Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 35
Found at i:5680924 original size:2 final size:2
Alignment explanation
Indices: 5680913--5680951 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5680903 TAAAGGAGAT
*
5680913 TA TA -A TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5680952 CAATAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5682727 original size:45 final size:45
Alignment explanation
Indices: 5682678--5682830 Score: 157
Period size: 45 Copynumber: 3.4 Consensus size: 45
5682668 AGAGTCAATA
5682678 TTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAACCT
1 TTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAACCT
* * * *
5682723 TTTAGTGGTGGT-GTTCTTGACTTTCTTGTGAAGAGAAGTCAATCT
1 TTTAGTGAT-GTCATTCTTGACTTTCTCGTGAAGAGAAGTCAACCT
* * * ** * * *
5682768 TTCAATGTTGTC-TTCCCTTGACTTTCTCACGAAGTGGAGTAAACCT
1 TTTAGTGATGTCATT--CTTGACTTTCTCGTGAAGAGAAGTCAACCT
5682814 TTTAGTGATGTCATTCT
1 TTTAGTGATGTCATTCT
5682831 CAACTTTACT
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
44 4 0.05
45 46 0.53
46 34 0.40
47 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.41
Consensus pattern (45 bp):
TTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAACCT
Found at i:5682895 original size:51 final size:51
Alignment explanation
Indices: 5682824--5682963 Score: 176
Period size: 51 Copynumber: 2.8 Consensus size: 51
5682814 TTTAGTGATG
*
5682824 TCATT-CTCAACTTTACTTTCTCGTGGAGAGGAGTCAACTTTTAAGTAGTA
1 TCATTCCTCAACTTGACTTTCTCGTGGAGAGGAGTCAACTTTTAAGTAGTA
** * * * *
5682874 TCATTTTTCAACTTGACTTTCTCATGGAGAGAAGTAAACTTTTCAGTAGTA
1 TCATTCCTCAACTTGACTTTCTCGTGGAGAGGAGTCAACTTTTAAGTAGTA
* *
5682925 TCGTTCCTCAACTTGACTTTATCGTGTG-GAGGAGTCAAC
1 TCATTCCTCAACTTGACTTTCTCGTG-GAGAGGAGTCAAC
5682964 CTGTCTATAA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
50 5 0.07
51 69 0.92
52 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (51 bp):
TCATTCCTCAACTTGACTTTCTCGTGGAGAGGAGTCAACTTTTAAGTAGTA
Found at i:5683807 original size:136 final size:136
Alignment explanation
Indices: 5683581--5683937 Score: 531
Period size: 136 Copynumber: 2.6 Consensus size: 136
5683571 AATCGTTTCT
* * *
5683581 GATTCAATCTTCCCTGAAGA-ACAGTGAAGTGAATTAAAG-TTTTTCTCGAGTCTAACCTCCCCT
1 GATTCAATCTTCCCTGAAGAGA-AGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTAACCTCCCCT
* *
5683644 AAAGAGTAGCGAAGTAGATTCTTTTTCTTTTACATTTGGGCTTCCTGAAGAGTAGTGAAGCAAAT
65 AAAGAGTAGCGGAGTAGATTCTTTTTCTTTCACATTTGGGCTTCCTGAAGAGTAGTGAAGCAAAT
5683709 CACATTC
130 CACATTC
5683716 GATTCAATCTTCCCTGAAGAGAAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTAACC-CACCCT
1 GATTCAATCTTCCCTGAAGAGAAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTAACCTC-CCCT
* * **
5683780 AAAGAGTAGCGGAGTATATTCTTTTTCTTTCAGATTTGGTTTTCCTGAAGAGTAGTGAAGCAAAT
65 AAAGAGTAGCGGAGTAGATTCTTTTTCTTTCACATTTGGGCTTCCTGAAGAGTAGTGAAGCAAAT
5683845 CACATTC
130 CACATTC
* * * *
5683852 GATTTAATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGCCTGACCTCCCCTA
1 GATTCAATCTTCCCTGAAGAGAAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTAACCTCCCCTA
* * *
5683917 AAGGGTATCGGAGCAGATTCT
66 AAGAGTAGCGGAGTAGATTCT
5683938 GTTGAAAATT
Statistics
Matches: 201, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
135 35 0.17
136 165 0.82
137 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (136 bp):
GATTCAATCTTCCCTGAAGAGAAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTAACCTCCCCTA
AAGAGTAGCGGAGTAGATTCTTTTTCTTTCACATTTGGGCTTCCTGAAGAGTAGTGAAGCAAATC
ACATTC
Found at i:5688686 original size:12 final size:12
Alignment explanation
Indices: 5688669--5688694 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5688659 TATCTTCACT
5688669 TAGTGTTTAAAA
1 TAGTGTTTAAAA
5688681 TAGTGTTTAAAA
1 TAGTGTTTAAAA
5688693 TA
1 TA
5688695 AATTTAGCAC
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:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (12 bp):
TAGTGTTTAAAA
Found at i:5688982 original size:23 final size:23
Alignment explanation
Indices: 5688940--5689024 Score: 136
Period size: 23 Copynumber: 3.7 Consensus size: 23
5688930 ATAGGGTAGA
* * *
5688940 GGGAATCGATACCCCC-TTGATG
1 GGGAACCGATTCCCCCTTTGAAG
5688962 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
5688985 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
5689008 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
5689025 AGGGGAATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
22 14 0.24
23 45 0.76
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:5692104 original size:136 final size:136
Alignment explanation
Indices: 5691903--5693473 Score: 1727
Period size: 136 Copynumber: 11.6 Consensus size: 136
5691893 ATTAACTCAA
* * * * *
5691903 CAGATTCTTTTTTCTTTCAAATTTGGTCTTCCTGAAAAGCAGTGAAGCAAATAACATTCAATTCA
1 CAGATTC-TTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCA
* ** *
5691968 ATCTTCCCTGAAGATCAGAGAAGTATATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGTGT
65 ATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGT
5692033 AGCGGAG
130 AGCGGAG
* * * **
5692040 TAGATTCTTTTTATTTCAGATTTGGTATTCCTGAAGAGCAATGAATTAAATCACATTCGATTCAA
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCAA
* * * *
5692105 TCTTCCCTGAAGAGCAGAGAAGTGTATCAAAGTTTTTTCTCGAGTTTAACCTCCCCTAAGGAGTA
66 TCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGTA
5692170 GCGGAG
131 GCGGAG
* *
5692176 CAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAG-AAGTAAAGCAAAT-ATCATTCGATTC
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAA-TGAAGCAAATCA-CATTCGATTC
* * * * * * *
5692239 AATCTTTCCTGAAGAACACAGAAGTGGATTAAAGATTTTTCTTGAGTGTGACCTCCCCTAAAGAG
64 AATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAG
*
5692304 TAGCAGAG
129 TAGCGGAG
* * * * ** * *
5692312 CATATTCTTTTTCTTTGATATTTGGTCTTCATTCAGAG-AAGTGAAGCAAATCATATTCGACAT-
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAA-TGAAGCAAATCACATTCGA-TTC
* * * * * * *
5692375 AATCTTCCCTGAGGAGCAAATAAGTGGATAAAAGTTTTTTCTCGAGTCTTACTTTCCCTAAAGAG
64 AATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAG
5692440 TAGCGGAG
129 TAGCGGAG
* * * *
5692448 CAAATTCATTTTCTTTCAGATTTGGTCTTCGTGAAGAGCAATGAAGCAAATCACATTTGATTCAA
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCAA
* * * * *
5692513 TCTTCCCTAAAGAGAATAGAAGTGGATCAAAGTTTTTTCTAGAGTCTAACCTCCCCTAAAGAGTA
66 TCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGTA
5692578 GCGGAG
131 GCGGAG
* * * *
5692584 CATATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAG-AAGTGAAGCAAATAACATTCGAATCA
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAA-TGAAGCAAATCACATTCGATTCA
* * * * *
5692648 ATCTTCCCTGAAGAACACAGAAGTGGATCAAAGTTTTTTCTCAAGTCTGAGCTCCCCTAAAGAAT
65 ATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGT
*
5692713 AGCAGAG
130 AGCGGAG
* * *
5692720 CAGATTCTTTTTCTTTTAGATTTGGTCTTCATAAAGAG-AAGTGAAGCAAATCACATTCGATAT-
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAA-TGAAGCAAATCACATTCGAT-TC
* * * * *
5692783 AATCTTCCCTGAAGAGCAAAGAAGTGGATAAAAGTTTTTTTTCTCGAGTTTAACCTTCCCTAAAG
64 AATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAG--TTTTTTCTCGAGTCTGACCTCCCCTAAAG
5692848 AGTAGCGGAG
127 AGTAGCGGAG
* * *
5692858 CAAATTCTTTTCCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTTGATTCAA
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCAA
* *
5692923 TCTTCCCTGAAGAAG-AGAGAAGTGGATCAAGGTTTTTTCTCTAGTCTGACCTCCCCTAAAGAGT
66 TCTTCCCTGAAG-AGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGT
* *
5692987 AGTGGGG
130 AGCGGAG
* * * *
5692994 CAGATTCTTTCTTCTTTCAGAATTGGTCTTCCTGAAGAGCAGTGAAACAAACCACATTCGATTCA
1 CAGATTCTTT-TTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCA
***** *
5693059 ATCTTCCCTGAAGAGCA-ACGAAGT-GAT-AAAAAAAATT-TCGAGTCTGACCTCCCCTAAAGAA
65 ATCTTCCCTGAAGAGCAGA-GAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAG
5693120 TAGCGGAG
129 TAGCGGAG
* * * * * * * *
5693128 CATATTCTCTTTATTTCAGATTTAGTCTTCCTAAAGAG-AAAGAAAGCAAATCAAATTCGATTAA
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATG-AAGCAAATCACATTCGATTCA
* * ** * * * *
5693192 ATATTCCCTGAAGAGAATTGAAGTGAATCAAA--ATTTTCTCGAGTTTGACATCCCCTAAAGAGT
65 ATCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGT
*
5693255 AGCAGAG
130 AGCGGAG
** * *
5693262 CAGATTCTCCTTCTTTCAGATTTGGTCTTCCTGAGGAGCAATTAAGCAAATCACATTCGATTCAA
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCAA
* * * * * * * * * *
5693327 TCTTCCCTGAAAAGCAGCGAAGTGAATCAAA--ATTTCCTTGAGTCCGACTTCCCTTTAAGAGTA
66 TCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGTA
*
5693390 GCAGAG
131 GCGGAG
* * ** * * *** * *
5693396 AAGATTCTTCTTCTTTCAGATTTCATCTTTCTAAAGAGCAGCAAAACAAAACACATTCGATTCAA
