Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 90 of 333
Found at i:28265054 original size:23 final size:23
Alignment explanation
Indices: 28265024--28265067 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
28265014 CCTCTCGAGT
28265024 ATACGTTATGATTAGGGTTTAAC
1 ATACGTTATGATTAGGGTTTAAC
28265047 ATACGTTATGATTAGGGTTTA
1 ATACGTTATGATTAGGGTTTA
28265068 GCCTGGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
ATACGTTATGATTAGGGTTTAAC
Found at i:28266435 original size:20 final size:20
Alignment explanation
Indices: 28266410--28266457 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
28266400 TGCTACATTG
28266410 GAAAATTTTTAAAATGTCGT
1 GAAAATTTTTAAAATGTCGT
28266430 GAAAATTTTTAAAATGTCGT
1 GAAAATTTTTAAAATGTCGT
28266450 GAAAATTT
1 GAAAATTT
28266458 CTTAGAGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (20 bp):
GAAAATTTTTAAAATGTCGT
Found at i:28269549 original size:43 final size:42
Alignment explanation
Indices: 28269457--28269563 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 42
28269447 GATGCCTCTA
* * *
28269457 TCCCAGACAGGGTCTTACACGAAATTAGATACGATGCCAATG
1 TCCCAGACACGGTCTTATACGAAATTAGATACGAGGCCAATG
* *
28269499 TCCCAGACATGGTCTTATACGTAAATCTCA-AT-CGAGGCCTATG
1 TCCCAGACACGGTCTTATACG-AAAT-T-AGATACGAGGCCAATG
28269542 TCCCAGACACGGTCTTATACGA
1 TCCCAGACACGGTCTTATACGA
28269564 TGTATCAGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 20 0.35
43 33 0.58
44 3 0.05
45 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (42 bp):
TCCCAGACACGGTCTTATACGAAATTAGATACGAGGCCAATG
Found at i:28282293 original size:51 final size:51
Alignment explanation
Indices: 28282216--28282413 Score: 326
Period size: 51 Copynumber: 3.9 Consensus size: 51
28282206 CGGATACACG
*
28282216 GTGGCCTTCACATAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAA
*
28282267 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCATAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
28282318 GTGGCCTTCACATAGTACCACACTTGTTTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
28282369 GTGGCCTTCACATAGTACCATACTTGTGTCCAAAGTTATTTTATT
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATT
28282414 ACTAAGGTTC
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 1 0.01
51 136 0.99
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:28282494 original size:52 final size:52
Alignment explanation
Indices: 28282438--28282716 Score: 452
Period size: 52 Copynumber: 5.4 Consensus size: 52
28282428 GGGAAATTTC
* *
28282438 TCACTTGGCACCA-TGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
28282490 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
* * *
28282542 TCACTTAGCACATTTCCATGGACTTATTTCATTTAGATGACATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
*
28282594 TCACTTAGCACATTGTCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
* *
28282646 TCATTTAGCACATTGCCATGGACTTATTTCACTTAGATGACATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
* *
28282698 TCAATTAGCACAATGCCAT
1 TCACTTAGCACATTGCCAT
28282717 ATCCTAGATA
Statistics
Matches: 212, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
51 2 0.01
52 210 0.99
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (52 bp):
TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
Found at i:28304619 original size:40 final size:40
Alignment explanation
Indices: 28304587--28304888 Score: 265
Period size: 40 Copynumber: 7.6 Consensus size: 40
28304577 CCAGCATGAT
* * * * *
28304587 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
28304627 TGCTCTTCGGAACTTAGTCCGGATACCTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
28304667 TGCTCTTCGGAACTTAGCCCGGAAACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* * *
28304707 TGCTCTTCGGGACTTAGCCCGGTTATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
** * * *
28304747 TGCTCTTCGGAACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGAACTTAGCCCGGATACA-TCACTAGCACGAA
* * * * *
28304788 TGC-CTTCGG-GCTTAGCCCGGAATTA-GTAACTCGCACAAA
1 TGCTCTTCGGAACTTAGCCCGG-A-TACATCACTAGCACGAA
* * **
28304827 TGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGAACTTAGCCCGGATA-CATCAC-TAGCACGAA
* *
28304867 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGAACTTAGCCCGGA
28304889 CATCATTCAA
Statistics
Matches: 221, Mismatches: 34, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.14
40 168 0.76
41 19 0.09
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28304795 original size:120 final size:119
Alignment explanation
Indices: 28304574--28304809 Score: 323
Period size: 120 Copynumber: 2.0 Consensus size: 119
28304564 CGAATACACG
*
28304574 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAA
* * *
28304639 CTTAGTCCGGATACCTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAAACA
66 CTTAGCCCGGATACCTAACTAGCACCAATGCTCTTCGG-ACTTAGCCCGGAAACA
* * * * *
28304694 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATATCACTAGCACGAATGCTCTTCGGAA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAA
* * *
28304759 CTTAGCCCGGATTTA-GTAACTCGCACCAATGC-CTTCGGGCTTAGCCCGGAA
66 CTTAGCCCGGA--TACCTAACTAGCACCAATGCTCTTCGGACTTAGCCCGGAA
28304810 TTAGTAACTC
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
119 12 0.12
120 75 0.74
121 13 0.13
122 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (119 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAA
CTTAGCCCGGATACCTAACTAGCACCAATGCTCTTCGGACTTAGCCCGGAAACA
Found at i:28304829 original size:120 final size:120
Alignment explanation
Indices: 28304587--28304888 Score: 321
Period size: 120 Copynumber: 2.5 Consensus size: 120
28304577 CCAGCATGAT
* * * *
28304587 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
* * * **
28304652 CCTCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAAACATCACTAGCATGAA
66 CCTAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGAAACATAACTAGCACAAA
*
28304707 TGCTCTTCGGGACTTAGCCCGGTTATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA--
* * * ** *
28304772 TA-GTAACTCGCACCAATGC-CTTCGG-GCTTAGCCCGGAATTAGTAACTCGCACAAA
64 TACCTAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGAAACA-TAACTAGCACAAA
* * * *
28304827 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGG
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAATGCTCTTCGGAACTTAGCCCGG
28304888 A
63 A
28304889 CATCATTCAA
Statistics
Matches: 155, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.02
119 47 0.30
120 84 0.54
121 19 0.12
122 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (120 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
CCTAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGAAACATAACTAGCACAAA
Found at i:28305231 original size:29 final size:29
Alignment explanation
Indices: 28305190--28305270 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
28305180 TGCTTAATAA
* *
28305190 TCAAGCCCGCACACTTAGTGCCATGTACTT
1 TCAAACCCGCACACTTAGTGCCATGCA-TT
*
28305220 T-AAACTCGCACACTTAGTGCCATGCATT
1 TCAAACCCGCACACTTAGTGCCATGCATT
*
28305248 TCAAGCCCGCACACTTAGTGCCA
1 TCAAACCCGCACACTTAGTGCCA
28305271 ATCTCACAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.07
29 41 0.91
30 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (29 bp):
TCAAACCCGCACACTTAGTGCCATGCATT
Found at i:28305313 original size:43 final size:43
Alignment explanation
Indices: 28305252--28305397 Score: 283
Period size: 43 Copynumber: 3.4 Consensus size: 43
28305242 TGCATTTCAA
28305252 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
28305295 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACGTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
28305338 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
28305381 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
28305398 TGAAAACCAA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:28307325 original size:37 final size:37
Alignment explanation
Indices: 28307264--28307342 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
28307254 TTATTACGAA
* * *
28307264 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
* *
28307301 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
28307338 GTCTT
1 GTCTT
28307343 TAGAGCTCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
Found at i:28307539 original size:47 final size:47
Alignment explanation
Indices: 28307463--28307796 Score: 506
Period size: 47 Copynumber: 7.0 Consensus size: 47
28307453 CTTCGGGACT
* * * * * * *
28307463 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGACCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
28307510 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
28307557 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
* *
28307604 TATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
28307651 TATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
28307702 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
28307751 TATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
28307797 TTACTATCAT
Statistics
Matches: 269, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
47 175 0.65
49 48 0.18
51 46 0.17
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:28307757 original size:147 final size:145
Alignment explanation
Indices: 28307516--28307799 Score: 541
Period size: 147 Copynumber: 1.9 Consensus size: 145
28307506 ACCCTGTCAC
28307516 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACAT
28307581 TCATCACATCGGCCATTAGGCCCTATCACGTATATACACTTTCACATTCATCACATCGGCCATTA
66 TCATCACATCGGCCATTAGGCCCTATCACGTATATACACTTTCACATTCATCACATCGGCCATTA
28307646 GGCCTTATCACATAT
131 GGCCTTATCACATAT
*
28307661 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATACACTTTCAC
28307726 ATTCATCACATCGGCCATTAGGCCCTATCACGTATATACACTTTCACATTCATCACATCGGCCAT
64 ATTCATCACATCGGCCATTAGGCCCTATCACGTATATACACTTTCACATTCATCACATCGGCCAT
28307791 TAGGCCTTA
129 TAGGCCTTA
