTAT
984468 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
984488 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
984508 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
984528 TATCTCGTTGCGA
1 TATCGCGTTGCGA
984541 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:984585 original size:41 final size:41
Alignment explanation
Indices: 984448--984583 Score: 152
Period size: 41 Copynumber: 3.3 Consensus size: 41
984438 CGCTTTGAAA
*
984448 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
984489 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * *
984529 ATCTCGTTGCGATTTTGTATTATCGCATTGC-AATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAA-AGTCAGT
984570 ATCGCATTGCGATT
1 ATCGCATTGCGATT
984584 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
39 3 0.04
40 33 0.42
41 40 0.51
42 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:993521 original size:13 final size:13
Alignment explanation
Indices: 993499--993532 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
993489 AGGGGGAGTA
*
993499 ATTTTCAAAATTG
1 ATTTTCAAAAATG
993512 A-TTTCAAAAATG
1 ATTTTCAAAAATG
993524 ATTTTCAAA
1 ATTTTCAAA
993533 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:994828 original size:13 final size:14
Alignment explanation
Indices: 994784--994826 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
994774 GAAAACGAGT
994784 AAATA-ATAATAAA
1 AAATAGATAATAAA
994797 AAATAGATAATAAA
1 AAATAGATAATAAA
994811 AAATAGATAATAAA
1 AAATAGATAATAAA
994825 AA
1 AA
994827 TAATATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (14 bp):
AAATAGATAATAAA
Found at i:994920 original size:34 final size:33
Alignment explanation
Indices: 994833--995134 Score: 207
Period size: 35 Copynumber: 8.5 Consensus size: 33
994823 AAAATAATAT
* * *
994833 ACTATATAATATATATTTTAAAAAATTTGTTTTAAA
1 ACTATATATTATATA-TTTCAAAAA--TATTTTAAA
*
994869 ATCTATACATAATATATATTTCAAAAATATTTTCAAA
1 A-CTAT--ATATTATATATTTCAAAAATATTTT-AAA
* * * *
994906 ACCATATATTATATAATTTAAAAAATGTTTTCAA
1 ACTATATATTATAT-ATTTCAAAAATATTTTAAA
*
994940 ACTATATATTATATAGCTTTCAAAAATGTTTTAAA
1 ACTATATATTATATA--TTTCAAAAATATTTTAAA
* *
994975 A-T-TATATTATATGTTTTCAAAAAAATATTTAAA
1 ACTATATATTATAT-ATTTCAAAAATAT-TTTAAA
995008 ACTATATATTATATATGTTTTC-AAAATATTTTAAAA
1 ACTATATATTATATA---TTTCAAAAATATTTT-AAA
** *
995044 ACTATATAATATATATATGTTTTTAAAATGATTTAAAA
1 ACTATAT-AT-TATATA--TTTCAAAAAT-ATTTTAAA
*
995082 ACTATATATTATATATTTTTTC-AAAATGTTTTAAA
1 ACTATATATTATATA---TTTCAAAAATATTTTAAA
995117 CACTATATATATATATAT
1 -ACTATATAT-TATATAT
995135 ATATATATAT
Statistics
Matches: 221, Mismatches: 23, Indels: 46
0.76 0.08 0.16
Matches are distributed among these distances:
32 10 0.05
33 18 0.08
34 26 0.12
35 50 0.23
36 45 0.20
37 29 0.13
38 29 0.13
39 14 0.06
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (33 bp):
ACTATATATTATATATTTCAAAAATATTTTAAA
Found at i:994937 original size:35 final size:35
Alignment explanation
Indices: 994833--995134 Score: 249
Period size: 36 Copynumber: 8.5 Consensus size: 35
994823 AAAATAATAT
*
994833 ACTATATAATATATA-TTTTAAAAAATTTGTTTTAAA
1 ACTATATATTATATATTTTTAAAAAA--TGTTTTAAA
* * * * *
994869 ATCTATACATAATATATATTTCAAAAATATTTTCAAA
1 A-CTATATATTATATATTTTTAAAAAATGTTTT-AAA
* * *
994906 ACCATATATTATATA-ATTTAAAAAATGTTTTCAA
1 ACTATATATTATATATTTTTAAAAAATGTTTTAAA
** *
994940 ACTATATATTATATAGCTTTCAAAAATGTTTTAAA
1 ACTATATATTATATATTTTTAAAAAATGTTTTAAA
* * *
994975 A-T-TATATTATATGTTTTCAAAAAAAT-ATTTAAA
1 ACTATATATTATATATTTT-TAAAAAATGTTTTAAA
* *
995008 ACTATATATTATATATGTTTTCAAAATAT-TTTAAAA
1 ACTATATATTATATAT-TTTT-AAAAAATGTTTTAAA
* *
995044 ACTATATAATATATATATGTTTT-TAAAATGATTTAAAA
1 ACTATAT-AT-TATATAT-TTTTAAAAAATG-TTTTAAA
**
995082 ACTATATATTATATATTTTTTCAAAATGTTTTAAA
1 ACTATATATTATATATTTTTAAAAAATGTTTTAAA
995117 CACTATATATATATATAT
1 -ACTATATAT-TATATAT
995135 ATATATATAT
Statistics
Matches: 219, Mismatches: 31, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
33 19 0.09
34 24 0.11
35 52 0.24
36 64 0.29
37 26 0.12
38 34 0.16
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (35 bp):
ACTATATATTATATATTTTTAAAAAATGTTTTAAA
Found at i:995002 original size:21 final size:20
Alignment explanation
Indices: 994965--995003 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
994955 GCTTTCAAAA
**
994965 ATGTTTTAAAATTATATTAT
1 ATGTTTTAAAAAAATATTAT
994985 ATGTTTTCAAAAAAATATT
1 ATGTTTT-AAAAAAATATT
995004 TAAAACTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
ATGTTTTAAAAAAATATTAT
Found at i:995057 original size:36 final size:36
Alignment explanation
Indices: 994833--995212 Score: 232
Period size: 36 Copynumber: 10.4 Consensus size: 36
994823 AAAATAATAT
** *
994833 ACTATATAATATATAT-TTTAAAAAATTTGTTTTAAAA
1 ACTATATAATATATATGTTTTCAAAA--TATTTTAAAA
* *
994870 TCTATACATAATATATA---TTTCAAAAATATTTTCAAA
1 ACTAT--ATAATATATATGTTTTC-AAAATATTTTAAAA
* * * ** * *
994906 ACCATATATTATATA-ATTTAAAAAATGTTTT-CAA
1 ACTATATAATATATATGTTTTCAAAATATTTTAAAA
* * *
994940 ACTATATATTATATA-GCTTTCAAAA-ATGTTTTAAA
1 ACTATATAATATATATGTTTTCAAAATAT-TTTAAAA
*
994975 A-T-TAT-AT-TATATGTTTTCAAAAAAATATTT-AAA
1 ACTATATAATATATATGTTTTC-AAAATAT-TTTAAAA
*
995008 ACTATATATTATATATGTTTTCAAAATATTTTAAAA
1 ACTATATAATATATATGTTTTCAAAATATTTTAAAA
*
995044 ACTATATAATATATATATGTTTTTAAAATGA-TTTAAAA
1 ACTATAT-A-ATATATATGTTTTCAAAAT-ATTTTAAAA
* * *
995082 ACTATATATTATATATTTTTTCAAAATGTTTTAAACA
1 ACTATATAATATATATGTTTTCAAAATATTTTAAA-A
* * ***
995119 CTATATATATATATATATATATATATTCAAAACGCTTTAAAA
1 --A-CTATATA-ATATATATGT-T-TTCAAAATATTTTAAAA
*
995161 ACTATAT-ATGATATAAGTTTTCAAAATATTTTAAAA
1 ACTATATAAT-ATATATGTTTTCAAAATATTTTAAAA
*
995197 ACTATATTATATATAT
1 ACTATATAATATATAT
995213 ATATATATAT
Statistics
Matches: 273, Mismatches: 42, Indels: 57
0.73 0.11 0.15
Matches are distributed among these distances:
31 4 0.01
32 6 0.02
33 12 0.04
34 41 0.15
35 18 0.07
36 78 0.29
37 25 0.09
38 41 0.15
39 17 0.06
40 7 0.03
41 8 0.03
42 2 0.01
43 14 0.05
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
ACTATATAATATATATGTTTTCAAAATATTTTAAAA
Found at i:995127 original size:2 final size:2
Alignment explanation
Indices: 995120--995144 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
995110 TTTTAAACAC
995120 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
995145 TCAAAACGCT
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:995211 original size:2 final size:2
Alignment explanation
Indices: 995199--995229 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
995189 TTTTAAAAAC
995199 TA TA T- 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 TA TA TA
995230 AACAATTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:996376 original size:84 final size:84
Alignment explanation
Indices: 996004--996379 Score: 425
Period size: 84 Copynumber: 4.5 Consensus size: 84
995994 TGAAATGCGC
* * * * * ** * ** *
996004 TTGAGCTGAATGGAATCGAACTCGAAGGT-ATTTGATGACATATAACCCTTCTTACCTTGAGTTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTA
** *
996068 TGTTGTAAATTGGATGTGCCT
66 TACTGCAAA-T-GATGTGCCT
*
996089 TTGAGCTGAGTGTAATCGAAA-TCGAAGGTCTTTTGTT-GTCAGATAACCCTTATTCGCCTTGAG
1 TTGAGCTGAGTGTAATC-AAACTCGAAGGTCTTTTGTTGGT-AGATAACCCTT-CTCGCCTTGAG
*
996152 CTATACTGCAAATGATGTACCT
63 CTATACTGCAAATGATGTGCCT
* * * * *
996174 TTGAGCCGAGTGTAATCGAACTCGAAGGTCTTTTATTGGAAGATAACCCTTCTCGACTTGAGCTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTA
996239 TACTGCAAATGATGTGCCT
66 TACTGCAAATGATGTGCCT
* *
996258 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAGCCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTA
*
996323 TACTGCAAATTATGTGCCT
66 TACTGCAAATGATGTGCCT
* * * * *
996342 TTAAGCTTAGTGTAATAAAACTCGAATGTATTTTGTTG
1 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTG
996380 AAGGTGCTTT
Statistics
Matches: 250, Mismatches: 35, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
84 142 0.57
85 73 0.29
86 19 0.08
87 16 0.06
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (84 bp):
TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTCGCCTTGAGCTA
TACTGCAAATGATGTGCCT
Found at i:1000089 original size:16 final size:17
Alignment explanation
Indices: 1000068--1000101 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1000058 AATAAAATAT
1000068 TCTACCCCATATG-ATA
1 TCTACCCCATATGCATA
1000084 TCTACCCCATATGCATA
1 TCTACCCCATATGCATA
1000101 T
1 T
1000102 TATTCCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.32
Consensus pattern (17 bp):
TCTACCCCATATGCATA
Found at i:1000973 original size:19 final size:19
Alignment explanation
Indices: 1000949--1000998 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1000939 TAAAAAGATA
