Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 45 of 143
Found at i:14204672 original size:17 final size:17
Alignment explanation
Indices: 14204652--14204688 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
14204642 TTAAATTTAT
14204652 TTTGAATTCAATTTAAA
1 TTTGAATTCAATTTAAA
*
14204669 TTTGAATTTAATTTAAA
1 TTTGAATTCAATTTAAA
14204686 TTT
1 TTT
14204689 AACATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTGAATTCAATTTAAA
Found at i:14204708 original size:6 final size:6
Alignment explanation
Indices: 14204625--14204690 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
14204615 CATTTTGAAA
* * * * *
14204625 TTAAAT TT-ATT TTAATT TTAAAT TT-ATT TTGAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
14204670 TTGAAT TT-AAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
14204691 CATTATTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 17 0.35
6 32 0.65
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:14206182 original size:30 final size:30
Alignment explanation
Indices: 14206148--14206399 Score: 405
Period size: 30 Copynumber: 8.4 Consensus size: 30
14206138 AACTATCTAG
*
14206148 AAATTATATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
*
14206178 AAATTACATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
* *
14206208 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
*
14206238 AAATTACATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
* * *
14206268 AAATTATATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
14206298 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
* *
14206328 AAATTACATTTTAACCCTAAAAATTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
*
14206358 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCA
14206388 AAATTACATTTT
1 AAATTACATTTT
14206400 TGACCCCGGT
Statistics
Matches: 204, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 204 1.00
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.37
Consensus pattern (30 bp):
AAATTACATTTTAACCCCAAAACTTTTCCA
Found at i:14206428 original size:60 final size:57
Alignment explanation
Indices: 14206148--14206516 Score: 352
Period size: 60 Copynumber: 6.2 Consensus size: 57
14206138 AACTATCTAG
* * *
14206148 AAATTATATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCC--AA-TTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCA
* *
14206208 AAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCC--AA-TTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCA
* *
14206268 AAATTATATTTTGACCCTAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCC--CAA-TTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCA
* * *
14206328 AAATTACATTTTAACCCTAAAAATTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCC---CAATTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCA
** *
14206388 AAATTACATTTTTGACCCCGGTTTTACCAAAATTACCATTTT-ACCACC-GAAC-TTTCCA
1 AAATTACA-TTTTGACCCCAATTTT-CCAAAATTA-CATTTTAACC-CCAAAACTTTTCCA
* * * * *
14206446 AAATTCCATTTTTGACCTCGATTTTGCCAAAATTTACCATTTT-ACCCCTAAAC-TTTCTA
1 AAATTACA-TTTTGACCCCAATTTT-CCAAAA-TTA-CATTTTAACCCCAAAACTTTTCCA
*
14206505 AAATTCCATTTT
1 AAATTACATTTT
14206517 TAGCCTCGAT
Statistics
Matches: 282, Mismatches: 18, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
58 44 0.16
59 44 0.16
60 182 0.65
61 12 0.04
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (57 bp):
AAATTACATTTTGACCCCAATTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCA
Found at i:14206428 original size:90 final size:88
Alignment explanation
Indices: 14206148--14206430 Score: 406
Period size: 90 Copynumber: 3.1 Consensus size: 88
14206138 AACTATCTAG
* * *
14206148 AAATTATATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATT
*
14206213 ATATTTTGACCCCAAAACTTTTCCA
66 ACATTTTGACCCC--AACTTTTCCA
*
14206238 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATT
*
14206303 ACATTTTAACCCCAAAACTTTTCCA
66 ACATTTTGACCCC--AACTTTTCCA
* *
14206328 AAATTACATTTTAACCCTAAAAATTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATT
**
14206393 ACATTTTTGACCCC-GGTTTTACCA
66 ACA-TTTTGACCCCAACTTTT-CCA
14206417 AAATTACCATTTTA
1 AAATTA-CATTTTA
14206431 CCACCGAACT
Statistics
Matches: 178, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
88 4 0.02
89 9 0.05
90 156 0.88
91 9 0.05
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (88 bp):
AAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATT
ACATTTTGACCCCAACTTTTCCA
Found at i:14206429 original size:29 final size:28
Alignment explanation
Indices: 14206201--14206576 Score: 146
Period size: 30 Copynumber: 12.8 Consensus size: 28
14206191 ACCCTAAAAC
* *
14206201 TTTTCCAAAATTA-TATTTTGACCCCAAAA
1 TTTTCCAAAATTACCATTTTGACCCC--GA
* **
14206230 CTTTTCCAAAATTA-CATTTTAACCCTAAAA
1 -TTTTCCAAAATTACCATTTTGACCC--CGA
* **
14206260 CTTTTCCAAAATTA-TATTTTGACCCTAAAA
1 -TTTTCCAAAATTACCATTTTGACCC--CGA
* *
14206290 CTTTTCCAAAATTA-CATTTTAACCCCAAAA
1 -TTTTCCAAAATTACCATTTTGACCCC--GA
* **
14206320 CTTTTCCAAAATTA-CATTTTAACCCTAAAAA
1 -TTTTCCAAAATTACCATTTTGACCC---CGA
*
14206351 TTTTCCAAAATTA-CATTTTGACCCCAAAA
1 TTTTCCAAAATTACCATTTTGACCCC--GA
*
14206380 CTTTTCCAAAATTA-CATTTTTGACCCCGG
1 -TTTTCCAAAATTACCA-TTTTGACCCCGA
14206409 TTTTACCAAAATTACCATTTT-ACCACCGAA
1 TTTT-CCAAAATTACCATTTTGACC-CCG-A
* *
14206439 CTTTCCAAAATT-CCATTTTTGACCTCGA
1 TTTTCCAAAATTACCA-TTTTGACCCCGA
*
14206467 TTTTGCCAAAATTTACCATTTT-ACCCCTAAA
1 TTTT-CCAAAA-TTACCATTTTGACCCC--GA
* * * *
14206498 CTTTCTAAAATT-CCATTTTTAGCCTCGA
1 TTTTCCAAAATTACCATTTTGA-CCCCGA
*
14206526 -TTTCACAAAAAATTACCATTTTGCCCCCGA
1 TTTTC-C--AAAATTACCATTTTGACCCCGA
*** *
14206556 AAGTCTAAAATTACCATTTTG
1 TTTTCCAAAATTACCATTTTG
14206577 CCCTCGGGTA
Statistics
Matches: 287, Mismatches: 30, Indels: 60
0.76 0.08 0.16
Matches are distributed among these distances:
27 4 0.01
28 37 0.13
29 45 0.16
30 173 0.60
31 28 0.10
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (28 bp):
TTTTCCAAAATTACCATTTTGACCCCGA
Found at i:14206573 original size:59 final size:57
Alignment explanation
Indices: 14206387--14206575 Score: 166
Period size: 59 Copynumber: 3.2 Consensus size: 57
14206377 AAACTTTTCC
* * * * * * * *
14206387 AAAATTACATTTTTGACCCCGGTTTTAC-CAAAATTACCATTTTACCACCGAACTTTCC
1 AAAATTCCATTTTTGACCTCGATTTCACAAAAAATTACCATTTT-CCCCCGAA-ATTCT
** * * * *
14206445 AAAATTCCATTTTTGACCTCGATTTTGCCAAAATTTACCATTTTACCCCTAAACTTTCT
1 AAAATTCCATTTTTGACCTCGATTTCACAAAAAATTACCATTTTCCCCCGAAA--TTCT
*
14206504 AAAATTCCATTTTT-AGCCTCGATTTCACAAAAAATTACCATTTTGCCCCCGAAAGTCT
1 AAAATTCCATTTTTGA-CCTCGATTTCACAAAAAATTACCATTTT-CCCCCGAAATTCT
14206562 AAAATTACCATTTT
1 AAAATT-CCATTTT
14206576 GCCCTCGGGT
Statistics
Matches: 107, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
58 39 0.36
59 61 0.57
60 7 0.07
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCTCGATTTCACAAAAAATTACCATTTTCCCCCGAAATTCT
Found at i:14208023 original size:34 final size:34
Alignment explanation
Indices: 14207984--14208092 Score: 111
Period size: 34 Copynumber: 3.4 Consensus size: 34
14207974 TAATAAAAAC
*
14207984 AATATTTAATGATTAAAAACAACCTAAATATTTA
1 AATATTTAATTATTAAAAACAACCTAAATATTTA
* * *
14208018 AATATTTAATTATT-TAAACATCC--CA-A-TTA
1 AATATTTAATTATTAAAAACAACCTAAATATTTA
* * *
14208047 ATTAATTAATTATTAAAAACAATCTAAATATTTA
1 AATATTTAATTATTAAAAACAACCTAAATATTTA
*
14208081 ATTATTTAATTA
1 AATATTTAATTA
14208093 AATATTTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
29 15 0.25
30 7 0.12
31 1 0.02
32 1 0.02
33 8 0.14
34 27 0.46
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (34 bp):
AATATTTAATTATTAAAAACAACCTAAATATTTA
Found at i:14208096 original size:20 final size:19
Alignment explanation
Indices: 14208071--14208162 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 19
14208061 AAAAACAATC
14208071 TAAATATTTAATTATTTAA
1 TAAATATTTAATTATTTAA
*
14208090 TTAAATATTTAATTATTCAA
1 -TAAATATTTAATTATTTAA
* *** *
14208110 -ACA-ACCCAAATATTTAA
1 TAAATATTTAATTATTTAA
14208127 TTCAAATATTTAATTATTTAA
1 -T-AAATATTTAATTATTTAA
*
14208148 T-CATATTTAATTATT
1 TAAATATTTAATTATT
14208163 AAAAACAACC
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
17 9 0.16
18 15 0.27
20 21 0.38
21 10 0.18
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAATATTTAATTATTTAA
Found at i:14208102 original size:46 final size:45
Alignment explanation
Indices: 14208042--14208194 Score: 126
Period size: 46 Copynumber: 3.1 Consensus size: 45
14208032 TAAACATCCC
* * *
14208042 AATTAATTAATTAATTATTAAAAACAATCTAAATATTTAATTATTT
1 AATTAAATAATTAATTATT-AAAACAACCCAAATATTTAATTATTT
* *
14208088 AATTAAATATTTAATTATTCAAACAACCCAAATATTTAATTCAAATATTT
1 AATTAAATAATTAATTATTAAAACAACCCAAATATTTAA-T----TATTT
* *
14208138 AATTATTTAATCATATTTAATTATTAAAAACAACCCAAATACTGAATTATTT
1 AATTA---AAT-A-A-TTAATTATT-AAAACAACCCAAATATTTAATTATTT
14208190 AATTA
1 AATTA
14208195 TTTAAAACAA
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
45 17 0.20
46 18 0.21
50 10 0.12
52 10 0.12
53 3 0.03
54 1 0.01
56 10 0.12
57 17 0.20
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (45 bp):
AATTAAATAATTAATTATTAAAACAACCCAAATATTTAATTATTT
Found at i:14208134 original size:13 final size:13
Alignment explanation
Indices: 14208116--14208141 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14208106 TCAAACAACC
14208116 CAAATATTTAATT
1 CAAATATTTAATT
14208129 CAAATATTTAATT
1 CAAATATTTAATT
14208142 ATTTAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
CAAATATTTAATT
Found at i:14208156 original size:165 final size:160
Alignment explanation
Indices: 14207985--14208282 Score: 395
Period size: 165 Copynumber: 1.8 Consensus size: 160
14207975 AATAAAAACA
* * * *
14207985 ATATTTAATGATTAAAAACAACCTAAATATTTAAATATTTAATTATTT-AAACATCCCAATTAAT
1 ATATTTAATGATTAAAAACAACCCAAATACTGAAATATTTAATTATTTAAAACAACCC-A--AA-
* *
14208049 TAATTAATTATTAAAAACAATCTAA-ATATTTAATTATTTAATTAAATATTTAATTA-TTCAAAC
62 T-ATT--TAATTAAAAA-AATCTAATATATTTAATTATTTAATTAAATATTTAATTATTTAAAAC
14208112 AACCCAAATATTTAATTCAAATATTTAATTATTTAATC
123 AACCCAAATATTTAATTCAAATATTTAATTATTTAATC
* *
