Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 61 of 132
Found at i:17151434 original size:39 final size:38
Alignment explanation
Indices: 17151378--17151463 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 38
17151368 TTTATAAGTT
*
17151378 TTTTTTATAAAATTTTAAATATTTTA-GATATATTT-TA
1 TTTTTTATAAAATTTT-AATAATTTATGATATATTTATA
*
17151415 TTAATTTTAT-AAATATTTAATAATTTATTATATATTTATA
1 TT--TTTTATAAAAT-TTTAATAATTTATGATATATTTATA
17151455 TTTTTTATA
1 TTTTTTATA
17151464 TTTCTATAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
37 2 0.05
38 18 0.44
39 17 0.41
40 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (38 bp):
TTTTTTATAAAATTTTAATAATTTATGATATATTTATA
Found at i:17151457 original size:17 final size:19
Alignment explanation
Indices: 17151405--17151511 Score: 61
Period size: 19 Copynumber: 5.7 Consensus size: 19
17151395 AATATTTTAG
*
17151405 ATATATTTTATTAATTT-TAT
1 ATATA-TTTAATAATTTAT-T
*
17151425 AAATATTTAATAATTTATT
1 ATATATTTAATAATTTATT
17151444 ATATATTT-AT-ATTT-TT
1 ATATATTTAATAATTTATT
*
17151460 -TATATTTCTATAAGTTTA-T
1 ATATATTT-AATAA-TTTATT
17151479 ATCA-ATTTTAATATATTT-TT
1 AT-ATA-TTTAATA-ATTTATT
17151499 A-ATATTTAATAAT
1 ATATATTTAATAAT
17151512 ATTTGTGATT
Statistics
Matches: 71, Mismatches: 4, Indels: 27
0.70 0.04 0.26
Matches are distributed among these distances:
15 7 0.10
16 2 0.03
17 8 0.11
18 11 0.15
19 23 0.32
20 15 0.21
21 5 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (19 bp):
ATATATTTAATAATTTATT
Found at i:17151550 original size:10 final size:10
Alignment explanation
Indices: 17151535--17151571 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
17151525 AATATTTTAT
17151535 ATTTTTATGA
1 ATTTTTATGA
17151545 ATTTTTAT-A
1 ATTTTTATGA
*
17151554 ATTTTTAAGA
1 ATTTTTATGA
17151564 ATTTTTAT
1 ATTTTTAT
17151572 ACATTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (10 bp):
ATTTTTATGA
Found at i:17151577 original size:10 final size:9
Alignment explanation
Indices: 17151348--17151728 Score: 101
Period size: 9 Copynumber: 40.2 Consensus size: 9
17151338 TTAAATAACT
17151348 TTTTTATAA
1 TTTTTATAA
17151357 TTTTTAT-A
1 TTTTTATAA
17151365 TTATTTATAA
1 TT-TTTATAA
17151375 GTTTTTTTTATAAA
1 ----TTTTTAT-AA
*
17151389 ATTTTA-AA
1 TTTTTATAA
*
17151397 TATTTTAGATA
1 T-TTTTATA-A
17151408 TATTTTATTAA
1 T-TTTTA-TAA
17151419 -TTTTATAAA
1 TTTTTAT-AA
*
17151428 TATTTAATAA
1 T-TTTTATAA
17151438 TTTATTAT-A
1 TTT-TTATAA
* *
17151447 TATTTATAT
1 TTTTTATAA
17151456 TTTTTAT-A
1 TTTTTATAA
*
17151464 TTTCTATAA
1 TTTTTATAA
*
17151473 GTTTATATCAA
1 -TTTTTAT-AA
*
17151484 TTTTAAT-A
1 TTTTTATAA
17151492 TATTTT-TAA
1 T-TTTTATAA
*
17151501 TATTTAATAA
1 T-TTTTATAA
* * *
17151511 TATTTGTGA
1 TTTTTATAA
*
17151520 -TTGT-TAA
1 TTTTTATAA
17151527 TATTTTAT-A
1 T-TTTTATAA
17151536 TTTTTATGAA
1 TTTTTAT-AA
17151546 TTTTTATAA
1 TTTTTATAA
*
17151555 TTTTTAAGAA
1 TTTTT-ATAA
17151565 TTTTTATACA
1 TTTTTATA-A
*
17151575 TTTTTGTAAA
1 TTTTTAT-AA
*
17151585 ATTTTA-AA
1 TTTTTATAA
*
17151593 TGTGTTTTATTA
1 --T-TTTTATAA
*
17151605 CTTTTATAA
1 TTTTTATAA
*
17151614 TTTTTTATAC
1 -TTTTTATAA
*
17151624 TTTGTTAGAA
1 TTT-TTATAA
* *
17151634 TTTATTAGATT
1 TTT-TTATA-A
17151645 TTTTTATAAA
1 TTTTTAT-AA
* *
17151655 ATTTTAT-G
1 TTTTTATAA
17151663 TTTTTATAA
1 TTTTTATAA
17151672 TTTTTATAA
1 TTTTTATAA
17151681 GTTTATT-TCAA
1 -TTT-TTAT-AA
* *
17151692 TCTTAAT-A
1 TTTTTATAA
17151700 TTTGTTA-AA
1 TTT-TTATAA
17151709 TATTTT-TAA
1 T-TTTTATAA
17151718 TTTTTATAA
1 TTTTTATAA
17151727 TT
1 TT
17151729 GTTAATAAAA
Statistics
Matches: 276, Mismatches: 48, Indels: 96
0.66 0.11 0.23
Matches are distributed among these distances:
7 2 0.01
8 42 0.15
9 97 0.35
10 94 0.34
11 30 0.11
12 2 0.01
13 5 0.02
14 4 0.01
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17152082 original size:9 final size:9
Alignment explanation
Indices: 17152067--17152164 Score: 62
Period size: 9 Copynumber: 10.8 Consensus size: 9
17152057 AACATGATTT
17152067 ATTTTTATA
1 ATTTTTATA
*
17152076 TTTTTTATAA
1 ATTTTTAT-A
*
17152086 AATTTTAT-
1 ATTTTTATA
*
17152094 TTTTTTATA
1 ATTTTTATA
17152103 ATTTTTATA
1 ATTTTTATA
17152112 AGTTTATT-TA
1 A-TTT-TTATA
* *
17152122 AATCTTA-A
1 ATTTTTATA
17152130 TATTTGTTA-A
1 -ATTT-TTATA
17152140 ATATTTT-TA
1 AT-TTTTATA
17152149 ATTTTTATA
1 ATTTTTATA
17152158 ATTTTTA
1 ATTTTTA
17152165 ATAAAAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
8 13 0.19
9 35 0.51
10 19 0.28
11 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:17152096 original size:17 final size:16
Alignment explanation
Indices: 17152074--17152107 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17152064 TTTATTTTTA
17152074 TATTTTTTATAAAATTT
1 TATTTTTT-TAAAATTT
*
17152091 TATTTTTTTATAATTT
1 TATTTTTTTAAAATTT
17152107 T
1 T
17152108 TATAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTTTAAAATTT
Found at i:17152117 original size:25 final size:26
Alignment explanation
Indices: 17152068--17152120 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
17152058 ACATGATTTA
* *
17152068 TTTTTATATTTTTTATAAAATTTTATT
1 TTTTTATAATTTTTAT-AAAGTTTATT
17152095 TTTTTATAATTTTTAT-AAGTTTATT
1 TTTTTATAATTTTTATAAAGTTTATT
17152120 T
1 T
17152121 AAATCTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
27 15 0.62
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTATAATTTTTATAAAGTTTATT
Found at i:17153121 original size:189 final size:189
Alignment explanation
Indices: 17152795--17153160 Score: 678
Period size: 189 Copynumber: 1.9 Consensus size: 189
17152785 AAATCTGATT
*
17152795 TAAAGAACCTTTAAATCAATTTGATTAGAATAAAATCATATTGAGATATTTTGTCTTTTTAAAAC
1 TAAAGAACCTTTAAATCAATTTGATTAGAATAAAATCATATTGAGATATTTTGTCCTTTTAAAAC
* *
17152860 AGATTCTTTTTAATATTTGCTGAGGGAAAAACTTAAATTACGTAATTGGACTAAAATATTCGTAG
66 AGATTCTTTTTAATATTTGCTGAGGGAAAAAATTAAATTACGTAATTGGACTAAAATATTCATAG
* *
17152925 GCCTTTTTTGGGCCCAATCTATTTGAACATTTCGTGTCTCCCACATCGTGCGGGTGCAC
131 GCCTTTTTTGGGCCCAATCGATTTGAACATTTCATGTCTCCCACATCGTGCGGGTGCAC
*
17152984 TAAAGGACCTTTAAATCAATTTGATTAGAATAAAATCATATTGAGATATTTTGTCCTTTTAAAAC
1 TAAAGAACCTTTAAATCAATTTGATTAGAATAAAATCATATTGAGATATTTTGTCCTTTTAAAAC
17153049 AGATTCTTTTTAATATTTGCTGAGGGAAAAAATTAAATTACGTAATTGGACTAAAATATTCATAG
66 AGATTCTTTTTAATATTTGCTGAGGGAAAAAATTAAATTACGTAATTGGACTAAAATATTCATAG
17153114 GCCTTTTTTGGGCCCAATCGATTTGAACATTTCATGTCTCCCACATC
131 GCCTTTTTTGGGCCCAATCGATTTGAACATTTCATGTCTCCCACATC
17153161 ATGCAAGTGC
Statistics
Matches: 171, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 171 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (189 bp):
TAAAGAACCTTTAAATCAATTTGATTAGAATAAAATCATATTGAGATATTTTGTCCTTTTAAAAC
AGATTCTTTTTAATATTTGCTGAGGGAAAAAATTAAATTACGTAATTGGACTAAAATATTCATAG
GCCTTTTTTGGGCCCAATCGATTTGAACATTTCATGTCTCCCACATCGTGCGGGTGCAC
Found at i:17156206 original size:28 final size:31
Alignment explanation
Indices: 17156175--17156238 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 31
17156165 TCACATCAAC
*
17156175 AAATAATTAAAA-ATTATA-AAAATATTCA-
1 AAATAATTAAAAGAATATATAAAATATTCAT
17156203 AAATAA--AAAAGAATATATAAAATATTCAT
1 AAATAATTAAAAGAATATATAAAATATTCAT
17156232 AAA-AATT
1 AAATAATT
17156239 CTAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
26 4 0.13
27 5 0.17
28 18 0.60
29 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (31 bp):
AAATAATTAAAAGAATATATAAAATATTCAT
Found at i:17158288 original size:26 final size:27
Alignment explanation
Indices: 17158233--17158299 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
17158223 TATTTTGGAG
* *
17158233 ATATT-TTTCATTAATTAATTAGTTAA
1 ATATTATTTTATTAATTAATTACTTAA
* *
17158259 ATATTATTTTATTAA-TATTTACTTAT
1 ATATTATTTTATTAATTAATTACTTAA
17158285 ATATTTATTATTATT
1 ATA-TTATT-TTATT
17158300 TTATTTAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 16 0.47
27 13 0.38
28 5 0.15
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (27 bp):
ATATTATTTTATTAATTAATTACTTAA
Found at i:17164931 original size:37 final size:37
Alignment explanation
Indices: 17164875--17165035 Score: 205
Period size: 37 Copynumber: 4.4 Consensus size: 37
17164865 CTTGGGTCAT
** * *
17164875 CGGCACAAAGCCTGGTAGGCACATAACCTGAAAACAC
1 CGGCACAAAGCCTACTAGGCACACAGCCTGAAAACAC
17164912 CGGCACAAAGCCTACTAGGCACACAGCCTGAAAACAC
1 CGGCACAAAGCCTACTAGGCACACAGCCTGAAAACAC
* * *
17164949 AGACACAAAGTCTACTAGGCACACAGCCTGAAAACAC
1 CGGCACAAAGCCTACTAGGCACACAGCCTGAAAACAC
* * * * *
17164986 CGGTACAAAGCCTATTACGCACGCAGCCTGAAAATAC
1 CGGCACAAAGCCTACTAGGCACACAGCCTGAAAACAC
*
17165023 TGGCACAAAGCCT
1 CGGCACAAAGCCT
17165036 GAAAATTGTG
Statistics
Matches: 107, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 107 1.00
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.12
Consensus pattern (37 bp):
CGGCACAAAGCCTACTAGGCACACAGCCTGAAAACAC
Found at i:17171139 original size:37 final size:37
Alignment explanation
Indices: 17171084--17171173 Score: 153
Period size: 37 Copynumber: 2.4 Consensus size: 37
17171074 GTTCTTGGGT
*
17171084 CACCGGCACAAAGCCTACTAGGCACATAGCCTAAAAA
1 CACCGGCACAAAGCCTACTAGGCACACAGCCTAAAAA
* *
17171121 CACCAGCACAAAGCCTACTAGGCACACAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCACACAGCCTAAAAA
17171158 CACCGGCACAAAGCCT
1 CACCGGCACAAAGCCT
17171174 GAAAATTGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.39, C:0.36, G:0.17, T:0.09
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACACAGCCTAAAAA
Found at i:17172886 original size:12 final size:12
Alignment explanation
Indices: 17172869--17172981 Score: 60
Period size: 12 Copynumber: 9.8 Consensus size: 12
17172859 ATAACATCCA
17172869 AACAACAAAAAT
1 AACAACAAAAAT
*
17172881 AACAACCAAAAT
1 AACAACAAAAAT
*
17172893 ---AAC-AGAA-
1 AACAACAAAAAT
*
17172900 AACAACATTAAA-
1 AACAACA-AAAAT
*
17172912 AACAATAAAAAT
1 AACAACAAAAAT
* *
17172924 AGCAACAAAAAC
1 AACAACAAAAAT
* *
17172936 AGCAATAAAAAT
1 AACAACAAAAAT
* *
17172948 AACAGCAAAAAC
1 AACAACAAAAAT
*
17172960 AAC-ACGAAAAT
1 AACAACAAAAAT
17172971 AACAACCAAAA
1 AACAA-CAAAA
17172982 CATTAAAAAA
Statistics
Matches: 74, Mismatches: 19, Indels: 15
0.69 0.18 0.14
Matches are distributed among these distances:
8 3 0.04
9 3 0.04
10 3 0.04
11 11 0.15
12 50 0.68
13 4 0.05
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:17172941 original size:24 final size:24
Alignment explanation
Indices: 17172914--17172983 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
17172904 ACATTAAAAA
*
17172914 CAATAAAAATAGCAACAAAAACAG
1 CAATAAAAATAACAACAAAAACAG
* *
17172938 CAATAAAAATAACAGCAAAAACAA
1 CAATAAAAATAACAACAAAAACAG
** *
17172962 C-ACGAAAATAACAACCAAAACA
1 CAATAAAAATAACAACAAAAACA
17172984 TTAAAAAAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 17 0.44
24 22 0.56
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (24 bp):
CAATAAAAATAACAACAAAAACAG
Found at i:17173008 original size:26 final size:23
Alignment explanation
Indices: 17172898--17173032 Score: 75
Period size: 24 Copynumber: 5.8 Consensus size: 23
17172888 AAAATAACAG
** *
17172898 AAAACAACATTAAAAACAATAAA
1 AAAACAACACAAAAAACAGTAAA
* * *
17172921 AATAGCAACA-AAAACAGCAATAAA
1 AA-AACAACACAAAA-AACAGTAAA
*
17172945 AATAACAGCA-AAAACAACACG-AAA
1 AA-AACAACACAAAA-AACA-GTAAA
* *
17172969 ATAACAAC-C--AAAACATTAAA
1 AAAACAACACAAAAAACAGTAAA
17172989 AAAACAAAACAGCAAAAAACAGTAAA
