Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 35 of 93
Found at i:13691808 original size:40 final size:38
Alignment explanation
Indices: 13691713--13691818 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 38
13691703 ATAGTGCTCG
*
13691713 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
* * *
13691751 TATGCACTATGTGGGGGGATGCACATGATGGTGTCGACT-A-
1 TGTGCACGATGTGGGGGGATGTACATGAT-G-G-C-ACTGAT
13691791 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
13691819 GCCGGGTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
38 25 0.44
39 1 0.02
40 26 0.46
41 2 0.04
42 3 0.05
ACGTcount: A:0.22, C:0.14, G:0.39, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
Found at i:13693267 original size:22 final size:22
Alignment explanation
Indices: 13693237--13693340 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
13693227 ATCAAAACAT
*
13693237 GTCACACAATGCCTAAAACTTA
1 GTCATACAATGCCTAAAACTTA
* * * *
13693259 ATCATACAATGCTTACAACCTA
1 GTCATACAATGCCTAAAACTTA
* * *
13693281 GTCATATAATACCTAAAA-TCCA
1 GTCATACAATGCCTAAAACT-TA
*
13693303 GTCATGCAATGCCTAAAAAC-TA
1 GTCATACAATGCCT-AAAACTTA
*
13693325 GTCATGCAATGCCTAA
1 GTCATACAATGCCTAA
13693341 GTCACCAATT
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
21 2 0.03
22 57 0.90
23 4 0.06
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (22 bp):
GTCATACAATGCCTAAAACTTA
Found at i:13693340 original size:44 final size:44
Alignment explanation
Indices: 13693237--13693340 Score: 102
Period size: 44 Copynumber: 2.4 Consensus size: 44
13693227 ATCAAAACAT
* * * * *
13693237 GTCACACAATGCCTAAAACTTAATCATACAATGCTTACAACCTA
1 GTCATACAATGCCTAAAACTCAATCATACAATGCCTAAAAACTA
* * * *
13693281 GTCATATAATACCTAAAA-TCCAGTCATGCAATGCCTAAAAACTA
1 GTCATACAATGCCTAAAACT-CAATCATACAATGCCTAAAAACTA
*
13693325 GTCATGCAATGCCTAA
1 GTCATACAATGCCTAA
13693341 GTCACCAATT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 1 0.02
44 46 0.98
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (44 bp):
GTCATACAATGCCTAAAACTCAATCATACAATGCCTAAAAACTA
Found at i:13693477 original size:22 final size:22
Alignment explanation
Indices: 13693433--13693493 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
13693423 ATTAAGTCAT
* *
13693433 GCAATGCCT-AAAAGTCAGTCTC
1 GCAATGCCTAAAAACT-AGACTC
*
13693455 GCAATGTCTAAAAACTAGACTC
1 GCAATGCCTAAAAACTAGACTC
*
13693477 GTAATGCCTAAAAACTA
1 GCAATGCCTAAAAACTA
13693494 TTGACACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (22 bp):
GCAATGCCTAAAAACTAGACTC
Found at i:13695317 original size:94 final size:95
Alignment explanation
Indices: 13695186--13695366 Score: 276
Period size: 94 Copynumber: 1.9 Consensus size: 95
13695176 ATTGAATATC
* * *
13695186 GAAAATATCCTTCAAAAACTCAAAAATAACAATGCCACATGTTAGACTGTAGAC-CTCTATGCAT
1 GAAAATATCCTTCAAAAACTCAAAAATAACAACGCCACATGTCAGACTGTAGACTCTCTATACAT
13695250 GAGATTCATTATAAAGTAGATTGAAAGCTT
66 GAGATTCATTATAAAGTAGATTGAAAGCTT
* *
13695280 GAAAATA-CCTTTCAAAAACTCAAAAATGACAACGCCACATGTCAGATTGTAGACTTCTCTATAC
1 GAAAATATCC-TTCAAAAACTCAAAAATAACAACGCCACATGTCAGACTGTAGAC-TCTCTATAC
*
13695344 ATGAGATTCATTATATAGTAGAT
64 ATGAGATTCATTATAAAGTAGAT
13695367 AGCTTATATT
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
93 2 0.03
94 47 0.60
96 29 0.37
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (95 bp):
GAAAATATCCTTCAAAAACTCAAAAATAACAACGCCACATGTCAGACTGTAGACTCTCTATACAT
GAGATTCATTATAAAGTAGATTGAAAGCTT
Found at i:13700682 original size:18 final size:17
Alignment explanation
Indices: 13700659--13700701 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
13700649 TTAAGAGGCC
*
13700659 CTTAAAAAACAGTTTTTT
1 CTTAAAAAAC-GATTTTT
*
13700677 CTTAAAGAACGATTTTT
1 CTTAAAAAACGATTTTT
13700694 -TTAAAAAA
1 CTTAAAAAA
13700702 AAAAGCTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (17 bp):
CTTAAAAAACGATTTTT
Found at i:13702340 original size:3 final size:3
Alignment explanation
Indices: 13702332--13702359 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13702322 ATATCTCTAC
13702332 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
13702360 GTATGCTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:13738447 original size:2 final size:2
Alignment explanation
Indices: 13738440--13738518 Score: 94
Period size: 2 Copynumber: 41.0 Consensus size: 2
13738430 TTCATGTTAA
* * *
13738440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T GNT CT -T CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
13738481 AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13738519 TGCATCAAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
1 4 0.06
2 65 0.93
3 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:13744719 original size:30 final size:29
Alignment explanation
Indices: 13744684--13744744 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
13744674 GTTTTAGGTT
* *
13744684 GACTAGAATTCTATATCTTATTTGATTAG
1 GACTAGAATTCTAGACCTTATTTGATTAG
13744713 GNACTAGAATTCTAGACCTTATTTGATTAG
1 G-ACTAGAATTCTAGACCTTATTTGATTAG
13744743 GA
1 GA
13744745 TTCTTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.39
Consensus pattern (29 bp):
GACTAGAATTCTAGACCTTATTTGATTAG
Found at i:13746186 original size:18 final size:20
Alignment explanation
Indices: 13746150--13746186 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13746140 GAGGAGCCTT
13746150 AAGGCCCATAACGAAAGAAA
1 AAGGCCCATAACGAAAGAAA
13746170 AAGGCCCA-AAC-AAAGAA
1 AAGGCCCATAACGAAAGAA
13746187 TTCCAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.57, C:0.22, G:0.19, T:0.03
Consensus pattern (20 bp):
AAGGCCCATAACGAAAGAAA
Found at i:13749070 original size:13 final size:13
Alignment explanation
Indices: 13749052--13749081 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13749042 GAAATGACCC
*
13749052 TTTCTTTTTCTTG
1 TTTCTTTTACTTG
13749065 TTTCTTTTACTTG
1 TTTCTTTTACTTG
13749078 TTTC
1 TTTC
13749082 CAATGCTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.17, G:0.07, T:0.73
Consensus pattern (13 bp):
TTTCTTTTACTTG
Found at i:13755591 original size:18 final size:18
Alignment explanation
Indices: 13755563--13755600 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
13755553 CCTCTCTCTC
13755563 TTTTCCTGTTTTTT-TTT
1 TTTTCCTGTTTTTTCTTT
13755580 TTTTCTCTGTTTTTTCTTT
1 TTTTC-CTGTTTTTTCTTT
13755599 TT
1 TT
13755601 CTTTTTGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTCCTGTTTTTTCTTT
Found at i:13755592 original size:17 final size:18
Alignment explanation
Indices: 13755563--13755602 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
13755553 CCTCTCTCTC
*
13755563 TTTTC-CTGTTTTTTTTT
1 TTTTCTCTGTTTTTTTCT
13755580 TTTTCTCTG-TTTTTTCT
1 TTTTCTCTGTTTTTTTCT
13755597 TTTTCT
1 TTTTCT
13755603 TTTTGCTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTCTCTGTTTTTTTCT
Found at i:13755599 original size:24 final size:23
Alignment explanation
Indices: 13755571--13755622 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
13755561 TCTTTTCCTG
13755571 TTTTTTTT-TTTTT-CTCTGTTT
1 TTTTTTTTCTTTTTGCTCTGTTT
13755592 TTTCTTTTTCTTTTTGCTCTGTTT
1 TTT-TTTTTCTTTTTGCTCTGTTT
13755616 TTTTTTT
1 TTTTTTT
13755623 CTTACTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.11
22 5 0.18
23 9 0.32
24 11 0.39
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.83
Consensus pattern (23 bp):
TTTTTTTTCTTTTTGCTCTGTTT
Found at i:13756314 original size:3 final size:3
Alignment explanation
Indices: 13756308--13756332 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13756298 ATAATAATAA
13756308 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
13756333 CTTGTGCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13758266 original size:26 final size:26
Alignment explanation
Indices: 13758236--13758301 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
13758226 TCCTCACTAC
*
13758236 AAGCTTACCTCGTTTAAAAGTTCGAT
1 AAGCTTACCTCGTTTAAAAGGTCGAT
13758262 AAGCTTACCTCGTTTAAAAGGTCGAT
1 AAGCTTACCTCGTTTAAAAGGTCGAT
13758288 AAGCTTACCTCGTT
1 AAGCTTACCTCGTT
13758302 AGCAGGGCTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (26 bp):
AAGCTTACCTCGTTTAAAAGGTCGAT
Found at i:13766311 original size:221 final size:225
Alignment explanation
Indices: 13765877--13766298 Score: 541
Period size: 221 Copynumber: 1.9 Consensus size: 225
13765867 CACCAATGTG
** * *
13765877 TAAATGAAAACTCCAAGAAATCAATCATGTAACAATGCCCCATGTGAATCTATTTAATGAAAGTA
1 TAAATGAAAACTCCAAGAAATCAATCATGTAACAACACCCCATGTGAATCTATCT-ATGAAACTA
* *
13765942 CCAGATTAAATTAAAAAAAAAAGGAAATAACCAAAACATTAAAAAAAAAAAAAAGCTAAGGAACA
65 CCAAATTAAATT-AAAAAAAAAGGAAATAACCAAAACATT-AAAAAAAAAAAAAGCTAAGGAAAA
* *
13766007 TAAGATTAACAGGAGAACAATCTTTGTTCCCTGATACCAAATTAAATTCTTAAAAAGAAAATAAC
128 TAAGATTAACAGGAGAACAATCATTGTTCCCTGATACCAAATTAAATTATTAAAAAGAAAATAAC
13766072 CAAAATATTGAAAAAAAAAAAAGCAGCATATTA
193 CAAAATATTGAAAAAAAAAAAAGCAGCATATTA
* * *
13766105 TAAATGAAAACTCCGAGCATTCAATCATGTAACAACACCCCATGTGAATCTA-CT-T-AAACTAC
