Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 93 of 109
Found at i:29561014 original size:15 final size:15
Alignment explanation
Indices: 29560994--29561024 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29560984 TATTGAGTCT
29560994 AGTTTCTCATAGAAG
1 AGTTTCTCATAGAAG
29561009 AGTTTCTCATAGAAG
1 AGTTTCTCATAGAAG
29561024 A
1 A
29561025 AATGATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (15 bp):
AGTTTCTCATAGAAG
Found at i:29561577 original size:17 final size:18
Alignment explanation
Indices: 29561555--29561588 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29561545 TTTGGGCCGA
29561555 GTGGG-CCACACAGGCAT
1 GTGGGCCCACACAGGCAT
*
29561572 GTGGGCCCACACGGGCA
1 GTGGGCCCACACAGGCA
29561589 GACCACATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.32, G:0.38, T:0.09
Consensus pattern (18 bp):
GTGGGCCCACACAGGCAT
Found at i:29562842 original size:24 final size:24
Alignment explanation
Indices: 29562814--29562860 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
29562804 TGGTGTTATT
* *
29562814 ATGACTAAGTTGATGTATGATGGA
1 ATGACCAAGTTGATATATGATGGA
* *
29562838 ATGACCAATTTGGTATATGATGG
1 ATGACCAAGTTGATATATGATGG
29562861 TATGTTTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (24 bp):
ATGACCAAGTTGATATATGATGGA
Found at i:29572298 original size:18 final size:18
Alignment explanation
Indices: 29572268--29572306 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29572258 ATTGTTGAAG
29572268 TTAAATCCCTAAGGGGTT
1 TTAAATCCCTAAGGGGTT
29572286 TTAAA-CCCTTAAGGGGTT
1 TTAAATCCC-TAAGGGGTT
29572304 TTA
1 TTA
29572307 TGGAAGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (18 bp):
TTAAATCCCTAAGGGGTT
Found at i:29574461 original size:15 final size:16
Alignment explanation
Indices: 29574427--29574469 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29574417 TATTTTATGA
29574427 ATTATTTATTAATTTAT
1 ATTATTTA-TAATTTAT
*
29574444 ATTATTTA-AATTTTT
1 ATTATTTATAATTTAT
*
29574459 ATTTTTTATAA
1 ATTATTTATAA
29574470 ATATTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATTTATAATTTAT
Found at i:29575520 original size:16 final size:17
Alignment explanation
Indices: 29575486--29575536 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
29575476 AATCTTAATA
*
29575486 TATTATTAATAAATTTT
1 TATTATTAATAAATATT
*
29575503 TATTTTTAA-AAATATT
1 TATTATTAATAAATATT
**
29575519 TAAAATTAATAAAATATT
1 TATTATTAAT-AAATATT
29575537 ATAATTTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 12 0.44
17 8 0.30
18 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATTAATAAATATT
Found at i:29580714 original size:22 final size:22
Alignment explanation
Indices: 29580668--29580720 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
29580658 AACATGTACA
* *
29580668 TGTGCGAACCTCTTCCATGCAT
1 TGTGCAAACCTCATCCATGCAT
**
29580690 TGTGCAAACCTCATCCATGTGT
1 TGTGCAAACCTCATCCATGCAT
29580712 TGTGCAAAC
1 TGTGCAAAC
29580721 TCTTAGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (22 bp):
TGTGCAAACCTCATCCATGCAT
Found at i:29581503 original size:192 final size:192
Alignment explanation
Indices: 29581176--29581546 Score: 634
Period size: 192 Copynumber: 1.9 Consensus size: 192
29581166 GTTTATGCGA
* * *
29581176 GCTTAATGCTTTGCAAGTTGTTCTATGACGTGTTGTGGTACTGTCAGCTATATTAAAATTTGTGA
1 GCTTAATGCTTTGCAAGCTATTCTATGACGTGTTGTGGTACTGTCAGCTATATTAAAAATTGTGA
* *
29581241 GCCTAAAATGACGTGACCTGTAAATGTGTATTATTGCGATATGTTGGTATTGTGAATTTTTGGAA
66 GCCTAAAATGACGTGACCTGTAAATGTGTATTACTGCGATATGTTGGCATTGTGAATTTTTGGAA
*
29581306 CCATTGGATATAGTTGGCATGCCATAGGATTATGAGTGCTCACCTATATAATGTGATAGGGC
131 CCATTGGATATAGTTGGAATGCCATAGGATTATGAGTGCTCACCTATATAATGTGATAGGGC
* *
29581368 GCTTAATGCTTTGCAAGCTATTCTATGACGTGTTGTGGTACTGTGAGCTCTATTAAAAATTGTGA
1 GCTTAATGCTTTGCAAGCTATTCTATGACGTGTTGTGGTACTGTCAGCTATATTAAAAATTGTGA
* *
29581433 GCCTAAAATGACGTGACCTGTACATGTGTATTACTGCGTTATGTTGGCATTGTGAATTTTTGGAA
66 GCCTAAAATGACGTGACCTGTAAATGTGTATTACTGCGATATGTTGGCATTGTGAATTTTTGGAA
* *
29581498 CCATTGGATATAGTTGGAATGCCATAGGATTGTGAGTGCTCACTTATAT
131 CCATTGGATATAGTTGGAATGCCATAGGATTATGAGTGCTCACCTATAT
29581547 GTGAATTAGT
Statistics
Matches: 167, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
192 167 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (192 bp):
GCTTAATGCTTTGCAAGCTATTCTATGACGTGTTGTGGTACTGTCAGCTATATTAAAAATTGTGA
GCCTAAAATGACGTGACCTGTAAATGTGTATTACTGCGATATGTTGGCATTGTGAATTTTTGGAA
CCATTGGATATAGTTGGAATGCCATAGGATTATGAGTGCTCACCTATATAATGTGATAGGGC
Found at i:29583670 original size:44 final size:44
Alignment explanation
Indices: 29583557--29585816 Score: 1687
Period size: 44 Copynumber: 50.6 Consensus size: 44
29583547 CATTATGGCG
* * * * *
29583557 AATCTTATC-CCCTAAAGTTACAGCAGAGCAAATTGAAGTTTCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * ** * *
29583600 AGTCTTATCTCCCTGATGTTATAGTGGAGCAGATTGAAGTTATA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * * * *
29583644 GATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATCGGAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * *
29583689 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * *
29583733 CACCTTATCT-CCTCGAAGTTGCAGTGGAGCAGATTAAAAATAAACA
1 AATCTTATCTCCCT-GAAGTTGCAGTAGAGCAGATT-GAAGT-TACA
* *
29583779 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGATAGGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAG-T----TACA
* * * ***
29583828 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * **
29583872 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAATAAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * *
29583917 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTTAAAATTGCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TTGAAGTTACA
* * * * * * **
29583962 AATATTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * * ** *
29584007 AATCTTATCACTCTAAAGTTGCAGTAGAGCATATTGAAACTATA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * * **
29584051 AATCTTATCTCCTTGAAGTTGCAG-GGTGTAAATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* *
29584095 AATCTTTTCTCCCTGAAGTTGCAGT-GAG-ATGGATTGAAATCATTATGGCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCA--GATTG-AA--GTTA---CA
**
29584145 AATCTTATC-CTCCTGAAGTTGCAGCGGAGCAGATTGAAGTTACA
1 AATCTTATCTC-CCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * *
29584189 AGTCTTATCTCCCTGAAGTTGCAATAGAGCAAATTGAAGTTATA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * *
29584233 GATCTTATCTTCCTAAAGTTGCAGTAGAGTAGA-TCAGAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGA-AGTTA-CA
* * * * * * *
29584278 AATTTTATCTCTCTAAAGTTGCAGTAAAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * * * * *
29584322 CACCTTGTCT-CCTCGAAGTTGCAGTGGAACAGGTTAAAAATAAACA
1 AATCTTATCTCCCT-GAAGTTGCAGTAGAGCAGATT-GAAGT-TACA
* * * * *
29584368 AATCTTATCTCTCTGAAATTGCAGTGGAGCAAATTGAAGACAGGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT---GA-A-GTTACA
* * * * ***
29584417 AATCTTATCTCCTTAAAGTTGCAGTAGAGCAAATTAAAGCCGCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * *
29584461 AATCTTATCTCACTGAAGTTGCAGTGGAGCAAAATGAAGATA-A
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* *
29584504 TGAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAAATTACA
1 --AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTG-AAGTTACA
* * * * **
29584551 AATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29584596 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29584640 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29584685 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29584729 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29584774 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29584818 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29584863 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29584907 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29584952 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29584996 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29585041 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29585085 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29585130 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29585174 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * * **
29585219 AATCTTATCTCTCTGAATTTGTAGTAGAGCAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29585263 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CA
* * *
29585308 AATCTTTTCTCCCTGAAGTTGCAGTGGAGCATATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * ** * **
29585352 ACTATTATCTCTCTAAAGTTATAGTGGAGTGGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * **
29585396 ACTCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * *
29585440 ACTCTTATCTCCCTAAAGTTGCAGTAGAGCGGATTGAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * *
29585484 ACTATTATCTCCCTGAATTTGCAGTGGAGCCGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * **
29585528 ACTCTTATCTCCCTGAAGTTGCAATGGAGTGGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * *
29585572 ACTTTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTTTCA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* *
29585616 AATATTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * *
29585660 AATCTTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * *
29585704 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* * * * * **
29585748 AGTCTAATCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCAACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
* *
29585792 AATCCTATAC-CTCTGAAGTTGCAGT
1 AATCTTAT-CTCCCTGAAGTTGCAGT
29585817 GGGTTAGAAT
Statistics
Matches: 1764, Mismatches: 402, Indels: 101
0.78 0.18 0.04
Matches are distributed among these distances:
43 27 0.02
44 992 0.56
45 554 0.31
46 71 0.04
47 9 0.01
48 4 0.00
49 76 0.04
50 27 0.02
51 3 0.00
52 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
Found at i:29583720 original size:89 final size:89
Alignment explanation
Indices: 29583557--29585795 Score: 1857
Period size: 89 Copynumber: 25.0 Consensus size: 89
29583547 CATTATGGCG
* * * * * * * *
29583557 AATCTTATC-CCCTAAAGTTACAGCAGAGCAAATTGAAG-T-TTCAAGTCTTATCTCCCTGATGT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGT-AAATCTTATCTCTCTGAAGT
** * *
29583619 TATAGTGGAGCAGATTGAAGTTATA
65 TGCAGTGGAGCAGATTGAAGCTACA
* * * * * * * *
29583644 GATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATCGGAGATAGCAAATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29583709 GCAGTAGAGCAGATTAAAGCTATA
66 GCAGTGGAGCAGATTGAAGCTACA
* * * * * * * ** * *
29583733 CACCTTATCT-CCTCGAAGTTGCAGTGGAGCAGATTAAAAATAAACAAATCTTATCTCCCTGAAA
1 AATCTTATCTCCCT-AAAGTTGCAGTAGAGTAGATTGAAGAT-AGTAAATCTTATCTCTCTGAAG
29583797 TTGCAGTGGAGCAGATTGAAGATAGGCTACA
64 TTGCAGTGGAGCAGATT---GA-A-GCTACA
* * * * * ** * * *
29583828 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAG-CCGCAAATCTTATCTCCCTAAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * **
29583892 GCAGTGGAGCAGAATAAAGATAGTG
66 GCAGTGGAGCAGATTGAAGCTA-CA
* * * * * * * * *
29583917 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTT-AAAATTGCAAATATTATCTCCCTAAAGT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGA-TTGAAGATAGTAAATCTTATCTCTCTGAAGT
* * * **
29583981 TGCAGTGGAGTAGATTAAAGATAGTG
65 TGCAGTGGAGCAGATTGAAGCTA-CA
* * * *
29584007 AATCTTATCACTCTAAAGTTGCAGTAGAGCATATTGAA-ACTA-TAAATCTTATCTC-CTTGAAG
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGA-TAGTAAATCTTATCTCTC-TGAAG
* * * * **
29584069 TTGCAG-GGTGTAAATTGAAGATAGTG
64 TTGCAGTGGAGCAGATTGAAGCTA-CA
* * * * *
29584095 AATCTTTTCTCCCTGAAGTTGCAGT-GAGATGGATTGAAATCATTATGGCAAATCTTATC-CTCC
1 AATCTTATCTCCCTAAAGTTGCAGTAGAG-TAGATTG-AA-GA-TA--GTAAATCTTATCTCT-C
* *
29584158 TGAAGTTGCAGCGGAGCAGATTGAAGTTACA
59 TGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * * * * * *
29584189 AGTCTTATCTCCCTGAAGTTGCAATAGAGCAAATTGAAGTTA-TAGATCTTATCT-TCCTAAAGT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCT-CTGAAGT
* * * *
29584252 TGCAGTAGAGTAGA-TCAGAGATAGCA
65 TGCAGTGGAGCAGATTGA-AGCTA-CA
* * * * * * * * *
29584278 AATTTTATCTCTCTAAAGTTGCAGTAAAGCAGATTAAAGCTA-TACACCTTGTCTC-CTCGAAGT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCT-GAAGT
* * * **
29584341 TGCAGTGGAACAGGTTAAAAATAAACA
65 TGCAGTGGAGCAGATTGAAGCT--ACA
* * * * *
29584368 AATCTTATCTCTCTGAAA-TTGCAGTGGAGCAAATTGAAGACAGGCTACAAATCTTATCTC-CTT
1 AATCTTATCTCCCT-AAAGTTGCAGTAGAGTAGATTGAAGATA-G-T--AAATCTTATCTCTC-T
* * * * **
29584431 AAAGTTGCAGTAGAGCAAATTAAAGCCGCA
60 GAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * * * * * *
29584461 AATCTTATCTCACTGAAGTTGCAGTGGAGCAAAATGAAGATAATGAATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* **
29584526 GCAGTAGAGCAGATTGAAAATTACA
66 GCAGTGGAGCAGATTG-AAGCTACA
* * * * *
29584551 AATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29584616 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* *
29584640 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29584705 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* *
29584729 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29584794 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* *
29584818 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29584883 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* *
29584907 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29584972 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* *
29584996 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29585061 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* *
29585085 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29585150 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* *
29585174 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTATCTCTCTGAATTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29585239 GTAGTAGAGCAGATTGAAACTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* * *
29585263 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTGAATCTTTTCTCCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* *
29585328 GCAGTGGAGCATATTGAAGTTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* * * ** * * * * * *
29585352 ACTATTATCTCTCTAAAGTTATAGTGGAGTGGATTGAAGTTA-CAACTCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
** *
29585416 GCAGTGGAGTGGATTGAAGTTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* ** * * *
29585440 ACTCTTATCTCCCTAAAGTTGCAGTAGAGCGGATTGAA-AT--TACAACTATTATCTCCCTGAAT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTA-AA-TCTTATCTCTCTGAAG
* *
29585502 TTGCAGTGGAGCCGATTGAAGTTACA
64 TTGCAGTGGAGCAGATTGAAGCTACA
* * * * * * * * * *
29585528 ACTCTTATCTCCCTGAAGTTGCAATGGAGTGGATTGAAGTTA-CAACTTTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * *
29585592 GCAGTGGAGCGGATTAAAGTTTCA
66 GCAGTGGAGCAGATTGAAGCTACA
* * * * * * * *
29585616 AATATTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA-CAAATCTTATCTCCCTAAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * * *
29585680 GTAGTGGAGCGGATTAAAGTTACA
66 GCAGTGGAGCAGATTGAAGCTACA
* * * * * * * *
29585704 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAGTCTAATCTCCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
* * *
29585768 GCAGTGGAGTACATTGAAGCAACA
66 GCAGTGGAGCAGATTGAAGCTACA
29585792 AATC
1 AATC
29585796 CTATACCTCT
Statistics
Matches: 1869, Mismatches: 233, Indels: 99
0.85 0.11 0.04
Matches are distributed among these distances:
86 1 0.00
87 15 0.01
88 437 0.23
89 963 0.52
90 231 0.12
91 10 0.01
92 2 0.00
93 76 0.04
94 48 0.03
95 83 0.04
96 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (89 bp):
AATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAGATAGTAAATCTTATCTCTCTGAAGTT
GCAGTGGAGCAGATTGAAGCTACA
Found at i:29586717 original size:14 final size:15
Alignment explanation
Indices: 29586698--29586729 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29586688 GTGGTTATAG
29586698 TTAAAATA-ATAAAA
1 TTAAAATAGATAAAA
29586712 TTAAAATAGATAAAA
1 TTAAAATAGATAAAA
29586727 TTA
1 TTA
29586730 TGATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TTAAAATAGATAAAA
Found at i:29588649 original size:19 final size:19
Alignment explanation
Indices: 29588624--29588661 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29588614 AAAAACATGT
*
29588624 AAAAAAAAGGAAAGAAATCG
1 AAAAAAAA-AAAAGAAATCG
29588644 AAAAAAAAAAAAGAAATC
1 AAAAAAAAAAAAGAAATC
29588662 AAATACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAAAGAAATCG
Found at i:29589587 original size:27 final size:26
Alignment explanation
Indices: 29589557--29589616 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
29589547 TGCATGTTTG
29589557 TTTATTTATTATTATTG-TCATTATTAT
1 TTTATTTATTATT-TTGTTC-TTATTAT
* *
29589584 TTTATTTTATTCTTTTGTTCTTGTTAT
1 TTTA-TTTATTATTTTGTTCTTATTAT
29589611 TTTATT
1 TTTATT
29589617 ATTTCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 2 0.07
27 17 0.59
28 10 0.34
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTATTTATTATTTTGTTCTTATTAT
Found at i:29589750 original size:3 final size:3
Alignment explanation
Indices: 29589735--29589769 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
29589725 ATGATATGAT
*
29589735 TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29589770 TTATTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:29589811 original size:3 final size:3
Alignment explanation
Indices: 29589768--29589796 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29589758 ATAATAATAA
29589768 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29589797 CATCATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29590642 original size:14 final size:14
Alignment explanation
Indices: 29590606--29590651 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
29590596 AATAAAAAAT
29590606 ACAAAATAATATTATA
1 ACAAAATAA-ATT-TA
*
29590622 ATAAAAATAAATTTA
1 A-CAAAATAAATTTA
29590637 ACAAAATAAATTTA
1 ACAAAATAAATTTA
29590651 A
1 A
29590652 TAATACTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.48
15 3 0.11
16 4 0.15
17 7 0.26
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAAATAAATTTA
Found at i:29592127 original size:20 final size:21
Alignment explanation
Indices: 29592093--29592132 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29592083 AAGTCAATTT
*
29592093 TTATTTTTATTTTATTTATGA
1 TTATTTTTATATTATTTATGA
29592114 TTATTTTTA-ATTATTTATG
1 TTATTTTTATATTATTTATG
29592133 GTATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTATTTTTATATTATTTATGA
Found at i:29592523 original size:33 final size:35
Alignment explanation
Indices: 29592484--29592550 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 35
29592474 AATTAAGAGC
*
29592484 TATATAATAAGTATAGA-TAATTATTT-TTTAATA
1 TATATAAGAAGTATAGATTAATTATTTATTTAATA
* * *
29592517 TATATAAGAATTATTGATTAATTTTTTATTTAAT
1 TATATAAGAAGTATAGATTAATTATTTATTTAAT
29592551 TAAAAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 14 0.50
34 8 0.29
35 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (35 bp):
TATATAAGAAGTATAGATTAATTATTTATTTAATA
Found at i:29594862 original size:29 final size:29
Alignment explanation
Indices: 29594810--29594865 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
29594800 ATAAGGACTA
* * *
29594810 GATCAAATTAGTCTCTCTAGTATTAAATG
1 GATCAAATTAGTCTATATACTATTAAATG
*
29594839 GATCAATTTAGTCTATATACTATTAAA
1 GATCAAATTAGTCTATATACTATTAAA
29594866 AAATCAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
GATCAAATTAGTCTATATACTATTAAATG
Found at i:29596245 original size:31 final size:31
Alignment explanation
Indices: 29596186--29596250 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
29596176 TTAAACCGAG
* * *
29596186 TCAAACAAATAATTTAAAAATTACAAAATAT
1 TCAAAAAAATAATTAAAAAAATACAAAATAT
*
29596217 TCAAAAAAATAAATTAAAAAAATA-AAAATGT
1 TCAAAAAAAT-AATTAAAAAAATACAAAATAT
29596248 TCA
1 TCA
29596251 TAATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.26
Consensus pattern (31 bp):
TCAAAAAAATAATTAAAAAAATACAAAATAT
Found at i:29598623 original size:17 final size:17
Alignment explanation
Indices: 29598580--29598624 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
29598570 CAAAATGTAA
*
29598580 AGTCCAGAAATTTAAAC
1 AGTCCAAAAATTTAAAC
*
29598597 AGTCTAAAAATTTAAAC
1 AGTCCAAAAATTTAAAC
*
29598614 AGTCCCAAAAT
1 AGTCCAAAAAT
29598625 GGCCAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (17 bp):
AGTCCAAAAATTTAAAC
Found at i:29605666 original size:40 final size:39
Alignment explanation
Indices: 29605607--29605901 Score: 136
Period size: 40 Copynumber: 7.8 Consensus size: 39
29605597 GAAAGTTGCA
* * * *
29605607 CCCAGCGCTAG-CGGATAAACCGACAAATATAGTGATGTA
1 CCCAGCACTAGTCAGATAAACTGACAAATATAGT-ATGTG
* *
29605646 CCCAGCACTAGTCAGATAAACTGAC-GA-A-AGT-TGCG
1 CCCAGCACTAGTCAGATAAACTGACAAATATAGTATGTG
* * *
29605681 CCCAACGCTAGTCAGATAAACTGACAAATATAATGATGTG
1 CCCAGCACTAGTCAGATAAACTGACAAATATAGT-ATGTG
* * * ***
29605721 CCCAACACTAGTCAAATAAACTGAC-GA-A-AGT-TACA
1 CCCAGCACTAGTCAGATAAACTGACAAATATAGTATGTG
* * * * *
29605756 CTCAGCGCTAGTC-GAATAAA-TCAAAAAATATAATAATGTG
1 CCCAGCACTAGTCAG-ATAAACT-GACAAATATAGT-ATGTG
*
29605796 CCCAGCACTAGTCAGATAAACTGAC-AA-A-AGTTACGT-
1 CCCAGCACTAGTCAGATAAACTGACAAATATAG-TATGTG
* * * ** * * * *
29605832 -CCAGCGCTAGTCGGATAAACCGATGAGTATAATGGTATG
1 CCCAGCACTAGTCAGATAAACTGACAAATATAGT-ATGTG
29605871 CCCAGCACTAGTCAGATAAACTGACGAAATA
1 CCCAGCACTAGTCAGATAAACTGAC-AAATA
29605902 ATTTGCCCAC
Statistics
Matches: 183, Mismatches: 50, Indels: 44
0.66 0.18 0.16
Matches are distributed among these distances:
34 1 0.01
35 62 0.34
36 3 0.02
37 13 0.07
38 10 0.05
39 14 0.08
40 75 0.41
41 5 0.03
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (39 bp):
CCCAGCACTAGTCAGATAAACTGACAAATATAGTATGTG
Found at i:29605740 original size:75 final size:75
Alignment explanation
Indices: 29605527--29605899 Score: 446
Period size: 75 Copynumber: 5.0 Consensus size: 75
29605517 TAACAAAGTT
* * *