28307800 CTATCATTTC
Statistics
Matches: 136, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
145 46 0.34
147 90 0.66
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (145 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCCTATCACGTATATACACTTTCACATTCATCACATCGGCCATTA
GGCCTTATCACATAT
Found at i:28312726 original size:20 final size:19
Alignment explanation
Indices: 28312693--28312743 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
28312683 ATAGAAGATA
*
28312693 TTATTTTATTTTATTTAGTT
1 TTATTTT-TATTATTTAGTT
*
28312713 TTATTATTTATTATTTATTT
1 TTATT-TTTATTATTTAGTT
28312733 TTATTTTTATT
1 TTATTTTTATT
28312744 TTATTAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATTTTTATTATTTAGTT
Found at i:28312737 original size:6 final size:6
Alignment explanation
Indices: 28312706--28312745 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
28312696 TTTTATTTTA
*
28312706 TTTAGT TTTATT ATTTATT ATTTATT TTTATT TTTATT TT
1 TTTATT TTTATT -TTTATT -TTTATT TTTATT TTTATT TT
28312746 ATTAATTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:28314606 original size:20 final size:19
Alignment explanation
Indices: 28314578--28314619 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
28314568 GTTTCAAGGA
* *
28314578 TTTTTTTTAATTTAATATAG
1 TTTTATTTAAATTAATA-AG
28314598 TTTTATTTAAATTAATAAG
1 TTTTATTTAAATTAATAAG
28314617 TTT
1 TTT
28314620 GTATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTATTTAAATTAATAAG
Found at i:28316851 original size:20 final size:19
Alignment explanation
Indices: 28316828--28316892 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
28316818 AAGCTCAAAC
28316828 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
28316848 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
28316868 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
28316888 GAGCT
1 GAGCT
28316893 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:28319300 original size:15 final size:15
Alignment explanation
Indices: 28319280--28319327 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
28319270 TCAAAGATGG
28319280 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
28319295 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
28319309 GTTTATGGATATAAA
1 GTTTATGGATATGAA
28319324 GTTT
1 GTTT
28319328 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:28319314 original size:14 final size:14
Alignment explanation
Indices: 28319274--28319317 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28319264 AAGGATTCAA
28319274 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
28319288 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
28319303 AGATGGGTTTATGG
1 AGATGGGTTTATGG
28319317 A
1 A
28319318 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:28319343 original size:29 final size:29
Alignment explanation
Indices: 28319274--28319333 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
28319264 AAGGATTCAA
*
28319274 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
28319303 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
28319332 AG
1 AG
28319334 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:28320352 original size:14 final size:14
Alignment explanation
Indices: 28320310--28320354 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
28320300 TTAAAGAAGC
28320310 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
28320324 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
28320337 AACTCATTTAATTA
1 AACTCATTAAATTA
28320351 AACT
1 AACT
28320355 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:28331070 original size:18 final size:17
Alignment explanation
Indices: 28331047--28331081 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28331037 TATGTTCAAA
*
28331047 TTTTCAGATTTTGTTTTT
1 TTTTCAAATTTT-TTTTT
28331065 TTTTCAAATTTTTTTTT
1 TTTTCAAATTTTTTTTT
28331082 GAACTTTTTT
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:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTCAAATTTTTTTTT
Found at i:28331344 original size:15 final size:15
Alignment explanation
Indices: 28331324--28331371 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
28331314 TCAAAGATGG
28331324 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
28331339 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
28331353 GTTTATGGATATAAA
1 GTTTATGGATATGAA
28331368 GTTT
1 GTTT
28331372 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:28331358 original size:14 final size:14
Alignment explanation
Indices: 28331318--28331361 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28331308 AAGGATTCAA
28331318 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
28331332 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
28331347 AGATGGGTTTATGG
1 AGATGGGTTTATGG
28331361 A
1 A
28331362 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:28331387 original size:29 final size:29
Alignment explanation
Indices: 28331318--28331377 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
28331308 AAGGATTCAA
*
28331318 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
28331347 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
28331376 AG
1 AG
28331378 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:28332396 original size:14 final size:14
Alignment explanation
Indices: 28332354--28332398 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
28332344 TTAAAGAAGC
28332354 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
28332368 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
28332381 AACTCATTTAATTA
1 AACTCATTAAATTA
28332395 AACT
1 AACT
28332399 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:28333850 original size:49 final size:49
Alignment explanation
Indices: 28333773--28333960 Score: 200
Period size: 49 Copynumber: 3.8 Consensus size: 49
28333763 TAGCCGAAGC
* * *
28333773 TATCTGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGAACTTAGTACTACACATGCGACCAAT
* * * * * *
28333822 AATCTGGTACATGTAGTAGCTTGAACTTAGTACTATACACGCGATCACAGT
1 TATCTGGTACACGTAGTAGCCTGAACTTAGTACTACACATGCGA-C-CAAT
* * * * *
28333873 TTTC-GAGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
1 TATCTG-GTACACGTAGTAGCCTGAACTTAGTACTACACATGCGACCAAT
28333922 TATCTGGTACACGTAGTAGCCT-ACACTTAGTACTACACA
1 TATCTGGTACACGTAGTAGCCTGA-ACTTAGTACTACACA
28333961 CGTGACCTCA
Statistics
Matches: 110, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
49 71 0.65
50 4 0.04
51 35 0.32
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGAACTTAGTACTACACATGCGACCAAT
Found at i:28333952 original size:100 final size:100
Alignment explanation
Indices: 28333779--28333962 Score: 298
Period size: 100 Copynumber: 1.8 Consensus size: 100
28333769 AAGCTATCTG
* * *
28333779 GTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAATAATCTGGTACATGTAGTAGCTT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCT
*
28333844 GAACTTAGTACTATACACGCGATCACAGTTTTCGA
66 GAACTTAGTACTACACACGCGATCACAGTTTTCGA
* *
28333879 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCTGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCT
28333944 -ACACTTAGTACTACACACG
66 GA-ACTTAGTACTACACACG
28333963 TGACCTCACA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
99 1 0.01
100 76 0.99
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (100 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCT
GAACTTAGTACTACACACGCGATCACAGTTTTCGA
Found at i:28340334 original size:30 final size:31
Alignment explanation
Indices: 28340300--28340394 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
28340290 AGCTCACTCC
*
28340300 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
28340330 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
28340360 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
28340390 TAGCT
1 TAGCT
28340395 AATTTTAGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
30 45 0.92
31 4 0.08
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:28344471 original size:43 final size:42
Alignment explanation
Indices: 28344417--28344573 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 42
28344407 AACATATACA
28344417 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAA-ATCG
* * * * *
28344460 ATGCCACTGTCCTAGACAG-GGCCTTACATGAAATC-AGATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCAAAAT-CG
* * * * *
28344502 ATGCCGATGTCCCAGACATGGTCTTACAAGTAAAACAGAAGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AATCA-AAATCG
*
28344546 ATGCCAATGTCCCAGATGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
28344574 CGATAACACA
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 26 0.29
43 32 0.36
44 28 0.31
45 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAAATCG
Found at i:28349403 original size:27 final size:27
Alignment explanation
Indices: 28349350--28349403 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28349340 AAAGAAATTG
* * * *
28349350 AAGAAAGAAGAGAAAATGACTTAGAAA
1 AAGAAACAAAAGAAAAAGACATAGAAA
*
28349377 AAGAAACAAAAGAAAAAGACATGGAAA
1 AAGAAACAAAAGAAAAAGACATAGAAA
28349404 GGGTAGTGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.67, C:0.06, G:0.20, T:0.07
Consensus pattern (27 bp):
AAGAAACAAAAGAAAAAGACATAGAAA
Found at i:28360370 original size:21 final size:21
Alignment explanation
Indices: 28360346--28360387 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28360336 TCATCAGATC
*
28360346 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
28360367 TACAGGTTGAGGAATCGGGGG
1 TACACCTTGAGGAATCGGGGG
28360388 AGGTGGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:28362973 original size:30 final size:30
Alignment explanation
Indices: 28362888--28362984 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
28362878 TAAACTAAAA
* *
28362888 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