1 TAAATGAAAACTCCAAGAAATCAATCATGTAACAACACCCCATGTGAATCTATCTATGAAACTAC
** * * * * * * *
13766167 CAAATTAAATT-ATTAAAAAGGAAATAACTAAAACATCT-AAAAAGAAACAATCTGAGTAAAATT
66 CAAATTAAATTAAAAAAAAAGGAAATAACCAAAACAT-TAAAAAAAAAAAAAGCTAAGGAAAATA
** * *
13766230 AGATTATTAGGAGAACGCA-CATTGTTCCCTGATACCAAATTAAATTATTAATAAGAAAATAACC
130 AGATTAACAGGAGAAC-AATCATTGTTCCCTGATACCAAATTAAATTATTAAAAAGAAAATAACC
13766294 AAAAT
194 AAAAT
13766299 TTGGGGAAAA
Statistics
Matches: 168, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
221 79 0.47
222 23 0.14
223 1 0.01
224 16 0.10
225 1 0.01
227 1 0.01
228 47 0.28
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (225 bp):
TAAATGAAAACTCCAAGAAATCAATCATGTAACAACACCCCATGTGAATCTATCTATGAAACTAC
CAAATTAAATTAAAAAAAAAGGAAATAACCAAAACATTAAAAAAAAAAAAAGCTAAGGAAAATAA
GATTAACAGGAGAACAATCATTGTTCCCTGATACCAAATTAAATTATTAAAAAGAAAATAACCAA
AATATTGAAAAAAAAAAAAGCAGCATATTA
Found at i:13768654 original size:28 final size:28
Alignment explanation
Indices: 13768623--13768721 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 28
13768613 TAACTGTTAG
13768623 TTATAAAATTTATTTAATTTAAAATAAA
1 TTATAAAATTTATTTAATTTAAAATAAA
* * * *
13768651 TTATAAAAATTAATTGAATATAATA-AAA
1 TTAT-AAAATTTATTTAATTTAAAATAAA
* *
13768679 TAATAAATATTTATTTAAATTTTTAAAT-AA
1 TTATAAA-ATTTATTT-AA-TTTAAAATAAA
13768709 TT-TAAAA-TTATTT
1 TTATAAAATTTATTT
13768722 TAAATTATTA
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
27 9 0.16
28 17 0.31
29 22 0.40
30 7 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TTATAAAATTTATTTAATTTAAAATAAA
Found at i:13769032 original size:18 final size:18
Alignment explanation
Indices: 13769011--13769046 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
13769001 GAGTATTTAA
13769011 TAAATCAAGA-AAAAAAAT
1 TAAATCAA-ATAAAAAAAT
13769029 TAAATCAAATAAAAAAAT
1 TAAATCAAATAAAAAAAT
13769047 AAGTGTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (18 bp):
TAAATCAAATAAAAAAAT
Found at i:13771231 original size:17 final size:17
Alignment explanation
Indices: 13771209--13771241 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13771199 GAGCTATCAT
*
13771209 AACCGAACTATCCAAAA
1 AACCGAACTAACCAAAA
13771226 AACCGAACTAACCAAA
1 AACCGAACTAACCAAA
13771242 TCAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.30, G:0.06, T:0.09
Consensus pattern (17 bp):
AACCGAACTAACCAAAA
Found at i:13773283 original size:2 final size:2
Alignment explanation
Indices: 13773276--13773303 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13773266 CTACACTTCC
13773276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13773304 CTATCTGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13775294 original size:2 final size:2
Alignment explanation
Indices: 13775287--13775321 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13775277 AAGATCACCC
13775287 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
13775322 CTACTACNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13775376 original size:2 final size:2
Alignment explanation
Indices: 13775369--13775403 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13775359 NNNNNNNNNN
13775369 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
13775404 GACTTACACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13777489 original size:124 final size:124
Alignment explanation
Indices: 13777267--13777611 Score: 458
Period size: 124 Copynumber: 2.8 Consensus size: 124
13777257 CACTTCAGTA
* ** * * * * *
13777267 GAAGATGTTACATACCAAAACTTCAGCTGCAGATGTTACACGCTAATGTCAAATCTTCAA-CACT
1 GAAGATGTTACACATAAAAACTTCAGCAGCAGATGCTACACGCCAAGGTCAAAGCTT-AAGCACT
* * * * * * *
13777331 AGATATCACACGCCAAGGTCAAAACTTTAACATCAAATGTTACACATCAAAGCTAAAGCC
65 AGATGTTACATGCCAAGGCCAAAGCTTTAGCATCAAATGTTACACACCAAAGCTAAAGCC
13777391 GAAGATGTTACACATAAAAACTTCAGCAGCAGATGCTACACGCCAAGGTCAAAGCTTAAGCACTA
1 GAAGATGTTACACATAAAAACTTCAGCAGCAGATGCTACACGCCAAGGTCAAAGCTTAAGCACTA
*
13777456 GATGTTACATGTCAAGGCCAAAGCTTTAGCATCAAATGTTACACACCAAAGCTAAAGCC
66 GATGTTACATGCCAAGGCCAAAGCTTTAGCATCAAATGTTACACACCAAAGCTAAAGCC
* * * * * *
13777515 GAAAATGTTACACATTAAAACTTTAGTAGCAGATGCTACACGCCAAGGTCAAAGCTTTAGCACCA
1 GAAGATGTTACACATAAAAACTTCAGCAGCAGATGCTACACGCCAAGGTCAAAGCTTAAGCACTA
* *
13777580 GATGCTACATGCCAAGGCCAAAGCTTCAGCAT
66 GATGTTACATGCCAAGGCCAAAGCTTTAGCAT
13777612 TAGATATTAC
Statistics
Matches: 195, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
123 2 0.01
124 193 0.99
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (124 bp):
GAAGATGTTACACATAAAAACTTCAGCAGCAGATGCTACACGCCAAGGTCAAAGCTTAAGCACTA
GATGTTACATGCCAAGGCCAAAGCTTTAGCATCAAATGTTACACACCAAAGCTAAAGCC
Found at i:13777495 original size:34 final size:34
Alignment explanation
Indices: 13777434--13777498 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
13777424 TGCTACACGC
* *
13777434 CAAGGTCAAAGCTTAAGCACTAGATGTTACATGT
1 CAAGGCCAAAGCTTAAGCACTAAATGTTACATGT
*
13777468 CAAGGCCAAAGCTTTAGCA-TCAAATGTTACA
1 CAAGGCCAAAGCTTAAGCACT-AAATGTTACA
13777499 CACCAAAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 26 0.96
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (34 bp):
CAAGGCCAAAGCTTAAGCACTAAATGTTACATGT
Found at i:13777582 original size:34 final size:34
Alignment explanation
Indices: 13777535--13777610 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
13777525 CACATTAAAA
* * *
13777535 CTTTAGTAGCAGATGCTACACGCCAAGGTCAAAG
1 CTTTAGCACCAGATGCTACACGCCAAGGCCAAAG
*
13777569 CTTTAGCACCAGATGCTACATGCCAAGGCCAAAG
1 CTTTAGCACCAGATGCTACACGCCAAGGCCAAAG
*
13777603 CTTCAGCA
1 CTTTAGCA
13777611 TTAGATATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (34 bp):
CTTTAGCACCAGATGCTACACGCCAAGGCCAAAG
Found at i:13777628 original size:34 final size:34
Alignment explanation
Indices: 13777544--13777628 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
13777534 ACTTTAGTAG
* * * *
13777544 CAGATGCTACACGCCAAGGTCAAAGCTTTAGCAC
1 CAGATACTACAAGCCAAGGCCAAAGCTTCAGCAC
* * *
13777578 CAGATGCTACATGCCAAGGCCAAAGCTTCAGCAT
1 CAGATACTACAAGCCAAGGCCAAAGCTTCAGCAC
* *
13777612 TAGATATTACAAGCCAA
1 CAGATACTACAAGCCAA
13777629 AGCTTCCTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (34 bp):
CAGATACTACAAGCCAAGGCCAAAGCTTCAGCAC
Found at i:13777694 original size:27 final size:27
Alignment explanation
Indices: 13777664--13777715 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
13777654 CACATCCAGG
*
13777664 CATGAATCACTTTGTTACACGCCAAGA
1 CATGAATCACTTTATTACACGCCAAGA
** *
13777691 CATGAATTGCTTTATTACATGCCAA
1 CATGAATCACTTTATTACACGCCAA
13777716 AGCATGTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (27 bp):
CATGAATCACTTTATTACACGCCAAGA
Found at i:13777721 original size:27 final size:26
Alignment explanation
Indices: 13777663--13777721 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
13777653 ACACATCCAG
*
13777663 GCATGAATCACTTTGTTACACGCCAA
1 GCATGAATCACTTTATTACACGCCAA
** *
13777689 GACATGAATTGCTTTATTACATGCCAAA
1 G-CATGAATCACTTTATTACACGCC-AA
13777717 GCATG
1 GCATG
13777722 TTCTACCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 23 0.85
28 3 0.11
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (26 bp):
GCATGAATCACTTTATTACACGCCAA
Found at i:13779641 original size:11 final size:11
Alignment explanation
Indices: 13779625--13779658 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13779615 GGCAATACTT
13779625 TCCGTTGGAAA
1 TCCGTTGGAAA
*
13779636 TCCGTTGAAAA
1 TCCGTTGGAAA
*
13779647 TCTGTTGGAAA
1 TCCGTTGGAAA
13779658 T
1 T
13779659 TTCTCACGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (11 bp):
TCCGTTGGAAA
Found at i:13779760 original size:13 final size:13
Alignment explanation
Indices: 13779729--13779761 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
13779719 GAAATCCGTT
13779729 GGAAATTTCCAAC
1 GGAAATTTCCAAC
13779742 --AAATTTCCAAC
1 GGAAATTTCCAAC
13779753 GGAAATTTC
1 GGAAATTTC
13779762 GTTGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.61
13 7 0.39
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (13 bp):
GGAAATTTCCAAC
Found at i:13780789 original size:2 final size:2
Alignment explanation
Indices: 13780782--13780841 Score: 95
Period size: 2 Copynumber: 30.0 Consensus size: 2
13780772 AATCATAATC
13780782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
13780824 TA TA TC T- TGA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA
13780842 ACATGTATAG
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
1 1 0.02
2 53 0.96
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13782312 original size:6 final size:6
Alignment explanation
Indices: 13782301--13782356 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
13782291 GCTCCACATG
* * *
13782301 ATCTTC ATCTTC ATCTTC ATATTC ATCCTC ATCTTC ATCTTC ATCATC
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC
13782349 ATCTTC AT
1 ATCTTC AT
13782357 TATCTTCTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.46
Consensus pattern (6 bp):
ATCTTC
