Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 52 of 136
Found at i:17234436 original size:19 final size:19
Alignment explanation
Indices: 17234412--17234449 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17234402 AATAAATAAC
17234412 CAAGAAATTACCTCAGTCT
1 CAAGAAATTACCTCAGTCT
17234431 CAAGAAATTACCTCAGTCT
1 CAAGAAATTACCTCAGTCT
17234450 AGTGGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (19 bp):
CAAGAAATTACCTCAGTCT
Found at i:17235690 original size:28 final size:28
Alignment explanation
Indices: 17235658--17235717 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
17235648 ATTATTACTA
* *
17235658 TTTATGCATGGTATGCAGTTGAAACTTG
1 TTTATACATGGTATGCAATTGAAACTTG
17235686 TTTATACATGGTATGCAATTGAAACTTG
1 TTTATACATGGTATGCAATTGAAACTTG
17235714 TTTA
1 TTTA
17235718 CTATCATCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (28 bp):
TTTATACATGGTATGCAATTGAAACTTG
Found at i:17236118 original size:45 final size:46
Alignment explanation
Indices: 17236014--17236120 Score: 114
Period size: 45 Copynumber: 2.3 Consensus size: 46
17236004 TGCAAGCCGA
*
17236014 TTGTGTATGCACAAC-TATTGGCAGCGTATTAACCTACAAGCACTCG
1 TTGTGTATCCACAACTTATTGGCAGCGTATTAACCTACAA-CACTCG
* * *
17236060 TGGTTTATCCACAACTTATATCGGCAGC-TATT-ATCTACAA-ACTCG
1 TTGTGTATCCACAACTTAT-T-GGCAGCGTATTAACCTACAACACTCG
*
17236105 TTGTGTATTCACAACT
1 TTGTGTATCCACAACT
17236121 ACTGGCAACA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
45 18 0.35
46 12 0.24
47 10 0.20
48 5 0.10
49 6 0.12
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (46 bp):
TTGTGTATCCACAACTTATTGGCAGCGTATTAACCTACAACACTCG
Found at i:17240631 original size:84 final size:82
Alignment explanation
Indices: 17240485--17240689 Score: 259
Period size: 84 Copynumber: 2.5 Consensus size: 82
17240475 AGACGAGAAG
* * * * *
17240485 GAAAGTCAAATATGAGAAAAGAAAGAGAATAACAACTATGTAAAATAGTGATCTAAAAGGGAATT
1 GAAAATCAAATATGGGAAAGGAAAGAGAATAAC-A-TATGGAAAATAGTGATATAAAAGGGAATT
*
17240550 GAATATTTTATGGAAAATA
64 GAATATTTTAGGGAAAATA
*
17240569 GAAAATCAAACATGGGAAAGGAAAGAGAATAACATATGGGGAAAATAGAT-ATATAAAAGGGAAT
1 GAAAATCAAATATGGGAAAGGAAAGAGAATAACATAT--GGAAAATAG-TGATATAAAAGGGAAT
*
17240633 TTAATATTTTAGGGAAAATA
63 TGAATATTTTAGGGAAAATA
* * *
17240653 GAAAACCAAATATGGTAAAGGAAAAAGAATAACATAT
1 GAAAATCAAATATGGGAAAGGAAAGAGAATAACATAT
17240690 ATGGAAGATC
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
82 3 0.03
83 1 0.01
84 101 0.95
85 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (82 bp):
GAAAATCAAATATGGGAAAGGAAAGAGAATAACATATGGAAAATAGTGATATAAAAGGGAATTGA
ATATTTTAGGGAAAATA
Found at i:17241091 original size:9 final size:9
Alignment explanation
Indices: 17241079--17241125 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
17241069 AATATTCGGT
*
17241079 TTATTCAAA
1 TTATTCGAA
*
17241088 TTATTCGAG
1 TTATTCGAA
17241097 TTATTCGAA
1 TTATTCGAA
*
17241106 TTATTCGAG
1 TTATTCGAA
*
17241115 TTATTCAAA
1 TTATTCGAA
17241124 TT
1 TT
17241126 TGAAAACCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:17241094 original size:18 final size:18
Alignment explanation
Indices: 17241079--17241125 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
17241069 AATATTCGGT
17241079 TTATTCAAATTATTCGAG
1 TTATTCAAATTATTCGAG
*
17241097 TTATTCGAATTATTCGAG
1 TTATTCAAATTATTCGAG
17241115 TTATTCAAATT
1 TTATTCAAATT
17241126 TGAAAACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (18 bp):
TTATTCAAATTATTCGAG
Found at i:17251193 original size:44 final size:44
Alignment explanation
Indices: 17251141--17251707 Score: 315
Period size: 44 Copynumber: 12.5 Consensus size: 44
17251131 TCGTGGCAAT
* * *
17251141 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTACAAA
* * * * *
17251185 -CATTATCTCTCTGAAGTTGCAAT-GAAGCAGATTGAAGATAGCAAA
1 TC-TTATCTCCCTGAAGTTGCAGTAG-AGCAAATTAAAGCTA-CAAA
* *
17251230 TCTTATCTCTCTGAAGTTGCAGTAGAACAAATTAAAGCTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTACAAA
* * * *
17251274 ACTTATCTCCCTGAAGTTGTAGTAGAGGAAATTAAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTACAAA
* * * * * * **
17251318 TCTTATCTTCTTGAAGTTGCAGTAGAACAGATTGAAGATAGTGAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTA-CAAA
* * * * * *
17251363 TCTAATATCCCAGAAGTTGCAGTGGAACAGATTAAAGTTGCAAGTCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAA---GC---T-ACAAA
* * * *
17251414 TCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTCAAGCGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTACAAA
* * * ** * * *
17251458 TAC-TATAC-CTCTGAAGTTGCAAT-GGGTCGGATTAAATCTACCGTGCGAG
1 T-CTTAT-CTCCCTGAAGTTGCAGTAGAG-CAAATTAAAGCTA-----CAAA
* ** * * **
17251507 TCTTATTTCTTTGAAG-T-CAGAAGAGATTAAAGCCACAAGCTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAG--CAAA-TTA-AAGCTACAAA
* *
17251553 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA--TGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATT-AAAGCT-ACAAA
* * * * *
17251597 TCTTATTTCCCTGAAGTTGTAATAGAGCAGATTGAAGCTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTACAAA
* * * *
17251641 TCTTATCTCCCTGAAGTTACAGTGGAGCAAATTGAAGCTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTACAAA
*
17251685 TCTTATCTCCCTGAAGTTACAGT
1 TCTTATCTCCCTGAAGTTGCAGT
17251708 CGAGTAGATT
Statistics
Matches: 398, Mismatches: 92, Indels: 66
0.72 0.17 0.12
Matches are distributed among these distances:
43 7 0.02
44 230 0.58
45 71 0.18
46 20 0.05
47 3 0.01
48 13 0.03
49 15 0.04
50 1 0.00
51 37 0.09
52 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTACAAA
Found at i:17251261 original size:89 final size:89
Alignment explanation
Indices: 17251136--17251346 Score: 250
Period size: 89 Copynumber: 2.4 Consensus size: 89
17251126 AGTCATCGTG
* * * * * *
17251136 GCAATTCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCAC-AAACATTATCTCTCTGAA
1 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAACAAATTAAAGCCACAAAAC-TTATCTCCCTGAA
* *
17251200 GTTGCAAT-GAAGCAGATTGAAGATA
65 GTTGCAATAG-AGCAAATTAAAGATA
*
17251225 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAACAAATTAAAGCTACAAAACTTATCTCCCTGAAG
1 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAACAAATTAAAGCCACAAAACTTATCTCCCTGAAG
* * * *
17251290 TTGTAGTAGAGGAAATTAAAGTTA
66 TTGCAATAGAGCAAATTAAAGATA
17251314 -CAAATCTTATCT-TCTTGAAGTTGCAGTAGAACA
1 GCAAATCTTATCTCTC-TGAAGTTGCAGTAGAACA
17251347 GATTGAAGAT
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
87 2 0.02
88 30 0.28
89 69 0.65
90 5 0.05
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (89 bp):
GCAAATCTTATCTCTCTGAAGTTGCAGTAGAACAAATTAAAGCCACAAAACTTATCTCCCTGAAG
TTGCAATAGAGCAAATTAAAGATA
Found at i:17251380 original size:133 final size:133
Alignment explanation
Indices: 17251142--17251481 Score: 364
Period size: 133 Copynumber: 2.5 Consensus size: 133
17251132 CGTGGCAATT
*
17251142 CTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCACAAACATTATCTCTCTGAAGTTGCAA
1 CTTATCTCCCTGAAGTTGTAGTAGAGCAAATTAAAGCCACAAACATTATCTCTCTGAAGTTGCAA
* * * *
17251207 TGAAGCAGATTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAACAAATTAAAGCTACA
66 TGAAGCAGATTGAAGATAGCAAATCTAATATCCCAGAAGTTGCAGTAGAACAAATTAAAGCTACA
17251272 AAA
131 AAA
* **
17251275 CTTATCTCCCTGAAGTTGTAGTAGAGGAAATTAAAGTTACAAATC-TTATCT-TCTTGAAGTTGC
1 CTTATCTCCCTGAAGTTGTAGTAGAGCAAATTAAAGCCACAAA-CATTATCTCTC-TGAAGTTGC
* ** * *
17251338 AGTAGAA-CAGATTGAAGATAGTGAATCTAATATCCCAGAAGTTGCAGTGGAACAGATTAAAGTT
64 AAT-GAAGCAGATTGAAGATAGCAAATCTAATATCCCAGAAGTTGCAGTAGAACAAATTAAA---
*
17251402 GCAAGTCACAAAT
125 GC---T-ACAAAA
* * * * * * *
17251415 CTTATCTCCCTGAAGTTGCAGTGGAGTAAATTCAAGCGACAAATACTATAC-CTCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGTAGTAGAGCAAATTAAAGCCACAAACATTAT-CTCTCTGAAGTTGCA
17251479 ATG
65 ATG
17251482 GGTCGGATTA
Statistics
Matches: 171, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
132 2 0.01
133 102 0.60
134 4 0.02
136 2 0.01
139 2 0.01
140 56 0.33
141 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (133 bp):
CTTATCTCCCTGAAGTTGTAGTAGAGCAAATTAAAGCCACAAACATTATCTCTCTGAAGTTGCAA
TGAAGCAGATTGAAGATAGCAAATCTAATATCCCAGAAGTTGCAGTAGAACAAATTAAAGCTACA
AAA
Found at i:17251684 original size:139 final size:138
Alignment explanation
Indices: 17251141--17251684 Score: 406
Period size: 139 Copynumber: 3.9 Consensus size: 138
17251131 TCGTGGCAAT
* * *
17251141 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAA-GCCACAAA-CATTATCTCTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAATG--ACAAATC-TTATTTCCCTGAAGTTG
* *
17251204 CAATGAAGCAGATTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAACAAATTAAAGCT
63 CAATG-AGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCT
17251269 ---A-C-A-AAA
127 ACAAGCTACAAA
* * * * *
17251275 -CTTATCTCCCTGAAGTTGTAGTAGAGGAAATTAAAGTTACAAATCTTATCTT-CTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAA-TGACAAATCTTAT-TTCCCTGAAGTTGC
* * ** * * * * * *
17251338 AGTAGAACAGATTGAAGATAGTGAATCTAATATCCCAGAAGTTGCAGTGGAACAGATTAAAGTTG
64 AAT-GAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTA
17251403 CAAG-TCACAAA
128 CAAGCT-ACAAA
* ** *
17251414 TCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTCAAGCGACAAATAC-TA-TACCTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATT-AAATGACAAAT-CTTATTTCC-CTGAAGTTG
* * * ** * * * ** * *
17251477 CAATGGGTCGGATTAAATCTACCGTGCGAGTCTTATTTCTTTGAAG-T-CA---GAAGAGATTAA
63 CAATGAG-CAGATTGAAGATA----GCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAA
*
17251537 AGCCACAAGCTACAAA
123 AGCTACAAGCTACAAA
* *
17251553 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATGACAAATCTTATTTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATT-AAATGACAAATCTTATTTCCCTGAAGTTGCA
* * * *
17251618 ATAGAGCAGATTGAAGCTA-CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTGAAGCTAC
65 AT-GAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTAC
17251682 AAG
129 AAG
17251685 TCTTATCTCC
Statistics
Matches: 315, Mismatches: 64, Indels: 57
0.72 0.15 0.13
Matches are distributed among these distances:
133 102 0.32
134 18 0.06
135 1 0.00
136 3 0.01
138 3 0.01
139 105 0.33
140 63 0.20
141 3 0.01
142 2 0.01
143 1 0.00
144 14 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (138 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAATGACAAATCTTATTTCCCTGAAGTTGCAA
TGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAA
GCTACAAA
Found at i:17251719 original size:44 final size:44
Alignment explanation
Indices: 17251543--17251726 Score: 244
Period size: 44 Copynumber: 4.2 Consensus size: 44
17251533 TTAAAGCCAC
*
17251543 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTG
* * ** * *
17251587 AA-ATGACAAATCTTATTTCCCTGAAGTTGTAATAGAGCAGATTG
1 AAGCT-ACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTG
*