1 AAAAC--AACA-CAAAAAACAGTAAA
17173015 AAAACAACACAAAAAACA
1 AAAACAACACAAAAAACA
17173033 ACAATATAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
20 11 0.12
21 2 0.02
22 3 0.03
23 19 0.21
24 39 0.44
26 15 0.17
ACGTcount: A:0.70, C:0.18, G:0.04, T:0.07
Consensus pattern (23 bp):
AAAACAACACAAAAAACAGTAAA
Found at i:17173035 original size:26 final size:26
Alignment explanation
Indices: 17172978--17173035 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
17172968 AATAACAACC
* *
17172978 AAAACATTAAAAAAACAAAACAGCAA
1 AAAACAGTAAAAAAACAAAACAGAAA
*
17173004 AAAACAGTAAAAAAACAACACA-AAA
1 AAAACAGTAAAAAAACAAAACAGAAA
17173029 AACAACA
1 AA-AACA
17173036 ATATAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.74, C:0.17, G:0.03, T:0.05
Consensus pattern (26 bp):
AAAACAGTAAAAAAACAAAACAGAAA
Found at i:17173222 original size:12 final size:12
Alignment explanation
Indices: 17173205--17173258 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
17173195 CCAATAAAAG
*
17173205 TTTTTGCTATTA
1 TTTTTGCTGTTA
* *
17173217 TTTTTGTTGTTG
1 TTTTTGCTGTTA
* *
17173229 TTTTTGTTGCTA
1 TTTTTGCTGTTA
17173241 TTTTTGCTGTTA
1 TTTTTGCTGTTA
17173253 TTTTTG
1 TTTTTG
17173259 AGATTAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.07, C:0.06, G:0.17, T:0.70
Consensus pattern (12 bp):
TTTTTGCTGTTA
Found at i:17173778 original size:19 final size:18
Alignment explanation
Indices: 17173736--17173769 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17173726 AAATAGTTAA
17173736 AAAAATTAAAACATTTTT
1 AAAAATTAAAACATTTTT
*
17173754 AAAAATTTAAAC-TTTT
1 AAAAATTAAAACATTTT
17173770 CTTTAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATTAAAACATTTTT
Found at i:17173828 original size:28 final size:28
Alignment explanation
Indices: 17173788--17173851 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
17173778 TGACTAAATT
17173788 TTTTTTTTGTTTTTTTAAAAATCTAAAC
1 TTTTTTTTGTTTTTTTAAAAATCTAAAC
17173816 TTTTTTTTGTTTTTTTAAAAATCTAAAC
1 TTTTTTTTGTTTTTTTAAAAATCTAAAC
17173844 TTTTTTTT
1 TTTTTTTT
17173852 AATGAAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTTTTTGTTTTTTTAAAAATCTAAAC
Found at i:17173911 original size:51 final size:52
Alignment explanation
Indices: 17173856--17173961 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 52
17173846 TTTTTTAATG
** *
17173856 AAAATCACTACTTTACTT-AAAAATTCG-AACTTTTAT-TTTGAAATAATTAAA
1 AAAATCAAAACTTTACTTAAAAAATT-GAAACTTTT-TCTTTAAAATAATTAAA
**
17173907 AAAATCAAAACTTTGTTTAAAAAATTGAAACTTTTTCTTTAAAATAATTAAA
1 AAAATCAAAACTTTACTTAAAAAATTGAAACTTTTTCTTTAAAATAATTAAA
17173959 AAA
1 AAA
17173962 TATATTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 16 0.34
52 31 0.66
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (52 bp):
AAAATCAAAACTTTACTTAAAAAATTGAAACTTTTTCTTTAAAATAATTAAA
Found at i:17174075 original size:20 final size:21
Alignment explanation
Indices: 17174050--17174096 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
17174040 TTCTAAATAG
17174050 TTAAAAAATCAAAATTTTG-T
1 TTAAAAAATCAAAATTTTGCT
* * *
17174070 TTAAAAATTTAAACTTTTGCT
1 TTAAAAAATCAAAATTTTGCT
17174091 TTAAAA
1 TTAAAA
17174097 TGACTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAAAAAATCAAAATTTTGCT
Found at i:17174118 original size:146 final size:145
Alignment explanation
Indices: 17173827--17174212 Score: 528
Period size: 146 Copynumber: 2.6 Consensus size: 145
17173817 TTTTTTTGTT
* *
17173827 TTTTTAAAAATCTAAAC-TTTTTTTTAATGAAAATCACTACTTTACTTAAAAATTCGAACTTTTA
1 TTTTTAAAAATCTAAACTTTTTTTTTAATGAAAATCACTATTTTACTTAAAAATTCAAACTTTTA
* * *
17173891 TTT-TGAAATAATTAAAAAAATCAAAACTTTGTTTAAAAAATTGAAACTTTTTCTTTAAAATAAT
66 TTTCT-AAATAGTT-AAAAAATCAAAACTTTGTTTAAAAAATTGAAACTTTTGCTTTAAAATAAC
*
17173955 TAAAAAATATATTTTTA
129 TAAAAAACATATTTTTA
* *
17173972 TTTTTAAAAATCTAAACTTTCTTTTTTTAATGAAAATCTCTATTTTATTTAAAAATTCAAACTTT
1 TTTTTAAAAATCTAAAC-TT-TTTTTTTAATGAAAATCACTATTTTACTTAAAAATTCAAACTTT
* * *
17174037 TATTTCTAAATAGTTAAAAAATCAAAATTTTGTTT-AAAAATTTAAACTTTTGCTTTAAAATGAC
64 TATTTCTAAATAGTTAAAAAATCAAAACTTTGTTTAAAAAATTGAAACTTTTGCTTTAAAATAAC
17174101 TAAAAAACATATTTTTA
129 TAAAAAACATATTTTTA
** * *
17174118 TTTTTAAAAATCTAAACTTTTTTTAAAAAGAAAATCACTATTTTACTTAAAAA-TCAAATTTTTA
1 TTTTTAAAAATCTAAACTTTTTTTTTAATGAAAATCACTATTTTACTTAAAAATTCAAACTTTTA
* * *
17174182 TTTCGAAATTGTTTAAAAAAACCAAAACTTT
66 TTTCTAAATAG-TT-AAAAAATCAAAACTTT
17174213 TCCCAAAATT
Statistics
Matches: 214, Mismatches: 21, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
143 19 0.09
144 31 0.14
145 33 0.15
146 58 0.27
147 20 0.09
148 52 0.24
149 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (145 bp):
TTTTTAAAAATCTAAACTTTTTTTTTAATGAAAATCACTATTTTACTTAAAAATTCAAACTTTTA
TTTCTAAATAGTTAAAAAATCAAAACTTTGTTTAAAAAATTGAAACTTTTGCTTTAAAATAACTA
AAAAACATATTTTTA
Found at i:17174379 original size:2 final size:2
Alignment explanation
Indices: 17174372--17174435 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
17174362 TGTCCATGGC
17174372 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17174414 AG AG AG AG AG AG AG AG A- AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
17174436 AGAAGAAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17174676 original size:3 final size:3
Alignment explanation
Indices: 17174668--17174706 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
17174658 ATGAAACCCA
*
17174668 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17174707 TTGGGCCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17175488 original size:42 final size:42
Alignment explanation
Indices: 17175176--17175480 Score: 430
Period size: 42 Copynumber: 7.3 Consensus size: 42
17175166 TCTATGTCTA
*
17175176 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * * *
17175218 GGCCTCTTAATGCGATGAAAAGTAAATGGACCTCCATATCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * * *
17175260 GGACTCTAAATACGATGAAAAGTAAATGGACCTCCATACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
*
17175302 GGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* *
17175344 GGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * * * *
17175386 AGCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACACTTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* *
17175428 GGCCTCTTAATGCAATGAAAAGTAAATAGACCTCCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
*
17175470 GGCTTCTAAAT
1 GGCCTCTAAAT
17175481 ATAATGAATG
Statistics
Matches: 236, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 236 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
Found at i:17175916 original size:17 final size:17
Alignment explanation
Indices: 17175896--17175950 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
17175886 TCTCTTTCTA
17175896 TTTTTTTCTTCTTTTTT
1 TTTTTTTCTTCTTTTTT
17175913 TTTTTTT-TCTCTTTTTT
1 TTTTTTTCT-TCTTTTTT
* *
17175930 CTTTTCTCTTCTTTTTT
1 TTTTTTTCTTCTTTTTT
17175947 TTTT
1 TTTT
17175951 ATTTTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTTT
Found at i:17186251 original size:23 final size:20
Alignment explanation
Indices: 17186202--17186251 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
17186192 ACGACATTAG
*
17186202 ACAATTAAATAAATTAATGC
1 ACAAATAAATAAATTAATGC
*
17186222 ACGAATAAATAAATCTAATATGC
1 ACAAATAAATAAAT-T-A-ATGC
17186245 ACAAATA
1 ACAAATA
17186252 CTAAAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 1 0.04
22 1 0.04
23 10 0.42
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (20 bp):
ACAAATAAATAAATTAATGC
Found at i:17187145 original size:236 final size:237
Alignment explanation
Indices: 17186675--17187147 Score: 779
Period size: 237 Copynumber: 2.0 Consensus size: 237
17186665 AAAAAAATGT
* * *
17186675 CTCCGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATTTACAATTTAAATT
1 CTCCGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATTTAAAACTTAAAAT
* * *
17186740 AGAGATTTTTACTTCTAACAAGAACCCTAAATGATACCTAAATAATTATAGTATACTACCTTCAA
66 AGAGATTTTTACTTCTAACAAGAACCCTAAATGATAACTAAATAATTATAGTAAAATACCTTCAA
*
17186805 TTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAA
131 TTATTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAA
*
17186870 ATATTAAAATTCATCTACAACTTATTCAATCTTTTATCATTA
196 ATACTAAAATTCATCTACAACTTATTCAATCTTTTATCATTA
* *
17186912 CTCCGATTTACTTGTAACTTGACTAAGATGTGTTCACCAAATTTATCTAATTTAAAACTTAAAAT
1 CTCCGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATTTAAAACTTAAAAT
* * * *
17186977 AGAGATTTTTACTTCTAACGAGAACCCTAAATGATAATTAAATAATTCTAGTAAAATAGCTTC-A
66 AGAGATTTTTACTTCTAACAAGAACCCTAAATGATAACTAAATAATTATAGTAAAATACCTTCAA
* *
17187041 TTATTAAAATTAATTTTATTTTAGAATTCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAA
131 TTATTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAA
17187106 ATACTAAAATTCATCTACAACTTATT-AGATCTTTTATCATTA
196 ATACTAAAATTCATCTACAACTTATTCA-ATCTTTTATCATTA
17187148 TTATTATTAT
Statistics
Matches: 219, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
235 1 0.00
236 102 0.47
237 116 0.53
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (237 bp):
CTCCGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATTTAAAACTTAAAAT
AGAGATTTTTACTTCTAACAAGAACCCTAAATGATAACTAAATAATTATAGTAAAATACCTTCAA
TTATTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAA
ATACTAAAATTCATCTACAACTTATTCAATCTTTTATCATTA
Found at i:17188574 original size:28 final size:28
Alignment explanation
Indices: 17188542--17188745 Score: 103
Period size: 28 Copynumber: 7.3 Consensus size: 28
17188532 ATAAAGAAAA
* *
17188542 CCTTTGTGGTAGACTTTGGAAAGGTAAG
1 CCTTTGTGGTAAACTTTAGAAAGGTAAG
* * ** *
17188570 CCTTTGTGGCAAACCTCTATTAA-GAAAG
1 CCTTTGTGGTAAA-CTTTAGAAAGGTAAG
*
17188598 CCTTTGTGGCAAACTATT-GAAAGGTAAG
1 CCTTTGTGGTAAACT-TTAGAAAGGTAAG
** * * * *
17188626 CCCCTGTGGTGAACCTCTATAAA-GAAAG
1 CCTTTGTGGT-AAACTTTAGAAAGGTAAG
** *
17188654 CCTTTGTGAAAAACTTTGGAAAGGTAAG
1 CCTTTGTGGTAAACTTTAGAAAGGTAAG
* * * *
17188682 CCTTTGTGGTGAACCTCTATAAA-GAAAG
1 CCTTTGTGGT-AAACTTTAGAAAGGTAAG
* ** *
17188710 CCTTTATGACAAA-TCCTAGAAAGGTAAG
1 CCTTTGTGGTAAACT-TTAGAAAGGTAAG
17188738 CCTTTGTG
1 CCTTTGTG
17188746 ATGAACCTCT
Statistics
Matches: 126, Mismatches: 41, Indels: 18
0.68 0.22 0.10
Matches are distributed among these distances:
26 1 0.01
27 20 0.16
28 85 0.67
29 20 0.16
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (28 bp):
CCTTTGTGGTAAACTTTAGAAAGGTAAG
Found at i:17188621 original size:56 final size:56
Alignment explanation
Indices: 17188532--17188780 Score: 322
Period size: 56 Copynumber: 4.4 Consensus size: 56
17188522 TAAAACATCG
* * * **
17188532 ATAAAGAAAACCTTTGTGGTAGACTTTGGAAAGGTAAGCCTTTGTGGCAAACCTCT
1 ATAAAGAAAGCCTTTGTGGCAAACTTTGGAAAGGTAAGCCTTTGTGGTGAACCTCT
* **
17188588 ATTAAGAAAGCCTTTGTGGCAAACTATT-GAAAGGTAAGCCCCTGTGGTGAACCTCT
1 ATAAAGAAAGCCTTTGTGGCAAACT-TTGGAAAGGTAAGCCTTTGTGGTGAACCTCT
**
17188644 ATAAAGAAAGCCTTTGTGAAAAACTTTGGAAAGGTAAGCCTTTGTGGTGAACCTCT
1 ATAAAGAAAGCCTTTGTGGCAAACTTTGGAAAGGTAAGCCTTTGTGGTGAACCTCT
* * * * *
17188700 ATAAAGAAAGCCTTTATGACAAA-TCCTAGAAAGGTAAGCCTTTGTGATGAACCTCT
1 ATAAAGAAAGCCTTTGTGGCAAACT-TTGGAAAGGTAAGCCTTTGTGGTGAACCTCT
*
17188756 ATAAAGAAAGCCTTCGTGGCAAACT
1 ATAAAGAAAGCCTTTGTGGCAAACT
17188781 CTATTAAAGG
Statistics
Matches: 168, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