28362918 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
28362948 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
28362977 ATGAGCTA
1 -TGAGCTA
28362985 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:28364317 original size:30 final size:30
Alignment explanation
Indices: 28364281--28364341 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28364271 CATTTAATAC
*
28364281 AAACTTTGGAAAAATTACATTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
28364311 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
28364341 A
1 A
28364342 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:28367485 original size:18 final size:18
Alignment explanation
Indices: 28367464--28367499 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28367454 AGTTATCTAA
28367464 TTTTAAAAGTATATAAAAT
1 TTTTAAAAG-ATATAAAAT
*
28367483 TTTTGAAAGATATAAAA
1 TTTTAAAAGATATAAAA
28367500 CCCTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TTTTAAAAGATATAAAAT
Found at i:28369587 original size:28 final size:28
Alignment explanation
Indices: 28369555--28369638 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
28369545 AACTTCGATC
28369555 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
28369583 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
28369605 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
28369633 ACGTGT
1 ACGTGT
28369639 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:28369628 original size:50 final size:51
Alignment explanation
Indices: 28369507--28369697 Score: 208
Period size: 50 Copynumber: 3.8 Consensus size: 51
28369497 TGAGGTCGCA
* * * *
28369507 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
* ** *
28369558 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-GGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
* * * *
28369608 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
** * * *
28369657 CATGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAAC
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAC
28369698 CTTGTCTACA
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
49 39 0.33
50 46 0.39
51 34 0.29
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (51 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
Found at i:28373251 original size:13 final size:14
Alignment explanation
Indices: 28373233--28373261 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28373223 ATTTATTTGT
28373233 ATATGG-CCATGTG
1 ATATGGTCCATGTG
28373246 ATATGGTCCATGTG
1 ATATGGTCCATGTG
28373260 AT
1 AT
28373262 CATTTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (14 bp):
ATATGGTCCATGTG
Found at i:28390182 original size:217 final size:217
Alignment explanation
Indices: 28389802--28390206 Score: 702
Period size: 217 Copynumber: 1.9 Consensus size: 217
28389792 TCATCGGCCG
28389802 TAGCCCTAAATTCTTCAACCCTATGTTTTCTGATTTTATCTACTAGAGCCTTACCAATTCTAACA
1 TAGCCCTAAATTCTTCAACCCTATGTTTTCTGATTTTATCTACTAGAGCCTTACCAATTCTAACA
*
28389867 GATCTAGCATCCTGTGGCACTTCATCATGTTGTAAAGCAGGTGGGGGAGGTCGTTGAACAGCGAG
66 GATCTAGCATCCTGTGGCACTTCATCATGTTGTAAAGCAGGTGGGGGAGGTCGTTGAACAGAGAG
28389932 ATTTGTTCTCATATATTCACTAAACCATTCATCCATCAATTCAAAGAAGGCTGCTTTTAACTTTA
131 ATTTGTTCTCATATATTCACTAAACCATTCATCCATCAATTCAAAGAAGGCTGCTTTTAACTTTA
28389997 TCTACTGGATCATTATTGGTCA
196 TCTACTGGATCATTATTGGTCA
* * * *
28390019 TAGCTCTAAATTCTTCAGCCCTATGTTTTCTGATTTTATCTACTGGAGCCTTACCAATTCTAATA
1 TAGCCCTAAATTCTTCAACCCTATGTTTTCTGATTTTATCTACTAGAGCCTTACCAATTCTAACA
* * * * *
28390084 GATCTAGCATCCTGTGGCATTTCATCATGTTGTGAAGCATGTGGGGGAGGTTGTTGAACAGAGGG
66 GATCTAGCATCCTGTGGCACTTCATCATGTTGTAAAGCAGGTGGGGGAGGTCGTTGAACAGAGAG
* *
28390149 ATTTGTTCTCATATATTCACTAAACCATTCATCCATCAATTTAAAGAAGGTTGCTTTT
131 ATTTGTTCTCATATATTCACTAAACCATTCATCCATCAATTCAAAGAAGGCTGCTTTT
28390207 GATGCCTCAC
Statistics
Matches: 176, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 176 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (217 bp):
TAGCCCTAAATTCTTCAACCCTATGTTTTCTGATTTTATCTACTAGAGCCTTACCAATTCTAACA
GATCTAGCATCCTGTGGCACTTCATCATGTTGTAAAGCAGGTGGGGGAGGTCGTTGAACAGAGAG
ATTTGTTCTCATATATTCACTAAACCATTCATCCATCAATTCAAAGAAGGCTGCTTTTAACTTTA
TCTACTGGATCATTATTGGTCA
Found at i:28391255 original size:22 final size:22
Alignment explanation
Indices: 28391230--28391274 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28391220 GTATTATCTC
*
28391230 ATGCATCAATAGATATAACCTT
1 ATGCATCAATAGATATAAACTT
28391252 ATGCATCAATAGATATAAACTT
1 ATGCATCAATAGATATAAACTT
28391274 A
1 A
28391275 CTCATGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (22 bp):
ATGCATCAATAGATATAAACTT
Found at i:28394554 original size:43 final size:43
Alignment explanation
Indices: 28394506--28394663 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 43
28394496 GTTACCGAGA
* * *
28394506 TGTGATTACATGTAAGACCATGTTTAGGACATTGACATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * *
28394549 TGTGATTACGTGTACGACCATGTCTGGGACATTGGCATCGTTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TAT
** * * *
28394593 T-CAATTTCGTGTAAGACCATGTCTGGGACAGTGGCATTG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
** *
28394634 ATGTGACGACATGTAAGACCATATCTGGGA
1 -TGTGATTACATGTAAGACCATGTCTGGGA
28394664 TATGGCTTTC
Statistics
Matches: 93, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 86 0.92
44 4 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:28398795 original size:29 final size:29
Alignment explanation
Indices: 28398711--28398808 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 29
28398701 TACCTGTATC
* * *
28398711 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * *
28398739 TGGCCCATTA-GCCCAAATGACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
28398767 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* *
28398796 TGACCCGTTAGGC
1 TGGCCCATTAGGC
28398809 GTAGTCAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.07
28 28 0.48
29 26 0.45
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:28400161 original size:16 final size:17
Alignment explanation
Indices: 28400130--28400169 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
28400120 ACAAAGAAAG
28400130 TTTGGGATTTCAGGATT
1 TTTGGGATTTCAGGATT
*
28400147 TTTGGG-TTTCGGGATT
1 TTTGGGATTTCAGGATT
28400163 TTTGGGA
1 TTTGGGA
28400170 CGTTACAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.12, C:0.05, G:0.35, T:0.47
Consensus pattern (17 bp):
TTTGGGATTTCAGGATT
Found at i:28401094 original size:23 final size:23
Alignment explanation
Indices: 28401062--28401125 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
28401052 AATTTTAATT
*
28401062 AGGAAACTCACAAAGAGCCTATC
1 AGGAAGCTCACAAAGAGCCTATC
28401085 AGGAAGCTCACAAAGAGCCTATC
1 AGGAAGCTCACAAAGAGCCTATC
*
28401108 AGGAAGCCCACAAAGAGC
1 AGGAAGCTCACAAAGAGC
28401126 TATGTAACAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.42, C:0.27, G:0.22, T:0.09
Consensus pattern (23 bp):
AGGAAGCTCACAAAGAGCCTATC
Found at i:28401210 original size:24 final size:24
Alignment explanation
Indices: 28401168--28401219 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
28401158 AAGTTTCAGC
*
28401168 GAGCCATGTCAGGAAGCTCAT-AA
1 GAGCCATATCAGGAAGCTCATGAA
*
28401191 GAGCCTATATCAGGATGCTCATGAA
1 GAGCC-ATATCAGGAAGCTCATGAA
28401216 GAGC
1 GAGC
28401220 TGTGTTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATGAA
Found at i:28402570 original size:28 final size:28
Alignment explanation
Indices: 28402538--28402592 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
28402528 GTGACCAAAG
28402538 TAAGTTCATATGTTAATAAGCATTAATA
1 TAAGTTCATATGTTAATAAGCATTAATA
28402566 TAAGTTCATATGTTAATAAGCATTAAT
1 TAAGTTCATATGTTAATAAGCATTAAT
28402593 GTAATTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (28 bp):
TAAGTTCATATGTTAATAAGCATTAATA
Found at i:28403188 original size:36 final size:37
Alignment explanation
Indices: 28403115--28403188 Score: 105
Period size: 41 Copynumber: 1.9 Consensus size: 37
28403105 AACATATATA
28403115 TTAGCCTTGTGATTAAATGGAATTGTAGTATATTATATGTG
1 TTAGCCTTGTGATTAAATGGAATTGTAG----TTATATGTG
28403156 TTAGCCTTGTGATTAAATGGAATTGTAG-TATAT
1 TTAGCCTTGTGATTAAATGGAATTGTAGTTATAT
28403189 TATGTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 5 0.15
41 28 0.85
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (37 bp):
TTAGCCTTGTGATTAAATGGAATTGTAGTTATATGTG
Found at i:28414636 original size:27 final size:26
Alignment explanation
Indices: 28414592--28414643 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28414582 GGACTACCGA
* *
28414592 TTTACCCCTGGAGGGTAAAATGACTAT
1 TTTACCCCTCGAGCGT-AAATGACTAT
*
28414619 TTTACCCCTCGTGCGTAAATGACTA
1 TTTACCCCTCGAGCGTAAATGACTA
28414644 ACTTCTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (26 bp):
TTTACCCCTCGAGCGTAAATGACTAT
Found at i:28420672 original size:25 final size:25
Alignment explanation
Indices: 28420644--28420713 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
28420634 CTCTTTTAAT
*
28420644 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
28420669 AACTGGGGTAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
28420694 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28420714 AGCACTTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:28421551 original size:27 final size:27
Alignment explanation
Indices: 28421521--28421585 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
28421511 GGGCATATTC
28421521 GTCATTTTACCATACAGGGG-TACTACG
1 GTCATTTTACCATACAGGGGCT-CTACG
* * *
28421548 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAGGGGCTCTACG
*
28421575 GTCTTTTTACC
1 GTCATTTTACC
28421586 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGCTCTACG
Found at i:28421669 original size:27 final size:27
Alignment explanation
Indices: 28421616--28421855 Score: 135
Period size: 27 Copynumber: 8.8 Consensus size: 27
