Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 51 of 79
Found at i:17220848 original size:16 final size:17
Alignment explanation
Indices: 17220829--17220865 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17220819 CAGTAATATA
*
17220829 ATTATATTTCT-TAAAT
1 ATTATATTACTATAAAT
17220845 ATTA-ATTACTATAAAT
1 ATTATATTACTATAAAT
17220861 ATTAT
1 ATTAT
17220866 TAAGTATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATATTACTATAAAT
Found at i:17232660 original size:13 final size:13
Alignment explanation
Indices: 17232642--17232676 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
17232632 AATTTTAAAA
17232642 TATTTTTAATTTT
1 TATTTTTAATTTT
*
17232655 TATTTTTATTTTT
1 TATTTTTAATTTT
17232668 TATTTTTAA
1 TATTTTTAA
17232677 AATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTAATTTT
Found at i:17232666 original size:5 final size:6
Alignment explanation
Indices: 17232642--17232675 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
17232632 AATTTTAAAA
17232642 TATTTT TAATTTT TATTTT TATTTTT TATTTT TA
1 TATTTT T-ATTTT TATTTT TA-TTTT TATTTT TA
17232676 AAATAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:17235624 original size:22 final size:22
Alignment explanation
Indices: 17235596--17235666 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
17235586 TAATATTATA
17235596 TATATTATGATTTTTATTAAAT
1 TATATTATGATTTTTATTAAAT
* * * *
17235618 TATATTAAGAATGTTATTAAAA
1 TATATTATGATTTTTATTAAAT
*
17235640 TATA-TATTATTTTTATTAAAT
1 TATATTATGATTTTTATTAAAT
17235661 TATATT
1 TATATT
17235667 TAATAATAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 16 0.41
22 23 0.59
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TATATTATGATTTTTATTAAAT
Found at i:17236433 original size:5 final size:5
Alignment explanation
Indices: 17236419--17236448 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
17236409 CACAGTGCGT
17236419 CCCCA CCCCCA CCCCA CCCCA CCCCA CCCC
1 CCCCA -CCCCA CCCCA CCCCA CCCCA CCCC
17236449 GATTGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCCA
Found at i:17240162 original size:42 final size:42
Alignment explanation
Indices: 17240116--17240243 Score: 256
Period size: 42 Copynumber: 3.0 Consensus size: 42
17240106 TTTTTATCTG
17240116 TTAGTACTATCACTAAAGCCTTAAATTGTAAACTTGAATTCT
1 TTAGTACTATCACTAAAGCCTTAAATTGTAAACTTGAATTCT
17240158 TTAGTACTATCACTAAAGCCTTAAATTGTAAACTTGAATTCT
1 TTAGTACTATCACTAAAGCCTTAAATTGTAAACTTGAATTCT
17240200 TTAGTACTATCACTAAAGCCTTAAATTGTAAACTTGAATTCT
1 TTAGTACTATCACTAAAGCCTTAAATTGTAAACTTGAATTCT
17240242 TT
1 TT
17240244 CTTGGTCATT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (42 bp):
TTAGTACTATCACTAAAGCCTTAAATTGTAAACTTGAATTCT
Found at i:17242758 original size:20 final size:20
Alignment explanation
Indices: 17242733--17242772 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17242723 TCAGCATTGA
*
17242733 ATAGCTAATCTTTAGGGATT
1 ATAGCTAATCTTTAGAGATT
* *
17242753 ATAGCTGATTTTTAGAGATT
1 ATAGCTAATCTTTAGAGATT
17242773 CTAATTAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (20 bp):
ATAGCTAATCTTTAGAGATT
Found at i:17246732 original size:276 final size:277
Alignment explanation
Indices: 17246236--17247001 Score: 1151
Period size: 277 Copynumber: 2.8 Consensus size: 277
17246226 GGATCCAGCT
17246236 AATGGGTATGGGTCAAACTACTTTTTGTATCATTGGAACTGCTTAAAAGGGTTACCATAAATCAG
1 AATGGGTATGGGTCAAACTACTTTTTGTATCATTGGAACTGCTTAAAAGGGTTACCATAAATCAG
* *
17246301 CTAGATCAAAAAGACGGATCATTGAGTAAAAAGGTTACTCGGTAGAAAATCCTATCCACATGAAT
66 CTAGATCAAAAAGATGGATCATTGAG-CAAAAGGTTACTCGGTAGAAAATCCTATCCACATGAAT
* * *
17246366 GGTAATCTACTTGTAAGTAGAATGGTCAATGGCTGTTTAGCATTGGATAATATTTTGCTC-GACA
130 GGTAGTCTACTTGGAAGTAGAATGGTCAATGGCTGTTAAGCATTGGATAATATTTTGC-CAGACA
* ** *
17246430 GAATCATCCACACTGATGAGCAGCTAGATCAAAAAGATGGATCATTAAACAAAAGGTTAC-TCGT
194 GAATCATCCACATTGACAAACAGCTAGATCAAAAAGATGGATCATTAAACAAAAGGTTACTTCGT
*
17246494 AGAAAATCCTATTCACATG
259 AGAAAATCCTATCCACATG
**
17246513 AATGGGTATGGGTCAAACTACTTTTTGTATCATTGGAACTGCTTAAAAGGACTACCATAAATCAG
1 AATGGGTATGGGTCAAACTACTTTTTGTATCATTGGAACTGCTTAAAAGGGTTACCATAAATCAG
*
17246578 CTAGATCAAAAAGATGGATCATTGAGCAAAAGGCTAC-CTGGTAGAAAATCCTATCCACATGAAT
66 CTAGATCAAAAAGATGGATCATTGAGCAAAAGGTTACTC-GGTAGAAAATCCTATCCACATGAAT
* **
17246642 GGTAGTCTGCTTGGAAGTAGAATGGTCAATGGCTGCCAAGCATTGGATAATATTTTGCCAGACAG
130 GGTAGTCTACTTGGAAGTAGAATGGTCAATGGCTGTTAAGCATTGGATAATATTTTGCCAGACAG
* * * *
17246707 AATCATCCACATTGACAAACAGCTAGATCAAAAAGATGGATCATTGAGCATAAGGTTACTTGGTA
195 AATCATCCACATTGACAAACAGCTAGATCAAAAAGATGGATCATTAAACAAAAGGTTACTTCGTA
*
17246772 GAAAATCCTATCCACGTG
260 GAAAATCCTATCCACATG
* * *
17246790 AATGGGTATGAGTCAAACTACATTTTGTATCATTGGAACTGCTTTTAAAAGGGTTGCCATAAATC
1 AATGGGTATGGGTCAAACTACTTTTTGTATCATTGGAACTGC--TTAAAAGGGTTACCATAAATC
* * * * * *
17246855 AGCTAGACCGAAAAGATGGATCATTGAGCAAAAGGTTACTCAGTAGAAATTCCTATCCAAATGAC
64 AGCTAGATCAAAAAGATGGATCATTGAGCAAAAGGTTACTCGGTAGAAAATCCTATCCACATGAA
* * * *
17246920 TGGTAGTCTACTTGGAAGTAAAATGGTCAATGGCAGTTTAAGCATTAGATAATATTTTGCTAGAC
129 TGGTAGTCTACTTGGAAGTAGAATGGTCAATGGCTG-TTAAGCATTGGATAATATTTTGCCAGAC
17246985 AGAATCATCCACATTGA
193 AGAATCATCCACATTGA
17247002 TGAGCAGCAG
Statistics
Matches: 442, Mismatches: 40, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
275 2 0.00
276 143 0.32
277 148 0.33
279 107 0.24
280 42 0.10
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (277 bp):
AATGGGTATGGGTCAAACTACTTTTTGTATCATTGGAACTGCTTAAAAGGGTTACCATAAATCAG
CTAGATCAAAAAGATGGATCATTGAGCAAAAGGTTACTCGGTAGAAAATCCTATCCACATGAATG
GTAGTCTACTTGGAAGTAGAATGGTCAATGGCTGTTAAGCATTGGATAATATTTTGCCAGACAGA
ATCATCCACATTGACAAACAGCTAGATCAAAAAGATGGATCATTAAACAAAAGGTTACTTCGTAG
AAAATCCTATCCACATG
Found at i:17249088 original size:17 final size:17
Alignment explanation
Indices: 17249062--17249095 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17249052 TTCTGCACGT
*
17249062 ATATGTAAAACATGAAA
1 ATATGGAAAACATGAAA
*
17249079 ATATGGAAAACTTGAAA
1 ATATGGAAAACATGAAA
17249096 TATAAAGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (17 bp):
ATATGGAAAACATGAAA
Found at i:17256034 original size:3 final size:3
Alignment explanation
Indices: 17256026--17256096 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
17256016 GGTTATGGAA
17256026 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
17256073 TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT
17256097 AAGTTTCCTT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:17256488 original size:27 final size:27
Alignment explanation
Indices: 17256450--17256532 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
17256440 ATACAAAGTA
* *
17256450 GTGGCGCCTATCTCAGAGGCGCCAATG
1 GTGGTGCCTATCTGAGAGGCGCCAATG
* * * *
17256477 GTGGTGCCTATCTGACAGACGCCATTA
1 GTGGTGCCTATCTGAGAGGCGCCAATG
*
17256504 GTGGTGCC-ATGTTGAGAGGCGCCAATG
1 GTGGTGCCTAT-CTGAGAGGCGCCAATG
17256531 GT
1 GT
17256533 CTTATTTTTC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 2 0.05
27 42 0.95
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.23
Consensus pattern (27 bp):
GTGGTGCCTATCTGAGAGGCGCCAATG
Found at i:17257842 original size:27 final size:27
Alignment explanation
Indices: 17257776--17257844 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
17257766 GAAAAATAAG
17257776 ACCATTGGCGCCTCTCAACATGGCACC
1 ACCATTGGCGCCTCTCAACATGGCACC
* * * * * *
17257803 ACTAATGGTGCCTGTC-AGATAGGCACT
1 ACCATTGGCGCCTCTCAACAT-GGCACC
17257830 ACCATTGGCGCCTCT
1 ACCATTGGCGCCTCT
17257845 GAGATAAGCG
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (27 bp):
ACCATTGGCGCCTCTCAACATGGCACC
Found at i:17258648 original size:27 final size:27
Alignment explanation
Indices: 17258610--17258664 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
17258600 TTAATTGATT
17258610 TCTAAGTTCTAACTAGCCCATTTTTTG
1 TCTAAGTTCTAACTAGCCCATTTTTTG
*
17258637 TCTAAGTTCTAACTAGCTCATTTTTTG
1 TCTAAGTTCTAACTAGCCCATTTTTTG
17258664 T
1 T
17258665 AATCTTAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (27 bp):
TCTAAGTTCTAACTAGCCCATTTTTTG
Found at i:17261234 original size:113 final size:114
Alignment explanation
Indices: 17261036--17261264 Score: 451
Period size: 113 Copynumber: 2.0 Consensus size: 114
17261026 ATGAGAGTGT
17261036 AATTAAAGGTGTATTACTTCAACCCATCTTCTGAGTTTAAATAAACGCAATACAACTCTACCTTG
1 AATTAAAGGTGTATTACTTCAACCCATCTTCTGAGTTTAAATAAACGCAATACAACTCTACCTTG
17261101 AAAAGCTAAAACAAAAGTTTTATCTTAAAAAAATTATAT-AATATCTTA
66 AAAAGCTAAAACAAAAGTTTTATCTTAAAAAAATTATATAAATATCTTA
17261149 AATTAAAGGTGTATTACTTCAACCCATCTTCTGAGTTTAAATAAACGCAATACAACTCTACCTTG
1 AATTAAAGGTGTATTACTTCAACCCATCTTCTGAGTTTAAATAAACGCAATACAACTCTACCTTG
17261214 AAAAGCTAAAACAAAAGTTTTATCTTAAAAAAATTATATAAATATCTTA
66 AAAAGCTAAAACAAAAGTTTTATCTTAAAAAAATTATATAAATATCTTA
17261263 AA
1 AA
17261265 AGATTAAATT
Statistics
Matches: 115, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 104 0.90
114 11 0.10
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (114 bp):
AATTAAAGGTGTATTACTTCAACCCATCTTCTGAGTTTAAATAAACGCAATACAACTCTACCTTG
AAAAGCTAAAACAAAAGTTTTATCTTAAAAAAATTATATAAATATCTTA
Found at i:17262895 original size:64 final size:64
Alignment explanation
Indices: 17262771--17262895 Score: 205
Period size: 64 Copynumber: 2.0 Consensus size: 64
17262761 CAAAGCCACT
* * *
17262771 TAGTCATAATAGTCATACTCCGCATAGCCCTCTTAAAGTCCATCCGAACCTCCACGAAACCGTA
1 TAGTCATAATAGTCATACCCCGCATAGCCCTCTTAAAGCCCATCCGAACCTCCACAAAACCGTA
* *
17262835 TAGTCATAATAGTCATACCCCGCATAGCCCTCTTAACGCCCATCCGAACCTCCGCAAAACC
1 TAGTCATAATAGTCATACCCCGCATAGCCCTCTTAAAGCCCATCCGAACCTCCACAAAACC
17262896 ACATCATCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.22
Consensus pattern (64 bp):
TAGTCATAATAGTCATACCCCGCATAGCCCTCTTAAAGCCCATCCGAACCTCCACAAAACCGTA
Found at i:17264446 original size:18 final size:18
Alignment explanation
Indices: 17264423--17264465 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
17264413 ACCCAATCTA
**
17264423 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