1000949 GAAATGTTAAATATGTAAT
1 GAAATGTTAAATATGTAAT
1000968 GAAATGTTAAATATGTAAT
1 GAAATGTTAAATATGTAAT
*
1000987 GAAATGTCAAAT
1 GAAATGTTAAAT
1000999 CAGATTAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (19 bp):
GAAATGTTAAATATGTAAT
Found at i:1001075 original size:28 final size:28
Alignment explanation
Indices: 1001026--1001100 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
1001016 TGCTAAATAT
*
1001026 AAAAATAATAAACGAAACAATAAGATATA-GA
1 AAAAATAATAAA--ATA-AATAAGATA-AGGA
* *
1001057 AAAAATAATAAAATAAATAATATAAGGG
1 AAAAATAATAAAATAAATAAGATAAGGA
1001085 AAAAATAA-AAAATAAA
1 AAAAATAATAAAATAAA
1001101 CGGTAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 9 0.22
28 17 0.43
29 2 0.05
31 12 0.30
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (28 bp):
AAAAATAATAAAATAAATAAGATAAGGA
Found at i:1001091 original size:20 final size:19
Alignment explanation
Indices: 1001066--1001115 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1001056 AAAAAATAAT
*
1001066 AAAATAAATAATATAAGGGA
1 AAAATAAATAATA-AACGGA
* *
1001086 AAAATAAAAAATAAACGGT
1 AAAATAAATAATAAACGGA
1001105 AAAATAAATAA
1 AAAATAAATAA
1001116 ACATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.18
Consensus pattern (19 bp):
AAAATAAATAATAAACGGA
Found at i:1001124 original size:15 final size:16
Alignment explanation
Indices: 1001094--1001127 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1001084 GAAAAATAAA
*
1001094 AAATAAACGGTAAAAT
1 AAATAAACGATAAAAT
1001110 AAATAAAC-ATAAAAT
1 AAATAAACGATAAAAT
1001125 AAA
1 AAA
1001128 AAAATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATAAACGATAAAAT
Found at i:1001131 original size:23 final size:21
Alignment explanation
Indices: 1001105--1001242 Score: 68
Period size: 23 Copynumber: 6.3 Consensus size: 21
1001095 AATAAACGGT
1001105 AAAATAAATAAACATA-AAATAAA
1 AAAATAAATAAA-A-AGAAAT-AA
*
1001128 AAAATGAATAAAAAGAAATAA
1 AAAATAAATAAAAAGAAATAA
* *
1001149 AAAATAAAAGAAAAAGAAAAAGA
1 AAAAT-AAATAAAAAGAAATA-A
* * *
1001172 AAAAGAAA-AAGAA-AAAGAA
1 AAAATAAATAAAAAGAAATAA
* * *
1001191 AAAGAAAAAGAAAAAGAAAAAGA
1 AAA-ATAAATAAAAAGAAATA-A
* *
1001214 AAAAGAAAAGAAAAAGAAA-AA
1 AAAA-TAAATAAAAAGAAATAA
1001235 GAAAATAA
1 -AAAATAA
1001243 GAATAAGAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.04
20 8 0.08
21 19 0.20
22 30 0.32
23 34 0.36
ACGTcount: A:0.81, C:0.01, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAATAAATAAAAAGAAATAA
Found at i:1001141 original size:1 final size:1
Alignment explanation
Indices: 1001137--1001239 Score: 53
Period size: 1 Copynumber: 103.0 Consensus size: 1
1001127 AAAAATGAAT
* * * * * * * * * * *
1001137 AAAAAGAAATAAAAAATAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
1001202 AAAAGAAAAAGAAAAAGAAAAGAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1001240 TAAGAATAAG
Statistics
Matches: 68, Mismatches: 34, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (1 bp):
A
Found at i:1001252 original size:6 final size:6
Alignment explanation
Indices: 1001137--1001239 Score: 167
Period size: 6 Copynumber: 17.7 Consensus size: 6
1001127 AAAAATGAAT
* *
1001137 AAAAAG AAATA- AAAAA- TAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1001183 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1001230 AAAAAG AAAA
1 AAAAAG AAAA
1001240 TAAGAATAAG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
5 13 0.14
6 78 0.86
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:1002360 original size:6 final size:6
Alignment explanation
Indices: 1002351--1002409 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
1002341 AAAAATGAGT
* * *
1002351 AAATAA AAATAA AAATAA TAATAA TAATAA TAAATAGA TAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA -AAATA-A AAATAA AAATAA
*
1002401 ATATAA AAA
1 AAATAA AAA
1002410 ATATAATGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 36 0.80
7 8 0.18
8 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (6 bp):
AAATAA
Found at i:1002372 original size:3 final size:3
Alignment explanation
Indices: 1002352--1002400 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
1002342 AAAATGAGTA
* * *
1002352 AAT AAA AAT AAA AAT AAT AAT AAT AAT AAT AAAT AGAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT AAT
1002399 AA
1 AA
1002401 ATATAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:1002403 original size:24 final size:25
Alignment explanation
Indices: 1002377--1002429 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 25
1002367 AATAATAATA
1002377 ATAATAAATAGATAAT-AAAAATAAAT
1 ATAA-AAA-AGATAATGAAAAATAAAT
*
1002403 ATAAAAAATATAATGAAAAAT-AAT
1 ATAAAAAAGATAATGAAAAATAAAT
1002427 ATA
1 ATA
1002430 CTATATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 12 0.48
25 9 0.36
26 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (25 bp):
ATAAAAAAGATAATGAAAAATAAAT
Found at i:1002416 original size:38 final size:38
Alignment explanation
Indices: 1002352--1002424 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1002342 AAAATGAGTA
*
1002352 AATAAAAATAAAAATAATAATAATAAT-AATAAATAGAT
1 AATAAAAATAAAAATAAAAATAATAATGAA-AAATAGAT
*
1002390 AATAAAAATAAATATAAAAA-ATATAATGAAAAATA
1 AATAAAAATAAAAATAAAAATA-ATAATGAAAAATA
1002425 ATATACTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 1 0.03
38 28 0.90
39 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.25
Consensus pattern (38 bp):
AATAAAAATAAAAATAAAAATAATAATGAAAAATAGAT
Found at i:1002517 original size:34 final size:33
Alignment explanation
Indices: 1002478--1002658 Score: 168
Period size: 35 Copynumber: 5.2 Consensus size: 33
1002468 CTATACATAA
1002478 TATATATTTCAAAAATATTTTCAAAACCATATAT
1 TATATATTTCAAAAATATTTT-AAAACCATATAT
* * *
1002512 TATATAATTTTAAAAATATTTTCAAACTATATAT
1 TATAT-ATTTCAAAAATATTTTAAAACCATATAT
*
1002546 TATATAGTTTTCAAAAATGTTTTAAAA-C-TATAT
1 TATATA--TTTCAAAAATATTTTAAAACCATATAT
* *
1002579 TATATGTTTTCAAAAATGATTTTTTAAAACTATATATT
1 TATAT-ATTTCAAAAAT-A--TTTTAAAACCATATA-T
* * *
1002617 ATATATATTTTTAAAAATATTTTAAAAACATATAA
1 -TATATA-TTTCAAAAATATTTTAAAACCATATAT
1002652 TATATAT
1 TATATAT
1002659 ATATATATTT
Statistics
Matches: 120, Mismatches: 15, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
32 10 0.08
33 12 0.10
34 26 0.22
35 39 0.32
36 13 0.11
37 4 0.03
38 2 0.02
39 14 0.12
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (33 bp):
TATATATTTCAAAAATATTTTAAAACCATATAT
Found at i:1002517 original size:36 final size:35
Alignment explanation
Indices: 1002459--1003105 Score: 499
Period size: 36 Copynumber: 17.9 Consensus size: 35
1002449 TTAAAAATTG
* *
1002459 TTTTAAAAACTATACATAATATATATTTCAAAAATA
1 TTTTAAAAACTATATATTATATATATTTC-AAAATA
* * *
1002495 TTTTCAAAACCATATATTATATA-ATTTTAAAAATA
1 TTTTAAAAACTATATATTATATATA-TTTCAAAATA
*
1002530 TTTT-CAAACTATATATTATATAGT-TTTCAAAA-A
1 TTTTAAAAACTATATATTATATA-TATTTCAAAATA
* *
1002563 TGTTTTAAAAC--TATATTATATGT-TTTCAAAAATGA
1 T-TTTAAAAACTATATATTATATATATTTC-AAAAT-A
* *
1002598 TTTTTTAAAACTATATATTATATATATTTTTAAAAATA
1 -TTTTAAAAACTATATATTATATATA--TTTCAAAATA
*
1002636 TTTTAAAAACATATAATATATATATATATATTTTCAAAATG
1 TTTTAAAAAC---T-ATATAT-TATATATA-TTTCAAAATA
* ** *
1002677 TTATAAAAACTATATATTATATATATTTTTTAAATG
1 TTTTAAAAACTATATATTATATATA-TTTCAAAATA
*
1002713 TTTTAAAAA--ACTATATTATATATA--T--ATATA
1 TTTTAAAAACTA-TATATTATATATATTTCAAAATA
* * *
1002743 -TATATATA-TATATA-TATATAT-TTTCAAAATGA
1 TTTTAAAAACTATATATTATATATATTTCAAAAT-A
*
1002775 -TTTAAAAACTATATATTATATATATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATA-TTTCAAAATA
* *
1002810 TTTTAAAAATTATATATTATATATATATTTTCAAAACA
1 TTTTAAAAACTATATA-T-TATATATA-TTTCAAAATA
* *
1002848 CTTTAAAAAATATATATTATATA-AGTTTTCAAAATA
1 TTTTAAAAACTATATATTATATATA--TTTCAAAATA
* *
1002884 TTTTAAAAACTATATATTATATATATTTTTAAAATG
1 TTTTAAAAACTATATATTATATATA-TTTCAAAATA
1002920 TTTTAAAAAAACTATATATTATATATATATTTTTCAAAATGA
1 TTTT--AAAAACTATATA-T-TATATATA--TTTCAAAAT-A
*
1002962 -TTTAAAAACTATATATTATATATATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATA-TTTCAAAATA
* **
1002997 TTTTAAAAACTATATATTATATAAAATTTTTCAAAACG
1 TTTTAAAAACTATATATTATAT---ATATTTCAAAATA
1003035 TTTTAAAAACTATATATTATATA-AGTTTTCAAAATA
1 TTTTAAAAACTATATATTATATATA--TTTCAAAATA
* *
1003071 TTTTAAAAATTATGTATTATATATATATTTCAAAA
1 TTTTAAAAACTATATA-T-TATATATATTTCAAAA
1003106 AAATCATTTA
Statistics
Matches: 512, Mismatches: 49, Indels: 99
0.78 0.07 0.15
Matches are distributed among these distances:
28 7 0.01
29 10 0.02
30 4 0.01
31 3 0.01
32 12 0.02
33 22 0.04
34 34 0.07
35 40 0.08
36 174 0.34
37 46 0.09
38 83 0.16
39 21 0.04
40 12 0.02
41 36 0.07
42 8 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATATATTTCAAAATA
Found at i:1002622 original size:106 final size:108
Alignment explanation
Indices: 1002429--1003106 Score: 402
Period size: 113 Copynumber: 6.2 Consensus size: 108
1002419 AAAATAATAT
* *
1002429 ACTATATAATATATATTTTTTTAAAAATTGTTTTAAAAACTATACATAATATATATTTCAAAAAT
1 ACTATATAATATATATGTTTTCAAAAATTGTTTTAAAAACTATA-ATAATATATATTTCAAAAAT
*
1002494 ATTTTCAAAACCATATATTATATAATTTTAAAAATATTTT-CAA
65 ATTTTCAAAACCATATATTATATAATTTTAAAAATATTTTAAAA
* * *
1002537 ACTATATATTATATA-GTTTTCAAAAA-TGTTTT-AAAACTAT-ATTATATGT-TTTCAAAAATG
1 ACTATATAATATATATGTTTTCAAAAATTGTTTTAAAAACTATAATAATATATATTTCAAAAAT-
* *
1002597 ATTTTTTAAAACTATATATTATATATATTTTTAAAAATATTTTAAAA
65 A-TTTTCAAAACCATATATTATATA-A-TTTTAAAAATATTTTAAAA
* * * **
1002644 ACATATAATATATATATATATATTTTC-AAAA-TGTTATAAAAACTATATATTATATATATTTTT
1 AC---T-ATATA-ATATATATGTTTTCAAAAATTGTTTTAAAAACTATA-ATAATATATATTTCA
* * * * * * * *
1002707 TAAATGTTTTAAAAAAC-TATATTATAT-A---T--ATATA-TATATAT
60 AAAATATTTTCAAAACCATATATTATATAATTTTAAAAATATTTTAAAA
* * *
1002748 A-TATAT-ATATATATATTTTC-AAAA-TGATTTAAAAACTATATATTATATATATTTTC-AAAA
1 ACTATATAATATATATGTTTTCAAAAATTGTTTTAAAAACTATA-ATAATATATA-TTTCAAAAA
* * ** * * *
1002808 TGTTTTAAAAATTATATATTATATATATATTTTCAAAACACTTTAAAA
64 TATTTTCAAAACCATATA-T-TATATA-ATTTTAAAAATATTTTAAAA
* * * * * **
1002856 AATATATATTATATAAGTTTTC-AAAA-TATTTTAAAAACTATATATTATATATATTTTTAAAAT
1 ACTATATAATATATATGTTTTCAAAAATTGTTTTAAAAACTATA-ATAATATATATTTCAAAAAT
* * * *
1002919 GTTTTAAAAAAACTATATATTATATATATATTTTTCAAAATGA-TTTAAAA
65 ATTTT--CAAAACCATATA-T-TATATA-A-TTTTAAAAAT-ATTTTAAAA
* * * *
1002969 ACTATATATTATATATATTTTC-AAAA-TGTTTTAAAAACTATATATTATATAAAATTTTTC-AA
1 ACTATATAATATATATGTTTTCAAAAATTGTTTTAAAAACTATA-A-TA-AT-ATATATTTCAAA
** * * *
1003031 AACGTTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTAAAA
62 AATATTTTCAAAACCATATATTATATAA-TTTTAAAAATATTTTAAAA
* * * *
1003079 ATTATGTATTATATATATATTTCAAAAA
1 ACTATATAATATATATGT-TTTCAAAAA
1003107 AATCATTTAC
Statistics
Matches: 476, Mismatches: 54, Indels: 76
0.79 0.09 0.13
Matches are distributed among these distances:
97 57 0.12
98 7 0.01
99 5 0.01
100 6 0.01
102 11 0.02
103 8 0.02
104 26 0.05
105 14 0.03
106 21 0.04
107 17 0.04
108 19 0.04
109 9 0.02
110 85 0.18
111 16 0.03
112 42 0.09
113 91 0.19
114 10 0.02
115 19 0.04
116 13 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (108 bp):
ACTATATAATATATATGTTTTCAAAAATTGTTTTAAAAACTATAATAATATATATTTCAAAAATA
TTTTCAAAACCATATATTATATAATTTTAAAAATATTTTAAAA
Found at i:1002734 original size:2 final size:2
Alignment explanation
Indices: 1002724--1002763 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1002714 TTTAAAAAAC
1002724 TA TA T- 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
1002764 TTTCAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1002795 original size:60 final size:60
Alignment explanation
Indices: 1002687--1002799 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 60
1002677 TTATAAAAAC
** *
1002687 TATATATTATATATATTTTTTAAATGTTTTAAAAAACTATATTATATATATATATATATA
1 TATATATTATATATATTTTCAAAATGATTTAAAAAACTATATTATATATATATATATATA
1002747 TATATATATATATATATTTTCAAAATGATTT-AAAAACTATA-TAT-TATATATAT
1 TATATAT-TATATATATTTTCAAAATGATTTAAAAAACTATATTATATATATATAT
1002800 TTTCAAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 9 0.18
59 3 0.06
60 17 0.35
61 20 0.41
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (60 bp):
TATATATTATATATATTTTCAAAATGATTTAAAAAACTATATTATATATATATATATATA
Found at i:1002963 original size:187 final size:190
Alignment explanation
Indices: 1002743--1003105 Score: 617
Period size: 187 Copynumber: 1.9 Consensus size: 190
1002733 TATATATATA
1002743 TATATATATATATATATATATTTTCAAAATGATTTAAAAACTATATATTATATATATTTTCAAAA
1 TATATATATATATATATATATTTTCAAAATGATTTAAAAACTATATATTATATATATTTTCAAAA
* *
1002808 TGTTTTAAAAATTATATATTATAT-ATATATTTTCAAAACACTTTAAAAAATATATATTATATAA
66 TGTTTTAAAAACTATATATTATATAAAAT-TTTTCAAAACACTTTAAAAAATATATATTATATAA
*
1002872 GTTTTCAAAATATTTTAAAAACTATATATTATATATAT-TTTTAAAATGTTTTAAAAAAAC
130 GTTTTCAAAATATTTTAAAAACTATATATTATATATATATTTCAAAATGTTTTAAAAAAAC
1002932 TATATAT-TATATATATAT-TTTTCAAAATGATTTAAAAACTATATATTATATATATTTTCAAAA
1 TATATATATATATATATATATTTTCAAAATGATTTAAAAACTATATATTATATATATTTTCAAAA
** *
1002995 TGTTTTAAAAACTATATATTATATAAAATTTTTCAAAACGTTTTAAAAACTATATATTATATAAG
66 TGTTTTAAAAACTATATATTATATAAAATTTTTCAAAACACTTTAAAAAATATATATTATATAAG
* *
1003060 TTTTCAAAATATTTTAAAAATTATGTATTATATATATATTTCAAAA
131 TTTTCAAAATATTTTAAAAACTATATATTATATATATATTTCAAAA
1003106 AAATCATTTA
Statistics
Matches: 164, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
187 136 0.83
188 21 0.13
189 7 0.04
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (190 bp):
TATATATATATATATATATATTTTCAAAATGATTTAAAAACTATATATTATATATATTTTCAAAA
TGTTTTAAAAACTATATATTATATAAAATTTTTCAAAACACTTTAAAAAATATATATTATATAAG
TTTTCAAAATATTTTAAAAACTATATATTATATATATATTTCAAAATGTTTTAAAAAAAC
Found at i:1003130 original size:74 final size:72
Alignment explanation
Indices: 1002429--1003134 Score: 500
Period size: 74 Copynumber: 9.8 Consensus size: 72
1002419 AAAATAATAT
* * * * *
1002429 ACTATATAATATATATTTTTTTAAAAATTGTTTTAAAAACTATA-CATA-ATATATATTTCAAAA
1 ACTATATATTATATATATTTTCAAAAA--ATTTTAAAAACTATATAATATATATAT-TTTC-AAA
*
1002492 ATATTTTCAAA
62 ATATTTTAAAA
* *
1002503 ACCATATATTATATA-ATTTT-AAAAATATTTT-CAAACTATAT-AT-TATATAGTTTTCAAAA-
1 ACTATATATTATATATATTTTCAAAAA-ATTTTAAAAACTATATAATATATATA-TTTTCAAAAT
*
1002562 ATGTTTTAAA
64 AT-TTTAAAA
* * * *
1002572 AC--TATA-T-TATATGTTTTCAAAAATGATTTTTTAAAACTATATATTATATATATTTTTAAAA
1 ACTATATATTATATATATTTTCAAAAA--A-TTTTAAAAACTATATAATATATATA-TTTTCAAA
1002633 ATATTTTAAAA
62 ATATTTTAAAA
** * * **
1002644 ACATATAATATATATATATATATTTTCAAAATGTTATAAAAACTATATATTATATATATTTTTTA
1 AC---T-ATATAT-TATATATATTTTCAAAAAATTTTAAAAACTATATAATATATATATTTTCAA
*
1002709 AATGTTTTAAAA
61 AATATTTTAAAA
* * * *
1002721 A--ACTATATTATATATA---T----ATA-TATATATA-TATAT-ATATATATATTTTCAAAATG
1 ACTA-TATATTATATATATTTTCAAAAAATTTTAAAAACTATATAATATATATATTTTCAAAAT-
1002774 A-TTTAAAA
64 ATTTTAAAA
** * *
1002782 ACTATATATTATATATATTTTCAAAATGTTTTAAAAATTATATATTATATATATATTTTCAAAAC
1 ACTATATATTATATATATTTTCAAAAAATTTTAAAAACTATATA--ATATATATATTTTCAAAAT
*
1002847 ACTTTAAAA
64 ATTTTAAAA
* * * * *
1002856 AATATATATTATATA-AGTTTTCAAAATATTTTAAAAACTATATATTATATATATTTTTAAAATG
1 ACTATATATTATATATA-TTTTCAAAAAATTTTAAAAACTATATAATATATATATTTTCAAAATA
1002920 TTTTAAAAAA
65 TTTT--AAAA
* *
1002930 ACTATATATTATATATATATTTTTCAAAATGA-TTTAAAAACTATATATTATATATATTTTCAAA
1 ACTATATA-T-TATATATA-TTTTCAAAA-AATTTTAAAAACTATATAATATATATATTTTCAAA
*
1002994 ATGTTTTAAAA
62 ATATTTTAAAA
* ** *
1003005 ACTATATATTATATAAAATTTTTCAAAACGTTTTAAAAACTATATATTATATA-AGTTTTCAAAA
1 ACTATATATTATAT-ATA-TTTTCAAAAAATTTTAAAAACTATATAATATATATA-TTTTCAAAA
1003069 TATTTTAAAA
63 TATTTTAAAA
* * *
1003079 ATTATGTATTATATATATATTTCAAAAAAATCATTTACAAA-T-TATAATATATATAT
1 ACTATATATTATATATAT-TTTC-AAAAAAT--TTTAAAAACTATATAATATATATAT
1003135 ATATATTAGA
Statistics
Matches: 523, Mismatches: 56, Indels: 106
0.76 0.08 0.15
Matches are distributed among these distances:
61 24 0.05
62 18 0.03
63 7 0.01
64 2 0.00
65 5 0.01
66 5 0.01
67 9 0.02
68 4 0.01
69 18 0.03
70 33 0.06
71 21 0.04
72 52 0.10
73 20 0.04
74 169 0.32
75 15 0.03
76 13 0.02
77 65 0.12
78 28 0.05
80 1 0.00
81 14 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (72 bp):
ACTATATATTATATATATTTTCAAAAAATTTTAAAAACTATATAATATATATATTTTCAAAATAT
TTTAAAA
Found at i:1008965 original size:14 final size:14
Alignment explanation
Indices: 1008946--1008982 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1008936 TCAAGAAAAA
1008946 TGAATAGCTAGAGC
1 TGAATAGCTAGAGC
1008960 TGAATAGCTAGAGC
1 TGAATAGCTAGAGC
*
1008974 TGCATAGCT
1 TGAATAGCT
1008983 TAGCTGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (14 bp):
TGAATAGCTAGAGC
Found at i:1015525 original size:32 final size:32
Alignment explanation
Indices: 1015459--1015538 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
1015449 ACATTTAAAA
*
1015459 TATATTTATTAATATTTTTAATAATAAAATAT
1 TATATTTATTAATATTTATAATAATAAAATAT
1015491 TATATTT-TTAATA-TTATAATAA-AATAATCAAT
1 TATATTTATTAATATTTATAATAATAA-AAT--AT
*
1015523 TATATTATAATAATAT
1 TATATT-TATTAATAT
1015539 AAGATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 2 0.05
30 11 0.28
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATAAAATAT
Found at i:1021408 original size:20 final size:20
Alignment explanation
Indices: 1021383--1021420 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1021373 GTCGACACTT
*
1021383 ATTCATGTAGTATCGATATC
1 ATTCATATAGTATCGATATC
*
1021403 ATTCATATAGTATTGATA
1 ATTCATATAGTATCGATA
