Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 104 of 171
Found at i:33526737 original size:271 final size:272
Alignment explanation
Indices: 33526224--33526761 Score: 880
Period size: 271 Copynumber: 2.0 Consensus size: 272
33526214 ACTTATTAGA
*
33526224 CATAATTTTTCTCAATTGATTCAAAATAAATGAGCTTCGTCCACAAAATTCGATTTTTAAATGAC
1 CATAATTTTTCTCAATTAATTCAAAATAAATGAGCTTCGTCCACAAAATTCGATTTTTAAATGAC
* * *
33526289 ATTAAAACATCTCATTCGTGTATTTATGGATCGTATTTTTAAATTTTACTCGAGTTTTCAATCTT
66 ATTAAAACATCTCATTCGTGTATTTATGGATCGTATTTTTAAATATTACTCAAGTTTTCAATCTC
* * * * *
33526354 CAACAATTAAGACCTTAAATAATCGACTAGGTACCAATTTTGGGCGTGTGAGGGTGCTAATCCTT
131 CAACAATTAAGACATTAAATAACCGACTAGGTACCAAATTTGGGCATGTGAGGATGCTAATCCTT
* * *
33526419 CCTCACACGTAACCGACTCCCGAACCTATTTTCTGGATTTTGAAGACCAAAACTTATGTTTAAAT
196 CCTCACACGTAACCGACTCCCGAACCTATTTTCTAGAATTCGAAGACCAAAACTTATGTTTAAAT
33526484 AAACTTACTGGG
261 AAACTTACTGGG
* * *
33526496 CATAATTTTTCTCGA-TAATTCAAAATAAATGAGCTTCGTCCACAAAATTCGTTTTTTAAATTAC
1 CATAATTTTTCTCAATTAATTCAAAATAAATGAGCTTCGTCCACAAAATTCGATTTTTAAATGAC
33526560 ATTAAAACATCTCATTCGTGTATTTATGGATCGTATTTTTAAATATTACTCAAGTTTTCAATCTC
66 ATTAAAACATCTCATTCGTGTATTTATGGATCGTATTTTTAAATATTACTCAAGTTTTCAATCTC
33526625 CAACAATTAAGACATTAAATAACCGACTAGGTACCAAATTTGGGCATGTGAGGATGCTAATCCTT
131 CAACAATTAAGACATTAAATAACCGACTAGGTACCAAATTTGGGCATGTGAGGATGCTAATCCTT
* * * * * *
33526690 CCTCACACGTAATCGACTCTCGAACTTGTTTTCTAGAATTCGAAGACCGAAACTTGTGTTTAAAT
196 CCTCACACGTAACCGACTCCCGAACCTATTTTCTAGAATTCGAAGACCAAAACTTATGTTTAAAT
33526755 AAACTTA
261 AAACTTA
33526762 AATATTTTAT
Statistics
Matches: 245, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
271 231 0.94
272 14 0.06
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (272 bp):
CATAATTTTTCTCAATTAATTCAAAATAAATGAGCTTCGTCCACAAAATTCGATTTTTAAATGAC
ATTAAAACATCTCATTCGTGTATTTATGGATCGTATTTTTAAATATTACTCAAGTTTTCAATCTC
CAACAATTAAGACATTAAATAACCGACTAGGTACCAAATTTGGGCATGTGAGGATGCTAATCCTT
CCTCACACGTAACCGACTCCCGAACCTATTTTCTAGAATTCGAAGACCAAAACTTATGTTTAAAT
AAACTTACTGGG
Found at i:33528591 original size:16 final size:16
Alignment explanation
Indices: 33528566--33528598 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33528556 TATGCATACA
33528566 TGCATTCATTA-GCAT
1 TGCATTCATTATGCAT
33528581 TGCATTTCATTATGCAT
1 TGCA-TTCATTATGCAT
33528598 T
1 T
33528599 AAAAAATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (16 bp):
TGCATTCATTATGCAT
Found at i:33529513 original size:22 final size:21
Alignment explanation
Indices: 33529488--33529547 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
33529478 TCTTGAAACC
33529488 TAAGAAAAAGAAAAAAGAAAAA
1 TAAG-AAAAGAAAAAAGAAAAA
*
33529510 TAAGAAAAGAGAAAAGAAAAGAA
1 TAAGAAAAGAAAAAAG-AAA-AA
* *
33529533 AAAGGAAAGAAAAAA
1 TAAGAAAAGAAAAAA
33529548 ATCAAGATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 11 0.34
22 7 0.22
23 14 0.44
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (21 bp):
TAAGAAAAGAAAAAAGAAAAA
Found at i:33529516 original size:16 final size:17
Alignment explanation
Indices: 33529493--33529545 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
33529483 AAACCTAAGA
33529493 AAAAGAAAAAAGAAAA-
1 AAAAGAAAAAAGAAAAG
* *
33529509 ATAAGAAAAGAGAAAAG
1 AAAAGAAAAAAGAAAAG
*
33529526 AAAAG-AAAAAGGAAAG
1 AAAAGAAAAAAGAAAAG
33529542 AAAA
1 AAAA
33529546 AAATCAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:33529526 original size:12 final size:11
Alignment explanation
Indices: 33529493--33529546 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
33529483 AAACCTAAGA
33529493 AAAAGAAAAA-
1 AAAAGAAAAAG
*
33529503 AGAAA-AATAAG
1 A-AAAGAAAAAG
33529514 AAAAGAGAAAAG
1 AAAAGA-AAAAG
33529526 AAAAGAAAAAG
1 AAAAGAAAAAG
*
33529537 GAAAGAAAAA
1 AAAAGAAAAA
33529547 AATCAAGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.22
11 19 0.51
12 10 0.27
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:33531432 original size:99 final size:99
Alignment explanation
Indices: 33531301--33531813 Score: 436
Period size: 99 Copynumber: 5.2 Consensus size: 99
33531291 GGACTAGTGA
* * *
33531301 AACACCAAATCATAAACCCCTACAA-TTATAGTGGGTCAGATTAAAACAAGTAACAGATCTCAAT
1 AACACCAAATCCTATACCCCTA-AAGTTACAGTGGGTCAGATTAAAACAAGTAACAGATCTCAAT
*
33531365 GTCCCTAAGGTTACAGTGGAATGGAGTGAAGTTAC
65 GTCCCTAAGGTTATAGTGGAATGGAGTGAAGTTAC
* * ** * * * * *
33531400 AAGACCAAATCTTATACCCCTAAAGTTGTAGTGGGTCAGATTAAAGCCAGAAACAAATCCCAATG
1 AACACCAAATCCTATACCCCTAAAGTTACAGTGGGTCAGATTAAAACAAGTAACAGATCTCAATG
* * * * **
33531465 TCCTTGAA-GTTACAGTGGAATAGAGTGAAGCTGT
66 TCCCT-AAGGTTATAGTGGAATGGAGTGAAGTTAC
* * * * * *
33531499 AACAACAAATCCTAT-CTTCCTGAAGTTACAATGAAGT-GGATTAAAACAAGTAACAGATCTCAA
1 AACACCAAATCCTATAC-CCCTAAAGTTACAGTG-GGTCAGATTAAAACAAGTAACAGATCTCAA
* * *
33531562 TGTCCCTGAGGTAATAGTGGAACGGAGTGAAGTTAC
64 TGTCCCTAAGGTTATAGTGGAATGGAGTGAAGTTAC
* * * * * *
33531598 AACATCAAATCCTATACCCTTGAAGTTACAGTGGGTCGGATTAAAGCCA--AA-AGATCTCAATG
1 AACACCAAATCCTATACCCCTAAAGTTACAGTGGGTCAGATTAAAACAAGTAACAGATCTCAATG
*
33531660 TCCCTAAGGTTATAGTAGAATGGAGTGAAGCTT-C
66 TCCCTAAGGTTATAGTGGAATGGAGTGAAG-TTAC
* * * * * * * * *
33531694 AACAACAAATCCTAT-CTTCCTAAATTTACATTGAAG-CAAAATT-AAATAAGTAACAAATCTTA
1 AACACCAAATCCTATAC-CCCTAAAGTTACAGTG-GGTC-AGATTAAAACAAGTAACAGATCTCA
* * * *
33531756 ATGTCCCTGAGGTTATAATGAAATGAAGTGAAGTTAC
63 ATGTCCCTAAGGTTATAGTGGAATGGAGTGAAGTTAC
*
33531793 AACACCAAATTCTATACCCCT
1 AACACCAAATCCTATACCCCT
33531814 GAACTTGTAG
Statistics
Matches: 327, Mismatches: 71, Indels: 32
0.76 0.17 0.07
Matches are distributed among these distances:
95 1 0.00
96 67 0.20
97 8 0.02
98 10 0.03
99 235 0.72
100 6 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (99 bp):
AACACCAAATCCTATACCCCTAAAGTTACAGTGGGTCAGATTAAAACAAGTAACAGATCTCAATG
TCCCTAAGGTTATAGTGGAATGGAGTGAAGTTAC
Found at i:33531766 original size:195 final size:197
Alignment explanation
Indices: 33531340--33531838 Score: 630
Period size: 195 Copynumber: 2.5 Consensus size: 197
33531330 AGTGGGTCAG
* * *
33531340 ATTAAAACAAGTAACAGATCTCAATGTCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAAGAC
1 ATTAAAACAAGTAACAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAGTTACAACAC
* * * *
33531405 CAAATCTTATACCCCTAAAGTTGTAGTGGGTCAGATTAAAGCCAGAAACAAATCCCAATGTCCTT
66 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCGGATTAAAGCCA-AAACAAATCCCAATGTCCCT
* *
33531470 GAAGTTACAGTGGAATAGAGTGAAGCTGTAACAACAAATCCTATCTTCCTGAAGTTACAATGAAG
130 GAAGTTACAGTAGAATAGAGTGAAGCTGTAACAACAAATCCTATCTTCCTAAAGTTACAATGAAG
***
33531535 TGG
195 AAA
* * *
33531538 ATTAAAACAAGTAACAGATCTCAATGTCCCTGAGGTAATAGTGGAACGGAGTGAAGTTACAACAT
1 ATTAAAACAAGTAACAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAGTTACAACAC
* ** * *
33531603 CAAATCCTATACCCTTGAAGTTACAGTGGGTCGGATTAAAGCC-AAA-AGATCTCAATGTCCCT-
66 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCGGATTAAAGCCAAAACAAATCCCAATGTCCCTG
* * * *
33531665 AAGGTTATAGTAGAATGGAGTGAAGCT-TCAACAACAAATCCTATCTTCCTAAATTTACATTGAA
131 AA-GTTACAGTAGAATAGAGTGAAGCTGT-AACAACAAATCCTATCTTCCTAAAGTTACAATGAA
33531729 GCAAA
194 G-AAA
* * * * * *
33531734 ATT-AAATAAGTAACAAATCTTAATGTCCCTGAGGTTATAATGAAATGAAGTGAAGTTACAACAC
1 ATTAAAACAAGTAACAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAGTTACAACAC
* * *
33531798 CAAATTCTATACCCCTGAACTTGTAGTGGGTCGAATTAAAG
66 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCGGATTAAAG
33531839 TTACAAAAGT
Statistics
Matches: 259, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
194 3 0.01
195 154 0.59
196 6 0.02
198 96 0.37
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (197 bp):
ATTAAAACAAGTAACAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAGTTACAACAC
CAAATCCTATACCCCTGAAGTTGTAGTGGGTCGGATTAAAGCCAAAACAAATCCCAATGTCCCTG
AAGTTACAGTAGAATAGAGTGAAGCTGTAACAACAAATCCTATCTTCCTAAAGTTACAATGAAGA
AA
Found at i:33531919 original size:50 final size:50
Alignment explanation
Indices: 33531858--33532349 Score: 228
Period size: 50 Copynumber: 9.8 Consensus size: 50
33531848 TTGTAGAGGG
* * *
33531858 GTAGATTGAAGCCACAAGGGCGAGTTTTATACCCCTAAAGTTGTAAAAAA
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * * * ***
33531908 GTAGATTGAAGCCGCCAGGGCGAATCTCATACACCTAAAGCTGTAAAGGG
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * * * **
33531958 GCAGATTGAAGCTGCAAGGGAGAATCTTATACCCCTAAAGTTGTAGAGCA
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * * ** * * * * * ***
33532008 GCAGATTTAAGCCGCAAGAGTAAATCTCATACACTTAAAGCTGTAGAGGG
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* ** * * * ***
33532058 GCAGATTGAAGTTGTAAGGGCGAATCTTATACCCTTAAAGTTGTAGAGGG
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * ** * * * * * ***
33532108 GCAAATTGAAGCCGCAAAAGCTAATCTCATACACCTAAAGCTGTAGAGGG
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * * ** * * * * **
33532158 GCAGATTAAAGCCGTAAAAGTGAATCTTATATCCCTAAAGCTGTAGATGA
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * * * * * * * ***
33532208 GTAAACTAAAGCCGTAAGGGTGAATCTTATACACATAAAGTTGTAGAGGG
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * * * * **
33532258 GCAAATTGAAGCCGCAAGGGTGTATCTTATACCCCTAAAGTTGTAGATGA
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
* * * * *
33532308 GCAGATTGAAGTCGCAATGCCAAATCTTATACCCCTAAAGTT
1 GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTT
33532350 ACAGAGAAGT
Statistics
Matches: 353, Mismatches: 89, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 353 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (50 bp):
GTAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAAAAAA
Found at i:33532116 original size:150 final size:148
Alignment explanation
Indices: 33531924--33532324 Score: 435
Period size: 150 Copynumber: 2.7 Consensus size: 148
33531914 TGAAGCCGCC
* * * * *
33531924 AGGGCGAATCTCATACACCTAAAGCTGTAAAGGGGCAGATTGAAGCTGCAAGGGAGAATCTTATA
1 AGGGCGAATCTTATAC-CCTAAAGTTGTAGAGGGGCAAATTGAAGCCGCAAGGGAGAATCTTATA
* * *
33531989 CCCCTAAAGTTGTAGAGCAGCAGATTTAAGCCGCAAGAGTAAATCTCATA-CACTTAAAGCTGTA
65 CCCCTAAAGTTGTAGAG-AGCAGATTAAAGCCGCAAAAGTAAATCTCATATC-CCTAAAGCTGTA
* * * * **
33532053 GAGGGGCAGATTGAAGTTGTA
128 GAGGAGCAAACTAAAGCCGTA
** ** *
33532074 AGGGCGAATCTTATACCCTTAAAGTTGTAGAGGGGCAAATTGAAGCCGCAAAAGCTAATCTCATA
1 AGGGCGAATCTTATACCC-TAAAGTTGTAGAGGGGCAAATTGAAGCCGCAAGGGAGAATCTTATA
* * * * * *
33532139 CACCTAAAGCTGTAGAGGGGCAGATTAAAGCCGTAAAAGTGAATCTTATATCCCTAAAGCTGTAG
65 CCCCTAAAGTTGTAGA-GAGCAGATTAAAGCCGCAAAAGTAAATCTCATATCCCTAAAGCTGTAG
* *
33532204 ATGAGTAAACTAAAGCCGTA
129 AGGAGCAAACTAAAGCCGTA
* * * *
33532224 AGGGTGAATCTTATACACATAAAGTTGTAGAGGGGCAAATTGAAGCCGCAAGGGTGTATCTTATA
1 AGGGCGAATCTTATAC-CCTAAAGTTGTAGAGGGGCAAATTGAAGCCGCAAGGGAGAATCTTATA
* *
33532289 CCCCTAAAGTTGTAGATGAGCAGATTGAAGTCGCAA
65 CCCCTAAAGTTGTAGA-GAGCAGATTAAAGCCGCAA
33532325 TGCCAAATCT
Statistics
Matches: 205, Mismatches: 42, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
149 2 0.01
150 200 0.98
151 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (148 bp):
AGGGCGAATCTTATACCCTAAAGTTGTAGAGGGGCAAATTGAAGCCGCAAGGGAGAATCTTATAC
CCCTAAAGTTGTAGAGAGCAGATTAAAGCCGCAAAAGTAAATCTCATATCCCTAAAGCTGTAGAG
GAGCAAACTAAAGCCGTA
Found at i:33532349 original size:100 final size:100
Alignment explanation
Indices: 33531844--33532347 Score: 515
Period size: 100 Copynumber: 5.0 Consensus size: 100
33531834 TAAAGTTACA
* * * * * * **
33531844 AAAGTTGTAGAGGGGTAGATTGAAGCCACAAGGGCGAGTTTTATACCCCTAAAGTTGTAAAAAAG
