Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 396 of 444
Found at i:114910067 original size:30 final size:30
Alignment explanation
Indices: 114910031--114910161 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
114910021 GACAAGATTG
* * * * *
114910031 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
114910061 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
114910089 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
114910119 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
114910148 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
114910162 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:114910122 original size:58 final size:58
Alignment explanation
Indices: 114910031--114910161 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
114910021 GACAAGATTG
* * * * * *
114910031 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
114910089 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
114910148 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
114910162 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:114918021 original size:30 final size:30
Alignment explanation
Indices: 114917985--114918115 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
114917975 GACAAGATTG
* * * * *
114917985 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
114918015 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
114918043 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
114918073 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
114918102 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
114918116 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:114918076 original size:58 final size:58
Alignment explanation
Indices: 114917985--114918115 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
114917975 GACAAGATTG
* * * * * *
114917985 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
114918043 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
114918102 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
114918116 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:114919664 original size:49 final size:49
Alignment explanation
Indices: 114919582--114919675 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
114919572 TTCAAGAAGG
* * * * *
114919582 ATAAATCGTGATAAGAGTGTAAACAGTGGAAGACTAAGTTTATCAATGT
1 ATAAATAGTGATAAAAGTGTAAACAATGAAAGACCAAGTTTATCAATGT
**
114919631 ATAAATAGTGATAAAAGTGTAGGCAATGAAAGACCAAGTTTATCA
1 ATAAATAGTGATAAAAGTGTAAACAATGAAAGACCAAGTTTATCA
114919676 TTACATAGCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.27
Consensus pattern (49 bp):
ATAAATAGTGATAAAAGTGTAAACAATGAAAGACCAAGTTTATCAATGT
Found at i:114924930 original size:40 final size:39
Alignment explanation
Indices: 114924762--114924932 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
114924752 AGAAATTGAA
* *
114924762 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
114924802 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
114924842 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
114924882 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
114924922 TGATATCCGGG
1 TGATATCCGGG
114924933 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:114927051 original size:46 final size:46
Alignment explanation
Indices: 114926997--114927098 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
114926987 AATTGAATTA
114926997 TTAT-AGCATAGTTAATGCTACCGTATTGTTCTGTTAAAAGCATAG
1 TTATAAGCATAGTTAATGCTACCGTATTGTTCTGTTAAAAGCATAG
* *
114927042 TTATAAGCATATTTAATGCTACTGTATTGTTCTGTTAAAAGCATAG
1 TTATAAGCATAGTTAATGCTACCGTATTGTTCTGTTAAAAGCATAG
114927088 TTATAAGCATA
1 TTATAAGCATA
114927099 ACTAAATTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
45 4 0.07
46 50 0.93
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (46 bp):
TTATAAGCATAGTTAATGCTACCGTATTGTTCTGTTAAAAGCATAG
Found at i:114927332 original size:85 final size:86
Alignment explanation
Indices: 114927162--114927440 Score: 229
Period size: 85 Copynumber: 3.2 Consensus size: 86
114927152 ACAGAGGAAC
* *
114927162 AGTGGCAGTTTAATCTACAAATAGTGTGGTTCAATCACGAACCGAGTAACAATTTGTTTAATCTG
1 AGTGGCAG--TAA-CTATAAATAGTGTGGTTCAATCACGAACCAAGTAACAATTTGTTTAATCTG
*
114927227 CAAATGTAAAATGCACTCACAACA
63 CAAATATAAAATGCACTCACAACA
* * *** * *
114927251 AGTGGCAGTAACTGTAAATA-TGTGGTTCAATCATGAACCAAGTGGTAGTTTGTTTAATCTGCTA
1 AGTGGCAGTAACTATAAATAGTGTGGTTCAATCACGAACCAAGTAACAATTTGTTTAATCTGCAA
*** *
114927315 ATATATTGTGCATTCACAACA
66 ATATAAAATGCACTCACAACA
* * * * * ** * * *
114927336 GGTGGTAGTAACTATAAATAGTTTCGTTCAATCAGGAATGAAGTGACAATTT-TTGTATTTTGCA
1 AGTGGCAGTAACTATAAATAGTGTGGTTCAATCACGAACCAAGTAACAATTTGTT-TAATCTGCA
**** * *
114927400 AATATGTTGTGTACCCACAACA
65 AATATAAAATGCACTCACAACA
*
114927422 AGTGGCAGTAACTAGAAAT
1 AGTGGCAGTAACTATAAAT
114927441 GAACTATGGT
Statistics
Matches: 153, Mismatches: 35, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
85 72 0.47
86 70 0.46
87 3 0.02
89 8 0.05
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (86 bp):
AGTGGCAGTAACTATAAATAGTGTGGTTCAATCACGAACCAAGTAACAATTTGTTTAATCTGCAA
ATATAAAATGCACTCACAACA
Found at i:114939267 original size:29 final size:27
Alignment explanation
Indices: 114939233--114939335 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 27
114939223 TACTCAATCA
*
114939233 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * **
114939262 CGCACACATAGTGCCATATAGTCCAAATT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
114939291 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
114939320 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
114939336 ATCTCGTCAC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 2 0.03
29 58 0.97
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:114947193 original size:29 final size:28
Alignment explanation
Indices: 114947159--114947260 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
114947149 TACTCAATCA
*
114947159 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
114947188 CGCACACATAGTGCCATATAGTCCAA-AT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
*
114947216 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
114947245 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
114947261 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.02
28 22 0.36
29 38 0.62
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:114951566 original size:18 final size:18
Alignment explanation
Indices: 114951511--114951556 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
114951501 TTGTTCATGT
114951511 TTTCAA-TCTCATATCTCAA
1 TTTCAATTCTCA-AT-TCAA
114951530 TTTCAATTCTCAATTCAA
1 TTTCAATTCTCAATTCAA
114951548 TTTCTAATT
1 TTTC-AATT
114951557 TCATTCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 12 0.48
20 5 0.20
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTCAATTCTCAATTCAA
Found at i:114951686 original size:23 final size:23
Alignment explanation
Indices: 114951656--114951713 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
114951646 GTGGATTCCT
114951656 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
114951679 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
*
114951702 TCCAAACACACC
1 CCCAAACACACC
114951714 CGGAATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.47, C:0.41, G:0.03, T:0.09
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:114952235 original size:15 final size:15
Alignment explanation
Indices: 114952215--114952246 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
114952205 TAATATATAT
114952215 TTCAATCAATATAAA
1 TTCAATCAATATAAA
114952230 TTCAATCAATATAAA
1 TTCAATCAATATAAA
114952245 TT
1 TT
114952247 TGATAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:114953451 original size:4 final size:4
Alignment explanation
Indices: 114953442--114953477 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
114953432 CCTTTTCTCC
114953442 CTTT CTTT CTTT CTTT CCTTT CTTT CCTTT CTTT CT
1 CTTT CTTT CTTT CTTT -CTTT CTTT -CTTT CTTT CT
114953478 CCCCTGCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 22 0.73
5 8 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:114953462 original size:9 final size:9
Alignment explanation
Indices: 114953441--114953476 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
114953431 CCCTTTTCTC
114953441 CCTTTCTTT
1 CCTTTCTTT
114953450 -CTTTCTTT
1 CCTTTCTTT
114953458 CCTTTCTTT
1 CCTTTCTTT
114953467 CCTTTCTTT
1 CCTTTCTTT
114953476 C
1 C
114953477 TCCCCTGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (9 bp):
CCTTTCTTT
Found at i:114953462 original size:13 final size:13
Alignment explanation
Indices: 114953441--114953477 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
114953431 CCCTTTTCTC
114953441 CCTTTCTTTCTTT
1 CCTTTCTTTCTTT
114953454 -CTTTCCTTTCTTT
1 CCTTT-CTTTCTTT
114953467 CCTTTCTTTCT
1 CCTTTCTTTCT
114953478 CCCCTGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
CCTTTCTTTCTTT
Found at i:114953553 original size:13 final size:13
Alignment explanation
Indices: 114953535--114953566 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
114953525 TTTTATTTCA
114953535 TTTATTTCTTTAT
1 TTTATTTCTTTAT
114953548 TTTATTTCTTTAT
1 TTTATTTCTTTAT
114953561 TTTATT
1 TTTATT
114953567 ATTAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTCTTTAT
Found at i:114958022 original size:43 final size:42
Alignment explanation
Indices: 114957942--114958075 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 42
114957932 AGACATCGTG
* * * * *
114957942 TAAGACCGTGTCTGGGACACAGGCCTCGAT-TGAGATTTATGTA
1 TAAGACCATGTTTGGGACAGAGGCATCGATAT-TGATTTAT-TA
** * *
114957985 TAAGACCATGTTTGGGACATTGGCATCG-TATCTGATTTCTTG
