Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 49 of 126
Found at i:9623864 original size:30 final size:28
Alignment explanation
Indices: 9623830--9623980 Score: 88
Period size: 30 Copynumber: 5.1 Consensus size: 28
9623820 ATAATGAAAG
9623830 AATTTTGAATTTTCTAACTT-TATTTAAATA
1 AATTTT-AATTTT-TAA-TTGTATTTAAATA
* *
9623860 AATTTTTATGTTTTTATTGTATTTAAATA
1 AATTTTAAT-TTTTAATTGTATTTAAATA
* * **
9623889 AATTTTTAATTCTTAATTTGAATAAAAATA
1 AA-TTTTAATTTTTAA-TTGTATTTAAATA
* * * **
9623919 ATTCTTTAATATTTATTATGTAAGTAAATGA
1 AAT-TTTAATTTTTAAT-TGTATTTAAAT-A
**
9623950 GTTTTTAATTTTTAATTTGTATTTAAATA
1 AATTTTAATTTTTAA-TTGTATTTAAATA
9623979 AA
1 AA
9623981 ACTTAAATGC
Statistics
Matches: 90, Mismatches: 23, Indels: 17
0.69 0.18 0.13
Matches are distributed among these distances:
28 2 0.02
29 23 0.26
30 61 0.68
31 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (28 bp):
AATTTTAATTTTTAATTGTATTTAAATA
Found at i:9623978 original size:60 final size:58
Alignment explanation
Indices: 9623830--9623979 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 58
9623820 ATAATGAAAG
* * * **
9623830 AATTTTGAATTTTCTAACTT-TATTTAAATAAATTTTTATGTTTTTATTGTATTTAAATA
1 AATTTTTAATTTT-TAATTTGTATTTAAAT-AATTTTTATATTTTTATTGTAAGTAAATA
* * ** *
9623889 AATTTTTAATTCTTAATTTGAATAAAAATAATTCTTTAATATTTATTA-TGTAAGTAAATG
1 AATTTTTAATTTTTAATTTGTATTTAAATAATT-TTT-ATATTT-TTATTGTAAGTAAATA
*
9623949 AGTTTTTAATTTTTAATTTGTATTTAAATAA
1 AATTTTTAATTTTTAATTTGTATTTAAATAA
9623980 AACTTAAATG
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
58 9 0.12
59 20 0.28
60 40 0.56
61 3 0.04
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (58 bp):
AATTTTTAATTTTTAATTTGTATTTAAATAATTTTTATATTTTTATTGTAAGTAAATA
Found at i:9626360 original size:22 final size:21
Alignment explanation
Indices: 9626324--9626368 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
9626314 CCATGTTTGG
**
9626324 TTATTTCTATTTTTAGTTCATT
1 TTATTTCTAGCTTTA-TTCATT
*
9626346 TTATTTCTAGCTTTATTTATT
1 TTATTTCTAGCTTTATTCATT
9626367 TT
1 TT
9626369 GCCTTATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69
Consensus pattern (21 bp):
TTATTTCTAGCTTTATTCATT
Found at i:9627921 original size:17 final size:17
Alignment explanation
Indices: 9627901--9627948 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
9627891 CCTAACATTT
9627901 TATTTTTAGTAACTTAC
1 TATTTTTAGTAACTTAC
*
9627918 TA-TTTTAGATAA-TTGC
1 TATTTTTAG-TAACTTAC
*
9627934 CATTTTTAGTAACTT
1 TATTTTTAGTAACTT
9627949 TTCATTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (17 bp):
TATTTTTAGTAACTTAC
Found at i:9628140 original size:18 final size:18
Alignment explanation
Indices: 9628102--9628136 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9628092 TATTAGTACT
*
9628102 AAATAAATAATATGTTTG
1 AAATAAAAAATATGTTTG
9628120 AAATAAAAAATAT-TTTG
1 AAATAAAAAATATGTTTG
9628137 GAAAATGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATAAAAAATATGTTTG
Found at i:9634857 original size:15 final size:16
Alignment explanation
Indices: 9634827--9634864 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
9634817 AAAAAATATC
9634827 AATAATAAATAATCAA
1 AATAATAAATAATCAA
*
9634843 AATAATCAA-AATCAA
1 AATAATAAATAATCAA
9634858 AATAATA
1 AATAATA
9634865 GTAGAGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAATAAATAATCAA
Found at i:9648976 original size:34 final size:32
Alignment explanation
Indices: 9648945--9649039 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 32
9648935 ATAACTGAGT
9648945 CGCAAGTTAAAAAATTAAATGACCTGGACTGAA
1 CGCAAGTTAAAAAA-TAAATGACCTGGACTGAA
* * *
9648978 C-CGAGGTT-GAAAATGAATGA-CTGAGACTGAA
1 CGC-AAGTTAAAAAATAAATGACCTG-GACTGAA
*
9649009 CTGCAAGTTAAAAAAATAAATGACCTAGACT
1 C-GCAAGTT-AAAAAATAAATGACCTGGACT
9649040 AAGCTGAGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
30 3 0.06
31 14 0.29
32 9 0.19
33 6 0.12
34 14 0.29
35 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (32 bp):
CGCAAGTTAAAAAATAAATGACCTGGACTGAA
Found at i:9649015 original size:65 final size:65
Alignment explanation
Indices: 9648946--9649097 Score: 171
Period size: 65 Copynumber: 2.3 Consensus size: 65
9648936 TAACTGAGTC
* * * * **
9648946 GCAAGTTAAAAAATTAAATGACCTGGACTGAA-CCGAGGTTGAAAATGAATGACTGAGACTGAAC
1 GCAAGTTAAAAAATTAAATGACCTAGACT-AAGCCGAGGTCGAAAATAAACGACCAAGACTGAAC
9649010 T
65 T
* * * *
9649011 GCAAGTTAAAAAAATAAATGACCTAGACTAAGCTGAGGTCGAAAATAAACGACCAAGATTGAATT
1 GCAAGTTAAAAAATTAAATGACCTAGACTAAGCCGAGGTCGAAAATAAACGACCAAGACTGAACT
* * *
9649076 GCAAGTCAACAAATGAAATGAC
1 GCAAGTTAAAAAATTAAATGAC
9649098 TTAAACTAGG
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 2 0.03
65 70 0.97
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (65 bp):
GCAAGTTAAAAAATTAAATGACCTAGACTAAGCCGAGGTCGAAAATAAACGACCAAGACTGAACT
Found at i:9649118 original size:65 final size:65
Alignment explanation
Indices: 9649049--9649170 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 65
9649039 TAAGCTGAGG
*** *
9649049 TCGAAAATAAACGACCAAGATTGAATTGCAAGTCAACAAATGAAATGACTTAAACTAGGTTAAGA
1 TCGAAAATAAACGACCAAGATTGAACCACAAGTCAAAAAATGAAATGACTTAAACTAGGTTAAGA
* * ** *
9649114 TCGAAAATAAATGATCGGGATTGAACCATAAGTCAAAAAATGAAATGACTTAAACTA
1 TCGAAAATAAACGACCAAGATTGAACCACAAGTCAAAAAATGAAATGACTTAAACTA
9649171 AGTCCAGGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 48 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.22
Consensus pattern (65 bp):
TCGAAAATAAACGACCAAGATTGAACCACAAGTCAAAAAATGAAATGACTTAAACTAGGTTAAGA
Found at i:9649186 original size:65 final size:65
Alignment explanation
Indices: 9649078--9649213 Score: 164
Period size: 65 Copynumber: 2.1 Consensus size: 65
9649068 ATTGAATTGC
* * * * ** *
9649078 AAGTCAACAAATGAAATGACTTAAACTAGGTTAAGATCGAAAATAAATGATCGGGATTGAACCAT
1 AAGTCAAAAAATGAAATGACTTAAACTAAGTCAAGATCAAAAATAAATGATCGAAATTAAACCAT
* * * * *
9649143 AAGTCAAAAAATGAAATGACTTAAACTAAGTCCAGGTCAAAAATGAGTGATCGAAATTAAACCGT
1 AAGTCAAAAAATGAAATGACTTAAACTAAGTCAAGATCAAAAATAAATGATCGAAATTAAACCAT
9649208 AAGTCA
1 AAGTCA
9649214 GAAATAAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (65 bp):
AAGTCAAAAAATGAAATGACTTAAACTAAGTCAAGATCAAAAATAAATGATCGAAATTAAACCAT
Found at i:9658220 original size:16 final size:16
Alignment explanation
Indices: 9658199--9658231 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9658189 AGAAGCCATT
9658199 GTCCTAAAAATTCATG
1 GTCCTAAAAATTCATG
*
9658215 GTCCTAAAAGTTCATG
1 GTCCTAAAAATTCATG
9658231 G
1 G
9658232 CAAGGCACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (16 bp):
GTCCTAAAAATTCATG
Found at i:9659254 original size:29 final size:29
Alignment explanation
Indices: 9659208--9659297 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
9659198 TAATTTATTT
*
9659208 AAATATGATATGAATAATATAAATATATAC
1 AAATA-GATATGATTAATATAAATATATAC
* *
9659238 AAATAGATATGATTAATATAGATATATAT
1 AAATAGATATGATTAATATAAATATATAC
* * * **
9659267 GAATAAATATGATTAACACGAATATATAC
1 AAATAGATATGATTAATATAAATATATAC
9659296 AA
1 AA
9659298 GAATATGACT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.32
Consensus pattern (29 bp):
AAATAGATATGATTAATATAAATATATAC
Found at i:9659426 original size:11 final size:11
Alignment explanation
Indices: 9659410--9659451 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
9659400 TAAAAAATAA
9659410 TTAATATTTAT
1 TTAATATTTAT
*
9659421 TTAATATGTAT
1 TTAATATTTAT
*
9659432 TTAATATATAT
1 TTAATATTTAT
9659443 TTAA-ATTTA
1 TTAATATTTA
9659452 AATTATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 4 0.14
11 24 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTAATATTTAT
Found at i:9659550 original size:6 final size:6
Alignment explanation
Indices: 9659539--9659577 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
9659529 AATGTATAAG
9659539 ATTAAT ATTAAT ATTAAT ATT-AT ATTTATAT ATTAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT A-TTA-AT ATTAAT AT
9659578 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 3 0.10
6 21 0.70
7 3 0.10
8 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTAAT
Found at i:9659590 original size:25 final size:24
Alignment explanation
Indices: 9659543--9659599 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
9659533 TATAAGATTA
* *
9659543 ATATTAATATTAATATTATATTTAT
1 ATATTAATATAAAAATTATATTT-T
9659568 ATATTAATATAAAAAATTA-ATTTT
1 ATATTAATAT-AAAAATTATATTTT
*
9659592 ATAATAAT
1 ATATTAAT
9659600 TATTAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.29
25 14 0.50
26 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTAATATAAAAATTATATTTT
Found at i:9659768 original size:16 final size:17
Alignment explanation
Indices: 9659735--9659768 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9659725 TACATATAAA
9659735 AAATATATTAAACGTGTT
1 AAATATATTAAAC-TGTT
9659753 AAATATATTAAA-TGTT
1 AAATATATTAAACTGTT
9659769 TATTCACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (17 bp):
AAATATATTAAACTGTT
Found at i:9661119 original size:2 final size:2
Alignment explanation
Indices: 9661112--9661141 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9661102 AAGAAAACAT
*
9661112 TA TA TA TA CA 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
9661142 ATTTACTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9669011 original size:45 final size:45
Alignment explanation
Indices: 9668950--9669046 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 45
9668940 CTCTCAATTT
*
9668950 CATACAACTCTTATGCATGTGAAGTCAATCCACCTTTAATCTATA
1 CATACAACTCTTATGCATGTGAAGTCAATCCACCTCTAATCTATA
* * *
9668995 CATATAACTCTTATGCATGTGAAGTCAATCCATCTCTAATTTATA
1 CATACAACTCTTATGCATGTGAAGTCAATCCACCTCTAATCTATA
9669040 CATACAA
1 CATACAA
9669047 TCTAAGTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (45 bp):
CATACAACTCTTATGCATGTGAAGTCAATCCACCTCTAATCTATA
Found at i:9674403 original size:17 final size:17
Alignment explanation