Found at i:13782411 original size:30 final size:29
Alignment explanation
Indices: 13782302--13782417 Score: 101
Period size: 24 Copynumber: 4.3 Consensus size: 29
13782292 CTCCACATGA
13782302 TCTTCATCTTCATCTTCAT-AT-TCATC-
1 TCTTCATCTTCATCTTCATCATATCATCT
13782328 -C-TCATCTTCATCTTCATC--ATCATCT
1 TCTTCATCTTCATCTTCATCATATCATCT
* *
13782353 TCATT-ATCTTC-TCTT--TCCATGTCGTCT
1 TC-TTCATCTTCATCTTCAT-CATATCATCT
*
13782380 TCTTCATCTTCATCTTTATCGATATCATCT
1 TCTTCATCTTCATCTTCATC-ATATCATCT
13782410 TCTTCATC
1 TCTTCATC
13782418 CTCAATCGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
24 22 0.31
25 2 0.03
26 7 0.10
27 19 0.26
28 5 0.07
29 1 0.01
30 16 0.22
ACGTcount: A:0.17, C:0.31, G:0.03, T:0.49
Consensus pattern (29 bp):
TCTTCATCTTCATCTTCATCATATCATCT
Found at i:13787039 original size:35 final size:35
Alignment explanation
Indices: 13787000--13787068 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
13786990 ACAAAAAAAT
* * *
13787000 TTAAATTTAAATTTAAATAATAAAAAACAAATATC
1 TTAAACTTAAAATTAAATAACAAAAAACAAATATC
*
13787035 TTAAACTTAAAATTAAATAACAAAAAATAAATAT
1 TTAAACTTAAAATTAAATAACAAAAAACAAATAT
13787069 ATGGGGAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (35 bp):
TTAAACTTAAAATTAAATAACAAAAAACAAATATC
Found at i:13788039 original size:91 final size:89
Alignment explanation
Indices: 13787936--13788212 Score: 243
Period size: 90 Copynumber: 3.1 Consensus size: 89
13787926 GCCGCTGACG
* * **
13787936 AAAGGAAAAAGCGAGAGAGAGAAGATCTGAGTTACTGTGCCGTTGATTATAGAGAAAGCTGGGTC
1 AAAGGAAGAAGCGAGAGAGACAAGATCTGAGTTACTGTGCCGCCGATTATAGAGAAAGCTGGG--
*
13788001 GATTTGGCCTTGTGTCGTCGG-CTGAA
64 GATTCGGCCTTGTGTCG-CGGACTGAA
* * * * * * *
13788027 AAAGGAAGAAGCGAAAGAGACAAGATTTGGGTTGCTGTGCCGCCGATTCTAGAGACAGCTGGGGC
1 AAAGGAAGAAGCGAGAGAGACAAGATCTGAGTTACTGTGCCGCCGATTATAGAGAAAGCTGGGGA
** *
13788092 TTCGGGGTTGTGTTGCGGACTGAA
66 TTCGGCCTTGTGTCGCGGACTGAA
* * ** * * * *
13788116 AAAGGAAGAAGCGAGAGCCA-ACCAGATCTGGGTTTTTGTGCCGTCGGTTGTAGAGAGAGCTGGG
1 AAAGGAAGAAGCGAGAG--AGACAAGATCTGAGTTACTGTGCCGCCGATTATAGAGAAAGCTGGG
* ** * *
13788180 GCTTCGGCCTTCCGTCGCCGACTGGA
64 GATTCGGCCTTGTGTCGCGGACTGAA
13788206 AAAGGAA
1 AAAGGAA
13788213 TGCCTTTAGA
Statistics
Matches: 152, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
88 3 0.02
89 33 0.22
90 62 0.41
91 54 0.36
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.22
Consensus pattern (89 bp):
AAAGGAAGAAGCGAGAGAGACAAGATCTGAGTTACTGTGCCGCCGATTATAGAGAAAGCTGGGGA
TTCGGCCTTGTGTCGCGGACTGAA
Found at i:13788178 original size:90 final size:89
Alignment explanation
Indices: 13787936--13788186 Score: 236
Period size: 91 Copynumber: 2.8 Consensus size: 89
13787926 GCCGCTGACG
* * * * * ** * *
13787936 AAAGGAAAAAGCGAGAGAGAGAAGATCTGAGTTACTGTGCCGTTGATTATAGAGAAAGCTGGGTC
1 AAAGGAAGAAGCGAAAGAGACAAGATCTGGGTTGCTGTGCCGCCGATTCTAGAGACAGCTGGG--
* * ** *
13788001 GATTTGGCCTTGTGTCGTCGG-CTGAA
64 GCTTCGGGGTTGTGTTG-CGGACTGAA
*
13788027 AAAGGAAGAAGCGAAAGAGACAAGATTTGGGTTGCTGTGCCGCCGATTCTAGAGACAGCTGGGGC
1 AAAGGAAGAAGCGAAAGAGACAAGATCTGGGTTGCTGTGCCGCCGATTCTAGAGACAGCTGGGGC
13788092 TTCGGGGTTGTGTTGCGGACTGAA
66 TTCGGGGTTGTGTTGCGGACTGAA
* * ** * * * *
13788116 AAAGGAAGAAGCGAGAGCCA-ACCAGATCTGGGTTTTTGTGCCGTCGGTTGTAGAGAGAGCTGGG
1 AAAGGAAGAAGCGAAAG--AGACAAGATCTGGGTTGCTGTGCCGCCGATTCTAGAGACAGCTGGG
13788180 GCTTCGG
64 GCTTCGG
13788187 CCTTCCGTCG
Statistics
Matches: 133, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
88 3 0.02
89 33 0.25
90 43 0.32
91 54 0.41
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (89 bp):
AAAGGAAGAAGCGAAAGAGACAAGATCTGGGTTGCTGTGCCGCCGATTCTAGAGACAGCTGGGGC
TTCGGGGTTGTGTTGCGGACTGAA
Found at i:13789892 original size:85 final size:86
Alignment explanation
Indices: 13789779--13789956 Score: 252
Period size: 85 Copynumber: 2.1 Consensus size: 86
13789769 TTTTAATATG
*
13789779 TTGGAAACTGTAAAAAAATTTAAATTTTTTTTTAAAGTTTAATGTTCCAACGG-ATTTCCAACAG
1 TTGGAAACTGCAAAAAAATTTAAATTTTTTTTTAAAGTTTAATGTTCCAACGGAATTTCCAACAG
*
13789843 AAATTTTCGTT-GAAAATCCC
66 AAATTTCCGTTGGAAAATCCC
* * * * *
13789863 TTGGAAACTGCAACAAGATTGTAAATTTTTTTTTAAAGTTTTATGTTCCAACGGAATTTTCAACG
1 TTGGAAACTGCAAAAAAATT-TAAATTTTTTTTTAAAGTTTAATGTTCCAACGGAATTTCCAACA
* *
13789928 GAAATTTCCGTTGGAAATTCCG
65 GAAATTTCCGTTGGAAAATCCC
13789950 TTGGAAA
1 TTGGAAA
13789957 TATTGTACAC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
84 17 0.21
85 32 0.39
86 19 0.23
87 14 0.17
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (86 bp):
TTGGAAACTGCAAAAAAATTTAAATTTTTTTTTAAAGTTTAATGTTCCAACGGAATTTCCAACAG
AAATTTCCGTTGGAAAATCCC
Found at i:13789943 original size:13 final size:13
Alignment explanation
Indices: 13789927--13789957 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
13789917 AATTTTCAAC
13789927 GGAAATTTCCGTT
1 GGAAATTTCCGTT
13789940 GGAAA-TTCCGTT
1 GGAAATTTCCGTT
13789952 GGAAAT
1 GGAAAT
13789958 ATTGTACACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (13 bp):
GGAAATTTCCGTT
Found at i:13790147 original size:11 final size:11
Alignment explanation
Indices: 13790116--13790158 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
13790106 AACTATATTT
* *
13790116 CGTTGGAAATT
1 CGTTGAAAATC
*
13790127 CGTTGCAAATC
1 CGTTGAAAATC
*
13790138 CGTTTAAAATC
1 CGTTGAAAATC
13790149 CGTTGAAAAT
1 CGTTGAAAAT
13790159 TTCCAACGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (11 bp):
CGTTGAAAATC
Found at i:13796025 original size:60 final size:60
Alignment explanation
Indices: 13795906--13796031 Score: 200
Period size: 61 Copynumber: 2.1 Consensus size: 60
13795896 CTAAAATTTA
* *
13795906 TTTTTAAATTGTAAATGAAATTTTATGTTATAATTTAATTTTATTTCAAAAGTGATTAAT
1 TTTTTAAATTGTAAATGAAATTTTATATTATAATTTAATTTTACTTCAAAAGTGATTAAT
* *
13795966 TTTTTAACATTGTTAATGAAATTTTATATTATAATTTAATTTTGCTTC-AAAGTGATTAAT
1 TTTTTAA-ATTGTAAATGAAATTTTATATTATAATTTAATTTTACTTCAAAAGTGATTAAT
13796026 TTTTTA
1 TTTTTA
13796032 TTTTGAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 25 0.41
61 36 0.59
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (60 bp):
TTTTTAAATTGTAAATGAAATTTTATATTATAATTTAATTTTACTTCAAAAGTGATTAAT
Found at i:13798935 original size:2 final size:2
Alignment explanation
Indices: 13798928--13798993 Score: 114
Period size: 2 Copynumber: 32.0 Consensus size: 2
13798918 TTCTTATGAC
13798928 TA TA TA TA TA TA TA TA TA TA TGA CTA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA
13798972 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
13798994 ATGTTGCTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 59 0.95
3 2 0.03
4 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13808919 original size:15 final size:16
Alignment explanation
Indices: 13808890--13808919 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13808880 ACCACTGCTG
13808890 AATTCCCAGTCACAAT
1 AATTCCCAGTCACAAT
13808906 AATTCCCA-TCACAA
1 AATTCCCAGTCACAA
13808920 CAGGACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.23
Consensus pattern (16 bp):
AATTCCCAGTCACAAT
Found at i:13813317 original size:63 final size:63
Alignment explanation
Indices: 13813195--13813331 Score: 150
Period size: 63 Copynumber: 2.2 Consensus size: 63
13813185 GCATTTTGTC
* * *
13813195 TTGTAAGAATCGATTAGTGCATTCCCAAGAAGTTGATTCTTCTTGCCCTTAGGGTATTCTATT
1 TTGTAAGAATCGATTAGTGCATTCCCAAGAAGTCGATTCTTCTTGCCCTTAGAGAATTCTATT
**** * * *
13813258 TTGTAAGAATCGATTAGTGCATTTTTGATAAGTCGATTCTTCTTG-ACTCTAGAGAATTCTGTT
1 TTGTAAGAATCGATTAGTGCATTCCCAAGAAGTCGATTCTTCTTGCCCT-TAGAGAATTCTATT
* *
13813321 TTCTAGGAATC
1 TTGTAAGAATC
13813332 AATCTTTACA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 2 0.03
63 59 0.97
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (63 bp):
TTGTAAGAATCGATTAGTGCATTCCCAAGAAGTCGATTCTTCTTGCCCTTAGAGAATTCTATT
Found at i:13817076 original size:19 final size:19
Alignment explanation
Indices: 13817032--13817069 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13817022 CCATTTGACT
*
13817032 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
13817051 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
13817070 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:13832625 original size:52 final size:52
Alignment explanation
Indices: 13832564--13832662 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
13832554 GATGAAATAT
* * *
13832564 AAGATAAATGTGACAAAACACGTGACAAGTAATGTGACGAAATACGATATAG
1 AAGATAAATGTAACAAAACACCTGACAAGTAATGTGACAAAATACGATATAG
* **
13832616 AAGATAAATGTAACAAAGCACCTGACAAGTGGTGTGACAAAATACGA
1 AAGATAAATGTAACAAAACACCTGACAAGTAATGTGACAAAATACGA
13832663 CACAAATAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (52 bp):
AAGATAAATGTAACAAAACACCTGACAAGTAATGTGACAAAATACGATATAG
Found at i:13834965 original size:15 final size:14
Alignment explanation
Indices: 13834934--13834963 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
13834924 AGTTTTTCCA
13834934 TTTCTTTCTCTTTT
1 TTTCTTTCTCTTTT
13834948 TTTCTTT-TCTTTT
1 TTTCTTTCTCTTTT
13834961 TTT
1 TTT