17251631 AAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTG
* * *
17251675 AAGCTACAAGTCTTATCTCCCTGAAGTTACAGTCGAGTAGATTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTG
*
17251719 AAACTACA
1 AAGCTACA
17251727 CCTCCTGTAC
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
43 1 0.01
44 119 0.98
45 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
AAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTG
Found at i:17252371 original size:2 final size:2
Alignment explanation
Indices: 17252366--17252397 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17252356 TTTAATCCAT
*
17252366 TA TA TA TA TA TA TG 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
17252398 ACTCACCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17253369 original size:4 final size:3
Alignment explanation
Indices: 17253332--17253381 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
17253322 TATTTTTCGA
* *
17253332 ATT ATT CTT ATT ATT ATT ATC ATT ATT ATT ATTT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT
17253379 ATT
1 ATT
17253382 TAATTAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 35 0.83
4 7 0.17
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17253375 original size:17 final size:17
Alignment explanation
Indices: 17253333--17253393 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
17253323 ATTTTTCGAA
*
17253333 TTATTCTTATTA-TTAT
1 TTATTATTATTATTTAT
17253349 TATCATTATTATTATTTAT
1 T-T-ATTATTATTATTTAT
*
17253368 TTATTATTATTATTTAA
1 TTATTATTATTATTTAT
*
17253385 TTAGTATTA
1 TTATTATTA
17253394 GAATTAGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 23 0.59
18 10 0.26
19 5 0.13
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATTATTATTATTTAT
Found at i:17254304 original size:9 final size:9
Alignment explanation
Indices: 17254290--17254327 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
17254280 TATAGTTTGA
17254290 TATTCGAAT
1 TATTCGAAT
17254299 TATTCGAAT
1 TATTCGAAT
*
17254308 TATTCGAGT
1 TATTCGAAT
17254317 TATTCCGAAT
1 TATT-CGAAT
17254327 T
1 T
17254328 CGAAACTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 21 0.81
10 5 0.19
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17257567 original size:22 final size:22
Alignment explanation
Indices: 17257537--17257579 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17257527 ACACCAAAAC
*
17257537 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGCGGCGTTTTTTT
17257559 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
17257580 AGCGCTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGTTTTTTT
Found at i:17257680 original size:43 final size:43
Alignment explanation
Indices: 17257632--17257851 Score: 334
Period size: 43 Copynumber: 5.1 Consensus size: 43
17257622 AATGACAGCA
17257632 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACG
* *
17257675 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACGAACA
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACG
* *
17257718 CCGCTAAAGACCAAGATCTTTAGCAGCGCT-TTCCCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACG
* * *
17257760 CCGCTAAAGACCAAAATCTTTAGCGGCGCTATTCCCACAAATG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACG
* * * *
17257803 CCACTAAAGACCATGACCTTTAGCGGCGCTTTTCACACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACG
17257846 CCGCTA
1 CCGCTA
17257852 TAGAATAGAT
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 38 0.24
43 121 0.76
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (43 bp):
CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACG
Found at i:17257781 original size:85 final size:85
Alignment explanation
Indices: 17257630--17257851 Score: 336
Period size: 85 Copynumber: 2.6 Consensus size: 85
17257620 CTAATGACAG
*
17257630 CACCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACGCCGCTAAAGACCAAGACCTT
1 CACCGCTAAAGACCAAGACCTTTAGCGGCGCT-TTCCCACAAACGCCGCTAAAGACCAAAACCTT
*
17257695 TAGCGGCGCTATTCCCACGAA
65 TAGCGGCGCTATTCCCACAAA
* * *
17257716 CACCGCTAAAGACCAAGATCTTTAGCAGCGCTTTCCCACAAACGCCGCTAAAGACCAAAATCTTT
1 CACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCAAAACCTTT
17257781 AGCGGCGCTATTCCCACAAA
66 AGCGGCGCTATTCCCACAAA
** * * *
17257801 TGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCACACAAACGCCGCTA
1 CACCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTA
17257852 TAGAATAGAT
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
85 75 0.61
86 48 0.39
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.18
Consensus pattern (85 bp):
CACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCAAAACCTTT
AGCGGCGCTATTCCCACAAA
Found at i:17257792 original size:128 final size:127
Alignment explanation
Indices: 17257632--17257868 Score: 359
Period size: 128 Copynumber: 1.9 Consensus size: 127
17257622 AATGACAGCA
* *
17257632 CCGCTAAAGACCAAGACCTTTAGCGGCGCTATTCCCACAAACGCCGCTAAAGACCAAGACCTTTA
1 CCGCTAAAGACCAAAACCTTTAGCGGCGCTATTCCCACAAACGCCACTAAAGACCAAGACCTTTA
* *
17257697 GCGGCGCTATTCCCACGAACACCGCTAAAGACCA-AGATCTTTAGCAGCGCTTTCCCACAAACG
66 GCGGCGCTATTCACACAAACACCGCTAAAGA--ATAGATCTTTAGCAGCGCTTTCCCACAAACG
* * *
17257760 CCGCTAAAGACCAAAATCTTTAGCGGCGCTATTCCCACAAATGCCACTAAAGACCATGACCTTTA
1 CCGCTAAAGACCAAAACCTTTAGCGGCGCTATTCCCACAAACGCCACTAAAGACCAAGACCTTTA
* * *
17257825 GCGGCGCTTTTCACACAAACGCCGCTATAGAATAGATCTTTAGC
66 GCGGCGCTATTCACACAAACACCGCTAAAGAATAGATCTTTAGC
17257869 GGTGCTTTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
126 1 0.01
127 11 0.11
128 86 0.88
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (127 bp):
CCGCTAAAGACCAAAACCTTTAGCGGCGCTATTCCCACAAACGCCACTAAAGACCAAGACCTTTA
GCGGCGCTATTCACACAAACACCGCTAAAGAATAGATCTTTAGCAGCGCTTTCCCACAAACG
Found at i:17258966 original size:5 final size:5
Alignment explanation
Indices: 17258956--17258983 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
17258946 TCTCTCTATC
17258956 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
17258984 TAATTCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:17263144 original size:77 final size:78
Alignment explanation
Indices: 17263080--17263228 Score: 216
Period size: 75 Copynumber: 1.9 Consensus size: 78
17263070 TTTTTTTTGC
* *
17263080 GGCG-TTTTTATGAAAACGTCGCTAAATGTTTTGCTATATAAAAT-GC-CTA-TTTTTAAAGTAA
1 GGCGTTTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCGCTATTTTTTAAAGTAA
17263141 AATTATTTTTTAT
66 AATTATTTTTTAT
* * *
17263154 GGCGTTTTTTATAAAAACGCCGCTAAATGTTTTGTTATATGAAATGGCGTTATTTTTTTAAAGTA
1 GGCGTTTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCGCTA-TTTTTTAAAGTA
17263219 AAATTATTTT
65 AAATTATTTT
17263229 ACTATCAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
74 4 0.06
75 36 0.55
76 2 0.03
77 2 0.03
79 21 0.32
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (78 bp):
GGCGTTTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCGCTATTTTTTAAAGTAA
AATTATTTTTTAT
Found at i:17264042 original size:14 final size:14
Alignment explanation
Indices: 17264025--17264119 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 14
17264015 ACTAATTAAT
17264025 CTAACCCTTAATCC
1 CTAACCCTTAATCC
* *
17264039 CTAACCCCTAACCC
1 CTAACCCTTAATCC
17264053 CTAA-CCTTAAATCC
1 CTAACCCTT-AATCC
* *
17264067 CTAACTCTTAATCT
1 CTAACCCTTAATCC
*
17264081 CTAACCCTTAACCC
1 CTAACCCTTAATCC
*
17264095 CTAACCCCTAA-CC
1 CTAACCCTTAATCC
*
17264108 CATAAACCTTAA
1 C-TAACCCTTAA
17264120 ATCACAACNN
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
13 6 0.09
14 57 0.86
15 3 0.05
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (14 bp):
CTAACCCTTAATCC
Found at i:17264045 original size:82 final size:81
Alignment explanation
Indices: 17263883--17264045 Score: 227
Period size: 82 Copynumber: 2.0 Consensus size: 81
17263873 ACTAGCTCTT
*
17263883 AACCCCAAACCCCAAACCACTAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
1 AACCCCAAACCCCAAACCACTAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
*
17263948 TCATAAACCCTAACCC
66 CCATAAACCCTAACCC
* * * * *
17263964 AACCCCAAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAA
1 AACCCCAAACCCCAAACCACT-AACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
* * *
17264029 CCCTTAATCCCTAACCC
65 ACCATAAACCCTAACCC
17264046 CTAACCCCTA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 18 0.25
82 53 0.75
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (81 bp):
AACCCCAAACCCCAAACCACTAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
CCATAAACCCTAACCC
Found at i:17264057 original size:28 final size:28
Alignment explanation
Indices: 17264025--17264119 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 28
17264015 ACTAATTAAT
17264025 CTAACCCTTAATCCCTAACCCCTAACCC
1 CTAACCCTTAATCCCTAACCCCTAACCC
* * * *
17264053 CTAA-CCTTAAATCCCTAACTCTTAATCT
1 CTAACCCTT-AATCCCTAACCCCTAACCC
*
17264081 CTAACCCTTAACCCCTAACCCCTAACCC
1 CTAACCCTTAATCCCTAACCCCTAACCC
* *
17264109 ATAAACCTTAA
1 CTAACCCTTAA
17264120 ATCACAACNN
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 4 0.07
28 46 0.85
29 4 0.07
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (28 bp):
CTAACCCTTAATCCCTAACCCCTAACCC
Found at i:17264096 original size:8 final size:7
Alignment explanation
Indices: 17264025--17264108 Score: 71
Period size: 7 Copynumber: 12.0 Consensus size: 7
17264015 ACTAATTAAT
17264025 CTAACCC
1 CTAACCC
* *
17264032 TTAATCC
1 CTAACCC
17264039 CTAACCC
1 CTAACCC
17264046 CTAACCC
1 CTAACCC
17264053 CTAA-CC
1 CTAACCC
* *
17264059 TTAAATCC
1 CT-AACCC
*
17264067 CTAACTC
1 CTAACCC
* * *
17264074 TTAATCT
1 CTAACCC
17264081 CTAACCC
1 CTAACCC
*
17264088 TTAACCC
1 CTAACCC
17264095 CTAACCC
1 CTAACCC
17264102 CTAACCC
1 CTAACCC
17264109 ATAAACCTTA
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
6 3 0.05
7 52 0.90
8 3 0.05
ACGTcount: A:0.30, C:0.45, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAACCC
Found at i:17264680 original size:41 final size:41
Alignment explanation
Indices: 17264622--17264945 Score: 452
Period size: 41 Copynumber: 7.9 Consensus size: 41
17264612 AAATGTTTTT
* * **
17264622 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
17264663 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
17264704 GCGGCGCATTT-TCAGAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGC-TTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
17264745 GCGGCGCATTCTCAGAAACGCCGCTAAAGCTCTGAGCGTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
17264786 GCGGCGCTTTCTCAGAAACGCCGCTAAAGATCTGAGCTTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
17264827 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGAATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
17264868 GCGGCGCTTCTCTCAAAAACACCGCTAAAGATCTGAGCATTA
1 GCGGCGCTT-TCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