1 AAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAGATGAG
* * *
33531909 TAGATTGAAGCCGCCAGGGCGAATCTCATACACCT
66 CAGATTGAAGCCGCAAGGGCAAATCTCATACACCT
* * *
33531944 AAAGCTGTAAAGGGGCAGATTGAAGCTGCAAGGGAGAATCTTATACCCCTAAAGTTGTAGA-GCA
1 AAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAGATG-A
* * * *
33532008 GCAGATTTAAGCCGCAAGAGTAAATCTCATACACTT
65 GCAGATTGAAGCCGCAAGGGCAAATCTCATACACCT
** * * * *
33532044 AAAGCTGTAGAGGGGCAGATTGAAGTTGTAAGGGCGAATCTTATACCCTTAAAGTTGTAGAGGGG
1 AAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAGATGAG
* ** *
33532109 CAAATTGAAGCCGCAAAAGCTAATCTCATACACCT
66 CAGATTGAAGCCGCAAGGGCAAATCTCATACACCT
* * ** * * *
33532144 AAAGCTGTAGAGGGGCAGATTAAAGCCGTAAAAGTGAATCTTATATCCCTAAAGCTGTAGATGAG
1 AAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAGATGAG
* * * * * ** * *
33532209 TAAACTAAAGCCGTAAGGGTGAATCTTATACACAT
66 CAGATTGAAGCCGCAAGGGCAAATCTCATACACCT
* * * *
33532244 AAAGTTGTAGAGGGGCAAATTGAAGCCGCAAGGGTGTATCTTATACCCCTAAAGTTGTAGATGAG
1 AAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAGATGAG
* * * * *
33532309 CAGATTGAAGTCGCAATGCCAAATCTTATACCCCT
66 CAGATTGAAGCCGCAAGGGCAAATCTCATACACCT
33532344 AAAG
1 AAAG
33532348 TTACAGAGAA
Statistics
Matches: 331, Mismatches: 71, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
100 330 1.00
101 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (100 bp):
AAAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTAAAGTTGTAGATGAG
CAGATTGAAGCCGCAAGGGCAAATCTCATACACCT
Found at i:33566509 original size:19 final size:19
Alignment explanation
Indices: 33566462--33566510 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
33566452 TTTATTAACA
* *
33566462 ATATCTTAAACTTTTAAAT
1 ATATTTTAAACTGTTAAAT
*
33566481 ATGCTTTTAAACTGTTAAAT
1 AT-ATTTTAAACTGTTAAAT
33566501 ATATTTTAAA
1 ATATTTTAAA
33566511 AATATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (19 bp):
ATATTTTAAACTGTTAAAT
Found at i:33566592 original size:24 final size:25
Alignment explanation
Indices: 33566546--33566597 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 25
33566536 CTTAAATAAT
33566546 TTTAATTAACTTTTTAAATTTTA-A
1 TTTAATTAACTTTTTAAATTTTATA
33566570 TTTAATTTAA-TTTTT-AATATTTATA
1 TTTAA-TTAACTTTTTAAAT-TTTATA
33566595 TTT
1 TTT
33566598 TTAACAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.12
24 14 0.56
25 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTAATTAACTTTTTAAATTTTATA
Found at i:33567128 original size:26 final size:27
Alignment explanation
Indices: 33567081--33567132 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
33567071 TTTAAGATAA
*
33567081 TTTTAATTTTAGATTCAAAATATATTTT
1 TTTTAATTTTAAATT-AAAATATATTTT
*
33567109 TTTTAATTTTAAATT-TAATATATT
1 TTTTAATTTTAAATTAAAATATATT
33567133 AAGTTTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
28 14 0.64
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTAATTTTAAATTAAAATATATTTT
Found at i:33569680 original size:21 final size:21
Alignment explanation
Indices: 33569642--33569681 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33569632 TGGGGTTCAA
* * *
33569642 GTTTTGGATTCTATATTTTGG
1 GTTTAGGATTCGAAATTTTGG
33569663 GTTTAGGATTCGAAATTTT
1 GTTTAGGATTCGAAATTTT
33569682 AGATTCATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.53
Consensus pattern (21 bp):
GTTTAGGATTCGAAATTTTGG
Found at i:33571442 original size:20 final size:19
Alignment explanation
Indices: 33571392--33571443 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 19
33571382 AAATGTAATT
33571392 TTATTTTTTGATAAAAGTAA
1 TTATTTTTT-ATAAAAGTAA
33571412 TTACTTATTTT-TAAAATGCTAA
1 TTA-TT-TTTTATAAAA-G-TAA
33571434 TTATTTTTTA
1 TTATTTTTTA
33571444 ATTTTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
20 12 0.44
21 5 0.19
22 10 0.37
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (19 bp):
TTATTTTTTATAAAAGTAA
Found at i:33583522 original size:19 final size:20
Alignment explanation
Indices: 33583494--33583541 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
33583484 ATCTAAATTC
33583494 ATTT-AATATT-TTCATT-AA
1 ATTTAAATATTATT-ATTCAA
33583512 ATTTAAATATTATTATTCAA
1 ATTTAAATATTATTATTCAA
*
33583532 ATCTAAATAT
1 ATTTAAATAT
33583542 AAATTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 9 0.35
20 13 0.50
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAAATATTATTATTCAA
Found at i:33586894 original size:29 final size:29
Alignment explanation
Indices: 33586855--33586951 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 29
33586845 ATCTAAATAA
* *
33586855 TTGACATGATGTGTTGTGAAAAATTAATT
1 TTGACAAGATGTGTTCTGAAAAATTAATT
* * * **
33586884 TTGAGAAGATGGGTTCT-AAAAAATAAAA
1 TTGACAAGATGTGTTCTGAAAAATTAATT
* *
33586912 TTGACATGATGTGTTCTGAAAAATTTTATT
1 TTGACAAGATGTGTTCTGAAAAA-TTAATT
*
33586942 TTGACGAGAT
1 TTGACAAGAT
33586952 AGATTTTTTT
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
28 22 0.44
29 18 0.36
30 10 0.20
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (29 bp):
TTGACAAGATGTGTTCTGAAAAATTAATT
Found at i:33587149 original size:17 final size:17
Alignment explanation
Indices: 33587129--33587214 Score: 100
Period size: 17 Copynumber: 5.1 Consensus size: 17
33587119 CCAATATTAA
* *
33587129 ATTTTAAATTTTAATTC
1 ATTTTAAATTTAAATTT
*
33587146 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* **
33587163 ATTGTAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
* *
33587180 ATTTGAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
33587197 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
33587214 A
1 A
33587215 CTTTGAAATA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:33588515 original size:21 final size:22
Alignment explanation
Indices: 33588477--33588517 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33588467 AATAGAAACT
**
33588477 TTAAAAATTGAGGCTCGACGTG
1 TTAAAAAAAGAGGCTCGACGTG
33588499 TTAAAAAAAGAGG-TCGACG
1 TTAAAAAAAGAGGCTCGACG
33588518 AAAACCCGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (22 bp):
TTAAAAAAAGAGGCTCGACGTG
Found at i:33589310 original size:9 final size:9
Alignment explanation
Indices: 33589296--33589335 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
33589286 AAAAGAAAGG
33589296 AAAAAAACA
1 AAAAAAACA
33589305 AAAAAAACA
1 AAAAAAACA
*
33589314 AAAAAAAAA
1 AAAAAAACA
*
33589323 AAGAAAAAGA
1 AA-AAAAACA
33589333 AAA
1 AAA
33589336 TAGAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:33589340 original size:13 final size:13
Alignment explanation
Indices: 33589280--33589344 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
33589270 CGGATTCAAT
33589280 AAAGAAAAAAGAAA
1 AAAGAAAAAA-AAA
33589294 GGAAA-AAAACAAAAA
1 --AAAGAAAA-AAAAA
*
33589309 AAACAAAAAAAAA
1 AAAGAAAAAAAAA
*
33589322 AAAGAAAAAGAAA
1 AAAGAAAAAAAAA
*
33589335 ATAGAAAAAA
1 AAAGAAAAAA
33589345 CGGGTAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
13 27 0.63
14 4 0.09
15 7 0.16
16 5 0.12
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:33590327 original size:50 final size:50
Alignment explanation
Indices: 33590273--33590446 Score: 122
Period size: 49 Copynumber: 3.5 Consensus size: 50
33590263 AAGATTTGAA
*
33590273 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATATTAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATATAAT
* * * * * **
33590323 GGGAAA--TATGAAGGCCGCAACGGTGAATCCGGTTCCAT-AGAGATGCAAT
1 GGGAAAGGT-TG-AGGCCGCAACGGCGAACCCGGTACCTTAAAAGATATAAT
* * * ** * * *
33590372 GGGAAAGGTTGAGGCCGTAACGACAAACTTGATACCTTAAAA-ATATGAC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATATAAT
* * * *
33590421 GAGAAAGATTGAGGCTGCAATGGCGA
1 GGGAAAGGTTGAGGCCGCAACGGCGA
33590447 GTCTCATACC
Statistics
Matches: 89, Mismatches: 30, Indels: 11
0.68 0.23 0.08
Matches are distributed among these distances:
48 1 0.01
49 54 0.61
50 33 0.37
51 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.18
Consensus pattern (50 bp):
GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAAAAGATATAAT
Found at i:33590746 original size:39 final size:38
Alignment explanation
Indices: 33590654--33590763 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 38
33590644 GCAGTCAACT
*
33590654 GATCTTTTACCCCGAGCTTGGGGCAGA-T-C-ACCATCA
1 GATCTTTTACCCCGAG-ATGGGGCAGATTGCAACCATCA
*
33590690 GCCAATCTCTTACCCCGAGATAGGGGCAGATTGCAACCATCA
1 G---ATCTTTTACCCCGAGAT-GGGGCAGATTGCAACCATCA
* *
33590732 GATCTTTTATCCCGATCATGGGGCAGATTGCA
1 GATCTTTTACCCCGA-GATGGGGCAGATTGCA
33590764 GTTATCCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
36 1 0.02
38 1 0.02
39 47 0.77
40 3 0.05
41 1 0.02
42 8 0.13
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (38 bp):
GATCTTTTACCCCGAGATGGGGCAGATTGCAACCATCA
Found at i:33591248 original size:171 final size:171
Alignment explanation
Indices: 33590950--33591316 Score: 601
Period size: 171 Copynumber: 2.1 Consensus size: 171
33590940 CCAGATCCGT
* * * *
33590950 CTTCCTGATGAGATACAGAGAAATGGATCAAAATAACGAGGTGGTCATCTTCCTGATAAGATACT
1 CTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAGGCGGTCATCTTCCTGATAAGATACT
* *
33591015 GAGAAGTAGACCAAATCAATGAAACCAAGTTCAAAGTGAGCAAATCTTTGGACCCTAGCTTCCTG
66 GAGAAGTAGACCAAATCAATGAAACCAAGTTCAAAGTGAGCAAATCTTCGAACCCTAGCTTCCTG
* *
33591080 ATGAGATATTGAGAAGCAGGTCGAAGTAATAAAGCGATTAC
131 ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATTAC
* *
33591121 CTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAGGCGGTCATCTTCTTGATGAGATACT
1 CTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAGGCGGTCATCTTCCTGATAAGATACT
*
33591186 GAGAAGTAGACCAAATCAATGAAACCAGGTTCAAAGTGAGCAAATCTTCGAAACCC-AGCTTCCT
66 GAGAAGTAGACCAAATCAATGAAACCAAGTTCAAAGTGAGCAAATCTTCG-AACCCTAGCTTCCT
*
33591250 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTAC
130 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATTAC
*
33591292 CTTCCTGATGAGATACATAGAAGTG
1 CTTCCTGATGAGATACAAAGAAGTG
33591317 AACCAGATCC
Statistics
Matches: 182, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
171 178 0.98
172 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (171 bp):
CTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAGGCGGTCATCTTCCTGATAAGATACT
GAGAAGTAGACCAAATCAATGAAACCAAGTTCAAAGTGAGCAAATCTTCGAACCCTAGCTTCCTG
ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATTAC
Found at i:33591474 original size:379 final size:378
Alignment explanation
Indices: 33590783--33591523 Score: 1155
Period size: 379 Copynumber: 2.0 Consensus size: 378
33590773 AATAGGTGAT
* * *
33590783 GCGGTCATCTTCCTGATAAGATATAGAGAATATACCGAATCAATGAAACGAGGCTTAAAGTGAGC
1 GCGGTCATCTTCCTGATAAGATATAGAGAATAGACCAAATCAATGAAACCAGGCTTAAAGTGAGC
*
33590848 AAATCTTCGAACCCTAGCTTTCTAATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCGGTTAC
66 AAATCTTCGAACCCTAGCTTCCTAATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCGGTTAC
* *
33590913 CTTCTTGATGAGATATAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGATACAGAGAAATGGAT
131 CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGATACAGAGAAATGGAT
* *
33590978 CAAAATAACGAGGTGGTCATCTTCCTGATAAGATACTGAGAAGTAGACCAAATCAATGAAACCAA
196 CAAAACAACGAGGTGGTCATCTTCCTGATAAGATACTGAGAAGTAAACCAAATCAATGAAACCAA
** * * * *
33591043 GTTCAAAGTGAGCAAATCTTTGGACCCTAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGTA
261 GTTCAAAGTGAGCAAATCTTTAAACCCCAGCTTCCTGATGACATACTGAGAAGCAGGTCGAAGCA
33591108 ATAAAGCGATTACCTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAG
326 ATAAAGCGATTACCTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAG
