Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 68 of 126
Found at i:20274376 original size:44 final size:44
Alignment explanation
Indices: 20274200--20274446 Score: 144
Period size: 44 Copynumber: 5.6 Consensus size: 44
20274190 TTCTATCTCT
*
20274200 CTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTACCTCC
1 CTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTACCTCC
** * * ** **** *
20274244 CTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCC
1 CTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTACCTCC
* * * * *
20274288 CTGAGGTTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCC
1 CTG-GG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATCTTACCTCC
*
20274332 CTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTACCTCC
1 CTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTACCTCC
** * * * ** * *
20274376 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
1 CTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTACCTCC
* *
20274420 CTGAGGTTA-CAGTGGAGTACATTGAAG
1 CTG-GG-CAGCAGTGGAGTAGATTGAAG
20274447 CCAGTAATTC
Statistics
Matches: 143, Mismatches: 50, Indels: 19
0.67 0.24 0.09
Matches are distributed among these distances:
41 3 0.02
42 2 0.01
43 20 0.14
44 85 0.59
45 30 0.21
46 2 0.01
47 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (44 bp):
CTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTACCTCC
Found at i:20274917 original size:44 final size:43
Alignment explanation
Indices: 20274725--20275578 Score: 141
Period size: 44 Copynumber: 19.4 Consensus size: 43
20274715 TAATTCTACT
* * * * *
20274725 TCCCTAAGCAGTAGTGGAATAGATTGAGGATTTTAGATATTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGA-TTAAGATCTTACC
* * ** * *
20274769 TCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGA-ATTTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGAT--TAAGATCTTACC
** ** * * * *
20274813 TCCCTGTGGTTGTAGTGGAGTACATTGAAGCCAGTAA-TTC-TACT
1 TCCCT-AAGCAGTAGTGGAGTAGATTGAAG--ATTAAGATCTTACC
** *
20274857 TCCCTGGGCAGTAGTGGAATAGATTGAAGATTGAAGATCTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGATT-AAGATCTTACC
* * ** *
20274901 TCCCTAAGCAGTAGTGGAGCAGA-TCAAGGATGGCAGATTTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAA-GAT-TAAGATCTTACC
* * * * *
20274945 TCCCTGAG--GTTACAGTGGAGTACATTGAAGCCAGTAA-TTC-TATC
1 TCCCTAAGCAG-T--AGTGGAGTAGATTGAAG--ATTAAGATCTTACC
* ** * *
20274989 TTCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGATTA-AGATCTTACC
* * *** *
20275033 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGAT-TAAGATCTTACC
* * * * *
20275077 TCCCTGAG--GTTACAGTGGAGTACATTGAAGCCAGTAA-TTC-TATC
1 TCCCTAAGCAG-T--AGTGGAGTAGATTGAAG--ATTAAGATCTTACC
* ** * * *
20275121 TCCCTAGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGA-TTAAGATCTTACC
* ** * * * *** *
20275165 TCCCCAAGCAGTAGCAGAGCAGTTTAAAGATGGCGGATTTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGAT-TAAGATCTTACC
** * * * *
20275209 TCCCT--GTGGTTACAGTGGAGTATATTGAAGCCAATAA-TTC-TACT
1 TCCCTAAGCAG-T--AGTGGAGTAGATTGAAG--ATTAAGATCTTACC
** * * ** **
20275253 TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGA-TTAAGATCTTACC
* * * ** *** *
20275297 TCCCTAAACAGTAGTGGAGCAGGTCAAAGATGGCGGATTTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGAT-TAAGATCTTACC
* ** * * * *
20275341 TCCCTATGGTTGCAGTGGAGTACATTGAAGCCATTAA-TTC-TACT
1 TCCCTA-AGCAGTAGTGGAGTAGATTGAAG--ATTAAGATCTTACC
** ** *
20275385 TCCCTGGGCAGCGGTGGAATAGATTGAAGATTACAGATCTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGATTA-AGATCTTACC
* * * *
20275429 TCCCTAAGCAGTAGTGGAGCAGA-TCAAGGATGACAGATTTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAA-GATTA-AGATCTTACC
* * * * * *
20275473 TCCCTGAGGTTA-TAGTGGAGTACATTGAAGCCAGTAA-TTC-TATC
1 TCCCT-AAG-CAGTAGTGGAGTAGATTGAAG--ATTAAGATCTTACC
** ** *
20275517 TCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTACC
1 TCCCTAAGCAGTAGTGGAGTAGATTGAAGATTA-AGATCTTACC
* *
20275561 TCCTTAAGTAGTAGTGGA
1 TCCCTAAGCAGTAGTGGA
20275579 ACAGATCAAT
Statistics
Matches: 549, Mismatches: 201, Indels: 120
0.63 0.23 0.14
Matches are distributed among these distances:
41 14 0.03
42 13 0.02
43 123 0.22
44 292 0.53
45 87 0.16
46 12 0.02
47 8 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
TCCCTAAGCAGTAGTGGAGTAGATTGAAGATTAAGATCTTACC
Found at i:20276458 original size:43 final size:43
Alignment explanation
Indices: 20276409--20276590 Score: 106
Period size: 44 Copynumber: 4.2 Consensus size: 43
20276399 CCTGTGGTTA
20276409 CAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGGCAG
1 CAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGGCAG
* * * * *
20276452 CAGTGGAATAGATTAAAG--ATTACAGATCTTATCT-TCCTAGGCAG
1 CAGTGGAGTACATTAAAGCCAGTA-A-TTC-TATCTCT-CTGGGCAG
* * * * * * * *
20276496 TAGTGGAGTAGATCGAAGATGGCAG--ATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTACAT-TAA-A-GCCAGTAATTCTATCTCTCTG-GG-CAG
* *
20276541 CAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGTCGG
1 CAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGGCAG
20276584 CAGTGGA
1 CAGTGGA
20276591 ATCGATTGAA
Statistics
Matches: 99, Mismatches: 25, Indels: 30
0.64 0.16 0.19
Matches are distributed among these distances:
41 3 0.03
42 5 0.05
43 28 0.28
44 42 0.42
45 16 0.16
46 3 0.03
47 1 0.01
49 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
CAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGGCAG
Found at i:20276619 original size:132 final size:132
Alignment explanation
Indices: 20274145--20276602 Score: 3379
Period size: 132 Copynumber: 18.6 Consensus size: 132
20274135 TTGATGGCAT
* *
20274145 ATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGGGCAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * *
20274210 GTGGAATAGATTGAAGATTACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20274275 GG
131 GG
20274277 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * *
20274342 GTGGAATAGATTGAAGATTACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20274407 GG
131 GG
** *
20274409 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCCAGACAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * * * *
20274474 GTGGAATAGATTGAAGATTTCAGATATTGTTTCCCTAAGCAGTAGCGGAGCAGGTCAAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20274539 GG
131 GG
* * *
20274541 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTA-CTTCCTTGGGCAGC
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGC
** * * * *
20274605 AGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAACAGTAGTAGAGCAGGTCAAAGATGG
65 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
20274670 CGG
130 CGG
* * * ** *
20274673 ATTTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTA-CTTCCCTAAGCAGT
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGC
* * * *
20274737 AGTGGAATAGATTGAGGATTTTAGATATTATCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGG
65 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
* *
20274802 TGA
130 CGG
* ** *
20274805 ATTTTACCTCCCTGTGGTTGTAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGCAGT
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGC
** * *
20274869 AGTGGAATAGATTGAAGATTGAAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGG
65 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
*
20274934 CAG
130 CGG
*
20274937 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCCTGGGCAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * *
20275002 GTGGAATAGATTGAAGATTACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20275067 GG
131 GG
* *
20275069 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAACA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* ** * *
20275134 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGCAGAGCAGTTTAAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20275199 GG
131 GG
* * *
20275201 ATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCAATAATTCTA-CTTCCCTGGGCAGC
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGC
** * * *
20275265 AGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAACAGTAGTGGAGCAGGTCAAAGATGG
65 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
20275330 CGG
130 CGG
* *
20275333 ATTTTACCTCCCT-ATGGTTGCAGTGGAGTACATTGAAGCCATTAATTCTA-CTTCCCTGGGCAG
1 ATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAG
* * * *
20275396 CGGTGGAATAGATTGAAGATTACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATG
64 CAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
* *
20275461 ACAG
129 GCGG
* *
20275465 ATTTTACCTCCCTGAGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * * * * * *
20275530 GTGGAATAGATTGAAGATTACAGATCTTACCTCCTTAAGTAGTAGTGGAACAGATCAATGATGGT
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20275595 GG
131 GG
* ** *
20275597 ATTTTACCTCCCAGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCATTGGGAAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * * *
20275662 GTGGAATAGATTGAAGATTACAGATCTTACCTCCCTAAGCAGTAATGGAGCAGATCGAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20275727 GG
131 GG
* *
20275729 ATTTTACTTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCTGGGCAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * * * * *
20275794 GTGGAATAGATTGAAGGTTTCAGATCTTGTCTCCCCAAGCAGTAGCGGAACAGGTCAAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20275859 GG
131 GG
* * *
20275861 ATTTTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAATAATTCTA-CTTCCCTGGGCAGC
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGC
* ** * * * * **
20275925 AGTGGGATAGATTGAAGATTTTGGATCTTGTCTCCTTAAACAGTAGTGGAGCAGGTCAAAGATAA
65 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
20275990 CGG
130 CGG
* * * * *
20275993 ATTTTACCTCCCTGTGGTTACAGTGGAGTACTTTGAAGCCAATAATTCTA-CTTCCCTGAGCAGT
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGC
* * * * *
20276057 AGTGGAATAGATT-AAGGATTTTAGATCTTGTCTCCCCAAGCAGTAGTGGAACAGATCAAAAATG
65 AGTGGAATAGATTGAA-GATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
* *
20276121 GTGA
129 GCGG
* * * *
20276125 ATTTTACCTCCCTGTGGTTGCAGTGGAGTACATTGAATCCAGTAATTCTA-CTTCCATGGGCAGC
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGC
* * *