17264910 GCGGCGCTTTTTTTAAAAACGCCACTAAAGATCTGA
1 GCGGCGC-TTTCTCAAAAACGCCGCTAAAGATCTGA
17264946 AAGGTACAAA
Statistics
Matches: 259, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
40 2 0.01
41 193 0.75
42 62 0.24
43 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:17265027 original size:40 final size:39
Alignment explanation
Indices: 17264977--17265089 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 39
17264967 GGGCTTAGAC
*
17264977 TTTTT-GCGGCGTTTTTTGGAAAAACGCCGCTAATGCT-AA
1 TTTTTAGCGGCGTTTTCT--AAAAACGCCGCTAATGCTCAA
* * *
17265016 TTTTTAGCGGCGCTTTCCTAGAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCG-TTTTCTAAAAACGCCGCTAATGCTCAA
* *
17265056 TTTTTAGTGGCGTTTTCTATCCAAACGCCGCTAA
1 TTTTTAGCGGCGTTTTCTA--AAAACGCCGCTAA
17265090 AAGCCTGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
39 28 0.45
40 18 0.29
41 16 0.26
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCTAAAAACGCCGCTAATGCTCAA
Found at i:17265041 original size:39 final size:40
Alignment explanation
Indices: 17264998--17265089 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 40
17264988 TTTTTTGGAA
*
17264998 AAACGCCGCTAATGCT-AATTTTTAGCGGCGCTTTCCTA-G
1 AAACGCCGCTAATGCTCAATTTTTAGCGGCG-TTTCCTACC
* * *
17265037 AAACGCCGCTAATGCTCGATTTTTAGTGGCGTTTTCTATCC
1 AAACGCCGCTAATGCTCAATTTTTAGCGGCGTTTCCTA-CC
17265078 AAACGCCGCTAA
1 AAACGCCGCTAA
17265090 AAGCCTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 22 0.48
40 12 0.26
41 12 0.26
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (40 bp):
AAACGCCGCTAATGCTCAATTTTTAGCGGCGTTTCCTACC
Found at i:17269398 original size:17 final size:17
Alignment explanation
Indices: 17269378--17269416 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
17269368 TAACACAAAT
*
17269378 ATATAATTAAA-AATAAC
1 ATATAA-TAAATAATAAA
17269395 ATATAATAAATAATAAA
1 ATATAATAAATAATAAA
17269412 ATATA
1 ATATA
17269417 TTGTTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAATAAATAATAAA
Found at i:17269407 original size:24 final size:22
Alignment explanation
Indices: 17269367--17269412 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
17269357 TTATATATTT
*
17269367 ATAACACAAATATATAATTAAAA
1 ATAACACAAATAAATAA-TAAAA
*
17269390 ATAACATATAATAAATAATAAAA
1 ATAACACA-AATAAATAATAAAA
17269413 TATATTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAACACAAATAAATAATAAAA
Found at i:17276926 original size:36 final size:34
Alignment explanation
Indices: 17276859--17276926 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 34
17276849 GTCTCCTGCT
*
17276859 GGTTAGGGTTTTGGGTTTTTAGTTTAGGGTTTAG
1 GGTTAGAGTTTTGGGTTTTTAGTTTAGGGTTTAG
17276893 GGTTAGAGTTTTGGGGTTTTTAAGTTTAGGGTTT
1 GGTTAGAGTTTT-GGGTTTTT-AGTTTAGGGTTT
17276927 TAAAGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 11 0.35
35 8 0.26
36 12 0.39
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (34 bp):
GGTTAGAGTTTTGGGTTTTTAGTTTAGGGTTTAG
Found at i:17277503 original size:125 final size:126
Alignment explanation
Indices: 17277131--17277544 Score: 677
Period size: 126 Copynumber: 3.3 Consensus size: 126
17277121 TTTAAAAAAA
*
17277131 CTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTG
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTG
17277196 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
66 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
* * * *
17277257 TTCCCACGTGGACGCTCTTTTGCTACAGTAGCACCTGAAAAAATAATTTCGAGAAGAAGTTTCTG
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTG
*
17277322 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTATTGAAAGAAG
66 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
* * * *
17277383 CTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCTTG-AAAAATAATTTCGAGTAGACGTTTCTA
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTG
* * * *
17277447 AGCAAATAGTTTCAAAAACACCTTAAGCAAGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
66 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
* *
17277508 CTCCCACGTGGATGGGCTTTTGCTACAGTAGCTCCTG
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
17277545 TTTGGCCTGA
Statistics
Matches: 267, Mismatches: 21, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
125 113 0.42
126 154 0.58
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (126 bp):
CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTG
AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
Found at i:17280599 original size:13 final size:13
Alignment explanation
Indices: 17280581--17280606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17280571 AATATTCAAA
17280581 AGATAATCTATTT
1 AGATAATCTATTT
17280594 AGATAATCTATTT
1 AGATAATCTATTT
17280607 TATTAAAAAT
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
AGATAATCTATTT
Found at i:17281903 original size:7 final size:7
Alignment explanation
Indices: 17281893--17281925 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
17281883 TATAATACAT
17281893 AATACTA
1 AATACTA
17281900 AATACTA
1 AATACTA
*
17281907 AACACTA
1 AATACTA
17281914 AATACTA
1 AATACTA
17281921 AATAC
1 AATAC
17281926 CAATCGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (7 bp):
AATACTA
Found at i:17283168 original size:22 final size:23
Alignment explanation
Indices: 17283143--17283190 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
17283133 GCTTTTTTTA
17283143 AGAGGAAT-TT-GAGAAGAATTTG
1 AGAGGAATATTGGAGAA-AATTTG
17283165 AGA-GAATATTGGAGAAAATTTG
1 AGAGGAATATTGGAGAAAATTTG
17283187 AGAG
1 AGAG
17283191 AAAGGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 14 0.61
23 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (23 bp):
AGAGGAATATTGGAGAAAATTTG
Found at i:17283179 original size:10 final size:10
Alignment explanation
Indices: 17283147--17283192 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
17283137 TTTTTAAGAG
17283147 GAATTTGAGAA
1 GAATTTGAG-A
17283158 GAATTTGAGA
1 GAATTTGAGA
17283168 GAATATTGGAGA
1 GAAT-TT-GAGA
*
17283180 AAATTTGAGA
1 GAATTTGAGA
17283190 GAA
1 GAA
17283193 AGGATTTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 11 0.35
11 13 0.42
12 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (10 bp):
GAATTTGAGA
Found at i:17289110 original size:25 final size:24
Alignment explanation
Indices: 17289082--17289130 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
17289072 AAATAAAACT
17289082 TTTATTTTTATATATAATT-TATTTA
1 TTTA-TTTTA-ATATAATTGTATTTA
*
17289107 TTTATTTTAATTTAATTGTATTTA
1 TTTATTTTAATATAATTGTATTTA
17289131 AAAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 11 0.50
25 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTATTTTAATATAATTGTATTTA
Found at i:17290330 original size:32 final size:31
Alignment explanation
Indices: 17290260--17290331 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
17290250 TGGCGAGGAT
*
17290260 GGCTTAATTGATTTTTTTATTATTTCACAAT
1 GGCTTAATTGATTTTTTTATTATTTCACAAG
** * *
17290291 GATTTAATTGATTTTTTTAGTTATTTTACGAG
1 GGCTTAATTGATTTTTTTA-TTATTTCACAAG
17290323 GGCTTAATT
1 GGCTTAATT
17290332 TATTATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (31 bp):
GGCTTAATTGATTTTTTTATTATTTCACAAG
Found at i:17293343 original size:56 final size:57
Alignment explanation
Indices: 17293252--17293360 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 57
17293242 CGTGTGTCCT
** * *
17293252 CTATTTTTCAGATTATATAGTTTTGCCCAT-GTTTTTCATATTTTACAATTTTACCC
1 CTATTTTTCAGATTATATAAATTTGCCCATATTTTTTCAAATTTTACAATTTTACCC
* * *
17293308 CTATTTTTTAGATTTTATAAATTTGTCCC-TATTTTTTCAAATTTTATAATTTT
1 CTATTTTTCAGATTATATAAATTTG-CCCATATTTTTTCAAATTTTACAATTTT
17293361 TCCCTGCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
56 22 0.50
57 22 0.50
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.56
Consensus pattern (57 bp):
CTATTTTTCAGATTATATAAATTTGCCCATATTTTTTCAAATTTTACAATTTTACCC
Found at i:17293364 original size:28 final size:28
Alignment explanation
Indices: 17293255--17293365 Score: 109
Period size: 28 Copynumber: 3.9 Consensus size: 28
17293245 GTGTCCTCTA
* * *
17293255 TTTTTCAGATTATATAGTTTTGCCC-AT
1 TTTTTCAGATTTTATAATTTTTCCCTAT
* * *
17293282 GTTTTTCATATTTTACAATTTTACCCCTAT
1 -TTTTTCAGATTTTATAATTTT-TCCCTAT
*
17293312 TTTTT-AGATTTTATAAATTTGTCCCTAT
1 TTTTTCAGATTTTAT-AATTTTTCCCTAT
*
17293340 TTTTTCAAATTTTATAATTTTTCCCT
1 TTTTTCAGATTTTATAATTTTTCCCT
17293366 GCTTTATAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
28 45 0.66
29 21 0.31
30 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.56
Consensus pattern (28 bp):
TTTTTCAGATTTTATAATTTTTCCCTAT
Found at i:17293681 original size:34 final size:34
Alignment explanation
Indices: 17293643--17293716 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
17293633 AACATGACTT
17293643 TTGCTACT-AAGTTGAACTGTTATAAGCATATTAA
1 TTGCTACTGAA-TTGAACTGTTATAAGCATATTAA
* * * *
17293677 TTGCTATTGTATTGAATTGTTATAAGCATATTGA
1 TTGCTACTGAATTGAACTGTTATAAGCATATTAA
17293711 TTGCTA
1 TTGCTA
17293717 TCGTATTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.43
Consensus pattern (34 bp):
TTGCTACTGAATTGAACTGTTATAAGCATATTAA
Found at i:17293717 original size:34 final size:34
Alignment explanation
Indices: 17293654--17293724 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
17293644 TGCTACTAAG
*
17293654 TTGAACTGTTATAAGCATATTAATTGCTATTGTA
1 TTGAACTGTTATAAGCATATTAATTGCTATCGTA
* *
17293688 TTGAATTGTTATAAGCATATTGATTGCTATCGTA
1 TTGAACTGTTATAAGCATATTAATTGCTATCGTA
17293722 TTG
1 TTG
17293725 TTATAGTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (34 bp):
TTGAACTGTTATAAGCATATTAATTGCTATCGTA
Found at i:17299925 original size:26 final size:26
Alignment explanation
Indices: 17299896--17299950 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
17299886 CATTAGGGCA
17299896 TAGTAGGCTTTGTGCCGGTGTATATT
1 TAGTAGGCTTTGTGCCGGTGTATATT
*
17299922 TAGTAGGCTTTGTGTCGGTGTATATT
1 TAGTAGGCTTTGTGCCGGTGTATATT
17299948 TAG
1 TAG
17299951 CAAGTTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.09, G:0.31, T:0.44
Consensus pattern (26 bp):
TAGTAGGCTTTGTGCCGGTGTATATT
Found at i:17300417 original size:38 final size:38
Alignment explanation
Indices: 17300375--17300447 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
17300365 GTCTAAGCTA
17300375 TTTTGTTTTACAAACTTACTAAGCTTTATGTAAGCCTT
1 TTTTGTTTTACAAACTTACTAAGCTTTATGTAAGCCTT
17300413 TTTTGTTTTACAAACTTACTAAGCTTTATGTAAGC
1 TTTTGTTTTACAAACTTACTAAGCTTTATGTAAGC
17300448 TTACTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (38 bp):
TTTTGTTTTACAAACTTACTAAGCTTTATGTAAGCCTT
Found at i:17307392 original size:18 final size:18
Alignment explanation
Indices: 17307365--17307399 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17307355 CCCAAGTCAA
17307365 AATAAGCAGTTAAAAAAT
