Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 132 of 228
Found at i:39400990 original size:25 final size:25
Alignment explanation
Indices: 39400962--39401013 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
39400952 AAGGAATTCG
39400962 CACACACACAGTGCCTCTAATT-ATT
1 CACACACACAGTG-CTCTAATTCATT
* * *
39400987 CACATACATAGTGCTCTTATTCATT
1 CACACACACAGTGCTCTAATTCATT
39401012 CA
1 CA
39401014 TTAATACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (25 bp):
CACACACACAGTGCTCTAATTCATT
Found at i:39401246 original size:40 final size:40
Alignment explanation
Indices: 39401189--39401371 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 40
39401179 CCAGCATGAT
* *
39401189 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
39401229 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * * *
39401269 TGCTCTTCGGGACTTAGCCCAGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
39401310 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
39401350 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
39401372 CATCATTCGA
Statistics
Matches: 117, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 3 0.03
40 94 0.80
41 20 0.17
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:39401716 original size:29 final size:29
Alignment explanation
Indices: 39401677--39401755 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
39401667 CTTAATAATC
*
39401677 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
39401707 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39401736 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39401756 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39401783 original size:28 final size:28
Alignment explanation
Indices: 39401743--39401810 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
39401733 TCAAGCCCGC
39401743 ACACTTAGTGCCAATCTCACAACCGTGA
1 ACACTTAGTGCCAATCTCACAACCGTGA
39401771 ACACTTAGTGCCAATCTCACAACCGTGA
1 ACACTTAGTGCCAATCTCACAACCGTGA
*
39401799 ACACTTATTGCC
1 ACACTTAGTGCC
39401811 CGCACACTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.31, C:0.32, G:0.13, T:0.24
Consensus pattern (28 bp):
ACACTTAGTGCCAATCTCACAACCGTGA
Found at i:39401832 original size:43 final size:43
Alignment explanation
Indices: 39401771--39401867 Score: 194
Period size: 43 Copynumber: 2.3 Consensus size: 43
39401761 ACAACCGTGA
39401771 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
1 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
39401814 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
1 ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
39401857 ACACTTAGTGC
1 ACACTTAGTGC
39401868 TGAAAACCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (43 bp):
ACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGC
Found at i:39403946 original size:45 final size:45
Alignment explanation
Indices: 39403876--39404159 Score: 370
Period size: 47 Copynumber: 6.1 Consensus size: 45
39403866 CCCTTCGGGA
* * * * * *
39403876 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACA--TATACACTTTCACATTCATCACATCGGCCATTAGGC
***
39403923 CCCGTCACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACTTTCACATTCATCACATCGGCCATTAGGC
39403968 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
39404015 CTTATCACACATATACACTTTCACATTCATCACATCGGATATTAGGC
1 CTTAT--CACATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39404062 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTAT--CACATATACACTTTCACATTCATCACATCGGCCATTAGGC
39404109 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTAT--CACATATACACTTTCACATTCATCACATCGGCCATTAGGC
39404156 CTTA
1 CTTA
39404160 CTATCATTTC
Statistics
Matches: 217, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
45 35 0.16
47 179 0.82
49 3 0.01
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (45 bp):
CTTATCACATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39403997 original size:47 final size:47
Alignment explanation
Indices: 39403928--39404159 Score: 428
Period size: 47 Copynumber: 4.9 Consensus size: 47
39403918 TCGGCCCCGT
39403928 CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
*
39403975 CATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
**
39404022 CACATATACACTTTCACATTCATCACATCGGATATTAGGCCTTATCA
1 CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
*
39404069 CACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
1 CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
39404116 CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
39404160 CTATCATTTC
Statistics
Matches: 179, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 179 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
Found at i:39404060 original size:94 final size:94
Alignment explanation
Indices: 39403876--39404159 Score: 428
Period size: 94 Copynumber: 3.0 Consensus size: 94
39403866 CCCTTCGGGA
* * * * * * * ***
39403876 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCCGT--CACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
39403939 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39403968 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
**
39404033 TTTCACATTCATCACATCGGATATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
39404062 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
39404127 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39404156 CTTA
1 CTTA
39404160 CTATCATTTC
Statistics
Matches: 174, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
92 42 0.24
94 132 0.76
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:39412834 original size:28 final size:28
Alignment explanation
Indices: 39412803--39412880 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
39412793 TGTCTTATTT
*
39412803 TAATACAAGTTTTTAATATGTCATA-ACC
1 TAATACATGTTTTTAATATGTCATAGA-C
* * *
39412831 TAATACATGTTATTAATTTGTCCTAGAC
1 TAATACATGTTTTTAATATGTCATAGAC
* *
39412859 TAAAACATGTTTTTATTATGTC
1 TAATACATGTTTTTAATATGTC
39412881 CTAGCTACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (28 bp):
TAATACATGTTTTTAATATGTCATAGAC
Found at i:39416367 original size:10 final size:11
Alignment explanation
Indices: 39416342--39416369 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39416332 ATATTTGTAA
39416342 AAAAAATTCGT
1 AAAAAATTCGT
39416353 AAAAAATTCGT
1 AAAAAATTCGT
39416364 AAAAAA
1 AAAAAA
39416370 AGGTTGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (11 bp):
AAAAAATTCGT
Found at i:39427841 original size:28 final size:28
Alignment explanation
Indices: 39427680--39427834 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
39427670 AACAGTACAG
* *
39427680 TGTGAGCCTTAGCCCAATACAGCAACAG
1 TGTGGGCCTTAGCCCAATACAGCAACAA
*
39427708 TATGGGCCTTAGCCCAATACAGCAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
**
39427736 TGTGGGCCTTAGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
* * * *
39427764 TATGGGCCTTAGCCCAAAATAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
39427792 TGTGGGCCTTAGCCCAATACAGCAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
39427820 TGTGGGCCTTAGCCC
1 TGTGGGCCTTAGCCC
39427835 TAAACAGTAT
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 113 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGCAACAA
Found at i:39427982 original size:26 final size:26
Alignment explanation
Indices: 39427951--39428057 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
39427941 AACACACCAA
*
39427951 TATCGCAGCAAAGCTACCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
*
39427977 AATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* * *
39428003 TATCACAGTAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* *
39428029 TATTGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
39428055 TAT
1 TAT
39428058 ACTTCCTCCA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:39428606 original size:108 final size:107
Alignment explanation
Indices: 39428203--39428910 Score: 560
Period size: 108 Copynumber: 6.6 Consensus size: 107
39428193 GGGGTATAAT
* * * * * * *
39428203 AGTCATTTTACCATATGGGGGTATTTTGGTTATTTTACCCTATCG-TGGTAATTCAGTCATTTTA
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCT-TCGAGGGTATTTCAGTCATTTTA
* * * *
39428267 CCCTATGGGGGTATTTCGATCATTTCACCCTTCGGGGGTATTTC
65 CCCT-TGAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
* * * * *
39428311 -GATCATTTCA-CCTTTCGGGGTATTTTGGTCATTTTACCCTAT-GAGGGTAATTCAGTCATCTT