14208150 ATATTTAATTATTAAAAACAACCCAAATACTGAATTATTTAATTATTTAAAACAACCCAAATATT
1 ATATTTAATGATTAAAAACAACCCAAATACTGAAATATTTAATTATTTAAAACAACCCAAATATT
* * *
14208215 TAATTCAAAATATTTAATTATATTTAATTATTTAATTAAATATTTAATTATTTAAAACAACCCAA
66 TAATTAAAAAAATCTAA-TATATTTAATTATTTAATTAAATATTTAATTATTTAAAACAACCCAA
14208280 ATA
130 ATA
14208283 ATTTTGATGA
Statistics
Matches: 118, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
158 5 0.04
159 8 0.07
160 31 0.26
161 19 0.16
162 1 0.01
163 2 0.02
165 44 0.37
166 8 0.07
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (160 bp):
ATATTTAATGATTAAAAACAACCCAAATACTGAAATATTTAATTATTTAAAACAACCCAAATATT
TAATTAAAAAAATCTAATATATTTAATTATTTAATTAAATATTTAATTATTTAAAACAACCCAAA
TATTTAATTCAAATATTTAATTATTTAATC
Found at i:14208259 original size:20 final size:18
Alignment explanation
Indices: 14208225--14208269 Score: 72
Period size: 20 Copynumber: 2.4 Consensus size: 18
14208215 TAATTCAAAA
14208225 TATTTAATTATATTTAAT
1 TATTTAATTATATTTAAT
14208243 TATTTAATTAAATATTTAAT
1 TATTTAATT--ATATTTAAT
14208263 TATTTAA
1 TATTTAA
14208270 AACAACCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTAATTATATTTAAT
Found at i:14214378 original size:43 final size:43
Alignment explanation
Indices: 14214312--14214612 Score: 347
Period size: 43 Copynumber: 7.0 Consensus size: 43
14214302 AATCTATTAA
* *
14214312 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCGTGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTC
* * *
14214355 TTTAGCGGCCTTTGTGGGGAAAGC-ACTGCTAAAGACCGTGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGTC-GCTAAAGACCATGTTC
* * * * * * *
14214398 TTTAGCGGCGTTTGTAGGGAAAGTGCCGTTAAAAATCGTGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTC
*
14214441 TTTAGCAGCGTTTGTGGGGAAAGCG-CTGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGTC-GCTAAAGACCATGTTC
* * * **
14214484 TTTAGCGGCTTTTGAGGGGAAAGCATTACTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTC
*
14214527 TTTAGCGGCGTTTGT-GGGAAAGTGTCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTC
* * * * *
14214569 TTTAGCGGTGTTTGTGGGAAAAACGCCGGTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTC
14214612 T
1 T
14214613 ATAGTGGCAT
Statistics
Matches: 218, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
42 39 0.18
43 178 0.82
44 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTC
Found at i:14214530 original size:129 final size:128
Alignment explanation
Indices: 14214312--14214612 Score: 424
Period size: 129 Copynumber: 2.3 Consensus size: 128
14214302 AATCTATTAA
* *
14214312 TTTAGCGGCGTTTGTGGGAAAAGCG-TCGCTAAAGACCGTGTTCTTTAGCGGCCTTTGTGGGGAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCT-GCTAAAGACCATGTTCTTTAGCGGCCTTTGAGGGGAA
* * * * *
14214376 AGCACTGCTAAAGACCGTGTTCTTTAGCGGCGTTTGTAGGGAAAGTGCCGTTAAAAATCGTGTTC
65 AGCACTACTAAAGACCATGTTCTTTAGCGGCGTTTGT-GGGAAAGTGCCGCTAAAAACCATGTTC
* * *
14214441 TTTAGCAGCGTTTGTGGGGAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCTTTTGAGGGGAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCCTTTGAGGGGAAA
* * *
14214506 GCATTACTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAGTGTCGCTAAAGACCATGTTC
66 GCACTACTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAGTGCCGCTAAAAACCATGTTC
* * * *
14214569 TTTAGCGGTGTTTGTGGGAAAAACGCCGGTAAAGACCATGTTCT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCATGTTCT
14214613 ATAGTGGCAT
Statistics
Matches: 152, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
128 60 0.39
129 91 0.60
130 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (128 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCCTTTGAGGGGAAA
GCACTACTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAGTGCCGCTAAAAACCATGTTC
Found at i:14217206 original size:13 final size:13
Alignment explanation
Indices: 14217188--14217217 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
14217178 TCTAAATCCT
*
14217188 TTGATTGAAAATC
1 TTGATTCAAAATC
14217201 TTGATTCAAAATC
1 TTGATTCAAAATC
14217214 TTGA
1 TTGA
14217218 GAAATTTCAG
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:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (13 bp):
TTGATTCAAAATC
Found at i:14218703 original size:53 final size:50
Alignment explanation
Indices: 14218596--14218734 Score: 158
Period size: 49 Copynumber: 2.7 Consensus size: 50
14218586 TAGATCTAAT
*
14218596 TTTTTAAATAAATATAAACATTTATTTAATTTATTTTTTTAAATATGATG
1 TTTTTAAATAAATATAAATATTTATTTAATTTATTTTTTTAAATATGATG
* *
14218646 -TTTTAAATAAATATAAATATTTATTTAATTTGTTTTTGTTTAAGAT-TAGGTG
1 TTTTTAAATAAATATAAATATTTATTTAATTT-ATTTT-TTTAA-ATAT-GATG
* * *
14218698 TTTTTACATAAAAATAAATGTTTATTT-ATATTATTTT
1 TTTTTAAATAAATATAAATATTTATTTAAT-TTATTTT
14218735 GTACAAATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
49 30 0.39
50 4 0.05
51 6 0.08
52 11 0.14
53 25 0.33
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (50 bp):
TTTTTAAATAAATATAAATATTTATTTAATTTATTTTTTTAAATATGATG
Found at i:14218908 original size:15 final size:15
Alignment explanation
Indices: 14218878--14218906 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14218868 TAAAATACAC
14218878 AAAAAAATATAATTT
1 AAAAAAATATAATTT
14218893 AAAAAAATA-AATTT
1 AAAAAAATATAATTT
14218907 TATATACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAAAATATAATTT
Found at i:14219207 original size:22 final size:23
Alignment explanation
Indices: 14219179--14219229 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
14219169 TTTTATATTG
14219179 TTTAAATCGTATTTTAACAAT-T
1 TTTAAATCGTATTTTAACAATAT
* *
14219201 TTTAAATTGTATTTTAACACTAT
1 TTTAAATCGTATTTTAACAATAT
14219224 TTTAAA
1 TTTAAA
14219230 CAAACATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTAAATCGTATTTTAACAATAT
Found at i:14229142 original size:19 final size:19
Alignment explanation
Indices: 14229118--14229154 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
14229108 TCACATTCTT
14229118 ATTCTCTCATCCTCTCTCA
1 ATTCTCTCATCCTCTCTCA
*
14229137 ATTCTCTCATCCTTTCTC
1 ATTCTCTCATCCTCTCTC
14229155 TCATTGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTCTCTCATCCTCTCTCA
Found at i:14231036 original size:30 final size:29
Alignment explanation
Indices: 14231000--14231059 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
14230990 AAAACCATCC
14231000 TACAACCACTTGAAAATGTGTGGGGGGTCT
1 TACAACCACTTGAAAATGT-TGGGGGGTCT
*
14231030 TACAACCACTTGAAAATGTTGGGGTGTCT
1 TACAACCACTTGAAAATGTTGGGGGGTCT
14231059 T
1 T
14231060 TGATAGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (29 bp):
TACAACCACTTGAAAATGTTGGGGGGTCT
Found at i:14240724 original size:17 final size:17
Alignment explanation
Indices: 14240699--14240741 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
14240689 ATGCATCTTA
14240699 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* *
14240716 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
*
14240733 TTTACTTGT
1 TTTAATTGT
14240742 TAGTTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:14240750 original size:17 final size:17
Alignment explanation
Indices: 14240710--14240768 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
14240700 TTAATTGTCA
*
14240710 TTGCATTT-TAGTTGTCG
1 TTGCATTTGTA-TTGTAG
14240727 TTGCATTT-TACTTGTTAG
1 TTGCATTTGTA-TTG-TAG
14240745 TT-CATTTGTATTGTAG
1 TTGCATTTGTATTGTAG
14240761 TTGCATTT
1 TTGCATTT
14240769 CCATTCTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 5 0.14
17 26 0.70
18 6 0.16
ACGTcount: A:0.15, C:0.10, G:0.19, T:0.56
Consensus pattern (17 bp):
TTGCATTTGTATTGTAG
Found at i:14242927 original size:24 final size:23
Alignment explanation
Indices: 14242890--14242939 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
14242880 ACTATTCATT
*
14242890 TTATTTTAATTTGC-TCTGACAAA
1 TTATTTCAATTTGCAT-TGACAAA
14242913 TTATTTCATATTTGCATTGACAAA
1 TTATTTCA-ATTTGCATTGACAAA
14242937 TTA
1 TTA
14242940 ACTCTTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 16 0.67
25 1 0.04
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (23 bp):
TTATTTCAATTTGCATTGACAAA
Found at i:14244983 original size:48 final size:49
Alignment explanation
Indices: 14244903--14245019 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 49
14244893 TCAGATCTTG
* * *
14244903 TTTAATTAATTTT-TTTAGATCTGATGTTTTAAAT-ATATAAACATTTA
1 TTTAATTTATTTTGTTTAAATATGATGTTTTAAATAATATAAACATTTA
*
14244950 TTTAATTTATTTTGTTTAAATATGATGTTTTAAATAAATATAAATATTTA
1 TTTAATTTATTTTGTTTAAATATGATGTTTTAAAT-AATATAAACATTTA
*
14245000 TTTAATTTGTTTTTGTTTAA
1 TTTAATTT-ATTTTGTTTAA
14245020 GATCTGGTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
47 12 0.20
48 19 0.31
50 20 0.33
51 10 0.16
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (49 bp):
TTTAATTTATTTTGTTTAAATATGATGTTTTAAATAATATAAACATTTA
Found at i:14245053 original size:53 final size:50
Alignment explanation
Indices: 14244903--14245067 Score: 158
Period size: 53 Copynumber: 3.3 Consensus size: 50
14244893 TCAGATCTTG
* * * * *
14244903 TTTAATTAATTTT-TTTAGATCTGATGTTTTAAAT--ATATAAACATTTA
1 TTTAATTTATTTTGTTTAAATATGATGTTTTAAATAAACATAAATATTTA
*
14244950 TTTAATTTATTTTGTTTAAATATGATGTTTTAAATAAATATAAATATTTA
1 TTTAATTTATTTTGTTTAAATATGATGTTTTAAATAAACATAAATATTTA
* * * ** *
14245000 TTTAATTTGTTTTTGTTTAAGATCTGGTGTTTTTGCATAAACATAAATTTTTA
1 TTTAATTT-ATTTTGTTTAA-ATATGATG-TTTTAAATAAACATAAATATTTA
14245053 TTT-ATATTATTTTGT
1 TTTAAT-TTATTTTGT
14245068 ACAAATCTTG
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
47 12 0.12
48 19 0.19
50 20 0.20
51 10 0.10
52 14 0.14
53 24 0.24
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (50 bp):
TTTAATTTATTTTGTTTAAATATGATGTTTTAAATAAACATAAATATTTA
Found at i:14245430 original size:72 final size:73
Alignment explanation
Indices: 14245352--14245486 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 73
14245342 TTCTATTTTG
** * *
14245352 GGATTTATTCCTGCTGTTTAAC-ATATTTGATTCTA-TTTTGATTTTGTTGTCAAAATAAGAATA
1 GGATTTATTCCCACTGTTCAACAATATTTGATTCTATTTTTGATTTTGTT-TCAAAACAAGAATA
14245415 AGTTTTTCA
65 AGTTTTTCA