1 AATAAGCAGTTAAAAAAT
*
17307383 AATAATCAGTTAAAAAA
1 AATAAGCAGTTAAAAAA
17307400 AATCTAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (18 bp):
AATAAGCAGTTAAAAAAT
Found at i:17309644 original size:17 final size:18
Alignment explanation
Indices: 17309611--17309660 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
17309601 AATATTACTG
17309611 TATTATTATCAGT-TTAT-
1 TATTATTATCA-TATTATA
17309628 TATTATTATCATATTATA
1 TATTATTATCATATTATA
* *
17309646 TAGTATTATTATATT
1 TATTATTATCATATT
17309661 TATTTATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 1 0.03
17 15 0.52
18 13 0.45
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
TATTATTATCATATTATA
Found at i:17316436 original size:8 final size:8
Alignment explanation
Indices: 17316423--17316452 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
17316413 GATTCAGTTA
17316423 AAAAAAAC
1 AAAAAAAC
17316431 AAAAAAAC
1 AAAAAAAC
17316439 -AAAAAAC
1 AAAAAAAC
17316446 AAAAAAA
1 AAAAAAA
17316453 AAGAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:17316467 original size:18 final size:17
Alignment explanation
Indices: 17316431--17316493 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
17316421 TAAAAAAAAC
* * *
17316431 AAAAAAACAAAAAACAA
1 AAAAAAAGAAAAGAGAA
17316448 AAAAAAAGAAAGAGAGAA
1 AAAAAAAGAAA-AGAGAA
* *
17316466 AAAAATAGAAAATAGAA
1 AAAAAAAGAAAAGAGAA
17316483 AAAAAAGAGAA
1 AAAAAA-AGAA
17316494 CATAAAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 20 0.53
18 18 0.47
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAGAGAA
Found at i:17317018 original size:8 final size:8
Alignment explanation
Indices: 17317005--17317044 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
17316995 AAAAGATGAG
17317005 AAATGAAA
1 AAATGAAA
17317013 AAATGAAA
1 AAATGAAA
*
17317021 AAGTGAAA
1 AAATGAAA
17317029 AAATGAAA
1 AAATGAAA
*
17317037 AAGTGAAA
1 AAATGAAA
17317045 TGGAGAGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:17317027 original size:16 final size:16
Alignment explanation
Indices: 17316994--17317044 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
17316984 AGTCGCAAAA
*
17316994 AAAAAGATGAGAAA-TG
1 AAAAA-ATGAAAAAGTG
17317010 AAAAAATGAAAAAGTG
1 AAAAAATGAAAAAGTG
17317026 AAAAAATGAAAAAGTG
1 AAAAAATGAAAAAGTG
17317042 AAA
1 AAA
17317045 TGGAGAGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
15 7 0.21
16 26 0.79
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.12
Consensus pattern (16 bp):
AAAAAATGAAAAAGTG
Found at i:17318441 original size:50 final size:50
Alignment explanation
Indices: 17318376--17319403 Score: 765
Period size: 50 Copynumber: 20.6 Consensus size: 50
17318366 CGCAATTAAA
**
17318376 AGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
**
17318426 AGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
**
17318476 AGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
**
17318526 AGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
**
17318576 AGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
**
17318626 AGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* *
17318676 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGCGGATC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* ** *** * * * **** **
17318726 AGATTGAAGTCACAACGATGGATCTGGTTTCCC-CGACAGCGTAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCG-CGGTGCAGCGGAGC
* *
17318776 AGATTGAAGCAACAACGGCGGATCTTACTTCCCTGGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* *** ** * * **** **
17318826 AGATTGAAGTCACAACGGCGGATCTGGTTTTTC-CGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCG-CGGTGCAGCGGAGC
* *
17318876 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGCGGTGCAGCAGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* * ** * * **** **
17318926 AGATTGAAGTCACAACGACGGATC-TGGTTTCCTCGACAGTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCG-CGGTGCAGCGGAGC
* * * *
17318976 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTAGCGGTGCAGCAGAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* * ** * * **** **
17319026 AGATTGAAGTCACAACGACGGATC-TGGTTTCCTCGACAGTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCG-CGGTGCAGCGGAGC
* * * * *
17319076 AGATTGAAGCCACAACGACAGATCTTACTTCCCTGGCAGTGCAGCGGAGT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* * *** * * **** **
17319126 AGATTGAAGTCACAACGGGGGATCTGGTTTCCC-CGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCG-CGGTGCAGCGGAGC
** * * *
17319176 AGATTGAAGCCACAACGGTAGATCTTACTTCCCTGGTGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* * * *** * * **** **
17319226 AAATTGAAGTCACAACGACGGATCTGGTTTCCC-CGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCG-CGGTGCAGCGGAGC
* * * * ** *
17319276 AGATTGAAGCCACAACGGCAGATTTTACTTCTCTGGCGGTGCAATGGAGT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
* * ** * * **** **
17319326 AGATTGAAGTCACAACGGCAGATC-TGGTTTCCTCGACAGTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCG-CGGTGCAGCGGAGC
17319376 AGATTGAAGCCACAACGGCGGATCTTAC
1 AGATTGAAGCCACAACGGCGGATCTTAC
17319404 CTCCTTAGTA
Statistics
Matches: 766, Mismatches: 198, Indels: 27
0.77 0.20 0.03
Matches are distributed among these distances:
49 24 0.03
50 723 0.94
51 19 0.02
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCCTCGCGGTGCAGCGGAGC
Found at i:17319463 original size:100 final size:100
Alignment explanation
Indices: 17318319--17319403 Score: 1217
Period size: 100 Copynumber: 10.9 Consensus size: 100
17318309 TTAGCGTTGT
* * * *
17318319 AGCGGAGCAGATTGAAGTCACAACGGCGGATCTAGTTTCCCCGACCGCGCAATT-AAAAGATTGA
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
* ** *
17318383 AGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * ** ** * * * **** **
17318418 AGCGGAGCAGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCG-CGGTGCAGCGGAGCAGATTG
1 AGCGGAGCAGATTGAAGTCACAACGACGGATC-TGGTTTCCTCGACAGCGCAATTAAAAAGATTG
* ** *
17318482 AAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGC
65 AAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * ** ** * * * **** **
17318518 AGCGGAGCAGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCG-CGGTGCAGCGGAGCAGATTG
1 AGCGGAGCAGATTGAAGTCACAACGACGGATC-TGGTTTCCTCGACAGCGCAATTAAAAAGATTG
* ** *
17318582 AAGCCACAACGGCGGGGCTTACTTCCCTCGCGGTGC
65 AAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * ** ** * * * **** **
17318618 AGCGGAGCAGATTGAAGCCACAACGGCGGGGCTTACTTCCCTCG-CGGTGCAGCGGAGCAGATTG
1 AGCGGAGCAGATTGAAGTCACAACGACGGATC-TGGTTTCCTCGACAGCGCAATTAAAAAGATTG
*
17318682 AAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGC
65 AAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * * *
17318718 AGCGGATCAGATTGAAGTCACAACGATGGATCTGGTTTCCCCGACAGCGTAATTAAAAAGATTGA
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
* *
17318783 AGCAACAACGGCGGATCTTACTTCCCTGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* *
17318818 AGCGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTT-TTCCGACAGCGCAATTAAAAAGATTG
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCT-CGACAGCGCAATTAAAAAGATTG
* *
17318882 AAGCCACAACGGCGGATCTTACTTCCCTAGCGGTGC
65 AAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* *
17318918 AGCAGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGTGCAATTAAAAAGATTGA
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
*
17318983 AGCCACAACGGCAGATCTTACTTCCCTAGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
17319018 AGCAGAACAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGTGCAATTAAAAAGATTGA
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
* *
17319083 AGCCACAACGACAGATCTTACTTCCCTGGCAGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* ** *
17319118 AGCGGAGTAGATTGAAGTCACAACGGGGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
* *
17319183 AGCCACAACGGTAGATCTTACTTCCCTGGTGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
17319218 AGTGGAGCAAATTGAAGTCACAACGACGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
* *
17319283 AGCCACAACGGCAGATTTTACTTCTCTGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
** * * * *
17319318 AATGGAGTAGATTGAAGTCACAACGGCAGATCTGGTTTCCTCGACAGTGCAATTAAAAAGATTGA
1 AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
*
17319383 AGCCACAACGGCGGATCTTAC
66 AGCCACAACGGCAGATCTTAC
17319404 CTCCTTAGTA
Statistics
Matches: 899, Mismatches: 82, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
99 41 0.05
100 857 0.95
101 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (100 bp):
AGCGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGATTGA
AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
Found at i:17320740 original size:20 final size:21
Alignment explanation
Indices: 17320714--17320764 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
17320704 TAATATTACT
17320714 GTATTATTATCAGT-TTAT-TA
1 GTATTATTATCA-TATTATATA
*
17320734 TTATTATTATCATATTATATA
1 GTATTATTATCATATTATATA
17320755 GTATTATTAT
1 GTATTATTAT
17320765 ATTTATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 15 0.56
21 11 0.41
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (21 bp):
GTATTATTATCATATTATATA
Found at i:17320761 original size:18 final size:17
Alignment explanation
Indices: 17320729--17320767 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
17320719 ATTATCAGTT
*
17320729 TATTATTATTATTATCA
1 TATTATTAGTATTATCA
*
17320746 TATTATATAGTATTATTA
1 TATTAT-TAGTATTATCA
17320764 TATT
1 TATT
17320768 TATTTATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTATTAGTATTATCA
Found at i:17322013 original size:8 final size:7
Alignment explanation
Indices: 17321996--17322027 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
17321986 TAAAACATTT
17321996 AAAAAGA
1 AAAAAGA
17322003 AAAAAGA
1 AAAAAGA
17322010 AAAAAGAA
1 AAAAAG-A
17322018 AAAAAGA
1 AAAAAGA
17322025 AAA
1 AAA
17322028 TCCTTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:17322015 original size:14 final size:15
Alignment explanation
Indices: 17321996--17322027 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17321986 TAAAACATTT
17321996 AAAAAG-AAAAAAGA
1 AAAAAGAAAAAAAGA
17322010 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
17322025 AAA
1 AAA
17322028 TCCTTTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:17327976 original size:50 final size:50
Alignment explanation
Indices: 17327852--17328032 Score: 163
Period size: 50 Copynumber: 3.6 Consensus size: 50
17327842 GATAATAACA
* * * * *
17327852 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACGGGA-GTTCTCATAT-CGG
* * *
17327901 TGCCAATTCCATATCCCAGATATGGTCTTACACGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACGGGAGTTCTCATATCGG
* * * * * *