55 3 0.02
56 162 0.96
57 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (56 bp):
ATAAAGAAAGCCTTTGTGGCAAACTTTGGAAAGGTAAGCCTTTGTGGTGAACCTCT
Found at i:17188766 original size:28 final size:28
Alignment explanation
Indices: 17188630--17188769 Score: 122
Period size: 28 Copynumber: 5.0 Consensus size: 28
17188620 GGTAAGCCCC
*
17188630 TGTGGTGAACCTCTATAAAGAAAGCCTT
1 TGTGATGAACCTCTATAAAGAAAGCCTT
* * * ** *
17188658 TGTGA-AAAACTTTGGAAAGGTAAGCCTT
1 TGTGATGAACCTCTATAAA-GAAAGCCTT
*
17188686 TGTGGTGAACCTCTATAAAGAAAGCCTT
1 TGTGATGAACCTCTATAAAGAAAGCCTT
* ** * * *
17188714 TATGACAAATC-CTAGAAAGGTAAGCCTT
1 TGTGATGAACCTCTATAAA-GAAAGCCTT
17188742 TGTGATGAACCTCTATAAAGAAAGCCTT
1 TGTGATGAACCTCTATAAAGAAAGCCTT
17188770 CGTGGCAAAC
Statistics
Matches: 81, Mismatches: 27, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
27 14 0.17
28 53 0.65
29 14 0.17
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (28 bp):
TGTGATGAACCTCTATAAAGAAAGCCTT
Found at i:17188827 original size:28 final size:28
Alignment explanation
Indices: 17188752--17188892 Score: 124
Period size: 28 Copynumber: 5.1 Consensus size: 28
17188742 TGTGATGAAC
* * * *
17188752 CTCTA-TAAAGAAAGCCTTCGTGGCAAA
1 CTCTATTAAAGGAAGTCTTTGTGGCAAT
*
17188779 CTCTATTAAAGGAA-TATTTTGTGGCAAT
1 CTCTATTAAAGGAAGT-CTTTGTGGCAAT
* * **
17188807 CTCTATTAAATGAAGTCTTTGTAGCGCT
1 CTCTATTAAAGGAAGTCTTTGTGGCAAT
* * **
17188835 CTTTGTTAAAGGAAGTCTTTGTGGCGCT
1 CTCTATTAAAGGAAGTCTTTGTGGCAAT
* *
17188863 CTCTGTTAAAGGAAGTCTTTGTGGCTAT
1 CTCTATTAAAGGAAGTCTTTGTGGCAAT
17188891 CT
1 CT
17188893 ATGAAAAGGA
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.05
28 88 0.94
29 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (28 bp):
CTCTATTAAAGGAAGTCTTTGTGGCAAT
Found at i:17191825 original size:33 final size:34
Alignment explanation
Indices: 17191754--17191832 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 34
17191744 TTATTGAAAG
*
17191754 TGTTGAAGACACCAATGAAGTAATAAGAGTACTG
1 TGTTGAAGACACCAATGAAGTAATAAGAGTACTC
*
17191788 TGTTGAAGACACCAATGAAGT-ATTAGAGTACTC
1 TGTTGAAGACACCAATGAAGTAATAAGAGTACTC
17191821 TGTTGAAGACAC
1 TGTTGAAGACAC
17191833 TTTCAACTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
33 22 0.51
34 21 0.49
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (34 bp):
TGTTGAAGACACCAATGAAGTAATAAGAGTACTC
Found at i:17192581 original size:18 final size:18
Alignment explanation
Indices: 17192558--17192592 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17192548 AGGCGCTCTC
* *
17192558 CACCAAGTTATTCTCGAT
1 CACCAAGATATGCTCGAT
17192576 CACCAAGATATGCTCGA
1 CACCAAGATATGCTCGA
17192593 AGTTACTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (18 bp):
CACCAAGATATGCTCGAT
Found at i:17195493 original size:26 final size:25
Alignment explanation
Indices: 17195453--17195540 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
17195443 TTATTTAATT
17195453 TTATTA-TTATGTTTTATAATAAAACA
1 TTATTATTTAT-TTTTA-AATAAAACA
* *
17195479 TTATTATTTATTTTTAAACTCAAACG
1 TTATTATTTATTTTTAAA-TAAAACA
* *
17195505 TT-TT-TTTA--CTCAAATAAAACA
1 TTATTATTTATTTTTAAATAAAACA
17195526 TTATTATTTATTTTT
1 TTATTATTTATTTTT
17195541 TAAAACTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
21 7 0.15
22 6 0.12
23 4 0.08
24 4 0.08
25 5 0.10
26 18 0.38
27 4 0.08
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.53
Consensus pattern (25 bp):
TTATTATTTATTTTTAAATAAAACA
Found at i:17200447 original size:71 final size:71
Alignment explanation
Indices: 17200365--17200508 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
17200355 ATTTTGACTT
17200365 GAAGATTTTAGTGACTTCGATATTGATGAGGTTCTGGAAGATATCGACGTTGAAGGCCGAAGGAG
1 GAAGATTTTAGTGACTTCGATATTGATGAGGTTCTGGAAGATATCGACGTTGAAGGCCGAAGGAG
17200430 GTTGAA
66 GTTGAA
*
17200436 GAAGATTTTAGTGACTTCGATATTGATGAGGTTCTGGAAGATATCGACGTTGAAGGTCGAAGGAG
1 GAAGATTTTAGTGACTTCGATATTGATGAGGTTCTGGAAGATATCGACGTTGAAGGCCGAAGGAG
17200501 GTTGAA
66 GTTGAA
17200507 GA
1 GA
17200509 TGCTCACGCC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (71 bp):
GAAGATTTTAGTGACTTCGATATTGATGAGGTTCTGGAAGATATCGACGTTGAAGGCCGAAGGAG
GTTGAA
Found at i:17203858 original size:34 final size:28
Alignment explanation
Indices: 17203789--17203845 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
17203779 ACTAATAATT
*
17203789 AACATATTTCATGACCAAAATTAATACA
1 AACATATTTCATGACCAAAATTAACACA
17203817 AACATATTTCATGACCAAAATTAACACA
1 AACATATTTCATGACCAAAATTAACACA
17203845 A
1 A
17203846 GGTACAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (28 bp):
AACATATTTCATGACCAAAATTAACACA
Found at i:17208440 original size:26 final size:27
Alignment explanation
Indices: 17208389--17208442 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
17208379 TAAAACAATT
*
17208389 AAAATTAATCATAAATGAACTGATTAA
1 AAAATTAATCATAAATGAACTCATTAA
*
17208416 AAAATTAATCGA-ATATGAA-TCATTAA
1 AAAATTAATC-ATAAATGAACTCATTAA
17208442 A
1 A
17208443 TAAAAGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 16 0.67
28 1 0.04
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (27 bp):
AAAATTAATCATAAATGAACTCATTAA
Found at i:17208828 original size:29 final size:29
Alignment explanation
Indices: 17208796--17208865 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
17208786 TAATTTATAT
* *
17208796 TTTTATAATTTTTAAAAGA-TTAAATTAAA
1 TTTT-TAATTTTTAAAAGAGTCAAAATAAA
*
17208825 TTTTTATATTTTTAGAAGAGTCAAAATAAA
1 TTTTTA-ATTTTTAAAAGAGTCAAAATAAA
*
17208855 ATTTTAATTTT
1 TTTTTAATTTT
17208866 AATAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.06
29 20 0.57
30 13 0.37
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (29 bp):
TTTTTAATTTTTAAAAGAGTCAAAATAAA
Found at i:17208830 original size:30 final size:29
Alignment explanation
Indices: 17208785--17208865 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 29
17208775 TTTCATCATT
* *
17208785 TTAATTTATATTTTTATAATTTTTAAAAGA
1 TTAAATTAAATTTTTAT-ATTTTTAAAAGA
*
17208815 TTAAATTAAATTTTTATATTTTTAGAAGA
1 TTAAATTAAATTTTTATATTTTTAAAAGA
* * *
17208844 GTCAAAATAAAATTTTA-ATTTT
1 -TTAAATTAAATTTTTATATTTT
17208866 AATAATTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.36
30 28 0.64
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (29 bp):
TTAAATTAAATTTTTATATTTTTAAAAGA
Found at i:17208881 original size:16 final size:17
Alignment explanation
Indices: 17208852--17208894 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
17208842 GAGTCAAAAT
17208852 AAAATTTT--AATTTTA
1 AAAATTTTAAAATTTTA
*
17208867 ATAA-TTTAAAATTTTA
1 AAAATTTTAAAATTTTA
17208883 AAAATTTTAAAA
1 AAAATTTTAAAA
17208895 GGTTTAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 3 0.13
15 3 0.13
16 10 0.43
17 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTTTAAAATTTTA
Found at i:17209656 original size:42 final size:41
Alignment explanation
Indices: 17209364--17209874 Score: 426
Period size: 41 Copynumber: 12.4 Consensus size: 41
17209354 AAAGGTAAAA
* * * ***
17209364 CATTAGCGGCGCTTT-TCTTAATGCGCCGCAAAAGGTAAAG-
1 CATTAGCGGCGCTTTCCCTCAA-GCGCCGCTAAAGGTCGGGT
** *
17209404 CATTAGCGGCGCTTT-TGTTAAGCGCCGCTAAAGGT-GAGGT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCG-GGT
* ** * * **
17209444 CATTAGCGGTGCTTTATCACAAGCGCCGCTAAAGTTCAAGT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGT
* * *
17209485 CATTAGCGGCGCTTTCTCT-AATACGCCGCTAAAGGTAGGGT
1 CATTAGCGGCGCTTTCCCTCAA-GCGCCGCTAAAGGTCGGGT
* * *
17209526 AATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGCCAGGT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGT
* ** * ** *
17209567 AATTAGCGGCGCTTTAACTTAAGCGCCGCTAAAGGTATGAT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGT
* * *
17209608 CATTAGCGGCGCTTTCCCTAAAGCGCCACGAAAAGGTCGGGT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGC-TAAAGGTCGGGT
* *
17209650 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTAGGAT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGT
**
17209691 CATTTAGCGGCGCTTTCATTCAAGCGCCGCTAAAAGGTCGGGT
1 CA-TTAGCGGCGCTTTCCCTCAAGCGCCGCT-AAAGGTCGGGT
* * *
17209734 CATTAGCGGCGCTTTTCCTCAAGTGCCGCTAAAGTTCGGGT
1 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGT
*** * *
17209775 CATTAGCGGCGCTTATATATAAAGCGCCGCTAAAGGTCAGGT
1 CATTAGCGGCGCTT-TCCCTCAAGCGCCGCTAAAGGTCGGGT
* * * * * *
17209817 TATTAGCAGCGCTTT-TCTAATAAGCGTCGCTAAAGGT-GTG-
1 CATTAGCGGCGCTTTCCCT--CAAGCGCCGCTAAAGGTCGGGT
*
17209857 AATTAGCGGCGCTTTCCC
1 CATTAGCGGCGCTTTCCC
17209875 ATAAGCACTG
Statistics
Matches: 386, Mismatches: 72, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
39 14 0.04
40 51 0.13
41 176 0.46
42 134 0.35
43 11 0.03
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.25
Consensus pattern (41 bp):
CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTCGGGT
Found at i:17211463 original size:6 final size:6
Alignment explanation
Indices: 17211453--17211485 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
17211443 AGCAAGCGGT
*
17211453 GGCACT GGCACC GGCACC GGCACC GGCACC GGC
1 GGCACC GGCACC GGCACC GGCACC GGCACC GGC
17211486 GACTCATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.45, G:0.36, T:0.03
Consensus pattern (6 bp):
GGCACC
Found at i:17214396 original size:18 final size:18
Alignment explanation
Indices: 17214345--17215200 Score: 136
Period size: 18 Copynumber: 48.8 Consensus size: 18
17214335 TATCAGCTTG
17214345 ATTATAATTATTTAATTAT
1 ATTA-AATTATTTAATTAT
* **
17214364 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
* *
17214382 ATTAAGTTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
17214400 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
17214422 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
*
17214437 ATTAAA-TATTTAAGTTAAAAA
1 ATTAAATTATTTAA-TT---AT
* *
17214458 ATTTAATTATTTAATGAT
1 ATTAAATTATTTAATTAT
*
17214476 ATTAAATT-TTATGATTAT
1 ATTAAATTATT-TAATTAT
17214494 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
17214508 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
17214524 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
17214542 ATTAAATTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
17214560 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
17214582 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
* *
17214597 ATTAAA-TATTTAAGGTAAAAG
1 ATTAAATTATTTAA--T--TAT
*
17214618 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
17214636 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
17214654 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
17214667 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
*
17214685 ATTAAAGTAAATGATTATATTA-
1 ATTAAA-T-TAT--TTA-ATTAT
**
17214707 AGTTAAAAGATTTAATTAT
1 A-TTAAATTATTTAATTAT
* ** *
17214726 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
17214744 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
17214757 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
17214775 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
**
17214793 ATTAAATTAAATAATTAT
1 ATTAAATTATTTAATTAT
* **
17214811 ATT-AA-T-TTAAAAGAT
1 ATTAAATTATTTAATTAT
17214826 A-T-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
17214842 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
* *
17214860 ATTAAGTTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