1 AG-TCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCT-TCGAGGGTATTTCAGTCATTTT
* * * *
39428373 ACCCTATG-GGGATATTTCGGTTATTTCT-CCTTTCAG-GAGTATTTC
64 ACCCT-TGAGGG-TATTTCGATCATTT-TACCCTT-AGAGGGTATTTC
* * * * * * * **
39428418 AGTTATTTCACCCTTTGGGGGTATTTCGGCCATTTTACTCATCGATGGTATTTTGGTCATTTTAC
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
* *
39428483 CCTTTGAGGGCATTTCGATCATTTTACTCTGTAGA-GGTATTTC
66 CC-TTGAGGGTATTTCGATCATTTTACCCT-TAGAGGGTATTTC
* * * *
39428526 AGTCATTTTACCCTGTAGGGGTATTTCGATCATTTTACTCTTCGAGGGTATTTCAATCATTTTAC
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
* * ** *
39428591 CCTTCAGGGGTATTTCGGTCATTTTACATTTTGAGGGTATTTC
66 CCTTGA-GGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
* * * * * ** * * * *
39428634 GGTCATTTTACCCATCAAGGATATTTTAGTCATTTTACCCTTCGAGGGCATCTCAATTATTTTAC
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
* *
39428699 CCTTCGAGGGTATTTTGATCATTTTACCCTTTGAGGGTATTTC
66 CCTT-GAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
** * * * **
39428742 -GATCATTTTACCCTTTAAAGGTATTTCAGTCATTTTACCAATT-GAGGATATTTTGGTCATTTT
1 AG-TCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACC-CTTCGAGGGTATTTCAGTCATTTT
* * * *
39428805 ACCTTTCGAGGGCATTTCGATCATTTTACCCTTCGAGGGTATTTT
64 ACCCTT-GAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
* * * *
39428850 GGT-ATTTTACCCTGTAGGGGTATTTTGGTCATTTCA-CCTATC-AGGGGTATTTCAGTCATTT
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCT-TCGA-GGGTATTTCAGTCATTT
39428911 GCCCACAAAT
Statistics
Matches: 485, Mismatches: 93, Indels: 45
0.78 0.15 0.07
Matches are distributed among these distances:
105 1 0.00
106 7 0.01
107 134 0.28
108 334 0.69
109 9 0.02
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (107 bp):
AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
CCTTGAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
Found at i:39428658 original size:27 final size:27
Alignment explanation
Indices: 39428204--39428910 Score: 503
Period size: 27 Copynumber: 26.3 Consensus size: 27
39428194 GGGTATAATA
* * *
39428204 GTCATTTTACCATAT-GGGGGTATTTTG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * * *
39428231 GTTATTTTACCCTATCG-TGGTAATTCA
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
39428258 GTCATTTTACCCTAT-GGGGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * *
39428285 ATCATTTCACCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * *
39428312 ATCATTTCACCTTTCG-GGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
39428338 GTCATTTTACCCTAT-GAGGGTAATTCA
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
39428365 GTCATCTTACCCTAT-G-GGGATATTTCG
1 GTCATTTTACCCT-TCGAGGG-TATTTCG
* * *
39428392 GTTATTTCT-CCTTTC-AGGAGTATTTCA
1 GTCATTT-TACCCTTCGAGG-GTATTTCG
* * * *
39428419 GTTATTTCACCCTTTGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * * *
39428446 GCCATTTTACTCATCGATGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
39428473 GTCATTTTACCCTTTGAGGGCATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * *
39428500 ATCATTTTACTCTGTAGA-GGTATTTCA
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
39428527 GTCATTTTACCCTGTAG-GGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * *
39428554 ATCATTTTACTCTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
39428581 ATCATTTTACCCTTC-AGGGGTATTTCG
1 GTCATTTTACCCTTCGA-GGGTATTTCG
** *
39428608 GTCATTTTACATTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * **
39428635 GTCATTTTACCCATCAAGGATATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
39428662 GTCATTTTACCCTTCGAGGGCATCTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
39428689 ATTATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
39428716 ATCATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* ** * *
39428743 ATCATTTTACCCTTTAAAGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
39428770 GTCATTTTACCAATT-GAGGATATTTTG
1 GTCATTTTACC-CTTCGAGGGTATTTCG
* *
39428797 GTCATTTTACCTTTCGAGGGCATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
39428824 ATCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
39428851 GT-ATTTTACCCTGTAG-GGGTATTTTG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* *
39428877 GTCATTTCA-CCTATC-AGGGGTATTTCA
1 GTCATTTTACCCT-TCGA-GGGTATTTCG
39428904 GTCATTT
1 GTCATTT
39428911 GCCCACAAAT
Statistics
Matches: 543, Mismatches: 114, Indels: 46
0.77 0.16 0.07
Matches are distributed among these distances:
26 57 0.10
27 475 0.87
28 11 0.02
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:39448046 original size:40 final size:39
Alignment explanation
Indices: 39447962--39448146 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
39447952 TTGAATGATG
* * * * *
39447962 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
39448002 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
39448042 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
39448081 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTA-AA
*
39448122 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
39448147 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 36 0.29
40 77 0.62
41 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39448101 original size:79 final size:81
Alignment explanation
Indices: 39447962--39448146 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
39447952 TTGAATGATG
* *
39447962 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
39448026 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39448041 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATC-CGAAGGCA
*
39448103 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
39448121 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39448147 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 2 0.02
79 56 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:39448168 original size:79 final size:78
Alignment explanation
Indices: 39447992--39448169 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 78
39447982 CTTTGTGCTA
* * *
39447992 AGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AGTGACTATATCCGG-TTAAGATCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCG
**
39448057 AAGGCATTTGTGCG
65 AAGGCATTTGAACG
* * * *
39448071 AGTTACTAAATCCGGGTTAAG-TCTCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 AGTGACTATATCC-GGTTAAGATC-CGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-C
39448134 CCGAAGGCATTTGAACG
62 CCGAAGGCATTTGAACG
39448151 AG-GAGCTATATCCGGTTAA
1 AGTGA-CTATATCCGGTTAA
39448170 ATTCCAAAGG
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
78 4 0.05
79 52 0.63
80 27 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
AGTGACTATATCCGGTTAAGATCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGA
AGGCATTTGAACG
Found at i:39452278 original size:20 final size:20
Alignment explanation
Indices: 39452255--39452303 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
39452245 GGGTTAAGAT
39452255 TGAGCTGAATTGAGCACAAA
1 TGAGCTGAATTGAGCACAAA
* * * * *
39452275 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCACAAA
39452295 TGAGCTGAA
1 TGAGCTGAA
39452304 CTAAGTTAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (20 bp):
TGAGCTGAATTGAGCACAAA
Found at i:39453213 original size:33 final size:33
Alignment explanation
Indices: 39453167--39453238 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
39453157 TTTAGGAGGC
*
39453167 TTACCTTTAGGAGCAGGAAAATAAAGTTCGGTT
1 TTACCTTTAGGAGCAGGAAAACAAAGTTCGGTT
* * *
39453200 TTACCTTTTGGAGCAGGGAAGCAAAGTTCGGTT
1 TTACCTTTAGGAGCAGGAAAACAAAGTTCGGTT
39453233 TTACCT
1 TTACCT
39453239 GGCTCGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (33 bp):
TTACCTTTAGGAGCAGGAAAACAAAGTTCGGTT
Found at i:39454197 original size:18 final size:17
Alignment explanation
Indices: 39454144--39454189 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
39454134 TTTCTCACTC
*
39454144 TCATTTTCTTTTTCGATT
1 TCATGTTCTTTTTCG-TT
39454162 TCATGTTCTTTTTC-TT
1 TCATGTTCTTTTTCGTT
39454178 TCAT-TTCTTTTT
1 TCATGTTCTTTTT
39454190 TTCGTTTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.30
16 6 0.22
18 13 0.48
ACGTcount: A:0.09, C:0.17, G:0.04, T:0.70
Consensus pattern (17 bp):
TCATGTTCTTTTTCGTT
Found at i:39455227 original size:17 final size:18
Alignment explanation
Indices: 39455207--39455253 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39455197 TCACTTTTTT
39455207 TTCGAATTTTTTTTTA-C
1 TTCGAATTTTTTTTTATC