1021421 CCATAGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTCATATAGTATCGATATC
Found at i:1045637 original size:74 final size:74
Alignment explanation
Indices: 1045516--1045664 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 74
1045506 GTGAAGTATA
* * *
1045516 TCATCGTTTACACAAGCGACAAAACAATTCAAGGACATCATGTCTATTTATTAGCTAGTAAAGTA
1 TCATCGTTTACACAAGCGACAAAACAATTCAAGGACATCATGTCTATTGATTAGCCAATAAAGTA
1045581 AATATATTG
66 AATATATTG
* *
1045590 TCATCGTTTACACAAGCGACAAAACAGTTCAATGACATCATGTCTATTGATTAGCCAATAAAGTA
1 TCATCGTTTACACAAGCGACAAAACAATTCAAGGACATCATGTCTATTGATTAGCCAATAAAGTA
1045655 AATATATTG
66 AATATATTG
1045664 T
1 T
1045665 GACACGGGAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (74 bp):
TCATCGTTTACACAAGCGACAAAACAATTCAAGGACATCATGTCTATTGATTAGCCAATAAAGTA
AATATATTG
Found at i:1050909 original size:2 final size:2
Alignment explanation
Indices: 1050902--1050954 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1050892 ATTTACATGA
1050902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1050944 AT AT AT AT AT A
1 AT AT AT AT AT A
1050955 AATGAATACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1051521 original size:20 final size:20
Alignment explanation
Indices: 1051482--1051522 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1051472 ATTTTAGAGA
*
1051482 AAATTATATGAAATATTATT
1 AAATTATATGAAATACTATT
* *
1051502 AAATTATATTAAGTACTATT
1 AAATTATATGAAATACTATT
1051522 A
1 A
1051523 TTTGAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
AAATTATATGAAATACTATT
Found at i:1051651 original size:18 final size:16
Alignment explanation
Indices: 1051619--1051653 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1051609 AAATTACAAA
1051619 AAATATTATTAAATTT
1 AAATATTATTAAATTT
1051635 AAATATTTATATAAATTT
1 AAATA-TTAT-TAAATTT
1051653 A
1 A
1051654 GAAATGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATATTATTAAATTT
Found at i:1051822 original size:24 final size:22
Alignment explanation
Indices: 1051778--1051843 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
1051768 AAATGAACTT
*
1051778 ATAAAAT-T-TTAAGAAATATAA
1 ATAAAATATATTAA-AAGTATAA
*
1051799 ATAAATTATCGATTAAAAGTATAA
1 ATAAAATAT--ATTAAAAGTATAA
*
1051823 ATAAAATATATTAAATGTATA
1 ATAAAATATATTAAAAGTATA
1051844 CGAATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.16
22 12 0.32
24 15 0.41
25 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (22 bp):
ATAAAATATATTAAAAGTATAA
Found at i:1051842 original size:22 final size:23
Alignment explanation
Indices: 1051794--1051843 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
1051784 TTTTAAGAAA
*
1051794 TATAAATAAATTATCGATTAAAAG
1 TATAAATAAAATATC-ATTAAAAG
*
1051818 TATAAATAAAATAT-ATTAAATG
1 TATAAATAAAATATCATTAAAAG
1051840 TATA
1 TATA
1051844 CGAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
24 13 0.54
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (23 bp):
TATAAATAAAATATCATTAAAAG
Found at i:1055561 original size:18 final size:20
Alignment explanation
Indices: 1055538--1055575 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1055528 ATGGTATTGA
1055538 TACCC-TTA-GTATCGATAC
1 TACCCTTTAGGTATCGATAC
1055556 TACCCTTTAGGTATCGATAC
1 TACCCTTTAGGTATCGATAC
1055576 CCCTTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (20 bp):
TACCCTTTAGGTATCGATAC
Found at i:1055579 original size:18 final size:18
Alignment explanation
Indices: 1055530--1055580 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
1055520 CTTGACATAT
*
1055530 GGTATTGATA-CCC-TTA
1 GGTATCGATACCCCTTTA
1055546 -GTATCGATACTACCCTTTA
1 GGTATCGATAC--CCCTTTA
1055565 GGTATCGATACCCCTT
1 GGTATCGATACCCCTT
1055581 GAATAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 8 0.28
18 8 0.28
19 3 0.10
20 10 0.34
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (18 bp):
GGTATCGATACCCCTTTA
Found at i:1060153 original size:17 final size:17
Alignment explanation
Indices: 1060131--1060173 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1060121 CTCTAGTAAG
*
1060131 CTATTTTGGTATCAATA
1 CTATTTTAGTATCAATA
* *
1060148 CTATTTCAGTATCGATA
1 CTATTTTAGTATCAATA
1060165 CTACTTTTA
1 CTA-TTTTA
1060174 ACAGTAGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (17 bp):
CTATTTTAGTATCAATA
Found at i:1061237 original size:2 final size:2
Alignment explanation
Indices: 1061230--1061256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1061220 ATTTTACCTC
1061230 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
1061257 TCATATGATA
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:1066174 original size:29 final size:29
Alignment explanation
Indices: 1066131--1066213 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1066121 CTCACCTAAC
1066131 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1066161 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1066190 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1066214 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1078888 original size:29 final size:31
Alignment explanation
Indices: 1078855--1078914 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
1078845 ATAAGTGAAT
1078855 TTAAACTTT-TAAAA-TTTCAA-GAGACGAAA
1 TTAAA-TTTATAAAATTTTCAAGGAGACGAAA
*
1078884 TTAAATTTATAAAATTTTGAAGGAGACGAAA
1 TTAAATTTATAAAATTTTCAAGGAGACGAAA
1078915 ATAGATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 3 0.11
29 10 0.37
30 5 0.19
31 9 0.33
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (31 bp):
TTAAATTTATAAAATTTTCAAGGAGACGAAA
Found at i:1080690 original size:308 final size:308
Alignment explanation
Indices: 1080132--1080748 Score: 1108
Period size: 308 Copynumber: 2.0 Consensus size: 308
1080122 ACTTAGCCCC
* *
1080132 GCCATTAACTAATTTATTTGGCATTGGGTTTGCTTCGAATGATTTTTATTTAGTGTTAATGAATG
1 GCCATTAACTAATTTATTTGGCATTGGGTTTGATTCGAATGATTTTTATGTAGTGTTAATGAATG
* **
1080197 GTTAAAGTATTTTTATGTTTAAATGTTGTTTTGCTCATTGTTTATATTTTATTTGCTTAGTCTTT
66 GTTAAAGTATTTTTATATTTAAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTT
1080262 TAAGAGCTTTCGAGGGATAGCCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAG
131 TAAGAGCTTTCGAGGGATAGCCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAG
* *
1080327 ATCGACGTGAGCAAGGGAGTTAAATCGGGATGGTGAGGTTTTAATCTGCCTTAGAAATAAAGAGA
196 ATCGACGTGAGAAAGGGAGTTAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGAGA
1080392 GGGTTTCTGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAA
261 GGGTTTCTGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAA
*
1080440 GCCATTAACTAATTTATTTGGCATTGGGTTTGATTCGAATGATTTTTCTGTAGTGTTAATGAATG
1 GCCATTAACTAATTTATTTGGCATTGGGTTTGATTCGAATGATTTTTATGTAGTGTTAATGAATG
*
1080505 GTTGAAGTATTTTTATATTTAAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTT
66 GTTAAAGTATTTTTATATTTAAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTT
* * *
1080570 TAAGAGCTTTCGAGTGATAGCCATTTTCTAAGTATAGATGCCTAATATCGAGAGATTTAGGCTAG
131 TAAGAGCTTTCGAGGGATAGCCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAG
*
1080635 ATCGACGTGAGAAAGGGAGTTAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGATA
196 ATCGACGTGAGAAAGGGAGTTAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGAGA
*
1080700 GGGTTTCTGTTGAACTATGTTTTATAATATTTTGATATAACAAATTAA
261 GGGTTTCTGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAA
1080748 G
1 G
1080749 GCAAAATGTT
Statistics
Matches: 295, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
308 295 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (308 bp):
GCCATTAACTAATTTATTTGGCATTGGGTTTGATTCGAATGATTTTTATGTAGTGTTAATGAATG
GTTAAAGTATTTTTATATTTAAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTT
TAAGAGCTTTCGAGGGATAGCCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAG
ATCGACGTGAGAAAGGGAGTTAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGAGA
GGGTTTCTGTTGAACCATGTTTTATAATATTTTGATATAACAAATTAA
Found at i:1080839 original size:308 final size:305
Alignment explanation
Indices: 1080217--1080844 Score: 793
Period size: 308 Copynumber: 2.0 Consensus size: 305
1080207 TTTTATGTTT
**
1080217 AAATGTTGTTTTGCTCATTGTTTATATTTTATTTGCTTAGTCTTTTAAGAGCTTTCGAGGGATAG
1 AAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTTTAAGAGCTTTCGAGGGATAG
*
1080282 CCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAGATCGACGTGAGCAAGGGAGT
66 CCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAGATCGACGTGAGAAAGGGAGT
*
1080347 TAAATCGGGATGGTGAGGTTTTAATCTGCCTTAGAAATAAAGAGAGGGTTTCTGTTGAACCATGT
131 TAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGAGAGGGTTTCTGTTGAACCATGT
* * * **
1080412 TTTATAATATTTTGATATAACAAATTAAGCCATTAACTAATTTATTTGGCATTGGGTTTGATTCG
196 TTTATAATATTTTGATATAACAAATTAAGCCA-TAAATAATTTACTTGGAATTGAATTTGATTCG
