Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 13 of 18
Found at i:2184709 original size:19 final size:19
Alignment explanation
Indices: 2184653--2184715 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2184643 TGGTTGTCGA
**
2184653 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
2184672 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2184691 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2184710 GTTACT
1 GGTACT
2184716 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2188847 original size:34 final size:34
Alignment explanation
Indices: 2188781--2188965 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
2188771 AAGTGGGAGA
* *
2188781 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2188814 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2188848 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2188882 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2188916 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2188950 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2188966 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2188956 original size:102 final size:101
Alignment explanation
Indices: 2188781--2188965 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
2188771 AAGTGGGAGA
2188781 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
2188846 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2188882 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
2188947 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
2188966 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2189397 original size:2 final size:2
Alignment explanation
Indices: 2189390--2189415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2189380 TTATCGATAC
2189390 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
2189416 GAAAATGATC
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):
AT
Found at i:2190260 original size:34 final size:34
Alignment explanation
Indices: 2190214--2190398 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
2190204 GTAAAAACCA
*
2190214 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2190248 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2190282 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2190316 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2190350 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2190383 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2190399 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2194491 original size:19 final size:19
Alignment explanation
Indices: 2194464--2194507 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2194454 TCACGTGTAC
* *
2194464 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2194483 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
2194502 AGTACC
1 AGTACC
2194508 TCGACAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2197455 original size:30 final size:29
Alignment explanation
Indices: 2197421--2197484 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
2197411 ATTGCAGTTG
2197421 AATAAA-TTCTAAATATTTAATTTACATTCA
1 AATAAACTTC-AAAT-TTTAATTTACATTCA
* *
2197451 AATAAAACTTCAACTTTTAATTTATATTCA
1 AAT-AAACTTCAAATTTTAATTTACATTCA
2197481 AATA
1 AATA
2197485 TATAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 1 0.03
30 20 0.67
31 6 0.20
32 3 0.10
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAAACTTCAAATTTTAATTTACATTCA
Found at i:2198013 original size:15 final size:12
Alignment explanation
Indices: 2197976--2198043 Score: 61
Period size: 12 Copynumber: 5.9 Consensus size: 12
2197966 AATTTAAAAG
*
2197976 TTTATTTTATTA
1 TTTATTATATTA
2197988 TTTATTATATTA
1 TTTATTATATTA
*
2198000 TTTATTATACTA
1 TTTATTATATTA
**
2198012 -TTAAAATATT-
1 TTTATTATATTA
* *
2198022 TTTATTTTAATA
1 TTTATTATATTA
2198034 TTTA-TATATT
1 TTTATTATATT
2198044 TTATAATTAA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
11 17 0.40
12 26 0.60
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:2198025 original size:22 final size:22
Alignment explanation
Indices: 2197994--2198045 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2197984 ATTATTTATT
*
2197994 ATATTATTTATTATACTATTAAA
1 ATATT-TTTATTATAATATTAAA
* * *
2198017 ATATTTTTATTTTAATATTTAT
1 ATATTTTTATTATAATATTAAA
2198039 ATATTTT
1 ATATTTT
2198046 ATAATTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTTTTATTATAATATTAAA
Found at i:2201794 original size:2 final size:2
Alignment explanation
Indices: 2201787--2201818 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2201777 GAATTGATTG
*
2201787 AT AT AT AT AT AG 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
2201819 CTGTGAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2202904 original size:2 final size:2
Alignment explanation
Indices: 2202897--2202929 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2202887 ACCCACACTA
2202897 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2202930 TGAAGATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2203309 original size:2 final size:2
Alignment explanation
Indices: 2203302--2203336 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2203292 GAATTAAGTG
*
2203302 TA TA TA TA TA TA CA 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 T
2203337 CTATGCCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2210346 original size:2 final size:2
Alignment explanation
Indices: 2210294--2210332 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2210284 TTCAGATCGA
*
2210294 TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2210333 TCTTTTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2210737 original size:22 final size:21
Alignment explanation
Indices: 2210725--2210767 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2210715 TAATTTAATT
2210725 TTTTTATTTAATTAAATTATA
1 TTTTTATTTAATTAAATTATA
*
2210746 TTTTTATTTAAATTTAATTATA
1 TTTTTATTT-AATTAAATTATA
2210768 AAATATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTATTTAATTAAATTATA
Found at i:2210902 original size:18 final size:17
Alignment explanation
Indices: 2210874--2210913 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2210864 TTATGTTAAT
2210874 AATTTATAATTATATAA
1 AATTTATAATTATATAA
* *
2210891 AATTTAATAATTTTATAT
1 AATTT-ATAATTATATAA
2210909 AATTT
1 AATTT
2210914 TATTTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTATAATTATATAA
Found at i:2210910 original size:10 final size:10
Alignment explanation
Indices: 2210850--2210916 Score: 51
Period size: 10 Copynumber: 7.5 Consensus size: 10
2210840 ATATTTTAAA
2210850 TTTATATAAT
1 TTTATATAAT
2210860 TTTAT-T-AT
1 TTTATATAAT
*
2210868 GTTA-ATAA-
1 TTTATATAAT
2210876 -TT-TATAAT
1 TTTATATAAT
* *
2210884 TATATA-AAA
1 TTTATATAAT
2210893 TTTA-ATAAT
1 TTTATATAAT