* *
39455224 TTCGTACTTTTTTTTATC
1 TTCGAATTTTTTTTTATC
*
39455242 CTC-AATTTTTTT
1 TTCGAATTTTTTT
39455254 CCTTTTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.66
Consensus pattern (18 bp):
TTCGAATTTTTTTTTATC
Found at i:39476512 original size:28 final size:28
Alignment explanation
Indices: 39476455--39476516 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
39476445 GGACAAAACA
* * *
39476455 AAGACATGATTTTAATGTGTAATATACT
1 AAGACATGATTTAAATATGTAACATACT
* *
39476483 AAGACATGATTTAAATATGTACCATGCT
1 AAGACATGATTTAAATATGTAACATACT
39476511 AAGACA
1 AAGACA
39476517 AAATAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (28 bp):
AAGACATGATTTAAATATGTAACATACT
Found at i:39482215 original size:50 final size:50
Alignment explanation
Indices: 39482135--39482316 Score: 203
Period size: 50 Copynumber: 3.7 Consensus size: 50
39482125 GGGAATAAGA
**
39482135 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * *
39482185 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * * * * *
39482235 TCCCATGTAAGACCATATCTAGGATATGGCATTGGTA--GTACAGGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAAC
*
39482283 ATCCCATGTAAGACCATGTCT-AGACATGGC-TTGG
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
39482317 GCATGTTATT
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
47 4 0.04
48 11 0.10
49 23 0.20
50 76 0.67
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
Found at i:39482546 original size:20 final size:20
Alignment explanation
Indices: 39482521--39482569 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39482511 TGAGTTATTT
39482521 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
39482541 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
39482561 AAG-AAGCAA
1 AAGTAAGCAA
39482570 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:39483800 original size:28 final size:28
Alignment explanation
Indices: 39483743--39483804 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
39483733 GGAAAAAACA
* * *
39483743 AAGACATGATTTTAATGTGTAATATACT
1 AAGACATGATTTAAATATGTAACATACT
* *
39483771 AAGACATGATTTAAATATGTAGCATGCT
1 AAGACATGATTTAAATATGTAACATACT
39483799 AAGACA
1 AAGACA
39483805 AAATAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (28 bp):
AAGACATGATTTAAATATGTAACATACT
Found at i:39495209 original size:20 final size:20
Alignment explanation
Indices: 39495184--39495238 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
39495174 CGTAAATTTA
39495184 ATCAAGCTAAAGTTGAACTC
1 ATCAAGCTAAAGTTGAACTC
* *
39495204 ATCAAGCT-GATTTGAACTC
1 ATCAAGCTAAAGTTGAACTC
** *
39495223 ATGGAGCTAAGGTTGA
1 ATCAAGCTAAAGTTGA
39495239 GTTGAGTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (20 bp):
ATCAAGCTAAAGTTGAACTC
Found at i:39496411 original size:46 final size:46
Alignment explanation
Indices: 39496358--39496451 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
39496348 CAAAGAAAAG
*
39496358 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
39496404 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
39496450 AC
1 AC
39496452 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:39499296 original size:18 final size:17
Alignment explanation
Indices: 39499275--39499309 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
39499265 CCTCAATCTC
*
39499275 TTTTTCAATTTTCTTTTT
1 TTTTTCAA-ATTCTTTTT
39499293 TTTTTCAAATTCTTTTT
1 TTTTTCAAATTCTTTTT
39499310 CACTCTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCAAATTCTTTTT
Found at i:39501875 original size:46 final size:46
Alignment explanation
Indices: 39501823--39501910 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 46
39501813 AAAGACCTTG
39501823 ACCCACTATCAA-GAATGATAGGA-ACCTTGGTATATGATGAACCTCA
1 ACCCACTATCAATG-ATGATAGGACA-CTTGGTATATGATGAACCTCA
39501869 ACCCACTATCAATGATGATAGGACACTTGGTATATGATGAAC
1 ACCCACTATCAATGATGATAGGACACTTGGTATATGATGAAC
39501911 GCCACACTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
46 38 0.95
47 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (46 bp):
ACCCACTATCAATGATGATAGGACACTTGGTATATGATGAACCTCA
Found at i:39504729 original size:27 final size:27
Alignment explanation
Indices: 39504699--39504757 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
39504689 CTTTCTCACA
*
39504699 TTTTTTTCAATCTCA-ATCTCGTTTTTC
1 TTTTTCTCAATCTCACATCT-GTTTTTC
* *
39504726 TTTTTCTCACTCTCACTATCTTTTTTTC
1 TTTTTCTCAATCTCAC-ATCTGTTTTTC
39504754 TTTT
1 TTTT
39504758 CTCGAGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.48
28 10 0.37
29 4 0.15
ACGTcount: A:0.12, C:0.24, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTTCTCAATCTCACATCTGTTTTTC
Found at i:39505707 original size:15 final size:15
Alignment explanation
Indices: 39505687--39505715 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39505677 CTTTTTTTGG
39505687 TTTTTTTTTCACAAA
1 TTTTTTTTTCACAAA
39505702 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
39505716 CTTGATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTTTTCACAAA
Found at i:39505772 original size:12 final size:13
Alignment explanation
Indices: 39505755--39505783 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39505745 GGAAATAAAA
39505755 TTTTTTC-AAATT
1 TTTTTTCAAAATT
39505767 TTTTTTCAAAATT
1 TTTTTTCAAAATT
39505780 TTTT
1 TTTT
39505784 CGAAGAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTCAAAATT
Found at i:39506154 original size:46 final size:46
Alignment explanation
Indices: 39506101--39506194 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 46
39506091 CAAAGAAAAG
39506101 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGTATATGATGA
39506147 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
39506193 AC
1 AC
39506195 GCCACACTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 46 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
Found at i:39519159 original size:2 final size:2
Alignment explanation
Indices: 39519154--39519220 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
39519144 ATTATAAATA
39519154 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
39519196 TG TG CG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
39519221 TAAAACATGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.01, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:39534970 original size:40 final size:40
Alignment explanation
Indices: 39534921--39535003 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
39534911 TTGAAATATT
39534921 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
1 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
39534961 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
1 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
39535001 GGA
1 GGA
39535004 CATGCTGAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (40 bp):
GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
Found at i:39536718 original size:20 final size:21
Alignment explanation
Indices: 39536687--39536731 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
39536677 TTGGAAGCCA
39536687 TCTTTCGGTTAAAGAATGGTT
1 TCTTTCGGTTAAAGAATGGTT
39536708 TCTTT-GGTTAAAGAATGGTT
1 TCTTTCGGTTAAAGAATGGTT
39536728 TCTT
1 TCTT
39536732 CTCATCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (21 bp):
TCTTTCGGTTAAAGAATGGTT
Found at i:39541012 original size:28 final size:28
Alignment explanation
Indices: 39540962--39541017 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
39540952 GTGATTGTAT
** *
39540962 AGTGTGGGCCTTAGCCCTTTACAGTAAC
1 AGTGTGGGCCTTAGCCCAATACAATAAC
*
39540990 AGTGTGGGTCTTAGCCCAATACAATAAC
1 AGTGTGGGCCTTAGCCCAATACAATAAC
39541018 CAGTACAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAATAAC
Found at i:39541373 original size:27 final size:26
Alignment explanation
Indices: 39541355--39541417 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
39541345 TATAATAGTT
*
39541355 ATTTTACCCTATGGGGGTATTCGATC
1 ATTTTACCCTATGGGGGTATTAGATC
* * *
39541381 ATTTTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTA-TTAGATC
39541408 ATTTTACCCT
1 ATTTTACCCT
39541418 TCGAGATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (26 bp):
ATTTTACCCTATGGGGGTATTAGATC
Found at i:39541428 original size:27 final size:27
Alignment explanation
Indices: 39541355--39541628 Score: 270
Period size: 27 Copynumber: 10.2 Consensus size: 27
39541345 TATAATAGTT
* *
39541355 ATTTTACCCTAT-GGGGGTA-TTCGATC
1 ATTTTACCCT-TCGAGGGTATTTCGGTC