** * *
14245424 GGATTTATTCCCACTGTTCAACAATATTTTTTTCTATTTTTTATTTTGTTTCTAAACAAGAAT
1 GGATTTATTCCCACTGTTCAACAATATTTGATTCTATTTTTGATTTTGTTTCAAAACAAGAAT
14245487 TAAAATTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
72 19 0.36
73 22 0.42
74 12 0.23
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (73 bp):
GGATTTATTCCCACTGTTCAACAATATTTGATTCTATTTTTGATTTTGTTTCAAAACAAGAATAA
GTTTTTCA
Found at i:14245573 original size:78 final size:79
Alignment explanation
Indices: 14245466--14245875 Score: 395
Period size: 85 Copynumber: 5.1 Consensus size: 79
14245456 TCTATTTTTT
* * * * * *
14245466 ATTTTGTTTCTAAACAAGAATTAAAATTAAATAATTATGTGTCAAGATTTATTCCCGTCGTTCAG
1 ATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTCTGTTTCAGGATTTATTCCCGCCGTTCAA
14245531 CAGATTTGA-TATG
66 CAGATTTGATTATG
* * * *
14245544 ATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCGGGATTTATTCCTGCAGTTCAA
1 ATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTCTGTTTCAGGATTTATTCCCGCCGTTCAA
*
14245609 CAGATTTAATTTGATTTTG
66 CAG-----ATTTGATTATG
* * * *
14245628 ATTTTTGTTTCCAAATAAGAATTAAAATTGAATAATTCTGTTTCAGGATTTATTTCCGCCGTTTA
1 A-TTTTGTTTCCAAACAAGAATTAAAATTAAATAATTCTGTTTCAGGATTTATTCCCGCCGTTCA
*
14245693 ACAGATTTGATTTGATTTTA
65 ACAGATTTGA-TT-A---TG
* * *
14245713 ATTTTGTTTCCAAATAAGAATT--AATTAAATAATTTTGTTTC-GGAATTTATTCCCGCCATTCA
1 ATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTCTGTTTCAGG-ATTTATTCCCGCCGTTCA
14245775 ACAGATTTGATT-TG
65 ACAGATTTGATTATG
* * * * ** *
14245789 ATTTTGTTTCAAAACAAGAA--ATAATTAAATAATTCTGTTTCAAGATTTAATCCTACCACTT-A
1 ATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTCTGTTTCAGGATTTATTCCCGCC-GTTCA
* *
14245851 ATAGAATTGATTATG
65 ACAGATTTGATTATG
14245866 ATTTTGTTTC
1 ATTTTGTTTC
14245876 AGAATTTCAA
Statistics
Matches: 278, Mismatches: 36, Indels: 37
0.79 0.10 0.11
Matches are distributed among these distances:
76 58 0.21
77 15 0.05
78 59 0.21
80 6 0.02
81 6 0.02
82 42 0.15
83 6 0.02
84 25 0.09
85 61 0.22
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (79 bp):
ATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTCTGTTTCAGGATTTATTCCCGCCGTTCAA
CAGATTTGATTATG
Found at i:14245648 original size:85 final size:85
Alignment explanation
Indices: 14245461--14245794 Score: 406
Period size: 85 Copynumber: 4.1 Consensus size: 85
14245451 TTTTTTCTAT
* * * * * *
14245461 TTTTTATTTTGTTTCTAAACAAGAATTAAAATTAAATAATTATGTGTCAAGATTTATTCCCGTC-
1 TTTTGATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCAGGATTTATTCCCGCCA
*
14245525 GTTCAGCAGATTTGA--T-A
66 GTTCAACAGATTTGATTTGA
* *
14245542 ---TGATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCGGGATTTATTCCTG-CA
1 TTTTGATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCAGGATTTATTCCCGCCA
*
14245603 GTTCAACAGATTTAATTTGA
66 GTTCAACAGATTTGATTTGA
* * * *
14245623 TTTTGATTTTTGTTTCCAAATAAGAATTAAAATTGAATAATTCTGTTTCAGGATTTATTTCCGCC
1 TTTTGA-TTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCAGGATTTATTCCCGCC
*
14245688 -GTTTAACAGATTTGATTTGA
65 AGTTCAACAGATTTGATTTGA
* *
14245708 TTTTAATTTTGTTTCCAAATAAGAATT--AATTAAATAATTTTGTTTC-GGAATTTATTCCCGCC
1 TTTTGATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCAGG-ATTTATTCCCGCC
14245770 A-TTCAACAGATTTGATTTGA
65 AGTTCAACAGATTTGATTTGA
14245790 TTTTG
1 TTTTG
14245795 TTTCAAAACA
Statistics
Matches: 219, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
77 1 0.00
78 65 0.30
80 1 0.00
81 3 0.01
82 51 0.23
84 24 0.11
85 73 0.33
86 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (85 bp):
TTTTGATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCAGGATTTATTCCCGCCA
GTTCAACAGATTTGATTTGA
Found at i:14245664 original size:163 final size:164
Alignment explanation
Indices: 14245467--14245794 Score: 439
Period size: 163 Copynumber: 2.0 Consensus size: 164
14245457 CTATTTTTTA
* * *
14245467 TTTTGTTTCTAAACAAGAATTAAAATTAAATAATTATGTGTCAAGATTTATTCCCGTCGTTCAGC
1 TTTTGTTTCCAAACAAGAATTAAAATTAAATAATTATGTGTCAAGATTTATTCCCGCCGTTCAAC
* *
14245532 AGATTTGA-T-A-TGATTTTGTTTCCAAACAAGAATTAAAATTAAATAATTTTGTTTCGGGATTT
66 AGATTTGATTGATTAATTTTGTTTCCAAACAAGAATT--AATTAAATAATTTTGTTTCGGAATTT
*
14245594 ATTCCTG-CAGTTCAACAGATTTAATTTGATTTTGAT
129 ATTCCCGCCA-TTCAACAGATTTAATTTGATTTTGAT
* * * * * * *
14245630 TTTTGTTTCCAAATAAGAATTAAAATTGAATAATTCTGTTTCAGGATTTATTTCCGCCGTTTAAC
1 TTTTGTTTCCAAACAAGAATTAAAATTAAATAATTATGTGTCAAGATTTATTCCCGCCGTTCAAC
*
14245695 AGATTTGATTTGATTTTAATTTTGTTTCCAAATAAGAATTAATTAAATAATTTTGTTTCGGAATT
66 AGATTTGA-TTGA--TTAATTTTGTTTCCAAACAAGAATTAATTAAATAATTTTGTTTCGGAATT
*
14245760 TATTCCCGCCATTCAACAGATTTGATTTGATTTTG
128 TATTCCCGCCATTCAACAGATTTAATTTGATTTTG
14245795 TTTCAAAACA
Statistics
Matches: 143, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
163 63 0.44
165 1 0.01
166 1 0.01
167 54 0.38
168 2 0.01
169 22 0.15
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (164 bp):
TTTTGTTTCCAAACAAGAATTAAAATTAAATAATTATGTGTCAAGATTTATTCCCGCCGTTCAAC
AGATTTGATTGATTAATTTTGTTTCCAAACAAGAATTAATTAAATAATTTTGTTTCGGAATTTAT
TCCCGCCATTCAACAGATTTAATTTGATTTTGAT
Found at i:14247406 original size:30 final size:30
Alignment explanation
Indices: 14247369--14247489 Score: 145
Period size: 30 Copynumber: 4.1 Consensus size: 30
14247359 TAGAAAACCA
14247369 TCCTACAACCACTTGAAAATGTTGGGGGTG
1 TCCTACAACCACTTGAAAATGTTGGGGGTG
* * **
14247399 ACCTACAACCACTTGAAAGTGTAAGGGGTG
1 TCCTACAACCACTTGAAAATGTTGGGGGTG
*** *
14247429 TTAGACAACCACTTGAAGATG-TGGGGGTG
1 TCCTACAACCACTTGAAAATGTTGGGGGTG
* *
14247458 TCCTACAACCACTTGAAAATGTAGGTGGTG
1 TCCTACAACCACTTGAAAATGTTGGGGGTG
14247488 TC
1 TC
14247490 TTGCTAACGT
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
29 23 0.32
30 49 0.68
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (30 bp):
TCCTACAACCACTTGAAAATGTTGGGGGTG
Found at i:14247468 original size:59 final size:60
Alignment explanation
Indices: 14247373--14247488 Score: 182
Period size: 59 Copynumber: 1.9 Consensus size: 60
14247363 AAACCATCCT
*
14247373 ACAACCACTTGAAAATGTTGGGGGTGACCTACAACCACTTGAAAGTGTAAGG-GGTGTTAG
1 ACAACCACTTGAAAATGTTGGGGGTGACCTACAACCACTTGAAAATGT-AGGTGGTGTTAG
* *
14247433 ACAACCACTTGAAGATG-TGGGGGTGTCCTACAACCACTTGAAAATGTAGGTGGTGT
1 ACAACCACTTGAAAATGTTGGGGGTGACCTACAACCACTTGAAAATGTAGGTGGTGT
14247489 CTTGCTAACG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 3 0.06
59 33 0.63
60 16 0.31
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (60 bp):
ACAACCACTTGAAAATGTTGGGGGTGACCTACAACCACTTGAAAATGTAGGTGGTGTTAG
Found at i:14248514 original size:21 final size:20
Alignment explanation
Indices: 14248477--14248516 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
14248467 TGCATTTTTA
*
14248477 GCATTTTAAACTTAGTGATT
1 GCATTTTAAACTCAGTGATT
*
14248497 GCATTTTCTAACTCAGTGAT
1 GCATTTT-AAACTCAGTGAT
14248517 GCTTGGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
GCATTTTAAACTCAGTGATT
Found at i:14254496 original size:22 final size:22
Alignment explanation
Indices: 14254466--14254530 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
14254456 GTTCTTCCTT
14254466 TTGTCGACGCATGAAAAACTCC
1 TTGTCGACGCATGAAAAACTCC
*
14254488 TTGTTGACGCATGAAAAACTCC
1 TTGTCGACGCATGAAAAACTCC
14254510 TTGTCGACGCATGAAAAACTC
1 TTGTCGACGCATGAAAAACTC
14254531 ATCACAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (22 bp):
TTGTCGACGCATGAAAAACTCC
Found at i:14256235 original size:12 final size:12
Alignment explanation
Indices: 14256214--14256256 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
14256204 GGAGACGAAT
14256214 GAGGAAAAAGAA
1 GAGGAAAAAGAA
* *
14256226 GAGGACAAAGAG
1 GAGGAAAAAGAA
14256238 GAGGAAAAAGAA
1 GAGGAAAAAGAA
*
14256250 GAAGAAA
1 GAGGAAA
14256257 GAAGTGCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (12 bp):
GAGGAAAAAGAA
Found at i:14256717 original size:17 final size:17
Alignment explanation
Indices: 14256688--14256734 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
14256678 TTGTAATATC
14256688 ATTGTCA-TCGCATTTCTT
1 ATTGTCACT-GCATTT-TT
*
14256706 -TTGTCCCTGCATTTTT
1 ATTGTCACTGCATTTTT
14256722 ATTGTCACTGCAT
1 ATTGTCACTGCAT
14256735 CTGCATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Found at i:14257574 original size:21 final size:20
Alignment explanation
Indices: 14257535--14257574 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
14257525 TGCATTTTTA
* *
14257535 GCATTTTTAACTTAGTGATT
1 GCATTTTTAACTCAATGATT
14257555 GCATTTTCTAACTCAATGAT
1 GCATTTT-TAACTCAATGAT
14257575 GCTTGGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (20 bp):
GCATTTTTAACTCAATGATT
Found at i:14298386 original size:13 final size:13
Alignment explanation
Indices: 14298368--14298392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14298358 CCCATTTTAT
14298368 CATTTTTAGCATG
1 CATTTTTAGCATG
14298381 CATTTTTAGCAT
1 CATTTTTAGCAT
14298393 TTTTAACTTA
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:14308465 original size:24 final size:24
Alignment explanation
Indices: 14308419--14308465 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
14308409 GTAGTAAGAA
*
14308419 GAAGAAAAAGAAGAACGAGAGGAG
1 GAAGAAAAAGAAGAACGAAAGGAG
*
14308443 GAAGGAAAAGAAGGAA-GAAAGGA
1 GAAGAAAAAGAA-GAACGAAAGGA
14308466 AGAACCTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (24 bp):
GAAGAAAAAGAAGAACGAAAGGAG
Found at i:14314983 original size:45 final size:45
Alignment explanation
Indices: 14314932--14315078 Score: 115
Period size: 45 Copynumber: 3.2 Consensus size: 45
14314922 AGCAATAAAA
14314932 CAAGAAAATGCAGTAAAACTATGAGAATAATTTGTCAAAGCAATT
1 CAAGAAAATGCAGTAAAACTATGAGAATAATTTGTCAAAGCAATT
* * * * **
14314977 CAAGAAAATTC--TAAAGAGATTCTAATGAATAA--TGTCGGAGCAATAAAAT
1 CAAGAAAATGCAGT-AA-A-ACTATGA-GAATAATTTGTCAAAGCAAT----T
* *
14315026 -AAGAAAATGAAGTAAAACTATGAGAATAATTTGTCAAAGAAATT
1 CAAGAAAATGCAGTAAAACTATGAGAATAATTTGTCAAAGCAATT
14315070 CAAGAAAAT
1 CAAGAAAAT
14315079 TTGAGTAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 26
0.65 0.12 0.23
Matches are distributed among these distances:
43 1 0.01
44 3 0.04
45 29 0.39
46 10 0.13
47 10 0.13
48 18 0.24
49 3 0.04
50 1 0.01