1 TAAGACCATGTTTGGGACAGAGGCATCGATAT-TGATTTATTA
* *
114958027 TAAGACCCTGTTTGGGACAGAGGCATCGATATTGAATTATATA
1 TAAGACCATGTTTGGGACAGAGGCATCGATATTGATTTAT-TA
114958070 TAAGAC
1 TAAGAC
114958076 TACGTCAGGG
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
42 33 0.45
43 40 0.55
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (42 bp):
TAAGACCATGTTTGGGACAGAGGCATCGATATTGATTTATTA
Found at i:114958095 original size:85 final size:85
Alignment explanation
Indices: 114957940--114958095 Score: 181
Period size: 85 Copynumber: 1.8 Consensus size: 85
114957930 TGAGACATCG
* * * * **
114957940 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTATGTATAAGACCATGTTTGGGACAT
1 TGTAAGACCCTGTCTGGGACACAGGCATCGATTGAGATTTATATATAAGACCACGTCAGGGACAT
*
114958005 TGGCATCGTATCTGATTTCT
66 CGGCATCGTATCTGATTTCT
* * *
114958025 TGTAAGACCCTGTTTGGGACAGAGGCATCGATATTGA-A-TTATATATAAGACTACGTCAGGGAC
1 TGTAAGACCCTGTCTGGGACACAGGCATCG--ATTGAGATTTATATATAAGACCACGTCAGGGAC
*
114958088 GTCGGCAT
64 ATCGGCAT
114958096 TGTACTTGGT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
85 52 0.90
86 1 0.02
87 5 0.09
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (85 bp):
TGTAAGACCCTGTCTGGGACACAGGCATCGATTGAGATTTATATATAAGACCACGTCAGGGACAT
CGGCATCGTATCTGATTTCT
Found at i:114972384 original size:40 final size:40
Alignment explanation
Indices: 114972310--114972455 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
114972300 CCGCACCAAG
* * * * * *
114972310 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
114972350 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
114972390 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
114972430 GCCTTCGGGTCTTAACCCGGATATAA
1 GCCTTCGGGTCTTAGCCCGGATATAA
114972456 TTTTCAGCAT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:114972470 original size:40 final size:40
Alignment explanation
Indices: 114972342--114972493 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
114972332 ATCACGATTT
* * * * *
114972342 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
114972382 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * **
114972422 GCACAATTGCCTTCGGGTCTTAACCCGGATATA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
114972462 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
114972494 CATTCAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
39 4 0.04
40 91 0.94
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:114980488 original size:40 final size:40
Alignment explanation
Indices: 114980414--114980559 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
114980404 CCGCACCAAG
* * * * * *
114980414 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
114980454 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
114980494 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
114980534 GCCTTCGGGTCTTAACCCGGATATAA
1 GCCTTCGGGTCTTAGCCCGGATATAA
114980560 TTTTCAGCAT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:114980574 original size:40 final size:40
Alignment explanation
Indices: 114980446--114980597 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
114980436 ATCACGATTT
* * * * *
114980446 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
114980486 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * **
114980526 GCACAATTGCCTTCGGGTCTTAACCCGGATATA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
114980566 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
114980598 CATTCAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
39 4 0.04
40 91 0.94
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:114986388 original size:42 final size:43
Alignment explanation
Indices: 114986331--114986412 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
114986321 TTAGACCATG
** * *
114986331 TCTGGGACATTGGCATC-ATATT-TGATTTCATGTAAGACCCTA
1 TCTGGGACAGAGGCATCGATATTGT-ATTACATATAAGACCCTA
114986373 TCTGGGACAGAGGCATCGATATTGTATTACATATAAGACC
1 TCTGGGACAGAGGCATCGATATTGTATTACATATAAGACC
114986413 ACGTCCGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 15 0.44
43 18 0.53
44 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (43 bp):
TCTGGGACAGAGGCATCGATATTGTATTACATATAAGACCCTA
Found at i:114986411 original size:43 final size:42
Alignment explanation
Indices: 114986331--114986412 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
114986321 TTAGACCATG
** * *
114986331 TCTGGGACATTGGCATCATATTTGATTTCATGTAAGACCCTA
1 TCTGGGACAGAGGCATCATATTTGATTACATATAAGACCCTA
114986373 TCTGGGACAGAGGCATCGATA-TTGTATTACATATAAGACC
1 TCTGGGACAGAGGCATC-ATATTTG-ATTACATATAAGACC
114986413 ACGTCCGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 18 0.53
43 16 0.47
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (42 bp):
TCTGGGACAGAGGCATCATATTTGATTACATATAAGACCCTA
Found at i:114995274 original size:21 final size:20
Alignment explanation
Indices: 114995244--114995282 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
114995234 CAAAACTTGT
*
114995244 ATAACTATCATTAAACATTC
1 ATAACTATCATCAAACATTC
114995264 ATAATCTATCATCAAACAT
1 ATAA-CTATCATCAAACAT
114995283 AAAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:115018197 original size:40 final size:40
Alignment explanation
Indices: 115018119--115018220 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
115018109 TGATGACATA
*
115018119 TCGGCTAAATATGGCACTTAGTGTGCAGTTCAATATAGCT
1 TCGGCTAAATATGGCACTTAGTGTGCAGTTCAAGATAGCT
* **
115018159 TCGGCTAAATTTGGCACTTAGTGTGC-GATTTGAGATAGCT
1 TCGGCTAAATATGGCACTTAGTGTGCAG-TTCAAGATAGCT
** *
115018199 TCGGCTATGTACGGCACTTAGT
1 TCGGCTAAATATGGCACTTAGT
115018221 TTGCGAGATA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.02
40 52 0.98
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
TCGGCTAAATATGGCACTTAGTGTGCAGTTCAAGATAGCT
Found at i:115018286 original size:28 final size:27
Alignment explanation
Indices: 115018214--115018287 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
115018204 TATGTACGGC
* * *
115018214 ACTTAGTTTGCGAGATATCAAGAATGC
1 ACTTAGTGTGCGAGACATCAAGAATGA
* * **
115018241 ACTTAGTGTGGGAAACATTGAGAATGGA
1 ACTTAGTGTGCGAGACATCAAGAAT-GA
115018269 ACTTAGTGTGCGAGACATC
1 ACTTAGTGTGCGAGACATC
115018288 GAGTATGCAA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 19 0.53
28 17 0.47
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (27 bp):
ACTTAGTGTGCGAGACATCAAGAATGA
Found at i:115018299 original size:28 final size:28
Alignment explanation
Indices: 115018214--115018299 Score: 93
Period size: 28 Copynumber: 3.1 Consensus size: 28
115018204 TATGTACGGC
* * *
115018214 ACTTAGTTTGCGAGATATCAAGAATGC-
1 ACTTAGTGTGCGAGACATCGAGAATGCA
* * * *
115018241 ACTTAGTGTGGGAAACATTGAGAATGGA
1 ACTTAGTGTGCGAGACATCGAGAATGCA
*
115018269 ACTTAGTGTGCGAGACATCGAGTATGCA
1 ACTTAGTGTGCGAGACATCGAGAATGCA
115018297 ACT
1 ACT
115018300 GCATTCCGTG
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 20 0.43
28 26 0.57
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (28 bp):
ACTTAGTGTGCGAGACATCGAGAATGCA
Found at i:115022622 original size:2 final size:2
Alignment explanation
Indices: 115022615--115022650 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
115022605 TAAGTCATGC
115022615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115022651 AAAACCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115030387 original size:36 final size:34
Alignment explanation
Indices: 115030340--115030406 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
115030330 GTTTATACAT
115030340 AAAAAATAAAAACTTCCCCCATAATTTTAGATTTTC
1 AAAAAATAAAAA-TT-CCCCATAATTTTAGATTTTC
* * *
115030376 AAAAATTAAAAATTTCCCTTAATTTTAGATT
1 AAAAAATAAAAATTCCCCATAATTTTAGATT
115030407 AAAAAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 15 0.54
35 2 0.07
36 11 0.39
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAAAATAAAAATTCCCCATAATTTTAGATTTTC
Found at i:115031724 original size:34 final size:34
Alignment explanation
Indices: 115031618--115031797 Score: 148
Period size: 34 Copynumber: 5.3 Consensus size: 34
115031608 ATGCAACATG
* *
115031618 ACATGCTTATAATAGATCAATACAGAAGCAAT-A
1 ACATGCTTATAATAGATCAATATAGTAGCAATAA
* ** * * *
115031651 ACATGCTTATAATA-AGTCGATGCAATAGTAATTA
1 ACATGCTTATAATAGA-TCAATATAGTAGCAATAA
* *
115031685 TCATGCTTATAATAGATCAATATGGTAGCAATAA
1 ACATGCTTATAATAGATCAATATAGTAGCAATAA
* * ** *
115031719 ACATGCTTATAACAGGGTTGATATAGTAGCAATTA
1 ACATGCTTATAATA-GATCAATATAGTAGCAATAA
* * *
115031754 ACATGTTTTATAACAGATCATTATAGTAGCAATAA
1 ACATG-CTTATAATAGATCAATATAGTAGCAATAA
*
115031789 ACTTGCTTA
1 ACATGCTTA
115031798 ACACGTATTT
Statistics
Matches: 114, Mismatches: 28, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
32 1 0.01
33 25 0.22
34 40 0.35
35 40 0.35
36 8 0.07
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (34 bp):
ACATGCTTATAATAGATCAATATAGTAGCAATAA
Found at i:115035563 original size:33 final size:33
Alignment explanation
Indices: 115035523--115035671 Score: 129
Period size: 33 Copynumber: 4.4 Consensus size: 33
115035513 ATGCAATATG
*
115035523 ACATGCTTATAACAAATCAATACGGTAGCAATA
1 ACATGCTTATAACAAATCAATACAGTAGCAATA
* * * * *
115035556 ATATGCTTATAATAAGTCGATATAGTAGCAATTA
1 ACATGCTTATAACAAATCAATACAGTAGCAA-TA
* * * * *
115035590 TCATGCCTATAATAGATCAATAC-GGAGCAATAA
1 ACATGCTTATAACAAATCAATACAGTAGCAAT-A
* * *
115035623 ACATGCTTATAACAAGTCGATACAGCAGCAATTA
1 ACATGCTTATAACAAATCAATACAGTAGCAA-TA
115035657 ACATGCATTATAACA
1 ACATGC-TTATAACA
115035672 GATAATTATA
Statistics
Matches: 90, Mismatches: 21, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
32 1 0.01
33 49 0.54
34 31 0.34
35 9 0.10
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (33 bp):
ACATGCTTATAACAAATCAATACAGTAGCAATA
Found at i:115035609 original size:67 final size:67
Alignment explanation