29605527 TTACACCTAACGCTAGTCGGATAAA-TCGACAAATATAATAATGTGCCCAGCACTAGTCAGATAA
1 TTACACCCAGCGCTAGTCGGATAAACT-GACAAATATAATGATGTGCCCAGCACTAGTCAGATAA
* *
29605591 ATTGATGAAAG
65 ACTGACGAAAG
* * * *
29605602 TTGCACCCAGCGCTAG-CGGATAAACCGACAAATATAGTGATGTACCCAGCACTAGTCAGATAAA
1 TTACACCCAGCGCTAGTCGGATAAACTGACAAATATAATGATGTGCCCAGCACTAGTCAGATAAA
29605666 CTGACGAAAG
66 CTGACGAAAG
* * * * * *
29605676 TTGCGCCCAACGCTAGTCAGATAAACTGACAAATATAATGATGTGCCCAACACTAGTCAAATAAA
1 TTACACCCAGCGCTAGTCGGATAAACTGACAAATATAATGATGTGCCCAGCACTAGTCAGATAAA
29605741 CTGACGAAAG
66 CTGACGAAAG
* * * * *
29605751 TTACACTCAGCGCTAGTCGAATAAA-TCAAAAAATATAATAATGTGCCCAGCACTAGTCAGATAA
1 TTACACCCAGCGCTAGTCGGATAAACT-GACAAATATAATGATGTGCCCAGCACTAGTCAGATAA
*
29605815 ACTGACAAAAG
65 ACTGACGAAAG
** * ** * * *
29605826 TTACGTCCAGCGCTAGTCGGATAAACCGATGAGTATAATGGTATGCCCAGCACTAGTCAGATAAA
1 TTACACCCAGCGCTAGTCGGATAAACTGACAAATATAATGATGTGCCCAGCACTAGTCAGATAAA
29605891 CTGACGAAA
66 CTGACGAAA
29605900 TAATTTGCCC
Statistics
Matches: 252, Mismatches: 42, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
74 66 0.26
75 186 0.74
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (75 bp):
TTACACCCAGCGCTAGTCGGATAAACTGACAAATATAATGATGTGCCCAGCACTAGTCAGATAAA
CTGACGAAAG
Found at i:29605843 original size:35 final size:35
Alignment explanation
Indices: 29605647--29605851 Score: 103
Period size: 35 Copynumber: 5.6 Consensus size: 35
29605637 AGTGATGTAC
* * *
29605647 CCAGCACTAGTCAGATAAACTGACGAAAGTTGCGC
1 CCAGCACTAGTCAGATAAACTGACAAAAGTTACGT
* * *
29605682 CCAACGCTAGTCAGATAAACTGACAAATA-TAATGATGT
1 CCAGCACTAGTCAGATAAACTGACAAA-AGT--T-ACGT
* * * *
29605720 GCCCAACACTAGTCAAATAAACTGACGAAAGTTAC-A
1 --CCAGCACTAGTCAGATAAACTGACAAAAGTTACGT
* * * * *
29605756 CTCAGCGCTAGTC-GAATAAA-TCAAAAAATATAATAATGT
1 C-CAGCACTAGTCAG-ATAAACTGACAAAA-GT--T-ACGT
29605795 GCCCAGCACTAGTCAGATAAACTGACAAAAGTTACGT
1 --CCAGCACTAGTCAGATAAACTGACAAAAGTTACGT
* *
29605832 CCAGCGCTAGTCGGATAAAC
1 CCAGCACTAGTCAGATAAAC
29605852 CGATGAGTAT
Statistics
Matches: 125, Mismatches: 27, Indels: 36
0.66 0.14 0.19
Matches are distributed among these distances:
34 6 0.05
35 58 0.46
36 1 0.01
37 6 0.05
38 4 0.03
39 1 0.01
40 41 0.33
41 8 0.06
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (35 bp):
CCAGCACTAGTCAGATAAACTGACAAAAGTTACGT
Found at i:29610328 original size:22 final size:21
Alignment explanation
Indices: 29610288--29610330 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29610278 TAATAAAATG
*
29610288 ATTTTTTAAAATTTTAATATT
1 ATTTTTTAAAATTTAAATATT
*
29610309 ATTTTTTAAAGTTTCAAATATT
1 ATTTTTTAAAATTT-AAATATT
29610331 TGTTCACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTTTAAAATTTAAATATT
Found at i:29626224 original size:3 final size:3
Alignment explanation
Indices: 29626216--29626249 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29626206 AATCTAATAC
29626216 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29626250 GTTGTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:29626254 original size:3 final size:3
Alignment explanation
Indices: 29626248--29626281 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29626238 ATTATTATTA
29626248 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
29626282 CATTATTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:29626359 original size:21 final size:23
Alignment explanation
Indices: 29626333--29626386 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
29626323 TGCACATTAA
29626333 ATATATATACAT-TTTTAC-AAT
1 ATATATATACATATTTTACTAAT
* *
29626354 ATATATACACATATTTTGCTAAT
1 ATATATATACATATTTTACTAAT
29626377 ATATATATAC
1 ATATATATAC
29626387 GTACATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.39
22 5 0.18
23 12 0.43
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATATATACATATTTTACTAAT
Found at i:29635069 original size:23 final size:23
Alignment explanation
Indices: 29635043--29635086 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29635033 TGGAAGCTTG
*
29635043 ATAAAAAAAGATTGGATTTTTCC
1 ATAAAAAAAGATTGCATTTTTCC
* *
29635066 ATAAAAGATGATTGCATTTTT
1 ATAAAAAAAGATTGCATTTTT
29635087 GTAGAAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (23 bp):
ATAAAAAAAGATTGCATTTTTCC
Found at i:29636831 original size:12 final size:12
Alignment explanation
Indices: 29636816--29636840 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29636806 CTGTGAGAGT
29636816 TTCTGATGATTG
1 TTCTGATGATTG
29636828 TTCTGATGATTG
1 TTCTGATGATTG
29636840 T
1 T
29636841 GATGGAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (12 bp):
TTCTGATGATTG
Found at i:29645434 original size:3 final size:3
Alignment explanation
Indices: 29645426--29645454 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29645416 AAAAATTCAT
29645426 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
29645455 TTTTGCAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:29660808 original size:24 final size:24
Alignment explanation
Indices: 29660793--29660844 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
29660783 AATCAAAGTC
29660793 AAATATATTATGCTAATAAATACT
1 AAATATATTATGCTAATAAATACT
* *
29660817 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATACT
29660841 AAAT
1 AAAT
29660845 CTTCTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATACT
Found at i:29664735 original size:24 final size:24
Alignment explanation
Indices: 29664708--29664759 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29664698 AATCAAAGTC
*
29664708 AAATACATTATGCTAATAAATACT
1 AAATACATTATACTAATAAATACT
* *
29664732 AAATATATTATACTCATAAATACT
1 AAATACATTATACTAATAAATACT
29664756 AAAT
1 AAAT
29664760 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATACATTATACTAATAAATACT
Found at i:29666799 original size:2 final size:2
Alignment explanation
Indices: 29666792--29666819 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29666782 ATAATCAAAG
29666792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29666820 AACAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29673657 original size:2 final size:2
Alignment explanation
Indices: 29673650--29673676 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29673640 CAAGAATCAA
29673650 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29673677 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29673858 original size:42 final size:42
Alignment explanation
Indices: 29673797--29673887 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
29673787 TGATCCAATC
* *
29673797 GAAAGCTAACGGTGGTTGGAGGCCTCGGCGTCATCGAAAATG
1 GAAAGCTAACGGTGGTTGGAGGCCTCGCCGCCATCGAAAATG
* ** * *
29673839 GAAAGCTAACGGTGTTTGGAGGGTTCGCCGCCATTGGAAATG
1 GAAAGCTAACGGTGGTTGGAGGCCTCGCCGCCATCGAAAATG
29673881 GAAAGCT
1 GAAAGCT
29673888 GCTAAGTGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (42 bp):
GAAAGCTAACGGTGGTTGGAGGCCTCGCCGCCATCGAAAATG
Found at i:29674556 original size:21 final size:22
Alignment explanation
Indices: 29674522--29674573 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
29674512 ATATGAATCA
29674522 TTTTTTTTAAAAAAATTATTAAC
1 TTTTTTTT-AAAAAATTATTAAC
* * *
29674545 TTTTTTTT-AAAATTTATTGAT
1 TTTTTTTTAAAAAATTATTAAC
29674566 TTTTTTTT
1 TTTTTTTT
29674574 GAATTTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.69
23 8 0.31
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTTTTAAAAAATTATTAAC
Found at i:29697923 original size:22 final size:24
Alignment explanation
Indices: 29697897--29697950 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
29697887 TTATAAATTC
29697897 AATTTAAA-AGATATAAT-ACAAT
1 AATTTAAACAGATATAATAACAAT
* *
29697919 AATTTCAAACATATTTAATAACAAT
1 AATTT-AAACAGATATAATAACAAT
29697944 AATTTAA
1 AATTTAA
29697951 TCATCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 3 0.11
24 9 0.33
25 10 0.37
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTTAAACAGATATAATAACAAT
Found at i:29699923 original size:8 final size:8
Alignment explanation
Indices: 29699891--29699921 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
29699881 TTTTAAATAA
29699891 TATTTTAG
1 TATTTTAG
29699899 TATTTTAG
1 TATTTTAG
*
29699907 TATTTTAT
1 TATTTTAG
29699915 TATTTTA
1 TATTTTA
29699922 TTTAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (8 bp):
TATTTTAG
Found at i:29706316 original size:29 final size:29
Alignment explanation
Indices: 29706284--29706367 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 29
29706274 TTACAAATTT
* *
29706284 AGAATTTAGTCCTTATACTTTTATTTTTA
1 AGAATTTAGTCCCTATACTTTTATTTTCA
29706313 AGAATTTAGTTAGTCCCTATACTTTTATTTTCA
1 AGAA--T--TTAGTCCCTATACTTTTATTTTCA
* *
29706346 AGAATTTAATCCCTCTACTTTT
1 AGAATTTAGTCCCTATACTTTT
29706368 CAAATTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
29 19 0.40
31 2 0.04
33 26 0.55
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.50
Consensus pattern (29 bp):
AGAATTTAGTCCCTATACTTTTATTTTCA
Found at i:29706334 original size:33 final size:33
Alignment explanation
Indices: 29706289--29706353 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
29706279 AATTTAGAAT
* *
29706289 TTAGTCCTTATACTTTTATTTTTAAGAATTTAG
1 TTAGTCCCTATACTTTTATTTTCAAGAATTTAG
29706322 TTAGTCCCTATACTTTTATTTTCAAGAATTTA
1 TTAGTCCCTATACTTTTATTTTCAAGAATTTA
29706354 ATCCCTCTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (33 bp):
TTAGTCCCTATACTTTTATTTTCAAGAATTTAG
Found at i:29706951 original size:21 final size:19
Alignment explanation
Indices: 29706916--29706976 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 19
29706906 TATATTACAA
*
29706916 TTTATAATCATTAAAATGTT
1 TTTATAATAATTAAAAT-TT
29706936 TTTATAACTAATTAAAATTT
1 TTTATAA-TAATTAAAATTT
**
29706956 TATTATTTTTAATTAAAATTT
1 T-TTA-TAATAATTAAAATTT
29706977 ATTGGATATG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 10 0.29
21 24 0.69
22 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTATAATAATTAAAATTT
Found at i:29718925 original size:31 final size:30
Alignment explanation
Indices: 29718867--29718925 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
29718857 GTGTAATTTG
* * *
29718867 ATACATGAATTTTGATTTTGGTGCAATTAT
1 ATACATGAATTTTGATCTCGATGCAATTAT
*
29718897 ATACATGAAATTTTGATCTCGATTCAATT
1 ATACATG-AATTTTGATCTCGATGCAATT
29718926 GTACACATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (30 bp):
ATACATGAATTTTGATCTCGATGCAATTAT
Found at i:29727450 original size:151 final size:152
Alignment explanation
Indices: 29727260--29727567 Score: 503
Period size: 151 Copynumber: 2.0 Consensus size: 152
29727250 TAAACCTGGT
* * * * * *
29727260 AAATTAAATCAAACGATAATTAAAAATGTGATCATGTGATGTTCTAAATTTCAGCCAAAGT-CTC
1 AAATTAAATCAAACAATAATTAAAAATATGATAATGTGATATTCTAAATTTCAACCAAAGTGAT-
29727324 GCATCATCACATTTTAACCAAATCTAAATTTAATGACTAAATTGAGAAAATGTAAT-AAAAAATT
65 GCATCATCACATTTTAACCAAATCTAAATTTAATGACTAAATTGAGAAAATGTAATAAAAAAATT
29727388 AAAAGTTAAGATGAAAAATTACC
130 AAAAGTTAAGATGAAAAATTACC
29727411 AAATTAAATCAAACAATAATTAAAAATATGATAATGTGATATTCTAAATTTCAACCAAAGTGATG