28421606 TTTCATCCTA
* * * **
28421616 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTGTAAAC
* **
28421643 CAATGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTGTAAAC
* * *
28421670 CAATGGTATTTCT-ATAATTTT-TAGAAAGT
1 CAAGGGTATTT-TGGTAATTTTGT--AAA-C
* * *
28421699 CAAGGGTATTTTTGTAATTTTGTGAAT
1 CAAGGGTATTTTGGTAATTTTGTAAAC
* ** *
28421726 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTGTAAAC
** * ***
28421753 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTGTAAAC
* **
28421779 CTAGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTGTAAAC
* *
28421807 TAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTGTAAAC
* *
28421834 CAATGGTATTTTAGTAATTTTG
1 CAAGGGTATTTTGGTAATTTTG
28421856 AAAATTGAGT
Statistics
Matches: 168, Mismatches: 37, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
26 3 0.02
27 140 0.83
28 7 0.04
29 17 0.10
30 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTGTAAAC
Found at i:28421788 original size:54 final size:54
Alignment explanation
Indices: 28421730--28421920 Score: 183
Period size: 54 Copynumber: 3.5 Consensus size: 54
28421720 GTGAATCAGG
* *
28421730 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGT
1 GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCATAAACCAGT
* * ** *
28421784 GGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTGTAAACCAAT
1 GGTATTTTGGTAATTTTACAAATTGA-GGGTATTTCGGTAATTTCATAAACCAGT
* * *** *
28421838 GGTATTTTAGTAATTTTGA-AAATTGAGTGTAAAAACGGTAA-TTCTATAAATCGAG-
1 GGTATTTTGGTAATTTT-ACAAATTGAGGGT-ATTTCGGTAATTTC-ATAAA-CCAGT
*
28421893 GGTACTTTGGTAATTTTACAAATTGAGG
1 GGTATTTTGGTAATTTTACAAATTGAGG
28421921 ACATTTTAGT
Statistics
Matches: 109, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
53 1 0.01
54 71 0.65
55 35 0.32
56 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (54 bp):
GGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCATAAACCAGT
Found at i:28421915 original size:27 final size:27
Alignment explanation
Indices: 28421701--28421935 Score: 145
Period size: 27 Copynumber: 8.7 Consensus size: 27
28421691 TAGAAAGTCA
* ***
28421701 AGGGTATTTTTGTAATTTTGTGAATC-
1 AGGGTATTTTGGTAATTTTACAAATCG
*
28421727 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTTGGTAATTTTACAAATCG
* * *
28421755 AGGGTATTTCGGTAATTTCACAAA-CT
1 AGGGTATTTTGGTAATTTTACAAATCG
*
28421781 AGTGGTATTTTGGTAATTTTACAAA-CT
1 AG-GGTATTTTGGTAATTTTACAAATCG
** * *
28421808 AGGGGTATTTTGGTAATTTTGTAAACCA
1 A-GGGTATTTTGGTAATTTTACAAATCG
* * *
28421836 ATGGTATTTTAGTAATTTTGA-AAATTG
1 AGGGTATTTTGGTAATTTT-ACAAATCG
* **** * *
28421863 AGTGTAAAAACGGTAATTCTATAAATCG
1 AGGGT-ATTTTGGTAATTTTACAAATCG
* *
28421891 AGGGTACTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTACAAATCG
** *
28421918 AGGACATTTTAGTAATTT
1 AGGGTATTTTGGTAATTT
28421936 GGTAAACTAA
Statistics
Matches: 160, Mismatches: 41, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
26 3 0.02
27 136 0.85
28 21 0.13
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAATCG
Found at i:28422941 original size:42 final size:43
Alignment explanation
Indices: 28422872--28423013 Score: 139
Period size: 42 Copynumber: 3.3 Consensus size: 43
28422862 TCTTACATGT
28422872 AATCAAATATCGATGCCACTGTCCCAGACAAGGTCTTACACAA
1 AATCAAATATCGATGCCACTGTCCCAGACAAGGTCTTACACAA
* *
28422915 AATCAAATA-CGATGTCGA-TGTCCCAGACATGGTCTTACACGTAA
1 AATCAAATATCGATG-CCACTGTCCCAGACAAGGTCTTACAC--AA
* * * ** *
28422959 ATCTCAAAT-T-GATGCCAATGTCCTAGACGTGGTCTTACACGA
1 A-ATCAAATATCGATGCCACTGTCCCAGACAAGGTCTTACACAA
*
28423001 AATCACATATCGA
1 AATCAAATATCGA
28423014 AATCCTATGT
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
41 5 0.06
42 29 0.35
43 15 0.18
44 27 0.33
45 6 0.07
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
AATCAAATATCGATGCCACTGTCCCAGACAAGGTCTTACACAA
Found at i:28422992 original size:44 final size:43
Alignment explanation
Indices: 28422850--28423010 Score: 150
Period size: 44 Copynumber: 3.8 Consensus size: 43
28422840 AATGCCGACA
* * * * *
28422850 TCCCTGACGTGGTCTTACATGTAA-TCAAATATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGAAACTCAAATAT-GATGCCAATG
* * * * *
28422893 TCCCAGACAAGGTCTTACAC-AAAATCAAATACGATGTCGATG
1 TCCCAGACATGGTCTTACACGAAACTCAAATATGATGCCAATG
28422935 TCCCAGACATGGTCTTACACGTAAATCTCAAAT-TGATGCCAATG
1 TCCCAGACATGGTCTTACACG-AAA-CTCAAATATGATGCCAATG
* * *
28422979 TCCTAGACGTGGTCTTACACGAAA-TCACATAT
1 TCCCAGACATGGTCTTACACGAAACTCAAATAT
28423011 CGAAATCCTA
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
41 5 0.05
42 29 0.30
43 26 0.27
44 30 0.31
45 6 0.06
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAACTCAAATATGATGCCAATG
Found at i:28423024 original size:44 final size:42
Alignment explanation
Indices: 28422850--28423013 Score: 163
Period size: 43 Copynumber: 3.8 Consensus size: 42
28422840 AATGCCGACA
* * * *
28422850 TCCCTGACGTGGTCTTACATGTAATCAAATATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCA-TG
* * *
28422893 TCCCAGACAAGGTCTTACACAAAATCAAATA-CGATGTCGATG
1 TCCCAGACATGGTCTTACACGAAATCAAATATCGATG-CCATG
28422935 TCCCAGACATGGTCTTACACGTAAATCTCAAAT-T-GATGCCAATG
1 TCCCAGACATGGTCTTACACG-AAA--TCAAATATCGATGCC-ATG
* * *
28422979 TCCTAGACGTGGTCTTACACGAAATCACATATCGA
1 TCCCAGACATGGTCTTACACGAAATCAAATATCGA
28423014 AATCCTATGT
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.05
42 27 0.27
43 36 0.36
44 26 0.26
45 6 0.06
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCATG
Found at i:28426517 original size:25 final size:25
Alignment explanation
Indices: 28426483--28426534 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28426473 ATATTTATAC
28426483 ATCGCAAAATTGCTAACACAACAAG
1 ATCGCAAAATTGCTAACACAACAAG
28426508 ATCGCAAAATTGCTAACACAACAAG
1 ATCGCAAAATTGCTAACACAACAAG
28426533 AT
1 AT
28426535 ATACTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.17
Consensus pattern (25 bp):
ATCGCAAAATTGCTAACACAACAAG
Found at i:28428047 original size:38 final size:38
Alignment explanation
Indices: 28428005--28428135 Score: 136
Period size: 38 Copynumber: 3.2 Consensus size: 38
28427995 TTTCAAATTA
28428005 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * *
28428043 ACATGTTTAACTGTGGAATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
* *
28428084 GAATCAATATATGTAACCATGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
28428128 ACATGTAT
1 ACATGTAT
28428136 CAATATGTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 18
0.74 0.09 0.18
Matches are distributed among these distances:
38 34 0.45
39 1 0.01
40 4 0.05
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 3 0.04
46 1 0.01
47 26 0.35
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:28428161 original size:48 final size:48
Alignment explanation
Indices: 28428062--28428183 Score: 165
Period size: 48 Copynumber: 2.6 Consensus size: 48
28428052 ACTGTGGAAT
* *
28428062 ATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAACCATGGCAT
1 ATCCACTTAGCACCACGTTACATGTATCAATATATGTAACCATGGCAA
* * * *
28428109 ATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCGTGGTAA
1 ATCCACTTAGCACCACGTTACATGTATCAATATATGTAACCATGGCAA
* *
28428157 ATCCACTTAGCACCACATTACACGTAT
1 ATCCACTTAGCACCACGTTACATGTAT
28428184 AGCCGTGGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 20 0.30
48 46 0.70
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (48 bp):
ATCCACTTAGCACCACGTTACATGTATCAATATATGTAACCATGGCAA
Found at i:28443996 original size:19 final size:19
Alignment explanation
Indices: 28443969--28444012 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
28443959 AATCCCTAGC
28443969 TTTCCCTTTTTCTT-TTTCT
1 TTTCCC-TTTTCTTCTTTCT
*
28443988 TTTCTCTTTTCTTCTTTC-
1 TTTCCCTTTTCTTCTTTCT
28444006 TTTCCCT
1 TTTCCCT
28444013 GCTAACCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCCCTTTTCTTCTTTCT
Found at i:28445970 original size:42 final size:44
Alignment explanation
Indices: 28445857--28446026 Score: 163
Period size: 43 Copynumber: 4.0 Consensus size: 44
28445847 TAGGATTCCG
* * * * *
28445857 ATATGTGATTTCGTGTAAGACCAC-ATATGGGACGTTGGCATCG
1 ATATTTGATTTCGTGTAAGACCACTGTTTGGGACATTGGCATCA
*
28445900 AT-TTGAGATTTACGTGTAAGACCA-TGTTTGGGACATTGGCATC-
1 ATATT-TGATTT-CGTGTAAGACCACTGTTTGGGACATTGGCATCA
* *
28445943 ATATTTGATTTCGTGTAAGACC-CTGTTTGGGATAGTGGCATCA
1 ATATTTGATTTCGTGTAAGACCACTGTTTGGGACATTGGCATCA
* * * * *
28445986 ATATTTGATTACATGGAAGACCACT-TCTGGGACGTTGGCAT
1 ATATTTGATTTCGTGTAAGACCACTGTTTGGGACATTGGCAT
28446027 TGTATGAGCT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
42 29 0.28
43 45 0.43
44 31 0.30
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (44 bp):
ATATTTGATTTCGTGTAAGACCACTGTTTGGGACATTGGCATCA
Found at i:28445991 original size:43 final size:43
Alignment explanation
Indices: 28445857--28446008 Score: 143
Period size: 42 Copynumber: 3.6 Consensus size: 43
28445847 TAGGATTCCG
* ** *
28445857 ATATGTGATTT-CGTGTAAGACCACATATGGGAC-GTTGGCATC
1 ATATTTGATTTACGTGTAAGACCATGTTTGGGACAG-TGGCATC
* *
28445899 GAT-TTGAGATTTACGTGTAAGACCATGTTTGGGACATTGGCATC
1 -ATATT-TGATTTACGTGTAAGACCATGTTTGGGACAGTGGCATC
* *
28445943 ATATTTGATTT-CGTGTAAGACCCTGTTTGGGATAGTGGCATC
1 ATATTTGATTTACGTGTAAGACCATGTTTGGGACAGTGGCATC
* *
28445985 AATATTTGA-TTACATGGAAGACCA
1 -ATATTTGATTTACGTGTAAGACCA
28446009 CTTCTGGGAC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
42 31 0.34
43 31 0.34
44 28 0.31
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
ATATTTGATTTACGTGTAAGACCATGTTTGGGACAGTGGCATC
Found at i:28452890 original size:47 final size:47
Alignment explanation
Indices: 28452830--28452950 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
28452820 GCATTGGCAC
*
28452830 TAAGACAATGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
28452877 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
28452924 TAAGATAAGGATATCATGTAAGACCAT
1 TAAGACAAGGATACCATGTAAGACCAT