* *
33591161 GCGGTCATCTTCTTGATGAGATACT-GAGAAGTAGACCAAATCAATGAAACCAGG-TTCAAAGTG
1 GCGGTCATCTTCCTGATAAGATA-TAGAGAA-TAGACCAAATCAATGAAACCAGGCTT-AAAGTG
* *
33591224 AGCAAATCTTCGAAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGG
63 AGCAAATCTTCG-AACCCTAGCTTCCTAATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCGG
* *
33591288 TTACCTTCCTGATGAGATACATAGAAGTGAACCAGATCCGTCTTCCTGATGAGATACAGAGAAGT
127 TTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGATACAGAGAAAT
* * * *
33591353 GGATCAAAACAATGAGGTGGTCATGTTCTTGATGAGATACTGAGAAGTAAACCAAATCAATGAAA
192 GGATCAAAACAACGAGGTGGTCATCTTCCTGATAAGATACTGAGAAGTAAACCAAATCAATGAAA
** * *
33591418 CCTGGTTCAAAGTGAGCAAATCTTTAAACCCCAGCTTCCTGATGACATACTGAGAAGCGGGTTGA
257 CCAAGTTCAAAGTGAGCAAATCTTTAAACCCCAGCTTCCTGATGACATACTGAGAAGCAGGTCGA
* *
33591483 AGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGT
322 AGCAATAAAGCGATTACCTTCCTGATGAGATACAAAGAAGT
33591524 AGACCAAATC
Statistics
Matches: 329, Mismatches: 30, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
378 28 0.09
379 296 0.90
380 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (378 bp):
GCGGTCATCTTCCTGATAAGATATAGAGAATAGACCAAATCAATGAAACCAGGCTTAAAGTGAGC
AAATCTTCGAACCCTAGCTTCCTAATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCGGTTAC
CTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGATACAGAGAAATGGAT
CAAAACAACGAGGTGGTCATCTTCCTGATAAGATACTGAGAAGTAAACCAAATCAATGAAACCAA
GTTCAAAGTGAGCAAATCTTTAAACCCCAGCTTCCTGATGACATACTGAGAAGCAGGTCGAAGCA
ATAAAGCGATTACCTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAG
Found at i:33591487 original size:208 final size:208
Alignment explanation
Indices: 33591121--33591627 Score: 766
Period size: 208 Copynumber: 2.4 Consensus size: 208
33591111 AAGCGATTAC
* * **
33591121 CTTCCTGATGAGATACAAAGAAGTGGATCAAAATAACAAGGCGGTCATCTTCTTGATGAGATACT
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCTTGATGAGATACT
33591186 GAGAAGTAGACCAAATCAATGAAACCAGGTTCAAAGTGAGCAAATCTTCGAAACCCAGCTTCCTG
66 GAGAAGTAGACCAAATCAATGAAACCAGGTTCAAAGTGAGCAAATCTTCGAAACCCAGCTTCCTG
* *
33591251 ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACATAGAAGT
131 ATGACATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGT
*
33591316 -GAACCAGATCCGT
196 AG-ACCAAATCCGT
* *
33591329 CTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAGGTGGTCATGTTCTTGATGAGATACT
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCTTGATGAGATACT
* * *
33591394 GAGAAGTAAACCAAATCAATGAAACCTGGTTCAAAGTGAGCAAATCTT-TAAACCCCAGCTTCCT
66 GAGAAGTAGACCAAATCAATGAAACCAGGTTCAAAGTGAGCAAATCTTCGAAA-CCCAGCTTCCT
* *
33591458 GATGACATACTGAGAAGCGGGTTGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAG
130 GATGACATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAG
*
33591523 TAGACCAAATCTGT
195 TAGACCAAATCCGT
* ** * * ** *
33591537 CTTCTTGATGAGATACAGAGAAGCAGATCAAAACAACTGATGCGATTGTCTTCATGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAACAA-TGAGGCGGTCATCTTCTTGATGAGATAC
33591602 TGAGAAGTAGACCAAATCAATGAAAC
65 TGAGAAGTAGACCAAATCAATGAAAC
33591628 TAAAGCTCGA
Statistics
Matches: 270, Mismatches: 26, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
207 3 0.01
208 220 0.81
209 47 0.17
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (208 bp):
CTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCTTGATGAGATACT
GAGAAGTAGACCAAATCAATGAAACCAGGTTCAAAGTGAGCAAATCTTCGAAACCCAGCTTCCTG
ATGACATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGT
AGACCAAATCCGT
Found at i:33593977 original size:30 final size:29
Alignment explanation
Indices: 33593943--33594081 Score: 120
Period size: 30 Copynumber: 4.7 Consensus size: 29
33593933 CTAAACTGTC
33593943 TAAAAATTACATTTTGACCCCCGAACATTT
1 TAAAAATTACATTTTGACCCCCGAAC-TTT
* * *
33593973 TAAAAATCACATTTTTACCCTCGAACTTTT
1 TAAAAATTACATTTTGACCCCCGAAC-TTT
* * * *
33594003 TAAAAATCACATTTTTGA-TCCCAAACTTC
1 TAAAAATTACA-TTTTGACCCCCGAACTTT
* * *
33594032 CAAAAATTACATTTTGA-TCCTGAACTTCT
1 TAAAAATTACATTTTGACCCCCGAACTT-T
* *
33594061 AAAAAATTACATTTTTACCCC
1 TAAAAATTACATTTTGACCCC
33594082 TAAATTTTCC
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
28 14 0.16
29 26 0.29
30 44 0.49
31 5 0.06
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (29 bp):
TAAAAATTACATTTTGACCCCCGAACTTT
Found at i:33594095 original size:29 final size:29
Alignment explanation
Indices: 33593944--33594104 Score: 119
Period size: 29 Copynumber: 5.4 Consensus size: 29
33593934 TAAACTGTCT
*
33593944 AAAAATTACATTTTGACCCCCGAACATTTT-
1 AAAAATTACATTTTTA-CCCCGAA-ATTTTC
* * *
33593974 AAAAATCACATTTTTACCCTCGAACTTTTT
1 AAAAATTACATTTTTACCC-CGAAATTTTC
* * * *
33594004 AAAAATCACATTTTTGATCCC-AAACTTCC
1 AAAAATTACATTTTT-ACCCCGAAATTTTC
* * * * * *
33594033 AAAAATTACATTTTGATCCTGAACTTCTA
1 AAAAATTACATTTTTACCCCGAAATTTTC
*
33594062 AAAAATTACATTTTTACCCCTAAATTTTC
1 AAAAATTACATTTTTACCCCGAAATTTTC
*
33594091 CAAAATTACCATTT
1 AAAAATTA-CATTT
33594105 AACCCTCAAA
Statistics
Matches: 102, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
28 4 0.04
29 56 0.55
30 39 0.38
31 3 0.03
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCCGAAATTTTC
Found at i:33594219 original size:29 final size:29
Alignment explanation
Indices: 33594187--33594278 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
33594177 CAATAATTGA
*
33594187 CATTTTGCCCCCGATTATCCAAAAATTAC
1 CATTTTGCCCCCGAGTATCCAAAAATTAC
** *
33594216 CATTTTGCCCCTAAAGTGTCC-AAAATTAC
1 CATTTTGCCCC-CGAGTATCCAAAAATTAC
* * * *
33594245 CATTTTACCCTCGGGCATCCAAAAATTA-
1 CATTTTGCCCCCGAGTATCCAAAAATTAC
33594273 CATTTT
1 CATTTT
33594279 TGACTCCATT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
28 10 0.20
29 35 0.70
30 5 0.10
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (29 bp):
CATTTTGCCCCCGAGTATCCAAAAATTAC
Found at i:33594280 original size:58 final size:57
Alignment explanation
Indices: 33594117--33594282 Score: 149
Period size: 59 Copynumber: 2.8 Consensus size: 57
33594107 CCCTCAAACA
* ** * *
33594117 TCCAAAATTACCATTCTACCCTC-GGATGACCAAAAATTGTATTTTTGACCCTGAACTT
1 TCCAAAATTACCATTTTACCCTCGGGAT--CCAAAAATTACATTTTTGACCCTAAACTG
* * ** * *
33594175 TCCAATAATTGA-CATTTTGCCCCCGATTATCCAAAAATTACCA-TTTTGCCCCTAAAGTG
1 TCCAA-AATT-ACCATTTTACCCTCG-GGATCCAAAAATTA-CATTTTTGACCCTAAACTG
33594234 TCCAAAATTACCATTTTACCCTCGGGCATCCAAAAATTACATTTTTGAC
1 TCCAAAATTACCATTTTACCCTCGGG-ATCCAAAAATTACATTTTTGAC
33594283 TCCATTTATT
Statistics
Matches: 84, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
57 3 0.04
58 38 0.45
59 39 0.46
60 2 0.02
61 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.33
Consensus pattern (57 bp):
TCCAAAATTACCATTTTACCCTCGGGATCCAAAAATTACATTTTTGACCCTAAACTG
Found at i:33599128 original size:30 final size:31
Alignment explanation
Indices: 33599092--33599153 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
33599082 CAAAATAGCA
*
33599092 AAATTTAGATATATTA-TTTTGAATTTTTAG
1 AAATTTAGATATATTAGTTTTGAAATTTTAG
33599122 AAATTTAGATATATTAGTTTTGAAATTTTAG
1 AAATTTAGATATATTAGTTTTGAAATTTTAG
33599153 A
1 A
33599154 CTTTAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (31 bp):
AAATTTAGATATATTAGTTTTGAAATTTTAG
Found at i:33600619 original size:14 final size:14
Alignment explanation
Indices: 33600581--33600611 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
33600571 TTTATGTATA
*
33600581 TTTAATATTTTAAT
1 TTTAAAATTTTAAT
33600595 TTTAAAATTTTAAT
1 TTTAAAATTTTAAT
33600609 TTT
1 TTT
33600612 TTATTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAAAATTTTAAT
Found at i:33602292 original size:21 final size:21
Alignment explanation
Indices: 33602267--33602309 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
33602257 ACTAAAACTG
33602267 AAATTGATATAATGTT-ACAAT
1 AAATT-ATATAATGTTCACAAT
*
33602288 AAATTATTTAATGTTCACAAT
1 AAATTATATAATGTTCACAAT
33602309 A
1 A
33602310 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTATATAATGTTCACAAT
Found at i:33603942 original size:21 final size:21
Alignment explanation
Indices: 33603918--33603964 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
33603908 GAATCTCGAG
33603918 CCAAAACTC-TAAACCCTAAAC
1 CCAAAA-TCATAAACCCTAAAC
*
33603939 CCAAAATCATAAACCTTAAAC
1 CCAAAATCATAAACCCTAAAC
33603960 CCAAA
1 CCAAA
33603965 CGTTAAGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (21 bp):
CCAAAATCATAAACCCTAAAC
Found at i:33607333 original size:12 final size:13
Alignment explanation
Indices: 33607307--33607337 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
33607297 ATTAAACATG
33607307 AATTTTAGTTTTC
1 AATTTTAGTTTTC
33607320 AATTTTAG-TTTC
1 AATTTTAGTTTTC
33607332 AATTTT
1 AATTTT
33607338 CAATTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (13 bp):
AATTTTAGTTTTC
Found at i:33608064 original size:7 final size:7
Alignment explanation
Indices: 33608054--33608080 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
33608044 ATAAATATAA
33608054 AATTATT
1 AATTATT
33608061 AATTATT
1 AATTATT
33608068 AATTATT
1 AATTATT
33608075 AATTAT
1 AATTAT
33608081 GCTCAACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTATT
Found at i:33608236 original size:59 final size:57
Alignment explanation
Indices: 33608163--33608272 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 57
33608153 TTAATATAAT
* * * * * *
33608163 ATTTGGTACTTGAACTTGATATTTTTTTTTTAATTTGGTACCTAAATTTTTTTGATTGA
1 ATTTGATACTTGAACTT-ACA-CTTTTTCTTAACTTAGTACCTAAATTTTTTTGATTGA
*
33608222 ATTTGATACTTGAACTTACACTTTTTCTTAACTTAGTATCTAAATTTTTTT
1 ATTTGATACTTGAACTTACACTTTTTCTTAACTTAGTACCTAAATTTTTTT
33608273 TGACCCAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 26 0.59
58 2 0.05
59 16 0.36
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (57 bp):
ATTTGATACTTGAACTTACACTTTTTCTTAACTTAGTACCTAAATTTTTTTGATTGA
Found at i:33608283 original size:58 final size:59
Alignment explanation
Indices: 33608163--33608322 Score: 138
Period size: 54 Copynumber: 2.8 Consensus size: 59
33608153 TTAATATAAT
* * * * * * ***
33608163 ATTTGGTACTTGAACTTGATATTTTTTTTTTAATTTGGTACCTAAATTTTTTTGATTGA
1 ATTTGATACTTGAACTTGACATCTTTTTCTTAACTTAGTACCTAAATTTTTTTGACCCA
*
33608222 ATTTGATACTTGAACTT-ACA-CTTTTTCTTAACTTAGTATCTAAATTTTTTTTGACCCA
1 ATTTGATACTTGAACTTGACATCTTTTTCTTAACTTAGTACCTAAA-TTTTTTTGACCCA
* * *
33608280 ATTTG--A--T-AACTTAACAT-TTTTTCTTAATTTGGTACCTAAATTT
1 ATTTGATACTTGAACTTGACATCTTTTTCTTAACTTAGTACCTAAATTT
33608323 ATTAAATCTT
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
53 8 0.09
54 24 0.28
56 1 0.01
57 19 0.22
58 17 0.20
59 16 0.19
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (59 bp):
ATTTGATACTTGAACTTGACATCTTTTTCTTAACTTAGTACCTAAATTTTTTTGACCCA
Found at i:33608322 original size:54 final size:55
Alignment explanation
Indices: 33608185--33608322 Score: 147
Period size: 54 Copynumber: 2.5 Consensus size: 55
33608175 AACTTGATAT
* ***
33608185 TTTTTTTTTAATTTGGTACCTAAA-TTTTTTTGATTGAATTTGATACTTGAACTTACA
1 TTTTTTCTTAATTTGGTACCTAAATTTTTTTTGACCCAATTTGATACTT-AA--TACA
* * * *
33608242 CTTTTTCTTAACTTAGTATCTAAATTTTTTTTGACCCAATTTGATAACTT-A-ACA
1 TTTTTTCTTAATTTGGTACCTAAATTTTTTTTGACCCAATTTGAT-ACTTAATACA
33608296 TTTTTTCTTAATTTGGTACCTAAATTT
1 TTTTTTCTTAATTTGGTACCTAAATTT
33608323 ATTAAATCTT
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
54 26 0.39
57 20 0.30
58 17 0.25
59 4 0.06
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (55 bp):
TTTTTTCTTAATTTGGTACCTAAATTTTTTTTGACCCAATTTGATACTTAATACA