17264441 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
17264459 AACCCAA
1 AACCCAA
17264466 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:17264587 original size:9 final size:9
Alignment explanation
Indices: 17264569--17264644 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
17264559 TTAGTGATTC
*
17264569 AATTCAGTT
1 AATTCGGTT
17264578 AATTCGGTT
1 AATTCGGTT
*
17264587 AATTCGGGT
1 AATTCGGTT
*
17264596 AATCCGGTT
1 AATTCGGTT
17264605 AATTCGGTT
1 AATTCGGTT
* *
17264614 AATTTGGGT
1 AATTCGGTT
17264623 AATTCGGTT
1 AATTCGGTT
17264632 AATTCGGTT
1 AATTCGGTT
17264641 AATT
1 AATT
17264645 TTTAACCAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:17264645 original size:27 final size:27
Alignment explanation
Indices: 17264569--17264645 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
17264559 TTAGTGATTC
* *
17264569 AATTCAGTTAATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTTGGGT
*
17264596 AATCCGGTTAATTCGGTTAATTTGGGT
1 AATTCGGTTAATTCGGTTAATTTGGGT
17264623 AATTCGGTTAATTCGGTTAATTT
1 AATTCGGTTAATTCGGTTAATTT
17264646 TTAACCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (27 bp):
AATTCGGTTAATTCGGTTAATTTGGGT
Found at i:17266212 original size:2 final size:2
Alignment explanation
Indices: 17266205--17266233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17266195 ACCAACAAAC
17266205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17266234 CAAGGGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17269442 original size:33 final size:33
Alignment explanation
Indices: 17269405--17269470 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17269395 TTACCGCCTT
17269405 TTCGAGAAGTCGAATTTCCTATTGAAGTTACCC
1 TTCGAGAAGTCGAATTTCCTATTGAAGTTACCC
17269438 TTCGAGAAGTCGAATTTCCTATTGAAGTTACCC
1 TTCGAGAAGTCGAATTTCCTATTGAAGTTACCC
17269471 CAAACACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (33 bp):
TTCGAGAAGTCGAATTTCCTATTGAAGTTACCC
Found at i:17276767 original size:21 final size:21
Alignment explanation
Indices: 17276741--17276783 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17276731 AGGAGAAAGC
17276741 TTAGAACACTCTTTTGTGTAA
1 TTAGAACACTCTTTTGTGTAA
17276762 TTAGAACACTCTTTTGTGTAA
1 TTAGAACACTCTTTTGTGTAA
17276783 T
1 T
17276784 ATGGCTGCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (21 bp):
TTAGAACACTCTTTTGTGTAA
Found at i:17289216 original size:29 final size:30
Alignment explanation
Indices: 17289184--17289243 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
17289174 AAGATATATA
*
17289184 TAAATATTATATGTATA-TAATTAT-TTATT
1 TAAATAGTA-ATGTATATTAATTATATTATT
* *
17289213 TAAATGGTAATTTATATTAATTATATTATT
1 TAAATAGTAATGTATATTAATTATATTATT
17289243 T
1 T
17289244 TATTATGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 14 0.54
30 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (30 bp):
TAAATAGTAATGTATATTAATTATATTATT
Found at i:17289374 original size:4 final size:4
Alignment explanation
Indices: 17289365--17289392 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
17289355 AGTAAAAGAT
17289365 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
17289393 TATCATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:17303114 original size:27 final size:28
Alignment explanation
Indices: 17303084--17303137 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
17303074 CAAAATTCAT
*
17303084 ACTTTAATTA-TAAAATAATTAATTTTC
1 ACTTAAATTATTAAAATAATTAATTTTC
*
17303111 ACTTAAATTATTAAAATATTTAATTTT
1 ACTTAAATTATTAAAATAATTAATTTT
17303138 AATTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATTAATTTTC
Found at i:17304506 original size:20 final size:21
Alignment explanation
Indices: 17304468--17304506 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
17304458 TTTATGGTTT
*
17304468 TAAATAATTTTTGGCTAAAAA
1 TAAATAATTTTGGGCTAAAAA
*
17304489 TAAAT-ATTTTGGGTTAAA
1 TAAATAATTTTGGGCTAAA
17304507 TTGAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (21 bp):
TAAATAATTTTGGGCTAAAAA
Found at i:17311230 original size:30 final size:30
Alignment explanation
Indices: 17311194--17311250 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
17311184 AGTTTGGACG
* *
17311194 CATTTATTCTGAAGGTTCGATGCAAGTACA
1 CATTTATTCCGAAGGTTCAATGCAAGTACA
17311224 CATTTATTCCGAAGGTTCAATGCAAGT
1 CATTTATTCCGAAGGTTCAATGCAAGT
17311251 TGGGTCTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (30 bp):
CATTTATTCCGAAGGTTCAATGCAAGTACA
Found at i:17311863 original size:81 final size:82
Alignment explanation
Indices: 17311728--17311894 Score: 327
Period size: 81 Copynumber: 2.0 Consensus size: 82
17311718 ACAAAAATAT
17311728 ATAAACTTTTTTAGTACCTTTTGAGCTCTAATTCATGCAATTTTGTAGTGATTTTTGTCGAAATT
1 ATAAACTTTTTTAGTACCTTTTGAGCTCTAATTCATGCAATTTTGTAGTGATTTTTGTCGAAATT
17311793 CACACTTT-ATTATAAA
66 CACACTTTAATTATAAA
17311809 ATAAACTTTTTTAGTACCTTTTGAGCTCTAATTCATGCAATTTTGTAGTGATTTTTGTCGAAATT
1 ATAAACTTTTTTAGTACCTTTTGAGCTCTAATTCATGCAATTTTGTAGTGATTTTTGTCGAAATT
17311874 CACACTTTAATTATAAA
66 CACACTTTAATTATAAA
17311891 ATAA
1 ATAA
17311895 TTAATTTGCA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 73 0.86
82 12 0.14
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (82 bp):
ATAAACTTTTTTAGTACCTTTTGAGCTCTAATTCATGCAATTTTGTAGTGATTTTTGTCGAAATT
CACACTTTAATTATAAA
Found at i:17314682 original size:49 final size:50
Alignment explanation
Indices: 17314611--17314947 Score: 306
Period size: 51 Copynumber: 6.7 Consensus size: 50
17314601 TCATTCGATA
*
17314611 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
* * * **
17314661 CATGTAGTGGCC-TCACATAGTACTACACATGTGATAAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
* *
17314710 CACGAAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGGTT
* * * * *** *
17314761 CACATAGTAGCCTTTACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CGGTT
* **
17314812 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATT--GGCA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TT-TTACGGTT
* * * * * * * *
17314863 CACATTGTAGCCTTCACTTAGTACTACACATGTGGCC-ATTATTTATCGATA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGT-TTTA-CGGTT
* *
17314914 CACGTAGTAGCCTTCACACAATACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
17314948 TTCATCGATA
Statistics
Matches: 228, Mismatches: 47, Indels: 23
0.77 0.16 0.08
Matches are distributed among these distances:
48 3 0.01
49 49 0.21
50 32 0.14
51 136 0.60
52 5 0.02
53 1 0.00
54 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
Found at i:17314841 original size:102 final size:102
Alignment explanation
Indices: 17314605--17314947 Score: 426
Period size: 102 Copynumber: 3.4 Consensus size: 102
17314595 CTTTTATCAT
* * * **
17314605 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGTTCATGTAG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAG
* * ** ***
17314668 TGGCC-TCACATAGTACTACACATGTGATAAAGTTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
17314705 -CGGTTCACGAAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
*
17314769 AGCCTTTACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * *
17314806 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATT-GGCACACATTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT-TTCGGTACACATAG
* *
17314870 TAGCCTTCACTTAGTACTACACATGTGGCCATTATTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
*
17314908 TCGATACACGTAGTAGCCTTCACACAATACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
17314948 TTCATCGATA
Statistics
Matches: 213, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
99 38 0.18
100 16 0.08
101 29 0.14
102 128 0.60
103 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (102 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:17314916 original size:153 final size:148
Alignment explanation
Indices: 17314604--17314947 Score: 361
Period size: 153 Copynumber: 2.3 Consensus size: 148
17314594 ACTTTTATCA
* ** * *
17314604 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCATGTAGT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTACGATTCACGTAGT
* * * * **
17314669 GGCCTCACATAGTACTACACATGTGATAAAGTTTTACGGTTCACGAAGTAGCCTTCACATAGTAC
66 AGCCTCACACAGTACTACACACGTGACAAAGTTTTA-GGCACACGAAGTAGCCTTCACATAGTAC
17314734 TACACACGTGACCAAAGCTT
130 TACACACGTGACCAAA-CTT
* * * * * *
17314754 TTCGGTACACATAGTAGCCTTTACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA-CGATTCACGTAG
* *
17314819 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATT-GGCACAC-ATTGTAGCCTTCACTT
65 TAGCC-TCACACAGTACTACACACGTGA-CAAAG-TT-TTAGGCACACGA-AGTAGCCTTCACAT
* * *
17314882 AGTACTACACATGTGGCCATTA-TT
125 AGTACTACACACGTGACCA-AACTT
* *
17314906 TATCGATACACGTAGTAGCCTTCACACAATACTACACACGTG
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
17314948 TTCATCGATA
Statistics
Matches: 157, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
150 43 0.27
151 14 0.09
152 24 0.15
153 71 0.45
154 3 0.02
155 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (148 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTACGATTCACGTAGT
AGCCTCACACAGTACTACACACGTGACAAAGTTTTAGGCACACGAAGTAGCCTTCACATAGTACT
ACACACGTGACCAAACTT
Found at i:17319839 original size:43 final size:42
Alignment explanation
Indices: 17319789--17319931 Score: 178
Period size: 43 Copynumber: 3.3 Consensus size: 42
17319779 GATTTTGGAG
**
17319789 AAGCGCCGCTAAAGATCATGGTCTATAGCGGTGTTTGTGGGA
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGTGGGA
* *
17319831 AATGCGCCGCTAAAGGTCATGGTCTATAGCAACGTTTGTGGGAA
1 AA-GCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGTGGG-A
* * **
17319875 AAGCGCCGCTATAGACCATGACCTATAGCGACGTTTGTGGGGA
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGT-GGGA
*
17319918 AAGCACCGCTAAAG
1 AAGCGCCGCTAAAG
17319932 TTAGCGACGC
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.02
43 78 0.91
44 6 0.07
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (42 bp):
AAGCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGTGGGA
Found at i:17320039 original size:22 final size:22
Alignment explanation
Indices: 17320003--17320045 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17319993 TAGCGGTGCT
* *
17320003 AAAAAGTGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
17320025 AAAAAGCGCCTCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
17320046 GTTTTGGTGT
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:0.42, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:17328255 original size:38 final size:39
Alignment explanation
Indices: 17328171--17328267 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 39
17328161 TTTGTTTGGA
*
17328171 CAAAAAACGCCGCTAAAAATCGAGCATTAGCGGTGCTTTTT
1 CAAAAAACGCCGC-AAAAA-AGAGCATTAGCGGTGCTTTTT
* *
17328212 C-AAAAACGCCACAAAAAAGAGCATTAG-TG-GCTTTTT
1 CAAAAAACGCCGCAAAAAAGAGCATTAGCGGTGCTTTTT
17328248 CCAAAAAACGCCGCAAAAAA
1 -CAAAAAACGCCGCAAAAAA
17328268 CCTAAGCCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
36 7 0.14
37 2 0.04
38 25 0.50
39 5 0.10
40 10 0.20
41 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (39 bp):
CAAAAAACGCCGCAAAAAAGAGCATTAGCGGTGCTTTTT
Found at i:17332890 original size:43 final size:43
Alignment explanation
Indices: 17332828--17332970 Score: 187
Period size: 43 Copynumber: 3.3 Consensus size: 43
17332818 GATTTTGGAG
**
17332828 AAGCGCCGCTAAAGATCATGGTCTATAGCGGTGTTTGTGGGAA
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGTGGGAA
* *
17332871 AAGCGCCGCTAAAGGTCATGGTCTATAGCAACGTTTGTGGGAA
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGTGGGAA
* * * ** *
17332914 AAGCGTCGCTATAGACCATGACCTATAGCGACGTTTGTGGGGA
1 AAGCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGTGGGAA
*
17332957 AAGCACCGCTAAAG
1 AAGCGCCGCTAAAG
17332971 TTAGGGACGC
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 85 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (43 bp):
AAGCGCCGCTAAAGATCATGGTCTATAGCGACGTTTGTGGGAA
Found at i:17335531 original size:13 final size:13
Alignment explanation
Indices: 17335515--17335540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17335505 TCGAACGAAA
17335515 TTTTCTCGAAATT
1 TTTTCTCGAAATT
17335528 TTTTCTCGAAATT
1 TTTTCTCGAAATT
17335541 GTAGACCATA
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:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTTCTCGAAATT
Found at i:17346119 original size:43 final size:42
Alignment explanation
Indices: 17345978--17346222 Score: 172
Period size: 43 Copynumber: 5.7 Consensus size: 42
17345968 GTTAAGTTTT
* * * * * *
17345978 TAGCGGCGTTTTTGGAGAAGCGCCGCTAAAGGT-TTGTTCTT
1 TAGCAGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * * *
17346019 TAGCAGCGTTTGTGATAAAAGTGCTGCTAAAGATCATGGTCTA
1 TAGCAGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
17346062 TAGCGGTGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGGTATA
1 TAGCAGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTA
** * ** **
17346105 TAGCAGCGTTTGTGGGAAAAGCATCGCTATAGACCATGACCTA
1 TAGCAGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
* ** * *
17346148 TAG-AGGCGTTTGTAGGTAAAGCATCGCTAAAGGTCTTGGTCTT
1 TAGCA-GCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
*
17346191 TAG-AGGCGTTTGTGGGGAAAGCGCCGCTAAAG
1 TAGCA-GCGTTTGT-GGAAAAGCGCCGCTAAAG
17346223 TTAGCGACGC
Statistics
Matches: 159, Mismatches: 40, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
41 12 0.08
42 15 0.09
43 130 0.82
44 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (42 bp):
TAGCAGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:17346319 original size:22 final size:22
Alignment explanation
Indices: 17346294--17346336 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17346284 TAGCGGTGCT
*
17346294 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
17346316 AAAAAGCGCCTCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
17346337 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.28, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:17346740 original size:51 final size:51
Alignment explanation
Indices: 17346616--17346910 Score: 296
Period size: 51 Copynumber: 5.8 Consensus size: 51
17346606 ACTTTTATCA
* * *
17346616 TTCGATACACGTAGTAACCTTCCCATAGTACTACACACGTGATC-AAG-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * *
17346665 TTACGGTTCACGTATTAGCCTTCACATAGTACTATACACATGACCAAAGCTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * *
17346717 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TT
* *
17346767 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * * * * *
17346819 ATCGGTACACATTGTAGCCTTTACTTAGTACTACACACGTGACCATTA--TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGCTT
*
17346869 TATCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
17346911 TTCATCGATA
Statistics
Matches: 198, Mismatches: 39, Indels: 16
0.78 0.15 0.06
Matches are distributed among these distances:
49 4 0.02
50 39 0.20
51 146 0.74
52 7 0.04
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (51 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:17346811 original size:102 final size:102
Alignment explanation
Indices: 17346616--17346910 Score: 403
Period size: 102 Copynumber: 2.9 Consensus size: 102
17346606 ACTTTTATCA
* * * * * * *** * *
17346616 TTCGATACACGTAGTAACCTTCCCATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAT
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACACGTGACCATCATTTATCGATTCACGTAG
* * *
17346680 TAGCCTTCACATAGTACTATACACATGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
*
17346717 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACACGTGACCATCATTTATCGATTCACGTAG
17346782 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
* * * * *
17346819 ATCGGTACACATTGTAGCCTTTACTTAGTACTACACACGTGACCATTATTTATCGATACACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACACGTGACCATCATTTATCGATTCACGTAG
17346884 TAGCCTTCACACAGTACTACACACGTG
66 TAGCCTTCACACAGTACTACACACGTG
17346911 TTCATCGATA
Statistics
Matches: 172, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
101 42 0.24
102 130 0.76
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
TTCGGTACACATAGTAGCCTTCACTTAGTACTACACACGTGACCATCATTTATCGATTCACGTAG
TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
Found at i:17346902 original size:153 final size:151
Alignment explanation
Indices: 17346617--17346906 Score: 352
Period size: 153 Copynumber: 1.9 Consensus size: 151
17346607 CTTTTATCAT
* * * * * *
17346617 TCGATACACGTAGTAACCTTCCCATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTATTA
1 TCGATACACGTAGTAACCTTCACACAGTACTACACACGTGACCAAGTTATACGGTACACATATTA
* * **
17346682 GCCTTCACATAGTACTATACACATGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTA
66 GCCTTCACATAGTACTACACACATGACCAAA-CTTTTCGATACACATAGTAGCCTTCACACAGTA
17346747 CTACACATGTGACCATCATTTA
130 CTACACATGTGACCATCATTTA
* *
17346769 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTAT-CGGTACACAT-T
1 TCGATACACGTAGTAACCTTCACACAGTACTACACACGTGACC-AAG-TTATACGGTACACATAT
* * * * *
17346832 GTAGCCTTTACTTAGTACTACACACGTGACCATTA-TTTATCGATACACGTAGTAGCCTTCACAC
64 -TAGCCTTCACATAGTACTACACACATGACCA-AACTTT-TCGATACACATAGTAGCCTTCACAC
17346896 AGTACTACACA
126 AGTACTACACA
17346907 CGTGTTCATC
Statistics
Matches: 116, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
152 42 0.36
153 70 0.60
154 4 0.03
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (151 bp):
TCGATACACGTAGTAACCTTCACACAGTACTACACACGTGACCAAGTTATACGGTACACATATTA
GCCTTCACATAGTACTACACACATGACCAAACTTTTCGATACACATAGTAGCCTTCACACAGTAC
TACACATGTGACCATCATTTA
Found at i:17347430 original size:29 final size:31
Alignment explanation
Indices: 17347379--17347439 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
17347369 GCTTCGATTC
* *
17347379 AACTTTTTCAAAATTATGA-TTTTGTCCCAA
1 AACTTTTGCAAAATTATCATTTTTGTCCCAA
*
17347409 AACTTTTGCATAATTA-CATTTTTGTCCCAA
1 AACTTTTGCAAAATTATCATTTTTGTCCCAA
17347439 A
1 A
17347440 GCTCAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.43
Consensus pattern (31 bp):
AACTTTTGCAAAATTATCATTTTTGTCCCAA
Found at i:17348649 original size:23 final size:23
Alignment explanation
Indices: 17348615--17348672 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
17348605 CGTCTGGTAA
* *
17348615 TTCCTTTCGTGCAGCTATGACTT
1 TTCCTTTCGTGCAACTATGAATT
*
17348638 TTCCTTTTGTGCAACTATGAATT
1 TTCCTTTCGTGCAACTATGAATT
*
17348661 TTCCATTC-TGCA
1 TTCCTTTCGTGCA
17348673 TAAGGACACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (23 bp):
TTCCTTTCGTGCAACTATGAATT
Found at i:17351341 original size:12 final size:12
Alignment explanation
Indices: 17351324--17351349 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17351314 TAAAAGCATG
17351324 TTGCTAATCAAT
1 TTGCTAATCAAT
17351336 TTGCTAATCAAT
1 TTGCTAATCAAT
17351348 TT
1 TT
17351350 TAACATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (12 bp):
TTGCTAATCAAT
Found at i:17352484 original size:12 final size:12
Alignment explanation
Indices: 17352469--17352493 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17352459 GAGAGAAAAA
17352469 GCTCTCAATTCG
1 GCTCTCAATTCG
17352481 GCTCTCAATTCG
1 GCTCTCAATTCG
17352493 G
1 G
17352494 GTTAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.32
Consensus pattern (12 bp):
GCTCTCAATTCG
Found at i:17361474 original size:21 final size:22
Alignment explanation
Indices: 17361434--17361474 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17361424 ATTAACATCT
* *
17361434 TTTTGTTTTAATTAACTTTTAA
1 TTTTATTTTAATTAAATTTTAA
17361456 TTTTATTTT-ATTAAATTTT
1 TTTTATTTTAATTAAATTTT
17361475 TCATAACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTATTTTAATTAAATTTTAA
Found at i:17362771 original size:27 final size:26
Alignment explanation
Indices: 17362675--17362776 Score: 152
Period size: 26 Copynumber: 3.9 Consensus size: 26
17362665 GGTTATCAGT
*
17362675 GTAGTTCACCGGGACAATAAACACGG
1 GTAGTTCACCGGGACAATAAACATGG
17362701 GTAGTTCACCGGGACAATAAACATGG
1 GTAGTTCACCGGGACAATAAACATGG
*