20276189 AGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAATAGTGGAGCAGATCAAAGATGG
65 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
* *
20276254 TGA
130 CGG
* * *
20276257 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAACA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * *
20276322 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGT
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
*
20276387 GA
131 GG
* * *
20276389 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGGCAGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
* * * * * *
20276454 GTGGAATAGATTAAAGATTACAGATCTTATCTTCCTAGGCAGTAGTGGAGTAGATCGAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
*
20276519 AG
131 GG
* * * *
20276521 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCTCTGGTCGGCA
1 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
*
20276586 GTGGAATCGATTGAAGA
66 GTGGAATAGATTGAAGA
20276603 AAGCAGATCT
Statistics
Matches: 2097, Mismatches: 219, Indels: 20
0.90 0.09 0.01
Matches are distributed among these distances:
131 5 0.00
132 2086 0.99
133 6 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCA
GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
GG
Found at i:20276760 original size:44 final size:44
Alignment explanation
Indices: 20276697--20276816 Score: 129
Period size: 44 Copynumber: 2.7 Consensus size: 44
20276687 GAAGATACAA
* *
20276697 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA-AAAATAACCG
1 GTCTTATCTCCTTGAAGTTGCAGTGGAGCAGA-ATAAAATAACAG
* * *
20276741 GTCTTATCTCCTTGAAGTTGCAATGGAG-TGAATTAAAATCACAG
1 GTCTTATCTCCTTGAAGTTGCAGTGGAGCAGAA-TAAAATAACAG
* *
20276785 ATCTTATCT-CTCTGAAGTTGCAGTAGAGCAGA
1 GTCTTATCTCCT-TGAAGTTGCAGTGGAGCAGA
20276817 TCGCATTAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.02
43 4 0.06
44 56 0.89
45 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
GTCTTATCTCCTTGAAGTTGCAGTGGAGCAGAATAAAATAACAG
Found at i:20278221 original size:3 final size:3
Alignment explanation
Indices: 20278208--20278287 Score: 74
Period size: 3 Copynumber: 26.0 Consensus size: 3
20278198 TTACTATTTA
*
20278208 ATT ATTT ATT ATT ATT A-T ATT A-T ACTT GTTT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT A-TT -ATT ATT ATT ATT ATT ATT
* * *
20278254 ATT ATT ATTT ATT ATT AAT ATT GTA ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
20278288 TTCGTGTACA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.06
3 50 0.79
4 9 0.14
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:20278264 original size:25 final size:25
Alignment explanation
Indices: 20278208--20278288 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
20278198 TTACTATTTA
20278208 ATTATTTATTATTATTA-TATTA-T
1 ATTATTTATTATTATTATTATTATT
*
20278231 ACTTGTTTATTATTATTATTATTATT
1 A-TTATTTATTATTATTATTATTATT
* * *
20278257 ATTATTTATTATTAATATTGTAATT
1 ATTATTTATTATTATTATTATTATT
20278282 ATTATTT
1 ATTATTT
20278289 TCGTGTACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
23 1 0.02
24 15 0.30
25 32 0.64
26 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTATTTATTATTATTATTATTATT
Found at i:20281351 original size:6 final size:6
Alignment explanation
Indices: 20281340--20281372 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
20281330 TGTCAAGGAT
*
20281340 AGGGGA AGGGGA AGGGGA AGGGGA AGGGAA AGG
1 AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGG
20281373 AAAATTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:20282037 original size:28 final size:25
Alignment explanation
Indices: 20281983--20282053 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 25
20281973 AAATCATAGT
20281983 TTACTTATGATAATTTA--TTTAAAA
1 TTACTTA-GATAATTTATTTTTAAAA
20282007 TTACTTAGATAATTTATTGTTTAGATAA
1 TTACTTAGATAATTTATT-TTTA-A-AA
*
20282035 TTATTTAGATAAATTTATT
1 TTACTTAGAT-AATTTATT
20282054 AAGAATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 9 0.22
24 7 0.17
26 4 0.10
27 1 0.03
28 11 0.28
29 8 0.20
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (25 bp):
TTACTTAGATAATTTATTTTTAAAA
Found at i:20282043 original size:12 final size:13
Alignment explanation
Indices: 20281991--20282053 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 13
20281981 GTTTACTTAT
20281991 GATAATTTATTTA
1 GATAATTTATTTA
*
20282004 -A-AA-TTACTTA
1 GATAATTTATTTA
20282014 GATAATTTATTGTTTA
1 GATAATTTA---TTTA
20282030 GATAA-TTATTTA
1 GATAATTTATTTA
20282042 GATAAATTTATT
1 GAT-AATTTATT
20282054 AAGAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
10 6 0.15
11 3 0.08
12 10 0.25
13 5 0.12
14 5 0.12
15 3 0.08
16 8 0.20
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (13 bp):
GATAATTTATTTA
Found at i:20282659 original size:18 final size:18
Alignment explanation
Indices: 20282615--20282660 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
20282605 TGTAATTTGA
* *
20282615 AAATAATATATTTATTAC
1 AAATTATATTTTTATTAC
*
20282633 AAA-TATATTTTTATTTC
1 AAATTATATTTTTATTAC
20282650 AAATTATATTT
1 AAATTATATTT
20282661 GCTTTGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATTATATTTTTATTAC
Found at i:20292019 original size:106 final size:106
Alignment explanation
Indices: 20291847--20292055 Score: 325
Period size: 106 Copynumber: 2.0 Consensus size: 106
20291837 CATAGCATTG
* * *
20291847 AAGAAGACCATATCGTGTAAGATAGTAACTGATGGGTTATGACATCATATGTGAAGAAGTCTATA
1 AAGAAGACCATATCGTGTAAGATAGTAACTGATAGGTTATGACATCATATGTGAAGAAGACCATA
**
20291912 TCATGTAAGACTATAACTGGTGGGTTATGGCATCATATATA
66 TCATGTAAGACTATAACTGGTGGGTTATGAAATCATATATA
20291953 AAGAAGACCATATCGTGTAAGACT-GTAACT-AGTAGGTTATGACATCATATG-GAAAGAAGACC
1 AAGAAGACCATATCGTGTAAGA-TAGTAACTGA-TAGGTTATGACATCATATGTG-AAGAAGACC
20292015 ATATCATGTAAGACTATAACTGGTGGGTTATGAAATCATAT
63 ATATCATGTAAGACTATAACTGGTGGGTTATGAAATCATAT
20292056 GGGGAAGTTT
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
105 2 0.02
106 92 0.97
107 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (106 bp):
AAGAAGACCATATCGTGTAAGATAGTAACTGATAGGTTATGACATCATATGTGAAGAAGACCATA
TCATGTAAGACTATAACTGGTGGGTTATGAAATCATATATA
Found at i:20292057 original size:53 final size:53
Alignment explanation
Indices: 20291847--20292057 Score: 282
Period size: 53 Copynumber: 4.0 Consensus size: 53
20291837 CATAGCATTG
* *
20291847 AAGAAGACCATATCGTGTAAGA-TAGTAACTGATGGGTTATGACATCATATGTG-
1 AAGAAGACCATATCATGTAAGACTA-TAACTGGTGGGTTATGACATCATATG-GA
* * * **
20291900 AAGAAGTCTATATCATGTAAGACTATAACTGGTGGGTTATGGCATCATATATA
1 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGGA
* * * *
20291953 AAGAAGACCATATCGTGTAAGACTGTAACTAGTAGGTTATGACATCATATGGA
1 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGGA
*
20292006 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGAAATCATATGG
1 AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGG
20292058 GGAAGTTTAA
Statistics
Matches: 135, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 133 0.99
54 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (53 bp):
AAGAAGACCATATCATGTAAGACTATAACTGGTGGGTTATGACATCATATGGA
Found at i:20293359 original size:20 final size:20
Alignment explanation
Indices: 20293334--20293373 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20293324 AACCTAATAA
*
20293334 AAGGTATTGATACTTTTTGT
1 AAGGTACTGATACTTTTTGT
*
20293354 AAGGTACTGATATTTTTTGT
1 AAGGTACTGATACTTTTTGT
20293374 GAAAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (20 bp):
AAGGTACTGATACTTTTTGT
Found at i:20295479 original size:3 final size:3
Alignment explanation
Indices: 20295471--20295523 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
20295461 TGGCCCAAAC
* * *
20295471 TAT TAT TAT TAT TAT CAT TAC TAC TAT TAT TAAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
20295517 TAT TAT T
1 TAT TAT T
20295524 TTTTTTACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:20296207 original size:99 final size:97
Alignment explanation
Indices: 20296018--20296199 Score: 260
Period size: 96 Copynumber: 1.9 Consensus size: 97
20296008 AAAAAAAGAG
* * *
20296018 AGTTTTGATTTTTAAAAATAAAAATATGTTTTTTTTAGTCATTCTAAAGGAAAGTTTAAAATTTT
1 AGTTTAGACTTTTAAAAATAAAAATA--TTATTTTTAGTCATTCTAAAGGAAAGTTTAAAATTTT
*
20296083 AAAACAATGTAGTGATTTTTTAAATAAAAGGGAA
64 AAAACAAAGTAGTGATTTTTTAAATAAAAGGGAA
*
20296117 AGTTTAGACTTTTAAAAATAAAAATA-TATTTTTAGTCATTTTAAAGGAAAGTTT-AAATGTTTA
1 AGTTTAGACTTTTAAAAATAAAAATATTATTTTTAGTCATTCTAAAGGAAAGTTTAAAAT-TTTA
**
20296180 AAACAAAGTTTTGATTTTTT
65 AAACAAAGTAGTGATTTTTT
20296200 TTAAAATATT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
95 4 0.05
96 47 0.63
99 24 0.32
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (97 bp):
AGTTTAGACTTTTAAAAATAAAAATATTATTTTTAGTCATTCTAAAGGAAAGTTTAAAATTTTAA
AACAAAGTAGTGATTTTTTAAATAAAAGGGAA
Found at i:20296373 original size:158 final size:154
Alignment explanation
Indices: 20296108--20296413 Score: 454
Period size: 158 Copynumber: 2.0 Consensus size: 154
20296098 TTTTTTAAAT
*
20296108 AAAAGGGAAAGTTTAGACTTTTAAAAATAAAAATATATTTTTAGTCATTTTAAAGGAAAGTTTAA
1 AAAAGAGAAAGTTTAGACTTTTAAAAATAAAAATATATTTTTAGTCATTTTAAAGGAAAGTTTAA
* *
20296173 ATGTTTAAAACAAAGTTTTGATTTTTTTTAAAATATTTCGAAATAAAAGCTTTAA-TCTTTAAGA
66 ATGTTTAAAACAAAATTTTGATTTTTTCT-AAATATTTCGAAATAAAA-CTTTAATTCTTTAAGA
20296237 AAAGTAGTGAATTTTTTAAAAGAAGAA
129 AAAGTAGTG-ATTTTTTAAAAGAAGAA
* *
20296264 AAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGTAAAGTT
1 AAAAGAGAAAGTTTAGACTTTTAAAAATAAAAATA--TATTTTTAGTCATTTTAAAGG-AAAGTT
* * * *
20296329 TAAATTTTTAAAACAAAATTTTGATCTTTTTCT-ACTATTTCGAAATAAAACTTTAATTTTTTTA
63 TAAATGTTTAAAACAAAATTTTGAT-TTTTTCTAAATATTTCGAAATAAAACTTTAATTCTTTAA
20296393 GAAAAGTAGTGATTTTTTAAA
127 GAAAAGTAGTGATTTTTTAAA
20296414 GGAAATTTTG
Statistics
Matches: 136, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
156 33 0.24
157 16 0.12
158 52 0.38
159 29 0.21
160 6 0.04
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.41
Consensus pattern (154 bp):
AAAAGAGAAAGTTTAGACTTTTAAAAATAAAAATATATTTTTAGTCATTTTAAAGGAAAGTTTAA
ATGTTTAAAACAAAATTTTGATTTTTTCTAAATATTTCGAAATAAAACTTTAATTCTTTAAGAAA
AGTAGTGATTTTTTAAAAGAAGAA
Found at i:20298436 original size:23 final size:24
Alignment explanation
Indices: 20298398--20298443 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
20298388 GTTTGAGAGC