2210902 TTTATATAAT
1 TTTATATAAT
2210912 TTTAT
1 TTTAT
2210917 TTAACTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 16
0.68 0.08 0.25
Matches are distributed among these distances:
7 6 0.14
8 7 0.16
9 14 0.32
10 17 0.39
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (10 bp):
TTTATATAAT
Found at i:2210983 original size:3 final size:3
Alignment explanation
Indices: 2210975--2211005 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2210965 TCATATTTAT
2210975 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2211006 TGTGTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2211257 original size:2 final size:2
Alignment explanation
Indices: 2211250--2211279 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2211240 TTTAAATTTA
2211250 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2211280 TATCAAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2213976 original size:2 final size:2
Alignment explanation
Indices: 2213969--2214035 Score: 91
Period size: 2 Copynumber: 33.5 Consensus size: 2
2213959 TCCAAAAAGC
* * *
2213969 TA TA TA TA TA TA TA TA TA TA TG GA -A TC TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2214010 TA TA TA TA TA CTA TA TA TA TA TA TA T
1 TA TA TA TA TA -TA TA TA TA TA TA TA T
2214036 GGAATCTTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2214004 original size:25 final size:25
Alignment explanation
Indices: 2213971--2214042 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
2213961 CAAAAAGCTA
2213971 TATATATATATATATATATGGAATC
1 TATATATATATATATATATGGAATC
2213996 TATATATATATATATATAT---A--
1 TATATATATATATATATATGGAATC
2214016 TATACTATATATATATATATGGAATC
1 TATA-TATATATATATATATGGAATC
2214042 T
1 T
2214043 TAGGATCGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.10
21 15 0.37
22 1 0.02
24 1 0.02
25 19 0.46
26 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (25 bp):
TATATATATATATATATATGGAATC
Found at i:2214006 original size:27 final size:25
Alignment explanation
Indices: 2213968--2214035 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 25
2213958 CTCCAAAAAG
2213968 CTATATATATATATATATATATGGA-A
1 CTATATATATATATATATATAT--ATA
2213994 TCTATATATATATATATATATATATA
1 -CTATATATATATATATATATATATA
2214020 CTATATATATATATAT
1 CTATATATATATATAT
2214036 GGAATCTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
25 17 0.43
26 1 0.03
27 22 0.55
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (25 bp):
CTATATATATATATATATATATATA
Found at i:2214747 original size:2 final size:2
Alignment explanation
Indices: 2214740--2214772 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2214730 GATTTGGTTG
2214740 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 A
2214773 CACACTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2215738 original size:24 final size:24
Alignment explanation
Indices: 2215702--2215760 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2215692 TTATTTTATT
2215702 ATTTATA-ATAATATAAAAAATTAA
1 ATTTATATA-AATATAAAAAATTAA
* ** *
2215726 TTTTATATAAATATTTATAATTAA
1 ATTTATATAAATATAAAAAATTAA
2215750 ATTTATATAAA
1 ATTTATATAAA
2215761 AAATTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTTATATAAATATAAAAAATTAA
Found at i:2215768 original size:26 final size:25
Alignment explanation
Indices: 2215720--2215778 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
2215710 TAATATAAAA
* *
2215720 AATTAATTTTATATAAATATTTA-T
1 AATTAAATTTATATAAAAATTTATT
2215744 AATTAAATTTATATAAAAAATTTTATT
1 AATTAAATTTATAT-AAAAA-TTTATT
*
2215771 ATTTAAAT
1 AATTAAAT
2215779 AATAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.45
25 4 0.14
26 4 0.14
27 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTAAATTTATATAAAAATTTATT
Found at i:2216395 original size:2 final size:2
Alignment explanation
Indices: 2216388--2216424 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2216378 TTTAGGTGAA
2216388 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 A
2216425 GTTACCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2218757 original size:56 final size:56
Alignment explanation
Indices: 2218689--2218794 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 56
2218679 TAACTTATTC
* *
2218689 AGTATTGTCATCTAAACAATAATAAAATATTTTGAAA-TATAAAAGTGACACCATTA
1 AGTATTATCATCTAAACAATAATAAAATAATTT-AAATTATAAAAGTGACACCATTA
* **
2218745 AGTATTATCATCTAAATAATAATAGGATAATTTAAATTATAAAAGTGACA
1 AGTATTATCATCTAAACAATAATAAAATAATTTAAATTATAAAAGTGACA
2218795 TCGTATAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
55 3 0.07
56 41 0.93
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.33
Consensus pattern (56 bp):
AGTATTATCATCTAAACAATAATAAAATAATTTAAATTATAAAAGTGACACCATTA
Found at i:2229292 original size:2 final size:2
Alignment explanation
Indices: 2229279--2229310 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2229269 AACGATGGGG
*
2229279 GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2229311 AGCTTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2230190 original size:17 final size:17
Alignment explanation
Indices: 2230159--2230201 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2230149 TTATTATATT
*
2230159 ATAAAAT-ATATAAATA
1 ATAAAATAAAATAAATA
* *
2230175 TTAATATAAAATAAATA
1 ATAAAATAAAATAAATA
2230192 ATAAAATAAA
1 ATAAAATAAA
2230202 TCAAGCTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAATAAAATAAATA
Found at i:2230892 original size:13 final size:11
Alignment explanation
Indices: 2230849--2230917 Score: 59
Period size: 13 Copynumber: 5.7 Consensus size: 11
2230839 AAATAATTTA
*
2230849 AAATATGATAT
1 AAATATAATAT
2230860 AATGATATAATAT
1 AA--ATATAATAT
2230873 AAATATAATAT
1 AAATATAATAT
2230884 AAAATTATAATATTTT
1 -AAA-TATAATA---T
2230900 AAATATAATA-
1 AAATATAATAT
2230910 AAATATAA
1 AAATATAA
2230918 AAAATAATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
10 8 0.16
11 11 0.22
12 3 0.06
13 17 0.34
14 7 0.14
15 3 0.06
16 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAATATAATAT
Found at i:2230983 original size:29 final size:29
Alignment explanation
Indices: 2230929--2231007 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
2230919 AAATAATGAT
* *
2230929 ATTATATTA-ACA-TATAAATTTGTTAAA
1 ATTATATTATAAATTATAAATTTATTAAA
* *
2230956 ATTATATTATAAATTATTAATTTATTAAT
1 ATTATATTATAAATTATAAATTTATTAAA
2230985 ATT-TA-TATAAATATATAATATTT
1 ATTATATTATAAAT-TATAA-ATTT
2231008 TAAATATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 16 0.37
28 8 0.19
29 19 0.44
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
ATTATATTATAAATTATAAATTTATTAAA
Found at i:2231003 original size:27 final size:27
Alignment explanation
Indices: 2230930--2231011 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 27
2230920 AATAATGATA
*
2230930 TTATATTAACATATA-AATTTGTTAAAAT