17327951 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGGGCCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACGGGAG-TTCTCATATCGG
* *
17328001 TGCCAACGCCATGTCCTAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
17328033 TAGGACCTCT
Statistics
Matches: 107, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
48 4 0.04
49 39 0.36
50 64 0.60
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACACGGGAGTTCTCATATCGG
Found at i:17336444 original size:30 final size:30
Alignment explanation
Indices: 17336405--17336473 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
17336395 ACTAAAAAAA
*
17336405 GCCGTTTTTTTTCAAAATTTACCGAAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
* ** *
17336435 GCCGATTTTTTTGATTATTTACCGGAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
*
17336465 TCC-ATTTTT
1 GCCGATTTTT
17336474 CGGGAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45
Consensus pattern (30 bp):
GCCGATTTTTTTCAAAATTTACCGAAATGG
Found at i:17336680 original size:22 final size:22
Alignment explanation
Indices: 17336652--17336723 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
17336642 ACAAATCCTA
17336652 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
17336674 TCTCAATTTCCTTCCAAATTCC
1 TCTCAATTTCCTTCCAAAATCC
17336696 TCTCAATTTCCTTCCAAAAAT-C
1 TCTCAATTTCCTTCC-AAAATCC
17336718 TCTCAA
1 TCTCAA
17336724 ATCCACATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 43 0.91
23 4 0.09
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:17336685 original size:11 final size:11
Alignment explanation
Indices: 17336652--17336707 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
17336642 ACAAATCCTA
17336652 TCTCAATTTCC
1 TCTCAATTTCC
**
17336663 T-TCCAAAATCC
1 TCT-CAATTTCC
17336674 TCTCAATTTCC
1 TCTCAATTTCC
*
17336685 T-TCCAAATTCC
1 TCT-CAATTTCC
17336696 TCTCAATTTCC
1 TCTCAATTTCC
17336707 T
1 T
17336708 TCCAAAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 2 0.06
11 31 0.89
12 2 0.06
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.41
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:17336797 original size:28 final size:29
Alignment explanation
Indices: 17336759--17336819 Score: 115
Period size: 28 Copynumber: 2.1 Consensus size: 29
17336749 TCAATTTCAT
17336759 TTTTTAAAATAATTTT-AAATTTTTTATA
1 TTTTTAAAATAATTTTAAAATTTTTTATA
17336787 TTTTTAAAATAATTTTAAAATTTTTTATA
1 TTTTTAAAATAATTTTAAAATTTTTTATA
17336816 TTTT
1 TTTT
17336820 CATCAATGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTTAAAATAATTTTAAAATTTTTTATA
Found at i:17336931 original size:14 final size:15
Alignment explanation
Indices: 17336912--17336941 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17336902 TTTGTAATTA
17336912 TTATTTAAG-ATTTT
1 TTATTTAAGTATTTT
17336926 TTATTTAAGTATTTT
1 TTATTTAAGTATTTT
17336941 T
1 T
17336942 AGATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTATTTAAGTATTTT
Found at i:17338817 original size:18 final size:18
Alignment explanation
Indices: 17338791--17338825 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17338781 AGGTGTGTTT
* *
17338791 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
17338809 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
17338826 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:17339352 original size:29 final size:29
Alignment explanation
Indices: 17339310--17339864 Score: 536
Period size: 29 Copynumber: 19.2 Consensus size: 29
17339300 TTATTTGATA
* * *
17339310 TAATTAAAGTAAAAATCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
*
17339339 TAATTTAATTAAAAACCCTAACCTTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
* *
17339368 TAATTTATTTAAAAACCCTAATCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
*
17339397 TAATTTATTTAAAAACCCTAACCCCTAACCCC
1 TAATTTAATTAAAAACCCTAA-CCCTAA--CC
****
17339429 TAA--CCCCT--AAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
*
17339454 TAA---AAGTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
* * *
17339480 TAATTGAATAAAAAAACCTTAACCCTAACC
1 TAATTTAAT-TAAAAACCCTAACCCTAACC
* ** *
17339510 TAATTTAATAAAAAAACTGTAACACTAACC
1 TAATTTAAT-TAAAAACCCTAACCCTAACC
*
17339540 CAATTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
17339569 TAATTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
*
17339598 TAATTTAATTAAAAACCCTAACCCTAACT
1 TAATTTAATTAAAAACCCTAACCCTAACC
***
17339627 TAATTTAATCCTAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
***
17339656 TAATTTAATCCTAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
17339685 TAATTTAATT-AAAACCCTAACCCTTAAAAACC
1 TAATTTAATTAAAAACCCTAACCC-T---AACC
* *
17339717 TTAGCCTAATTTAATTAAAAACTCTAAACCCT---C
1 -TA----ATTT-AATTAAAAACCCT-AACCCTAACC
17339750 ------AATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
* *
17339773 TAATATAATTAAAAACCCTAGCCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
*
17339802 TAATTTATTTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
17339831 TAATTTAATTAAAAACCCGT--CCCTAACC
1 TAATTTAATTAAAAACCC-TAACCCTAACC
17339859 TAATTT
1 TAATTT
17339865 TACATAATTT
Statistics
Matches: 452, Mismatches: 43, Indels: 63
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.01
21 12 0.03
23 1 0.00
24 1 0.00
25 5 0.01
26 20 0.04
27 6 0.01
28 35 0.08
29 275 0.61
30 59 0.13
32 9 0.02
33 3 0.01
37 3 0.01
38 4 0.01
39 8 0.02
40 5 0.01
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (29 bp):
TAATTTAATTAAAAACCCTAACCCTAACC
Found at i:17339424 original size:7 final size:7
Alignment explanation
Indices: 17339412--17339453 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
17339402 TATTTAAAAA
17339412 CCCTAAC
1 CCCTAAC
17339419 CCCTAAC
1 CCCTAAC
17339426 CCCTAAC
1 CCCTAAC
*
17339433 CCCTAAA
1 CCCTAAC
17339440 CCCTAA-
1 CCCTAAC
17339446 CCCTAAC
1 CCCTAAC
17339453 C
1 C
17339454 TAAAAGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.31, C:0.55, G:0.00, T:0.14
Consensus pattern (7 bp):
CCCTAAC
Found at i:17339766 original size:20 final size:21
Alignment explanation
Indices: 17339729--17339768 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17339719 AGCCTAATTT
*
17339729 AATTAAAAACTCTAAACCCTC
1 AATTAAAAACCCTAAACCCTC
17339750 AATTAAAAACCCT-AACCCT
1 AATTAAAAACCCTAAACCCT
17339769 AACCTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AATTAAAAACCCTAAACCCTC
Found at i:17341535 original size:76 final size:76
Alignment explanation
Indices: 17341409--17341561 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
17341399 CCAAAATAGG
17341409 CGTTTGAACACTTGACATCCACGTAGCAATCGGCCGTTGTAGTACGCATGTTCCGTTTCAAGGTC
1 CGTTTGAACACTTGACATCCACGTAGCAATCGGCCGTTGTAGTACGCATGTTCCGTTTCAAGGTC
17341474 TGTGATGGCAC
66 TGTGATGGCAC
* *
17341485 CGTTTGAACACTTGGCATCCACGTAGCAATCGGCCGTTGTAGTACGCATGTTCCGTTTCAATGTC
1 CGTTTGAACACTTGACATCCACGTAGCAATCGGCCGTTGTAGTACGCATGTTCCGTTTCAAGGTC
17341550 TGTGATGGCAC
66 TGTGATGGCAC
17341561 C
1 C
17341562 TCGGACGTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (76 bp):
CGTTTGAACACTTGACATCCACGTAGCAATCGGCCGTTGTAGTACGCATGTTCCGTTTCAAGGTC
TGTGATGGCAC
Found at i:17343385 original size:125 final size:124
Alignment explanation
Indices: 17343159--17343425 Score: 437
Period size: 125 Copynumber: 2.1 Consensus size: 124
17343149 CCACGAGGGC
* *
17343159 GCGATTTTATAGTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTAAATACCCAACTGTAGCG
1 GCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATTATTTCTTAAATACCCAACTGTAGCG
* * *
17343224 AAATCGCGTCTACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGGTAGAA
66 AAATCGCATCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGGTAGAA
* *
17343283 GCGATTTTATACTATTTGCTCAGAAGCGTAAAAAAAAAATTATTTCTTACATGA-CCAACTGTAG
1 GCGATTTTATACTATTTGCTCAGAAACGT-AAAAAAAAATTATTTCTTAAAT-ACCCAACTGTAG
*
17343347 CGAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
64 CGAAATCGCATCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGGTAGAA
17343408 GCGATTTTATACTATTTG
1 GCGATTTTATACTATTTG
17343426 ACCAAAAACG
Statistics
Matches: 133, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
124 27 0.20
125 105 0.79
126 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (124 bp):
GCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAATTATTTCTTAAATACCCAACTGTAGCG
AAATCGCATCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:17346887 original size:18 final size:17
Alignment explanation
Indices: 17346864--17346916 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
17346854 ATATATTATG
*
17346864 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
17346882 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
17346899 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
17346917 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:17350197 original size:111 final size:113
Alignment explanation
Indices: 17349975--17350197 Score: 335
Period size: 111 Copynumber: 2.0 Consensus size: 113
17349965 GACCATATTC
17349975 GATTTGAATCTTACTACTCACTGTCAATTTCCTTTTATAGATAATTTTATCATTTAAGTCCAAGA
1 GATTTGAATCTTACTACTCACTGTCAATTT-CTTTTATAGATAATTTTATCATTTAAGTCCAAGA
* *
17350040 GCTAGTAAGTGGAAATTTTTTTATTTACACCCTTTTATAGTATATAATT
65 GCTAGCAAGTGGAAATTTTTTTATTTACACCCTTTTATAATATATAATT
* * * *
17350089 GATTTGAATCTTACTAGTTACTGTCAATTT-TTTTATAGAT-TTTTTATCACTTTAAGTCCAAGG
1 GATTTGAATCTTACTACTCACTGTCAATTTCTTTTATAGATAATTTTATCA-TTTAAGTCCAAGA
* *
17350152 GCTAGCAAGT-GAAATTTTTTTATTTAGACCCTTTTATAATTTATAA
65 GCTAGCAAGTGGAAATTTTTTTATTTACACCCTTTTATAATATATAA
17350198 AATTTTAAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
111 41 0.41
112 31 0.31
114 28 0.28
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (113 bp):
GATTTGAATCTTACTACTCACTGTCAATTTCTTTTATAGATAATTTTATCATTTAAGTCCAAGAG
CTAGCAAGTGGAAATTTTTTTATTTACACCCTTTTATAATATATAATT
Found at i:17350862 original size:73 final size:73
Alignment explanation
Indices: 17350710--17350853 Score: 216
Period size: 73 Copynumber: 2.0 Consensus size: 73
17350700 TCTTGGATTT
* * * *
17350710 AAAAAAGGGATCATGCACAGTAAGTTAGGACACGATTTTTTCTTAATTCCCGACATCGCTTAAAA
1 AAAAAAGGGATCATGCACAGTAAGTTAGGACACGATCTCTTCTCAATTCCCGACATCACTTAAAA
17350775 CTTGAGAA
66 CTTGAGAA
* * * *
17350783 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTCAATTCTCGAGATCATTTAAAA
1 AAAAAAGGGATCATGCACAGTAAGTTAGGACACGATCTCTTCTCAATTCCCGACATCACTTAAAA
17350848 CTTGAG
66 CTTGAG
17350854 TTTGAAAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (73 bp):
AAAAAAGGGATCATGCACAGTAAGTTAGGACACGATCTCTTCTCAATTCCCGACATCACTTAAAA
CTTGAGAA
Found at i:17351282 original size:20 final size:21
Alignment explanation
Indices: 17351254--17351308 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
17351244 ATATATATGT
*
17351254 ATATGTATATAAATTATAA-A
1 ATATATATATAAATTATAAGA
* * *
17351274 ATATATATAAAAAATATAAGT
