Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 67 of 182
Found at i:20427450 original size:3 final size:3
Alignment explanation
Indices: 20427442--20427485 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
20427432 ATCACATGTT
20427442 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTGA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
20427486 TGGATGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20441217 original size:17 final size:17
Alignment explanation
Indices: 20441195--20441246 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
20441185 AATATGGAAG
20441195 GTGATCTTTAGAGATAT
1 GTGATCTTTAGAGATAT
*
20441212 GTGATC-TTAGATATTAAT
1 GTGATCTTTAGAGA-T-AT
*
20441230 GTAATCTTTAGAAGATA
1 GTGATCTTTAG-AGATA
20441247 CGATTATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 8 0.29
19 5 0.18
20 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (17 bp):
GTGATCTTTAGAGATAT
Found at i:20442742 original size:202 final size:202
Alignment explanation
Indices: 20442391--20442795 Score: 711
Period size: 202 Copynumber: 2.0 Consensus size: 202
20442381 AAGCAAGAGC
20442391 TGCAACGCCGAGGAGTTCAAGAGCTTACCAATAGCTTACAATTGAAGGAACTTTTGGATACGAGA
1 TGCAACGCCGAGGAGTTCAAGAGCTTACCAATAGCTTACAATTGAAGGAACTTTTGGATACGAGA
* * *
20442456 TTCATTAGACCATCTAAATCCCCATTCGGCGCGCCAGTGTTGTTTCAAAAGAAACATGATGGGTC
66 TTCATTAGACCATCTAAATCCCCATACGGCGCGCCAGTGCTATTTCAAAAGAAACATGATGGGTC
* * *
20442521 TTTGAAAATGTGCATCGATTATCAGGCTTTAAACAAGATCACTGTGAAGAATAGGTACCCTATTC
131 CTTGAAAATGTGCATCGATTATCAGGCTTTAAACAAGATCACTGTGAAGAATAAGTACCATATTC
20442586 CTCTTAT
196 CTCTTAT
* *
20442593 TGCAGCGCCGAGGAGTTCAAGAGCTTACCAATAGCTTACAATTGAAGGAACTTTTGGATGCGAGA
1 TGCAACGCCGAGGAGTTCAAGAGCTTACCAATAGCTTACAATTGAAGGAACTTTTGGATACGAGA
*
20442658 TTCATTAGACCATCTAAATCCCCATACGGTGCGCCAGTGCTATTTCAAAAGAAACATGATGGGTC
66 TTCATTAGACCATCTAAATCCCCATACGGCGCGCCAGTGCTATTTCAAAAGAAACATGATGGGTC
* *
20442723 CTTGAGAATGTGCATCGATTATCAGGCTTTAAACAAGATCATTGTGAAGAATAAGTACCATATTC
131 CTTGAAAATGTGCATCGATTATCAGGCTTTAAACAAGATCACTGTGAAGAATAAGTACCATATTC
20442788 CTCTTAT
196 CTCTTAT
20442795 T
1 T
20442796 ACAGATTTGT
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
202 192 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (202 bp):
TGCAACGCCGAGGAGTTCAAGAGCTTACCAATAGCTTACAATTGAAGGAACTTTTGGATACGAGA
TTCATTAGACCATCTAAATCCCCATACGGCGCGCCAGTGCTATTTCAAAAGAAACATGATGGGTC
CTTGAAAATGTGCATCGATTATCAGGCTTTAAACAAGATCACTGTGAAGAATAAGTACCATATTC
CTCTTAT
Found at i:20450196 original size:26 final size:26
Alignment explanation
Indices: 20450160--20450211 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
20450150 GAGGATTTGG
20450160 GTAAAAATATAAGCCCGAAAAATGGA
1 GTAAAAATATAAGCCCGAAAAATGGA
20450186 GTAAAAATATAAGCCCGAAAAATGGA
1 GTAAAAATATAAGCCCGAAAAATGGA
20450212 CTTGGCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.19, T:0.15
Consensus pattern (26 bp):
GTAAAAATATAAGCCCGAAAAATGGA
Found at i:20455589 original size:3 final size:3
Alignment explanation
Indices: 20455583--20455608 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20455573 GCTTACTTGT
20455583 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
20455609 CCTTGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20462688 original size:43 final size:43
Alignment explanation
Indices: 20462620--20462745 Score: 141
Period size: 43 Copynumber: 2.9 Consensus size: 43
20462610 AAAGCTCGTA
* *
20462620 CAATGCCAAC-GTCCCAGACGTGGTCTTACATGTAACCACATA-T
1 CAATGCC-ACTGTCCCAGACGTGGTCTTACACGTAAACACA-AGT
*
20462663 CCATGCCACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGT
1 CAATGCCACTGTCCCAGAC-GTGGTCTTACACGTAAACACAAGT
* * * *
20462706 CAATGCCAATGTCCCAGACGTGCTGTTACACGAAAACACA
1 CAATGCCACTGTCCCAGACGTGGTCTTACACGTAAACACA
20462746 TATCGGAGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
42 4 0.06
43 66 0.93
44 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (43 bp):
CAATGCCACTGTCCCAGACGTGGTCTTACACGTAAACACAAGT
Found at i:20463383 original size:28 final size:28
Alignment explanation
Indices: 20463349--20463405 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
20463339 GGCAAATTTC
20463349 AAAATCTTCATCAAAATAAAAAATTAAG
1 AAAATCTTCATCAAAATAAAAAATTAAG
20463377 AAAATCTTCATCAAAATAAAAAATTAAG
1 AAAATCTTCATCAAAATAAAAAATTAAG
20463405 A
1 A
20463406 CATGAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAATCTTCATCAAAATAAAAAATTAAG
Found at i:20463876 original size:11 final size:11
Alignment explanation
Indices: 20463862--20463890 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
20463852 AATTAACACA
20463862 TAAAATAATAT
1 TAAAATAATAT
20463873 TAAAATAATAT
1 TAAAATAATAT
20463884 TAAAATA
1 TAAAATA
20463891 TTTTTGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:20465189 original size:143 final size:143
Alignment explanation
Indices: 20464796--20466716 Score: 2418
Period size: 143 Copynumber: 13.4 Consensus size: 143
20464786 GATTGAAGTC
* * * * *
20464796 ATTATGGTGAATCATATCTTCCTGAAGTTGCAATGGAGTAGATTGAAGCCACCAGCCTTATCTTC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * ** *
20464861 CTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCCTATTTCCCTGGCGTTATAGTAGAGTAT
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
* *
20464926 ATTAAAACTAAAA
131 ATTAAAGCTACAA
* * * *
20464939 ATTATGGCGACTCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTG-AGCCACCAGCTTTATCTTC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
20465003 CTGAAGTTGCAGCAGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAGCATTGTAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
*
20465068 ATTACAGCTACAA
131 ATTAAAGCTACAA
* * * * *
20465081 TTTATGGCTAATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CGGACCTTATCTC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAG-CCTTATCTC
* *
20465145 CCTAAAGTTGTAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACA
65 CCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACA
20465210 GATTAAAGCTACAA
130 GATTAAAGCTACAA
* * * * * * * ** *
20465224 ATTATAGCGGATCTTCTCTTTCTAAAGTTGAAGTGGAGCAAACCGAAGCCACCAACCTTATCTCC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* ** * * *
20465289 ATGAAGTTATAGTGGAGCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
*
20465354 ATTCAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
20465367 ATTATGAC-AGATCTTCTCATCCTAAAGTTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
1 ATTATGGCGA-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
* * * * * *
20465431 CCTGAAGTTGTAGCGGAGCAGACTAAAGACAGCGAATTTTATTTCCCTAGCGTTGCAGTGGAATA
65 CCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACA
20465496 GATTAAAGCTACAA
130 GATTAAAGCTACAA
* * *
20465510 ATCATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
20465575 CTGAAGTTGCAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCGTTGCAGTAGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
20465640 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* *
20465653 ATTATGGCGAATCTTATCTTTCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* ** * * * * ** *
20465718 CTAAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCTTAGCATTACAGTAGG-ATA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGT-GGAACA
*
20465782 GTTTAAAGCTACAA
130 GATTAAAGCTACAA
* * * * *
20465796 ATTATGGCGAATCGTATCTTCCTAAAGTTGCAATGGAGCAGATTGAAGTCACCAACCTTATCTCC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
20465861 CTGAAGTTGTAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAACAA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
20465926 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
20465939 ATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTTGAGTATATTAAAGCCACCAGCCTTATCTCC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * * * *
20466004 CTAAAGTTACAGCGGAGCAGGCTGAAGAAAACGAATCTTATTTCCTTGGAGTTGAAGTAGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
*
20466069 ATTAAAGCTGCAA
131 ATTAAAGCTACAA
* * *
20466082 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCATATTGAAGCCACCAGTCTTATCTCC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * *
20466147 TTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCATTGTAGTGGAACAT
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
20466212 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * ** * * *
20466225 ATTATGACGAATCTTATTTTTATAAAGTTGTAGTGGAGCAGATTGAAGCCACCTA-CATTATCTC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACC-AGCCTTATCTC
* * * * *
20466289 CCTGAAGTTGCAGCAGAGCAGACTGAAGACAGTGAATCTTATTTCCCTGACATTGTAGTGGAATA
65 CCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACA
20466354 GATTAAAGCTACAA
130 GATTAAAGCTACAA
* *
20466368 ATTATGGC-AGATCTTATCTTCCTGAAGGTT-CAGTGGAGCAAATTGAAGCCACCAACCTTATCT
1 ATTATGGCGA-ATCTTATCTTCCTGAA-GTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT
* ** * * * *
20466431 CCCTGAAGTTTTCAATGCAGCAGATTGAAAACA-TGAATCTTATTTCCCTGGCGTTGTAGTGGAA
64 CCCTGAAG-TTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAA
20466495 CAGATTAAAGCTACAA
128 CAGATTAAAGCTACAA
* * * * * *
20466511 ATTATGGTGAATCTTATTTTCCTGATGTTGCAGTAGAGTAGATTGAACCCACCAGCCTTATCTCC
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
20466576 CTGAAGTTACAGCAGAGCAGACTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
20466641 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * *
20466654 ATTATGGCAAATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAATCCACCAGCCTTATCT
1 ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT
20466717 TATTTCCCTG
Statistics
Matches: 1532, Mismatches: 231, Indels: 30
0.85 0.13 0.02
Matches are distributed among these distances:
142 146 0.10
143 1361 0.89
144 25 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (143 bp):
ATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAG
ATTAAAGCTACAA
Found at i:20465585 original size:44 final size:44
Alignment explanation
Indices: 20465522--20465744 Score: 149
Period size: 44 Copynumber: 4.8 Consensus size: 44
20465512 CATGGCGAAT
* *
20465522 CTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
* * * * **
20465566 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CCACTAGC
* ** * * * *
20465611 CTTATTTCCCTGGCGTTGCAGTAGAACAGATTAAAGCTACAAATTATGGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--C--ACTA--GC
** * *
20465661 GAATCTTATCTTTCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
* * *
20465709 CTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
20465745 ATAGCGAATC
Statistics
Matches: 130, Mismatches: 38, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
44 63 0.48
45 32 0.25
48 4 0.03
50 2 0.02
52 1 0.01
54 28 0.22
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
Found at i:20466742 original size:103 final size:103
Alignment explanation
Indices: 20466610--20466819 Score: 366