13834964 TTGAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTTTCTCTTTT
Found at i:13835450 original size:117 final size:117
Alignment explanation
Indices: 13835243--13835477 Score: 409
Period size: 117 Copynumber: 2.0 Consensus size: 117
13835233 GAAGTGTACT
*
13835243 CAAATCCTACCTCGGGAGTTATCCTACGCGCCTCTCCAATCAAGGTAAGCTCAATAATTGGGAAC
1 CAAATCCTACCTCGGGAGTTATCCTACGCGCCTCTCCAATCAAGGTAAGCTCAATAATTGAGAAC
*
13835308 CGTGCCCCTCTAATTAGGCTAGCCCACGGAACCCCCGTCACTGCAGTGCCCA
66 CGTGCCCCTCTAATTAAGCTAGCCCACGGAACCCCCGTCACTGCAGTGCCCA
*
13835360 CAAATCCTACCTCGGGAGTTAAT-CTACGCGCCTCTCCAATCGAGGTAAGCTCAATAATTGAGAA
1 CAAATCCTACCTCGGGAGTT-ATCCTACGCGCCTCTCCAATCAAGGTAAGCTCAATAATTGAGAA
* *
13835424 CCGTGCCCCTCTAATTAAGCTGGCCCACGGAACCCCCGTCATTGCAGTGCCCA
65 CCGTGCCCCTCTAATTAAGCTAGCCCACGGAACCCCCGTCACTGCAGTGCCCA
13835477 C
1 C
13835478 TTTATAATCC
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
117 110 0.98
118 2 0.02
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (117 bp):
CAAATCCTACCTCGGGAGTTATCCTACGCGCCTCTCCAATCAAGGTAAGCTCAATAATTGAGAAC
CGTGCCCCTCTAATTAAGCTAGCCCACGGAACCCCCGTCACTGCAGTGCCCA
Found at i:13837401 original size:2 final size:2
Alignment explanation
Indices: 13837394--13837437 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
13837384 TTATTAGATG
* * *
13837394 TA TA TA TA TA -A AA TA TA TG TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13837435 TA T
1 TA T
13837438 TGAACTATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:13840457 original size:2 final size:2
Alignment explanation
Indices: 13840450--13840506 Score: 75
Period size: 2 Copynumber: 29.5 Consensus size: 2
13840440 ATACCTTTTA
*
13840450 AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT AT AT -T TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13840489 AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT A-T AT A
13840507 AAAATAATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
1 3 0.06
2 45 0.90
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:13840520 original size:8 final size:8
Alignment explanation
Indices: 13840507--13840554 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
13840497 ATATAGTATA
13840507 AAAATAAT
1 AAAATAAT
*
13840515 ATAATAAT
1 AAAATAAT
13840523 AAAATATAAT
1 -AAA-ATAAT
13840533 AAAA-AAT
1 AAAATAAT
*
13840540 AAAACAAT
1 AAAATAAT
13840548 AAAATAA
1 AAAATAA
13840555 GAAATAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.21
8 17 0.50
9 5 0.15
10 5 0.15
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:13840524 original size:17 final size:17
Alignment explanation
Indices: 13840504--13840543 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
13840494 TATATATAGT
*
13840504 ATAAAA-ATAATATAATA
1 ATAAAATATAATA-AAAA
13840521 ATAAAATATAATAAAAA
1 ATAAAATATAATAAAAA
13840538 ATAAAA
1 ATAAAA
13840544 CAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAATATAATAAAAA
Found at i:13840530 original size:13 final size:13
Alignment explanation
Indices: 13840512--13840553 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
13840502 GTATAAAAAT
13840512 AATATAATAATAA
1 AATATAATAATAA
13840525 AATATAATAA-AA
1 AATATAATAATAA
* *
13840537 AATAAAACAATAA
1 AATATAATAATAA
13840550 AATA
1 AATA
13840554 AGAAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
AATATAATAATAA
Found at i:13840548 original size:20 final size:20
Alignment explanation
Indices: 13840507--13840562 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
13840497 ATATAGTATA
*
13840507 AAAATAATATAATAATAA-AAT
1 AAAATAA-AAAATAA-AACAAT
*
13840528 ATAATAAAAAATAAAACAAT
1 AAAATAAAAAATAAAACAAT
*
13840548 AAAATAAGAAATAAA
1 AAAATAAAAAATAAA
13840563 TTAAAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.73
21 6 0.20
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAATAAAAAATAAAACAAT
Found at i:13840548 original size:25 final size:24
Alignment explanation
Indices: 13840503--13840553 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
13840493 ATATATATAG
* * *
13840503 TATAAAAATAATATAATAATAAAA
1 TATAAAAAAAATAAAACAATAAAA
13840527 TATAATAAAAAATAAAACAATAAAA
1 TATAA-AAAAAATAAAACAATAAAA
13840552 TA
1 TA
13840554 AGAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
TATAAAAAAAATAAAACAATAAAA
Found at i:13840554 original size:33 final size:33
Alignment explanation
Indices: 13840507--13840576 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
13840497 ATATAGTATA
* *
13840507 AAAATAATATAATAATAAAATATAA-TAAAAAAT-
1 AAAACAATAAAATAA-AAAATA-AATTAAAAAATG
*
13840540 AAAACAATAAAATAAGAAATAAATTAAAAAATG
1 AAAACAATAAAATAAAAAATAAATTAAAAAATG
13840573 AAAA
1 AAAA
13840577 AAAGGAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 2 0.06
32 13 0.41
33 17 0.53
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.21
Consensus pattern (33 bp):
AAAACAATAAAATAAAAAATAAATTAAAAAATG
Found at i:13840562 original size:12 final size:12
Alignment explanation
Indices: 13840506--13840576 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
13840496 TATATAGTAT
*
13840506 AAAAATAATAT-
1 AAAAATAAAATA
*
13840517 AATAATAAAATA
1 AAAAATAAAATA
*
13840529 TAATAA-AAAATA
1 -AAAAATAAAATA
13840541 AAACAATAAAATA
1 AAA-AATAAAATA
* *
13840554 AGAAATAAATTA
1 AAAAATAAAATA
13840566 AAAAATGAAAA
1 AAAAAT-AAAA
13840577 AAAGGAATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
11 11 0.23
12 21 0.44
13 16 0.33
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:13842487 original size:67 final size:68
Alignment explanation
Indices: 13842394--13842569 Score: 227
Period size: 67 Copynumber: 2.6 Consensus size: 68
13842384 AAGTTAGTTG
* ** *
13842394 TTGGATTTTGGTTGATCCCGTGAAAAACCATTGTTG-TAGGTTGTGATTGAA-CCCTTGAAAAAC
1 TTGGGTTTTGGTTGATCTTGTGAAAAACCATTGTTGAAAGGTTGTGATT-AAGCCCTTGAAAAAC
13842457 CACT
65 CACT
* * * *
13842461 TTGGGTTTTGGTTGAGCTTGTGAAAAACCATTG-TGAAAGGTTGTGGTTAAGCCTTTGAAAAATC
1 TTGGGTTTTGGTTGATCTTGTGAAAAACCATTGTTGAAAGGTTGTGATTAAGCCCTTGAAAAACC
13842525 ACT
66 ACT
13842528 TTGGGTTTTGGTTGATCTTG-GTAAAAACCATTG-TGAAAGGTT
1 TTGGGTTTTGGTTGATCTTGTG-AAAAACCATTGTTGAAAGGTT
13842570 TTGGCTAAGC
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
66 5 0.05
67 92 0.95
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (68 bp):
TTGGGTTTTGGTTGATCTTGTGAAAAACCATTGTTGAAAGGTTGTGATTAAGCCCTTGAAAAACC
ACT
Found at i:13842490 original size:32 final size:32
Alignment explanation
Indices: 13842449--13842557 Score: 107
Period size: 32 Copynumber: 3.3 Consensus size: 32
13842439 ATTGAACCCT
13842449 TGAAAAACCACTTTGGGTTTTGGTTGAGCTTG
1 TGAAAAACCACTTTGGGTTTTGGTTGAGCTTG
* *
13842481 TGAAAAACCA-TTGTGAAAGGTTGTGGTTAAGCCTT-
1 TGAAAAACCACTT-TG---GGTTTTGGTTGAG-CTTG
* *
13842516 TGAAAAATCACTTTGGGTTTTGGTTGATCTTG
1 TGAAAAACCACTTTGGGTTTTGGTTGAGCTTG
13842548 -GTAAAAACCA
1 TG-AAAAACCA
13842558 TTGTGAAAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
31 6 0.10
32 29 0.47
35 22 0.35
36 5 0.08
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (32 bp):
TGAAAAACCACTTTGGGTTTTGGTTGAGCTTG
Found at i:13842520 original size:35 final size:33
Alignment explanation
Indices: 13842414--13842581 Score: 98
Period size: 35 Copynumber: 5.0 Consensus size: 33
13842404 GTTGATCCCG
* * *
13842414 TGAAAAACCATTGTTGTAGGTTGTGATTGAA-CCCT
1 TGAAAAACCATTG-TG-AGGTTTTGGTT-AAGCCTT
*
13842449 TGAAAAACCACTT-TG-GGTTTTGGTTGAG-CTT
1 TGAAAAACCA-TTGTGAGGTTTTGGTTAAGCCTT
*
13842480 GTGAAAAACCATTGTGAAAGGTTGTGGTTAAGCCTT
1 -TGAAAAACCATTGTG--AGGTTTTGGTTAAGCCTT
* * *
13842516 TGAAAAATCACTT-TG-GGTTTTGGTTGA-TCTT
1 TGAAAAACCA-TTGTGAGGTTTTGGTTAAGCCTT
* *
13842547 GGTAAAAACCATTGTGAAAGGTTTTGGCTAAGCCT
1 TG-AAAAACCATTGTG--AGGTTTTGGTTAAGCCT
13842582 AGTAAAAGCC
Statistics
Matches: 103, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
31 11 0.11
32 39 0.38
34 2 0.02
35 42 0.41
36 9 0.09
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (33 bp):
TGAAAAACCATTGTGAGGTTTTGGTTAAGCCTT
Found at i:13843397 original size:2 final size:2
Alignment explanation
Indices: 13843390--13843424 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13843380 AGCAAAGGAT
13843390 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13843425 GTTTTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13844399 original size:22 final size:23
Alignment explanation
Indices: 13844373--13844415 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
13844363 TAGGTCTCTA
13844373 ATTTATA-AAAAAAAATATAATT
1 ATTTATATAAAAAAAATATAATT
* *
13844395 ATTTATATTAAAAATATATAA
1 ATTTATATAAAAAAAATATAA
13844416 AAATTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTATATAAAAAAAATATAATT
Found at i:13847008 original size:19 final size:17
Alignment explanation
Indices: 13846967--13847010 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
13846957 AACTTTTAAC
13846967 ATATTCTTTAATAATATA
1 ATATT-TTTAATAATATA
13846985 A-ATTTTTAAATAATATA
1 ATATTTTT-AATAATATA
13847002 TATATTTTT
1 -ATATTTTT