1 AAATTAAATCAAACAATAATTAAAAATATGATAATGTGATATTCTAAATTTCAACCAAAGTGATG
* * *
29727476 CATGATCGCATTTTAACTAAATCTAAATTTAATGACTAAATTGAGAAAATGTAATAAAAAAATTA
66 CATCATCACATTTTAACCAAATCTAAATTTAATGACTAAATTGAGAAAATGTAATAAAAAAATTA
*
29727541 AAATTTAAGATGAAAAATTACC
131 AAAGTTAAGATGAAAAATTACC
29727563 AAATT
1 AAATT
29727568 CAAGAATAAG
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
151 109 0.75
152 36 0.25
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.31
Consensus pattern (152 bp):
AAATTAAATCAAACAATAATTAAAAATATGATAATGTGATATTCTAAATTTCAACCAAAGTGATG
CATCATCACATTTTAACCAAATCTAAATTTAATGACTAAATTGAGAAAATGTAATAAAAAAATTA
AAAGTTAAGATGAAAAATTACC
Found at i:29727566 original size:22 final size:20
Alignment explanation
Indices: 29727533--29727572 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
29727523 AATGTAATAA
*
29727533 AAAAATTAAAATTTAAGATG
1 AAAAATTAAAATTCAAGATG
29727553 AAAAATTACCAAATTCAAGA
1 AAAAATTA--AAATTCAAGA
29727573 ATAAGTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAAATTAAAATTCAAGATG
Found at i:29728421 original size:3 final size:3
Alignment explanation
Indices: 29728406--29728440 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
29728396 CCAAAGACAC
*
29728406 CAA CAA AAA CAA CAA CAA CAA CAA CAA CAA -AA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
29728441 TGTTTTCTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:29732984 original size:20 final size:20
Alignment explanation
Indices: 29732961--29732999 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29732951 CATTGAGATT
29732961 TCGAAACATCTTGCATCAGG
1 TCGAAACATCTTGCATCAGG
29732981 TCGAAACATCTTGCATCAG
1 TCGAAACATCTTGCATCAG
29733000 AACCGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
TCGAAACATCTTGCATCAGG
Found at i:29736005 original size:6 final size:6
Alignment explanation
Indices: 29735989--29736027 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
29735979 TATTGGAGTG
29735989 TAAAAA T-AAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA
29736028 GCGAAGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:29736665 original size:24 final size:24
Alignment explanation
Indices: 29736609--29736708 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
29736599 CGGTGTTCCC
* * *
29736609 GGTGAAGGTGGCTTCACGATAGGA
1 GGTGATGGTGGGTTCACAATAGGA
* * *
29736633 GGCGTTGGTGGGTTCACAATAGGT
1 GGTGATGGTGGGTTCACAATAGGA
* * * *
29736657 GGTGATGGTGGTGGT-AGAATCGGC
1 GGTGATGGTGG-GTTCACAATAGGA
* *
29736681 GGTGTTGGTGGATTCACAATAGGA
1 GGTGATGGTGGGTTCACAATAGGA
29736705 GGTG
1 GGTG
29736709 GCAGAATCGG
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 53 0.95
25 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.44, T:0.26
Consensus pattern (24 bp):
GGTGATGGTGGGTTCACAATAGGA
Found at i:29736889 original size:144 final size:144
Alignment explanation
Indices: 29736729--29737024 Score: 565
Period size: 144 Copynumber: 2.1 Consensus size: 144
29736719 CGGTGTTGGT
29736729 GGGTTCACTATTGGTGGACTGGGGTAGACTGGTGGCTTTGGAGGCAGTGTTGGTGGTGATATGAC
1 GGGTTCACTATTGGTGGACTGGGGTAGACTGGTGGCTTTGGAGGCAGTGTTGGTGGTGATATGAC
29736794 CGGCGGTATTGGATAGTAAGGTGGCTTGGGTGTATATGGCGGAGGCTTCACAACCGGCGGTTTGG
66 CGGCGGTATTGGATAGTAAGGTGGCTTGGGTGTATATGGCGGAGGCTTCACAACCGGCGGTTTGG
*
29736859 GTGTATATGGTGGA
131 GTGTATATGGCGGA
29736873 GGGTTCACTATTGGTGGACTGGGGTAGACTGGTGGCTTTGGAGGCAGTGTTGGTGGTGATATGAC
1 GGGTTCACTATTGGTGGACTGGGGTAGACTGGTGGCTTTGGAGGCAGTGTTGGTGGTGATATGAC
*
29736938 CGGCGGTATTGGATAGTAAGGTGGCTTGGGTGTATATGGTGGAGGCTTCACAACCGGCGGTTTGG
66 CGGCGGTATTGGATAGTAAGGTGGCTTGGGTGTATATGGCGGAGGCTTCACAACCGGCGGTTTGG
29737003 GTGTATATGGCGGA
131 GTGTATATGGCGGA
*
29737017 GGCTTCAC
1 GGGTTCAC
29737025 AACCGGTGGT
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 149 1.00
ACGTcount: A:0.17, C:0.12, G:0.42, T:0.29
Consensus pattern (144 bp):
GGGTTCACTATTGGTGGACTGGGGTAGACTGGTGGCTTTGGAGGCAGTGTTGGTGGTGATATGAC
CGGCGGTATTGGATAGTAAGGTGGCTTGGGTGTATATGGCGGAGGCTTCACAACCGGCGGTTTGG
GTGTATATGGCGGA
Found at i:29737069 original size:36 final size:36
Alignment explanation
Indices: 29736956--29737108 Score: 168
Period size: 36 Copynumber: 4.3 Consensus size: 36
29736946 TTGGATAGTA
29736956 AGGTGGCTTGGGTGTATATGGTGGAGGCTTCACAAC
1 AGGTGGCTTGGGTGTATATGGTGGAGGCTTCACAAC
* * * *
29736992 CGGCGGTTTGGGTGTATATGGCGGAGGCTTCACAAC
1 AGGTGGCTTGGGTGTATATGGTGGAGGCTTCACAAC
* * * * *
29737028 CGGTGGTTTGGGTGTATACGGTGGAGGCTTTACAAT
1 AGGTGGCTTGGGTGTATATGGTGGAGGCTTCACAAC
* * * *
29737064 AGGTGGCTT-AG-GTACATAG-GGAGGCTTTACAAC
1 AGGTGGCTTGGGTGTATATGGTGGAGGCTTCACAAC
29737097 AGGTGGCTTGGG
1 AGGTGGCTTGGG
29737109 AGGATGCGGG
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
33 22 0.22
34 6 0.06
35 1 0.01
36 70 0.71
ACGTcount: A:0.19, C:0.14, G:0.39, T:0.27
Consensus pattern (36 bp):
AGGTGGCTTGGGTGTATATGGTGGAGGCTTCACAAC
Found at i:29737198 original size:42 final size:42
Alignment explanation
Indices: 29737128--29737210 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
29737118 GGGATGTTTT
* *
29737128 GGTGGCTTAGGGTGATATGGGGGTTTCACCACCGGAGGCTTA
1 GGTGGCTTAGGGTGATACGGGGGCTTCACCACCGGAGGCTTA
* * *
29737170 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTT
1 GGTGGCTTAGGGTGATACGGGGGCTTCACCACCGGAGGCTT
29737211 CACCACCGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.14, C:0.18, G:0.40, T:0.28
Consensus pattern (42 bp):
GGTGGCTTAGGGTGATACGGGGGCTTCACCACCGGAGGCTTA
Found at i:29737207 original size:15 final size:15
Alignment explanation
Indices: 29737187--29737226 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
29737177 TAGGGTGATA
29737187 CGGTGGCTTCACCAC
1 CGGTGGCTTCACCAC
29737202 CGGTGGCTTCACCAC
1 CGGTGGCTTCACCAC
29737217 CGGTGGCTTC
1 CGGTGGCTTC
29737227 GGTGGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.10, C:0.38, G:0.30, T:0.23
Consensus pattern (15 bp):
CGGTGGCTTCACCAC
Found at i:29737267 original size:57 final size:57
Alignment explanation
Indices: 29737152--29737267 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 57
29737142 ATATGGGGGT
*
29737152 TTCACCACCGGAGGCTTAGGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGC
1 TTCACCACCGGAGGCTTAGGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGAGGC
* * * * * * *
29737209 TTCACCACCGGTGGCTTCGGTGGTTTAGGGTGATATGGTGGGTTTACCGCGGGAGGC
1 TTCACCACCGGAGGCTTAGGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGAGGC
29737266 TT
1 TT
29737268 AGGTGGCTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.14, C:0.22, G:0.37, T:0.28
Consensus pattern (57 bp):
TTCACCACCGGAGGCTTAGGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGAGGC
Found at i:29739906 original size:22 final size:23
Alignment explanation
Indices: 29739868--29739914 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
29739858 ACTTACTTTA
* *
29739868 TTTTTATTTTAAGAAATTTAAAT
1 TTTTTAATTTAAGAAATATAAAT
29739891 TTTTTAATTTAA-AAATATAAAT
1 TTTTTAATTTAAGAAATATAAAT
29739913 TT
1 TT
29739915 AATTGTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTTAATTTAAGAAATATAAAT
Found at i:29742331 original size:18 final size:17
Alignment explanation
Indices: 29742310--29742352 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
29742300 TACTAAATGG
*
29742310 ATAAAGAATTTTAAAATT
1 ATAAA-AATTTTAAAATA
*
29742328 ATAAATATCTTTAAAATA
1 ATAAAAAT-TTTAAAATA
29742346 ATAAAAA
1 ATAAAAA
29742353 ATTCCAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAAAAATTTTAAAATA
Found at i:29747426 original size:10 final size:10
Alignment explanation
Indices: 29747387--29747432 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
29747377 TAAAAAAAAT
29747387 AAAATTCAATA
1 AAAATTC-ATA
29747398 AGAAATT-ATA
1 A-AAATTCATA
29747408 AAAATTTCATA
1 AAAA-TTCATA
29747419 AAAATTCA-A
1 AAAATTCATA
29747428 AAAAT
1 AAAAT
29747433 AACAAGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 9 0.28
10 10 0.31
11 8 0.25
12 5 0.16
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAATTCATA
Found at i:29751352 original size:24 final size:24
Alignment explanation
Indices: 29751324--29751369 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
29751314 CATTGGAAAT
*
29751324 GATGATAAGAAGAATGTACAGGAA
1 GATGATAAGAAGAATATACAGGAA
29751348 GATGATAAGAAGAATATACAGG
1 GATGATAAGAAGAATATACAGG
29751370 TATGTGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.28, T:0.17
Consensus pattern (24 bp):
GATGATAAGAAGAATATACAGGAA
Found at i:29754201 original size:57 final size:57
Alignment explanation
Indices: 29754113--29754227 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
29754103 AGCTAAAATA
*
29754113 TCAGTAGTCCAGTTCACCTCTCTTAGTACTTATTTAAAGAGTACTTTCAAATCACAC
1 TCAGTAGTCCAGTTCACCTCTCTTAGTACTTATTTAAAAAGTACTTTCAAATCACAC
* * *
29754170 TCAGTAGTCGAGTTCACCTCTCTTGGTACTTATTTAAAAAGTACTTTCCAATCACAC
1 TCAGTAGTCCAGTTCACCTCTCTTAGTACTTATTTAAAAAGTACTTTCAAATCACAC
29754227 T
1 T
29754228 GGCATAGTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (57 bp):
TCAGTAGTCCAGTTCACCTCTCTTAGTACTTATTTAAAAAGTACTTTCAAATCACAC
Found at i:29754430 original size:23 final size:23
Alignment explanation
Indices: 29754398--29754464 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
29754388 AGCTTGTAAA
29754398 ACACTGCATCTTCTAATACTTCT
1 ACACTGCATCTTCTAATACTTCT
*
29754421 ATACTGCATCTTCTAATACTTCT
1 ACACTGCATCTTCTAATACTTCT
*
29754444 ACACCGCATCTTCTAATACTT
1 ACACTGCATCTTCTAATACTT
29754465 GTTCCTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.27, C:0.30, G:0.04, T:0.39
Consensus pattern (23 bp):
ACACTGCATCTTCTAATACTTCT
Found at i:29760189 original size:24 final size:25
Alignment explanation
Indices: 29760108--29760222 Score: 110
Period size: 25 Copynumber: 4.6 Consensus size: 25
29760098 GCGGACACAC
* *
29760108 CACATCTCGTATGAGCTTACCAATT
1 CACAGCTCGTATGAGCTTACCGATT
*
29760133 TACAGCTCGTGA-GAGCTTACCGATT
1 CACAGCTCGT-ATGAGCTTACCGATT
*
29760158 CTCAGCTCGTATGAGCTT-CCGATT
1 CACAGCTCGTATGAGCTTACCGATT
* * *
29760182 CACTGCTCGTGA-AAGCATACCGATT
1 CACAGCTCGT-ATGAGCTTACCGATT
* *
29760207 CATAGCTCTTATGAGC
1 CACAGCTCGTATGAGC
29760223 ATACATGTAC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
24 20 0.28
25 51 0.71
26 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCGATT
Found at i:29760203 original size:49 final size:50
Alignment explanation
Indices: 29760113--29760222 Score: 143
Period size: 49 Copynumber: 2.2 Consensus size: 50
29760103 CACACCACAT
* * *
29760113 CTCGTATGAGCTTACCAATTTACAGCTCGTGAGAGCTTACCGATTC-TCAG
1 CTCGTATGAGCTTACCAATTCACAGCTCGTGAAAGCATACCGATTCAT-AG
* *
29760163 CTCGTATGAGCTT-CCGATTCACTGCTCGTGAAAGCATACCGATTCATAG
1 CTCGTATGAGCTTACCAATTCACAGCTCGTGAAAGCATACCGATTCATAG
*
29760212 CTCTTATGAGC
1 CTCGTATGAGC
29760223 ATACATGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
49 39 0.74
50 14 0.26
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (50 bp):
CTCGTATGAGCTTACCAATTCACAGCTCGTGAAAGCATACCGATTCATAG
Found at i:29770435 original size:49 final size:49
Alignment explanation
Indices: 29770376--29770582 Score: 121