*
20298398 TAGATTTTTTAGTATTTGTGCATAT
1 TAGATTTTTTA-TATTCGTGCATAT
20298423 TAGATTTTTT-TATTCGTGCAT
1 TAGATTTTTTATATTCGTGCAT
20298444 TAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (24 bp):
TAGATTTTTTATATTCGTGCATAT
Found at i:20299645 original size:34 final size:35
Alignment explanation
Indices: 20299602--20299686 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
20299592 ATTTTATTTG
*
20299602 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
* *
20299635 TTTATATTATAGAATTTATGATAATTAAATTATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
* *
20299670 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
20299687 ATAAATCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 4 0.09
34 34 0.79
35 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:20300675 original size:6 final size:6
Alignment explanation
Indices: 20300658--20300708 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
20300648 ATGTGAGGTA
* * * * *
20300658 AGTATT AATATT AGTATT AGTAAT AGTATT ATTATT ATTATT ATTATT
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT
20300706 AGT
1 AGT
20300709 GGGAATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:20300675 original size:12 final size:12
Alignment explanation
Indices: 20300658--20300708 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
20300648 ATGTGAGGTA
*
20300658 AGTATTAATATT
1 AGTATTATTATT
* *
20300670 AGTATTAGTAAT
1 AGTATTATTATT
20300682 AGTATTATTATT
1 AGTATTATTATT
*
20300694 ATTATTATTATT
1 AGTATTATTATT
20300706 AGT
1 AGT
20300709 GGGAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (12 bp):
AGTATTATTATT
Found at i:20301036 original size:23 final size:23
Alignment explanation
Indices: 20301017--20301063 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
20301007 ATTATCAAAC
20301017 CATCAAAAAAATTAACATCATAA
1 CATCAAAAAAATTAACATCATAA
* * *
20301040 CATTAAATAAATTAATCATAATAA
1 CATCAAAAAAATTAA-CATCATAA
20301064 AAACCAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
CATCAAAAAAATTAACATCATAA
Found at i:20304455 original size:46 final size:46
Alignment explanation
Indices: 20304304--20304466 Score: 134
Period size: 46 Copynumber: 3.5 Consensus size: 46
20304294 TCTGTATAGT
* **
20304304 TTGCAGACTCAAGAATATAGGAATAGGTTGTGAGCTCTTGCATATG
1 TTGCAGACTCGAGAATATAGGAATAGGTTCCGAGCTCTTGCATATG
* * * * * * * *
20304350 TTGC-GAACTCGAGAACACAAGAATAGGTTTCGAGCTCCTACATCTA
1 TTGCAG-ACTCGAGAATATAGGAATAGGTTCCGAGCTCTTGCATATG
** * *
20304396 TTGTGGAC-CTGAGAATTTAGGTATAGGTTCCGAGCTCTTGCATATG
1 TTGCAGACTC-GAGAATATAGGAATAGGTTCCGAGCTCTTGCATATG
*
20304442 TTGCAGACTTGAGAATACT-GGAATA
1 TTGCAGACTCGAGAATA-TAGGAATA
20304467 TTAAGCCCTA
Statistics
Matches: 86, Mismatches: 26, Indels: 10
0.70 0.21 0.08
Matches are distributed among these distances:
45 2 0.02
46 82 0.95
47 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (46 bp):
TTGCAGACTCGAGAATATAGGAATAGGTTCCGAGCTCTTGCATATG
Found at i:20305313 original size:27 final size:27
Alignment explanation
Indices: 20305259--20305314 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
20305249 ATCATCATAT
* *
20305259 ATATACACACATAACATAGCATTTATC
1 ATATACACACATAACATAGCACTCATC
*
20305286 ATATATACACATAACATAGCACTCATC
1 ATATACACACATAACATAGCACTCATC
20305313 AT
1 AT
20305315 TAACATGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.29
Consensus pattern (27 bp):
ATATACACACATAACATAGCACTCATC
Found at i:20306498 original size:13 final size:13
Alignment explanation
Indices: 20306468--20306492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20306458 TATTTGGTTA
20306468 TTCAAATGACCAC
1 TTCAAATGACCAC
20306481 TTCAAATGACCA
1 TTCAAATGACCA
20306493 TATCAACTCC
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCAAATGACCAC
Found at i:20307791 original size:25 final size:25
Alignment explanation
Indices: 20307762--20307826 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
20307752 TCTTGTACAT
*
20307762 GTATGCTCATATGAGCTATGAACCG
1 GTATGCTCATATGAGCTATAAACCG
* **
20307787 GTATGCTC-TCACGAGCTATAAATTG
1 GTATGCTCAT-ATGAGCTATAAACCG
*
20307812 GTAAGCTCATATGAG
1 GTATGCTCATATGAG
20307827 TTGAGAATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (25 bp):
GTATGCTCATATGAGCTATAAACCG
Found at i:20307860 original size:24 final size:24
Alignment explanation
Indices: 20307832--20307882 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
20307822 ATGAGTTGAG
*
20307832 AATCGGTAAACTTTAACGAGCTGA
1 AATCGGTAAACTCTAACGAGCTGA
* *
20307856 AATCGGTAAGCTCTCACGAGCTGA
1 AATCGGTAAACTCTAACGAGCTGA
20307880 AAT
1 AAT
20307883 AAAAAATCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (24 bp):
AATCGGTAAACTCTAACGAGCTGA
Found at i:20309873 original size:44 final size:44
Alignment explanation
Indices: 20309814--20309902 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
20309804 ATTCCCATAC
*
20309814 TTAAAGATAAACTCAAATGTATATAACTCAATTTACTTTTCAAA
1 TTAAAGATAAACTCAAATGCATATAACTCAATTTACTTTTCAAA
* *
20309858 TTAAATATAAGCTCAAATGCATATAACTCAATTTACTTTTCAAA
1 TTAAAGATAAACTCAAATGCATATAACTCAATTTACTTTTCAAA
20309902 T
1 T
20309903 GAATAACTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (44 bp):
TTAAAGATAAACTCAAATGCATATAACTCAATTTACTTTTCAAA
Found at i:20313861 original size:14 final size:14
Alignment explanation
Indices: 20313842--20313871 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20313832 AGTGAGAGAG
*
20313842 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
20313856 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
20313870 GA
1 GA
20313872 ATGCGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:20314446 original size:20 final size:22
Alignment explanation
Indices: 20314421--20314468 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
20314411 CGAATCTGTA
20314421 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
20314441 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
20314463 AAAAAT
1 AAAAAT
20314469 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:20314521 original size:18 final size:20
Alignment explanation
Indices: 20314492--20314531 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
20314482 TTTTTAATAC
20314492 AATTTAATTATTTTAT-AAA
1 AATTTAATTATTTTATGAAA
20314511 AATTT-ATTATTTTATGAAA
1 AATTTAATTATTTTATGAAA
20314530 AA
1 AA
20314532 AATTCTATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTTAATTATTTTATGAAA
Found at i:20319794 original size:62 final size:62
Alignment explanation
Indices: 20319697--20319820 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
20319687 AGTATAAGAG
20319697 AAGAATTCCCTTCTTGTGGCTCCAATCTGGACAAGTGATCTGCTACTTGATTTTTGACTCCC
1 AAGAATTCCCTTCTTGTGGCTCCAATCTGGACAAGTGATCTGCTACTTGATTTTTGACTCCC
20319759 AAGAATTCCCTTCTTGTGGCTCCAATCTGGACAAGTGATCTGCTACTTGATTTTTGACTCCC
1 AAGAATTCCCTTCTTGTGGCTCCAATCTGGACAAGTGATCTGCTACTTGATTTTTGACTCCC
20319821 TTTCGATATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (62 bp):
AAGAATTCCCTTCTTGTGGCTCCAATCTGGACAAGTGATCTGCTACTTGATTTTTGACTCCC
Found at i:20324169 original size:5 final size:5
Alignment explanation
Indices: 20324159--20324206 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
20324149 AAAAAAAAGG
20324159 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
20324207 GTTCTAATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20325184 original size:14 final size:14
Alignment explanation
Indices: 20325165--20325194 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20325155 AGTGAGAGAG
*
20325165 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
20325179 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
20325193 GA
1 GA
20325195 ATGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:20325595 original size:20 final size:22
Alignment explanation
Indices: 20325570--20325619 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
20325560 CGAATCTGTC
20325570 AAAAATAA-T-AAAAATTCACT
1 AAAAATAATTGAAAAATTCACT
* *
20325590 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGAAAAATTCACT
20325612 AAAAATAA
1 AAAAATAA
20325620 CATGTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
22 17 0.65
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAAATAATTGAAAAATTCACT
Found at i:20327195 original size:12 final size:12
Alignment explanation
Indices: 20327178--20327203 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20327168 TTGGAGCAAA
20327178 TGCCCAATTATG
1 TGCCCAATTATG
20327190 TGCCCAATTATG
1 TGCCCAATTATG
20327202 TG
1 TG
20327204 TAATCCATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (12 bp):
TGCCCAATTATG
Found at i:20335968 original size:40 final size:40
Alignment explanation
Indices: 20335931--20336960 Score: 1059
Period size: 40 Copynumber: 25.8 Consensus size: 40
20335921 CGAGTACCAG
* * * * * *
20335931 AGTACTAACAAGGGCACATATGTGCTTTCAGGGGTACCAA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* *
20335971 AGTACAAACAGGGGCACGTATGTGCATTTAGGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * * *
20336011 AGTACAAATAGGGGCACGTATGTTCATTCAGGGGTACTGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * * * * * *
20336051 AGTACAAATAAGGGCACATATGTGAATTTAGGGGTATCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
*
20336091 AGTACAAACAGGGGGACGTGTGTGCATTCAGGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* *
20336131 AGTACAAACAGGGGCACTTGTGTGCATTCAGGGGTACCAA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
*
20336171 AGTATAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * *
20336211 AGTACAAACAGGGGAACTTGTGTTCATTCAGGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * *
20336251 AGTACAAACAAGGGCACATGTGTGCATTCAGGGGTACTGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * *
20336291 AGTACAAATAGGGGCACGTCTGTGCATTCAAGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * *
20336331 AGTAAAAACAGGGGCAAGTGTGTGCATTCAGGGGTA-CTA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * * *
20336370 AGTACAAACCA-GGGCACGTAG-GTGAATTTAGAGGTATCGA
1 AGTACAAA-CAGGGGCACGT-GTGTGCATTCAGGGGTACCGA
* * * * *
20336410 AGTACAAATAGGGGGACGTGTGTGCATTTAGGGGTATCAA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* *
20336450 AGTACAAACA-GGGCGATGTGTGTGCATTCAGGGGTATCGA
1 AGTACAAACAGGGGC-ACGTGTGTGCATTCAGGGGTACCGA
* *