* *** * * ** * * * * * ***
1080477 AATGATTTTTCTGTAGTGTTAATGAATGGTTGAAGTATTTTTATATTT
260 AAAGA-TTTTCAAAAATATTAA-GAATCATTAAAATAATTTGACACAA
*
1080525 AAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTTTAAGAGCTTTCGAGTGATAG
1 AAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTTTAAGAGCTTTCGAGGGATAG
* *
1080590 CCATTTTCTAAGTATAGATGCCTAATATCGAGAGATTTAGGCTAGATCGACGTGAGAAAGGGAGT
66 CCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAGATCGACGTGAGAAAGGGAGT
* *
1080655 TAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGATAGGGTTTCTGTTGAACTATGT
131 TAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGAGAGGGTTTCTGTTGAACCATGT
* **
1080720 TTTATAATATTTTGATATAACAAATTAAGGCA-AAATGTTTTTGGACTT-GAATTGAATTTG-TT
196 TTTATAATATTTTGATATAACAAATTAAGCCATAAAT-AATTT--ACTTGGAATTGAATTTGATT
*
1080782 C-AAAGA-TTTCAAAAATAATTCAA-AGTCCATTAAAATAAAATTTGAGCACAA
258 CGAAAGATTTTCAAAAAT-ATT-AAGAAT-CATTAAAAT--AATTTGA-CACAA
1080833 AAATGTT-TTTTG
1 AAATGTTGTTTTG
1080845 GGTACGTAGT
Statistics
Matches: 277, Mismatches: 34, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
304 8 0.03
305 7 0.03
306 9 0.03
307 16 0.06
308 234 0.84
309 3 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (305 bp):
AAATGTTGTTTTGCTCATTGTTTATATTTTAAATGCTTAGTCTTTTAAGAGCTTTCGAGGGATAG
CCATTTTCTAACTATAGATGCCTAATATCGAGAGAGTTAGGCTAGATCGACGTGAGAAAGGGAGT
TAAATCGGGATGGTGAGGTTTTAATATGCCTTAGAAATAAAGAGAGGGTTTCTGTTGAACCATGT
TTTATAATATTTTGATATAACAAATTAAGCCATAAATAATTTACTTGGAATTGAATTTGATTCGA
AAGATTTTCAAAAATATTAAGAATCATTAAAATAATTTGACACAA
Found at i:1081155 original size:21 final size:22
Alignment explanation
Indices: 1081119--1081159 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1081109 TCAAATAATA
*
1081119 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
1081141 TAAAGG-AGTACCGATACTC
1 TAAAGGAAGTACCGATACTC
1081160 CCTCTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:1090137 original size:13 final size:13
Alignment explanation
Indices: 1090119--1090143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1090109 ATTACAGGCG
1090119 TGCATATGAAGAC
1 TGCATATGAAGAC
1090132 TGCATATGAAGA
1 TGCATATGAAGA
1090144 TTGTTCAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
TGCATATGAAGAC
Found at i:1095164 original size:19 final size:20
Alignment explanation
Indices: 1095140--1095201 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
1095130 AATTTGACCA
1095140 TTTAGCCGCCCATGCATTG-
1 TTTAGCCGCCCATGCATTGT
1095159 TTTAGCCGCCC---CACTTGT
1 TTTAGCCGCCCATGCA-TTGT
1095177 TTTCAGCCGCCCATGCATTGAT
1 TTT-AGCCGCCCATGCATTG-T
1095199 TTT
1 TTT
1095202 CAACAATCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.06
17 3 0.08
18 3 0.08
19 19 0.53
21 3 0.08
22 6 0.17
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (20 bp):
TTTAGCCGCCCATGCATTGT
Found at i:1102076 original size:18 final size:19
Alignment explanation
Indices: 1102049--1102084 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1102039 AATTCGATCC
1102049 TTTTACATTTTTTTATTTT
1 TTTTACATTTTTTTATTTT
1102068 TTTTA-ATTTTTTTATTT
1 TTTTACATTTTTTTATTT
1102085 CAATAGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTACATTTTTTTATTTT
Found at i:1102112 original size:16 final size:17
Alignment explanation
Indices: 1102091--1102124 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1102081 ATTTCAATAG
1102091 TATATTTATTA-TTATT
1 TATATTTATTATTTATT
*
1102107 TATATTTTTTATTTATT
1 TATATTTATTATTTATT
1102124 T
1 T
1102125 TTTTCGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TATATTTATTATTTATT
Found at i:1112808 original size:12 final size:12
Alignment explanation
Indices: 1112791--1112821 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1112781 TTTCCTAAGT
1112791 CAAAAAAATAGA
1 CAAAAAAATAGA
1112803 CAAAAAAATAGA
1 CAAAAAAATAGA
1112815 -AAAAAAA
1 CAAAAAAA
1112822 GAGAAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (12 bp):
CAAAAAAATAGA
Found at i:1113521 original size:14 final size:14
Alignment explanation
Indices: 1113502--1113528 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1113492 AATCAAAACT
1113502 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
1113516 TCAAGATTCCAGA
1 TCAAGATTCCAGA
1113529 CAGGCAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:1113881 original size:43 final size:41
Alignment explanation
Indices: 1113832--1113951 Score: 159
Period size: 43 Copynumber: 2.9 Consensus size: 41
1113822 ACGGAGGAGT
*
1113832 CATCCACGATTTCAACTCCACGATGGAGAATATCGTACCCA
1 CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCA
* * * *
1113873 CAAATCCACGATTTCAACTCCATGACGGAGGATATCATGCCCA
1 C--ATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCA
* *
1113916 CATCCACGATTTCAACTTCACGATGAAGGATATCGT
1 CATCCACGATTTCAACTCCACGATGGAGGATATCGT
1113952 TCCAACTCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 31 0.46
43 36 0.54
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (41 bp):
CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCA
Found at i:1116089 original size:12 final size:12
Alignment explanation
Indices: 1116053--1116119 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
1116043 TTATAATTTT
1116053 TATTTATTTATTA
1 TATTTA-TTATTA
* *
1116066 T-TTAAATATTA
1 TATTTATTATTA
1116077 TATTTATTATTA
1 TATTTATTATTA
* *
1116089 TCTATATTTAATTA
1 TATTTA-TT-ATTA
*
1116103 TATTTTTTATTA
1 TATTTATTATTA
1116115 TATTT
1 TATTT
1116120 TTTCATTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
11 6 0.14
12 24 0.57
13 5 0.12
14 7 0.17
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTTATTATTA
Found at i:1116120 original size:12 final size:12
Alignment explanation
Indices: 1116072--1116122 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
1116062 ATTATTTAAA
*
1116072 TATTATATTTAT
1 TATTATATTTTT
*
1116084 TATTATCTATATTT
1 TATTA--TATTTTT
*
1116098 AATTATATTTTT
1 TATTATATTTTT
1116110 TATTATATTTTT
1 TATTATATTTTT
1116122 T
1 T
1116123 CATTTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 23 0.72
14 9 0.28
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATATTTTT
Found at i:1116158 original size:10 final size:9
Alignment explanation
Indices: 1116041--1116158 Score: 55
Period size: 10 Copynumber: 12.3 Consensus size: 9
1116031 TCGTTTTACA
*
1116041 TTTTATAAT
1 TTTTATTAT
1116050 TTTTATT-T
1 TTTTATTAT
*
1116058 ATTTATTAT
1 TTTTATTAT
*
1116067 TTAAATATTAT
1 TT--TTATTAT
*
1116078 ATTTATTAT
1 TTTTATTAT
*
1116087 TATCTA-TAT
1 T-TTTATTAT
1116096 TTAATTA-TATT
1 TT--TTATTA-T
1116107 TTTTATTAT
1 TTTTATTAT
1116116 ATTTT-TTCAT
1 -TTTTATT-AT
1116126 TTTTATTCAT
1 TTTTATT-AT
*
1116136 TATTATTACT
1 TTTTATTA-T
1116146 TTTTCATTAT
1 TTTT-ATTAT
1116156 TTT
1 TTT
1116159 AATCTATATA
Statistics
Matches: 85, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
8 8 0.09
9 29 0.34
10 34 0.40
11 14 0.16
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTATTAT
Found at i:1116216 original size:18 final size:17
Alignment explanation
Indices: 1116173--1116217 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1116163 TATATATTTG
1116173 TAAATATATTTTATATC
1 TAAATATATTTTATATC
* *
1116190 TATACTATATTTTATTATT
1 TA-AATATATTTTA-TATC
1116209 TAAATATAT
1 TAAATATAT
1116218 ACTATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.09
18 16 0.70
19 5 0.22
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATATATTTTATATC
Found at i:1116351 original size:15 final size:15
Alignment explanation
Indices: 1116310--1116365 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1116300 TATATACATG
* *
1116310 TTTTTTTCTTTTTCT
1 TTTTTTTATTTTTCA
1116325 TTTTACTTTATTTTTCA
1 TTTT--TTTATTTTTCA
*
1116342 TTTTTTTATTTCAT-A
1 TTTTTTTATTT-TTCA
1116357 TTTTTTTAT
1 TTTTTTTAT
1116366 ATTATTGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 21 0.60
16 1 0.03
17 13 0.37
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTATTTTTCA
Found at i:1120792 original size:24 final size:24
Alignment explanation
Indices: 1120758--1120812 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1120748 ATATTACAAC
* *
1120758 TCACTCTTATAAGACTTTGCTTCT
1 TCACTCATATAAGACTTTACTTCT
1120782 TCACTCATATAAGACTTTACTTCT
1 TCACTCATATAAGACTTTACTTCT
*
1120806 TTACTCA
1 TCACTCA
1120813 CTTAGAAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.44
Consensus pattern (24 bp):
TCACTCATATAAGACTTTACTTCT
Found at i:1120973 original size:11 final size:11
Alignment explanation
Indices: 1120942--1120975 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
1120932 TACCTAACAC
1120942 TCACCTAACTT
1 TCACCTAACTT
1120953 TCATACCTAACTT
1 TC--ACCTAACTT
1120966 TCACCTAACT
1 TCACCTAACT
