Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 103 of 144
Found at i:31674781 original size:46 final size:43
Alignment explanation
Indices: 31674717--31674815 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
31674707 AATAATAACA
*
31674717 GATACACGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAAT
1 GATAC-CGGTGGATTCAGCACACAGCAACCA-CC-TTATAATCAAT
* *
31674763 GATATCCGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAAT
1 GATA-CCGGT-GGATTCAGCACACAGCAACCACCTTATAATCAAT
31674807 GATACCGGT
1 GATACCGGT
31674816 TCACATAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 13 0.27
45 2 0.04
46 24 0.50
47 4 0.08
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (43 bp):
GATACCGGTGGATTCAGCACACAGCAACCACCTTATAATCAAT
Found at i:31676234 original size:27 final size:27
Alignment explanation
Indices: 31676196--31676250 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
31676186 ACTTATTTTC
31676196 AAAGAATATTCTAAATAGATTGAGTCT
1 AAAGAATATTCTAAATAGATTGAGTCT
*
31676223 AAAGAATATTCTGAATAGATTGAGTCT
1 AAAGAATATTCTAAATAGATTGAGTCT
31676250 A
1 A
31676251 GTGTTTGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (27 bp):
AAAGAATATTCTAAATAGATTGAGTCT
Found at i:31680733 original size:50 final size:50
Alignment explanation
Indices: 31680591--31680831 Score: 270
Period size: 50 Copynumber: 4.8 Consensus size: 50
31680581 GATAATAACA
* ** * * *
31680591 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * ** *
31680640 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
31680690 TGCCCATGCCATGTCCCAGACATGGTGTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
31680740 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTTATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
31680790 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31680832 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 31, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
49 38 0.24
50 121 0.76
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:31681788 original size:16 final size:16
Alignment explanation
Indices: 31681767--31681798 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31681757 GTCTACCAAC
31681767 TTAACCAATGGTCTAA
1 TTAACCAATGGTCTAA
31681783 TTAACCAATGGTCTAA
1 TTAACCAATGGTCTAA
31681799 CCAATGGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
TTAACCAATGGTCTAA
Found at i:31681801 original size:12 final size:12
Alignment explanation
Indices: 31681784--31681809 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31681774 ATGGTCTAAT
31681784 TAACCAATGGTC
1 TAACCAATGGTC
31681796 TAACCAATGGTC
1 TAACCAATGGTC
31681808 TA
1 TA
31681810 TTTCACTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (12 bp):
TAACCAATGGTC
Found at i:31685810 original size:50 final size:50
Alignment explanation
Indices: 31685777--31686006 Score: 250
Period size: 50 Copynumber: 4.6 Consensus size: 50
31685767 TGCCCATGAT
31685777 ATGTCCCAGACATGGTGTTACGGGGGACCTCTCATCTCGGTG-CCAGCGCC
1 ATGTCCCAGACATGGTGTTACGGGGGACCTCTCATCTCGGTGCCCA-CGCC
* *
31685827 ATGTCTCAGACATGGTGTTACGGGGGACCTCTCATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTGTTACGGGGGACCTCTCATCTCGGTGCCCACGCC
* * ** * *
31685877 ATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTGTTACGGGGGACCTCTCATCTCGGTGCCCACGCC
* * * ** * *
31685927 ATGTCCCAAACATGATCTTATATGGGG-CCTCTTATCTCGGTG-CCACCGTC
1 ATGTCCCAGACATGGTGTTA-CGGGGGACCTCTCATCTCGGTGCCCA-CGCC
* **
31685977 ATGTCCCAGACATGGTCTTACAAGGGACCT
1 ATGTCCCAGACATGGTGTTACGGGGGACCT
31686007 ATTTACCTAA
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
49 5 0.03
50 147 0.94
51 5 0.03
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.25
Consensus pattern (50 bp):
ATGTCCCAGACATGGTGTTACGGGGGACCTCTCATCTCGGTGCCCACGCC
Found at i:31685940 original size:150 final size:150
Alignment explanation
Indices: 31685675--31686006 Score: 339
Period size: 150 Copynumber: 2.2 Consensus size: 150
31685665 ACATGCCAAA
* * * * * * *
31685675 GCCATGTCCCAGACATGGTCTTACATGGGA--TGT-TTCCCGTACTGCCAATGCCATATCCCAGA
1 GCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCG--GTGCCAACGCCATATCCCAAA
* ** * * * * * * * *
31685737 TATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGATATGTCCCAGACATGGTGTTA-CGGG
64 CATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGACATGTCCCAAACATGATCTTATAGGG
*
31685801 GGACCTCTCATCTCGGTGCCAGC
129 GG-CCTCTCATCTCGGTGCCACC
* * ** *
31685824 GCCATGTCTCAGACATGGTGTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACA
1 GCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCGGTGCCAACGCCATATCCCAAACA
* * * *
31685889 TGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCCAAACATGATCTTATATGGGG
66 TGGTCTTACATGGGACCTCTCATATCGGTGCCAACGACATGTCCCAAACATGATCTTATAGGGGG
*
31685954 CCTCTTATCTCGGTGCCACC
131 CCTCTCATCTCGGTGCCACC
*
31685974 GTCATGTCCCAGACATGGTCTTACAAGGGACCT
1 GCCATGTCCCAGACATGGTCTTACAAGGGACCT
31686007 ATTTACCTAA
Statistics
Matches: 146, Mismatches: 33, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
149 26 0.18
150 110 0.75
151 6 0.04
152 4 0.03
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (150 bp):
GCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCGGTGCCAACGCCATATCCCAAACA
TGGTCTTACATGGGACCTCTCATATCGGTGCCAACGACATGTCCCAAACATGATCTTATAGGGGG
CCTCTCATCTCGGTGCCACC
Found at i:31686360 original size:51 final size:51
Alignment explanation
Indices: 31686300--31686402 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
31686290 TAATAGCAAA
31686300 TTTAGCTTATTTAATACTCACAATCATCAAAACAATTCTTGACTCAAACTT
1 TTTAGCTTATTTAATACTCACAATCATCAAAACAATTCTTGACTCAAACTT
31686351 TTTAGCTTATTTAATACTCACAATCATCAAAACAATTCTTGACTCAAACTT
1 TTTAGCTTATTTAATACTCACAATCATCAAAACAATTCTTGACTCAAACTT
31686402 T
1 T
31686403 AGAAAAATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (51 bp):
TTTAGCTTATTTAATACTCACAATCATCAAAACAATTCTTGACTCAAACTT
Found at i:31692763 original size:25 final size:24
Alignment explanation
Indices: 31692723--31692809 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 24
31692713 TCTTGTACAT
*
31692723 GTATGCTCATACGAGCTGTGAATCA
1 GTATGCTCACACGAGCTGT-AATCA
**
31692748 GTATGCTCACTTGAGCTGTAGATCA
1 GTATGCTCACACGAGCTGTA-ATCA
* *
31692773 GTATGCTCTCACGAGCTATAAATCA
1 GTATGCTCACACGAGCTGT-AATCA
*
31692798 ATATGCTCACAC
1 GTATGCTCACAC
31692810 AAGCAGTGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.02
25 49 0.96
26 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (24 bp):
GTATGCTCACACGAGCTGTAATCA
Found at i:31694067 original size:19 final size:20
Alignment explanation
Indices: 31694043--31694082 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
31694033 GGCAATAAAA
31694043 TTATAATAAAAT-AATTTTT
1 TTATAATAAAATAAATTTTT
31694062 TTATAATAAAATAAATTTTT
1 TTATAATAAAATAAATTTTT
31694082 T
1 T
31694083 GACTTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATAATAAAATAAATTTTT
Found at i:31698439 original size:102 final size:102
Alignment explanation
Indices: 31698208--31698529 Score: 371
Period size: 102 Copynumber: 3.2 Consensus size: 102
31698198 CTTTTATTAT
* * ** * *
31698208 TCGATACACGTAGTAGCTTTTACATAGTACTACACACGTGA-TTAAG-TTTTACGGTTCACGTAG
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTA-GGTACACATAG
* * * ***
31698271 TAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * * *
31698309 -CGGTCCACTTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTAGGTACACATAAT
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTAGGTACACATAGT
**
31698373 AGCCTTCACTTAGTACTACACATGCCACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * * * *
31698410 TCGATTCACGTAGTAGCCTTCACACAGTACTACAAACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTAGGTACACATAGT
* *
31698475 AGCCTTCACTTAGTACTACACATTTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
31698512 TCGATACACGTAGTAGCC
1 TCGATACACGTAGTAGCC
31698530 ATCTATTTCA
Statistics
Matches: 184, Mismatches: 34, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
100 34 0.18
101 41 0.22
102 109 0.59
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTAGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:31698503 original size:51 final size:51
Alignment explanation
Indices: 31698207--31698504 Score: 257
Period size: 51 Copynumber: 5.9 Consensus size: 51
31698197 ACTTTTATTA
* * * * * **
31698207 TTCGATACACGTAGTAGCTTTTACATAGTACTACACACGTGA-TTAAG-TT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * * *
31698256 TTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TT
1 TT-CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* *
31698306 TTACGGTCCACTTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
1 TT-CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * * ** *
31698358 TTAGGTACACATAATAGCCTTCACTTAGTACTACACATGCCACC--ATCATT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAAGC-TT
* * * * * *
31698408 TATCGATTCACGTAGTAGCCTTCACACAGTACTACAAACGTGACCAAAGCTT
1 T-TCGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * * *
31698460 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATTTGACCA
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCA
31698505 TTATTTATCG
Statistics
Matches: 202, Mismatches: 39, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
49 4 0.02
50 85 0.42
51 105 0.52
52 6 0.03
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
TTCGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
Found at i:31704441 original size:40 final size:40
Alignment explanation
Indices: 31704393--31704548 Score: 249
Period size: 40 Copynumber: 3.9 Consensus size: 40
31704383 GCAAACACAT
* *
31704393 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* *
31704433 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* *
31704473 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
*
31704513 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGC
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGC
31704549 TCATGCACAC
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
Found at i:31704896 original size:203 final size:203
Alignment explanation