1 CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCAA
5693461 TCTTCCCTGAAGA
66 TCTTCCCTGAAGA
5693474 ACAGCAAAGT
Statistics
Matches: 1212, Mismatches: 200, Indels: 47
0.83 0.14 0.03
Matches are distributed among these distances:
132 2 0.00
133 64 0.05
134 240 0.20
135 15 0.01
136 696 0.57
137 79 0.07
138 112 0.09
139 4 0.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (136 bp):
CAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCAATGAAGCAAATCACATTCGATTCAA
TCTTCCCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTTCTCGAGTCTGACCTCCCCTAAAGAGTA
GCGGAG
Found at i:5695836 original size:13 final size:13
Alignment explanation
Indices: 5695820--5695848 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5695810 GTTGACTTTT
5695820 ATTTAGTTCTTAG
1 ATTTAGTTCTTAG
5695833 ATTTAGTTCTTAG
1 ATTTAGTTCTTAG
5695846 ATT
1 ATT
5695849 AATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (13 bp):
ATTTAGTTCTTAG
Found at i:5697147 original size:14 final size:14
Alignment explanation
Indices: 5697128--5697156 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5697118 CATTCATGTA
5697128 TCTCTGTTAAATTC
1 TCTCTGTTAAATTC
5697142 TCTCTGTTAAATTC
1 TCTCTGTTAAATTC
5697156 T
1 T
5697157 GTTTTTGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.52
Consensus pattern (14 bp):
TCTCTGTTAAATTC
Found at i:5699975 original size:113 final size:112
Alignment explanation
Indices: 5699523--5699986 Score: 802
Period size: 112 Copynumber: 4.1 Consensus size: 112
5699513 TTGACGGTTT
* * *
5699523 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
5699588 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
5699635 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
5699700 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTAAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
5699747 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
5699812 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
5699859 GTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* * * *
5699924 TGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
5699972 GTGTCAATACTTTAT
1 GTGTCGATACTTTAT
5699987 TATAAATATC
Statistics
Matches: 334, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 262 0.78
113 72 0.22
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:5700186 original size:182 final size:182
Alignment explanation
Indices: 5699856--5700306 Score: 715
Period size: 182 Copynumber: 2.5 Consensus size: 182
5699846 GGATATATTG
* *
5699856 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAAATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAA
* ** *
5699921 AACTGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATGTTGATAGTGTCAATACTTTA
65 AACCGGTCTCGAAATGACAAAACAGGTAAAACGCTACCGGATATGTTGAAAGTGTCAATACTTTA
* * * *
5699986 TTATAAATATCAACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCTAAT
130 TTATAAATATCAACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGCCAAT
5700039 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
5700104 ACCGGTCTCGAAATGACAAAACCGGTAAAGA-GCTATCGGATATGTTGAAAGTGTCGATACTTTA
66 ACCGGTCTCGAAATGACAAAACAGGTAAA-ACGCTACCGGATATGTTGAAAGTGTCAATACTTTA
* *
5700168 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGCCAAT
130 TTATAAATATCAACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGCCAAT
5700221 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
5700286 ATCGGTATCGAAATGAAAAAA
66 ACCGGTCTCGAAATGACAAAA
5700307 TCGATAGTAA
Statistics
Matches: 249, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
182 198 0.80
183 51 0.20
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACAGGTAAAACGCTACCGGATATGTTGAAAGTGTCAATACTTTAT
TATAAATATCAACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGCCAAT
Found at i:5700774 original size:23 final size:23
Alignment explanation
Indices: 5700745--5700792 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5700735 AAATAGGTCA
*
5700745 ATATAAGCGATACCTATTACATT
1 ATATAAGCGATACCTAATACATT
* * *
5700768 ATATAAGTGCTACCTAATATATT
1 ATATAAGCGATACCTAATACATT
5700791 AT
1 AT
5700793 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGATACCTAATACATT
Found at i:5702119 original size:17 final size:17
Alignment explanation
Indices: 5702097--5702129 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5702087 ATATTAATTT
5702097 AAATAATTAC-ATTTTTA
1 AAATAA-TACTATTTTTA
5702114 AAATAATACTATTTTT
1 AAATAATACTATTTTT
5702130 TATCACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATAATACTATTTTTA
Found at i:5704222 original size:15 final size:15
Alignment explanation
Indices: 5704204--5704233 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5704194 AGCTTACAAG
5704204 AAAGAATCCTAAAGA
1 AAAGAATCCTAAAGA
5704219 AAAGAATCCTAAAGA
1 AAAGAATCCTAAAGA
5704234 TTTGCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAGAATCCTAAAGA
Found at i:5711921 original size:65 final size:65
Alignment explanation
Indices: 5711784--5711907 Score: 153
Period size: 65 Copynumber: 1.9 Consensus size: 65
5711774 AATAGCTAGA
* ** *
5711784 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTTTGAGTGTATCGATGCATAGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATAAAACCATGAGTGCATCGATGCATAGTAT
* * **
5711849 GTGCATCGATGCATGAAATGCATTCGATG-TTTAATTTATTCCATG-GTGCATCGATGCAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTAA-TAAAACCATGAGTGCATCGATGCAT
5711908 GGATTGGTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 17 0.34
65 33 0.66
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTAATAAAACCATGAGTGCATCGATGCATAGTAT
Found at i:5715547 original size:20 final size:20
Alignment explanation
Indices: 5715522--5715577 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
5715512 GAATGTAATT
5715522 AGGGTATCGATACCTAGTAG
1 AGGGTATCGATACCTAGTAG
5715542 AGGGTATCGATACCTAGTAG
1 AGGGTATCGATACCTAGTAG
*
5715562 AGGGTACCGATACCTA
1 AGGGTATCGATACCTA
5715578 CCTTAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (20 bp):
AGGGTATCGATACCTAGTAG
Found at i:5716135 original size:21 final size:22
Alignment explanation
Indices: 5716109--5716163 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
5716099 GTCGAGGGTT
5716109 TCATAGGTCCTTTGGGACA-AC
1 TCATAGGTCCTTTGGGACATAC
5716130 TCATAGGTCCTTTGGGACATAC
1 TCATAGGTCCTTTGGGACATAC
5716152 TCATAGGTCCTT
1 TCATAGGTCCTT
5716164 CGAGAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (22 bp):
TCATAGGTCCTTTGGGACATAC
Found at i:5722935 original size:21 final size:22
Alignment explanation
Indices: 5722909--5722967 Score: 93
Period size: 21 Copynumber: 2.7 Consensus size: 22
5722899 TCGAGGGTTG
5722909 CATAGGTCCTTCGGGACA-ACT
1 CATAGGTCCTTCGGGACATACT
*
5722930 CATAGGTCTTTCGGGACATACT
1 CATAGGTCCTTCGGGACATACT
*
5722952 CACAGGTCCTTCGGGA
1 CATAGGTCCTTCGGGA
5722968 TAAATTTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (22 bp):
CATAGGTCCTTCGGGACATACT
Found at i:5722958 original size:22 final size:21
Alignment explanation
Indices: 5722912--5722967 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
5722902 AGGGTTGCAT
*
5722912 AGGTCCTTCGGGACAACTCAT
1 AGGTCCTTCGGGACAACTCAC
*
5722933 AGGTCTTTCGGGACATACTCAC
1 AGGTCCTTCGGGACA-ACTCAC
5722955 AGGTCCTTCGGGA
1 AGGTCCTTCGGGA
5722968 TAAATTTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (21 bp):
AGGTCCTTCGGGACAACTCAC
Found at i:5725631 original size:22 final size:21
Alignment explanation
Indices: 5725572--5725631 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
5725562 TTAGTCACTG
* *
5725572 AAGTGCCTTAGCACTAATACTA
1 AAGTG-CTTAGCACTGATACAA
5725594 AAGTGCTTCAGCACTGATACAA
1 AAGTGCTT-AGCACTGATACAA
5725616 AAGTGCATTAGCACTG
1 AAGTGC-TTAGCACTG
5725632 GGGGAGAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (21 bp):
AAGTGCTTAGCACTGATACAA
Found at i:5726878 original size:19 final size:21
Alignment explanation
Indices: 5726843--5726885 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
5726833 AAAAACAAAG
*
5726843 GAAAGAAGAGATGAAGAATAT
1 GAAAGAAGAGATGAAGAAAAT
5726864 GAAA-AAGAG-TGAAGAAAAT
1 GAAAGAAGAGATGAAGAAAAT
5726883 GAA
1 GAA
5726886 GGGAAAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 5 0.24
21 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAAGAAGAGATGAAGAAAAT
Found at i:5727756 original size:409 final size:408
Alignment explanation
Indices: 5726998--5727816 Score: 1298
Period size: 409 Copynumber: 2.0 Consensus size: 408
5726988 TTTTATCCAA
*
5726998 ATAAAAAATACATTTTTTATCACCTTGTGGGTTTTCCTATAAGAACAAGTCTTTCATCTTTGACC
1 ATAAAAAATACATTTTTTATCACCTTGTGGGTTTTCCTATAAGAACAAGTCTTTCATCTTTGACA
* * * * *
5727063 CATATGATTAAGTTAGCATAATATAGGCACTCTAAGTCTAACGATAATGCCCAAAACTACTAACT