Period size: 50 Copynumber: 4.2 Consensus size: 49
29770366 TTTATATTTA
29770376 AATATAAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGC
1 AATAT-AAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGC
* * * * *
29770426 AATATAAATACATGGTATTAAC--TA-AAAAATACAAAAAAACATATAA-A-T--
1 AATATAAATAC-T--T-TAAACATTATTATAATA-TAATAAA-ATATAATAGTGC
* * * * * * **
29770474 -ATATAAA-ATTTTATAATATGTATTATTAATAT-CTCAAAT-TTATATTTA
1 AATATAAATACTTTA-AACAT-TATTA-TAATATAATAAAATATAATAGTGC
29770522 AATATAAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGC
1 AATAT-AAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGC
29770572 AATATAAATAC
1 AATATAAATAC
29770583 ATGGTATTAA
Statistics
Matches: 113, Mismatches: 23, Indels: 43
0.63 0.13 0.24
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 2 0.02
45 4 0.04
46 6 0.05
47 8 0.07
48 10 0.09
49 26 0.23
50 29 0.26
51 13 0.12
52 7 0.06
53 4 0.04
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.36
Consensus pattern (49 bp):
AATATAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGC
Found at i:29770464 original size:146 final size:147
Alignment explanation
Indices: 29770301--29770595 Score: 583
Period size: 146 Copynumber: 2.0 Consensus size: 147
29770291 AAATTTATTT
29770301 TAAAAAATACAACAAAAACATATAAATATATAAAATTTTATAATATGTATTATTAATATCTCAAA
1 TAAAAAATACAACAAAAACATATAAATATATAAAATTTTATAATATGTATTATTAATATCTCAAA
29770366 TTTATATTTAAATATAAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGCAATAT
66 TTTATATTTAAATATAAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGCAATAT
29770431 AAATACATGGTATTAAC
131 AAATACATGGTATTAAC
29770448 TAAAAAATACAA-AAAAACATATAAATATATAAAATTTTATAATATGTATTATTAATATCTCAAA
1 TAAAAAATACAACAAAAACATATAAATATATAAAATTTTATAATATGTATTATTAATATCTCAAA
29770512 TTTATATTTAAATATAAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGCAATAT
66 TTTATATTTAAATATAAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGCAATAT
29770577 AAATACATGGTATTAAC
131 AAATACATGGTATTAAC
29770594 TA
1 TA
29770596 TTTTCAAAAT
Statistics
Matches: 148, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 136 0.92
147 12 0.08
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.37
Consensus pattern (147 bp):
TAAAAAATACAACAAAAACATATAAATATATAAAATTTTATAATATGTATTATTAATATCTCAAA
TTTATATTTAAATATAAAATACTTTAAACATTATTATAATATAATAAAATATAATAGTGCAATAT
AAATACATGGTATTAAC
Found at i:29778497 original size:35 final size:34
Alignment explanation
Indices: 29778444--29778541 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 34
29778434 CTTTTTCTTT
*
29778444 TTTTGAAAACACGAAATTTTTTTTAAAATACA-AGAA
1 TTTTG-AAACAC-AAATTTTTTTTAAAA-ACACAAAA
29778480 TTTTAGAAACACAAATTTTTTTTTAAAAACACGAAAA
1 TTTT-GAAACACAAA-TTTTTTTTAAAAACAC-AAAA
29778517 TTTTGAAACAC-AA-TTTTTTTAAAAA
1 TTTTGAAACACAAATTTTTTTTAAAAA
29778542 GTACCGTATT
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
33 12 0.21
35 8 0.14
36 29 0.51
37 8 0.14
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (34 bp):
TTTTGAAACACAAATTTTTTTTAAAAACACAAAA
Found at i:29778520 original size:20 final size:19
Alignment explanation
Indices: 29778441--29778520 Score: 58
Period size: 20 Copynumber: 4.2 Consensus size: 19
29778431 CAACTTTTTC
* *
29778441 TTTTTTTGAAAACACGAAA
1 TTTTTTTAAAAACACAAAA
* *
29778460 TTTTTTTTAAAATACAAGAA
1 TTTTTTTAAAAACACAA-AA
* *
29778480 ---TTTTAGAAACACAAATT
1 TTTTTTTAAAAACACAAA-A
29778497 TTTTTTTAAAAACACGAAAA
1 TTTTTTTAAAAACAC-AAAA
29778517 TTTT
1 TTTT
29778521 GAAACACAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
16 1 0.02
17 11 0.24
19 14 0.30
20 17 0.37
21 3 0.07
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (19 bp):
TTTTTTTAAAAACACAAAA
Found at i:29778649 original size:21 final size:20
Alignment explanation
Indices: 29778620--29778659 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29778610 GACACGAAAA
29778620 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACACAAAATTTG
*
29778640 TTTTTGAAAACATAAAATTT
1 TTTTT-AAAACACAAAATTT
29778660 TTGATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTTAAAACACAAAATTTG
Found at i:29778713 original size:17 final size:17
Alignment explanation
Indices: 29778687--29779009 Score: 150
Period size: 17 Copynumber: 17.8 Consensus size: 17
29778677 ACGAGGATTT
29778687 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * * *
29778704 TTTATGAAACATGGTCAAT
1 TTTTTGAAACA-CG-AAAA
*
29778723 TTTTTAAAAACACGAAAA
1 TTTTT-GAAACACGAAAA
* *
29778741 TTTTTGAAAGACGAAATTT
1 TTTTTGAAACACGAAA--A
* *
29778760 TTTTTAAAACACGGAAA
1 TTTTTGAAACACGAAAA
*
29778777 TTTATGAAACACGGAAAA
1 TTTTTGAAACAC-GAAAA
* *
29778795 TTTTTTTTTAAAACAAGAAAA
1 ----TTTTTGAAACACGAAAA
* * *
29778816 TTTTCGAAATACGAGAA
1 TTTTTGAAACACGAAAA
* *
29778833 TATTTGAAAACACAGGAAA
1 TTTTTG-AAACAC-GAAAA
* *
29778852 -TCTTGAAAACACAAAAA
1 TTTTTG-AAACACGAAAA
* *
29778869 TTTTTGACACACTG-GAA
1 TTTTTGAAACAC-GAAAA
*
29778886 -TTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
* *
29778903 TTTTTGAAACATGAGAA
1 TTTTTGAAACACGAAAA
* *
29778920 TTTTTGAAAACTCGAAATT
1 TTTTTG-AAACACGAAA-A
* *
29778939 TTTTTAAAAAAC-AAGGAA
1 TTTTTGAAACACGAA--AA
29778957 TTTTTTGAAACACGAGAAA
1 -TTTTTGAAACACGA-AAA
29778976 TTATTTTGAAAACACGAAAA
1 -T-TTTTG-AAACACGAAAA
29778996 TTTTTGAAACACGA
1 TTTTTGAAACACGA
29779010 TTTTTTTAAG
Statistics
Matches: 224, Mismatches: 56, Indels: 52
0.67 0.17 0.16
Matches are distributed among these distances:
16 6 0.03
17 85 0.38
18 52 0.23
19 44 0.20
20 14 0.06
21 14 0.06
22 9 0.04
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:29778713 original size:37 final size:37
Alignment explanation
Indices: 29778670--29778833 Score: 165
Period size: 37 Copynumber: 4.4 Consensus size: 37
29778660 TTGATAAAAA
* *
29778670 ATGAAACACGAGGATTTTTTTTGAAACACGAAAATTT
1 ATGAAACACGAGAATTTTTTTTAAAACACGAAAATTT
* *
29778707 ATGAAACATG-GTCAA-TTTTTTAAAAACACGAAAATTT
1 ATGAAACACGAG--AATTTTTTTTAAAACACGAAAATTT
* * *
29778744 TTGAAAGACGA-AATTTTTTTTAAAACACGGAAATTT
1 ATGAAACACGAGAATTTTTTTTAAAACACGAAAATTT
* *
29778780 ATGAAACACGGAAAATTTTTTTTTAAAACAAGAAAATTT
1 ATGAAACAC-GAGAA-TTTTTTTTAAAACACGAAAATTT
*
29778819 -TCGAAATACGAGAAT
1 AT-GAAACACGAGAAT
29778834 ATTTGAAAAC
Statistics
Matches: 104, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
35 2 0.02
36 28 0.27
37 39 0.38
38 8 0.08
39 27 0.26
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (37 bp):
ATGAAACACGAGAATTTTTTTTAAAACACGAAAATTT
Found at i:29778770 original size:73 final size:74
Alignment explanation
Indices: 29778683--29778829 Score: 197
Period size: 73 Copynumber: 2.0 Consensus size: 74
29778673 AAACACGAGG
* * ** * *
29778683 ATTTTTTTTGAAACACGAAAATTTATGAAACATGGTCAA-TTTTTTAAAAACACGAAAATTTTTG
1 ATTTTTTTTAAAACACGAAAATTTATGAAACACGGAAAATTTTTTTAAAAACAAGAAAATTTTCG
29778747 AAAGACGAA
66 AAAGACGAA
* *
29778756 ATTTTTTTTAAAACACGGAAATTTATGAAACACGGAAAATTTTTTTTTAAAACAAGAAAATTTTC
1 ATTTTTTTTAAAACACGAAAATTTATGAAACACGGAAAA-TTTTTTTAAAAACAAGAAAATTTTC
*
29778821 GAAATACGA
65 GAAAGACGA
29778830 GAATATTTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 34 0.54
75 29 0.46
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (74 bp):
ATTTTTTTTAAAACACGAAAATTTATGAAACACGGAAAATTTTTTTAAAAACAAGAAAATTTTCG
AAAGACGAA
Found at i:29778875 original size:18 final size:18
Alignment explanation
Indices: 29778835--29779004 Score: 80
Period size: 18 Copynumber: 9.4 Consensus size: 18
29778825 TACGAGAATA
*
29778835 TTTGAAAACACAGGAAA-T
1 TTTGAAAACACA-AAAATT
*
29778853 CTTGAAAACACAAAAATT
1 TTTGAAAACACAAAAATT
* ***
29778871 TTTG-ACACACTGGAA-T
1 TTTGAAAACACAAAAATT
* *
29778887 TTTGAAAACACGAAGATT
1 TTTGAAAACACAAAAATT
** *
29778905 TTTG-AAACATGAGAATT
1 TTTGAAAACACAAAAATT
* * *
29778922 TTTGAAAACTCGAAATTT
1 TTTGAAAACACAAAAATT
* * *
29778940 TTTTAAAAAACAAGGAATTT
1 TTTGAAAACACAA--AAATT
*
29778960 TTTG-AAACACGAGAAATTAT
1 TTTGAAAACAC-A-AAAAT-T
*
29778980 TTTGAAAACACGAAAATT
1 TTTGAAAACACAAAAATT
29778998 TTTGAAA
1 TTTGAAA
29779005 CACGATTTTT
Statistics
Matches: 115, Mismatches: 27, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
16 5 0.04
17 30 0.26
18 46 0.40
19 13 0.11
20 14 0.12
21 7 0.06
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (18 bp):
TTTGAAAACACAAAAATT
Found at i:29778982 original size:21 final size:20
Alignment explanation
Indices: 29778958--29779009 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
29778948 AACAAGGAAT
*
29778958 TTTTTGAAACACGA-GAAAT
1 TTTTTGAAACACGACGAAAA
29778977 TATTTTGAAA-AC-ACGAAAA
1 T-TTTTGAAACACGACGAAAA
29778996 TTTTTGAAACACGA
1 TTTTTGAAACACGA
29779010 TTTTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 9 0.32
19 10 0.36
20 9 0.32
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (20 bp):
TTTTTGAAACACGACGAAAA
Found at i:29778988 original size:38 final size:37
Alignment explanation
Indices: 29778739--29779009 Score: 115
Period size: 38 Copynumber: 7.4 Consensus size: 37
29778729 AAAACACGAA
* * * *
29778739 AATTTTTGAAAGAC--GAAATTTTTTTTAAAACACGG
1 AATTTTTGAAACACGAGAAATTATTTTGAAAACAAGG
* * * *
29778774 AAATTTATGAAACACG-GAAAATTTTTTTTTAAAACAAGAA
1 -AATTTTTGAAACACGAG-AAA-TTATTTTGAAAACAAG-G
* *
29778814 AATTTTCGAAATACGAG-AA-TA-TTTGAAAACACAGG
1 AATTTTTGAAACACGAGAAATTATTTTGAAAACA-AGG
* * * * *
29778849 AAATCTTGAAAACAC-A-AAAAT-TTTTG-ACACACTGG
1 AATTTTTG-AAACACGAGAAATTATTTTGAAAACA-AGG
* *
29778884 AA-TTTTGAAAACACGA-AGA-T-TTTTG-AAACATGAG
1 AATTTTTG-AAACACGAGAAATTATTTTGAAAACAAG-G
** * *
29778918 AATTTTTGAAA-ACTCGAAATTTTTTTAAAAAACAAGG
1 AATTTTTGAAACACGAGAAATTATTTT-GAAAACAAGG
* *
29778955 AATTTTTTGAAACACGAGAAATTATTTTGAAAACACGAA
1 AA-TTTTTGAAACACGAGAAATTATTTTGAAAACAAG-G
29778994 AATTTTTGAAACACGA
1 AATTTTTGAAACACGA
29779010 TTTTTTTAAG
Statistics
Matches: 184, Mismatches: 30, Indels: 40
0.72 0.12 0.16
Matches are distributed among these distances:
33 4 0.02
34 29 0.16
35 35 0.19
36 29 0.16
37 4 0.02
38 41 0.22
39 41 0.22
40 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (37 bp):
AATTTTTGAAACACGAGAAATTATTTTGAAAACAAGG
Found at i:29779754 original size:4 final size:4
Alignment explanation
Indices: 29779747--29779784 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
29779737 TTCTTCCTTC
29779747 TTCT TTCT TT-T TTCT CTT-T TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTC
29779785 CCGTTCAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 5 0.16
4 24 0.77
5 2 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:29779757 original size:19 final size:19
Alignment explanation
Indices: 29779733--29779781 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
29779723 TTTGCTCCTT
29779733 TTTTTTCTTCCTTCTTCTTTC
1 TTTTTTC-T-CTTCTTCTTTC
*
29779754 TTTTTTCTCTTTTTCTTTC
1 TTTTTTCTCTTCTTCTTTC
29779773 TTTCTTTCT
1 TTT-TTTCT
29779782 TTCCCGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.50
20 6 0.23
21 7 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTCTCTTCTTCTTTC
Found at i:29779760 original size:7 final size:7
Alignment explanation