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.24
Consensus pattern (45 bp):
CAAGAAAATGCAGTAAAACTATGAGAATAATTTGTCAAAGCAATT
Found at i:14315030 original size:93 final size:93
Alignment explanation
Indices: 14314894--14315079 Score: 345
Period size: 93 Copynumber: 2.0 Consensus size: 93
14314884 AAAGTTAAAC
*
14314894 CTAAAGAGATTCTAATGAATAATGTCGGAGCAATAAAACAAGAAAATGCAGTAAAACTATGAGAA
1 CTAAAGAGATTCTAATGAATAATGTCGGAGCAATAAAACAAGAAAATGAAGTAAAACTATGAGAA
*
14314959 TAATTTGTCAAAGCAATTCAAGAAAATT
66 TAATTTGTCAAAGAAATTCAAGAAAATT
*
14314987 CTAAAGAGATTCTAATGAATAATGTCGGAGCAATAAAATAAGAAAATGAAGTAAAACTATGAGAA
1 CTAAAGAGATTCTAATGAATAATGTCGGAGCAATAAAACAAGAAAATGAAGTAAAACTATGAGAA
14315052 TAATTTGTCAAAGAAATTCAAGAAAATT
66 TAATTTGTCAAAGAAATTCAAGAAAATT
14315080 TGAGTAAAAA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (93 bp):
CTAAAGAGATTCTAATGAATAATGTCGGAGCAATAAAACAAGAAAATGAAGTAAAACTATGAGAA
TAATTTGTCAAAGAAATTCAAGAAAATT
Found at i:14331218 original size:984 final size:984
Alignment explanation
Indices: 14329367--14331225 Score: 2559
Period size: 984 Copynumber: 1.9 Consensus size: 984
14329357 GATAGGTTAC
* * *
14329367 TGTGGCAATGCAGAGCAGAATCAAGCAGCGAGCCTGGTGTTCGTTTTGCGTCTCAACAGGAGTAC
1 TGTGGAAATGCAGAGCAGAATCAAGCAGCGAGCCTGATGTTCGTTTTGCGTCTCAACAGAAGTAC
*
14329432 TATTGATCTCTAAATTTGAAAGTAATTTTGTTTAAACAATATTTTACACCCTTTTACTGATCATT
66 TATTGATCTCTAAATTTGAAAGTAATTTTGTTTAAACAACATTTTACACCCTTTTACTGATCATT
* * * * * *
14329497 TAGGGGTTGAATATTCTGATACTTTTTTTACTTTTATGAATGATTACCAATATTTTTTCTGATGA
131 CAAGGGTTGAATATTCTGATACTTTATTTACTTTTATGAATGATTACCAATATCTTTTCTAATAA
* * * * *
14329562 ATCTCTTCAATTGATTTATGTTCAATTGTTGTTAATTCTACATGTTAGCAATCTCAAGAATGAGC
196 ATCTCTTCAATTGAATTATGTTCAAGTGTTGTTAATTCTACATGCTAACAATCTCAAGAATAAGC
** * * * *
14329627 ACTTGTTTTGCATGTGAATAATCTTGATTGAAAGCAGGACATATTTGCTAGAGCATAATTCAGTG
261 ACTTGTTTTGCATGTGAATAATCTCAATTGAAAGCAAGACAGATTTGCTAGAGCATAACTCAATG
* * * * *
14329692 TAATGAGCATATATCGGAAGCTATGTGTAGTAACTCTTAATGTTAAGCTGCATTCATTAAGGGTG
326 TAATGAGCATATATCAGAAGATATGTGTAGTAACTCTTAATGATAAGCTACATTCATTAAGAGTG
** * **
14329757 AGATAAGTCTTTGTTGGGACAATACATGTTATAGGAATATAATATGGAATTGCTGTAAAAGTTGC
391 AGATAAGTCTTTGTTGAAACAATACATGTTATAGGAATATAATATGGAATTACCATAAAAGTTGC
* * * * **
14329822 AATGAAACGACACACTATTTCTTAGTCATTTTGGGAAATTTGTAGAAACAAATATTTGTTATGAC
456 AATGAAACGACACACCATTGCTTAGTCATTCTAGGAAATTCATAGAAACAAATATTTGTTATGAC
* * *
14329887 ATTCGTATATCTAGACTTAGAATTGAAATATTCTAGATCTAGTGATCACAACTTAGTCCTGTACT
521 ATTCGTAGATCTAAACTTAGAATTGAAATATTCAAGATCTAGTGATCACAACTTAGTCCTGTACT
* *
14329952 GAAGTTCTTGGCAATCATTTCTGCTAAGAGTGATGAGTACTTAGTAGATCTGATGCTTTGCTTGG
586 GAAGCTCTTGCCAATCATTTCTGCTAAGAGTGATGAGTACTTAGTAGATCTGATGCTTTGCTTGG
* * * * *
14330017 TTGATTCTTGATCATTTTACTATTTTTTCATTTTTTATGACACGCAAGTTGCAATCACAATTATC
651 TTGATTCTCGACCATTTCACTATTTTTGCATTTTTTATGACACGCAAGTTGCAAACACAATTATC
* * * * * * *
14330082 TTTGTTACCATATTTACTTTACTTGCATAATTCTTTTGTCAATAGTTTAAGGAATTTCTTCTGAA
716 ATTGTTACCACATTTACTTAAATTGCACAATTCTTTTGTCAACAGTTTAAGGAATTTCTTCTAAA
* * *
14330147 TATCAATATCTCTGTGGGTACGATACTCTACTTATCACTTTATCACTTGAACGTTGTGTACACTT
781 TACCAATATCTCTGAGGGTACGATACTCTACTTATCAATTTATCACTTGAACGTTGTGTACACTT
14330212 GCACATTTACTACAACAATATATTTTACACGCGATAGTCACATGGCAGATCAAAAGTGCAGAGGC
846 GCACATTTACTACAACAATATATTTTACACGCGATAGTCACATGGCAGATCAAAAGTGCAGAGGC
14330277 AAAGTTGATAGCTAGTGCTGGGAGCGAAGCCTTGACAACGCGATCGCAAAACCACCTAAGCAAAG
911 AAAGTTGATAGCTAGTGCTGGGAGCGAAGCCTTGACAACGCGATCGCAAAACCACCTAAGCAAAG
14330342 ATACGTTGT
976 ATACGTTGT
* * * * *
14330351 TGTGGAAATGCGGAGCAGAATCAAGCAGCGAGCCTGATGTT-TTTTTGGGTCTCGACAGAATTAC
1 TGTGGAAATGCAGAGCAGAATCAAGCAGCGAGCCTGATGTTCGTTTTGCGTCTCAACAGAAGTAC
* * * * **
14330415 TCTTGATCTCTAAGTTTGAATGTCATTTTGTTTAAACAACATTTTATGCCCTTTTACTGATCATT
66 TATTGATCTCTAAATTTGAAAGTAATTTTGTTTAAACAACATTTTACACCCTTTTACTGATCATT
* * **
14330480 CAATGGTTGAATATTTCTGATACTTTATTTATTTTTATGAATGATTACTGATATCTTTTCTAATA
131 CAAGGGTTGAATA-TTCTGATACTTTATTTACTTTTATGAATGATTACCAATATCTTTTCTAATA
* * * * *
14330545 AATCTCTTCACTTGAATTATGTTC-AGTGTTGTTAATTTTACGTGCTAACAATCTTAGGAATAAG
195 AATCTCTTCAATTGAATTATGTTCAAGTGTTGTTAATTCTACATGCTAACAATCTCAAGAATAAG
* * * *
14330609 CTCTTGTTTTTGCATGTGCATAATCTCAATTGAAAGCAAGACAGATTTGTTGGAGCATAACTCAA
260 CACTTG-TTTTGCATGTGAATAATCTCAATTGAAAGCAAGACAGATTTGCTAGAGCATAACTCAA
* * * * *
14330674 TGTATTGAGTATATATCAGAAGATGTTTGTAGTAACT-TTAGAT-ATAGAGCTACGTTCATTAAG
324 TGTAATGAGCATATATCAGAAGATATGTGTAGTAACTCTTA-ATGATA-AGCTACATTCATTAAG
* * * * *
14330737 AGTGAGATTAGTCTTTGTTGAAACTATGCATGTTGTAGGAATATAATATGGATTTACCATAAAAG
387 AGTGAGATAAGTCTTTGTTGAAACAATACATGTTATAGGAATATAATATGGAATTACCATAAAAG
* * * * *
14330802 TTGCTATGACACGGCACACCATTGCTTAGTCATTCTAGGAAATTCATAGGAACAAATATTTGTTT
452 TTGCAATGAAACGACACACCATTGCTTAGTCATTCTAGGAAATTCATAGAAACAAATATTTGTTA
* * *
14330867 TGACATTCGTAGATCTAAACTTAG-ATCTTAAATATTCCAAG-TTTAGTGATCACAACTTAGTCT
517 TGACATTCGTAGATCTAAACTTAGAAT-TGAAATATT-CAAGATCTAGTGATCACAACTTAGTCC
* * *
14330930 TGTGCTGAAGCTCTTGCCAATCATTTCTGCTCAGAGTGATGAGTACTTAGTAGATCTTATG-TCT
580 TGTACTGAAGCTCTTGCCAATCATTTCTGCTAAGAGTGATGAGTACTTAGTAGATCTGATGCT-T
*
14330994 TGCTTGTTTGATAT-TCGAACCA-TTCACTA-TTTTGCATTTTGTTATGACACGCAAGTTGCAAA
644 TGCTTGGTTGAT-TCTCG-ACCATTTCACTATTTTTGCATTTT-TTATGACACGCAAGTTGCAAA
* *
14331056 CACAGTTATCATTGTTATCACATTTACTTAAATTGCACAATTCTTTTGTCAACAGTTTAAGGAAT
706 CACAATTATCATTGTTACCACATTTACTTAAATTGCACAATTCTTTTGTCAACAGTTTAAGGAAT
* * * *
14331121 TTCTTTTAAATACCAATCTCTCTGAGGGTATGATACTCTACTTATCAATTTATTACTTGAACGTT
771 TTCTTCTAAATACCAATATCTCTGAGGGTACGATACTCTACTTATCAATTTATCACTTGAACGTT
* *
14331186 GTGTACACTTGCATATTTGCTACAACAATATATTTTACAC
836 GTGTACACTTGCACATTTACTACAACAATATATTTTACAC
14331226 ACGACAGTGC
Statistics
Matches: 754, Mismatches: 111, Indels: 20
0.85 0.13 0.02
Matches are distributed among these distances:
983 141 0.19
984 606 0.80
985 7 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (984 bp):
TGTGGAAATGCAGAGCAGAATCAAGCAGCGAGCCTGATGTTCGTTTTGCGTCTCAACAGAAGTAC
TATTGATCTCTAAATTTGAAAGTAATTTTGTTTAAACAACATTTTACACCCTTTTACTGATCATT
CAAGGGTTGAATATTCTGATACTTTATTTACTTTTATGAATGATTACCAATATCTTTTCTAATAA
ATCTCTTCAATTGAATTATGTTCAAGTGTTGTTAATTCTACATGCTAACAATCTCAAGAATAAGC
ACTTGTTTTGCATGTGAATAATCTCAATTGAAAGCAAGACAGATTTGCTAGAGCATAACTCAATG
TAATGAGCATATATCAGAAGATATGTGTAGTAACTCTTAATGATAAGCTACATTCATTAAGAGTG
AGATAAGTCTTTGTTGAAACAATACATGTTATAGGAATATAATATGGAATTACCATAAAAGTTGC
AATGAAACGACACACCATTGCTTAGTCATTCTAGGAAATTCATAGAAACAAATATTTGTTATGAC
ATTCGTAGATCTAAACTTAGAATTGAAATATTCAAGATCTAGTGATCACAACTTAGTCCTGTACT
GAAGCTCTTGCCAATCATTTCTGCTAAGAGTGATGAGTACTTAGTAGATCTGATGCTTTGCTTGG
TTGATTCTCGACCATTTCACTATTTTTGCATTTTTTATGACACGCAAGTTGCAAACACAATTATC
ATTGTTACCACATTTACTTAAATTGCACAATTCTTTTGTCAACAGTTTAAGGAATTTCTTCTAAA
TACCAATATCTCTGAGGGTACGATACTCTACTTATCAATTTATCACTTGAACGTTGTGTACACTT
GCACATTTACTACAACAATATATTTTACACGCGATAGTCACATGGCAGATCAAAAGTGCAGAGGC
AAAGTTGATAGCTAGTGCTGGGAGCGAAGCCTTGACAACGCGATCGCAAAACCACCTAAGCAAAG
ATACGTTGT
Found at i:14345553 original size:18 final size:19
Alignment explanation
Indices: 14345526--14345568 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
14345516 TTGTGTGACC
*
14345526 CATG-TTTTCC-AAATTTT
1 CATGTTTTTCCTAAAATTT
14345543 CATGTTTTTCCTAAAATTT
1 CATGTTTTTCCTAAAATTT
14345562 -ATGTTTT
1 CATGTTTT
14345569 GTTTCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (19 bp):
CATGTTTTTCCTAAAATTT
Found at i:14352846 original size:21 final size:21
Alignment explanation
Indices: 14352822--14352861 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14352812 TAGAAACATG
*
14352822 ACTTGTTTCGGTAGAAGTTAT
1 ACTTGTATCGGTAGAAGTTAT
*
14352843 ACTTGTATCGTTAGAAGTT
1 ACTTGTATCGGTAGAAGTT
14352862 TGCACTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGTTAT
Found at i:14353570 original size:16 final size:16
Alignment explanation
Indices: 14353530--14353572 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
14353520 GAAAAAAAAG
* *
14353530 AAGAAAAAAATGTTAA
1 AAGAAAAATATGTAAA
*
14353546 AAGAAAAATTTGTAAA
1 AAGAAAAATATGTAAA
14353562 AAGAAAAATAT
1 AAGAAAAATAT
14353573 TTTTTAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (16 bp):
AAGAAAAATATGTAAA
Found at i:14356587 original size:16 final size:19
Alignment explanation
Indices: 14356557--14356594 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
14356547 TTATTTACTA
14356557 TTTGAGATAATTTTTAT-T
1 TTTGAGATAATTTTTATGT
14356575 TTTGA-ATAA-TTTTATGT
1 TTTGAGATAATTTTTATGT
14356592 TTT
1 TTT
14356595 ATTTTTAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (19 bp):
TTTGAGATAATTTTTATGT
Found at i:14378944 original size:134 final size:133
Alignment explanation
Indices: 14378703--14378970 Score: 491
Period size: 134 Copynumber: 2.0 Consensus size: 133
14378693 GAGATACCTC
*
14378703 TTTGCCAAAAAATATGCCAAACCCAGCTGATTAGATGGATCCTGTTATTACAAGAGTTTGATATT
1 TTTGCCAAAAAAGATGCCAAACCCAGCTGATTAGATGGATCCTGTTATTACAAGAGTTTGATATT
* * *
14378768 GAGATTCAAGATAGAAAAGGATCGGAGAATCAGGTAGTAGACCACCTATCTCGTCTGGAATCTAG
66 GAGATTCAAGACAGAAAAGGATCGGAGAATCAGGTAGCAGACCACCTATCTCGTCTAGAATCTAG
14378833 AAG
131 AAG
14378836 TTTGCCAAAAAAGATGCCAAACCCAGGCTGATTAGATGGATCCTGTTATTACAAGAGTTTGATAT
1 TTTGCCAAAAAAGATGCCAAACCCA-GCTGATTAGATGGATCCTGTTATTACAAGAGTTTGATAT
14378901 TGAGATTCAAGACAGAAAAGGATCGGAGAATCAGGTAGCAGACCACCTATCTCGTCTAGAATCTA
65 TGAGATTCAAGACAGAAAAGGATCGGAGAATCAGGTAGCAGACCACCTATCTCGTCTAGAATCTA
14378966 GAAG
130 GAAG
14378970 T
1 T
14378971 GAAGATGGAA
Statistics
Matches: 130, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
133 24 0.18
134 106 0.82
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (133 bp):
TTTGCCAAAAAAGATGCCAAACCCAGCTGATTAGATGGATCCTGTTATTACAAGAGTTTGATATT
GAGATTCAAGACAGAAAAGGATCGGAGAATCAGGTAGCAGACCACCTATCTCGTCTAGAATCTAG
AAG
Found at i:14396429 original size:16 final size:15
Alignment explanation
Indices: 14396408--14396452 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
14396398 TCAATCACTT
14396408 GAAAAAGAA-AAAATGA
1 GAAAAAGAAGAAAA--A
14396424 GAAAAAGGAAGAAAAA
1 GAAAAA-GAAGAAAAA