Period size: 103 Copynumber: 2.0 Consensus size: 103
20466600 AAGGCAGCGA
20466610 ATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGCAAATCTTATCTTC
1 ATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGCAAATCTTATCTTC
* *
20466675 CTGAAGTTACAATGGAGCAGATTGAATCCACCAGCCTT
66 CTAAAGTTACAATGGAGCAGATTGAAGCCACCAGCCTT
**
20466713 ATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGTGAATCTTATCTTC
1 ATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGCAAATCTTATCTTC
* *
20466778 CTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTT
66 CTAAAGTTACAATGGAGCAGATTGAAGCCACCAGCCTT
20466816 ATCT
1 ATCT
20466820 CCTGGAAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (103 bp):
ATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGCAAATCTTATCTTC
CTAAAGTTACAATGGAGCAGATTGAAGCCACCAGCCTT
Found at i:20466748 original size:246 final size:246
Alignment explanation
Indices: 20466467--20466931 Score: 736
Period size: 246 Copynumber: 1.9 Consensus size: 246
20466457 GAAAACATGA
* *
20466467 ATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTACAAATTATGGTGAATCTTATTTTC
1 ATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGAATCTTATCTTC
* * * * *
20466532 CTGATGTTGCAGTAGAGTAGATTGAACCCACCAGCCTTATCTCCCT-GAAGTTACAGC-AGAGCA
66 CTAAAGTTGCAGTAGAGCAGATTGAACCCACCAGCCTTATCT-CCTGGAAATTACAACGA-AGCA
* * * *
20466595 GACTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATG
129 GACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAAATTATG
20466660 GCAAATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAATCCACCAGCCTT
194 GCAAATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAATCCACCAGCCTT
*
20466713 ATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGTGAATCTTATCTTC
1 ATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGAATCTTATCTTC
* * *
20466778 CTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTGGAAATTGCAACGAAGCAGA
66 CTAAAGTTGCAGTAGAGCAGATTGAACCCACCAGCCTTATCTCCTGGAAATTACAACGAAGCAGA
*
20466843 CTGAAGATAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAAATTATGGC
131 CTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAAATTATGGC
**
20466908 GGATCTTATCTTCCTGAAGTTACA
196 AAATCTTATCTTCCTGAAGTTACA
20466932 GTATACCAGA
Statistics
Matches: 199, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
245 3 0.02
246 195 0.98
247 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (246 bp):
ATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGTGAATCTTATCTTC
CTAAAGTTGCAGTAGAGCAGATTGAACCCACCAGCCTTATCTCCTGGAAATTACAACGAAGCAGA
CTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAAATTATGGC
AAATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAATCCACCAGCCTT
Found at i:20466787 original size:54 final size:53
Alignment explanation
Indices: 20466609--20466793 Score: 139
Period size: 54 Copynumber: 3.5 Consensus size: 53
20466599 GAAGGCAGCG
** *
20466609 AATCTTAT-TTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGCA
1 AATCTTATCTT-CCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTATGG-T
* * ** * * * * ***
20466663 AATCTTATCTTCCTGAAGTTACAATGGAGCAGATTGAATCCAC-CAGCCT--T
1 AATCTTATCTTCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGT
**
20466713 -ATCTTAT-TTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGT
1 AATCTTATCTT-CCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGT
*
20466765 GAATCTTATCTTCCTAAAGTTGCAGTGGA
1 -AATCTTATCTTCCTGAAGTTGCAGTGGA
20466794 GCAGATTGAA
Statistics
Matches: 93, Mismatches: 30, Indels: 16
0.67 0.22 0.12
Matches are distributed among these distances:
48 2 0.02
49 30 0.32
50 2 0.02
52 1 0.01
53 2 0.02
54 52 0.56
55 4 0.04
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (53 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGT
Found at i:20467491 original size:20 final size:19
Alignment explanation
Indices: 20467458--20467506 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
20467448 CCAGGCCCAA
20467458 CAAAAT-AAATTACAAACC
1 CAAAATAAAATTACAAACC
*
20467476 CAAAATAAACATTACAAGCC
1 CAAAATAAA-ATTACAAACC
20467496 CAAAAATAAAA
1 C-AAAATAAAA
20467507 AAAAAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 6 0.22
19 2 0.07
20 11 0.41
21 8 0.30
ACGTcount: A:0.63, C:0.20, G:0.02, T:0.14
Consensus pattern (19 bp):
CAAAATAAAATTACAAACC
Found at i:20468680 original size:3 final size:3
Alignment explanation
Indices: 20468674--20468699 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20468664 ATCTGCTTAC
20468674 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
20468700 CGTTGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20471194 original size:319 final size:319
Alignment explanation
Indices: 20470615--20471254 Score: 1088
Period size: 319 Copynumber: 2.0 Consensus size: 319
20470605 AAACGAGGTG
20470615 AAAACACTTTGAAACATTGATTTTATTCAAAATCCCGAATTTCACCATTAACGCCCAAAATTCCA
1 AAAACACTTTGAAACATTGATTTTATTCAAAATCCCGAATTTCACCATTAACGCCCAAAATTCCA
* **
20470680 GCATTTACACAAAAGCTTTGATTCAATTGATTTAAAACTCGATTTAAATAGCTAGAGTTCATAAA
66 GCATTTACACAAAACCTTTGATTCAATTGATAAAAAACTCGATTTAAATAGCTAGAGTTCATAAA
* *
20470745 AAAACTATTAGGAAAATGAAACATTACCTTGATTGAGGGGAAAAGGAGTGTTTGATTGAAAATTC
131 AAAACTATTAGGAAAACGAAACATTACCTTGATTGAGGGGAAAAGGAGTGTTTAATTGAAAATTC
* *
20470810 AGAAAACCCACAAGTTGAATGACAAGGAAATTAAGGGTGTTCTTTGTGCTCTTCTTGGCTTTCAA
196 AGAAAACCCACAAGTTGAATGAAAAGGAAATTAAGGGTGTTCTTTCTGCTCTTCTTGGCTTTCAA
* * *
20470875 AGGGGGTTTTAATACTAGGAAGATTATAGAAAATAAGGGATTAGAGTT-TGGAAGATTGA
261 AAGGGGTTTTAATACTAGGAAGATTATAGAAAACAAAGGATTAGAGTTCT-GAAGATTGA
* **
20470934 AAAACACTTTGAAA-ATTTGATTTTATTCAAAATCTCGAATTTCACCATTAACGCCCAAAATTTT
1 AAAACACTTTGAAACA-TTGATTTTATTCAAAATCCCGAATTTCACCATTAACGCCCAAAATTCC
*
20470998 GGCATTTACACAAAACCTTTGATTCAATTGATAAAAAAACTCGATTTAAATAGCTAGAGTTCAT-
65 AGCATTTACACAAAACCTTTGATTCAATTGAT-AAAAAACTCGATTTAAATAGCTAGAGTTCATA
20471062 AAAAAACTATTAGGAAAACGAAACATTACCTTGATTGAGGGGAAAAGGAGTGTTTAATTGAAAAT
129 AAAAAACTATTAGGAAAACGAAACATTACCTTGATTGAGGGGAAAAGGAGTGTTTAATTGAAAAT
20471127 TCAGAAAACCCACAAGTTGAATGAAAAGGAAATTAAGGGTGTTCTTTCTGCTCTTCTTGGCTTTC
194 TCAGAAAACCCACAAGTTGAATGAAAAGGAAATTAAGGGTGTTCTTTCTGCTCTTCTTGGCTTTC
* *
20471192 AAAAGGGGTTTTAATGCTAGGAAGATTATAGAAAACAAAGGATTGGAGTTCTGAAGATTGA
259 AAAAGGGGTTTTAATACTAGGAAGATTATAGAAAACAAAGGATTAGAGTTCTGAAGATTGA
20471253 AA
1 AA
20471255 TTGAGGGATA
Statistics
Matches: 302, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
318 1 0.00
319 271 0.90
320 30 0.10
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (319 bp):
AAAACACTTTGAAACATTGATTTTATTCAAAATCCCGAATTTCACCATTAACGCCCAAAATTCCA
GCATTTACACAAAACCTTTGATTCAATTGATAAAAAACTCGATTTAAATAGCTAGAGTTCATAAA
AAAACTATTAGGAAAACGAAACATTACCTTGATTGAGGGGAAAAGGAGTGTTTAATTGAAAATTC
AGAAAACCCACAAGTTGAATGAAAAGGAAATTAAGGGTGTTCTTTCTGCTCTTCTTGGCTTTCAA
AAGGGGTTTTAATACTAGGAAGATTATAGAAAACAAAGGATTAGAGTTCTGAAGATTGA
Found at i:20472608 original size:30 final size:30
Alignment explanation
Indices: 20472572--20472692 Score: 134
Period size: 30 Copynumber: 4.0 Consensus size: 30
20472562 GGTGAATAAG
20472572 TGCTCACACAAGCTGACTTTATAACAAGGT
1 TGCTCACACAAGCTGACTTTATAACAAGGT
* * *
20472602 TGCTCACACAAGCTAACTTTATACCACGGT
1 TGCTCACACAAGCTGACTTTATAACAAGGT
* * * * *
20472632 TGCTCACACATGATGAATTTATAAAAAGTT
1 TGCTCACACAAGCTGACTTTATAACAAGGT
* * * *
20472662 TGATCACACAAGTTGACATTATATCAAGGT
1 TGCTCACACAAGCTGACTTTATAACAAGGT
20472692 T
1 T
20472693 ACCCATCCGA
Statistics
Matches: 72, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (30 bp):
TGCTCACACAAGCTGACTTTATAACAAGGT
Found at i:20479542 original size:19 final size:19
Alignment explanation
Indices: 20479508--20479562 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
20479498 ATTTATAAAA
*
20479508 AATAAAAATCAATAAAATTT
1 AATAAAAAT-ATTAAAATTT
20479528 -ATAAAAATGATT-AAATTT
1 AATAAAAAT-ATTAAAATTT
20479546 AAATAAAAATATTAAAA
1 -AATAAAAATATTAAAA
20479563 GTATTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.20
19 13 0.43
20 11 0.37
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAAAAATATTAAAATTT
Found at i:20480671 original size:29 final size:31
Alignment explanation
Indices: 20480628--20480691 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
20480618 TAGGAGCAAT
*
20480628 TTTTTCAATTTGTTTGTTGTTTTAATA-TTG
1 TTTTTCAATTTGTTTGTTATTTTAATATTTG
20480658 TTTTT-AATTTGTTTGTTATTTTAATATTTG
1 TTTTTCAATTTGTTTGTTATTTTAATATTTG
20480688 TTTT
1 TTTT
20480692 AATGTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.17, C:0.02, G:0.11, T:0.70
Consensus pattern (31 bp):
TTTTTCAATTTGTTTGTTATTTTAATATTTG
Found at i:20483869 original size:14 final size:14
Alignment explanation
Indices: 20483850--20483879 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20483840 CCATTGTAGT
*
20483850 TTCTTCTCGAAACA
1 TTCTTCTCAAAACA
20483864 TTCTTCTCAAAACA
1 TTCTTCTCAAAACA
20483878 TT
1 TT
20483880 TTCAACAACA
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:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (14 bp):
TTCTTCTCAAAACA
Found at i:20491433 original size:21 final size:22
Alignment explanation
Indices: 20491386--20491430 Score: 54
Period size: 25 Copynumber: 1.9 Consensus size: 22
20491376 TACAAAGCGG
20491386 GTAATAAATACATAAAAATAAGCAT
1 GTAATAAATACATAAAAAT-A--AT
*
20491411 GTAATTAATACATAAAAATA
1 GTAATAAATACATAAAAATA
20491431 TGTCATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
24 1 0.05
25 18 0.95
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (22 bp):
GTAATAAATACATAAAAATAAT
Found at i:20496839 original size:14 final size:15
Alignment explanation
Indices: 20496816--20496846 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
20496806 AGCGAAAATG
20496816 AAAATGAAAAACAAA
1 AAAATGAAAAACAAA
20496831 AAAAT-AAAAACAAA
1 AAAATGAAAAACAAA
20496845 AA
1 AA
20496847 TAACCTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAATGAAAAACAAA
Found at i:20498484 original size:16 final size:17
Alignment explanation
Indices: 20498463--20498496 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20498453 TTTATAATAC
*
20498463 TTTATA-TTATGTTATT
1 TTTATACTTATGTAATT
20498479 TTTATACTTATGTAATT
1 TTTATACTTATGTAATT
20498496 T
1 T
20498497 GTAACACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTATACTTATGTAATT
Found at i:20499057 original size:17 final size:18
Alignment explanation
Indices: 20499024--20499065 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
20499014 AAATATAAAG
20499024 TTTTAAATATTTCTTTAT
1 TTTTAAATATTTCTTTAT
*
20499042 TTTTAAAT-TTTTTTTAT
1 TTTTAAATATTTCTTTAT
20499059 TTTTAAA
1 TTTTAAA
20499066 ATTGACTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTAAATATTTCTTTAT
Found at i:20499276 original size:13 final size:13
Alignment explanation
Indices: 20499260--20499303 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
20499250 TTGAAAAGAA
20499260 AAAATAATTAAAT
1 AAAATAATTAAAT
20499273 AAAATATATT-AAT