1 TTATA-TAA-ATATATAATTTATTAAAAT
*
2230958 TATATTATAAAT-TATTAATTTATTAATAT
1 T-TA-TATAAATATA-TAATTTATTAAAAT
2230987 TTATATAAATATATAATATT-TTAAA
1 TTATATAAATATATAAT-TTATTAAA
2231012 TATAATTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
27 17 0.38
28 9 0.20
29 17 0.38
30 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
TTATATAAATATATAATTTATTAAAAT
Found at i:2232342 original size:18 final size:18
Alignment explanation
Indices: 2232319--2232353 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2232309 GCTTCCATTT
2232319 TATATATAATTTATATAA
1 TATATATAATTTATATAA
*
2232337 TATATATTATTTATATA
1 TATATATAATTTATATA
2232354 TAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATATAATTTATATAA
Found at i:2233040 original size:2 final size:2
Alignment explanation
Indices: 2233033--2233072 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2233023 GTCGACATAG
2233033 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
2233073 GTTCGTGCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2235006 original size:12 final size:13
Alignment explanation
Indices: 2234986--2235018 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2234976 AAATTATAAC
2234986 TTAAA-TTATT-T
1 TTAAATTTATTGT
2234997 TTAAATTTATTGT
1 TTAAATTTATTGT
2235010 TTAAATTTA
1 TTAAATTTA
2235019 ATTTGACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 5 0.25
13 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
TTAAATTTATTGT
Found at i:2236813 original size:16 final size:16
Alignment explanation
Indices: 2236787--2236826 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2236777 TTTTTTTCTC
*
2236787 TAAATTCTTATTT-TT
1 TAAATTTTTATTTATT
2236802 TAAAATTTTTATTTATT
1 T-AAATTTTTATTTATT
2236819 TAAATTTT
1 TAAATTTT
2236827 AAATTATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.82
17 3 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TAAATTTTTATTTATT
Found at i:2237070 original size:19 final size:19
Alignment explanation
Indices: 2237046--2237084 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2237036 AGTGTAATTG
2237046 AGCTAAATTAATGAGTTTA
1 AGCTAAATTAATGAGTTTA
2237065 AGCTAAATTAATGAGTTTA
1 AGCTAAATTAATGAGTTTA
2237084 A
1 A
2237085 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (19 bp):
AGCTAAATTAATGAGTTTA
Found at i:2237331 original size:22 final size:23
Alignment explanation
Indices: 2237306--2237356 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2237296 GTTATTCAAA
* *
2237306 TTAATT-ATTAAAAAATTTGAAT
1 TTAATTCACTAAAAAATTTAAAT
*
2237328 TTAATTCACTAAATAATTTAAAT
1 TTAATTCACTAAAAAATTTAAAT
2237351 TTAATT
1 TTAATT
2237357 TAATAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAATTCACTAAAAAATTTAAAT
Found at i:2237779 original size:2 final size:2
Alignment explanation
Indices: 2237721--2237760 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2237711 AAGAGAGCAC
2237721 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
2237761 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2238294 original size:23 final size:24
Alignment explanation
Indices: 2238241--2238294 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
2238231 TTAAAAAAAT
* * *
2238241 ATTATTTAATAAATTTAATGTTTG
1 ATTATTTAATAAATATAATGTATA
*
2238265 ATT-TTTAATATATATAAT-TATA
1 ATTATTTAATAAATATAATGTATA
2238287 ATTATTTA
1 ATTATTTA
2238295 TTTTATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 5 0.20
23 17 0.68
24 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTATTTAATAAATATAATGTATA
Found at i:2239330 original size:2 final size:2
Alignment explanation
Indices: 2239323--2239355 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2239313 ATGAGATTGG
2239323 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2239356 CATATCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2242195 original size:2 final size:2
Alignment explanation
Indices: 2242188--2242234 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2242178 AAGATTTTAA
2242188 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
2242230 AT AT A
1 AT AT A
2242235 CACACTGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2242658 original size:23 final size:23
Alignment explanation
Indices: 2242632--2242675 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2242622 TTTTATAGAA
* *
2242632 TTTTTGATATTATTTTTTATTAT
1 TTTTTGAAATTATATTTTATTAT
*
2242655 TTTTTTAAATTATATTTTATT
1 TTTTTGAAATTATATTTTATT
2242676 TTAATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTTGAAATTATATTTTATTAT
Found at i:2243216 original size:1 final size:1
Alignment explanation
Indices: 2243205--2243234 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2243195 AATTCATTTC
*
2243205 GGGGGGTGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2243235 AACTGAGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:2247128 original size:33 final size:33
Alignment explanation
Indices: 2247086--2247152 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2247076 TTTGAGAGAT
2247086 AGTTTTATTATAAATAAATAAAAACATTAATCA
1 AGTTTTATTATAAATAAATAAAAACATTAATCA
*
2247119 AGTTTTATTATAAATAAATAAAAATATTAATCA
1 AGTTTTATTATAAATAAATAAAAACATTAATCA
2247152 A
1 A
2247153 ACATAACATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.37
Consensus pattern (33 bp):
AGTTTTATTATAAATAAATAAAAACATTAATCA
Found at i:2247320 original size:31 final size:31
Alignment explanation
Indices: 2247268--2247359 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
2247258 GGATATTTAT
*
2247268 ATAAAGTAATT-TTTT-AA-ATCAAAAATAAA
1 ATAAA-TAATTATTTTAAACATCAATAATAAA
2247297 ATAAATAATTATTTTAAACATCAATAATAAA
1 ATAAATAATTATTTTAAACATCAATAATAAA
2247328 ATAAATAATTATTTTAAACATCAATAATAAA
1 ATAAATAATTATTTTAAACATCAATAATAAA
2247359 A
1 A
2247360 AATTTTAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
28 5 0.08
29 9 0.15
30 2 0.03
31 43 0.73
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (31 bp):
ATAAATAATTATTTTAAACATCAATAATAAA
Found at i:2247324 original size:19 final size:19
Alignment explanation
Indices: 2247300--2247355 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
2247290 AAATAAAATA
2247300 AATAATTATTTTAAACATC
1 AATAATTATTTTAAACATC
*
2247319 AAT-A--A---TAAA-ATA
1 AATAATTATTTTAAACATC
2247331 AATAATTATTTTAAACATC
1 AATAATTATTTTAAACATC
2247350 AATAAT
1 AATAAT
2247356 AAAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
15 1 0.04
16 1 0.04
18 5 0.18
19 11 0.39
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATTATTTTAAACATC
Found at i:2247372 original size:14 final size:14
Alignment explanation
Indices: 2247353--2247384 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2247343 AAACATCAAT
2247353 AATAAAAAATTTTA
1 AATAAAAAATTTTA
2247367 AAT-AAAAATTTTA
1 AATAAAAAATTTTA
2247380 AATAA
1 AATAA