Found at i:33615377 original size:18 final size:18
Alignment explanation
Indices: 33615351--33615402 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
33615341 TAATGAATAA
33615351 TTATATTTTAGAATTATTT
1 TTAT-TTTTAGAATTATTT
***
33615370 TTATTTTTATTTTTATTT
1 TTATTTTTAGAATTATTT
* *
33615388 TTATTCTCAGAATTA
1 TTATTTTTAGAATTA
33615403 ATTTAATCAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (18 bp):
TTATTTTTAGAATTATTT
Found at i:33615382 original size:5 final size:6
Alignment explanation
Indices: 33615364--33615392 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
33615354 TATTTTAGAA
33615364 TTATTT TTATTT TTATTT TTATTT TTATT
1 TTATTT TTATTT TTATTT TTATTT TTATT
33615393 CTCAGAATTA
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:33619556 original size:31 final size:31
Alignment explanation
Indices: 33619498--33619556 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
33619488 AAATTAGTCA
*
33619498 TTGAACTTGACAATTATTCCTATATTAGGAT
1 TTGAACTTGACAATTATTCCTAAATTAGGAT
33619529 TTGAACTTGACAATTATT-CTCAAATTAG
1 TTGAACTTGACAATTATTCCT-AAATTAG
33619557 ACTGGAACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (31 bp):
TTGAACTTGACAATTATTCCTAAATTAGGAT
Found at i:33626259 original size:861 final size:858
Alignment explanation
Indices: 33624597--33626311 Score: 2859
Period size: 861 Copynumber: 2.0 Consensus size: 858
33624587 GGCAATATGT
*
33624597 TCGTGATGTGGTGCACCATGGAAAATTGAATCGTTACTCCCTTGTGTTTAAAGGAAAGAAATTTA
1 TCGTGATGTGGTGCACCATGGAAAATTGAACCGTTACTCCCTTGTGTTTAAAGGAAAGAAATTTA
*
33624662 CTCTAGCCCATTTGGATCCAAAAGATGTACACAATGATCAACTTAAGATGAAAAAGTTTTTTGAG
66 CTCTAGCCCATTTGGATCCAAAAGATGTACACAATGATCAACTCAAGATGAAAAAGTTTTTTGAG
33624727 GGGGTTATAGGAAAGAAAGATAAATTAGAAAAGATAGAGAGAAAAAAGGCCATTAGTGATAAAAG
131 GGGGTTATAGGAAAGAAAGATAAATTAGAAAAGATAGAGAGAAAAAAGGCCATTAGTGATAAAAG
* * **
33624792 TCAAAATACAAATAGCCTAATAGTGAACCCTCTAATGGTAAAAATAGAGTGCGAAATTTATTTGC
196 TCAAAATACAAATAGCCCAATAGTGAACCCTCTAATGGTAAAAACAGAGCACGAAATTTATTTGC
*
33624857 AAGTAAAAAAGATGTGAGCAGAGCCCTATTACACAAACAACCTTGTATCCTTGTGAGGTTTAGGA
261 AAGTAAAAAAGATATGAGCAGAGCCCTATTACACAAACAACCTTGTATCCTTGTGAGGTTTAGGA
* *
33624922 AAAATTCTTTATCTTTAACTAACCTTAACGATTTTTTGCCTAGTGTCTTTACATCTTTTTTGTAG
326 AAAATTCTTTATCTTTAACTAACCTTAACGATTTTTTACCTAGTGTCTTTACATCTCTTTTGTAG
33624987 GATTATGAGGATGTTTTCAATGAGACACTTGAAGGTTTACCACCTTTGTAAGGCGTAGAGCACCA
391 GATTATGAGGATGTTTTCAATGAGACACTTGAAGGTTTACCACCTTTGTAAGGCGTAGAGCACCA
33625052 AATTGACTTAGTACCCAATGTAACCATTCCAAACCATCCAACTTATAGAAGCAATCCCGAGGAGA
456 AATTGACTTAGTACCCAATGTAACCATTCCAAACCATCCAACTTATAGAAGCAATCCCGAGGAGA
** *
33625117 CAAAGGAGTTAAAAAGGCAAGTGAAAGAGTTATTACAAAATGGGTACATTAGAGGAAAGTTTGAG
521 CAAAGGAGTTAAAAAGGCAAGTGAAAGAGTTATTACAAAACAGGCACATTAGAGGAAAGTTTGAG
* *
33625182 CCCTTGTGCCGTCCCTGTCCTGTTGGTGTCTAAGAAGGATGTTTCCTTCCAAATGTGTTGATTGT
586 CCCTTGTGCCGTCCCTGTCCTGTTGGTGCCTAAGAAGGATGGTTCCTTCCAAATGTGTTGATTGT
* * *
33625247 CGCCCAATCAACAAAATAACGATAAAGTATAGACATTCAATCCTTAGACTTGAAGACATGCTTGA
651 CGCCCAATCAACAAAATAACGATAAAGTATAAACATTCAATCCCTAGACTTAAAGACATGCTTGA
*
33625312 TGAGTTACATGGTTCAACAATATTTACAAAAATTGATTTAAAAAGTGGTTATCATCAAATTCGTA
716 TGAGTTACATGGTTCAACAATATTTACAAAAATTGATTTAAAAAGCGGTTATCATCAAATTCGTA
* * * * *
33625377 TGAGGGAAAGGGACAAATGGAAAATAGCCTTTAAAATTAAGTTTGGATTATATGAGTGGCTTGTT
781 TAAGGGAAAGGGACAAATGGAAAACAACCTTTAAAACTAAGTTTGGATTATATGAATGGCTTGTT
33625442 ATGCCTTTCGGGA
846 ATGCCTTTCGGGA
*
33625455 TCGTGATGTGGTGCACCATGGAAAATTGAACCGTTACTCCCTTGTGTTTAAAGGGAAGAAATTTA
1 TCGTGATGTGGTGCACCATGGAAAATTGAACCGTTACTCCCTTGTGTTTAAAGGAAAGAAATTTA
*
33625520 CTCTAGTCCC-TTTGGATCTAAAAGATGTACACAATGATCAACTCAAGATGAAAAAGTTTTTTGA
66 CTCTAG-CCCATTTGGATCCAAAAGATGTACACAATGATCAACTCAAGATGAAAAAGTTTTTTGA
* *
33625584 GGGGGTTATAGGGAAA-AAAGATAAATTTGAAAAGATAGAGAGAAAAGAGGCCATTAGTGATAAA
130 GGGGGTTATA-GGAAAGAAAGATAAATTAGAAAAGATAGAGAGAAAAAAGGCCATTAGTGATAAA
33625648 AGTCAAAATACAAATAGCCCAATGGTGAGTGAACCCTCTAATGGTAAAAAACAGAGCACGAAATT
194 AGTCAAAATACAAATAGCCCAA---T-AGTGAACCCTCTAATGGT-AAAAACAGAGCACGAAATT
* * *
33625713 TATTTGCAAGT-AAAAAGATATGAGCAGAGTCTTATTACACAAACAACCTTTTATCCTTGTGAGG
254 TATTTGCAAGTAAAAAAGATATGAGCAGAGCCCTATTACACAAACAACCTTGTATCCTTGTGAGG
*
33625777 TTTAGGAAAAATTCTTTATCTTTAACTAACCTTAACGATTTTTTACCTGGTGT-TTTACATCTCT
319 TTTAGGAAAAATTCTTTATCTTTAACTAACCTTAACGATTTTTTACCTAGTGTCTTTACATCTCT
* * * *
33625841 TTTGTAGGATTATGAGGATGTTTTCAATGAGGCGCTTGAAGGTTTACCACCTTTGTGAGGCGTAT
384 TTTGTAGGATTATGAGGATGTTTTCAATGAGACACTTGAAGGTTTACCACCTTTGTAAGGCGTAG
* * *
33625906 AGCACCAAATTGACTTAGTACCCAATGTAACCATTCTAAACCATCTAGCTTACT-GAAGCAATCC
449 AGCACCAAATTGACTTAGTACCCAATGTAACCATTCCAAACCATCCAACTTA-TAGAAGCAATCC
* * *
33625970 CGAGGAGACAATGGAGTTACAAAGGCAAGTGGAAGAGTTATTACAAAACAGGCACATTAGA-GAA
513 CGAGGAGACAAAGGAGTTAAAAAGGCAAGTGAAAGAGTTATTACAAAACAGGCACATTAGAGGAA
* * * *
33626034 CGTTTTAGCCCTTGTGTCGTCTCTGTCCTGTTGGTGCCTAAGAAGGATGGTTCCTTCCAAATGTG
578 AGTTTGAGCCCTTGTGCCGTCCCTGTCCTGTTGGTGCCTAAGAAGGATGGTTCCTTCCAAATGTG
33626099 TTTTGATTGTCGCCCAATCAACAAAATAACGATAAAGTATAAACATTCAATCCCTAGACTTAAAG
643 --TTGATTGTCGCCCAATCAACAAAATAACGATAAAGTATAAACATTCAATCCCTAGACTTAAAG
*
33626164 ACATGCTTGATGAGTTA-ATGGTTCAATAATATTTACAAAAATTGATTTAAAAAGCGGTTATCAT
706 ACATGCTTGATGAGTTACATGGTTCAACAATATTTACAAAAATTGATTTAAAAAGCGGTTATCAT
* *
33626228 CAAATTCGTATAAGGGAAGGGGACGAATGGAAAACAACCTTTAAAACTAAGTTTGGATTATATGA
771 CAAATTCGTATAAGGGAAAGGGACAAATGGAAAACAACCTTTAAAACTAAGTTTGGATTATATGA
33626293 ATGGCTTGTTATGCCTTTC
836 ATGGCTTGTTATGCCTTTC
33626312 AGTCTAATTA
Statistics
Matches: 799, Mismatches: 48, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
858 198 0.25
859 8 0.01
860 62 0.08
861 308 0.39
862 196 0.25
863 27 0.03
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (858 bp):
TCGTGATGTGGTGCACCATGGAAAATTGAACCGTTACTCCCTTGTGTTTAAAGGAAAGAAATTTA
CTCTAGCCCATTTGGATCCAAAAGATGTACACAATGATCAACTCAAGATGAAAAAGTTTTTTGAG
GGGGTTATAGGAAAGAAAGATAAATTAGAAAAGATAGAGAGAAAAAAGGCCATTAGTGATAAAAG
TCAAAATACAAATAGCCCAATAGTGAACCCTCTAATGGTAAAAACAGAGCACGAAATTTATTTGC
AAGTAAAAAAGATATGAGCAGAGCCCTATTACACAAACAACCTTGTATCCTTGTGAGGTTTAGGA
AAAATTCTTTATCTTTAACTAACCTTAACGATTTTTTACCTAGTGTCTTTACATCTCTTTTGTAG
GATTATGAGGATGTTTTCAATGAGACACTTGAAGGTTTACCACCTTTGTAAGGCGTAGAGCACCA
AATTGACTTAGTACCCAATGTAACCATTCCAAACCATCCAACTTATAGAAGCAATCCCGAGGAGA
CAAAGGAGTTAAAAAGGCAAGTGAAAGAGTTATTACAAAACAGGCACATTAGAGGAAAGTTTGAG
CCCTTGTGCCGTCCCTGTCCTGTTGGTGCCTAAGAAGGATGGTTCCTTCCAAATGTGTTGATTGT
CGCCCAATCAACAAAATAACGATAAAGTATAAACATTCAATCCCTAGACTTAAAGACATGCTTGA
TGAGTTACATGGTTCAACAATATTTACAAAAATTGATTTAAAAAGCGGTTATCATCAAATTCGTA
TAAGGGAAAGGGACAAATGGAAAACAACCTTTAAAACTAAGTTTGGATTATATGAATGGCTTGTT
ATGCCTTTCGGGA
Found at i:33629066 original size:26 final size:27
Alignment explanation
Indices: 33629007--33629066 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
33628997 TATACTAGTT
*
33629007 AAACTCTATTTGGGCTTATAAGAGCTA
1 AAACTCTATTTGAGCTTATAAGAGCTA
* * *
33629034 AAA-TCTATTTGATCTTCTAAGA-TTA
1 AAACTCTATTTGAGCTTATAAGAGCTA
33629059 AAACTCTA
1 AAACTCTA
33629067 ACTGGCTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 5 0.18
26 20 0.71
27 3 0.11
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (27 bp):
AAACTCTATTTGAGCTTATAAGAGCTA
Found at i:33651669 original size:21 final size:20
Alignment explanation
Indices: 33651645--33651699 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
33651635 GGAGTTTTTA
*
33651645 GTATCGGTAGAAGAGTCAATT
1 GTATCAGTAGAAGA-TCAATT
* *
33651666 GTATCAGTAGAACTATCATTT
1 GTATCAGTAGAA-GATCAATT
33651687 GTATCAGTAGAAG
1 GTATCAGTAGAAG
33651700 TTTACACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (20 bp):
GTATCAGTAGAAGATCAATT
Found at i:33657901 original size:41 final size:41
Alignment explanation
Indices: 33657846--33658051 Score: 234
Period size: 41 Copynumber: 5.0 Consensus size: 41
33657836 GGATGGTAAT
** * * *
33657846 TTCAATCTATCCCTCTTAATTAGGGGTAAAAGA-CGGGATGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT-C
*
33657887 TTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAATC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
* * * *
33657928 TTCAATCTACCCTTCTTGATTAAGGGTAAAAGATTGGAATT
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
**
33657969 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTAAAATGGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT--C
* * * *
33658012 TTCAATCTGCCCCTCTTGACTAAGGGTAACAGACTGGAAT
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT
33658052 GTATGCAGTT
Statistics
Matches: 139, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
41 101 0.73
42 4 0.03
43 34 0.24
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (41 bp):
TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
Found at i:33659097 original size:17 final size:18
Alignment explanation
Indices: 33659077--33659135 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 18
33659067 GACTTTTCCC
33659077 TTTTGTTTCTTTT-TTCT
1 TTTTGTTTCTTTTCTTCT
*
33659094 TTTTATTT-TTTTCTTCT
1 TTTTGTTTCTTTTCTTCT
33659111 TTTTGTTTTCTTTTTCTTCT
1 TTTTG-TTTC-TTTTCTTCT
33659131 TTTTG
1 TTTTG
33659136 GGTGAAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 4 0.11
17 15 0.42
18 3 0.08
20 14 0.39
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTGTTTCTTTTCTTCT
Found at i:33659105 original size:14 final size:13
Alignment explanation
Indices: 33659086--33659125 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
33659076 CTTTTGTTTC
33659086 TTTTTTCTTTTTAT
1 TTTTTTCTTTTT-T
33659100 TTTTTTCTTCTTTT
1 TTTTTTCTT-TTTT
*
33659114 TGTTTTCTTTTT
1 TTTTTTCTTTTT
33659126 CTTCTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 3 0.12
14 18 0.75
15 3 0.12
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:33659133 original size:14 final size:13
Alignment explanation
Indices: 33659082--33659133 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
33659072 TTCCCTTTTG
33659082 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
*
33659095 TTTATTTTTTTCTT
1 TTT-CTTTTTTCTT
33659109 CTTT-TTGTTTTCTT
1 -TTTCTT-TTTTCTT
33659123 TTTCTTCTTTT
1 TTTCTT-TTTT
33659134 TGGGTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 8 0.24
14 22 0.67
15 3 0.09
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTTCTT
Found at i:33663813 original size:16 final size:15
Alignment explanation
Indices: 33663792--33663839 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
33663782 GGACTTTTTA
33663792 ATTTAAAGTTAAATTG
1 ATTTAAA-TTAAATTG
*
33663808 ATTTAAATTGAAATTT
1 ATTTAAATT-AAATTG
33663824 ATCTTAAATTTAAATT
1 AT-TTAAA-TTAAATT
33663840 TAATTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 2 0.07
16 14 0.50
17 10 0.36
18 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (15 bp):
ATTTAAATTAAATTG
Found at i:33663832 original size:17 final size:16
Alignment explanation
Indices: 33663794--33663872 Score: 81
Period size: 17 Copynumber: 4.9 Consensus size: 16
33663784 ACTTTTTAAT
* * *
33663794 TTAAAGTTAAATTGAT
1 TTAAATTTAAATTTAC
*
33663810 TTAAATTGAAATTTATC
1 TTAAATTTAAATTTA-C
*
33663827 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAC
33663843 TT--ATTTAAATTTACC
1 TTAAATTTAAATTTA-C
33663858 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
33663873 AATTTAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 14 0.27
17 25 0.48
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (16 bp):
TTAAATTTAAATTTAC
Found at i:33663836 original size:6 final size:6
Alignment explanation