1 AAAATA-ATTAAAT
* *
20499286 ATAATAAATAAAT
1 AAAATAATTAAAT
20499299 AAAAT
1 AAAAT
20499304 TTCCTTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 21 0.81
14 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATAATTAAAT
Found at i:20502089 original size:19 final size:19
Alignment explanation
Indices: 20502065--20502103 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20502055 TAGGTTTTTA
20502065 AAATATTATTTAATAAATT
1 AAATATTATTTAATAAATT
* *
20502084 AAATATTTTTTATTAAATT
1 AAATATTATTTAATAAATT
20502103 A
1 A
20502104 TCCAACAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTATTTAATAAATT
Found at i:20504405 original size:15 final size:17
Alignment explanation
Indices: 20504372--20504409 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
20504362 ATTATTAAAA
20504372 TAAAATTAGTAATTTAT
1 TAAAATTAGTAATTTAT
20504389 TAAAATTA-TAA-TTAT
1 TAAAATTAGTAATTTAT
20504404 TAAAAT
1 TAAAAT
20504410 AATTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAAATTAGTAATTTAT
Found at i:20506634 original size:3 final size:3
Alignment explanation
Indices: 20506626--20506671 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
20506616 ACTAACTCTT
20506626 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20506672 CTTTTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20507695 original size:29 final size:29
Alignment explanation
Indices: 20507650--20507729 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
20507640 AAGTGGCACT
*
20507650 GAAGTGCAAT-ATCAGAACAGAATGACATC
1 GAAGTGCATTAAT-AGAACAGAATGACATC
* * * * *
20507679 GAAGTGCTTTAGTAGAACAAAATGGCATT
1 GAAGTGCATTAATAGAACAGAATGACATC
*
20507708 GAAGTGCATTAATAGAATAGAA
1 GAAGTGCATTAATAGAACAGAA
20507730 AGCGTGCTAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (29 bp):
GAAGTGCATTAATAGAACAGAATGACATC
Found at i:20511440 original size:31 final size:31
Alignment explanation
Indices: 20511400--20511462 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
20511390 ACTTATCATT
*
20511400 TATCTCTTGTCACTGATCAGATAAGTGTAGC
1 TATCACTTGTCACTGATCAGATAAGTGTAGC
* *
20511431 TATCACTTGTTACTGATTAGATAAGTGTAGC
1 TATCACTTGTCACTGATCAGATAAGTGTAGC
20511462 T
1 T
20511463 GAGCTACCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (31 bp):
TATCACTTGTCACTGATCAGATAAGTGTAGC
Found at i:20511546 original size:51 final size:51
Alignment explanation
Indices: 20511485--20511582 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
20511475 ATCCCTTATT
*
20511485 ACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTC
1 ACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACTTGTC
20511536 ACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACT
1 ACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACT
20511583 GATCAGAAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (51 bp):
ACTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCACTTGTC
Found at i:20511575 original size:44 final size:44
Alignment explanation
Indices: 20511431--20511589 Score: 185
Period size: 51 Copynumber: 3.5 Consensus size: 44
20511421 TAAGTGTAGC
* * *
20511431 TATCACTTGTTACTGATTAGATAAGTGTAGCT-GAGCTACCACT
1 TATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACT
* * *
20511474 TATCCCTTATTACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 TATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC-T
*
20511519 ATCACTTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCACT
1 -T-A----TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACT
20511569 TATCACTTGTCACTGATCAGA
1 TATCACTTGTCACTGATCAGA
20511590 AGAACTCAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
43 29 0.29
44 28 0.28
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 37 0.37
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (44 bp):
TATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACT
Found at i:20512784 original size:88 final size:88
Alignment explanation
Indices: 20512635--20512810 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
20512625 TTCTAACGAA
*
20512635 ACTTTAATACCAACTCAATGACACTCTATAAATATTTCTAAAAGTATTTATGGCTCGATTTATGA
1 ACTTTAATACCAACTCAATGACACTCTATAAATATTTCTAAAAATATTTATGGCTCGATTTATGA
20512700 GTTTGAGGTTTCGATACCTCATT
66 GTTTGAGGTTTCGATACCTCATT
*
20512723 ACTTTAATACCAACTCAATGACATTCTATAAATATTTCTAAAAATATTTATGGCTCGATTTATGA
1 ACTTTAATACCAACTCAATGACACTCTATAAATATTTCTAAAAATATTTATGGCTCGATTTATGA
20512788 GTTTGAGGTTTCGATACCTCATT
66 GTTTGAGGTTTCGATACCTCATT
20512811 TTCAATTCTA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (88 bp):
ACTTTAATACCAACTCAATGACACTCTATAAATATTTCTAAAAATATTTATGGCTCGATTTATGA
GTTTGAGGTTTCGATACCTCATT
Found at i:20519197 original size:40 final size:39
Alignment explanation
Indices: 20519113--20519376 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 39
20519103 TCGAATGATG
* * * *
20519113 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
20519153 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
20519193 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
20519232 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
* *
20519272 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
20519311 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTA-AA
*
20519352 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
20519377 AACGAGTAGC
Statistics
Matches: 195, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 71 0.36
40 113 0.58
41 11 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:20519249 original size:79 final size:80
Alignment explanation
Indices: 20519113--20519374 Score: 372
Period size: 79 Copynumber: 3.3 Consensus size: 80
20519103 TCGAATGATG
* * * * * **
20519113 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
20519176 TTGTGCGAGTTACTAAT
64 TTGTGCGAGTTACTAAT
20519193 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
20519257 GTGCGAGTTACTAAT
66 GTGCGAGTTACTAAT
*
20519272 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCTCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
20519336 GTGCGAGTTACT-AT
66 GTGCGAGTTACTAAT
* *
20519350 AACCGGGCTATGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCATT
20519375 TGAACGAGTA
Statistics
Matches: 168, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
78 3 0.02
79 136 0.81
80 29 0.17
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
GTGCGAGTTACTAAT
Found at i:20519329 original size:119 final size:121
Alignment explanation
Indices: 20519113--20519376 Score: 360
Period size: 119 Copynumber: 2.2 Consensus size: 121
20519103 TCGAATGATG
* *
20519113 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGACCCGAAGGCATT
* *
20519177 TGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTA-AA
66 GGTGCGAGTTACTAAATCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTATAA
* * * *
20519232 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGACCCGAAGGCAT
* * *
20519294 TGGTGCGAGTTACTAAATCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
65 TGGTGCGAGTTACTAAATCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTATAA
*
20519352 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20519377 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
118 35 0.27
119 82 0.64
120 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (121 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGACCCGAAGGCATT
GGTGCGAGTTACTAAATCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTATAA
Found at i:20519408 original size:79 final size:79
Alignment explanation
Indices: 20519113--20519409 Score: 345
Period size: 79 Copynumber: 3.7 Consensus size: 79
20519103 TCGAATGATG
* * * * * **
20519113 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGA-TCCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAA-ATTCCGAAGGCAT
20519176 TTGTGCGAGTTACTAAT
63 TTGTGCGAGTTACTAAT
* *
20519193 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAATTCCGAAGGCATTTG
20519258 TGCGAGTTACTAAT
66 TGCGAGTTACTAAT
*
20519272 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTT-AAGTCTCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAATTC-CGAAGGCATTT
20519336 GTGCGAGTTACT-AT
65 GTGCGAGTTACTAAT
* * * ** *
20519350 AACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 -TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAATTCCGAAGG
20519410 TACGTGATTC
Statistics
Matches: 191, Mismatches: 19, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
78 4 0.02
79 142 0.74
80 45 0.24
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAATTCCGAAGGCATTTG
TGCGAGTTACTAAT
Found at i:20521855 original size:42 final size:42
Alignment explanation
Indices: 20521801--20521900 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
20521791 GCTCTCGGTA
* *
20521801 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTAATCAACATCATCATTTTAATT
* *
20521843 TCGCACACTTAGTGCCCATTAATCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTAATCAACATCATCATTTTAATT
*
20521885 TTGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
20521901 GTTCATATAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTAATCAACATCATCATTTTAATT
Found at i:20530375 original size:2 final size:2
Alignment explanation
Indices: 20530368--20530397 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20530358 AAAGACAAAT
20530368 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20530398 GAACAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20532764 original size:2 final size:2
Alignment explanation
Indices: 20532759--20532789 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20532749 ATATATATAT
20532759 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
20532790 AATATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20534865 original size:17 final size:18
Alignment explanation
Indices: 20534838--20534879 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
20534828 TTAAAGAATT
*
20534838 TACAA-ATAAAT-GCAAA
1 TACAATATAAATCACAAA
20534854 TACAATATAAATCACAAA
1 TACAATATAAATCACAAA
20534872 TA-AATATA
1 TACAATATA
20534880 TATTTGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (18 bp):
TACAATATAAATCACAAA
Found at i:20539221 original size:22 final size:23
Alignment explanation
Indices: 20539195--20539240 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20539185 TTTTAATATA
*
20539195 TATTTT-TAAATTTAAATTATTT
1 TATTTTATAAATTTAAATGATTT
*
20539217 TATTTTATAATTTTAAATGATTT
1 TATTTTATAAATTTAAATGATTT
20539240 T
1 T
20539241 TAGCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTTATAAATTTAAATGATTT
Found at i:20540884 original size:12 final size:12
Alignment explanation
Indices: 20540869--20540910 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20540859 TAAGGTATGT
20540869 TTTATTCCATTA
1 TTTATTCCATTA
**
20540881 TTTATTTAATGT-
1 TTTATTCCAT-TA
20540893 TTTATTCCATTA
1 TTTATTCCATTA
20540905 TTTATT
1 TTTATT