Indices: 29779733--29779784 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
29779723 TTTGCTCCTT
29779733 TTTTTTC
1 TTTTTTC
**
29779740 TTCCTTC
1 TTTTTTC
*
29779747 TTCTTTC
1 TTTTTTC
29779754 TTTTTTC
1 TTTTTTC
29779761 TCTTTTTC
1 T-TTTTTC
29779769 TTTCTTTC
1 TTT-TTTC
29779777 TTTCTTTC
1 TTT-TTTC
29779785 CCGTTCAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
7 20 0.51
8 19 0.49
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTTC
Found at i:29779764 original size:23 final size:23
Alignment explanation
Indices: 29779730--29779784 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
29779720 TTTTTTGCTC
*
29779730 CTTTTTTTTCTTCCTTC-TTCTTT
1 CTTTTTTCTCTT-CTTCTTTCTTT
*
29779753 CTTTTTTCTCTTTTTCTTTCTTT
1 CTTTTTTCTCTTCTTCTTTCTTT
29779776 CTTTCTTTC
1 CTTT-TTTC
29779785 CCGTTCAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 21 0.75
24 4 0.14
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (23 bp):
CTTTTTTCTCTTCTTCTTTCTTT
Found at i:29780298 original size:29 final size:31
Alignment explanation
Indices: 29780260--29780321 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
29780250 AAAAGTGCAA
29780260 TTTTAGGAAAATAT-GGGGCCAAAAAGTAAT
1 TTTTAGGAAAATATAGGGGCCAAAAAGTAAT
* * * *
29780290 TTTTA-GAAAGTTTAGGGGCCCAAATGTAAT
1 TTTTAGGAAAATATAGGGGCCAAAAAGTAAT
29780320 TT
1 TT
29780322 ACAAATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (31 bp):
TTTTAGGAAAATATAGGGGCCAAAAAGTAAT
Found at i:29780691 original size:13 final size:13
Alignment explanation
Indices: 29780673--29780697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29780663 TCTAAAATTA
29780673 TTATATTTTTTGT
1 TTATATTTTTTGT
29780686 TTATATTTTTTG
1 TTATATTTTTTG
29780698 AAAGCCTAAA
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTATATTTTTTGT
Found at i:29781104 original size:155 final size:153
Alignment explanation
Indices: 29780768--29781310 Score: 664
Period size: 155 Copynumber: 3.5 Consensus size: 153
29780758 TGAGTTGACC
* * ** * *
29780768 TTTGAAAAATAGAAATTGAAAAATACCTCGGCATATGACCCAAGGCTCAATTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAAATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTCGCAAT
* * * * *
29780833 ATAAGTTGATTTTTTTGAAAACCAAAAATTGAAAAATACATC-GACGTGACTCGAGGCTCAACTC
66 ATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAG-CGTGACCCGAGGCTCAACTC
*
29780897 ACCTCTCGCAATATGAGTT-A-ATT
129 ACCTCTCGCAATATGAGTTGATTTT
* **
29780920 TTTG-AAAACAGAAATTTAAAAGAAATACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAA-TT-GAA-AAATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTCGC
* * *
29780984 AATATGAGTTGA-TTTTTGAAAAACGGAAATTTAAAAAATACCTCAGTGTGTAACCCGAGGCTCA
63 AATATGAGTTGATTTTTTGAAAAACAGAAA-TTGAAAAATACCTCAGCGTG--ACCCGAGGCTCA
29781048 ACTCACCTCTCGCAATATGAGTTGATTTT
125 ACTCACCTCTCGCAATATGAGTTGATTTT
* * * * *
29781077 TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGATCCGAGGCTCAACTCAACTCTCGCATT
1 TTTGAAAAACAGAAATTGAAAAATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTCGCAAT
*
29781142 ATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTACGACCCGAGGCCCAACT
66 ATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGT--GACCCGAGGCTCAACT
29781207 CACCTCTCGCAATATGAGTTGATTTT
128 CACCTCTCGCAATATGAGTTGATTTT
** * * *
29781233 TTTGAAAAGTAAAAATTGAAAAGAATACCTCGGCATGCGACCCGAGGCTCAACTCACCTCTTGCA
1 TTTGAAAAACAGAAATTG-AAA-AATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTCGCA
*
29781298 TTATGAGTTGATT
64 ATATGAGTTGATT
29781311 GATTTTTTTT
Statistics
Matches: 338, Mismatches: 37, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
151 9 0.03
152 20 0.06
153 17 0.05
154 47 0.14
155 83 0.25
156 75 0.22
157 29 0.09
158 58 0.17
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (153 bp):
TTTGAAAAACAGAAATTGAAAAATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
CTCTCGCAATATGAGTTGATTTT
Found at i:29781216 original size:233 final size:231
Alignment explanation
Indices: 29780756--29781310 Score: 717
Period size: 233 Copynumber: 2.4 Consensus size: 231
29780746 CTTCTCAAAT
** * * * *
29780756 TATGAGTTGACCTTTGAAAAATAGAAA-TTGAAAAATACCTCGGCATATGACCCAAGGCTCAATT
1 TATGAGTTGATTTTTGAAAAATAGAAATTTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACT
* *
29780820 CACCTCTCGCAATATAAGTTGATTTTTTTGAAAACCAAAAATTGAAAAATACATCGACGTGACTC
66 CACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAAATACATCGACGTGACTC
*
29780885 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAACAGAAATTTAAAAGAAATACCT
131 GAGGCTCAACTCAACTCTCGCAATATGAGTTAATTTTTGAAAACAGAAATTTAAAAGAAATACCT
* * *
29780950 CAGTGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
196 CAGCGTACGACCCGAGGCCCAACTCACCTCTCGCAA
** * ** *
29780986 TATGAGTTGATTTTTGAAAAACGGAAATTTAAAAAATACCTCAGTGTGTAACCCGAGGCTCAACT
1 TATGAGTTGATTTTTGAAAAATAGAAATTTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACT
* *
29781051 CACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTC-AGCGTGTGA
66 CACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAAATACATCGA-C--GTGA
* * *
29781115 -TCCGAGGCTCAACTCAACTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAA-TT-GAA-A
128 CT-CGAGGCTCAACTCAACTCTCGCAATATGAGTT-A-ATTTTTG-AAAACAGAAATTTAAAAGA
29781176 AATACCTCAGCGTACGACCCGAGGCCCAACTCACCTCTCGCAA
189 AATACCTCAGCGTACGACCCGAGGCCCAACTCACCTCTCGCAA
* * * *
29781219 TATGAGTTGATTTTTTTGAAAAGTAAAAATTGAAAAGAATACCTCGGCATGCGACCCGAGGCTCA
1 TATGAGTTGA--TTTTTGAAAAATAGAAATTTAAAA-AATACCTCGGCATGTGACCCGAGGCTCA
* *
29781284 ACTCACCTCTTGCATTATGAGTTGATT
63 ACTCACCTCTCGCAATATGAGTTGATT
29781311 GATTTTTTTT
Statistics
Matches: 279, Mismatches: 35, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
230 24 0.09
231 81 0.29
232 1 0.00
233 85 0.30
234 3 0.01
235 27 0.10
236 58 0.21
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (231 bp):
TATGAGTTGATTTTTGAAAAATAGAAATTTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAAATACATCGACGTGACTC
GAGGCTCAACTCAACTCTCGCAATATGAGTTAATTTTTGAAAACAGAAATTTAAAAGAAATACCT
CAGCGTACGACCCGAGGCCCAACTCACCTCTCGCAA
Found at i:29781327 original size:80 final size:78
Alignment explanation
Indices: 29780768--29781310 Score: 670
Period size: 78 Copynumber: 7.0 Consensus size: 78
29780758 TGAGTTGACC
* * * ** * *
29780768 TTTGAAAAATAGAAATTGAAAAATACCTCGGCATATGACCCAAGGCTCAATTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
*
29780833 ATAAGTTGATTTT
66 ATGAGTTGATTTT
* * * *
29780846 TTTGAAAACCAAAAATTGAAAAATACATC-GACGT--GACTCGAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAATTGAAAAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
*
29780908 TATGAGTT-A-ATT
65 TATGAGTTGATTTT
* *
29780920 TTTG-AAAACAGAAATTTAAAAGAAATACCTCAGTGTGCGACCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAA-TT-GAA-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGC
29780984 AATATGAGTTGA--TT
63 AATATGAGTTGATTTT
* * * **
29780998 TTTGAAAAACGGAAATTTAAAAAATACCTCAGTGTGTAACCCGAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAA-TTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
29781063 TATGAGTTGATTTT
65 TATGAGTTGATTTT
* * * *
29781077 TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGATCCGAGGCTCAACTCAACTCTCGCATT
1 TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
29781142 ATGAGTTGATTTT
66 ATGAGTTGATTTT
* *
29781155 TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTACGACCCGAGGCCCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
29781220 ATGAGTTGATTTT
66 ATGAGTTGATTTT
** * * * *
29781233 TTTGAAAAGTAAAAATTGAAAAGAATACCTCGGCATGCGACCCGAGGCTCAACTCACCTCTTGCA
1 TTTGAAAAACAGAAATTG-AAA-AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
*
29781298 TTATGAGTTGATT
64 ATATGAGTTGATT
29781311 GATTTTTTTT
Statistics
Matches: 411, Mismatches: 41, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
73 8 0.02
74 8 0.02
75 3 0.01
76 42 0.10
77 54 0.13
78 215 0.52
79 32 0.08
80 49 0.12
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (78 bp):
TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATTTT
Found at i:29783051 original size:19 final size:20
Alignment explanation
Indices: 29783022--29783059 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
29783012 GTACAAAGAT
29783022 TTTTTTAAATTTATTTTTAG
1 TTTTTTAAATTTATTTTTAG
29783042 TTTTTT-AATTTATTTTTA
1 TTTTTTAAATTTATTTTTA
29783060 ATTTGGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTTAAATTTATTTTTAG
Found at i:29784623 original size:19 final size:19
Alignment explanation
Indices: 29784599--29784635 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29784589 TCTCAGAAAC
29784599 ACTTTTG-GAACAAAAAAAT
1 ACTTTTGAG-ACAAAAAAAT
29784618 ACTTTTGAGACAAAAAAA
1 ACTTTTGAGACAAAAAAA
29784636 AATATTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (19 bp):
ACTTTTGAGACAAAAAAAT
Found at i:29785605 original size:14 final size:15
Alignment explanation
Indices: 29785578--29785607 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29785568 ATATATTTAA
29785578 TCATTTTTATTATAT
1 TCATTTTTATTATAT
29785593 TCATTTTTA-TATAT
1 TCATTTTTATTATAT
29785607 T
1 T
29785608 TGACGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TCATTTTTATTATAT
Found at i:29793245 original size:76 final size:78
Alignment explanation
Indices: 29793156--29793343 Score: 310
Period size: 78 Copynumber: 2.4 Consensus size: 78
29793146 AAGTCAGATA
29793156 TAAACATAACCTACATGGATCGGATTAAATTTTTT-AATA-TTTTTATCACATGATGAAAATTAA
1 TAAACATAACCTACATGGATCGGATTAAATTTTTTAAATATTTTTTATCACATGATGAAAATTAA
29793219 ATCAAAATAAATC
66 ATCAAAATAAATC
**
29793232 TAAACATAACCTACATGGATCGGATTATTTTTTTTAAATATTTTTTATCACATGATGAAAATTAA
1 TAAACATAACCTACATGGATCGGATTAAATTTTTTAAATATTTTTTATCACATGATGAAAATTAA
29793297 ATCAAAATAAATC
66 ATCAAAATAAATC
* * *
29793310 TAAACATAACCTATATGGATCAGACT-AATTTTTT
1 TAAACATAACCTACATGGATCGGATTAAATTTTTT
29793344 CATCAATCAA
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
76 33 0.32
77 10 0.10
78 60 0.58
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (78 bp):
TAAACATAACCTACATGGATCGGATTAAATTTTTTAAATATTTTTTATCACATGATGAAAATTAA
ATCAAAATAAATC
Found at i:29793673 original size:31 final size:31
Alignment explanation
Indices: 29793638--29793696 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
29793628 ATAGTCATTG
*
29793638 AATTATTTAAAAGATTTCATTTAAGTTATTA
1 AATTATTCAAAAGATTTCATTTAAGTTATTA
* * *
29793669 AATTATTCGAAAGTTTTTATTTAAGTTA
1 AATTATTCAAAAGATTTCATTTAAGTTA
29793697 CTAGGCTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.49
Consensus pattern (31 bp):
AATTATTCAAAAGATTTCATTTAAGTTATTA
Found at i:29796319 original size:45 final size:45
Alignment explanation
Indices: 29796192--29797471 Score: 1248
Period size: 45 Copynumber: 28.8 Consensus size: 45
29796182 TATCTTCAAC
** * * *
29796192 CTACTTCGCTGCCGTTACAGGAAGACAAGACCTGCTAT-TTTCAA
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *** * * *
29796236 CTTACTTCACT-ACTGCACAGGGAGATAAG-GCTGCTATCTTTGAT
1 C-TACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