Indices: 31704547--31704947 Score: 802
Period size: 203 Copynumber: 2.0 Consensus size: 203
31704537 ATATCAACTC
31704547 GCTCATGCACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGGCTCAA
1 GCTCATGCACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGGCTCAA
31704612 ACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATAATTTC
66 ACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATAATTTC
31704677 AATTGGCTTTATAACATAGTCTCTAAGCACATTCGACTATCCGTCATAGTATGACTATTCATTTC
131 AATTGGCTTTATAACATAGTCTCTAAGCACATTCGACTATCCGTCATAGTATGACTATTCATTTC
31704742 AATCCAAT
196 AATCCAAT
31704750 GCTCATGCACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGGCTCAA
1 GCTCATGCACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGGCTCAA
31704815 ACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATAATTTC
66 ACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATAATTTC
31704880 AATTGGCTTTATAACATAGTCTCTAAGCACATTCGACTATCCGTCATAGTATGACTATTCATTTC
131 AATTGGCTTTATAACATAGTCTCTAAGCACATTCGACTATCCGTCATAGTATGACTATTCATTTC
31704945 AAT
196 AAT
31704948 ATAATTCAAG
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 198 1.00
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (203 bp):
GCTCATGCACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGGCTCAA
ACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATAATTTC
AATTGGCTTTATAACATAGTCTCTAAGCACATTCGACTATCCGTCATAGTATGACTATTCATTTC
AATCCAAT
Found at i:31710503 original size:44 final size:44
Alignment explanation
Indices: 31710440--31710527 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
31710430 ACATATGTAA
* *
31710440 GAATGGGTAGAACCAGGGTCAATCAAAGCAATTACATTAGTATC
1 GAATGAGTAGAACCAGGGTCAATCAAAGAAATTACATTAGTATC
*
31710484 GAATGAGTAGAACCGGGGTCAATCAAAGAAATTACATTAGTATC
1 GAATGAGTAGAACCAGGGTCAATCAAAGAAATTACATTAGTATC
31710528 AAAGAGAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (44 bp):
GAATGAGTAGAACCAGGGTCAATCAAAGAAATTACATTAGTATC
Found at i:31713401 original size:40 final size:40
Alignment explanation
Indices: 31713353--31713503 Score: 239
Period size: 40 Copynumber: 3.8 Consensus size: 40
31713343 GCAAACACAT
* *
31713353 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* *
31713393 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* *
31713433 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
*
31713473 TTGCCTTCGGGTCTTAGCCCGGATATATCAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAA
31713504 AATGCTCATG
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
Found at i:31713486 original size:80 final size:80
Alignment explanation
Indices: 31713353--31713502 Score: 264
Period size: 80 Copynumber: 1.9 Consensus size: 80
31713343 GCAAACACAT
* *
31713353 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
31713418 TATCATCTCGCATAA
66 TATCATCTCGCATAA
* *
31713433 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
31713498 TATCA
66 TATCA
31713503 AAATGCTCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (80 bp):
TTGCCTTCGGGTCATAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCATCTCGCATAA
Found at i:31713769 original size:161 final size:161
Alignment explanation
Indices: 31713504--31713823 Score: 640
Period size: 161 Copynumber: 2.0 Consensus size: 161
31713494 GATATATCAA
31713504 AATGCTCATGCACACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGG
1 AATGCTCATGCACACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGG
31713569 CTCAAACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATA
66 CTCAAACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATA
31713634 ATTTCAATTGGCTTTATAACATAGTCTCTCC
131 ATTTCAATTGGCTTTATAACATAGTCTCTCC
31713665 AATGCTCATGCACACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGG
1 AATGCTCATGCACACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGG
31713730 CTCAAACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATA
66 CTCAAACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATA
31713795 ATTTCAATTGGCTTTATAACATAGTCTCT
131 ATTTCAATTGGCTTTATAACATAGTCTCT
31713824 AAGCACATTC
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 159 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (161 bp):
AATGCTCATGCACACACATATATCAATAATCATAACACATCCATTTCATTTCTTCGTTACTAAGG
CTCAAACACAAAACATTTATTAAACCTTTCAAATTTCGGCTCAGTAGCCGCACACAAAGAGTATA
ATTTCAATTGGCTTTATAACATAGTCTCTCC
Found at i:31718361 original size:26 final size:26
Alignment explanation
Indices: 31718320--31718396 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
31718310 AGCCCCATGG
* *
31718320 GCGTGCTGTCTGGCCGTGTGTCCCTG
1 GCGTACTGTCTGGCCGTGTGTCCCTA
* *
31718346 GTGTACTGTCTGGCCGTGTGTCCCCA
1 GCGTACTGTCTGGCCGTGTGTCCCTA
* *
31718372 GCGTGCTGTCTGGCCATGTGTCCCT
1 GCGTACTGTCTGGCCGTGTGTCCCT
31718397 TGCACGTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.04, C:0.31, G:0.34, T:0.31
Consensus pattern (26 bp):
GCGTACTGTCTGGCCGTGTGTCCCTA
Found at i:31724711 original size:11 final size:11
Alignment explanation
Indices: 31724697--31724723 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31724687 GTAAACATCA
31724697 AAAATAATTTT
1 AAAATAATTTT
31724708 AAAATAATTTT
1 AAAATAATTTT
31724719 AAAAT
1 AAAAT
31724724 CTCAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:31726021 original size:10 final size:11
Alignment explanation
Indices: 31725998--31726022 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31725988 ACCAATAGTC
31725998 AAAATGAGCAA
1 AAAATGAGCAA
31726009 AAAATGAGCAA
1 AAAATGAGCAA
31726020 AAA
1 AAA
31726023 GGGGACAAAA
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:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAATGAGCAA
Found at i:31727071 original size:367 final size:367
Alignment explanation
Indices: 31726398--31727130 Score: 1351
Period size: 367 Copynumber: 2.0 Consensus size: 367
31726388 AGCAAGACGA
31726398 TCCATCCCAAAAGCCGGAACTACTCCAAGATCTAAGATCTCTCTCAGAATTCCTTCAGGGGTTTT
1 TCCATCCCAAAAGCCGGAACTACTCCAAGATCTAAGATCTCTCTCAGAATTCCTTCAGGGGTTTT
31726463 AGAGTTTTCTTCATGTTTTGTTATTTTTATACTTTTGAGATGTACTCTTATTTTATTATGAACTA
66 AGAGTTTTCTTCATGTTTTGTTATTTTTATACTTTTGAGATGTACTCTTATTTTATTATGAACTA
** *
31726528 AACCCCTTAGATACTTAAGGGGGATAAAACCTATGATGGATCTTGTTATTATTATCTGAACTGTA
131 AACCCCTTAGATACCAAACGGGGATAAAACCTATGATGGATCTTGTTATTATTATCTGAACTGTA
*
31726593 TGATAAATACTTGATTTGTTTTTAATTATGTGTTCTTAATGCTTGAGTTAATATTCCAGGTATTA
196 TGATAAATACTTGATTTGTTTTTAATTATGTGTTCTTAATGCTTGAGTTAATATTCCAAGTATTA
*
31726658 ATTCATGATTTGATGTGCTTATGTAGAGGAGGAATAGACCCTGCCTAAGAGTAGATTGGGCATAA
261 ATTCATGATTTGATGTGCTTATGTAGAGGAGGAATAGACCCTGCCTAAGAGTAGATTGGGAATAA
*
31726723 TTAGGCGGAGTTGATCGAACGCCTAGAAATAGGGTTACGAGT
326 TTAAGCGGAGTTGATCGAACGCCTAGAAATAGGGTTACGAGT
*
31726765 TCCATCCCAAAAGCCGGAACTATTCCAAGA-CTGAAGATCTCTCTCAGAATTCCTTCAGGGGTTT
1 TCCATCCCAAAAGCCGGAACTACTCCAAGATCT-AAGATCTCTCTCAGAATTCCTTCAGGGGTTT
*
31726829 TAGAGTTTTCTTTATGTTTTGTTATTTTTATACTTTTGAGATGTACTCTTATTTTATTATGAACT
65 TAGAGTTTTCTTCATGTTTTGTTATTTTTATACTTTTGAGATGTACTCTTATTTTATTATGAACT
*
31726894 AAACCCCTTAGATACCAAACGGGGATAAAACCTATGTTGGATCTTGTTATTATTATCTGAACTGT
130 AAACCCCTTAGATACCAAACGGGGATAAAACCTATGATGGATCTTGTTATTATTATCTGAACTGT
*
31726959 ATGATAAATATTTGATTTGTTTTTAATTATGTGTTCTTAATGCTTGAGTTAATATTCCAAGTATT
195 ATGATAAATACTTGATTTGTTTTTAATTATGTGTTCTTAATGCTTGAGTTAATATTCCAAGTATT
*
31727024 AATTCATGATTTGATGTGCTTATGTAGAGGAGGAATAGACCCTGCCTAAGAGTAGATTTGGAATA
260 AATTCATGATTTGATGTGCTTATGTAGAGGAGGAATAGACCCTGCCTAAGAGTAGATTGGGAATA
31727089 ATTAAGCGGAGTTGATCGAACGCCTAGAAATAGGGTTACGAG
325 ATTAAGCGGAGTTGATCGAACGCCTAGAAATAGGGTTACGAG
31727131 ATTTTCTCGG
Statistics
Matches: 354, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
366 2 0.01
367 352 0.99
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (367 bp):
TCCATCCCAAAAGCCGGAACTACTCCAAGATCTAAGATCTCTCTCAGAATTCCTTCAGGGGTTTT
AGAGTTTTCTTCATGTTTTGTTATTTTTATACTTTTGAGATGTACTCTTATTTTATTATGAACTA
AACCCCTTAGATACCAAACGGGGATAAAACCTATGATGGATCTTGTTATTATTATCTGAACTGTA
TGATAAATACTTGATTTGTTTTTAATTATGTGTTCTTAATGCTTGAGTTAATATTCCAAGTATTA
ATTCATGATTTGATGTGCTTATGTAGAGGAGGAATAGACCCTGCCTAAGAGTAGATTGGGAATAA
TTAAGCGGAGTTGATCGAACGCCTAGAAATAGGGTTACGAGT
Found at i:31727447 original size:13 final size:13
Alignment explanation
Indices: 31727431--31727476 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
31727421 TTTAATTAAA
*
31727431 TTAGTTAATTAGT
1 TTAGATAATTAGT
31727444 TTAGATAATTAGT
1 TTAGATAATTAGT
31727457 TTAGATAATTAGT
1 TTAGATAATTAGT
31727470 TTA-ATAA
1 TTAGATAA
31727477 ACAAACCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 4 0.12
13 28 0.88
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:31732875 original size:28 final size:29
Alignment explanation
Indices: 31732833--31732892 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
31732823 CCTCCTATCT
31732833 TTTTATTCTTATTTTT-TTACTTATTTT-A
1 TTTTATTCTTATTTTTATTAC-TATTTTCA
* *
31732861 TTTTATTTTTCTTTTTATTACTATTTTCA
1 TTTTATTCTTATTTTTATTACTATTTTCA
31732890 TTT
1 TTT
31732893 CAATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTTATTCTTATTTTTATTACTATTTTCA
Found at i:31732899 original size:29 final size:28
Alignment explanation
Indices: 31732844--31732908 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
31732834 TTTATTCTTA
* *
31732844 TTTTTTTACTTATTTTATTTTATTTTTC
1 TTTTTTTACTTATTTTATTTCAATTTTC
*
31732872 TTTTTATTAC-TATTTTCATTTCAATTTTA
1 TTTTT-TTACTTATTTT-ATTTCAATTTTC
*
31732901 TTATTTTA
1 TTTTTTTA
31732909 TTTTGAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTTTTTACTTATTTTATTTCAATTTTC
Found at i:31735798 original size:13 final size:13
Alignment explanation
Indices: 31735782--31735814 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
31735772 TTTAATTAAA
*
31735782 TTAGTTAATTAGT
1 TTAGATAATTAGT
31735795 TTAGATAATTAGT
1 TTAGATAATTAGT
31735808 TTA-ATAA
1 TTAGATAA
31735815 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:31738858 original size:14 final size:14
Alignment explanation
Indices: 31738835--31738868 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31738825 ACACACGCCC
*
31738835 GTGCCTCTACCTAT
1 GTGCCACTACCTAT
*