20540911 TAATGTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (12 bp):
TTTATTCCATTA
Found at i:20540892 original size:24 final size:24
Alignment explanation
Indices: 20540865--20540916 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
20540855 GTTGTAAGGT
20540865 ATGTTTTATTCCATTATTTATTTA
1 ATGTTTTATTCCATTATTTATTTA
20540889 ATGTTTTATTCCATTATTTATTTA
1 ATGTTTTATTCCATTATTTATTTA
20540913 ATGT
1 ATGT
20540917 CAAGAACCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (24 bp):
ATGTTTTATTCCATTATTTATTTA
Found at i:20544770 original size:10 final size:10
Alignment explanation
Indices: 20544755--20544784 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20544745 TCTTCTTCTC
20544755 TTTTTCTTTT
1 TTTTTCTTTT
20544765 TTTTTCTTTT
1 TTTTTCTTTT
*
20544775 TTTTACTTTT
1 TTTTTCTTTT
20544785 GTAGCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:20548028 original size:25 final size:25
Alignment explanation
Indices: 20547992--20548048 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
20547982 CTTCCTAATT
*
20547992 ATGGCTCTTATGAGCTTCCCGTTAC
1 ATGGCTCATATGAGCTTCCCGTTAC
* *
20548017 ATGGCTCATATGAGCTTCTCGTTAT
1 ATGGCTCATATGAGCTTCCCGTTAC
20548042 ATGGCTC
1 ATGGCTC
20548049 GAGAGAGAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (25 bp):
ATGGCTCATATGAGCTTCCCGTTAC
Found at i:20548066 original size:27 final size:25
Alignment explanation
Indices: 20548003--20548070 Score: 59
Period size: 25 Copynumber: 2.7 Consensus size: 25
20547993 TGGCTCTTAT
* * * *
20548003 GAGCTTCCCGTTACATGGCTCATAT
1 GAGCTTTCCGTTATATGGCTCAGAA
20548028 GAGC-TTCTCGTTATATGGCTCGAGAGA
1 GAGCTTTC-CGTTATATGGCTC-AGA-A
20548055 GAGCTTTCCGTT-TATG
1 GAGCTTTCCGTTATATG
20548071 TACTCATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.06
25 16 0.46
26 6 0.17
27 8 0.23
28 3 0.09
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (25 bp):
GAGCTTTCCGTTATATGGCTCAGAA
Found at i:20555011 original size:42 final size:42
Alignment explanation
Indices: 20554955--20555130 Score: 185
Period size: 42 Copynumber: 4.2 Consensus size: 42
20554945 CGTGTTTTAC
* * *
20554955 TTTCAGTTTAGCTCTTATGAGCTTTTGTTCAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * * *
20554997 TTTCTGTTCAGCTCTTACT-AG-TTCCTATTTAACTCATACGAG
1 TTTCTGTTCAGCTCTTA-TGAGCTT-CTGTTCAACTCTTATGAG
* * ** *
20555039 TTTTTGTTTAGCTCTTACAAGCTTTTGTTCAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * *
20555081 TTTTTGTTCAACTCTTATGAGCTTCTGTTCAACTCTTAAGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
20555123 TTTCTGTT
1 TTTCTGTT
20555131 AATGATGTAC
Statistics
Matches: 108, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.02
42 103 0.95
43 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
Found at i:20555115 original size:84 final size:84
Alignment explanation
Indices: 20554955--20555130 Score: 230
Period size: 84 Copynumber: 2.1 Consensus size: 84
20554945 CGTGTTTTAC
* ** *
20554955 TTTCAGTTTAGCTCTTATGAGCTTTTGTTCAACTCTTATGAGTTTCTGTTCAGCTCTTACTAGTT
1 TTTCTGTTTAGCTCTTACAAGCTTTTGTTCAACTCTTATGAGTTTCTGTTCAACTCTTACTAGTT
* *
20555020 CCTATTTAACTCATACGAG
66 CCTATTCAACTCATAAGAG
* *
20555039 TTTTTGTTTAGCTCTTACAAGCTTTTGTTCAACTCTTATGAGTTTTTGTTCAACTCTTA-TGAGC
1 TTTCTGTTTAGCTCTTACAAGCTTTTGTTCAACTCTTATGAGTTTCTGTTCAACTCTTACT-AG-
* *
20555103 TT-CTGTTCAACTCTTAAGAG
64 TTCCTATTCAACTCATAAGAG
20555123 TTTCTGTT
1 TTTCTGTT
20555131 AATGATGTAC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
83 1 0.01
84 76 0.96
85 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (84 bp):
TTTCTGTTTAGCTCTTACAAGCTTTTGTTCAACTCTTATGAGTTTCTGTTCAACTCTTACTAGTT
CCTATTCAACTCATAAGAG
Found at i:20555127 original size:21 final size:21
Alignment explanation
Indices: 20554966--20555130 Score: 156
Period size: 21 Copynumber: 7.9 Consensus size: 21
20554956 TTCAGTTTAG
20554966 CTCTTATGAGCTTT-TGTTCAA
1 CTCTTATGAG-TTTCTGTTCAA
*
20554987 CTCTTATGAGTTTCTGTTCAG
1 CTCTTATGAGTTTCTGTTCAA
* * *
20555008 CTCTTACT-AGTTCCTATTTAA
1 CTCTTA-TGAGTTTCTGTTCAA
* * * * *
20555029 CTCATACGAGTTTTTGTTTAG
1 CTCTTATGAGTTTCTGTTCAA
**
20555050 CTCTTACAAGCTTT-TGTTCAA
1 CTCTTATGAG-TTTCTGTTCAA
*
20555071 CTCTTATGAGTTTTTGTTCAA
1 CTCTTATGAGTTTCTGTTCAA
*
20555092 CTCTTATGAGCTTCTGTTCAA
1 CTCTTATGAGTTTCTGTTCAA
*
20555113 CTCTTAAGAGTTTCTGTT
1 CTCTTATGAGTTTCTGTT
20555131 AATGATGTAC
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.05
21 108 0.92
22 4 0.03
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (21 bp):
CTCTTATGAGTTTCTGTTCAA
Found at i:20557882 original size:12 final size:12
Alignment explanation
Indices: 20557865--20557903 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
20557855 TTTTAATAAG
20557865 ATTTAATATTAA
1 ATTTAATATTAA
*
20557877 ATTTAATATAATGA
1 ATTTAATAT--TAA
20557891 ATTTAATATTAA
1 ATTTAATATTAA
20557903 A
1 A
20557904 GTGATTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:20559537 original size:20 final size:20
Alignment explanation
Indices: 20559503--20559544 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20559493 AACTATTTAA
** *
20559503 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
20559523 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
20559543 AT
1 AT
20559545 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:20567643 original size:59 final size:58
Alignment explanation
Indices: 20567550--20567699 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 58
20567540 GTACTTGTGG
* *
20567550 CTTGTGA-TTGCGGTTGCTTTTAGTGCCCAAACAAATTCAATCCTTGACATGCTGGTT
1 CTTGTGACTTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTA
* * * *
20567607 CTTGTGACTTGTGGTTTACTTTTGGTGCCAAAACAAATTTAATCCTTGACATGCTGGTA
1 CTTGTGACTTGCGG-TTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTA
* *
20567666 GTTGTGGCTTGCGGTTGCTTTTAGTGCCAAAACA
1 CTTGTGACTTGCGGTTGCTTTTAGTGCCAAAACA
20567700 TAGCAACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 7 0.09
58 23 0.29
59 50 0.62
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (58 bp):
CTTGTGACTTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTA
Found at i:20567794 original size:26 final size:26
Alignment explanation
Indices: 20567741--20567796 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
20567731 AATGTCACAC
* *
20567741 ATTTTGAAGCTTCATTTTCTTTGATT
1 ATTTTGAAGCTTCAATTTCTATGATT
*
20567767 ATTTTGAA-CTTCAATTTCATATGCTT
1 ATTTTGAAGCTTCAATTTC-TATGATT
20567793 ATTT
1 ATTT
20567797 CAGATGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.55
Consensus pattern (26 bp):
ATTTTGAAGCTTCAATTTCTATGATT
Found at i:20568262 original size:18 final size:17
Alignment explanation
Indices: 20568234--20568268 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20568224 ATTATTAAGA
*
20568234 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20568251 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20568269 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20568525 original size:16 final size:16
Alignment explanation
Indices: 20568504--20568539 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
20568494 AATTTGTTAT
20568504 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
20568520 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
20568536 TACA
1 TACA
20568540 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:20584180 original size:30 final size:30
Alignment explanation
Indices: 20584144--20584201 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
20584134 GTGCCATTGC
20584144 TTGAAACTTTGCAGAACCATGATGAGATGT
1 TTGAAACTTTGCAGAACCATGATGAGATGT
20584174 TTGAAACTTTGCAGAACCATGATGAGAT
1 TTGAAACTTTGCAGAACCATGATGAGAT
20584202 CATCCATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (30 bp):
TTGAAACTTTGCAGAACCATGATGAGATGT
Found at i:20586426 original size:25 final size:26
Alignment explanation
Indices: 20586380--20586435 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
20586370 TAATTTTGCC
*
20586380 ATTTTAATCAATATTTTATTATCATT
1 ATTTTAATAAATATTTTATTATCATT
**
20586406 ATTTT-ATAAATATATTT-TTATTTTT
1 ATTTTAATAAATAT-TTTATTATCATT
20586431 ATTTT
1 ATTTT
20586436 CACTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
ATTTTAATAAATATTTTATTATCATT
Found at i:20594386 original size:189 final size:186
Alignment explanation
Indices: 20594053--20594431 Score: 686
Period size: 189 Copynumber: 2.0 Consensus size: 186
20594043 AGAGCTAGAC
20594053 AGTAAAGACCCTTAGAAATATGTCAGGCTTCTTAATATCACTTATATCTTAAGTCAATAATGATA
1 AGTAAAGACCCTTAGAAATATGTCAGGCTTCTTAATATCACTTATATCTTAAGTCAATAATGATA
* *
20594118 ATTGCAAGTCTATAATTCAGAGCTCAACTAACAAAATATTCCCCCTTTTGGTTCCATCAATTCTC
66 ATTGCAAGTCAATAATTCAGAGCTCAACTAACAAAATATTCCCCCTTTTGATTCCATCAATTCTC
20594183 ACATGCATGCACACACTCAAAATTCATGTGCAAAAACCATCTAAACAAAGGTTTCA
131 ACATGCATGCACACACTCAAAATTCATGTGCAAAAACCATCTAAACAAAGGTTTCA
*
20594239 AGTAAAGACCCTTAGAAGAAATATGTTAGGCTTCTTAATATCACTTATATCTTAAGTCAATAATG
1 AGTAAAGACCCTT---AGAAATATGTCAGGCTTCTTAATATCACTTATATCTTAAGTCAATAATG
*
20594304 ATAATTGCAAGTCAATAATTCAGAGCTCAACTAACAAAATATTCCCGCTTTTGATTCCATCAATT
63 ATAATTGCAAGTCAATAATTCAGAGCTCAACTAACAAAATATTCCCCCTTTTGATTCCATCAATT
*
20594369 CTCACATGCATGCACACACTCATAATTCATGTGCAAAAACCATCTAAACAAAGGTTTCA
128 CTCACATGCATGCACACACTCAAAATTCATGTGCAAAAACCATCTAAACAAAGGTTTCA
20594428 AGTA
1 AGTA
20594432 GAAAATTTTC
Statistics
Matches: 185, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
186 13 0.07
189 172 0.93
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (186 bp):
AGTAAAGACCCTTAGAAATATGTCAGGCTTCTTAATATCACTTATATCTTAAGTCAATAATGATA
ATTGCAAGTCAATAATTCAGAGCTCAACTAACAAAATATTCCCCCTTTTGATTCCATCAATTCTC
ACATGCATGCACACACTCAAAATTCATGTGCAAAAACCATCTAAACAAAGGTTTCA
Found at i:20596242 original size:24 final size:23
Alignment explanation
Indices: 20596214--20596266 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
20596204 TTGTTTGATA
20596214 AATTTTCCTACAATCATATTTTTG
1 AATTTT-CTACAATCATATTTTTG
* ** *
20596238 AATTTTTTTTAATGATATTTTTG
1 AATTTTCTACAATCATATTTTTG
20596261 AATTTT
1 AATTTT
20596267 GTTTTTAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (23 bp):
AATTTTCTACAATCATATTTTTG
Found at i:20598749 original size:25 final size:22
Alignment explanation
Indices: 20598732--20598773 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20598722 CTCTCCGATT
20598732 ATTAGCACATTAGTGCTCTCCG
1 ATTAGCACATTAGTGCTCTCCG
* *
20598754 CTTAGCACATTTGTGCTCTC
1 ATTAGCACATTAGTGCTCTC
20598774 TATTTAACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.36
Consensus pattern (22 bp):
ATTAGCACATTAGTGCTCTCCG
Found at i:20604864 original size:22 final size:21
Alignment explanation
Indices: 20604834--20604891 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
20604824 ATGCAATCGT
*
20604834 AGATTTGATATGTAATCTTAG
1 AGATTTGATTTGTAATCTTAG
*
20604855 AAGATATGATTTTGTAATCTTAG
1 -AGATTTGA-TTTGTAATCTTAG
20604878 AGATTTGATTTGTA
1 AGATTTGATTTGTA