17214878 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
17214900 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
* *
17214915 ATTAAA-TATTTAAGGTAAAAG
1 ATTAAATTATTTAA--T--TAT
*
17214936 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
17214954 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
17214972 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
17214985 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
17215003 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
17215021 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
17215034 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
17215052 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
17215070 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
17215083 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* * **
17215101 ATTAGAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
**
17215119 ATTAAATTAAATAATTAT
1 ATTAAATTATTTAATTAT
* **
17215137 ATT-AA-T-TTAAAAGAT
1 ATTAAATTATTTAATTAT
17215152 A-T-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
17215168 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
17215186 ATTAAGTTATTTAAT
1 ATTAAATTATTTAAT
17215201 CATGTTTAAT
Statistics
Matches: 584, Mismatches: 166, Indels: 175
0.63 0.18 0.19
Matches are distributed among these distances:
12 5 0.01
13 42 0.07
14 9 0.02
15 29 0.05
16 53 0.09
17 24 0.04
18 302 0.52
19 27 0.05
20 7 0.01
21 22 0.04
22 55 0.09
23 9 0.02
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTAAATTATTTAATTAT
Found at i:17214508 original size:30 final size:30
Alignment explanation
Indices: 17214474--17214545 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
17214464 TTATTTAATG
* *
17214474 ATATTAAATT-TTATGATTATATTAAATTAA
1 ATATTAAATTATT-TAATTATATTAAACTAA
*
17214504 ATATTTAATTATTTAATTATATTAAACTAA
1 ATATTAAATTATTTAATTATATTAAACTAA
*
17214534 ATAATTATATTA
1 AT-ATTAAATTA
17214546 AATTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
ATATTAAATTATTTAATTATATTAAACTAA
Found at i:17214513 original size:48 final size:48
Alignment explanation
Indices: 17214458--17214550 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
17214448 AAGTTAAAAA
* ** *
17214458 ATTTAATTATTTAATGATATTAAATTTTATGATTATATTAAATTAAAT
1 ATTTAATTATTTAATGATATTAAACTAAATAATTATATTAAATTAAAT
*
17214506 ATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTA
1 ATTTAATTATTTAATGATATTAAACTAAATAATTATATTAAATTA
17214551 TTTAATCATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (48 bp):
ATTTAATTATTTAATGATATTAAACTAAATAATTATATTAAATTAAAT
Found at i:17214667 original size:49 final size:49
Alignment explanation
Indices: 17214606--17214803 Score: 313
Period size: 49 Copynumber: 4.2 Consensus size: 49
17214596 AATTAAATAT
*
17214606 TTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
17214655 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
17214704 TTAAGTTAAAAG--------ATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
*
17214745 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
*
17214794 TTAAATTAAA
1 TTAAGTTAAA
17214804 TAATTATATT
Statistics
Matches: 138, Mismatches: 3, Indels: 16
0.88 0.02 0.10
Matches are distributed among these distances:
41 41 0.30
49 97 0.70
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
Found at i:17214672 original size:41 final size:41
Alignment explanation
Indices: 17214626--17214770 Score: 211
Period size: 41 Copynumber: 3.4 Consensus size: 41
17214616 AGATTTAATT
17214626 ATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG
1 ATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG
17214667 ATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG
1 --------ATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG
17214716 ATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG
1 ATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG
17214757 ATTTAATTAT-TTAA
1 ATTTAATTATATTAA
17214771 TTATATTAAA
Statistics
Matches: 96, Mismatches: 0, Indels: 9
0.91 0.00 0.09
Matches are distributed among these distances:
40 4 0.04
41 51 0.53
49 41 0.43
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (41 bp):
ATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG
Found at i:17214790 original size:67 final size:67
Alignment explanation
Indices: 17214606--17215190 Score: 325
Period size: 67 Copynumber: 8.8 Consensus size: 67
17214596 AATTAAATAT
* * *
17214606 TTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATT-AAGTTAAAAGATT
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAAG-TAAATGATT
17214670 -TAA
65 AT-A
* * * * * ** *
17214673 TT-ATTTAATTATATTAAAGTAAATGATTATATT-AAGTTAAAAGATTTAATTATATTAAAGTAA
1 TTAAGTTAA-AAGATTTAATTATTTAATTATATTAAAG-T--AA-A--TAATTATATTAAAGTAA
17214736 ATGATTATA
59 ATGATTATA
* *
17214745 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAATAATTA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAAGTAAATGATTA
17214810 TA
66 TA
* * * *
17214812 TTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATT-AAGT-TAT--TTA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAAGTAAATGATTA
17214873 -A
66 TA
* * * ** ** * * * * *
17214874 TCATGTTTAATTATGTATTTAATTA--TAAACACTA-TCGATTAATTAAATAT-TTAAGGTAAAA
1 TTAAG-TTAA--AAG-ATTTAATTATTTAATTA-TATTAAAGTAAATAATTATATTAAAGTAAAT
17214935 GATT-TAA
61 GATTAT-A
* * * * * ** * * * * ** *
17214942 TT-ATTTAATTATATTAAAGTAAATGATTATATT-AAGTTAA-AA-GAT-TT-AATTATTTAATT
1 TTAAGTTAA-AAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAAGTAAATGATT
17215001 ATA
65 ATA
* * * * * * **
17215004 TTAAAG-TAAATGA-TTATATTAAGTTAA-AAGATTTAATTATTTAATTATATTAAAGTAAATGA
1 TT-AAGTTAAAAGATTTA-ATT-ATTTAATTATATTAAAGTAAATAATTATATTAAAGTAAATGA
17215066 TTATA
63 TTATA
* * *
17215071 TTAAGTTAAAAGATTTAATTATTTAATTATATTAGAGTAAATAATTATATTAAATTAAATAATTA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAAGTAAATGATTA
17215136 TA
66 TA
* * *
17215138 TTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATTAA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAA
17215191 GTTATTTAAT
Statistics
Matches: 382, Mismatches: 98, Indels: 76
0.69 0.18 0.14
Matches are distributed among these distances:
61 2 0.01
62 19 0.05
63 23 0.06
64 30 0.08
65 15 0.04
66 36 0.09
67 196 0.51
68 5 0.01
69 3 0.01
70 3 0.01
72 38 0.10
73 12 0.03
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.45
Consensus pattern (67 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAAGTAAATGATTA
TA
Found at i:17214846 original size:26 final size:27
Alignment explanation
Indices: 17214801--17214873 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
17214791 ATATTAAATT
17214801 AAATAATTATATT-A---ATTTAAAAG
1 AAATAATTATATTAAGTTATTTAAAAG
* **
17214824 ATATAATTAT-TTAA-TTATATTAAACT
1 AAATAATTATATTAAGTTAT-TTAAAAG
17214850 AAATAATTATATTAAGTTATTTAA
1 AAATAATTATATTAAGTTATTTAA
17214874 TCATGTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.05
23 10 0.25
25 2 0.05
26 14 0.35
27 8 0.20
28 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (27 bp):
AAATAATTATATTAAGTTATTTAAAAG
Found at i:17214985 original size:49 final size:49
Alignment explanation
Indices: 17214924--17215129 Score: 376
Period size: 49 Copynumber: 4.2 Consensus size: 49
17214914 AATTAAATAT
*
17214924 TTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
17214973 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
17215022 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
* *
17215071 TTAAGTTAAAAGATTTAATTATTTAATTATATTAGAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
*
17215120 TTAAATTAAA
1 TTAAGTTAAA
17215130 TAATTATATT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 153 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
Found at i:17215062 original size:277 final size:270
Alignment explanation
Indices: 17214655--17215399 Score: 823
Period size: 277 Copynumber: 2.7 Consensus size: 270
17214645 AATGATTATA
17214655 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG----
1 TTAAG-TAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTT
17214716 ----ATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATAT
65 AATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATAT
* **
17214777 TAAAGTAAATAATTATATTAAATTAAATAATTATATTAATTTAAAAGATA-TA-ATTATTTAATT
130 TAAAGTAAATAATTATATTAAATTAAATAATTATATT-ATTTAAAAGATATTAGAGTAAATAATT
* * *
17214840 ATATTAAACTAAATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATA-AAC
194 ATATTAAACTAAATAATTATATT-A---ATTTAA--AAG-AT-ATAAT-TATTTAATTATATAA-
*
17214904 ACT-ATCGATTA-ATTAA-ATAT
249 ACTAAT-AATTATATTAAGATAT
17214924 TTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTT
1 TTAA-GTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTT
17214989 AATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATAT
65 AATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATAT
* * **
17215054 TAAAGTAAATGATTATATTAAGTTAAA-AGATT-TAATTATTT-AATTATATTAGAGTAAATAAT
130 TAAAGTAAATAATTATATTAAATTAAATA-ATTAT-ATTATTTAAAAGATATTAGAGTAAATAAT
*
17215116 TATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATA
193 TATATTAAACTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATA-TAAACT-AATA
*
17215181 ATTATATTAAGTTAT
256 ATTATATTAAGATAT
* * * * * * * * * *
17215196 TTAA-T-CATG-TTTAATAAAGTAAATGATTATAAACACTATCGATTAATTAAATATTTAAGTTA
1 TTAAGTAAAAGATTTAAT-TATTTAATTA-TATTAA-AGTA---AATGATT--ATA-TTAAGTTA
* *
17215258 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGACTTAATCATTT
57 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTT
* * ** *
17215323 AATTATACTAAAGTAAATAATTATATTAAATTAAATATTTA-ATTATTT-AATTATATTAAAGTA
122 AATTATATTAAAGTAAATAATTATATTAAATTAAATAATTATATTATTTAAAAGATATTAGAGTA
17215386 AATAATTATATTAA
187 AATAATTATATTAA
17215400 GTTAAAAGAT
Statistics
Matches: 416, Mismatches: 30, Indels: 53
0.83 0.06 0.11
Matches are distributed among these distances:
268 18 0.04
269 74 0.18
270 14 0.03
271 12 0.03
272 7 0.02
273 6 0.01
274 5 0.01
275 5 0.01
276 47 0.11
277 227 0.55
278 1 0.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (270 bp):
TTAAGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTA
ATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATT
AAAGTAAATAATTATATTAAATTAAATAATTATATTATTTAAAAGATATTAGAGTAAATAATTAT
ATTAAACTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATAAACTAATAATTAT
ATTAAGATAT
Found at i:17215118 original size:326 final size:326
Alignment explanation
Indices: 17214469--17215447 Score: 1665
Period size: 326 Copynumber: 3.0 Consensus size: 326
17214459 TTTAATTATT
* ** * * * *
17214469 TAATGATATTAAATTTTATGATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAACTA
1 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
*
17214533 AATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
66 AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
17214598 TTAAATATTTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
131 TTAAATATTTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
17214663 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG--------ATTT
196 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTT
17214720 AATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