17362727 GTAGTTCACCGGGACAATAAACATGAA
1 GTAGTTCACCGGGACAATAAACATG-G
*
17362754 GTAGTTCGCCAGGG-CAATAAACA
1 GTAGTTCACC-GGGACAATAAACA
17362777 CAGGGACATC
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
26 50 0.70
27 18 0.25
28 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (26 bp):
GTAGTTCACCGGGACAATAAACATGG
Found at i:17367274 original size:16 final size:16
Alignment explanation
Indices: 17367253--17367312 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
17367243 TTTCAATGGT
17367253 TTTTCTTTCTTCTCGA
1 TTTTCTTTCTTCTCGA
**
17367269 TTTTCTTT-TTACTCTCT
1 TTTTCTTTCTT-CTC-GA
17367286 TTTTCATTCTTCTTCTCGA
1 TTTTC--T-TTCTTCTCGA
17367305 TTTTCTTT
1 TTTTCTTT
17367313 TCACTCTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 2 0.06
16 13 0.38
17 6 0.18
19 6 0.18
20 5 0.15
21 2 0.06
ACGTcount: A:0.07, C:0.23, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTCTTTCTTCTCGA
Found at i:17367302 original size:18 final size:19
Alignment explanation
Indices: 17367279--17367332 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
17367269 TTTTCTTTTT
17367279 ACTCTCTTTTTCATTCTTC
1 ACTCTCTTTTTCATTCTTC
* *
17367298 -TTCTCGATTTTC-TT-TTC
1 ACTCTC-TTTTTCATTCTTC
17367315 ACTCTCTTTTTCATTCTT
1 ACTCTCTTTTTCATTCTT
17367333 TTATTTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
17 8 0.30
18 12 0.44
19 7 0.26
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.61
Consensus pattern (19 bp):
ACTCTCTTTTTCATTCTTC
Found at i:17367306 original size:36 final size:36
Alignment explanation
Indices: 17367259--17367332 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
17367249 TGGTTTTTCT
*
17367259 TTCTTCTCGATTTTCTTTTTACTCTCTTTTTCATTC
1 TTCTTCTCGATTTTCTTTTCACTCTCTTTTTCATTC
17367295 TTCTTCTCGATTTTCTTTTCACTCTCTTTTTCATTC
1 TTCTTCTCGATTTTCTTTTCACTCTCTTTTTCATTC
17367331 TT
1 TT
17367333 TTATTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.08, C:0.26, G:0.03, T:0.64
Consensus pattern (36 bp):
TTCTTCTCGATTTTCTTTTCACTCTCTTTTTCATTC
Found at i:17374542 original size:30 final size:28
Alignment explanation
Indices: 17374508--17374563 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
17374498 GTGATTAAAT
17374508 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
17374538 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
17374564 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:17378836 original size:25 final size:26
Alignment explanation
Indices: 17378808--17378864 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
17378798 GTTATCGATT
17378808 TCAGCTCT-TATAAGCTTACCGATAC
1 TCAGCTCTGTATAAGCTTACCGATAC
* * *
17378833 TCAGCT-TGTATGAGCTTACCGTTAT
1 TCAGCTCTGTATAAGCTTACCGATAC
17378858 TCAGCTC
1 TCAGCTC
17378865 AGAGGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (26 bp):
TCAGCTCTGTATAAGCTTACCGATAC
Found at i:17379068 original size:26 final size:26
Alignment explanation
Indices: 17379037--17379088 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
17379027 CACAGGTATT
17379037 TACATGAGATATATGA-AAATGATTTG
1 TACATGAGATATA-GATAAATGATTTG
* *
17379063 TACATGATATATAGATACATGATTTG
1 TACATGAGATATAGATAAATGATTTG
17379089 GAAATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (26 bp):
TACATGAGATATAGATAAATGATTTG
Found at i:17385161 original size:46 final size:43
Alignment explanation
Indices: 17385080--17385178 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
17385070 TACTATATGA
* *
17385080 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCT-AATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTCGCTATGTGCTGAAT-CC
* *
17385123 ACCGGATATCATTGATTACAAAGGGTGGTCGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTCGCTATGTGCTGAATCC
17385169 ACCGTGTATC
1 ACCG-GTATC
17385179 TGTTATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 25 0.53
47 4 0.09
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTCGCTATGTGCTGAATCC
Found at i:17395118 original size:16 final size:17
Alignment explanation
Indices: 17395094--17395133 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
17395084 TGCCCAAAAT
* *
17395094 ATTATTTATTTAA-TCA
1 ATTAATTATTTAACTAA
17395110 ATTAATTATTTAACTAA
1 ATTAATTATTTAACTAA
17395127 ATTAATT
1 ATTAATT
17395134 TCTCAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAATTATTTAACTAA
Found at i:17405392 original size:36 final size:37
Alignment explanation
Indices: 17405323--17405397 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 37
17405313 TTTAATATTG
* * *
17405323 TATATATTTCATATGTTATTATTTATTAATTTTAAAT
1 TATAAATTTCATATGTTATTATATACTAATTTTAAAT
*
17405360 TATAAATTTCAT-TGTTATTATATACTATTTTTAAAT
1 TATAAATTTCATATGTTATTATATACTAATTTTAAAT
17405396 TA
1 TA
17405398 ACATCCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 23 0.68
37 11 0.32
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (37 bp):
TATAAATTTCATATGTTATTATATACTAATTTTAAAT
Found at i:17415030 original size:20 final size:20
Alignment explanation
Indices: 17415005--17415043 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17414995 GTATTGAGCT
*
17415005 TTTAATTTCTAGTCGATTTC
1 TTTAATTTCAAGTCGATTTC
*
17415025 TTTAATTTCAAGTTGATTT
1 TTTAATTTCAAGTCGATTT
17415044 TAAAGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTAATTTCAAGTCGATTTC
Found at i:17415196 original size:36 final size:36
Alignment explanation
Indices: 17415149--17415221 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
17415139 GTAACAAATG
*
17415149 CACAAGGTTGACCGGCAACTGATATATATATATTGA
1 CACAAGGTTGACCGACAACTGATATATATATATTGA
* * *
17415185 CACAAGGTTGACTGACAAGTGATATATATATTTTGA
1 CACAAGGTTGACCGACAACTGATATATATATATTGA
17415221 C
1 C
17415222 CCATGATGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (36 bp):
CACAAGGTTGACCGACAACTGATATATATATATTGA
Found at i:17415937 original size:20 final size:20
Alignment explanation
Indices: 17415912--17415968 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
17415902 GGAAAAACTT
17415912 TTACCAAAATATTTAAGGAC
1 TTACCAAAATATTTAAGGAC
*
17415932 TTACCAATAT-TTCTAA-GAC
1 TTACCAAAATATT-TAAGGAC
*
17415951 -TACCAAAATATCTAAGGA
1 TTACCAAAATATTTAAGGA
17415969 TTTAACAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 11 0.35
19 8 0.26
20 12 0.39
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.30
Consensus pattern (20 bp):
TTACCAAAATATTTAAGGAC
Found at i:17415954 original size:18 final size:20
Alignment explanation
Indices: 17415933--17415985 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
17415923 TTTAAGGACT
17415933 TACCAATATTTCTAA-GA-C
1 TACCAATATTTCTAAGGATC
* * *
17415951 TACCAAAATATCTAAGGATT
1 TACCAATATTTCTAAGGATC
*
17415971 TAACAATATTTCTAA
1 TACCAATATTTCTAA
17415986 AGTTTTATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 12 0.44
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (20 bp):
TACCAATATTTCTAAGGATC
Found at i:17415967 original size:38 final size:38
Alignment explanation
Indices: 17415913--17415985 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
17415903 GAAAAACTTT
* *
17415913 TACCAAAATATTTAAGGACTTACCAATATTTCTAAGAC
1 TACCAAAATATCTAAGGACTTAACAATATTTCTAAGAC
*
17415951 TACCAAAATATCTAAGGATTTAACAATATTTCTAA
1 TACCAAAATATCTAAGGACTTAACAATATTTCTAA
17415986 AGTTTTATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (38 bp):
TACCAAAATATCTAAGGACTTAACAATATTTCTAAGAC
Found at i:17415992 original size:20 final size:20
Alignment explanation
Indices: 17415969--17416006 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17415959 TATCTAAGGA
*
17415969 TTTAACAATATTTCTAAAGT
1 TTTAACAATATTTATAAAGT
*
17415989 TTTATCAATATTTATAAA
1 TTTAACAATATTTATAAA
17416007 CCCTAAACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTAACAATATTTATAAAGT
Found at i:17416419 original size:50 final size:50
Alignment explanation
Indices: 17416328--17416426 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
17416318 ACCTTATCAT
* ** * * *
17416328 AATCAATGTCAAATAGAAGGAGAGAATTTCTATACAGATTCTACTTGTAC
1 AATCAATATCAAATAGAAAAAGAGAAGTTATATACAAATTCTACTTGTAC
* *
17416378 AATCAATATCAAATAGAAAAAGAGTAGTTATATGCAAATTCTACTTGTA
1 AATCAATATCAAATAGAAAAAGAGAAGTTATATACAAATTCTACTTGTA
17416427 TTTTATTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (50 bp):
AATCAATATCAAATAGAAAAAGAGAAGTTATATACAAATTCTACTTGTAC
Found at i:17416534 original size:29 final size:29
Alignment explanation
Indices: 17416488--17416545 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
17416478 CCACCTTGAT
* * *
17416488 ACGAACTCTCAACGAATAATTTCTTCACC
1 ACGAACTCTCAACAAATAAGTTCTCCACC
17416517 ACGAACTCTCAACAAATAAGTTCTCCACC
1 ACGAACTCTCAACAAATAAGTTCTCCACC
17416546 TCTTCTACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.24
Consensus pattern (29 bp):
ACGAACTCTCAACAAATAAGTTCTCCACC
Found at i:17420654 original size:30 final size:30
Alignment explanation
Indices: 17420620--17420683 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
17420610 TCTGATCCTT
* * *
17420620 ATACAGTAGCAGTGTATGGGCCATAGCCCA
1 ATACAGTAACAGAGTATAGGCCATAGCCCA
* *
17420650 ATACAGTAACAGAGTGTAGGCCTTAGCCCA
1 ATACAGTAACAGAGTATAGGCCATAGCCCA
17420680 ATAC
1 ATAC
17420684 TGATACGCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (30 bp):
ATACAGTAACAGAGTATAGGCCATAGCCCA
Found at i:17421557 original size:29 final size:29
Alignment explanation
Indices: 17421523--17421595 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
17421513 ATGTATTAGT
* *
17421523 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
17421552 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
17421581 TTAGGACATATTTAA
1 TTAGGACATATTTAA
17421596 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:17422175 original size:26 final size:26
Alignment explanation
Indices: 17422120--17422195 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
17422110 TGCTAGTAAT
* * * **
17422120 AGTAACGCAACAAAGTTGCCAATAAA
1 AGTAACGCAGCAAAGCTGCCAGTATC
* *
17422146 AGTAATGCAGCAGAGCTGCCAGTATC
1 AGTAACGCAGCAAAGCTGCCAGTATC
*
17422172 AGTAACGCAGCAAATCTGCCAGTA