31738849 GTGCCACTACCTGT
1 GTGCCACTACCTAT
31738863 GTGCCA
1 GTGCCA
31738869 AATTTTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.35, G:0.21, T:0.29
Consensus pattern (14 bp):
GTGCCACTACCTAT
Found at i:31746142 original size:48 final size:48
Alignment explanation
Indices: 31746075--31746301 Score: 165
Period size: 48 Copynumber: 4.7 Consensus size: 48
31746065 GTGAATTGCC
* * * *
31746075 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGGCT
* * * * * *
31746123 GATGCCCTGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGGCT
* * * *
31746171 GATGCCATGTCCCAGACATGGTCATACACCGGCTCTCA--T-AATGTGCCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAA-G-G-CT
* * * * * * * *
31746219 AATGCCATGTCCTAGTCATGGTCTTACACTAG-TGCATATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-CACATCTCAAGGCT
* * *
31746267 GATGCCATGTCCCAAACATGGTCATACACTAGCTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC
31746302 TCACAACATC
Statistics
Matches: 139, Mismatches: 32, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
45 2 0.01
46 1 0.01
47 2 0.01
48 129 0.93
49 2 0.01
50 1 0.01
51 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGGCT
Found at i:31746239 original size:96 final size:95
Alignment explanation
Indices: 31746124--31746344 Score: 250
Period size: 96 Copynumber: 2.3 Consensus size: 95
31746114 GTCGAGGCTG
* * * ** *
31746124 ATGCCCTGTCCCAGACATGGTCTTACACTAGCT-C-TCGTCTCAATGTTGATGCCATGTCCCAGA
1 ATGCCATGT-CCAGACATGGTCTTACACTAG-TGCAT-ATATCAATGCCGATGCCATGTCCCAAA
* * **
31746187 CATGGTCATACACCGGCTCTCATAATGTGC-CCA
63 CATGGTCATACACCAGCTCTCACAACAT-CACCA
*
31746220 ATGCCATGTCCTAGTCATGGTCTTACACTAGTGCATATATCAATGCCGATGCCATGTCCCAAACA
1 ATGCCATGTCC-AGACATGGTCTTACACTAGTGCATATATCAATGCCGATGCCATGTCCCAAACA
*
31746285 TGGTCATACACTAGCTCTCACAACATCACCA
65 TGGTCATACACCAGCTCTCACAACATCACCA
*
31746316 ATGCCATGTTCCAAACATGGTCTTACACT
1 ATGCCATG-TCCAGACATGGTCTTACACT
31746345 GACTCCCATA
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
95 4 0.04
96 98 0.92
97 4 0.04
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (95 bp):
ATGCCATGTCCAGACATGGTCTTACACTAGTGCATATATCAATGCCGATGCCATGTCCCAAACAT
GGTCATACACCAGCTCTCACAACATCACCA
Found at i:31746320 original size:48 final size:47
Alignment explanation
Indices: 31746172--31746344 Score: 152
Period size: 48 Copynumber: 3.6 Consensus size: 47
31746162 CTCAATGTTG
* ** **
31746172 ATGCCATGTCCCAGACATGGTCATACACCGGCTCTCATAATGTGCCCA
1 ATGCCATGTCCCAAACATGGTCATACACTAGCTCTCATAACAT-CCCA
* ** * * * *
31746220 ATGCCATGTCCTAGTCATGGTCTTACACTAG-TGCAT-ATATCAATGCCG
1 ATGCCATGTCCCAAACATGGTCATACACTAGCT-C-TCATAAC-ATCCCA
*
31746268 ATGCCATGTCCCAAACATGGTCATACACTAGCTCTCACAACATCACCA
1 ATGCCATGTCCCAAACATGGTCATACACTAGCTCTCATAACATC-CCA
* *
31746316 ATGCCATGTTCCAAACATGGTCTTACACT
1 ATGCCATGTCCCAAACATGGTCATACACT
31746345 GACTCCCATA
Statistics
Matches: 99, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
47 4 0.04
48 92 0.93
49 3 0.03
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (47 bp):
ATGCCATGTCCCAAACATGGTCATACACTAGCTCTCATAACATCCCA
Found at i:31746370 original size:96 final size:95
Alignment explanation
Indices: 31746174--31746385 Score: 225
Period size: 96 Copynumber: 2.2 Consensus size: 95
31746164 CAATGTTGAT
* * * ** **
31746174 GCCATGTCCCAGACATGGTCATACACCGGCTCTCATAATGTGCCCAATGCCATGTCCTAGTCATG
1 GCCATGTCCCAAACATGGTCATACACCAGCTCTCACAACATGCCCAATGCCATGTCCTAAACATG
* * *
31746239 GTCTTACACTAGTGCATATATCAATGCCGAT
66 GTCTTACACTACTCCATATAT-AATGCCGAC
*
31746270 GCCATGTCCCAAACATGGTCATACACTAGCTCTCACAACAT-CACCAATGCCATGTTCC-AAACA
1 GCCATGTCCCAAACATGGTCATACACCAGCTCTCACAACATGC-CCAATGCCATG-TCCTAAACA
*
31746333 TGGTCTTACACTGACTCCCATAT-T-GTGCCTGAC
64 TGGTCTTACACT-ACT-CCATATATAATGCC-GAC
*
31746366 GCCATGTTCCAAACATGGTC
1 GCCATGTCCCAAACATGGTC
31746386 TTATGTTGGC
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
95 5 0.05
96 82 0.84
97 6 0.06
98 5 0.05
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (95 bp):
GCCATGTCCCAAACATGGTCATACACCAGCTCTCACAACATGCCCAATGCCATGTCCTAAACATG
GTCTTACACTACTCCATATATAATGCCGAC
Found at i:31746383 original size:144 final size:144
Alignment explanation
Indices: 31746078--31746388 Score: 315
Period size: 144 Copynumber: 2.2 Consensus size: 144
31746068 AATTGCCGAT
* * * * * *
31746078 GCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCCTGTCCCAGACATG
1 GCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTCCCAAACATG
* * * **** * * *
31746143 GTCTTACACTAGCTCTCGTCTCAATGTTGATGCCATGTCCCAGACATGGTCATACACCGGCTCTC
66 GTCATACACTAGCTCTCGACACAATACCAATGCCATGTCCCAAACATGGTCATACACCGACTCCC
*
31746208 ATAATGTGCCCAAT
131 ATAATGTGCCCAAC
** * *
31746222 GCCATG-TCCTAGTCATGGTCTTACACTAG-TGCATATATCAATGCCGATGCCATGTCCCAAACA
1 GCCATGTTCC-AAACATGGTCTTACACTAGCT-CACATATCAAGGCCGATGCCATGTCCCAAACA
* * *
31746285 TGGTCATACACTAGCTCTC-ACA-ACATCACCAATGCCATGTTCCAAACATGGTCTTACACTGAC
64 TGGTCATACACTAGCTCTCGACACA-AT-ACCAATGCCATGTCCCAAACATGGTCATACACCGAC
* **
31746348 TCCCATATTGTGCCTGAC
127 TCCCATAATGTGCCCAAC
31746366 GCCATGTTCCAAACATGGTCTTA
1 GCCATGTTCCAAACATGGTCTTA
31746389 TGTTGGCACA
Statistics
Matches: 133, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
142 1 0.01
143 7 0.05
144 122 0.92
145 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (144 bp):
GCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTCCCAAACATG
GTCATACACTAGCTCTCGACACAATACCAATGCCATGTCCCAAACATGGTCATACACCGACTCCC
ATAATGTGCCCAAC
Found at i:31750359 original size:14 final size:14
Alignment explanation
Indices: 31750342--31750381 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31750332 CGAATGGAAT
*
31750342 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
31750356 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
31750370 GATATGAACAAA
1 GGTAGGAACAAA
31750382 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:31758348 original size:11 final size:12
Alignment explanation
Indices: 31758344--31758377 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31758334 TTTTTTGATT
*
31758344 TTTTTTATTTTGA
1 TTTTTT-TTTCGA
31758357 TTTTTTTTTCGA
1 TTTTTTTTTCGA
31758369 TTTTTTTTT
1 TTTTTTTTT
31758378 AACTTGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTCGA
Found at i:31758356 original size:15 final size:14
Alignment explanation
Indices: 31758332--31758377 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
31758322 CACAAATCAA
31758332 TTTTTTTTGATTTT
1 TTTTTTTTGATTTT
31758346 TTTTATTTTGA--TT
1 TTTT-TTTTGATTTT
*
31758359 TTTTTTTCGATTTT
1 TTTTTTTTGATTTT
31758373 TTTTT
1 TTTTT
31758378 AACTTGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 5 0.18
13 6 0.21
14 11 0.39
15 6 0.21
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTTTTTTGATTTT
Found at i:31758778 original size:14 final size:14
Alignment explanation
Indices: 31758731--31758778 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
31758721 GTACGAATGG
*
31758731 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
31758745 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
31758759 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
31758773 ATTGGT
1 AATGGT
31758779 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:31765694 original size:27 final size:27
Alignment explanation
Indices: 31765664--31765841 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31765654 ATATTGAGTC
* * * *
31765664 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31765691 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31765718 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31765746 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31765773 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31765800 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31765827 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31765842 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:31765803 original size:82 final size:81
Alignment explanation
Indices: 31765685--31765840 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31765675 TGCTATATAA
* *
31765685 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31765750 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31765767 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31765831 CACTTAGTGC
65 CACTTAGTGC
31765841 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:31773034 original size:27 final size:27
Alignment explanation
Indices: 31773004--31773181 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
31772994 ATATTGAGTC
* *
31773004 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
31773031 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
31773058 CGCACCCTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
31773086 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
31773113 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
31773140 TGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
31773167 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31773182 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31773150 original size:82 final size:81
Alignment explanation
Indices: 31773025--31773180 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
31773015 TGCTATATAA
* *
31773025 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACCCTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31773090 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
31773107 TCAATTCGCACACTTAGTGC-ATCATATTCATTTTGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31773171 CACTTAGTGC
65 CACTTAGTGC
31773181 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31776918 original size:38 final size:38
Alignment explanation
Indices: 31776875--31776950 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
31776865 TTCATCCTTT
31776875 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
31776913 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
31776951 GGAGTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:31778231 original size:40 final size:40
Alignment explanation