2247385 TATATGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAAAAAATTTTA
Found at i:2249106 original size:23 final size:22
Alignment explanation
Indices: 2249075--2249134 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
2249065 TAATTTTTAT
*
2249075 TAATATAAATTTTAATAAATTAA
1 TAATATAAATTAT-ATAAATTAA
*
2249098 TAATTTAAATTATATAAATTTAA
1 TAATATAAATTATATAAA-TTAA
2249121 -AA-ATAAATTTATAT
1 TAATATAAA-TTATAT
2249135 TATATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.12
22 13 0.41
23 15 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATAAATTATATAAATTAA
Found at i:2252853 original size:16 final size:16
Alignment explanation
Indices: 2252832--2252884 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
2252822 ATACATATTT
2252832 TAAATTTTATATAATA
1 TAAATTTTATATAATA
2252848 TAAATTATTA-AT-ATA
1 TAAATT-TTATATAATA
*
2252863 TTAAAATTTATATAAATA
1 -TAAATTTTATAT-AATA
2252881 TAAA
1 TAAA
2252885 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
15 6 0.19
16 15 0.48
17 7 0.23
18 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:2252854 original size:60 final size:60
Alignment explanation
Indices: 2252790--2252911 Score: 131
Period size: 60 Copynumber: 2.0 Consensus size: 60
2252780 CACAAGAAAT
* * * * *
2252790 AATTAAAAAAATA-TATACATTTGCATAAATATATACATATTTTAAATTTTA-TATAATATA
1 AATTAAAAAAATATTA-AAATTTACATAAATATA-AAATATTTTAAATATAATTATAATATA
** * *
2252850 AATTATTAATATATTAAAATTTATATAAATATAAAATATTTTAAATATAATTATAATATA
1 AATTAAAAAAATATTAAAATTTACATAAATATAAAATATTTTAAATATAATTATAATATA
2252910 AA
1 AA
2252912 AAACTTTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 14 0.27
60 35 0.69
61 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (60 bp):
AATTAAAAAAATATTAAAATTTACATAAATATAAAATATTTTAAATATAATTATAATATA
Found at i:2252873 original size:32 final size:33
Alignment explanation
Indices: 2252816--2252889 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
2252806 ACATTTGCAT
* *
2252816 AAATATATACATATTTTAAATTTTATAT-AATATA
1 AAATAT-TA-ATATATTAAAATTTATATAAATATA
*
2252850 AATTATTAATATATTAAAATTTATATAAATATA
1 AAATATTAATATATTAAAATTTATATAAATATA
2252883 AAATATT
1 AAATATT
2252890 TTAAATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 16 0.46
33 14 0.40
34 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
AAATATTAATATATTAAAATTTATATAAATATA
Found at i:2264235 original size:3 final size:3
Alignment explanation
Indices: 2264227--2264264 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2264217 TTAATTCTGA
2264227 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2264265 ACTAGCACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2267065 original size:6 final size:6
Alignment explanation
Indices: 2267033--2267066 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2267023 TTTTTACTGA
* *
2267033 ATGTAT ATATAT ATATAT ATGTAT ATGTAT ATGT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGT
2267067 GACAGGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:2267707 original size:61 final size:61
Alignment explanation
Indices: 2267642--2267761 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
2267632 AAATCGTTAG
** *
2267642 AAAAAATAATAAATTTTCGTAAAATACGATGACATTGCATCAGTAAATTTTATATGACAAA
1 AAAAAATAATAAATTCACGTAAAATACGATGACATTGCATCAGTAAATCTTATATGACAAA
* * * *
2267703 AAAAAATAATGAATTCAGGTGAAATACGATGATATTGCATCAGTAAATCTTATATGACA
1 AAAAAATAATAAATTCACGTAAAATACGATGACATTGCATCAGTAAATCTTATATGACA
2267762 TCTTCTGTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (61 bp):
AAAAAATAATAAATTCACGTAAAATACGATGACATTGCATCAGTAAATCTTATATGACAAA
Found at i:2269030 original size:2 final size:2
Alignment explanation
Indices: 2268993--2269022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2268983 TCTGTCACAC
2268993 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
2269023 GCATATATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2277263 original size:2 final size:2
Alignment explanation
Indices: 2277256--2277292 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2277246 GTTCAATTAA
2277256 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2277293 ACTTTGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2284271 original size:6 final size:6
Alignment explanation
Indices: 2284262--2284295 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2284252 CAGGCTTGAA
2284262 GAAACT GAAACT GAAACT GAAACT GAAACT GAAA
1 GAAACT GAAACT GAAACT GAAACT GAAACT GAAA
2284296 TAGGAACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (6 bp):
GAAACT
Found at i:2284276 original size:110 final size:112
Alignment explanation
Indices: 2284071--2284284 Score: 315
Period size: 110 Copynumber: 1.9 Consensus size: 112
2284061 CTGAATCAGA
2284071 AAGAACTCGATTAGAATTATTATGGGTTCTGATCCAAAATCAATTGAAAGTAAGTATAGAACACA
1 AAGAACTCGATTAGAATTATTATGGGTTCTGATCCAAAATCAATTGAAAGTAAGTATAGAACACA
* * *
2284136 GAGAGACAGGCTTGAAGAAACTGGAGCTGAAACTGAAACAGGAACTTG
66 -AGACACAGGCTTGAAGAAACTGAAACTGAAACTGAAACAGGAACTTG
* * * ** * *
2284184 AAGAACTCGGTTGGAATTATTATGTGTTCTGAT-CTGAATCAATTGAAATTAGGTATAGAACAC-
1 AAGAACTCGATTAGAATTATTATGGGTTCTGATCCAAAATCAATTGAAAGTAAGTATAGAACACA
2284247 AGACACAGGCTTGAAGAAACTGAAACTGAAACTGAAAC
66 AGACACAGGCTTGAAGAAACTGAAACTGAAACTGAAAC
2284285 TGAAACTGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
110 35 0.38
112 26 0.29
113 30 0.33
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (112 bp):
AAGAACTCGATTAGAATTATTATGGGTTCTGATCCAAAATCAATTGAAAGTAAGTATAGAACACA
AGACACAGGCTTGAAGAAACTGAAACTGAAACTGAAACAGGAACTTG
Found at i:2288813 original size:19 final size:19
Alignment explanation
Indices: 2288786--2288835 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
2288776 TTTTTATCTA
* *
2288786 ATTATAAATATGAATTATT
1 ATTAAAAATATAAATTATT
2288805 ATTAAAAATAATAAATTATT
1 ATTAAAAAT-ATAAATTATT
2288825 -TTCAAAAATAT
1 ATT-AAAAATAT
2288836 TTATATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAAAATATAAATTATT
Found at i:2288862 original size:28 final size:28
Alignment explanation
Indices: 2288843--2288897 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
2288833 TATTTATATA
2288843 TTTA-TAATTAAATTTAAATAAATTATT
1 TTTATTAATTAAATTTAAATAAATTATT
*
2288870 TTTATTAATTAAATAATAAATTAAATTA
1 TTTATTAATTAAAT-TTAAA-TAAATTA
2288898 AATTATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 9 0.38
29 4 0.17
30 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTATTAATTAAATTTAAATAAATTATT
Found at i:2291655 original size:120 final size:119
Alignment explanation
Indices: 2291420--2291669 Score: 351
Period size: 120 Copynumber: 2.1 Consensus size: 119
2291410 GTATGCATAT
* * * * * * * *
2291420 GCTTATAAAAGTTAATTTGTGGAGATTCGTTTCTTTGAGTCTGAGACTGAAGCAATGTTATTAAT
1 GCTTGTAAAAGTTAATTTGTGAAGATACATGTCTTTGAGTCTAAGACTAAAGCAATGTTATCAAT
* *
2291485 GATGTTTTCTCTTGTGCTTGTCAAAATCGTAGGCCATGATCATGGGTGACATTG