39541381 ATTTTACCCTAT-GAGGGTATTTCGGTC
1 ATTTTACCCT-TCGAGGGTATTTCGGTC
** **
39541408 ATTTTACCCTTCGAGATTATTTTTGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
** *
39541435 ATTTTACCAATCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
* * **
39541462 ATTTTATCCATCGAGGGTATTTCAATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
39541489 ATTTTACCCTTC-AGGGGTATTTCGGTC
1 ATTTTACCCTTCGA-GGGTATTTCGGTC
* * *
39541516 ATTTTACCCTTCGAGGATATTTTGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
** **
39541543 ATTTTATGCTTC-AGGGGTATTTTAGTC
1 ATTTTACCCTTCGA-GGGTATTTCGGTC
*
39541570 ATTTTACCCTTCGAGGGTATTTCAGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
**
39541597 ATTTTACCCTTCGAGGGTATTTCAATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
39541624 ATTTT
1 ATTTT
39541629 CCCACGAATC
Statistics
Matches: 210, Mismatches: 32, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
26 21 0.10
27 187 0.89
28 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTC
Found at i:39541491 original size:81 final size:81
Alignment explanation
Indices: 39541355--39541628 Score: 324
Period size: 81 Copynumber: 3.4 Consensus size: 81
39541345 TATAATAGTT
* * *
39541355 ATTTTACCCTAT-GGGGGTA-TTCGATCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACCC
1 ATTTTACCCT-TCGAGGGTATTTCGATCATTTTATCC-ATCGAGGGTATTTCAGTCATTTTACCC
** **
39541417 TTCGAGATTATTTTTGTC
64 TTCGAGGGTATTTCAGTC
** *
39541435 ATTTTACCAATCGAGGGTATTTCGATCATTTTATCCATCGAGGGTATTTCAATCATTTTACCCTT
1 ATTTTACCCTTCGAGGGTATTTCGATCATTTTATCCATCGAGGGTATTTCAGTCATTTTACCCTT
*
39541500 C-AGGGGTATTTCGGTC
66 CGA-GGGTATTTCAGTC
* * * * *
39541516 ATTTTACCCTTCGAGGATATTTTGATCATTTTATGCTTC-AGGGGTATTTTAGTCATTTTACCCT
1 ATTTTACCCTTCGAGGGTATTTCGATCATTTTATCCATCGA-GGGTATTTCAGTCATTTTACCCT
39541580 TCGAGGGTATTTCAGTC
65 TCGAGGGTATTTCAGTC
*
39541597 ATTTTACCCTTCGAGGGTATTTCAATCATTTT
1 ATTTTACCCTTCGAGGGTATTTCGATCATTTT
39541629 CCCACGAATC
Statistics
Matches: 166, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 18 0.11
81 146 0.88
82 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (81 bp):
ATTTTACCCTTCGAGGGTATTTCGATCATTTTATCCATCGAGGGTATTTCAGTCATTTTACCCTT
CGAGGGTATTTCAGTC
Found at i:39542245 original size:34 final size:35
Alignment explanation
Indices: 39542206--39542278 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
39542196 AAAGAGGGAG
* * * *
39542206 AGAAAGGTAGTATTCGGCCA-AGAGAGAAGAAGAA
1 AGAAAGGCAATATTCGGCCACAAAGAAAAGAAGAA
*
39542240 AGAAAGGCAATATTCGGCCACAAAGAAAAGAGGAA
1 AGAAAGGCAATATTCGGCCACAAAGAAAAGAAGAA
39542275 AGAA
1 AGAA
39542279 CCAAAGGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.51, C:0.11, G:0.29, T:0.10
Consensus pattern (35 bp):
AGAAAGGCAATATTCGGCCACAAAGAAAAGAAGAA
Found at i:39544331 original size:20 final size:20
Alignment explanation
Indices: 39544306--39544360 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
39544296 TGTGGTTCAA
* *
39544306 CTCATTCGAGTTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
39544326 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
39544346 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
39544361 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:39547335 original size:5 final size:5
Alignment explanation
Indices: 39547325--39547351 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39547315 TACTTATTTA
39547325 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
39547352 TTGAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:39557578 original size:28 final size:28
Alignment explanation
Indices: 39557515--39557692 Score: 225
Period size: 28 Copynumber: 6.4 Consensus size: 28
39557505 ATAATAAGTC
* * *
39557515 CGCACACTCAATGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
39557542 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
39557570 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
39557598 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
39557626 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * * *
39557653 CGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAA-TCAAACT
39557682 CGCACACTTAG
1 CGCACACTTAG
39557693 CGCCAATCTC
Statistics
Matches: 135, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
27 42 0.31
28 80 0.59
29 13 0.10
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:39565764 original size:28 final size:28
Alignment explanation
Indices: 39565701--39565878 Score: 225
Period size: 28 Copynumber: 6.4 Consensus size: 28
39565691 ATAATAAGTC
* *
39565701 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
39565728 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
39565756 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
39565784 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
39565812 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * * * *
39565839 CGCAGACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAA-TCAAACT
39565868 CGCACACTTAG
1 CGCACACTTAG
39565879 CGCCAATCTC
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
27 42 0.31
28 80 0.60
29 12 0.09
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:39571409 original size:22 final size:24
Alignment explanation
Indices: 39571375--39571418 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
39571365 CTTGGACTAA
39571375 GATTTCCAAGA-T-TTGAAATCTT
1 GATTTCCAAGATTCTTGAAATCTT
* *
39571397 GATTTTCATGATTCTTGAAATC
1 GATTTCCAAGATTCTTGAAATC
39571419 ACTCAACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (24 bp):
GATTTCCAAGATTCTTGAAATCTT
Found at i:39589542 original size:25 final size:25
Alignment explanation
Indices: 39589483--39589585 Score: 118
Period size: 25 Copynumber: 4.1 Consensus size: 25
39589473 GTACATCTAT
* ** *
39589483 GCTCATACGAGCTATGAATTAGTAT
1 GCTCATACGAGCTATAAATCGGTAA
*
39589508 GCT-GTCACGAGCTATAAATCGGTAA
1 GCTCAT-ACGAGCTATAAATCGGTAA
*
39589533 GCTCATACGAGCTGTAAATCGGTAA
1 GCTCATACGAGCTATAAATCGGTAA
* *
39589558 GCTTATACGAGCTGTAAATCGGTAA
1 GCTCATACGAGCTATAAATCGGTAA
39589583 GCT
1 GCT
39589586 TGTATGAGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.01
25 66 0.97
26 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCGGTAA
Found at i:39589603 original size:25 final size:25
Alignment explanation
Indices: 39589514--39589586 Score: 128
Period size: 25 Copynumber: 2.9 Consensus size: 25
39589504 GTATGCTGTC
* *
39589514 ACGAGCTATAAATCGGTAAGCTCAT
1 ACGAGCTGTAAATCGGTAAGCTTAT
39589539 ACGAGCTGTAAATCGGTAAGCTTAT
1 ACGAGCTGTAAATCGGTAAGCTTAT
39589564 ACGAGCTGTAAATCGGTAAGCTT
1 ACGAGCTGTAAATCGGTAAGCTT
39589587 GTATGAGTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (25 bp):
ACGAGCTGTAAATCGGTAAGCTTAT
Found at i:39594352 original size:23 final size:22
Alignment explanation
Indices: 39594301--39594352 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
39594291 CCTCGTCTTT
*
39594301 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
39594323 -TCATTTTCTATTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
39594346 TTCTTTT
1 TTCTTTT
39594353 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:39594367 original size:18 final size:18
Alignment explanation
Indices: 39594346--39594384 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
39594336 TTTCTTCAAC
*
39594346 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTTCTT
*
39594364 TTCTGTTTCACATTTCTT
1 TTCTGTTTCAAATTTCTT
39594382 TTC
1 TTC
39594385 ACTCTCAATC
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:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (18 bp):
TTCTGTTTCAAATTTCTT
Found at i:39619599 original size:39 final size:40
Alignment explanation
Indices: 39619448--39619617 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
39619438 GGACTAAGAT
* * * *
39619448 CCGAAGGCCTTTGTGCGAGATACTAAATCTGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
39619488 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
39619528 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * * *
39619568 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
39619607 CCGAAGGCATT
1 CCGAAGGCATT
39619618 TGAACGAGGA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
39 32 0.29
40 79 0.71
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:39619637 original size:79 final size:80
Alignment explanation
Indices: 39619470--39619652 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 80
39619460 GTGCGAGATA
* * * * *