Indices: 115035523--115035671 Score: 192
Period size: 67 Copynumber: 2.2 Consensus size: 67
115035513 ATGCAATATG
* * * * *
115035523 ACATGCTTATAACAAATCAATACGGTAGCAAT-AATATGCTTATAATAAGTCGATATAGTAGCAA
1 ACATGCCTATAACAAATCAATACGG-AGCAATAAACATGCTTATAACAAGTCGATACAGCAGCAA
115035587 TTA
65 TTA
* * *
115035590 TCATGCCTATAATAGATCAATACGGAGCAATAAACATGCTTATAACAAGTCGATACAGCAGCAAT
1 ACATGCCTATAACAAATCAATACGGAGCAATAAACATGCTTATAACAAGTCGATACAGCAGCAAT
115035655 TA
66 TA
*
115035657 ACATGCATTATAACA
1 ACATGC-CTATAACA
115035672 GATAATTATA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
66 6 0.09
67 57 0.83
68 6 0.09
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (67 bp):
ACATGCCTATAACAAATCAATACGGAGCAATAAACATGCTTATAACAAGTCGATACAGCAGCAAT
TA
Found at i:115038882 original size:3 final size:3
Alignment explanation
Indices: 115038874--115038903 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
115038864 AAAAAATATG
115038874 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
115038904 CTATATATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:115040377 original size:15 final size:16
Alignment explanation
Indices: 115040359--115040392 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
115040349 AATTATTAAT
115040359 ATAATAATTTTAAA-A
1 ATAATAATTTTAAATA
115040374 ATAATAATTTTAAATA
1 ATAATAATTTTAAATA
115040390 ATA
1 ATA
115040393 TTATTCACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATAATTTTAAATA
Found at i:115043306 original size:4 final size:4
Alignment explanation
Indices: 115043299--115043334 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
115043289 CACACACACT
115043299 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
115043335 TTTGTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:115045751 original size:27 final size:27
Alignment explanation
Indices: 115045721--115045775 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
115045711 ATGAGATTAT
* *
115045721 AGTTATTATATGATAATTTAAAAAAAA
1 AGTTATTATATGATAAGTAAAAAAAAA
115045748 AGTTATTATATGATAAGTAAAAAAAAA
1 AGTTATTATATGATAAGTAAAAAAAAA
115045775 A
1 A
115045776 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (27 bp):
AGTTATTATATGATAAGTAAAAAAAAA
Found at i:115045784 original size:27 final size:27
Alignment explanation
Indices: 115045723--115045787 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
115045713 GAGATTATAG
* * *
115045723 TTATTATATGATAATTTAAAAAAAAAG
1 TTATTATATGATAAGTAAAAAAAAAAA
115045750 TTATTATATGATAAGTAAAAAAAAAAA
1 TTATTATATGATAAGTAAAAAAAAAAA
115045777 TATATATATAT
1 T-TAT-TATAT
115045788 ATATATAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 25 0.76
28 3 0.09
29 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (27 bp):
TTATTATATGATAAGTAAAAAAAAAAA
Found at i:115048933 original size:31 final size:30
Alignment explanation
Indices: 115048876--115048935 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
115048866 TTTCAAATTT
* *
115048876 ATATTATTTAAAAATTAACAAGAATTAAAA
1 ATATTATTTAAAAAATAACAAAAATTAAAA
*
115048906 ATATTATTTAAAAAATAATTAAAAATTAAA
1 ATATTATTTAAAAAATAA-CAAAAATTAAA
115048936 TGCAACGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (30 bp):
ATATTATTTAAAAAATAACAAAAATTAAAA
Found at i:115055116 original size:59 final size:58
Alignment explanation
Indices: 115055043--115055162 Score: 231
Period size: 59 Copynumber: 2.1 Consensus size: 58
115055033 GTTTAAATAA
115055043 TGAAATTTTTACATCATATTTTTATTTTTATTTTCAATAAAAGTAATATATCTAGGAG
1 TGAAATTTTTACATCATATTTTTATTTTTATTTTCAATAAAAGTAATATATCTAGGAG
115055101 TGAAATTTTTTACATCATATTTTTATTTTTATTTTCAATAAAAGTAATATATCTAGGAG
1 TGAAA-TTTTTACATCATATTTTTATTTTTATTTTCAATAAAAGTAATATATCTAGGAG
115055160 TGA
1 TGA
115055163 TTTTATCTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 5 0.08
59 56 0.92
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (58 bp):
TGAAATTTTTACATCATATTTTTATTTTTATTTTCAATAAAAGTAATATATCTAGGAG
Found at i:115055269 original size:44 final size:44
Alignment explanation
Indices: 115055220--115055307 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
115055210 GTTATGATTC
115055220 AAATTTTAGATTTAAATTTTATTTATTATGTAAATGATAAGAAT
1 AAATTTTAGATTTAAATTTTATTTATTATGTAAATGATAAGAAT
115055264 AAATTTTAGATTTAAATTTTATTTATTATGTAAATGATAAGAAT
1 AAATTTTAGATTTAAATTTTATTTATTATGTAAATGATAAGAAT
115055308 GAGATGCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (44 bp):
AAATTTTAGATTTAAATTTTATTTATTATGTAAATGATAAGAAT
Found at i:115055810 original size:43 final size:43
Alignment explanation
Indices: 115055755--115055983 Score: 332
Period size: 43 Copynumber: 5.3 Consensus size: 43
115055745 TTTTTCGAAA
* *
115055755 AAACGCCACTAAAGACCATGACCTTTAGCTGCGCTTTTTTCGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
* *
115055798 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTTCGT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
*
115055841 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTAGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
* * * *
115055884 AAACGCCACGAAAGACCATAACCTTTAGCGGCGCTTTTTTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
* * * * *
115055927 AAACGCCGCTAAAGATCATAACCTTTAGCGGCACTTTTTCCCC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
115055970 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
115055984 GTCATGAAAT
Statistics
Matches: 168, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 168 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
Found at i:115056298 original size:19 final size:19
Alignment explanation
Indices: 115056253--115056299 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
115056243 TAAATATTAA
*
115056253 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
115056272 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
115056291 AATAAAAAT
1 AATAAAAAT
115056300 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:115060982 original size:14 final size:15
Alignment explanation
Indices: 115060946--115060982 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
115060936 AACCATTAAA
115060946 CTTAAACCATAGAAC
1 CTTAAACCATAGAAC
*
115060961 CCTAAACCATAG-AC
1 CTTAAACCATAGAAC
115060975 CTTAAACC
1 CTTAAACC
115060983 TTAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.43, C:0.32, G:0.05, T:0.19
Consensus pattern (15 bp):
CTTAAACCATAGAAC
Found at i:115060983 original size:7 final size:7
Alignment explanation
Indices: 115060935--115061003 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
115060925 GGTTTACGAC
115060935 AAACCATT
1 AAACC-TT
115060943 AAA-CTT
1 AAACCTT
*
115060949 AAACCAT
1 AAACCTT
*
115060956 AGAACCCT
1 A-AACCTT
*
115060964 AAACCAT
1 AAACCTT
*
115060971 AGACCTT
1 AAACCTT
115060978 AAACCTT
1 AAACCTT
**
115060985 AAATATT
1 AAACCTT
*
115060992 AAACCCT
1 AAACCTT
115060999 AAACC
1 AAACC
115061004 CAAAAATAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
6 5 0.10
7 34 0.71
8 9 0.19
ACGTcount: A:0.48, C:0.28, G:0.03, T:0.22
Consensus pattern (7 bp):
AAACCTT
Found at i:115061301 original size:41 final size:41
Alignment explanation
Indices: 115061244--115061356 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
115061234 GTCATATGAC
*
115061244 TTTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGCTCTGGT
* *
115061285 TTTTAGCGGCGTTTTACAAAAAGCGCCGCTAATTCTCTGGT
1 TTTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGCTCTGGT
* *
115061326 TTTTAGCGGCGTTTTACCGAAAGCGCTGCTA
1 TTTTAGCGGCGTTTTACAGAAAGCGCCGCTA
115061357 TTGACCTATT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGCTCTGGT
Found at i:115061394 original size:82 final size:83
Alignment explanation
Indices: 115061244--115061411 Score: 193
Period size: 82 Copynumber: 2.0 Consensus size: 83
115061234 GTCATATGAC
* *
115061244 TTTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACAAAAAGC
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGATTTTTAGCGGCGTTTTACAAAAAGC
115061309 GCCGCTAATT-CTCTG-GT
66 GCCGCT-ATTGCTCTGTGT
* * * ***
115061326 TTTTAGCGGCGTTTTACCGAAAGCGCTGCTATTGAC-CT-ATTTTTAGCGGCATTTTTTGTTAAA
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATG-CTCTGATTTTTAGCGGC--GTTTTACAAAA
115061389 A-CGCCGCTATTGCTCTGTGT
63 AGCGCCGCTATTGCTCTGTGT
115061409 TTT
1 TTT
115061412 ACAATTTTTG
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
81 14 0.19
82 45 0.62
83 14 0.19
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (83 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGATTTTTAGCGGCGTTTTACAAAAAGC
GCCGCTATTGCTCTGTGT
Found at i:115061452 original size:12 final size:12
Alignment explanation
Indices: 115061437--115061461 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
115061427 TTTTTTGATG
115061437 AAACGCCGCTAA
1 AAACGCCGCTAA
115061449 AAACGCCGCTAA
1 AAACGCCGCTAA
115061461 A
1 A
115061462 GCCCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.16, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:115064860 original size:49 final size:49
Alignment explanation
Indices: 115064701--115065080 Score: 621
Period size: 49 Copynumber: 7.9 Consensus size: 49
115064691 GTAGGAGATG
*
115064701 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAG--
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
115064748 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT-AAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
115064796 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
115064845 TATACATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAG--
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
115064892 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTA
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
115064941 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAG--