20336490 AGTACAAAAAGGGGCACGTGTGTGCATTCAGGGGTATCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * *
20336530 AGTACAAATAGGGGCACATGTGTACATTCAGGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * * *
20336570 AGTACAAACAGGTGCACGTCTGTGCATTTAGGGGTACTGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * * * * *
20336610 AGTACAAATAAGGGCACGTCTTTGCATTTAGAGGGTA-CTA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAG-GGGTACCGA
* * * * **
20336650 AGTACGAACAAGGGCACATCTGTGCATTCAGGGGTATTGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * ** * * *
20336690 AGTACAAAAAAGGGCATATGTGTGCATTTAGGGGTATCAA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* *
20336730 AGTACAAATAGGGGCACGTGTGTGCATTCACGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
** * * *
20336770 AGTAC-AACTATTGGCATGTGTGTGCATTCGGGGGTATCGA
1 AGTACAAAC-AGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * * ** *
20336810 AGCAC-AACAGGAGCATGCATGTGCATTCAAGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * *
20336849 AGTACAAACAGGGGCATGTATGTGGATTCAGGGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
* * * **
20336889 AGTACAAATAAGGGCATGCATGTGCATTCCA-GGGTACCGA
1 AGTACAAACAGGGGCACGTGTGTGCATT-CAGGGGTACCGA
* * * *
20336929 AGTACAGACAAGGGCATGTATGTGCATTCAGG
1 AGTACAAACAGGGGCACGTGTGTGCATTCAGG
20336961 TAATAATTAC
Statistics
Matches: 840, Mismatches: 137, Indels: 26
0.84 0.14 0.03
Matches are distributed among these distances:
39 69 0.08
40 760 0.90
41 11 0.01
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (40 bp):
AGTACAAACAGGGGCACGTGTGTGCATTCAGGGGTACCGA
Found at i:20336003 original size:20 final size:20
Alignment explanation
Indices: 20335980--20336044 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
20335970 AAGTACAAAC
*
20335980 AGGGGCACGTATGTGCATTT
1 AGGGGCACGTATGTACATTT
* * **
20336000 AGGGGTACCG-AAGTACAAAT
1 AGGGGCA-CGTATGTACATTT
* *
20336020 AGGGGCACGTATGTTCATTC
1 AGGGGCACGTATGTACATTT
20336040 AGGGG
1 AGGGG
20336045 TACTGAAGTA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.23
Consensus pattern (20 bp):
AGGGGCACGTATGTACATTT
Found at i:20336142 original size:20 final size:20
Alignment explanation
Indices: 20336119--20336260 Score: 56
Period size: 20 Copynumber: 7.1 Consensus size: 20
20336109 TGTGTGCATT
20336119 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * * **
20336139 CAGGGGCACTTG-TGTGCATT
1 CAGGGGTAC-CGAAGTACAAA
* *
20336159 CAGGGGTACCAAAGTATAAA
1 CAGGGGTACCGAAGTACAAA
* ** * **
20336179 CAGGGGCA-CGTGTGTGCATT
1 CAGGGGTACCG-AAGTACAAA
20336199 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * * **
20336219 CAGGGGAACTTG-TGTTCATT
1 CAGGGGTAC-CGAAGTACAAA
20336239 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
20336259 CA
1 CA
20336261 AGGGCACATG
Statistics
Matches: 76, Mismatches: 40, Indels: 12
0.59 0.31 0.09
Matches are distributed among these distances:
19 2 0.03
20 70 0.92
21 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:20337671 original size:7 final size:7
Alignment explanation
Indices: 20337639--20337663 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20337629 AAAATATTTT
20337639 AAAATTA
1 AAAATTA
20337646 AAAATTA
1 AAAATTA
20337653 AAAATTA
1 AAAATTA
20337660 AAAA
1 AAAA
20337664 ATCAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:20339968 original size:13 final size:13
Alignment explanation
Indices: 20339950--20339975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20339940 ATTATTGGAT
20339950 GATTTTAATTTAA
1 GATTTTAATTTAA
20339963 GATTTTAATTTAA
1 GATTTTAATTTAA
20339976 ACTTCGTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
GATTTTAATTTAA
Found at i:20344403 original size:46 final size:46
Alignment explanation
Indices: 20344353--20344455 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
20344343 TGCAGAATCA
*
20344353 AGAATATAGGAATAGGTTCTAAGCTCCAACATATGTTGAAGACTTG
1 AGAATATAGGAATAGGTTCCAAGCTCCAACATATGTTGAAGACTTG
* * * * ** ** *
20344399 AGAATATATGTATTGGTTCCGAGCTCTTACATATGTTGCGGAGTTG
1 AGAATATAGGAATAGGTTCCAAGCTCCAACATATGTTGAAGACTTG
20344445 AGAATATAGGA
1 AGAATATAGGA
20344456 CAAAGCCCTG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (46 bp):
AGAATATAGGAATAGGTTCCAAGCTCCAACATATGTTGAAGACTTG
Found at i:20348766 original size:40 final size:40
Alignment explanation
Indices: 20348668--20348930 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
20348658 TCCTCGTTCA
* * * * *
20348668 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
20348707 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20348747 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20348787 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
20348827 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
20348867 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
20348907 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20348931 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:20353361 original size:30 final size:30
Alignment explanation
Indices: 20353264--20353540 Score: 225
Period size: 30 Copynumber: 9.4 Consensus size: 30
20353254 TCAGCTATCG
* * *
20353264 AATTATGAAAAGAGATTGTGATGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
20353294 ACA--ATG-AAAGGGATGGTGACGACCATCA
1 A-ATTATGAAAAGGGATGGTGACGACCATCA
*
20353322 ACA--ATGAAAAGGGATTGTGACGACCATCA
1 A-ATTATGAAAAGGGATGGTGACGACCATCA
* * *
20353351 AATTATGAAAAGGGATGGCT-TCGGCTATCA
1 AATTATGAAAAGGGATGG-TGACGACCATCA
* * *
20353381 AATTATGAAAAGGGATGGCT-TCGACTATCG
1 AATTATGAAAAGGGATGG-TGACGACCATCA
* * * * *
20353411 AATTATAAAAAGGGATAGCT-TCGGCTATCA
1 AATTATGAAAAGGGAT-GGTGACGACCATCA
* *
20353441 AATTATGAAAAGGGATGTTGATGACCATC-
1 AATTATGAAAAGGGATGGTGACGACCATCA
* *
20353470 AATAATGAAAAGGGATGGTGATGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
** *
20353500 ACA--ATGAGCAGGGATGGTGATGACCATCA
1 A-ATTATGAAAAGGGATGGTGACGACCATCA
20353529 AATTATGAAAAG
1 AATTATGAAAAG
20353541 AGTTTGCTTT
Statistics
Matches: 210, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
28 27 0.13
29 79 0.38
30 100 0.48
31 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (30 bp):
AATTATGAAAAGGGATGGTGACGACCATCA
Found at i:20353415 original size:60 final size:59
Alignment explanation
Indices: 20353325--20353606 Score: 209
Period size: 60 Copynumber: 4.7 Consensus size: 59
20353315 ACCATCAACA
* *
20353325 ATGAAAAGGGATTGTGACGACCATCAAATTATGAAAAGGGATGGCTTCGGCTATCAAATT
1 ATGAAAAGGGATGGT-TCGACCATCAAATTATGAAAAGGGATGGCTTCGGCTATCAAATT
* * * *
20353385 ATGAAAAGGGATGGCTTCGACTATCGAATTATAAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATGG-TTCGACCATCAAATTATGAAAAGGGATGGCTTCGGCTATCAAATT
* * * *
20353445 ATGAAAAGGGAT-GTTGATGACCATC-AATAATGAAAAGGGATGG-TGAT-GACCATCAACA--
1 ATGAAAAGGGATGGTT--CGACCATCAAATTATGAAAAGGGATGGCT--TCGGCTATCAA-ATT
** * * * ** *
20353503 ATGAGCAGGGATGGTGAT-GACCATCAAATTATGAAAAGAGTTTGCTTTTGCTATCAAAAT
1 ATGAAAAGGGATGGT--TCGACCATCAAATTATGAAAAGGGATGGCTTCGGCTATCAAATT
* * * * * *
20353563 ATGGAAAGGGATAGCTTCGGCTATCGAACTATGAAAAGGGATGG
1 ATGAAAAGGGAT-GGTTCGACCATCAAATTATGAAAAGGGATGG
20353607 TAACAACCAT
Statistics
Matches: 173, Mismatches: 33, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
58 22 0.13
59 46 0.27
60 101 0.58
61 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (59 bp):
ATGAAAAGGGATGGTTCGACCATCAAATTATGAAAAGGGATGGCTTCGGCTATCAAATT
Found at i:20353540 original size:178 final size:177
Alignment explanation
Indices: 20353242--20353604 Score: 512
Period size: 178 Copynumber: 2.0 Consensus size: 177
20353232 CGACTAATGG
*
20353242 AAAGGGATAACTTCAGCTATCGAATTATGAAAAGAGATTGTGATGACCATCAACAATGAAAGGGA
1 AAAGGGATAACTTCAGCTATCAAATTATGAAAAGAGATTGTGATGACCATCAACAATGAAAGGGA
* *
20353307 TGGTGACGACCATCAACAATGAAAAGGGATTGTGACGACCATCAAATTATGAAAAGGGATGGCTT
66 TGGTGACGACCATCAACAATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAGAGATGGCTT
* * *
20353372 CGGCTATCAAATTATGAAAAGGGATGGCTTCGACTATCGAATTATAA
131 CGGCTATCAAAATATGAAAAGGGATAGCTTCGACTATCGAACTATAA
* * * *
20353419 AAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGA-TGTTGATGACCATCAATAATGAAAAGG
1 AAAGGGATAACTTCAGCTATCAAATTATGAAAAGAGATTG-TGATGACCATCAACAATG-AAAGG
* ** * * *
20353483 GATGGTGATGACCATCAACAATGAGCAGGGATGGTGATGACCATCAAATTATGAAAAGAGTTTGC
64 GATGGTGACGACCATCAACAATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAGAGATGGC
** * * *
20353548 TTTTGCTATCAAAATATGGAAAGGGATAGCTTCGGCTATCGAACTATGA
129 TTCGGCTATCAAAATATGAAAAGGGATAGCTTCGACTATCGAACTATAA
20353597 AAAGGGAT
1 AAAGGGAT
20353605 GGTAACAACC
Statistics
Matches: 163, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
176 2 0.01
177 50 0.31
178 111 0.68
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (177 bp):
AAAGGGATAACTTCAGCTATCAAATTATGAAAAGAGATTGTGATGACCATCAACAATGAAAGGGA
TGGTGACGACCATCAACAATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAGAGATGGCTT
CGGCTATCAAAATATGAAAAGGGATAGCTTCGACTATCGAACTATAA
Found at i:20354486 original size:20 final size:20
Alignment explanation
Indices: 20354437--20354486 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
20354427 GGGTCATACG
*
20354437 GCCAAGCCGCACGTCCTTGT
1 GCCAAGCCGTACGTCCTTGT
20354457 GCCAAGCCGTACGTCCTTGT
1 GCCAAGCCGTACGTCCTTGT
20354477 GCCAAGCCGT
1 GCCAAGCCGT
20354487 GTACCCTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.38, G:0.26, T:0.20
Consensus pattern (20 bp):
GCCAAGCCGTACGTCCTTGT
Found at i:20358119 original size:19 final size:19
Alignment explanation
Indices: 20358083--20358130 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
20358073 GTGTTATACT
*
20358083 AATCCCTCAAACTCTCTTA
1 AATCCCTCAAACTATCTTA
20358102 AATCCCTCAAAAC-ATCTTA
1 AATCCCTC-AAACTATCTTA
20358121 AA-CCCT-AAAC
1 AATCCCTCAAAC
20358131 CCCCAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
18 4 0.15
19 15 0.56
20 4 0.15
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (19 bp):
AATCCCTCAAACTATCTTA
Found at i:20365626 original size:27 final size:27
Alignment explanation
Indices: 20365596--20365773 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
20365586 ATATTGAGTC
* * *
20365596 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCAACT
* *
20365623 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