66 CATATGATTAAGTTAGCATAATATAAGCACTATAAGCCCAAAGATAATGCCCAAAACTACTAACT
* **
5727128 CAATTTTTGGGGCGTTACAACTCTCCCCTCCTAAAAAGAATTTTATCCTTGAAATTTTCCTGATC
131 CAATTTTTGGGGCGTTACAACTCTCCCCTCCTAAAAAGAATTTCATCCTTGAAATTTGACTGATC
* *
5727193 CGAACAAGTACAGGTACAATAGTTGCATGGCTTCCTCAATTTCCAACATTGTTTCCTCCACTCTG
196 CGAACAAGTACAGGTACAATAGTTGCATGGCTTCCTCAATTTCCAACATTGTTTCATCCACTATG
* * *
5727258 TGATTCCTCCATAGGACCTTAACTACCGATATCGTCTTGTTTCATAATTCCTTGGCCTCTCAGAC
261 TGATTCCTCCATAGGACCTTAACTACCGAAATCGTCTTGTTTCATAATTCCTTGACCTATCAGAC
*
5727323 CAAAATATTTAATGGTTCCTCAATATATGACATGTCTAGGTGAACTTCGATTCGCTCCAATAGAA
326 CAAAATATTTAATGGTTCCTCAATATATGACATGTCTAGGTGAACTTCGATTCGCTCCAACAGAA
*
5727388 CCACATGCGACGAGTCTG
391 CCACATGCGACAAGTCTG
* *
5727406 ATAAAAAATACCA-TTTTTATCACCTTGTGGGTTTTCCTATAAGCACAAGTTTTTCATCTTTGAC
1 ATAAAAAATA-CATTTTTTATCACCTTGTGGGTTTTCCTATAAGAACAAGTCTTTCATCTTTGAC
5727470 ACATATGATTAAGTTAGCATAATATAAGCACTATAAGCCCAAAGATAATGCCCAAAAACTACTAA
65 ACATATGATTAAGTTAGCATAATATAAGCACTATAAGCCCAAAGATAATGCCC-AAAACTACTAA
* * *
5727535 CTCGATTTTTGGGGTGTTACAACTCTCCCCTCCTAAAAAGAATTTCATCCTTGAAATTTGACTGG
129 CTCAATTTTTGGGGCGTTACAACTCTCCCCTCCTAAAAAGAATTTCATCCTTGAAATTTGACTGA
* * *
5727600 TCTGAACAAGTACAGGTACTATAGTTGCATGGCTTCCTCAATTTCCAACATTGTTTTATCCACTA
194 TCCGAACAAGTACAGGTACAATAGTTGCATGGCTTCCTCAATTTCCAACATTGTTTCATCCACTA
* * * * * * **
5727665 TGTGATTCCTCCGTAGGACTTTCACTACTGAAATCGTCTTGTTTCATAATTCTTTGACTTATTGG
259 TGTGATTCCTCCATAGGACCTTAACTACCGAAATCGTCTTGTTTCATAATTCCTTGACCTATCAG
* *
5727730 GCCAAAATATTTAATGGTTCCTCAATATATGACATGTCTAGGTGCACTTCGATTCGCTCCAACAG
324 ACCAAAATATTTAATGGTTCCTCAATATATGACATGTCTAGGTGAACTTCGATTCGCTCCAACAG
*
5727795 AACCACATGCGACAAGTTTG
389 AACCACATGCGACAAGTCTG
5727815 AT
1 AT
5727817 GGGTACCCCC
Statistics
Matches: 374, Mismatches: 35, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
408 106 0.28
409 268 0.72
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (408 bp):
ATAAAAAATACATTTTTTATCACCTTGTGGGTTTTCCTATAAGAACAAGTCTTTCATCTTTGACA
CATATGATTAAGTTAGCATAATATAAGCACTATAAGCCCAAAGATAATGCCCAAAACTACTAACT
CAATTTTTGGGGCGTTACAACTCTCCCCTCCTAAAAAGAATTTCATCCTTGAAATTTGACTGATC
CGAACAAGTACAGGTACAATAGTTGCATGGCTTCCTCAATTTCCAACATTGTTTCATCCACTATG
TGATTCCTCCATAGGACCTTAACTACCGAAATCGTCTTGTTTCATAATTCCTTGACCTATCAGAC
CAAAATATTTAATGGTTCCTCAATATATGACATGTCTAGGTGAACTTCGATTCGCTCCAACAGAA
CCACATGCGACAAGTCTG
Found at i:5731231 original size:22 final size:22
Alignment explanation
Indices: 5731205--5731280 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
5731195 CTAATCAAGG
* *
5731205 AAGTGTCTTAGCACTAATACTA
1 AAGTGCCTTAGCACTAATACAA
* * *
5731227 AAGTGCCTCAACACTTATACAA
1 AAGTGCCTTAGCACTAATACAA
* * *
5731249 AAGTGCATTTGCACTGATACAA
1 AAGTGCCTTAGCACTAATACAA
5731271 AAGTGCCTTA
1 AAGTGCCTTA
5731281 TCATTAGGGG
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (22 bp):
AAGTGCCTTAGCACTAATACAA
Found at i:5735858 original size:23 final size:23
Alignment explanation
Indices: 5735798--5735861 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
5735788 CAGCTCATAT
* * *
5735798 AATTGCACCGAAGTGCCACGTAT
1 AATTACACCGAAGTTCCACGTAG
* *
5735821 AATTCCACCGGAGTTCCACGTAG
1 AATTACACCGAAGTTCCACGTAG
*
5735844 AATTACACCGTAGTTCCA
1 AATTACACCGAAGTTCCA
5735862 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (23 bp):
AATTACACCGAAGTTCCACGTAG
Found at i:5736043 original size:105 final size:104
Alignment explanation
Indices: 5735861--5736092 Score: 389
Period size: 105 Copynumber: 2.2 Consensus size: 104
5735851 CCGTAGTTCC
** * *
5735861 ATATA-ATA-ATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGAT
1 ATATATATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGAT
5735924 CAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAG
66 CAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAG
*
5735963 AATATATATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGA
1 -ATATATATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGA
5736028 TCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAG
65 TCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAG
5736068 A-ATATATATATGTCCCGAAGGACCA
1 ATATATATATATGTCCCGAAGGACCA
5736093 TATAGACCCT
Statistics
Matches: 122, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
103 29 0.24
104 4 0.03
105 89 0.73
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (104 bp):
ATATATATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGAT
CAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAG
Found at i:5747454 original size:13 final size:13
Alignment explanation
Indices: 5747436--5747477 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
5747426 TGGGTTGAGC
*
5747436 TTAATATATGTAT
1 TTAATATATATAT
5747449 TTAATATATATAT
1 TTAATATATATAT
*
5747462 ATAATATATAATAT
1 TTAATATAT-ATAT
5747476 TT
1 TT
5747478 GGTAATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TTAATATATATAT
Found at i:5750261 original size:20 final size:20
Alignment explanation
Indices: 5750236--5750325 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
5750226 CAATCAGTTG
* *
5750236 GGGTATCGATGCCTTAGGT-A
1 GGGTATCGATG-CTGAAGTAA
*
5750256 GGGTATCAATGCTGAAGTAA
1 GGGTATCGATGCTGAAGTAA
*
5750276 GGGTATCGATACT-AA--AA
1 GGGTATCGATGCTGAAGTAA
* *
5750293 GGGTAATATCGATACTGAAGCAA
1 GGG---TATCGATGCTGAAGTAA
5750316 GGGTATCGAT
1 GGGTATCGAT
5750326 ACTACAAGGG
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
17 5 0.09
19 7 0.12
20 39 0.67
21 2 0.03
23 5 0.09
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (20 bp):
GGGTATCGATGCTGAAGTAA
Found at i:5750311 original size:40 final size:40
Alignment explanation
Indices: 5750267--5750353 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
5750257 GGTATCAATG
5750267 CTGAAGTAAGGGTATCGATACTAAAAGGGTAATATCGATA
1 CTGAAGTAAGGGTATCGATACTAAAAGGGTAATATCGATA
* * *
5750307 CTGAAGCAAGGGTATCGATACTACAAGGGTAATATTGATA
1 CTGAAGTAAGGGTATCGATACTAAAAGGGTAATATCGATA
*
5750347 CTAAAGT
1 CTGAAGT
5750354 GATGTTTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.25
Consensus pattern (40 bp):
CTGAAGTAAGGGTATCGATACTAAAAGGGTAATATCGATA
Found at i:5750326 original size:20 final size:19
Alignment explanation
Indices: 5750255--5750328 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 19
5750245 TGCCTTAGGT
* *
5750255 AGGGTATCAATGCTGAAGTA
1 AGGGTATCGATACTGAAG-A
5750275 AGGGTATCGATACT-AA-A
1 AGGGTATCGATACTGAAGA
5750292 AGGGTAATATCGATACTGAAGCA
1 AGGG---TATCGATACTGAAG-A
5750315 AGGGTATCGATACT
1 AGGGTATCGATACT
5750329 ACAAGGGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
17 5 0.11
19 2 0.04
20 32 0.70
21 2 0.04
23 5 0.11
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (19 bp):
AGGGTATCGATACTGAAGA
Found at i:5750346 original size:20 final size:20
Alignment explanation
Indices: 5750279--5750349 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
5750269 GAAGTAAGGG
*
5750279 TATCGATACTAAAAGGGTAA
1 TATCGATACTACAAGGGTAA
5750299 TATCGATACTGAAGCAAGGG---
1 TATCGATACT--A-CAAGGGTAA
5750319 TATCGATACTACAAGGGTAA
1 TATCGATACTACAAGGGTAA
*
5750339 TATTGATACTA
1 TATCGATACTA
5750350 AAGTGATGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
17 6 0.14
18 1 0.02
20 30 0.70
22 1 0.02
23 5 0.12
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (20 bp):
TATCGATACTACAAGGGTAA
Found at i:5760523 original size:21 final size:21
Alignment explanation
Indices: 5760453--5760544 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
5760443 AATATATCGG
* * * *
5760453 ATCCTAAATGATGGGAGGTGG
1 ATCCTGAACGATGAGAGGTGA
* * *
5760474 ATCCTGAACGATGGGAGGGGC
1 ATCCTGAACGATGAGAGGTGA
* *
5760495 CTCTTGAACGATGAGAGGTGA
1 ATCCTGAACGATGAGAGGTGA
5760516 ATCCTGAA-GAATGAGAGGTGA
1 ATCCTGAACG-ATGAGAGGTGA
*
5760537 ACCCTGAA
1 ATCCTGAA
5760545 TAAAGGTTGG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 1 0.02
21 57 0.98
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (21 bp):
ATCCTGAACGATGAGAGGTGA
Found at i:5760945 original size:21 final size:21
Alignment explanation
Indices: 5760895--5761054 Score: 166
Period size: 21 Copynumber: 7.7 Consensus size: 21
5760885 TGAAACAATC
* *
5760895 TCACGTAGAGCACCTACT-TCA
1 TCACGTAAAGCACC-ATTGTCA
5760916 TCA-GTAAAGCACCATTGTCA
1 TCACGTAAAGCACCATTGTCA
* ***
5760936 TCATGTAAAGCACCAACCTCA
1 TCACGTAAAGCACCATTGTCA
5760957 TCACGTAAAGCACCATTGTCA
1 TCACGTAAAGCACCATTGTCA
5760978 TCACGTAAAGCACCATTGTCA
1 TCACGTAAAGCACCATTGTCA
**
5760999 TCACGTAAAGCACCGA-CCTCA
1 TCACGTAAAGCACC-ATTGTCA
* **
5761020 TCACATAAAGCACC-TACCTCA
1 TCACGTAAAGCACCAT-TGTCA
5761041 TCACGTAAAGCACC
1 TCACGTAAAGCACC
5761055 TAACTCATCC
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
19 2 0.02
20 15 0.12
21 103 0.85
22 1 0.01
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGCACCATTGTCA
Found at i:5760972 original size:42 final size:42
Alignment explanation
Indices: 5760895--5761054 Score: 198
Period size: 42 Copynumber: 3.8 Consensus size: 42
5760885 TGAAACAATC
* * *
5760895 TCACGTAGAGCACCTACTTCATCA-GTAAAGCACCATTGTCA
1 TCACGTAAAGCACCAACCTCATCACGTAAAGCACCATTGTCA
*
5760936 TCATGTAAAGCACCAACCTCATCACGTAAAGCACCATTGTCA
1 TCACGTAAAGCACCAACCTCATCACGTAAAGCACCATTGTCA
*** **
5760978 TCACGTAAAGCACCATTGTCATCACGTAAAGCACCGA-CCTCA
1 TCACGTAAAGCACCAACCTCATCACGTAAAGCACC-ATTGTCA
* *
5761020 TCACATAAAGCACCTACCTCATCACGTAAAGCACC
1 TCACGTAAAGCACCAACCTCATCACGTAAAGCACC
5761055 TAACTCATCC
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
41 20 0.20
42 81 0.79
43 1 0.01
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (42 bp):
TCACGTAAAGCACCAACCTCATCACGTAAAGCACCATTGTCA
Found at i:5761063 original size:63 final size:63
Alignment explanation
Indices: 5760903--5761054 Score: 227
Period size: 63 Copynumber: 2.4 Consensus size: 63
5760893 TCTCACGTAG
* * *
5760903 AGCACCTACTTCATCA-GTAAAGCACCATTGTCATCATGTAAAGCACCAACCTCATCACGTAA
1 AGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCAACCTCATCACATAA
** *
5760965 AGCACC-ATTGTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCGACCTCATCACATAA
1 AGCACCTA-CCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCAACCTCATCACATAA
5761028 AGCACCTACCTCATCACGTAAAGCACC
1 AGCACCTACCTCATCACGTAAAGCACC
5761055 TAACTCATCC
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.01
62 12 0.15
63 66 0.82
64 1 0.01
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (63 bp):
AGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCAACCTCATCACATAA
Found at i:5761227 original size:21 final size:21
Alignment explanation
Indices: 5761201--5761265 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
5761191 GAGTCAACTA
5761201 GAGGTGATGGATCTCGGTGTC
1 GAGGTGATGGATCTCGGTGTC
* *
5761222 GAGGTG-TAGA-ATCGG-GTC
1 GAGGTGATGGATCTCGGTGTC
5761240 GATGAGGTGATGGATCTCGGTGTC
1 ---GAGGTGATGGATCTCGGTGTC
5761264 GA
1 GA
5761266 AGTGGAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 3 0.09
21 14 0.41
22 3 0.09
23 4 0.12
24 3 0.09
ACGTcount: A:0.18, C:0.12, G:0.43, T:0.26
Consensus pattern (21 bp):
GAGGTGATGGATCTCGGTGTC
Found at i:5761260 original size:42 final size:42
Alignment explanation
Indices: 5761166--5761370 Score: 299
Period size: 42 Copynumber: 5.0 Consensus size: 42
5761156 ATGAAATAGA
* * *
5761166 TGATGGATCTCGGTGTCGAGGTGTAGAGTCAACT--A-GAGG
1 TGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAGG
* **
5761205 TGATGGATCTCGGTGTCGAGGTGTAGAATCGGGTCGATGAGG
1 TGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAGG
*
5761247 TGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATGAGG
1 TGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAGG
*
5761289 TGATGGATCACGGTGTCGAAGTGTAGAATCGACTCGATGAGG
1 TGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAGG
* *
5761331 TGATGGATCTCGGTGTCAAAGTGGAGAATCGACTCGATGA
1 TGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGA
5761371 AAAAGTGGGG
Statistics
Matches: 150, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 30 0.20
41 1 0.01
42 119 0.79
ACGTcount: A:0.24, C:0.14, G:0.38, T:0.25
Consensus pattern (42 bp):
TGATGGATCTCGGTGTCGAAGTGTAGAATCGACTCGATGAGG
Found at i:5763799 original size:20 final size:19
Alignment explanation
Indices: 5763736--5763803 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
5763726 AAACATTTGT
* *
5763736 GTTGCGAAATTAAAAGCTGA
1 GTTGCGAATTTAAAATC-GA
* * *
5763756 GTTGCAAAATTTAAATTCGC
1 GTTGC-GAATTTAAAATCGA
5763776 GTTGCGAATTTAAAAATCGA
1 GTTGCGAATTT-AAAATCGA
5763796 GTTGCGAA
1 GTTGCGAA
5763804 AAAGAAATTC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.13
20 25 0.66
21 8 0.21
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
GTTGCGAATTTAAAATCGA
Found at i:5763901 original size:20 final size:19
Alignment explanation
Indices: 5763854--5763905 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
5763844 GATTCGACTT
5763854 CTGTGTTGCGAATTCCAAA
1 CTGTGTTGCGAATTCCAAA
* * *
5763873 TTGGAGTTGCGAATTCGGAAA
1 CT-GTGTTGCGAATTC-CAAA
5763894 CTGTGTTGCGAA
1 CTGTGTTGCGAA
5763906 ATTGGCTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 21 0.81
21 4 0.15
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (19 bp):
CTGTGTTGCGAATTCCAAA
Found at i:5764668 original size:17 final size:15
Alignment explanation
Indices: 5764635--5764672 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5764625 TTTTATATAA
5764635 ATATTATTTCAAGAT
1 ATATTATTTCAAGAT
5764650 ATATTATATTCAA-AT
1 ATATTAT-TTCAAGAT
5764665 ATA-TATTT
1 ATATTATTT
5764673 ACATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 3 0.14
15 12 0.55
16 5 0.23
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATTATTTCAAGAT
Found at i:5766519 original size:23 final size:24
Alignment explanation
Indices: 5766490--5766553 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
5766480 CACATAATTA
5766490 TCCCGAAGGACCACATAGG-TTTG
1 TCCCGAAGGACCACATAGGTTTTG
*
5766513 TCCCGAAGGACCACACAGGTTTTG
1 TCCCGAAGGACCACATAGGTTTTG
* * *
5766537 TACCGATGTACCACATA
1 TCCCGAAGGACCACATA
5766554 AAACCGTCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (24 bp):
TCCCGAAGGACCACATAGGTTTTG
Found at i:5776361 original size:556 final size:543
Alignment explanation
Indices: 5775300--5776395 Score: 1845
Period size: 556 Copynumber: 2.0 Consensus size: 543
5775290 TTAATTAATG
5775300 TCACCAGGATGTTCACAAAACTCCCCCCAACCTCGTTGTGTAACCGTTTGAGAAATATAATTGAA
1 TCACCAGGATGTTCACAAAACTCCCCCCAACCTCGTTGTGTAACCGTTTGAGAAATATAATTGAA
*
5775365 TATTTGAGGATCCTCTTCCATAGTTAAATCAAAACCCTACTCATAACAAAAATCTCAGCCATCAA
66 GATTTGAGGATCCTCTTCCATAGTTAAATCAAAACCCTACTCATAACAAAAATCTCAGCCATCAA
* * *
5775430 ATTCCTCTTCACAACGCCGTCATAAATCTGGTGACTTCCTCCGTCGGATAAACTTTTTGTGGCGT
131 ATTCCTCTTCACAACGCCGTCATAAATCTGGTGACTTCCTCCGACAGAGAAACTTTTTGTGGCGT
*
5775495 AGATATAGTAGGAGGCAGTGTAGGCGTATGGTCAAATGACTTTGTGCTTGCCTTATTTTTGTGTG
196 AGATATAGTAGGAGGCAGTGTAGGCGTACGGTCAAATGACTTTGTGCTTGCCTTATTTTTGTGTG
* * *
5775560 CCATGGTGGTTTGTAAATAGATGAGAAAAATAAAGGAGAGGGTAACAAGGGTTTTAGACTCATTA
261 CCACGGTGGTTAGTAAATAGATGAGAAAAATAAAGGAGAGGGTAACAAGGGTTTTAGACTCATGA
*
5775625 AGAAGAATAAGGTAAAGTAAATAGGAGTAAATGGCTTGTGTGAAATAGGGGATAATATTTTTAAA
326 AGAAGAATAAGGTAAAGTAAACAGGAGTAAATGGCTTGTGTGAAATAGGGGATAATATTTTTAAA
* * *
5775690 ATTTAAAACTCAAGGGTGGAGGGATAAGGGTTGATTTTAAATGGACGGTTATGATTGGGTAAGGT
391 ATTTAAAACTCAAGGGGGGAGGGATAAGGGTTGATTTTAAATGGACGATTATGATTGAGTAAGGT
* * *
5775755 GGTCGGTGAAAATACAAGGGGAGTAATTTGTGGATAGCTCATACTGAGTTATAATGTAAAAAATA
456 GGTCGGTGAAAATACAAGGGGAGTAAATTATGGACAGCTCATACTGAGTTATAATGTAAAAAATA
5775820 TTTGGTTATCCTTGTATTGAATA
521 TTTGGTTATCCTTGTATTGAATA
*
5775843 TCACCCGGATGTTCACAAAACT-CCCCCAACCTCGTTGTGTAACCGTTTGAGAAATATAATTGAA
1 TCACCAGGATGTTCACAAAACTCCCCCCAACCTCGTTGTGTAACCGTTTGAGAAATATAATTGAA
* *
5775907 GATTTGAGGATCCTCTTCCATAGTTAAATCAAAACCCTACTCATAACAAAAATCTTAGCTATCAA
66 GATTTGAGGATCCTCTTCCATAGTTAAATCAAAACCCTACTCATAACAAAAATCTCAGCCATCAA
*
5775972 ATTCCTCTTTACAACGCCGTTGTTGTTCGTCATCCATAAATCTGGTGACTTCCTCCGACAGAGAA
131 ATTCCTCTTCACAACG-C---------CG---T-CATAAATCTGGTGACTTCCTCCGACAGAGAA
*
5776037 ACTTTTTGTGGCGTAGATATAGTAGGAGGCGGTGTAGGCGTACGGTCAAATGACTTTGTGCTTGC
182 ACTTTTTGTGGCGTAGATATAGTAGGAGGCAGTGTAGGCGTACGGTCAAATGACTTTGTGCTTGC
*
5776102 CTTATTTTTGTGTGCCACGGTGGTTAGTAAATAGATGAGAAAAATAAAGTAGAGGGTAACAAGGG
247 CTTATTTTTGTGTGCCACGGTGGTTAGTAAATAGATGAGAAAAATAAAGGAGAGGGTAACAAGGG
*
5776167 TTTTAGACTCATGAAGTAGAATAAGGTAAAGTAAACAGGAGTAAATGGCTTGTGTGAAATAGGGG
312 TTTTAGACTCATGAAGAAGAATAAGGTAAAGTAAACAGGAGTAAATGGCTTGTGTGAAATAGGGG
5776232 ATAATATTTTTAAAATTTAAAACTCAAGGGGGGAGGGATAAGGGTTGATTTTAAATGGGA-GATT
377 ATAATATTTTTAAAATTTAAAACTCAAGGGGGGAGGGATAAGGGTTGATTTTAAAT-GGACGATT
5776296 ATGATTGAGTAAGGTGGTCGGTGAAAATACAAGGGGAGTAAATTATGGACAGCTCATACTGAGTT
441 ATGATTGAGTAAGGTGGTCGGTGAAAATACAAGGGGAGTAAATTATGGACAGCTCATACTGAGTT
5776361 ATAATGTAAAAAATATTTGGTTATCCTTGTATTGA
506 ATAATGTAAAAAATATTTGGTTATCCTTGTATTGA
5776396 TGTGGCTCTA
Statistics
Matches: 516, Mismatches: 22, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
542 119 0.23
543 22 0.04
552 2 0.00
555 1 0.00
556 369 0.72
557 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (543 bp):
TCACCAGGATGTTCACAAAACTCCCCCCAACCTCGTTGTGTAACCGTTTGAGAAATATAATTGAA
GATTTGAGGATCCTCTTCCATAGTTAAATCAAAACCCTACTCATAACAAAAATCTCAGCCATCAA
ATTCCTCTTCACAACGCCGTCATAAATCTGGTGACTTCCTCCGACAGAGAAACTTTTTGTGGCGT
AGATATAGTAGGAGGCAGTGTAGGCGTACGGTCAAATGACTTTGTGCTTGCCTTATTTTTGTGTG
CCACGGTGGTTAGTAAATAGATGAGAAAAATAAAGGAGAGGGTAACAAGGGTTTTAGACTCATGA
AGAAGAATAAGGTAAAGTAAACAGGAGTAAATGGCTTGTGTGAAATAGGGGATAATATTTTTAAA