261 AATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
17214785 A
326 A
17214786 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
1 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
17214851 AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
66 AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
17214916 TTAAATATTTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
131 TTAAATATTTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
17214981 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTT
196 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTT
*
17215046 AATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAGAGTAA
261 AATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
17215111 A
326 A
17215112 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
1 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
* * ** *
17215177 AATAATTATATTAAGTTATTTAATCATGTTTAATAAAGTAAATGATTATAAACACTATCGATTAA
66 AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
*
17215242 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
131 TTAAATATTTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
* * * * * *
17215307 AAAGACTTAATCATTTAATTATACTAAAGTAAATAATTATATTAAATT-AAATATTTAATTATTT
196 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTT
* *
17215371 AATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATGATATTAAAGTAA
261 AATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
*
17215436 C
326 A
17215437 TAATTAT-TTAA
1 TAATTATATTAA
17215448 TTATATTAAA
Statistics
Matches: 628, Mismatches: 25, Indels: 11
0.95 0.04 0.02
Matches are distributed among these distances:
317 28 0.04
318 211 0.34
324 4 0.01
325 84 0.13
326 301 0.48
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (326 bp):
TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
TTAAATATTTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTT
AATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
A
Found at i:17215129 original size:98 final size:98
Alignment explanation
Indices: 17214446--17214803 Score: 340
Period size: 90 Copynumber: 3.6 Consensus size: 98
17214436 AATTAAATAT
* * * ** * *
17214446 TTAAGTTAAAAAATTTAATTATTTAATGATATTAAATTTTATGATTATATTAAATT-AAATATTT
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTT
* *
17214510 AATTATTTAATTATATTAAACTAAATAATTATA
66 AATTATTTAATTATATTAAAGTAAATGATTATA
* * * * * *
17214543 TTAAATTATTTAATCATG-TTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATT
1 TTAAGTTA---AA--A-GATTTAATTATTTAATT-A-TATTAA-AGTA---AATAATT--ATA-T
**
17214607 TAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
51 TAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
* *
17214655 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAG----
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTT
17214716 ----ATTTAATTATATTAAAGTAAATGATTATA
66 AATTATTTAATTATATTAAAGTAAATGATTATA
17214745 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAA
17214804 TAATTATATT
Statistics
Matches: 218, Mismatches: 26, Indels: 41
0.76 0.09 0.14
Matches are distributed among these distances:
90 86 0.39
97 7 0.03
98 11 0.05
99 3 0.01
100 2 0.01
101 5 0.02
102 13 0.06
103 1 0.00
104 8 0.04
105 7 0.03
106 2 0.01
107 14 0.06
108 4 0.02
109 2 0.01
110 3 0.01
111 5 0.02
112 45 0.21
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (98 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTT
AATTATTTAATTATATTAAAGTAAATGATTATA
Found at i:17215172 original size:26 final size:27
Alignment explanation
Indices: 17215127--17215199 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
17215117 ATATTAAATT
17215127 AAATAATTATATT-A---ATTTAAAAG
1 AAATAATTATATTAAGTTATTTAAAAG
* **
17215150 ATATAATTAT-TTAA-TTATATTAAACT
1 AAATAATTATATTAAGTTAT-TTAAAAG
17215176 AAATAATTATATTAAGTTATTTAA
1 AAATAATTATATTAAGTTATTTAA
17215200 TCATGTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.05
23 10 0.25
25 2 0.05
26 14 0.35
27 8 0.20
28 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (27 bp):
AAATAATTATATTAAGTTATTTAAAAG
Found at i:17215307 original size:49 final size:49
Alignment explanation
Indices: 17215250--17215447 Score: 310
Period size: 49 Copynumber: 4.1 Consensus size: 49
17215240 AATTAAATAT
*
17215250 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
17215299 TTAAGTTAAAAGACTTAATCATTTAATTATACTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* *
17215348 TTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* *
17215396 TTAAGTTAAAAGATTTAATTATTTAATGATATTAAAGTAACTAATTAT-
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
17215444 TTAA
1 TTAA
17215448 TTATATTAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
48 47 0.35
49 88 0.65
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:17215374 original size:30 final size:31
Alignment explanation
Indices: 17215340--17215398 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
17215330 CTAAAGTAAA
* *
17215340 TAATTATATTAAATTAAATATTTA-ATTATT
1 TAATTATATTAAAGTAAATAATTATATTATT
17215370 TAATTATATTAAAGTAAATAATTATATTA
1 TAATTATATTAAAGTAAATAATTATATTA
17215399 AGTTAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
TAATTATATTAAAGTAAATAATTATATTATT
Found at i:17215391 original size:18 final size:18
Alignment explanation
Indices: 17215322--17215399 Score: 78
Period size: 18 Copynumber: 4.7 Consensus size: 18
17215312 CTTAATCATT
*
17215322 TAATTATACTAAAGTAAA
1 TAATTATATTAAAGTAAA
*
17215340 TAATTATATTAAATTAAA
1 TAATTATATTAAAGTAAA
* *
17215358 TATTTA-ATT--A-T--T
1 TAATTATATTAAAGTAAA
17215370 TAATTATATTAAAGTAAA
1 TAATTATATTAAAGTAAA
17215388 TAATTATATTAA
1 TAATTATATTAA
17215400 GTTAAAAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
12 5 0.10
13 3 0.06
14 1 0.02
15 2 0.04
16 1 0.02
17 3 0.06
18 33 0.69
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (18 bp):
TAATTATATTAAAGTAAA
Found at i:17220979 original size:65 final size:66
Alignment explanation
Indices: 17220874--17221013 Score: 203
Period size: 65 Copynumber: 2.1 Consensus size: 66
17220864 CAAATTGCTC
*
17220874 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTC-AAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
17220937 AA
65 AA
* ** *
17220939 AACTTAAAGAGGAGGTTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
17221004 C
66 A
17221005 AACTTAAAG
1 AACTTAAAG
17221014 TAGAGGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 36 0.54
66 31 0.46
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:17221042 original size:21 final size:21
Alignment explanation
Indices: 17221016--17221067 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
17221006 ACTTAAAGTA
17221016 GAGGCAGCAGCGAGGCAAGCG
1 GAGGCAGCAGCGAGGCAAGCG
*
17221037 GAGGCAGCAGTGAGGCAAGCG
1 GAGGCAGCAGCGAGGCAAGCG
* *
17221058 AAGGAAGCAG
1 GAGGCAGCAG
17221068 AGGCTACAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.46, T:0.02
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGCAAGCG
Found at i:17221416 original size:43 final size:43
Alignment explanation
Indices: 17221368--17221508 Score: 237
Period size: 43 Copynumber: 3.3 Consensus size: 43
17221358 CTGTTATATT
* *
17221368 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAATATGTCCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
17221411 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
* *
17221454 AGCGGCGCTTCTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
*
17221497 AGTGGCGCTTGT
1 AGCGGCGCTTGT
17221509 TAATCCTGCG
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 92 1.00
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.19
Consensus pattern (43 bp):
AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
Found at i:17223323 original size:19 final size:17
Alignment explanation
Indices: 17223296--17223337 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17223286 AACAAAATTA
17223296 TTTTAATCTTTCCTTTAAT
1 TTTTAATCTTT--TTTAAT
*
17223315 TTTTCATCTTTTTTAAT
1 TTTTAATCTTTTTTAAT
17223332 TTTTAA
1 TTTTAA
17223338 ATTTACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.52
19 10 0.48
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATCTTTTTTAAT
Found at i:17227617 original size:21 final size:20
Alignment explanation
Indices: 17227593--17227650 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
17227583 CAGTGCAGAA
*
17227593 TTCTATCGATACAAGTGACAG
1 TTCTA-CGATACAAGTGACAC
* *
17227614 TTCTACTGATACAGGTGACTC
1 TTCTAC-GATACAAGTGACAC
*
17227635 TTCTACCGAAACAAGT
1 TTCTA-CGATACAAGT
17227651 CTTACATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (20 bp):
TTCTACGATACAAGTGACAC
Found at i:17228403 original size:25 final size:25
Alignment explanation
Indices: 17228361--17228552 Score: 140
Period size: 25 Copynumber: 7.4 Consensus size: 25
17228351 TTTAACTCAA
*
17228361 ACGAGCCTAGACAGAATATCGCTCAT
1 ACGAGCC-AGACAGAATATCGCTCTT
*
17228387 ACGAGCCAGACAGAATATTGCTCTT
1 ACGAGCCAGACAGAATATCGCTCTT
* * * *
17228412 ACGAGCTAGAGTTAGAATATTGCTCAT
1 ACGAGCCAGA--CAGAATATCGCTCTT
* * *
17228439 ACAAGCCAGACAAAATTAT-ACTCTT
1 ACGAGCCAGACAGAA-TATCGCTCTT
*
17228464 ACGAGCCAGAATCAAAAT-TACGCTCTT
1 ACGAGCCAG-A-CAGAATAT-CGCTCTT
*
17228491 ACAAGCCAGACAGAAT-TACGCTCTT
1 ACGAGCCAGACAGAATAT-CGCTCTT
*
17228516 ACGAGCCAAAATCAGAAT-TACGCTCTT
1 ACGAGCC-AGA-CAGAATAT-CGCTCTT
*
17228543 ACAAGCCAGA
1 ACGAGCCAGA
17228553 ATTAGAATTT
Statistics
Matches: 138, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
25 61 0.44
26 17 0.12
27 60 0.43
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (25 bp):
ACGAGCCAGACAGAATATCGCTCTT
Found at i:17228437 original size:52 final size:52
Alignment explanation
Indices: 17228372--17228552 Score: 190
Period size: 52 Copynumber: 3.5 Consensus size: 52
17228362 CGAGCCTAGA
* * * *
17228372 CAGAATATCGCTCATACGAGCCAGACAGAA-TATTGCTCTTACGAGCTAGAGT
1 CAGAATATTGCTCATACAAGCCAGACAGAATTA-TGCTCTTACGAGCCAGAAT
* * *
17228424 TAGAATATTGCTCATACAAGCCAGACAAAATTATACTCTTACGAGCCAGAAT
1 CAGAATATTGCTCATACAAGCCAGACAGAATTATGCTCTTACGAGCCAGAAT
* * *
17228476 CA-AA-ATTACGCTCTTACAAGCCAGACAGAATTACGCTCTTACGAGCCAAAAT
1 CAGAATATT--GCTCATACAAGCCAGACAGAATTATGCTCTTACGAGCCAGAAT
* *
17228528 CAGAAT-TACGCTCTTACAAGCCAGA
1 CAGAATAT-TGCTCATACAAGCCAGA
17228553 ATTAGAATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
50 3 0.03
51 2 0.02
52 99 0.91
53 5 0.05
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (52 bp):
CAGAATATTGCTCATACAAGCCAGACAGAATTATGCTCTTACGAGCCAGAAT
Found at i:17228559 original size:27 final size:27
Alignment explanation
Indices: 17228433--17228561 Score: 149
Period size: 27 Copynumber: 4.9 Consensus size: 27
17228423 TTAGAATATT
* * *
17228433 GCTCATACAAGCCAG-A-CAAAATTAT
1 GCTCTTACAAGCCAGAATCAGAATTAC
* * *
17228458 ACTCTTACGAGCCAGAATCAAAATTAC
1 GCTCTTACAAGCCAGAATCAGAATTAC
17228485 GCTCTTACAAGCCAG-A-CAGAATTAC
1 GCTCTTACAAGCCAGAATCAGAATTAC
* *
17228510 GCTCTTACGAGCCAAAATCAGAATTAC
1 GCTCTTACAAGCCAGAATCAGAATTAC
*
17228537 GCTCTTACAAGCCAGAATTAGAATT
1 GCTCTTACAAGCCAGAATCAGAATT
17228562 TCTTCTTTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
25 33 0.38
26 3 0.03
27 52 0.59
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (27 bp):
GCTCTTACAAGCCAGAATCAGAATTAC
Found at i:17230363 original size:25 final size:25