39619470 CTAAATCTGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
39619535 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
39619550 TTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
39619614 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
39619629 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
39619653 TACGTGATTT
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
78 14 0.17
79 47 0.56
80 23 0.27
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:39622851 original size:47 final size:47
Alignment explanation
Indices: 39622773--39623199 Score: 683
Period size: 47 Copynumber: 9.1 Consensus size: 47
39622763 CCCTTCGGGA
* * * * * * *
39622773 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39622820 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39622867 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39622914 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39622961 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39623008 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTATGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39623055 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39623102 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39623149 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39623196 CTTA
1 CTTA
39623200 CTATCATTTC
Statistics
Matches: 362, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 362 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39645875 original size:14 final size:14
Alignment explanation
Indices: 39645856--39645882 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39645846 TGCATCTCCC
39645856 CATGCATGAATCTA
1 CATGCATGAATCTA
39645870 CATGCATGAATCT
1 CATGCATGAATCT
39645883 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:39649271 original size:25 final size:24
Alignment explanation
Indices: 39649243--39649289 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39649233 TTTTATTACT
* *
39649243 CATTTTTTTCTTTTCTTCTTTTCTA
1 CATTCTTTTC-TTTATTCTTTTCTA
39649268 CATTCTTTTCTTTATTCTTTTC
1 CATTCTTTTCTTTATTCTTTTC
39649290 ATTTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (24 bp):
CATTCTTTTCTTTATTCTTTTCTA
Found at i:39652497 original size:14 final size:14
Alignment explanation
Indices: 39652478--39652504 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39652468 TGCATCTCCC
39652478 CATGCATGAATCTA
1 CATGCATGAATCTA
39652492 CATGCATGAATCT
1 CATGCATGAATCT
39652505 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:39659201 original size:15 final size:15
Alignment explanation
Indices: 39659181--39659235 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
39659171 ACTCTCCTCA
*
39659181 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
39659196 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
39659211 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
39659225 TTCTTTT-TCTC
1 TTCTTTTCTCTC
39659236 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:39661518 original size:40 final size:40
Alignment explanation
Indices: 39661427--39661596 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
39661417 TCCTCGTTCA
* * * * *
39661427 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
39661466 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39661506 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
39661546 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
39661586 AAGGCCTTCGG
1 AATGCCTTCGG
39661597 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39664394 original size:11 final size:10
Alignment explanation
Indices: 39664362--39664393 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
39664352 TTTTAATCAC
39664362 TTCTTTTTTT
1 TTCTTTTTTT
39664372 TTCTTTTTTT
1 TTCTTTTTTT
39664382 TTCTTTTTTT
1 TTCTTTTTTT
39664392 TT
1 TT
39664394 TAATTTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:39670749 original size:21 final size:21
Alignment explanation
Indices: 39670691--39670749 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
39670681 TCACTCTCTT
39670691 TTTCAA-TTTCTTTCTC-TTTC
1 TTTCAATTTTCTTT-TCATTTC
*
39670711 TCTTC-TTTTTCTTTTTCATTTC
1 T-TTCAATTTTC-TTTTCATTTC
39670733 TTTCAATTTTCTTTTCA
1 TTTCAATTTTCTTTTCA
39670750 ATGTTGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.03
21 18 0.56
22 13 0.41
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCAATTTTCTTTTCATTTC
Found at i:39671380 original size:18 final size:18
Alignment explanation
Indices: 39671359--39671393 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39671349 TAAATTAGAA
*
39671359 AGAAAAATAATCCTCACT
1 AGAAAAAAAATCCTCACT
*
39671377 AGAAAAAAAATTCTCAC
1 AGAAAAAAAATCCTCAC
39671394 AAGTTCTCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.20, G:0.06, T:0.20
Consensus pattern (18 bp):
AGAAAAAAAATCCTCACT
Found at i:39671830 original size:14 final size:13
Alignment explanation
Indices: 39671808--39671841 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
39671798 CAAAATAAAC
39671808 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
39671821 TTTCTTTTTTTGAA
1 TTT-TTTTTTTGAA
39671835 TTTTTTT
1 TTTTTTT
39671842 ACAATCTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:39675466 original size:17 final size:18
Alignment explanation
Indices: 39675434--39675470 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
39675424 TTTTGAGCTA
39675434 AACTTAATTAAATTAACT
1 AACTTAATTAAATTAACT
*
39675452 AACTT-ATTTAATTAACT
1 AACTTAATTAAATTAACT
39675469 AA
1 AA
39675471 GTTTATTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AACTTAATTAAATTAACT
Found at i:39682886 original size:29 final size:29
Alignment explanation
Indices: 39682854--39682977 Score: 115
Period size: 29 Copynumber: 4.3 Consensus size: 29
39682844 GGTTGTCACC
* **
39682854 ATCCCTTTTCATAATTGATAGTTGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
*
39682883 ATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * * * * * *
39682912 ATTCCTTTTCATATTCAATGGTCGTCATC-
1 ATCCCTTTTCATAATCGATAGCCG-AAGCT
* *
39682941 ATCCCTTTTCATAGTCGATAGCTGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
39682970 ATCCCTTT
1 ATCCCTTT
39682978 CCATTGGTTG
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
28 2 0.03
29 69 0.95
30 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAGCT
Found at i:39683069 original size:12 final size:12
Alignment explanation
Indices: 39683052--39683081 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
39683042 AAATGATAAC
39683052 ATTTAAAACAGT
1 ATTTAAAACAGT
39683064 ATTTAAAACAGT
1 ATTTAAAACAGT
39683076 ATTTAA
1 ATTTAA
39683082 TGTACGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (12 bp):
ATTTAAAACAGT
Found at i:39687829 original size:25 final size:25
Alignment explanation
Indices: 39687796--39687853 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
39687786 GCTCGAGAGA
*
39687796 GAGCTTACCGATATTCAACTCGCAT
1 GAGCTTACCGATAGTCAACTCGCAT
* * *
39687821 GAGCTTACCGTTAGTCAGCTCGTAT
1 GAGCTTACCGATAGTCAACTCGCAT
39687846 GAGCTTAC
1 GAGCTTAC
39687854 TGATTATAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
GAGCTTACCGATAGTCAACTCGCAT
Found at i:39688938 original size:26 final size:26
Alignment explanation
Indices: 39688889--39688938 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
39688879 TTTGGTATCT
*
39688889 TGATGGTATAATGGCAAAGTTTGGCA
1 TGATGGTATAATGGCAAAGCTTGGCA
*
39688915 TGATGGTATGATGGACAAA-CTTGG
1 TGATGGTATAATGG-CAAAGCTTGG
39688939 ATTGTTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (26 bp):
TGATGGTATAATGGCAAAGCTTGGCA
Found at i:39689430 original size:7 final size:7
Alignment explanation
Indices: 39689414--39689451 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
39689404 TAAAACCCTA
39689414 AAACTTT
1 AAACTTT
*
39689421 AAACTCT
1 AAACTTT
39689428 AAACTTT
1 AAACTTT
39689435 AAACTTT
1 AAACTTT
*
39689442 AAACCTT
1 AAACTTT
39689449 AAA
1 AAA
39689452 ATCCTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (7 bp):
AAACTTT
Found at i:39694078 original size:20 final size:20
Alignment explanation
Indices: 39694044--39694083 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39694034 CAGCTCAACG
* *
39694044 AGCTCATTTTTAGCTCATTT
1 AGCTCATCTTAAGCTCATTT
*
39694064 AGCTCATCTTAAGCTTATTT
1 AGCTCATCTTAAGCTCATTT
39694084 TAGTTTGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (20 bp):
AGCTCATCTTAAGCTCATTT