Indices: 31778137--31778281 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
31778127 TACTCGAATG
* *
31778137 ATATCCGGGCTAAGTCCCGAACGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
31778178 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
31778218 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
31778258 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
31778282 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.68
41 27 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:31784264 original size:65 final size:65
Alignment explanation
Indices: 31784190--31784315 Score: 234
Period size: 65 Copynumber: 1.9 Consensus size: 65
31784180 GTTAATGCCA
31784190 TTGCATGCTAAATATGAAGCTTGTTAATGATGCATGTGATGATGGATTGATGATTCTTGAATCTC
1 TTGCATGCTAAATATGAAGCTTGTTAATGATGCATGTGATGATGGATTGATGATTCTTGAATCTC
* *
31784255 TTGCATGCTAAATATGAAGCTTGTTAATGATGCATGTGATGGTGGCTTGATGATTCTTGAA
1 TTGCATGCTAAATATGAAGCTTGTTAATGATGCATGTGATGATGGATTGATGATTCTTGAA
31784316 CCTCCTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (65 bp):
TTGCATGCTAAATATGAAGCTTGTTAATGATGCATGTGATGATGGATTGATGATTCTTGAATCTC
Found at i:31785203 original size:40 final size:40
Alignment explanation
Indices: 31785119--31785503 Score: 564
Period size: 40 Copynumber: 9.7 Consensus size: 40
31785109 TTGAATGATG
* * * * *
31785119 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
31785159 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
31785199 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
31785238 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
31785278 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
31785318 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31785358 TCCGGGTCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGT-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
31785398 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31785438 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
31785479 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
31785504 AACGAGGAGC
Statistics
Matches: 319, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
39 38 0.12
40 267 0.84
41 14 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31790090 original size:27 final size:27
Alignment explanation
Indices: 31790052--31790107 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
31790042 AGCATACGTA
* * *
31790052 GGTCAAAGCCCATTACAATATCATTTG
1 GGTCAAAGCCCATAACAAAATCAATTG
31790079 GGTCACAA-CCCATAACAAAATCAATTG
1 GGTCA-AAGCCCATAACAAAATCAATTG
31790106 GG
1 GG
31790108 CCTAGCCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (27 bp):
GGTCAAAGCCCATAACAAAATCAATTG
Found at i:31790420 original size:27 final size:27
Alignment explanation
Indices: 31790389--31790492 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 27
31790379 CAGCGATGGT
*
31790389 AATATAATCGGCACAAAGCCATGGGTA
1 AATATAATCGGCACAAAGCCATAGGTA
* * * * *
31790416 AATATGATCGACACAGAGTCATCA-ATA
1 AATATAATCGGCACAAAGCCAT-AGGTA
* * * *
31790443 AATATGATAGGCACATAGCCACAGGTA
1 AATATAATCGGCACAAAGCCATAGGTA
*
31790470 AATATAATTGGCACAAAGCCATA
1 AATATAATCGGCACAAAGCCATA
31790493 ATCAAGATAG
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
26 1 0.02
27 58 0.98
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (27 bp):
AATATAATCGGCACAAAGCCATAGGTA
Found at i:31790920 original size:27 final size:27
Alignment explanation
Indices: 31790890--31790964 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
31790880 TACCCTATAG
*
31790890 AGGTATTTTTGTAATTTTACACTACAA
1 AGGTATTTTAGTAATTTTACACTACAA
* *
31790917 AGGTA-TTTCGATAATTTTACACTACAG
1 AGGTATTTTAG-TAATTTTACACTACAA
* *
31790944 GGGTATTTCAGTAATTTTACA
1 AGGTATTTTAGTAATTTTACA
31790965 AAATTAGGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.10
27 34 0.83
28 3 0.07
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
AGGTATTTTAGTAATTTTACACTACAA
Found at i:31791006 original size:27 final size:27
Alignment explanation
Indices: 31790944--31791101 Score: 149
Period size: 27 Copynumber: 5.8 Consensus size: 27
31790934 TACACTACAG
* *
31790944 GGGTATTTCAGTAATTTTACAAAAT-TA
1 GGGTATTTTAGTAATTTTAC-AAATCGA
* *
31790971 GGAGTATTTTAGTAATTTCATAAATCGA
1 GG-GTATTTTAGTAATTTTACAAATCGA
* *
31790999 GGGCATTTTGGTAATTTTACAAA-CTGA
1 GGGTATTTTAGTAATTTTACAAATC-GA
* * *
31791026 GGGTATTTCAGTAATTTTATAAATCAA
1 GGGTATTTTAGTAATTTTACAAATCGA
* * * *
31791053 GGGTATTTCAATAATTTTACAAATTGG
1 GGGTATTTTAGTAATTTTACAAATCGA
*
31791080 GGGTATTTTGGTAATTTTACAA
1 GGGTATTTTAGTAATTTTACAA
31791102 TTTGGAGTCT
Statistics
Matches: 106, Mismatches: 21, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 86 0.81
28 19 0.18
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.41
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTACAAATCGA
Found at i:31791048 original size:54 final size:54
Alignment explanation
Indices: 31790948--31791098 Score: 185
Period size: 54 Copynumber: 2.8 Consensus size: 54
31790938 CTACAGGGGT
* * *
31790948 ATTTCAGTAATTTTACAAAATTAGGAGTATTTTAGTAATTTCATAAATCGAGGGC
1 ATTTCAGTAATTTTACAAAATGAGG-GTATTTTAGTAATTTTATAAATCAAGGGC
** * * *
31791003 ATTTTGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTATAAATCAAGGGT
1 ATTTCAGTAATTTTACAAAATGAGGGTATTTTAGTAATTTTATAAATCAAGGGC
* * * *
31791057 ATTTCAATAATTTTACAAATTGGGGGTATTTTGGTAATTTTA
1 ATTTCAGTAATTTTACAAAATGAGGGTATTTTAGTAATTTTA
31791099 CAATTTGGAG
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
54 60 0.74
55 21 0.26
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (54 bp):
ATTTCAGTAATTTTACAAAATGAGGGTATTTTAGTAATTTTATAAATCAAGGGC
Found at i:31797225 original size:27 final size:27
Alignment explanation
Indices: 31797123--31797227 Score: 86
Period size: 27 Copynumber: 3.9 Consensus size: 27
31797113 AATACTTTAG
* *
31797123 TTTACCAAATTACTGAAATACCCTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
* ** *
31797150 CTTGTAAAATTACC-AAAGTACCCCCGA
1 TTTACAAAATTACCGAAA-TACCCTCGA
* ***
31797177 TTTACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
**
31797204 TTTACAAAATTATTGAAATACCCT
1 TTTACAAAATTACCGAAATACCCT
31797228 TGTAGGGTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
26 3 0.05
27 53 0.95
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (27 bp):
TTTACAAAATTACCGAAATACCCTCGA
Found at i:31797241 original size:27 final size:27
Alignment explanation
Indices: 31797211--31797350 Score: 190
Period size: 27 Copynumber: 5.2 Consensus size: 27
31797201 CGATTTACAA
31797211 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTATTGAAATACCCTTGTAGGGTAG
* *
31797238 AATTATTGAAATACCCCTGTAGGCTAG
1 AATTATTGAAATACCCTTGTAGGGTAG
31797265 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTATTGAAATACCCTTGTAGGGTAG
* * *
31797292 AAATATCGAAATACCCCTGTAGGGTAG
1 AATTATTGAAATACCCTTGTAGGGTAG
** * * *
31797319 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTATTGAAATACCCTTGTAGGGTAG
31797346 AATTA
1 AATTA
31797351 CCATTTTGCC
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (27 bp):
AATTATTGAAATACCCTTGTAGGGTAG
Found at i:31797899 original size:22 final size:22
Alignment explanation
Indices: 31797869--31797921 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
31797859 AATTATTCTG
31797869 ATTATGGCTTTGCGCCAACCTA
1 ATTATGGCTTTGCGCCAACCTA
*
31797891 CA-TATGGCTTTGTGCCAACCTA
1 -ATTATGGCTTTGCGCCAACCTA
31797913 ATTATGGCT
1 ATTATGGCT
31797922 GTGTATCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (22 bp):
ATTATGGCTTTGCGCCAACCTA
Found at i:31797941 original size:20 final size:20
Alignment explanation
Indices: 31797924--31797971 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
31797914 TTATGGCTGT
*
31797924 GTATCGTTATTGTGGGCTTC
1 GTATCGATATTGTGGGCTTC
*
31797944 GTATCGATCTTGTGGGCTTC
1 GTATCGATATTGTGGGCTTC
*
31797964 GTACCGAT
1 GTATCGAT
31797972 TATAGACCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (20 bp):
GTATCGATATTGTGGGCTTC
Found at i:31798045 original size:27 final size:27
Alignment explanation
Indices: 31798015--31798077 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
31798005 ATTCTGTTAA
* * *
31798015 GTGGCTTTGCTACATTATCTG-ATTCTG
1 GTGGCTCTGCCACAATATCTGTA-TCTG
31798042 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
*
31798069 GTGACTCTG
1 GTGGCTCTG
31798078 TTATAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTATCTG
Found at i:31798244 original size:25 final size:25
Alignment explanation
Indices: 31798216--31798305 Score: 135
Period size: 25 Copynumber: 3.6 Consensus size: 25
31798206 CATTCACATT
* *
31798216 CTGATTTTGATTCTGTCATCTAATA
1 CTGATTCTGATTCTGTCACCTAATA
*
31798241 CTGATTCTGATTCTGTTACCTAATA
1 CTGATTCTGATTCTGTCACCTAATA
*
31798266 CTGATTCTGATTCTGTCACCTAATT
1 CTGATTCTGATTCTGTCACCTAATA
*
31798291 CTGATTCTAATTCTG
1 CTGATTCTGATTCTG
31798306 ATTCTGATTC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGTCACCTAATA
Found at i:31798252 original size:6 final size:6
Alignment explanation
Indices: 31798213--31798334 Score: 79
Period size: 6 Copynumber: 19.8 Consensus size: 6
31798203 TTGCATTCAC
* * * *
31798213 ATTCTG ATTTTG ATTCTG -TCATCTA ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * *
31798263 ATACTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTA ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
31798312 ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
31798335 AGTTCTCATA
Statistics
Matches: 87, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
5 4 0.05
6 73 0.84
7 7 0.08
8 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:31798341 original size:18 final size:18
Alignment explanation
Indices: 31798288--31798343 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
31798278 CTGTCACCTA
* *
31798288 ATTCTGATTCTAATTCTG
1 ATTCTGATTCTAGTTCTC
31798306 ATTCTGATTCT-GATTCTC
1 ATTCTGATTCTAG-TTCTC
*
31798324 ATTTTGATTCTAGTTCTC
1 ATTCTGATTCTAGTTCTC
31798342 AT
1 AT
31798344 AATGTTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 32 0.97
19 1 0.03
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.52
Consensus pattern (18 bp):
ATTCTGATTCTAGTTCTC
Found at i:31801188 original size:41 final size:41