1 AGTAACGCAGCAAAGCTGCCAGTA
17422196 ACAATGTTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (26 bp):
AGTAACGCAGCAAAGCTGCCAGTATC
Found at i:17422396 original size:27 final size:26
Alignment explanation
Indices: 17422376--17422735 Score: 194
Period size: 27 Copynumber: 13.3 Consensus size: 26
17422366 GGGTATAACA
*
17422376 GTCATTTTACCCTATGAGGGTATTTC
1 GTCATTTTACCCTATAAGGGTATTTC
* *
17422402 GATCATTTTACCCTTTAAGGGTTTTTC
1 G-TCATTTTACCCTATAAGGGTATTTC
* **
17422429 GGTCATTTTACCCT-TCGAGCCTATTTC
1 -GTCATTTTACCCTAT-AAGGGTATTTC
* *
17422456 GGTAATTTTACCC-ATCGAGGGTATTTC
1 -GTCATTTTACCCTAT-AAGGGTATTTC
* * *
17422483 AATCATTTAACCCT-TCAGGGGTATTTC
1 -GTCATTTTACCCTAT-AAGGGTATTTC
* *
17422510 GGTCATTTTA-CCTTTCAAGGGTATTTTG
1 -GTCATTTTACCCTAT-AAGGGTA-TTTC
* * ** *
17422538 GTCATGTTACCCTTTGGGGGTATTCC
1 GTCATTTTACCCTATAAGGGTATTTC
* ** *
17422564 GATCATTTTACCAT-TCGGGGGTATTTTG
1 G-TCATTTTACCCTAT-AAGGGTA-TTTC
* ** *
17422592 GTCATTTTACCCTTTGGGGGTATTCC
1 GTCATTTTACCCTATAAGGGTATTTC
*
17422618 GGTCATTTTACCCT-TCGAGGGTATTTC
1 -GTCATTTTACCCTAT-AAGGGTATTTC
* * *
17422645 AGTCATTTTACCCTTTGAGGGTATTTTG
1 -GTCATTTTACCCTATAAGGGTA-TTTC
* * *
17422673 GTAATTTTACCCTTTGAGGGTATTTC
1 GTCATTTTACCCTATAAGGGTATTTC
17422699 GGTCATTTTACCCT-TCAAGGGTATTTC
1 -GTCATTTTACCCTAT-AAGGGTATTTC
17422726 GATCATTTTA
1 G-TCATTTTA
17422736 GAGGCCCATT
Statistics
Matches: 274, Mismatches: 41, Indels: 37
0.78 0.12 0.11
Matches are distributed among these distances:
26 17 0.06
27 240 0.88
28 17 0.06
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (26 bp):
GTCATTTTACCCTATAAGGGTATTTC
Found at i:17422440 original size:54 final size:53
Alignment explanation
Indices: 17422376--17422735 Score: 387
Period size: 54 Copynumber: 6.7 Consensus size: 53
17422366 GGGTATAACA
* ** *
17422376 GTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTTTAAGGGTTTTTCG
1 GTCATTTTACCCT-TGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCG
** * * *
17422430 GTCATTTTACCCTTCGAGCCTATTTCGGTAATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCTT-GAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCG
* * * * * *
17422484 ATCATTTAACCCTTCAGGGGTATTTCGGTCATTTTACCTTTCAAGGGTATTTTG
1 GTCATTTTACCCTTGA-GGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCG
* * * * * * *
17422538 GTCATGTTACCCTTTGGGGGTATTCCGATCATTTTACCATTCGGGGGTATTTTG
1 GTCATTTTACCC-TTGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCG
* * *
17422592 GTCATTTTACCCTTTGGGGGTATTCCGGTCATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTACCC-TTGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCG
* * *
17422646 GTCATTTTACCCTTTGAGGGTATTTTGGTAATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCC-TTGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCG
* *
17422700 GTCATTTTACCCTTCAAGGGTATTTCGATCATTTTA
1 GTCATTTTACCCTT-GAGGGTATTTCGGTCATTTTA
17422736 GAGGCCCATT
Statistics
Matches: 256, Mismatches: 46, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
53 4 0.02
54 250 0.98
55 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (53 bp):
GTCATTTTACCCTTGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCG
Found at i:17422488 original size:81 final size:81
Alignment explanation
Indices: 17422376--17422735 Score: 429
Period size: 81 Copynumber: 4.4 Consensus size: 81
17422366 GGGTATAACA
*
17422376 GTCATTTTACCCTAT-GAGGGTATTTCGATCATTTTACCCTTTAAGGGT-TTTTCGGTCATTTTA
1 GTCATTTTACCCT-TCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTT-GGTCATTTTA
**
17422439 CCCTTCGAGCCTATTTCG
64 CCCTTCGAGGGTATTTCG
* * * * * *
17422457 GTAATTTTACCCATCGAGGGTATTTCAATCATTTAACCCTTCAGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTTGGTCATTTTACC
* * *
17422522 TTTCAAGGGTATTTTG
66 CTTCGAGGGTATTTCG
* * * * * **
17422538 GTCATGTTACCCTTTGGGGGTATTCCGATCATTTTACCATTCGGGGGTATTTTGGTCATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTTGGTCATTTTACC
* * *
17422603 CTTTGGGGGTATTCCG
66 CTTCGAGGGTATTTCG
** *
17422619 GTCATTTTACCCTTCGAGGGTATTTC-AGTCATTTTACCCTTTGAGGGTATTTTGGTAATTTTAC
1 GTCATTTTACCCTTCGAGGGTATTTCGA-TCATTTTACCCTTCAAGGGTATTTTGGTCATTTTAC
*
17422683 CCTTTGAGGGTATTTCG
65 CCTTCGAGGGTATTTCG
*
17422700 GTCATTTTACCCTTCAAGGGTATTTCGATCATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTA
17422736 GAGGCCCATT
Statistics
Matches: 235, Mismatches: 40, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
80 2 0.01
81 229 0.97
82 4 0.02
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (81 bp):
GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTTGGTCATTTTACC
CTTCGAGGGTATTTCG
Found at i:17493751 original size:16 final size:15
Alignment explanation
Indices: 17493716--17493751 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17493706 CAAAATCAAG
17493716 ATTTTTACAACATCC
1 ATTTTTACAACATCC
* *
17493731 ATTTTTACAATATTC
1 ATTTTTACAACATCC
17493746 ATTTTT
1 ATTTTT
17493752 CTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTACAACATCC
Found at i:17495466 original size:22 final size:23
Alignment explanation
Indices: 17495439--17495487 Score: 82
Period size: 22 Copynumber: 2.1 Consensus size: 23
17495429 TATATTTTAT
17495439 TTCAAATGTTTCATATT-TACAC
1 TTCAAATGTTTCATATTATACAC
17495461 TTCAAATGTTTCATATTCATACAC
1 TTCAAATGTTTCATATT-ATACAC
17495485 TTC
1 TTC
17495488 TCGATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 17 0.68
24 8 0.32
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (23 bp):
TTCAAATGTTTCATATTATACAC
Found at i:17498073 original size:23 final size:23
Alignment explanation
Indices: 17498047--17498103 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
17498037 ATAGAAATAA
17498047 ATTAAAACATAATTATAAATATC
1 ATTAAAACATAATTATAAATATC
*
17498070 ATTAAATCATAATTATAAATATC
1 ATTAAAACATAATTATAAATATC
17498093 ATTAATAACAT
1 ATTAA-AACAT
17498104 CACAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTAAAACATAATTATAAATATC
Found at i:17502867 original size:86 final size:86
Alignment explanation
Indices: 17502763--17502978 Score: 283
Period size: 86 Copynumber: 2.5 Consensus size: 86
17502753 CTAAAGAACG
** * ** * *
17502763 ATGCT-TTTAGCGACGTTTGTGAAAAAAAAGCCGCTAAAAGTCATTCTCTATAGA-GACGTTTGT
1 ATGCTCTTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAAGGTCATTCTCTATA-ACGACGTTTAT
*
17502826 GATAAAAGCGCCACTAAAGGTT
65 GATAAAAGCGCCACTAAAGGTC
* * *
17502848 ATGCTCTTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAAGGTTATTTTCTTTAACGACGTTTATG
1 ATGCTCTTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAAGGTCATTCTCTATAACGACGTTTATG
17502913 ATAAAAGCGCCACTAAAGGTC
66 ATAAAAGCGCCACTAAAGGTC
* * *
17502934 AAGTTCTTTAGCAGTGTTTGTGATAAAAGCGCCGCTAAAGGTCAT
1 ATGCTCTTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAAGGTCAT
17502979 GTTCTTTAGC
Statistics
Matches: 114, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
85 6 0.05
86 108 0.95
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (86 bp):
ATGCTCTTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAAGGTCATTCTCTATAACGACGTTTATG
ATAAAAGCGCCACTAAAGGTC
Found at i:17502988 original size:43 final size:44
Alignment explanation
Indices: 17502768--17502988 Score: 238
Period size: 43 Copynumber: 5.1 Consensus size: 44
17502758 GAACGATGCT
* ** *
17502768 TTTAGC-GACGTTTGTGAAAAAAAAGCCGCTAAAAGTCAT-TCTC
1 TTTAGCAGACGTTTGTGATAAAAGCGCCGCTAAAGGTCATGT-TC
* * * *
17502811 TATAG-AGACGTTTGTGATAAAAGCGCCACTAAAGGTTATGCTC
1 TTTAGCAGACGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
** * *
17502854 TTTAGC-GGTGTTTGTGATAAAAGCGCCGCTAAAGGTTATTTTC
1 TTTAGCAGACGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * * *
17502897 TTTAAC-GACGTTTATGATAAAAGCGCCACTAAAGGTCAAGTTC
1 TTTAGCAGACGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
*
17502940 TTTAGCAG-TGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCAGACGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
17502983 TTTAGC
1 TTTAGC
17502989 TGCTTAAAAG
Statistics
Matches: 147, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
43 146 0.99
44 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (44 bp):
TTTAGCAGACGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:17515450 original size:20 final size:20
Alignment explanation
Indices: 17515425--17515463 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
17515415 TGCATGTCGT
17515425 TAATTATTTATCCTTTGTGC
1 TAATTATTTATCCTTTGTGC
17515445 TAATTATTTATCCTTTGTG
1 TAATTATTTATCCTTTGTG
17515464 TTGTCAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.56
Consensus pattern (20 bp):
TAATTATTTATCCTTTGTGC
Found at i:17516105 original size:13 final size:12
Alignment explanation
Indices: 17516082--17516144 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
17516072 AATAATTTTA
17516082 TATTAAAATTAT
1 TATTAAAATTAT
17516094 TATT-AAA-TAT
1 TATTAAAATTAT
17516104 TATTAATAATTA-
1 TATTAA-AATTAT
*
17516116 TATTAAGAA-TGT
1 TATTAA-AATTAT
17516128 TATT-AAATTAT
1 TATTAAAATTAT
17516139 ATATTA
1 -TATTA
17516145 TTTTATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
10 9 0.22
11 8 0.20
12 22 0.54
13 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
TATTAAAATTAT
Found at i:17516109 original size:22 final size:23
Alignment explanation
Indices: 17516082--17516144 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
17516072 AATAATTTTA
17516082 TATTAAAATTATTATTA-AATAT
1 TATTAAAATTATTATTAGAATAT
*
17516104 TATTAATAATTA-TATTAAGAATGT
1 TATTAA-AATTATTATT-AGAATAT
17516128 TATT-AAATTATATATTA
1 TATTAAAATTAT-TATTA
17516145 TTTTATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 15 0.43
23 8 0.23
24 12 0.34
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
TATTAAAATTATTATTAGAATAT
Found at i:17516223 original size:61 final size:57
Alignment explanation
Indices: 17516107--17516243 Score: 157
Period size: 61 Copynumber: 2.3 Consensus size: 57
17516097 TAAATATTAT
* * * *
17516107 TAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTGTATTTAA
1 TAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