13847011 TTATTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 2 0.09
19 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTTAATAATATA
Found at i:13849399 original size:28 final size:28
Alignment explanation
Indices: 13849337--13849537 Score: 278
Period size: 28 Copynumber: 7.0 Consensus size: 28
13849327 TCTGTATACA
* *
13849337 AAGACAAGTCCAATGGATGGAG-AGATG
1 AAGAAAAGGCCAATGGATGGAGAAGATG
13849364 AAGAAAAGGCCAATGGATGGAGAAGATG
1 AAGAAAAGGCCAATGGATGGAGAAGATG
13849392 AAGAAAAGGCCAATGGATGGAGAAGATG
1 AAGAAAAGGCCAATGGATGGAGAAGATG
13849420 AAGAAAAGGCCAATGGATGGAGAAGATG
1 AAGAAAAGGCCAATGGATGGAGAAGATG
13849448 AAGAAAAGGCCAATGGATGGAGAAGATG
1 AAGAAAAGGCCAATGGATGGAGAAGATG
* * * *
13849476 AAGACAAGTCCAATGTTATTTGCTATTGAGAGATG
1 AAGAAAAGGCCAATG-GA--TG-GA--GA-AGATG
13849511 AAGAAAAGGCCAATGGATGGAGAAGAT
1 AAGAAAAGGCCAATGGATGGAGAAGAT
13849538 CGGTCACGCC
Statistics
Matches: 156, Mismatches: 10, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
27 20 0.13
28 106 0.68
29 3 0.02
31 3 0.02
32 3 0.02
34 3 0.02
35 18 0.12
ACGTcount: A:0.44, C:0.08, G:0.33, T:0.15
Consensus pattern (28 bp):
AAGAAAAGGCCAATGGATGGAGAAGATG
Found at i:13849892 original size:26 final size:26
Alignment explanation
Indices: 13849843--13849893 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
13849833 AAATAGAATG
**
13849843 AAAATAAAATAATCGTTTTGATATAT
1 AAAATAAAATAATAATTTTGATATAT
13849869 AAAATAAAATAATAATTATT-ATATA
1 AAAATAAAATAATAATT-TTGATATA
13849894 ATTTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (26 bp):
AAAATAAAATAATAATTTTGATATAT
Found at i:13850718 original size:2 final size:2
Alignment explanation
Indices: 13850711--13850748 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13850701 NNNNNNNNNN
13850711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13850749 ATTGCAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13863859 original size:26 final size:26
Alignment explanation
Indices: 13863829--13863905 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 26
13863819 CAATAGACAT
* *
13863829 AATTATTTTTCAAATAAACATAACTG
1 AATTATTTTTCAAACAAACATAACCG
13863855 AATTATTTTTTAAATTCAAACAAACATAACCG
1 AATTA---TTT---TTCAAACAAACATAACCG
13863887 AATTATTTTTCAAACAAAC
1 AATTATTTTTCAAACAAAC
13863906 TTATCTGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
26 16 0.37
29 6 0.14
32 21 0.49
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (26 bp):
AATTATTTTTCAAACAAACATAACCG
Found at i:13864190 original size:33 final size:33
Alignment explanation
Indices: 13864132--13864227 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
13864122 ATTTGGGTAA
* * *
13864132 AATAAGCCTTTCTTCTTAACCGTTGACTAATAG
1 AATAAGCCATTCTCCCTAACCGTTGACTAATAG
* *
13864165 AATAAGCCCTTCTCCCTAACTGTTGACTAATAG
1 AATAAGCCATTCTCCCTAACCGTTGACTAATAG
*
13864198 AATAAGCCATTCTCGCTAACCGTTGACTAA
1 AATAAGCCATTCTCCCTAACCGTTGACTAA
13864228 CTTCTATTAG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (33 bp):
AATAAGCCATTCTCCCTAACCGTTGACTAATAG
Found at i:13878520 original size:24 final size:24
Alignment explanation
Indices: 13878492--13878550 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
13878482 TTTTTTAATA
13878492 ATCTTG-GTTATATAAAAGGAAATG
1 ATCTTGAG-TATATAAAAGGAAATG
* *
13878516 ATCTTGAGTATATAAGAGGAAATT
1 ATCTTGAGTATATAAAAGGAAATG
13878540 ATCTTGAGTAT
1 ATCTTGAGTAT
13878551 TTAGTCCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (24 bp):
ATCTTGAGTATATAAAAGGAAATG
Found at i:13882969 original size:21 final size:21
Alignment explanation
Indices: 13882945--13882996 Score: 50
Period size: 26 Copynumber: 2.2 Consensus size: 21
13882935 TCCAACAGAT
13882945 ATAATTATTTTTCAAACAAAC
1 ATAATTATTTTTCAAACAAAC
13882966 ATAACCGAATTATTTTTCAAACAAAC
1 AT-----AATTATTTTTCAAACAAAC
*
13882992 TTAAT
1 ATAAT
13882997 CGTTTTGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 10
0.69 0.03 0.28
Matches are distributed among these distances:
21 5 0.20
26 20 0.80
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAATTATTTTTCAAACAAAC
Found at i:13883716 original size:16 final size:16
Alignment explanation
Indices: 13883697--13883742 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
13883687 AACAATTCTT
*
13883697 ATTTGAAATGAATCGA
1 ATTTGAAAAGAATCGA
*
13883713 ATTTGAAAAGATTCGA
1 ATTTGAAAAGAATCGA
* *
13883729 ACTTGAAAACAATC
1 ATTTGAAAAGAATC
13883743 TTATTTAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (16 bp):
ATTTGAAAAGAATCGA
Found at i:13920549 original size:28 final size:27
Alignment explanation
Indices: 13920513--13920565 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
13920503 ATATCCTGGT
*
13920513 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
13920540 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
13920566 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:13920635 original size:20 final size:20
Alignment explanation
Indices: 13920610--13920655 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
13920600 CTTCTAAACC
13920610 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
* *
13920630 TCAAATTATACTCGAATAAG
1 TCAAATCATACTCCAATAAG
13920650 TCAAAT
1 TCAAAT
13920656 GGGGCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:13921766 original size:15 final size:14
Alignment explanation
Indices: 13921741--13921793 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
13921731 CTTGCTTGAA
*
13921741 TTTCTTTTCTTTTTTT
1 TTTC-TTTC-TTTTTC
13921757 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
*
13921771 TTTCTTACCTTTTTC
1 TTTCTT-TCTTTTTC
13921786 TTTCTTTC
1 TTTCTTTC
13921794 CATAAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 12 0.36
15 17 0.52
16 4 0.12
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTCTTTTTC
Found at i:13925800 original size:15 final size:15
Alignment explanation
Indices: 13925782--13925811 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13925772 GAAAAAGCAT
*
13925782 GAAAGGAAATTATTA
1 GAAAGGAAATCATTA
13925797 GAAAGGAAATCATTA
1 GAAAGGAAATCATTA
13925812 TTTAGGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.23
Consensus pattern (15 bp):
GAAAGGAAATCATTA
Found at i:13927199 original size:16 final size:17
Alignment explanation
Indices: 13927168--13927202 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13927158 GAATTTTTAT
13927168 TTTTAAAAAGATAAAAA
1 TTTTAAAAAGATAAAAA
*
13927185 TTTTAAAAATA-AAAAA
1 TTTTAAAAAGATAAAAA
13927201 TT
1 TT
13927203 ATAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TTTTAAAAAGATAAAAA
Found at i:13932852 original size:32 final size:32
Alignment explanation
Indices: 13932768--13932859 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
13932758 TCATAAATGT
* * *
13932768 CCAAGGTGTAATGGGGTTAAAACATTACCAAC
1 CCAAGGTGCAATGGGGTTTAAACATTGCCAAC
*
13932800 TCAA-G-GCATACTGGGGTTTAAACATTGCCAAC
1 CCAAGGTGCA-A-TGGGGTTTAAACATTGCCAAC
*
13932832 CCAAGGTGCAATGGGATTTAAACATTGC
1 CCAAGGTGCAATGGGGTTTAAACATTGC
13932860 TGGTTCAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
30 2 0.04
31 2 0.04
32 41 0.82
33 2 0.04
34 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (32 bp):
CCAAGGTGCAATGGGGTTTAAACATTGCCAAC
Found at i:13944158 original size:30 final size:30
Alignment explanation
Indices: 13944122--13944182 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
13944112 ATACAAATAG
13944122 GGAAAACAATATCTACT-GTTTCATGCTTTT
1 GGAAAACAATATCTACTGGTTT-ATGCTTTT
*
13944152 GGAAAACAATGTCTACTGGTTTATGCTTTT
1 GGAAAACAATATCTACTGGTTTATGCTTTT
13944182 G
1 G
13944183 CTATGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (30 bp):
GGAAAACAATATCTACTGGTTTATGCTTTT
Found at i:13946299 original size:60 final size:59
Alignment explanation
Indices: 13946227--13946347 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 59
13946217 ATTTATTTGT
* * * *
13946227 TAAAAGATAAAAATATTCTAAGTAATAAATTCAAAATACGTTTTATTATAATTAAATAA
1 TAAAAGATAAAAATATTCTAAGTAATAAAATCAAAATACCTTATACTATAATTAAATAA
13946286 TNAAAAGATAAAAATATTCTAAGTAATAAAATCAAAATACCTTATACTATAATTAAATAA
1 T-AAAAGATAAAAATATTCTAAGTAATAAAATCAAAATACCTTATACTATAATTAAATAA
13946346 TA
1 TA
13946348 TTTTCACCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
59 2 0.04
60 55 0.96
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (59 bp):
TAAAAGATAAAAATATTCTAAGTAATAAAATCAAAATACCTTATACTATAATTAAATAA
Found at i:13946410 original size:23 final size:22
Alignment explanation
Indices: 13946367--13946410 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
13946357 AAATACAAAC
* **
13946367 ATATTTTCATTATAATTTAATA
1 ATATTTTCATTAGAAGATAATA
13946389 ATATTTTACATTAGAAGATAAT
1 ATATTTT-CATTAGAAGATAAT
13946411 TAACCTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (22 bp):
ATATTTTCATTAGAAGATAATA
Found at i:13946542 original size:45 final size:49
Alignment explanation
Indices: 13946489--13946594 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 49
13946479 ATAAATGTAC
* *
13946489 TAAATAATATTCTTTTTTACATTTATTATA-TTCAAAT-A-A-TA-ATAT