20365650 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
20365678 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
20365705 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
20365732 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
20365759 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20365774 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20365735 original size:82 final size:81
Alignment explanation
Indices: 20365622--20365772 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
20365612 TATAATCATC
* *
20365622 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
20365687 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
20365704 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
20365768 AGTGC
65 AGTGC
20365773 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:20370879 original size:93 final size:93
Alignment explanation
Indices: 20370772--20370942 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
20370762 GCCCCTAAGT
* *
20370772 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
20370837 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* * * *
20370865 GAACTCGGACTCAACTCAACGAGTTCGGACATTTTCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
20370930 CGAGTTCGGATGC
66 CGAGTTCGGATGC
20370943 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:20370939 original size:46 final size:46
Alignment explanation
Indices: 20370767--20370939 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
20370757 AACCCGCCCC
* * * * *
20370767 TAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
* * *
20370813 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTACATCCA
* * *
20370861 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTTCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
20370906 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
20370940 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 2 0.02
46 59 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
Found at i:20371396 original size:30 final size:30
Alignment explanation
Indices: 20371362--20371421 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20371352 ATTTAATACG
20371362 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
20371392 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
20371422 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:20375257 original size:47 final size:47
Alignment explanation
Indices: 20375178--20375272 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
20375168 ATCTAAAACA
* *
20375178 TGCACCGCTCTTCACTCGACATTCTCCGTAGTGAAATTTGTTGCAAC
1 TGCACCGCTCTTCACTCGACATTATCCATAGTGAAATTTGTTGCAAC
* *
20375225 TGCACTGCTCTTCACTCGGCATTATCCATAGTGAAATTTGTTGCAAC
1 TGCACCGCTCTTCACTCGACATTATCCATAGTGAAATTTGTTGCAAC
20375272 T
1 T
20375273 CTTACACTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (47 bp):
TGCACCGCTCTTCACTCGACATTATCCATAGTGAAATTTGTTGCAAC
Found at i:20378590 original size:19 final size:19
Alignment explanation
Indices: 20378566--20378605 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
20378556 TAATCTAACT
20378566 AAACCATTATTGAAATCCA
1 AAACCATTATTGAAATCCA
20378585 AAACCATTATTGAAATCCA
1 AAACCATTATTGAAATCCA
20378604 AA
1 AA
20378606 CATTCCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (19 bp):
AAACCATTATTGAAATCCA
Found at i:20379645 original size:16 final size:17
Alignment explanation
Indices: 20379624--20379663 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
20379614 AAGAAAATTT
20379624 TTATATTTTAA-TTTTG
1 TTATATTTTAATTTTTG
*
20379640 TTATA-TTAAATTTTTG
1 TTATATTTTAATTTTTG
20379656 TTAT-TTTT
1 TTATATTTT
20379664 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TTATATTTTAATTTTTG
Found at i:20380367 original size:38 final size:37
Alignment explanation
Indices: 20380323--20380395 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
20380313 TAATTTAAAG
*
20380323 AAAAAACATTATAATTTAAAAAA-ATTAAAAATATATGA
1 AAAAAACATTA-AAATTAAAAAATA-TAAAAATATATGA
*
20380361 AAAAAACTTTAAAATTAAAAAATATAAAAATATAT
1 AAAAAACATTAAAATTAAAAAATATAAAAATATAT
20380396 TTTTAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 21 0.66
38 11 0.34
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (37 bp):
AAAAAACATTAAAATTAAAAAATATAAAAATATATGA
Found at i:20380633 original size:21 final size:21
Alignment explanation
Indices: 20380593--20380634 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20380583 AACAACGGTG
* *
20380593 GCGGTGAGATTAGTTTCTGTA
1 GCGGTGAGATTAGATACTGTA
*
20380614 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
20380635 ACAATGGTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.36, T:0.33
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:20380855 original size:22 final size:23
Alignment explanation
Indices: 20380785--20380868 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 23
20380775 ATATGTTAAT
*
20380785 TTATAAATTAATTTAATAAAATA
1 TTATAAATTAATTTAATAAATTA
* **
20380808 TTA-AAATGTATCTTTTAATATTTTA
1 TTATAAAT-TA--ATTTAATAAATTA
*
20380833 TTATAAA-TATTTTAATAAATTA
1 TTATAAATTAATTTAATAAATTA
20380855 -TAT-AATTAATTTAA
1 TTATAAATTAATTTAA
20380869 ATTATTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 2 0.04
21 10 0.20
22 15 0.31
23 5 0.10
24 2 0.04
25 12 0.24
26 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
TTATAAATTAATTTAATAAATTA
Found at i:20387438 original size:19 final size:16
Alignment explanation
Indices: 20387405--20387454 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
20387395 TAAATTTTGG
20387405 AATTTTTTATATTTTA
1 AATTTTTTATATTTTA
*
20387421 AATTCTTTTATATTTTT
1 AATT-TTTTATATTTTA
*
20387438 TATTTTTTGA-ATTTTA
1 AATTTTTT-ATATTTTA
20387454 A
1 A
20387455 TGAGTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (16 bp):
AATTTTTTATATTTTA
Found at i:20387973 original size:17 final size:16
Alignment explanation
Indices: 20387946--20387982 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
20387936 TATTATTTTT
20387946 ATTTAATATTTAATAA
1 ATTTAATATTTAATAA
*
20387962 ATTTATATATTTAATTA
1 ATTTA-ATATTTAATAA
20387979 ATTT
1 ATTT
20387983 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTAATATTTAATAA
Found at i:20387974 original size:24 final size:24
Alignment explanation
Indices: 20387945--20388023 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
20387935 ATATTATTTT
20387945 TATTTAATATTTAATAAATTTATA
1 TATTTAATATTTAATAAATTTATA
**
20387969 TATTTAATTAATTTTTTAAATATTATA
1 TATTTAA-T-ATTTAATAAAT-TTATA
* *
20387996 TTTTTAATA-TTCATAAATTATATA
1 TATTTAATATTTAATAAATT-TATA
20388020 TATT
1 TATT
20388024 ATTAGTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.02
24 21 0.47
25 2 0.04
26 10 0.22
27 11 0.24
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTAATATTTAATAAATTTATA
Found at i:20388001 original size:27 final size:28
Alignment explanation
Indices: 20387939--20388003 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
20387929 TTGACTATAT
*
20387939 TATTTTTATTTAATATTTAATAAATTTA
1 TATTTTTAATTAATATTTAATAAATTTA
* *
20387967 TATATTTAATTAAT-TTT-TTAAATATTA
1 TATTTTTAATTAATATTTAATAAAT-TTA
20387994 TATTTTTAAT
1 TATTTTTAAT
20388004 ATTCATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 5 0.16
27 15 0.47
28 12 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TATTTTTAATTAATATTTAATAAATTTA
Found at i:20388714 original size:3 final size:3
Alignment explanation
Indices: 20388706--20388741 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
20388696 GTAATTACAT
20388706 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20388742 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20405234 original size:50 final size:50
Alignment explanation
Indices: 20405117--20405463 Score: 365
Period size: 50 Copynumber: 6.8 Consensus size: 50
20405107 GTATATAACA
* * * ** * * * *
20405117 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * ** *
20405166 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
*
20405216 TGCCCATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-G
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-AGG
* *
20405266 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* ** * *
20405316 TGCCAACGTTATCTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * *
20405366 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATAATCTTAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-A-GG
* *
20405422 TGCCAATGACATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
20405464 TTACCCAAAT
Statistics
Matches: 252, Mismatches: 37, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
49 37 0.15
50 171 0.68
51 1 0.00
53 3 0.01
54 1 0.00
56 39 0.15
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:20405387 original size:150 final size:154
Alignment explanation
Indices: 20405179--20405458 Score: 415
Period size: 150 Copynumber: 1.8 Consensus size: 154
20405169 CAATGCCATA
* ** * *
20405179 TCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCT
* *
20405244 TACATGGGACCTCTC-ATC-TCA-G-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACA
66 TACATGGGACCTCTCAATCTTAATGATGCCAATGACATGTCCCAGACATGGTCTTACATGGGACA
20405305 TCTCATCTCGGTGCCAACGTTATC
131 TCTCATCTCGGTGCCAACGTTATC
* * *
20405329 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCT
*
20405394 TATATGGGACCTCTCATAATCTTAATGATGCCAATGACATGTCCCAGACATGGTCTTACATGGGA
66 TACATGGGACCTCTC--AATCTTAATGATGCCAATGACATGTCCCAGACATGGTCTTACATGGGA
20405459 TCTCTTTACC
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
150 71 0.63
153 3 0.03
154 2 0.02
155 1 0.01
156 36 0.32
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (154 bp):
TCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCT
TACATGGGACCTCTCAATCTTAATGATGCCAATGACATGTCCCAGACATGGTCTTACATGGGACA
TCTCATCTCGGTGCCAACGTTATC
Found at i:20421459 original size:45 final size:45
Alignment explanation
Indices: 20421389--20421521 Score: 144
Period size: 45 Copynumber: 3.0 Consensus size: 45
20421379 GCTATACATC
* * * * *
20421389 AAAGATGAGTAAGACCGTAGTTGAAAGATGCTATGGCATCATGGT
1 AAAGATAAGTAAGACCATAGCTGAAAGATGATATGGCATCATGAT
* *
20421434 AAAGATAAGTAAGACCATAGCTGAAAGATGTTATAGCATCATGAT
1 AAAGATAAGTAAGACCATAGCTGAAAGATGATATGGCATCATGAT
* * *