Alignment explanation
Indices: 31801116--31801425 Score: 345
Period size: 41 Copynumber: 7.6 Consensus size: 41
31801106 TAGTGGCATT
* * * * *
31801116 TGCAAAAGGTCAAACACTAGCTGTGTTTATGATAAAAACGC
1 TGCAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAACGC
* *
31801157 TACAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAATGC
1 TGCAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAACGC
* * * * *
31801198 TGCAAAAGGTCAAGTAGTAGCGGTGTTTATGATAAAAACGT
1 TGCAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAACGC
* *
31801239 TACAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAATGC
1 TGCAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAACGC
* * * * *
31801280 TGCAAAAGGTCAAGTAGTAGCGGTGTTTATGATAAAAACGT
1 TGCAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAACGC
* *
31801321 TACAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAATGC
1 TGCAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAACGC
* * * * *
31801362 TGCAAAAGGTCAAGCAGTAGTGGCA-T-TTTTATCATAAACGC
1 TGCAAAAGGTCAAGCAATAGCGG-AGTGTATGAT-AAAAACGC
*
31801403 TGTAAAAGGTCAAGCAATAGCGG
1 TGCAAAAGGTCAAGCAATAGCGG
31801426 CGTTTTTATC
Statistics
Matches: 222, Mismatches: 45, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
40 4 0.02
41 217 0.98
42 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.23
Consensus pattern (41 bp):
TGCAAAAGGTCAAGCAATAGCGGAGTGTATGATAAAAACGC
Found at i:31801253 original size:82 final size:82
Alignment explanation
Indices: 31801116--31801425 Score: 480
Period size: 82 Copynumber: 3.8 Consensus size: 82
31801106 TAGTGGCATT
* * *
31801116 TGCAAAAGGTCAAACACTAGCTGTGTTTATGATAAAAACGCTACAAAAGGTCAAGCAATAGCGGA
1 TGCAAAAGGTCAAGCAGTAGCGGTGTTTATGATAAAAACGCTACAAAAGGTCAAGCAATAGCGGA
31801181 GTGTATGATAAAAATGC
66 GTGTATGATAAAAATGC
* *
31801198 TGCAAAAGGTCAAGTAGTAGCGGTGTTTATGATAAAAACGTTACAAAAGGTCAAGCAATAGCGGA
1 TGCAAAAGGTCAAGCAGTAGCGGTGTTTATGATAAAAACGCTACAAAAGGTCAAGCAATAGCGGA
31801263 GTGTATGATAAAAATGC
66 GTGTATGATAAAAATGC
* *
31801280 TGCAAAAGGTCAAGTAGTAGCGGTGTTTATGATAAAAACGTTACAAAAGGTCAAGCAATAGCGGA
1 TGCAAAAGGTCAAGCAGTAGCGGTGTTTATGATAAAAACGCTACAAAAGGTCAAGCAATAGCGGA
31801345 GTGTATGATAAAAATGC
66 GTGTATGATAAAAATGC
* * * **
31801362 TGCAAAAGGTCAAGCAGTAGTGGCATTTTTATCAT--AAACGCTGTAAAAGGTCAAGCAATAGCG
1 TGCAAAAGGTCAAGCAGTAGCGG--TGTTTATGATAAAAACGCTACAAAAGGTCAAGCAATAGCG
31801425 G
64 G
31801426 CGTTTTTATC
Statistics
Matches: 214, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
82 206 0.96
84 8 0.04
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.23
Consensus pattern (82 bp):
TGCAAAAGGTCAAGCAGTAGCGGTGTTTATGATAAAAACGCTACAAAAGGTCAAGCAATAGCGGA
GTGTATGATAAAAATGC
Found at i:31801581 original size:28 final size:27
Alignment explanation
Indices: 31801514--31801592 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 27
31801504 CTATGGTTTA
* *
31801514 TAGTTTTAGGGTTTATGGTTTAATGTT
1 TAGTATTAGGGTTTAGGGTTTAATGTT
*
31801541 TAGTATATTGGGTTTAGGGTTTAATGTGT
1 TAGTAT-TAGGGTTTAGGGTTTAATGT-T
*
31801570 TA-TAGTTAGGGTATTAGTGTTTA
1 TAGTA-TTAGGGT-TTAGGGTTTA
31801593 GGGTTTTAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.12
28 25 0.58
29 13 0.30
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.51
Consensus pattern (27 bp):
TAGTATTAGGGTTTAGGGTTTAATGTT
Found at i:31801749 original size:7 final size:7
Alignment explanation
Indices: 31801739--31801829 Score: 92
Period size: 7 Copynumber: 13.0 Consensus size: 7
31801729 GGGTTTAATA
*
31801739 TTTAGAG
1 TTTAGGG
31801746 TTTAGGG
1 TTTAGGG
* **
31801753 TATATAG
1 TTTAGGG
31801760 TTTAGGG
1 TTTAGGG
*
31801767 TTTAGGA
1 TTTAGGG
**
31801774 TTTAGTA
1 TTTAGGG
*
31801781 TTTATGG
1 TTTAGGG
31801788 TTTAGGG
1 TTTAGGG
31801795 TTTAGGG
1 TTTAGGG
31801802 TTTAGGG
1 TTTAGGG
*
31801809 TTTAGGC
1 TTTAGGG
*
31801816 ATTAGGG
1 TTTAGGG
31801823 TTTAGGG
1 TTTAGGG
31801830 ATAAAATTTG
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 67 1.00
ACGTcount: A:0.21, C:0.01, G:0.34, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:31801799 original size:21 final size:21
Alignment explanation
Indices: 31801727--31801814 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
31801717 ATAATATATA
* *
31801727 TAGGGTTTAATATTTAGAGTT
1 TAGGGTTTAGTATTTAGGGTT
*
31801748 TAGGGTATA-TAGTTTAGGGTT
1 TAGGGTTTAGTA-TTTAGGGTT
* *
31801769 TAGGATTTAGTATTTATGGTT
1 TAGGGTTTAGTATTTAGGGTT
**
31801790 TAGGGTTTAGGGTTTAGGGTT
1 TAGGGTTTAGTATTTAGGGTT
31801811 TAGG
1 TAGG
31801815 CATTAGGGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (21 bp):
TAGGGTTTAGTATTTAGGGTT
Found at i:31802291 original size:41 final size:41
Alignment explanation
Indices: 31802231--31802326 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
31802221 GTGGCGTTTG
* * *
31802231 CAAAAGGTCAAGCAGTAGCTGTGTTTATGATAAAAACGCTA
1 CAAAAGGTCAAGCAATAGCTGAGTGTATGATAAAAACGCTA
* * * *
31802272 CAAAAGTTCAGGCAATAGCTGAGTGTATGATAAAAATGCTG
1 CAAAAGGTCAAGCAATAGCTGAGTGTATGATAAAAACGCTA
31802313 CAAAAGGTCAAGCA
1 CAAAAGGTCAAGCA
31802327 GTAGTGGCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.22
Consensus pattern (41 bp):
CAAAAGGTCAAGCAATAGCTGAGTGTATGATAAAAACGCTA
Found at i:31802360 original size:41 final size:41
Alignment explanation
Indices: 31802303--31802399 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 41
31802293 AGTGTATGAT
* * * *
31802303 AAAAATGCTGCAAAAGGTCAAGCAGTAGTGGCATTGTTATC
1 AAAAACGCTGTAAAAGGTCAAGCAATAGCGGCATTGTTATC
* * *
31802344 ATAAACGCTGTAAAAGGTCAAGCAATAGCGGCGTTTTTATC
1 AAAAACGCTGTAAAAGGTCAAGCAATAGCGGCATTGTTATC
* *
31802385 AAAAACACCGTAAAA
1 AAAAACGCTGTAAAA
31802400 AAGTTTTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAAACGCTGTAAAAGGTCAAGCAATAGCGGCATTGTTATC
Found at i:31802426 original size:14 final size:14
Alignment explanation
Indices: 31802409--31802492 Score: 57
Period size: 14 Copynumber: 5.9 Consensus size: 14
31802399 AAAGTTTTTA
31802409 TTTTAAGGTTTAGG
1 TTTTAAGGTTTAGG
* *
31802423 TTTTAAGATTTA-A
1 TTTTAAGGTTTAGG
*
31802436 TGTTTAAGGTCTAAGG
1 T-TTTAAGGT-TTAGG
* *
31802452 -TCTATGGTTTATGG
1 TTTTAAGGTTTA-GG
31802466 TTTTAAGGTTTATGG
1 TTTTAAGGTTTA-GG
*
31802481 -TTTAATGTTTAG
1 TTTTAAGGTTTAG
31802493 TATATTGGGT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
13 4 0.07
14 36 0.67
15 14 0.26
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (14 bp):
TTTTAAGGTTTAGG
Found at i:31802490 original size:22 final size:22
Alignment explanation
Indices: 31802422--31802490 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
31802412 TAAGGTTTAG
*
31802422 GTTTTAAGATTTAAT-GTTTAA-
1 GTTTTAAGGTTT-ATGGTTTAAT
* * *
31802443 GGTCTAAGGTCTATGGTTT-AT
1 GTTTTAAGGTTTATGGTTTAAT
31802464 GGTTTTAAGGTTTATGGTTTAAT
1 -GTTTTAAGGTTTATGGTTTAAT
31802487 GTTT
1 GTTT
31802491 AGTATATTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
20 3 0.08
21 12 0.32
22 20 0.54
23 2 0.05
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (22 bp):
GTTTTAAGGTTTATGGTTTAAT
Found at i:31802715 original size:35 final size:35
Alignment explanation
Indices: 31802676--31802750 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
31802666 TAATATATGC
* *
31802676 AGGGTTTAAGATTTAG-AGTTTAGGGTGTATTGTTT
1 AGGGTTTAAGATTTAGTA-TTTAGGGTATATGGTTT
* *
31802711 AGGGTTTAGGATTTAGTATTTATGGTATATGGTTT
1 AGGGTTTAAGATTTAGTATTTAGGGTATATGGTTT
31802746 AGGGT
1 AGGGT
31802751 CTAGGGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (35 bp):
AGGGTTTAAGATTTAGTATTTAGGGTATATGGTTT
Found at i:31802717 original size:7 final size:7
Alignment explanation
Indices: 31802676--31802777 Score: 69
Period size: 7 Copynumber: 14.6 Consensus size: 7
31802666 TAATATATGC
31802676 AGGGTTT
1 AGGGTTT
* *
31802683 AAGATTT
1 AGGGTTT
*
31802690 AGAGTTT
1 AGGGTTT
*
31802697 AGGGTGT
1 AGGGTTT
**
31802704 ATTGTTT
1 AGGGTTT
31802711 AGGGTTT
1 AGGGTTT
*
31802718 AGGATTT
1 AGGGTTT
**
31802725 AGTATTT
1 AGGGTTT
* *
31802732 ATGGTAT
1 AGGGTTT
*
31802739 ATGGTTT
1 AGGGTTT
*
31802746 AGGGTCT
1 AGGGTTT
31802753 AGGGTTT
1 AGGGTTT
**
31802760 AGGCATT
1 AGGGTTT
31802767 AGGGTTT
1 AGGGTTT
31802774 AGGG
1 AGGG
31802778 ATAAAATTTG
Statistics
Matches: 69, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:31805322 original size:49 final size:49
Alignment explanation
Indices: 31805090--31805314 Score: 297
Period size: 49 Copynumber: 4.5 Consensus size: 49
31805080 TGAGGTCGCA
* * ** *
31805090 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTAAAAATTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTG-G-TCACG
* * **
31805141 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCACG
*
31805191 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* *
31805240 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* *
31805289 AGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
31805315 TGCGTACCAA
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 77 0.50
50 42 0.27
51 35 0.23
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
Found at i:31810654 original size:49 final size:49
Alignment explanation
Indices: 31810533--31810720 Score: 250
Period size: 49 Copynumber: 3.8 Consensus size: 49
31810523 TGAGGTCGCA
* * * *
31810533 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAATTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTG-G-TCACG
*
31810584 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * * *
31810633 TGTGTTGTACTAAGTGTAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
31810682 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
31810721 GCTTTGGCTA
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
49 83 0.67
50 1 0.01
51 39 0.32
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:31831260 original size:13 final size:13
Alignment explanation
Indices: 31831242--31831266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31831232 AACAAAGTCA
31831242 GACACAGCCGTGC
1 GACACAGCCGTGC
31831255 GACACAGCCGTG
1 GACACAGCCGTG
31831267 TGCACCCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.36, G:0.32, T:0.08
Consensus pattern (13 bp):
GACACAGCCGTGC