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
115064988 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTA
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
115065037 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
115065081 CATATGTGTG
Statistics
Matches: 310, Mismatches: 16, Indels: 12
0.92 0.05 0.04
Matches are distributed among these distances:
46 5 0.02
47 126 0.41
48 39 0.13
49 140 0.45
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:115064940 original size:96 final size:96
Alignment explanation
Indices: 115064700--115065080 Score: 642
Period size: 96 Copynumber: 4.0 Consensus size: 96
115064690 TGTAGGAGAT
*
115064700 GTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAG--TATATATGTGATAAG
1 GTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
* *
115064763 GCCTAATGGCCGATGTGATGAATGT-AAAGT
66 GCCTAATGGCCAATGTGATGAATGTGAAAGA
*
115064793 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATACATGTGATA
1 G--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATA
115064858 AGGCCTAATGGCCAATGTGATGAATGTGAAAGA
64 AGGCCTAATGGCCAATGTGATGAATGTGAAAGA
* *
115064891 GTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAG
1 GTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
115064956 GCCTAATGGCCAATGTGATGAATGTGAAAGA
66 GCCTAATGGCCAATGTGATGAATGTGAAAGA
* *
115064987 GTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAG
1 GTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
*
115065052 GCCTAATGGCCGATGTGATGAATGTGAAA
66 GCCTAATGGCCAATGTGATGAATGTGAAA
115065081 CATATGTGTG
Statistics
Matches: 275, Mismatches: 8, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
93 1 0.00
95 46 0.17
96 185 0.67
97 38 0.14
98 5 0.02
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (96 bp):
GTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
GCCTAATGGCCAATGTGATGAATGTGAAAGA
Found at i:115065128 original size:48 final size:48
Alignment explanation
Indices: 115065072--115065271 Score: 355
Period size: 48 Copynumber: 4.2 Consensus size: 48
115065062 CGATGTGATG
*
115065072 AATGTGAAACATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
115065120 AATGTGAAATATATGTGTGATGTGTATATGTGGTAAAGCCGAAGGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
115065168 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
115065216 AATGTGAAATATATGTGTGATGTGTATGTGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
115065264 AATGTGAA
1 AATGTGAA
115065272 TGTTGTAACA
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 145 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.32
Consensus pattern (48 bp):
AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
Found at i:115065365 original size:37 final size:37
Alignment explanation
Indices: 115065311--115065438 Score: 238
Period size: 37 Copynumber: 3.4 Consensus size: 37
115065301 AACTTGGAAA
*
115065311 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTAAGACCCGATGACTACGTGTGGAGAT
115065349 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
115065386 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
115065423 TATGTCCGGGTAAGAC
1 TATGTCCGGGTAAGAC
115065439 TTCGTAATAA
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
37 85 0.96
38 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (37 bp):
TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:115067390 original size:40 final size:40
Alignment explanation
Indices: 115067344--115067643 Score: 281
Period size: 40 Copynumber: 7.5 Consensus size: 40
115067334 TGAATGATAC
**
115067344 CCGGGCTAAGTCCCGAAG-GCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG-ATATAT
* * * *
115067384 CCGGGCTAAGACCCGAAG-GCATTTGTG-TGAGTTGTTATAC
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AG-TGATATAT
* * * *
115067424 CCGGGTTAAGACCCGAAG-GCAATT-GTGCTTGTGGTTATAT
1 CCGGGCTAAGTCCCGAAGAGC-ATTCGTGCTAGT-GATATAT
* *
115067464 CC-GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
* * *
115067503 -CGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
* * * *
115067542 CCGGGCTAAATTCCGAAGAGCATTCGTGCTAATGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
* * * *
115067582 CCGGACTAAGTTCCAAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
**
115067622 CCGGGCTGGGTCCCGAAGAGCA
1 CCGGGCTAAGTCCCGAAGAGCA
115067644 ATCATGCTGG
Statistics
Matches: 225, Mismatches: 26, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
38 1 0.00
39 58 0.26
40 160 0.71
41 6 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
Found at i:115071482 original size:49 final size:48
Alignment explanation
Indices: 115071266--115071696 Score: 674
Period size: 47 Copynumber: 9.0 Consensus size: 48
115071256 TGTAGGAGAT
115071266 GTATAT-ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
1 GTATATAATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
115071313 GTATAT-ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
1 GTATATAATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
* * *
115071360 GTATAT-ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGT
1 GTATATAATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
*
115071407 GTATATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGT
1 G--TATATA-ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
115071458 GTATATACATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
1 GTATATA-ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
* * *
115071507 GTATAT-ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGT
1 GTATATAATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
115071554 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
1 GTATATA-ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
* * *
115071603 GTATAT-ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGT
1 GTATATAATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
*
115071650 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTATATA-ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
115071697 CATATGTGTG
Statistics
Matches: 359, Mismatches: 17, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
47 180 0.50
49 139 0.39
51 40 0.11
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (48 bp):
GTATATAATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
Found at i:115071540 original size:96 final size:96
Alignment explanation
Indices: 115071267--115071696 Score: 720
Period size: 96 Copynumber: 4.5 Consensus size: 96
115071257 GTAGGAGATG
115071267 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCC
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCC
*
115071332 TAATGGCCAATGTGATGAATGTGAAAGAG--
66 TAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
115071361 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATATGTGATAA
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA--AG-A-GTATATATGTGATAA
115071426 GGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
62 GGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
115071461 TATACATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCC
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCC
* *
115071526 TAATGGCCGATGTGATGAATGTGAAGGTGTA
66 TAATGGCCAATGTGATGAATGTGAAAGTGTA
115071557 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCC
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCC
* *
115071622 TAATGGCCGATGTGATGAATGTGAAGGTGTA
66 TAATGGCCAATGTGATGAATGTGAAAGTGTA
*
115071653 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
115071697 CATATGTGTG
Statistics
Matches: 318, Mismatches: 12, Indels: 10
0.94 0.04 0.03
Matches are distributed among these distances:
94 42 0.13
96 186 0.58
97 2 0.01
98 47 0.15
100 41 0.13
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (96 bp):
TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCC
TAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:115071744 original size:48 final size:48
Alignment explanation
Indices: 115071688--115071887 Score: 355
Period size: 48 Copynumber: 4.2 Consensus size: 48
115071678 CGATGTGATG
*
115071688 AATGTGAAACATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
115071736 AATGTGAAATATATGTGTGATGTGTATATGTGGTAAAGCCGAAGGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
115071784 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
115071832 AATGTGAAATATATGTGTGATGTGTATGTGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
115071880 AATGTGAA
1 AATGTGAA
115071888 TGTTGTAACA
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 145 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.32
Consensus pattern (48 bp):
AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
Found at i:115071983 original size:37 final size:37
Alignment explanation
Indices: 115071927--115072014 Score: 149
Period size: 37 Copynumber: 2.4 Consensus size: 37
115071917 AACTTAGAAA
* *
115071927 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTAAAACCCGATGACTACGTGTGGAGAT
115071965 TATGTCCGGGTAAAACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAAACCCGATGACTACGTGTGGAGAT
115072002 TATGTCCGGGTAA
1 TATGTCCGGGTAA
115072015 GACTTCGTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 44 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (37 bp):
TATGTCCGGGTAAAACCCGATGACTACGTGTGGAGAT
Found at i:115074052 original size:29 final size:29
Alignment explanation
Indices: 115074020--115074122 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
115074010 GTGACGAGAT
* *
115074020 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
115074049 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
115074078 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
115074107 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