14396440 GAAAAAGAAGAAA
1 GAAAAAGAAGAAA
14396453 CTTTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.26
16 13 0.48
17 3 0.11
18 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:14398006 original size:13 final size:14
Alignment explanation
Indices: 14397977--14398006 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14397967 TTCAGTACAT
14397977 TGACATTTAACCTC
1 TGACATTTAACCTC
14397991 TGACATTTAA-CTC
1 TGACATTTAACCTC
14398004 TGA
1 TGA
14398007 TTGCGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:14404961 original size:18 final size:18
Alignment explanation
Indices: 14404925--14404963 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
14404915 TATTAATTGC
* **
14404925 TTTGATTGTTTCATGTAA
1 TTTGACTGTTTCACATAA
14404943 TTTGACTGTTTCACATAA
1 TTTGACTGTTTCACATAA
14404961 TTT
1 TTT
14404964 CACATCACCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (18 bp):
TTTGACTGTTTCACATAA
Found at i:14406778 original size:5 final size:5
Alignment explanation
Indices: 14406768--14406811 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
14406758 TCAGTCTTGA
* * * *
14406768 AAAAG AAAAG AACAT AATAG AAAAT AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
14406812 AAATACCCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (5 bp):
AAAAG
Found at i:14408092 original size:17 final size:17
Alignment explanation
Indices: 14408067--14408109 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
14408057 GAATAAACCA
*
14408067 ATTGCAAACATATTATG
1 ATTGCAAACATATTACG
*
14408084 ATTGAAAACATATTACG
1 ATTGCAAACATATTACG
14408101 ATTGCAAAC
1 ATTGCAAAC
14408110 CTATATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (17 bp):
ATTGCAAACATATTACG
Found at i:14413236 original size:15 final size:15
Alignment explanation
Indices: 14413211--14413249 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
14413201 ACAACATATA
14413211 TTTCT-TTTTCTTCT
1 TTTCTCTTTTCTTCT
14413225 TTTCTCTTTTCTTCT
1 TTTCTCTTTTCTTCT
14413240 TCTT-TCTTTT
1 T-TTCTCTTTT
14413250 TTTTAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.22
15 16 0.70
16 2 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTCTTTTCTTCT
Found at i:14413876 original size:18 final size:18
Alignment explanation
Indices: 14413835--14413868 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14413825 ATGTGCTAAC
*
14413835 AAAT-AAAATGCAGTGAA
1 AAATAAAAATGCAATGAA
14413852 AAATAAAAATGCAATGA
1 AAATAAAAATGCAATGA
14413869 CAACTAAATG
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:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (18 bp):
AAATAAAAATGCAATGAA
Found at i:14414329 original size:24 final size:24
Alignment explanation
Indices: 14414277--14414333 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
14414267 TCGGGGCATT
*
14414277 TTCCTTCTCTTCATCCTTCTTCTC
1 TTCCTTCTCTTCATCATTCTTCTC
* *
14414301 TTCCTTCTCTTCCTCATT-TTCTT
1 TTCCTTCTCTTCATCATTCTTCTC
14414324 TCTCCTTCTC
1 T-TCCTTCTC
14414334 AGGTTCCGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.04, C:0.40, G:0.00, T:0.56
Consensus pattern (24 bp):
TTCCTTCTCTTCATCATTCTTCTC
Found at i:14426727 original size:15 final size:16
Alignment explanation
Indices: 14426683--14426731 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
14426673 AAAACTTCTA
*
14426683 AAAAAATCAACAACAAT
1 AAAAAATAAACAA-AAT
14426700 AAAAAATGAAACAAAAT
1 AAAAAAT-AAACAAAAT
*
14426717 TAAAAAT-AACAAAAT
1 AAAAAATAAACAAAAT
14426732 CAAATGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 8 0.28
17 16 0.55
18 5 0.17
ACGTcount: A:0.73, C:0.10, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAAAATAAACAAAAT
Found at i:14431796 original size:18 final size:17
Alignment explanation
Indices: 14431773--14431806 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
14431763 CCCACAGAAT
14431773 TTTTTTCGTATTTTTTTG
1 TTTTTTC-TATTTTTTTG
*
14431791 TTTTTTCTCTTTTTTT
1 TTTTTTCTATTTTTTT
14431807 ATCAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTCTATTTTTTTG
Found at i:14435598 original size:15 final size:15
Alignment explanation
Indices: 14435551--14435599 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 15
14435541 TAAAACTTCT
*
14435551 ACAAAAGTTTATAATA
1 ACAAAA-TTAATAATA
*
14435567 ACAAAA--ACTAA-A
1 ACAAAATTAATAATA
14435579 ACAAAATTAATAATA
1 ACAAAATTAATAATA
14435594 ACAAAA
1 ACAAAA
14435600 CAAATGTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
14 4 0.15
15 7 0.26
16 6 0.22
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.20
Consensus pattern (15 bp):
ACAAAATTAATAATA
Found at i:14436034 original size:15 final size:15
Alignment explanation
Indices: 14436004--14436116 Score: 66
Period size: 15 Copynumber: 7.5 Consensus size: 15
14435994 GCTTGGAAGA
**
14436004 TGCGAGCACTGGTGT
1 TGCGAGCACTCATGT
14436019 TGCGAGCACTCATGT
1 TGCGAGCACTCATGT
* * * *
14436034 TGTGAACACTGGA-GC
1 TGCGAGCACT-CATGT
* *
14436049 TACGAACACTCATGT
1 TGCGAGCACTCATGT
* **
14436064 TGCGTGCACTCACAT
1 TGCGAGCACTCATGT
* *
14436079 TGAGAGCACTGATGT
1 TGCGAGCACTCATGT
* * *
14436094 TGCAAACACTCGTGT
1 TGCGAGCACTCATGT
14436109 TGCGAGCA
1 TGCGAGCA
14436117 TAAACAAAGG
Statistics
Matches: 69, Mismatches: 27, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
14 1 0.01
15 67 0.97
16 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (15 bp):
TGCGAGCACTCATGT
Found at i:14438453 original size:19 final size:20
Alignment explanation
Indices: 14438402--14438451 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
14438392 AAAATGGGGT
*
14438402 AAAAATAAAAGAAATAGAGAG
1 AAAAA-AAAAGAAATAGAAAG
*
14438423 AAGAAAAAAAGAAATTGAAAG
1 AA-AAAAAAAGAAATAGAAAG
14438444 AAAAAAAA
1 AAAAAAAA
14438452 GAGAGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 17 0.65
22 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAGAAATAGAAAG
Found at i:14440954 original size:15 final size:15
Alignment explanation
Indices: 14440913--14440994 Score: 56
Period size: 15 Copynumber: 5.5 Consensus size: 15
14440903 AAGCACAGGT
* *
14440913 GTTGCGAACACTGAA
1 GTTGCGAACACTCAC
* * *
14440928 GCTACGAACACTCAT
1 GTTGCGAACACTCAC
*
14440943 GTTGCGAGCACTCAC
1 GTTGCGAACACTCAC
* * * *
14440958 ATTGAGAACACTGAT
1 GTTGCGAACACTCAC
* *
14440973 GTTGTGAACACTCGC
1 GTTGCGAACACTCAC
14440988 GTTGCGA
1 GTTGCGA
14440995 GCATGAACGA
Statistics
Matches: 48, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (15 bp):
GTTGCGAACACTCAC
Found at i:14441153 original size:18 final size:18
Alignment explanation
Indices: 14441130--14441173 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
14441120 TCATGCATTC
14441130 CATGCATTTCATACAACT
1 CATGCATTTCATACAACT
* * * *
14441148 CGTGCACTTCTTGCAACT
1 CATGCATTTCATACAACT
14441166 CATGCATT
1 CATGCATT
14441174 CCATGCAATG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (18 bp):
CATGCATTTCATACAACT
Found at i:14441180 original size:18 final size:17
Alignment explanation
Indices: 14441130--14441181 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
14441120 TCATGCATTC
*
14441130 CATGCATTTCATACAACT
1 CATGCA-TTCATGCAACT
* *
14441148 CGTGCACTTCTTGCAACT
1 CATGCA-TTCATGCAACT
14441166 CATGCATTCCATGCAA
1 CATGCATT-CATGCAA
14441182 TGTGCTGCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (17 bp):
CATGCATTCATGCAACT
Found at i:14444305 original size:22 final size:22
Alignment explanation
Indices: 14444280--14444362 Score: 130
Period size: 22 Copynumber: 3.8 Consensus size: 22
14444270 ATTGAATTAT
*
14444280 AATCAATCAATTAAATTGGTGC
1 AATCAATCAATTATATTGGTGC
***
14444302 AATCAATCAATTATATTTCCGC
1 AATCAATCAATTATATTGGTGC
14444324 AATCAATCAATTATATTGGTGC
1 AATCAATCAATTATATTGGTGC
14444346 AATCAATCAATTATATT
1 AATCAATCAATTATATT
14444363 TGCATAATAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (22 bp):
AATCAATCAATTATATTGGTGC
Found at i:14444333 original size:44 final size:44
Alignment explanation
Indices: 14444280--14444363 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
14444270 ATTGAATTAT
14444280 AATCAATCAATTAAATTGGTGCAATCAATCAATTATATTTCCGC
1 AATCAATCAATTAAATTGGTGCAATCAATCAATTATATTTCCGC
*
14444324 AATCAATCAATTATATTGGTGCAATCAATCAATTATATTT
1 AATCAATCAATTAAATTGGTGCAATCAATCAATTATATTT
14444364 GCATAATACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (44 bp):
AATCAATCAATTAAATTGGTGCAATCAATCAATTATATTTCCGC
Found at i:14445773 original size:75 final size:75
Alignment explanation
Indices: 14445643--14445801 Score: 295
Period size: 75 Copynumber: 2.1 Consensus size: 75
14445633 AGCAAAAGAT
*
14445643 GATTGAA--AACAACTTAAAAATGAATTTAGAGTTAAGAATTACCTTCAATTGATCTCAGATCAT
1 GATTGAATCAACAACTTAAAAATGAATTTAGAGTTAAGAATTACCTTCAATTGATCTCAAATCAT
14445706 CAATTTAGAA
66 CAATTTAGAA
14445716 GATTGAATCAACAACTTAAAAATGAATTTAGAGTTAAGAATTACCTTCAATTGATCTCAAATCAT
1 GATTGAATCAACAACTTAAAAATGAATTTAGAGTTAAGAATTACCTTCAATTGATCTCAAATCAT
14445781 CAATTTAGAA
66 CAATTTAGAA
14445791 GATTGAATCAA
1 GATTGAATCAA
14445802 GATCCTTGAA
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
73 7 0.08
75 76 0.92
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (75 bp):
GATTGAATCAACAACTTAAAAATGAATTTAGAGTTAAGAATTACCTTCAATTGATCTCAAATCAT
CAATTTAGAA
Found at i:14447771 original size:33 final size:33
Alignment explanation
Indices: 14447726--14447795 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
14447716 ACAGAATATT
14447726 GCAAAAAATTTTGTCAAAGAAAAAGTCATTCTA
1 GCAAAAAATTTTGTCAAAGAAAAAGTCATTCTA
*
14447759 GCAAAAATTTTTGTCAAAGAAAAAGTCATTCTA
1 GCAAAAAATTTTGTCAAAGAAAAAGTCATTCTA
14447792 GCAA
1 GCAA
14447796 TTTAAATCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (33 bp):
GCAAAAAATTTTGTCAAAGAAAAAGTCATTCTA
Found at i:14448610 original size:17 final size:17
Alignment explanation
Indices: 14448588--14448624 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
14448578 AAAAATGCAG
14448588 ATGTAGTGACAATAAAA
1 ATGTAGTGACAATAAAA
14448605 ATGTAGTGACAATAAAA
1 ATGTAGTGACAATAAAA
14448622 ATG
1 ATG
14448625 CAAAGACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (17 bp):
ATGTAGTGACAATAAAA