1 TAAATAATATTCTTTATAACATTTATTATAGTT-AAATCATATTATATAT
*
13946534 TAAATAATATTCTTTATAATATTTATTATAGTTAAATCATATTTATATAT
1 TAAATAATATTCTTTATAACATTTATTATAGTTAAATCATA-TTATATAT
13946584 TAAATAATATT
1 TAAATAATATT
13946595 TAAATATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 31 0.60
46 3 0.06
47 1 0.02
49 2 0.04
50 15 0.29
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (49 bp):
TAAATAATATTCTTTATAACATTTATTATAGTTAAATCATATTATATAT
Found at i:13946588 original size:18 final size:18
Alignment explanation
Indices: 13946549--13946602 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
13946539 AATATTCTTT
13946549 ATAATATTTATTATAGTTAA
1 ATAATATTTA-TATA-TTAA
*
13946569 ATCATATTTATATATTAA
1 ATAATATTTATATATTAA
*
13946587 ATAATATTTAAATATT
1 ATAATATTTATATATT
13946603 TTCATTTCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 18 0.58
19 4 0.13
20 9 0.29
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATAATATTTATATATTAA
Found at i:13947730 original size:68 final size:66
Alignment explanation
Indices: 13947604--13947784 Score: 202
Period size: 67 Copynumber: 2.7 Consensus size: 66
13947594 GAATGCAACC
* * * *
13947604 ATGCTAGGTATATGATGT-AATCCCATATACCATATGAGATGATTAAACATGCATGATAAATGCC
1 ATGCTA-GTATATGATGTAAATTCCATATACCACATGAGATGA-TAAACATACATGATAAATGAC
13947668 ATG
64 ATG
* * *
13947671 ATGCTATGTATATGATGTAAATTCCATATGCCACATGAGATGATAAATAGTACATGATAAATGAT
1 ATGCTA-GTATATGATGTAAATTCCATATACCACATGAGATGATAAACA-TACATGATAAATGAC
13947736 ATG
64 ATG
* * * * * *
13947739 ATGCTAGTATGTCAAGTAGATTCCACATAACACATGAGATGATAAA
1 ATGCTAGTATATGATGTAAATTCCATATACCACATGAGATGATAAA
13947785 GAATACTTAT
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 55 0.57
68 42 0.43
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (66 bp):
ATGCTAGTATATGATGTAAATTCCATATACCACATGAGATGATAAACATACATGATAAATGACAT
G
Found at i:13949567 original size:16 final size:17
Alignment explanation
Indices: 13949535--13949570 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
13949525 TTATTATGGC
13949535 TATTTAATTCTCTTTTT
1 TATTTAATTCTCTTTTT
*
13949552 TATTTTATTC-CTTTTT
1 TATTTAATTCTCTTTTT
13949568 TAT
1 TAT
13949571 GCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTAATTCTCTTTTT
Found at i:13951202 original size:19 final size:19
Alignment explanation
Indices: 13951178--13951217 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
13951168 AAAAATAATA
*
13951178 CATATATGTTTGTATTTAG
1 CATATATGTTTGTATCTAG
13951197 CATATATGTTTGTATCTAG
1 CATATATGTTTGTATCTAG
13951216 CA
1 CA
13951218 AATTGTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (19 bp):
CATATATGTTTGTATCTAG
Found at i:13955602 original size:27 final size:24
Alignment explanation
Indices: 13955543--13955594 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
13955533 TATTCGATAT
* *
13955543 ATATGATATGTATGAATCACAATC
1 ATATGATATATATGAATAACAATC
13955567 ATAT-ATATATATGATATAACAATC
1 ATATGATATATATGA-ATAACAATC
13955591 ATAT
1 ATAT
13955595 TCGATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (24 bp):
ATATGATATATATGAATAACAATC
Found at i:13956839 original size:14 final size:14
Alignment explanation
Indices: 13956789--13956842 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
13956779 AATTAAACCG
13956789 AGTTCGGTTAGTTC
1 AGTTCGGTTAGTTC
* *
13956803 AGATCGATTAGTTC
1 AGTTCGGTTAGTTC
13956817 AAAGTTCGGTTAGTTC
1 --AGTTCGGTTAGTTC
*
13956833 GGTTCGGTTA
1 AGTTCGGTTA
13956843 TTTCGGTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 21 0.64
16 12 0.36
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (14 bp):
AGTTCGGTTAGTTC
Found at i:13956847 original size:14 final size:14
Alignment explanation
Indices: 13956790--13956850 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
13956780 ATTAAACCGA
*
13956790 GTTCGGTTAGTTCA
1 GTTCGGTTAGTTCG
* * *
13956804 GATCGATTAGTTCAAA
1 GTTCGGTTAGTTC--G
13956820 GTTCGGTTAGTTCG
1 GTTCGGTTAGTTCG
*
13956834 GTTCGGTTATTTCG
1 GTTCGGTTAGTTCG
13956848 GTT
1 GTT
13956851 AATGAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 27 0.69
16 12 0.31
ACGTcount: A:0.16, C:0.13, G:0.28, T:0.43
Consensus pattern (14 bp):
GTTCGGTTAGTTCG
Found at i:13969888 original size:28 final size:29
Alignment explanation
Indices: 13969847--13969906 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
13969837 GTCTATGGGC
*
13969847 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
13969875 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
13969905 AA
1 AA
13969907 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:13980789 original size:15 final size:15
Alignment explanation
Indices: 13980769--13980803 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13980759 GAATAACAAC
13980769 ATAAAGAAACTGAAA
1 ATAAAGAAACTGAAA
* *
13980784 ATAAAGAAATTGAAT
1 ATAAAGAAACTGAAA
13980799 ATAAA
1 ATAAA
13980804 TAATTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (15 bp):
ATAAAGAAACTGAAA
Found at i:13987478 original size:2 final size:2
Alignment explanation
Indices: 13987413--13987459 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
13987403 TTGAGTCATG
13987413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13987455 TA TA T
1 TA TA T
13987460 CATAATATNC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13990783 original size:298 final size:297
Alignment explanation
Indices: 13990196--13990794 Score: 722
Period size: 298 Copynumber: 2.0 Consensus size: 297
13990186 TCAACTTGAG
* * * *
13990196 TGGCTCGTGAGCTTTATCGAACTTTTGAAATGTTATTAATATTTAATATTTTATTTATGTACAAA
1 TGGCTCGTAAGCTTTATCGAACTTTTGAAATGTTATTAATATCTAATATTTTATTCATATACAAA
* ** *
13990261 TAAAAAATTATATTTATTTACATATTTTCAACTTTTATTTGAGTTTTAACTTCAAGCTTGAGCTC
66 TAAAAAATTATATTTATTTACATATTTTCAACTTTTATTTGAGTATTAACTTCAAGCTCAAGCAC
** * **
13990326 GAGTTTTGAGCTCCTTACTCCAGCTGATGATAATTGAGCCTAATCGGTTGAGATTGTACAAAAAT
131 GAGTTTCAAGCTCCTTACTCAAGCTGATGATAATTGAGCCTAATAAGTTGAGATTGTACAAAAAT
* ** * *
13990391 TAAAGCTTAATCAAGTTCAAGTTGGGCTCAAGCCTCAAGTTATTTAATTGAGCAGAGCTCAAGCT
196 TAAAGCTCAATCAAGTTCAAGCAGGGCTCAAGCCTCAAGTTATTTAATCGAGCAGAGCTCAAGCC
* * *
13990456 TGGCACTATATTGGCTTGGCTTTTTTACACCATTTAGT
261 TGGCACTATATTGGATTGGCTTGTTTACACC-CTTAGT
* * *
13990494 TGGCTCGTAAGCTTTATTGAACTTTTGAATTGTTATTAATA-CTAATATTTTATTCGTATAC-AA
1 TGGCTCGTAAGCTTTATCGAACTTTTGAAATGTTATTAATATCTAATATTTTATTCATATACAAA
* * * * *
13990557 -AAAATATTATATTTATTTGCATATTTTCAAGTTTTATTTGAGTATTGAGTTCAAGCTCAAGCAC
66 TAAAAAATTATATTTATTTACATATTTTCAACTTTTATTTGAGTATTAACTTCAAGCTCAAGCAC
* * * * *
13990621 GGGTTTCAAGTTCCTTACTCAAGTTGATGATAATTGAGCCTAATAAAGTTGAGCTTGAGTGCAAA
131 GAGTTTCAAGCTCCTTACTCAAGCTGATGATAATTGAGCCTAAT-AAGTTGAGATT--GTACAAA
* * * ** *
13990686 AATTAAAGCTCGATCGAGTTTAAGCAGGGCTTGAGCCTCAAGGTT-TTTAATCGAGCCA-AGCTT
193 AATTAAAGCTCAATCAAGTTCAAGCAGGGCTCAAGCCTCAA-GTTATTTAATCGAG-CAGAGCTC
* * *
13990749 GAGCCTGGCATTGTATTGGATTGGCTTGTTTACACCCTTAGT
256 AAGCCTGGCACTATATTGGATTGGCTTGTTTACACCCTTAGT
13990791 TGGC
1 TGGC
13990795 ATATGCAATA
Statistics
Matches: 253, Mismatches: 43, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
295 93 0.37
296 10 0.04
297 25 0.10
298 120 0.47
299 5 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (297 bp):
TGGCTCGTAAGCTTTATCGAACTTTTGAAATGTTATTAATATCTAATATTTTATTCATATACAAA
TAAAAAATTATATTTATTTACATATTTTCAACTTTTATTTGAGTATTAACTTCAAGCTCAAGCAC
GAGTTTCAAGCTCCTTACTCAAGCTGATGATAATTGAGCCTAATAAGTTGAGATTGTACAAAAAT
TAAAGCTCAATCAAGTTCAAGCAGGGCTCAAGCCTCAAGTTATTTAATCGAGCAGAGCTCAAGCC
TGGCACTATATTGGATTGGCTTGTTTACACCCTTAGT
Found at i:13992836 original size:18 final size:18
Alignment explanation
Indices: 13992813--13992847 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13992803 AAAACATAGG
13992813 ACACTAATCTGATGGACT
1 ACACTAATCTGATGGACT
13992831 ACACTAATCTGATGGAC
1 ACACTAATCTGATGGAC
13992848 AGTAATTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (18 bp):
ACACTAATCTGATGGACT
Found at i:13996884 original size:18 final size:18
Alignment explanation
Indices: 13996852--13996910 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
13996842 ACATATGAGA
*
13996852 AAATAAAATAGAAATAAAT
1 AAAT-AAATAAAAATAAAT
13996871 AAATAAATAAAAAT-AAT
1 AAATAAATAAAAATAAAT
* *
13996888 AATATAAATTAAAAGAAA-
1 AA-ATAAATAAAAATAAAT
13996906 AAATA
1 AAATA
13996911 TAAAAACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 8 0.23
18 21 0.60
19 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAAATAAAT
Found at i:13997042 original size:21 final size:22
Alignment explanation
Indices: 13997012--13997052 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13997002 GGGGGGGGCT
*
13997012 ATTAAGAAAATT-TATAAAAAA
1 ATTAAAAAAATTATATAAAAAA
13997033 ATTAAAAAAATTATATAAAA
1 ATTAAAAAAATTATATAAAA
13997053 CGAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
ATTAAAAAAATTATATAAAAAA
Found at i:14001979 original size:2 final size:2
Alignment explanation
Indices: 14001972--14002008 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