ATTTAAAACTCAAGGGGGGAGGGATAAGGGTTGATTTTAAATGGACGATTATGATTGAGTAAGGT
GGTCGGTGAAAATACAAGGGGAGTAAATTATGGACAGCTCATACTGAGTTATAATGTAAAAAATA
TTTGGTTATCCTTGTATTGAATA
Found at i:5792883 original size:100 final size:98
Alignment explanation
Indices: 5792765--5792959 Score: 336
Period size: 100 Copynumber: 2.0 Consensus size: 98
5792755 AGATTCTACT
5792765 ATATCGACTGTCTCAAGCTTTCATCTATTCATTCTTTTCTTTTGTTTGTCACAACAGTCATAGAA
1 ATATCGACTGTCTCAAGCTTTCATCTATTCATTCTTTTCTTTTGTTTGTCACAAC--TCATAGAA
*
5792830 CGCTTTCGATGCTCCATCATCTTCTCAAAAGCACC
64 CACTTTCGATGCTCCATCATCTTCTCAAAAGCACC
* * *
5792865 ATATCGTCTGTCTCAAGCTTTCATCTATTTATTCTTTTCTTTTTTTTGTCACAACTCATAGAACA
1 ATATCGACTGTCTCAAGCTTTCATCTATTCATTCTTTTCTTTTGTTTGTCACAACTCATAGAACA
5792930 CTTTCGATGCTCCATCATCTTCTCAAAAGC
66 CTTTCGATGCTCCATCATCTTCTCAAAAGC
5792960 CAAGGCAAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 39 0.43
100 52 0.57
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.41
Consensus pattern (98 bp):
ATATCGACTGTCTCAAGCTTTCATCTATTCATTCTTTTCTTTTGTTTGTCACAACTCATAGAACA
CTTTCGATGCTCCATCATCTTCTCAAAAGCACC
Found at i:5818096 original size:19 final size:17
Alignment explanation
Indices: 5818055--5818087 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5818045 AAAATCATGA
5818055 TAATCAATATAAATCAG
1 TAATCAATATAAATCAG
*
5818072 TAATCAATATCAATCA
1 TAATCAATATAAATCA
5818088 TAGTAATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (17 bp):
TAATCAATATAAATCAG
Found at i:5819528 original size:33 final size:31
Alignment explanation
Indices: 5819462--5819532 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
5819452 ATTAATTCAA
* * *
5819462 CCTAACATCAAATTCATTGAATTCCAATCAT
1 CCTAACATCAAATTAATTAAATTCCAATAAT
5819493 CCTAACATCAAATTAAATTTAAATT-CAATAAAT
1 CCTAACATCAAATT-AA-TTAAATTCCAAT-AAT
5819526 CCTAACA
1 CCTAACA
5819533 ATACCCTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 14 0.41
32 5 0.15
33 15 0.44
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (31 bp):
CCTAACATCAAATTAATTAAATTCCAATAAT
Found at i:5820404 original size:30 final size:30
Alignment explanation
Indices: 5820368--5820458 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
5820358 CAAAATATAT
* * *
5820368 AACTTTTAAAAATTATATTTTTTGTCTCTA
1 AACTTTTAAAAATTATATTTTTAGCCACTA
* *
5820398 AACTTTTACAAAGTT-TATACTTTAGCCACTA
1 AACTTTTA-AAAATTATAT-TTTTAGCCACTA
* * *
5820429 AACTTTCAAAACTTATA-TTTTAGTCACTA
1 AACTTTTAAAAATTATATTTTTAGCCACTA
5820458 A
1 A
5820459 CCCAAATTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
29 11 0.22
30 16 0.33
31 22 0.45
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.44
Consensus pattern (30 bp):
AACTTTTAAAAATTATATTTTTAGCCACTA
Found at i:5823182 original size:5 final size:5
Alignment explanation
Indices: 5823172--5823238 Score: 88
Period size: 5 Copynumber: 13.8 Consensus size: 5
5823162 ATGAAAATAA
5823172 GAAAT GAAAT GAAA- GAAAT GAAAT GAAAT GATAA- GAAAT GAAA- GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GA-AAT GAAAT GAAAT GAAAT
5823220 GAAAT GATAA- GAAAT GAAA
1 GAAAT GA-AAT GAAAT GAAA
5823239 GGGATAGAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
4 12 0.21
5 40 0.71
6 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (5 bp):
GAAAT
Found at i:5823191 original size:9 final size:9
Alignment explanation
Indices: 5823147--5823223 Score: 79
Period size: 9 Copynumber: 8.4 Consensus size: 9
5823137 ACAATATAAA
5823147 GAAAGAAAT
1 GAAAGAAAT
**
5823156 G-ATTAAAT
1 GAAAGAAAT
5823164 GAAA-ATAA-
1 GAAAGA-AAT
5823172 GAAATGAAAT
1 GAAA-GAAAT
5823182 GAAAGAAAT
1 GAAAGAAAT
5823191 GAAATGAAAT
1 GAAA-GAAAT
5823201 GATAAGAAAT
1 GA-AAGAAAT
5823211 GAAAGAAAT
1 GAAAGAAAT
5823220 GAAA
1 GAAA
5823224 TGATAAGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
8 11 0.19
9 26 0.45
10 19 0.33
11 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (9 bp):
GAAAGAAAT
Found at i:5823209 original size:24 final size:24
Alignment explanation
Indices: 5823144--5823239 Score: 107
Period size: 24 Copynumber: 4.2 Consensus size: 24
5823134 TACACAATAT
*
5823144 AAAGAAA-GAAATGAT--TAAATG
1 AAAGAAATGAAATGATAAGAAATG
5823165 AAA-ATAA-GAAATGA-AATGAAA-G
1 AAAGA-AATGAAATGATAA-GAAATG
5823187 AAATGAAATGAAATGATAAGAAATG
1 AAA-GAAATGAAATGATAAGAAATG
5823212 AAAGAAATGAAATGATAAGAAATG
1 AAAGAAATGAAATGATAAGAAATG
5823236 AAAG
1 AAAG
5823240 GGATAGAATT
Statistics
Matches: 65, Mismatches: 1, Indels: 15
0.80 0.01 0.19
Matches are distributed among these distances:
20 1 0.02
21 12 0.18
22 4 0.06
23 5 0.08
24 37 0.57
25 6 0.09
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.17
Consensus pattern (24 bp):
AAAGAAATGAAATGATAAGAAATG
Found at i:5823211 original size:34 final size:34
Alignment explanation
Indices: 5823147--5823236 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 34
5823137 ACAATATAAA
*
5823147 GAAAGAAATG--ATTAAATGAAA--ATAAGAAAT
1 GAAAGAAATGAAATGAAATGAAATGATAAGAAAT
5823177 GAAATGAAA-GAAATGAAATGAAATGATAAGAAAT
1 GAAA-GAAATGAAATGAAATGAAATGATAAGAAAT
5823211 GAAAGAAATGAAATGATAA-GAAATGA
1 GAAAGAAATGAAATGA-AATGAAATGA
5823237 AAGGGATAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
30 5 0.10
31 4 0.08
32 10 0.19
33 4 0.08
34 27 0.52
35 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (34 bp):
GAAAGAAATGAAATGAAATGAAATGATAAGAAAT
Found at i:5823247 original size:15 final size:15
Alignment explanation
Indices: 5823160--5823240 Score: 66
Period size: 14 Copynumber: 5.7 Consensus size: 15
5823150 AGAAATGATT
5823160 AAATGAAA--ATAAG
1 AAATGAAAGGATAAG
*
5823173 AAATGAAATGA-AAG
1 AAATGAAAGGATAAG
*
5823187 AAATGAAATGA-AATG
1 AAATGAAAGGATAA-G
*
5823202 ATAA-GAAATGA-AAG
1 A-AATGAAAGGATAAG
*
5823216 AAATGAAATGATAAG
1 AAATGAAAGGATAAG
5823231 AAATGAAAGG
1 AAATGAAAGG
5823241 GATAGAATTG
Statistics
Matches: 61, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
13 10 0.16
14 25 0.41
15 24 0.39
16 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (15 bp):
AAATGAAAGGATAAG
Found at i:5825280 original size:165 final size:165
Alignment explanation
Indices: 5825008--5825337 Score: 660
Period size: 165 Copynumber: 2.0 Consensus size: 165
5824998 GATTTTCAAA
5825008 GGTCACATCTTCTAAACCTTTATTTTGACAAATGGTGTCTCTTGGTACATCCTACAAGTCAAAGA
1 GGTCACATCTTCTAAACCTTTATTTTGACAAATGGTGTCTCTTGGTACATCCTACAAGTCAAAGA
5825073 AAAAATCTACATTTTCAAAGTTAGAATAATCATCTTTAACTTTGCGTTTTGTTAGTAGGCATTCT
66 AAAAATCTACATTTTCAAAGTTAGAATAATCATCTTTAACTTTGCGTTTTGTTAGTAGGCATTCT
5825138 CGTTTCAAGCACTTTGAATAATAAACACTTGTCTT
131 CGTTTCAAGCACTTTGAATAATAAACACTTGTCTT
5825173 GGTCACATCTTCTAAACCTTTATTTTGACAAATGGTGTCTCTTGGTACATCCTACAAGTCAAAGA
1 GGTCACATCTTCTAAACCTTTATTTTGACAAATGGTGTCTCTTGGTACATCCTACAAGTCAAAGA
5825238 AAAAATCTACATTTTCAAAGTTAGAATAATCATCTTTAACTTTGCGTTTTGTTAGTAGGCATTCT
66 AAAAATCTACATTTTCAAAGTTAGAATAATCATCTTTAACTTTGCGTTTTGTTAGTAGGCATTCT
5825303 CGTTTCAAGCACTTTGAATAATAAACACTTGTCTT
131 CGTTTCAAGCACTTTGAATAATAAACACTTGTCTT
5825338 TAGATCAGTT
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 165 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (165 bp):
GGTCACATCTTCTAAACCTTTATTTTGACAAATGGTGTCTCTTGGTACATCCTACAAGTCAAAGA
AAAAATCTACATTTTCAAAGTTAGAATAATCATCTTTAACTTTGCGTTTTGTTAGTAGGCATTCT
CGTTTCAAGCACTTTGAATAATAAACACTTGTCTT
Found at i:5827479 original size:24 final size:24
Alignment explanation
Indices: 5827447--5827500 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
5827437 TTTGAGTGTA
5827447 TTTTGCAACTTTGCTTCACTTTTC
1 TTTTGCAACTTTGCTTCACTTTTC
5827471 TTTTGCAACTTTGCTTCACTTTTC
1 TTTTGCAACTTTGCTTCACTTTTC
5827495 TTTTGC
1 TTTTGC
5827501 TTAGAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.11, C:0.24, G:0.09, T:0.56
Consensus pattern (24 bp):
TTTTGCAACTTTGCTTCACTTTTC
Found at i:5827568 original size:8 final size:8
Alignment explanation
Indices: 5827555--5827579 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5827545 AAGAGTCTTT
5827555 TCTTTTTC
1 TCTTTTTC
5827563 TCTTTTTC
1 TCTTTTTC
5827571 TCTTTTTC
1 TCTTTTTC
5827579 T
1 T
5827580 TCTCTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TCTTTTTC
Found at i:5827574 original size:21 final size:22
Alignment explanation
Indices: 5827552--5827593 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5827542 TGTAAGAGTC
*
5827552 TTTTCTTTTTCTCTT-TTTCTCT
1 TTTTC-TTCTCTCTTCTTTCTCT
5827574 TTTTCTTCTCTCTTCTTTCT
1 TTTTCTTCTCTCTTCTTTCT
5827594 TTTGTTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTCTTCTCTCTTCTTTCTCT
Found at i:5827813 original size:15 final size:14
Alignment explanation
Indices: 5827787--5827818 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5827777 TGGAAATAAT
5827787 AAATGAAAGAAATG
1 AAATGAAAGAAATG
5827801 AAATGATAAGAAATG
1 AAATGA-AAGAAATG