Found at i:14448632 original size:17 final size:17
Alignment explanation
Indices: 14448595--14448634 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
14448585 CAGATGTAGT
* **
14448595 GACAATAAAAATGTAGT
1 GACAATAAAAATGCAAA
14448612 GACAATAAAAATGCAAA
1 GACAATAAAAATGCAAA
14448629 GACAAT
1 GACAAT
14448635 TATACTACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.17
Consensus pattern (17 bp):
GACAATAAAAATGCAAA
Found at i:14455723 original size:82 final size:84
Alignment explanation
Indices: 14455550--14455794 Score: 298
Period size: 82 Copynumber: 2.9 Consensus size: 84
14455540 GACTGCTACG
* * * * *
14455550 TGTAAGATAATATTGCTGTAGCAACTATGCAAGTGTACACGACGTTCAAGAAATAAAGTGATAAG
1 TGTAAAATAATATTGCTGTAGCAA-TGTGCAAGTGTACACAATGTTCAAGTAATAAAGTGATAAG
*
14455615 TAGAGTATCGTACAATAGCG
65 TAGAGTATCGTACAATAGCA
* * * * *
14455635 TATAAAATAATATTGTTATAGC-ATGTGCAAGTTTACACAATGTCCAAGTAATAAAGT-ATAAGT
1 TGTAAAATAATATTGCTGTAGCAATGTGCAAGTGTACACAATGTTCAAGTAATAAAGTGATAAGT
**
14455698 AGAGTATCGTACTGTCA-CA
66 AGAGTATCGTACAAT-AGCA
**
14455717 TGTAAAATAATATTGCTGTAGCAAATGAACAAGTGTACACAATGTTCAAGTAATAAAGTGATAAG
1 TGTAAAATAATATTGCTGTAGC-AATGTGCAAGTGTACACAATGTTCAAGTAATAAAGTGATAAG
*
14455782 TAAAGTATCGTAC
65 TAGAGTATCGTAC
14455795 CCACAGAGAG
Statistics
Matches: 135, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
82 39 0.29
83 29 0.21
84 32 0.24
85 35 0.26
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (84 bp):
TGTAAAATAATATTGCTGTAGCAATGTGCAAGTGTACACAATGTTCAAGTAATAAAGTGATAAGT
AGAGTATCGTACAATAGCA
Found at i:14457788 original size:15 final size:16
Alignment explanation
Indices: 14457762--14457803 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
14457752 CTAAAAAATT
*
14457762 ATTTTTCTTTTTACAA
1 ATTTTTCTTTTAACAA
*
14457778 ATTTTTCTTTTAACAT
1 ATTTTTCTTTTAACAA
*
14457794 TTTTTTCTTT
1 ATTTTTCTTT
14457804 CTTTTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTCTTTTAACAA
Found at i:14461513 original size:14 final size:14
Alignment explanation
Indices: 14461494--14461520 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14461484 AGCAAGCACG
14461494 TCATTACTTAGTCT
1 TCATTACTTAGTCT
14461508 TCATTACTTAGTC
1 TCATTACTTAGTC
14461521 ATTTTGAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (14 bp):
TCATTACTTAGTCT
Found at i:14469653 original size:15 final size:16
Alignment explanation
Indices: 14469635--14469673 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
14469625 AAAAGAAAAG
*
14469635 AAAGAAAAA-ATGTTA
1 AAAGAAAAATATGTAA
*
14469650 AAAGAAAAATTTGTAA
1 AAAGAAAAATATGTAA
14469666 AAAGAAAA
1 AAAGAAAA
14469674 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (16 bp):
AAAGAAAAATATGTAA
Found at i:14470836 original size:89 final size:88
Alignment explanation
Indices: 14470650--14470880 Score: 259
Period size: 89 Copynumber: 2.5 Consensus size: 88
14470640 TTAAGGGTAT
* * * *
14470650 AAAAAGA-CCTCAAACTTTTTCAAAAGAAGCAATTGAGCCCCTCATTATTATTTTTTTGCACTAA
1 AAAAAGACCCTCAAAC-TTTTCAAAAAAAGCAATTAAG-CCC-C--TACT-TTTTTTTACACTAA
*
14470714 TTTGGATACTTGAACTTTCAAAATACATC
60 TTTGGATACTTAAACTTTCAAAATACATC
*
14470743 AAAAAGGCCCTCAAACATTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTACACTCAA-TTG
1 AAAAAGACCCTCAAAC-TTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTACACT-AATTTG
* * *
14470807 GGTACTTAAACTTTTAAAATGCATC
64 GATACTTAAACTTTCAAAATACATC
* * *
14470832 AAAAAGACCCTCAAACTCTTTCAAATAAAGCAATTAAGTCTCTACTTTT
1 AAAAAGACCCTCAAACT-TTTCAAAAAAAGCAATTAAGCCCCTACTTTT
14470881 ATTAAAAAAT
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
88 1 0.01
89 78 0.64
90 5 0.04
92 1 0.01
93 9 0.07
94 27 0.22
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (88 bp):
AAAAAGACCCTCAAACTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTACACTAATTTGGA
TACTTAAACTTTCAAAATACATC
Found at i:14470990 original size:22 final size:22
Alignment explanation
Indices: 14470965--14471011 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
14470955 TTAAAATTAG
14470965 AAAAAAAAATATAAAA-ATTGTA
1 AAAAAAAAATA-AAAAGATTGTA
* *
14470987 AAAAGAATATAAAAAGATTGTA
1 AAAAAAAAATAAAAAGATTGTA
14471009 AAA
1 AAA
14471012 TTTATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAAAAAAATAAAAAGATTGTA
Found at i:14471001 original size:20 final size:19
Alignment explanation
Indices: 14470939--14471011 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
14470929 AAATATTATT
* * *
14470939 AAATTTTAAAAAATTATTA
1 AAATTGTAAAAAAATATAA
*
14470958 AAATTAGAAAAAAAAATATAA
1 AAATT-G-TAAAAAAATATAA
14470979 AAATTGTAAAAAGAATATAAA
1 AAATTGTAAAAA-AATAT-AA
14471000 AAGATTGTAAAA
1 AA-ATTGTAAAA
14471012 TTTATAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.23
20 6 0.14
21 19 0.43
22 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
AAATTGTAAAAAAATATAA
Found at i:14471052 original size:20 final size:20
Alignment explanation
Indices: 14471027--14471110 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 20
14471017 AAAAAACGTA
14471027 AAATATTATAAAATATATAG
1 AAATATTATAAAATATATAG
* *
14471047 AAATA-TA-AAAAAATACA-
1 AAATATTATAAAATATATAG
* *
14471064 AAATTTTATAAAGT-TATAAG
1 AAATATTATAAAATATAT-AG
*
14471084 AAA-ATTATACAGAATATAAAG
1 AAATATTATA-A-AATATATAG
14471105 AAATAT
1 AAATAT
14471111 AAAATTCGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
17 4 0.09
18 12 0.26
19 11 0.23
20 9 0.19
21 7 0.15
22 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (20 bp):
AAATATTATAAAATATATAG
Found at i:14471057 original size:28 final size:26
Alignment explanation
Indices: 14470992--14471114 Score: 75
Period size: 28 Copynumber: 4.3 Consensus size: 26
14470982 TTGTAAAAAG
* *
14470992 AATATAAAAAGATTGTAAAATTTATAA
1 AATATAAAAA-ATTATAAAATATATAA
* *
14471019 AAAACGTAAAATATTATAAAATATATAGA
1 AATA--TAAAAAATTATAAAATATATA-A
* * *
14471048 AATATAAAAAAATACAAAATTTTATAA
1 AATATAAAAAATTATAAAA-TATATAA
* *
14471075 AGTTATAAGAAAATTATACAGAATATAAAGA
1 A-ATATAA-AAAATTATA-A-AATATATA-A
14471106 AATATAAAA
1 AATATAAAA
14471115 TTCGTAAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
27 17 0.24
28 23 0.32
29 18 0.25
30 10 0.14
31 4 0.06
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (26 bp):
AATATAAAAAATTATAAAATATATAA
Found at i:14471135 original size:10 final size:10
Alignment explanation
Indices: 14470939--14471140 Score: 59
Period size: 10 Copynumber: 20.7 Consensus size: 10
14470929 AAATATTATT
*
14470939 AAATTTTAAA
1 AAATTATAAA
*
14470949 AAATTAT-TA
1 AAATTATAAA
*
14470958 AAATTAGAAA
1 AAATTATAAA
**
14470968 AAAAAATATAA
1 AAATTATA-AA
*
14470979 AAATTGTAAA
1 AAATTATAAA
*
14470989 AAGAATATAAA
1 AA-ATTATAAA
*
14471000 AAGATTGT-AA
1 AA-ATTATAAA
*
14471010 AATTTATAAA
1 AAATTATAAA
**
14471020 AAA-CGTAAA
1 AAATTATAAA
*
14471029 ATATTATAAA
1 AAATTATAAA
* *
14471039 ATA-TAT-AG
1 AAATTATAAA
14471047 AAA-TATAAA
1 AAATTATAAA
*
14471056 AAA--ATACA
1 AAATTATAAA
* *
14471064 AAATTTTATA
1 AAATTATAAA
*
14471074 AAGTTATAAGA
1 AAATTATAA-A
*
14471085 AAATTATACA
1 AAATTATAAA
*
14471095 GAA-TATAAA
1 AAATTATAAA
14471104 GAAA-TAT-AA
1 -AAATTATAAA
* *
14471113 AATTCGTAAAAA
1 AAAT--TATAAA
14471125 AAATTAT-AA
1 AAATTATAAA
14471134 AAATTAT
1 AAATTAT
14471141 CGTACCAAAA
Statistics
Matches: 138, Mismatches: 40, Indels: 29
0.67 0.19 0.14
Matches are distributed among these distances:
8 15 0.11
9 39 0.28
10 50 0.36
11 29 0.21
12 5 0.04
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (10 bp):
AAATTATAAA
Found at i:14471700 original size:89 final size:90
Alignment explanation
Indices: 14471494--14471711 Score: 280
Period size: 90 Copynumber: 2.4 Consensus size: 90
14471484 TAAGAGCAAT
** *
14471494 GGCTTAATTGC-TTTTTTGAAAATTTTTTAGGGTCTTTTTTTATGCATTTTGAAAGTTCAAGCAC
1 GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTC-TTTTTTATGCATTTTGAAAGTTCAAGCAC
** *
14471558 CCAATTGAGTGGGGAAAACAAACAAG
65 CCAATTGAGTGGCAAAAAAAAACAAG
* * ** *
14471584 GGCTTAATTGCTTTTTTTGAATAAGTTTGAGGGTCTTTTTTATGCATTTTGAAAGTTCATGTGCT
1 GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTTATGCATTTTGAAAGTTCAAGCACC
* *
14471649 CAATTGAGT-GCAAAAAAAAAGATG
66 CAATTGAGTGGCAAAAAAAAACAAG
*
14471673 GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGTG-CTTTTT
1 GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTT
14471712 ACGCCCTTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
88 6 0.05
89 41 0.37
90 46 0.41
91 19 0.17
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (90 bp):
GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTTATGCATTTTGAAAGTTCAAGCACC
CAATTGAGTGGCAAAAAAAAACAAG
Found at i:14471891 original size:18 final size:17
Alignment explanation
Indices: 14471857--14471907 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
14471847 ATCACTTTTA
*
14471857 AATTTATTACTTGAATTT
1 AATTTATT-CTTTAATTT
*
14471875 CATTTATTCCTTTAA-TT
1 AATTTATT-CTTTAATTT
14471892 AATTTATTCTTTAATT
1 AATTTATTCTTTAATT
14471908 ATTTAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 6 0.21
17 10 0.36
18 12 0.43
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTTATTCTTTAATTT
Found at i:14471919 original size:15 final size:15
Alignment explanation
Indices: 14471876--14471923 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
14471866 CTTGAATTTC
14471876 ATTTATTCCTTTAATT
1 ATTTATT-CTTTAATT
14471892 AATTTATTCTTTAATT
1 -ATTTATTCTTTAATT
14471908 ATTTAATT-TTTAATT
1 ATTT-ATTCTTTAATT
14471923 A
1 A
14471924 AAATAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.40
16 11 0.37
17 7 0.23
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTATTCTTTAATT
Found at i:14472069 original size:32 final size:33
Alignment explanation
Indices: 14472033--14472118 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 33
14472023 AGATAAATTT
*
14472033 ATTTAAAGGAATAAATGAAATTTCAATAA-TAA
1 ATTTAAAGGAATAAATGAAATTTAAATAACTAA
* *
14472065 ATTTAAAAGTAATAAATGAAA-TTAAATAACTTTA
1 ATTT-AAAGGAATAAATGAAATTTAAATAAC-TAA
14472099 A-TTAAAGG-ATAAATGAAATT
1 ATTTAAAGGAATAAATGAAATT
14472119 AAAGTAGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