Found at i:31838277 original size:9 final size:9
Alignment explanation
Indices: 31838263--31838402 Score: 76
Period size: 9 Copynumber: 15.9 Consensus size: 9
31838253 TTCTTTAAAA
31838263 TTACATAAC
1 TTACATAAC
31838272 TTACAT-AC
1 TTACATAAC
*
31838280 TCACATAAC
1 TTACATAAC
*
31838289 ATACATAAC
1 TTACATAAC
*
31838298 TTATATAA-
1 TTACATAAC
* * *
31838306 ATATATATC
1 TTACATAAC
*
31838315 ATATCATAAC
1 TTA-CATAAC
31838325 TTACATAA-
1 TTACATAAC
31838333 -TACATAA-
1 TTACATAAC
* * *
31838340 ATATATATC
1 TTACATAAC
* *
31838349 ATATCATAAA
1 TTA-CATAAC
31838359 TGT-CATAAC
1 T-TACATAAC
*
31838368 CTACATAAC
1 TTACATAAC
*
31838377 TTACATAAT
1 TTACATAAC
31838386 TTACATAAC
1 TTACATAAC
*
31838395 TAACATAA
1 TTACATAA
31838403 ATAAATATCA
Statistics
Matches: 101, Mismatches: 22, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
7 7 0.07
8 19 0.19
9 65 0.64
10 9 0.09
11 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.34
Consensus pattern (9 bp):
TTACATAAC
Found at i:31838345 original size:34 final size:35
Alignment explanation
Indices: 31838283--31838375 Score: 118
Period size: 34 Copynumber: 2.6 Consensus size: 35
31838273 TACATACTCA
*
31838283 CATAACATACATAACTTATATAAATATATATCATAT
1 CATAACATACATAAC-TACATAAATATATATCATAT
*
31838319 CATAACTTACATAA-TACATAAATATATATCATAT
1 CATAACATACATAACTACATAAATATATATCATAT
*
31838353 CATAA-ATGTCATAACCTACATAA
1 CATAACAT-ACATAA-CTACATAA
31838376 CTTACATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.58
36 20 0.40
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33
Consensus pattern (35 bp):
CATAACATACATAACTACATAAATATATATCATAT
Found at i:31843083 original size:16 final size:15
Alignment explanation
Indices: 31843057--31843088 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
31843047 GCTAGATCGG
31843057 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
31843072 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
31843088 C
1 C
31843089 GGTATTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.28, G:0.19, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:31843240 original size:16 final size:17
Alignment explanation
Indices: 31843207--31843240 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31843197 ATATTTGGGC
31843207 TTAATGGGCCAAAACGGG
1 TTAATGGGCC-AAACGGG
31843225 TTAATGGGCC-AACGGG
1 TTAATGGGCCAAACGGG
31843241 CCCAATTCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.18, G:0.35, T:0.18
Consensus pattern (17 bp):
TTAATGGGCCAAACGGG
Found at i:31843375 original size:28 final size:28
Alignment explanation
Indices: 31843335--31843398 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
31843325 TGTACTAGAG
*
31843335 TACCCCTATGTATGCAAAATTACCAT-TA
1 TACCCCTATGTATGCAAAATGACC-TCTA
31843363 TACCCCTATGTATGCAAAATGACCTCTA
1 TACCCCTATGTATGCAAAATGACCTCTA
31843391 TACCCCTA
1 TACCCCTA
31843399 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.33, C:0.30, G:0.08, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATGACCTCTA
Found at i:31843562 original size:27 final size:27
Alignment explanation
Indices: 31843504--31843593 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
31843494 AGGAAGCGTC
*
31843504 CTGGTGGCTA-TGCCACAAATTATCTATT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
31843532 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
31843559 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
31843588 CTGGTG
1 CTGGTG
31843594 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 22 0.41
28 25 0.46
29 7 0.13
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:31843604 original size:29 final size:28
Alignment explanation
Indices: 31843514--31843604 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
31843504 CTGGTGGCTA
* * * *
31843514 TGCCACAAATTATCTATTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* *
31843542 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
31843569 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
31843598 TGTCACA
1 TGCCACA
31843605 TTTTCTGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.43
28 15 0.28
29 15 0.28
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:31843612 original size:55 final size:56
Alignment explanation
Indices: 31843504--31843618 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
31843494 AGGAAGCGTC
* *
31843504 CTGGTGGCTATGCCACAAATTATCTATTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT
* * * *
31843559 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTAT-TCTGGTGACCCTGCCACATATATCTGTAT
31843615 CTGG
1 CTGG
31843619 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:31848728 original size:17 final size:18
Alignment explanation
Indices: 31848696--31848730 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31848686 GGGCCGAAAG
31848696 GGGCCATATAGGCCCAAT
1 GGGCCATATAGGCCCAAT
*
31848714 GGGCC-TATGGGCCCAAT
1 GGGCCATATAGGCCCAAT
31848731 TGGATAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.23, C:0.29, G:0.31, T:0.17
Consensus pattern (18 bp):
GGGCCATATAGGCCCAAT
Found at i:31848931 original size:27 final size:28
Alignment explanation
Indices: 31848901--31849000 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 28
31848891 TTTAGTTTAC
31848901 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * * *
31848928 TAAAAATACTGAAATATCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
** * *
31848955 TAAAATTATTGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
31848982 TAAAATTACC-AAAGTACCC
1 TAAAATTACCGAAA-TACCC
31849001 CCGATTTACA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.12
27 51 0.85
28 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:31849015 original size:27 final size:27
Alignment explanation
Indices: 31848985--31849043 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
31848975 CGACTTGTAA
31848985 AATTACCAAAGTACCCCCGATTTACAT
1 AATTACCAAAGTACCCCCGATTTACAT
* ***
31849012 AATTACTATTTTACCCCCGATTTACAT
1 AATTACCAAAGTACCCCCGATTTACAT
31849039 AATTA
1 AATTA
31849044 TTGTTTTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (27 bp):
AATTACCAAAGTACCCCCGATTTACAT
Found at i:31849050 original size:27 final size:27
Alignment explanation
Indices: 31848996--31849180 Score: 235
Period size: 27 Copynumber: 6.9 Consensus size: 27
31848986 ATTACCAAAG
* * *
31848996 TACCCCCGATTTACATAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
31849023 TACCCCCGATTTACATAATTATTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
31849050 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
31849077 TACCCTTGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
31849104 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
31849131 TACCCTTGATTTACAGAATTACTTTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
31849158 TACCCTTGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
31849181 AAAATACCCT
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 142 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:31849059 original size:81 final size:81
Alignment explanation
Indices: 31848969--31849152 Score: 188
Period size: 81 Copynumber: 2.3 Consensus size: 81
31848959 ATTATTGAAA
* ** * *
31848969 TACCTTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACATAATTACTATTTTACCCCCGATT
1 TACCCTCGACTTACAAAATTACCAAAGTACCCCCGATTTACAGAATTACCATTTTACCCCCGATT
* *
31849034 TACATAATTATTGTTT
66 TACAGAATTACTGTTT
* **** ** * *
31849050 TACCCTCGACTTACAGAATTACCGTTTTACCCTTGATTTACAGAATTACCGTTTTACCCTCGATT
1 TACCCTCGACTTACAAAATTACCAAAGTACCCCCGATTTACAGAATTACCATTTTACCCCCGATT
*
31849115 TATAGAATTACTGTTT
66 TACAGAATTACTGTTT
* * *
31849131 TACCCTTGATTTACAGAATTAC
1 TACCCTCGACTTACAAAATTAC
31849153 TTTTTTACCC
Statistics
Matches: 84, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (81 bp):
TACCCTCGACTTACAAAATTACCAAAGTACCCCCGATTTACAGAATTACCATTTTACCCCCGATT
TACAGAATTACTGTTT
Found at i:31849188 original size:27 final size:27
Alignment explanation
Indices: 31849131--31849379 Score: 162
Period size: 27 Copynumber: 9.1 Consensus size: 27
31849121 ATTACTGTTT
* *****
31849131 TACCCTTGATTTACAGAATTACTTTTT
1 TACCCTTGATTTACAAAATTACCAAAA
*
31849158 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* **
31849185 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* *
31849212 TACCCCT-AGTTTATAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACCAAAA
* ***
31849239 TACCCTTGGTTTGTGAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
** ***
31849266 TACCCTCAATTTGTGAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* *
31849293 TACCCCTGATTTACAAAGTTA-CAGAAA
1 TACCCTTGATTTACAAAATTACCA-AAA
* * *
31849320 TACCCTAGACTTTATAAAAATTA-TAGAAA
1 TACCCTTGA-TTTA-CAAAATTACCA-AAA
* * **
31849349 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACCAAAA
31849376 TACC
1 TACC
31849380 TTTGGTTTGT
Statistics
Matches: 180, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
26 2 0.01
27 152 0.84
28 9 0.05
29 17 0.09
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACCAAAA
Found at i:31849205 original size:54 final size:54
Alignment explanation
Indices: 31849167--31849297 Score: 183
Period size: 54 Copynumber: 2.4 Consensus size: 54
31849157 TTACCCTTGA
*
31849167 TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAG
1 TTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAG
* * *
31849221 TTTATAAAATTACCAAAATACCCTTGGTTTGTGAAATTACCAAAATA-CCCTCAA
1 TTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCT-AG
***
31849275 TTTGTGAAATTACCAAAATACCC
1 TTTACAAAATTACCAAAATACCC
31849298 CTGATTTACA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
53 4 0.06
54 66 0.94
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
TTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAG
Found at i:31849205 original size:81 final size:81
Alignment explanation
Indices: 31849023--31849206 Score: 206
Period size: 81 Copynumber: 2.3 Consensus size: 81
31849013 ATTACTATTT
* * * *
31849023 TACCCCCGATTTACATAATTATTGTTTTACCCTCGACTTACAGAATTACCGTTTTACCCTTGATT
1 TACCCTCGATTTATAAAATTACTGTTTTACCCTCGACTTACAGAATTACCGTTTTACCCTTGATT
* ****
31849088 TACAGAATTACCGTTT