5827816 AAA
1 AAA
5827819 GGGATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.16
Consensus pattern (14 bp):
AAATGAAAGAAATG
Found at i:5831428 original size:49 final size:49
Alignment explanation
Indices: 5831374--5831710 Score: 436
Period size: 49 Copynumber: 7.0 Consensus size: 49
5831364 AAAATGAATG
* *
5831374 AATGAAAGTTAAATACATAACGGTGCATTT-AGGCATAAAAAGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCA-GCATAAAAGGTGCCACT
* * **
5831423 AATGAAAGTTAAATGTATAACGGTGTATTTTGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
* * **
5831472 AATGAAAGTTAAATGCATAATGATGCATTTTGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
* * *
5831521 AATGAAAGTTAAATGCACAACGGTGTATTTCAGTATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
* * * *
5831570 AATGAATGTTATATGCATAACGGTGTATTTCAGCATAAAAGGTTCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
**
5831619 AAT----G--AAATGCATAACAATGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
*
5831662 AATGAAAGTTAAATGCATAACGATGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
5831711 CATGGTATTC
Statistics
Matches: 254, Mismatches: 27, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
43 37 0.15
45 1 0.00
47 1 0.00
49 215 0.85
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (49 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
Found at i:5837941 original size:2 final size:2
Alignment explanation
Indices: 5837869--5837924 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
5837859 TTTTAAGAAA
5837869 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5837909 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5837925 TTTTATAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5839636 original size:13 final size:14
Alignment explanation
Indices: 5839602--5839639 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5839592 TTTGGGTTAG
5839602 TCTGTTTGGGCCAA
1 TCTGTTTGGGCCAA
*
5839616 TATG-TTGGGCC-A
1 TCTGTTTGGGCCAA
5839628 TCTGTTTGGGCC
1 TCTGTTTGGGCC
5839640 TAAAATGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 4 0.19
13 14 0.67
14 3 0.14
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.37
Consensus pattern (14 bp):
TCTGTTTGGGCCAA
Found at i:5839655 original size:3 final size:3
Alignment explanation
Indices: 5839647--5839722 Score: 64
Period size: 3 Copynumber: 25.0 Consensus size: 3
5839637 GCCTAAAATG
* ** * *
5839647 TAA TAA TAA TAA TAT TTT TTA TTAA TAA AAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA
* *
5839694 TAA T-A TAA TAA TAA CAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5839723 ATAGCAAATG
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 53 0.88
4 5 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5839689 original size:15 final size:16
Alignment explanation
Indices: 5839669--5839725 Score: 77
Period size: 15 Copynumber: 3.8 Consensus size: 16
5839659 TATTTTTTAT
5839669 TAATAA-AAATAATAA
1 TAATAATAAATAATAA
5839684 TAATAATAAATAAT-A
1 TAATAATAAATAATAA
5839699 TAATAATAACAT--TAA
1 TAATAATAA-ATAATAA
5839714 TAATAATAAATA
1 TAATAATAAATA
5839726 GCAAATGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.08
15 26 0.68
16 9 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAATAAATAATAA
Found at i:5840364 original size:124 final size:123
Alignment explanation
Indices: 5840101--5840653 Score: 616
Period size: 124 Copynumber: 4.6 Consensus size: 123
5840091 GAATTATGGC
* * *
5840101 AAGGTTGAACAAATTATTATCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * * ** **
5840165 TGAACTCTTTTGAAAATGTTGATGTTGATCTATTTTCTTCTATGATAGAATTAAGCAA
66 TGAACTCTTCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAATCGAGCAA
* *
5840223 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTCATATGAGTTCTTCT-ACTT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TT
* *
5840287 ATGAACTCCTTCTGGAAATGTTGGTGCTGATTTATCTCCTTCTGGGATAGAATCGAGTAA
65 ATGAACT-CTTCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAATCGAGCAA
* * * * * * *
5840347 AAGGTTAAACCAGTTCTTCTCTTTATGAACTTCTTCTTCC-TCTTCAGATGTGTTCATCCCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * ** ** *
5840411 TGAACACTTATGGAAATGTTGAT-C--------CAGC--GAGTGAT-GAATTCGAGCAA
66 TGAACTCTTCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAA-TCGAGCAA
* * *
5840458 AAGGTTGAATAAATTCTTCTCATTATAAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
5840523 TGAACTCTACCTGGCAATGTTGATGCTGATTTATCTTCTTCTGGGATAGAATCGAGCAA
66 TGAACTCT-TCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAATCGAGCAA
*
5840582 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
5840646 TGAACTCT
66 TGAACTCT
5840654 ACCTGACAAT
Statistics
Matches: 354, Mismatches: 58, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
110 3 0.01
111 44 0.12
112 28 0.08
113 14 0.04
114 1 0.00
121 1 0.00
122 51 0.14
123 84 0.24
124 125 0.35
125 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAATCGAGCAA
Found at i:5840552 original size:235 final size:235
Alignment explanation
Indices: 5840218--5840650 Score: 690
Period size: 235 Copynumber: 1.8 Consensus size: 235
5840208 GATAGAATTA
* *
5840218 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTCATATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTCTTCCTTATTCAGATGAGTTCTTCT
* * *
5840283 ACTTATGAACTCCTTCTGGAAATGTTGGTGCTGATTTATCTCCTTCTGGGATAGAATCGAGTAAA
66 ACTTATGAACTCCTCCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAATCGAGCAAA
* * *
5840348 AGGTTAAACCAGTTCTTCTCTTTATGAACTTCTTCTTCCTCTTCAGATGTGTTCATCCCATTATG
131 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCATCCCATTATG
5840413 AACACTTATGGAAATGTTGATCCAGCGAGTGATGAATTCG
196 AACACTTATGGAAATGTTGATCCAGCGAGTGATGAATTCG
* * *
5840453 AGCAAAAGGTTGAATAAATTCTTCTCATTATAAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTCTTCCTTATTCAGATGAGTTCTTCT
* *
5840518 -CATTATGAACT-CTACCTGGCAATGTTGATGCTGATTTATCTTCTTCTGGGATAGAATCGAGCA
66 AC-TTATGAACTCCT-CCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAATCGAGCA
* * *
5840581 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
129 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCATCCCATTA
5840646 TGAAC
194 TGAAC
5840651 TCTACCTGAC
Statistics
Matches: 180, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
234 3 0.02
235 177 0.98
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (235 bp):
AGCAAAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTCTTCCTTATTCAGATGAGTTCTTCT
ACTTATGAACTCCTCCTGGAAATGTTGATGCTGATTTATCTCCTTCTGGGATAGAATCGAGCAAA
AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCATCCCATTATG
AACACTTATGGAAATGTTGATCCAGCGAGTGATGAATTCG
Found at i:5841077 original size:21 final size:22
Alignment explanation
Indices: 5841036--5841092 Score: 98
Period size: 21 Copynumber: 2.6 Consensus size: 22
5841026 AATAAAACTT
*
5841036 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
5841058 TCATCTTTGAAGAG-GAATCTA
1 TCATCTTTGAAGAGAGAATCTA
5841079 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
5841093 TGTAGATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:5841740 original size:18 final size:18
Alignment explanation
Indices: 5841717--5841756 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5841707 TATGTGAAAG
* *
5841717 AATAAATTGAATTTCGAA
1 AATAAATTGAACTTCAAA
5841735 AATAAATTGAACTTCAAA
1 AATAAATTGAACTTCAAA
5841753 AATA
1 AATA
5841757 TAAACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (18 bp):
AATAAATTGAACTTCAAA
Found at i:5849418 original size:14 final size:16
Alignment explanation
Indices: 5849401--5849432 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5849391 ATTATTTTTT
5849401 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
5849415 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
5849431 TG
1 TG
5849433 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:5855009 original size:12 final size:12
Alignment explanation
Indices: 5854989--5855019 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5854979 TAATCCCGGG
*
5854989 TTTGTTTTTTCA
1 TTTGATTTTTCA
5855001 TTTGATTTTTCA
1 TTTGATTTTTCA
5855013 TTTGATT
1 TTTGATT
5855020 ATCAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTGATTTTTCA
Found at i:5856449 original size:2 final size:2
Alignment explanation
Indices: 5856435--5856469 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
5856425 TTATTTGTTA
5856435 AT AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
5856470 ATTTACGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.94
3 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5856673 original size:28 final size:29
Alignment explanation
Indices: 5856639--5856706 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 29