31 10 0.22
32 16 0.35
33 17 0.37
34 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (33 bp):
ATTTAAAGGAATAAATGAAATTTAAATAACTAA
Found at i:14472104 original size:33 final size:30
Alignment explanation
Indices: 14472033--14472131 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 30
14472023 AGATAAATTT
*
14472033 ATTTAAAGGAATAAATGAAATTTCAATAATAA
1 ATTTAAA-GAATAAATGAAA-TTAAATAATAA
*
14472065 ATTTAAAAGTAATAAATGAAATTAAATAACTTTA
1 ATTT-AAAG-AATAAATGAAATTAAATAA--TAA
* *
14472099 A-TTAAAGGATAAATGAAATTAAAGTAGTAA
1 ATTTAAAGAATAAATGAAATTAAA-TAATAA
14472129 ATT
1 ATT
14472132 GAAAAGTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
30 3 0.05
31 16 0.29
32 18 0.32
33 16 0.29
34 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (30 bp):
ATTTAAAGAATAAATGAAATTAAATAATAA
Found at i:14482448 original size:18 final size:19
Alignment explanation
Indices: 14482420--14482455 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14482410 TCGTAGGGGT
*
14482420 TATTATAGTCAATATTCAG
1 TATTATAGTCAAGATTCAG
14482439 TATT-TAGTCAAGATTCA
1 TATTATAGTCAAGATTCA
14482456 TCGACTTACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
TATTATAGTCAAGATTCAG
Found at i:14484643 original size:5 final size:5
Alignment explanation
Indices: 14484633--14484663 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
14484623 GATTCAAACC
*
14484633 AGAAA AGAAA ATAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
14484664 AATATCCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (5 bp):
AGAAA
Found at i:14490489 original size:286 final size:287
Alignment explanation
Indices: 14489970--14490542 Score: 977
Period size: 286 Copynumber: 2.0 Consensus size: 287
14489960 GCTTAGTGTG
*
14489970 AGCAGCATCATTAGGGAACAGTTATATATGTACAGATACTGTATCGATGGCTGAGGTATCGCATA
1 AGCAGCATCATTAGGGAACAGTTATATATGTACAGATACTGTATCGATGGCTGAGGTACCGCATA
*
14490035 TGTTTCGAGTCCTCATTAGCTTAGTGTGAACAGCATCGTATACTAGTAACAAGAATGACCTTAGG
66 TGTTTCGAGTCCTCAGTAGCTTAGTGTGAACAGCATCGTATACTAGTAACAAGAATGACCTTAGG
* *
14490100 TCAAAAAGGATGAAATCTGATTATAGATTATTGAAGTACAATCGTGTGATTACAGATTGTACAAC
131 CCAAAAAGGATGAAATCTGATTATAGATTACTGAAGTACAATCGTGTGATTACAGATTGTACAAC
* * *
14490165 TCATGTTATTTGGTAAATTATTAAACTCTACGAACTTGCTAAGCTATGAAAACTTACCTGTGAAT
196 TCATGTTATTCGGTAAATTATTAAACTCTACAAACTTGCTAAGCTATGAAAACTTACCTATGAAT
**
14490230 TTGTTGTTGTTTTGTAAATTCTACTTT
261 TTGTTGTTGTTTTACAAATTCTACTTT
* *
14490257 AGCAGCATCGTTAGGGAACAGTTATATATGTACAGATACTGTATCGATGGTTGAGGTACCGCATA
1 AGCAGCATCATTAGGGAACAGTTATATATGTACAGATACTGTATCGATGGCTGAGGTACCGCATA
* * *
14490322 TGTTTTGAGTCCTC-GTCGCTTAGTGTGAACAGCATCGTATACTAGTAACAAGAATGACCTTGGG
66 TGTTTCGAGTCCTCAGTAGCTTAGTGTGAACAGCATCGTATACTAGTAACAAGAATGACCTTAGG
* *
14490386 CCAAAAGGGATGAAATCTGATTATAGATTACTGAAGTACAGTCGTGTGATTACAGATTGTACAAC
131 CCAAAAAGGATGAAATCTGATTATAGATTACTGAAGTACAATCGTGTGATTACAGATTGTACAAC
*
14490451 TCATGTTATTCGGTAAATTATTAAACTCTACAAACTTGCTAAGCTATGAAAGCTTACCTATGAAT
196 TCATGTTATTCGGTAAATTATTAAACTCTACAAACTTGCTAAGCTATGAAAACTTACCTATGAAT
*
14490516 TTGTTGTTGTTTTACAGATTCTACTTT
261 TTGTTGTTGTTTTACAAATTCTACTTT
14490543 GTTGCTTGAA
Statistics
Matches: 268, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
286 193 0.72
287 75 0.28
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (287 bp):
AGCAGCATCATTAGGGAACAGTTATATATGTACAGATACTGTATCGATGGCTGAGGTACCGCATA
TGTTTCGAGTCCTCAGTAGCTTAGTGTGAACAGCATCGTATACTAGTAACAAGAATGACCTTAGG
CCAAAAAGGATGAAATCTGATTATAGATTACTGAAGTACAATCGTGTGATTACAGATTGTACAAC
TCATGTTATTCGGTAAATTATTAAACTCTACAAACTTGCTAAGCTATGAAAACTTACCTATGAAT
TTGTTGTTGTTTTACAAATTCTACTTT
Found at i:14491114 original size:21 final size:21
Alignment explanation
Indices: 14491064--14491115 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
14491054 AGTTTTTAGT
* *
14491064 ATCGGTAGAAGTATGACTTGT
1 ATCGGTAGAAGTATCACTTGC
* *
14491085 TTCGATAGAAGT-TACACTTGC
1 ATCGGTAGAAGTAT-CACTTGC
14491106 ATCGGTAGAA
1 ATCGGTAGAA
14491116 ATTTGCACTG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (21 bp):
ATCGGTAGAAGTATCACTTGC
Found at i:14506487 original size:2 final size:2
Alignment explanation
Indices: 14506442--14506475 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14506432 TGTATCTATC
14506442 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
14506476 AGTATTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14507670 original size:99 final size:99
Alignment explanation
Indices: 14507499--14507704 Score: 351
Period size: 99 Copynumber: 2.1 Consensus size: 99
14507489 GCCACTTTTT
* *
14507499 AGAATCGTAAAATAAATCTGAAATAAAACTTAATAAACCATAAGCCAGAATCTGTCATATCAAAT
1 AGAATCGTAAAATAAATCTAAAATAAAACTTAATAAACCATAAACCAGAATCTGTCATATCAAAT
*
14507564 CATCAAGAATAAATCAAGAACAAAATTATATGCG
66 CATCAAGAATAAATCAAGAACAAAACTATATGCG
* *
14507598 AGAATCGTAAAATAAATCTAAAATAAAACTTAATAAACCATAAATCAGAATCTGTCATGTCAAAT
1 AGAATCGTAAAATAAATCTAAAATAAAACTTAATAAACCATAAACCAGAATCTGTCATATCAAAT
14507663 CATCAAGAATAAATCAAGAACAAAACTATATGCG
66 CATCAAGAATAAATCAAGAACAAAACTATATGCG
*
14507697 -GAAACGTA
1 AGAATCGTA
14507705 CTTGAATCCA
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 7 0.07
99 94 0.93
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (99 bp):
AGAATCGTAAAATAAATCTAAAATAAAACTTAATAAACCATAAACCAGAATCTGTCATATCAAAT
CATCAAGAATAAATCAAGAACAAAACTATATGCG
Found at i:14510813 original size:31 final size:32
Alignment explanation
Indices: 14510778--14510838 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
14510768 AGCTTCCAGC
*
14510778 TGAAAGTGTTTTTAAG-TG-AAATGTTTTCAGT
1 TGAAAATG-TTTTAAGTTGAAAATGTTTTCAGT
*
14510809 TGAAAATGTTTTCAGTTGAAAATGTTTTCA
1 TGAAAATGTTTTAAGTTGAAAATGTTTTCA
14510839 ACGTGTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 6 0.23
31 9 0.35
32 11 0.42
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (32 bp):
TGAAAATGTTTTAAGTTGAAAATGTTTTCAGT
Found at i:14510815 original size:16 final size:16
Alignment explanation
Indices: 14510796--14510838 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
14510786 TTTTTAAGTG
14510796 AAATGTTTTCAGTTGA
1 AAATGTTTTCAGTTGA
14510812 AAATGTTTTCAGTTGA
1 AAATGTTTTCAGTTGA
14510828 AAATGTTTTCA
1 AAATGTTTTCA
14510839 ACGTGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (16 bp):
AAATGTTTTCAGTTGA
Found at i:14513749 original size:30 final size:29
Alignment explanation
Indices: 14513675--14513802 Score: 96
Period size: 30 Copynumber: 4.2 Consensus size: 29
14513665 ATTAATCACG
** *
14513675 TTAATATTAAATTAATAAAATATTATCTAGA
1 TTAATATTAAATTAATTTAATA-TATC-ATA
* *
14513706 TAAATATTAAATTAAATTTGATATATCATA
1 TTAATATTAAATT-AATTTAATATATCATA
* * *
14513736 TTAATATTGAATTAA-TAAATACTATCTAGA
1 TTAATATTAAATTAATTTAATA-TATC-ATA
* * *
14513766 TAAATATTTAATTTAATTTAATATTTCATA
1 TTAATA-TTAAATTAATTTAATATATCATA
14513796 TTAATAT
1 TTAATAT
14513803 CTAGATAAAT
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
28 4 0.05
29 7 0.09
30 27 0.36
31 26 0.35
32 11 0.15
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (29 bp):
TTAATATTAAATTAATTTAATATATCATA
Found at i:14513770 original size:60 final size:61
Alignment explanation
Indices: 14513675--14513802 Score: 195
Period size: 60 Copynumber: 2.1 Consensus size: 61
14513665 ATTAATCACG
* *
14513675 TTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTGATATATCATA
1 TTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATATATCATA
* * * *
14513736 TTAATATTGAATTAAT-AAATACTATCTAGATAAATATTTAATTTAATTTAATATTTCATA
1 TTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATATATCATA
14513796 TTAATAT
1 TTAATAT
14513803 CTAGATAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 46 0.75
61 15 0.25
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (61 bp):
TTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTTAATATATCATA
Found at i:14516912 original size:28 final size:28
Alignment explanation
Indices: 14516881--14516947 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
14516871 TTCTGAGTTG
*
14516881 GAAACAGATTAACACTCTACTCGAGCCA
1 GAAACAGATTAACACTCTACCCGAGCCA
* * * *
14516909 GAAACAGAATACCATTCTACCCGAGCTA
1 GAAACAGATTAACACTCTACCCGAGCCA
14516937 GAAACAGATTA
1 GAAACAGATTA
14516948 CTCCTTAAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (28 bp):
GAAACAGATTAACACTCTACCCGAGCCA
Found at i:14517170 original size:26 final size:26
Alignment explanation
Indices: 14517140--14517190 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
14517130 CTTCCAGAAA
*
14517140 TTTAGCTCATACGAGCCCAGACGGAG
1 TTTAGCTCATACGAGCCCAAACGGAG
* *
14517166 TTTAGCTCTTACGAGCTCAAACGGA
1 TTTAGCTCATACGAGCCCAAACGGA
14517191 ATATCGTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (26 bp):
TTTAGCTCATACGAGCCCAAACGGAG
Found at i:14517217 original size:25 final size:25
Alignment explanation
Indices: 14517170--14517253 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
14517160 ACGGAGTTTA
*
14517170 GCTCTTACGAGCTCAAACGGAATATC
1 GCTCTTACGAGC-CAAACAGAATATC
* * *
14517196 GTTCTTATGAGCCAAACAGAATATT
1 GCTCTTACGAGCCAAACAGAATATC
**
14517221 GCTCTTACGAGCCAGTCAGAATATC
1 GCTCTTACGAGCCAAACAGAATATC
14517246 GCTCTTAC
1 GCTCTTAC
14517254 AAGCTAGAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 39 0.80
26 10 0.20
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (25 bp):
GCTCTTACGAGCCAAACAGAATATC
Found at i:14517827 original size:11 final size:11
Alignment explanation
Indices: 14517813--14517838 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14517803 AAACTTCCAT
14517813 AAACTTTCAAG
1 AAACTTTCAAG
14517824 AAACTTTCAAG
1 AAACTTTCAAG
14517835 AAAC
1 AAAC
14517839 AACTCATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (11 bp):
AAACTTTCAAG
Found at i:14520131 original size:33 final size:33
Alignment explanation
Indices: 14520072--14520142 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 33
14520062 AATTTTCAAT
*
14520072 AAATAAAAAATTTATAAAATTATT-AAATATTAA
1 AAATAAAAAA-TTATAAAATTATTAAAAAATTAA
*
14520105 AAATAAAAAA-TATAAATATTTTTTAAAAAATTAA
1 AAATAAAAAATTATAAA-A-TTATTAAAAAATTAA
14520139 AAAT
1 AAAT