Indices: 33663791--33663899 Score: 84
Period size: 6 Copynumber: 18.3 Consensus size: 6
33663781 TGGACTTTTT
* * *
33663791 AATTTA AAGTTA AA-TT- GATTTA AATTGA AATTT- -ATCTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT-TTA AATTTA
** *
33663836 AATTTA ATTATTTA AATTT- ACCTTA AATTTA AATTTA AATTTA AATTAA
1 AATTTA A--ATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
33663885 AATACTA AATTTA AA
1 AAT-TTA AATTTA AA
33663900 CATTAAAAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
4 3 0.04
5 9 0.11
6 57 0.70
7 6 0.07
8 6 0.07
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:33663861 original size:31 final size:29
Alignment explanation
Indices: 33663808--33663882 Score: 114
Period size: 31 Copynumber: 2.5 Consensus size: 29
33663798 AGTTAAATTG
* *
33663808 ATTTAAATTGAAATTTATCTTAAATTTAA
1 ATTTAAATTTAAATTTACCTTAAATTTAA
33663837 ATTTAATTATTTAAATTTACCTTAAATTTAA
1 ATTTAA--ATTTAAATTTACCTTAAATTTAA
33663868 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
33663883 AAAATACTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 15 0.36
31 27 0.64
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (29 bp):
ATTTAAATTTAAATTTACCTTAAATTTAA
Found at i:33663884 original size:11 final size:11
Alignment explanation
Indices: 33663788--33663885 Score: 76
Period size: 11 Copynumber: 9.0 Consensus size: 11
33663778 GCTTGGACTT
*
33663788 TTTAATTTAAA
1 TTTAAATTAAA
* *
33663799 GTTAAATT-GA
1 TTTAAATTAAA
33663809 TTTAAATTGAAA
1 TTTAAATT-AAA
**
33663821 TTTATCTTAAA
1 TTTAAATTAAA
*
33663832 TTTAAATTTAA
1 TTTAAATTAAA
*
33663843 -TT-ATTTAAA
1 TTTAAATTAAA
**
33663852 TTTACCTTAAA
1 TTTAAATTAAA
33663863 TTTAAATTTAAA
1 TTTAAA-TTAAA
33663875 TTTAAATTAAA
1 TTTAAATTAAA
33663886 ATACTAAATT
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
9 5 0.08
10 12 0.18
11 31 0.47
12 18 0.27
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:33663884 original size:17 final size:17
Alignment explanation
Indices: 33663788--33663887 Score: 73
Period size: 17 Copynumber: 6.1 Consensus size: 17
33663778 GCTTGGACTT
* *
33663788 TTTAATTTAAAGTTAAA
1 TTTAAATTAAATTTAAA
* * *
33663805 -TTGATTTAAATTGAAA
1 TTTAAATTAAATTTAAA
**
33663821 TTTATCTTAAATTTAAA
1 TTTAAATTAAATTTAAA
33663838 TTT-AATT--ATTTAAA
1 TTTAAATTAAATTTAAA
**
33663852 TTTACCTTAAATTTAAA
1 TTTAAATTAAATTTAAA
*
33663869 TTTAAATTTAAATTAAAA
1 TTTAAA-TTAAATTTAAA
33663887 T
1 T
33663888 ACTAAATTTA
Statistics
Matches: 64, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
14 10 0.16
15 2 0.03
16 15 0.23
17 26 0.41
18 11 0.17
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTAAATTAAATTTAAA
Found at i:33663894 original size:31 final size:30
Alignment explanation
Indices: 33663827--33663899 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
33663817 GAAATTTATC
* **
33663827 TTAAATTTAAATTTAATTATTTAAATTTACC
1 TTAAATTTAAATTTAA-TATTTAAATTAAAA
33663858 TTAAATTTAAATTTAA-ATTTAAATTAAAA
1 TTAAATTTAAATTTAATATTTAAATTAAAA
33663887 TACTAAATTTAAA
1 T--TAAATTTAAA
33663900 CATTAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 11 0.30
31 26 0.70
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAAATTTAAATTTAATATTTAAATTAAAA
Found at i:33665821 original size:28 final size:28
Alignment explanation
Indices: 33665781--33665835 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
33665771 CAAACAATCC
* *
33665781 AAAATTACATTTTGACCCTAAAACTTTCA
1 AAAATTACATTTT-ACCCCAAAAATTTCA
*
33665810 AAAATTA-TTTTTACCCCAAAAATTTC
1 AAAATTACATTTTACCCCAAAAATTTC
33665836 CTAAATCCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 4 0.17
29 7 0.30
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTTACCCCAAAAATTTCA
Found at i:33665909 original size:59 final size:58
Alignment explanation
Indices: 33665838--33666004 Score: 210
Period size: 59 Copynumber: 2.8 Consensus size: 58
33665828 AAAATTTCCT
* * * *
33665838 AAATCCCATTTTTAACCCTGATTTCACCAAAATTTACCATTTTACCCTCG-AAGCTTCTA
1 AAATTCCATTTTTAACCCCGATTTCACCAAAA-TTACCATTTTACCCCCGAAACCTT-TA
* *
33665897 AAATTCCGTTTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCCCGAAACCTTTA
1 AAATTCCATTTTTAACCCCGATTTCAC-CAAAATTACCATTTTACCCCCGAAACCTTTA
* ** *
33665956 AAATTCCATTTTAAACCCCGATTTTGCCAAAATTACCATTTTGCCCCCG
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCG
33666005 GGTATCCATA
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
58 20 0.21
59 65 0.69
60 9 0.10
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (58 bp):
AAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGAAACCTTTA
Found at i:33665940 original size:30 final size:29
Alignment explanation
Indices: 33665847--33665997 Score: 75
Period size: 30 Copynumber: 5.1 Consensus size: 29
33665837 TAAATCCCAT
*
33665847 TTTTAACCCTGATTTCAC-CAAAATTTACCA
1 TTTTAACCCCGATTTC-CTCAAAA-TTACCA
* *
33665877 TTTT-ACCCTCGAAGCTT-CT-AAAATT-CCGT
1 TTTTAACCC-CG-A-TTTCCTCAAAATTACC-A
*
33665906 TTTTAACCCCGATTTCACTGAAAATTACCA
1 TTTTAACCCCGATTTC-CTCAAAATTACCA
* ** *
33665936 TTTTACCCCCGA-AACCTTTAAAATT-CCA
1 TTTTAACCCCGATTTCC-TCAAAATTACCA
*
33665964 TTTTAAACCCCGATTTTGC-CAAAATTACCA
1 TTTT-AACCCCGA-TTTCCTCAAAATTACCA
33665994 TTTT
1 TTTT
33665998 GCCCCCGGGT
Statistics
Matches: 92, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
27 2 0.02
28 11 0.12
29 35 0.38
30 38 0.41
31 4 0.04
32 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (29 bp):
TTTTAACCCCGATTTCCTCAAAATTACCA
Found at i:33678140 original size:68 final size:68
Alignment explanation
Indices: 33677944--33678362 Score: 490
Period size: 68 Copynumber: 6.0 Consensus size: 68
33677934 CTGCAGGTCT
* * * *
33677944 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTTTGAAA-T-AAG--A
1 CAACGCCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
33678005 -A-
66 GAG
* * * *
33678006 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGACTTCATCTCTGAAATTGAAGTA
1 CAACGCCATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTA
33678071 AGAG
65 AGAG
* * *
33678075 CAACGCCACCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCCTTATCTCTGAAATTGAAGTAA
1 CAACGCCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
33678140 GAG
66 GAG
* *
33678143 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
1 CAACGCCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
33678208 GAG
66 GAG
*
33678211 CAAGGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
1 CAA---C---GCC-ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATT
33678276 GAAGTAAGAG
59 GAAGTAAGAG
* * * *
33678286 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 C-A-A-C---GCC-ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAAT
33678351 TGAAGTAAGAG
58 TGAAGTAAGAG
33678362 C
1 C
33678363 GAGATCATTT
Statistics
Matches: 316, Mismatches: 24, Indels: 20
0.88 0.07 0.06
Matches are distributed among these distances:
62 29 0.09
63 21 0.07
64 1 0.00
65 3 0.01
67 1 0.00
68 102 0.32
69 27 0.09
71 1 0.00
74 1 0.00
75 91 0.29
76 38 0.12
77 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (68 bp):
CAACGCCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
GAG
Found at i:33678161 original size:31 final size:31
Alignment explanation
Indices: 33678058--33678169 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 31
33678048 ACTTCATCTC
*
33678058 TGAAATTGAAGTAAGAGCAACGCCA-CCCGCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCC-CT
** * ***
33678089 TGAAATTGAAGTAGAGTGGATAACACGTCCTTATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT
33678125 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCCCT
33678157 TGAAATTGAAGTA
1 TGAAATTGAAGTA
33678170 GAGTGGATAA
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
31 26 0.43
32 9 0.15
33 3 0.05
35 3 0.05
36 7 0.11
37 13 0.21
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCCCT
Found at i:33678198 original size:37 final size:37
Alignment explanation
Indices: 33678089--33678357 Score: 179
Period size: 37 Copynumber: 7.4 Consensus size: 37
33678079 GCCACCCGCT
*
33678089 TGAAATTGAAGTAGAGTGGATAACACGTCCTTATCTC
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
** * ***
33678126 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT-
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
33678157 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
* ** *
33678194 TGAAATTGAAGTAAGAGCAAGG-T--CATTTC-CTATCCTC
1 TGAAATTGAAGT-AGAG--TGGATAACACGTCTTTAT-CTC
33678231 TTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
* * * *
33678269 TGAAATTGAAGTA-AGAGCA-AGA-TC-TTTTCCTATCCTC
1 TGAAATTGAAGTAGAGTGGATA-ACACGTCTT--TAT-CTC
* * *
33678306 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTC
33678345 TGAAATTGAAGTA
1 TGAAATTGAAGTA
33678358 AGAGCGAGAT
Statistics
Matches: 177, Mismatches: 30, Indels: 49
0.69 0.12 0.19
Matches are distributed among these distances:
31 13 0.07
32 9 0.05
33 3 0.02
34 3 0.02
35 7 0.04
36 21 0.12
37 52 0.29
38 49 0.28
39 9 0.05
40 7 0.04
41 1 0.01
42 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (37 bp):
TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
Found at i:33678320 original size:38 final size:37
Alignment explanation
Indices: 33678188--33678396 Score: 169
Period size: 38 Copynumber: 5.6 Consensus size: 37
33678178 AACACGTCTT
*
33678188 TATCTC-TGAAATTGAAGTAAGAGCAAGGTCATTTCC
1 TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
** ** *
33678224 TATCCTCTTGAAATTGAAGT-AGAG-TGGATAACACGTCTT
1 TAT-CTCTTGAAATTGAAGTAAGAGCAAGAT--CATTTC-C
*
33678263 TATCTC-TGAAATTGAAGTAAGAGCAAGATCTTTTCC
1 TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
* * ** *
33678299 TATCCTCTTGAAATTGAAGTAA-AGCTGGATATCAAGTCTT
1 TAT-CTCTTGAAATTGAAGTAAGAGC--AAGATCATTTC-C
* *
33678339 TATCTC-TGAAATTGAAGTAAGAGCGAGATCATTTCA
1 TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
33678375 TATTCTCTTGAAATTGAAGTAA
1 TA-TCTCTTGAAATTGAAGTAA
33678397 AGCTGGATAA
Statistics
Matches: 136, Mismatches: 22, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
36 10 0.07
37 40 0.29
38 65 0.48
39 18 0.13
40 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (37 bp):
TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
Found at i:33678368 original size:76 final size:75
Alignment explanation
Indices: 33678013--33678445 Score: 500
Period size: 68 Copynumber: 5.9 Consensus size: 75
33678003 GAACAACGTC
* * *
33678013 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGACTTCATCTCTGAAATTGAAGTAAGAGC-A
1 ATCCTCTTGAAATTGAAGTAAAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
33678077 -A-C---GCC-
65 GATCATTTCCT
* * * * *
33678082 ACCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCCTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAAAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA-
33678147 G-TCA--T-C-
65 GATCATTTCCT
* *
33678153 --CC-CTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
1 ATCCTCTTGAAATTGAAGTAAAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
*
33678215 GTCATTTCCT
66 ATCATTTCCT
* *
33678225 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
1 ATCCTCTTGAAATTGAAGTAAAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
*
33678290 ATCTTTTCCT
66 ATCATTTCCT
* *
33678300 ATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCGA
1 ATCCTCTTGAAATTGAAGTAAAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
33678365 GATCATTTCAT
65 GATCATTTCCT
* * ** *
33678376 ATTCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGT
1 ATCCTCTTGAAATTGAAGTAAAG-TGGATAACAAGTCTT--TATCTCTGAAATTGAAGTAAGAGC
33678441 AAGAT
63 AAGAT
33678446 AAAGCACCAA
Statistics
Matches: 325, Mismatches: 23, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
67 1 0.00
68 96 0.30
69 24 0.07
70 1 0.00
71 3 0.01
74 2 0.01
75 90 0.28
76 83 0.26
78 25 0.08
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (75 bp):
ATCCTCTTGAAATTGAAGTAAAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
ATCATTTCCT
Found at i:33678788 original size:10 final size:11
Alignment explanation
Indices: 33678763--33678792 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
33678753 TAATTTAAAG
33678763 TTAAATTGATT
1 TTAAATTGATT
33678774 TTAAATTGA-T
1 TTAAATTGATT
33678784 TTAAATTGA
1 TTAAATTGA
33678793 AATTTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (11 bp):
TTAAATTGATT
Found at i:33678795 original size:27 final size:27
Alignment explanation
Indices: 33678755--33678807 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
33678745 GGACTTTTTA
*
33678755 ATTTAAAGTTAAATTGATTTTAAATTG
1 ATTTAAAGTTAAATTGATCTTAAATTG
*
33678782 ATTTAAA-TTGAAATTTATCTTAAATT
1 ATTTAAAGTT-AAATTGATCTTAAATT
33678808 TAAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (27 bp):
ATTTAAAGTTAAATTGATCTTAAATTG
Found at i:33678837 original size:31 final size:29
Alignment explanation
Indices: 33678782--33678858 Score: 109
Period size: 31 Copynumber: 2.6 Consensus size: 29
33678772 TTTTAAATTG
* * *
33678782 ATTTAAATTGAAATTTATCTTAAATTTAA
1 ATTTAAATTTAAATTTACCCTAAATTTAA
33678811 ATTTAATTATTTAAATTTACCCTAAATTTAA
1 ATTTAA--ATTTAAATTTACCCTAAATTTAA
33678842 ATTTAAATTTAAATTTA
1 ATTTAAATTTAAATTTA
33678859 AATACTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 17 0.40
31 26 0.60
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (29 bp):
ATTTAAATTTAAATTTACCCTAAATTTAA
Found at i:33678841 original size:17 final size:16
Alignment explanation
Indices: 33678785--33678873 Score: 62
Period size: 17 Copynumber: 5.6 Consensus size: 16
33678775 TAAATTGATT
* *
33678785 TAAATTGAAATTTATCT
1 TAAATTTAAATTTA-CA
33678802 TAAATTTAAATTTA-A
1 TAAATTTAAATTTACA
* *
33678817 T-TATTTAAATTTACCC
1 TAAATTTAAATTTA-CA
*
33678833 TAAATTTAAATTTAAA
1 TAAATTTAAATTTACA
33678849 TTTAAATTTAAA--TAC-
1 --TAAATTTAAATTTACA
33678864 TAAATTTAAA
1 TAAATTTAAA
33678874 CATTAAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
13 10 0.17
14 11 0.19
15 1 0.02
16 3 0.05
17 24 0.41
18 10 0.17
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (16 bp):
TAAATTTAAATTTACA
Found at i:33678867 original size:31 final size:28
Alignment explanation
Indices: 33678782--33678873 Score: 103
Period size: 31 Copynumber: 3.0 Consensus size: 28
33678772 TTTTAAATTG
*
33678782 ATTTAAATTGAAATTTATCTTAAATTTAA
1 ATTTAAATTTAAATTTATC-TAAATTTAA
*
33678811 ATTTAATTATTTAAATTTACCCTAAATTTAA
1 ATTTAA--ATTTAAATTTA-TCTAAATTTAA
33678842 ATTTAAATTTAAATTTAAATACTAAATTTAA
1 ATTTAAATTTAAATTT--AT-CTAAATTTAA
33678873 A
1 A
33678874 CATTAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
29 16 0.30
31 37 0.69
32 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTTAAATTTAAATTTATCTAAATTTAA
Found at i:33678880 original size:13 final size:12
Alignment explanation
Indices: 33678833--33678880 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
33678823 AAATTTACCC
*
33678833 TAAATTTAAATT
1 TAAAATTAAATT
*
33678845 TAAATTTAAATT
1 TAAAATTAAATT
*
33678857 TAAATACTAAATT
1 TAAA-ATTAAATT
33678870 TAAACATTAAA
1 TAAA-ATTAAA
33678881 AATTAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAAATTAAATT
Found at i:33678888 original size:6 final size:6
Alignment explanation
Indices: 33678782--33678873 Score: 82
Period size: 6 Copynumber: 15.2 Consensus size: 6
33678772 TTTTAAATTG
*
33678782 ATTTAA ATTGAA ATTT-- ATCTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA --ATTTAA ATTTAA
*** *
33678830 CCCTAA ATTTAA ATTTAA ATTTAA ATTTAA ATACTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA A
33678874 CATTAAAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.03
5 4 0.06
6 50 0.72
7 7 0.10
8 6 0.09
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:33680795 original size:29 final size:29
Alignment explanation
Indices: 33680733--33680789 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
33680723 CAAACAATCC
* *
33680733 AAAATTACATTTTGACCCTAAAACTTTCA
1 AAAATTACATTTTGACCCCAAAAATTTCA
* *
33680762 AAAATTATATTTTTACCCCAAAAATTTC
1 AAAATTACATTTTGACCCCAAAAATTTC
33680790 CTAAATCCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAAAATTTCA
Found at i:33680826 original size:59 final size:59
Alignment explanation
Indices: 33680772--33680897 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 59
33680762 AAAATTATAT
* *
33680772 TTTTACCCCAAAAATTTCCT-AAATCCCATTTTTAACCCCGATTTCACTAAAAATTACCA
1 TTTTACCCCAAAAACTT-CTAAAATCCCATTTTAAACCCCGATTTCACTAAAAATTACCA
** * * * *
33680831 TTTTACCCCCGAAGCTTCTAAAATTCCATTTTAAACCCCGATTTCGC-CAAAATTACCA
1 TTTTACCCCAAAAACTTCTAAAATCCCATTTTAAACCCCGATTTCACTAAAAATTACCA
*
33680889 TTTTGCCCC
1 TTTTACCCC
33680898 CGGGTATCCA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 20 0.35
59 37 0.65
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (59 bp):
TTTTACCCCAAAAACTTCTAAAATCCCATTTTAAACCCCGATTTCACTAAAAATTACCA
Found at i:33680835 original size:30 final size:28
Alignment explanation
Indices: 33680785--33680892 Score: 89
Period size: 30 Copynumber: 3.8 Consensus size: 28
33680775 TACCCCAAAA
*
33680785 ATTTCCT-AAA-TCCCATTTTTAACCCCG
1 ATTTCCTAAAATTACCA-TTTTAACCCCG
*
33680812 ATTTCACTAAAAATTACCATTTTACCCCCG
1 ATTTC-CT-AAAATTACCATTTTAACCCCG
*
33680842 AAGCTT-CTAAAATT-CCATTTTAAACCCCG
1 -A-TTTCCTAAAATTACCATTTT-AACCCCG
*
33680871 ATTTCGCCAAAATTACCATTTT
1 ATTTC-CTAAAATTACCATTTT
33680893 GCCCCCGGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
27 7 0.11
28 10 0.15
29 19 0.29
30 22 0.34
31 5 0.08
32 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTTCCTAAAATTACCATTTTAACCCCG
Found at i:33688180 original size:30 final size:30
Alignment explanation
Indices: 33688144--33688209 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
33688134 ATTAATAAAA
*
33688144 ATAAAATTACACTTTAA-CTCTTTAAAAATT
1 ATAAAATTACAATTTAATCT-TTTAAAAATT
*
33688174 ATAAAATTTCAATTTAATCTTTTAAAAATT
1 ATAAAATTACAATTTAATCTTTTAAAAATT
33688204 ATAAAA
1 ATAAAA
33688210 AAATTTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (30 bp):
ATAAAATTACAATTTAATCTTTTAAAAATT
Found at i:33693425 original size:3 final size:3
Alignment explanation
Indices: 33693415--33693452 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
33693405 TTTTTTCATA
*
33693415 ATT A-T ATT ATT ATT ATT ATT ATT -TT ATT AGT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
33693453 CAAAGTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:33693435 original size:17 final size:17
Alignment explanation
Indices: 33693415--33693452 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
33693405 TTTTTTCATA
*
33693415 ATTATATTATTATTATT
1 ATTATATTATTAGTATT
*
33693432 ATTATTTTATTAGTATT
1 ATTATATTATTAGTATT
33693449 ATTA
1 ATTA
33693453 CAAAGTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTATATTATTAGTATT
Found at i:33698665 original size:29 final size:29
Alignment explanation
Indices: 33698623--33698726 Score: 172
Period size: 29 Copynumber: 3.6 Consensus size: 29
33698613 AATCCATATT
*
33698623 GTCAAAATTATTTTTTCAGAACACATCTC
1 GTCAAAATTATTTTTTCAAAACACATCTC
* *
33698652 GTCAAATTTATTTTTTCAAAACCCATCTC
1 GTCAAAATTATTTTTTCAAAACACATCTC
*
33698681 GTCAAAATTATTTTTTCAAAACCCATCTC
1 GTCAAAATTATTTTTTCAAAACACATCTC
33698710 GTCAAAATTATTTTTTC
1 GTCAAAATTATTTTTTC
33698727 CAGAACAATA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (29 bp):
GTCAAAATTATTTTTTCAAAACACATCTC
Found at i:33703174 original size:21 final size:22
Alignment explanation
Indices: 33703150--33703192 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
33703140 ACTTTCATCA
33703150 TTAAGCTTAATT-AACCCATTT
1 TTAAGCTTAATTAAACCCATTT
* *
33703171 TTAATCTTGATTAAACCCATTT
1 TTAAGCTTAATTAAACCCATTT
33703193 ATACCTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (22 bp):
TTAAGCTTAATTAAACCCATTT
Found at i:33704977 original size:2 final size:2
Alignment explanation
Indices: 33704970--33705001 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33704960 AATATTTTTA
33704970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33705002 TAAATTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33706717 original size:39 final size:39
Alignment explanation
Indices: 33706672--33706859 Score: 175
Period size: 39 Copynumber: 4.8 Consensus size: 39
33706662 TTGGGAATAA
33706672 ACTGAACTGGTAGTGACACTGTAAACACTACAATGATAT
1 ACTGAACTGGTAGTGACACTGTAAACACTACAATGATAT
* * * * *
33706711 ATTGAACTAGCAGTGACACTGTAAACACTGCATTGATA-
1 ACTGAACTGGTAGTGACACTGTAAACACTACAATGATAT
* * * *
33706749 ACTGAACTGATAGTGACACTGTAAATATTACAATTGTTAT
1 ACTGAACTGGTAGTGACACTGTAAACACTACAA-TGATAT
* * * * *
33706789 ACTGAACTGG-CGATAACACTGTAAGCA-TCGCAATGTTAT
1 ACTGAACTGGTAG-TGACACTGTAAACACT-ACAATGATAT
* * *
33706828 ACTGAAGTTGTAGTGAGACTGTAAACACTACA
1 ACTGAACTGGTAGTGACACTGTAAACACTACA
33706860 GGCTGTTGTT
Statistics
Matches: 116, Mismatches: 27, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
38 25 0.22
39 66 0.57
40 25 0.22
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (39 bp):
ACTGAACTGGTAGTGACACTGTAAACACTACAATGATAT
Found at i:33711421 original size:13 final size:13
Alignment explanation
Indices: 33711403--33711427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33711393 ATGTTTATTT
33711403 ATAAAAAAATATA
1 ATAAAAAAATATA
33711416 ATAAAAAAATAT
1 ATAAAAAAATAT
33711428 GTATATAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAAAAAATATA
Found at i:33712499 original size:17 final size:17
Alignment explanation
Indices: 33712474--33712507 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33712464 TCGTTTTGGC
33712474 TTTTTTTAA-TTTAAAA
1 TTTTTTTAATTTTAAAA
33712490 TTTTTATTAATTTTAAAA
1 TTTTT-TTAATTTTAAAA
33712508 AAGATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTTAATTTTAAAA
Found at i:33713918 original size:159 final size:159
Alignment explanation
Indices: 33713738--33714386 Score: 1289
Period size: 159 Copynumber: 4.1 Consensus size: 159
33713728 ATGATGATTT
*
33713738 AATTTTAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
1 AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
33713803 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
66 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
33713868 TATAGGAAATTAGCTAAATACGTCTAGAG
131 TATAGGAAATTAGCTAAATACGTCTAGAG
33713897 AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
1 AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
33713962 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
66 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
33714027 TATAGGAAATTAGCTAAATACGTCTAGAG
131 TATAGGAAATTAGCTAAATACGTCTAGAG
33714056 AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
1 AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
33714121 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
66 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
33714186 TATAGGAAATTAGCTAAATACGTCTAGAG
131 TATAGGAAATTAGCTAAATACGTCTAGAG
33714215 AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
1 AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