14001962 TTATTTACGC
* *
14001972 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14002009 TTGAGTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14006842 original size:20 final size:20
Alignment explanation
Indices: 14006817--14006862 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
14006807 TTTTGACCCC
14006817 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
14006837 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
14006857 ATTTGA
1 ATTTGA
14006863 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:14018888 original size:3 final size:3
Alignment explanation
Indices: 14018880--14018948 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
14018870 TAAATATTTA
14018880 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14018928 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
14018949 TTCTCTACCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:14020388 original size:25 final size:25
Alignment explanation
Indices: 14020360--14020407 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
14020350 AGTGTCTCTC
14020360 ACACTCTAAGTAAACAAGAAATAAG
1 ACACTCTAAGTAAACAAGAAATAAG
14020385 ACACTCTAAGTAAACAAGAAATA
1 ACACTCTAAGTAAACAAGAAATA
14020408 GATAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (25 bp):
ACACTCTAAGTAAACAAGAAATAAG
Found at i:14021588 original size:30 final size:29
Alignment explanation
Indices: 14021522--14021577 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
14021512 AAAGCTTTAT
14021522 AATATCCACAATAGCTAAACAAGATATAC
1 AATATCCACAATAGCTAAACAAGATATAC
* *
14021551 AATATCCA-AGTAGCTAAGCAAGATATA
1 AATATCCACAATAGCTAAACAAGATATA
14021578 TTGAATATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (29 bp):
AATATCCACAATAGCTAAACAAGATATAC
Found at i:14022295 original size:19 final size:20
Alignment explanation
Indices: 14022258--14022295 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
14022248 TATTCTTAAT
14022258 TGATTAAAATATGCTTCAAG
1 TGATTAAAATATGCTTCAAG
14022278 TGATTACAAA-AT-CTTCAA
1 TGATTA-AAATATGCTTCAA
14022296 ATTTGGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
TGATTAAAATATGCTTCAAG
Found at i:14027654 original size:162 final size:163
Alignment explanation
Indices: 14027384--14027709 Score: 548
Period size: 162 Copynumber: 2.0 Consensus size: 163
14027374 TAGTTGAAAA
*
14027384 TAAATAATTATGCATGCAAATCGAAAAAACAAAATAAATCGGACATACTTGATCATACCTCTTCT
1 TAAATAATTATGCATGCAAATCGAAAAAACAAAATAAATCGGACATACTTGATCATACCTCATCT
*
14027449 ATACAATATGCACATAGAAAATAAAGAAAAGTGTATTCTATCAAATATTAAATCAATATACAGAT
66 ATACAATATGCACATAGAAAATAAAGAAAAGTGTATCCTATCAAATATTAAATCAATATACAGAT
*
14027514 CCTGAAGTTATAAAGAGTTGCACCTTTGATAGC
131 ACTGAAGTTATAAAGAGTTGCACCTTTGATAGC
* * * * *
14027547 TAAATAATTATGTATGCAAATC-AAAAAATAAAATAAATTGGGCATACTTGATCATGCCTCATCT
1 TAAATAATTATGCATGCAAATCGAAAAAACAAAATAAATCGGACATACTTGATCATACCTCATCT
14027611 ATACAATATGCACATAGAAAAT-AAGAAAAAGTGTATCCTATCAAATATTAAATCAATATACAGA
66 ATACAATATGCACATAGAAAATAAAG-AAAAGTGTATCCTATCAAATATTAAATCAATATACAGA
*
14027675 TACTGAAGTTATAAAGAGTTGTACCTTTGATAGC
130 TACTGAAGTTATAAAGAGTTGCACCTTTGATAGC
14027709 T
1 T
14027710 GAAAACTGAG
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
161 3 0.02
162 129 0.84
163 21 0.14
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (163 bp):
TAAATAATTATGCATGCAAATCGAAAAAACAAAATAAATCGGACATACTTGATCATACCTCATCT
ATACAATATGCACATAGAAAATAAAGAAAAGTGTATCCTATCAAATATTAAATCAATATACAGAT
ACTGAAGTTATAAAGAGTTGCACCTTTGATAGC
Found at i:14029252 original size:102 final size:102
Alignment explanation
Indices: 14029076--14029273 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
14029066 CATTAGGTGC
*
14029076 CTGAATGTTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATTTAAGCA
1 CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATTTAAGCA
* * * *
14029141 TTGCGTGACAGGTAGTATGTGACTGAATATTACCTAA
66 TTACGTGACAAGCAGTACGTGACTGAATATTACCTAA
* *
14029178 CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTATGTGACTGAATAT-TTGTTAGC
1 CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATT-TAAGC
* *
14029242 GTTACGTGACAAGCATTACGTGACTGAATATT
65 ATTACGTGACAAGCAGTACGTGACTGAATATT
14029274 TATTGAGCAT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 2 0.02
102 84 0.98
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (102 bp):
CTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATTTAAGCA
TTACGTGACAAGCAGTACGTGACTGAATATTACCTAA
Found at i:14029920 original size:30 final size:30
Alignment explanation
Indices: 14029884--14029944 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
14029874 AAGAGATGCC
14029884 CTTGAGTGTGAGGGACCAGTTGCACATATT
1 CTTGAGTGTGAGGGACCAGTTGCACATATT
14029914 CTTGAGTGTGAGGGACCAGTTGCACATATT
1 CTTGAGTGTGAGGGACCAGTTGCACATATT
14029944 C
1 C
14029945 CAGCAGGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (30 bp):
CTTGAGTGTGAGGGACCAGTTGCACATATT
Found at i:14030815 original size:111 final size:111
Alignment explanation
Indices: 14030584--14030978 Score: 538
Period size: 111 Copynumber: 3.5 Consensus size: 111
14030574 AGTGCGTGAC
* * *
14030584 TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCAGTGCATGAC
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTGCATGAC
* * * * *
14030649 TGGTTTTTATATATTACGTTACTTGTTGTAGCGAGAGTGGTGGTGCA
65 TTGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
* *
14030696 TGACTTGTGTAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCATGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCATGACT
* * *
14030761 TGTTTTTATATATTGCCTTACCTATTGTAGCGTGAGTGGTGGCGCG
66 TGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
* * *
14030807 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAGTAGTTTTTTAGGCTTACGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCATGACT
* * * *
14030872 TGTTTTTATATATTGCGTGACCTGTTGTTATGTATTACGAAAGTGGTGACACG
66 TGTTTTTATATATTGCGTTACCTGTTG-TA-G-----CGAGAGTGGTGGCGCG
14030925 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGG
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGG
14030979 ATTACGTTAC
Statistics
Matches: 252, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
111 131 0.52
112 55 0.22
113 1 0.00
118 65 0.26
ACGTcount: A:0.18, C:0.11, G:0.26, T:0.45
Consensus pattern (111 bp):
TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCATGACT
TGTTTTTATATATTGCGTTACCTGTTGTAGCGAGAGTGGTGGCGCG
Found at i:14030890 original size:22 final size:22
Alignment explanation
Indices: 14030865--14030907 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
14030855 TTTAGGCTTA
* *
14030865 CGTGACTTGTTTTTATATATTG
1 CGTGACCTGTTGTTATATATTG
*
14030887 CGTGACCTGTTGTTATGTATT
1 CGTGACCTGTTGTTATATATT
14030908 ACGAAAGTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.21, T:0.51
Consensus pattern (22 bp):
CGTGACCTGTTGTTATATATTG
Found at i:14030958 original size:118 final size:117
Alignment explanation
Indices: 14030584--14031088 Score: 532
Period size: 111 Copynumber: 4.4 Consensus size: 117
14030574 AGTGCGTGAC
* * * * *
14030584 TGACTTGTGCAATTCATGTGTTGTTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCAGTGCATGAC
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGC-TTACGTGAC
* * * * * * *
14030649 TGGTTTTTATATATTACGTTA-C--TTG-T-TGTA-GCGAGAGTGGTGGTGCA
65 TTGTTTTTATATATTGCATGACCTGTTGTTATGTATTCGAGAGTGGTGGCGCG
* * * *
14030696 TGACTTGTGTAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCATGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTACGTGACT
* * * *
14030761 TGTTTTTATATATTGCCTTACCTATTG-TA-G----CGTGAGTGGTGGCGCG
66 TGTTTTTATATATTGCATGACCTGTTGTTATGTATTCGAGAGTGGTGGCGCG
*
14030807 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAGTAGTTTTTTAGGCTTACGTGACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTACGTGACT
* * * *
14030872 TGTTTTTATATATTGCGTGACCTGTTGTTATGTATTACGAAAGTGGTGACACG
66 TGTTTTTATATATTGCATGACCTGTTGTTATGTATT-CGAGAGTGGTGGCGCG
* *
14030925 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGATTACGTTACT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTACGTGACT
* * * * * * *
14030990 AG-TTTTATAGATTACATGACCTGCTGTTATATATTGCGAGAGTAGTGGCGTG
66 TGTTTTTATATATTGCATGACCTGTTGTTATGTATT-CGAGAGTGGTGGCGCG
** * * * *
14031042 TGACTTGTGCAATTCACCTCTTGTTTAGGGGCGTTTGTTCACTAGTT
1 TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTT
14031089 ATTAGGCATT
Statistics
Matches: 340, Mismatches: 42, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
111 123 0.36
112 56 0.16
113 1 0.00
114 5 0.01
117 80 0.24
118 75 0.22
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.44
Consensus pattern (117 bp):
TGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTACGTGACT
TGTTTTTATATATTGCATGACCTGTTGTTATGTATTCGAGAGTGGTGGCGCG
Found at i:14040813 original size:23 final size:23
Alignment explanation
Indices: 14040787--14040841 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
14040777 TTAGTGACAC
*
14040787 GATTCCATATTAACAACTGACGT