66 GATGTTTTCTCTTGTGCTTGTCAAAATCATAGGCCATGATCATGGATGACATTG
*
2291539 GCTTGTAAGAGTTAATTTGTGAAGATACATGTCTTTGAGTCTAAGAGC-AAAG-ATATGTTATCA
1 GCTTGTAAAAGTTAATTTGTGAAGATACATGTCTTTGAGTCTAAGA-CTAAAGCA-ATGTTATCA
2291602 ATGATGTTTTTCTCTTGTGCTTGTCAAAATCATAGGCCATGATCATGGATGACATTG
64 ATGATG-TTTTCTCTTGTGCTTGTCAAAATCATAGGCCATGATCATGGATGACATTG
*
2291659 GCTTGTCAAAG
1 GCTTGTAAAAG
2291670 CCTACTTAAG
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
118 1 0.01
119 56 0.49
120 58 0.50
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (119 bp):
GCTTGTAAAAGTTAATTTGTGAAGATACATGTCTTTGAGTCTAAGACTAAAGCAATGTTATCAAT
GATGTTTTCTCTTGTGCTTGTCAAAATCATAGGCCATGATCATGGATGACATTG
Found at i:2294980 original size:5 final size:5
Alignment explanation
Indices: 2294970--2295023 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
2294960 AATATTAAAA
* *
2294970 ATAAT ATAAT A-AAT ATGAT ATAAT AT-AT TTAAAT ATAAT -TAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT
2295017 ATAAT AT
1 ATAAT AT
2295024 TTATTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
4 15 0.38
5 22 0.55
6 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:2294994 original size:19 final size:20
Alignment explanation
Indices: 2294970--2295020 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2294960 AATATTAAAA
*
2294970 ATAATATA-ATAAATATGAT
1 ATAATATATATAAATATAAT
*
2294989 ATAATATATTTAAATATAAT
1 ATAATATATATAAATATAAT
2295009 -TAATATATATAA
1 ATAATATATATAA
2295021 TATTTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATAATATATATAAATATAAT
Found at i:2297644 original size:206 final size:206
Alignment explanation
Indices: 2297313--2297693 Score: 514
Period size: 206 Copynumber: 1.8 Consensus size: 206
2297303 TTGTTGGCAT
* * * * * * * *
2297313 AATTTAATACTCTGTTAAGCTTATATCTTATTTTAGAAAGTAATTCAATCTGAGTCAATTTGATA
1 AATTTAATACACTGTTAAACTTACATCTTATTTTAAAAAGCAATTCAATATGACTCAATTTGACA
* * * * *
2297378 TTTTGCCATTTGGCATATTGTATTACTGTATGAATCAAATTAATTAAATTTTAGATTTTAACT-A
66 TTTTACCATTTGACATATTGTATTACTGAATGAATCAAATTAATTAAATTTAAAATTTTAACTGA
*
2297442 TGTATTGCCTTATTACGAAACTTTAATGAATTAATAGAATAATTTATATGAAACTTTAAATATTA
131 -GTATTACCTTATTACGAAACTTTAATGAATTAATAGAATAATTTATATGAAACTTTAAATATTA
2297507 TTTTATTAATAC
195 TTTTATTAATAC
* *
2297519 AATTTAATACACTTTTAAACTTACATCTTGTTTTAAAAAGCAATTCAATATGAACT-AATTTGAC
1 AATTTAATACACTGTTAAACTTACATCTTATTTTAAAAAGCAATTCAATATG-ACTCAATTTGAC
* * *
2297583 ATTTTACCATTTGACATATTGTATTACTGAATGAATCAACTTAGTTAAGTTTAAAATTTTAACTG
65 ATTTTACCATTTGACATATTGTATTACTGAATGAATCAAATTAATTAAATTTAAAATTTTAACTG
* * * * *
2297648 AGTATTATCTTATTACGGAACTTTGATGAATTGATAGAGTAATTTA
130 AGTATTACCTTATTACGAAACTTTAATGAATTAATAGAATAATTTA
2297694 CATCTTTTTG
Statistics
Matches: 149, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
206 146 0.98
207 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (206 bp):
AATTTAATACACTGTTAAACTTACATCTTATTTTAAAAAGCAATTCAATATGACTCAATTTGACA
TTTTACCATTTGACATATTGTATTACTGAATGAATCAAATTAATTAAATTTAAAATTTTAACTGA
GTATTACCTTATTACGAAACTTTAATGAATTAATAGAATAATTTATATGAAACTTTAAATATTAT
TTTATTAATAC
Found at i:2301299 original size:2 final size:2
Alignment explanation
Indices: 2301294--2301324 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2301284 ATATATGTTC
2301294 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 A
2301325 ACTTCAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2305904 original size:2 final size:2
Alignment explanation
Indices: 2305899--2305927 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2305889 TATATATATA
2305899 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2305928 ACATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2306081 original size:2 final size:2
Alignment explanation
Indices: 2306074--2306119 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2306064 TGCACGCTTC
2306074 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
2306116 AT AT
1 AT AT
2306120 CCTTCAGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2306154 original size:2 final size:2
Alignment explanation
Indices: 2306149--2306180 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2306139 ACACACACAC
2306149 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
2306181 CAGTGTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2307335 original size:3 final size:3
Alignment explanation
Indices: 2307327--2307383 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
2307317 TTTCTCCAAC
2307327 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2307374 ATA ATA ATA A
1 ATA ATA ATA A
2307384 AAAGTAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2312473 original size:4 final size:4
Alignment explanation
Indices: 2312464--2312492 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2312454 TTTTTATCCA
2312464 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
2312493 CATGCTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:2317752 original size:15 final size:15
Alignment explanation
Indices: 2317734--2317772 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2317724 AATGAAAAAA
*
2317734 ATTAATTTTTATATT
1 ATTAATTTTAATATT
*
2317749 ATTAAATTTAATATT
1 ATTAATTTTAATATT
2317764 -TTAATTTTA
1 ATTAATTTTA
2317773 TAATTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTAATTTTAATATT
Found at i:2317760 original size:21 final size:21
Alignment explanation
Indices: 2317735--2317778 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2317725 ATGAAAAAAA
2317735 TTAAT-TTTTATATTATTA-AAT
1 TTAATATTTTA-ATT-TTATAAT
2317756 TTAATATTTTAATTTTATAAT
1 TTAATATTTTAATTTTATAAT
2317777 TT
1 TT
2317779 TAAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.14
21 13 0.62
22 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTAATATTTTAATTTTATAAT
Found at i:2318041 original size:29 final size:29
Alignment explanation
Indices: 2318008--2318064 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2317998 TATTTATTAT
*
2318008 AATTTAAAAATATAAAGATTAAAATATTG
1 AATTTAAAAATATAAAAATTAAAATATTG
* *
2318037 AATTTAATAATGTAAAAATTAAAATATT
1 AATTTAAAAATATAAAAATTAAAATATT
2318065 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (29 bp):
AATTTAAAAATATAAAAATTAAAATATTG
Found at i:2319498 original size:25 final size:27
Alignment explanation
Indices: 2319443--2319499 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
2319433 TGTGTCTATC
2319443 ATATATTTAAACATGAGTAAAAAGAAT
1 ATATATTTAAACATGAGTAAAAAGAAT
* *
2319470 ATAT-TTTGAAACATGGGTAAAAAAAAT
1 ATATATTT-AAACATGAGTAAAAAGAAT
2319497 ATA
1 ATA
2319500 CCCTCCTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (27 bp):
ATATATTTAAACATGAGTAAAAAGAAT
Found at i:2324894 original size:23 final size:23
Alignment explanation
Indices: 2324862--2324906 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2324852 AATAAATTAT