1120976 AATTTGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (11 bp):
TCACCTAACTT
Found at i:1123292 original size:20 final size:21
Alignment explanation
Indices: 1123253--1123292 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1123243 AGTATGCTCG
1123253 GAGGGAACCGATTCCCCCCCA
1 GAGGGAACCGATTCCCCCCCA
*
1123274 GAGGGTACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
1123293 TGTGTAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.42, G:0.25, T:0.12
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCA
Found at i:1124825 original size:6 final size:6
Alignment explanation
Indices: 1124810--1124841 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1124800 GAGTGATTCG
*
1124810 GATGAA GATGAC GATGAC GATGAC GATGAC GA
1 GATGAC GATGAC GATGAC GATGAC GATGAC GA
1124842 GGAAATGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.34, T:0.16
Consensus pattern (6 bp):
GATGAC
Found at i:1129131 original size:21 final size:21
Alignment explanation
Indices: 1129105--1129144 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1129095 ACCCCTTTGA
*
1129105 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1129126 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1129145 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1140713 original size:11 final size:11
Alignment explanation
Indices: 1140682--1140715 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
1140672 TACCTAACAC
1140682 TCACCTAACTT
1 TCACCTAACTT
1140693 TCATACCTAACTT
1 TC--ACCTAACTT
1140706 TCACCTAACT
1 TCACCTAACT
1140716 AATATGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (11 bp):
TCACCTAACTT
Found at i:1144370 original size:15 final size:15
Alignment explanation
Indices: 1144347--1144376 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1144337 ATGAAAATCT
*
1144347 CTTCTTCTTCTTCAC
1 CTTCATCTTCTTCAC
1144362 CTTCATCTTCTTCAC
1 CTTCATCTTCTTCAC
1144377 TTTCGTGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.40, G:0.00, T:0.50
Consensus pattern (15 bp):
CTTCATCTTCTTCAC
Found at i:1147002 original size:29 final size:29
Alignment explanation
Indices: 1146949--1147025 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
1146939 TAGACGAGCT
* *
1146949 TAATTGAT-TTTTTGACTAAGTTTGAGGGCC
1 TAATTGATCTTTTAGA--AAGTTTGAGGACC
* *
1146979 TAATTGATCTTTTAGAAAGTTTGATGACT
1 TAATTGATCTTTTAGAAAGTTTGAGGACC
* *
1147008 TATTTAATCTTTTAGAAA
1 TAATTGATCTTTTAGAAA
1147026 AATTAAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.65
30 8 0.20
31 6 0.15
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (29 bp):
TAATTGATCTTTTAGAAAGTTTGAGGACC
Found at i:1153010 original size:106 final size:106
Alignment explanation
Indices: 1152820--1153012 Score: 316
Period size: 106 Copynumber: 1.8 Consensus size: 106
1152810 TTATATGTAT
* *
1152820 ACAATAAAGTTGAGCTATTCCTCTAAAGTAATTGGTTAAAACCATTGGCTTTATGGATAGATTCC
1 ACAATAAAGTTGAGCTATTCCGCTAAAGTAATTAGTTAAAACCATTGGCTTTATGGATAGATTCC
*
1152885 TTCAACTAGCCAAATAAAGGCACACACATATATATACACAC
66 TTCAACTAGCCAAAAAAAGGCACACACATATATATACACAC
* *
1152926 ACAATAAATTTGAGCTATTTCGCTAAAGTAATTAGTTAAAAGCC-TTGGCTTTATGGATAGATTC
1 ACAATAAAGTTGAGCTATTCCGCTAAAGTAATTAGTTAAAA-CCATTGGCTTTATGGATAGATTC
*
1152990 CTTCAGCTAGCCAAAAAAAGGCA
65 CTTCAACTAGCCAAAAAAAGGCA
1153013 AATTAAGTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
106 78 0.98
107 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (106 bp):
ACAATAAAGTTGAGCTATTCCGCTAAAGTAATTAGTTAAAACCATTGGCTTTATGGATAGATTCC
TTCAACTAGCCAAAAAAAGGCACACACATATATATACACAC
Found at i:1154744 original size:13 final size:14
Alignment explanation
Indices: 1154687--1154746 Score: 77
Period size: 14 Copynumber: 4.1 Consensus size: 14
1154677 AATAATTAAT
*
1154687 AATAAAAATGAAAA
1 AATAGAAATGAAAA
1154701 AATTA-ATGAATGAAAA
1 AA-TAGA--AATGAAAA
1154717 AATAGAAATGAAAA
1 AATAGAAATGAAAA
1154731 AATAGAAATGAAAA
1 AATAGAAATGAAAA
1154745 AA
1 AA
1154747 ATAAAGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 27 0.64
15 4 0.10
16 11 0.26
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.17
Consensus pattern (14 bp):
AATAGAAATGAAAA
Found at i:1154747 original size:30 final size:29
Alignment explanation
Indices: 1154687--1154751 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1154677 AATAATTAAT
*
1154687 AATAAAAATGAAAAAATTAATGAATGAAAA
1 AATAAAAATGAAAAAATAAATGAA-GAAAA
*
1154717 AATAGAAATGAAAAAATAGAAATG-A-AAAA
1 AATAAAAATGAAAAAAT--AAATGAAGAAAA
1154746 AATAAA
1 AATAAA
1154752 GATAAATCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 9 0.30
30 16 0.53
31 1 0.03
32 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (29 bp):
AATAAAAATGAAAAAATAAATGAAGAAAA
Found at i:1159919 original size:24 final size:24
Alignment explanation
Indices: 1159828--1159912 Score: 111
Period size: 24 Copynumber: 3.5 Consensus size: 24
1159818 TACGATTTGA
* *
1159828 ATTCTGTTATGATACCAT-ACTTGG
1 ATTCTGTTATGATA-CTTGACCTGG
*
1159852 ATTCTGATATGATACTTGACCTGG
1 ATTCTGTTATGATACTTGACCTGG
1159876 ATTCTGATT-TGATACTTGACCTGG
1 ATTCTG-TTATGATACTTGACCTGG
1159900 ATTCTGTTATGAT
1 ATTCTGTTATGAT
1159913 GTATGACTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.07
24 49 0.91
25 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (24 bp):
ATTCTGTTATGATACTTGACCTGG
Found at i:1160145 original size:15 final size:13
Alignment explanation
Indices: 1160117--1160141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1160107 GGTTTTTGAA
1160117 TTTTAAAAATATG
1 TTTTAAAAATATG
1160130 TTTTAAAAATAT
1 TTTTAAAAATAT
1160142 ATGTATCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTTAAAAATATG
Found at i:1166615 original size:20 final size:20
Alignment explanation
Indices: 1166590--1166630 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1166580 TCCAGCAAGC
1166590 CCAGAACAACTGTCCCTCCA
1 CCAGAACAACTGTCCCTCCA
**
1166610 CCAGAACAGTTGTCCCTCCA
1 CCAGAACAACTGTCCCTCCA
1166630 C
1 C
1166631 GTTTCAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (20 bp):
CCAGAACAACTGTCCCTCCA
Found at i:1168268 original size:136 final size:136
Alignment explanation
Indices: 1168003--1168262 Score: 330
Period size: 137 Copynumber: 1.9 Consensus size: 136
1167993 TCATATTTTA
* * *
1168003 AATATTTATTTATTTTTCAATATTAAGAAATGACAGTCTTAAAGCAACTGGATGTCCATTTTCTG
1 AATATTTATTTATTTTTCAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCATTTTCTG
* * * * *
1168068 ATATTTTTAAATAAATAAATATTTTACTTTTATAAATTATATATATTAATCTATTTTTTAATTAT
66 ATATTTCTAAATAAATAAATATCTTAC-TTAATAAATTATATAAATTAATATATTTTTTAATTAT
1168133 TTTTATT
130 TTTTATT
* ** * * *
1168140 AATATTTATTTATTTTTTAATATTAA-AAAAGAGTTGTCTTAAATCACCTAGAAG-CCTTTTTCT
1 AATATTTATTTATTTTTCAATATTAAGAAAAGA-CAGTCTTAAAGCAACTAGAAGTCCATTTTCT
*
1168203 GATATTTCTAAATAAATAAATATCTTA-TTAATATA-TATATAAATTAATATATTTTCTTAA
65 GATATTTCTAAATAAATAAATATCTTACTTAATAAATTATATAAATTAATATATTTT-TTAA
1168263 AATTATAAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
133 18 0.17
134 10 0.09
136 38 0.36
137 40 0.38
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.48
Consensus pattern (136 bp):
AATATTTATTTATTTTTCAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCATTTTCTG
ATATTTCTAAATAAATAAATATCTTACTTAATAAATTATATAAATTAATATATTTTTTAATTATT
TTTATT
Found at i:1178589 original size:72 final size:73
Alignment explanation
Indices: 1178347--1178668 Score: 432
Period size: 73 Copynumber: 4.4 Consensus size: 73
1178337 CTATTTCCAA
* * * * * *
1178347 CATCCGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTTATTTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTTGGGAGCTTTTTGA--TCTT--A
*
1178412 AACCCTCAGGGT
62 AAGCCTCAGGGT
* *
1178424 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGACTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTTGGGAGCTTTTTGATCTTAAAGC
*
1178489 CTCAGAGT
66 CTCAGGGT
* * * * *
1178497 CGTCTGTAAGACCTATAGTGCATGATGTTCTCAAAAAGCCTTTAGAAGC-ATTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTTGGGAGCTTTTTGATCTTAAAGC
1178561 CTCAGGGT
66 CTCAGGGT
1178569 CATCTGTAAGACCTACAGTGCATGATGCTT-TCAAAAAGCCTTTGGGAGCTTTTTGATCTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATG-TTCTCAAAAAGCCTTTGGGAGCTTTTTGATCTTAAAG
1178633 CCTCAGGGT
65 CCTCAGGGT
* *
1178642 CATCTGTAAGCCCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
1178669 ATAAGACTGG
Statistics
Matches: 218, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
72 63 0.29
73 103 0.47
75 3 0.01
77 49 0.22
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTTGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:1178914 original size:113 final size:114
Alignment explanation
Indices: 1178709--1179442 Score: 971
Period size: 113 Copynumber: 6.6 Consensus size: 114