5856629 GCGTGTCATA
5856639 AATTTATGACACACAAA-TGTGTCATCTT
1 AATTTATGACACACAAAGTGTGTCATCTT
*
5856667 AATTTATGACATACAAATGTGTGTCATCTT
1 AATTTATGACACACAAA-GTGTGTCATCTT
5856697 AATTTATGAC
1 AATTTATGAC
5856707 GGGGACTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 16 0.43
30 21 0.57
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (29 bp):
AATTTATGACACACAAAGTGTGTCATCTT
Found at i:5856752 original size:13 final size:13
Alignment explanation
Indices: 5856734--5856764 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5856724 GCAATGAGCA
5856734 TCATAAATCCGCG
1 TCATAAATCCGCG
*
5856747 TCATAAATGCGCG
1 TCATAAATCCGCG
5856760 TCATA
1 TCATA
5856765 GATTCATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (13 bp):
TCATAAATCCGCG
Found at i:5866266 original size:21 final size:23
Alignment explanation
Indices: 5866240--5866289 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
5866230 TCACTTGTAC
*
5866240 AATTTACCTTT-TATTTT-AAAT
1 AATTTACCTTTAAATTTTGAAAT
*
5866261 AATTTACCTTTAAATTTTGAACT
1 AATTTACCTTTAAATTTTGAAAT
5866284 AATTTA
1 AATTTA
5866290 TAATTATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.44
22 5 0.20
23 9 0.36
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (23 bp):
AATTTACCTTTAAATTTTGAAAT
Found at i:5866393 original size:18 final size:18
Alignment explanation
Indices: 5866370--5866417 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
5866360 TCGAGCGTTG
*
5866370 TAGAATCATGCAAAAACA
1 TAGAATCATCCAAAAACA
5866388 TAGAATCATCCAAAAACA
1 TAGAATCATCCAAAAACA
5866406 TAGAATCATCCA
1 TAGAATCATCCA
5866418 TATATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.52, C:0.21, G:0.08, T:0.19
Consensus pattern (18 bp):
TAGAATCATCCAAAAACA
Found at i:5867761 original size:20 final size:20
Alignment explanation
Indices: 5867736--5867781 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5867726 ATTTTTGATC
5867736 TAAAATGAAACATCCAGTAG
1 TAAAATGAAACATCCAGTAG
*
5867756 TAAAATGAAACGTCCAGTAG
1 TAAAATGAAACATCCAGTAG
5867776 TAAAAT
1 TAAAAT
5867782 TTTGACACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (20 bp):
TAAAATGAAACATCCAGTAG
Found at i:5879169 original size:17 final size:17
Alignment explanation
Indices: 5879122--5879193 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
5879112 AATTAAGAGT
* * *
5879122 TAGTCTAATAAATGAGC
1 TAGTTTAATTAATGAAC
* *
5879139 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
5879156 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
5879173 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
5879191 TAG
1 TAG
5879194 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:5879187 original size:18 final size:18
Alignment explanation
Indices: 5879149--5879192 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5879139 TAGTTTGATG
*
5879149 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
5879166 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
5879183 CAATGAACTA
1 -AATGAACTA
5879193 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:5881286 original size:18 final size:18
Alignment explanation
Indices: 5881263--5881335 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
5881253 AGGGATTATC
*
5881263 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
5881281 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
5881300 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
5881319 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
5881336 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 30 0.62
19 4 0.08
20 14 0.29
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5881316 original size:38 final size:38
Alignment explanation
Indices: 5881260--5881336 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
5881250 TTGAGGGATT
* *
5881260 ATCAGTGGTCCTTTGGGACATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
*
5881298 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
5881336 A
1 A
5881337 ATATTCAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
Found at i:5887455 original size:64 final size:64
Alignment explanation
Indices: 5887387--5887511 Score: 155
Period size: 64 Copynumber: 2.0 Consensus size: 64
5887377 CGATGCACTC
** * *
5887387 TTAAATAATGAACATCGAATGCCA-TTAGTGCATCGATGCATAAGG-AGTGCATCGATGCACCTG
1 TTAAATAACAAACATCGAATGCCATTTA-TCCACCGATGCAT-AGGAAGTGCATCGATGCACCTG
5887450 T
64 T
* **
5887451 TTAAATTACAAACATCGAATGGGATTTATCCACCGATGCATAGGAAGTGCATCGATGCACC
1 TTAAATAACAAACATCGAATGCCATTTATCCACCGATGCATAGGAAGTGCATCGATGCACC
5887512 CGTCAAGGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 3 0.06
64 46 0.88
65 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (64 bp):
TTAAATAACAAACATCGAATGCCATTTATCCACCGATGCATAGGAAGTGCATCGATGCACCTGT
Found at i:5888105 original size:18 final size:18
Alignment explanation
Indices: 5888082--5888154 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
5888072 AGGGATTATC
*
5888082 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
* **
5888100 AGTGGTTCTTCGAAACAAT
1 AGTGGTCCTTCGGGAC-AT
5888119 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
5888138 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
5888155 AATATTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5890662 original size:9 final size:9
Alignment explanation
Indices: 5890627--5890680 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
5890617 CTCTTTAAAA
*
5890627 TTTTCTTTT
1 TTTTATTTT
5890636 CTTTTA-TTT
1 -TTTTATTTT
5890645 TTTTA--TT
1 TTTTATTTT
5890652 TTTTATTTT
1 TTTTATTTT
5890661 TTTTATTTT
1 TTTTATTTT
*
5890670 TTTAATTTT
1 TTTTATTTT
5890679 TT
1 TT
5890681 AATTTTTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 7 0.17
8 5 0.12
9 24 0.60
10 4 0.10
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTATTTT
Found at i:5890664 original size:24 final size:25
Alignment explanation
Indices: 5890627--5890688 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
5890617 CTCTTTAAAA
*
5890627 TTTTCTTTTCTTTTATTTTTTT-ATT
1 TTTTATTTT-TTTTATTTTTTTAATT
5890652 TTTTATTTTTTTTATTTTTTTAATT
1 TTTTATTTTTTTTATTTTTTTAATT
*
5890677 TTTTAATTTTTT
1 TTTTATTTTTTT
5890689 ACTAACCCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 12 0.35
25 22 0.65
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTATTTTTTTTATTTTTTTAATT
Found at i:5890687 original size:9 final size:8
Alignment explanation
Indices: 5890637--5890689 Score: 72
Period size: 8 Copynumber: 6.6 Consensus size: 8
5890627 TTTTCTTTTC
5890637 TTTTATTT
1 TTTTATTT
5890645 TTTTA-TT
1 TTTTATTT
5890652 TTTTATTTT
1 TTTTA-TTT
5890661 TTTTATTT
1 TTTTATTT
*
5890669 TTTTAATT
1 TTTTATTT
*
5890677 TTTTAATT
1 TTTTATTT
5890685 TTTTA
1 TTTTA
5890690 CTAACCCGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
7 7 0.17
8 28 0.67
9 7 0.17
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:5890689 original size:24 final size:24
Alignment explanation
Indices: 5890637--5890689 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5890627 TTTTCTTTTC
*
5890637 TTTTATTTTTTTATTTTTTATTTT
1 TTTTATTTTTTTATTTTTTATATT
5890661 TTTTATTTTTTTAATTTTTTA-ATT
1 TTTTATTTTTTT-ATTTTTTATATT
5890685 TTTTA
1 TTTTA
5890690 CTAACCCGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTATTTTTTTATTTTTTATATT
Found at i:5892264 original size:17 final size:17
Alignment explanation
Indices: 5892244--5892283 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
5892234 TAGTCCAATA
*
5892244 AATGAACTAGTTTGATG
1 AATGAACTAGTTTAATG
*
5892261 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATG
5892278 AATGAA
1 AATGAA
5892284 GTAACTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTAATG
Found at i:5893201 original size:24 final size:24
Alignment explanation
Indices: 5893174--5893220 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5893164 AACTCTAAGT
5893174 TTGTATTATTTTAATTTAAACTAC
1 TTGTATTATTTTAATTTAAACTAC
**
5893198 TTGTATTATTTTGTTTTAAACTA
1 TTGTATTATTTTAATTTAAACTA
5893221 TGTGTTACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
TTGTATTATTTTAATTTAAACTAC
Found at i:5893957 original size:14 final size:14
Alignment explanation
Indices: 5893929--5893992 Score: 51
Period size: 15 Copynumber: 4.5 Consensus size: 14
5893919 TTTTTATTAT
5893929 TTATTTTTAATATAA
1 TTATTTTTAA-ATAA
5893944 TTATTTTTAAATAAA
1 TTATTTTTAAAT-AA
** *
5893959 AAATTATT-AATAA
1 TTATTTTTAAATAA
*
5893972 TCTATTTTTAAA-AC
1 T-TATTTTTAAATAA
5893986 TTATTTT
1 TTATTTT
5893993 ATCCAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 8 0.21
14 12 0.31
15 19 0.49
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATTTTTAAATAA
Found at i:5903103 original size:12 final size:12
Alignment explanation