115074123 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:115077871 original size:9 final size:9
Alignment explanation
Indices: 115077857--115077883 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
115077847 ATGTTCGATA
115077857 TAGTCAGTC
1 TAGTCAGTC
115077866 TAGTCAGTC
1 TAGTCAGTC
115077875 TAGTCAGTC
1 TAGTCAGTC
115077884 ACATCTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (9 bp):
TAGTCAGTC
Found at i:115090923 original size:21 final size:21
Alignment explanation
Indices: 115090897--115090941 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
115090887 AAAATGATAG
*
115090897 ATAAATAA-ATAAATAAAATAA
1 ATAAATAATA-AAATAAAAAAA
*
115090918 ATAAATGATAAAATAAAAAAA
1 ATAAATAATAAAATAAAAAAA
115090939 ATA
1 ATA
115090942 GTATGCTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
ATAAATAATAAAATAAAAAAA
Found at i:115092474 original size:40 final size:40
Alignment explanation
Indices: 115092402--115092626 Score: 273
Period size: 40 Copynumber: 5.7 Consensus size: 40
115092392 GCTACTCGTT
* *
115092402 CAAATGCCTTCAGGA-CATAGACCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCA
**
115092442 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
115092482 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
*
115092522 CGAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
* * * *
115092562 CGAATGCCTTTGGATCTTAGTCCGGA-TTAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAAC-TCGCA
*
115092602 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGTCCGGA
115092627 CATCATTCGA
Statistics
Matches: 168, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
39 25 0.15
40 141 0.84
41 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
Found at i:115100689 original size:39 final size:40
Alignment explanation
Indices: 115100571--115100793 Score: 246
Period size: 40 Copynumber: 5.7 Consensus size: 40
115100561 GCTACTCGTT
* *
115100571 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCA
**
115100611 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
115100651 CAAATGCCTTCGGATCTTAGTCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
** *
115100690 TGAATGCCTT-GGATCTTAGTCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
* * *
115100729 CGAATGCCTTCGGATCTTAGTCCGGA-TTAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAAC-TCGCA
*
115100769 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGTCCGGA
115100794 CATCATTCGA
Statistics
Matches: 164, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
38 12 0.07
39 74 0.45
40 76 0.46
41 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
Found at i:115100735 original size:78 final size:79
Alignment explanation
Indices: 115100571--115100793 Score: 242
Period size: 78 Copynumber: 2.8 Consensus size: 79
115100561 GCTACTCGTT
* * *
115100571 CAAATGCCTTCGGGA-CATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTC-GGATCTTAGTCCGATTATAGTAACTCGCACAAATGCCTTC-GGACTTAACCCG
*
115100635 GATTTAGTAACTCGCA
64 GATTTAGTAACTCACA
** **
115100651 CAAATGCCTTCGGATCTTAGTCCGATT-TAGTAACTCGCATGAATGCCTT-GGATCTTAGTCCGG
1 CAAATGCCTTCGGATCTTAGTCCGATTATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGG
115100714 ATTTAGTAACTCACA
65 ATTTAGTAACTCACA
* * * *
115100729 CGAATGCCTTCGGATCTTAGTCCGGA-T-TAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGATCTTAGTCC-GATTATAGTAAC-TCGCACAAATGCCTTC-GGACTTAACCC
115100791 GGA
63 GGA
115100794 CATCATTCGA
Statistics
Matches: 123, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
77 3 0.02
78 56 0.46
79 41 0.33
80 23 0.19
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (79 bp):
CAAATGCCTTCGGATCTTAGTCCGATTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGA
TTTAGTAACTCACA
Found at i:115104714 original size:47 final size:45
Alignment explanation
Indices: 115104642--115104811 Score: 202
Period size: 47 Copynumber: 3.7 Consensus size: 45
115104632 GGTATAATGC
* * *
115104642 CGATGCCATGTCCCAGAAATTGTCTTACACTGGCTCATCCATCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCAT-C-TCAAGT
* *
115104689 CGATGCCATGTCCCAGACATGGTCTTACACTGACAT-ATCTCGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-TCATCTC-AAGT
115104735 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCATCTCAATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACT-G-ACTCATCTCAA-GT
*
115104781 CGATGCCATGTCCAAGACATGGTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
115104812 AGCTCACAAT
Statistics
Matches: 107, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
44 10 0.09
45 19 0.18
46 21 0.20
47 46 0.43
48 11 0.10
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (45 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCATCTCAAGT
Found at i:115104799 original size:92 final size:93
Alignment explanation
Indices: 115104640--115104811 Score: 262
Period size: 92 Copynumber: 1.9 Consensus size: 93
115104630 AGGGTATAAT
* *
115104640 GCCGATGCCATGTCCCAGAAATTGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTCCCAG
1 GCCGATGCCATGTCCCAGAAATTGTCTTACACTGACTCATCCATCAAGTCGATGCCATGTCCAAG
115104705 ACATGGTCTTACACTGACATATCTCGTA
66 ACATGGTCTTACACTGACATATCTCGTA
*
115104733 GCCGATG-CATGTCCCAGACA-TGTCTTACACTAGCACTCAT-C-TCAATGTCGATGCCATGTCC
1 GCCGATGCCATGTCCCAGAAATTGTCTTACACT-G-ACTCATCCATCAA-GTCGATGCCATGTCC
115104794 AAGACATGGTCTTACACT
63 AAGACATGGTCTTACACT
115104812 AGCTCACAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
91 15 0.21
92 46 0.63
93 12 0.16
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (93 bp):
GCCGATGCCATGTCCCAGAAATTGTCTTACACTGACTCATCCATCAAGTCGATGCCATGTCCAAG
ACATGGTCTTACACTGACATATCTCGTA
Found at i:115106374 original size:20 final size:20
Alignment explanation
Indices: 115106349--115106387 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
115106339 TGAAGTATTT
**
115106349 TAAAAAAAGGTAAAAAATAA
1 TAAAAAAACCTAAAAAATAA
115106369 TAAAAAAACCTAAAAAATA
1 TAAAAAAACCTAAAAAATA
115106388 GTTCATAAAG
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:0.74, C:0.05, G:0.05, T:0.15
Consensus pattern (20 bp):
TAAAAAAACCTAAAAAATAA
Found at i:115109068 original size:40 final size:40
Alignment explanation
Indices: 115108964--115109180 Score: 314
Period size: 40 Copynumber: 5.5 Consensus size: 40
115108954 CGGATGATAA
* *
115108964 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
115109004 CCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
115109043 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
115109083 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
115109123 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
115109163 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
115109181 TACTTGGTTT
Statistics
Matches: 164, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 48 0.29
40 116 0.71
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:115109178 original size:119 final size:119
Alignment explanation
Indices: 115108960--115109180 Score: 329
Period size: 119 Copynumber: 1.9 Consensus size: 119
115108950 TATTCGGATG
* *
115108960 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
* ** * *
115109025 TTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGAGCAAGTAACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
*
115109079 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
115109143 ATTTGAGCAAGTAACTATATCC-GGCTAAATTCCGAAGG
64 ATTTGAGCAAGTAACTATATCCGGGCTAAATCCCGAAGG
115109181 TACTTGGTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
118 2 0.02
119 62 0.68
120 27 0.30
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
TTGAGCAAGTAACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
Found at i:115111330 original size:48 final size:48
Alignment explanation
Indices: 115111257--115111584 Score: 299
Period size: 48 Copynumber: 6.9 Consensus size: 48
115111247 GTAAATTGCT
* *
115111257 GATGCCATGTCCCAGACATGCTCTTACACTAGCTCACATGTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * *
115111305 AATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG-C
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * * *
115111352 AATGCCATGTCCCAGACCTGGTCTTACACTAGCTCTCATAAT-GTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCC
* * *
115111400 GACGCCATGTCCCAGACATGGTCTTACACTAG--CACATAATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCC
* * * * * * *
115111447 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCACAAC-ATTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGA-GGCC
* * * * * *
115111495 GATACCATGTTCCAAACATGGTCTTACACTAGCACACGAAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCAC-ATATCGAGGCC
* * * *
115111543 GATACCATGTCCCAGACATAGTCTTACACTGGCACACATATC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATC
115111585 ACCTAAATGT
Statistics
Matches: 232, Mismatches: 39, Indels: 18
0.80 0.13 0.06
Matches are distributed among these distances:
46 7 0.03
47 74 0.32
48 146 0.63
49 5 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
Found at i:115111421 original size:95 final size:96
Alignment explanation
Indices: 115111258--115111572 Score: 320
Period size: 95 Copynumber: 3.3 Consensus size: 96
115111248 TAAATTGCTG
* * * * *
115111258 ATGCCATGTCCCAGACATGCTCTTACACTAGCTCACAT-GTCGAGGCCAATGCCATGTCCCAGAC
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTGGCCGATGCCATGTCCCAGAC
*
115111322 ATGGTCTTACACTAGCTCTCAT-ATCAATG-CA
65 ATGGTCTTACACTAGC-CACATAATCAATGCCA
* * *
115111353 ATGCCATGTCCCAGACCTGGTCTTACACTAGCTCTCATAATGTGGCTGACGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCCGATGCCATGTCCCAGACA
*
115111418 TGGTCTTACACTAG-CACATAATCAATGCCG
66 TGGTCTTACACTAGCCACATAATCAATGCCA
* * * * ** * * * *
115111448 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCACAACATTGCCGATACCATGTTCCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCCGATGCCATGTCCCAGACA
* *
115111513 TGGTCTTACACTAGCACACGA-AAT--GTGGCCG
66 TGGTCTTACACTAGC-CAC-ATAATCAAT-GCCA
* *
115111544 ATACCATGTCCCAGACATAGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
115111573 GGCACACATA
Statistics
Matches: 185, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
93 4 0.02
94 7 0.04
95 137 0.74
96 30 0.16
97 6 0.03
98 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (96 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCCGATGCCATGTCCCAGACA
TGGTCTTACACTAGCCACATAATCAATGCCA
Found at i:115111517 original size:143 final size:141
Alignment explanation
Indices: 115111254--115111578 Score: 391
Period size: 143 Copynumber: 2.3 Consensus size: 141
115111244 AGGGTAAATT
* * *
115111254 GCTGATGCCATGTCCCAGACATGCTCTTACACTAGCTCACATGTCGAGGCCAATGCCATGTCCCA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAG--CACATATCAAGGCCAATGCCATGTCCCA
* * * * * *
115111319 GACATGGTCTTACACTAGCTCTCATATCAATGCAATGCCATGTCCCAGACCTGGTCTTACACTAG
64 AACATGGTCTTACACTAGCTCTCACAACAATGCAATACCATGTCCCAAACATGGTCTTACACTAG
* *
115111384 CTCTC-ATAATGTG
129 CACACGA-AATGTG
* * * *
115111397 GCTGACGCCATGTCCCAGACATGGTCTTACACTAGCACATAATCAATGCCGATGCCATGTTCCAA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACAT-ATCAAGGCCAATGCCATGTCCCAA
* * * *
115111462 ACATGGTCTTACACTGGCTCTCACAACATTGCCGATACCATGTTCCAAACATGGTCTTACACTAG
65 ACATGGTCTTACACTAGCTCTCACAACAATG-CAATACCATGTCCCAAACATGGTCTTACACTAG
115111527 CACACGAAATGTG
129 CACACGAAATGTG
* * * *
115111540 GCCGATACCATGTCCCAGACATAGTCTTACACTGGCACA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACA
115111579 CATATCACCT
Statistics
Matches: 155, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
141 5 0.03
142 45 0.29
143 104 0.67
144 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (141 bp):
GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACATATCAAGGCCAATGCCATGTCCCAAA
CATGGTCTTACACTAGCTCTCACAACAATGCAATACCATGTCCCAAACATGGTCTTACACTAGCA
CACGAAATGTG
Found at i:115125206 original size:5 final size:5
Alignment explanation
Indices: 115125196--115125276 Score: 51
Period size: 5 Copynumber: 15.8 Consensus size: 5
115125186 TATGTATTTC
* * * * *
115125196 AAAAT AAAAT AACA- AAATT TAAAT GAAAT AAAAAT CAAAAGA AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAA-T AAAAT
115125243 AAAA- AAAAT AAAAT AAAAAT AAGAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAA
115125277 AATAGGAGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
4 9 0.15
5 30 0.51
6 20 0.34
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:115125230 original size:6 final size:6
Alignment explanation
Indices: 115125221--115125280 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
115125211 AATTTAAATG
* * * *
115125221 AAATAA AAATCA AAAGAA AAATAAA AAAAATA AAATAA AAATAA GAATAA
1 AAATAA AAATAA AAATAA AAAT-AA AAATA-A AAATAA AAATAA AAATAA
*
115125271 ATA-AA AAATA
1 AAATAA AAATA
115125281 GGAGGAGTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
5 4 0.10
6 27 0.66
7 10 0.24
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:115125258 original size:32 final size:30
Alignment explanation
Indices: 115125216--115125278 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 30
115125206 AACAAAATTT
*
115125216 AAATGAAATAAAAATCAAAAGAA-AAATAAAAA
1 AAATAAAATAAAAAT---AAGAATAAATAAAAA
115125248 AAATAAAATAAAAATAAGAATAAATAAAAA
1 AAATAAAATAAAAATAAGAATAAATAAAAA
115125278 A
1 A
115125279 TAGGAGGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
32 14 0.48
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (30 bp):
AAATAAAATAAAAATAAGAATAAATAAAAA
Found at i:115125269 original size:12 final size:11
Alignment explanation
Indices: 115125216--115125280 Score: 64
Period size: 12 Copynumber: 5.9 Consensus size: 11
115125206 AACAAAATTT
*
115125216 AAATGAAATAA
1 AAATAAAATAA
*
115125227 AAATCAAAAGAA
1 AAAT-AAAATAA
115125239 AAAT-AAA-AA
1 AAATAAAATAA
115125248 AAATAAAATAA
1 AAATAAAATAA
115125259 AAATAAGAATAA
1 AAATAA-AATAA
115125271 ATAA-AAAATA
1 A-AATAAAATA
115125281 GGAGGAGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
9 6 0.13
10 6 0.13
11 16 0.34
12 17 0.36
13 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:115125269 original size:26 final size:28
Alignment explanation
Indices: 115125221--115125277 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
115125211 AATTTAAATG
*
115125221 AAATAAAAATCAAAAGAAAAATAAA-AA
1 AAATAAAAATAAAAAGAAAAATAAATAA
* *
115125248 AAAT-AAAATAAAAATAAGAATAAATAA
1 AAATAAAAATAAAAAGAAAAATAAATAA
115125275 AAA
1 AAA
115125278 ATAGGAGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.14
Consensus pattern (28 bp):
AAATAAAAATAAAAAGAAAAATAAATAA
Found at i:115125272 original size:21 final size:20
Alignment explanation
Indices: 115125225--115125276 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
115125215 TAAATGAAAT
115125225 AAAAATCAAAAGAAAAATAAA
1 AAAAAT-AAAAGAAAAATAAA
*
115125246 AAAAATAAAATAAAAATAAGA
1 AAAAATAAAAGAAAAATAA-A
*
115125267 ATAAATAAAA
1 AAAAATAAAA
115125277 AATAGGAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAATAAAAGAAAAATAAA
Found at i:115125278 original size:17 final size:16
Alignment explanation
Indices: 115125234--115125280 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
115125224 TAAAAATCAA
115125234 AAGAAAAATAAAAAA-
1 AAGAAAAATAAAAAAT
*
115125249 AA-TAAAAT-AAAAAT
1 AAGAAAAATAAAAAAT
115125263 AAGAATAAATAAAAAAT
1 AAGAA-AAATAAAAAAT
115125280 A
1 A
115125281 GGAGGAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 3 0.12
16 4 0.15
17 7 0.27
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (16 bp):
AAGAAAAATAAAAAAT
Found at i:115127975 original size:40 final size:40
Alignment explanation
Indices: 115127920--115128176 Score: 319
Period size: 40 Copynumber: 6.5 Consensus size: 40
115127910 CGGATGATAA
* *
115127920 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTA-TAT
*
115127960 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
* * * *
115128000 CCGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
115128040 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCT-ACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACTATAT
* *
115128080 CCGGGCTATGTCCCGAAGGCATTGGTGCGAGTTG-CTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACTATAT
* *
115128120 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAGT-AGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATAT
* *
115128159 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
115128177 TACTTGGCTT
Statistics
Matches: 195, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
38 14 0.07
39 16 0.08
40 164 0.84
41 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:115132592 original size:41 final size:40
Alignment explanation
Indices: 115132540--115132620 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 40
115132530 TGTTAGTTCC
115132540 TCGAATGAATGACATGATTGAAATATGATTGCTATGATGA
1 TCGAATGAATGACATGATTGAAATATGATTGCTATGATGA
115132580 TCGAACTGAATGACATGATTGAAATATGATTGCTATGATGA
1 TCGAA-TGAATGACATGATTGAAATATGATTGCTATGATGA
115132621 AAACTGTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 5 0.12
41 35 0.88
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (40 bp):
TCGAATGAATGACATGATTGAAATATGATTGCTATGATGA
Found at i:115133389 original size:15 final size:16
Alignment explanation
Indices: 115133371--115133404 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
115133361 TCTCGTATTA
115133371 TGGATTTCTTTAT-CT
1 TGGATTTCTTTATACT
115133386 TGGATTTCTTTATACT
1 TGGATTTCTTTATACT
115133402 TGG
1 TGG
115133405 CTGCTCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.56
Consensus pattern (16 bp):
TGGATTTCTTTATACT
Found at i:115135482 original size:30 final size:30
Alignment explanation
Indices: 115135446--115135505 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
115135436 TTCCCGAGCC
115135446 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
115135476 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
115135506 CGTATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:115136219 original size:49 final size:49
Alignment explanation
Indices: 115136147--115136433 Score: 385
Period size: 49 Copynumber: 5.8 Consensus size: 49
115136137 TGAGGTCACG
115136147 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * *
115136196 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCGCA
* ** * *
115136247 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
* *
115136297 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * *
115136346 TGTGTAGTACTAAGTACAGGCTACTACGTGTACCGGATAATTGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
115136395 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
115136434 GCTTCAGCTA
Statistics
Matches: 210, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
49 124 0.59
50 48 0.23
51 38 0.18
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:115136276 original size:28 final size:28
Alignment explanation
Indices: 115136244--115136327 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
115136234 AACTTCGATC
115136244 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
115136272 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
115136294 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
115136322 ACGTGT
1 ACGTGT
115136328 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:115162491 original size:40 final size:40
Alignment explanation
Indices: 115162401--115162586 Score: 232
Period size: 40 Copynumber: 4.6 Consensus size: 40
115162391 TGGATAATAA
* * **
115162401 CCGGGCTAAGTCCCGAAGGCATTTTGTGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCA-TTTGTGCGAGTTACTAAAT