* * *
2324862 TAAAATATTATTGATTTGATTGG
1 TAAAAAATTATTAAATTGATTGG
2324885 TAAAAAATTATTAAATTGATTG
1 TAAAAAATTATTAAATTGATTG
2324907 AAATATTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (23 bp):
TAAAAAATTATTAAATTGATTGG
Found at i:2325762 original size:27 final size:26
Alignment explanation
Indices: 2325699--2325762 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
2325689 TTTAATCGTT
2325699 ATTTTTTATAT--TATTTAAATTTAA
1 ATTTTTTATATAATATTTAAATTTAA
* *
2325723 ATATATTT-GATAATATTTAAAATTTAA
1 AT-TTTTTATATAATATTT-AAATTTAA
2325750 ATTTTTTATATAA
1 ATTTTTTATATAA
2325763 GTAAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 4 0.13
25 4 0.13
26 9 0.29
27 14 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
ATTTTTTATATAATATTTAAATTTAA
Found at i:2325812 original size:17 final size:16
Alignment explanation
Indices: 2325779--2325821 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2325769 AATTATATTT
* *
2325779 TTATAATTATATTTAA
1 TTATAATTAAATATAA
2325795 TTATATATTAAATATAA
1 TTATA-ATTAAATATAA
2325812 TTATTAATTA
1 TTA-TAATTA
2325822 TTTTAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 16 0.70
18 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATAATTAAATATAA
Found at i:2325844 original size:22 final size:22
Alignment explanation
Indices: 2325777--2325847 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
2325767 AAAATTATAT
*
2325777 TTTTATAAT-TATATTTAATTATA
1 TTTTA-AATATATATATAATT-TA
*
2325800 TATTAAATATA-ATTATTAA-TTA
1 TTTTAAATATATA-TA-TAATTTA
2325822 TTTTAAATATATATATAATTTA
1 TTTTAAATATATATATAATTTA
2325844 TTTT
1 TTTT
2325848 TAACGGTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
21 3 0.08
22 25 0.62
23 9 0.22
24 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTAAATATATATATAATTTA
Found at i:2326735 original size:15 final size:14
Alignment explanation
Indices: 2326715--2326771 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
2326705 TCTATTGATA
2326715 TTATTTTGTTATAAT
1 TTATTTT-TTATAAT
*
2326730 TTATTTTTTAAAAT
1 TTATTTTTTATAAT
*
2326744 ATATATTTTTA-AAT
1 TTAT-TTTTTATAAT
*
2326758 TTAATTTTTATAAT
1 TTATTTTTTATAAT
2326772 GTAATAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 6 0.17
14 17 0.47
15 13 0.36
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTATTTTTTATAAT
Found at i:2326782 original size:29 final size:28
Alignment explanation
Indices: 2326727--2326802 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
2326717 ATTTTGTTAT
* *
2326727 AATTTATTTTTTAAAATATATATTTTTA
1 AATTTAATTTTTAAAATATATAATTTTA
* * *
2326755 AATTTAATTTTTATAATGTAATAATTTTT
1 AATTTAATTTTTAAAATAT-ATAATTTTA
* *
2326784 TA-TTAAGTTTTAAAATATA
1 AATTTAATTTTTAAAATATA
2326803 AACAACTCAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.76
29 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
AATTTAATTTTTAAAATATATAATTTTA
Found at i:2334294 original size:29 final size:29
Alignment explanation
Indices: 2334222--2334329 Score: 83
Period size: 29 Copynumber: 3.6 Consensus size: 29
2334212 TTGATATAAT
* * *
2334222 ATAATTATAAAATATAAATTTAATACAAAAAA
1 ATAAATATAAAATAT-AATATAA-A-TAAAAA
* *
2334254 ATAATATTTAAAATATAATATATAATAAAAT
1 ATAA-ATATAAAATATAATATA-AATAAAAA
* * *
2334285 AT-GATATAAAAAATTATATAAATAAAAA
1 ATAAATATAAAATATAATATAAATAAAAA
2334313 ATAAATATAAAAATATA
1 ATAAATAT-AAAATATA
2334330 TCAAGATTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
28 9 0.15
29 18 0.31
30 6 0.10
31 6 0.10
32 10 0.17
33 10 0.17
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (29 bp):
ATAAATATAAAATATAATATAAATAAAAA
Found at i:2334322 original size:17 final size:16
Alignment explanation
Indices: 2334290--2334323 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2334280 AAAATATGAT
*
2334290 ATAAAAAATTATATAA
1 ATAAAAAATAATATAA
2334306 ATAAAAAATAAATATAA
1 ATAAAAAAT-AATATAA
2334323 A
1 A
2334324 AATATATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAATAATATAA
Found at i:2339500 original size:16 final size:16
Alignment explanation
Indices: 2339479--2339510 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2339469 CTGAATACTC
2339479 GTATCAATTATCATTA
1 GTATCAATTATCATTA
2339495 GTATCAATTATCATTA
1 GTATCAATTATCATTA
2339511 TGATAGTTTC
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:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
GTATCAATTATCATTA
Found at i:2343062 original size:6 final size:7
Alignment explanation
Indices: 2343044--2343068 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2343034 TTTATAATAC
2343044 TAAAAAA
1 TAAAAAA
2343051 TAAAAAA
1 TAAAAAA
2343058 TAAAAAA
1 TAAAAAA
2343065 TAAA
1 TAAA
2343069 GATAGACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:2343324 original size:14 final size:14
Alignment explanation
Indices: 2343305--2343331 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2343295 TATAGTTAGT
2343305 TTTTCTTATTATTA
1 TTTTCTTATTATTA
2343319 TTTTCTTATTATT
1 TTTTCTTATTATT
2343332 TAATGTAATA
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:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTATTATTA
Found at i:2343361 original size:2 final size:2
Alignment explanation
Indices: 2343354--2343386 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2343344 TTAAAAGTAT
2343354 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 T
2343387 TTCAAGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2343887 original size:18 final size:20
Alignment explanation
Indices: 2343859--2343895 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2343849 AAATTTGAAA
2343859 TTAATAAAAT-AAACATATT
1 TTAATAAAATAAAACATATT
2343878 TTAA-AAAATAAAACATAT
1 TTAATAAAATAAAACATAT
2343896 AATAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAATAAAATAAAACATATT
Found at i:2344623 original size:5 final size:5
Alignment explanation
Indices: 2344606--2344639 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
2344596 AATTTATTTG
*
2344606 AAAAT AAAGT AAAAT AAAAT AAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
2344640 TCTTTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2345905 original size:26 final size:26
Alignment explanation
Indices: 2345876--2345975 Score: 68
Period size: 26 Copynumber: 3.9 Consensus size: 26
2345866 ATATATATAT
2345876 TTATAATTTAATATATTATTAATAAA
1 TTATAATTTAATATATTATTAATAAA
*
2345902 TTAT-ATGATAATAT-TTCATTAATAAA
1 TTATAAT-TTAATATATT-ATTAATAAA
* * *
2345928 TTTTAA--AAATA-AATATTAAT-AA
1 TTATAATTTAATATATTATTAATAAA
* *
2345950 TTATAAATTTTAATAGATGATTAATA
1 TTAT-AA-TTTAATATATTATTAATA
2345976 CATCGATCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
22 5 0.09
23 8 0.14
24 5 0.09
25 4 0.07
26 26 0.46
27 8 0.14
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (26 bp):
TTATAATTTAATATATTATTAATAAA
Found at i:2345938 original size:13 final size:14