1 ATATATATATAAATTATAAGA
*
17351295 ATGTATATATAAAT
1 ATATATATATAAAT
17351309 CAAAGATCTG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATATATATATAAATTATAAGA
Found at i:17351676 original size:3 final size:3
Alignment explanation
Indices: 17351607--17351656 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
17351597 AAACTAATAC
* *
17351607 AAT AAT AAT ACCT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17351652 AAT AA
1 AAT AA
17351657 CCTAATTAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 39 0.95
4 1 0.02
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17353187 original size:100 final size:100
Alignment explanation
Indices: 17353023--17354587 Score: 2081
Period size: 100 Copynumber: 15.7 Consensus size: 100
17353013 AGATTCATCA
* * *
17353023 TTGTAGCTTCAATCTGTTCCACTACAACGCCAGGGAAGTAAAATTCACCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* *
17353088 TTTCAATTGCAATGTCGGGGAAGTAAGATTCGCCG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * * * *
17353123 TTATAACTTCAATCTGTTCCACTGCACCGCTAAGTAAGTAAGATTCACCGTTGTGGCTTTAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* * * * *
17353188 TTTCAAATGCAATGTCAGGGAAGAAAGATTCACCG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * * * *
17353223 TTGTAACTTCAATTTGTTCAACTGCACCGCCAGGTAAGTAAGATTCGCCGTTGTGGCTTCAATAT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* *
17353288 TTTTAATTGTAATGTCGGGGAAGCAAGATTCGCTG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * *
17353323 TTATAGCTTCAATCTGTTCCACTGCACCACCAAGGAAGTAAAATTCACCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* *
17353388 TTTTAATTACAATGTCGGGGAAGCAAGATTTGCCG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * * *
17353423 TTGTAGCTTCCATCTGTTGCACTGCACCACCAGGAAAGTAAGATTCACCATTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
17353488 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * *
17353523 TTGTAGCTTCAATCTGTTCCACTGCATCTCCAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* *
17353588 TTTTAATTGCAATGTCGGGGAAGCAAGATTTGCCA
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * * ** *
17353623 TTGTAGCTTCAATTTGTTCCATTGCACCACTAGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCA
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
*
17353688 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCA
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * *
17353723 TTGTAGCTTCAATATGTTCCACTGCACCTCCAGGGAAGTAAGATTTC-CCGTTGTGGCATCAATC
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA-TTCACCGTTGTGGCTTCAATC
* *
17353787 TTTTTAATTGCAATGTCAGGGAAGCAAGATTCGCTG
65 TTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* *
17353823 TTGTACCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* * * *
17353888 TTTTAATTGTAATGTCGGGGAAGTAAGATTCACTG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * **
17353923 TTGCAGCTTGAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATTTGCCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* * *
17353988 TTTTAATAT-CAATATCGGGGAAGTAAGATTCACCG
66 TTTTAAT-TGCAATGTCGGGGAAGCAAGATTCGCCG
* * * * * ** * *
17354023 TTCTACCTTTAATCTATTTCACTGCACCGCCAGGGAAGTAAGATTCGTCGTTGTGGCTTAAATAT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* * *
17354088 TTTTAATTGCAATGTCGAGGAAGCAAGATTCACCA
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* *
17354123 TTGTAGCTTCAATTTGTTCCACTGCACCGCCAGGGGAGTAAGATTCACCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* * *
17354188 TTTTAATTGCAATGTCGAGAAAGCAAGATTTGCCG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * * * *
17354223 TTGTACCTTCAATCTGATCCACTGCACCACCAGAGAAGTAAGATTCGCCGTTGTGGCTTCAAGCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* *
17354288 TTTTAATTGTAATGTCCGGGAAGCAAGATTCGCCG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * *
17354323 TTGTACCTTCAATTTGTTCCACTGCACCGCTAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* *
17354388 TTTTAATTGCAATGTCGGGGAAGCAAGATTCACCA
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * * *
17354423 TTGTAACTTCAATTTGTTGCACTGCACCACCAGGGAAGTAAGATTCACTGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
* * *
17354488 TTTTAATTACAATGTCAGGGAAGCAAGATTCACCG
66 TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * ** *
17354523 TTGTAGTTTCAATCTGTTCCACTGCATCGCTAGGGAAGTAAGATTTTCCGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
17354588 GTTCCACTGC
Statistics
Matches: 1291, Mismatches: 170, Indels: 8
0.88 0.12 0.01
Matches are distributed among these distances:
99 4 0.00
100 1283 0.99
101 4 0.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (100 bp):
TTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
Found at i:17354826 original size:99 final size:100
Alignment explanation
Indices: 17354503--17354842 Score: 452
Period size: 100 Copynumber: 3.4 Consensus size: 100
17354493 ATTACAATGT
* * * * ** * * *
17354503 CAGGGAAGCAAGATTCACCGTTGTAGTTTCAATCTGTTCCACTGC-ATCGCTA-GGGAAGTAAGA
1 CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTACAAT-G-TAGGGGAAGCAAGA
** *
17354566 TTTTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
64 TTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
* * * *
17354603 CAGGGAAGTAAGATTCATCATTGTGGCTTCAATCTTTTTAATTTCAATGTCGGGGAAGCAAGATT
1 CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTACAATGTAGGGGAAGCAAGATT
* **
17354668 CACCGTTGCAGCTTCAATCTATTCCACTGCACTAC
66 CACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
*
17354703 CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTACAATGTAGGGGAAGCATGATT
1 CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTACAATGTAGGGGAAGCAAGATT
*
17354768 CACCG-TGTAGCTTCAATCCATTCCACTGCACCGC
66 CACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
17354802 CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAA
1 CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAA
17354843 CTGCAACCTT
Statistics
Matches: 211, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
99 67 0.32
100 142 0.67
101 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (100 bp):
CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTACAATGTAGGGGAAGCAAGATT
CACCGTTGTAGCTTCAATCTATTCCACTGCACCGC
Found at i:17355735 original size:13 final size:11
Alignment explanation
Indices: 17355715--17355765 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
17355705 TGGCCTCTCT
17355715 TTTTCTTTTTC
1 TTTTCTTTTTC
17355726 GTTCTTC-TTTTC
1 -TT-TTCTTTTTC
17355738 TTTTCTTTTTTC
1 TTTTC-TTTTTC
17355750 TTTTCATTTTT-
1 TTTTC-TTTTTC
17355761 TTTTC
1 TTTTC
17355766 AAGTGAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
10 3 0.09
11 7 0.20
12 22 0.63
13 3 0.09
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:17355750 original size:17 final size:17
Alignment explanation
Indices: 17355715--17355765 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
17355705 TGGCCTCTCT
* *
17355715 TTTTCTTTTTCGTTCTTC
1 TTTTC-TTTTCTTTTTTC
17355733 TTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTTTTTTC
*
17355750 TTTTCATTT-TTTTTTC
1 TTTTCTTTTCTTTTTTC
17355766 AAGTGAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 7 0.23
17 18 0.60
18 5 0.17
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTTC
Found at i:17356220 original size:14 final size:15
Alignment explanation
Indices: 17356201--17356231 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
17356191 GTAGAAGGTT
17356201 TTTTGTTT-TTTTTG
1 TTTTGTTTCTTTTTG
17356215 TTTTGTTTCTTTTTG
1 TTTTGTTTCTTTTTG
17356230 TT
1 TT
17356232 GCCTCCACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (15 bp):
TTTTGTTTCTTTTTG
Found at i:17358869 original size:74 final size:74
Alignment explanation
Indices: 17358755--17358892 Score: 240
Period size: 74 Copynumber: 1.9 Consensus size: 74
17358745 TTTAAAAATA
* *
17358755 GGATCATGCCCAGTATGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGCTTAAAACTTGAGA
1 GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGCTTAAAACTTGAGA
17358820 AAAAAAAAG
66 AAAAAAAAG
* *
17358829 GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCTCGAGATCGTTTAAAACTTGAG
1 GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGCTTAAAACTTGAG
17358893 TTTGAAAAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (74 bp):
GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGCTTAAAACTTGAGA
AAAAAAAAG
Found at i:17359291 original size:16 final size:16
Alignment explanation
Indices: 17359270--17359300 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17359260 GTAAAAGATA
17359270 TATATATATGTATATG
1 TATATATATGTATATG
17359286 TATATATATGTATAT
1 TATATATATGTATAT
17359301 AAAAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
TATATATATGTATATG
Found at i:17359293 original size:10 final size:10
Alignment explanation
Indices: 17359267--17359301 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
17359257 AAAGTAAAAG
*
17359267 ATATATATAT
1 ATATATATGT
*
17359277 ATGTATATGT
1 ATATATATGT
17359287 ATATATATGT
1 ATATATATGT
17359297 ATATA
1 ATATA
17359302 AAAATTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (10 bp):
ATATATATGT
Found at i:17361320 original size:17 final size:18
Alignment explanation
Indices: 17361287--17361327 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
17361277 TATAGCACCA
17361287 AAAAAGTATACATTTGATT
1 AAAAAGTATA-ATTTGATT
17361306 AAAAAGTAT-ATTTGATT
1 AAAAAGTATAATTTGATT
17361323 AAAAA
1 AAAAA
17361328 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (18 bp):
AAAAAGTATAATTTGATT
Found at i:17362275 original size:6 final size:6
Alignment explanation
Indices: 17362266--17362294 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17362256 TCAAAAATAA
17362266 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
17362295 ATTTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:17362312 original size:19 final size:17
Alignment explanation
Indices: 17362303--17362335 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
17362293 ATATTTATAA
17362303 ATTTTTAAAAAAATTAT
1 ATTTTTAAAAAAATTAT
17362320 ATTTTT-AAAAAATTAT
1 ATTTTTAAAAAAATTAT
17362336 NNNNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTTAAAAAAATTAT
Found at i:17362502 original size:3 final size:3
Alignment explanation
Indices: 17362494--17362520 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17362484 NNNNNNNNNN
17362494 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
17362521 TTGCTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17364140 original size:15 final size:17
Alignment explanation
Indices: 17364120--17364151 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
17364110 ACAAAACGAG
17364120 AATAA-TTAAT-ACAAA
1 AATAATTTAATCACAAA
17364135 AATAATTTAATCACAAA
1 AATAATTTAATCACAAA