33714280 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
66 TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
33714345 TATAGGAAATTAGCTAAATACGTCTAGAG
131 TATAGGAAATTAGCTAAATACGTCTAGAG
33714374 AATTATAATTTTT
1 AATTATAATTTTT
33714387 TGTATAGAAA
Statistics
Matches: 489, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 489 1.00
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (159 bp):
AATTATAATTTTTATTATTTTTTTAGAAATTTTTATCGTGCTCATAATTTTTATAGTAATTAATA
TTTTTTAAAATTTAATTTATATAATTGTGTAATTATAATTTGTAATACTAAACATGGTATAATTG
TATAGGAAATTAGCTAAATACGTCTAGAG
Found at i:33714872 original size:90 final size:86
Alignment explanation
Indices: 33714723--33714969 Score: 280
Period size: 88 Copynumber: 2.8 Consensus size: 86
33714713 CCTCAAATTT
* * * * *
33714723 AAAAAAAACAATTAAACTCTTTTTTTTTTTCACTTAATTGAGTACTTAAACTTATAAAATGTATC
1 AAAAAAAACAATTAAGCCCTTATTTTTTTTCACTTAATTGAGTACTTGAACTT-TAAAATGCATC
33714788 AAAAAGA-CCTTCAAACTTTTTAAA
65 AAAAAGACCCTT-AAA-TTTTT-AA
* * * *
33714812 AAAAAAAACAATTAAGCCCTTACTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATACAT
1 AAAAAAAACAATTAAGCCCTTA-TTTTTTTTCACTTAATTGAGTACTTGAACTTT-AAAATGCAT
* **
33714877 TAAAAAGACCCTTAAATTTTTTC
64 CAAAAAGACCCTTAAATTTTTAA
** * *
33714900 AAAAAAAGGAATTAAGCCCTTGATTTTTTTTCACTTAATTAAGTACTTGAACTATAAAATGCATC
1 AAAAAAAACAATTAAGCCCTT-ATTTTTTTTCACTTAATTGAGTACTTGAACTTTAAAATGCATC
33714965 AAAAA
65 AAAAA
33714970 AGCTATTTGA
Statistics
Matches: 133, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
87 13 0.10
88 46 0.35
89 26 0.20
90 44 0.33
91 4 0.03
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (86 bp):
AAAAAAAACAATTAAGCCCTTATTTTTTTTCACTTAATTGAGTACTTGAACTTTAAAATGCATCA
AAAAGACCCTTAAATTTTTAA
Found at i:33715148 original size:21 final size:21
Alignment explanation
Indices: 33715124--33715167 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33715114 AAACTTAAAT
33715124 AAAAAAAATAT-TAAAATTT-
1 AAAAAAAATATATAAAATTTG
*
33715143 AGAAAAAAATTTATAAAATTTG
1 A-AAAAAAATATATAAAATTTG
33715165 AAA
1 AAA
33715168 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 1 0.05
20 9 0.43
21 10 0.48
22 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAAAAATATATAAAATTTG
Found at i:33715150 original size:20 final size:20
Alignment explanation
Indices: 33715125--33715167 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
33715115 AACTTAAATA
33715125 AAAAAAATAT-TAAAATTTAG
1 AAAAAAATATATAAAATTT-G
*
33715145 AAAAAAATTTATAAAATTTG
1 AAAAAAATATATAAAATTTG
33715165 AAA
1 AAA
33715168 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAAAATATATAAAATTTG
Found at i:33715390 original size:19 final size:19
Alignment explanation
Indices: 33715366--33715439 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
33715356 TTAGTATGAT
33715366 AATTTTTATATTTTTTACG
1 AATTTTTATATTTTTTACG
33715385 AA-TTTTATATTTATTTAC-
1 AATTTTTATATTT-TTTACG
*
33715403 -ATTTTTAAATTTTTTTTACG
1 AATTTTT--ATATTTTTTACG
* *
33715423 AATTTATAAATTTTTTA
1 AATTTTTATATTTTTTA
33715440 TATTTATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
17 1 0.02
18 14 0.31
19 20 0.44
20 5 0.11
21 5 0.11
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (19 bp):
AATTTTTATATTTTTTACG
Found at i:33715444 original size:17 final size:17
Alignment explanation
Indices: 33715424--33715458 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
33715414 TTTTTTACGA
*
33715424 ATTTATAAATTTTTTAT
1 ATTTATAAATATTTTAT
*
33715441 ATTTATATATATTTTAT
1 ATTTATAAATATTTTAT
33715458 A
1 A
33715459 ATTTTTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTATAAATATTTTAT
Found at i:33715474 original size:19 final size:19
Alignment explanation
Indices: 33715452--33715560 Score: 73
Period size: 19 Copynumber: 5.7 Consensus size: 19
33715442 TTTATATATA
**
33715452 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTACAAT
***
33715471 TTTTATAAAAATTTACAAT
1 TTTTATAATTTTTTACAAT
* *
33715490 TGATTATAATTTTTTTACGAT
1 T-TTTATAA-TTTTTTACAAT
*
33715511 TTTTAT-ATTTTTTTCTAAT
1 TTTTATAATTTTTTAC-AAT
33715530 TTTTAGTAA-TTTTTA-AAT
1 TTTTA-TAATTTTTTACAAT
33715548 ATTTTAT-ATTTTT
1 -TTTTATAATTTTT
33715561 ATTAAAATTT
Statistics
Matches: 69, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
17 1 0.01
18 15 0.22
19 28 0.41
20 16 0.23
21 9 0.13
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:33715831 original size:91 final size:89
Alignment explanation
Indices: 33715667--33715898 Score: 241
Period size: 91 Copynumber: 2.6 Consensus size: 89
33715657 TTAGAGGTGA
* *
33715667 TTCAAGTAACCAATTGAGTGAAAAAAAAAAAAAGGGCTTAATTGCTTTTTTTTTGAAAAGGTTTG
1 TTCAAGTAACCAATTGAGTGAAAAAAAAAAGAAGGGCTTAATTG-TTTTTTGTTGAAAAGGTTTG
* * ** * *
33715732 AGGGTCTTTTTTATGTATTTTAAAAG
65 AAGATCTTTTCGATGCA-TATAAAAG
* * * * * * *
33715758 TTTAAGTATCCAATTGAGTGCAAAAAAATAGTAGTGGCTTAATTGATTTTTGTTG-ATAGAGTTT
1 TTCAAGTAACCAATTGAGTGAAAAAAAAAAGAAG-GGCTTAATTGTTTTTTGTTGAAAAG-GTTT
*
33715822 GAAGATCTTTTCGATGCATATGAAAG
64 GAAGATCTTTTCGATGCATATAAAAG
* * *
33715848 TTCAAGTACCCAAATGAGTGTAAAAAAAAAGGAAGGGCTTAATTGTTTTTT
1 TTCAAGTAACCAATTGAGTG-AAAAAAAAAAGAAGGGCTTAATTGTTTTTT
33715899 TAAAAAAACT
Statistics
Matches: 114, Mismatches: 24, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
90 41 0.36
91 63 0.55
92 10 0.09
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.37
Consensus pattern (89 bp):
TTCAAGTAACCAATTGAGTGAAAAAAAAAAGAAGGGCTTAATTGTTTTTTGTTGAAAAGGTTTGA
AGATCTTTTCGATGCATATAAAAG
Found at i:33722511 original size:13 final size:12
Alignment explanation
Indices: 33722484--33722518 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
33722474 AAATAAATGG
*
33722484 ATTTTTATTTGT
1 ATTTTTATTTCT
33722496 ATTTTTATATTCT
1 ATTTTTAT-TTCT
33722509 ATTTTTATTT
1 ATTTTTATTT
33722519 GGTTTGGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTATTTCT
Found at i:33754316 original size:43 final size:42
Alignment explanation
Indices: 33754252--33754350 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 42
33754242 CTGTAAATTA
*
33754252 GATAA-ATTTGCTATTAATTTTAATTTTGAAATAATGAATTTT
1 GATAAGATTT-CTTTTAATTTTAATTTTGAAATAATGAATTTT
** * * * *
33754294 GATAATTTTTCTTTTAATTTTTAATTTTTAAATACTTAGTTTT
1 GATAAGATTTCTTTTAA-TTTTAATTTTGAAATAATGAATTTT
33754337 GATAAGATTTCTTT
1 GATAAGATTTCTTT
33754351 AAGTTTTCCT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 11 0.23
43 36 0.77
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (42 bp):
GATAAGATTTCTTTTAATTTTAATTTTGAAATAATGAATTTT
Found at i:33759443 original size:5 final size:5
Alignment explanation
Indices: 33759435--33759460 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33759425 GAGATAGAAT
33759435 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
33759461 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:33763867 original size:133 final size:133
Alignment explanation
Indices: 33763689--33763948 Score: 466
Period size: 133 Copynumber: 2.0 Consensus size: 133
33763679 AACGGAGACG
*
33763689 ATAAAATTAAATATTGAAGTGATATTAGAATAAGAGACAAAAAAATAAACTAAATTTACCATACT
1 ATAAAATTAAATATTGAAGTGATATTAGAACAAGAGACAAAAAAATAAACTAAATTTACCATACT
33763754 ATTCATCTAAACTCGCACCTACCTTGATTACTAAAATGAAATTCTTGCAACTTTTTATCTAAATG
66 ATTCATCTAAACTCGCACCTACCTTGATTACTAAAATGAAATTCTTGCAACTTTTTATCTAAATG
33763819 GTC
131 GTC
* ** *
33763822 ATAAAATTAAATATTGAAGTGATATTGGAACGTGAGACAAAAAAATAAACTAAATTTACCGTACT
1 ATAAAATTAAATATTGAAGTGATATTAGAACAAGAGACAAAAAAATAAACTAAATTTACCATACT
*
33763887 ATTCATCTAAACTCGCACCTACCTTGATTATTAAAATGAAATTCTTGCAACTTTTTATCTAA
66 ATTCATCTAAACTCGCACCTACCTTGATTACTAAAATGAAATTCTTGCAACTTTTTATCTAA
33763949 TTTTTAGGAC
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 121 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (133 bp):
ATAAAATTAAATATTGAAGTGATATTAGAACAAGAGACAAAAAAATAAACTAAATTTACCATACT
ATTCATCTAAACTCGCACCTACCTTGATTACTAAAATGAAATTCTTGCAACTTTTTATCTAAATG
GTC
Found at i:33771490 original size:15 final size:15
Alignment explanation
Indices: 33771425--33771506 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 15
33771415 ACGGTAACAT
33771425 TCCCAACAATCACAA
1 TCCCAACAATCACAA
* * *
33771440 TCCTAACGACCACAA
1 TCCCAACAATCACAA
* * *
33771455 TTCCAACAGTTAC-A
1 TCCCAACAATCACAA
*
33771469 CCCCAACAATCACAA
1 TCCCAACAATCACAA
* *
33771484 TCCCAACGACCACAA
1 TCCCAACAATCACAA
*
33771499 TTCCAACA
1 TCCCAACA
33771507 GTTACACCCC
Statistics
Matches: 48, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
14 10 0.21
15 38 0.79
ACGTcount: A:0.41, C:0.40, G:0.04, T:0.15
Consensus pattern (15 bp):
TCCCAACAATCACAA
Found at i:33771492 original size:44 final size:44
Alignment explanation
Indices: 33771426--33771520 Score: 181
Period size: 44 Copynumber: 2.2 Consensus size: 44
33771416 CGGTAACATT
*
33771426 CCCAACAATCACAATCCTAACGACCACAATTCCAACAGTTACAC
1 CCCAACAATCACAATCCCAACGACCACAATTCCAACAGTTACAC
33771470 CCCAACAATCACAATCCCAACGACCACAATTCCAACAGTTACAC
1 CCCAACAATCACAATCCCAACGACCACAATTCCAACAGTTACAC
33771514 CCCAACA
1 CCCAACA
33771521 GTCATATTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (44 bp):
CCCAACAATCACAATCCCAACGACCACAATTCCAACAGTTACAC
Found at i:33772065 original size:34 final size:35
Alignment explanation
Indices: 33772027--33772094 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
33772017 GATGAAACGC
*
33772027 GAATCGAGCCGACAATGATTGCTTG-GTGAAATGT
1 GAATCGAGCCGACAACGATTGCTTGTGTGAAATGT
* * *
33772061 GAATCGGGTCGATAACGATTGCTTGTGTGAAATG
1 GAATCGAGCCGACAACGATTGCTTGTGTGAAATG
33772095 ACAATAGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (35 bp):
GAATCGAGCCGACAACGATTGCTTGTGTGAAATGT
Found at i:33772113 original size:35 final size:34
Alignment explanation
Indices: 33772038--33772113 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 34
33772028 AATCGAGCCG
* ** * *
33772038 ACAATGATTGCTTGGTGAAATGTGAATCGGGTCG
1 ACAACGATTGCTTGGTGAAATGACAATAGGGTCA
*
33772072 ATAACGATTGCTTGTGTGAAATGACAATAGGGTCA
1 ACAACGATTGCTTG-GTGAAATGACAATAGGGTCA
33772107 ACAACGA
1 ACAACGA
33772114 CTGTCTGTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 12 0.35
35 22 0.65
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (34 bp):
ACAACGATTGCTTGGTGAAATGACAATAGGGTCA
Found at i:33773287 original size:15 final size:15
Alignment explanation
Indices: 33773267--33773300 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
33773257 ATTAAGAATG
33773267 TTATTAAATTATATA
1 TTATTAAATTATATA
*
33773282 TTATTAAATTATTTA
1 TTATTAAATTATATA
33773297 TTAT
1 TTAT
33773301 CATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTAAATTATATA
Found at i:33775182 original size:24 final size:24
Alignment explanation
Indices: 33775166--33775216 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
33775156 AGTTTGCCTT
33775166 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
33775190 AAACAAATAAATAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
33775214 AAA
1 AAA
33775217 GATTGTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:33776152 original size:9 final size:9
Alignment explanation
Indices: 33776138--33776163 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
33776128 ATTATTCGAA
33776138 TCGAGTTAT
1 TCGAGTTAT
33776147 TCGAGTTAT
1 TCGAGTTAT
33776156 TCGAGTTA
1 TCGAGTTA
33776164 AGCGAATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:33777834 original size:24 final size:24
Alignment explanation
Indices: 33777785--33777835 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