Indices: 9674383--9674434 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
9674373 TTTGGTTTGA
*
9674383 TTTACCATTTTTTAATT
1 TTTAACATTTTTTAATT
**
9674400 TTTAATTTTTTTTAATT
1 TTTAACATTTTTTAATT
*
9674417 TTTATATATTATTTTAAT
1 TTTA-ACATT-TTTTAAT
9674435 ATAAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 18 0.62
18 4 0.14
19 7 0.24
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTAACATTTTTTAATT
Found at i:9674436 original size:13 final size:13
Alignment explanation
Indices: 9674414--9674452 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
9674404 ATTTTTTTTA
*
9674414 ATTTTTATATATT
1 ATTTTAATATATT
**
9674427 ATTTTAATATAAA
1 ATTTTAATATATT
9674440 ATTTTAATATATT
1 ATTTTAATATATT
9674453 TAAGTAGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:9676304 original size:30 final size:30
Alignment explanation
Indices: 9676270--9676345 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
9676260 TTTTGCACCC
*
9676270 AAATAAATCATTAAATTTTAATTTGTATAT
1 AAATAAATCTTTAAATTTTAATTTGTATAT
** *
9676300 AAATAAATCTTTAACCTTTAATTTGTATCT
1 AAATAAATCTTTAAATTTTAATTTGTATAT
9676330 AAATAAATCTTTAAAT
1 AAATAAATCTTTAAAT
9676346 AAATCTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (30 bp):
AAATAAATCTTTAAATTTTAATTTGTATAT
Found at i:9676346 original size:12 final size:12
Alignment explanation
Indices: 9676329--9676362 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
9676319 AATTTGTATC
9676329 TAAATAAATCTT
1 TAAATAAATCTT
9676341 TAAATAAATCTT
1 TAAATAAATCTT
9676353 TAAATAAATC
1 TAAATAAATC
9676363 AATTTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAATAAATCTT
Found at i:9676440 original size:29 final size:30
Alignment explanation
Indices: 9676375--9676447 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
9676365 TTTTTACTTG
*
9676375 AAATAAAGACTTATTTGGATACTAATTAAA
1 AAATAAAGATTTATTTGGATACTAATTAAA
*
9676405 GAATAAAGATTTATTT-GAGTA-TAA-TAAA
1 AAATAAAGATTTATTTGGA-TACTAATTAAA
*
9676433 AATATAAAAATTTAT
1 AA-ATAAAGATTTAT
9676448 CTAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 5 0.14
29 16 0.43
30 16 0.43
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (30 bp):
AAATAAAGATTTATTTGGATACTAATTAAA
Found at i:9677392 original size:21 final size:22
Alignment explanation
Indices: 9677367--9677407 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9677357 ATATATAACT
9677367 CAAATATTTTATA-ATAAATGC
1 CAAATATTTTATACATAAATGC
* *
9677388 CAAATCTTTTTTACATAAAT
1 CAAATATTTTATACATAAAT
9677408 TATAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41
Consensus pattern (22 bp):
CAAATATTTTATACATAAATGC
Found at i:9677882 original size:216 final size:213
Alignment explanation
Indices: 9677480--9678126 Score: 680
Period size: 217 Copynumber: 3.0 Consensus size: 213
9677470 TTATTTGGAT
* * * *
9677480 TATTGACTTTTGATTTGCTTATA-T-ATATTTTTTAAAACCATTATTTTCTTAAAATGTAGTAAT
1 TATTGACTTTTGATTT-CTTGTATTCAT-TTTTTTAAAACCATTA-TTTGTTAAAATTTATTAAT
9677543 C-AATCCTTT-AGTTTTGTAACATTTATATTTTTTACTTTTGGTTTTCTTGTGACTTATAATTTT
63 CAAAT-CTTTGA-TTTTGTAACATTTATA--TTTTACTTTT-GTTTTCTTGTGACTTATAA-TTT
** * * * * * *
9677606 TTATCTCTTTTAAGGATGAGAGTTATATGAATGTCTTTCATGTTTGTGTTACACTTTTTTCTCCC
122 TCCTCTCTTTTAAGGATGAGAGTTATATGAATTTCTTTCATGTCTCTATTACATTTTTTTCTCTC
*
9677671 AATTATTGTTTGTCATAATACTTAGA-
187 AATTATTGTTTGTCATATTACTTAGAC
9677697 TATTGACTTTTGATATTCTTGTATTCATTTTATTTAAAACCATTATTTGTTAAAATTTATTAATC
1 TATTGACTTTTGAT-TTCTTGTATTCATTTT-TTTAAAACCATTATTTGTTAAAATTTATTAATC
* * * *
9677762 AAATCTTTGATTTTATAACATTTATATTGTTGACTTTTAGTTTTCTTATGAATTAT-AGTTTCCT
64 AAATCTTTGATTTTGTAACATTTATATT-TT-ACTTTT-GTTTTCTTGTGACTTATAATTTTCCT
* * *
9677826 CTCTTTTAAGGGTGAGAGTTATATAAATTTCTTTCATGTCTCTATTACATTTTTTTCTCTCGATT
126 CTCTTTTAAGGATGAGAGTTATATGAATTTCTTTCATGTCTCTATTACATTTTTTTCTCTCAATT
* * * *
9677891 ATTATTTTTCATATTATTTGGAC
191 ATTGTTTGTCATATTACTTAGAC
* * * *
9677914 TATTAACTTTTAATTTTCTTGTATGCATTTTCTTTAAAACCATTATTTGTTAAAATTTATTTATC
1 TATTGACTTTTGA-TTTCTTGTATTCATTTT-TTTAAAACCATTATTTGTTAAAATTTATTAATC
* * * * *
9677979 AAATCTATGGTTTTGTAAGATTTATATTTTACTTTTGATTTTCATGTGACTTATGATTTTCCATC
64 AAATCTTTGATTTTGTAACATTTATATTTTACTTTTG-TTTTCTTGTGACTTATAATTTTCC-TC
* ** * * * *
9678044 TCGTTTAAAAATGAGAGGTTATATGAGTGTT-TTTAATG-CTTCTATTATATTTTCTTCTCTCAA
127 TCTTTTAAGGATGAGA-GTTATATGAAT-TTCTTTCATGTC-TCTATTACATTTTTTTCTCTCAA
*
9678107 TTTTTGTTTGTCATATTACT
189 TTATTGTTTGTCATATTACT
9678127 AACTATAAGG
Statistics
Matches: 362, Mismatches: 52, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
214 1 0.00
215 19 0.05
216 87 0.24
217 119 0.33
218 115 0.32
219 21 0.06
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (213 bp):
TATTGACTTTTGATTTCTTGTATTCATTTTTTTAAAACCATTATTTGTTAAAATTTATTAATCAA
ATCTTTGATTTTGTAACATTTATATTTTACTTTTGTTTTCTTGTGACTTATAATTTTCCTCTCTT
TTAAGGATGAGAGTTATATGAATTTCTTTCATGTCTCTATTACATTTTTTTCTCTCAATTATTGT
TTGTCATATTACTTAGAC
Found at i:9681222 original size:2 final size:2
Alignment explanation
Indices: 9681215--9681246 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9681205 TTGACATCGC
*
9681215 TA TA TA TA TA TA CA 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
9681247 AACTTGATTG
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9682526 original size:609 final size:614
Alignment explanation
Indices: 9681428--9682660 Score: 1942
Period size: 609 Copynumber: 2.0 Consensus size: 614
9681418 CAATAACTTA
*
9681428 TAATAATATAACTTTCTTGAATTCATACTTTAAAAATATAAAGAAAGGACACATAAAGATATTAA
1 TAATAATAGAACTTTCTTGAATTCATACTTTAAAAATATAAAGAAAGGACACATAAAGATATTAA
*
9681493 TATTATAAATATATGTGAATTTGGATCATTTTTTATTTAATGCTAATTCATAAAACCCATAATTG
66 TATTATAAATATATGTGAATTTGGATCATTTTTTATTTAATGCTAATTCATAAAACCCACAATTG
*
9681558 AAACCAAAAATAAATTTATTAACTTTTTTTTATATCTTTTTCTCAATTTAATTTTTATCAAAAGA
131 AAACCAAAAATAAATTTATTAAC-TTTTTTTATATCTCTTTCTCAATTTAATTTTTATCAAAAGA
* * *
9681623 ATGTTTTGAAAATTTGTTAATAAGAATAGTTCTTTTTAAGCATGGCATTAATTAGTGGCTCTAAG
195 ATGTGTTGAAAATTTGTCAATAAGAATAGTTCTTTTTAAACATGGCATTAATTAGTGGCTCTAAG
* * *
9681688 ATCAAGTCCAAGGTCTTACCTTCCTAGCCAATTTATGCTTTTATTAATTAGCAAAAAGATATATA
260 ATCAAGTCCAAGATCTTACATTACTAGCCAATTTATGCTTTTATTAATTAGCAAAAAG--A-ATA
*
9681753 TATATATATAAAAACTTTTTTTTTTACATTTTTCCCTCCACATTCATAACTTAAAACTCAAATTT
322 TATATATAT----A-TTTTTTTTTTACATTTTTCCCTCCACATCCATAACTTAAAACTCAAATTT
**
9681818 GAACTGTAAAATTTTATATAAATTTTCATTTATGAAAAGCACAAGTATAACTAAAAAGAAAAGTT
382 GAACTACAAAATTTTATATAAATTTTCATTTATGAAAAGCACAAGTATAACTAAAAAGAAAAGTT
* *
9681883 GAAAATTTTCTTATTAAATAAATTTGTGGTCAAATGAACACTAGAGATTTATTGCCAAATTCACA
447 GAAAATTTTCCTATTAAATAAATTTGTGGTCAAATGAACACTAGAGATTTAATGCCAAATTCACA
* *
9681948 TATTTTATCATTTAAATATGATAGTTTTATTTAGAATAAAATAAAACACTAAGTGAAAAGTACTC
512 TATTTCATCATTTAAATATGATAGTTTTATTTAGAATAAAATAAAACACTAAGTGAAAAATACTC
* * **
9682013 TAAGTAACATTTTTGCTTCTTAAGGGTTGACCTCTTCT
577 TAAATAACATTTTTGCTTCTTAAAGGCGGACCTCTTCT
* *
9682051 TAATAATAGAATTTTCTTGAATTCATACTTTAAAAATATAACGAAAGGACACATAAAGATATTAA
1 TAATAATAGAACTTTCTTGAATTCATACTTTAAAAATATAAAGAAAGGACACATAAAGATATTAA
* *
9682116 TATTATAAATATATGTGAATTTGGATCTTTTTTTTAATTTAATGCTACTTCATAAAACCCACAAT
66 TATTATAAATATATGTGAATTTGGATC-ATTTTTT-ATTTAATGCTAATTCATAAAACCCACAAT
9682181 TGAAACCAAAAATAAATTTATTAAC-TTTTTT-TATCTCTTTCTCAATTTAATTTTTATCAAAAG
129 TGAAACCAAAAATAAATTTATTAACTTTTTTTATATCTCTTTCTCAATTTAATTTTTATCAAAAG
* ** *
9682244 AATGTGTTGAAAATTTGTCAATAAGAATAGTTTTTTTTAAATGTGGCATTGATTAGTGGCTCTAA
194 AATGTGTTGAAAATTTGTCAATAAGAATAGTTCTTTTTAAACATGGCATTAATTAGTGGCTCTAA
* * * *
9682309 GATTAAGTCTAAGATCTTACATTACTAGGCAATTTATGTTTTTATTAATTAGCAAAAAG-ATA-A
259 GATCAAGTCCAAGATCTTACATTACTAGCCAATTTATGCTTTTATTAATTAGCAAAAAGAATATA
* *
9682372 -AT-TGT-TTTTTTTTTTACA-TTTTCTCCTCCATATCCATAACTTAAAACTCAAATTTGAACTA
324 TATATATATTTTTTTTTTACATTTTTC-CCTCCACATCCATAACTTAAAACTCAAATTTGAACTA
* * *
9682433 CAAATTTTTATATAAATTTTTATTTATGAAATGCACAAGTATAACTAAAAAGAAAAGTTGAAAAT
388 CAAAATTTTATATAAATTTTCATTTATGAAAAGCACAAGTATAACTAAAAAGAAAAGTTGAAAAT
* **
9682498 TTTCCTATTAAATAAATTTGTTGTCAAATGAATGCTAGAGATTTAATGCCAAATTCACATATTTC
453 TTTCCTATTAAATAAATTTGTGGTCAAATGAACACTAGAGATTTAATGCCAAATTCACATATTTC
9682563 ATCATTTAAATATGATAGTTTTATTTAGAATAAAATAAAACACTAAGTGAAAAATACTCTAAATA
518 ATCATTTAAATATGATAGTTTTATTTAGAATAAAATAAAACACTAAGTGAAAAATACTCTAAATA
9682628 ACATTTTTGCTTCTTAAAGGCGGACCTCTTCT
583 ACATTTTTGCTTCTTAAAGGCGGACCTCTTCT
9682660 T
1 T
9682661 CCTCATAATA
Statistics
Matches: 567, Mismatches: 40, Indels: 20
0.90 0.06 0.03
Matches are distributed among these distances:
608 5 0.01
609 260 0.46
615 2 0.00
616 2 0.00
617 1 0.00
618 3 0.01
622 141 0.25
623 95 0.17
624 6 0.01
625 52 0.09
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (614 bp):
TAATAATAGAACTTTCTTGAATTCATACTTTAAAAATATAAAGAAAGGACACATAAAGATATTAA
TATTATAAATATATGTGAATTTGGATCATTTTTTATTTAATGCTAATTCATAAAACCCACAATTG
AAACCAAAAATAAATTTATTAACTTTTTTTATATCTCTTTCTCAATTTAATTTTTATCAAAAGAA
TGTGTTGAAAATTTGTCAATAAGAATAGTTCTTTTTAAACATGGCATTAATTAGTGGCTCTAAGA
TCAAGTCCAAGATCTTACATTACTAGCCAATTTATGCTTTTATTAATTAGCAAAAAGAATATATA
TATATATTTTTTTTTTACATTTTTCCCTCCACATCCATAACTTAAAACTCAAATTTGAACTACAA
AATTTTATATAAATTTTCATTTATGAAAAGCACAAGTATAACTAAAAAGAAAAGTTGAAAATTTT
CCTATTAAATAAATTTGTGGTCAAATGAACACTAGAGATTTAATGCCAAATTCACATATTTCATC
ATTTAAATATGATAGTTTTATTTAGAATAAAATAAAACACTAAGTGAAAAATACTCTAAATAACA
TTTTTGCTTCTTAAAGGCGGACCTCTTCT
Found at i:9682770 original size:12 final size:12
Alignment explanation
Indices: 9682753--9682779 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9682743 AATTTCTTAC
9682753 TTTTTCACATTA
1 TTTTTCACATTA
9682765 TTTTTCACATTA
1 TTTTTCACATTA
9682777 TTT
1 TTT
9682780 AAGTATAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTTCACATTA
Found at i:9683624 original size:78 final size:77
Alignment explanation
Indices: 9683542--9683732 Score: 194
Period size: 78 Copynumber: 2.4 Consensus size: 77
9683532 AAACTTTTAA
* * * *
9683542 AAAATAAAAAATAAAAAAACCAAAAAGACACATTCAATTATCACAATTAA-TAGATAAATATTA-