Alignment explanation
Indices: 17230330--17230403 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
17230320 TGAAGTGAAT
* *
17230330 TATTTTGTCTCGCTCGTAAGAGCGA
1 TATTCTGTCTGGCTCGTAAGAGCGA
*
17230355 TATTCTGTCTGGCTCGTAAGAGTGA
1 TATTCTGTCTGGCTCGTAAGAGCGA
*
17230380 TATTCTGTCTGGGCTCGTATGAGC
1 TATTCTGTCT-GGCTCGTAAGAGC
17230404 TAAATTTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 32 0.74
26 11 0.26
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (25 bp):
TATTCTGTCTGGCTCGTAAGAGCGA
Found at i:17237284 original size:25 final size:26
Alignment explanation
Indices: 17237250--17237298 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
17237240 TGGAGCGAAT
17237250 TATTCTGTCT-CGCTCGTAAGAGCGA
1 TATTCTGTCTGCGCTCGTAAGAGCGA
* *
17237275 TATTCTGTCTGGGCTCGTATGAGC
1 TATTCTGTCTGCGCTCGTAAGAGC
17237299 TAAATTTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (26 bp):
TATTCTGTCTGCGCTCGTAAGAGCGA
Found at i:17241987 original size:80 final size:80
Alignment explanation
Indices: 17241885--17242118 Score: 342
Period size: 80 Copynumber: 2.9 Consensus size: 80
17241875 ACGGTCCGCA
*
17241885 TTACCTACTCACGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACGTATGCAGGATCTCAACC
1 TTACCTACTCACGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACGTATGCAGGATCTCAGCC
17241950 ATCGTAGGGTCCATG
66 ATCGTAGGGTCCATG
* * *
17241965 TTACCCACTCACGATGCTGCTCACACAACCTGTCAAGTAACTGCAACGTATGCAGGATCTCAGCC
1 TTACCTACTCACGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACGTATGCAGGATCTCAGCC
* *
17242030 ATCGTAAGGTCGATG
66 ATCGTAGGGTCCATG
* * * * * * **
17242045 TTACCTACTCACGATGCTTCTCACACAAGTTGTCAAGAAATTGTAACTTATGTATAATCTCAGCC
1 TTACCTACTCACGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACGTATGCAGGATCTCAGCC
17242110 ATCGTAGGG
66 ATCGTAGGG
17242119 GTTCTTACAA
Statistics
Matches: 136, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 136 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (80 bp):
TTACCTACTCACGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACGTATGCAGGATCTCAGCC
ATCGTAGGGTCCATG
Found at i:17242629 original size:189 final size:189
Alignment explanation
Indices: 17242309--17242681 Score: 737
Period size: 189 Copynumber: 2.0 Consensus size: 189
17242299 AGCATATGAA
17242309 ATTTGCTACAATAAAAATGGAGTAAAGAAATATTTAATACAATATAGAGAATAACAGTACAAACA
1 ATTTGCTACAATAAAAATGGAGTAAAGAAATATTTAATACAATATAGAGAATAACAGTACAAACA
17242374 TACCAAATAAAATTACAGTTAAGGTTAACTTTAGGAACTATTCTGCTAATTTCCCTTTTCATCGA
66 TACCAAATAAAATTACAGTTAAGGTTAACTTTAGGAACTATTCTGCTAATTTCCCTTTTCATCGA
17242439 TCTGCAGCACGCTCGTGATATAAATCAATAAATCATTCAATTTTCTCATTAATTGAATG
131 TCTGCAGCACGCTCGTGATATAAATCAATAAATCATTCAATTTTCTCATTAATTGAATG
*
17242498 ATTTGCTACAATAAAAATGGAGTAAAGAAATATTTAATACAATATAGAGAATAACAGTACGAACA
1 ATTTGCTACAATAAAAATGGAGTAAAGAAATATTTAATACAATATAGAGAATAACAGTACAAACA
17242563 TACCAAATAAAATTACAGTTAAGGTTAACTTTAGGAACTATTCTGCTAATTTCCCTTTTCATCGA
66 TACCAAATAAAATTACAGTTAAGGTTAACTTTAGGAACTATTCTGCTAATTTCCCTTTTCATCGA
17242628 TCTGCAGCACGCTCGTGATATAAATCAATAAATCATTCAATTTTCTCATTAATT
131 TCTGCAGCACGCTCGTGATATAAATCAATAAATCATTCAATTTTCTCATTAATT
17242682 CATGAAGTTT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 183 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (189 bp):
ATTTGCTACAATAAAAATGGAGTAAAGAAATATTTAATACAATATAGAGAATAACAGTACAAACA
TACCAAATAAAATTACAGTTAAGGTTAACTTTAGGAACTATTCTGCTAATTTCCCTTTTCATCGA
TCTGCAGCACGCTCGTGATATAAATCAATAAATCATTCAATTTTCTCATTAATTGAATG
Found at i:17244569 original size:4 final size:4
Alignment explanation
Indices: 17244560--17244608 Score: 62
Period size: 4 Copynumber: 11.8 Consensus size: 4
17244550 TGGTTGTCAT
* *
17244560 TTTA TTTA TTTA TTTA TTTA TTTTA TTTTA TTTA TTAA TTTT TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTT
17244609 TATTGTCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 31 0.77
5 9 0.22
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:17244590 original size:26 final size:26
Alignment explanation
Indices: 17244558--17244612 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
17244548 TTTGGTTGTC
*
17244558 ATTTTATTTATTTATTTATTTATTTT
1 ATTTTATTTATTAATTTATTTATTTT
*
17244584 ATTTTATTTATTAATTTTTTTATTTT
1 ATTTTATTTATTAATTTATTTATTTT
17244610 ATT
1 ATT
17244613 GTCTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (26 bp):
ATTTTATTTATTAATTTATTTATTTT
Found at i:17244609 original size:21 final size:22
Alignment explanation
Indices: 17244558--17244612 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
17244548 TTTGGTTGTC
*
17244558 ATTTTA-TTTATTTATTTATTT
1 ATTTTATTTTATTTATTAATTT
17244579 ATTTTATTTTATTTATTAATTT
1 ATTTTATTTTATTTATTAATTT
17244601 -TTTTATTTTATT
1 ATTTTATTTTATT
17244613 GTCTTTTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTTTATTTTATTTATTAATTT
Found at i:17247724 original size:18 final size:19
Alignment explanation
Indices: 17247687--17247728 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
17247677 GCCTAAAAGG
* *
17247687 AATTTTAATTTTTGTTTTC
1 AATTTTAATGTTTATTTTC
17247706 AATTTTAA-GTTTATTTTC
1 AATTTTAATGTTTATTTTC
17247724 -ATTTT
1 AATTTT
17247729 TTTATGCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
AATTTTAATGTTTATTTTC
Found at i:17249748 original size:25 final size:26
Alignment explanation
Indices: 17249720--17249768 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
17249710 AATTATTTCA
*
17249720 TTAATAAATTAGGTTTA-TTAATTTT
1 TTAATAAATTAGGTTAATTTAATTTT
* *
17249745 TTAATTAATTGGGTTAATTTAATT
1 TTAATAAATTAGGTTAATTTAATT
17249769 AATTTGACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (26 bp):
TTAATAAATTAGGTTAATTTAATTTT
Found at i:17266550 original size:11 final size:11
Alignment explanation
Indices: 17266514--17266555 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
17266504 ATAATATTAC
17266514 TTTT-TTAATA
1 TTTTATTAATA
*
17266524 TTTTAATAAGATA
1 TTTT-ATTA-ATA
17266537 TTTTATTAATA
1 TTTTATTAATA
17266548 TTTTATTA
1 TTTTATTA
17266556 TAAATGGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 11 0.41
12 5 0.19
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTTATTAATA
Found at i:17284621 original size:30 final size:30
Alignment explanation
Indices: 17284587--17284643 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
17284577 AATTTCATAA
*
17284587 CCAAATCTTAATACAATTGTCGAGTTTTAG
1 CCAAATCTTAATACAATTGTCAAGTTTTAG
*
17284617 CCAAATCTTAATACGATTGTCAAGTTT
1 CCAAATCTTAATACAATTGTCAAGTTT
17284644 GAGTTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (30 bp):
CCAAATCTTAATACAATTGTCAAGTTTTAG
Found at i:17288410 original size:19 final size:18
Alignment explanation
Indices: 17288382--17288427 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
17288372 GTCTAAGTTG
*
17288382 GTAAATTTAAAGCCGAGA
1 GTAAAATTAAAGCCGAGA
*
17288400 TGTAAAATTAAAGCTGAGA
1 -GTAAAATTAAAGCCGAGA
17288419 GCTAAAATT
1 G-TAAAATT
17288428 GAGCCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (18 bp):
GTAAAATTAAAGCCGAGA
Found at i:17299592 original size:17 final size:17
Alignment explanation
Indices: 17299576--17299607 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17299566 TTTTACTTGT
17299576 TAGTT-CATTTGCATTG
1 TAGTTGCATTTGCATTG
17299592 TAGTTGCATTTGCATT
1 TAGTTGCATTTGCATT
17299608 CTTATTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (17 bp):
TAGTTGCATTTGCATTG
Found at i:17302737 original size:25 final size:25
Alignment explanation
Indices: 17302532--17302736 Score: 196
Period size: 25 Copynumber: 8.2 Consensus size: 25
17302522 TCTTAAAACT
* * *
17302532 TGATAGGTAACACCAGCATAAAGCC
1 TGATAGATAACACCGGCAAAAAGCC
* *
17302557 TGATAGATAACACCGTCACAAA-CAC
1 TGATAGATAACACCGGCAAAAAGC-C
* *
17302582 TAAAAGATAACACCGGCAAAAAGCC
1 TGATAGATAACACCGGCAAAAAGCC
* * *
17302607 TGATAGATAACACTGCCAAAAAGTC
1 TGATAGATAACACCGGCAAAAAGCC
* * *
17302632 TGATAGATAACACTGACACAAAGCC
1 TGATAGATAACACCGGCAAAAAGCC
* * * *
17302657 TGATAGATAACATCAGCACAAAGCT
1 TGATAGATAACACCGGCAAAAAGCC
* * *
17302682 TTATAGATAACACCAGCACAAAGCC
1 TGATAGATAACACCGGCAAAAAGCC
* *
17302707 TGATATATAACACCGGTAAAAAGCC
1 TGATAGATAACACCGGCAAAAAGCC
17302732 TGATA
1 TGATA
17302737 TTCGGTAACA
Statistics
Matches: 149, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
24 1 0.01
25 147 0.99
26 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (25 bp):
TGATAGATAACACCGGCAAAAAGCC
Found at i:17306067 original size:8 final size:8
Alignment explanation
Indices: 17306054--17306079 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17306044 ACGGATCAAT
17306054 CACTATCA
1 CACTATCA
17306062 CACTATCA
1 CACTATCA
17306070 CACTATCA
1 CACTATCA
17306078 CA
1 CA
17306080 GGTTCATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (8 bp):
CACTATCA
Found at i:17306921 original size:158 final size:158
Alignment explanation
Indices: 17306669--17307017 Score: 477
Period size: 158 Copynumber: 2.2 Consensus size: 158
17306659 GGTCCTGCAT
* * * * ** *
17306669 TGGTTATGGATTCCCCACAGCTCGTGTAAGCAGCGTCGTGTAGTGTAACATCTCGACCCATAGCT
1 TGGTTGTGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCT
* * *
17306734 CGTGTGAGCAGGCCCACTTCACAGCTCGTGTG-TGCATTACAGGTTATAT-AGGTGTTAGTCTTA
66 CGTGTGAGCAAGCCAACTTCACAGCTCGTGTGAT-CATTACAGGTTATATGA-GTGATAGTCTTA
17306797 GATGTCCTACCGATGGCTGAGGTCTTAAAA
129 GATGTCCTACCGATGGCTGAGGTCTTAAAA
* * *
17306827 TGGTTGTGGATTCTACACAACTCGTGTGAGCAGCATTGTGTAGCCTAACATCTCGACCCACAGCT
1 TGGTTGTGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCT
* * *
17306892 CGTGTGAGCAAGCCAATTTCACAGCTCGTGTGATCATTACCGGTTATATGAGTGATGGTCTTAGA
66 CGTGTGAGCAAGCCAACTTCACAGCTCGTGTGATCATTACAGGTTATATGAGTGATAGTCTTAGA
* ** *
17306957 TGTCTTACCGATGGCTGAGGTCTTGCAT
131 TGTCCTACCGATGGCTGAGGTCTTAAAA
*
17306985 TGGTTGTAGATTCTCCACAGCTCGTGTGAGCAG
1 TGGTTGTGGATTCTCCACAGCTCGTGTGAGCAG
17307018 GCTTATTTCA
Statistics
Matches: 166, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
158 164 0.99
159 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (158 bp):
TGGTTGTGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCT
CGTGTGAGCAAGCCAACTTCACAGCTCGTGTGATCATTACAGGTTATATGAGTGATAGTCTTAGA
TGTCCTACCGATGGCTGAGGTCTTAAAA
Found at i:17313411 original size:158 final size:158
Alignment explanation
Indices: 17313117--17313518 Score: 567
Period size: 158 Copynumber: 2.5 Consensus size: 158
17313107 TACAGTTCCA
* * * *
17313117 GGTGCTGGTCTTGGATGTCCTATCGATGGTTGAGGTCCTGCATTGGTTGCGGATTCTCCACAACT
1 GGTGCTGGTCTTAGATGTCCTATCGATGGCTGAGGTCCTGCATTGGTTGCGGATTCTTCACAGCT
* * *
17313182 CGTGTGAGCAACATCGTGTAACCTAACATCTCGACCCACAACTCATGTGAGCAGGCCTATTTCAC
66 CGTGTGAGCAACATCGTGTAGCCTAACATCTCGACCCACAACTCATGTGAGAAGGCCCATTTCAC
17313247 TACTCGTGTGAGCATTACAAG-TTATATG
131 TACTCGTGTGAGCATTA-AAGTTTATATG
* * *
17313275 GGTGTTGGTCTTAGATGTCCTATCGATGGGTGAAGTCCTGCATTGGTTGCGGATTCTTCACAGCT
1 GGTGCTGGTCTTAGATGTCCTATCGATGGCTGAGGTCCTGCATTGGTTGCGGATTCTTCACAGCT
* *
17313340 TGTGTGAGCAACATCGTGTAGCCTAACATCTCGACCCACAGCTCATGTGAGAAGGCCCATTTCAC
66 CGTGTGAGCAACATCGTGTAGCCTAACATCTCGACCCACAACTCATGTGAGAAGGCCCATTTCAC
*
17313405 -AGCTCGTGTGAGCATTATAGTTTATATG
131 TA-CTCGTGTGAGCATTAAAGTTTATATG
* * * * *
17313433 GGTGCTAGTATTAGATGTCCTACCGATGGCTGAGGTCCTACATCGGTTGCGGATTC-TCTACAGC
1 GGTGCTGGTCTTAGATGTCCTATCGATGGCTGAGGTCCTGCATTGGTTGCGGATTCTTC-ACAGC
* * *