14520143 TAATATGGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 6 0.18
32 1 0.03
33 14 0.42
34 12 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATAAAAAATTATAAAATTATTAAAAAATTAA
Found at i:14521621 original size:16 final size:16
Alignment explanation
Indices: 14521600--14521652 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
14521590 TTTGAATAAT
14521600 GGGTACCCGAATTTTC
1 GGGTACCCGAATTTTC
* **
14521616 GGGTACTCGTAATAATC
1 GGGTACCCG-AATTTTC
14521633 GGGTACCC-ATATTTTC
1 GGGTACCCGA-ATTTTC
14521649 GGGT
1 GGGT
14521653 CACAAGGTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 16 0.55
17 12 0.41
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (16 bp):
GGGTACCCGAATTTTC
Found at i:14524625 original size:19 final size:20
Alignment explanation
Indices: 14524603--14524657 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
14524593 AAAATTAAGT
*
14524603 ATTTCTTAAAACAT-GAAAG
1 ATTTCTTAAAACATAAAAAG
* *
14524622 ATTTATTTAAAATATAAAAAG
1 ATTT-CTTAAAACATAAAAAG
*
14524643 ATTTC-TAAAAAATAA
1 ATTTCTTAAAACATAA
14524658 GTAATTCTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 13 0.45
20 8 0.28
21 8 0.28
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTCTTAAAACATAAAAAG
Found at i:14525176 original size:20 final size:19
Alignment explanation
Indices: 14525153--14525190 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
14525143 AAAAAAAATC
*
14525153 AAAATATTCTTTAAAATTTA
1 AAAATATT-TATAAAATTTA
14525173 AAAATATTTATAAAATTT
1 AAAATATTTATAAAATTT
14525191 TCTCAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATATTTATAAAATTTA
Found at i:14529540 original size:21 final size:21
Alignment explanation
Indices: 14529516--14529603 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
14529506 CAAATATATA
14529516 TACCTTAACAATCGAGTTACC
1 TACCTTAACAATCGAGTTACC
* * * *
14529537 TACCTTTACAATTGATTTATC
1 TACCTTAACAATCGAGTTACC
*
14529558 TACCTTTAA-AATCTAGTTACC
1 TACC-TTAACAATCGAGTTACC
* * * *
14529579 TAACTTTACAATCGATTTATC
1 TACCTTAACAATCGAGTTACC
14529600 TACC
1 TACC
14529604 CAAATTTTAC
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.06
21 44 0.88
22 3 0.06
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.39
Consensus pattern (21 bp):
TACCTTAACAATCGAGTTACC
Found at i:14529576 original size:42 final size:42
Alignment explanation
Indices: 14529516--14529603 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
14529506 CAAATATATA
* *
14529516 TACCTTAACAATCGAGTTACCTACCTTTACAATTGATTTATC
1 TACCTTAACAATCGAGTTACCTAACTTTACAATCGATTTATC
*
14529558 TACCTTTAA-AATCTAGTTACCTAACTTTACAATCGATTTATC
1 TACC-TTAACAATCGAGTTACCTAACTTTACAATCGATTTATC
14529600 TACC
1 TACC
14529604 CAAATTTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.39
Consensus pattern (42 bp):
TACCTTAACAATCGAGTTACCTAACTTTACAATCGATTTATC
Found at i:14531937 original size:20 final size:19
Alignment explanation
Indices: 14531899--14531941 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
14531889 AAATAAACCA
14531899 AATTTGATACTTGAATATT
1 AATTTGATACTTGAATATT
*
14531918 CAATTTGATACCTTG-CTATT
1 -AATTTGATA-CTTGAATATT
14531938 AATT
1 AATT
14531942 CTTCCTCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (19 bp):
AATTTGATACTTGAATATT
Found at i:14532576 original size:27 final size:26
Alignment explanation
Indices: 14532533--14532588 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
14532523 AAAACGCTTT
* *
14532533 TAAAAAAATAAATAATTTGTAAAA-A
1 TAAAAAAATAAACAATTTATAAAATA
14532558 TAAAAGAAATTAAACAATTTATAAAATA
1 TAAAA-AAA-TAAACAATTTATAAAATA
14532586 TAA
1 TAA
14532589 TAATGCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 3 0.12
27 14 0.54
28 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (26 bp):
TAAAAAAATAAACAATTTATAAAATA
Found at i:14538967 original size:27 final size:27
Alignment explanation
Indices: 14538937--14539014 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
14538927 ATATAACGGG
*
14538937 GTGGTGCCTACCTGAT-AGGCGGCACTA
1 GTGGTGCCTACCTG-TCAGGCGGCACCA
*
14538964 GTGGTGCCTACCTGTCAGGAGGCACCA
1 GTGGTGCCTACCTGTCAGGCGGCACCA
* *
14538991 ATGGTGCCTTCCTGTCAGGCGGCA
1 GTGGTGCCTACCTGTCAGGCGGCA
14539015 TCAACCCGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (27 bp):
GTGGTGCCTACCTGTCAGGCGGCACCA
Found at i:14543288 original size:26 final size:26
Alignment explanation
Indices: 14543239--14543288 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
14543229 TCTATTAAAA
**
14543239 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
14543265 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
14543289 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:14543365 original size:6 final size:6
Alignment explanation
Indices: 14543354--14543388 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
14543344 ATATTTGCAT
14543354 ACATAA ACATAA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATAA ACATAA ACATAA ACATA
14543389 TTTAATTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:14543834 original size:6 final size:6
Alignment explanation
Indices: 14543823--14543847 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14543813 ATAGTACTGC
14543823 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
14543848 CCGGTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:14545442 original size:25 final size:21
Alignment explanation
Indices: 14545395--14545440 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
14545385 AAAAATTGAG
14545395 ATTATCAATCCGTCAGAAGTA
1 ATTATCAATCCGTCAGAAGTA
*
14545416 ATTATCAATCTGTCAGAAGTA
1 ATTATCAATCCGTCAGAAGTA
14545437 ATTA
1 ATTA
14545441 ATATAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
ATTATCAATCCGTCAGAAGTA
Found at i:14546634 original size:17 final size:17
Alignment explanation
Indices: 14546612--14546644 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14546602 TTACAATAAA
*
14546612 TAAATAATATTTAAATT
1 TAAATAACATTTAAATT
14546629 TAAATAACATTTAAAT
1 TAAATAACATTTAAAT
14546645 AAATTTTTTT
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:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATAACATTTAAATT
Found at i:14547119 original size:15 final size:15
Alignment explanation
Indices: 14547080--14547113 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
14547070 TTAATATTTT
*
14547080 TTTAAAAAATTATTA
1 TTTAAATAATTATTA
*
14547095 TTTAAATAATTTTTA
1 TTTAAATAATTATTA
14547110 TTTA
1 TTTA
14547114 TTTAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAAATAATTATTA
Found at i:14561165 original size:4 final size:4
Alignment explanation
Indices: 14561156--14561199 Score: 63
Period size: 4 Copynumber: 10.8 Consensus size: 4
14561146 AGAAGAAAAG
14561156 GAAA GAAA GAAA GAAA GGAGAA G-AA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAA
14561200 GAAGGAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.08
4 29 0.78
5 3 0.08
6 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:14561176 original size:31 final size:31
Alignment explanation
Indices: 14561141--14561212 Score: 112
Period size: 31 Copynumber: 2.3 Consensus size: 31
14561131 GATAGCAGGG
14561141 GGAGAAGAAGAAAAGGAAAGAAAGAAAG-A-AA
1 GGAGAAGAAG-AAA-GAAAGAAAGAAAGAAGAA
14561172 GGAGAAGAAGAAAGAAAGAAAGAAAGAAGAA
1 GGAGAAGAAGAAAGAAAGAAAGAAAGAAGAA
14561203 GGAGAAGAAG
1 GGAGAAGAAG
14561213 GAGAAGAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
29 13 0.33
30 4 0.10
31 22 0.56
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (31 bp):
GGAGAAGAAGAAAGAAAGAAAGAAAGAAGAA
Found at i:14561177 original size:25 final size:25
Alignment explanation
Indices: 14561145--14561208 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
14561135 GCAGGGGGAG
14561145 AAGAAGAA-AAGGAAAGAAAGAAAGA
1 AAGAAGAAGAA-GAAAGAAAGAAAGA
*
14561170 AAGGAGAAGAAGAAAGAAAGAAAGA
1 AAGAAGAAGAAGAAAGAAAGAAAGA
*
14561195 AAGAAGAAGGAGAA
1 AAGAAGAAGAAGAA
14561209 GAAGGAGAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (25 bp):
AAGAAGAAGAAGAAAGAAAGAAAGA
Found at i:14561219 original size:25 final size:24
Alignment explanation
Indices: 14561148--14561220 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
14561138 GGGGGAGAAG
14561148 AAGAA-AAGGA-AAGAAAGAAAGA
1 AAGAAGAAGGAGAAGAAAGAAAGA
* *
14561170 AAGGAGAAGAAGAAAGAAAGAAAGA
1 AAGAAGAAGGAG-AAGAAAGAAAGA
*
14561195 AAGAAGAAGGAGAAGAAGGAGAAGA
1 AAGAAGAAGGAGAAGAAAGA-AAGA
14561220 A
1 A
14561221 TGTTAATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
22 4 0.10
23 4 0.10
24 7 0.17
25 27 0.64
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
AAGAAGAAGGAGAAGAAAGAAAGA
Found at i:14561400 original size:21 final size:21
Alignment explanation
Indices: 14561374--14561420 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
14561364 TAGGTTGATT
14561374 AAAGGAGAAAAAATCTAAAAG
1 AAAGGAGAAAAAATCTAAAAG
14561395 AAAGGAGAAAAAATCTAAAAG
1 AAAGGAGAAAAAATCTAAAAG
14561416 AAAGG
1 AAAGG
14561421 TAAATGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.66, C:0.04, G:0.21, T:0.09
Consensus pattern (21 bp):
AAAGGAGAAAAAATCTAAAAG
Found at i:14561511 original size:25 final size:24
Alignment explanation
Indices: 14561480--14561534 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
14561470 TTATTGTAAG
*
14561480 TTATTTGTTTTGTTTAATT-TAATTT
1 TTATTTGGTTTG-TT-ATTATAATTT
*
14561505 TTATTTGGTTTGTTATTATTATTT
1 TTATTTGGTTTGTTATTATAATTT
14561529 TTATTT
1 TTATTT
14561535 AGTAGAGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 3 0.11
24 13 0.48
25 11 0.41
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (24 bp):
TTATTTGGTTTGTTATTATAATTT
Found at i:14563012 original size:28 final size:28
Alignment explanation
Indices: 14562980--14563035 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
14562970 TATGGGTCAG
*
14562980 GGTTTCACGTTTAAGGATTAAGGTTTAT
1 GGTTTCACATTTAAGGATTAAGGTTTAT
* *
14563008 GGTTTCACATTTAGGGTTTAAGGTTTAT
1 GGTTTCACATTTAAGGATTAAGGTTTAT
14563036 AATTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.25, T:0.45
Consensus pattern (28 bp):
GGTTTCACATTTAAGGATTAAGGTTTAT
Done.