29796280 CTACTTCACTGCCAATACAGAAAAATAAGATCTGCTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* ** *
29796325 CTACTTCGCTGCCAATATAAAAAGACAAGAT-TCGTTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCT-GCTATCTTTGAT
* * * *
29796370 CTACTTCACTACCAATATAGGAAGACAAGATCTACTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
29796415 CTACTTC-ATGCCAATATAGGAAGACAAGATCTGTTAT-TTTCGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTT-GAT
* ** * * * * *
29796459 TTACTTTACTACCAATATAGGAAGACAAGATCCGGTATCTTCGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
29796504 CTACTTCACTACCAATATAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
29796549 CTACTTCACTACCAATATAGGAAGACAAGATCTGTTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * * *
29796594 CTACTTCACTGCTAATACAGGAAGACAAGATCTGTTTTCTTCGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * * *
29796639 ATACTTCGCTACCAATATAGGAAGACAAGATTTACTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * * * *
29796684 CTACTTCGCTACTAATATAAGAAGACAAGATCTGTTTTCTTCT-AT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT-TGAT
* * * * * *
29796729 CTACTTTGCTACCAATATAGGAAGATAAGATTTGATATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
29796774 CTACTTCGCTGTCAATACAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * ** * *
29796819 CTATTTCACTATCAATATAGGAAGATAAGATCTGCTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
29796864 CTACTTCGGTGCCAATTCAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
29796909 CTACTTCACTACCAATATAGGAAGACAAGA--T-CTATC--TG--
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
*
29796947 CT--TT-GCTGCCAATACAGGAAGACAAAATCTGCTATCTTT-AGT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGA-T
* * * * ** * * * *
29796989 CTGCTCCGCTACAAACCCAGGGAGGCAAG-GCTGGTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
29797033 CTACTTCGCTGCCAATACAGGAAGACAATATATGTTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* ** * * * *
29797078 CTATTTCATTGCCAATACAAGAAGATAAAATCTGCTATATTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
*
29797123 TTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
29797168 CTACTTCGCTGCCAATACAGGAAGACAATATATGTTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
** * * *
29797213 CTACTTCATTGCCAATACAAGAAGACAAAATCTGCTATATTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
29797258 TTACTTCGCTGCTAATACAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
29797303 CTACTTCGCTACCAATACAGGAAAACAAGATCTGCTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
29797348 CTACTTCACTGCCAGTACAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
29797393 CTACTTCGCTACTAATATAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
29797438 CTACTTCACTGCCAGTACAGGAAGACAAGATCTG
1 CTACTTCGCTGCCAATACAGGAAGACAAGATCTG
29797472 TTATTTTCAA
Statistics
Matches: 1017, Mismatches: 195, Indels: 47
0.81 0.15 0.04
Matches are distributed among these distances:
35 19 0.02
36 2 0.00
37 1 0.00
38 7 0.01
40 2 0.00
42 6 0.01
43 20 0.02
44 97 0.10
45 859 0.84
46 4 0.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (45 bp):
CTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
Found at i:29798524 original size:19 final size:19
Alignment explanation
Indices: 29798500--29798538 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29798490 TTTACAGGGT
29798500 TTGGCAAATCTTTACCATC
1 TTGGCAAATCTTTACCATC
*
29798519 TTGGCAAATCTTTACTATC
1 TTGGCAAATCTTTACCATC
29798538 T
1 T
29798539 ATCTCACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (19 bp):
TTGGCAAATCTTTACCATC
Found at i:29799326 original size:21 final size:21
Alignment explanation
Indices: 29799287--29799326 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29799277 AAGAAAATCC
*
29799287 AAAAGAATGAATAATTATTTG
1 AAAAGAATGAATAAATATTTG
29799308 AAAAGAATGAA-AGAATATT
1 AAAAGAATGAATA-AATATT
29799327 GGCTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAAGAATGAATAAATATTTG
Found at i:29801243 original size:19 final size:20
Alignment explanation
Indices: 29801219--29801265 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
29801209 TAACGGTATT
* *
29801219 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
29801238 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
29801258 -AATGCAAA
1 TAATGCAAA
29801266 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:29801725 original size:16 final size:16
Alignment explanation
Indices: 29801700--29801734 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29801690 ATCTATGATG
*
29801700 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
*
29801716 AAATGTCATGCAGCCA
1 AAATGCCATGCAGCCA
29801732 AAA
1 AAA
29801735 CAAAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:29807728 original size:31 final size:32
Alignment explanation
Indices: 29807690--29807756 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 32
29807680 ATATAAAATA
29807690 TAAAATTTAA-AT-AATTAATATAAATTAT-TTT
1 TAAAATTTAATATGAA-T-ATATAAATTATATTT
*
29807721 TAAAATTTAATTTGAATATATAAATTATATTT
1 TAAAATTTAATATGAATATATAAATTATATTT
29807753 TAAA
1 TAAA
29807757 TATTAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 21 0.66
32 9 0.28
33 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
TAAAATTTAATATGAATATATAAATTATATTT
Found at i:29807920 original size:31 final size:31
Alignment explanation
Indices: 29807885--29807962 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
29807875 TTAAATACCT
29807885 TTTTAATTAAT-TAATATAAAT-TATTTATATA
1 TTTTAATTAATAT-ATATAAATATATTTATA-A
*
29807916 TTTTAATTTATATATATAAATCATATTTATAA
1 TTTTAATTAATATATATAAAT-ATATTTATAA
*
29807948 TTTATAATAAATATA
1 TTT-TAATTAATATA
29807963 AATAGGGGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 18 0.45
32 5 0.12
33 17 0.43
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTTAATTAATATATATAAATATATTTATAA
Found at i:29816507 original size:39 final size:39
Alignment explanation
Indices: 29816462--29816540 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
29816452 TCTTTTATGG
29816462 TGAGCTAGTTTCTAGCTATAAGATGATGAAATTTGAAGA
1 TGAGCTAGTTTCTAGCTATAAGATGATGAAATTTGAAGA
29816501 TGAGCTAGTTTCTAGCTATAAGATGATGAAATTTGAAGA
1 TGAGCTAGTTTCTAGCTATAAGATGATGAAATTTGAAGA
29816540 T
1 T
29816541 ATTCACATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (39 bp):
TGAGCTAGTTTCTAGCTATAAGATGATGAAATTTGAAGA
Found at i:29822793 original size:1 final size:1
Alignment explanation
Indices: 29822787--29822813 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
29822777 AAATTTTCAG
29822787 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
29822814 TCAAAATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29824021 original size:31 final size:31
Alignment explanation
Indices: 29823956--29824024 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
29823946 GTTACTAAAT
* * *
29823956 AGTCATCAAATTATTCGATAATTTTGATTCA
1 AGTCATTAAACTATTCGATAATTTTCATTCA
*
29823987 AGTCATTAAACTATTCGA-AATTTTTCATTTA
1 AGTCATTAAACTATTCGATAA-TTTTCATTCA
29824018 AGTCATT
1 AGTCATT
29824025 GGTACCACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (31 bp):
AGTCATTAAACTATTCGATAATTTTCATTCA
Found at i:29828972 original size:31 final size:30
Alignment explanation
Indices: 29828919--29828993 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
29828909 TATTTGGAGG
29828919 TTGTATGATTAAAAAAATAGTAAA-TTAGTTA
1 TTGTATG-TTAAAAAAATAGTAAATTTA-TTA
29828950 TTGTATGTTAAATTAAAA-AGTAAATTTATTA
1 TTGTATGTTAAA--AAAATAGTAAATTTATTA
*
29828981 TT-TTTGTTAAAAA
1 TTGTATGTTAAAAA
29828994 TTTTATCCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 2 0.05
30 13 0.32
31 18 0.45
32 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.44
Consensus pattern (30 bp):
TTGTATGTTAAAAAAATAGTAAATTTATTA
Found at i:29836386 original size:7 final size:7
Alignment explanation
Indices: 29836374--29836399 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29836364 TAGTCGAATG
29836374 GTATTTA
1 GTATTTA
29836381 GTATTTA
1 GTATTTA
29836388 GTATTTA
1 GTATTTA
29836395 GTATT
1 GTATT
29836400 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:29837069 original size:18 final size:18
Alignment explanation
Indices: 29837048--29837082 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29837038 AGGTATGTTT
* *
29837048 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
29837066 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
29837083 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:29837677 original size:35 final size:35
Alignment explanation
Indices: 29837628--29837710 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
29837618 CTTAATTAAA
* * *
29837628 AACCCTAACCCTAACCTAACCTAACTAAAAACCCT
1 AACCCTAAACCTAACCTAAACTAACCAAAAACCCT
* *
29837663 AACCCTAAATCTAACCTAAATTAACCAAAAACCCT
1 AACCCTAAACCTAACCTAAACTAACCAAAAACCCT
29837698 AACCCT-AACCTAA
1 AACCCTAAACCTAA
29837711 ATTAACTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 6 0.14
35 36 0.86
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (35 bp):
AACCCTAAACCTAACCTAAACTAACCAAAAACCCT
Found at i:29837695 original size:64 final size:61
Alignment explanation
Indices: 29837594--29837770 Score: 227
Period size: 64 Copynumber: 2.9 Consensus size: 61
29837584 AATTTAATTG
* *
29837594 AAAACCCTAA-CTAACCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACCTAACTA
1 AAAACCCTAACCTAA-CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAACCTAACTA
* **
29837655 AAAACCCTAACCCTAAATCTAACCTAAATTAACCAAAAACCCTAACCCTAACCTAAATTAACTA
1 AAAACCCTAA-CCT-AA-CTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAACCTAACTA
*
29837719 AAAACCCTAACC---CTAACCTAAATTAACTAAAAACTCTAACCCTAACCGTAAC
1 AAAACCCTAACCTAACTAACCTAAATTAACTAAAAACCCTAACCCTAACC-TAAC
29837771 TATTAACACA
Statistics
Matches: 103, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
58 33 0.32
59 3 0.03
61 10 0.10
63 4 0.04
64 53 0.51
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (61 bp):
AAAACCCTAACCTAACTAACCTAAATTAACTAAAAACCCTAACCCTAACCTAACCTAACTA
Found at i:29837731 original size:35 final size:29
Alignment explanation
Indices: 29837594--29837765 Score: 209
Period size: 29 Copynumber: 5.6 Consensus size: 29
29837584 AATTTAATTG
* *
29837594 AAAACCCTAACTAACCTAACCTAACTTAATTA
1 AAAACCCTAAC---CCTAACCTAAATTAACTA
**
29837626 AAAACCCTAACCCTAACCTAACCTAACTA
1 AAAACCCTAACCCTAACCTAAATTAACTA
*
29837655 AAAACCCTAACCCTAAATCTAACCTAAATTAACCA
1 AAAACCCTAA-CC-----CTAACCTAAATTAACTA
29837690 AAAACCCTAACCCTAACCTAAATTAACTA
1 AAAACCCTAACCCTAACCTAAATTAACTA
29837719 AAAACCCTAACCCTAACCTAAATTAACTA
1 AAAACCCTAACCCTAACCTAAATTAACTA
*
29837748 AAAACTCTAACCCTAACC
1 AAAACCCTAACCCTAACC
29837766 GTAACTATTA
Statistics
Matches: 127, Mismatches: 7, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
29 88 0.69
30 2 0.02
32 11 0.09
34 2 0.02
35 24 0.19
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (29 bp):
AAAACCCTAACCCTAACCTAAATTAACTA
Found at i:29837863 original size:54 final size:56