20421479 AGAA-ATGAA-TAAGACCATAGCTAAAAGACGATATGGAATCATG
1 A-AAGAT-AAGTAAGACCATAGCTGAAAGATGATATGGCATCATG
20421522 CGAAAGCACA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
45 71 0.95
46 4 0.05
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (45 bp):
AAAGATAAGTAAGACCATAGCTGAAAGATGATATGGCATCATGAT
Found at i:20421851 original size:39 final size:39
Alignment explanation
Indices: 20421808--20421925 Score: 94
Period size: 39 Copynumber: 3.2 Consensus size: 39
20421798 CATATAAAGA
20421808 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
1 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
* * *
20421847 AATGAG-TGACTG-G----AGTG-AT-TAGTC-ATATA-AAGA
1 AATGAGTTG-GTGTGACCAAG-GAATATAGACTAT-TAGAA-T
20421880 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
1 AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
*
20421919 AAGGAGT
1 AATGAGT
20421926 GACGTCAAGG
Statistics
Matches: 58, Mismatches: 7, Indels: 28
0.62 0.08 0.30
Matches are distributed among these distances:
32 4 0.07
33 14 0.24
34 7 0.12
35 1 0.02
37 1 0.02
38 7 0.12
39 20 0.34
40 4 0.07
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (39 bp):
AATGAGTTGGTGTGACCAAGGAATATAGACTATTAGAAT
Found at i:20421895 original size:72 final size:72
Alignment explanation
Indices: 20421778--20421928 Score: 293
Period size: 72 Copynumber: 2.1 Consensus size: 72
20421768 TGGAGTTCAC
20421778 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
1 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
*
20421843 GAATAAT
66 GAATAAG
20421850 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
1 GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
20421915 GAATAAG
66 GAATAAG
20421922 GAGTGAC
1 GAGTGAC
20421929 GTCAAGGTTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.26
Consensus pattern (72 bp):
GAGTGACTGGAGTGATTAGTCATATAAAGAAATGAGTTGGTGTGACCAAGGAATATAGACTATTA
GAATAAG
Found at i:20422940 original size:42 final size:42
Alignment explanation
Indices: 20422867--20422950 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
20422857 GTGTCCCAAC
* * * * *
20422867 CCGTGTCTTTTCCCATGTAACTTATTGACTTGAGACACACGG
1 CCGTGTCTCTGCCCATGTAACTCACTAACTTGAGACACACGG
* *
20422909 CCGTGTCTCTGCCCATGTAACTCACTAACTTGGGTCACACGG
1 CCGTGTCTCTGCCCATGTAACTCACTAACTTGAGACACACGG
20422951 GTGCGTCGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (42 bp):
CCGTGTCTCTGCCCATGTAACTCACTAACTTGAGACACACGG
Found at i:20439370 original size:9 final size:9
Alignment explanation
Indices: 20439356--20439406 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
20439346 GAAATCATAA
20439356 AAAAATTAT
1 AAAAATTAT
20439365 AAAAATTAT
1 AAAAATTAT
**
20439374 AAATTTTCAT
1 AAAAATT-AT
*
20439384 AAAAATCAT
1 AAAAATTAT
20439393 AAAAAATTAT
1 -AAAAATTAT
20439403 AAAA
1 AAAA
20439407 TGCATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 20 0.59
10 14 0.41
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20439374 original size:29 final size:29
Alignment explanation
Indices: 20439338--20439417 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
20439328 TTAACTTTGT
*
20439338 AAAA-TATAGAAATCATAAAAAAATTAT-A
1 AAAATTATA-AAATCATAAAAAAATCATAA
*
20439366 AAAATTATAAATTTTCAT--AAAAATCATAA
1 AAAATTATAAA--ATCATAAAAAAATCATAA
20439395 AAAATTATAAAATGCATAAAAAA
1 AAAATTATAAAAT-CATAAAAAA
20439418 TTACCTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
27 1 0.02
28 17 0.40
29 16 0.38
30 8 0.19
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAATTATAAAATCATAAAAAAATCATAA
Found at i:20439404 original size:19 final size:19
Alignment explanation
Indices: 20439338--20439420 Score: 82
Period size: 19 Copynumber: 4.4 Consensus size: 19
20439328 TTAACTTTGT
*
20439338 AAAA-TATAGAAATCATAAA
1 AAAATTATAAAAATCAT-AA
*
20439357 AAAATTATAAAAATTAT-A
1 AAAATTATAAAAATCATAA
**
20439375 AATTTTCATAAAAATCATAA
1 AAAATT-ATAAAAATCATAA
20439395 AAAATTAT-AAAATGCATAA
1 AAAATTATAAAAAT-CATAA
20439414 AAAATTA
1 AAAATTA
20439421 CCTTTAACCA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 10 0.19
19 28 0.53
20 15 0.28
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATTATAAAAATCATAA
Found at i:20439412 original size:28 final size:28
Alignment explanation
Indices: 20439356--20439416 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
20439346 GAAATCATAA
* * *
20439356 AAAAATTATAAAAATTATAAATTTTCAT
1 AAAAATCATAAAAATTATAAATATGCAT
20439384 AAAAATCATAAAAAATTATAAA-ATGCAT
1 AAAAATCAT-AAAAATTATAAATATGCAT
20439412 AAAAA
1 AAAAA
20439417 ATTACCTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAATCATAAAAATTATAAATATGCAT
Found at i:20439418 original size:29 final size:27
Alignment explanation
Indices: 20439338--20439418 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 27
20439328 TTAACTTTGT
*
20439338 AAAA-TATAGAAATCATAAAAAAATTATA
1 AAAATTATA-AAATCAT-AAAAAATCATA
*
20439366 AAAATTATAAATTTTCAT-AAAAATCATAA
1 AAAATTATAAA--ATCATAAAAAATCAT-A
20439395 AAAATTATAAAATGCATAAAAAAT
1 AAAATTATAAAAT-CATAAAAAAT
20439419 TACCTTTAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
27 1 0.02
28 17 0.39
29 22 0.50
30 4 0.09
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAATTATAAAATCATAAAAAATCATA
Found at i:20439541 original size:15 final size:16
Alignment explanation
Indices: 20439523--20439553 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20439513 ACATGTGACA
20439523 AAAAAT-AATAAAAGT
1 AAAAATCAATAAAAGT
20439538 AAAAATCAATAAAAGT
1 AAAAATCAATAAAAGT
20439554 TATAGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAAATCAATAAAAGT
Found at i:20439740 original size:10 final size:9
Alignment explanation
Indices: 20439587--20439742 Score: 52
Period size: 9 Copynumber: 16.2 Consensus size: 9
20439577 TTCTGGTACA
20439587 ATAATTTTT
1 ATAATTTTT
20439596 ATAATTTTTT
1 ATAA-TTTTT
* *
20439606 TTACGAATTTT
1 ATA--ATTTTT
*
20439617 ATATTTCTTT
1 ATAATT-TTT
20439627 AT-ATTTTT
1 ATAATTTTT
20439635 ATAA-TTTT
1 ATAATTTTT
*
20439643 ATTACGA-CTTT
1 A-TA--ATTTTT
20439654 ATAATATTTT
1 ATAAT-TTTT
20439664 ATAATATTTTT
1 AT-A-ATTTTT
* *
20439675 CTTATTTTTT
1 -ATAATTTTT
*
20439685 CTAATTTTT
1 ATAATTTTT
20439694 A-ATATTTTT
1 ATA-ATTTTT
20439703 AT-ATTTTCT
1 ATAATTTT-T
* *
20439712 ATTAAAATTTA
1 A-T-AATTTTT
20439723 ATAATTTTT
1 ATAATTTTT
*
20439732 ATAACTTTT
1 ATAATTTTT
20439741 AT
1 AT
20439743 TGATTTATAA
Statistics
Matches: 110, Mismatches: 18, Indels: 38
0.66 0.11 0.23
Matches are distributed among these distances:
8 17 0.15
9 41 0.37
10 26 0.24
11 18 0.16
12 8 0.07
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:20440035 original size:88 final size:89
Alignment explanation
Indices: 20439863--20440035 Score: 206
Period size: 88 Copynumber: 2.0 Consensus size: 89
20439853 TCAAAGGAAC
* * *
20439863 TTTTTGATGCATTTTGACAGTTCAAATACTCAATTGAGTGCAAAAAAAAAATAGGGGCTTAATTG
1 TTTTTGATGCATTTTAAAAGTTCAAATACTCAATTGAGTGCAAAAAAAAAATAAGGGCTTAATTG
* ** **
20439928 CTTTTTTTTTAAAGTTTGAGGGTA
66 CTTTTTCTGAAAAAATTGAGGGTA
* * * * *
20439952 TTTTTTATGCATTTTAAAAGTTTAAGTAC-CTAATTGAGTG-AACAAGAAAATAAGGGCTTAATT
1 TTTTTGATGCATTTTAAAAGTTCAAATACTC-AATTGAGTGCAAAAAAAAAATAAGGGCTTAATT
20440015 GCTTTTTCTGAAAAAATTGAG
65 GCTTTTTCTGAAAAAATTGAG
20440036 AGCTTTTTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
88 37 0.53
89 33 0.47
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (89 bp):
TTTTTGATGCATTTTAAAAGTTCAAATACTCAATTGAGTGCAAAAAAAAAATAAGGGCTTAATTG
CTTTTTCTGAAAAAATTGAGGGTA
Found at i:20442236 original size:10 final size:9
Alignment explanation
Indices: 20442213--20442258 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
20442203 AACTATAACT
*
20442213 TCATTTTAA
1 TCATTTTTA
20442222 TCATTTTTA
1 TCATTTTTA
*
20442231 TACATTTTAA
1 T-CATTTTTA
20442241 TCATTTTTA
1 TCATTTTTA
20442250 TACATTTTT
1 T-CATTTTT
20442259 TTAATATGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (9 bp):
TCATTTTTA
Found at i:20442238 original size:19 final size:19
Alignment explanation
Indices: 20442214--20442257 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
20442204 ACTATAACTT
20442214 CATTTTAATCATTTTTATA
1 CATTTTAATCATTTTTATA
20442233 CATTTTAATCATTTTTATA
1 CATTTTAATCATTTTTATA
20442252 CATTTT
1 CATTTT
20442258 TTTAATATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (19 bp):
CATTTTAATCATTTTTATA
Found at i:20445333 original size:24 final size:24
Alignment explanation
Indices: 20445306--20445362 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
20445296 AAACCTAATT
* *
20445306 CTAATCAATGTCAAATAAATTATG
1 CTAATAAATGTCAAATAAATTATA
* *
20445330 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATAAATTATA
20445354 CTAATAAAT
1 CTAATAAAT
20445363 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATAAATTATA
Found at i:20445368 original size:24 final size:24
Alignment explanation
Indices: 20445318--20445369 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20445308 AATCAATGTC
* **
20445318 AAATAAATTATGCTAATAAATGTT
1 AAATAAATTATACTAATAAATACT
*
20445342 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
20445366 AAAT
1 AAAT
20445370 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:20445499 original size:29 final size:29
Alignment explanation
Indices: 20445462--20445518 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
20445452 CACTTTTACT
* *
20445462 CGAATTCTCAAGGAACAAGTTCTTCACCA
1 CGAACTCTCAAGGAACAAGTTCTCCACCA
*
20445491 CGAACTCTCAATGAACAAGTTCTCCACC
1 CGAACTCTCAAGGAACAAGTTCTCCACC
20445519 TCTTCAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.23
Consensus pattern (29 bp):
CGAACTCTCAAGGAACAAGTTCTCCACCA
Found at i:20448697 original size:24 final size:24
Alignment explanation
Indices: 20448670--20448726 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
20448660 AAACCTAATT
* *
20448670 CTAATCAATGTCAAATAAATTATG
1 CTAATAAATGTCAAATAAATTATA
* *
20448694 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATAAATTATA
20448718 CTAATAAAT
1 CTAATAAAT
20448727 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATAAATTATA
Found at i:20448732 original size:24 final size:24
Alignment explanation
Indices: 20448682--20448733 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20448672 AATCAATGTC
* **
20448682 AAATAAATTATGCTAATAAATGTT