* *
17516165 TAATAATTATGTTAAAATATGATTAAATTATTTATTTTTATTTTTATTAAAATATATTTAA
1 TAATAATTATATTAAAATATGATTAAATTA--TA-TATTA-TTTTATTAAAATATATTTAA
* *
17516226 CAATAATCATATTAAAAT
1 TAATAATTATATTAAAAT
17516244 TTAATAACAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
57 13 0.20
58 14 0.21
59 2 0.03
60 4 0.06
61 33 0.50
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (57 bp):
TAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
Found at i:17516256 original size:25 final size:26
Alignment explanation
Indices: 17516209--17516260 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
17516199 TTTTTATTTT
*
17516209 TATTAAAATATATTTAACAATAATCA
1 TATTAAAATATATATAACAATAATCA
*
17516235 TATTAAAATTTA-ATAACAATAATCA
1 TATTAAAATATATATAACAATAATCA
17516260 T
1 T
17516261 CTACCTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (26 bp):
TATTAAAATATATATAACAATAATCA
Found at i:17519845 original size:15 final size:15
Alignment explanation
Indices: 17519822--17519851 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17519812 AAATAATAGT
17519822 TATAATGTTTTTATC
1 TATAATGTTTTTATC
*
17519837 TATATTGTTTTTATC
1 TATAATGTTTTTATC
17519852 CCTCAACAAA
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:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (15 bp):
TATAATGTTTTTATC
Found at i:17527470 original size:88 final size:88
Alignment explanation
Indices: 17527199--17528173 Score: 1303
Period size: 88 Copynumber: 11.2 Consensus size: 88
17527189 ACTAGTGCTT
* ** * *
17527199 AGGAAGGCAATATCTGCT-TCTTTAACCAGCTCCA-CTGCAACCGATG-GAGGCAAGGCTTTGT-
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGA-GAGAGGCAAGG-TTTGTG
* * * *
17527260 T-TTTGGTCTGCTTCGCTGTTAATGT
63 TCTTCGATCTGCTTCGCTGTCAATGC
* * * ** * ** * *
17527285 AAGAAGACAGGATCTGCT-TCTTTAACCAGCTCCA-CTGTAACCGATAGAGGC-AGGGTT-TGTC
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAGAGAGGCAAGGTTTGTGTC
17527346 TTCGATCTGCTTCGCTGTCAATGC
65 TTCGATCTGCTTCGCTGTCAATGC
* *
17527370 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAGGTTTGTGTCC
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
* *
17527435 TCGACCTGCTTCGTTGTCAATGC
66 TCGATCTGCTTCGCTGTCAATGC
** * *
17527458 AGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCATCACAACCGAGAGAGGTAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
*
17527523 TTGATCTGCTTCGCTGTCAATGC
66 TCGATCTGCTTCGCTGTCAATGC
** * *
17527546 AGGAAGGCAAGATCTACTATCTTCAACTAGCTCCA-CTACAACCGAGAGAGGCAAGGTTTGTGTC
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAGAGAGGCAAGGTTTGTGTC
17527610 TTCGATCTGCTTCGCTGTCAATGC
65 TTCGATCTGCTTCGCTGTCAATGC
* * * * * *
17527634 AGGAAGGCAAGATCCTTTATATTCAACCAGCTCTATCACAACCGAGAGAGGCAAGGTTTTTGTCC
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
*
17527699 TCGACCTGCTTCGCTGTCAATGC
66 TCGATCTGCTTCGCTGTCAATGC
*
17527722 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
* *
17527787 TCGATTTGCTTCGCTGTCAATAC
66 TCGATCTGCTTCGCTGTCAATGC
** * *
17527810 AGGAAGGCAAGATCTACTATCTTCAACCAGCTCCA-CTACAACTGAGAGAGGCAAGGTTTGTGTC
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAGAGAGGCAAGGTTTGTGTC
17527874 TTCGATCTGCTTCGCTGTCAATGC
65 TTCGATCTGCTTCGCTGTCAATGC
* * *
17527898 AGGAAGGCAA-ATCTTTTGTCTTCAACCAGCTCTATCACAACTGAAAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
17527962 TCGATCTGCTTCGCTGTCAATGC
66 TCGATCTGCTTCGCTGTCAATGC
* * *
17527985 AGGAAGGCAA-ATCTTTTGTCTTCAACCAGCTCTATCACAACTGAAAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
17528049 TCGATCTGCTTCGCTGTCAATGC
66 TCGATCTGCTTCGCTGTCAATGC
* * *
17528072 AGGAAGGCAA-ATCTTTTGTCTTCAACCAGCTCTATCACAACTGAAAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
17528136 TCGATCTGCTTCGCTGTCAATGC
66 TCGATCTGCTTCGCTGTCAATGC
17528159 AGGAAGGCAAGATCT
1 AGGAAGGCAAGATCT
17528174 GCTATCTTCA
Statistics
Matches: 809, Mismatches: 68, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
83 1 0.00
84 3 0.00
85 36 0.04
86 70 0.09
87 262 0.32
88 436 0.54
89 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (88 bp):
AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCT
TCGATCTGCTTCGCTGTCAATGC
Found at i:17529274 original size:21 final size:21
Alignment explanation
Indices: 17529248--17529294 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
17529238 GGTATAGCAA
17529248 GATCACCGCATGCCCCAATCT
1 GATCACCGCATGCCCCAATCT
** *
17529269 GATCACTTCATGCCCCATTCT
1 GATCACCGCATGCCCCAATCT
17529290 GATCA
1 GATCA
17529295 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (21 bp):
GATCACCGCATGCCCCAATCT
Found at i:17532387 original size:19 final size:19
Alignment explanation
Indices: 17532363--17532427 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
17532353 GTGAAAATCC
* *
17532363 AATGCATATG-ATGCAATG
1 AATGCAAATGCATGAAATG
17532381 TAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
17532401 AATGCCAAATGCATG-AATG
1 AATG-CAAATGCATGAAATG
17532420 AATGCAAA
1 AATGCAAA
17532428 AAGAGACGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 4 0.10
19 21 0.50
20 17 0.40
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:17532409 original size:20 final size:19
Alignment explanation
Indices: 17532377--17532424 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
17532367 CATATGATGC
17532377 AATGTAATG-CAAATGCATG
1 AATG-AATGCCAAATGCATG
17532396 AAATGAATGCCAAATGCATG
1 -AATGAATGCCAAATGCATG
17532416 AATGAATGC
1 AATGAATGC
17532425 AAAAAGAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (19 bp):
AATGAATGCCAAATGCATG
Found at i:17537518 original size:18 final size:18
Alignment explanation
Indices: 17537495--17537532 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17537485 ATATATAAAT
17537495 TATAAGTATAAAAATATA
1 TATAAGTATAAAAATATA
* *
17537513 TATAAGTATGAATATATA
1 TATAAGTATAAAAATATA
17537531 TA
1 TA
17537533 AATCAAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (18 bp):
TATAAGTATAAAAATATA
Found at i:17538303 original size:21 final size:22
Alignment explanation
Indices: 17538257--17538303 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
17538247 GAAAAATAAA
* *
17538257 AAAAATCGAATACAAACAGTCG
1 AAAAATCGAAAACAAACAGTAG
*
17538279 -AAAATCGAAAACAAAGAG-AG
1 AAAAATCGAAAACAAACAGTAG
17538299 AAAAA
1 AAAAA
17538304 AAATAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.64, C:0.13, G:0.15, T:0.09
Consensus pattern (22 bp):
AAAAATCGAAAACAAACAGTAG
Found at i:17547280 original size:16 final size:15
Alignment explanation
Indices: 17547245--17547280 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17547235 CAAAATCAAG
17547245 ATTTTTACAACATCC
1 ATTTTTACAACATCC
* *
17547260 ATTTTTACAATATTC
1 ATTTTTACAACATCC
17547275 ATTTTT
1 ATTTTT
17547281 CCTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTACAACATCC
Found at i:17550125 original size:15 final size:15
Alignment explanation
Indices: 17550100--17550134 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17550090 GACTCTATTT
*
17550100 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
17550114 TAATTAATATTAAGA
1 TAATTAATATTAAGA
17550129 TAATTA
1 TAATTA
17550135 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:17554128 original size:4 final size:4
Alignment explanation
Indices: 17554119--17554188 Score: 56
Period size: 4 Copynumber: 16.5 Consensus size: 4
17554109 AATTTTTATT
17554119 TTTA TTTA TTT- TTTA TTTTA TTTTA TTTA TTTTAA TTTA TTTA -TTA
1 TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA -TTT-A TTTA TTTA TTTA
17554165 CTTTA TTTTA TTT- TATTA TTTA TT
1 -TTTA -TTTA TTTA T-TTA TTTA TT
17554189 ACTTATTTGG
Statistics
Matches: 57, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
3 7 0.12
4 26 0.46
5 23 0.40
6 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:17554133 original size:17 final size:17
Alignment explanation
Indices: 17554111--17554196 Score: 72
Period size: 17 Copynumber: 5.1 Consensus size: 17
17554101 GGCAACCCAA
17554111 TTTTTATTTTTATTTAT
1 TTTTTATTTTTATTTAT
17554128 TTTTTA-TTTTA-TT-T
1 TTTTTATTTTTATTTAT
* *
17554142 TATTTATTTTAATTTAT
1 TTTTTATTTTTATTTAT
* *
17554159 TTATTA-CTTTATTTTAT
1 TTTTTATTTTTA-TTTAT
*
17554176 TTTATTATTTATTACTTAT
1 TTT-TTATTT-TTATTTAT
17554195 TT
1 TT
17554197 GGATATTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 6 0.11
15 6 0.11
16 10 0.19
17 18 0.34
18 3 0.06
19 7 0.13
20 3 0.06
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTATTTAT
Found at i:17554137 original size:5 final size:5
Alignment explanation
Indices: 17554112--17554181 Score: 70
Period size: 5 Copynumber: 13.4 Consensus size: 5
17554102 GCAACCCAAT
* *
17554112 TTTTA TTTTTA TTTATT TTTTA TTTTA TTTTA -TTTA TTTTA ATTTA TTTATTA
1 TTTTA -TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA
*
17554165 CTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
17554182 ATTTATTACT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
4 4 0.07
5 36 0.67
6 11 0.20
7 3 0.06
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:17554151 original size:31 final size:32
Alignment explanation
Indices: 17554112--17554188 Score: 111
Period size: 31 Copynumber: 2.4 Consensus size: 32
17554102 GCAACCCAAT
* *
17554112 TTTTATTTTTATTTATTTTTTATTTTATTTTA
1 TTTTATTTTTATTTATTTATTACTTTATTTTA
*
17554144 -TTTATTTTAATTTATTTATTACTTTATTTTA
1 TTTTATTTTTATTTATTTATTACTTTATTTTA
17554175 TTTTATTATTTATT
1 TTTTATT-TTTATT
17554189 ACTTATTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 28 0.72
32 6 0.15
33 5 0.13
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTTATTTTTATTTATTTATTACTTTATTTTA
Found at i:17554195 original size:36 final size:35
Alignment explanation
Indices: 17554120--17554196 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
17554110 ATTTTTATTT
* *
17554120 TTATTTATTTTTTATTTTATTTTATTTATTTTAAT
1 TTATTTATTCTTTATTTTATTTTATTTATTTTAAC
*
17554155 TTATTTATTACTTTATTTTATTTTA-TTATTTATTAC
1 TTATTTATT-CTTTATTTTATTTTATTTATTT-TAAC
17554191 TTATTT
1 TTATTT