17313497 TCATGTGAGTAGCATCGTGTAG
65 TCGTGTGAGCAACATCGTGTAG
17313519 TCCCACAGCT
Statistics
Matches: 217, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
157 5 0.02
158 212 0.98
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (158 bp):
GGTGCTGGTCTTAGATGTCCTATCGATGGCTGAGGTCCTGCATTGGTTGCGGATTCTTCACAGCT
CGTGTGAGCAACATCGTGTAGCCTAACATCTCGACCCACAACTCATGTGAGAAGGCCCATTTCAC
TACTCGTGTGAGCATTAAAGTTTATATG
Found at i:17313832 original size:13 final size:14
Alignment explanation
Indices: 17313816--17313845 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17313806 GAATTTATGT
17313816 AATGGCTATGTG-A
1 AATGGCTATGTGCA
17313829 AATGGCTATGTGCA
1 AATGGCTATGTGCA
17313843 AAT
1 AAT
17313846 ATGTGTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (14 bp):
AATGGCTATGTGCA
Found at i:17315036 original size:31 final size:31
Alignment explanation
Indices: 17314998--17315062 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
17314988 TTCAAATTAA
17314998 AACTTAACAAAATTGAGCAAAGTAATAATTT
1 AACTTAACAAAATTGAGCAAAGTAATAATTT
17315029 AACTTAACAAAATTGAGCAAAGTAATAATTT
1 AACTTAACAAAATTGAGCAAAGTAATAATTT
17315060 AAC
1 AAC
17315063 ATCCTAGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.28
Consensus pattern (31 bp):
AACTTAACAAAATTGAGCAAAGTAATAATTT
Found at i:17315663 original size:25 final size:25
Alignment explanation
Indices: 17315635--17315698 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
17315625 TCTCAAAGTT
*
17315635 TGATAGATAACACCGGCACAAATCC
1 TGATAGATAACACCGGCACAAAGCC
* *
17315660 TGATAGATAACACCGGCACAGAGCT
1 TGATAGATAACACCGGCACAAAGCC
*
17315685 TGATATATAACACC
1 TGATAGATAACACC
17315699 AGTAAAATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (25 bp):
TGATAGATAACACCGGCACAAAGCC
Found at i:17331742 original size:53 final size:53
Alignment explanation
Indices: 17331656--17331904 Score: 365
Period size: 53 Copynumber: 4.7 Consensus size: 53
17331646 TTGTGCCAAT
* *
17331656 GATTAAAGGTTCGATGACTCTGTGTCATTGTGAGTTATATGAATCCTATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATG
* *
17331709 GATAAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATG
* * *
17331762 GATTAAAGGTCCGATAACTATGTGTCGTCGTGAGTTATATGAATCCTATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATG
* * * * * *
17331815 AATTAAGGGTCCGATGACTTTGTGTCATCGTGAGATACACGAATCC-ATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATG
*
17331867 GATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
17331905 CAAATGCGAA
Statistics
Matches: 175, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
52 40 0.23
53 135 0.77
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTATG
Found at i:17338909 original size:53 final size:53
Alignment explanation
Indices: 17338830--17339075 Score: 332
Period size: 53 Copynumber: 4.6 Consensus size: 53
17338820 TTATGCCAAA
* * * * * *
17338830 GATTAAAAGTCTGATGACTCTATGTCATCGTTAGTTGTATGAATCCTATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
17338883 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
* *
17338936 GATTAAAGGTCCGATAACTATGTGTCATCGTGAGTTATATGAATCCTATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
* * * * * * * *
17338989 GATTAAGGGTTCCAATGATTTTGTGTCATCGTGAGATACACGAATCC-ATTATG
1 GATTAAAGG-TCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
17339042 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAG
17339076 CTATCAAATG
Statistics
Matches: 171, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
52 22 0.13
53 119 0.70
54 30 0.18
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
Found at i:17340165 original size:21 final size:21
Alignment explanation
Indices: 17340119--17340169 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
17340109 TAGTACAGAG
*
17340119 TTCTACCGATACAAGTGACAG
1 TTCTACCGATACAAGTGACAC
* *
17340140 GTCTACCGATACAAGTGACTC
1 TTCTACCGATACAAGTGACAC
17340161 TTCTACCGA
1 TTCTACCGA
17340170 AACTAGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACAC
Found at i:17340974 original size:52 final size:52
Alignment explanation
Indices: 17340912--17341098 Score: 275
Period size: 52 Copynumber: 3.6 Consensus size: 52
17340902 ATTTAATTTA
* * * *
17340912 ATACTCACAATGACACATAGTCATCGGACCCCTTAATCCTTAAAGGAATCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* *
17340964 ATACTCACAATGACACATAGTTATCGGACCTCATAATCCATGAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
* *** *
17341016 ATTCTCGTGACGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
17341068 ATACTCACAATGACACATAGTCATCGGACCT
1 ATACTCACAATGACACATAGTCATCGGACCT
17341099 TTTTCATTTA
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 117 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
Found at i:17347188 original size:21 final size:21
Alignment explanation
Indices: 17347162--17347211 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
17347152 AATAGTGCAG
17347162 ACTTCTACCGAAACAAGTATT
1 ACTTCTACCGAAACAAGTATT
*
17347183 ACTTCTACCGAAATAAGTATT
1 ACTTCTACCGAAACAAGTATT
17347204 ACTTCTAC
1 ACTTCTAC
17347212 TGATACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (21 bp):
ACTTCTACCGAAACAAGTATT
Found at i:17347966 original size:52 final size:51
Alignment explanation
Indices: 17347893--17348027 Score: 216
Period size: 52 Copynumber: 2.6 Consensus size: 51
17347883 TTCGCATTTC
17347893 ATACTCACGATGACACATAGTCATCTGACCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATC-GACCTCATAATCCGTAAAAGATTCAT
* * *
17347945 ATGCTCATGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCG-ACCTCATAATCCGTAAAAGATTCAT
17347997 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATC-GACCT
17348028 TTTTCATTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
51 1 0.01
52 74 0.97
53 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGACCTCATAATCCGTAAAAGATTCAT
Found at i:17359323 original size:21 final size:21
Alignment explanation
Indices: 17359297--17359337 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17359287 CCGTTCCTCC
*
17359297 TTATGCATCATTTTTTTGTCT
1 TTATGCATCATTTTTCTGTCT
* *
17359318 TTATGCTTCCTTTTTCTGTC
1 TTATGCATCATTTTTCTGTC
17359338 CTTCGTACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.20, G:0.10, T:0.61
Consensus pattern (21 bp):
TTATGCATCATTTTTCTGTCT
Found at i:17367062 original size:18 final size:18
Alignment explanation
Indices: 17367036--17367089 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
17367026 ATGCATAGCA
* *
17367036 TTTAGTTGTTATTACATT
1 TTTATTTGTTACTACATT
*
17367054 TTTATTTGTCACTACA-T
1 TTTATTTGTTACTACATT
* *
17367071 TTCATTTGTTAGTACATT
1 TTTATTTGTTACTACATT
17367089 T
1 T
17367090 GCATTGTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTATTTGTTACTACATT
Found at i:17367079 original size:17 final size:18
Alignment explanation
Indices: 17367057--17367094 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
17367047 TTACATTTTT
17367057 ATTTGTCACTACATTT-C
1 ATTTGTCACTACATTTGC
* *
17367074 ATTTGTTAGTACATTTGC
1 ATTTGTCACTACATTTGC
17367092 ATT
1 ATT
17367095 GTAGTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.50
Consensus pattern (18 bp):
ATTTGTCACTACATTTGC
Found at i:17371958 original size:53 final size:52
Alignment explanation
Indices: 17371891--17371996 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 52
17371881 GGTAAGTAAG
*
17371891 AATAAGAGGAGTACTTGATTGAGCTCTTTATGCCTTTATTCTATCTTGCTTCT
1 AATAAGAGAAGTACTTGATTGAGCTCTTTATGCC-TTATTCTATCTTGCTTCT
*
17371944 AATAATAGAAGTACTTGATTGAGCTCTTTATGCCTTATTCTATCTTGCTTCT
1 AATAAGAGAAGTACTTGATTGAGCTCTTTATGCCTTATTCTATCTTGCTTCT
17371996 A
1 A
17371997 CCTTTCGCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 19 0.37
53 32 0.63
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (52 bp):
AATAAGAGAAGTACTTGATTGAGCTCTTTATGCCTTATTCTATCTTGCTTCT
Found at i:17377990 original size:105 final size:103
Alignment explanation
Indices: 17377870--17378082 Score: 338
Period size: 105 Copynumber: 2.0 Consensus size: 103
17377860 AATAGAAAAA
*
17377870 AATAAATTAGCAGTGTGTTGGGCTGAGTAACCGGGATGGGGTGCTTGGTTTATCATTCCATTTCG
1 AATAAATTAGCAGTGTGTTGGGCTGAGTAACCGGGATGGGGTGCTTGGGTTATCATTCCATTTCG
*
17377935 CGTCAAAAGGGCCAATATATTCTTAAGTAAAAAAAATGAT
66 CGTC-AAAGGGCCAATATATTCTTAAG-AAAAAAAATAAT
* *
17377975 AATAAATTGAG-AGTGTGTTGGGCTGAGTAACTGGGATGGGGTGCTTGGGTTGTCATTCCATTTC
1 AATAAATT-AGCAGTGTGTTGGGCTGAGTAACCGGGATGGGGTGCTTGGGTTATCATTCCATTTC
* *
17378039 GCGTCAAAGGGCTAATATATTCTTAAGCAAAAAAATAAT
65 GCGTCAAAGGGCCAATATATTCTTAAGAAAAAAAATAAT
17378078 AATAA
1 AATAA
17378083 TAAGAAAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
103 15 0.15
104 21 0.21
105 63 0.62
106 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (103 bp):
AATAAATTAGCAGTGTGTTGGGCTGAGTAACCGGGATGGGGTGCTTGGGTTATCATTCCATTTCG
CGTCAAAGGGCCAATATATTCTTAAGAAAAAAAATAAT
Found at i:17378110 original size:23 final size:24
Alignment explanation
Indices: 17378070--17378115 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
17378060 CTTAAGCAAA
* *
17378070 AAAATAATAATAATAAGAAAATTG
1 AAAATAATAAAAAGAAGAAAATTG
*
17378094 AAAA-AATAAAAAGAAGAGAATT
1 AAAATAATAAAAAGAAGAAAATT
17378116 AAATTTGGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.20
Consensus pattern (24 bp):
AAAATAATAAAAAGAAGAAAATTG
Found at i:17382004 original size:17 final size:17
Alignment explanation
Indices: 17381971--17382031 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
17381961 CATTAATTTA
*
17381971 CAATGACAAATGGAAATG
1 CAATGAC-AATGAAAATG
*
17381989 CAATGACAATGCAAATG
1 CAATGACAATGAAAATG
* *
17382006 CAGTGACAATTAAAATG
1 CAATGACAATGAAAATG
17382023 CAATGACAA
1 CAATGACAA
17382032 AGGGGATGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
17 31 0.82
18 7 0.18
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:17393643 original size:5 final size:5
Alignment explanation
Indices: 17393633--17393666 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
17393623 TGCAACAAGA
* *
17393633 TTTAT TTTAT TTTAT TTTAT TTTAG TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
17393667 ACATTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:17396650 original size:21 final size:21
Alignment explanation
Indices: 17396614--17396667 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
17396604 TAGAGGTGAA
* *
17396614 ACTTGTATCGGCAGAA-GAGTC
1 ACTTGTATCAGTAGAACGA-TC
*
17396635 ACTTGTATCAGTAGAACTATC
1 ACTTGTATCAGTAGAACGATC
17396656 ACTTGTATCAGT
1 ACTTGTATCAGT
17396668 TAAAATCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (21 bp):
ACTTGTATCAGTAGAACGATC
Found at i:17399503 original size:26 final size:26
Alignment explanation
Indices: 17399460--17399518 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
17399450 AATTCTGGGC
17399460 ACAATTCTGGACACGTTCATGCAGCA
1 ACAATTCTGGACACGTTCATGCAGCA
* * *
17399486 ACAATTCTGTACATGTTCATGCAGCG
1 ACAATTCTGGACACGTTCATGCAGCA
17399512 AC-ATTCT
1 ACAATTCT
17399519 TGGGTGCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (26 bp):
ACAATTCTGGACACGTTCATGCAGCA
Found at i:17399545 original size:37 final size:38
Alignment explanation
Indices: 17399504--17399600 Score: 128
Period size: 37 Copynumber: 2.6 Consensus size: 38
17399494 GTACATGTTC
17399504 ATGCAGCGACATTCTTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACATTCTTGGGTGCAATTTGAAGAATACTT