*
115162442 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
115162482 CCGGACTAAGAT-TCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * *
115162522 CCGGGTTAAGTCCCGAAGGCATTTGTACGGGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AAT
*
115162562 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
115162587 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 103 0.81
41 23 0.18
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:115162604 original size:80 final size:80
Alignment explanation
Indices: 115162397--115162619 Score: 233
Period size: 80 Copynumber: 2.8 Consensus size: 80
115162387 TATTTGGATA
* * *
115162397 ATAACCGGGCTAAGTCCCGAAGGCATTTTGTGCTAGT-GACTAGT-TTCGGGCTAAGTCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCA-TTTGTGCGAGTAG-CTA-TATCCGGGTTAAGTCCCGAAG
*
115162460 GCATTTGTGCGAGTTACT
63 GCATTTGTACGAGTTACT
* * *
115162478 A-AATCCGGACTAAGAT-TCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAGTCCCGAAG
1 ATAA-CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TAGCTATATCCGGGTTAAGTCCCGAAG
*
115162540 GCATTTGTACGGGTTACT
63 GCATTTGTACGAGTTACT
* ** * *
115162558 ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCC-GGTTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGGTTAAGTCCCGAAGG
115162620 TACGTGATTC
Statistics
Matches: 118, Mismatches: 16, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
79 17 0.14
80 79 0.67
81 21 0.18
82 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGGTTAAGTCCCGAAGGCA
TTTGTACGAGTTACT
Found at i:115170483 original size:40 final size:40
Alignment explanation
Indices: 115170434--115170646 Score: 263
Period size: 40 Copynumber: 5.3 Consensus size: 40
115170424 GGTCTAAGTC
* ** *
115170434 CCGAAGGCATTT-TGCGCTAGTGACTAGTTCCGGGCTAAG-T
1 CCGAAGGCATTTGTGCG--AGTTACTAAATCCGGACTAAGAT
*
115170474 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGATTAAGAT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
115170514 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
** *
115170554 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGAC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
* * *
115170594 CCGAAGGCATTTGTGCGGGTTACTATAA-CCGGGCTATG-T
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGACTAAGAT
115170633 CCCGAAGGCATTTG
1 -CCGAAGGCATTTG
115170647 AACGAGTAGC
Statistics
Matches: 156, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 16 0.10
40 134 0.86
41 6 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
Found at i:115170567 original size:80 final size:78
Alignment explanation
Indices: 115170434--115170679 Score: 293
Period size: 80 Copynumber: 3.1 Consensus size: 78
115170424 GGTCTAAGTC
* **
115170434 CCGAAGGCATTT-TGCGCTAGTGACTAGTTCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT
1 CCGAAGGCATTTGTGCG--AGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT
115170498 AAATCCGGATTAAGAT
64 AAATCCGG-TTAAGAT
*
115170514 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTA
*
115170579 AATCCGGGTTAAGAC
65 AATCC-GGTTAAGAT
* * **
115170594 CCGAAGGCATTTGTGCGGGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTA-C
*
115170657 TATATCCGGTTAA-ATT
63 TAAATCCGGTTAAGA-T
115170673 CCGAAGG
1 CCGAAGG
115170680 TACGTGATTC
Statistics
Matches: 147, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
78 1 0.01
79 33 0.22
80 105 0.71
81 8 0.05
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
ATCCGGTTAAGAT
Found at i:115176987 original size:13 final size:13
Alignment explanation
Indices: 115176969--115176995 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
115176959 TACTACTCTA
115176969 GCATCATTAGTAG
1 GCATCATTAGTAG
115176982 GCATCATTAGTAG
1 GCATCATTAGTAG
115176995 G
1 G
115176996 TAAAACTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (13 bp):
GCATCATTAGTAG
Found at i:115178749 original size:13 final size:13
Alignment explanation
Indices: 115178733--115178765 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
115178723 TTTAATTAAA
*
115178733 TTAGTTAATTAGT
1 TTAGATAATTAGT
115178746 TTAGATAATTAGT
1 TTAGATAATTAGT
115178759 TTA-ATAA
1 TTAGATAA
115178766 ACAAATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:115182172 original size:21 final size:20
Alignment explanation
Indices: 115182140--115182184 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
115182130 GCCATTCAGC
*
115182140 CGTGTACAATAATACACGGG
1 CGTGTACAATAACACACGGG
*
115182160 CGTGCTACCATAACACACGGG
1 CGTG-TACAATAACACACGGG
115182181 CGTG
1 CGTG
115182185 GGAGAAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (20 bp):
CGTGTACAATAACACACGGG
Found at i:115184073 original size:11 final size:11
Alignment explanation
Indices: 115184053--115184093 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
115184043 AATCCTCCTA
115184053 TCTT-TTTTAT
1 TCTTATTTTAT
115184063 TCTTATTTTAT
1 TCTTATTTTAT
115184074 T-TTATTTTTAT
1 TCTTA-TTTTAT
*
115184085 TTTTATTTT
1 TCTTATTTT
115184094 TATTTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 7 0.25
11 18 0.64
12 3 0.11
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTATTTTAT
Found at i:115184075 original size:5 final size:5
Alignment explanation
Indices: 115184057--115184125 Score: 61
Period size: 6 Copynumber: 13.0 Consensus size: 5
115184047 CTCCTATCTT
*
115184057 TTTTA TTCTTA TTTTA TTTTA TTTTTA TTTTTA TTTTTA TTTTCA TTTCAA
1 TTTTA TT-TTA TTTTA TTTTA -TTTTA -TTTTA -TTTTA TTTT-A TTT-TA
115184108 TTTTA --TTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA
115184126 AAGACAAATC
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
3 3 0.05
5 23 0.41
6 30 0.54
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:115184082 original size:6 final size:6
Alignment explanation
Indices: 115184056--115184104 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
115184046 CCTCCTATCT
* *
115184056 TTTTTA TTCTTA -TTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTTTCA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
115184102 TTT
1 TTT
115184105 CAATTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
5 9 0.23
6 30 0.77
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:115187044 original size:13 final size:13
Alignment explanation
Indices: 115187028--115187060 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
115187018 TTTAATTAAA
*
115187028 TTAGTTAATTAGT
1 TTAGATAATTAGT
115187041 TTAGATAATTAGT
1 TTAGATAATTAGT
115187054 TTA-ATAA
1 TTAGATAA
115187061 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:115192937 original size:40 final size:39
Alignment explanation
Indices: 115192892--115193099 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
115192882 CGGAATACAA
*
115192892 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
115192932 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
115192972 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
115193012 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
115193052 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
115193092 CCGGATAT
1 CCGGATAT
115193100 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:115193032 original size:80 final size:81
Alignment explanation
Indices: 115192892--115193097 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
115192882 CGGAATACAA
* * *
115192892 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
115192956 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
115192972 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
115193035 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
** * ** * *
115193052 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
115193098 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:115201083 original size:40 final size:39
Alignment explanation
Indices: 115201038--115201245 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
115201028 CGGAATACAA
*
115201038 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
115201078 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
115201118 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
115201158 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
115201198 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
115201238 CCGGATAT
1 CCGGATAT
115201246 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:115201178 original size:80 final size:81
Alignment explanation
Indices: 115201038--115201243 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
115201028 CGGAATACAA
* * *
115201038 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
115201102 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
115201118 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
115201181 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
** * ** * *
115201198 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
115201244 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:115206813 original size:5 final size:5
Alignment explanation
Indices: 115206803--115206832 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
115206793 AACCTAAATT
*
115206803 AATAA AATAA AATAA AATAA AACAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
115206833 TATCTTCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:115209388 original size:14 final size:14
Alignment explanation
Indices: 115209368--115209400 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
115209358 ATTTTGGGGG
115209368 TTCTTTTTTTTT-T
1 TTCTTTTTTTTTCT
115209381 TTCTTTTTTTTTCT
1 TTCTTTTTTTTTCT
115209395 TTCTTT
1 TTCTTT
115209401 CTTCTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTCTTTTTTTTTCT
Found at i:115209389 original size:10 final size:10
Alignment explanation