1 AAAATAAAAAGTAAAAAAACCAAAAAGACACAATAAATTAT-ACAATTAATTA-ATAAACATTAT
**
9683605 TTTTTAAAGTTGAAG
64 TTTTTAAA-TCAAAG
*
9683620 AAAATGAAAAGGT-AAAAAA-CAATAAATGA-ACAATAAATTATACAATTAATTAATAAACATTA
1 AAAAT-AAAAAGTAAAAAAACCAA-AAA-GACACAATAAATTATACAATTAATTAATAAACATTA
9683682 TTTTTTAAATCAAAG
63 TTTTTTAAATCAAAG
* *
9683697 AAAATAAAAAGGTAAAGAAAGCTAAAAAGACACAAT
1 AAAATAAAAA-GTAAA-AAAACCAAAAAGACACAAT
9683733 TAATAGATAA
Statistics
Matches: 93, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
76 4 0.04
77 31 0.33
78 38 0.41
79 18 0.19
80 2 0.02
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (77 bp):
AAAATAAAAAGTAAAAAAACCAAAAAGACACAATAAATTATACAATTAATTAATAAACATTATTT
TTTAAATCAAAG
Found at i:9683781 original size:66 final size:67
Alignment explanation
Indices: 9683661--9683799 Score: 169
Period size: 66 Copynumber: 2.1 Consensus size: 67
9683651 AATAAATTAT
*
9683661 ACAATTAATTAATAAACATTATTTTTTAAATCAAAGAAAATAAAAAGGTAAAGAAAG-CTAAAAA
1 ACAATTAATTAATAAACATTATTTTTTAAATCAAAGAAAACAAAAAGGTAAAGAAAGCCTAAAAA
9683725 GAC
66 -AC
* ** ** *
9683728 ACAATTAA-TAGATAAATATTA-TTTTTAAATTGAAGAAAACGTAAAGGTCAAGAAAGCCTAAAA
1 ACAATTAATTA-ATAAACATTATTTTTTAAATCAAAGAAAACAAAAAGGTAAAGAAAGCCTAAAA
9683791 AAC
65 AAC
9683794 -CAATTA
1 ACAATTA
9683800 TCAAAATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
65 6 0.10
66 33 0.52
67 24 0.38
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (67 bp):
ACAATTAATTAATAAACATTATTTTTTAAATCAAAGAAAACAAAAAGGTAAAGAAAGCCTAAAAA
AC
Found at i:9683837 original size:13 final size:13
Alignment explanation
Indices: 9683817--9683846 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9683807 TAATCATTAA
9683817 AATT-TATTATAT
1 AATTATATTATAT
9683829 AATTATATTATAT
1 AATTATATTATAT
9683842 AATTA
1 AATTA
9683847 ATTTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTATATTATAT
Found at i:9692911 original size:66 final size:67
Alignment explanation
Indices: 9692829--9692967 Score: 226
Period size: 66 Copynumber: 2.1 Consensus size: 67
9692819 GTTTGTATGG
*
9692829 TTTTGAGATTCAAAGTTTATTGTACATGATTGTGTTGCTATGAAGGTGCTATTGCGG-TATTCTC
1 TTTTGAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGAAGGTGCTATTGCGGTTATTCTC
9692893 AT
66 AT
* * *
9692895 TTTTTAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGGAGGTGCTATTGTGGTTATTCTC
1 TTTTGAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGAAGGTGCTATTGCGGTTATTCTC
9692960 AT
66 AT
*
9692962 TCTTGA
1 TTTTGA
9692968 TATTATGATG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
66 53 0.80
67 13 0.20
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (67 bp):
TTTTGAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGAAGGTGCTATTGCGGTTATTCTC
AT
Found at i:9693033 original size:23 final size:24
Alignment explanation
Indices: 9693006--9693053 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
9692996 TTGAGCTTCA
*
9693006 ATAATATTG-GCCTTGAGTTGATT
1 ATAATATTGTGCCTTGAATTGATT
9693029 ATAATATTGTTGCCTTGAATTGATT
1 ATAATATTG-TGCCTTGAATTGATT
9693054 GAGCAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
25 13 0.59
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (24 bp):
ATAATATTGTGCCTTGAATTGATT
Found at i:9696495 original size:66 final size:67
Alignment explanation
Indices: 9696407--9696542 Score: 229
Period size: 66 Copynumber: 2.0 Consensus size: 67
9696397 GTTTGTATGG
* *
9696407 TTTTGAGATTCAAATTTTATTGTACATGATTGTGTTGCTATGAAGGTGCTATTGTGG-TATTCTC
1 TTTTGAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGAAGGTGCTATTGTGGTTATTCTC
9696471 AT
66 AT
* *
9696473 TTTTTAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGGAGGTGCTATTGTGGTTATTCTC
1 TTTTGAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGAAGGTGCTATTGTGGTTATTCTC
9696538 AT
66 AT
9696540 TTT
1 TTT
9696543 GATATTATGA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 53 0.82
67 12 0.18
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.49
Consensus pattern (67 bp):
TTTTGAGATTCAAAGTTTATTGTACATGATTGTGTTACTATGAAGGTGCTATTGTGGTTATTCTC
AT
Found at i:9701547 original size:23 final size:21
Alignment explanation
Indices: 9701448--9701558 Score: 64
Period size: 24 Copynumber: 4.8 Consensus size: 21
9701438 AAAAAAAAAA
* *
9701448 AAAAAATTATTTTTCATAATTT
1 AAAAAA-TATTTTTTAAAATTT
9701470 AACAAAAATATATTTTTAAAA--T
1 -A-AAAAATAT-TTTTTAAAATTT
*
9701492 AAAAAATGACTTTTGTTAAAAGTATG
1 AAAAAAT-A-TTTT-TTAAAA-T-TT
9701518 AAAAAATATTTTTTAAAATTT
1 AAAAAATATTTTTTAAAATTT
9701539 AACAGAAATGATATTTTTAA
1 AA-A-AAAT-AT-TTTTTAA
9701559 GATAAAAAGT
Statistics
Matches: 71, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
20 6 0.08
21 8 0.11
22 10 0.14
23 14 0.20
24 18 0.25
25 8 0.11
26 7 0.10
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (21 bp):
AAAAAATATTTTTTAAAATTT
Found at i:9701601 original size:112 final size:112
Alignment explanation
Indices: 9701473--9701766 Score: 448
Period size: 112 Copynumber: 2.6 Consensus size: 112
9701463 ATAATTTAAC
9701473 AAAAAT-ATATTTTTAAAATAAAAAATGACTTTTGTTAAAAGTATGAAAAAATATTTTTTAAAAT
1 AAAAATGATATTTTTAAAATAAAAAATGACTTTTGTTAAAA-TATGAAAAAATATTTTTTAAAAT
*
9701537 TTAACAGAAATGATATTTTTAAGATAAAAAGTGTAATCTTTGATG-AA
65 TTAACAAAAATGATATTTTTAAGATAAAAAGTGTAATCTTTGATGAAA
9701584 AAAAATGATATTTTTAAAATAAAAAATGACTTTTGTTAAAAATATGAAAAAATATTTTTTAAAAT
1 AAAAATGATATTTTTAAAATAAAAAATGACTTTTGTT-AAAATATGAAAAAATATTTTTTAAAAT
9701649 TTAACAAAAATGATATTTTTAAGATAAAAAGTGTAATCTTTGATGAAAA
65 TTAACAAAAATGATATTTTTAAGATAAAAAGTGTAATCTTTGATG-AAA
* * * * * *
9701698 AAAATATGATATTTTAAAAATAAAAACTCAATTTTTATTATAAACATGAAGAAAATATTTTTTAA
1 AAAA-ATGATATTTTTAAAATAAAAAAT-GACTTTTGTTA-AAATATGAA-AAAATATTTTTTAA
9701763 AATT
62 AATT
9701767 CAGTAAAGAT
Statistics
Matches: 168, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
111 6 0.04
112 97 0.58
113 4 0.02
114 6 0.04
115 22 0.13
116 15 0.09
117 18 0.11
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (112 bp):
AAAAATGATATTTTTAAAATAAAAAATGACTTTTGTTAAAATATGAAAAAATATTTTTTAAAATT
TAACAAAAATGATATTTTTAAGATAAAAAGTGTAATCTTTGATGAAA
Found at i:9701608 original size:23 final size:23
Alignment explanation
Indices: 9701473--9701678 Score: 84
Period size: 21 Copynumber: 9.1 Consensus size: 23
9701463 ATAATTTAAC
9701473 AAAAAT-ATATTTTTAAAAT--A
1 AAAAATGATATTTTTAAAATAAA
*
9701493 AAAAATGACT-TTTGTTAAAAGTATGA
1 AAAAATGA-TATTT-TTAAAA-TA-AA
*
9701519 AAAAAT-AT-TTTTTAAAATTTAAC
1 AAAAATGATATTTTTAAAA--TAAA
* *
9701542 AGAAATGATATTTTTAAGAT--A
1 AAAAATGATATTTTTAAAATAAA
* * * *
9701563 AAAAGTG-TAATCTTT--GATGAA
1 AAAAATGAT-ATTTTTAAAATAAA
9701584 AAAAATGATATTTTTAAAAT--A
1 AAAAATGATATTTTTAAAATAAA
*
9701605 AAAAATGACT-TTTGTTAAAAATATGA
1 AAAAATGA-TATTT-TT-AAAATA-AA
*
9701631 AAAAAT-AT-TTTTTAAAATTTAAC
1 AAAAATGATATTTTTAAAA--TAAA
*
9701654 AAAAATGATATTTTTAAGATAAA
1 AAAAATGATATTTTTAAAATAAA
9701677 AA
1 AA
9701679 GTGTAATCTT
Statistics
Matches: 144, Mismatches: 16, Indels: 49
0.69 0.08 0.23
Matches are distributed among these distances:
19 3 0.02
20 7 0.05
21 38 0.26
22 15 0.10
23 33 0.23
24 16 0.11
25 18 0.12
26 14 0.10
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (23 bp):
AAAAATGATATTTTTAAAATAAA
Found at i:9701722 original size:23 final size:22
Alignment explanation
Indices: 9701582--9701723 Score: 78
Period size: 24 Copynumber: 6.2 Consensus size: 22
9701572 ATCTTTGATG
*
9701582 AAAAAAATGATATTTTTAAAAT
1 AAAAAAATGATATTTTAAAAAT
*
9701604 -AAAAAATGACTTTTGTTAAAAAT
1 AAAAAAATGA-TATT-TTAAAAAT
* *
9701627 ATGAAAAAAT-ATTTTTTAAAATTT
1 A--AAAAAATGATATTTTAAAA-AT
* *
9701651 AACAAAAATGATATTTTTAAGAT
1 AA-AAAAATGATATTTTAAAAAT
* *
9701674 -AAAAAGTG-TAATCTTTGATGAAA-
1 AAAAAAATGAT-AT-TTT-A-AAAAT
*
9701697 AAAAATATGATATTTTAAAAAT
1 AAAAAAATGATATTTTAAAAAT
9701719 AAAAA
1 AAAAA
9701724 CTCAATTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 30
0.67 0.10 0.22
Matches are distributed among these distances:
20 1 0.01
21 20 0.22
22 14 0.15
23 23 0.25
24 24 0.26
25 2 0.02
26 7 0.08
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
AAAAAAATGATATTTTAAAAAT
Found at i:9704179 original size:7 final size:7
Alignment explanation
Indices: 9704167--9704196 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
9704157 TCTCTTAATC
9704167 TTTATAT
1 TTTATAT
9704174 TTTATAT
1 TTTATAT
9704181 TTTATAT
1 TTTATAT
*
9704188 TTCATAT
1 TTTATAT
9704195 TT
1 TT
9704197 CATAATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATAT
Found at i:9705482 original size:3 final size:3
Alignment explanation
Indices: 9705474--9705526 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
9705464 TTATGCCTTG
*
9705474 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9705522 ATT AT
1 ATT AT
9705527 AAAAGAAGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9705927 original size:6 final size:7
Alignment explanation
Indices: 9705914--9705938 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9705904 TTTTATTTTT
9705914 AATAAAA
1 AATAAAA
9705921 AATAAAA
1 AATAAAA
9705928 AATAAAA
1 AATAAAA
9705935 AATA
1 AATA
9705939 GTTTATTTTT
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):
AATAAAA
Found at i:9706677 original size:3 final size:3
Alignment explanation
Indices: 9706669--9706709 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
9706659 GTTTATTTCA
*
9706669 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9706710 CTAGATAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:9708359 original size:30 final size:31
Alignment explanation
Indices: 9708303--9708363 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
9708293 TAGAAGTCCG
9708303 TTTAAGAAAATAATAATACAATAACTAAATA
1 TTTAAGAAAATAATAATACAATAACTAAATA
* *
9708334 TTTAAGAAAATAATAGTA-GATAACTAAATA
1 TTTAAGAAAATAATAATACAATAACTAAATA
9708364 CACATGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (31 bp):
TTTAAGAAAATAATAATACAATAACTAAATA