17554197 GGATATTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 15 0.41
36 22 0.59
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (35 bp):
TTATTTATTCTTTATTTTATTTTATTTATTTTAAC
Found at i:17554392 original size:22 final size:21
Alignment explanation
Indices: 17554343--17554402 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
17554333 GGCCAGAATG
* *
17554343 CCTGCAGCCAAACTACCCTATT
1 CCTGCAGCC-AACCACCCTATC
*
17554365 CTTGCAGCCAACCACCCTTATC
1 CCTGCAGCCAACCACCC-TATC
* *
17554387 CCTGCACCCAAGCACC
1 CCTGCAGCCAACCACC
17554403 ACCCCTCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.25, C:0.47, G:0.10, T:0.18
Consensus pattern (21 bp):
CCTGCAGCCAACCACCCTATC
Found at i:17555530 original size:101 final size:101
Alignment explanation
Indices: 17555341--17555531 Score: 260
Period size: 101 Copynumber: 1.9 Consensus size: 101
17555331 AAGAACATGT
* *
17555341 TGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCTCGTCAAAAAGTTCGATGTG
1 TGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAAGTTCGATATG
* * *
17555406 TTCTTAAGAAAAAATTATAATAAATTAGGAGTCTGC
66 TCCTAAAGAAAAAATAATAATAAATTAGGAGTCTGC
* * *
17555442 TGGGTTGAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATA
1 TGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAAGTTC-G-ATA
* *
17555507 T-TCCTAAAGCATAAATAAT-ATAAAT
64 TGTCCTAAAGAAAAAATAATAATAAAT
17555532 AATAAATAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
101 61 0.78
102 14 0.18
103 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (101 bp):
TGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAAGTTCGATATG
TCCTAAAGAAAAAATAATAATAAATTAGGAGTCTGC
Found at i:17557530 original size:30 final size:31
Alignment explanation
Indices: 17557494--17557554 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
17557484 CTTATTATGA
17557494 AAAGTCAAAGATAT-GAGTATC-AAATATTGG
1 AAAGTCAAAGATATAG-GTATCGAAATATTGG
17557524 AAAGTCAAAGATATAGGTATCGAAATATTGG
1 AAAGTCAAAGATATAGGTATCGAAATATTGG
17557555 CATAAGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (31 bp):
AAAGTCAAAGATATAGGTATCGAAATATTGG
Found at i:17560165 original size:21 final size:21
Alignment explanation
Indices: 17560141--17560182 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17560131 GATTGTTTTC
*
17560141 AGTAGAGATGTGACTTTTGAT
1 AGTAGAAATGTGACTTTTGAT
17560162 AGTAGAAATGTGACTTTTGAT
1 AGTAGAAATGTGACTTTTGAT
17560183 GAATCAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (21 bp):
AGTAGAAATGTGACTTTTGAT
Found at i:17562152 original size:30 final size:31
Alignment explanation
Indices: 17562118--17562181 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
17562108 ATCCATATTA
*
17562118 TGGAAAGTCAAAGATATGGGTATC-AAATAT
1 TGGAAAGTCAAAGATATGAGTATCGAAATAT
17562148 TGGAAAGTCAAAGATATGAGTATCGAAATAT
1 TGGAAAGTCAAAGATATGAGTATCGAAATAT
17562179 TGG
1 TGG
17562182 CATAAGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.27
Consensus pattern (31 bp):
TGGAAAGTCAAAGATATGAGTATCGAAATAT
Found at i:17562158 original size:15 final size:16
Alignment explanation
Indices: 17562116--17562165 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
17562106 TCATCCATAT
17562116 TATGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
** *
17562132 TATGGGTA-TCAAATA
1 TATGGAAAGTCAAAGA
17562147 T-TGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
17562162 TATG
1 TATG
17562166 AGTATCGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (16 bp):
TATGGAAAGTCAAAGA
Found at i:17563655 original size:13 final size:13
Alignment explanation
Indices: 17563603--17563655 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
17563593 TAAACCAAAC
17563603 TTTTCAAAAGCACT
1 TTTTCAAAAGCA-T
* * *
17563617 TTTTC-ACATCAC
1 TTTTCAAAAGCAT
*
17563629 TTTTCAAAAACAT
1 TTTTCAAAAGCAT
17563642 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
17563655 T
1 T
17563656 GCCAAACTAG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
12 5 0.16
13 21 0.68
14 5 0.16
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:17563800 original size:18 final size:17
Alignment explanation
Indices: 17563769--17563802 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17563759 CAGCTAAATT
17563769 AAAAATTATAATTTTTA
1 AAAAATTATAATTTTTA
*
17563786 AAAAATATATGATTTTT
1 AAAAAT-TATAATTTTT
17563803 TCTAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAAAATTATAATTTTTA
Found at i:17567909 original size:29 final size:29
Alignment explanation
Indices: 17567867--17567939 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
17567857 CTACAATTGG
*
17567867 AACAAAATGTAAGAAATCCATTTGCATTA
1 AACAAAATGTAAGAAATCCATGTGCATTA
* *
17567896 AACAAAATGTAAGAAATCTATGTGTATTA
1 AACAAAATGTAAGAAATCCATGTGCATTA
17567925 AACAAAATGTAAGAA
1 AACAAAATGTAAGAA
17567940 CACATATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (29 bp):
AACAAAATGTAAGAAATCCATGTGCATTA
Found at i:17569507 original size:9 final size:9
Alignment explanation
Indices: 17569490--17569565 Score: 116
Period size: 9 Copynumber: 8.4 Consensus size: 9
17569480 GTAGTGATTC
*
17569490 AATTTGGTT
1 AATTCGGTT
17569499 AATTCGGTT
1 AATTCGGTT
*
17569508 AATTCGGGT
1 AATTCGGTT
*
17569517 AATTCGGGT
1 AATTCGGTT
17569526 AATTCGGTT
1 AATTCGGTT
*
17569535 AATTCGGGT
1 AATTCGGTT
17569544 AATTCGGTT
1 AATTCGGTT
17569553 AATTCGGTT
1 AATTCGGTT
17569562 AATT
1 AATT
17569566 TGTTTAATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:17569574 original size:27 final size:27
Alignment explanation
Indices: 17569490--17569565 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
17569480 GTAGTGATTC
*
17569490 AATTTGGTTAATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
*
17569517 AATTCGGGTAATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
17569544 AATTCGGTTAATTCGGTTAATT
1 AATTCGGTTAATTCGGTTAATT
17569566 TGTTTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (27 bp):
AATTCGGTTAATTCGGTTAATTCGGGT
Found at i:17577042 original size:20 final size:20
Alignment explanation
Indices: 17577015--17577065 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
17577005 AAAATAAAAT
**
17577015 ATTTTTATTTATTTTGAAG-
1 ATTTTTATTTATTTACAAGA
17577034 ATGTTTTATTT-TTTACAAGA
1 AT-TTTTATTTATTTACAAGA
17577054 ATTTTTATTTAT
1 ATTTTTATTTAT
17577066 ATTTCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (20 bp):
ATTTTTATTTATTTACAAGA
Found at i:17577876 original size:20 final size:20
Alignment explanation
Indices: 17577849--17577899 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
17577839 AAAATAAAAT
**
17577849 ATTTTTATTTATTTTGAAG-
1 ATTTTTATTTATTTACAAGA
17577868 ATGTTTTATTT-TTTACAAGA
1 AT-TTTTATTTATTTACAAGA
17577888 ATTTTTATTTAT
1 ATTTTTATTTAT
17577900 ATTTCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (20 bp):
ATTTTTATTTATTTACAAGA
Found at i:17578471 original size:834 final size:834
Alignment explanation
Indices: 17576863--17578532 Score: 3340
Period size: 834 Copynumber: 2.0 Consensus size: 834
17576853 TTGTTTATTA
17576863 ATCAAATTAATTACATGTATTAACATTTCAATGCTACCTTTAGTAATGATGTTATTTTTACATGT
1 ATCAAATTAATTACATGTATTAACATTTCAATGCTACCTTTAGTAATGATGTTATTTTTACATGT
17576928 ATTTTAATATATGAGTTAGTAATAAATTAATTTAATTTATAATATTTAGTTATTCTCATAACTTA
66 ATTTTAATATATGAGTTAGTAATAAATTAATTTAATTTATAATATTTAGTTATTCTCATAACTTA
17576993 GTTTTAGTAAAGAAAATAAAATATTTTTATTTATTTTGAAGATGTTTTATTTTTTACAAGAATTT
131 GTTTTAGTAAAGAAAATAAAATATTTTTATTTATTTTGAAGATGTTTTATTTTTTACAAGAATTT
17577058 TTATTTATATTTCTATTTTCAAGTTTAAATTTATTATAACTATTCTTAGTTTGATATTTAACTAT
196 TTATTTATATTTCTATTTTCAAGTTTAAATTTATTATAACTATTCTTAGTTTGATATTTAACTAT
17577123 TGTAATACATGTACCCAATAAGTTTTTTCTTCATGTTATTACATTAATAACCGAATGAGGCATTA
261 TGTAATACATGTACCCAATAAGTTTTTTCTTCATGTTATTACATTAATAACCGAATGAGGCATTA
17577188 ATATATTTATATTAATAGTTAATTTCACCTTATTTCCTTAAACTATAACCTTCATTCTAAATTAG
326 ATATATTTATATTAATAGTTAATTTCACCTTATTTCCTTAAACTATAACCTTCATTCTAAATTAG
17577253 TCCTCAAATTTTAAAATATTTTAATTACATCCCAAACTGTTGATGTTTTATCAATAAGGTCATCC
391 TCCTCAAATTTTAAAATATTTTAATTACATCCCAAACTGTTGATGTTTTATCAATAAGGTCATCC
17577318 CATTACTAAAAAATAATTAATTTAACTGTTAAATGAAATGTCAAATCTTATGTGTCATGTTTAAA
456 CATTACTAAAAAATAATTAATTTAACTGTTAAATGAAATGTCAAATCTTATGTGTCATGTTTAAA
17577383 ATAAAGAATTGTAAAAAAAAATGAATGTTATAAAAATATTGGGTTTGAGGCTTTTACAAAAGTGT
521 ATAAAGAATTGTAAAAAAAAATGAATGTTATAAAAATATTGGGTTTGAGGCTTTTACAAAAGTGT
17577448 TATTGCTTACTTTCTTCTTTTTTCAGTTTTACTTCATTTTTAATTTAAAAGTTATGCAATAAAAT
586 TATTGCTTACTTTCTTCTTTTTTCAGTTTTACTTCATTTTTAATTTAAAAGTTATGCAATAAAAT
17577513 TTTAATTTTTTTAAAAAATTATCATTTTAAATTATGCCACATAAGATTTGACATATTATTTAAAG
651 TTTAATTTTTTTAAAAAATTATCATTTTAAATTATGCCACATAAGATTTGACATATTATTTAAAG
17577578 GTTAAATTAATTATTTTAATAATTGAAGGACCCTATTGATATATCATCAATAATTTGGGAAGATA
716 GTTAAATTAATTATTTTAATAATTGAAGGACCCTATTGATATATCATCAATAATTTGGGAAGATA
17577643 ATTAGACGTTTTGAAATTTAGGGGTCAATTTAGAATAAGTGCCATAGTTTGGGG
781 ATTAGACGTTTTGAAATTTAGGGGTCAATTTAGAATAAGTGCCATAGTTTGGGG
17577697 ATCAAATTAATTACATGTATTAACATTTCAATGCTACCTTTAGTAATGATGTTATTTTTACATGT
1 ATCAAATTAATTACATGTATTAACATTTCAATGCTACCTTTAGTAATGATGTTATTTTTACATGT
17577762 ATTTTAATATATGAGTTAGTAATAAATTAATTTAATTTATAATATTTAGTTATTCTCATAACTTA
66 ATTTTAATATATGAGTTAGTAATAAATTAATTTAATTTATAATATTTAGTTATTCTCATAACTTA
17577827 GTTTTAGTAAAGAAAATAAAATATTTTTATTTATTTTGAAGATGTTTTATTTTTTACAAGAATTT
131 GTTTTAGTAAAGAAAATAAAATATTTTTATTTATTTTGAAGATGTTTTATTTTTTACAAGAATTT
17577892 TTATTTATATTTCTATTTTCAAGTTTAAATTTATTATAACTATTCTTAGTTTGATATTTAACTAT
196 TTATTTATATTTCTATTTTCAAGTTTAAATTTATTATAACTATTCTTAGTTTGATATTTAACTAT
17577957 TGTAATACATGTACCCAATAAGTTTTTTCTTCATGTTATTACATTAATAACCGAATGAGGCATTA
261 TGTAATACATGTACCCAATAAGTTTTTTCTTCATGTTATTACATTAATAACCGAATGAGGCATTA
17578022 ATATATTTATATTAATAGTTAATTTCACCTTATTTCCTTAAACTATAACCTTCATTCTAAATTAG
326 ATATATTTATATTAATAGTTAATTTCACCTTATTTCCTTAAACTATAACCTTCATTCTAAATTAG
17578087 TCCTCAAATTTTAAAATATTTTAATTACATCCCAAACTGTTGATGTTTTATCAATAAGGTCATCC
391 TCCTCAAATTTTAAAATATTTTAATTACATCCCAAACTGTTGATGTTTTATCAATAAGGTCATCC
17578152 CATTACTAAAAAATAATTAATTTAACTGTTAAATGAAATGTCAAATCTTATGTGTCATGTTTAAA