20604892 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 14 0.44
23 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:20604874 original size:23 final size:22
Alignment explanation
Indices: 20604844--20604888 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
20604834 AGATTTGATA
20604844 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAG-AGATATGATTT
*
20604867 TGTAATCTTAGAGATTTGATTT
1 TGTAATCTTAGAGATATGATTT
20604889 GTAGATACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTAATCTTAGAGATATGATTT
Found at i:20615143 original size:30 final size:30
Alignment explanation
Indices: 20615100--20615157 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
20615090 CACGGGCTAA
*
20615100 CACATGGGCGTGTGGCCAGCCCGTGTGGCT
1 CACACGGGCGTGTGGCCAGCCCGTGTGGCT
* *
20615130 CACACGGGTGTGTGGCCAGCTCGTGTGG
1 CACACGGGCGTGTGGCCAGCCCGTGTGG
20615158 AACCTGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.10, C:0.28, G:0.41, T:0.21
Consensus pattern (30 bp):
CACACGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:20615450 original size:13 final size:13
Alignment explanation
Indices: 20615424--20615464 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
20615414 TCTCAATTTG
20615424 TAATTCTCATAAA
1 TAATTCTCATAAA
20615437 TAATATCTCA-AAA
1 TAAT-TCTCATAAA
20615450 TAA-TC-CATAAA
1 TAATTCTCATAAA
20615461 TAAT
1 TAAT
20615465 CATGCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.08
11 8 0.32
13 10 0.40
14 5 0.20
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATTCTCATAAA
Found at i:20616968 original size:6 final size:6
Alignment explanation
Indices: 20616950--20616988 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
20616940 TAAATAGAAG
* *
20616950 AAAATA ACAATA AACATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
20616989 TACAACAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:20618691 original size:28 final size:28
Alignment explanation
Indices: 20618642--20618695 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
20618632 CAAGAACACC
* *
20618642 TATAGATAAAAATAATAGAATAGATGAAA
1 TATAGATAAAAATAAAAAAATA-ATGAAA
*
20618671 TATA-ATAACAATAAAAAAATAATGA
1 TATAGATAAAAATAAAAAAATAATGA
20618696 TGAACTAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.18
28 14 0.64
29 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (28 bp):
TATAGATAAAAATAAAAAAATAATGAAA
Found at i:20633607 original size:37 final size:37
Alignment explanation
Indices: 20633558--20633647 Score: 128
Period size: 37 Copynumber: 2.4 Consensus size: 37
20633548 TCCCCTCGCC
* *
20633558 TGAGTTTCATTCAGTATAAT-AGTACGATTTACTCAAT
1 TGAGCTTCATTCAGTATAATGA-TAAGATTTACTCAAT
* *
20633595 TTAGCTTCATTCAGTATAATGATAAGATTTGCTCAAT
1 TGAGCTTCATTCAGTATAATGATAAGATTTACTCAAT
20633632 TGAGCTTCATTCAGTA
1 TGAGCTTCATTCAGTA
20633648 GGATCAATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 46 0.98
38 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
TGAGCTTCATTCAGTATAATGATAAGATTTACTCAAT
Found at i:20635374 original size:13 final size:13
Alignment explanation
Indices: 20635356--20635388 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
20635346 AAAATGACTA
20635356 AATTGAACTAACC
1 AATTGAACTAACC
20635369 AATTGAACTAACC
1 AATTGAACTAACC
20635382 AATTGAA
1 AATTGAA
20635389 GACCCAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (13 bp):
AATTGAACTAACC
Found at i:20635458 original size:3 final size:3
Alignment explanation
Indices: 20635450--20635489 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
20635440 CATTCGGTGT
*
20635450 AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
20635490 GGAAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20635581 original size:13 final size:13
Alignment explanation
Indices: 20635552--20635583 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
20635542 AACTTTATAC
20635552 TTTTAATTAAAAA
1 TTTTAATTAAAAA
20635565 -TTTAATTAAAAA
1 TTTTAATTAAAAA
20635577 TTTTAAT
1 TTTTAAT
20635584 ACTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAATTAAAAA
Found at i:20637899 original size:12 final size:12
Alignment explanation
Indices: 20637882--20637907 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20637872 ATATAAAGAT
20637882 AATTGAAGTGAC
1 AATTGAAGTGAC
20637894 AATTGAAGTGAC
1 AATTGAAGTGAC
20637906 AA
1 AA
20637908 ATACATGTAT
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:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (12 bp):
AATTGAAGTGAC
Found at i:20645016 original size:24 final size:24
Alignment explanation
Indices: 20644980--20645034 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
20644970 TTTCCAATAT
* **
20644980 ATGGCTATCCGGAGCTTTCCGTTA
1 ATGGCTCTCCGGAGCTACCCGTTA
*
20645004 ATGGCTCTTCGGAGCTACCCGTTA
1 ATGGCTCTCCGGAGCTACCCGTTA
*
20645028 TTGGCTC
1 ATGGCTC
20645035 GCATAAGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.25, T:0.33
Consensus pattern (24 bp):
ATGGCTCTCCGGAGCTACCCGTTA
Found at i:20645169 original size:25 final size:27
Alignment explanation
Indices: 20645111--20645162 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
20645101 TATGGCTTAC
*
20645111 ATGAGCTTCTTGTTATATGTGCTCGAG
1 ATGAGCTTCTTATTATATGTGCTCGAG
*
20645138 AGAGAGCTTCTTATT-TATGTGCTCG
1 A-TGAGCTTCTTATTATATGTGCTCG
20645163 TATGAGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.40
Consensus pattern (27 bp):
ATGAGCTTCTTATTATATGTGCTCGAG
Found at i:20645345 original size:12 final size:12
Alignment explanation
Indices: 20645328--20645353 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20645318 ATACAAAGAT
20645328 AATTGAAGTGAC
1 AATTGAAGTGAC
20645340 AATTGAAGTGAC
1 AATTGAAGTGAC
20645352 AA
1 AA
20645354 ATACATGTAT
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:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (12 bp):
AATTGAAGTGAC
Found at i:20655811 original size:18 final size:18
Alignment explanation
Indices: 20655770--20655814 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
20655760 AAAAGAAGGT
* * *
20655770 TATAAATTTATATAATTT
1 TATAAAATTATATAAATC
*
20655788 TTTAAAATTATATAAATC
1 TATAAAATTATATAAATC
20655806 TATAAAATT
1 TATAAAATT
20655815 TGAAAAACCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAAAATTATATAAATC
Found at i:20656383 original size:20 final size:20
Alignment explanation
Indices: 20656360--20656397 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20656350 TTTTTTCTAT
20656360 TTTTTATGAATTTT-TATAAG
1 TTTTTATG-ATTTTATATAAG
20656380 TTTTTATGATTTTATATA
1 TTTTTATGATTTTATATA
20656398 TATATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTTATGATTTTATATAAG
Found at i:20656406 original size:13 final size:13
Alignment explanation
Indices: 20656388--20656435 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
20656378 AGTTTTTATG
*
20656388 ATTTTATATATAT
1 ATTTTATAAATAT
*
20656401 ATTTTATAAATCT
1 ATTTTATAAATAT
* *
20656414 ATTTTTTAATTAT
1 ATTTTATAAATAT
20656427 -TTTTATAAA
1 ATTTTATAAA
20656436 ATTCCAAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTATAAATAT
Found at i:20660863 original size:22 final size:22
Alignment explanation
Indices: 20660812--20660866 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
20660802 TTGTGCCTAG
*
20660812 CAGGCTTAGTGTCGGTGTTATT
1 CAGGCTTTGTGTCGGTGTTATT
*
20660834 CAGGCTTTGTGTTGGTGTTATT
1 CAGGCTTTGTGTCGGTGTTATT
20660856 CAGGCTTTGTG
1 CAGGCTTTGTG
20660867 CCTAGTAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.11, C:0.13, G:0.33, T:0.44
Consensus pattern (22 bp):
CAGGCTTTGTGTCGGTGTTATT
Found at i:20660865 original size:60 final size:60
Alignment explanation
Indices: 20660789--20660905 Score: 182
Period size: 60 Copynumber: 1.9 Consensus size: 60
20660779 TGAGCTATAC
*
20660789 TGTTATTCAGGATTTGTGCCTAGCAGGCTTAGTG-TCGGTGTTATTCAGGCTTTGTGTTGG
1 TGTTATTCAGGATTTGTGCCTAGCAGGCTTAGTGCT-GGTGTTATTCAGGCTTAGTGTTGG
* * *
20660849 TGTTATTCAGGCTTTGTGCCTAGTAGGCTTAGTGCTGGTGTTATTTAGGCTTAGTGT
1 TGTTATTCAGGATTTGTGCCTAGCAGGCTTAGTGCTGGTGTTATTCAGGCTTAGTGT
20660906 CTAGCAGGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.14, C:0.13, G:0.31, T:0.43
Consensus pattern (60 bp):
TGTTATTCAGGATTTGTGCCTAGCAGGCTTAGTGCTGGTGTTATTCAGGCTTAGTGTTGG
Found at i:20660877 original size:38 final size:38
Alignment explanation
Indices: 20660834--20660930 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 38
20660824 CGGTGTTATT
*
20660834 CAGGCTTTGTGTTGGTGTTATTCAGGCTTTGTGCCTAG
1 CAGGCTTTGTGTTGGTGTTATTCAGGCTTAGTGCCTAG
* * * * *
20660872 TAGGCTTAGTGCTGGTGTTATTTAGGCTTAGTGTCTAG
1 CAGGCTTTGTGTTGGTGTTATTCAGGCTTAGTGCCTAG
*
20660910 CAGGCTTAT-TGTCGGTGTTAT
1 CAGGCTT-TGTGTTGGTGTTAT
20660931 AAAGGTTAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.13, C:0.13, G:0.31, T:0.42
Consensus pattern (38 bp):
CAGGCTTTGTGTTGGTGTTATTCAGGCTTAGTGCCTAG
Found at i:20667099 original size:20 final size:20
Alignment explanation
Indices: 20667074--20667123 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
20667064 TGGCTTAAAA
20667074 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
20667094 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
20667111 GTGGTAGTGGATT
1 TTGGTAGTGGATT
20667124 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:20671738 original size:20 final size:20
Alignment explanation
Indices: 20671713--20671762 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
20671703 TGGCTTAAAA
20671713 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
20671733 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
20671750 GTGGTAGTGGATT
1 TTGGTAGTGGATT
20671763 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:20672565 original size:20 final size:21
Alignment explanation
Indices: 20672540--20672581 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
20672530 GGCTTGGTCT
20672540 TATATTATTTTTAAA-TAATA
1 TATATTATTTTTAAATTAATA
20672560 TATATTATTTTTAAATTAATA
1 TATATTATTTTTAAATTAATA
20672581 T
1 T
20672582 TTAATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTATTTTTAAATTAATA
Found at i:20672581 original size:17 final size:19
Alignment explanation
Indices: 20672540--20672622 Score: 64
Period size: 20 Copynumber: 4.3 Consensus size: 19
20672530 GGCTTGGTCT
20672540 TATATTATTTTTAAATAATA
1 TATATTATTTTTAAAT-ATA
20672560 TATATTATTTTTAAATTAATA
1 TATATTATTTTTAAA-T-ATA
* * *
20672581 TTTAATAATTTT--ATATA
1 TATATTATTTTTAAATATA
*
20672598 T-TTTTATTTATTAAATTATA
1 TATATTATTT-TTAAA-TATA
20672618 TATAT
1 TATAT
20672623 AGAATATTAC
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
16 5 0.10
17 6 0.12
18 1 0.02
19 2 0.04
20 20 0.40
21 16 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTATTTTTAAATATA
Found at i:20672592 original size:21 final size:20
Alignment explanation
Indices: 20672548--20672593 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
20672538 CTTATATTAT
* *
20672548 TTTTAAATAATATATATTAT
1 TTTTAAATAATATATAATAA