Found at i:9710646 original size:52 final size:51
Alignment explanation
Indices: 9710494--9710650 Score: 215
Period size: 52 Copynumber: 3.0 Consensus size: 51
9710484 TATAACCATA
* * ** *
9710494 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCCGTAAGT
1 CAAACTTGCCTATTAAGAATCCCT-TTCTCTTAGAATTCTTCTCTTGCAAGT
*
9710546 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTT-CTCTTAGAATTCTTCTCTTGCAAGT
* *
9710598 CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-CTTTCTCTTAGAATTCTTCTCTTGCAAGT
9710650 C
1 C
9710651 TTCTTGTCCA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 1 0.01
52 89 0.95
53 4 0.04
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.38
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCCTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:9710693 original size:11 final size:11
Alignment explanation
Indices: 9710677--9710705 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
9710667 AATATCTGAA
9710677 AAATCTCAAAC
1 AAATCTCAAAC
9710688 AAATCTCAAAC
1 AAATCTCAAAC
9710699 AAATCTC
1 AAATCTC
9710706 TTATGGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATCTCAAAC
Found at i:9711330 original size:15 final size:16
Alignment explanation
Indices: 9711312--9711342 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9711302 ATATATCAAA
9711312 ATTATTAA-TATGATT
1 ATTATTAAGTATGATT
9711327 ATTATTAAGTATGATT
1 ATTATTAAGTATGATT
9711343 TTAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
ATTATTAAGTATGATT
Found at i:9720067 original size:11 final size:11
Alignment explanation
Indices: 9720051--9720089 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
9720041 AGCCTAATAC
9720051 AAAGAAACTAA
1 AAAGAAACTAA
9720062 AAAGAAACTAA
1 AAAGAAACTAA
* *
9720073 AAA-AAAATTA
1 AAAGAAACTAA
9720083 AAAGAAA
1 AAAGAAA
9720090 AGATGAACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (11 bp):
AAAGAAACTAA
Found at i:9721623 original size:21 final size:23
Alignment explanation
Indices: 9721594--9721638 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
9721584 TAAAATGGGA
* *
9721594 AAATCAAG-TTGG-ACTTTATTG
1 AAATAAAGTTTGGAACTTCATTG
9721615 AAATAAAGTTTGGAACTTCATTG
1 AAATAAAGTTTGGAACTTCATTG
9721638 A
1 A
9721639 CCTAATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (23 bp):
AAATAAAGTTTGGAACTTCATTG
Found at i:9724218 original size:19 final size:18
Alignment explanation
Indices: 9724185--9724222 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
9724175 TGATGAATGC
*
9724185 TATCTTGATTATTTCATA
1 TATCTTCATTATTTCATA
9724203 TATCTTCATATATTTCATA
1 TATCTTCAT-TATTTCATA
9724222 T
1 T
9724223 TATACCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (18 bp):
TATCTTCATTATTTCATA
Found at i:9725998 original size:61 final size:62
Alignment explanation
Indices: 9725914--9726039 Score: 202
Period size: 61 Copynumber: 2.0 Consensus size: 62
9725904 ATTCAAACTC
* *
9725914 CTTGATGCTTGCTTAAGTTTATAGATGGATTTTT-AAAGCTTGCACACCTTATTAACATTAT
1 CTTGATGCTTGCTTAAATCTATAGATGGATTTTTAAAAGCTTGCACACCTTATTAACATTAT
*
9725975 CTTGATGCTTAG-TTAAATCTATAGATGGATTTTTAAAAGCTTGTACACCTTATTAACATTAT
1 CTTGATGCTT-GCTTAAATCTATAGATGGATTTTTAAAAGCTTGCACACCTTATTAACATTAT
9726037 CTT
1 CTT
9726040 TGGATTTTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
61 30 0.50
62 30 0.50
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (62 bp):
CTTGATGCTTGCTTAAATCTATAGATGGATTTTTAAAAGCTTGCACACCTTATTAACATTAT
Found at i:9730476 original size:59 final size:60
Alignment explanation
Indices: 9730413--9730698 Score: 172
Period size: 63 Copynumber: 4.7 Consensus size: 60
9730403 AGGCATTTTC
*
9730413 AATAATCCCCTTCAATTTTTTTTAGGATTATTCAAGGCATTTCTGAC-AAAAATGCCTTG
1 AATAATCCCCTTCAATTTTTTTTAGGATTATTCAAGGCGTTTCTGACAAAAAATGCCTTG
* * * * * * *
9730472 AATAAT-CTCTTCCA-TTTTTTGAAGATTATTCAAGGTGTTTTTGGCAATAAAACT-CCTTG
1 AATAATCCCCTTCAATTTTTTTTAGGATTATTCAAGGCGTTTCTGACAA-AAAA-TGCCTTG
* ** *** * * *
9730531 AATAAT-CTCTTACAAAAAATTAAATAGGGTTATTCAAGGCGTTTCTGACAAAAAATACATTG
1 AATAATCCCCTT-C--AATTTTTTTTAGGATTATTCAAGGCGTTTCTGACAAAAAATGCCTTG
* * * * * * * *
9730593 AATAATCCCTTTCTATTTTTTTTTTTTGGATTATTCAAAGCTTTTTATG-CCAAAAATGCCTTT
1 AATAATCCCCTTC-A--ATTTTTTTTAGGATTATTCAAGGC-GTTTCTGACAAAAAATGCCTTG
* * *
9730656 AA-AAACACCCTTCCCATTTTTTTTAGGATTATTCAAGGTGTTT
1 AATAATC-CCCTT-CAATTTTTTTTAGGATTATTCAAGGCGTTT
9730699 TTTGCTAAAA
Statistics
Matches: 167, Mismatches: 46, Indels: 27
0.70 0.19 0.11
Matches are distributed among these distances:
57 25 0.15
58 7 0.04
59 26 0.16
60 5 0.03
61 22 0.13
62 19 0.11
63 57 0.34
64 6 0.04
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (60 bp):
AATAATCCCCTTCAATTTTTTTTAGGATTATTCAAGGCGTTTCTGACAAAAAATGCCTTG
Found at i:9730503 original size:57 final size:59
Alignment explanation
Indices: 9730429--9730541 Score: 142
Period size: 57 Copynumber: 1.9 Consensus size: 59
9730419 CCCCTTCAAT
* *
9730429 TTTTTTTAGGATTATTCAAGGCATTTCTGAC-A-AAAA-TGCCTTGAATAATCTCTTCCA
1 TTTTTTGAAGATTATTCAAGGCATTTCTGACAATAAAACT-CCTTGAATAATCTCTTCCA
** * *
9730486 TTTTTTGAAGATTATTCAAGGTGTTTTTGGCAATAAAACTCCTTGAATAATCTCTT
1 TTTTTTGAAGATTATTCAAGGCATTTCTGACAATAAAACTCCTTGAATAATCTCTT
9730542 ACAAAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 25 0.53
58 1 0.02
59 20 0.43
60 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (59 bp):
TTTTTTGAAGATTATTCAAGGCATTTCTGACAATAAAACTCCTTGAATAATCTCTTCCA
Found at i:9730556 original size:177 final size:180
Alignment explanation
Indices: 9730230--9730559 Score: 413
Period size: 177 Copynumber: 1.9 Consensus size: 180
9730220 CAAAAATACC
* *
9730230 TTCAATAATCCCTTCTAATTTTTTTAGGGATTATTCAAGGCGTTTCTAGCTAAAAACGCTTTCAA
1 TTCAATAATCCCTTCTAATTTTTTTAGGGATTATTCAAGGCATTTCTAGCTAAAAACGCCTTCAA
* * *
9730295 TAATCCCCTCTAATTTTTTTAGGGAGTATTCAAGATGCTTTTGGCCAGAAAATGCCTTAAATAAT
66 TAATCCCCTCTAATTTTTTGAGAGAGTATTCAAGATGCTTTTGGCAAGAAAATGCCTTAAATAAT
*
9730360 CCCATATAAAAAATTAAATAGGGATTTTTTTGGGGATTATTCAAGGCATT
131 CCCATACAAAAAATTAAATAGGGATTTTTTTGGGGATTATTCAAGGCATT
*
9730410 TTCAATAATCCCCTTC-AATTTTTTTTA-GGATTATTCAAGGCATTTCT-GAC-AAAAATGCCTT
1 TTCAATAAT-CCCTTCTAA-TTTTTTTAGGGATTATTCAAGGCATTTCTAG-CTAAAAACGCCTT
* * * * * * * * *
9730471 GAATAATCTCTTC-CATTTTTTGA-AGATTATTCAAGGTGTTTTTGGCAATAAAACT-CCTTGAA
63 CAATAATCCCCTCTAATTTTTTGAGAGAGTATTCAAGATGCTTTTGGCAAGAAAA-TGCCTTAAA
* *
9730533 TAATCTCTTACAAAAAATTAAATAGGG
127 TAATCCCATACAAAAAATTAAATAGGG
9730560 TTATTCAAGG
Statistics
Matches: 128, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
177 54 0.42
178 9 0.07
179 20 0.16
180 31 0.24
181 14 0.11
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (180 bp):
TTCAATAATCCCTTCTAATTTTTTTAGGGATTATTCAAGGCATTTCTAGCTAAAAACGCCTTCAA
TAATCCCCTCTAATTTTTTGAGAGAGTATTCAAGATGCTTTTGGCAAGAAAATGCCTTAAATAAT
CCCATACAAAAAATTAAATAGGGATTTTTTTGGGGATTATTCAAGGCATT
Found at i:9730787 original size:187 final size:183
Alignment explanation
Indices: 9730428--9730763 Score: 444
Period size: 187 Copynumber: 1.8 Consensus size: 183
9730418 TCCCCTTCAA
* * * * *
9730428 TTTTTTTTAGGATTATTCAAGGCATTTCTGACAAAAATGCCTTGAATAATCTCTTCCATTTTTTG
1 TTTTTTTTAGGATTATTCAAAGCATTTATGACAAAAATGCCTTGAAAAAACCCTTCCATTTTTTG
* *
9730493 AAGATTATTCAAGGTGTTTTTGGCAATAAAACTCCTTGAATAATCTCTTACAAAAAATTAAATAG
66 AAGATTATTCAAGGTGTTTTTGGCAATAAAACTCCTTGAATAATCCCTTACAAAAAATTAAAGAG
*
9730558 GGTTATTCAAGGCGTTTCTGACAAAAAATACATTGAATAATCCCTTTCTATTT
131 GCTTATTCAAGGCGTTTCTGACAAAAAATACATTGAATAATCCCTTTCTATTT
* * * *
9730611 TTTTTTTTTGGATTATTCAAAGCTTTTTATGCCAAAAATGCCTTTAAAAACACCCTTCCCATTTT
1 TTTTTTTTAGGATTATTCAAAGC-ATTTATGACAAAAATGCCTTGAAAAA-ACCCTT-CCA-TTT
* * *
9730676 TTTTAGGATTATTCAAGGTGTTTTTTGCTAA-AAAAC-CACTTGAATAATCCCTTACAAAAAATT
62 TTTGAAGATTATTCAAGGTGTTTTTGGC-AATAAAACTC-CTTGAATAATCCCTTACAAAAAATT
*
9730739 GAACGA-GCTTATTCAAGGCGTTTCT
125 -AAAGAGGCTTATTCAAGGCGTTTCT
9730764 AGCTAAAAAC
Statistics
Matches: 130, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
183 21 0.16
184 21 0.16
185 4 0.03
186 4 0.03
187 75 0.58
188 5 0.04
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (183 bp):
TTTTTTTTAGGATTATTCAAAGCATTTATGACAAAAATGCCTTGAAAAAACCCTTCCATTTTTTG
AAGATTATTCAAGGTGTTTTTGGCAATAAAACTCCTTGAATAATCCCTTACAAAAAATTAAAGAG
GCTTATTCAAGGCGTTTCTGACAAAAAATACATTGAATAATCCCTTTCTATTT
Found at i:9739189 original size:55 final size:55
Alignment explanation
Indices: 9739024--9739189 Score: 171
Period size: 56 Copynumber: 3.0 Consensus size: 55
9739014 TTTTTTTTTA
* * * * *
9739024 AATTTC-AAAATT-AAAGAAAAAAATTGAAAT-TCCATTTTTCCTTTAAATGAAACT
1 AATTTCAAAAATTAAAAG-AAAAAGTTAAAATATCAATTTTTCCTTAAAATCAAA-T
*
9739078 AATTTCAAAAATTAAAAGAAAAAGTTAAAGTATCAATTTTTCCTTAAAA-CAAAAAT
1 AATTTCAAAAATTAAAAGAAAAAGTTAAAATATCAATTTTTCCTTAAAATC--AAAT
* **
9739134 AATTTCAAAATTTTGAAGAAAAAGTTAAAATATCAA-TTTTCCTTAAATATCAAAT
1 AATTTCAAAAATTAAAAGAAAAAGTTAAAATATCAATTTTTCCTTAAA-ATCAAAT
9739189 A
1 A
9739190 TTTAAGACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
54 6 0.06
55 32 0.34
56 53 0.56
57 4 0.04
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (55 bp):
AATTTCAAAAATTAAAAGAAAAAGTTAAAATATCAATTTTTCCTTAAAATCAAAT
Found at i:9744725 original size:27 final size:27
Alignment explanation
Indices: 9744694--9744745 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9744684 ATGCTTGGTG
*
9744694 TTTGTTAGATTGTTAGATGAATTAAAA
1 TTTGTTAGATTATTAGATGAATTAAAA
* *
9744721 TTTGTTAGGTTATTATATGAATTAA
1 TTTGTTAGATTATTAGATGAATTAA
9744746 GTTACTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (27 bp):
TTTGTTAGATTATTAGATGAATTAAAA
Found at i:9746017 original size:18 final size:18
Alignment explanation
Indices: 9745954--9746018 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
9745944 TATTTTTAGA
9745954 AAAATAATTTAATAATTT
1 AAAATAATTTAATAATTT
* *
9745972 ATAATAATTTATTAATTTT
1 AAAATAATTTAATAA-TTT
*
9745991 ATAAAT-ATTAAATAATTT
1 A-AAATAATTTAATAATTT
*
9746009 AAAATTATTT