66 TACAAAATTACCAAAA
* * * **
31849104 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTTTTTTACCCTTGATT
1 TACCCTCGATTTATAAAATTACTGTTTTACCCTCGACTTACAGAATTACCGTTTTACCCTTGATT
*
31849169 TACAAAATTACTAAAA
66 TACAAAATTACCAAAA
* * *
31849185 TACCCTTGGTTTGTAAAATTAC
1 TACCCTCGATTTATAAAATTAC
31849207 CAAAATACCC
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (81 bp):
TACCCTCGATTTATAAAATTACTGTTTTACCCTCGACTTACAGAATTACCGTTTTACCCTTGATT
TACAAAATTACCAAAA
Found at i:31849216 original size:81 final size:81
Alignment explanation
Indices: 31849158--31849325 Score: 205
Period size: 81 Copynumber: 2.1 Consensus size: 81
31849148 ATTACTTTTT
* ***
31849158 TACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCT-AGT
1 TACCCTTGATTTACAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGA-T
*
31849222 TTATAAAATTACCAAAA
65 TTACAAAATTACCAAAA
* *** *
31849239 TACCCTTGGTTTGTGAAATTACCAAAATACCCTCAATTTGTGAAATTACCAAAATACCCCTGATT
1 TACCCTTGATTTACAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATT
*
31849304 TACAAAGTTA-CAGAAA
66 TACAAAATTACCA-AAA
31849320 TACCCT
1 TACCCT
31849326 AGACTTTATA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
80 2 0.03
81 71 0.96
82 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (81 bp):
TACCCTTGATTTACAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATT
TACAAAATTACCAAAA
Found at i:31849384 original size:27 final size:27
Alignment explanation
Indices: 31849336--31849387 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
31849326 AGACTTTATA
31849336 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
31849363 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
31849388 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:31849471 original size:27 final size:27
Alignment explanation
Indices: 31849441--31849532 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
31849431 ACCCCTATTA
*
31849441 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
*
31849468 GGTAAAGTGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
31849495 GGTAAAGTGACCGTAATA-CCCCTATAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
31849522 GGTAAAATGAC
1 GGTAAAATGAC
31849533 GAATATGCCC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:31850788 original size:9 final size:9
Alignment explanation
Indices: 31850776--31850832 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
31850766 TTTGATAAAC
31850776 ATGATATGT
1 ATGATATGT
*
31850785 ATGATATGCAC
1 ATGATATG--T
*
31850796 ATGACATGT
1 ATGATATGT
*
31850805 ATGATATGCAC
1 ATGATATG--T
31850816 ATGATATGT
1 ATGATATGT
31850825 ATGATATG
1 ATGATATG
31850833 CATATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:31850799 original size:20 final size:20
Alignment explanation
Indices: 31850774--31850844 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
31850764 ATTTTGATAA
31850774 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
31850794 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
31850814 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
31850834 ATATGAGATGT
1 ACATGATATGT
31850845 TTATAAATGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:31850947 original size:25 final size:25
Alignment explanation
Indices: 31850891--31851033 Score: 238
Period size: 25 Copynumber: 5.8 Consensus size: 25
31850881 AGGAAGTGCA
31850891 AAAGGGCTTATGCCCCAGTTAT--T
1 AAAGGGCTTATGCCCCAGTTATGAT
31850914 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
31850939 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
31850964 GAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
31850989 AAAGGGCTTATGCCCCAGTTAT-AA
1 AAAGGGCTTATGCCCCAGTTATGAT
*
31851013 AAAGGGCTTCTGCCCCAGTTA
1 AAAGGGCTTATGCCCCAGTTA
31851034 CTAAAAGAGG
Statistics
Matches: 114, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
23 22 0.19
24 21 0.18
25 71 0.62
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:31851045 original size:25 final size:24
Alignment explanation
Indices: 31850890--31851059 Score: 220
Period size: 25 Copynumber: 7.0 Consensus size: 24
31850880 GAGGAAGTGC
31850890 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATG
*
31850913 TAAAGGGCTTATGCCCCAGTTATG
1 AAAAGGGCTTATGCCCCAGTTATG
31850937 ATAAAGGGCTTATGCCCCAGTTATG
1 A-AAAGGGCTTATGCCCCAGTTATG
*
31850962 ATGAAGGGCTTATGCCCCAGTTATG
1 A-AAAGGGCTTATGCCCCAGTTATG
*
31850987 ATAAAGGGCTTATGCCCCAGTTATA
1 A-AAAGGGCTTATGCCCCAGTTATG
*
31851012 AAAAGGGCTTCTGCCCCAGTTACT-
1 AAAAGGGCTTATGCCCCAGTTA-TG
*
31851036 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
31851060 ATGATAAAGC
Statistics
Matches: 134, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
23 22 0.16
24 30 0.22
25 82 0.61
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATG
Found at i:31851291 original size:31 final size:31
Alignment explanation
Indices: 31851253--31851316 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
31851243 CGTTTACAGT
*
31851253 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
31851284 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
31851315 AA
1 AA
31851317 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:31858619 original size:27 final size:27
Alignment explanation
Indices: 31858588--31858765 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
31858578 TAAATTGTAC
*
31858588 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
31858615 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
31858641 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
31858669 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
31858697 AGCACTAAGTGTGCGACTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
31858724 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
31858751 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31858766 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:31858702 original size:82 final size:81
Alignment explanation
Indices: 31858589--31858744 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31858579 AAATTGTACA
* *
31858589 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31858653 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31858670 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGACTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31858735 TGCGAGTTGA
65 TGCGAATTGA
31858745 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31858756 original size:82 final size:81
Alignment explanation
Indices: 31858585--31858765 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
31858575 GATTAAATTG
* *
31858585 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31858650 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31858666 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGACTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31858730 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31858748 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31858766 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31866716 original size:27 final size:27
Alignment explanation
Indices: 31866685--31866862 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31866675 TAAATTGTAC
31866685 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31866712 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31866738 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31866766 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31866794 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31866821 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31866848 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31866863 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31866799 original size:82 final size:81
Alignment explanation
Indices: 31866686--31866841 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31866676 AAATTGTACA
* *
31866686 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31866750 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31866767 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31866832 TGCGAGTTGA
65 TGCGAATTGA
31866842 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31866853 original size:82 final size:81
Alignment explanation
Indices: 31866682--31866862 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
31866672 GATTAAATTG
* *
31866682 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31866747 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31866763 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31866827 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31866845 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31866863 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31869683 original size:137 final size:137
Alignment explanation
Indices: 31869433--31869702 Score: 353
Period size: 137 Copynumber: 2.0 Consensus size: 137
31869423 ATAAAATAGA
* * * * * *
31869433 TCTGCTCACACAAGTTGACGATTGGAATGTAAGCTACACGATGCTACTCACACAAGCTAATGAGT
1 TCTGCTCACACAAGCTGACGATCGAAATGTAAGCTACACAATGCCACTCACACAAGCTAACGAGT
* * *
31869498 ATCCGCAACTAATGCCGGACCTCAACCAACAATAGGACATTCAAGACCAACACCCGAAACATGGT
66 ATCCGCAACAAATGCCAGAACTCAACCAACAATAGGACATTCAAGACCAACA-CCGAAACATGGT
31869563 AACCTAGG
130 AACCTAGG
* * *
31869571 TCTGCTCACACAAGCTGACGGTCGAAATGT-AGCTACACAATGCCGCTCACACAAGCTGACGAGT
1 TCTGCTCACACAAGCTGACGATCGAAATGTAAGCTACACAATGCCACTCACACAAGCTAACGAGT
* * * * * * *
31869635 ATCTGCAACAAATGCCAGAACTCAGCCATCAGTAGGACATTTAGGACCATCACCGAAACATGGTA
66 ATCCGCAACAAATGCCAGAACTCAACCAACAATAGGACATTCAAGACCAACACCGAAACATGGTA
31869700 ACC
131 ACC
31869703 CTAATGACAT
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
136 16 0.14
137 71 0.63
138 26 0.23
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (137 bp):
TCTGCTCACACAAGCTGACGATCGAAATGTAAGCTACACAATGCCACTCACACAAGCTAACGAGT
ATCCGCAACAAATGCCAGAACTCAACCAACAATAGGACATTCAAGACCAACACCGAAACATGGTA
ACCTAGG
Found at i:31876152 original size:30 final size:30
Alignment explanation
Indices: 31876125--31876195 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
31876115 CTGAGCCCTG
* *