1178699 CCAGAAGAGG
* * ** *
1178709 TCATAATGAGAAGAACTCATCTAAAAAAATAAGAATAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * *
1178774 CTTTTGCTTTAATTCATCACCCAATGGATTAACATTGCCAGAG-AAAGT
66 CTTTTGCTTTAATTCATCACCCGATGGATCAGCATTGCCAGAGTAAAGT
* * * *
1178822 TCATAATAAGAAGAACTTATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*** * *
1178887 CTTTTG-TTTGAATTCATCATTTGATGGATCAGCATTACCAG-GTAGAGT
66 CTTTTGCTTT-AATTCATCACCCGATGGATCAGCATTGCCAGAGTAAAGT
*
1178935 TCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
1179000 CTTTTGCTTTAATTCATCACCCGATGGATTAGCATTGCCAGAGAAAAGT
66 CTTTTGCTTTAATTCATCACCCGATGGATCAGCATTGCCAGAGTAAAGT
* *
1179049 TCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
** * *
1179114 CTTTT-C----A-TCAT---TTGATGGATCAGCATTACCAG-GTAGAGT
66 CTTTTGCTTTAATTCATCACCCGATGGATCAGCATTGCCAGAGTAAAGT
* **
1179153 TCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGCCCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*
1179218 CTTTTGCTTTAATTCATCACCCGATGGATTAGCATTGCCAGAG-AAAGT
66 CTTTTGCTTTAATTCATCACCCGATGGATCAGCATTGCCAGAGTAAAGT
*
1179266 TCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * * * * * *
1179331 CTTTT-TTTTGAATTCATCACTCGATGGATCAACTTTTCTAGAG-AAGTGT
66 CTTTTGCTTT-AATTCATCACCCGATGGATCAGCATTGCCAGAGTAA-AGT
*
1179380 TCATAATGAGAAGAACTCATCTAAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1179443 TTTTTTTTTT
Statistics
Matches: 545, Mismatches: 60, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
104 70 0.13
105 18 0.03
108 4 0.01
109 2 0.00
110 4 0.01
112 7 0.01
113 336 0.62
114 104 0.19
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (114 bp):
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTTGCTTTAATTCATCACCCGATGGATCAGCATTGCCAGAGTAAAGT
Found at i:1179110 original size:20 final size:20
Alignment explanation
Indices: 1179047--1179111 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 20
1179037 CCAGAGAAAA
1179047 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * *
1179067 ATCTGAAGAATGAAGAAGAA---
1 GT-T-CATAATG-AGAAGAACTT
1179087 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1179107 GTTCA
1 GTTCA
1179112 ACCTTTTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 1 0.03
20 7 0.21
21 1 0.03
22 5 0.15
23 7 0.21
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1179204 original size:24 final size:23
Alignment explanation
Indices: 1179161--1179205 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1179151 GTTCATAATG
*
1179161 AGAAGAACTCATATGAAGAAGGA
1 AGAAGAACCCATATGAAGAAGGA
1179184 AGAAGAAGCCCATAATG-AGAAG
1 AGAAGAA-CCCAT-ATGAAGAAG
1179206 AACTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 9 0.47
25 3 0.16
ACGTcount: A:0.51, C:0.11, G:0.27, T:0.11
Consensus pattern (23 bp):
AGAAGAACCCATATGAAGAAGGA
Found at i:1179320 original size:331 final size:335
Alignment explanation
Indices: 1178709--1179442 Score: 993
Period size: 331 Copynumber: 2.2 Consensus size: 335
1178699 CCAGAAGAGG
* *
1178709 TCATAATGAGAAGAACTCATCTAAAAAAAT-AAGAATAAGTTCATAATGAGAAGAACTTGTTCAA
1 TCATAATGAGAAGAACTCATCT-AAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
1178773 CCTTTTGCTTTAATTCATCACCCAATGGATTAACATTGCCAGAGAAAGTTCATAATAAGAAGAAC
65 CCTTTTGC--T-ATTCAT--CCCAATGGATCAACATTACCAGAGAAAGTTCATAATAAGAAGAAC
* * **
1178838 TTATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTTTGTTTGAATTCA
125 TCATATAAAGAAGGAAGAAGAAGCCCATAATGAGAAGAACTTGTCCAACCTTTTGTTTGAATTCA
*** * *
1178903 TCATTTGATGGATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAT
190 TCACCCGATGGATCAGCATTACCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
* *
1178968 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTT-AATTCATCACCCGATGGATTAG
255 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-CTTTGAATTCATCACCCGATGGATCAA
1179032 CATTGCCAGAGAAAAGT
319 CATTGCCAGAGAAAAGT
* *
1179049 TCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*** * * *
1179114 CTTTT-C-A-TCAT-TTGATGGATCAGCATTACCAG-GTAGAGTTCATAATGAGAAGAACTCATA
66 CTTTTGCTATTCATCCCAATGGATCAACATTACCAGAG-AAAGTTCATAATAAGAAGAACTCATA
* *
1179174 TGAAGAAGGAAGAAGAAGCCCATAATGAGAAGAACTTGTTCAACCTTTTGCTTT-AATTCATCAC
130 TAAAGAAGGAAGAAGAAGCCCATAATGAGAAGAACTTGTCCAACCTTTTG-TTTGAATTCATCAC
* * *
1179238 CCGATGGATTAGCATTGCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAG
194 CCGATGGATCAGCATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * *
1179302 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTTTTGAATTCATCACTCGATGGATCAACTTT
258 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCTTTGAATTCATCACCCGATGGATCAACATT
* * **
1179367 TCTAGAGAAGTGT
323 GCCAGAGAAAAGT
1179380 TCATAATGAGAAGAACTCATCTAAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TCATAATGAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1179443 TTTTTTTTTT
Statistics
Matches: 352, Mismatches: 37, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
330 39 0.11
331 238 0.68
332 4 0.01
334 4 0.01
335 1 0.00
339 6 0.02
340 60 0.17
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (335 bp):
TCATAATGAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTTGCTATTCATCCCAATGGATCAACATTACCAGAGAAAGTTCATAATAAGAAGAACTCATAT
AAAGAAGGAAGAAGAAGCCCATAATGAGAAGAACTTGTCCAACCTTTTGTTTGAATTCATCACCC
GATGGATCAGCATTACCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAACTTGTTCAACCTTTTCTTTGAATTCATCACCCGATGGATCAACATTGCC
AGAGAAAAGT
Found at i:1179440 original size:20 final size:19
Alignment explanation
Indices: 1179372--1179441 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
1179362 ACTTTTCTAG
*
1179372 AGAAGTGTTCATAATGAGA
1 AGAACTGTTCATAATGAGA
** *
1179391 AGAACTCATC-TAAAGAAGA
1 AGAACTGTTCATAATG-AGA
**
1179410 AGAAGAAGTTCATAATGAGA
1 AGAA-CTGTTCATAATGAGA
1179430 AGAACTTGTTCA
1 AGAAC-TGTTCA
1179442 ATTTTTTTTT
Statistics
Matches: 36, Mismatches: 11, Indels: 7
0.67 0.20 0.13
Matches are distributed among these distances:
18 4 0.11
19 14 0.39
20 14 0.39
21 4 0.11
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (19 bp):
AGAACTGTTCATAATGAGA
Found at i:1179639 original size:123 final size:123
Alignment explanation
Indices: 1179378--1179698 Score: 430
Period size: 123 Copynumber: 2.6 Consensus size: 123
1179368 CTAGAGAAGT
* * *
1179378 GTTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
** * * * * *
1179443 TTTTTTTTTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCACCAACATTTCCATATGAA
66 ------CCTTTTGCATGACGCTATCACAGAAAGAGATAGATCAACACCAACATTTCCAAAAGAA
* *
1179507 GTTTATAATGAGAAGAGCTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
*
1179572 CCTTTTGC-TCGACGCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAAAA-AGA
66 CCTTTTGCAT-GACGCTATCACAGAAAGAGATAGATCAACACCAACATTTCCAAAAGA-A
*
1179630 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAGGAAGTTCATAATGAGAAGAATTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1179695 CCTT
66 CCTT
1179699 GCCTTAATTT
Statistics
Matches: 174, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
122 2 0.01
123 112 0.64
129 60 0.34
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (123 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
CCTTTTGCATGACGCTATCACAGAAAGAGATAGATCAACACCAACATTTCCAAAAGAA
Found at i:1180319 original size:14 final size:15
Alignment explanation
Indices: 1180285--1180319 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1180275 TATTTTTTTT
1180285 GAAATAAAAAAATCA
1 GAAATAAAAAAATCA
*
1180300 GTAATAAAAAAAT-A
1 GAAATAAAAAAATCA
1180314 GAAATA
1 GAAATA
1180320 TAAAGGAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (15 bp):
GAAATAAAAAAATCA
Found at i:1185112 original size:24 final size:27
Alignment explanation
Indices: 1185083--1185142 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
1185073 TATTTTTCAT
1185083 ATTTTGGCCT-TTTT-T-CTTTCTTTC
1 ATTTTGGCCTCTTTTCTCCTTTCTTTC
1185107 ATTTTGGCCTCCTTTTCTCCTTTCTTTC
1 ATTTTGGCCT-CTTTTCTCCTTTCTTTC
1185135 ATTTTGGC
1 ATTTTGGC
1185143 TCAATCATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 10 0.31
26 4 0.12
27 1 0.03
28 17 0.53
ACGTcount: A:0.05, C:0.25, G:0.10, T:0.60
Consensus pattern (27 bp):
ATTTTGGCCTCTTTTCTCCTTTCTTTC
Found at i:1186056 original size:130 final size:131
Alignment explanation
Indices: 1185811--1186179 Score: 497
Period size: 130 Copynumber: 2.8 Consensus size: 131
1185801 AATAATTTTA
* * * * *
1185811 AGAGAGAAAATGATAATATCTAATTATTTCCGATCGAGAATAAATGACCTCTCATGCCTTAAAGC
1 AGAGAGAAAACGATAATATCTAATGATTTCCAATTGAGAATAAATGACCTCTCATACCTTAAAGC
* * * * *
1185876 AGTCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCTTCTTAAAATTCAATATCGAT
66 AATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATCGAT
1185941 T
131 T
* * * * * *
1185942 CGAGTGAAAAC-ATAATATCTAATGATTTCCAATTGAGAATAAATGATCTTTTATACCTTAAAAC
1 AGAGAGAAAACGATAATATCTAATGATTTCCAATTGAGAATAAATGACCTCTCATACCTTAAAGC
* * *
1186006 AATCATTTATTGCTCCAATCGAAATGAAGAGATATCATTATTCCGTCTTAAAAATCAATATTGAT
66 AATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATCGAT
1186071 T
131 T
* *
1186072 AGAGAGAAAACGATAATATCTAATGATTTCCAACTGAAAATAAATGACCTCTCATACCTTAAAGC
1 AGAGAGAAAACGATAATATCTAATGATTTCCAATTGAGAATAAATGACCTCTCATACCTTAAAGC
* * * * *
1186137 ATTCATTTATTACTCCAACCGAAATGAAAATATATTACTATTC
66 AATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTC
1186180 TCAATATCGA
Statistics
Matches: 203, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
130 112 0.55
131 91 0.45
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (131 bp):
AGAGAGAAAACGATAATATCTAATGATTTCCAATTGAGAATAAATGACCTCTCATACCTTAAAGC
AATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATCGAT
T
Found at i:1187256 original size:108 final size:106
Alignment explanation
Indices: 1187067--1187262 Score: 302
Period size: 108 Copynumber: 1.8 Consensus size: 106
1187057 AAATAACCCT
* * *
1187067 AAAAATATATAACATGCATAAAAGTGGTATATTACAAAATTGGTCCCTATATGTGACTATTTTGC
1 AAAAATATATAACATGCATAAAAATGGTAAATTACAAAATCGGTCCCTATATGTGACTATTTTGC
****
1187132 AAAAACACGTGTAAGTTAGGGGATTAAATAACAATTACACC
66 AAAAACACACACAAGTTAGGGGATTAAATAACAATTACACC
*
1187173 AAAAATTTATAACATGCATAAGAAATGAGTAAATTACAAAATCGGTCCCTATATGTGACTATTTT
1 AAAAATATATAACATGCATAA-AAATG-GTAAATTACAAAATCGGTCCCTATATGTGACTATTTT
1187238 GCAAAAACACACACAAGTTAGGGGA
64 GCAAAAACACACACAAGTTAGGGGA
1187263 CGTAAGCGTA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 20 0.25
107 4 0.05
108 56 0.70
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (106 bp):
AAAAATATATAACATGCATAAAAATGGTAAATTACAAAATCGGTCCCTATATGTGACTATTTTGC
AAAAACACACACAAGTTAGGGGATTAAATAACAATTACACC
Found at i:1188330 original size:3 final size:3
Alignment explanation
Indices: 1188317--1188349 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1188307 TGCACAAAGA
*
1188317 AAT AGT AAT AAT AAT AAT AAT -AT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1188350 GCGGGACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1188698 original size:31 final size:30
Alignment explanation
Indices: 1188663--1188744 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
1188653 TCATGGATTG
**
1188663 AATTGATATTTTATCTAAATATCAAGGGTTA
1 AATTGATATTTTATCTAAAT-TCAAGGGCCA
1188694 AATTGATATTTTATCTAAAGTTC-AGGGCCA
1 AATTGATATTTTATCTAAA-TTCAAGGGCCA
* *
1188724 AATTAATATGTTATCTAAATT
1 AATTGATATTTTATCTAAATT
1188745 TCAATGATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 2 0.04
30 22 0.48
31 21 0.46
32 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (30 bp):
AATTGATATTTTATCTAAATTCAAGGGCCA
Found at i:1189569 original size:10 final size:10
Alignment explanation
Indices: 1189554--1189593 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1189544 TTTATCACAC
1189554 CAAATTCTCT
1 CAAATTCTCT
1189564 CAAATTCTCT
1 CAAATTCTCT
1189574 -AAATTTCTCT
1 CAAA-TTCTCT
*
1189584 CAAATACTCT
1 CAAATTCTCT
1189594 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1189918 original size:106 final size:108
Alignment explanation
Indices: 1189763--1190047 Score: 493
Period size: 106 Copynumber: 2.6 Consensus size: 108
1189753 TATCATTTTA
*
1189763 ATTTAATTTAAATTATTAGTAATATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAAT
1 ATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAAT
*
1189828 TAAATATATCGACACTTTGCTGATACGGTAACATTTTAACG-T
66 TAAATATATCGACACTTTGCTAATACGGTAACATTTTAACGTT
1189870 -TTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAAT
1 ATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAAT
*
1189934 TAAATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTT
66 TAAATATATCGACACTTTGCTAATACGGTAACATTTTAACG--TT
*
1189979 AATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAA
1 -ATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAA
1190044 TTAA
65 TTAA
1190048 TTTTTGTAAT
Statistics
Matches: 169, Mismatches: 4, Indels: 6
0.94 0.02 0.03
Matches are distributed among these distances:
106 102 0.60
109 1 0.01
111 66 0.39
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.45
Consensus pattern (108 bp):
ATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAAT
TAAATATATCGACACTTTGCTAATACGGTAACATTTTAACGTT
Found at i:1195888 original size:48 final size:48
Alignment explanation
Indices: 1195790--1195889 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 48
1195780 ATCAGGGGGC
* * * *
1195790 GCGCTATACCTACGTGGCGCCAGATCACCGTATATCGCGGGGCAGGGG
1 GCGCTATACCCACGTGACGCCAAATCACCGTATATCGCGGGGCAGAGG
* **
1195838 GCGCTATACCCACGTGACGCCAAATCAGCGTATAGT-GCGGTTCAGAGG
1 GCGCTATACCCACGTGACGCCAAATCACCGTATA-TCGCGGGGCAGAGG
1195886 GCGC
1 GCGC
1195890 GCTTTACAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 43 0.98
49 1 0.02
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (48 bp):
GCGCTATACCCACGTGACGCCAAATCACCGTATATCGCGGGGCAGAGG
Found at i:1196283 original size:32 final size:32
Alignment explanation
Indices: 1196247--1196310 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
1196237 ATTAAAGTAT
*
1196247 TATTTTTATAATTTTATT-AATAAAAATATTAA
1 TATTTGTAT-ATTTTATTAAATAAAAATATTAA
*
1196279 TATTTGTATATTTTATTGAAATAAAAGTATTA
1 TATTTGTATATTTTATT-AAATAAAAATATTA
1196311 TAAATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 8 0.29
32 8 0.29
33 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (32 bp):
TATTTGTATATTTTATTAAATAAAAATATTAA
Found at i:1196388 original size:18 final size:17
Alignment explanation
Indices: 1196345--1196394 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 17
1196335 AGTAATACTG
1196345 TTATATTA-TATTATAT
1 TTATATTATTATTATAT
**
1196361 TT-TAAAATTATTATAT
1 TTATATTATTATTATAT
*
1196377 CTTATATTATTATAATAT
1 -TTATATTATTATTATAT
1196395 AATTTATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 2 0.08
18 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTATTATTATAT
Found at i:1196428 original size:32 final size:34
Alignment explanation
Indices: 1196390--1196464 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 34
1196380 ATATTATTAT
* *
1196390 AATATAATTTATTATTTTGTTAT-AACATTAA-A
1 AATATAATTTATTATATTATTATAAACATTAATA
*
1196422 AATATAA--TATTATATTATTATAAATATTAATA
1 AATATAATTTATTATATTATTATAAACATTAATA
*
1196454 AATATATTTTA
1 AATATAATTTA
1196465 AATATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 12 0.34
31 7 0.20
32 14 0.40
34 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
AATATAATTTATTATATTATTATAAACATTAATA
Found at i:1196441 original size:22 final size:24
Alignment explanation
Indices: 1196416--1196477 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
1196406 TTGTTATAAC
*
1196416 ATTAAAAATA-TAAT-ATTATATT
1 ATTAAAAATATTAATAAATATATT
*
1196438 ATTATAAATATTAATAAATATATT
1 ATTAAAAATATTAATAAATATATT
* *
1196462 -TTAAATATTTTAATAA
1 ATTAAAAATATTAATAA
1196478 TTAATAGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 9 0.27
23 17 0.52
24 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAAAAATATTAATAAATATATT
Found at i:1197496 original size:2 final size:2
Alignment explanation
Indices: 1197437--1197477 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1197427 TAATTTTTTA
1197437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1197478 CATTGTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1198506 original size:19 final size:18
Alignment explanation
Indices: 1198482--1198524 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1198472 CTATTTAATT
1198482 CAACTCAAATTAAATTTTA
1 CAACTC-AATTAAATTTTA
* **
1198501 CAACTCGATTTTATTTTA
1 CAACTCAATTAAATTTTA
1198519 CAACTC
1 CAACTC
1198525 GATTTGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (18 bp):
CAACTCAATTAAATTTTA
Found at i:1198518 original size:18 final size:18
Alignment explanation
Indices: 1198495--1198534 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1198485 CTCAAATTAA
*
1198495 ATTTTACAACTCGATTTT
1 ATTTTACAACTCGATTTG
1198513 ATTTTACAACTCGATTTG
1 ATTTTACAACTCGATTTG
1198531 ATTT
1 ATTT
1198535 GAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTTTACAACTCGATTTG
Found at i:1204941 original size:21 final size:21
Alignment explanation
Indices: 1204917--1204961 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1204907 ATTCTGACTA
1204917 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1204938 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1204959 TCG
1 TCG
1204962 TAATGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Done.