1 AAAATAATTT
9746019 TGTATATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.11
18 20 0.53
19 11 0.29
20 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATAATTTAATAATTT
Found at i:9749671 original size:19 final size:20
Alignment explanation
Indices: 9749649--9749690 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
9749639 TTATAGTTTA
*
9749649 AAATGAATTT-TATAAAAT-T
1 AAAT-AATTTATACAAAATAT
9749668 AAATAATTTATACAAAATAT
1 AAATAATTTATACAAAATAT
9749688 AAA
1 AAA
9749691 AGTATTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
19 11 0.55
20 4 0.20
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATAATTTATACAAAATAT
Found at i:9755601 original size:12 final size:12
Alignment explanation
Indices: 9755584--9755619 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
9755574 GCACAAGGTT
9755584 CAAGATATTCCA
1 CAAGATATTCCA
*
9755596 CAAGATGTTCCA
1 CAAGATATTCCA
9755608 CAAGATATTCCA
1 CAAGATATTCCA
9755620 TAAAAAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (12 bp):
CAAGATATTCCA
Found at i:9758340 original size:61 final size:62
Alignment explanation
Indices: 9758256--9758381 Score: 202
Period size: 61 Copynumber: 2.0 Consensus size: 62
9758246 ATTCAAACTC
* *
9758256 CTTGATGCTTGCTTAAGTTTATAGATGGATTTTT-AAAGCTTGCACACCTTATTAACATTAT
1 CTTGATGCTTGCTTAAATCTATAGATGGATTTTTAAAAGCTTGCACACCTTATTAACATTAT
*
9758317 CTTGATGCTTAG-TTAAATCTATAGATGGATTTTTAAAAGCTTGTACACCTTATTAACATTAT
1 CTTGATGCTT-GCTTAAATCTATAGATGGATTTTTAAAAGCTTGCACACCTTATTAACATTAT
9758379 CTT
1 CTT
9758382 TGGATTTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
61 30 0.50
62 30 0.50
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (62 bp):
CTTGATGCTTGCTTAAATCTATAGATGGATTTTTAAAAGCTTGCACACCTTATTAACATTAT
Found at i:9762411 original size:23 final size:23
Alignment explanation
Indices: 9762385--9762429 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9762375 CAAAAGAAGA
9762385 TGAAAATT-GACCAAAAAAATGAC
1 TGAAAATTAG-CCAAAAAAATGAC
* *
9762408 TGAAACTTAGGCAAAAAAATGA
1 TGAAAATTAGCCAAAAAAATGA
9762430 GAAGAAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (23 bp):
TGAAAATTAGCCAAAAAAATGAC
Found at i:9762836 original size:60 final size:61
Alignment explanation
Indices: 9762758--9763072 Score: 180
Period size: 60 Copynumber: 5.2 Consensus size: 61
9762748 AGGCATTTTC
* * *
9762758 AATAATCCCCTTCAATTTTTTTTAGGGATTATTCAAGGCATTTCTGAC-AAAAATGCCTTG
1 AATAATCCCTTTCAATTTTTTTTAGGGATTATTCAAGGCGTTTCTGGCAAAAAATGCCTTG
* * * * * *
9762818 AATAATCTCTTTCCA-TTTTTTGA-AGATTATTCAAGGTGTTTTTGGCAATAAAACT-CCTTG
1 AATAATCCCTTTCAATTTTTTTTAGGGATTATTCAAGGCGTTTCTGGCAA-AAAA-TGCCTTG
* * ** *** * *
9762878 AATAATCTCTTACAAAAAATTAAATAGGG-TTATTCAAGGCGTTTCTGGCAAAAAATACATTG
1 AATAATCCCTTTC--AATTTTTTTTAGGGATTATTCAAGGCGTTTCTGGCAAAAAATGCCTTG
* * * * * * *
9762940 AATAATCCCTTTCTATTTTTTTT-TGGATTATTCAAAGC-TTTTTATGCCAAAAATGCCTTT
1 AATAATCCCTTTCAATTTTTTTTAGGGATTATTCAAGGCGTTTCT-GGCAAAAAATGCCTTG
* * * * * * * * * *
9763000 AAAAACACCCTTCCCA-TTTTTTTAAGGATTATTTAAGGTGTTTTTTGCTAAAAAA-CCACTTG
1 AATAA-TCCCTTTCAATTTTTTTTAGGGATTATTCAAGGCGTTTCTGGC-AAAAAATGC-CTTG
9763062 AATAATCCCTT
1 AATAATCCCTT
9763073 ACAAAAAATT
Statistics
Matches: 191, Mismatches: 49, Indels: 29
0.71 0.18 0.11
Matches are distributed among these distances:
58 18 0.09
59 14 0.07
60 69 0.36
61 29 0.15
62 37 0.19
63 23 0.12
64 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (61 bp):
AATAATCCCTTTCAATTTTTTTTAGGGATTATTCAAGGCGTTTCTGGCAAAAAATGCCTTG
Found at i:9762901 original size:179 final size:180
Alignment explanation
Indices: 9762575--9762906 Score: 397
Period size: 179 Copynumber: 1.9 Consensus size: 180
9762565 CAAAAATACC
* * *
9762575 TTCAATAATCTCTTCTAATTTTTTTAGAGATTATTCAAGGCGTTTCTAGCTAAAAACGCTTTCAA
1 TTCAATAATCCCTTCTAATTTTTTTAGAGATTATTCAAGGCATTTCTAGCTAAAAACGCCTTCAA
* * *
9762640 TAATCCCCTCTAATTTTTTTAGGGAGTATTCAAGATGCTTTTGGCCAGAAAATGCCTTAAATAAT
66 TAATCCCCTCTAATTTTTTGAGAGAGTATTCAAGATGCTTTTGGCAAGAAAATGCCTTAAATAAT
*
9762705 CCCATATAAAAAATTAAATAGGGATTTTTTTGGGGATTATTCAAGGCATT
131 CCCATACAAAAAATTAAATAGGGATTTTTTTGGGGATTATTCAAGGCATT
* *
9762755 TTCAATAATCCCCTTC-AATTTTTTTTAGGGATTATTCAAGGCATTTCT-GAC-AAAAATGCCTT
1 TTCAATAAT-CCCTTCTAA-TTTTTTTAGAGATTATTCAAGGCATTTCTAG-CTAAAAACGCCTT
* * * * * * * * *
9762817 GAATAAT-CTCTTTCCATTTTTTGA-AGATTATTCAAGGTGTTTTTGGCAATAAAACT-CCTTGA
63 CAATAATCCCCTCT-AATTTTTTGAGAGAGTATTCAAGATGCTTTTGGCAAGAAAA-TGCCTTAA
* *
9762879 ATAATCTCTTACAAAAAATTAAATAGGG
126 ATAATCCCATACAAAAAATTAAATAGGG
9762907 TTATTCAAGG
Statistics
Matches: 127, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
179 58 0.46
180 36 0.28
181 33 0.26
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (180 bp):
TTCAATAATCCCTTCTAATTTTTTTAGAGATTATTCAAGGCATTTCTAGCTAAAAACGCCTTCAA
TAATCCCCTCTAATTTTTTGAGAGAGTATTCAAGATGCTTTTGGCAAGAAAATGCCTTAAATAAT
CCCATACAAAAAATTAAATAGGGATTTTTTTGGGGATTATTCAAGGCATT
Found at i:9763097 original size:184 final size:182
Alignment explanation
Indices: 9762758--9763138 Score: 441
Period size: 184 Copynumber: 2.1 Consensus size: 182
9762748 AGGCATTTTC
* * *
9762758 AATAATCCCCTTCAATTTTTTTTAGGGATTATTCAAGGCATTTCTGACAAAAATGCCTTGAATAA
1 AATAATCCCCTTCAATTTTTTTTAGGGATTATTCAAAGCATTTATGACAAAAATGCCTTGAAAAA
* * * *
9762823 TCTCTTTCCATTTTTTGAAGATTATTCAAGGTGTTTTTGGCAATAAAACTCCTTGAATAATCTCT
66 ACCCTTCCCATTTTTTGAAGATTATTCAAGGTGTTTTTGGCAATAAAACTCCTTGAATAATCCCT
* * *
9762888 TACAAAAAATTAAATAGGGTTATTCAAGGCGTTTCTGGCAAAAAATACATTG
131 TACAAAAAATTAAAGAGGCTTATTCAAGGCGTTTCTAGCAAAAAATACATTG
* * * * * *
9762940 AATAATCCCTTTCTATTTTTTTT-TGGATTATTCAAAGCTTTTTATGCCAAAAATGCCTTTAAAA
1 AATAATCCCCTTCAATTTTTTTTAGGGATTATTCAAAGC-ATTTATGACAAAAATGCCTTGAAAA
* * *
9763004 ACACCCTTCCCATTTTTTTAAGGATTATTTAAGGTGTTTTTTGCTAA-AAAAC-CACTTGAATAA
65 A-ACCCTTCCCATTTTTTGAA-GATTATTCAAGGTGTTTTTGGC-AATAAAACTC-CTTGAATAA
* * *
9763067 TCCCTTACAAAAAATTGAACGA-GCTTATTCAAGGTGTTTCTAGCTAAAAACGT-C-TTG
126 TCCCTTACAAAAAATT-AAAGAGGCTTATTCAAGGCGTTTCTAGC-AAAAA-ATACATTG
*
9763124 AATAATCCTCTTCAA
1 AATAATCCCCTTCAA
9763139 CTAAAAGTTA
Statistics
Matches: 166, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
181 13 0.08
182 42 0.25
183 16 0.10
184 83 0.50
185 11 0.07
186 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (182 bp):
AATAATCCCCTTCAATTTTTTTTAGGGATTATTCAAAGCATTTATGACAAAAATGCCTTGAAAAA
ACCCTTCCCATTTTTTGAAGATTATTCAAGGTGTTTTTGGCAATAAAACTCCTTGAATAATCCCT
TACAAAAAATTAAAGAGGCTTATTCAAGGCGTTTCTAGCAAAAAATACATTG
Found at i:9771054 original size:20 final size:21
Alignment explanation
Indices: 9771029--9771067 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
9771019 GAGGCTTAAA
9771029 GGAGAGACAGAA-AAAAAAAG
1 GGAGAGACAGAAGAAAAAAAG
*
9771049 GGAGAGAGAGAAGAAAAAA
1 GGAGAGACAGAAGAAAAAA
9771068 CTGAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (21 bp):
GGAGAGACAGAAGAAAAAAAG
Found at i:9771360 original size:29 final size:29
Alignment explanation
Indices: 9771295--9771360 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
9771285 TACAAGACAT
* *
9771295 TTTTTTTAGTAATTTTTTTATTTTATCTA
1 TTTTTTTAGTAATTTTTTTATTTAATCAA
*
9771324 TTTATTTA-TAATTTTTTTATTTGAAT-AA
1 TTTTTTTAGTAATTTTTTTATTT-AATCAA
9771352 GTTTTTTTA
1 -TTTTTTTA
9771361 AAAATTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.70
Consensus pattern (29 bp):
TTTTTTTAGTAATTTTTTTATTTAATCAA
Found at i:9771457 original size:56 final size:55
Alignment explanation
Indices: 9771363--9771521 Score: 164
Period size: 56 Copynumber: 2.9 Consensus size: 55
9771353 TTTTTTTAAA
* * * * * *
9771363 AATTTC-AAAATTAAAGAAAAAAAATGAAAT-TCCATTTTTCCTTTAAATGAAACT
1 AATTTCAAAAATTAAA-AGAAAAAGTTAAATATCAATTTTTCCTTTAAATAAAAAT
* *
9771417 AATTTCAAAAATTAAAAGAAAAAGTTAAAGTATCAATTTTTCCTTAAAACAAAAAT
1 AATTTCAAAAATTAAAAGAAAAAGTTAAA-TATCAATTTTTCCTTTAAATAAAAAT
* **
9771473 AATTTCAAAATTTTGAAGAAAAAGTTAAAATATCAA-TTTTCC-TTAAATA
1 AATTTCAAAAATTAAAAGAAAAAGTT-AAATATCAATTTTTCCTTTAAATA
9771522 TCAAATATTT
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
54 21 0.24
55 16 0.18
56 48 0.55
57 3 0.03
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (55 bp):
AATTTCAAAAATTAAAAGAAAAAGTTAAATATCAATTTTTCCTTTAAATAAAAAT
Found at i:9772377 original size:83 final size:83
Alignment explanation
Indices: 9772256--9772421 Score: 280
Period size: 83 Copynumber: 2.0 Consensus size: 83
9772246 AATGTTAAAA
9772256 CTAAGATACTATGCAATGAAAAAAATGAATTATACACTAAGACCATTCACGGATAAATTGTCAAG
1 CTAAGATACTATGCAATGAAAAAAATGAATTATACACTAAGACCATTCACGGATAAATTGTCAAG
9772321 CCATATTGACTTTTCTTTT
66 CCATATTGACTTTT-TTTT
* * *
9772340 CTAAGATACTATGTAATG-AAAAAATGAATTATACACTAAGACCATTCATGGATAGATTGTCAAG
1 CTAAGATACTATGCAATGAAAAAAATGAATTATACACTAAGACCATTCACGGATAAATTGTCAAG
*
9772404 CCATGTTGACTTTTTTTT
66 CCATATTGACTTTTTTTT
9772422 AGTAATTGGG
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 4 0.05
83 57 0.73
84 17 0.22
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (83 bp):
CTAAGATACTATGCAATGAAAAAAATGAATTATACACTAAGACCATTCACGGATAAATTGTCAAG
CCATATTGACTTTTTTTT
Found at i:9777108 original size:27 final size:27
Alignment explanation
Indices: 9777077--9777128 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9777067 ATGCTTGGTG
*
9777077 TTTGTTAGATTGTTAGATGAATTAAAA
1 TTTGTTAGATTATTAGATGAATTAAAA
* *
9777104 TTTGTTAGGTTATTATATGAATTAA
1 TTTGTTAGATTATTAGATGAATTAA
9777129 GTTACTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (27 bp):
TTTGTTAGATTATTAGATGAATTAAAA
Found at i:9778272 original size:18 final size:18
Alignment explanation
Indices: 9778251--9778304 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
9778241 TTTTTAGAAA
9778251 AATAATTTAATAATTTAT
1 AATAATTTAATAATTTAT
*
9778269 AATAATTTATTAATTTTAT
1 AATAATTTAATAA-TTTAT
*
9778288 AA-ATATTAAATAATTTA
1 AATA-ATTTAATAATTTA
9778305 AAAATTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAATTTAATAATTTAT
Found at i:9781980 original size:19 final size:21