17364152 TAAACCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATTTAATCACAAA
Found at i:17364344 original size:19 final size:20
Alignment explanation
Indices: 17364311--17364350 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
17364301 AGGTAAAAAG
*
17364311 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
17364331 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
17364350 A
1 A
17364351 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:17366295 original size:46 final size:46
Alignment explanation
Indices: 17366239--17366400 Score: 197
Period size: 46 Copynumber: 3.6 Consensus size: 46
17366229 TCTGCTCTGT
17366239 TGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTATTCCAC
* * * ** **
17366285 TGTAATCTCAGGGAGATAGGAT-T-ACCA-GCTTCAATCTGCTCCGA-
1 TGTAATCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTATTCC-AC
*
17366329 TGTAATCTCAGGGAGATAAGATATGAAATTCTTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTATTCCAC
*
17366375 TGTAATCTCAGGGAGATAAGACCTGA
1 TGTAATCTCAGGGAGATAAGATCTGA
17366401 TGCGATCTAC
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
44 32 0.34
45 6 0.06
46 56 0.60
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (46 bp):
TGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTATTCCAC
Found at i:17366313 original size:90 final size:90
Alignment explanation
Indices: 17366191--17366566 Score: 446
Period size: 90 Copynumber: 4.3 Consensus size: 90
17366181 TTTAATCCGC
* * *
17366191 TCCACTGTAATCTCA-GGAGATAAGATTACCAGCTTCAATCTGCTCTGTTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
*
17366255 TAAGATCTGAAATTCTTCGGTCTAT
66 TAAGATATGAAATTCTTCGGTCTAT
17366280 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
17366345 TAAGATATGAAATTCTTCGGTCTAT
66 TAAGATATGAAATTCTTCGGTCTAT
* * * * * * * **
17366370 TCCACTGTAATCTCAGGGAGATA--A-GACCTGATGCGATCTACT-CTACTGTAA-CTTCATAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGA-TGTAATC-TCAGGGA
* ***** ** ***
17366430 GATAAAATCCCTTATT-TT-AATCCGC
64 GATAAGATATGAAATTCTTCGGTCTAT
17366455 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
17366520 TAAGATATGAAATTCTTCGGTCTAT
66 TAAGATATGAAATTCTTCGGTCTAT
*
17366545 TCCACTGTAATC-CAGAGAGATA
1 TCCACTGTAATCTCAGGGAGATA
17366567 AGACCTGATG
Statistics
Matches: 232, Mismatches: 45, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
85 25 0.11
86 5 0.02
87 33 0.14
88 33 0.14
89 29 0.12
90 107 0.46
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (90 bp):
TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
TAAGATATGAAATTCTTCGGTCTAT
Found at i:17366346 original size:44 final size:44
Alignment explanation
Indices: 17366184--17366828 Score: 298
Period size: 44 Copynumber: 14.8 Consensus size: 44
17366174 CCTTGATTTT
*
17366184 AATCCGCTCCACTGTAATCTCA-GGAGATAAGATTACCAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
*** * *
17366227 AATCTGCTCTGTTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACCA-GCTTC
** ** *
17366273 GGTCTATTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
* *
17366317 AATCTGCTCCGA-TGTAATCTCAGGGAGATAAGATATGA-AATTCTTC
1 AATCTGCTCC-ACTGTAATCTCAGGGAGATAAGAT-T-ACCA-GCTTC
** ** * * *
17366363 GGTCTATTCCACTGTAATCTCAGGGAGATAAG---ACCTGATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
* * * ** * * * *
17366404 GATCTACTCTACTGTAA-CTTCATAGAGATAA-AATCCCTTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACC--AGCTTC
* *
17366448 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
* *
17366492 AATCTGCTCCGA-TGTAATCTCAGGGAGATAAGATATGA-AATTCTTC
1 AATCTGCTCC-ACTGTAATCTCAGGGAGATAAGAT-T-ACCA-GCTTC
** ** * * * *
17366538 GGTCTATTCCACTGTAATC-CAGAGAGATAAG---ACCTGATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
* * * * * *
17366578 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-T-CCTTTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACC---AGCTTC
* * *
17366622 AATCCGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
* * * * * * *
17366666 AATCTACTCCGCTATAATCTCAAGGAGATAAG---ACCTGATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
* * * * ** *
17366707 TATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-T-CCATTATTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACCA--GCTTC
* * * *
17366751 AATCTGCTCCACTATAATCTCAGGGAGATAGGAGTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
*
17366795 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
17366829 CTGTTATATT
Statistics
Matches: 441, Mismatches: 116, Indels: 89
0.68 0.18 0.14
Matches are distributed among these distances:
39 1 0.00
40 19 0.04
41 68 0.15
42 4 0.01
43 22 0.05
44 212 0.48
45 32 0.07
46 83 0.19
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACCAGCTTC
Found at i:17366686 original size:174 final size:175
Alignment explanation
Indices: 17366280--17366698 Score: 732
Period size: 174 Copynumber: 2.4 Consensus size: 175
17366270 TTCGGTCTAT
17366280 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
*
17366345 TAAGATATGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
66 TAAGATATGAAATTCTTCGGTCTATTCCACTGTAATCTCAGAGAGATAAGACCTGATGCGATCTA
*
17366410 CTCTACTGTAACTTCATAGAGATAAAATCCCTTATTTTAATCCGC
131 CTCTACTGTAACTTCAGAGAGATAAAATCCCTTATTTTAATCCGC
17366455 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
17366520 TAAGATATGAAATTCTTCGGTCTATTCCACTGTAATC-CAGAGAGATAAGACCTGATGCGATCTA
66 TAAGATATGAAATTCTTCGGTCTATTCCACTGTAATCTCAGAGAGATAAGACCTGATGCGATCTA
* *
17366584 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
131 CTCTACTGTAACTTCAGAGAGATAAAATCCCTTATTTTAATCCGC
* * * * * * *
17366629 TCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCTCAAGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
17366694 TAAGA
66 TAAGA
17366699 CCTGATGCTA
Statistics
Matches: 233, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
174 131 0.56
175 102 0.44
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (175 bp):
TCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTGCTCCGATGTAATCTCAGGGAGA
TAAGATATGAAATTCTTCGGTCTATTCCACTGTAATCTCAGAGAGATAAGACCTGATGCGATCTA
CTCTACTGTAACTTCAGAGAGATAAAATCCCTTATTTTAATCCGC
Found at i:17366724 original size:129 final size:129
Alignment explanation
Indices: 17366561--17366827 Score: 444
Period size: 129 Copynumber: 2.1 Consensus size: 129
17366551 GTAATCCAGA
*
17366561 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATC
1 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCATTATTTTAATC
* *
17366626 CGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCTCAAG
66 CGCTCCACTATAATCTCAAGGAGATAAGAGTACTAGCTTCAATCTACTCCGCTATAATCTCAAG
*
17366690 GAGATAAGACCTGATGCTATCTACTCTACTGTAACTTCAGAGAGATAAGATCCATTATTTTAATC
1 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCATTATTTTAATC
* * * * * *
17366755 TGCTCCACTATAATCTCAGGGAGATAGGAGTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGG
66 CGCTCCACTATAATCTCAAGGAGATAAGAGTACTAGCTTCAATCTACTCCGCTATAATCTCAAG
17366819 GAGATAAGA
1 GAGATAAGA
17366828 TCTGTTATAT
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (129 bp):
GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCATTATTTTAATC
CGCTCCACTATAATCTCAAGGAGATAAGAGTACTAGCTTCAATCTACTCCGCTATAATCTCAAG
Found at i:17374781 original size:66 final size:66
Alignment explanation
Indices: 17374658--17375096 Score: 661
Period size: 66 Copynumber: 6.8 Consensus size: 66
17374648 TTTCCAATTC
* *** *
17374658 AGAGAGCACACTCCCGCGAACCTCATTTTTTATAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCACGAACCTCA-TCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
17374723 CA
65 CA
*
17374725 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGT
1 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
17374790 A
66 A
* ** * **
17374791 ATG-TA--A-ACTCATA-G-A-GT-AT---T--GTCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 A-GAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
17374843 CA
65 CA
17374845 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
1 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
17374910 A
66 A
17374911 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
1 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
17374976 A
66 A
17374977 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
1 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
17375042 A
66 A
17375043 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCT
1 AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCT
17375097 TTTAAGAATA
Statistics
Matches: 339, Mismatches: 19, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
53 1 0.00
54 33 0.10
56 2 0.01
57 5 0.01
58 1 0.00
59 3 0.01
60 2 0.01
61 3 0.01
62 1 0.00
63 5 0.01
64 2 0.01
66 256 0.76
67 25 0.07
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.18
Consensus pattern (66 bp):
AGAGAGCACACTCCCACGAACCTCATCCATACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
A
Found at i:17383248 original size:19 final size:18
Alignment explanation
Indices: 17383205--17383252 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
17383195 TTAATAATCT
*
17383205 TGAATG-AATATGATGACA
1 TGAATGCAA-ATGATGAAA
17383223 TGTAATGCAAATGCATGAAA
1 TG-AATGCAAATG-ATGAAA
17383243 TGAATGCAAA
1 TGAATGCAAA
17383253 AAGAGCATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 9 0.35
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (18 bp):
TGAATGCAAATGATGAAA
Found at i:17384373 original size:14 final size:14
Alignment explanation
Indices: 17384346--17384387 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
17384336 TATCTAACTT
*
17384346 AAAAACTAAGAAATA
1 AAAAAATAA-AAATA
*
17384361 AATAAATAAAAATA
1 AAAAAATAAAAATA
17384375 AAAAAATAAAAAT
1 AAAAAATAAAAAT
17384388 CATTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:17385302 original size:13 final size:13
Alignment explanation
Indices: 17385286--17385320 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17385276 TTTAAACAAA
*
17385286 TTAATTAACTTAT
1 TTAATTAACTAAT
17385299 TTAATTAACTAAT
1 TTAATTAACTAAT
*
17385312 TTAACTAAC
1 TTAATTAAC
17385321 AGCAACTTAT
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:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:17388135 original size:13 final size:14
Alignment explanation
Indices: 17388119--17388157 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
17388109 ATACTTCGAT
*
17388119 TTTTTTTTGAA-AA
1 TTTTTTTTCAACAA
17388132 TTTTTTTTCAATCAA
1 TTTTTTTTCAA-CAA
17388147 TTTTTTTTCAA
1 TTTTTTTTCAA
17388158 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
15 13 0.57
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (14 bp):
TTTTTTTTCAACAA
Found at i:17388165 original size:15 final size:15
Alignment explanation