*
20672568 TTTTAAATTAATATTTAATAA
1 TTTTAAA-TAATATATAATAA
20672589 TTTTA
1 TTTTA
20672594 TATATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAATAATATATAATAA
Found at i:20673841 original size:46 final size:46
Alignment explanation
Indices: 20673788--20673875 Score: 176
Period size: 46 Copynumber: 1.9 Consensus size: 46
20673778 CTATTCTATT
20673788 AATACTTAACCAATTAGGGAAGTTAGTTTCATGAAATGGACAATTC
1 AATACTTAACCAATTAGGGAAGTTAGTTTCATGAAATGGACAATTC
20673834 AATACTTAACCAATTAGGGAAGTTAGTTTCATGAAATGGACA
1 AATACTTAACCAATTAGGGAAGTTAGTTTCATGAAATGGACA
20673876 TGTATTGCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (46 bp):
AATACTTAACCAATTAGGGAAGTTAGTTTCATGAAATGGACAATTC
Found at i:20684432 original size:19 final size:19
Alignment explanation
Indices: 20684408--20684451 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
20684398 ACGTTTTTTT
* *
20684408 TGCATT-CATTTCATGCATC
1 TGCATTACATGTCAT-CATA
20684427 TGCATTACATGTCATCATA
1 TGCATTACATGTCATCATA
20684446 TGCATT
1 TGCATT
20684452 TAAGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (19 bp):
TGCATTACATGTCATCATA
Found at i:20692655 original size:44 final size:43
Alignment explanation
Indices: 20692558--20693124 Score: 216
Period size: 44 Copynumber: 12.9 Consensus size: 43
20692548 GAATATTTCA
* * *
20692558 GATCTTATCTCCTTGAGATTACAGCGGAGCAGATTG-AAGCTAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATC-AG
* * * * *
20692601 TAATCCTATCTCCCTGAGATTACAGTAGAGCGGATTGAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAAT-CAG
* * * * *
20692646 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCACATCAG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATCAG
* * * **
20692688 G-TATTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-A-A--TCAG
* *
20692734 GATCTTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAGTAAATG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAA-T-CA-G
** * * * *
20692779 G-TCTTATCTGTCTGA-AGTTACAGTAGAGTAGA-TCACATCAG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATCAG
* * * **
20692820 G-TATTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-A-A--TCAG
* * **
20692866 GATCTTATCTCCTTGAGATTACAGTGGAACAGACCGAAGAATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AA--TCAG
* * * *
20692912 GATCTTATCTCCTTGAGATTACAGCGGAGCGGATTG-AAGCTAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATC-AG
* * * * * *
20692955 TAATCCTATCTCCCTGATATTACAGTAGAGCGGATT-AAAGTAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAA-T-CAG
* * * *
20693000 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATTG-CATCA-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATCAG
* * * * **
20693041 GATCTTATCTCCCTAAGATTATAGTGGAACAAACCGAAGAATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AA--TCAG
* *
20693087 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAA
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA
20693125 GCTACTAATC
Statistics
Matches: 395, Mismatches: 90, Indels: 76
0.70 0.16 0.14
Matches are distributed among these distances:
41 73 0.18
42 10 0.03
43 16 0.04
44 145 0.37
45 11 0.03
46 70 0.18
47 70 0.18
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATCAG
Found at i:20692760 original size:47 final size:47
Alignment explanation
Indices: 20692691--20692935 Score: 237
Period size: 47 Copynumber: 5.4 Consensus size: 47
20692681 ACATCAGGTA
20692691 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATC
1 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATC
* * * *** ** *
20692738 TTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG-TAAAT--GGTC
1 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATC
* * ** * *
20692782 TTATCT-GTCTGA-AGTTACAGT-----AGA--GTAGATCACATCAGGTA
1 TTATCTCCT-TGAGA-TTACAGTGGAACAGACCGAAGAT-ATTTCAGATC
20692823 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATC
1 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATC
20692870 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGA-ATTTCAGATC
1 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATC
20692916 TTATCTCCTTGAGATTACAG
1 TTATCTCCTTGAGATTACAG
20692936 CGGAGCGGAT
Statistics
Matches: 161, Mismatches: 22, Indels: 31
0.75 0.10 0.14
Matches are distributed among these distances:
37 2 0.01
38 1 0.01
39 5 0.03
41 19 0.12
42 2 0.01
43 1 0.01
44 19 0.12
46 36 0.22
47 71 0.44
48 5 0.03
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (47 bp):
TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATC
Found at i:20692796 original size:132 final size:132
Alignment explanation
Indices: 20692562--20692893 Score: 521
Period size: 132 Copynumber: 2.5 Consensus size: 132
20692552 ATTTCAGATC
* * ** * * *
20692562 TTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTA-GT-A-ATCCTATCTCCCTGAGATTAC
1 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATCTTATCTCCCTGAGATTAC
*
20692624 AGTAGAGCGGATTGAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGG
66 AGTGGAGCGGATTGAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGG
20692689 TA
131 TA
20692691 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATCTTATCTCCCTGAGATTAC
1 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATCTTATCTCCCTGAGATTAC
*
20692756 AGTGGAGCGGATT-AAAGTAAATGG-TCTTATCTGTCTGAAGTTACAGTAGAGTAGATCACATCA
66 AGTGGAGCGGATTGAAA-TAAA-GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
20692819 GGTA
129 GGTA
*
20692823 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATCTTATCTCCTTGAGATTAC
1 TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATCTTATCTCCCTGAGATTAC
20692888 AGTGGA
66 AGTGGA
20692894 ACAGACCGAA
Statistics
Matches: 188, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
129 33 0.18
130 1 0.01
131 4 0.02
132 148 0.79
133 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (132 bp):
TTATCTCCTTGAGATTACAGTGGAACAGACCGAAGATATTTCAGATCTTATCTCCCTGAGATTAC
AGTGGAGCGGATTGAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGG
TA
Found at i:20706766 original size:22 final size:23
Alignment explanation
Indices: 20706740--20706783 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
20706730 TTCATATATG
20706740 TTAGATTAAAG-TAAATTGATTA
1 TTAGATTAAAGATAAATTGATTA
20706762 TTAGATTAAAGATTAAATTGAT
1 TTAGATTAAAGA-TAAATTGAT
20706784 CATTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (23 bp):
TTAGATTAAAGATAAATTGATTA
Found at i:20706933 original size:26 final size:26
Alignment explanation
Indices: 20706887--20706940 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
20706877 AATTACACCG
* *
20706887 TTTGTTAAAAATTGTATCCA-TTTAT
1 TTTGTTAAAAATTATACCCATTTTAT
20706912 TTTGTTAAAAATTCATACCCATTTTAT
1 TTTGTTAAAAATT-ATACCCATTTTAT
20706939 TT
1 TT
20706941 GAGGTAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
26 5 0.20
27 7 0.28
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (26 bp):
TTTGTTAAAAATTATACCCATTTTAT
Found at i:20710137 original size:38 final size:38
Alignment explanation
Indices: 20710095--20710171 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
20710085 TTATTTTTCA
* * *
20710095 CTCTTTACTCCTCTTCTTT-TTTCTCTATTTGCCCTAGT
1 CTCTTTACACCTCTT-TTTCCTTCTCCATTTGCCCTAGT
* *
20710133 CTCTTTACACTTCTTTTTCCTTCTCCATTTGTCCTAGT
1 CTCTTTACACCTCTTTTTCCTTCTCCATTTGCCCTAGT
20710171 C
1 C
20710172 GCCGCTTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 3 0.09
38 30 0.91
ACGTcount: A:0.09, C:0.32, G:0.05, T:0.53
Consensus pattern (38 bp):
CTCTTTACACCTCTTTTTCCTTCTCCATTTGCCCTAGT
Found at i:20717114 original size:48 final size:48
Alignment explanation
Indices: 20717058--20717207 Score: 160
Period size: 48 Copynumber: 3.1 Consensus size: 48
20717048 AACAACATTC
* *
20717058 GGACAGCATTGATTTGTACAAAAATGGACAGCATTTAAGCACCAATTT
1 GGACAGCATTAATTTGTACAAAAATGGACAGCAATTAAGCACCAATTT
** ** * *
20717106 GGACAGCATTAATATACTA-AAAAACAGACAGTAATTAAGCATCAATTT
1 GGACAGCATTAAT-TTGTACAAAAATGGACAGCAATTAAGCACCAATTT
* * *
20717154 GGACAACATTAATATGCT-CAAAAAATGGATAGCAATTAAGCACCAATTT
1 GGACAGCATTAATTTG-TAC-AAAAATGGACAGCAATTAAGCACCAATTT
20717203 GGACA
1 GGACA
20717208 ACATCTTATC
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
48 49 0.60
49 32 0.40
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (48 bp):
GGACAGCATTAATTTGTACAAAAATGGACAGCAATTAAGCACCAATTT
Found at i:20717201 original size:49 final size:48
Alignment explanation
Indices: 20717077--20717211 Score: 189
Period size: 48 Copynumber: 2.8 Consensus size: 48
20717067 TGATTTGTAC
* *
20717077 AAAAATGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATACTA
1 AAAAATGGACAGCAATTAAGCACCAATTTGGACAACATTAATATACTA
** * * *
20717125 AAAAACAGACAGTAATTAAGCATCAATTTGGACAACATTAATATGCTCA
1 AAAAATGGACAGCAATTAAGCACCAATTTGGACAACATTAATATACT-A
*
20717174 AAAAATGGATAGCAATTAAGCACCAATTTGGACAACAT
1 AAAAATGGACAGCAATTAAGCACCAATTTGGACAACAT
20717212 CTTATCATCA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
48 40 0.54
49 34 0.46
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (48 bp):
AAAAATGGACAGCAATTAAGCACCAATTTGGACAACATTAATATACTA
Found at i:20717871 original size:42 final size:43
Alignment explanation
Indices: 20717753--20717872 Score: 136
Period size: 42 Copynumber: 2.8 Consensus size: 43
20717743 AGCTCGTACA
* * ** *
20717753 ATGCC-ATATCCCAGATATGGTCTTACATGTTATAATATATCG
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCATATATCG
* * * *
20717795 ATGCCACTATCCTAGACAGGGTTTTACACGAAATCATATA-CG
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCATATATCG
*
20717837 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCA
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCA
20717873 CACCTCGGAA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
42 38 0.60
43 25 0.40
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCAATATCCCAGACATGGTCTTACACGAAATCATATATCG
Found at i:20722326 original size:42 final size:42
Alignment explanation
Indices: 20722275--20722393 Score: 220
Period size: 42 Copynumber: 2.8 Consensus size: 42
20722265 GTTTACAAAC
* *
20722275 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
20722317 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
20722359 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
20722394 TTTTTTTTCT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
Found at i:20722453 original size:41 final size:42
Alignment explanation
Indices: 20722277--20722489 Score: 194
Period size: 42 Copynumber: 5.1 Consensus size: 42
20722267 TTACAAACAA
* * * **** *
20722277 AAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAA
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTTTTAC
* * **** *
20722319 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTTTTAC
* * *
20722361 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTTC
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTTTTAC
* *