Alignment explanation
Indices: 9781953--9781995 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
9781943 TTATAGTTTA
9781953 AAATGAATTTTATA-AAAAT-T
1 AAATGAA-TTTATACAAAATAT
9781973 AAAT-AATTTATACAAAATAT
1 AAATGAATTTATACAAAATAT
9781993 AAA
1 AAA
9781996 AAGTATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 8 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATGAATTTATACAAAATAT
Found at i:9783073 original size:23 final size:23
Alignment explanation
Indices: 9783043--9783095 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
9783033 AAGTCACATC
9783043 CACCTCACCTTTCGTCTAAGTTT
1 CACCTCACCTTTCGTCTAAGTTT
9783066 CACCTCACCTTTCGTCTAAGTTT
1 CACCTCACCTTTCGTCTAAGTTT
9783089 CACCTCA
1 CACCTCA
9783096 TCACCACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.38, G:0.08, T:0.36
Consensus pattern (23 bp):
CACCTCACCTTTCGTCTAAGTTT
Found at i:9787325 original size:246 final size:246
Alignment explanation
Indices: 9786874--9787337 Score: 684
Period size: 246 Copynumber: 1.9 Consensus size: 246
9786864 ATGCTTTAGC
*
9786874 CATTAGCTCAAGTTTCATCCTAATTCCAATTTATATTTCTTGAACTTCTTCAAGTTGTACTTTAC
1 CATTAGCTCAAGTTTCATCCTAATTCCAATTTATATTTCTTGAACTTCTTCAAGTTCTACTTTAC
* * **
9786939 TCTTACTATTTTCTTCATGGATAAACTCTTTTTTCAAGAAGACATCATGTCTAGAAACAACATTT
66 TCATACTATTTTCTTCAAGGATAAACTCTTTTTTCAAGAAGACATCATGTCTAGAAACAACACCT
* **
9787004 TTTATTTTTCAGAGTTGTAGAAATAATATCCTTTTGTTTCTTTTGGATATCCTGTAAATTTACCC
131 TTTATTTTTCAGAGTTGTAAAAATAATATCCTTTTGTTTCTTTTGGATATCCTACAAATTTACCC
9787069 TTAACTGATCTAGCTCCAAACTTACGTTTCTTTGGATATCCTAGAAATTTA
196 TTAACTGATCTAGCTCCAAACTTACGTTTCTTTGGATATCCTAGAAATTTA
* * * *
9787120 CATTGGCTCAAGTTTCATCCTAGTGT-CAATTTATGTTTCTTGAACTTCTTCATGTTCTACTTTA
1 CATTAGCTCAAGTTTCATCCTAAT-TCCAATTTATATTTCTTGAACTTCTTCAAGTTCTACTTTA
* *
9787184 CTCATACTATTTTTTTCAAGGATAAACTC-TTTTTCTAAGAAGACATCATGTCTA-AAAGTAACA
65 CTCATACTATTTTCTTCAAGGATAAACTCTTTTTTC-AAGAAGACATCATGTCTAGAAA-CAACA
* *
9787247 CCTTTTGTTTTTCAGAGTTGTAAAAATAATATCCTTTTCTTTTCTTTT-GATATCCTACAAATTT
128 CCTTTTATTTTTCAGAGTTGTAAAAATAATATCCTTTT-GTTTCTTTTGGATATCCTACAAATTT
** * *
9787311 ATGCTTAGCTGATCTAGCTCTAAACTT
192 ACCCTTAACTGATCTAGCTCCAAACTT
9787338 GTCAACTTGA
Statistics
Matches: 194, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
245 9 0.05
246 176 0.91
247 9 0.05
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (246 bp):
CATTAGCTCAAGTTTCATCCTAATTCCAATTTATATTTCTTGAACTTCTTCAAGTTCTACTTTAC
TCATACTATTTTCTTCAAGGATAAACTCTTTTTTCAAGAAGACATCATGTCTAGAAACAACACCT
TTTATTTTTCAGAGTTGTAAAAATAATATCCTTTTGTTTCTTTTGGATATCCTACAAATTTACCC
TTAACTGATCTAGCTCCAAACTTACGTTTCTTTGGATATCCTAGAAATTTA
Found at i:9787859 original size:12 final size:12
Alignment explanation
Indices: 9787842--9787877 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
9787832 GCACAAGGTT
9787842 CAAGATATTCCA
1 CAAGATATTCCA
*
9787854 CAAGATGTTCCA
1 CAAGATATTCCA
9787866 CAAGATATTCCA
1 CAAGATATTCCA
9787878 TAAAAAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (12 bp):
CAAGATATTCCA
Found at i:9788887 original size:20 final size:20
Alignment explanation
Indices: 9788859--9788897 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9788849 AATTTGGTAA
*
9788859 AATTGAATTTAAATGTTTTG
1 AATTGAATTTAAATATTTTG
*
9788879 AATTTAATTTAAATATTTT
1 AATTGAATTTAAATATTTT
9788898 TCTAACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
AATTGAATTTAAATATTTTG
Found at i:9799246 original size:17 final size:17
Alignment explanation
Indices: 9799226--9799271 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
9799216 ATACCTTAAC
9799226 TAAAAAAATAAAAAACT
1 TAAAAAAATAAAAAACT
* *
9799243 TAAAAAAACTTAGAAACT
1 TAAAAAAA-TAAAAAACT
*
9799261 AAAAAAAATAA
1 TAAAAAAATAA
9799272 GAGAAGTGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (17 bp):
TAAAAAAATAAAAAACT
Found at i:9801799 original size:15 final size:15
Alignment explanation
Indices: 9801779--9801808 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9801769 GTTTTTATTG
9801779 ATTTCATTGATTTCA
1 ATTTCATTGATTTCA
9801794 ATTTCATTGATTTCA
1 ATTTCATTGATTTCA
9801809 TGTGAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTCATTGATTTCA
Found at i:9804675 original size:27 final size:27
Alignment explanation
Indices: 9804634--9804685 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
9804624 TTAGGTCCAG
* * *
9804634 GGGTATTTTAGTCTTTTCATTAACCCA
1 GGGTATTTCAGTCTTTACACTAACCCA
*
9804661 GGGTATTTCATTCTTTACACTAACC
1 GGGTATTTCAGTCTTTACACTAACC
9804686 TAACAGGTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (27 bp):
GGGTATTTCAGTCTTTACACTAACCCA
Found at i:9805307 original size:35 final size:35
Alignment explanation
Indices: 9805253--9805324 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
9805243 CAAAAACCTT
*
9805253 TTAGTATGGTTATGAAGTGATTGACT-GAAGTTTTC
1 TTAGTATGCTTATGAAGTGATTGA-TAGAAGTTTTC
*
9805288 TTAGTATGCTTAT-AGAGTGATTGATAGAGGTTTTC
1 TTAGTATGCTTATGA-AGTGATTGATAGAAGTTTTC
9805323 TT
1 TT
9805325 TGGGAGAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (35 bp):
TTAGTATGCTTATGAAGTGATTGATAGAAGTTTTC
Found at i:9806605 original size:2 final size:2
Alignment explanation
Indices: 9806594--9806630 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
9806584 TTCAACTTTC
*
9806594 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9806631 AAATACATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9806928 original size:8 final size:8
Alignment explanation
Indices: 9806911--9806940 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9806901 GAGCACCTTG
*
9806911 TTTTTGGT
1 TTTTTTGT
9806919 TTTTTTGT
1 TTTTTTGT
9806927 TTTTTTGT
1 TTTTTTGT
9806935 TTTTTT
1 TTTTTT
9806941 CTTATCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTGT
Found at i:9822276 original size:160 final size:160
Alignment explanation
Indices: 9822106--9822428 Score: 637
Period size: 160 Copynumber: 2.0 Consensus size: 160
9822096 TGGCTTTTTA
9822106 GGTTGTGGCATGCGTCATGTTATGGCTAAGGTAGTGACAAGTTAGGGTGTTATGCTCTTTTTCTT
1 GGTTGTGGCATGCGTCATGTTATGGCTAAGGTAGTGACAAGTTAGGGTGTTATGCTCTTTTTCTT
*
9822171 TTAAGGCCAAAGAAGCCTCCATCTCTTCATAACTTGGTTGTCTTTTCGTAGCTTATCGGCTAAGG
66 TTAAGGCCAAAGAAGCCTCCATCTCTTCATAACTTGGTTGTCTTTTCGTAGCTTATCGGCCAAGG
9822236 GTAACTAAATCTAGCACTTTTAAAACTTGT
131 GTAACTAAATCTAGCACTTTTAAAACTTGT
9822266 GGTTGTGGCATGCGTCATGTTATGGCTAAGGTAGTGACAAGTTAGGGTGTTATGCTCTTTTTCTT
1 GGTTGTGGCATGCGTCATGTTATGGCTAAGGTAGTGACAAGTTAGGGTGTTATGCTCTTTTTCTT
9822331 TTAAGGCCAAAGAAGCCTCCATCTCTTCATAACTTGGTTGTCTTTTCGTAGCTTATCGGCCAAGG
66 TTAAGGCCAAAGAAGCCTCCATCTCTTCATAACTTGGTTGTCTTTTCGTAGCTTATCGGCCAAGG
9822396 GTAACTAAATCTAGCACTTTTAAAACTTGT
131 GTAACTAAATCTAGCACTTTTAAAACTTGT
9822426 GGT
1 GGT
9822429 GGGGTTATGG
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (160 bp):
GGTTGTGGCATGCGTCATGTTATGGCTAAGGTAGTGACAAGTTAGGGTGTTATGCTCTTTTTCTT
TTAAGGCCAAAGAAGCCTCCATCTCTTCATAACTTGGTTGTCTTTTCGTAGCTTATCGGCCAAGG
GTAACTAAATCTAGCACTTTTAAAACTTGT
Found at i:9831688 original size:17 final size:17
Alignment explanation
Indices: 9831645--9831682 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9831635 GGTGCAAGGC
**
9831645 AAAGAAAAAATTGAAAA
1 AAAGAAAAAAAGGAAAA
9831662 AAAGAAAAAAAGGAAAA
1 AAAGAAAAAAAGGAAAA
9831679 AAAG
1 AAAG
9831683 CCAAAATGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAGAAAAAAAGGAAAA
Found at i:9835252 original size:11 final size:13
Alignment explanation
Indices: 9835214--9835254 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
9835204 AGAGGAAGGG
*
9835214 AAATCTTTGTGTTA
1 AAATCTTT-TGTCA
9835228 AAATCTTTTGTCA
1 AAATCTTTTGTCA
9835241 AAAT-TTTT-TCA
1 AAATCTTTTGTCA
9835252 AAA
1 AAA
9835255 AGGTTACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 4 0.15
13 8 0.31
14 8 0.31
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (13 bp):
AAATCTTTTGTCA
Found at i:9838631 original size:22 final size:21
Alignment explanation
Indices: 9838606--9838659 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
9838596 CAAGTTTTCC
* *
9838606 TCAAGCTTTCTTCATTTACATT
1 TCAAGCATTCTTAATTTAC-TT
*
9838628 TCAAGCATTC-AAATTTACTT
1 TCAAGCATTCTTAATTTACTT
9838648 TCAAGCATTCTT
1 TCAAGCATTCTT
9838660 TAAGTTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.44
21 6 0.22
22 9 0.33
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (21 bp):
TCAAGCATTCTTAATTTACTT
Found at i:9838651 original size:20 final size:21
Alignment explanation
Indices: 9838619--9838657 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
9838609 AGCTTTCTTC
9838619 ATTTACATTTCAAGCATTCAA
1 ATTTACATTTCAAGCATTCAA
9838640 ATTTAC-TTTCAAGCATTC
1 ATTTACATTTCAAGCATTC
9838658 TTTAAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTTACATTTCAAGCATTCAA
Found at i:9842862 original size:2 final size:2
Alignment explanation
Indices: 9842855--9842881 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9842845 GCTTATTAGC
9842855 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9842882 AGTAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9848815 original size:18 final size:18
Alignment explanation
Indices: 9848792--9848843 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
9848782 GATTTTACCA
9848792 AGGGTTTAGGTTTCACCT
1 AGGGTTTAGGTTTCACCT
*
9848810 AGGGTTTCGGATTT-ACCT
1 AGGGTTTAGG-TTTCACCT
*
9848828 AAGGTTTAGGGTTTCA
1 AGGGTTTA-GGTTTCA
9848844 TTTTAGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.38
Consensus pattern (18 bp):
AGGGTTTAGGTTTCACCT
Found at i:9849850 original size:3 final size:3
Alignment explanation
Indices: 9849842--9849876 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
9849832 TGGTATAGTC
* *
9849842 ATT ATT ATT ATT ACT ATT ATT AGT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9849877 CATAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:9853972 original size:38 final size:39
Alignment explanation