Alignment explanation
Indices: 29837767--29837968 Score: 270
Period size: 55 Copynumber: 3.6 Consensus size: 56
29837757 ACCCTAACCG
* ** *
29837767 TAACTATTAACACAATTTTTGGACTTAATAA-TTTAGTTTATTTCATAAATTTTAC
1 TAACCATTAACACAATTTTTGGACTTAATAATTTTAGCATATTTGATAAATTTTAC
*
29837822 TAACCATTAATACAATTTTTGG-CTTAATAATTTTA-CATATTTTGAT-AATTTTAC
1 TAACCATTAACACAATTTTTGGACTTAATAATTTTAGCATA-TTTGATAAATTTTAC
* **
29837876 TAACCATTAACACAATTTCTGGACTTAATAATTTTAGTTTATTTGATAAATTTTAC
1 TAACCATTAACACAATTTTTGGACTTAATAATTTTAGCATATTTGATAAATTTTAC
29837932 TAACCATTAACACAATTTTTTTGG-CTTAATAATTTTA
1 TAACCATTAACACAA--TTTTTGGACTTAATAATTTTA
29837969 CACAATTTTA
Statistics
Matches: 130, Mismatches: 10, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
54 38 0.29
55 48 0.37
56 25 0.19
57 13 0.10
58 6 0.05
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.47
Consensus pattern (56 bp):
TAACCATTAACACAATTTTTGGACTTAATAATTTTAGCATATTTGATAAATTTTAC
Found at i:29838801 original size:11 final size:11
Alignment explanation
Indices: 29838785--29838809 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29838775 AATTTATGCA
29838785 TGTTGGTCACT
1 TGTTGGTCACT
29838796 TGTTGGTCACT
1 TGTTGGTCACT
29838807 TGT
1 TGT
29838810 CGTCGTTCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (11 bp):
TGTTGGTCACT
Found at i:29840807 original size:126 final size:126
Alignment explanation
Indices: 29840582--29840810 Score: 397
Period size: 126 Copynumber: 1.8 Consensus size: 126
29840572 CCCAAACTTG
* * *
29840582 CTACTGTAGCAAAATCGTGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATTGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCCCAAATAGCATCCTGG
29840647 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
* *
29840708 CTACTGTAGCAAAATCGCGTCCACTAGGGTGCGATTTCACAATTTCTTCCCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCCCAAATAGCATCCTGG
29840773 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAAC
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAAC
29840811 TCGAAATAAT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 96 0.99
127 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCCCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
Found at i:29842038 original size:188 final size:189
Alignment explanation
Indices: 29841663--29842068 Score: 502
Period size: 188 Copynumber: 2.1 Consensus size: 189
29841653 TTTTTTTTTC
* *
29841663 TATCGAAATAGCGACTGTTTTTAATCCTTCTTCTATGTATATATATATCGATATAGTATCACTTG
1 TATCGAAATAGCGACTGTTTTTAATCCTGCTTCTATG-ATATATATATCGATATAGTATCACTTC
* *
29841728 TTACTGAGTTTTTTTGCTTTTGAATTTTGTGTTGTGGCTACGGAATTTATTTGCGTTTTGAACTC
65 TTACCGAG------TGCTTTTGAATTTTGTGTTGTGGCTACGGAATTTATCTGCGTTTTGAACTC
* * **
29841793 TTTAGATCGGTATTTGGTTGATTTTATTTTCTATTTACTTGCTGGATTCGAGAAAGTGGAAAGAA
124 TTTAGATCGGTATTTGGATGATTTTATTTTC-ATCTACTCACTGGATTCGAGAAAGTGGAAAGAA
29841858 AA
188 AA
29841860 TATCGAAATAGCGACTGTTTTTAATCCTGCTT-TCATG-TATATATATCGATATAGTATCACTTC
1 TATCGAAATAGCGACTGTTTTTAATCCTGCTTCT-ATGATATATATATCGATATAGTATCACTTC
* * ** *
29841923 TTACCGAG-GTTTTTGAATTTTGTGTTGTGGCTATGGGTTTTTATCT-CTGTTTTGAACTTTTTA
65 TTACCGAGTGCTTTTGAATTTTGTGTTGTGGCTA-CGGAATTTATCTGC-GTTTTGAACTCTTTA
29841986 GATCGGTATTTAGTTGATGATTTTATTTTC-TCT-C-CACTGGATTCGAGAAAGTGGAAAGAAAA
128 GATCGGTATTT-G--GATGATTTTATTTTCATCTACTCACTGGATTCGAGAAAGTGGAAAGAAAA
* *
29842048 GATCGAAATAGTGACTGTTTT
1 TATCGAAATAGCGACTGTTTT
29842069 CATCGTTTCT
Statistics
Matches: 188, Mismatches: 15, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
188 70 0.37
189 34 0.18
190 3 0.02
192 14 0.07
195 32 0.17
196 1 0.01
197 34 0.18
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (189 bp):
TATCGAAATAGCGACTGTTTTTAATCCTGCTTCTATGATATATATATCGATATAGTATCACTTCT
TACCGAGTGCTTTTGAATTTTGTGTTGTGGCTACGGAATTTATCTGCGTTTTGAACTCTTTAGAT
CGGTATTTGGATGATTTTATTTTCATCTACTCACTGGATTCGAGAAAGTGGAAAGAAAA
Found at i:29843902 original size:17 final size:17
Alignment explanation
Indices: 29843880--29843919 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29843870 CACTTAAACA
29843880 TAAACACAAT-AAATTAT
1 TAAACACAATAAAATT-T
*
29843897 TAAACACATTAAAATTT
1 TAAACACAATAAAATTT
29843914 TAAACA
1 TAAACA
29843920 TGAATGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAACACAATAAAATTT
Found at i:29854763 original size:31 final size:30
Alignment explanation
Indices: 29854736--29854795 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29854726 CAAAATTTAG
29854736 CAAAAAACTCT-AAATTTCTCCCTAAATTT
1 CAAAAAACTCTCAAATTTCTCCCTAAATTT
** * *
29854765 CTCAAAGCTCTCAAATTTCTCCTTAAATTT
1 CAAAAAACTCTCAAATTTCTCCCTAAATTT
29854795 C
1 C
29854796 TCAAAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAAAAACTCTCAAATTTCTCCCTAAATTT
Found at i:29854783 original size:30 final size:29
Alignment explanation
Indices: 29854743--29854800 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
29854733 TAGCAAAAAA
29854743 CTCTAAATTTCTCCCTAAATTTCTCAAAG
1 CTCTAAATTTCTCCCTAAATTTCTCAAAG
*
29854772 CTCTCAAATTTCTCCTTAAATTTCTCAAA
1 CTCT-AAATTTCTCCCTAAATTTCTCAAA
29854801 ACTGTCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.31, C:0.28, G:0.02, T:0.40
Consensus pattern (29 bp):
CTCTAAATTTCTCCCTAAATTTCTCAAAG
Found at i:29861742 original size:98 final size:98
Alignment explanation
Indices: 29861573--29861849 Score: 536
Period size: 98 Copynumber: 2.8 Consensus size: 98
29861563 ACAATAAAAT
*
29861573 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAAAATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
29861638 TCTAGAATCCCAAACTCGGAATATTTCATTTAC
66 TCTAGAATCCCAAACTCGGAATATTTCATTTAC
29861671 TTTAAAAGAAAATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAAAATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
29861736 TCTAGAATCCCAAACTCGGAATATTTCATTTAC
66 TCTAGAATCCCAAACTCGGAATATTTCATTTAC
29861769 TTTAAAAGAAAATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAAAATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
*
29861834 TTTAGAATCCCAAACT
66 TCTAGAATCCCAAACT
29861850 NNNNNNNNNN
Statistics
Matches: 177, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 177 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (98 bp):
TTTAAAAGAAAATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
TCTAGAATCCCAAACTCGGAATATTTCATTTAC
Found at i:29865510 original size:6 final size:6
Alignment explanation
Indices: 29865501--29865533 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
29865491 TTTTTTTCAT
29865501 TTTTTG TTTTTG TTTTTG -TTTT- TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
29865534 TTTGAATCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.32
6 17 0.68
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:29865516 original size:22 final size:22
Alignment explanation
Indices: 29865490--29865533 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29865480 AGCCTCTCCA
*
29865490 TTTTTTTTCATTTTTTGTTTTTG
1 TTTTTGTT-ATTTTTTGTTTTTG
*
29865513 TTTTTGTTTTTTTTTGTTTTT
1 TTTTTGTTATTTTTTGTTTTT
29865534 TTTGAATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (22 bp):
TTTTTGTTATTTTTTGTTTTTG
Found at i:29865534 original size:12 final size:12
Alignment explanation
Indices: 29865500--29865536 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29865490 TTTTTTTTCA
29865500 TTTTTTGTTTTT
1 TTTTTTGTTTTT
*
29865512 GTTTTTG--TTT
1 TTTTTTGTTTTT
29865522 TTTTTTGTTTTT
1 TTTTTTGTTTTT
29865534 TTT
1 TTT
29865537 GAATCTGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:29867953 original size:194 final size:194
Alignment explanation
Indices: 29867624--29868011 Score: 776
Period size: 194 Copynumber: 2.0 Consensus size: 194
29867614 AAACTAATAA
29867624 CCCTGTACAGCCCAAAAATTTTCAAAGAATAGCAAACCCTAAATAGCTAACAGCAAAATCAGCAG
1 CCCTGTACAGCCCAAAAATTTTCAAAGAATAGCAAACCCTAAATAGCTAACAGCAAAATCAGCAG
29867689 CCGCGGCAACCTCACCCACGCCTCAACATCGCCCCACGTTCAGCACTTTGCGCACATCCTCCATG
66 CCGCGGCAACCTCACCCACGCCTCAACATCGCCCCACGTTCAGCACTTTGCGCACATCCTCCATG
29867754 ACCTTCATACCTGCAAAAAACTGATCCAAACGGAAATAGATGTAAAAATAACAGAATAGAGTTT
131 ACCTTCATACCTGCAAAAAACTGATCCAAACGGAAATAGATGTAAAAATAACAGAATAGAGTTT
29867818 CCCTGTACAGCCCAAAAATTTTCAAAGAATAGCAAACCCTAAATAGCTAACAGCAAAATCAGCAG
1 CCCTGTACAGCCCAAAAATTTTCAAAGAATAGCAAACCCTAAATAGCTAACAGCAAAATCAGCAG
29867883 CCGCGGCAACCTCACCCACGCCTCAACATCGCCCCACGTTCAGCACTTTGCGCACATCCTCCATG
66 CCGCGGCAACCTCACCCACGCCTCAACATCGCCCCACGTTCAGCACTTTGCGCACATCCTCCATG
29867948 ACCTTCATACCTGCAAAAAACTGATCCAAACGGAAATAGATGTAAAAATAACAGAATAGAGTTT
131 ACCTTCATACCTGCAAAAAACTGATCCAAACGGAAATAGATGTAAAAATAACAGAATAGAGTTT
29868012 TATTTATTGA
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
194 194 1.00
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.19
Consensus pattern (194 bp):
CCCTGTACAGCCCAAAAATTTTCAAAGAATAGCAAACCCTAAATAGCTAACAGCAAAATCAGCAG
CCGCGGCAACCTCACCCACGCCTCAACATCGCCCCACGTTCAGCACTTTGCGCACATCCTCCATG
ACCTTCATACCTGCAAAAAACTGATCCAAACGGAAATAGATGTAAAAATAACAGAATAGAGTTT
Found at i:29868825 original size:14 final size:16
Alignment explanation
Indices: 29868806--29868837 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
29868796 AGGTACACGC
29868806 ATGTATGT-TA-ATAT
1 ATGTATGTATATATAT
29868820 ATGTATGTATATATAT
1 ATGTATGTATATATAT
29868836 AT
1 AT
29868838 ATTTAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
ATGTATGTATATATAT
Found at i:29873236 original size:9 final size:9
Alignment explanation
Indices: 29873211--29873250 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
29873201 AATAAATATT
29873211 ATTAAATTA
1 ATTAAATTA
* *
29873220 TTTTAATTA
1 ATTAAATTA
29873229 ATTAAATTA
1 ATTAAATTA
*
29873238 ACTAAATTA
1 ATTAAATTA
29873247 ATTA
1 ATTA
29873251 CCAATTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
ATTAAATTA
Found at i:29877271 original size:30 final size:31
Alignment explanation
Indices: 29877209--29877269 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
29877199 AAAAATTATG
*
29877209 TTGACTATTTTTCAAAAGGTTGATGTCAAAA
1 TTGACTATTTTTCAAAAGGTTAATGTCAAAA
* *
29877240 TTGACTCTTTTT-AAGAGGTTAAATGTCAAA
1 TTGACTATTTTTCAAAAGGTT-AATGTCAAA
29877270 TTTAGCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (31 bp):
TTGACTATTTTTCAAAAGGTTAATGTCAAAA
Found at i:29878446 original size:3 final size:3
Alignment explanation
Indices: 29878432--29878472 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
29878422 TAAAATCTTA
29878432 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29878473 TATTATTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:29878613 original size:21 final size:22
Alignment explanation
Indices: 29878587--29878636 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
29878577 TTATAATTAC
29878587 ATAATAAATATATTTA-TAAAA
1 ATAATAAATATATTTAGTAAAA
* * *
29878608 ATAAT-AATGTCTTTAGTTAAA
1 ATAATAAATATATTTAGTAAAA
29878629 ATAATAAA
1 ATAATAAA
29878637 GTTGAGACGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.33
21 14 0.58
22 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAATAAATATATTTAGTAAAA
Done.