28452951 TCCAAGGCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:28453110 original size:53 final size:54
Alignment explanation
Indices: 28452930--28453234 Score: 368
Period size: 55 Copynumber: 5.6 Consensus size: 54
28452920 TTGGTAAGAT
* * * *
28452930 AAGGATATCATGTAAGACCATTCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
28452984 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* ** *
28453039 AAAGG-T-CCTATGTAAGACCATGCCAAGGCATGAAATTGGTGAGTTC-ATAAGGC
1 -AAGGATACC-ATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
28453092 AAGGATGCCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * *
28453147 AAAGG-TCCCATCTAAGACCATGCCAAGACATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
28453200 AAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA
28453235 ATGGTAAGTT
Statistics
Matches: 217, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
52 8 0.04
53 72 0.33
54 46 0.21
55 83 0.38
56 8 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:28453114 original size:108 final size:108
Alignment explanation
Indices: 28452938--28453234 Score: 477
Period size: 108 Copynumber: 2.7 Consensus size: 108
28452928 ATAAGGATAT
* * * * *
28452938 CATGTAAGACCATTCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCATGTAAGACC
28453003 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
65 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
* ** *
28453047 TATGTAAGACCATGCCAAGGCATGAAATTGGTGAGTTCATAAGGCAAGGATGCCATGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATACCATGTAAGACCA
28453112 TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
66 TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
* * *
28453155 CATCTAAGACCATGCCAAGACATGGCATTGGTGAGTTCATAAGGCAAGGATACCACGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATACCATGTAAGACCA
28453220 TGTCAAGACATGGCA
66 TGTCAAGACATGGCA
28453235 ATGGTAAGTT
Statistics
Matches: 172, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 140 0.81
109 32 0.19
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (108 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATACCATGTAAGACCA
TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
Found at i:28456046 original size:43 final size:42
Alignment explanation
Indices: 28455963--28456054 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 42
28455953 CGAAAAGCTC
* * * *
28455963 ATACAATGCCAATGTCCCAGATGTAGTCTTACATGTAATCAG
1 ATACGATGCCAATGTCCCAGATGTAGTCTTACACGAAATCAA
* *
28456005 ATATCGATGCCACTGTCCCAGATAG-GGTCTTACACGAAATCAA
1 ATA-CGATGCCAATGTCCCAGAT-GTAGTCTTACACGAAATCAA
28456048 ATACGAT
1 ATACGAT
28456055 ACCGATCCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 7 0.17
43 34 0.81
44 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGATGTAGTCTTACACGAAATCAA
Found at i:28470685 original size:19 final size:19
Alignment explanation
Indices: 28470663--28470709 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
28470653 TATTTCTTTA
28470663 ATTTTAGTTAATTTATGT-T
1 ATTTTAGTTAA-TTATGTCT
*
28470682 ATTTT-GATTAATTATTTCT
1 ATTTTAG-TTAATTATGTCT
28470701 ATTTTAGTT
1 ATTTTAGTT
28470710 TTTCATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 6 0.25
19 17 0.71
20 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (19 bp):
ATTTTAGTTAATTATGTCT
Found at i:28475750 original size:15 final size:16
Alignment explanation
Indices: 28475730--28475759 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28475720 AATTCAACCC
28475730 AAAAATTA-ATTTTGG
1 AAAAATTACATTTTGG
28475745 AAAAATTACATTTTG
1 AAAAATTACATTTTG
28475760 CCCCCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (16 bp):
AAAAATTACATTTTGG
Found at i:28481867 original size:27 final size:27
Alignment explanation
Indices: 28481837--28481932 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 27
28481827 CAATATCGTA
* *
28481837 GCAAAGCTACCAGAAACAGTAAATGTG
1 GCAAAGCCACCAGTAACAGTAAATGTG
* * *
28481864 GCAAAGCCACCAGTATCAGTAATTGTA
1 GCAAAGCCACCAGTAACAGTAAATGTG
* *
28481891 GCATAGCCACCAGTAACAGTGAATGTG
1 GCAAAGCCACCAGTAACAGTAAATGTG
* * *
28481918 ACATAGTCACCAGTA
1 GCAAAGCCACCAGTA
28481933 CAGAACTTCC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.19
Consensus pattern (27 bp):
GCAAAGCCACCAGTAACAGTAAATGTG
Found at i:28482425 original size:27 final size:27
Alignment explanation
Indices: 28482167--28482429 Score: 206
Period size: 27 Copynumber: 9.7 Consensus size: 27
28482157 TTTCATCCTA
* * * *
28482167 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * *
28482194 CAAGGGTATTTCAGTAATTTTGCAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * **
28482221 CAATGGTATTTCT-ATAATTTTTGAAAGT
1 CAAGGGTATTT-TGGTAATTTTACAAA-T
* * *
28482249 TAAGGGTATTTTTGTAATTTTCCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * *
28482276 TAAGGGTATTTCGGTACTTTTCCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
28482303 CAGGGGTATTTTGGTAACTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
28482330 TAAGGGTATTTTAGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
28482357 CGAA-GGTATTTCGGTAATTTCACAAAT
1 C-AAGGGTATTTTGGTAATTTTACAAAT
* * ** *
28482384 CAGGGGTATTGTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
28482411 CAAGGGTATTTTGGTAATT
1 CAAGGGTATTTTGGTAATT
28482430 CTACCCTACA
Statistics
Matches: 186, Mismatches: 45, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
26 1 0.01
27 164 0.88
28 21 0.11
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:28482444 original size:27 final size:27
Alignment explanation
Indices: 28482414--28482467 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
28482404 TGTAAACCAA
*
28482414 GGGTATTTTGGTAATTCTACCCTACAG
1 GGGTATTTTAGTAATTCTACCCTACAG
28482441 GGGTATTTTAGTAATTCTACCCTACAG
1 GGGTATTTTAGTAATTCTACCCTACAG
28482468 ATATGAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (27 bp):
GGGTATTTTAGTAATTCTACCCTACAG
Found at i:28482869 original size:23 final size:23
Alignment explanation
Indices: 28482843--28482890 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28482833 AATTCTCATG
28482843 TTAGCTTCCCGATGTGGGATTAC
1 TTAGCTTCCCGATGTGGGATTAC
28482866 TTAGCTTCCCGATGTGGGATTAC
1 TTAGCTTCCCGATGTGGGATTAC
28482889 TT
1 TT
28482891 CCAACCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (23 bp):
TTAGCTTCCCGATGTGGGATTAC
Found at i:28484447 original size:27 final size:27
Alignment explanation
Indices: 28484417--28484513 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 27
28484407 CTTTGTAACA
* * *
28484417 TACTCTGAATGAATCTCCTTTACGGTG
1 TACTCTGTATGAATCGCCTTTACGGCG
* **
28484444 TACTGTGTATGAATCGCCTTTGTGGCG
1 TACTCTGTATGAATCGCCTTTACGGCG
* * **
28484471 TACTCTGTATGAATCGTCTATGTGGCG
1 TACTCTGTATGAATCGCCTTTACGGCG
*
28484498 TACTCTATATGAATCG
1 TACTCTGTATGAATCG
28484514 TGTAACCCTC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (27 bp):
TACTCTGTATGAATCGCCTTTACGGCG
Found at i:28484514 original size:27 final size:27
Alignment explanation
Indices: 28484451--28484514 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
28484441 GTGTACTGTG
* * *
28484451 TATGAATCGCCTTTGTGGCGTACTCTG
1 TATGAATCGTCTATGTGGCGTACTCTA
28484478 TATGAATCGTCTATGTGGCGTACTCTA
1 TATGAATCGTCTATGTGGCGTACTCTA
28484505 TATGAATCGT
1 TATGAATCGT
28484515 GTAACCCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (27 bp):
TATGAATCGTCTATGTGGCGTACTCTA
Found at i:28486770 original size:27 final size:28
Alignment explanation
Indices: 28486710--28486802 Score: 111
Period size: 27 Copynumber: 3.4 Consensus size: 28
28486700 ACGTTACAAA
* **
28486710 TGCCTTTGTGGC-ATACTCTGTATAAAT
1 TGCCTTTGTGGCAATACTCTGAATGGAT
*
28486737 AGCCTTTGTGGCAAT-CTCTGAATGGAT
1 TGCCTTTGTGGCAATACTCTGAATGGAT
*
28486764 TGTCTTTGTGG-AATACTCTGAATGGAT
1 TGCCTTTGTGGCAATACTCTGAATGGAT
*
28486791 TGCCTTAGTGGC
1 TGCCTTTGTGGC
28486803 CTATCTTACA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.05
27 50 0.91
28 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (28 bp):
TGCCTTTGTGGCAATACTCTGAATGGAT
Found at i:28491120 original size:13 final size:14
Alignment explanation
Indices: 28491092--28491126 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
28491082 CCATTATAAA
*
28491092 CCAAACATAGATAG
1 CCAAACATACATAG
28491106 CCAAACAT-CATAG
1 CCAAACATACATAG
28491119 CCAAACAT
1 CCAAACAT
28491127 TTTGTCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.49, C:0.29, G:0.09, T:0.14
Consensus pattern (14 bp):
CCAAACATACATAG
Found at i:28492739 original size:16 final size:15
Alignment explanation
Indices: 28492718--28492759 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
28492708 CACATTCGGC
*
28492718 TCACATATATATATT
1 TCACATATATACATT
28492733 ATCACAT-TATACATT
1 -TCACATATATACATT
28492748 TCAGCATATATA
1 TCA-CATATATA
28492760 ATTCATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (15 bp):
TCACATATATACATT
Found at i:28494873 original size:39 final size:40
Alignment explanation
Indices: 28494669--28494891 Score: 254
Period size: 40 Copynumber: 5.6 Consensus size: 40
28494659 TTGAATGCTG
* * * * * *
28494669 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
28494709 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
28494749 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
28494789 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
28494829 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
28494868 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28494892 TGAACGAGGA
Statistics
Matches: 163, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 36 0.22
40 119 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:28494911 original size:79 final size:80
Alignment explanation
Indices: 28494743--28494926 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
28494733 TGTGCGAGAT
* * *
28494743 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