Indices: 9853856--9853969 Score: 119
Period size: 38 Copynumber: 3.0 Consensus size: 39
9853846 AACTTAACCA
* * * * *
9853856 AAAGTTTAGAG-TTTCACCTAGAGTTTCAGAGTTTCGTTT
1 AAAGTTTTGAGATTTTACCTAGAGCTT-AGGGTTTCATTT
* *
9853895 -AGGATTTGAGATTTTACCTAGAGCTTAGGGTTTCATTT
1 AAAGTTTTGAGATTTTACCTAGAGCTTAGGGTTTCATTT
*
9853933 AAAGTTTTG-GATTTTACCTAG-GCTTAGGGTTTTATTT
1 AAAGTTTTGAGATTTTACCTAGAGCTTAGGGTTTCATTT
9853970 TAAGGTTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
37 15 0.24
38 29 0.46
39 19 0.30
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.44
Consensus pattern (39 bp):
AAAGTTTTGAGATTTTACCTAGAGCTTAGGGTTTCATTT
Found at i:9861413 original size:143 final size:143
Alignment explanation
Indices: 9861154--9861417 Score: 316
Period size: 143 Copynumber: 1.8 Consensus size: 143
9861144 TAGAGTACTG
* **
9861154 CTATGATTTCAAATGTACCAAAAATCATAAAATATTATGAAATTAAGATTTAAAAAGTTTCATGA
1 CTATGATTTCAAATGCACCAAAAATCATAAAATATTATGAAATTAAGAACTAAAAAGTTTCATGA
* * * * ** *
9861219 AAATTTGAGCTCAAGAAGGTCAAATTACGAAAATACTCTTAAGGGATATTTTAGTAATTTAACAC
66 AAATTCGAACTCAAGAAGGCCAAATTACGAAAACACTCAAAAGGGACATTTTAGTAATTTAACAC
9861284 CTCTCAGGGTATT
131 CTCTCAGGGTATT
* * ** *
9861297 CTATGATTTTAAATGCACCAAAAATCATGAAATATTATGAAATTAAGAACTGTAAAGTTTCGTGA
1 CTATGATTTCAAATGCACCAAAAATCATAAAATATTATGAAATTAAGAACTAAAAAGTTTCATGA
* * * * *
9861362 AAATTCGAATTTAGGAAGGCCAAATTTCTAAAACAC-CAAAAAAGGG-CATTTTAGTA
66 AAATTCGAACTCAAGAAGGCCAAATTACGAAAACACTC--AAAAGGGACATTTTAGTA
9861418 TTTTTGTAAT
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
142 1 0.01
143 93 0.94
144 5 0.05
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (143 bp):
CTATGATTTCAAATGCACCAAAAATCATAAAATATTATGAAATTAAGAACTAAAAAGTTTCATGA
AAATTCGAACTCAAGAAGGCCAAATTACGAAAACACTCAAAAGGGACATTTTAGTAATTTAACAC
CTCTCAGGGTATT
Found at i:9862229 original size:6 final size:6
Alignment explanation
Indices: 9862218--9862249 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
9862208 ATGAAAACAT
9862218 TTTTTG TTTTTG TTTTTG TTTTT- TTTTT- TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
9862250 GGAAAACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (6 bp):
TTTTTG
Found at i:9862517 original size:60 final size:60
Alignment explanation
Indices: 9862440--9862557 Score: 227
Period size: 60 Copynumber: 2.0 Consensus size: 60
9862430 ATAAGTAAAT
9862440 TATTTTTTTTCAATTTAAAATAAGAAATAATAAGATTAAATAAAAATAAATAAACTAATG
1 TATTTTTTTTCAATTTAAAATAAGAAATAATAAGATTAAATAAAAATAAATAAACTAATG
*
9862500 TATTTTTTTTCAATTTAAAATAAGACATAATAAGATTAAATAAAAATAAATAAACTAA
1 TATTTTTTTTCAATTTAAAATAAGAAATAATAAGATTAAATAAAAATAAATAAACTAA
9862558 CATAAACAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (60 bp):
TATTTTTTTTCAATTTAAAATAAGAAATAATAAGATTAAATAAAAATAAATAAACTAATG
Found at i:9863162 original size:50 final size:51
Alignment explanation
Indices: 9863083--9863227 Score: 150
Period size: 52 Copynumber: 2.8 Consensus size: 51
9863073 TGATTTTTGT
* *
9863083 TTTAATGAGAATTGATTCTAAAATCAAATCCCAAAATCTCTCC-CTATCA-A
1 TTTAATGAGAATTGATTCTAGAATTAAATCCCAAAATCTCTCCAC-ATCATA
* * * * * *
9863133 TTTAATGTGAATTGATTATGGAATTAAATCCTGACAATCTCTCCACATCATT
1 TTTAATGAGAATTGATTCTAGAATTAAATCC-CAAAATCTCTCCACATCATA
** *
9863185 TTTAATGCCAATTAATTCTAGAATTAAATCCCAAAAATCTCTC
1 TTTAATGAGAATTGATTCTAGAATTAAATCCC-AAAATCTCTC
9863228 GATTGAAGCC
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
50 26 0.34
51 14 0.18
52 36 0.47
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (51 bp):
TTTAATGAGAATTGATTCTAGAATTAAATCCCAAAATCTCTCCACATCATA
Found at i:9882592 original size:17 final size:17
Alignment explanation
Indices: 9882572--9882610 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
9882562 GGTATATTAG
9882572 TTGATGATT-ATATGACA
1 TTGA-GATTGATATGACA
*
9882589 TTGAGATTGATATGACC
1 TTGAGATTGATATGACA
9882606 TTGAG
1 TTGAG
9882611 TTGTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (17 bp):
TTGAGATTGATATGACA
Found at i:9885040 original size:34 final size:35
Alignment explanation
Indices: 9884977--9885042 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
9884967 AGATATTCAT
9884977 ATTTGCATCACTTGCATTTTCATCATAAGAAAGAA
1 ATTTGCATCACTTGCATTTTCATCATAAGAAAGAA
*
9885012 ATTTGCATCA-TTGCATTTGT-ATCCTAAGAAA
1 ATTTGCATCACTTGCATTT-TCATCATAAGAAA
9885043 AGGTATTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (35 bp):
ATTTGCATCACTTGCATTTTCATCATAAGAAAGAA
Found at i:9885051 original size:35 final size:35
Alignment explanation
Indices: 9884975--9885051 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
9884965 AAAGATATTC
9884975 ATATTTGCATCACTTGCATTTTCATCATAAGAAAG
1 ATATTTGCATCACTTGCATTTTCATCATAAGAAAG
* *
9885010 AAATTTGCATCA-TTGCATTTGT-ATCCTAAGAAAAG
1 ATATTTGCATCACTTGCATTT-TCATCATAAG-AAAG
*
9885045 GTATTTG
1 ATATTTG
9885052 TGGGGGCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 15 0.42
35 21 0.58
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (35 bp):
ATATTTGCATCACTTGCATTTTCATCATAAGAAAG
Found at i:9885154 original size:18 final size:18
Alignment explanation
Indices: 9885131--9885173 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9885121 GTTTACATTC
9885131 TTGCATT-TGCATTGACAT
1 TTGCATTCT-CATTGACAT
9885149 TTGCATTCTCATTGACAT
1 TTGCATTCTCATTGACAT
*
9885167 TTCCATT
1 TTGCATT
9885174 AGTATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (18 bp):
TTGCATTCTCATTGACAT
Found at i:9885235 original size:9 final size:9
Alignment explanation
Indices: 9885221--9885249 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9885211 CTTTGTATAC
9885221 ATTAAAAAA
1 ATTAAAAAA
9885230 ATT-AAAAA
1 ATTAAAAAA
9885238 ATTAAAAAA
1 ATTAAAAAA
9885247 ATT
1 ATT
9885250 GACTTAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:9885757 original size:69 final size:70
Alignment explanation
Indices: 9885614--9885757 Score: 184
Period size: 69 Copynumber: 2.1 Consensus size: 70
9885604 TTGGAAAAAA
* * * *
9885614 AAAACATTTCAAACTTTTAAAAGTTTCACGGCCTCTGATTGGAGGAGGATTCAAAAGTTTTCAGA
1 AAAACATTTCAAACTTTTAAAAGTCTCACGGCCTCTGATTAGAGGAGCATTCAAAAGATTTCAGA
9885679 CTTGC
66 CTTGC
* * *
9885684 AAAACATTTTAAACTTTT-AAAGTCTCATGGTCTCTGATTAGAGGAGCATTC-AAAGATTTCGAG
1 AAAACATTTCAAACTTTTAAAAGTCTCACGGCCTCTGATTAGAGGAGCATTCAAAAGATTTC-AG
* *
9885747 ATTTGT
65 ACTTGC
9885753 AAAAC
1 AAAAC
9885758 CTCAAACATA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 8 0.12
69 39 0.61
70 17 0.27
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (70 bp):
AAAACATTTCAAACTTTTAAAAGTCTCACGGCCTCTGATTAGAGGAGCATTCAAAAGATTTCAGA
CTTGC
Found at i:9885985 original size:54 final size:55
Alignment explanation
Indices: 9885927--9886034 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 55
9885917 AAACATTTTA
* * * *
9885927 AATTTCAAAGTTTCATGGCCTTTGATTA-ATGGAGCATTC-AAAGATTTTTAGATG
1 AATTTCAAAGTTTAATGGCCTCTGATTAGA-GGAACAATCAAAAGATTTTTAGATG
* *
9885981 AATTTTAAAGTTTAATGGCCTCTGATTAGAGGAACAATCAAAAGTTTTTTAGAT
1 AATTTCAAAGTTTAATGGCCTCTGATTAGAGGAACAATCAAAAGATTTTTAGAT
9886035 TTAATCTCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 32 0.70
55 14 0.30
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (55 bp):
AATTTCAAAGTTTAATGGCCTCTGATTAGAGGAACAATCAAAAGATTTTTAGATG
Found at i:9886083 original size:6 final size:5
Alignment explanation
Indices: 9886060--9886110 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
9886050 CCCAATCAAA
*
9886060 AAAAT AAAAC AAAAC AAAACC AAAAC AAAAAC AAAAAC AAAA- AAAA-
1 AAAAC AAAAC AAAAC AAAA-C AAAAC -AAAAC -AAAAC AAAAC AAAAC
9886106 AAAAC
1 AAAAC
9886111 TCTCAAAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
4 8 0.19
5 18 0.43
6 16 0.38
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.02
Consensus pattern (5 bp):
AAAAC
Found at i:9886106 original size:11 final size:11
Alignment explanation
Indices: 9886058--9886109 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
9886048 CCCCCAATCA
9886058 AAAAAATAAAAC
1 AAAAAA-AAAAC
* *
9886070 AAAACAAAACC
1 AAAAAAAAAAC
*
9886081 AAAACAAAAAC
1 AAAAAAAAAAC
9886092 AAAAACAAAAA-
1 AAAAA-AAAAAC
9886103 AAAAAAA
1 AAAAAAA
9886110 CTCTCAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 2 0.06
11 23 0.66
12 10 0.29
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:9889321 original size:2 final size:2
Alignment explanation
Indices: 9889314--9889344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9889304 TTTTCTATGT
9889314 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 T
9889345 TATCTTTTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9889615 original size:27 final size:27
Alignment explanation
Indices: 9889556--9889608 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
9889546 ATATTTTAAA
9889556 AAAATTAAGAATATTAATTTTTAATACC
1 AAAATTAAGAATATT-ATTTTTAATACC
*
9889584 AAAATTAAGACTATT-TTTGTTAATA
1 AAAATTAAGAATATTATTT-TTAATA
9889609 TTAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 6 0.26
28 14 0.61
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (27 bp):
AAAATTAAGAATATTATTTTTAATACC
Found at i:9891220 original size:17 final size:18
Alignment explanation
Indices: 9891184--9891226 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9891174 TGTACTTATC
*
9891184 TTATTATTTTTTAGTTTT
1 TTATTATTTTTTAGTATT
*
9891202 TTGTTATTTTTTA-TATT
1 TTATTATTTTTTAGTATT
9891219 TTATTATT
1 TTATTATT
9891227 ATTATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
TTATTATTTTTTAGTATT
Found at i:9896484 original size:142 final size:144
Alignment explanation
Indices: 9896094--9896492 Score: 377
Period size: 143 Copynumber: 2.8 Consensus size: 144
9896084 TTTAAAACAC
* * * * ** *
9896094 CAAAAATCATGAAATATTATAAAATTGAGATCTAAAAAATT-TAATAAAAATCTGAGCTCGAGAA
1 CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTCT-ATGAAAATCCAAGCTCGAAAA
* ** * * * **
9896158 AGTCAAATTAC-AAATACCTTTATAAG-GGTATTTTAATAATTTCACACTTTTTGAGGTACTACT