20722403 TAATCGCCGCTAAAGAACATGTTCTTTAGTGGC-ATTTTTTAC
1 -AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTTTTAC
* * * *
20722445 AAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTATAC
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTTTTAC
20722487 AAA
1 AAA
20722490 AACGCCACTA
Statistics
Matches: 151, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
41 30 0.20
42 92 0.61
43 29 0.19
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTTTTAC
Found at i:20722571 original size:14 final size:14
Alignment explanation
Indices: 20722548--20722581 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
20722538 GCCCTCCTGT
*
20722548 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
20722562 AGCAACATTTCAAA
1 AGCAACATTTCAAA
20722576 AGCAAC
1 AGCAAC
20722582 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:20722873 original size:21 final size:21
Alignment explanation
Indices: 20722805--20722875 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
20722795 TTTTGCTCTG
* *
20722805 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
20722826 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
20722847 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
20722868 CTCTGCTT
1 CTCTGCTT
20722876 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:20728349 original size:18 final size:18
Alignment explanation
Indices: 20728326--20728490 Score: 69
Period size: 18 Copynumber: 9.5 Consensus size: 18
20728316 AATTGCAATG
20728326 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
20728344 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
20728362 GTAAGTTAAATGTAAG-T-T
1 GTAAGTT--ATGTAAGTTAT
*
20728380 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
20728399 GTAAG-T-TGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
*
20728417 GT-A-TTGTGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
20728431 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
20728449 GTAAG-T-TGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
*
20728465 -TATGTATTATGTAAG-T-T
1 GTAAG--TTATGTAAGTTAT
20728482 GTAAGTTAT
1 GTAAGTTAT
20728491 TATGTATTGT
Statistics
Matches: 116, Mismatches: 5, Indels: 54
0.66 0.03 0.31
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 14 0.12
17 8 0.07
18 61 0.53
19 15 0.13
20 4 0.03
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (18 bp):
GTAAGTTATGTAAGTTAT
Found at i:20728374 original size:11 final size:9
Alignment explanation
Indices: 20728326--20728490 Score: 69
Period size: 7 Copynumber: 19.0 Consensus size: 9
20728316 AATTGCAATG
20728326 GTAAGTTAT
1 GTAAGTTAT
20728335 GTAAGTTAT
1 GTAAGTTAT
20728344 GTAAGTTAAAT
1 GTAAGTT--AT
20728355 GT-A-TTAT
1 GTAAGTTAT
20728362 GTAAGTTAAAT
1 GTAAGTT--AT
20728373 GTAAG-T-T
1 GTAAGTTAT
20728380 GTAAGTTAT
1 GTAAGTTAT
*
20728389 -TATGTATTAT
1 GTAAG--TTAT
20728399 GTAAG-T-T
1 GTAAGTTAT
20728406 GTAAGTTAAAT
1 GTAAGTT--AT
*
20728417 GT-A-TTGT
1 GTAAGTTAT
20728424 GTAAG-T-T
1 GTAAGTTAT
20728431 GTAAGTTAAAT
1 GTAAGTT--AT
20728442 GT-A-TTAT
1 GTAAGTTAT
20728449 GTAAG-T-T
1 GTAAGTTAT
20728456 GTAAGTTAT
1 GTAAGTTAT
*
20728465 -TATGTATTAT
1 GTAAG--TTAT
20728475 GTAAG-T-T
1 GTAAGTTAT
20728482 GTAAGTTAT
1 GTAAGTTAT
20728491 TATGTATTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 60
0.65 0.03 0.32
Matches are distributed among these distances:
7 41 0.34
8 18 0.15
9 27 0.22
10 12 0.10
11 23 0.19
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:20728401 original size:19 final size:19
Alignment explanation
Indices: 20728340--20728636 Score: 78
Period size: 19 Copynumber: 15.6 Consensus size: 19
20728330 GTTATGTAAG
*
20728340 TTATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
*
20728358 TTATGTAAGTTA-AATGTAA
1 TTATGTAAGTTATTATGT-A
*
20728377 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
20728395 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
*
20728420 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
20728445 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
20728461 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
20728479 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
20728497 TTGTGTAAGTTGCAAGTTAAATGTA
1 TTATGTAAGTT---A-TT--ATGTA
* *
20728522 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
20728538 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
20728556 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
* * *
20728574 TTGTGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
20728590 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
20728608 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
20728626 TTGTGTAAGTT
1 TTATGTAAGTT
20728637 GTAAGTTAAA
Statistics
Matches: 212, Mismatches: 31, Indels: 71
0.68 0.10 0.23
Matches are distributed among these distances:
14 3 0.01
15 18 0.08
16 11 0.05
17 3 0.01
18 53 0.25
19 60 0.28
20 3 0.01
21 1 0.00
22 2 0.01
23 5 0.02
24 1 0.00
25 52 0.25
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (19 bp):
TTATGTAAGTTATTATGTA
Found at i:20728405 original size:26 final size:26
Alignment explanation
Indices: 20728371--20728752 Score: 531
Period size: 26 Copynumber: 15.2 Consensus size: 26
20728361 TGTAAGTTAA
20728371 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
20728397 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
20728422 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
20728447 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
20728473 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* * *
20728499 GTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
20728524 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
20728550 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
20728576 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
20728602 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
20728628 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
20728653 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
20728671 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
20728696 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
20728722 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
20728749 ATGT
1 ATGT
20728753 CGACAAGATT
Statistics
Matches: 323, Mismatches: 21, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.04
19 1 0.00
21 3 0.01
22 3 0.01
24 1 0.00
25 104 0.32
26 179 0.55
27 11 0.03
28 9 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:20728676 original size:43 final size:46
Alignment explanation
Indices: 20728371--20728753 Score: 277
Period size: 51 Copynumber: 7.7 Consensus size: 46
20728361 TGTAAGTTAA
* * *
20728371 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TATATGTATT
* *
20728422 GTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTCA--TGTAA--TA-TATGTATT
* * * * *
20728473 ATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGCAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TATATGTATT
* *
20728524 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TA-TATGTATT
* * *
20728576 GTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTCA--TGTAA--TA-TATGTATT
* *
20728628 GTGTAAGTTGTAAGTTAAATGTATTATGTCA-GTCA-A-ATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTCATGTAATATATGTATT
*
20728671 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTCA--TGTAA--TA-TATGTATT
20728722 ATGTAAGTAATGTAAGTTAAATGTATTATGTC
1 ATGTAAGT--TGTAAGTTAAATGTATTATGTC
20728754 GACAAGATTT
Statistics
Matches: 300, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
43 36 0.12
45 1 0.00
46 3 0.01
48 3 0.01
49 1 0.00
50 24 0.08
51 114 0.38
52 97 0.32
53 21 0.07
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (46 bp):
ATGTAAGTTGTAAGTTAAATGTATTATGTCATGTAATATATGTATT
Found at i:20728704 original size:18 final size:18
Alignment explanation
Indices: 20728636--20728679 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
20728626 TTGTGTAAGT
20728636 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
* *
20728654 TGTCAGTCAAATGTATTA
1 TGTAAGTTAAATGTATTA
20728672 TGTAAGTT
1 TGTAAGTT
20728680 GTAAGTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:20731374 original size:7 final size:7
Alignment explanation
Indices: 20731321--20731396 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
20731311 ACCTTAATCA
*
20731321 CTAAACT
1 CTAAACC
20731328 CTCAAACC
1 CT-AAACC
20731336 CTAAACC
1 CTAAACC
** *
20731343 AAAAACA
1 CTAAACC
20731350 CTAAA-C
1 CTAAACC
* *
20731356 CTACATC
1 CTAAACC
*
20731363 GTAAACC
1 CTAAACC
20731370 CTAAACC
1 CTAAACC
*
20731377 CTAAACT
1 CTAAACC
20731384 CTAAACC
1 CTAAACC
20731391 CTAAAC
1 CTAAAC
20731397 TAGAATTCAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
6 4 0.08
7 43 0.81
8 6 0.11
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:20731459 original size:17 final size:17
Alignment explanation
Indices: 20731437--20731486 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
20731427 TATCCTATTT
20731437 CCTACATTATATAATAA
1 CCTACATTATATAATAA
20731454 CCTACATTATATAATAA
1 CCTACATTATATAATAA
*
20731471 ACTACA-TATATAATAA
1 CCTACATTATATAATAA
20731487 TCTAGCGGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (17 bp):
CCTACATTATATAATAA
Found at i:20731689 original size:113 final size:111
Alignment explanation
Indices: 20731508--20731858 Score: 411
Period size: 113 Copynumber: 3.1 Consensus size: 111
20731498 TTCCCACAAC
* * * *
20731508 GCGCCGCTAATAATATGTTTTACCGGCGTTTTACCATAAGCGCCAC-AACTGGTAGTATACATCA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTA-AATAAGCGCCACTAA-T-GTAGTATACATCA
20731572 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
63 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
* * *
20731621 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAAATAAGCGCCACTAATCGTAATGTACCTCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTT-AAATAAGCGCCACTAAT-GTAGTATACATCAA
* * * * *
20731686 GACCAAA-CTCTGCGTTTTGGTTAA-GAAATATTGCGGCGCTTTTCACTAC
64 GACCAAAGCGCTGCGTTTTGGTTAATG---TTTTGCGGCGCTTTACAATAA
* * * *
20731735 TCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCCACTACTGCTAGTATACATCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAA-ATAAGCGCCACTAATG-TAGTATACATCAA
* * *
20731800 GACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGTTTTCCAATAA
64 GACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
*
20731848 GCGCCACTAAT
1 GCGCCGCTAAT
20731859 CCTAATATAC
Statistics
Matches: 200, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
111 1 0.00
112 16 0.08
113 87 0.44
114 80 0.40
115 16 0.08
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (111 bp):
GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAATAAGCGCCACTAATGTAGTATACATCAAGA
CCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
Found at i:20731960 original size:188 final size:188