33777775 AGTTTGTCTC
*
33777785 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAACTG
*
33777809 AAACAAATAAATGGAGTTTAACTG
1 AAACAAATAAATAGAGTTTAACTG
33777833 AAA
1 AAA
33777836 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.25
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTTAACTG
Found at i:33782470 original size:147 final size:147
Alignment explanation
Indices: 33782252--33782702 Score: 744
Period size: 147 Copynumber: 3.1 Consensus size: 147
33782242 TAGGAGGCAC
* *
33782252 TGATTTGTGTTGAGAGAGTGGTAGCTGCAGACTGGGAAGCATGAGTTCGTCGGAGGACGGATAAC
1 TGATTTATGTTGAGAGAGTGGTGGCTGCAGACTGGGAAGCATGAGTTCGTCGGAGGACGGATAAC
* * * *
33782317 ATGTTTTTTTATCTTTGAAATT-GAAGAAGATTTGATGGAATCTCCAAGGACGACTTAAAAGTTG
66 AAGTTTTTTTAACTTTGAAATTAG-AGAAGGTTTGATGGAATCTCCAAGGAGGACTTAAAAGTTG
33782381 TTCCTTCCTATAGAGTGT
130 TTCCTTCCTATAGAGTGT
* *
33782399 TGATTTATGTTGAGAGAGTGGTGGCTGCAGACTGGGAAGCATGAGTTTGTCGGAGGATGGATAAC
1 TGATTTATGTTGAGAGAGTGGTGGCTGCAGACTGGGAAGCATGAGTTCGTCGGAGGACGGATAAC
* *
33782464 AAGTTTTTTTAACTTTGAAATTAGAGAAGGTTTGATAGAATCTCCAAGGAGGGCTTAAAAGTTGT
66 AAGTTTTTTTAACTTTGAAATTAGAGAAGGTTTGATGGAATCTCCAAGGAGGACTTAAAAGTTGT
33782529 TCCTTCCTATAGAGTGT
131 TCCTTCCTATAGAGTGT
* *
33782546 TGATTTATGTTGAGAGAGTGGTGGCTGCAGACTGGGAAGCATGAGTTCGTCAGAGGACGGATAGC
1 TGATTTATGTTGAGAGAGTGGTGGCTGCAGACTGGGAAGCATGAGTTCGTCGGAGGACGGATAAC
* *
33782611 AAGTTTTTTTAACTTTGAAATCAGAGAAGGTTTGATGGAATCTCTAAGGAGGACTTAAAAGTTGT
66 AAGTTTTTTTAACTTTGAAATTAGAGAAGGTTTGATGGAATCTCCAAGGAGGACTTAAAAGTTGT
*
33782676 TCCTTCCTATAGAGTGC
131 TCCTTCCTATAGAGTGT
33782693 TGATTT-TGTT
1 TGATTTATGTT
33782703 TTCATGGAGA
Statistics
Matches: 284, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
146 4 0.01
147 279 0.98
148 1 0.00
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (147 bp):
TGATTTATGTTGAGAGAGTGGTGGCTGCAGACTGGGAAGCATGAGTTCGTCGGAGGACGGATAAC
AAGTTTTTTTAACTTTGAAATTAGAGAAGGTTTGATGGAATCTCCAAGGAGGACTTAAAAGTTGT
TCCTTCCTATAGAGTGT
Found at i:33783847 original size:13 final size:13
Alignment explanation
Indices: 33783829--33783855 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33783819 ATTTAATTGA
33783829 AAAAATAAAAAAT
1 AAAAATAAAAAAT
33783842 AAAAATAAAAAAT
1 AAAAATAAAAAAT
33783855 A
1 A
33783856 TATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:33794288 original size:6 final size:6
Alignment explanation
Indices: 33794279--33794306 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
33794269 CAACCTTAGC
33794279 CTTGAG CTTGAG CTTGAG CTTGAG CTTG
1 CTTGAG CTTGAG CTTGAG CTTGAG CTTG
33794307 GCCTACTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (6 bp):
CTTGAG
Found at i:33797197 original size:51 final size:53
Alignment explanation
Indices: 33797089--33797217 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 53
33797079 TGAAAAAATG
* * * *
33797089 TGTAAATGTTATGGGCTAAATTTGTTAAATTAGGACCAAGTTAACAAAATTCA
1 TGTAAATGTTGTGGGCTAAATTTATTAAATCAAGACCAAGTTAACAAAATTCA
* *
33797142 --TAAATGTTGTGGGCTAAATTTATTAAATCAAGACCAAGTTGAC-ATATT-A
1 TGTAAATGTTGTGGGCTAAATTTATTAAATCAAGACCAAGTTAACAAAATTCA
* * * *
33797191 TGTAAATTTTGAGAGCTAAACTTATTA
1 TGTAAATGTTGTGGGCTAAATTTATTA
33797218 TATTAATGAT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.02
50 4 0.06
51 59 0.92
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (53 bp):
TGTAAATGTTGTGGGCTAAATTTATTAAATCAAGACCAAGTTAACAAAATTCA
Found at i:33804297 original size:22 final size:22
Alignment explanation
Indices: 33804271--33804312 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33804261 TTAGTCAAAG
*
33804271 TCAATGGGTCAGGTTGGGTCGA
1 TCAATGGGTCAGGTCGGGTCGA
*
33804293 TCAATGGGTCGGGTCGGGTC
1 TCAATGGGTCAGGTCGGGTC
33804313 ATACGATTCG
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:0.14, C:0.17, G:0.43, T:0.26
Consensus pattern (22 bp):
TCAATGGGTCAGGTCGGGTCGA
Found at i:33805644 original size:39 final size:39
Alignment explanation
Indices: 33805564--33805644 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
33805554 AATCATTGTA
* * *
33805564 GATTCTTGACTTAACGCTAATTCTTGGCAGACTTTTGCG
1 GATTCTTGACTTAACGCTAATCCTTGGCAGACTCTTACG
* *
33805603 GATTTTTGACTTAATGCTAATCCTTGGC-GAACTCTTACG
1 GATTCTTGACTTAACGCTAATCCTTGGCAG-ACTCTTACG
33805642 GAT
1 GAT
33805645 AATAGACATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (39 bp):
GATTCTTGACTTAACGCTAATCCTTGGCAGACTCTTACG
Found at i:33813317 original size:28 final size:29
Alignment explanation
Indices: 33813261--33813341 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
33813251 TCTTTACCCG
33813261 TTAATCGAATCGAAATTTTTTCAAAAAAA
1 TTAATCGAATCGAAATTTTTTCAAAAAAA
*
33813290 TTAATCGGATCGAAATTTTTTCAAAAAAA
1 TTAATCGAATCGAAATTTTTTCAAAAAAA
33813319 TTAATCGAATCG-AATTTTTTCAA
1 TTAATCGAATCGAAATTTTTTCAA
33813342 TTAATTCGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 11 0.22
29 39 0.78
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (29 bp):
TTAATCGAATCGAAATTTTTTCAAAAAAA
Found at i:33813395 original size:16 final size:15
Alignment explanation
Indices: 33813374--33813408 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33813364 TAATTGACCG
33813374 ATTATAATACTTATAT
1 ATTATAATA-TTATAT
*
33813390 ATTATAATATTATTT
1 ATTATAATATTATAT
33813405 ATTA
1 ATTA
33813409 AGTTCAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATAATATTATAT
Found at i:33813574 original size:16 final size:16
Alignment explanation
Indices: 33813552--33813603 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
33813542 TAAGAGGAAA
33813552 GAAAATTAGAAGGATG
1 GAAAATTAGAAGGATG
*
33813568 GAGAATT-GAAGGGATG
1 GAAAATTAGAA-GGATG
* *
33813584 GAAAACTAGAATGATG
1 GAAAATTAGAAGGATG
33813600 GAAA
1 GAAA
33813604 TATAAATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (16 bp):
GAAAATTAGAAGGATG
Found at i:33818941 original size:27 final size:27
Alignment explanation
Indices: 33818896--33818963 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
33818886 TCTACCTCAC
*
33818896 TTCATTTTATACCTCTTTTGTTCATCCT
1 TTCATTTT-TTCCTCTTTTGTTCATCCT
33818924 TTCATTTTTTCCTCTTTTGTTCATCCT
1 TTCATTTTTTCCTCTTTTGTTCATCCT
**
33818951 TTTGTTTTTTCCT
1 TTCATTTTTTCCT
33818964 TTCACCATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 29 0.78
28 8 0.22
ACGTcount: A:0.09, C:0.24, G:0.04, T:0.63
Consensus pattern (27 bp):
TTCATTTTTTCCTCTTTTGTTCATCCT
Found at i:33818982 original size:24 final size:24
Alignment explanation
Indices: 33818945--33819014 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
33818935 CTCTTTTGTT
33818945 CATCCTTTTGTTTTTTC-CTTTCAC
1 CATCC-TTTGTTTTTTCTCTTTCAC
33818969 CATCTCTTT-TTTTTTCTCTTTCAC
1 CATC-CTTTGTTTTTTCTCTTTCAC
*
33818993 C-T-ATTTGTTTTCTATCTCTTTC
1 CATCCTTTGTTTT-T-TCTCTTTC
33819015 GTTTTATCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
21 3 0.08
22 4 0.10
23 9 0.22
24 23 0.57
25 1 0.03
ACGTcount: A:0.09, C:0.27, G:0.03, T:0.61
Consensus pattern (24 bp):
CATCCTTTGTTTTTTCTCTTTCAC
Found at i:33823262 original size:33 final size:33
Alignment explanation
Indices: 33823199--33823356 Score: 207
Period size: 33 Copynumber: 4.9 Consensus size: 33
33823189 TAACATATAC
* *
33823199 CATACATAACAT--ACACGCTAATATATCATAA
1 CATACATAATATACACACACTAATATATCATAA
* * *
33823230 CATACATAATATATAGACACTAAAATATCATAA
1 CATACATAATATACACACACTAATATATCATAA
*
33823263 CATACATAATATACACACACTGATATATCATAA
1 CATACATAATATACACACACTAATATATCATAA
*
33823296 CATACATAATATACACACACTGATATATCATAA
1 CATACATAATATACACACACTAATATATCATAA
* *
33823329 CATACATAATAT--TCATACTAATATATCA
1 CATACATAATATACACACACTAATATATCA
33823357 ATTGATTGAC
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
31 24 0.21
33 90 0.79
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (33 bp):
CATACATAATATACACACACTAATATATCATAA
Found at i:33824125 original size:22 final size:22
Alignment explanation
Indices: 33824094--33824142 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
33824084 GGATTTTTAT
* **
33824094 TTAATGAATTTAATTAATAAAG
1 TTAATAAATTTAAGAAATAAAG
*
33824116 TTAATAAATTTAAGAAATAAAT
1 TTAATAAATTTAAGAAATAAAG
33824138 TTAAT
1 TTAAT
33824143 CATTTTTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (22 bp):
TTAATAAATTTAAGAAATAAAG
Found at i:33826229 original size:29 final size:28
Alignment explanation
Indices: 33826193--33826381 Score: 148
Period size: 29 Copynumber: 6.5 Consensus size: 28
33826183 TTAACAGAGA
33826193 TATCCACAAAGGCTCACATATAATCGAAT
1 TATCCACAAAGGCTCACATATAA-CGAAT
*
33826222 TATCCACAAAGGCTCACATATAA-TAGAT
1 TATCCACAAAGGCTCACATATAACGA-AT
* * * *
33826250 TCAACCATAAAGGTTCACATATAACAAAGT
1 T-ATCCACAAAGGCTCACATATAACGAA-T
* * *
33826280 CAGT-AACAAAGGCTCACATATAACAAAT
1 TA-TCCACAAAGGCTCACATATAACGAAT
* * *
33826308 TCAACTACAAAAGCTCACATATAACAGAAT
1 T-ATCCACAAAGGCTCACATATAAC-GAAT
* * *
33826338 CATCCACAAAGACTCGCATATAACAGAAT
1 TATCCACAAAGGCTCACATATAAC-GAAT
* *
33826367 CAGCCACAAAGGCTC
1 TATCCACAAAGGCTC
33826382 TCTTTTTTGT
Statistics
Matches: 129, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 119 0.92
30 5 0.04
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (28 bp):
TATCCACAAAGGCTCACATATAACGAAT
Found at i:33826268 original size:58 final size:57
Alignment explanation
Indices: 33826196--33826381 Score: 212
Period size: 58 Copynumber: 3.2 Consensus size: 57
33826186 ACAGAGATAT
* *
33826196 CCACAAAGGCTCACATATAATCGAATTATCCACAAAGGCTCACATATAATAGATTCAA
1 CCACAAAGGCTCACATATAA-CGAATCATCCACAAAGGCTCACATATAACAGATTCAA
* * * * *
33826254 CCATAAAGGTTCACATATAACAAAGTCAGT-AACAAAGGCTCACATATAACAAATTCAA
1 CCACAAAGGCTCACATATAACGAA-TCA-TCCACAAAGGCTCACATATAACAGATTCAA
* * * * * *
33826312 CTACAAAAGCTCACATATAACAGAATCATCCACAAAGACTCGCATATAACAGAATCAG
1 CCACAAAGGCTCACATATAAC-GAATCATCCACAAAGGCTCACATATAACAGATTCAA
33826370 CCACAAAGGCTC
1 CCACAAAGGCTC
33826382 TCTTTTTTGT
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
57 4 0.04
58 97 0.93
59 3 0.03
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (57 bp):
CCACAAAGGCTCACATATAACGAATCATCCACAAAGGCTCACATATAACAGATTCAA
Found at i:33826330 original size:87 final size:87
Alignment explanation
Indices: 33826198--33826381 Score: 219
Period size: 87 Copynumber: 2.1 Consensus size: 87
33826188 AGAGATATCC
* * * * * * *
33826198 ACAAAGGCTCACATATAATCGAATTATCCACAAAGGCTCACATATAATAGATTCAACCATAAAGG
1 ACAAAGGCTCACATATAATCAAATTAACCACAAAAGCTCACATATAACAGAATCAACCACAAAGA
* *
33826263 TTCACATATAACA-AAGTCAGTA
66 CTCACATATAACAGAA-TCAGCA
* *
33826285 ACAAAGGCTCACATATAA-CAAATTCAACTACAAAAGCTCACATATAACAGAATCATCCACAAAG
1 ACAAAGGCTCACATATAATCAAATT-AACCACAAAAGCTCACATATAACAGAATCAACCACAAAG
* *
33826349 ACTCGCATATAACAGAATCAGCC
65 ACTCACATATAACAGAATCAGCA
33826372 ACAAAGGCTC
1 ACAAAGGCTC
33826382 TCTTTTTTGT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 5 0.06
87 75 0.91
88 2 0.02
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.20
Consensus pattern (87 bp):
ACAAAGGCTCACATATAATCAAATTAACCACAAAAGCTCACATATAACAGAATCAACCACAAAGA
CTCACATATAACAGAATCAGCA
Found at i:33835266 original size:29 final size:29
Alignment explanation
Indices: 33835226--33835284 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
33835216 TTGTGGAAGA
* * *
33835226 GGTGGAGAACTTGTTCGTTGAGAGTTCGT
1 GGTGAAGAACTTGTTCGTAGAGAATTCGT
*
33835255 GGTGAAGAACTTGTTTGTAGAGAATTCGT
1 GGTGAAGAACTTGTTCGTAGAGAATTCGT
33835284 G
1 G
33835285 TCAAGGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.36, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTAGAGAATTCGT
Done.