Found at i:39698757 original size:20 final size:20
Alignment explanation
Indices: 39698722--39698760 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39698712 TCAGCTCAAC
39698722 TTTAGCTCAATGAGCTCATT
1 TTTAGCTCAATGAGCTCATT
* *
39698742 TTTAGCTCATTTAGCTCAT
1 TTTAGCTCAATGAGCTCAT
39698761 CTTAAGCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTAGCTCAATGAGCTCATT
Found at i:39698768 original size:20 final size:20
Alignment explanation
Indices: 39698704--39698773 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
39698694 AGTCTACTTC
* * *
39698704 AAGCTCACTCAGCTCAACTT
1 AAGCTCATTTAGCTCATCTT
* * * *
39698724 TAGCTCAATGAGCTCATTTT
1 AAGCTCATTTAGCTCATCTT
*
39698744 TAGCTCATTTAGCTCATCTT
1 AAGCTCATTTAGCTCATCTT
*
39698764 AAGCTTATTT
1 AAGCTCATTT
39698774 TAGGTTGCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (20 bp):
AAGCTCATTTAGCTCATCTT
Found at i:39707372 original size:20 final size:19
Alignment explanation
Indices: 39707349--39707413 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
39707339 AAGCTCAAAC
39707349 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39707369 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39707389 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39707409 GAGCT
1 GAGCT
39707414 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39714182 original size:11 final size:10
Alignment explanation
Indices: 39714157--39714217 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
39714147 ACCAATAAAA
39714157 TAAA-TGAGC
1 TAAATTGAGC
*
39714166 TGAATTGTAGC
1 TAAATTG-AGC
39714177 TAAATTGAGC
1 TAAATTGAGC
**
39714187 TCGATTGAGC
1 TAAATTGAGC
39714197 TGAAA-TGAGC
1 T-AAATTGAGC
*
39714207 TCAATTGAGC
1 TAAATTGAGC
39714217 T
1 T
39714218 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:39714218 original size:20 final size:20
Alignment explanation
Indices: 39714158--39714218 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
39714148 CCAATAAAAT
*
39714158 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
39714178 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
39714199 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
39714219 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:39720269 original size:20 final size:20
Alignment explanation
Indices: 39720222--39720269 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
39720212 AGTAAGCTCG
39720222 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
39720242 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
39720262 GTTGAGCT
1 GTTGAGCT
39720270 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:39723228 original size:21 final size:22
Alignment explanation
Indices: 39723199--39723249 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
39723189 TCTCTCTCGC
*
39723199 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
39723220 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
39723242 TTT-ATTTT
1 TTTCATTTT
39723250 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:39726194 original size:40 final size:40
Alignment explanation
Indices: 39726094--39726265 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
39726084 GCTCCTCGTT
* * *
39726094 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
39726134 C-AATGCCTTCGGGACATAACCTGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
** * *
39726173 TGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39726213 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
39726253 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39726266 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 33 0.29
40 78 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:39726278 original size:80 final size:79
Alignment explanation
Indices: 39726094--39726318 Score: 222
Period size: 80 Copynumber: 2.8 Consensus size: 79
39726084 GCTCCTCGTT
* * * * * *
39726094 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCTGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
39726158 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
** * *
39726173 TGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
39726238 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
39726253 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
39726317 GA
63 GA
39726319 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
78 1 0.01
79 38 0.32
80 67 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:39726327 original size:41 final size:41
Alignment explanation
Indices: 39726250--39726327 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39726240 TTTGTATCTC
* * *
39726250 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39726291 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39726328 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39733424 original size:40 final size:40
Alignment explanation
Indices: 39733324--39733495 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
39733314 GCCCCTCGTT
* * *
39733324 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
39733364 C-AATGCCTTCGGGACATAACCTGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
39733403 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39733443 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
39733483 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39733496 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:39733508 original size:80 final size:79
Alignment explanation
Indices: 39733324--39733548 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 79
39733314 GCCCCTCGTT
* * * * * *
39733324 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCTGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
39733388 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
39733403 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
39733468 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
39733483 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
39733547 GA
63 GA
39733549 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 68 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:39733557 original size:41 final size:41
Alignment explanation
Indices: 39733480--39733557 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39733470 TTTGTATCTC
* * *
39733480 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39733521 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39733558 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39737022 original size:20 final size:19
Alignment explanation
Indices: 39736958--39737022 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
39736948 TATAAACGCA
39736958 AATGAGCTTAAAATGAGCTG
1 AATGAGC-TAAAATGAGCTG
* * *
39736978 ATTGAGCTAAGAGTGAACTCG
1 AATGAGCTAA-AATGAGCT-G
39736999 -ATGAGCTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
39737018 AATGA
1 AATGA
39737023 ACTTGAAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 5 0.14
20 29 0.83
21 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:39744933 original size:20 final size:18
Alignment explanation
Indices: 39744896--39744944 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
39744886 AGACCGTATA
39744896 CAATTTTTTTTTTCTTTT
1 CAATTTTTTTTTTCTTTT
*
39744914 CAATTTTTTTGATTTGTTTT
1 CAATTTTTTT--TTTCTTTT
*
39744934 CGATTTTTTTT
1 CAATTTTTTTT
39744945 CAAATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
20 16 0.59
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.73
Consensus pattern (18 bp):
CAATTTTTTTTTTCTTTT
Found at i:39751079 original size:18 final size:18
Alignment explanation
Indices: 39751058--39751101 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
39751048 AAAAGAAGAC
39751058 AGAAAAAGA-AATTGAAAA
1 AGAAAAAGAGAA-TGAAAA
39751076 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
39751094 AGAGAAAA
1 AGA-AAAA
39751102 AAGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:39752815 original size:33 final size:34
Alignment explanation
Indices: 39752778--39752857 Score: 121
Period size: 33 Copynumber: 2.4 Consensus size: 34
39752768 GAGTTAGTTT
39752778 ATTAAATTTAGTTTAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTTAGCTCAAATAAGTGTTAGTA
* *
39752811 ATTAATTTTAGTTTAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTTAGCTCAAATAAGTGTTAGTA
39752845 ATT-AATTT-GTTTA
1 ATTAAATTTAGTTTA
39752858 AATTTGGACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.12