Alignment explanation
Indices: 2345922--2345964 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
2345912 ATATTTCATT
2345922 AATAAATTTTAA-A
1 AATAAATTTTAATA
*
2345935 AATAAATATTAATA
1 AATAAATTTTAATA
2345949 ATTATAAATTTTAATA
1 A--ATAAATTTTAATA
2345965 GATGATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.44
14 2 0.08
16 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAAATTTTAATA
Found at i:2346595 original size:2 final size:2
Alignment explanation
Indices: 2346588--2346620 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2346578 TTTCATGAAT
2346588 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 T
2346621 TCAACATTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2347010 original size:15 final size:16
Alignment explanation
Indices: 2346986--2347015 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2346976 TTTAAGTGCA
2346986 AAAAAGAAAAAAGAAG
1 AAAAAGAAAAAAGAAG
2347002 AAAAA-AAAAAAGAA
1 AAAAAGAAAAAAGAA
2347016 CATTTCCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAG
Found at i:2349439 original size:22 final size:21
Alignment explanation
Indices: 2349392--2349442 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2349382 ATGTATTACA
*
2349392 AAAATGAAAAAAAATTATCAT
1 AAAATTAAAAAAAATTATCAT
*
2349413 AAAATTAAAATAAAATT-TGAT
1 AAAATTAAAA-AAAATTATCAT
2349434 ATAAATTAA
1 A-AAATTAA
2349443 GAATTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATTAAAAAAAATTATCAT
Found at i:2352197 original size:14 final size:13
Alignment explanation
Indices: 2352163--2352202 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
2352153 ACATTCATTC
2352163 ATAAATTTAA-TT
1 ATAAATTTAATTT
*
2352175 ATTAATTTAATTT
1 ATAAATTTAATTT
2352188 GATAAATTTAATTT
1 -ATAAATTTAATTT
2352202 A
1 A
2352203 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.38
13 3 0.12
14 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATAAATTTAATTT
Found at i:2352215 original size:19 final size:19
Alignment explanation
Indices: 2352166--2352215 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
2352156 TTCATTCATA
2352166 AATTT-AATTA-TTAATTT
1 AATTTAAATTATTTAATTT
2352183 AATTTGATAA--ATTTAATTT
1 AATTT-A-AATTATTTAATTT
2352202 AATTTAAATTATTT
1 AATTTAAATTATTT
2352216 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 16 0.59
20 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTAAATTATTTAATTT
Found at i:2352699 original size:2 final size:2
Alignment explanation
Indices: 2352692--2352716 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2352682 CTTTCACATC
2352692 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
2352717 AAAGAGAGAT
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:2352897 original size:13 final size:14
Alignment explanation
Indices: 2352875--2352907 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2352865 TTTTTAATTT
2352875 ATATTT-AAATAAA
1 ATATTTAAAATAAA
2352888 AT-TTTAAAATAAA
1 ATATTTAAAATAAA
2352901 ATATTTA
1 ATATTTA
2352908 TTTATGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.17
13 11 0.61
14 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATTTAAAATAAA
Found at i:2353401 original size:20 final size:21
Alignment explanation
Indices: 2353362--2353401 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2353352 ATATGTCTTA
* *
2353362 TTTTTAAAATTATTATTTAAT
1 TTTTTAAAAATATTACTTAAT
2353383 TTTTTAAAAATA-TACTTAA
1 TTTTTAAAAATATTACTTAA
2353402 AGAATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTAAAAATATTACTTAAT
Found at i:2357680 original size:27 final size:28
Alignment explanation
Indices: 2357650--2357703 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
2357640 GAATCGATTA
2357650 AATTAATTAAAAATTA-TTAAAT-TTAAT
1 AATT-ATTAAAAATTATTTAAATATTAAT
**
2357677 AATTATTTTAAATTATTTAAATATTAA
1 AATTATTAAAAATTATTTAAATATTAA
2357704 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 9 0.39
27 10 0.43
28 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTATTAAAAATTATTTAAATATTAAT
Found at i:2357737 original size:21 final size:21
Alignment explanation
Indices: 2357704--2357745 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2357694 TAAATATTAA
2357704 AAAATAAAAAAATATT-TAATT
1 AAAATAAAAAAAT-TTATAATT
* *
2357725 AAAATTAATAAATTTATAATT
1 AAAATAAAAAAATTTATAATT
2357746 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATAAAAAAATTTATAATT
Found at i:2357791 original size:18 final size:19
Alignment explanation
Indices: 2357765--2357803 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2357755 TTTTAATCTC
2357765 AATTCAAATTTATTT-ATA
1 AATTCAAATTTATTTAATA
* *
2357783 AATTTAAATTTTTTTAATA
1 AATTCAAATTTATTTAATA
2357802 AA
1 AA
2357804 AAAGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTCAAATTTATTTAATA
Found at i:2358047 original size:14 final size:14
Alignment explanation
Indices: 2358028--2358055 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2358018 TTTTTCAGTT
2358028 TTAAATATATTTTA
1 TTAAATATATTTTA
2358042 TTAAATATATTTTA
1 TTAAATATATTTTA
2358056 AATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:2358383 original size:18 final size:17
Alignment explanation
Indices: 2358325--2358384 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
2358315 GTCACTTATG
2358325 TTATTTTTCTTTATTTT
1 TTATTTTTCTTTATTTT
*
2358342 TTAATTTTTTTTCTATTTT
1 TT-ATTTTTCTT-TATTTT
* *
2358361 CTATTTTTCTTAATTATT
1 TTATTTTTCTTTATT-TT
2358379 TTATTT
1 TTATTT
2358385 GATTAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.14
18 23 0.66
19 7 0.20
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTTCTTTATTTT
Found at i:2360325 original size:5 final size:6
Alignment explanation
Indices: 2360310--2360334 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2360300 TTTATATCAA
2360310 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
2360335 GGCACGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2367455 original size:13 final size:13
Alignment explanation
Indices: 2367437--2367464 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2367427 GAAGGCGACA
2367437 ATAAAGAGAAAAG
1 ATAAAGAGAAAAG
2367450 ATAAAGAGAAAAG
1 ATAAAGAGAAAAG
2367463 AT
1 AT
2367465 TACATGCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (13 bp):
ATAAAGAGAAAAG
Found at i:2371538 original size:15 final size:14
Alignment explanation
Indices: 2371518--2371602 Score: 56
Period size: 14 Copynumber: 6.1 Consensus size: 14
2371508 GGAGTTATTT
*
2371518 TTAAATTTAATAATA
1 TTAAATATAAT-ATA
2371533 TTAAATATAATATA
1 TTAAATATAATATA
2371547 TT--ATATAATATA
1 TTAAATATAATATA
*
2371559 --AAATA-ATTATA
1 TTAAATATAATATA
*
2371570 TATATATATATATGATA
1 T-TAAATATA-AT-ATA
2371587 TTAATATATAA-ATA
1 TTAA-ATATAATATA
2371601 TT
1 TT
2371603 TTAAAATTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