** *
28494808 GCATTCGTGCGAGTT
66 GCATTCGAACGAGTG
* * * *
28494823 ATTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
*
28494887 GCATTTGAACGAG-G
66 GCATTCGAACGAGTG
* *
28494901 AGCTATATCC-GGTTAAATCCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
28494927 TACGTGATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 15 0.17
79 45 0.51
80 28 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
GCATTCGAACGAGTG
Found at i:28502727 original size:40 final size:40
Alignment explanation
Indices: 28502672--28502795 Score: 182
Period size: 40 Copynumber: 3.2 Consensus size: 40
28502662 ATCGGAGCCG
*
28502672 AGGCATTC-TGCGAGTTATTAAATCCGGGTTAAGTCCCGA
1 AGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGA
*
28502711 AGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGA
1 AGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGA
* * *
28502751 AGGCATT-GTGTGAGTTACTAAA-CCGGGCTATGTCCCGA
1 AGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGA
28502789 AGGCATT
1 AGGCATT
28502796 TGAACGAGGA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 22 0.28
39 20 0.26
40 36 0.46
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
AGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGA
Found at i:28502815 original size:78 final size:78
Alignment explanation
Indices: 28502672--28502830 Score: 176
Period size: 78 Copynumber: 2.0 Consensus size: 78
28502662 ATCGGAGCCG
* * ** ** *
28502672 AGGCATTCTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCC
1 AGGCATTCTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAATCC
**
28502737 GGGTTATGTCCCGA
66 -GGTTAAATCCCGA
* * * * *
28502751 AGGCATTGTGTGAGTTACTAAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATATCC
1 AGGCATTCTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAATCC
28502815 GGTTAAATCCCGA
66 GGTTAAATCCCGA
28502828 AGG
1 AGG
28502831 TACGTGATTT
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
77 14 0.21
78 33 0.50
79 19 0.29
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (78 bp):
AGGCATTCTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAATCC
GGTTAAATCCCGA
Found at i:28505280 original size:21 final size:19
Alignment explanation
Indices: 28505256--28505311 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
28505246 AAAACACTTA
*
28505256 TTTTTTTATTTTCCATCTT
1 TTTTTTTTTTTTCCATCTT
*
28505275 TCTTTTTTCTTTTGTAC-TCTT
1 T-TTTTTT-TTTT-TCCATCTT
28505296 TTTTTTTTTTTTCCAT
1 TTTTTTTTTTTTCCAT
28505312 TGTTTTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.07
19 6 0.20
20 12 0.40
21 8 0.27
22 2 0.07
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTTTTTTTCCATCTT
Found at i:28507146 original size:16 final size:16
Alignment explanation
Indices: 28507125--28507157 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28507115 TTTGTTTTTC
*
28507125 TTTTTTTAATTCTGAA
1 TTTTTTTAATACTGAA
28507141 TTTTTTTAATACTGAA
1 TTTTTTTAATACTGAA
28507157 T
1 T
28507158 AAACAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTTTTAATACTGAA
Found at i:28518755 original size:18 final size:18
Alignment explanation
Indices: 28518731--28518774 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
28518721 CACTAAGCCA
28518731 ATTTTTA-CTTAATATATT
1 ATTTTTATCTTAAT-TATT
* *
28518749 CTTTTTATTTTAATTATT
1 ATTTTTATCTTAATTATT
28518767 ATTTTTAT
1 ATTTTTAT
28518775 TACTTAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTATCTTAATTATT
Found at i:28518775 original size:18 final size:19
Alignment explanation
Indices: 28518739--28518775 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28518729 CAATTTTTAC
*
28518739 TTAATATATTCTTTTTATT
1 TTAATATATTATTTTTATT
28518758 TTAAT-TATTATTTTTATT
1 TTAATATATTATTTTTATT
28518776 ACTTAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
TTAATATATTATTTTTATT
Found at i:28521736 original size:6 final size:6
Alignment explanation
Indices: 28521725--28521751 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28521715 ACAAACAAGA
28521725 CATGAT CATGAT CATGAT CATGAT CAT
1 CATGAT CATGAT CATGAT CATGAT CAT
28521752 TCCATCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (6 bp):
CATGAT
Found at i:28526063 original size:49 final size:51
Alignment explanation
Indices: 28526010--28526108 Score: 132
Period size: 54 Copynumber: 1.9 Consensus size: 51
28526000 ATTCTTGACA
28526010 TAAATTAGTT-GA-AATGATAACATGGGTTGCGAA-GTTGTTTTTCTTAATG
1 TAAATTAGTTAGACAATGATAACATGGGTTGC-AATGTTGTTTTTCTTAATG
*
28526059 TAAATTAGTTGAAGATCAATGCTAACATGGGTTGCAATGTTGTTTTTCTT
1 TAAATTAGTT--AGA-CAATGATAACATGGGTTGCAATGTTGTTTTTCTT
28526109 TTTGCAAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
49 10 0.23
52 2 0.05
53 2 0.05
54 29 0.67
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.41
Consensus pattern (51 bp):
TAAATTAGTTAGACAATGATAACATGGGTTGCAATGTTGTTTTTCTTAATG
Found at i:28528614 original size:51 final size:49
Alignment explanation
Indices: 28528442--28528636 Score: 264
Period size: 49 Copynumber: 3.9 Consensus size: 49
28528432 TAGCCAAAGC
* * * *
28528442 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* *
28528491 TATCCGGTACACGTAGTAGCTTGCACTTAGTACTACACATGTGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* *
28528540 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAAT
* * * *
28528591 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC
28528637 TCACAATAGA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 85 0.66
50 2 0.02
51 42 0.33
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
Found at i:28533324 original size:47 final size:47
Alignment explanation
Indices: 28533273--28533463 Score: 291
Period size: 47 Copynumber: 4.1 Consensus size: 47
28533263 TTAGGATTTT
28533273 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
28533320 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28533367 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
28533414 ATGTGGTGAATATGAACATG--TATATGTGGA-AA-GCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATATGT-GATAAGGCCGAATGGCCA
28533458 ATGTGA
1 ATGTGA
28533464 AATATATATA
Statistics
Matches: 135, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
44 16 0.12
45 8 0.06
46 2 0.01
47 109 0.81
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:28533326 original size:22 final size:22
Alignment explanation
Indices: 28533298--28533373 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
28533288 ACATGCATAT
28533298 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
28533320 ATGTGATGAATGTG-AGCAT-GCATA
1 ATGTGAT-AA-G-GCCGAATGGC-CA
28533344 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
28533367 ATGTGAT
1 ATGTGAT
28533374 GAATGTGAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 15 0.37
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:28533422 original size:25 final size:25
Alignment explanation
Indices: 28533347--28533422 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
28533337 ATGCATATAT
28533347 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
28533372 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
28533394 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
28533419 GTGA
1 GTGA
28533423 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:28533500 original size:94 final size:91
Alignment explanation
Indices: 28533273--28533505 Score: 238
Period size: 94 Copynumber: 2.5 Consensus size: 91
28533263 TTAGGATTTT
* * * * *
28533273 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGATGAATATGAGCATG--TATATGTGGTAAGGCCGAATGGCCAATGTGATGAATATGAACA
28533338 TGCATATATGTGATAAGGCCGAATGGCCA
64 TG-ATATATGTGATAAGGCCGAATGGCCA
* * *
28533367 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACA
1 ATGTGATGAATATGAGCATGTATATGTG-G-TAAGGCCGAATGGCCAATGTGATGAATATGAACA
*
28533432 TG-TATATGTGGA-AA-GCCGAATGGTCA
64 TGATATATGT-GATAAGGCCGAATGGCCA
* * *
28533458 ATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGC
1 ATGTG--AT-GA-ATATGAG-CATGTATATGTGGTAAGGCCGAATGGC
28533506 TAGTGTGAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
91 16 0.13
92 16 0.13
93 4 0.03
94 66 0.55
95 7 0.06
96 10 0.08
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (91 bp):
ATGTGATGAATATGAGCATGTATATGTGGTAAGGCCGAATGGCCAATGTGATGAATATGAACATG
ATATATGTGATAAGGCCGAATGGCCA
Found at i:28533504 original size:50 final size:48
Alignment explanation
Indices: 28533423--28533518 Score: 140
Period size: 50 Copynumber: 2.0 Consensus size: 48
28533413 AATGTGGTGA
28533423 ATATGAACATGTATATGTGGAAAGCCGAATGG-TCAATGTGAAATATAT
1 ATATGAACATGTATATGTGGAAAGCCGAATGGCT-AATGTGAAATATAT
* *
28533471 ATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 ATATGA-ACATGTATATGTGG-AAAGCCGAATGGCTAATGTGAAATAT
28533519 GTAGGCGATG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 6 0.14
49 13 0.30
50 23 0.53
51 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (48 bp):
ATATGAACATGTATATGTGGAAAGCCGAATGGCTAATGTGAAATATAT
Found at i:28533718 original size:37 final size:37
Alignment explanation
Indices: 28533668--28533775 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
28533658 GGAAATATAT
28533668 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28533705 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
28533742 TCCAGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
28533776 TCGTCTGAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28535189 original size:24 final size:23
Alignment explanation
Indices: 28535142--28535191 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
28535132 TAAAGTAGGT
*
28535142 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATTA
28535165 TATATTATGATTTTTATTAAT-TTA
1 TATA-TATGATTTTTA-TAATATTA
28535189 TAT
1 TAT
28535192 TTTAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 16 0.67
25 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TATATATGATTTTTATAATATTA