33 34 0.79
34 4 0.09
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (34 bp):
ATTAAATTTAGTTTAGCTCAAATAAGTGTTAGTA
Found at i:39757080 original size:20 final size:20
Alignment explanation
Indices: 39757029--39757082 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
39757019 TAATTCATGT
*
39757029 TTTAATTTAAGACATACTTAA
1 TTTAA-TTAAGACACACTTAA
** * *
39757050 TAAAATCAAGACACATTTAA
1 TTTAATTAAGACACACTTAA
39757070 TTTAATTAAGACA
1 TTTAATTAAGACA
39757083 AGACAAATTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTAATTAAGACACACTTAA
Found at i:39757163 original size:21 final size:22
Alignment explanation
Indices: 39757138--39757183 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
39757128 TAAAAAACAA
39757138 ATTAAACACTT-AACTAAATTT
1 ATTAAACACTTAAACTAAATTT
* *
39757159 ATTAAATACTTAAACTAATTTT
1 ATTAAACACTTAAACTAAATTT
39757181 ATT
1 ATT
39757184 CCAGCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAACACTTAAACTAAATTT
Found at i:39757249 original size:20 final size:20
Alignment explanation
Indices: 39757224--39757264 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39757214 ATTTAAACCG
39757224 AGCTCAAACGAGCTGAAATA
1 AGCTCAAACGAGCTGAAATA
***
39757244 AGCTCATGTGAGCTGAAATA
1 AGCTCAAACGAGCTGAAATA
39757264 A
1 A
39757265 AATTAGGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
AGCTCAAACGAGCTGAAATA
Found at i:39760973 original size:23 final size:22
Alignment explanation
Indices: 39760921--39760973 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39760911 TCCACGTCTT
*
39760921 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39760943 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39760966 TTTCTTTT
1 TTTCTTTT
39760974 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39767811 original size:21 final size:21
Alignment explanation
Indices: 39767785--39767837 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39767775 TTGGTATTTG
39767785 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
39767806 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
39767827 GGTATTTGGTA
1 GG-AATTGGTA
39767838 AAAATTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.34, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:39767816 original size:11 final size:11
Alignment explanation
Indices: 39767796--39767828 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39767786 GAATTGGTAC
39767796 GAAATGGTATG
1 GAAATGGTATG
*
39767807 GAATTGGTAT-
1 GAAATGGTATG
39767817 GAAATGGTATG
1 GAAATGGTATG
39767828 G
1 G
39767829 TATTTGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:39767842 original size:21 final size:21
Alignment explanation
Indices: 39767785--39767847 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
39767775 TTGGTATTTG
**
39767785 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTATAAAATGGTAT
*
39767806 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATAAAATGGTAT
*
39767827 GGTATTTGGTA-AAAATTGGTA
1 GG-AATTGGTATAAAA-TGGTA
39767848 AAGGTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.02, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTATAAAATGGTAT
Found at i:39773073 original size:16 final size:16
Alignment explanation
Indices: 39773052--39773083 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39773042 GTTTTGTTGC
*
39773052 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
39773068 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
39773084 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:39775250 original size:20 final size:19
Alignment explanation
Indices: 39775227--39775291 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
39775217 AAGCTCAAAC
39775227 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39775247 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39775267 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39775287 GAGCT
1 GAGCT
39775292 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39776580 original size:17 final size:18
Alignment explanation
Indices: 39776558--39776591 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39776548 ACAACACTCC
*
39776558 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
39776575 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
39776592 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:39776699 original size:15 final size:16
Alignment explanation
Indices: 39776674--39776705 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39776664 TATCTCACAC
39776674 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39776690 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39776705 T
1 T
39776706 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:39777688 original size:13 final size:13
Alignment explanation
Indices: 39777672--39777746 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
39777662 TTTTGCTCGA
*
39777672 TTTTTTTTTCACT
1 TTTTTTTTTCAAT
*
39777685 TTTTTTTTTGAAT
1 TTTTTTTTTCAAT
39777698 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
39777711 CAATTTTTTTTTCGAAT
1 ---TTTTTTTTTC-AAT
*
39777728 TTTTTTTTT-GAT
1 TTTTTTTTTCAAT
39777740 TTTTTTT
1 TTTTTTT
39777747 GTTACTCCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
12 9 0.17
13 23 0.43
14 9 0.17
16 10 0.19
17 3 0.06
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:39779239 original size:20 final size:19
Alignment explanation
Indices: 39779216--39779280 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
39779206 AAGCTCAAAC
39779216 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39779236 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39779256 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39779276 GAGCT
1 GAGCT
39779281 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39781270 original size:26 final size:26
Alignment explanation
Indices: 39781241--39781297 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
39781231 TCAACTTCTC
*
39781241 TTTTTAGTT-AATAAATTCTCTTTGAG
1 TTTTTAGTTCAAGAAATTCT-TTTGAG
** *
39781267 TTTTTCTTTCAAGAATTTCTTTTGAG
1 TTTTTAGTTCAAGAAATTCTTTTGAG
39781293 TTTTT
1 TTTTT
39781298 TTAGAAGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.60
Consensus pattern (26 bp):
TTTTTAGTTCAAGAAATTCTTTTGAG
Found at i:39781305 original size:25 final size:27
Alignment explanation
Indices: 39781256--39781305 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
39781246 AGTTAATAAA
*
39781256 TTCTCTTTGAGTTTTTCTTTCAAGAAT
1 TTCTCTTTGAGTTTTTCTTACAAGAAT
*
39781283 TTCT-TTTGAGTTTTT-TTAGAAGA
1 TTCTCTTTGAGTTTTTCTTACAAGA
39781306 GTTTTAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 11 0.52
27 4 0.19
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.56
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTTCTTACAAGAAT
Found at i:39788662 original size:11 final size:11
Alignment explanation
Indices: 39788627--39788665 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
39788617 AGCTCGATCC
*
39788627 AGCTCAA-TCG
1 AGCTCAATTCT
39788637 AGCTCAATT-T
1 AGCTCAATTCT
39788647 AGCTCAATTCT
1 AGCTCAATTCT
39788658 AGCTCAAT
1 AGCTCAAT
39788666 GAGCTCGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (11 bp):
AGCTCAATTCT
Found at i:39788663 original size:21 final size:20
Alignment explanation
Indices: 39788627--39788665 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39788617 AGCTCGATCC
39788627 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
*
39788647 AGCTCAATTCTAGCTCAAT
1 AGCTCAA-TCGAGCTCAAT
39788666 GAGCTCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:39788670 original size:20 final size:20
Alignment explanation
Indices: 39788627--39788671 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39788617 AGCTCGATCC
*
39788627 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTG
*
39788647 AGCTCAATTCTAGCTCAA-TG
1 AGCTCAA-TCGAGCTCAATTG
39788667 AGCTC
1 AGCTC
39788672 GTTCCTAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTG
Found at i:39796236 original size:21 final size:21
Alignment explanation
Indices: 39796191--39796253 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
39796181 TTTGAACCAT
* *
39796191 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
39796213 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
39796234 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
39796254 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:39797985 original size:54 final size:54