456 CATTACTAAAAAATAATTAATTTAACTGTTAAATGAAATGTCAAATCTTATGTGTCATGTTTAAA
17578217 ATAAAGAATTGTAAAAAAAAATGAATGTTATAAAAATATTGGGTTTGAGGCTTTTACAAAAGTGT
521 ATAAAGAATTGTAAAAAAAAATGAATGTTATAAAAATATTGGGTTTGAGGCTTTTACAAAAGTGT
17578282 TATTGCTTACTTTCTTCTTTTTTCAGTTTTACTTCATTTTTAATTTAAAAGTTATGCAATAAAAT
586 TATTGCTTACTTTCTTCTTTTTTCAGTTTTACTTCATTTTTAATTTAAAAGTTATGCAATAAAAT
17578347 TTTAATTTTTTTAAAAAATTATCATTTTAAATTATGCCACATAAGATTTGACATATTATTTAAAG
651 TTTAATTTTTTTAAAAAATTATCATTTTAAATTATGCCACATAAGATTTGACATATTATTTAAAG
17578412 GTTAAATTAATTATTTTAATAATTGAAGGACCCTATTGATATATCATCAATAATTTGGGAAGATA
716 GTTAAATTAATTATTTTAATAATTGAAGGACCCTATTGATATATCATCAATAATTTGGGAAGATA
17578477 ATTAGACGTTTTGAAATTTAGGGGTCAATTTAGAATAAGTGCCATAGTTTGGGG
781 ATTAGACGTTTTGAAATTTAGGGGTCAATTTAGAATAAGTGCCATAGTTTGGGG
17578531 AT
1 AT
17578533 GTTTAGTGCA
Statistics
Matches: 836, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
834 836 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.44
Consensus pattern (834 bp):
ATCAAATTAATTACATGTATTAACATTTCAATGCTACCTTTAGTAATGATGTTATTTTTACATGT
ATTTTAATATATGAGTTAGTAATAAATTAATTTAATTTATAATATTTAGTTATTCTCATAACTTA
GTTTTAGTAAAGAAAATAAAATATTTTTATTTATTTTGAAGATGTTTTATTTTTTACAAGAATTT
TTATTTATATTTCTATTTTCAAGTTTAAATTTATTATAACTATTCTTAGTTTGATATTTAACTAT
TGTAATACATGTACCCAATAAGTTTTTTCTTCATGTTATTACATTAATAACCGAATGAGGCATTA
ATATATTTATATTAATAGTTAATTTCACCTTATTTCCTTAAACTATAACCTTCATTCTAAATTAG
TCCTCAAATTTTAAAATATTTTAATTACATCCCAAACTGTTGATGTTTTATCAATAAGGTCATCC
CATTACTAAAAAATAATTAATTTAACTGTTAAATGAAATGTCAAATCTTATGTGTCATGTTTAAA
ATAAAGAATTGTAAAAAAAAATGAATGTTATAAAAATATTGGGTTTGAGGCTTTTACAAAAGTGT
TATTGCTTACTTTCTTCTTTTTTCAGTTTTACTTCATTTTTAATTTAAAAGTTATGCAATAAAAT
TTTAATTTTTTTAAAAAATTATCATTTTAAATTATGCCACATAAGATTTGACATATTATTTAAAG
GTTAAATTAATTATTTTAATAATTGAAGGACCCTATTGATATATCATCAATAATTTGGGAAGATA
ATTAGACGTTTTGAAATTTAGGGGTCAATTTAGAATAAGTGCCATAGTTTGGGG
Found at i:17578622 original size:16 final size:15
Alignment explanation
Indices: 17578597--17578626 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17578587 ATACTAAAGG
17578597 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
17578612 AAAAGGAAAAGAAAA
1 AAAA-GAAAAGAAAA
17578627 GAGAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAA
Found at i:17580201 original size:16 final size:15
Alignment explanation
Indices: 17580176--17580205 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17580166 ATACTAAAGG
17580176 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
17580191 AAAAGGAAAAGAAAA
1 AAAA-GAAAAGAAAA
17580206 GAGAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAA
Found at i:17588612 original size:16 final size:18
Alignment explanation
Indices: 17588581--17588613 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
17588571 GTTAATAGAA
17588581 TAAATTTAGTTTTAATTG
1 TAAATTTAGTTTTAATTG
17588599 TAAATTT-G-TTTAATT
1 TAAATTTAGTTTTAATT
17588614 TTTCATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
TAAATTTAGTTTTAATTG
Found at i:17589695 original size:309 final size:306
Alignment explanation
Indices: 17588933--17589777 Score: 849
Period size: 308 Copynumber: 2.7 Consensus size: 306
17588923 GAAAATTACA
* * * * * *
17588933 GGAACGCACATCCATAATTAAAATAAAGAATATTTTTTGAGTGTATTTTAGTCTTTTCACTTTAA
1 GGAATGCACATCCGTAATTAAAAT-AATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAA
* * * * ** ** * * *
17588998 AAATCAATAAAAAGCA-AGGATATGATAGGATTCAAACCCATGCCAAGTGCATTAGTAAAATATT
65 AAATCAATAAAAA-TATA-CATATGGTAAGATTTGAACCCACACCAATTGCATTAATAAAACATT
*
17589062 TAATTTACCACTCAACTAAAGCTTCATTTTAATATTTTTATACATTTTAGTTTTATTATGCACAT
128 TAATTTACCACTCAACTAAA-CTT-ATTTTAATATTTTTATACATTTTAATTTTATTATGCACAT
* * * * *
17589127 TCTATTATCTC-C--ATTA-A-ATGTATA-TTTATATCTATCTATACTATTGTTTAAACTCTTGA
191 TTTATTACCTCACTAATTATATATCTATACTTTATATCTATCTATACTATTATTTAAACTCCTGA
* * * *
17589186 CTGAGTTGGTGTCGCAAGTCAACCGAGCACGAACTAATTGGTTAGGAAATTATG
256 CTGAGTTGATGTCACAACTCAACCGAGCACCAACTAA---GTTAGGAAATTATG
* * * *
17589240 GGAATGCACATCCTTAATTAAAATAAGTAATATTATTC-AGGGTATTTTAGTCTTTTTTAATTTA
1 GGAATGCACATCCGTAATTAAAATAA-TAATATTATTCGAGTGTATTTTAGTC--TTTTCACTTA
* * ** * * * * *
17589304 AAAAATGAATAAAATTATGTATATGGTGAGATTTGAATCTACACCAATTGCATT-ATAAAGCCTT
63 AAAAATCAATAAAAATATACATATGGTAAGATTTGAACCCACACCAATTGCATTAATAAAACATT
*
17589368 TAATTTACCACTCAACTAAACATTAATTTTAATATTTTTATAAATTTTAATTTTATTATGCACAT
128 TAATTTACCACTCAACTAAAC-TT-ATTTTAATATTTTTATACATTTTAATTTTATTATGCACAT
* * *
17589433 TTTATTACCTCCACTAATTATATATCTATACTTGTATAT-TATTTATACTATTATTTCAGCTCCT
191 TTTATTACCT-CACTAATTATATATCTATACTT-TATATCTATCTATACTATTATTTAAACTCCT
* * *
17589497 G-CTGAGTTGATGTCAC-CCTCAACCGGGTCACCAACTCAA-TTAGGAAGTTATG
254 GACTGAGTTGATGTCACAACTCAACCGAG-CACCAACT-AAGTTAGGAAATTATG
* * *
17589549 GGAATGCACTTTCGTAATTAAAGTATATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAA
1 GGAATGCACATCCGTAATTAAAATA-ATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAA
* *
17589614 AAACCAATAAAAATATACATATGGTAAAATTTGAACCCACACCAATTGCATTAATAAAACATTTA
65 AAATCAATAAAAATATACATATGGTAAGATTTGAACCCACACCAATTGCATTAATAAAACATTTA
* * *
17589679 ATTTACC-GTGCAACTAAAGTT-TTTATATATATTTTTATACATTTTAATTTTATTATGCACACT
130 ATTTACCACT-CAACTAAACTTATTT-TA-ATATTTTTATACATTTTAATTTTATTATGCACATT
* *
17589742 TTATTACCTTCA-TCAGTTGTATATCTATACTATTAT
192 TTATTACC-TCACT-AATTATATATCTATACT-TTAT
17589778 TTAAATTCCT
Statistics
Matches: 444, Mismatches: 70, Indels: 47
0.79 0.12 0.08
Matches are distributed among these distances:
305 1 0.00
306 92 0.21
307 59 0.13
308 138 0.31
309 71 0.16
310 18 0.04
311 9 0.02
312 26 0.06
313 25 0.06
314 5 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (306 bp):
GGAATGCACATCCGTAATTAAAATAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAAA
AATCAATAAAAATATACATATGGTAAGATTTGAACCCACACCAATTGCATTAATAAAACATTTAA
TTTACCACTCAACTAAACTTATTTTAATATTTTTATACATTTTAATTTTATTATGCACATTTTAT
TACCTCACTAATTATATATCTATACTTTATATCTATCTATACTATTATTTAAACTCCTGACTGAG
TTGATGTCACAACTCAACCGAGCACCAACTAAGTTAGGAAATTATG
Found at i:17590838 original size:21 final size:21
Alignment explanation
Indices: 17590814--17590854 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17590804 GTCAATAACC
17590814 AAATGTTCACACAAACAGACA
1 AAATGTTCACACAAACAGACA
**
17590835 AAATGTTCTGACAAACAGAC
1 AAATGTTCACACAAACAGAC
17590855 GTATGTTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (21 bp):
AAATGTTCACACAAACAGACA
Found at i:17597990 original size:16 final size:17
Alignment explanation
Indices: 17597969--17598002 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
17597959 TGGTAGAGTT
17597969 GAAAGAAAA-TGGAGAG
1 GAAAGAAAATTGGAGAG
17597985 GAAAGAAAATTGGAGAG
1 GAAAGAAAATTGGAGAG
17598002 G
1 G
17598003 TAGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.38, T:0.09
Consensus pattern (17 bp):
GAAAGAAAATTGGAGAG
Found at i:17599743 original size:19 final size:19
Alignment explanation
Indices: 17599721--17599757 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17599711 CTTGCATGCT
17599721 AATATACAAATAACATATA
1 AATATACAAATAACATATA
* *
17599740 AATATATACATAACATAT
1 AATATACAAATAACATAT
17599758 TAGCTAGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATACAAATAACATATA
Found at i:17602994 original size:16 final size:17
Alignment explanation
Indices: 17602973--17603006 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17602963 TCTTTCATTT
17602973 TTTTAAATAT-ATTTAA
1 TTTTAAATATAATTTAA
*
17602989 TTTTAAATCTAATTTAA
1 TTTTAAATATAATTTAA
17603006 T
1 T
17603007 GATTAAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAATATAATTTAA
Found at i:17608347 original size:12 final size:12
Alignment explanation
Indices: 17608330--17608354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17608320 ACACAGTCAA
17608330 ATTTAGATTCAG
1 ATTTAGATTCAG
17608342 ATTTAGATTCAG
1 ATTTAGATTCAG
17608354 A
1 A
17608355 CTTAAGTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTTAGATTCAG
Found at i:17616805 original size:9 final size:9
Alignment explanation
Indices: 17616749--17616835 Score: 56
Period size: 9 Copynumber: 10.0 Consensus size: 9
17616739 TAAGTATAAT
17616749 TAAGTTATG
1 TAAGTTATG
*
17616758 TAACTTATG
1 TAAGTTATG
* * *
17616767 ATATGATATA
1 -TAAGTTATG
*
17616777 T-ATTTATG
1 TAAGTTATG
17616785 T-A-TTATG
1 TAAGTTATG
*
17616792 CAAGTTATG
1 TAAGTTATG
17616801 TAAGTTATG
1 TAAGTTATG
*
17616810 TGAG-TATG
1 TAAGTTATG
* *
17616818 CAAATTATG
1 TAAGTTATG
17616827 TAAGTTATG
1 TAAGTTATG
17616836 ATATATATTT
Statistics
Matches: 57, Mismatches: 17, Indels: 8
0.70 0.21 0.10
Matches are distributed among these distances:
7 5 0.09
8 11 0.19
9 36 0.63
10 5 0.09
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:17616825 original size:26 final size:25
Alignment explanation
Indices: 17616780--17616835 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
17616770 TGATATATAT
* *
17616780 TTATGTATTATGCAAGTTATGTAAG
1 TTATGTAGTATGCAAATTATGTAAG
17616805 TTATGTGAGTATGCAAATTATGTAAG
1 TTATGT-AGTATGCAAATTATGTAAG
17616831 TTATG
1 TTATG
17616836 ATATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (25 bp):
TTATGTAGTATGCAAATTATGTAAG
Found at i:17617288 original size:33 final size:33
Alignment explanation
Indices: 17617246--17617311 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
17617236 TAAAAAAGAG
17617246 TTGTTTTTGCGGCAATTTTAAAATGAAAATTAA
1 TTGTTTTTGCGGCAATTTTAAAATGAAAATTAA
* * *
17617279 TTGTTTTTGCTGCAATTTTAAGATGGAAATTAA
1 TTGTTTTTGCGGCAATTTTAAAATGAAAATTAA
17617312 AAAAATTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (33 bp):
TTGTTTTTGCGGCAATTTTAAAATGAAAATTAA
Found at i:17617997 original size:12 final size:12
Alignment explanation
Indices: 17617980--17618006 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17617970 AACTTGCAAC
17617980 AACATTAACCAG
1 AACATTAACCAG
17617992 AACATTAACCAG
1 AACATTAACCAG
17618004 AAC
1 AAC
17618007 TTGCAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (12 bp):
AACATTAACCAG
Done.