* * *
17399541 ATGCAGC-A-ATGTTTTGGATGCAATTTGAAGAATATTT
1 ATGCAGCGACAT-TCTTGGGTGCAATTTGAAGAATACTT
*
17399578 ATGCAGCGACAGTCTTGGGTGCA
1 ATGCAGCGACATTCTTGGGTGCA
17399601 TTCCGAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 2 0.04
36 11 0.22
37 26 0.52
38 10 0.20
39 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (38 bp):
ATGCAGCGACATTCTTGGGTGCAATTTGAAGAATACTT
Found at i:17404006 original size:26 final size:26
Alignment explanation
Indices: 17403977--17404032 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
17403967 ATTCTGGGTG
17403977 CAATTATGCACACGTTCATGCAGTGA
1 CAATTATGCACACGTTCATGCAGTGA
* * *
17404003 CAATTCTGTACATGTTCATGCAGTGA
1 CAATTATGCACACGTTCATGCAGTGA
17404029 -AATT
1 CAATT
17404033 CCTAGGTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (26 bp):
CAATTATGCACACGTTCATGCAGTGA
Found at i:17407464 original size:21 final size:21
Alignment explanation
Indices: 17407438--17407491 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
17407428 AGAGTTTTTA
17407438 GTATCGGTA-AAG-GTGAAACTT
1 GTATCGGTAGAAGAGT--AACTT
*
17407459 GTATCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAGTAACTT
17407480 GTATCGGTAGAA
1 GTATCGGTAGAA
17407492 ATCTGTACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 25 0.83
22 3 0.10
23 2 0.07
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (21 bp):
GTATCGGTAGAAGAGTAACTT
Found at i:17421748 original size:16 final size:17
Alignment explanation
Indices: 17421716--17421748 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17421706 ACCAATCCAA
17421716 CCCAAACCCTTGAATCGG
1 CCCAAACCC-TGAATCGG
17421734 CCCAAACCC-GAATCG
1 CCCAAACCCTGAATCG
17421749 ACCATAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.42, G:0.15, T:0.12
Consensus pattern (17 bp):
CCCAAACCCTGAATCGG
Found at i:17424732 original size:26 final size:26
Alignment explanation
Indices: 17424689--17424747 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
17424679 AATTCTAGGC
*
17424689 ACAATTCTGGGCACGTTCATGCAGCG
1 ACAATTCTGGACACGTTCATGCAGCG
* *
17424715 ACAATTCTGTACATGTTCATGCAGCG
1 ACAATTCTGGACACGTTCATGCAGCG
17424741 AC-ATTCT
1 ACAATTCT
17424748 TGGGTGCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (26 bp):
ACAATTCTGGACACGTTCATGCAGCG
Found at i:17426021 original size:17 final size:17
Alignment explanation
Indices: 17425982--17426039 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
17425972 ATATATATGG
**
17425982 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
17425999 AGATGCAACGACAATAA
1 AAATGCAATGACAATAA
*
17426016 AAATGCAGTGACAATAA
1 AAATGCAATGACAATAA
17426033 AAATGCA
1 AAATGCA
17426040 GGAACAATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:17429363 original size:37 final size:38
Alignment explanation
Indices: 17429322--17429412 Score: 87
Period size: 38 Copynumber: 2.4 Consensus size: 38
17429312 ATGTTCATGT
*
17429322 AGCGACATTCCTGGGTTCAA-TTGAAGAATACTTATAC
1 AGCGACATTCCTGGGTGCAATTTGAAGAATACTTATAC
* * * *
17429359 AGCGATAGTT-CTGGATGCAATTTGAAGAATATTTATGC
1 AGCGACA-TTCCTGGGTGCAATTTGAAGAATACTTATAC
* * *
17429397 AGTGACAGTCTTGGGT
1 AGCGACATTCCTGGGT
17429413 AAATTCCTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
37 15 0.37
38 26 0.63
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (38 bp):
AGCGACATTCCTGGGTGCAATTTGAAGAATACTTATAC
Found at i:17433642 original size:24 final size:24
Alignment explanation
Indices: 17433604--17433669 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
17433594 GTATACTAGT
17433604 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
* *
17433628 TAATCATTCTAGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
17433652 TAACCATTCTGGGCTCAT
1 TAACCATTCTGGGCTCAT
17433670 GTGAGTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:17435291 original size:52 final size:52
Alignment explanation
Indices: 17435212--17435447 Score: 298
Period size: 52 Copynumber: 4.6 Consensus size: 52
17435202 AATGGAAAAA
* *
17435212 AGGTCTGATGACTACGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
17435264 AGGTCCGATGACTACGTGTCATTGTGAGTATATGAATCCTTTATGGATAATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
17435316 AGGTCCGATGACTATGTGTCATCGTTAATATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * * *
17435368 AGGTCCGATGACTAGGTATCATCGTGAGTATGTG-ATTCTTTAACGAATTA-A
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTT-ACGGATTATG
**
17435419 AGGTCCGATGACTTTGTGTCATC-TGAGTA
1 AGGTCCGATGACTACGTGTCATCGTGAGTA
17435448 ATAAATATGC
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
50 6 0.04
51 26 0.16
52 129 0.80
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:17439728 original size:195 final size:191
Alignment explanation
Indices: 17439424--17439785 Score: 474
Period size: 195 Copynumber: 1.9 Consensus size: 191
17439414 ACTATAAACC
* * *
17439424 GTTCCCTAACGATGCTTCTCACACGAGCTGTCGAGAGTATGCATAAAGCATAGTCCCAGCCATCG
1 GTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCATAAAGCATAGTCCCAGCCATCG
* **
17439489 TAGGGACTGTAATCCATTTAGGATCCATTTCTCTTTTTCGACTCACGATGCTACTCACACT-AGT
66 TAAGGACTGTAATCCATTTAGGATCCATTTCTCTTTCCCGACTCACGATGCTACTCACA-TAAGT
* * * *
17439553 TGTCAAGGACTCGTAATATATACGGTGCCTCAGCCATCAATACGATATTTGTGCATATAACT
130 TATCAAGGACTCGCAACATATACGGTACCTCAGCCATCAATACGATATTTGTGCATATAACT
* * *
17439615 GTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCACTTATGCATAAGTCTCAGCCAT
1 GTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCA-TAAAGCAT-AGTCCCAGCCAT
* * * * * *
17439680 CGTAAGGCCTGTAATCCATTTTTGGATTCTTTTCTCATTTCCCGACTCATGATGCTGCTCACATA
64 CGTAAGGACTGTAATCCA-TTTAGGATCCATTTCTC-TTTCCCGACTCACGATGCTACTCACATA
* * *
17439745 AGTTATCGAGGACTTGCAACATATGCGGTACCTCAGCCATC
127 AGTTATCAAGGACTCGCAACATATACGGTACCTCAGCCATC
17439786 GCGTCGGTTT
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
191 40 0.28
192 6 0.04
193 27 0.19
194 15 0.10
195 56 0.39
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (191 bp):
GTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATATGCATAAAGCATAGTCCCAGCCATCG
TAAGGACTGTAATCCATTTAGGATCCATTTCTCTTTCCCGACTCACGATGCTACTCACATAAGTT
ATCAAGGACTCGCAACATATACGGTACCTCAGCCATCAATACGATATTTGTGCATATAACT
Found at i:17440168 original size:8 final size:8
Alignment explanation
Indices: 17440155--17440180 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17440145 ACATGCATAA
17440155 TTACCCTT
1 TTACCCTT
17440163 TTACCCTT
1 TTACCCTT
17440171 TTACCCTT
1 TTACCCTT
17440179 TT
1 TT
17440181 TTAATTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.54
Consensus pattern (8 bp):
TTACCCTT
Found at i:17442992 original size:21 final size:21
Alignment explanation
Indices: 17442968--17443018 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
17442958 ATGACAGTTT
* *
17442968 TACCGATACAAGTGAAGCTTC
1 TACCGATACAAATCAAGCTTC
* *
17442989 TACCGAAACAAATCATGCTTC
1 TACCGATACAAATCAAGCTTC
17443010 TACCGATAC
1 TACCGATAC
17443019 TAAAAATTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (21 bp):
TACCGATACAAATCAAGCTTC
Found at i:17444186 original size:195 final size:191
Alignment explanation
Indices: 17443771--17444209 Score: 443
Period size: 195 Copynumber: 2.3 Consensus size: 191
17443761 CTAGTACTCG
* * * * * * * *
17443771 ATGCTACTCACACGAGCTGTCGAGGACTCACAACGTATGCGGTACCCCAACCATCGGTAC-AGTG
1 ATGCTACTCACACGAGCTATCGAGGACTCTCAACATATGCAGTACCTCAGCCATCGATACGA-TA
* * * * *
17443835 CCTGT-CTATACTATAAATTGTTCCCTAACGATGCTGCTCATACGAGCTGTCGAGAGTATGCATA
65 TCTGTGC---A-TAT-AACTGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCATA
* * **
17443899 AGGCATAGTCCCAACCATCGTAGGGCTTATAATCCATTTAGGATCCATTTCTCTTTTTCGACTCA
125 AGGCATAATCCCAACCATCGTAGGGCCTATAATCCATTTAGGATCCATTTCTCTTTCCCGACTCA
*
17443964 CG
190 CA
* * * * *
17443966 ATGTTGCTCATACGAGCTGTCGAGGACTCGT-AACATATGTAGTACCTCAGCCATCGATACGATA
1 ATGCTACTCACACGAGCTATCGAGGACTC-TCAACATATGCAGTACCTCAGCCATCGATACGATA
* * * *
17444030 TCTGTGCATATAACTGTTCCCTAATAATGCTGCTCACACGAGCTGTCGAGAATATGTACTTATGC
65 TCTGTGCATATAACTGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCA-TAAGGC
* * * * * * *
17444095 ATAAATCTCAGCCATCGTAGGGCCTGTAGTCCATTCTTGGATTCTTTTCTCATTTCCCGACTCAC
129 AT-AATCCCAACCATCGTAGGGCCTATAATCCATT-TAGGATCCATTTCTC-TTTCCCGACTCAC
17444160 A
191 A
*
17444161 ATGCTACTCACACGAGCTATCGAGGACTCTCAACATATGCGGTACCTCA
1 ATGCTACTCACACGAGCTATCGAGGACTCTCAACATATGCAGTACCTCA
17444210 ATCATCGCGT
Statistics
Matches: 198, Mismatches: 38, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
191 41 0.21
192 9 0.05
193 27 0.14
194 13 0.07
195 106 0.54
196 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (191 bp):
ATGCTACTCACACGAGCTATCGAGGACTCTCAACATATGCAGTACCTCAGCCATCGATACGATAT
CTGTGCATATAACTGTTCCCTAACAATGCTGCTCACACGAGCTGTCGAGAATATGCATAAGGCAT
AATCCCAACCATCGTAGGGCCTATAATCCATTTAGGATCCATTTCTCTTTCCCGACTCACA
Found at i:17454655 original size:21 final size:21
Alignment explanation
Indices: 17454615--17454655 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17454605 GAAGTAAGAC
* *
17454615 TTGTATCGGTAGAAGAGTCAT
1 TTGTATCAGTAGAACAGTCAT
*
17454636 TTGTATCAGTAGAACTGTCA
1 TTGTATCAGTAGAACAGTCA
17454656 CATGGATCGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.34
Consensus pattern (21 bp):
TTGTATCAGTAGAACAGTCAT
Found at i:17463720 original size:22 final size:22
Alignment explanation
Indices: 17463692--17463733 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17463682 AAAAAATAAA
*
17463692 GTGAACAGTGAGATTCTCTGAC
1 GTGAACAGTAAGATTCTCTGAC
17463714 GTGAACAGTAAGATTCTCTG
1 GTGAACAGTAAGATTCTCTG
17463734 GCAATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (22 bp):
GTGAACAGTAAGATTCTCTGAC
Found at i:17463740 original size:69 final size:69
Alignment explanation
Indices: 17463667--17463801 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
17463657 ATGAACAGGA
* * *
17463667 AATATTCTCTGTAAGAAAAAATAAAGTGAACAGTGAGATTCTCTGACGTGAACAGT-AAGATTCT
1 AATATTCTCTGCAAGAAAAAACAAAATGAACAGTGAGATTCTCTGACGTGAACAGTGAA-ATTCT
17463731 CTGGC
65 CTGGC
17463736 AATATTCTCTGCAAGAAAAAACAAAATGAACAGTGAGATTCTCTGACGTGAACAGTGAAATTCTC
1 AATATTCTCTGCAAGAAAAAACAAAATGAACAGTGAGATTCTCTGACGTGAACAGTGAAATTCTC
17463801 T
66 T
17463802 AACGTAAACA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 60 0.97
70 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (69 bp):
AATATTCTCTGCAAGAAAAAACAAAATGAACAGTGAGATTCTCTGACGTGAACAGTGAAATTCTC
TGGC
Found at i:17463790 original size:22 final size:22
Alignment explanation
Indices: 17463762--17463811 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
17463752 AAAAACAAAA
* *
17463762 TGAACAGTGAGATTCTCTGACG
1 TGAACAGTGAAATTCTCTAACG
17463784 TGAACAGTGAAATTCTCTAACG
1 TGAACAGTGAAATTCTCTAACG
*
17463806 TAAACA
1 TGAACA
17463812 ATAAAGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (22 bp):
TGAACAGTGAAATTCTCTAACG
Found at i:17464166 original size:14 final size:14
Alignment explanation
Indices: 17464121--17464168 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
17464111 TTTAGCCTTC
17464121 AAATTTAAGTTTTA
1 AAATTTAAGTTTTA
* **
17464135 AAATTCAAAATTTA
1 AAATTTAAGTTTTA
*
17464149 AAATTTAAGTTTTC
1 AAATTTAAGTTTTA
17464163 AAATTT
1 AAATTT
17464169 TAATTACATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (14 bp):
AAATTTAAGTTTTA
Done.