Found at i:28535205 original size:16 final size:18
Alignment explanation
Indices: 28535166--28535205 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
28535156 ATAATATTAT
*
28535166 ATATTATGATTTTTATTA
1 ATATTATGATTTTTAATA
28535184 AT-TTAT-A-TTTTAATA
1 ATATTATGATTTTTAATA
28535199 ATATTAT
1 ATATTAT
28535206 TAAGAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 9 0.45
16 5 0.25
17 4 0.20
18 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
ATATTATGATTTTTAATA
Found at i:28535310 original size:61 final size:58
Alignment explanation
Indices: 28535165--28535319 Score: 192
Period size: 61 Copynumber: 2.7 Consensus size: 58
28535155 TATAATATTA
* * * *
28535165 TATATTATGATTTTTATTAATTTATATTTTAATAAT-ATTATTAAGAATGTTATTAAAT
1 TATATTATTATTTTTATTAAATTATA-TTTAATAATAATTATTAAGAATATAATTAAAT
*
28535223 TATA-TATTA-TTTTATTAAATTTTATTTAATAATAATTATGTTAA-AATATAATTAAAT
1 TATATTATTATTTTTATTAAATTATATTTAATAATAATTA--TTAAGAATATAATTAAAT
28535280 TATTCATTATTATTTTTATTAAATTATATTTAATAATAAT
1 TA-T-ATTATTATTTTTATTAAATTATATTTAATAATAAT
28535320 CATCTACTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
55 9 0.11
56 17 0.20
57 17 0.20
58 9 0.11
59 1 0.01
60 5 0.06
61 26 0.31
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (58 bp):
TATATTATTATTTTTATTAAATTATATTTAATAATAATTATTAAGAATATAATTAAAT
Found at i:28535502 original size:16 final size:16
Alignment explanation
Indices: 28535467--28535504 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28535457 TAAATTATTG
**
28535467 ATTACAACTTTATTTT
1 ATTACAACTTTATTAC
28535483 ATTACAACTTTATTAC
1 ATTACAACTTTATTAC
28535499 ATTACA
1 ATTACA
28535505 GCTCTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTACAACTTTATTAC
Found at i:28536561 original size:34 final size:34
Alignment explanation
Indices: 28536518--28536586 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
28536508 TTACTAGTTT
28536518 AATAATGTAAATATGGTAGGGGTATGCTCTTCTA
1 AATAATGTAAATATGGTAGGGGTATGCTCTTCTA
28536552 AATAATGTAAATATGGTAGGGGTATGCTCTTCTA
1 AATAATGTAAATATGGTAGGGGTATGCTCTTCTA
28536586 A
1 A
28536587 GTGACGACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (34 bp):
AATAATGTAAATATGGTAGGGGTATGCTCTTCTA
Found at i:28539563 original size:9 final size:9
Alignment explanation
Indices: 28539549--28539577 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
28539539 GAGGTAGATA
28539549 AATTGAAAG
1 AATTGAAAG
28539558 AATTGAAAG
1 AATTGAAAG
28539567 AATTGAAAG
1 AATTGAAAG
28539576 AA
1 AA
28539578 AAGAACTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (9 bp):
AATTGAAAG
Found at i:28558861 original size:27 final size:27
Alignment explanation
Indices: 28558831--28559008 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28558821 ATATTGAGTC
* * * *
28558831 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28558858 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28558885 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28558913 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28558940 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28558967 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28558994 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28559009 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28558970 original size:82 final size:81
Alignment explanation
Indices: 28558852--28559007 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28558842 TGCTATATAA
* *
28558852 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28558917 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28558934 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28558998 CACTTAGTGC
65 CACTTAGTGC
28559008 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28566951 original size:27 final size:27
Alignment explanation
Indices: 28566921--28567098 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28566911 ATATTGAGTC
* * * *
28566921 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28566948 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28566975 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28567003 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28567030 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28567057 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28567084 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28567099 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28567060 original size:82 final size:81
Alignment explanation
Indices: 28566942--28567097 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28566932 TGCTATATAA
* *
28566942 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28567007 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28567024 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28567088 CACTTAGTGC
65 CACTTAGTGC
28567098 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28602941 original size:18 final size:18
Alignment explanation
Indices: 28602912--28602984 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 18
28602902 CTTGGCCCAT
*
28602912 TGCAATAACAGTAAACAG
1 TGCAGTAACAGTAAACAG
* *
28602930 TGCAGTAGCAGTAATCAG
1 TGCAGTAACAGTAAACAG
* *
28602948 TGTAGTAACATTAAACAG
1 TGCAGTAACAGTAAACAG
* *
28602966 TGCACTAACAGTAAGCAG
1 TGCAGTAACAGTAAACAG
28602984 T
1 T
28602985 ATGCAAGTCC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (18 bp):
TGCAGTAACAGTAAACAG
Found at i:28605586 original size:47 final size:47
Alignment explanation
Indices: 28605534--28606080 Score: 896
Period size: 47 Copynumber: 11.6 Consensus size: 47
28605524 GATAATTGTG
* *
28605534 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
28605581 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28605628 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
28605675 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28605722 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28605771 ATGTGAAAGTGTATATTTGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28605818 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28605865 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28605914 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28605961 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * * *
28606008 ATGTGAAAGTGTATATTTGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28606055 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
28606081 TCCCGAAGGG
Statistics
Matches: 470, Mismatches: 26, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 378 0.80
49 92 0.20
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:28605651 original size:143 final size:142
Alignment explanation
Indices: 28605534--28606080 Score: 873
Period size: 143 Copynumber: 3.9 Consensus size: 142
28605524 GATAATTGTG
* *
28605534 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATA
* *
28605598 TGTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAG
66 TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
*
28605663 CCGATGTGATGA
131 ACGATGTGATGA
* *
28605675 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATAT
* *
28605740 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATTTGTGATAAGGCCTAATG
65 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
*
28605805 GCCGATGTGATGA
130 GACGATGTGATGA
28605818 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATAT
*
28605883 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
65 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
*
28605948 GCCGATGTGATGA
130 GACGATGTGATGA
* *
28605961 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-TATATT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATA
* * * * * * *
28606025 TGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAG
28606081 TCCCGAAGGG
Statistics
Matches: 383, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
141 107 0.28
143 276 0.72
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (142 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATA
TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
ACGATGTGATGA
Found at i:28605821 original size:190 final size:190
Alignment explanation
Indices: 28605534--28606080 Score: 913
Period size: 190 Copynumber: 2.9 Consensus size: 190
28605524 GATAATTGTG
28605534 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
28605597 ATGTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATA
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
28605662 GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
131 GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
28605722 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
28605787 TTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
* *
28605852 GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
131 GCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
28605914 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * *
28605977 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATTTGTGACAGGGCCGAGTG
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
* * * *
28606042 GCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
131 GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
28606081 TCCCGAAGGG
Statistics
Matches: 338, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
188 19 0.06
189 2 0.01
190 272 0.80
192 45 0.13
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (190 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:28607973 original size:27 final size:27
Alignment explanation
Indices: 28607936--28608123 Score: 191
Period size: 27 Copynumber: 7.0 Consensus size: 27
28607926 AAACATATAT
* *
28607936 CACATAGGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
28607963 CACAAAAGGGCAAAATAGCCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
28607990 CTCATAAGGGCAAAACTGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
28608017 CACATAAGGGCAAAACTGTCAATTTA-
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
28608043 -ACACAAGGGCAAAACAGTCGTTTTGC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * * *
28608069 TATATAAGGGAAAAACCGTCATTTTAA
1 CACATAAGGGCAAAACAGTCATTTTAC
**
28608096 CACATAAGGGCAAAACAACCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
28608123 C
1 C
28608124 TTACAGGGGT
Statistics
Matches: 128, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
25 20 0.16
27 108 0.84
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:28608213 original size:81 final size:81
Alignment explanation
Indices: 28608115--28608361 Score: 350
Period size: 81 Copynumber: 3.0 Consensus size: 81
28608105 GCAAAACAAC
* * *** **
28608115 CATTTTACCTTACAGGGGTATTACAGTCATTTTACCCTATGAAGGTATTTCGGTCATTTTACCCT
1 CATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCT
*
28608180 ATAGGGGTATTTTGGT
66 ATAGGGGTATTTCGGT
* * *
28608196 CATTTTACCCTATAGGGGTATTTTGGTCATTTTACCTTATGGGGGTATTTCGATCATTTTACCTT
1 CATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCT
*
28608261 ATGGGGGTATTTCGGT
66 ATAGGGGTATTTCGGT
* * * *
28608277 CATTTTATCCTATGGGGGTATTTTGGTAATTTTACCCTATGGGGGTATTTCGGTCATTATACCCT
1 CATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCT
28608342 ATAGGGGTATTTCGGT
66 ATAGGGGTATTTCGGT
28608358 CATT
1 CATT
28608362 ATTTTCGGTC
Statistics
Matches: 146, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 146 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (81 bp):
CATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCT
ATAGGGGTATTTCGGT
Found at i:28608363 original size:27 final size:27
Alignment explanation
Indices: 28608115--28608361 Score: 316
Period size: 27 Copynumber: 9.1 Consensus size: 27
28608105 GCAAAACAAC
* * * *
28608115 CATTTTACCTTACAGGGGTATTACAGT
1 CATTTTACCCTATAGGGGTATTTCGGT
*
28608142 CATTTTACCCTAT-GAAGGTATTTCGGT
1 CATTTTACCCTATAG-GGGTATTTCGGT
*
28608169 CATTTTACCCTATAGGGGTATTTTGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
*
28608196 CATTTTACCCTATAGGGGTATTTTGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
* * *
28608223 CATTTTACCTTATGGGGGTATTTCGAT
1 CATTTTACCCTATAGGGGTATTTCGGT
* *
28608250 CATTTTACCTTATGGGGGTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
* * *
28608277 CATTTTATCCTATGGGGGTATTTTGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
* *
28608304 AATTTTACCCTATGGGGGTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
*
28608331 CATTATACCCTATAGGGGTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
28608358 CATT
1 CATT
28608362 ATTTTCGGTC
Statistics
Matches: 197, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
26 1 0.01
27 195 0.99
28 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (27 bp):
CATTTTACCCTATAGGGGTATTTCGGT
Found at i:28608369 original size:13 final size:13
Alignment explanation
Indices: 28608351--28608378 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28608341 TATAGGGGTA
28608351 TTTCGGTCATTAT
1 TTTCGGTCATTAT
28608364 TTTCGGTCATTAT
1 TTTCGGTCATTAT
28608377 TT
1 TT
28608379 CGTCCCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (13 bp):
TTTCGGTCATTAT
Found at i:28608379 original size:12 final size:12
Alignment explanation
Indices: 28608349--28608380 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
28608339 CCTATAGGGG
28608349 TATTTCGGTCAT
1 TATTTCGGTCAT
28608361 TATTTTCGGTCAT
1 TA-TTTCGGTCAT
28608374 TATTTCG
1 TATTTCG
28608381 TCCCAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (12 bp):
TATTTCGGTCAT
Found at i:28612913 original size:24 final size:23
Alignment explanation
Indices: 28612862--28612926 Score: 112
Period size: 23 Copynumber: 2.7 Consensus size: 23
28612852 CCTATACATG
28612862 CAATTATACCAAAATGATTTTTA
1 CAATTATACCAAAATGATTTTTA
28612885 CAATTATACCAAAATGATTTTTA
1 CAATTATACCAAAATGATTTTTA
28612908 CTAATTATACCCAAAATGA
1 C-AATTATA-CCAAAATGA
28612927 CTAGTTGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 24 0.60
24 7 0.17
25 9 0.22
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (23 bp):
CAATTATACCAAAATGATTTTTA
Found at i:28615210 original size:11 final size:11
Alignment explanation
Indices: 28615196--28615220 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28615186 AAAGTATGAT
28615196 TAAAATGTAAC
1 TAAAATGTAAC
28615207 TAAAATGTAAC
1 TAAAATGTAAC
28615218 TAA
1 TAA
28615221 CTACCTGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (11 bp):
TAAAATGTAAC
Found at i:28618184 original size:44 final size:44
Alignment explanation
Indices: 28618104--28618483 Score: 278
Period size: 44 Copynumber: 8.6 Consensus size: 44
28618094 CTTTGATCCA
* * * *
28618104 CTCCACTG-AACTTTAAGGAGATAAGACTTGTAGCTTCTATATG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTG
* * * * *
28618147 CTCCACTGTAACTTCAGGGAAATGAGATTTGTGGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTG
* * * *
28618191 CTCCATTGCAACATCAGGGAGATAAGACTTGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTG
* *
28618235 CTCCACTGCAACTTTAGGGAGATAAGA----T---TT-AATATG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTG
* * * * * ** *
28618271 CTCTATTGCAACTTCAGAGAGATAAGATTTGCTATCTTTGATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTCAATCTG
* *
28618316 CTCCACTGCAACTTCAGGGAGA-AGATTTGTAATTTGTAGCTTTAATCT-
1 CTCCACTGCAACTTCAGGGAGATA-A---G--ACTTGTAGCTTCAATCTG
* * * * * *
28618364 TTCCACTGTAACTTCAGGGAAATAAAACTTGTAACTTCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTG
*
28618408 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCCTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTA----G-CTTCAATCTG
*
28618457 CTCCACTGCAACTTCAAGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
28618484 TTCGCCATGA
Statistics
Matches: 265, Mismatches: 49, Indels: 40
0.75 0.14 0.11
Matches are distributed among these distances:
36 27 0.10
37 2 0.01
40 1 0.00
41 1 0.00
43 22 0.08
44 117 0.44
45 23 0.09
48 21 0.08
49 46 0.17
50 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTG
Found at i:28618470 original size:49 final size:46
Alignment explanation
Indices: 28618277--28618485 Score: 180
Period size: 49 Copynumber: 4.5 Consensus size: 46
28618267 TATGCTCTAT
* *
28618277 TGCAACTTCAGAGAGATAAGATTTGCTATCT-TT-GATCTACTCCAC
1 TGCAACTTCAGGGAGATAAGATTTG-TATCTCTTCAATCTACTCCAC
* * *
28618322 TGCAACTTCAGGGAG--AAGATTTGTAATTTGTAGCTTTAATCT-TTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGT-A--TCT--CTTCAATCTACTCCAC
* * * * *
28618370 TGTAACTTCAGGGAAATAAAACTTGTA--ACTTCAATCTACTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGTATCTCTTCAATCTACTCCAC
*
28618414 TGCAACTTCAGGGAGATAAGATTTGTATCCTGTCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGTAT-C--TCTTCAATCTACTCCAC
*
28618463 TGCAACTTCAAGGAGATAAGATT
1 TGCAACTTCAGGGAGATAAGATT
28618486 CGCCATGATA
Statistics
Matches: 131, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
42 1 0.01
43 17 0.13
44 28 0.21
45 16 0.12
48 20 0.15
49 42 0.32
50 7 0.05
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (46 bp):
TGCAACTTCAGGGAGATAAGATTTGTATCTCTTCAATCTACTCCAC
Found at i:28618521 original size:50 final size:50
Alignment explanation
Indices: 28618395--28618522 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 50
28618385 ATAAAACTTG
* * * * *
28618395 TAACTTCAATCTA-CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCC
1 TAACTTCAATCCATCTCCACTGCAACTTCAAGGAGATAAGATTCGCATCA
** *
28618444 TGTCTTCAAT-C-TGCTCCACTGCAACTTCAAGGAGATAAGATTCGCCATGA
1 TAACTTCAATCCAT-CTCCACTGCAACTTCAAGGAGATAAGATTCG-CATCA
28618494 TAACTTCAATCCATC-CCACTGCAACTTCA
1 TAACTTCAATCCATCTCCACTGCAACTTCA
28618523 GGGGTATAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
49 37 0.58
50 24 0.38
51 2 0.03
52 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (50 bp):
TAACTTCAATCCATCTCCACTGCAACTTCAAGGAGATAAGATTCGCATCA
Found at i:28621673 original size:18 final size:18
Alignment explanation
Indices: 28621650--28621695 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
28621640 TTTTTGTATT
28621650 TGGCCTTGGGTTGGATTC
1 TGGCCTTGGGTTGGATTC
28621668 TGGCCTTGGGTTGGATTC
1 TGGCCTTGGGTTGGATTC
*
28621686 TTGCCTTGGG
1 TGGCCTTGGG
28621696 GCTGATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.04, C:0.17, G:0.39, T:0.39
Consensus pattern (18 bp):
TGGCCTTGGGTTGGATTC
Found at i:28628502 original size:50 final size:50
Alignment explanation
Indices: 28628335--28628719 Score: 373
Period size: 50 Copynumber: 7.6 Consensus size: 50
28628325 ATCTAGTCCG
* * *
28628335 CATAGTAGCCTTCACTTAGTACTGA-ACATGCGACC-AACAATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACT-ACACATGTGACCTAACTATCTGGTACA
* * * * * * * *
28628384 CGTAGTAGCCTACACTTAGTACTACACACGTGA-TTGAAGTTGTCAGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCT-AA-CTATCTGGTACA
* *
28628435 CATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCTGGTATA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGGTACA
* * * *
28628485 CGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGGTACA
* * * * * * **
28628535 CGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTTGTCGGGTATG
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCT-AA-CTATCTGGTACA
* * * *
28628586 CATAGTAGCTTACACTTTGTACTACACATATGACCTAACTATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGGTACA
* ***
28628636 CATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAAACCATCTTAAACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCT--AACTATCTGGTACA
*
28628688 CATAGTAGCCTGCACATAGTACTACACATGTG
1 CATAGTAGCCTGCACTTAGTACTACACATGTG
28628720 TTCTCACAAT
Statistics
Matches: 271, Mismatches: 55, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.00
49 28 0.10
50 127 0.47
51 72 0.27
52 43 0.16
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGGTACA
Done.