1 GATTCCATATTAACAACTCACGT
* * * **
14040810 GATTCAAAATTTAGTACTCACGT
1 GATTCCATATTAACAACTCACGT
14040833 GATTCCATA
1 GATTCCATA
14040842 ACAAATACTC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
GATTCCATATTAACAACTCACGT
Found at i:14041147 original size:26 final size:26
Alignment explanation
Indices: 14041115--14041167 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
14041105 ATGAATGAAT
*
14041115 ACAAAGAATAATATGTAAATAATACA
1 ACAAAGAATAATATGGAAATAATACA
*
14041141 ACAAAGAATAATATGGAAATGATACA
1 ACAAAGAATAATATGGAAATAATACA
14041167 A
1 A
14041168 ATAATGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (26 bp):
ACAAAGAATAATATGGAAATAATACA
Found at i:14044754 original size:23 final size:23
Alignment explanation
Indices: 14044728--14044772 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
14044718 CGTACAATTT
14044728 CCTACAACAA-TAGTCACGCAATG
1 CCTA-AACAATTAGTCACGCAATG
* *
14044751 CCTAATCAATTAGTCATGCAAT
1 CCTAAACAATTAGTCACGCAAT
14044773 TACTAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (23 bp):
CCTAAACAATTAGTCACGCAATG
Found at i:14047460 original size:24 final size:24
Alignment explanation
Indices: 14047432--14047551 Score: 95
Period size: 24 Copynumber: 5.1 Consensus size: 24
14047422 TTTGCATGTT
*
14047432 ACACGTCATATACAAAAATCTGTG
1 ACACGTCATATACAAAAACCTGTG
14047456 ACACGTCATATACAAAAACCTGTG
1 ACACGTCATATACAAAAACCTGTG
* * * * * *
14047480 ACAAGCCATGGT----TAGCGTGTG
1 ACACGTCAT-ATACAAAAACCTGTG
* *
14047501 ACACGTCATGTACAAAAACATGTG
1 ACACGTCATATACAAAAACCTGTG
* * *
14047525 ACAGGCCATGTACAAAAACCTGTG
1 ACACGTCATATACAAAAACCTGTG
14047549 ACA
1 ACA
14047552 AGCCATGGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.03
21 13 0.17
24 60 0.79
25 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (24 bp):
ACACGTCATATACAAAAACCTGTG
Found at i:14047505 original size:69 final size:69
Alignment explanation
Indices: 14047387--14047756 Score: 367
Period size: 69 Copynumber: 5.4 Consensus size: 69
14047377 CTATGATGTT
* * * * *
14047387 ACACGTCATGTACAAAAATCTGTGACAAGTCATGGTTTGCATGTTACACGTCATATACAAAAATC
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAAAAATC
14047452 TGTG
66 TGTG
* * * *
14047456 ACACGTCATATACAAAAACCTGTGACAAGCCATGGTTAGCGTGTGACACGTCATGTACAAAAA-C
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAAAAATC
14047520 ATGTG
66 -TGTG
* * *
14047525 ACAGGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGCCATGTACAAAAATA
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAAAAATC
14047590 TGTG
66 TGTG
* * * * * * * * *
14047594 ACACGCCATATATAAAAACTTGTGACACA-CCAT-GTACAAAAACCTGTAACAAGCCAT-T---A
1 ACACGCCATGTACAAAAACCTGTGACA-AGCCATGGT----TAGCATGTTACACGTCATGTACAA
** *
14047653 TTAGCGTGTG
61 AAATC-TGTG
* * * *
14047663 ACACGCCATGTATAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGTCATGTATAAAAACC
1 ACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAAAAATC
14047728 TGTG
66 TGTG
*
14047732 ACACGCCATGTACAAAAACTTGTGA
1 ACACGCCATGTACAAAAACCTGTGA
14047757 AACTTCAAAT
Statistics
Matches: 247, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
66 12 0.05
67 1 0.00
68 6 0.02
69 208 0.84
70 6 0.02
71 1 0.00
72 13 0.05
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (69 bp):
ACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAAAAATC
TGTG
Found at i:14047568 original size:45 final size:45
Alignment explanation
Indices: 14047519--14047741 Score: 232
Period size: 45 Copynumber: 4.9 Consensus size: 45
14047509 TGTACAAAAA
* *
14047519 CATGTGACAGGCCATGTACAAAAACCTGTGACAAGCCATGGTTAG
1 CATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAG
* ** * *
14047564 CATGTTACACGCCATGTACAAAAATATGTGACACGCCAT-ATATAAAAA
1 CATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGAT-T---AG
* * * *
14047612 CTTGTGACACACCATGTACAAAAACCTGTAACAAGCCATTATTAG
1 CATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAG
* * *
14047657 CGTGTGACACGCCATGTATAAAAACCTGTGACAAGCCATGGTTAG
1 CATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAG
* * * * *
14047702 CGTGTTACACGTCATGTATAAAAACCTGTGACACGCCATG
1 CATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATG
14047742 TACAAAAACT
Statistics
Matches: 149, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
44 1 0.01
45 112 0.75
48 34 0.23
49 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (45 bp):
CATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAG
Found at i:14047594 original size:93 final size:93
Alignment explanation
Indices: 14047497--14047695 Score: 263
Period size: 93 Copynumber: 2.1 Consensus size: 93
14047487 ATGGTTAGCG
* * ** * *
14047497 TGTGACACGTCATGTACAAAAACATGTGACAGGCCATGTACAAAAACCTGTGACAAGCCATGGTT
1 TGTGACACGCCATATACAAAAACATGTGACACACCATGTACAAAAACCTGTAACAAGCCATGATT
* *
14047562 AGCATGTTACACGCCATGTACAAAAATA
66 AGCATGTGACACGCCATGTACAAAAACA
* * *
14047590 TGTGACACGCCATATATAAAAACTTGTGACACACCATGTACAAAAACCTGTAACAAGCCATTATT
1 TGTGACACGCCATATACAAAAACATGTGACACACCATGTACAAAAACCTGTAACAAGCCATGATT
* * *
14047655 AGCGTGTGACACGCCATGTATAAAAACC
66 AGCATGTGACACGCCATGTACAAAAACA
*
14047683 TGTGACAAGCCAT
1 TGTGACACGCCAT
14047696 GGTTAGCGTG
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (93 bp):
TGTGACACGCCATATACAAAAACATGTGACACACCATGTACAAAAACCTGTAACAAGCCATGATT
AGCATGTGACACGCCATGTACAAAAACA
Found at i:14047663 original size:138 final size:137
Alignment explanation
Indices: 14047382--14047756 Score: 425
Period size: 138 Copynumber: 2.7 Consensus size: 137
14047372 ACATGCTATG
* * * * * *
14047382 ATGTTACACGTCATGTACAAAAATCTGTGACAAGTCATGGTTTGCATGTTACACGTCATATACAA
1 ATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAA
* * * * * * * *
14047447 AAATCTGTGACACGTCATATACAAAAACCTGTGACAAGCCATGGTTAGCGTGTGACACGTCATGT
66 AAATCTGTGACACGCCATATACAAAAACTTGTGACAAGCCATGGTAAACCTGTAACAAGCCATGT
14047512 ACAAAAAC
131 A-AAAAAC
* *
14047520 ATGTGACAGGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGCCATGTACAA
1 ATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAA
* *
14047585 AAATATGTGACACGCCATATATAAAAACTTGTGACACA-CCAT-GTACAAAAACCTGTAACAAGC
66 AAATCTGTGACACGCCATATACAAAAACTTGTGACA-AGCCATGGT----AAACCTGTAACAAGC
** *
14047648 CAT-T-ATTAGC
126 CATGTAAAAAAC
* * * *
14047658 GTGTGACACGCCATGTATAAAAACCTGTGACAAGCCATGGTTAGCGTGTTACACGTCATGTATAA
1 ATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAA
* *
14047723 AAACCTGTGACACGCCATGTACAAAAACTTGTGA
66 AAATCTGTGACACGCCATATACAAAAACTTGTGA
14047757 AACTTCAAAT
Statistics
Matches: 201, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
137 2 0.01
138 185 0.92
139 1 0.00
140 1 0.00
141 12 0.06
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (137 bp):
ATGTGACACGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGCATGTTACACGTCATGTACAA
AAATCTGTGACACGCCATATACAAAAACTTGTGACAAGCCATGGTAAACCTGTAACAAGCCATGT
AAAAAAC
Found at i:14052710 original size:25 final size:27
Alignment explanation
Indices: 14052664--14052721 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
14052654 AGTCATATAT
*
14052664 ATCATCATGCTATATTAGCATGTC-AC
1 ATCATCATGCTATATTAACATGTCAAC
14052690 ATCATCAT-CTAT-TATAACATGTCAAC
1 ATCATCATGCTATAT-TAACATGTCAAC
14052716 AT-ATCA
1 ATCATCA
14052722 CATTAGCGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.03
25 16 0.55
26 12 0.41
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (27 bp):
ATCATCATGCTATATTAACATGTCAAC
Found at i:14055413 original size:12 final size:11
Alignment explanation
Indices: 14055394--14055423 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
14055384 TTCTTTTTCA
14055394 TTTTTTTTTAT
1 TTTTTTTTTAT
14055405 TTTTATTTTTAT
1 TTTT-TTTTTAT
14055417 TTTTTTT
1 TTTTTTT
14055424 GTTGGGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:14059945 original size:29 final size:29
Alignment explanation
Indices: 14059899--14059958 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
14059889 TTTTCAGCAA
*
14059899 CTTGTTTTATGTCTTAGTGTATGTTTGGT
1 CTTGTTTTATGTCCTAGTGTATGTTTGGT
14059928 CTTGTTTTATGTCCTAGTGTATGTTTGGT
1 CTTGTTTTATGTCCTAGTGTATGTTTGGT
14059957 CT
1 CT
14059959 AACTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.57
Consensus pattern (29 bp):
CTTGTTTTATGTCCTAGTGTATGTTTGGT
Found at i:14060241 original size:18 final size:20
Alignment explanation
Indices: 14060218--14060259 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
14060208 CTTTTTTATG
*
14060218 ATAATTT-TAACAAAAA-TT
1 ATAATTTATAAAAAAAACTT
14060236 ATAATTTATAAAAAAAACTT
1 ATAATTTATAAAAAAAACTT
14060256 ATAA
1 ATAA
14060260 AAAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATTTATAAAAAAAACTT
Found at i:14060266 original size:14 final size:13
Alignment explanation
Indices: 14060241--14060265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14060231 AAATTATAAT
14060241 TTATAAAAAAAAC
1 TTATAAAAAAAAC
14060254 TTATAAAAAAAA
1 TTATAAAAAAAA
14060266 ATTTATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TTATAAAAAAAAC
Done.