1 AAATAAATTATACTAATAAATACT
*
20448706 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
20448730 AAAT
1 AAAT
20448734 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:20459003 original size:21 final size:21
Alignment explanation
Indices: 20458977--20459036 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
20458967 ATTTATTTAT
20458977 TTTTTATAGACAATTTGTTAA
1 TTTTTATAGACAATTTGTTAA
*
20458998 TTTTTATAAACAA--T-TT--
1 TTTTTATAGACAATTTGTTAA
20459014 TTTTTATAGA-AATTTGTTAA
1 TTTTTATAGACAATTTGTTAA
20459034 TTT
1 TTT
20459037 ATTCATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
15 2 0.06
16 9 0.28
17 1 0.03
18 4 0.12
19 1 0.03
20 3 0.09
21 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTTATAGACAATTTGTTAA
Found at i:20461932 original size:42 final size:41
Alignment explanation
Indices: 20461873--20461960 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 41
20461863 AAAAGCAACT
*
20461873 TTTTGACCTTGCCCTTGATGCAATGGAGATGATAGGGATGA
1 TTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
20461914 GTTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
1 -TTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
20461956 TTTTG
1 TTTTG
20461961 GTTTAGCTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (41 bp):
TTTTGACCTTGCCCTTGATACAATGGAGATGATAGGGATGA
Found at i:20463221 original size:25 final size:25
Alignment explanation
Indices: 20463189--20463238 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
20463179 TCGTTTTTAG
*
20463189 TTTGATGCCGAATTTGTTTGACTAA
1 TTTGATGCCGAATTTGTTGGACTAA
*
20463214 TTTGATGCTGAATTTGTTGGACTAA
1 TTTGATGCCGAATTTGTTGGACTAA
20463239 GCACTTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (25 bp):
TTTGATGCCGAATTTGTTGGACTAA
Found at i:20463457 original size:25 final size:25
Alignment explanation
Indices: 20463424--20463473 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20463414 TCACTAAGAG
20463424 ATAGAATAAAAATTATGAAAAGTAA
1 ATAGAATAAAAATTATGAAAAGTAA
20463449 ATAGAATAAAAATTATGAAAAGTAA
1 ATAGAATAAAAATTATGAAAAGTAA
20463474 GTAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (25 bp):
ATAGAATAAAAATTATGAAAAGTAA
Found at i:20463481 original size:25 final size:25
Alignment explanation
Indices: 20463428--20463486 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
20463418 TAAGAGATAG
*
20463428 AATAAAAATTATGAAAAGTAAATAG
1 AATAAAAATTATGAAAAGTAAATAA
*
20463453 AATAAAAATTATGAAAAGTAAGTAA
1 AATAAAAATTATGAAAAGTAAATAA
*
20463478 AATATAAAT
1 AATAAAAAT
20463487 AAAAGTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.25
Consensus pattern (25 bp):
AATAAAAATTATGAAAAGTAAATAA
Found at i:20465107 original size:30 final size:30
Alignment explanation
Indices: 20465071--20465168 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
20465061 AAAGTAAATC
20465071 AAAATTCAACTCAGTGCCAAAATTAAACTA
1 AAAATTCAACTCAGTGCCAAAATTAAACTA
* * * *
20465101 AAAATTCATTA-TCCA--ACCACACAGTAAA-TC
1 AAAATTCA--ACT-CAGTGCCA-AAATTAAACTA
20465131 AAAATTCAACTCAGTGCCAAAATTAAACTA
1 AAAATTCAACTCAGTGCCAAAATTAAACTA
20465161 AAAATTCA
1 AAAATTCA
20465169 TTATCCAACC
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
28 3 0.06
29 7 0.13
30 32 0.62
31 7 0.13
32 3 0.06
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.23
Consensus pattern (30 bp):
AAAATTCAACTCAGTGCCAAAATTAAACTA
Found at i:20465130 original size:60 final size:60
Alignment explanation
Indices: 20465058--20465185 Score: 247
Period size: 60 Copynumber: 2.1 Consensus size: 60
20465048 TTATTTAATT
*
20465058 CACAAAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
1 CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
20465118 CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
1 CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
20465178 CACACAGT
1 CACACAGT
20465186 TTCAATGAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.23
Consensus pattern (60 bp):
CACACAGTAAATCAAAATTCAACTCAGTGCCAAAATTAAACTAAAAATTCATTATCCAAC
Found at i:20478967 original size:37 final size:37
Alignment explanation
Indices: 20478917--20478990 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
20478907 CACCGAATTG
20478917 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
1 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
20478954 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
1 GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
20478991 AAACTCATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (37 bp):
GCTAAGCTAACTTATGTTACTTTTTAAGACTTTAAAT
Found at i:20488522 original size:79 final size:78
Alignment explanation
Indices: 20488420--20488642 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
20488410 GCTCCTCGTT
* *
20488420 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
20488485 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
20488500 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
20488564 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
20488578 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
20488641 GA
63 GA
20488643 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:20488537 original size:39 final size:40
Alignment explanation
Indices: 20488420--20488642 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
20488410 GCTCCTCGTT
* *
20488420 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
20488460 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
20488500 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
20488539 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
20488578 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
20488619 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20488643 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:20497992 original size:61 final size:60
Alignment explanation
Indices: 20497855--20498114 Score: 182
Period size: 61 Copynumber: 4.3 Consensus size: 60
20497845 TAAACAGAGG
* * * * * *
20497855 TTGCCACAAAGGCTTTTCTCTAT-AA-ATTTTTTCCACAAAGGTTATCCTTTATATTCGATGC
1 TTGCCACAAAGGC-TTTCT-TGTCAAGATTTTTACCACAAAGGCTATCCTTTACATTAG-TAC
*** * * *
20497916 TCATCACAAAAGCTTTCTTGTCTAGATTTTTTCCACAAAGGCTATCCTTTACAATTAGTAC
1 TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTAC-ATTAGTAC
* * * * * * * * * *
20497977 TTGCCATAAAGGCTTTCATGTCCAGAGTTGTGCCACAAAGACCATCCTTTATATCCAGTAC
1 TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTACAT-TAGTAC
* * * * * **
20498038 TCGCCACAAAGGCTTTCTCGTCAAAATTTTTACCACAAAGGTTGTATTTTACATTCAGTAC
1 TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTACATT-AGTAC
*
20498099 TTGCCACAAGGGCTTT
1 TTGCCACAAAGGCTTT
20498115 GCTTCTCCTG
Statistics
Matches: 151, Mismatches: 43, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
59 2 0.01
60 8 0.05
61 137 0.91
62 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (60 bp):
TTGCCACAAAGGCTTTCTTGTCAAGATTTTTACCACAAAGGCTATCCTTTACATTAGTAC
Found at i:20504945 original size:26 final size:26
Alignment explanation
Indices: 20504894--20504945 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
20504884 ATATAATTTC
*
20504894 CAAATCATGTATCTATATATCGTGTA
1 CAAATCATGTATCTATATATCATGTA
* *
20504920 CAAATCAT-TTTCATATATCTCATGTA
1 CAAATCATGTATC-TATATATCATGTA
20504946 AATACCTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (26 bp):
CAAATCATGTATCTATATATCATGTA
Found at i:20516655 original size:38 final size:39
Alignment explanation
Indices: 20516594--20516668 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
20516584 ATCCAACCCA
*
20516594 ACCCGATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCGATTACCCAACCCAATAAAAATAAAACTAAAGTCT
*
20516633 ACCCGATTA-CCGACCCAATAAAAATAAAACTAAAGT
1 ACCCGATTACCCAACCCAATAAAAATAAAACTAAAGT
20516669 TTAACTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (39 bp):
ACCCGATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:20516851 original size:37 final size:37
Alignment explanation
Indices: 20516801--20516875 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
20516791 TGTTAATTTC
*
20516801 AAGAATTATGTAAT-TTTTATAATTATGTAGTGATTCA
1 AAGAATTAAGTAATATTTT-TAATTATGTAGTGATTCA
*
20516838 AAGACTTAAGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTAAGTAATATTTTTAATTATGTAGTGATTCA
20516875 A
1 A
20516876 TTCGGATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 31 0.89
38 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (37 bp):
AAGAATTAAGTAATATTTTTAATTATGTAGTGATTCA
Found at i:20516888 original size:9 final size:9
Alignment explanation
Indices: 20516874--20516922 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
20516864 GTAGTGATTC
*
20516874 AATTCGGAT
1 AATTCGGGT
20516883 AATTCGGGT
1 AATTCGGGT
20516892 AATTCGGGT
1 AATTCGGGT
*
20516901 AATTCGGTT
1 AATTCGGGT
*
20516910 AATTCGGCT
1 AATTCGGGT
20516919 AATT
1 AATT
20516923 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (9 bp):
AATTCGGGT
Found at i:20517105 original size:12 final size:12
Alignment explanation
Indices: 20517088--20517118 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20517078 TTCAGGTCAA
*
20517088 TTAACCGGTTGG
1 TTAACCGGTCGG
20517100 TTAACCGGTCGG
1 TTAACCGGTCGG
20517112 TTAACCG
1 TTAACCG
20517119 AATGCACACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (12 bp):
TTAACCGGTCGG
Found at i:20520698 original size:93 final size:92
Alignment explanation
Indices: 20520590--20520770 Score: 317
Period size: 93 Copynumber: 2.0 Consensus size: 92
20520580 ATATAGGGTC
* * *
20520590 CCCCTATAGAACAACACTTCTTTAATCACATCAAATAGCACATGTAGAGGGTAGTCCATAACTCA
1 CCCCTATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTCA
*
20520655 AAATATGTAGATGGTAGTCCATAGATT
66 AAATATGTAGAGGGTAGTCCATAGATT
20520682 CCCCTGATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTC
1 CCCCT-ATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTC
20520747 AAAATATGTAGAGGGTAGTCCATA
65 AAAATATGTAGAGGGTAGTCCATA
20520771 ACGCAAAATA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
92 5 0.06
93 79 0.94
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (92 bp):
CCCCTATAGAACAACACATCTTTAATCACATCAAAGAGCACATGTAGAGGGTACTCCATAACTCA
AAATATGTAGAGGGTAGTCCATAGATT
Found at i:20520768 original size:28 final size:28
Alignment explanation