Alignment explanation
Indices: 20731643--20732040 Score: 688
Period size: 188 Copynumber: 2.1 Consensus size: 188
20731633 CTATGCTTTA
* * * *
20731643 GCGGCGTTTTCAAATAAGCGCCACTAATCGTAATGTACCTCAAGACCAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
20731708 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
66 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
20731773 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
131 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
20731831 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
* * *
20731896 AAGAAATCTTGCGGCGCTTTTCACTACTCGCTGCTAATACTATTCTTTAGTAGCGTTTTAATATA
66 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
* *
20731961 AGTGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
131 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
* * *
20732019 GCGACGCTTTACAATAAGCGCC
1 GCGGCGTTTTCCAATAAGCGCC
20732041 GCTACTACTA
Statistics
Matches: 198, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
188 198 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (188 bp):
GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
Found at i:20732081 original size:113 final size:114
Alignment explanation
Indices: 20731831--20732256 Score: 464
Period size: 114 Copynumber: 3.7 Consensus size: 114
20731821 TTAATATTTT
* ** *
20731831 GCGGCGTTTTCCA-ATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGT
1 GCGGCGTTTT-AATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGT
* * * *
20731895 TAAGAAATCTTGCGGCGCTTTTCACTACTCGCTGCTAATACTATTCTTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
** * * ** *
20731945 GTAGCGTTTTAATATAAGTGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGT
1 GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-CGCTGCGTTTTGGT
* * * * ** * * *
20732010 T-A-ATATTTTGCGACGCTTTACAATAAGCGCCGCTACTACTATGCGTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
* * *
20732058 GCGGCGTTTTTAA-ATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCGTTTTGGT
1 GCGGCG-TTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGT
*
20732122 TAAGAAATATTGCGGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
* ** * *
20732172 GCGGCGTTTGAATATAAGCGCCACTAAGGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGA
1 GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-CGCTGCGTTTTGGT
** *
20732237 TAAGAGCTTTTGCGGCGCTT
65 TAAGAAATATTGCGGCGCTT
20732257 GGTAGTAAAC
Statistics
Matches: 252, Mismatches: 53, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
112 14 0.06
113 76 0.30
114 119 0.47
115 43 0.17
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (114 bp):
GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGTT
AAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
Found at i:20738041 original size:47 final size:47
Alignment explanation
Indices: 20737990--20738082 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 47
20737980 AGTATAATTT
* * * *
20737990 GGATTTATTTATGCTTTACCTGGTGAGCTCCATTTAGGCTTCTAGGC
1 GGATTTACTTATACTTTACCTGGCGAGCTCCATTTAGCCTTCTAGGC
*
20738037 GGATTTACTTATACTTTACCTGGCGAGTTCCATTTAGCCTTCTAGG
1 GGATTTACTTATACTTTACCTGGCGAGCTCCATTTAGCCTTCTAGG
20738083 TGAGCTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (47 bp):
GGATTTACTTATACTTTACCTGGCGAGCTCCATTTAGCCTTCTAGGC
Found at i:20740678 original size:24 final size:24
Alignment explanation
Indices: 20740632--20740678 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20740622 AAAGATTTAG
**
20740632 TATTTATTAGCATAGTATATTTGA
1 TATTTATTAGCATAAAATATTTGA
*
20740656 TATTTATTAGCATAAAATCTTTG
1 TATTTATTAGCATAAAATATTTG
20740679 TTTTTCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (24 bp):
TATTTATTAGCATAAAATATTTGA
Found at i:20750228 original size:42 final size:43
Alignment explanation
Indices: 20750020--20750375 Score: 477
Period size: 43 Copynumber: 8.3 Consensus size: 43
20750010 ACGATATTTT
* * * *
20750020 TAGCGACGTTTGT-AATCAAAGCGTCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTGAA-AAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
20750063 TAGCGGCGTTTGTGAAAAAAAGCGTCGCTAAAGATCATGATCTA
1 TAGCGGCGTTTGTG-AAAAAAGCGCCGCTAAAGGTCTTGATCTA
*
20750107 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
20750150 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
*
20750193 TAGCGGCGTTTGT-AAAAAAGCGCCGCTAAATGTCTTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * *
20750235 TACCGGCGTTTGT-AAAAAAGCGCCGCTAAAGATCCTGAGCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
* ** *
20750277 TAGCGGCGTTTGTG-TAAAAGCATCGCTAAAGGTCATGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * **
20750319 TAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGGTCCGGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
20750362 TAGCGGCGTTTGTG
1 TAGCGGCGTTTGTG
20750376 GGAAAAAAAA
Statistics
Matches: 280, Mismatches: 29, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
42 113 0.40
43 128 0.46
44 37 0.13
45 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:20750375 original size:85 final size:85
Alignment explanation
Indices: 20750020--20750375 Score: 491
Period size: 85 Copynumber: 4.2 Consensus size: 85
20750010 ACGATATTTT
* * *
20750020 TAGCGACGTTTGT-AATCAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAAA
1 TAGCGGCGTTTGTGAA--AAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTG-AAAAAA
* *
20750084 GCGTCGCTAAAGATCATGATCTA
63 GCGCCGCTAAAGATCCTGATCTA
20750107 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGC
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGC
* *
20750172 GCCGCTAAAGGTCTTGATCTA
65 GCCGCTAAAGATCCTGATCTA
* * *
20750193 TAGCGGCGTTTGTAAAAAAGCGCCGCTAAATGTCTTGATCTATACCGGCGTTTGT-AAAAAAGCG
1 TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGCG
*
20750257 CCGCTAAAGATCCTGAGCTA
66 CCGCTAAAGATCCTGATCTA
* ** * *
20750277 TAGCGGCGTTTGTGTAAAAGCATCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGAAAAAGCG
1 TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGCG
* * *
20750342 CCACTAAAGGTCCGGATCTA
66 CCGCTAAAGATCCTGATCTA
20750362 TAGCGGCGTTTGTG
1 TAGCGGCGTTTGTG
20750376 GGAAAAAAAA
Statistics
Matches: 242, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
84 74 0.31
85 76 0.31
86 40 0.17
87 50 0.21
88 1 0.00
89 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (85 bp):
TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGCG
CCGCTAAAGATCCTGATCTA
Found at i:20752967 original size:54 final size:54
Alignment explanation
Indices: 20752901--20753010 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
20752891 TTTGGTAATG
20752901 GTTATATCCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
1 GTTATATCCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
* *
20752955 GTTATATGCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCGGGTTATGTT
1 GTTATATCCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
20753009 GT
1 GT
20753011 GCATTTATGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.19, C:0.08, G:0.26, T:0.46
Consensus pattern (54 bp):
GTTATATCCAATGTTTGGGATGCAATTTGGTGTATCTTTTATGCAGGTTATGTT
Found at i:20767363 original size:50 final size:49
Alignment explanation
Indices: 20767300--20767484 Score: 216
Period size: 50 Copynumber: 3.8 Consensus size: 49
20767290 CGTCAAGGGG
* * *
20767300 GTAAGATCTGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTCTTTAACTGCAATG-CAGGGAA
* ** * *
20767350 GTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTCTTTAACTGCAATGC-AGGGAA
* * *
20767400 ATAAGATCCGCTATTGTAGCTTCAATATCTTTAACTGC----CAGGGAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTCTTTAACTGCAATGCAGGGAA
*
20767445 GCAAGATCCGCTGTTGTAGCTTCAATCTCTTTAACTGCAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTCTTTAACTGCAA
20767485 ACTATGGTTT
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
45 39 0.34
46 1 0.01
49 1 0.01
50 73 0.64
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (49 bp):
GTAAGATCCGCTGTTGTAGCTTCAATCTCTTTAACTGCAATGCAGGGAA
Found at i:20767616 original size:44 final size:44
Alignment explanation
Indices: 20767568--20767838 Score: 153
Period size: 44 Copynumber: 6.2 Consensus size: 44
20767558 TAGTACGGGA
*
20767568 AGGCAAGATCTGCTATCTTTAACCAGCTCCATCACAACCGAGAG
1 AGGCAAGATCTGCTATCTTCAACCAGCTCCATCACAACCGAGAG
* ** * *
20767612 AGGCAAGGTCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAG
1 AGGCAAGATCTGCTATCTTCAACCAGCTCCATCACAACCGAGAG
* * * * * ** * *
20767656 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGC-TGTCAA-TGCAGAA
1 AGGCAAGATCTGCTATCTTCAACCAGC-TC-CATCACAACCG-AGAG
** * *
20767700 AGGCAAGATCTATTGTCTTCAACCAGCTCCATTACAACCGAGAG
1 AGGCAAGATCTGCTATCTTCAACCAGCTCCATCACAACCGAGAG
* * * * * * ** *
20767744 AGACAAGGTTTG-TGTCTTCGACCTGCTTCGC-TGTCAA-TGCAG-G
1 AGGCAAGATCTGCTATCTTCAACCAGC-TC-CATCACAACCG-AGAG
*
20767787 AAGGCAAGATCTG-TCGTCTTCAACCAGCTCCATCACAACCGAGAG
1 -AGGCAAGATCTGCT-ATCTTCAACCAGCTCCATCACAACCGAGAG
20767832 AGGCAAG
1 AGGCAAG
20767839 GTTTGTGTCT
Statistics
Matches: 172, Mismatches: 41, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
43 28 0.16
44 116 0.67
45 28 0.16
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTCAACCAGCTCCATCACAACCGAGAG
Found at i:20767731 original size:88 final size:88
Alignment explanation
Indices: 20767612--20768160 Score: 868
Period size: 88 Copynumber: 6.2 Consensus size: 88
20767602 CAACCGAGAG
* * *
20767612 AGGCAAGGTCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
*
20767677 CCTGCTTCGCTGTCAATGCAGAA
66 CCTGCTTCGCTGTCAATGCAGGA
* * *
20767700 AGGCAAGATCTATTGTCTTCAACCAGCTCCATTACAACCGAGAGAGACAAGGTTTGTGTCTTCGA
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
20767765 CCTGCTTCGCTGTCAATGCAGGA
66 CCTGCTTCGCTGTCAATGCAGGA
* *
20767788 AGGCAAGATCTGTCGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGA
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
20767853 CCTGCTTCGCTGTCAATGCAGGA
66 CCTGCTTCGCTGTCAATGCAGGA
* * ** * *
20767876 AGGCAAGATCTGCTATCTTTGACCAGCT-C-TGCTACAAACGAGGGAGGCAAGGTTTGTGTCTTC
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCAT-C-ACAACCGAGAGAGGCAAGGTTTGTGTCTTC
*
20767939 GACCTGCTTCGTTGTCAATGCAGGA
64 GACCTGCTTCGCTGTCAATGCAGGA
*
20767964 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
*
20768029 CCTGCTTCGCTATCAATGCAGGA
66 CCTGCTTCGCTGTCAATGCAGGA
* * * *
20768052 AGGCAAGATCTTTTGTCCTCAACCAGCTCTATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCGA
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
20768117 CCTGCTTCGCTGTCAATGCAGGA
66 CCTGCTTCGCTGTCAATGCAGGA
20768140 AGGCAAGATCTGTTGTCTTCA
1 AGGCAAGATCTGTTGTCTTCA
20768161 CTGATCTGTT
Statistics
Matches: 422, Mismatches: 35, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
86 1 0.00
87 2 0.00
88 416 0.99
89 2 0.00
90 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA
CCTGCTTCGCTGTCAATGCAGGA
Done.