Indices: 115209374--115209407 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
115209364 GGGGTTCTTT
115209374 TTTTTTTTTC
1 TTTTTTTTTC
115209384 TTTTTTTTTC
1 TTTTTTTTTC
*
115209394 TTTCTTTCTTC
1 TTT-TTTTTTC
115209405 TTT
1 TTT
115209408 GGGTCACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:115215908 original size:13 final size:13
Alignment explanation
Indices: 115215892--115215924 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
115215882 TTTAATTAAA
*
115215892 TTAGTTAATTAGT
1 TTAGATAATTAGT
115215905 TTAGATAATTAGT
1 TTAGATAATTAGT
115215918 TTA-ATAA
1 TTAGATAA
115215925 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:115219064 original size:68 final size:66
Alignment explanation
Indices: 115218992--115219147 Score: 174
Period size: 67 Copynumber: 2.3 Consensus size: 66
115218982 CATCATGTGT
* * *
115218992 ACAAGAGAGCTACGAGATACTATGTGGTAGCTAGGTCACATGTGT-GAT-ACG-GGATGTATACC
1 ACAAGAGAGCTACGAGATA--A-AT-GTAGCTAGGTCACATGTGTGGATCACGTGGA-GGACACC
115219054 ATGTAG
61 ATGTAG
* * * *
115219060 ACAAGAGAGCTACGGGATAAATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGGAGGACACCATGT
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGAT-CACGTGGAGGACACCATGT
115219125 AG
65 AG
115219127 ACAAGAGAGCTACGAGATAAA
1 ACAAGAGAGCTACGAGATAAA
115219148 ATAGGTCACA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
64 18 0.24
65 3 0.04
66 1 0.01
67 33 0.43
68 21 0.28
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGATCACGTGGAGGACACCATGTA
G
Found at i:115226504 original size:68 final size:67
Alignment explanation
Indices: 115226432--115226608 Score: 184
Period size: 67 Copynumber: 2.6 Consensus size: 67
115226422 CATCATGTGT
* * * *
115226432 ACAAGAGAGCTACGAGATACTATGTGGTAGCTAGGTCACATGTGT-GATAC-GG-GATGTATACC
1 ACAAGAGAGCTACGAGATA--A-AT-GTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACC
115226494 ATGTAG
62 ATGTAG
* ** * *
115226500 ACAAGAGAGCTACGGGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACCATGT
115226565 AG
66 AG
*
115226567 ACAAGAGAGCTACGAGATAAAATG--GCTAGGTCACATGGGTGG
1 ACAAGAGAGCTACGAGAT-AAATGTAGCTAGGTCACATGTGTGG
115226609 TACTAAGTGT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
64 17 0.18
65 4 0.04
66 18 0.20
67 30 0.33
68 23 0.25
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.22
Consensus pattern (67 bp):
ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACCATGT
AG
Found at i:115231195 original size:12 final size:11
Alignment explanation
Indices: 115231169--115231249 Score: 54
Period size: 12 Copynumber: 6.6 Consensus size: 11
115231159 TTGAATCCTC
*
115231169 TTATTTTTTTAT
1 TTATTTTATT-T
115231181 TTATTCTTATTT
1 TTATT-TTATTT
115231193 TTATTTTATTTTT
1 TTATTTTA--TTT
115231206 TTATTTTGATTT
1 TTATTTT-ATTT
*
115231218 TGATTTTGATTT
1 TTATTTT-ATTT
**
115231230 CAATTTTATTAT
1 TTATTTTATT-T
115231242 TTCATTTT
1 TT-ATTTT
115231250 GAAAGACATA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
11 6 0.11
12 31 0.54
13 19 0.33
14 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:115231196 original size:6 final size:6
Alignment explanation
Indices: 115231169--115231229 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
115231159 TTGAATCCTC
* * *
115231169 TTATTT TT-TTAT TTATTC TTATTT TTATTT TATTTTT TTATTT TGATTT
1 TTATTT TTATT-T TTATTT TTATTT TTATTT T-TATTT TTATTT TTATTT
* *
115231218 TGATTT TGATTT
1 TTATTT TTATTT
115231230 CAATTTTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
5 2 0.04
6 38 0.81
7 7 0.15
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:115231217 original size:25 final size:25
Alignment explanation
Indices: 115231169--115231229 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
115231159 TTGAATCCTC
115231169 TTATTTT-TTTATTTATTCTTATTT
1 TTATTTTATTTATTTATTCTTATTT
*
115231193 TTATTTTATTTTTTTATT-TTGATTT
1 TTATTTTATTTATTTATTCTT-ATTT
*
115231218 TGATTTTGATTT
1 TTATTTT-ATTT
115231230 CAATTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.28
25 19 0.59
26 4 0.12
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (25 bp):
TTATTTTATTTATTTATTCTTATTT
Found at i:115235248 original size:33 final size:33
Alignment explanation
Indices: 115235208--115235367 Score: 203
Period size: 33 Copynumber: 4.8 Consensus size: 33
115235198 TGAGTGGTAC
* * *
115235208 ACACAAAGTATACATTTCCTTTTCATATGATAT
1 ACACAAAGTATACCTTACCTTTTCAAATGATAT
* * *
115235241 ACACAAAGTATACCTTCCCTTTTCATATGGTAT
1 ACACAAAGTATACCTTACCTTTTCAAATGATAT
* *
115235274 ACACAAAGTATACCTAACCTTTTCAAATGGTAT
1 ACACAAAGTATACCTTACCTTTTCAAATGATAT
* * *
115235307 ACACAAAGTATACCTAACATTTTCAAATAATAT
1 ACACAAAGTATACCTTACCTTTTCAAATGATAT
* *
115235340 ACACAAAGTATACCTTTCCTTTCCAAAT
1 ACACAAAGTATACCTTACCTTTTCAAAT
115235368 TTGATAGCTG
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (33 bp):
ACACAAAGTATACCTTACCTTTTCAAATGATAT
Found at i:115235451 original size:29 final size:29
Alignment explanation
Indices: 115235357--115235443 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
115235347 GTATACCTTT
* *
115235357 CCTTTCCAAATTTGATAGCTGAAGCTATC
1 CCTTTTCACATTTGATAGCTGAAGCTATC
*
115235386 CCTTTTCACATTTGATAGCCGAAGCTATC
1 CCTTTTCACATTTGATAGCTGAAGCTATC
115235415 CCTTTTCACATTTGATAGCTGAAGCTATC
1 CCTTTTCACATTTGATAGCTGAAGCTATC
115235444 ACTATTCATT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (29 bp):
CCTTTTCACATTTGATAGCTGAAGCTATC
Found at i:115235503 original size:31 final size:31
Alignment explanation
Indices: 115235468--115235545 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
115235458 AGGTAGTTAG
115235468 AGCTACCACTTTTCACTAATCAGGTAGCCGA
1 AGCTACCACTTTTCACTAATCAGGTAGCCGA
* * *
115235499 AGCTACTACTTTTCACTGATTAGGTAGCCGA
1 AGCTACCACTTTTCACTAATCAGGTAGCCGA
115235530 AGCTACCACTTTTCAC
1 AGCTACCACTTTTCAC
115235546 ATTGTACACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
AGCTACCACTTTTCACTAATCAGGTAGCCGA
Found at i:115237658 original size:13 final size:13
Alignment explanation
Indices: 115237642--115237674 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
115237632 TTTAATTAAA
*
115237642 TTAGTTAATTAGT
1 TTAGATAATTAGT
115237655 TTAGATAATTAGT
1 TTAGATAATTAGT
115237668 TTA-ATAA
1 TTAGATAA
115237675 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:115249092 original size:31 final size:31
Alignment explanation
Indices: 115249054--115249131 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
115249044 TTTAACGGTT
115249054 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
115249085 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
115249116 ACAGGG-CAAAGCCTTT
1 ACTGGGCCGAAGCCTTT
115249132 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 9 0.20
31 36 0.80
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:115249220 original size:42 final size:42
Alignment explanation
Indices: 115249155--115249246 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
115249145 TGGCCCATAG
*
115249155 GCCCATTTCAATAACACACGAAATATCAATGAATGTATGCAA
1 GCCCATTTCAATAACACACGAAATACCAATGAATGTATGCAA
* *
115249197 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATAACACACGAAATACCAATGAATGTATGCAA
115249239 GCCCATTT
1 GCCCATTT
115249247 GGGGAGACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (42 bp):
GCCCATTTCAATAACACACGAAATACCAATGAATGTATGCAA
Found at i:115249426 original size:25 final size:25
Alignment explanation
Indices: 115249393--115249487 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
115249383 CTCTTTTAAT
* * *
115249393 AACTAGGGCAAAACCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
115249418 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
115249443 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
115249468 AACTGGGACAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
115249488 AGCACTTCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:115249539 original size:16 final size:16
Alignment explanation
Indices: 115249518--115249548 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115249508 AACCCAACCC
*
115249518 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
115249534 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
115249549 CCCATATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:115250358 original size:27 final size:27
Alignment explanation
Indices: 115250298--115250360 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
115250288 GCATATTCGA
115250298 CATTTTACCATACAAGGGTATTACGGT
1 CATTTTACCATACAAGGGTATTACGGT
* * *
115250325 CACTTTACCCTACAGGGGCT-TTACGGT
1 CATTTTACCATACAAGGG-TATTACGGT
*
115250352 CTTTTTACC
1 CATTTTACC
115250361 TGTTAGGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (27 bp):
CATTTTACCATACAAGGGTATTACGGT
Found at i:115250444 original size:27 final size:27
Alignment explanation
Indices: 115250414--115250465 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
115250404 GTAAATCTAC
*
115250414 AAACCAAGGGTATTTC-AGTAATTTTGT
1 AAACCAAAGGTATTTCTA-TAATTTTGT
115250441 AAACCAAAGGTATTTCTATAATTTT
1 AAACCAAAGGTATTTCTATAATTTT
115250466 TAGAAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (27 bp):
AAACCAAAGGTATTTCTATAATTTTGT
Found at i:115250596 original size:27 final size:27
Alignment explanation
Indices: 115250560--115250705 Score: 220
Period size: 27 Copynumber: 5.4 Consensus size: 27
115250550 GTAATTTCAC
*
115250560 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
115250587 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
115250614 AATCAAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
115250641 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
115250668 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
115250695 AATCGAGGGTA
1 AATCGAGGGTA
115250706 CTTTGGTAAT
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Done.