65 AGACAAATTACGAAATACCCCTA-AAGAGATATTTTAGTAATTTTACACTTTTCAAGGTACTACT
*
9896221 ATGACTTCAAATGCAT
129 ATGACTTCAAATACAT
* * * *
9896237 CAAAAATTATGAAATATTATGAAATTAAGATTTAAAAAGTTCTATGAAAATTCAAGCTCGAAAAG
1 CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTCTATGAAAATCCAAGCTCGAAAAA
* * * * *
9896302 GGCAAATTAGGAAATATCCTTAAAGAGATATTTT-GATAATTTTACACTTTTCAAGGTACTGCTA
66 GACAAATTACGAAATACCCCTAAAGAGATATTTTAG-TAATTTTACACTTTTCAAGGTACTACTA
* *
9896366 TGATTTTAAATACAT
130 TGACTTCAAATACAT
* * * *
9896381 TAAAAA-CATGAAATATTATGGAATTAAGATCT-GAAAGCTT-TATGAAAATCCGAGCTC-AAAA
1 CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAG-TTCTATGAAAATCCAAGCTCGAAAA
*
9896442 AGACTAAATTACGACAATACCCCCT-AA-AGATATTTTAGTAATTTTATACTT
65 AGAC-AAATTACGA-AATA-CCCCTAAAGAGATATTTTAGTAATTTTACACTT
9896493 CTCACAGTGC
Statistics
Matches: 210, Mismatches: 37, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
141 6 0.03
142 48 0.23
143 95 0.45
144 61 0.29
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (144 bp):
CAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTCTATGAAAATCCAAGCTCGAAAAA
GACAAATTACGAAATACCCCTAAAGAGATATTTTAGTAATTTTACACTTTTCAAGGTACTACTAT
GACTTCAAATACAT
Found at i:9898320 original size:37 final size:38
Alignment explanation
Indices: 9898247--9898325 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
9898237 TCTATGAATG
* *
9898247 GTCTTAGTGTATAACTAATATCCTTTCATCATATAGTA
1 GTCTTAATGTATAACTAATATCCTTTCATCACATAGTA
*
9898285 GTCTTAATGTATAACTAATA-CTTTTCATCACATAGTA
1 GTCTTAATGTATAACTAATATCCTTTCATCACATAGTA
9898322 -TCTT
1 GTCTT
9898326 GGTTTGAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 4 0.11
37 15 0.39
38 19 0.50
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (38 bp):
GTCTTAATGTATAACTAATATCCTTTCATCACATAGTA
Found at i:9913930 original size:26 final size:26
Alignment explanation
Indices: 9913892--9913942 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
9913882 TTTCACCCAT
*
9913892 TGAGTTAGGACAAAAATACTAAAAAA
1 TGAGTTAGAACAAAAATACTAAAAAA
* *
9913918 TGAGTTAGAACAAAGATACTTAAAA
1 TGAGTTAGAACAAAAATACTAAAAA
9913943 GATTCTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.22
Consensus pattern (26 bp):
TGAGTTAGAACAAAAATACTAAAAAA
Found at i:9914287 original size:104 final size:104
Alignment explanation
Indices: 9914077--9914288 Score: 311
Period size: 106 Copynumber: 2.0 Consensus size: 104
9914067 GCAAGCAAAG
*
9914077 AAAATTGAACTCTTAAAAAAAATTAATTTATGGTTTCATCCAAATATAATTTTTTTAGTAGTTTT
1 AAAATTGAACTCTTAAAAAAAATTAATTTATGATTTCATCCAAATATAATTTTTTTAGTAGTTTT
* *
9914142 AATCTTTTTTTTTTTAATTTTTATAAAGGCTTATGCTTA
66 AATCCTTCTTTTTTTAATTTTTATAAAGGCTTATGCTTA
* * * *
9914181 AAAAGTTGAACTTTTAAAAACACATTGATTTATGATTTCATCCAATTATAATTTTTTTAGTAGTT
1 AAAA-TTGAACTCTTAAAAA-AAATTAATTTATGATTTCATCCAAATATAATTTTTTTAGTAGTT
* *
9914246 TTTA-CCTTCTTTTTTT-ATTTTTATCAAGGCTTATGCTTA
64 TTAATCCTTCTTTTTTTAATTTTTATAAAGGCTTATGCTTA
9914285 AAAA
1 AAAA
9914289 CTTTGTTATT
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
104 30 0.31
105 24 0.25
106 43 0.44
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.49
Consensus pattern (104 bp):
AAAATTGAACTCTTAAAAAAAATTAATTTATGATTTCATCCAAATATAATTTTTTTAGTAGTTTT
AATCCTTCTTTTTTTAATTTTTATAAAGGCTTATGCTTA
Found at i:9915459 original size:34 final size:34
Alignment explanation
Indices: 9915421--9915566 Score: 123
Period size: 34 Copynumber: 4.3 Consensus size: 34
9915411 ACAATGTAAA
** * *
9915421 TCTTGAAAATCCATTTTCGAGAATTATATTGTAT
1 TCTTGAAAATAAATTTTTGAGAATTATATTATAT
** * * *
9915455 TCTTGAAAACGAATTTTTGA-AAATACAATATAAT
1 TCTTGAAAATAAATTTTTGAGAATTATATTAT-AT
* * **
9915489 TCTTAAAAATAAATTTTTGATAATTATATTGCAT
1 TCTTGAAAATAAATTTTTGAGAATTATATTATAT
* **
9915523 TCTCGAAAATAGGTTTTTGAGAATTATATTATAT
1 TCTTGAAAATAAATTTTTGAGAATTATATTATAT
*
9915557 TTTTGAAAAT
1 TCTTGAAAAT
9915567 GGATTTTCAA
Statistics
Matches: 85, Mismatches: 25, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
33 7 0.08
34 72 0.85
35 6 0.07
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (34 bp):
TCTTGAAAATAAATTTTTGAGAATTATATTATAT
Found at i:9940544 original size:13 final size:13
Alignment explanation
Indices: 9940526--9940551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9940516 AAACTATCTT
9940526 GCTAAAATATATA
1 GCTAAAATATATA
9940539 GCTAAAATATATA
1 GCTAAAATATATA
9940552 AGCATGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
GCTAAAATATATA
Found at i:9942195 original size:25 final size:23
Alignment explanation
Indices: 9942154--9942200 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
9942144 CCACTTGATT
9942154 GTTTTTTTTTTCATTTTCTTTTA
1 GTTTTTTTTTTCATTTTCTTTTA
*
9942177 GTTTTTTCTTTTCTGTTTTCTTTT
1 GTTTTTT-TTTTC-ATTTTCTTTT
9942201 GCAAGCTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 5 0.24
25 9 0.43
ACGTcount: A:0.04, C:0.11, G:0.06, T:0.79
Consensus pattern (23 bp):
GTTTTTTTTTTCATTTTCTTTTA
Found at i:9942866 original size:20 final size:20
Alignment explanation
Indices: 9942841--9942880 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9942831 AATTCAAGGT
9942841 AAAATTTAAG-AAAAATTTGA
1 AAAATTT-AGCAAAAATTTGA
*
9942861 AAAATTTTGCAAAAATTTGA
1 AAAATTTAGCAAAAATTTGA
9942881 GCTATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAATTTAGCAAAAATTTGA
Found at i:9946287 original size:106 final size:106
Alignment explanation
Indices: 9946133--9946335 Score: 264
Period size: 106 Copynumber: 1.9 Consensus size: 106
9946123 GGCTGGCCTT
* * ** * *
9946133 CTAATGCTAGGTTAAAATCTATTAAGATCAAGCATAGCGTAATCCCTAAATGCTCTAGTGTTTGC
1 CTAATGCTAGGTTAAAATCTATTAAGATCAAGCACAACACAATACCTAAATACTCTAGTGTTTGC
**
9946198 TTGACCATGGTGATGGTAAAATCAATTTGTCTCTCCCTTTC
66 TCAACCATGGTGATGGTAAAATCAATTTGTCTCTCCCTTTC
* * * *
9946239 CTAATGCTAGGTTAAAATCCT-TTAAGATTAGGCACAACACAATACCTAAGTACTTTAGTGTTTG
1 CTAATGCTAGGTTAAAAT-CTATTAAGATCAAGCACAACACAATACCTAAATACTCTAGTGTTTG
* *
9946303 CTCAACCATGGTGATGGTAAGATCAGTTTGTCT
65 CTCAACCATGGTGATGGTAAAATCAATTTGTCT
9946336 TTCTTTTCTA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
106 80 0.98
107 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (106 bp):
CTAATGCTAGGTTAAAATCTATTAAGATCAAGCACAACACAATACCTAAATACTCTAGTGTTTGC
TCAACCATGGTGATGGTAAAATCAATTTGTCTCTCCCTTTC
Found at i:9963308 original size:27 final size:27
Alignment explanation
Indices: 9963266--9963321 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
9963256 ATAACTTGAG
*
9963266 CCTAAAAATGATCCAAATCTAAATAAC
1 CCTAAAAATGACCCAAATCTAAATAAC
*
9963293 CCTAAAAATGACCCAAATCTGAATAAC
1 CCTAAAAATGACCCAAATCTAAATAAC
9963320 CC
1 CC
9963322 AAGTGTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.27, G:0.05, T:0.20
Consensus pattern (27 bp):
CCTAAAAATGACCCAAATCTAAATAAC
Found at i:9963789 original size:22 final size:22
Alignment explanation
Indices: 9963764--9963805 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
9963754 TTGTTTATCC
9963764 TAATTTTAG-GAATACAAATACT
1 TAATTTTAGAG-ATACAAATACT
9963786 TAATTTTAGAGATACAAATA
1 TAATTTTAGAGATACAAATA
9963806 TAAATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (22 bp):
TAATTTTAGAGATACAAATACT
Found at i:9967702 original size:22 final size:22
Alignment explanation
Indices: 9967677--9967719 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9967667 TTGTCTATCC
*
9967677 TAATTTTAGAAATACAAATACT
1 TAATTCTAGAAATACAAATACT
*
9967699 TAATTCTAGAGATACAAATAC
1 TAATTCTAGAAATACAAATAC
9967720 AAATATACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAAATACAAATACT
Found at i:9971270 original size:16 final size:17
Alignment explanation
Indices: 9971249--9971283 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9971239 GCGGAGTCTT
9971249 ATAATAA-AATCAGTAA
1 ATAATAATAATCAGTAA
*
9971265 ATAATAATAATCATTAA
1 ATAATAATAATCAGTAA
9971282 AT
1 AT
9971284 TTATACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAATAATAATCAGTAA
Found at i:9973453 original size:145 final size:141
Alignment explanation
Indices: 9973011--9973549 Score: 518
Period size: 143 Copynumber: 3.8 Consensus size: 141
9973001 AGGAAAGACA
* * ** * * *
9973011 AAATTACCAAAATACCCTTATAGGGGTATTTTCGTAATTTGAC-TTTCCTAAGC-TCAGATTTTC
1 AAATTACCAAAATA-CCTTTTAAGGGTATTTTTATAATTTGGCTTTTCC-GAGCTTGA-ATTTTC
* * * * * *
9973074 ATGAAACTTTTCAGATTTTAATTTTATAATATTTCATAATTTTTTA-TGCATTTAAAATCACA-T
63 ATAAAACTTTTCAGATCTTAATTTCATAATATTTCATGA-TTTTTAGTGCATTTGAAATCATAGT
9973137 CAGTACCCAAAAAGGGT
127 -AGTACCCAAAAA-GGT
* * * * * **
9973154 AAATTACCAAAATAACCTTTTAAGGGTATCTTTGTAATTTAGCTTTTCTGAGCTCGAATTTTTGT
1 AAATTACCAAAAT-ACCTTTTAAGGGTATTTTTATAATTTGGCTTTTCCGAGCTTGAATTTTCAT
* * * *
9973219 GAAATTTTTCAGAT-TTCAATTT-ATAATATTTCATGA-TTTTGGTG-AGTTTGAAACCATAGTA
65 AAAACTTTTCAGATCTT-AATTTCATAATATTTCATGATTTTTAGTGCA-TTTGAAATCATAGTA
9973280 GTACCTCAAAAAAGGT
128 GTACC-C-AAAAAGGT
* *
9973296 GAAATTACCAAAATACCTTTTAAGGGATATTTTTATAATTTGGCTTTCCCGAGCTTGAAATTTCA
1 -AAATTACCAAAATACCTTTTAAGGG-TATTTTTATAATTTGGCTTTTCCGAGCTTGAATTTTCA
* *
9973361 TAAAACTTTTTAGATCTTAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAATTATAGTAG
64 TAAAACTTTTCAGATCTTAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAATCATAGTAG
*
9973426 TACCCTAGAAAGTGT
129 TACCC-AAAAAG-GT
* * ** * * * *
9973441 AAAATTATCAAAATACCCTTATAAAAGTATTTTCATAATTTGGCTTTTTCAAGTTTGAATTTTCA
1 -AAATTACCAAAATA-CCTTTTAAGGGTATTTTTATAATTTGGCTTTTCCGAGCTTGAATTTTCA
*
9973506 TAAAACTTTTCAGATCTTAATTTCATAATATTTTTATGATTTTT
64 TAAAACTTTTCAGATCTTAATTTCATAATA-TTTCATGATTTTT
9973550 TATGCTTTAA
Statistics
Matches: 330, Mismatches: 48, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
140 5 0.02
141 17 0.05
142 32 0.10
143 126 0.38
144 28 0.08
145 101 0.31
146 21 0.06
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (141 bp):
AAATTACCAAAATACCTTTTAAGGGTATTTTTATAATTTGGCTTTTCCGAGCTTGAATTTTCATA
AAACTTTTCAGATCTTAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAATCATAGTAGTA
CCCAAAAAGGT
Done.