Indices: 17388130--17388158 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17388120 TTTTTTTGAA
17388130 AATTTTTTTTCAATC
1 AATTTTTTTTCAATC
17388145 AATTTTTTTTCAAT
1 AATTTTTTTTCAAT
17388159 TTTTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTTTTTCAATC
Found at i:17389955 original size:13 final size:13
Alignment explanation
Indices: 17389939--17389973 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17389929 TTTAAACAAA
*
17389939 TTAATTAACTTAT
1 TTAATTAACTAAT
17389952 TTAATTAACTAAT
1 TTAATTAACTAAT
*
17389965 TTAACTAAC
1 TTAATTAAC
17389974 AGCAACTTAT
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:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:17400659 original size:10 final size:9
Alignment explanation
Indices: 17400603--17400689 Score: 57
Period size: 10 Copynumber: 8.8 Consensus size: 9
17400593 GCAAGCTGAT
17400603 TTTAGCTCAA
1 TTTAGCTC-A
*
17400613 TTCTAGCTCC
1 TT-TAGCTCA
*
17400623 TTTAGCTCG
1 TTTAGCTCA
17400632 TTTCAGCTCCA
1 TTT-AGCT-CA
* *
17400643 ATCAGCTCA
1 TTTAGCTCA
17400652 TTTAAGCTCAA
1 TTT-AGCTC-A
17400663 TTTAGCTCA
1 TTTAGCTCA
*
17400672 TTCGAGCTCAA
1 TT-TAGCTC-A
17400683 TTTAGCT
1 TTTAGCT
17400690 TTCTATCAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
9 15 0.25
10 31 0.51
11 15 0.25
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (9 bp):
TTTAGCTCA
Found at i:17400669 original size:20 final size:20
Alignment explanation
Indices: 17400623--17400689 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
17400613 TTCTAGCTCC
* *
17400623 TTTAGCTCGTTTCAGCTCCAA
1 TTTAGCTCATTTAAGCT-CAA
*
17400644 -TCAGCTCATTTAAGCTCAA
1 TTTAGCTCATTTAAGCTCAA
**
17400663 TTTAGCTCATTCGAGCTCAA
1 TTTAGCTCATTTAAGCTCAA
17400683 TTTAGCT
1 TTTAGCT
17400690 TTCTATCAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.37
Consensus pattern (20 bp):
TTTAGCTCATTTAAGCTCAA
Found at i:17403258 original size:20 final size:20
Alignment explanation
Indices: 17403230--17403293 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
17403220 GCTGATAGAA
* **
17403230 AGCTAAATTGAGCTTGAATG
1 AGCTGAATTGAGCTCAAATG
17403250 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
* *
17403270 AGCTG-ATTGGAGCTGAAACG
1 AGCTGAATT-GAGCTCAAATG
17403290 AGCT
1 AGCT
17403294 AAAGGAGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 3 0.08
20 35 0.92
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:17405425 original size:29 final size:28
Alignment explanation
Indices: 17405380--17405461 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 28
17405370 TCTGGTTCGC
*
17405380 TCATC-TCTTTTTC--TTTCGTTTATTTT
1 TCATCATCTTTTTCTTTTTCGATT-TTTT
*
17405406 TCATCATCTTTTTCTTTTTCAATTTTTT
1 TCATCATCTTTTTCTTTTTCGATTTTTT
17405434 T-ATCAATCTTAATTTCTTTTTCGATTTT
1 TCATC-ATCTT--TTTCTTTTTCGATTTT
17405462 CTTTTCTTCG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 5 0.11
27 11 0.23
28 10 0.21
29 6 0.13
30 15 0.32
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (28 bp):
TCATCATCTTTTTCTTTTTCGATTTTTT
Found at i:17405478 original size:14 final size:13
Alignment explanation
Indices: 17405445--17405483 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
17405435 ATCAATCTTA
17405445 ATTTC-TTTTTCG
1 ATTTCTTTTTTCG
17405457 ATTTTCTTTTCTTCG
1 A-TTTCTTTT-TTCG
17405472 ATTTCTTTTTTC
1 ATTTCTTTTTTC
17405484 TTTTGCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 7 0.29
14 11 0.46
15 5 0.21
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.69
Consensus pattern (13 bp):
ATTTCTTTTTTCG
Found at i:17407906 original size:20 final size:20
Alignment explanation
Indices: 17407883--17407940 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
17407873 AGAAAGCTAT
*
17407883 ATTGAGCTCGAATGAGCTGA
1 ATTGAGCTCAAATGAGCTGA
17407903 ATTGAGCTCAAATGAGCTG-
1 ATTGAGCTCAAATGAGCTGA
* *
17407922 ATTGGAGCTGAAACGAGCT
1 ATT-GAGCTCAAATGAGCT
17407941 AAAGGAGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (20 bp):
ATTGAGCTCAAATGAGCTGA
Found at i:17413700 original size:19 final size:19
Alignment explanation
Indices: 17413678--17413774 Score: 97
Period size: 19 Copynumber: 5.2 Consensus size: 19
17413668 GTATAGTATT
*
17413678 TTTAGGCTCGCATAAAACA
1 TTTAAGCTCGCATAAAACA
* *
17413697 TTTAAGCTTGTATAAAACA
1 TTTAAGCTCGCATAAAACA
* ** *
17413716 TTT-GGCTCATATAAAATA
1 TTTAAGCTCGCATAAAACA
* * *
17413734 GTTAAGCTCACATGAAACA
1 TTTAAGCTCGCATAAAACA
17413753 TTTAAGCTCGCATAAAACA
1 TTTAAGCTCGCATAAAACA
17413772 TTT
1 TTT
17413775 GAAAGTAGGG
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
18 13 0.21
19 49 0.79
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (19 bp):
TTTAAGCTCGCATAAAACA
Found at i:17413723 original size:37 final size:38
Alignment explanation
Indices: 17413678--17413774 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 38
17413668 GTATAGTATT
***
17413678 TTTAGGCTCGCATAAAACATTTAAGCTTGTATAAAACA
1 TTTAGGCTCGCATAAAACATTTAAGCTCACATAAAACA
** * * *
17413716 TTT-GGCTCATATAAAATAGTTAAGCTCACATGAAACA
1 TTTAGGCTCGCATAAAACATTTAAGCTCACATAAAACA
*
17413753 TTTAAGCTCGCATAAAACATTT
1 TTTAGGCTCGCATAAAACATTT
17413775 GAAAGTAGGG
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
37 29 0.64
38 16 0.36
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (38 bp):
TTTAGGCTCGCATAAAACATTTAAGCTCACATAAAACA
Found at i:17413923 original size:22 final size:22
Alignment explanation
Indices: 17413898--17413939 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17413888 ATAAAGTTGG
*
17413898 CACAGTACTTTTATAGGGTTCA
1 CACAATACTTTTATAGGGTTCA
*
17413920 CACAATACTTTTATTGGGTT
1 CACAATACTTTTATAGGGTT
17413940 TGCATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (22 bp):
CACAATACTTTTATAGGGTTCA
Found at i:17418812 original size:28 final size:28
Alignment explanation
Indices: 17418773--17418829 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
17418763 TTTACTTTAT
17418773 TTTAATAATAAAAAATAACATATAAACA
1 TTTAATAATAAAAAATAACATATAAACA
17418801 TTTAATAATAAAAAATAACATATAAACA
1 TTTAATAATAAAAAATAACATATAAACA
17418829 T
1 T
17418830 ATAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (28 bp):
TTTAATAATAAAAAATAACATATAAACA
Found at i:17418825 original size:14 final size:14
Alignment explanation
Indices: 17418780--17418826 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
17418770 TATTTTAATA
17418780 ATAAAAAATAACAT
1 ATAAAAAATAACAT
* * *
17418794 ATAAACATTTA-AT
1 ATAAAAAATAACAT
17418807 AATAAAAAATAACAT
1 -ATAAAAAATAACAT
17418822 ATAAA
1 ATAAA
17418827 CATATAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 2 0.08
14 21 0.84
15 2 0.08
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAAAATAACAT
Found at i:17419067 original size:12 final size:12
Alignment explanation
Indices: 17419050--17419088 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
17419040 AACATTCCGT
*
17419050 AAATATTTATAA
1 AAATATTTACAA
17419062 AAATATTTACAA
1 AAATATTTACAA
17419074 ATAAT-TTTACAA
1 A-AATATTTACAA
17419086 AAA
1 AAA
17419089 CGAGGTCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 2 0.08
12 20 0.80
13 3 0.12
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATATTTACAA
Found at i:17421238 original size:17 final size:17
Alignment explanation
Indices: 17421216--17421252 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
17421206 TCGACATTTC
*
17421216 TTTATTTATTTGTTTAT
1 TTTATTTATTTCTTTAT
17421233 TTTATTTATTTCTTTAT
1 TTTATTTATTTCTTTAT
17421250 TTT
1 TTT
17421253 TACTTAAAAT
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:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATTTATTTCTTTAT
Found at i:17421870 original size:19 final size:19
Alignment explanation
Indices: 17421833--17421872 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17421823 TAATATTAGT
*
17421833 TTTACTATTATTATTATTA
1 TTTACTATTATTATAATTA
* *
17421852 TTTATTATTATTGTAATTA
1 TTTACTATTATTATAATTA
17421871 TT
1 TT
17421873 ATTCCCATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTACTATTATTATAATTA
Found at i:17422110 original size:2 final size:2
Alignment explanation
Indices: 17422103--17422153 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
17422093 TGAATATTCT
* ** * *
17422103 TA TA TA TA TA TA TA TA TG CG TA TA TA TC TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17422145 TA TA TA TA T
1 TA TA TA TA T
17422154 CCATTCTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17422506 original size:13 final size:14
Alignment explanation
Indices: 17422472--17422509 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
17422462 TCCCCTCATG
17422472 TATATTAGTTTCGTT
1 TATATTA-TTTCGTT
17422487 TAT-TTATTT-GTT
1 TATATTATTTCGTT
17422499 TATATTATTTC
1 TATATTATTTC
17422510 TATGCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:17422540 original size:15 final size:15
Alignment explanation
Indices: 17422520--17422550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17422510 TATGCCATTA
17422520 TTGTATTTATTATTG
1 TTGTATTTATTATTG
*
17422535 TTGTATTTGTTATTG
1 TTGTATTTATTATTG
17422550 T
1 T
17422551 GACATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (15 bp):
TTGTATTTATTATTG
Found at i:17426424 original size:20 final size:19
Alignment explanation
Indices: 17426395--17426444 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
17426385 GTACTTACGA
17426395 AATT-AAAAAAAATAAGTG
1 AATTAAAAAAAAATAAGTG
**
17426413 AATTGAAAAAAAAATTTGTG
1 AATT-AAAAAAAAATAAGTG
17426433 AATTAAAAAAAA
1 AATTAAAAAAAA
17426445 GTGTTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 8 0.29
20 16 0.57
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (19 bp):
AATTAAAAAAAAATAAGTG
Found at i:17426785 original size:14 final size:14
Alignment explanation
Indices: 17426766--17426792 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17426756 TTCGAGAGAT
17426766 TTGTGAGGTTTTTG
1 TTGTGAGGTTTTTG
17426780 TTGTGAGGTTTTT
1 TTGTGAGGTTTTT
17426793 ATATTCATGT
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:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (14 bp):
TTGTGAGGTTTTTG
Found at i:17431148 original size:20 final size:20
Alignment explanation
Indices: 17431123--17431176 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
17431113 TAACTTGTCT
*
17431123 TGTCTTAATTAAATTAAATG
1 TGTCTTAATTAAATTAAATA
** *
17431143 TGTCTTAATTTTATTAAGTA
1 TGTCTTAATTAAATTAAATA
17431163 TGTCTTAAATTAAA
1 TGTCTT-AATTAAA
17431177 ACATGAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (20 bp):
TGTCTTAATTAAATTAAATA
Found at i:17435415 original size:3 final size:3
Alignment explanation
Indices: 17435407--17435441 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17435397 AGTGTTAAAT
17435407 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17435442 TAAGAAGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.