31876125 TACAGTAGCAGTGTATGGGCCATAGCCCAA
1 TACAGTAACAGAGTATGGGCCATAGCCCAA
* * *
31876155 TACAGTAACAGAGTGTGGGCCCTAGTCCAA
1 TACAGTAACAGAGTATGGGCCATAGCCCAA
*
31876185 TACATTAACAG
1 TACAGTAACAG
31876196 TGAAAATGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (30 bp):
TACAGTAACAGAGTATGGGCCATAGCCCAA
Found at i:31876334 original size:26 final size:26
Alignment explanation
Indices: 31876304--31876400 Score: 124
Period size: 26 Copynumber: 3.7 Consensus size: 26
31876294 CACCAATATC
31876304 GCAGCAAAGCTGCCAGTAATAGTAAT
1 GCAGCAAAGCTGCCAGTAATAGTAAT
* * *
31876330 ACAGCAGAGCTGCCAGTAACAGTAAT
1 GCAGCAAAGCTGCCAGTAATAGTAAT
* * *
31876356 GCAGCAGAGCTACCAGT-ATCAGTAAC
1 GCAGCAAAGCTGCCAGTAAT-AGTAAT
31876382 GCAGCAAAGCTGCCAGTAA
1 GCAGCAAAGCTGCCAGTAA
31876401 GAGTGTTTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 58 0.97
27 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAGTAAT
Found at i:31876611 original size:27 final size:28
Alignment explanation
Indices: 31876581--31876858 Score: 231
Period size: 27 Copynumber: 10.3 Consensus size: 28
31876571 GGTATAACAG
* *
31876581 TCATTTTACCCTAT-GGGGGTATTTCGA
1 TCATTTTACCCTTTCGAGGGTATTTCGA
31876608 TCATTTTA-CCTTTC-AGGGGTATTTCGA
1 TCATTTTACCCTTTCGA-GGGTATTTCGA
* * *
31876635 TCATTTTACCCTTT-GGGGGTATTTTGG
1 TCATTTTACCCTTTCGAGGGTATTTCGA
* * *
31876662 TCATTTTACCC-ATCAAGGGTATTTTGA
1 TCATTTTACCCTTTCGAGGGTATTTCGA
* * *
31876689 TAATTTTACCC-ATCGAGGGTATTTCGG
1 TCATTTTACCCTTTCGAGGGTATTTCGA
* * *
31876716 TTATTTTACCCTTT-GAGGGTATTTTGT
1 TCATTTTACCCTTTCGAGGGTATTTCGA
31876743 TCATTTTACCC-TTCGAGGGTATTTC-A
1 TCATTTTACCCTTTCGAGGGTATTTCGA
* *
31876769 GTTATTTTA-CCTTTTGAGGGTATTTC-A
1 -TCATTTTACCCTTTCGAGGGTATTTCGA
** *
31876796 GTTGTTTTA-TCTTTCGAGGGTATTTCGA
1 -TCATTTTACCCTTTCGAGGGTATTTCGA
* * * *
31876824 TAATTTCACCC-TTCAAGTGTATTTCGA
1 TCATTTTACCCTTTCGAGGGTATTTCGA
31876851 TCATTTTA
1 TCATTTTA
31876859 GAGGCCCATT
Statistics
Matches: 207, Mismatches: 33, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
26 9 0.04
27 190 0.92
28 8 0.04
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (28 bp):
TCATTTTACCCTTTCGAGGGTATTTCGA
Found at i:31876804 original size:81 final size:79
Alignment explanation
Indices: 31876597--31876858 Score: 267
Period size: 81 Copynumber: 3.2 Consensus size: 79
31876587 TACCCTATGG
* * * * *
31876597 GGGTATTTCGATCATTTTACCTTTCAGGGGTATTTCGATCATTTTACCCTTTGGGGGTATTTTGG
1 GGGTATTTCGATAATTTTACCTTTGA-GGGTATTTCG-TTATTTTACCCTTTGAGGGTATTTTGA
*
31876662 TCATTTTACCCATCAA
64 TCATTTTACCCTTCAA
* * * *
31876678 GGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTTATTTTACCCTTTGAGGGTATTTTGT
1 GGGTATTTCGATAATTTTA-CCTTTGAGGGTATTTC-GTTATTTTACCCTTTGAGGGTATTTTGA
*
31876743 TCATTTTACCCTTCGA
64 TCATTTTACCCTTCAA
* * * *
31876759 GGGTATTTC-AGTTATTTTACCTTTTGAGGGTATTTCAGTTGTTTTA-TCTTTCGAGGGTATTTC
1 GGGTATTTCGA-TAATTTTACC-TTTGAGGGTATTTC-GTTATTTTACCCTTT-GAGGGTATTTT
* *
31876822 GATAATTTCACCCTTCAA
62 GATCATTTTACCCTTCAA
* *
31876840 GTGTATTTCGATCATTTTA
1 GGGTATTTCGATAATTTTA
31876859 GAGGCCCATT
Statistics
Matches: 151, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
80 7 0.05
81 138 0.91
82 6 0.04
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (79 bp):
GGGTATTTCGATAATTTTACCTTTGAGGGTATTTCGTTATTTTACCCTTTGAGGGTATTTTGATC
ATTTTACCCTTCAA
Found at i:31879090 original size:31 final size:30
Alignment explanation
Indices: 31879064--31879133 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
31879054 AATTCTAGTT
*
31879064 TTAATTCTAATTTTCATGTCTAATTCTAAAC
1 TTAATTCTAAGTTTCAT-TCTAATTCTAAAC
* *
31879095 TTAATTCTAAGTTTGATTCTAATACTAAAC
1 TTAATTCTAAGTTTCATTCTAATTCTAAAC
*
31879125 -TAGTTCTAA
1 TTAATTCTAA
31879134 ATGCTAATCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 8 0.23
30 12 0.34
31 15 0.43
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (30 bp):
TTAATTCTAAGTTTCATTCTAATTCTAAAC
Found at i:31881865 original size:27 final size:27
Alignment explanation
Indices: 31881835--31882012 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31881825 ATATTGAGTC
* * * *
31881835 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31881862 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31881889 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31881917 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31881944 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31881971 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31881998 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31882013 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:31881974 original size:82 final size:81
Alignment explanation
Indices: 31881856--31882011 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31881846 TGCTATATAA
* *
31881856 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31881921 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31881938 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31882002 CACTTAGTGC
65 CACTTAGTGC
31882012 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:31889928 original size:27 final size:27
Alignment explanation
Indices: 31889898--31890075 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31889888 ATATTGAGTC
* * * *
31889898 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31889925 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31889952 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31889980 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31890007 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31890034 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31890061 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31890076 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:31890037 original size:82 final size:81
Alignment explanation
Indices: 31889919--31890074 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31889909 TGCTATATAA
* *
31889919 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31889984 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31890001 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31890065 CACTTAGTGC
65 CACTTAGTGC
31890075 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:31893439 original size:52 final size:51
Alignment explanation
Indices: 31893382--31893489 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
31893372 AAATATGATG
* * *
31893382 AAATGGAGAAATAGGAAA-CATTTGGAAATGATTATGGTTTTCTCCAAAATGA
1 AAATGGAGAAAT--GAAATCATTTGGAAATGAATATGGTTTTCTCAAAAATAA
*
31893434 AAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCAAAAATAA
1 AAATGGAGAAATGAAATCATTTGGAAATGAATATGGTTTTCTCAAAAATAA
31893485 AAATG
1 AAATG
31893490 AAAATTACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
50 4 0.08
51 35 0.69
52 12 0.24
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.29
Consensus pattern (51 bp):
AAATGGAGAAATGAAATCATTTGGAAATGAATATGGTTTTCTCAAAAATAA
Found at i:31899480 original size:17 final size:20
Alignment explanation
Indices: 31899458--31899496 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
31899448 CTGTTCTATG
31899458 CAATT-ATAT-ATATA-TAA
1 CAATTAATATCATATATTAA
31899475 CAATTAATATCATATATTAA
1 CAATTAATATCATATATTAA
31899495 CA
1 CA
31899497 CACAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 5 0.26
20 5 0.26
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTAATATCATATATTAA
Found at i:31906659 original size:27 final size:27
Alignment explanation
Indices: 31906608--31906659 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
31906598 GATAGTCCGA
* **
31906608 TGGGACATTAAACATGGGATGGTCCAT
1 TGGGACACTAAACATGGGACAGTCCAT
31906635 TGGGACACTAAACATGGGACAGTCC
1 TGGGACACTAAACATGGGACAGTCC
31906660 TATGAGACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (27 bp):
TGGGACACTAAACATGGGACAGTCCAT
Found at i:31906668 original size:27 final size:26
Alignment explanation
Indices: 31906601--31906668 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
31906591 CATCGTAGAT
* *
31906601 AGTCCGATGGGACATTAAACATGGGAT
1 AGTCC-ATGGGACACTAAACATGGGAC
*
31906628 GGTCCATTGGGACACTAAACATGGGAC
1 AGTCCA-TGGGACACTAAACATGGGAC
*
31906655 AGTCCTATGAGACA
1 AGTCC-ATGGGACA
31906669 GTAGATGCGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (26 bp):
AGTCCATGGGACACTAAACATGGGAC
Found at i:31906809 original size:2 final size:2
Alignment explanation
Indices: 31906804--31906835 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31906794 AGAGAGAGTA
*
31906804 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31906836 AGGGAGAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:31915085 original size:5 final size:6
Alignment explanation
Indices: 31915070--31915095 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31915060 CAGTTTAAAA
31915070 TTTTTG TTTTTG TTTTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TT
31915096 ATAGTAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:31919296 original size:18 final size:18
Alignment explanation
Indices: 31919273--31919311 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31919263 TCAAGGATAG
* *
31919273 GGGAAGGGGAAGGGGAAA
1 GGGAAGGGAAAGAGGAAA
31919291 GGGAAGGGAAAGAGGAAA
1 GGGAAGGGAAAGAGGAAA
31919309 GGG
1 GGG
31919312 GAGAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (18 bp):
GGGAAGGGAAAGAGGAAA
Found at i:31919299 original size:5 final size:6
Alignment explanation
Indices: 31919271--31919313 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
31919261 TGTCAAGGAT
* * *
31919271 AGGGGA AGGGGA AGGGGA AAGGGA AGGGAA AGAGGAA AGGGGA
1 AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AG-GGGA AGGGGA
31919314 GAAGAAAGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:31919964 original size:17 final size:17
Alignment explanation
Indices: 31919941--31919978 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31919931 TTTTTCTCGA
* *
31919941 ATTTTTAAG-GTTTAGG
1 ATTTTTTAGAGTTTAAG
31919957 ATTTTTTAGAGTTTAAG
1 ATTTTTTAGAGTTTAAG
31919974 ATTTT
1 ATTTT
31919979 ATGTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
ATTTTTTAGAGTTTAAG
Done.