Indices: 20520724--20520797 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
20520714 CAAAGAGCAC
* *
20520724 ATGTAGAGGGTACTCCATAACTCAAAAT
1 ATGTAGAGGGTAGTCCATAACGCAAAAT
20520752 ATGTAGAGGGTAGTCCATAACGCAAAAT
1 ATGTAGAGGGTAGTCCATAACGCAAAAT
20520780 ATGTAGAGGGTAGTCCAT
1 ATGTAGAGGGTAGTCCAT
20520798 GACTTTGCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (28 bp):
ATGTAGAGGGTAGTCCATAACGCAAAAT
Found at i:20523561 original size:41 final size:41
Alignment explanation
Indices: 20523506--20523612 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
20523496 TGAATTTAAG
* *
20523506 GGGTTGCTAAGTGTATATTCCTCGAATCACTGATCAAAAAA
1 GGGTTGCTAAGTGTAGATTCCTCGAAACACTGATCAAAAAA
* * *
20523547 GGGTTGCTAAGTGTAGATTCCCCGAAACTCTGATCAAAAAG
1 GGGTTGCTAAGTGTAGATTCCTCGAAACACTGATCAAAAAA
*
20523588 GGGTTGCTAAGTGCAGATTCCTCGA
1 GGGTTGCTAAGTGTAGATTCCTCGA
20523613 GAGGTTGCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (41 bp):
GGGTTGCTAAGTGTAGATTCCTCGAAACACTGATCAAAAAA
Found at i:20523676 original size:42 final size:42
Alignment explanation
Indices: 20523615--20523754 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 42
20523605 TTCCTCGAGA
* * *
20523615 GGTTGCTAAGTGTTAATTCCCCGAATTATTGATTTTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGATTTTAAAGGT
* * *
20523657 GGTTGCTAAGTGCTGATTCCACC-ATATCCTTGATTGTGAAA-GA
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATCATTGATT-TTAAAGGT
* * * ** * *
20523700 GGTTGTTATGTGCTGATTCCCCGTATCACAGAATAT-AAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGATTTTAAAGGT
20523741 GGTTGCTAAGTGCT
1 GGTTGCTAAGTGCT
20523755 AATTTCACGG
Statistics
Matches: 75, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
40 2 0.03
41 13 0.17
42 27 0.36
43 29 0.39
44 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGATTTTAAAGGT
Found at i:20527731 original size:20 final size:21
Alignment explanation
Indices: 20527681--20527731 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
20527671 TAGAGATTTG
20527681 GTATCGATAC-CTTTGCTCAA
1 GTATCGATACTCTTTGCTCAA
*
20527701 GTATCGATACTC-TTGCTCGA
1 GTATCGATACTCTTTGCTCAA
20527721 GTATCGATACT
1 GTATCGATACT
20527732 TGGGGTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCTTTGCTCAA
Found at i:20530047 original size:26 final size:26
Alignment explanation
Indices: 20530011--20530063 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
20530001 TATTTTCTCG
*
20530011 AAATTTAACCAGGGGCAAAATCGTCA
1 AAATTTAACCAAGGGCAAAATCGTCA
* * *
20530037 AAATTTTACCAAGGGTAAAATCTTCA
1 AAATTTAACCAAGGGCAAAATCGTCA
20530063 A
1 A
20530064 TTTCTTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (26 bp):
AAATTTAACCAAGGGCAAAATCGTCA
Found at i:20538032 original size:31 final size:30
Alignment explanation
Indices: 20537996--20538064 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
20537986 TTACAAAACG
**
20537996 GTCACTAAGCTATTTGAAAG-TTTTCATTTAA
1 GTCACTAA-CTATTCAAAAGATTTT-ATTTAA
20538027 GTCACTGAACTATTCAAAAGATTTTATTTAA
1 GTCACT-AACTATTCAAAAGATTTTATTTAA
20538058 GTCACTA
1 GTCACTA
20538065 GATTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.79
32 6 0.18
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (30 bp):
GTCACTAACTATTCAAAAGATTTTATTTAA
Found at i:20554529 original size:26 final size:28
Alignment explanation
Indices: 20554490--20554548 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
20554480 AACTATAATT
20554490 AATATAATACTAATAAATA-AATTATTAA
1 AATATAATACTAATAAATATAA-TATTAA
*
20554518 AATA-AATA-TAATAATTATAATATTAA
1 AATATAATACTAATAAATATAATATTAA
20554544 AATAT
1 AATAT
20554549 TATGTCTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 18 0.64
27 6 0.21
28 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AATATAATACTAATAAATATAATATTAA
Found at i:20557893 original size:29 final size:29
Alignment explanation
Indices: 20557816--20557926 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
20557806 TTTTTTTATT
* * * * *
20557816 GAGATGGCCGCAAAGGCTTACTTTTAACA
1 GAGATCGCCACAAAGGCTTCCATTTAATA
* * *
20557845 GAGGTCACCACAAAAGCTTCCATTTAATA
1 GAGATCGCCACAAAGGCTTCCATTTAATA
*
20557874 GAGATCGCCACAAAGGCTTCC-TTACAATA
1 GAGATCGCCACAAAGGCTTCCATT-TAATA
* *
20557903 GAGATAGCCACAAAGGCATCCATT
1 GAGATCGCCACAAAGGCTTCCATT
20557927 CAGAGATAGC
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
28 2 0.03
29 62 0.94
30 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (29 bp):
GAGATCGCCACAAAGGCTTCCATTTAATA
Found at i:20557938 original size:26 final size:26
Alignment explanation
Indices: 20557902--20557971 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
20557892 TCCTTACAAT
20557902 AGAGATAGCCACAAAGGCATCCATTC
1 AGAGATAGCCACAAAGGCATCCATTC
20557928 AGAGATAGCCACCAAA-GCATCCATTC
1 AGAGATAGCCA-CAAAGGCATCCATTC
* * *
20557954 AAAGATTGCCAAAAAGGC
1 AGAGATAGCCACAAAGGC
20557972 TCACTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
25 3 0.08
26 32 0.82
27 4 0.10
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.14
Consensus pattern (26 bp):
AGAGATAGCCACAAAGGCATCCATTC
Found at i:20561470 original size:29 final size:29
Alignment explanation
Indices: 20561433--20561532 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
20561423 AAGCATCTTT
* **
20561433 TTTTTACAGAGATGGTCACAAAGGCTTCC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
*
20561462 TTTTAACAGAGATCATCACCAAGGCTTCC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
* * * *
20561491 ATTTAACAAAGATCACCACAAAGGCTTTC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
* *
20561520 TTATAATAGAGAT
1 TTTTAACAGAGAT
20561533 AGCCACAATG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTTAACAGAGATCATCACAAAGGCTTCC
Found at i:20563616 original size:23 final size:23
Alignment explanation
Indices: 20563590--20563633 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20563580 TGAAATAAGT
*
20563590 CTAAGAAAATAAAAATAAAGCAA
1 CTAAAAAAATAAAAATAAAGCAA
20563613 CTAAAAAAATAAAAATAAAGC
1 CTAAAAAAATAAAAATAAAGC
20563634 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (23 bp):
CTAAAAAAATAAAAATAAAGCAA
Found at i:20563715 original size:12 final size:12
Alignment explanation
Indices: 20563700--20563732 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
20563690 AAGGTAGTAG
20563700 TAAAAATAATAC
1 TAAAAATAATAC
20563712 T-AAAA-AATAC
1 TAAAAATAATAC
20563722 TAAAAATAATA
1 TAAAAATAATA
20563733 GAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.32
11 8 0.42
12 5 0.26
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAAAATAATAC
Found at i:20563741 original size:22 final size:22
Alignment explanation
Indices: 20563700--20563741 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20563690 AAGGTAGTAG
*
20563700 TAAAAATAATACTAAAAAATAC
1 TAAAAATAATACGAAAAAATAC
20563722 TAAAAATAATA-GAAATAAAT
1 TAAAAATAATACGAAA-AAAT
20563742 TAAAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAATAATACGAAAAAATAC
Found at i:20563788 original size:18 final size:18
Alignment explanation
Indices: 20563765--20563868 Score: 68
Period size: 19 Copynumber: 5.4 Consensus size: 18
20563755 AAATCTAAGC
20563765 ATAAGAAAAATAAAAAAA
1 ATAAGAAAAATAAAAAAA
20563783 ATAAGAAAAAATAAGAAAATA
1 ATAAG-AAAAATAA-AAAA-A
* * *
20563804 GATAAAAAATAATATAACAA
1 -ATAAGAAA-AATAAAAAAA
* *
20563824 ATAATAATAAAT-AATAAA
1 ATAAGAA-AAATAAAAAAA
*
20563842 ATAA-TAAAATAAAATAAA
1 ATAAGAAAAATAAAA-AAA
20563860 ATAAAGAAA
1 AT-AAGAAA
20563869 TGGGTAAAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.06
17 3 0.05
18 17 0.26
19 19 0.29
20 8 0.12
21 7 0.11
22 8 0.12
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (18 bp):
ATAAGAAAAATAAAAAAA
Found at i:20563836 original size:41 final size:37
Alignment explanation
Indices: 20563770--20563868 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 37
20563760 TAAGCATAAG
20563770 AAAAATAAAAAAAATAAGAAAAAATAAGAAAATAGATA
1 AAAAATAAAAAAAATAAGAAAAAATAAGAAAATA-ATA
* * *
20563808 AAAAATAATATAACAAATAATAATAAATAATAAAATAAT-
1 AAAAATAA-A-AA-AAATAAGAAAAAATAAGAAAATAATA
20563847 -AAAATAAAATAAAATAAAGAAA
1 AAAAATAAAA-AAAAT-AAGAAA
20563869 TGGGTAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
36 5 0.10
37 6 0.12
38 15 0.29
39 1 0.02
40 4 0.08
41 20 0.39
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (37 bp):
AAAAATAAAAAAAATAAGAAAAAATAAGAAAATAATA
Found at i:20563839 original size:25 final size:26
Alignment explanation
Indices: 20563776--20563863 Score: 53
Period size: 25 Copynumber: 3.5 Consensus size: 26
20563766 TAAGAAAAAT
* *
20563776 AAAA-AAAATAAGAAAA-AATAAGAA
1 AAAATAAAATAATAAAATAATAATAA
* *
20563800 AATAGATAAAA-AATAATATAACAA-ATA
1 AA-A-ATAAAATAATAAAATAATAATA-A
*
20563827 ATAAT-AAATAATAAAATAATAA-AA
1 AAAATAAAATAATAAAATAATAATAA
20563851 TAAAATAAAATAA
1 -AAAATAAAATAA
20563864 AGAAATGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
24 6 0.12
25 19 0.39
26 14 0.29
27 10 0.20
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAATAAAATAATAAAATAATAATAA
Found at i:20563864 original size:10 final size:9
Alignment explanation
Indices: 20563765--20563860 Score: 75
Period size: 10 Copynumber: 9.7 Consensus size: 9
20563755 AAATCTAAGC
*
20563765 ATAAGAAAA
1 ATAAAAAAA
20563774 ATAAAAAAA
1 ATAAAAAAA
20563783 ATAAGAAAAA
1 ATAA-AAAAA
20563793 ATAAGAAAATA
1 ATAA-AAAA-A
20563804 GATAAAAAATA
1 -ATAAAAAA-A
* *
20563815 ATATAACAA
1 ATAAAAAAA
*
20563824 ATAATAATAA
1 ATAA-AAAAA
20563834 ATAATAAAATA
1 ATAA-AAAA-A
20563845 ATAAAATAAA
1 ATAAAA-AAA
20563855 ATAAAA
1 ATAAAA
20563861 TAAAGAAATG
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
9 16 0.21
10 41 0.55
11 14 0.19
12 4 0.05
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:20566022 original size:29 final size:29
Alignment explanation
Indices: 20565985--20566084 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
20565975 AAGCATCTTT
* **
20565985 TTTTTACAGAGATGGTCACAAAGGCTTCC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
*
20566014 TTTTAACAGAGATCATCACCAAGGCTTCC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
* * * *
20566043 ATTTAACAAAGATCACCACAAAGGCTTTC
1 TTTTAACAGAGATCATCACAAAGGCTTCC
* *
20566072 TTATAATAGAGAT
1 TTTTAACAGAGAT
20566085 AGCCACAATG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTTAACAGAGATCATCACAAAGGCTTCC
Done.