Alignment explanation
Indices: 39797901--39798025 Score: 164
Period size: 54 Copynumber: 2.3 Consensus size: 54
39797891 GAATAAGTAT
* * * *
39797901 TTAGTTGCTGTAATAAATTACTCGACTTAGTTAATTGAGTTCATCTTTGTT-AA
1 TTAGTTGCTGGAATAAATTACTCGACTTAGTTAATTAAGTTCAACTTAGTTCAA
*
39797954 TTAAGTTGCTGGAATAAATTACTC-ATCTTAGTTAATTAAGTTCAACTTAGTTCAC
1 TT-AGTTGCTGGAATAAATTACTCGA-CTTAGTTAATTAAGTTCAACTTAGTTCAA
*
39798009 TTAGTTGCTGGATTAAA
1 TTAGTTGCTGGAATAAA
39798026 CTTTTAATGT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
53 3 0.05
54 57 0.90
55 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (54 bp):
TTAGTTGCTGGAATAAATTACTCGACTTAGTTAATTAAGTTCAACTTAGTTCAA
Found at i:39804736 original size:21 final size:21
Alignment explanation
Indices: 39804694--39804738 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
39804684 TCATGTCTCA
* * *
39804694 TATAATTGCTCTCTCTCGAGC
1 TATAATTGCTCTCACACAAGC
39804715 TATAATTGCTCTCACACAAGC
1 TATAATTGCTCTCACACAAGC
39804736 TAT
1 TAT
39804739 CAGTCAGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.36
Consensus pattern (21 bp):
TATAATTGCTCTCACACAAGC
Found at i:39805215 original size:20 final size:20
Alignment explanation
Indices: 39805182--39805225 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
39805172 TAGCTTCCCA
* *
39805182 AGCTTCTTTCAGCTCCAATC
1 AGCTTATTTCAGCTCAAATC
* *
39805202 AGCTTATTTGAGCTTAAATC
1 AGCTTATTTCAGCTCAAATC
39805222 AGCT
1 AGCT
39805226 CGTTTAAGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (20 bp):
AGCTTATTTCAGCTCAAATC
Found at i:39806613 original size:20 final size:20
Alignment explanation
Indices: 39806588--39806683 Score: 90
Period size: 20 Copynumber: 4.9 Consensus size: 20
39806578 TTCCATGCGG
39806588 TTCAGCTCACTTGAGCTCAA
1 TTCAGCTCACTTGAGCTCAA
**
39806608 TTCAGCT-ACTCCAGCTCAA
1 TTCAGCTCACTTGAGCTCAA
*
39806627 GTCAGCTCA-TTCGAGCTCAA
1 TTCAGCTCACTT-GAGCTCAA
* * **
39806647 GTCAGCTCCCACGAGCTCAA
1 TTCAGCTCACTTGAGCTCAA
*
39806667 TTCATCTCA-TTGAGCTC
1 TTCAGCTCACTTGAGCTC
39806684 GTTATTAGCT
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 23 0.38
20 37 0.62
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (20 bp):
TTCAGCTCACTTGAGCTCAA
Found at i:39806614 original size:10 final size:10
Alignment explanation
Indices: 39806588--39806654 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
39806578 TTCCATGCGG
*
39806588 TTCAGCTCAC
1 TTCAGCTCAA
*
39806598 TTGAGCTCAA
1 TTCAGCTCAA
*
39806608 TTCAGCT-AC
1 TTCAGCTCAA
*
39806617 TCCAGCTCAA
1 TTCAGCTCAA
*
39806627 GTCAGCTC-A
1 TTCAGCTCAA
39806636 TTCGAGCTCAA
1 TTC-AGCTCAA
*
39806647 GTCAGCTC
1 TTCAGCTC
39806655 CCACGAGCTC
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 10 0.23
10 31 0.70
11 3 0.07
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:39806633 original size:39 final size:39
Alignment explanation
Indices: 39806589--39806683 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 39
39806579 TCCATGCGGT
* *
39806589 TCAGCTCACTTGAGCTCAATTCAGCTACTC-C-AGCTCAAG
1 TCAGCTCA-TTGAGCTCAAGTCAGCT-CCCACGAGCTCAAG
*
39806628 TCAGCTCATTCGAGCTCAAGTCAGCTCCCACGAGCTCAAT
1 TCAGCTCATT-GAGCTCAAGTCAGCTCCCACGAGCTCAAG
*
39806668 TCATCTCATTGAGCTC
1 TCAGCTCATTGAGCTC
39806684 GTTATTAGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
38 4 0.08
39 29 0.59
40 16 0.33
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (39 bp):
TCAGCTCATTGAGCTCAAGTCAGCTCCCACGAGCTCAAG
Found at i:39809152 original size:33 final size:33
Alignment explanation
Indices: 39809114--39809176 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
39809104 GATTACTCAC
39809114 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
39809147 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
39809177 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:39809199 original size:15 final size:13
Alignment explanation
Indices: 39809173--39809229 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
39809163 TCAAGCTCTC
*
39809173 TTTCAATTTCTTT
1 TTTCATTTTCTTT
39809186 TTTCACTTTT-TCTT
1 TTTCA-TTTTCT-TT
39809200 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
39809214 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
39809228 TT
1 TT
39809230 CTCTCACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.18
14 26 0.68
15 5 0.13
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:39809203 original size:27 final size:27
Alignment explanation
Indices: 39809173--39809230 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
39809163 TCAAGCTCTC
39809173 TTTCAA-TTTCTTTT-TTCACTTTTTCTT
1 TTTCAATTTTCTTTTCTTCA--TTTTCTT
39809200 TTTCAATTTTCTTTTCTTCATTTTCTT
1 TTTCAATTTTCTTTTCTTCATTTTCTT
39809227 TTTC
1 TTTC
39809231 TCTCACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 17 0.59
28 8 0.28
29 4 0.14
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTCAATTTTCTTTTCTTCATTTTCTT
Found at i:39809289 original size:18 final size:18
Alignment explanation
Indices: 39809191--39809329 Score: 88
Period size: 18 Copynumber: 7.7 Consensus size: 18
39809181 TCTTTTTTCA
39809191 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
39809210 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
39809230 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
39809248 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
39809266 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
39809284 CTTTTT-GTTTTC--TTT
1 CTTTTTCTTTTTCATTTT
** * *
39809299 CAATTTCTTTTTCAATCT
1 CTTTTTCTTTTTCATTTT
*
39809317 CTTTTTCCTTTTC
1 CTTTTTCTTTTTC
39809330 TCGCTCAATG
Statistics
Matches: 91, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
15 7 0.08
16 5 0.05
17 6 0.07
18 54 0.59
19 3 0.03
20 8 0.09
21 8 0.09
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:39809311 original size:6 final size:6
Alignment explanation
Indices: 39809191--39809298 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
39809181 TCTTTTTTCA
* * * **
39809191 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
39809242 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
39809290 -GTTTT CTTT
1 CTTTTT CTTT
39809299 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:39809330 original size:81 final size:83
Alignment explanation
Indices: 39809176--39809330 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 83
39809166 AGCTCTCTTT
* * **
39809176 CAATTTCTTTTTTCACTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTT
1 CAATTTCTTTTTT-ACTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTT
*
39809241 TCGATTTCTTTTTCTTTTG
65 TCCATTTCTTTTTCTTTTG
* * *
39809260 CAATTTC-TTTTT-CTTTTTCGTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTCTTTT
1 CAATTTCTTTTTTACTTTTTCGTTTTCAATTTTCTTTTC-TTCAATTTCTTTTTCAATCACTTTT
*
39809322 TCCTTTTCT
65 TCCATTTCT
39809331 CGCTCAATGG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 9 0.15
81 40 0.66
83 5 0.08
84 7 0.11
ACGTcount: A:0.09, C:0.20, G:0.03, T:0.68
Consensus pattern (83 bp):
CAATTTCTTTTTTACTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTTT
CCATTTCTTTTTCTTTTG
Found at i:39810362 original size:28 final size:28
Alignment explanation
Indices: 39810331--39810391 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
39810321 TTTAACTTGA
*
39810331 TTTTTTTGCTC-ACTTTTTTT-TCTTTCTT
1 TTTTTTTGCTCGA-TTTTTTTCACTTT-TT
39810359 TTTTTTTGCTCGATTTTTTTCACTTTTT
1 TTTTTTTGCTCGATTTTTTTCACTTTTT
39810387 TTTTT
1 TTTTT
39810392 GAATTTCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTTTTGCTCGATTTTTTTCACTTTTT
Found at i:39812739 original size:11 final size:11
Alignment explanation
Indices: 39812725--39812774 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
39812715 AGTCATTGTG
*
39812725 AAAAAAAATTG
1 AAAAAAAATTC
*
39812736 AAAAAAAAATC
1 AAAAAAAATTC
39812747 --AAAAAATTC
1 AAAAAAAATTC
39812756 AAAAAAAATTC
1 AAAAAAAATTC
39812767 AAAAAAAA
1 AAAAAAAA
39812775 GTTTATTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.24
11 26 0.76
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:39812752 original size:20 final size:20
Alignment explanation
Indices: 39812727--39812772 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
39812717 TCATTGTGAA
*
39812727 AAAAAATTGAAAAAAAAATC
1 AAAAAATTCAAAAAAAAATC
*
39812747 AAAAAATTCAAAAAAAATTC
1 AAAAAATTCAAAAAAAAATC
39812767 AAAAAA
1 AAAAAA
39812773 AAGTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (20 bp):
AAAAAATTCAAAAAAAAATC
Done.