11 5 0.09
12 13 0.23
14 14 0.25
15 11 0.20
16 4 0.07
17 9 0.16
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (14 bp):
TTAAATATAATATA
Found at i:2371558 original size:17 final size:17
Alignment explanation
Indices: 2371536--2371702 Score: 83
Period size: 17 Copynumber: 9.7 Consensus size: 17
2371526 AATAATATTA
2371536 AATATAATATATTATAT
1 AATATAATATATTATAT
*
2371553 AATATAAAATAATTATAT
1 AATATAATAT-ATTATAT
*
2371571 -ATATATATATATGATATT
1 AATATA-ATATATTATA-T
* * *
2371589 AATATATAAATATTTTAA
1 AATATA-ATATATTATAT
* * *
2371607 AAT-TTATAT-TTTTTT
1 AATATAATATATTATAT
* * *
2371622 AATATATTATTTTTTTAT
1 AATATAATA-TATTATAT
* *
2371640 AAATATAAAATATTTTA-
1 -AATATAATATATTATAT
* *
2371657 AATGTAAT-TATAATAT
1 AATATAATATATTATAT
* *
2371673 AATAAAATATATAATAT
1 AATATAATATATTATAT
2371690 AATATAAATATAT
1 AATAT-AATATAT
2371703 ATTATTAAGT
Statistics
Matches: 115, Mismatches: 24, Indels: 21
0.72 0.15 0.13
Matches are distributed among these distances:
15 12 0.10
16 18 0.16
17 33 0.29
18 32 0.28
19 20 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (17 bp):
AATATAATATATTATAT
Found at i:2371593 original size:23 final size:24
Alignment explanation
Indices: 2371540--2371601 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
2371530 ATATTAAATA
2371540 TAATATATTATATAATATAAAATAAT
1 TAATATA-TATAT-ATATAAAATAAT
**
2371566 T-ATATATATATATATATGAT-AT
1 TAATATATATATATATAAAATAAT
*
2371588 TAATATATAAATAT
1 TAATATATATATAT
2371602 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 3 0.09
23 18 0.56
24 5 0.16
25 5 0.16
26 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAATATATATATATATAAAATAAT
Found at i:2371594 original size:25 final size:23
Alignment explanation
Indices: 2371527--2371601 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 23
2371517 TTTAAATTTA
2371527 ATAATATTAAATATAATATAT-TAT
1 ATAATA-TAAA-ATAATATATATAT
2371551 ATAATATAAAATAATTATATATAT
1 ATAATATAAAATAA-TATATATAT
* * *
2371575 ATATATATGATATTAATATATAAAT
1 ATA-ATAT-AAAATAATATATATAT
2371600 AT
1 AT
2371602 TTTAAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.09
23 9 0.20
24 12 0.27
25 14 0.32
26 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
ATAATATAAAATAATATATATAT
Found at i:2371692 original size:28 final size:30
Alignment explanation
Indices: 2371636--2371701 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 30
2371626 TATTATTTTT
* *
2371636 TTATAA-AT-ATAAAATATTTTAAATGTAA
1 TTATAATATAATAAAATATTATAAATATAA
2371664 TTATAATATAATAAAATA-TAT-AATATAA
1 TTATAATATAATAAAATATTATAAATATAA
2371692 -TATAAATATA
1 TTAT-AATATA
2371702 TATTATTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
28 18 0.55
29 4 0.12
30 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TTATAATATAATAAAATATTATAAATATAA
Found at i:2371997 original size:24 final size:23
Alignment explanation
Indices: 2371962--2372016 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2371952 ATTTATATTA
2371962 ATAATAATTTTTTAGTTTAAAAT
1 ATAATAATTTTTTAGTTTAAAAT
* * *
2371985 ATAATTATATTTTTATTTTGAAAT
1 ATAATAAT-TTTTTAGTTTAAAAT
*
2372009 AAAATAAT
1 ATAATAAT
2372017 CTTATAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATAATAATTTTTTAGTTTAAAAT
Found at i:2372030 original size:22 final size:22
Alignment explanation
Indices: 2372005--2372048 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2371995 TTTTATTTTG
2372005 AAATA-AAATAATCTTATAAATA
1 AAATATAAAT-ATCTTATAAATA
*
2372027 AAATATAAATATTTTATAAATA
1 AAATATAAATATCTTATAAATA
2372049 TTTTTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATATAAATATCTTATAAATA
Found at i:2372142 original size:18 final size:20
Alignment explanation
Indices: 2372119--2372163 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
2372109 TAAAAAATAT
2372119 ATTTTACCATT-AAT-TTTA
1 ATTTTACCATTAAATATTTA
*
2372137 ATTTTACTATTACAATATTTA
1 ATTTTACCATTA-AATATTTA
2372158 ATTTTA
1 ATTTTA
2372164 TTATTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
20 3 0.13
21 10 0.43
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTACCATTAAATATTTA
Found at i:2372159 original size:21 final size:21
Alignment explanation
Indices: 2372133--2372174 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2372123 TACCATTAAT
2372133 TTTAATTTTACTATTACAATA
1 TTTAATTTTACTATTACAATA
* *
2372154 TTTAATTTTATTATTATAATA
1 TTTAATTTTACTATTACAATA
2372175 ATCAATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATTTTACTATTACAATA
Found at i:2372181 original size:21 final size:21
Alignment explanation
Indices: 2372136--2372187 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2372126 CATTAATTTT
* * *
2372136 AATTTTACTATTACAATATTT
1 AATTTTATTATTACAATAATC
*
2372157 AATTTTATTATTATAATAATC
1 AATTTTATTATTACAATAATC
*
2372178 AATTTCATTA
1 AATTTTATTA
2372188 CTATTATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTATTATTACAATAATC
Found at i:2376123 original size:22 final size:23
Alignment explanation
Indices: 2376098--2376141 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2376088 AAATTTTGAA
*
2376098 TTATTATG-CTTATTATTTATTT
1 TTATTATGAATTATTATTTATTT
*
2376120 TTATTATGAATTTTTATTTATT
1 TTATTATGAATTATTATTTATT
2376142 ATGTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TTATTATGAATTATTATTTATTT
Found at i:2376689 original size:3 final size:3
Alignment explanation
Indices: 2376681--2376705 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2376671 ATTTGATGAG
2376681 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2376706 TGTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2377251 original size:27 final size:31
Alignment explanation
Indices: 2377221--2377281 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
2377211 TATAATAACT
*
2377221 TTAA-AAAA-TATATTTTTAAGAT-A-TTTA
1 TTAATAAAATTATATTTATAAGATAATTTTA
*
2377248 TTAATAAAATTGTATTTATAAGATAATTTTA
1 TTAATAAAATTATATTTATAAGATAATTTTA
2377279 TTA
1 TTA
2377282 TCATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.14
28 4 0.14
29 12 0.43
30 1 0.04
31 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (31 bp):
TTAATAAAATTATATTTATAAGATAATTTTA
Found at i:2379732 original size:2 final size:2
Alignment explanation
Indices: 2379725--2379750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2379715 TAAGGCGATC
2379725 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
2379751 AATTCTTAGA
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:2387871 original size:25 final size:25
Alignment explanation
Indices: 2387826--2387873 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2387816 ATAAAGATAT
*
2387826 ATATATATAAATAATGTAATATAAC
1 ATATATATAAATAATGAAATATAAC
*
2387851 ATATATATATATAGAT-AAATATA
1 ATATATATAAATA-ATGAAATATA
2387874 TTTGTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
ATATATATAAATAATGAAATATAAC
Done.