Indices: 5903086--5903110 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5903076 TACTTAAATA
5903086 TTAATAACCATT
1 TTAATAACCATT
5903098 TTAATAACCATT
1 TTAATAACCATT
5903110 T
1 T
5903111 GATCACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAATAACCATT
Found at i:5907748 original size:108 final size:108
Alignment explanation
Indices: 5907581--5907899 Score: 467
Period size: 108 Copynumber: 3.0 Consensus size: 108
5907571 TCAAACTTTG
* * * *
5907581 GATTAGACTCTAGTTATTAGCTAAAACCCATTGTTCATGTTGATATTCTCCTAGTTTCTCTCGAA
1 GATTAGGCTCTAGTTATTAGCTAAAACCCATTATTCATGTTGATCTTCCCCTAGTTTCTCTCGAA
* *
5907646 CACTAAGGATTTTTAACTTAATTTCTCTTGAACACTAATATTA
66 CACTAAGGATCTTTAACTTAGTTTCTCTTGAACACTAATATTA
* * * * * *
5907689 GATTAGGCTCTAATTATTAGCTAAAACCCATTATACATATTGTTCTTCCCCTACTTTCTCTTGAA
1 GATTAGGCTCTAGTTATTAGCTAAAACCCATTATTCATGTTGATCTTCCCCTAGTTTCTCTCGAA
* * * * *
5907754 CATTTAGGATCTTTAACTTAGTTTCTCCTGAACACTAATTTTG
66 CACTAAGGATCTTTAACTTAGTTTCTCTTGAACACTAATATTA
5907797 GATTAGGCTCTAGTTATTAGCTAAAACCCATTATTCATGTTGATCTTCCCCTAGTTTCTCTCGAA
1 GATTAGGCTCTAGTTATTAGCTAAAACCCATTATTCATGTTGATCTTCCCCTAGTTTCTCTCGAA
**
5907862 CACTAAGGATCTTTAACTTAGTTTCTCTCAAACACTAA
66 CACTAAGGATCTTTAACTTAGTTTCTCTTGAACACTAA
5907900 GTAATATACT
Statistics
Matches: 183, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
108 183 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (108 bp):
GATTAGGCTCTAGTTATTAGCTAAAACCCATTATTCATGTTGATCTTCCCCTAGTTTCTCTCGAA
CACTAAGGATCTTTAACTTAGTTTCTCTTGAACACTAATATTA
Found at i:5917849 original size:32 final size:31
Alignment explanation
Indices: 5917798--5917859 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
5917788 ACCCATTGTT
* * *
5917798 GATCTTTCACTATTTTCTCTCGAACACTAAG
1 GATCTTTAACTAGTTTCTCTCAAACACTAAG
5917829 GATCTTTAACTTAGTTTCTCTCAAACACTAA
1 GATCTTTAAC-TAGTTTCTCTCAAACACTAA
5917860 TGTTGGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (31 bp):
GATCTTTAACTAGTTTCTCTCAAACACTAAG
Found at i:5917956 original size:107 final size:104
Alignment explanation
Indices: 5917736--5918073 Score: 448
Period size: 107 Copynumber: 3.2 Consensus size: 104
5917726 GAAATCCTAC
* * * *
5917736 CTTAGTTTCTCTCGAACACTAATATTGGATTAAGATCTAGTTATTAGCTAAAACCCA--T-TGTT
1 CTTAGTTTCTCTCAAACACTAATGTTGGATTAGGCTCTAGTTATTAGCTAAAACCCATTTATGTT
* *
5917798 GATCTTTCACTATTTTCTCTCGAACACTAAGGATCTTTAA
66 GATC-TTCCCTAGTTTCTCTCGAACACTAAGGATCTTTAA
*
5917838 CTTAGTTTCTCTCAAACACTAATGTTGGATTAGGCTCTAATTATTAGCTAAAACCCATTTTTCAT
1 CTTAGTTTCTCTCAAACACTAATGTTGGATTAGGCTCTAGTTATTAGCTAAAACCCA--TTT-AT
* *
5917903 GTTGTTCTTCCCTAGTCTCTCTCGAACACTAAGGATCTTTAA
63 GTTGATCTTCCCTAGTTTCTCTCGAACACTAAGGATCTTTAA
* ** *
5917945 CTTAGATTCTCTCAAACACTAATGTCAGATTAGGCTCTAGTTATTATCTAAAACCCATTACTAAT
1 CTTAGTTTCTCTCAAACACTAATGTTGGATTAGGCTCTAGTTATTAGCTAAAACCCATT--T-AT
*
5918010 GTTGATCTTCCCCTAGTTTCTCTCAAACACTAAGGATCTTTAA
63 GTTGATCTT-CCCTAGTTTCTCTCGAACACTAAGGATCTTTAA
*
5918053 CTTAGTTTCTCTTAAACACTA
1 CTTAGTTTCTCTCAAACACTA
5918074 TGTAATATAC
Statistics
Matches: 207, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
102 52 0.25
105 2 0.01
106 1 0.00
107 95 0.46
108 57 0.28
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (104 bp):
CTTAGTTTCTCTCAAACACTAATGTTGGATTAGGCTCTAGTTATTAGCTAAAACCCATTTATGTT
GATCTTCCCTAGTTTCTCTCGAACACTAAGGATCTTTAA
Found at i:5934033 original size:22 final size:21
Alignment explanation
Indices: 5934001--5934056 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
5933991 CCCTCGAGGG
5934001 GTATCGATACATA-TCAAGGAAT
1 GTATCGATACATATTCAAGG--T
* *
5934023 GTATCGGTACACATTCAAGGT
1 GTATCGATACATATTCAAGGT
5934044 GTATCGATACATA
1 GTATCGATACATA
5934057 GATATGCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 12 0.41
22 11 0.38
23 6 0.21
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (21 bp):
GTATCGATACATATTCAAGGT
Found at i:5936021 original size:12 final size:12
Alignment explanation
Indices: 5936004--5936028 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5935994 ATGATGGTTC
5936004 TCCAACGTCATG
1 TCCAACGTCATG
5936016 TCCAACGTCATG
1 TCCAACGTCATG
5936028 T
1 T
5936029 GCATTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:5938319 original size:18 final size:19
Alignment explanation
Indices: 5938276--5938320 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
5938266 GCAACTCCAA
*
5938276 CATTCTTCTTTTTCTCAGT
1 CATTCTTCTTTGTCTCAGT
*
5938295 C-TCCTTCTTTGTCTCA-T
1 CATTCTTCTTTGTCTCAGT
5938312 CATTCTTCT
1 CATTCTTCT
5938321 CGAGGTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.09
18 19 0.86
19 1 0.05
ACGTcount: A:0.09, C:0.31, G:0.04, T:0.56
Consensus pattern (19 bp):
CATTCTTCTTTGTCTCAGT
Found at i:5940364 original size:59 final size:60
Alignment explanation
Indices: 5940270--5940396 Score: 184
Period size: 59 Copynumber: 2.1 Consensus size: 60
5940260 TTAATTTTCA
* *
5940270 CTTATCCAAAGGTCATAAACCAATGTAAAATTTAAAAAGTTTTAGACTATATATTTAGAT
1 CTTATCCAAAGGTCATAAACCAATGTAAAATTTAAAAAGTTTTAGACTACACATTTAGAT
* * * * *
5940330 C-TATCCAAAGGTCATAACCCTATGTAATATTTAAAAAGTTTTAGGCTACGCATTTAGAT
1 CTTATCCAAAGGTCATAAACCAATGTAAAATTTAAAAAGTTTTAGACTACACATTTAGAT
5940389 CTTATCCA
1 CTTATCCA
5940397 TATATATATA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 52 0.88
60 7 0.12
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (60 bp):
CTTATCCAAAGGTCATAAACCAATGTAAAATTTAAAAAGTTTTAGACTACACATTTAGAT
Found at i:5940447 original size:2 final size:2
Alignment explanation
Indices: 5940396--5940429 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5940386 GATCTTATCC
5940396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5940430 CAACAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5953490 original size:17 final size:17
Alignment explanation
Indices: 5953468--5953501 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5953458 TTCAATATTT
*
5953468 TGGATTGTTTGATTTTA
1 TGGATTGTTGGATTTTA
5953485 TGGATTGTTGGATTTTA
1 TGGATTGTTGGATTTTA
5953502 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTA
Found at i:5956501 original size:22 final size:22
Alignment explanation
Indices: 5956471--5956542 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
5956461 ATAGATGGTC
*
5956471 CGAAGGACTTACACATCATGCT
1 CGAAAGACTTACACATCATGCT
* *
5956493 CGAAAGACTT--AC-TGATGGCC
1 CGAAAGACTTACACATCAT-GCT
* *
5956513 CGAAGGACTTACACATCAAGCT
1 CGAAAGACTTACACATCATGCT
5956535 CGAAAGAC
1 CGAAAGAC
5956543 ATACTGATGG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.08
20 13 0.34
22 20 0.53
23 2 0.05
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (22 bp):
CGAAAGACTTACACATCATGCT
Found at i:5956503 original size:42 final size:42
Alignment explanation
Indices: 5956423--5956564 Score: 207
Period size: 42 Copynumber: 3.4 Consensus size: 42
5956413 AGGTCTTATG
* * *
5956423 GATGACCCGAAGGACTTA-TCATCTTGCTCGAAAGACTTA-T
1 GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
*
5956463 AGATGGTCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
1 -GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
* *
5956506 GATGGCCCGAAGGACTTACACATCAAGCTCGAAAGACATACT
1 GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
5956548 GATGGCCCGAAGGACTT
1 GATGGCCCGAAGGACTT
5956565 CAGCTGATTT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
41 16 0.17
42 75 0.82
43 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.22
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
Found at i:5956521 original size:20 final size:20
Alignment explanation
Indices: 5956493--5956564 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
5956483 ACATCATGCT
5956493 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* ** * *
5956513 CGAAGGACTTACACATCAAGCT
1 CGAAAGACTTACTGAT--GGCC
*
5956535 CGAAAGACATACTGATGGCC
1 CGAAAGACTTACTGATGGCC
*
5956555 CGAAGGACTT
1 CGAAAGACTT
5956565 CAGCTGATTT
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
20 23 0.62
22 14 0.38
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:5956747 original size:20 final size:20
Alignment explanation
Indices: 5956722--5956795 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
5956712 CATCTTGCTT
5956722 GAAAGACTTATAGATGACCC
1 GAAAGACTTATAGATGACCC
* *
5956742 GAAAGATTTA-AGCATCACGCTC
1 GAAAGACTTATAG-ATGAC-C-C
5956764 GAAAGACTTACT-GATTG-CCC
1 GAAAGACTTA-TAGA-TGACCC
*
5956784 GAAGGACTTATA
1 GAAAGACTTATA
5956796 CTAATTCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
19 3 0.07
20 23 0.55
21 2 0.05
22 12 0.29
23 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAAGACTTATAGATGACCC
Found at i:5956898 original size:228 final size:228
Alignment explanation
Indices: 5956458--5957009 Score: 736
Period size: 228 Copynumber: 2.4 Consensus size: 228
5956448 GCTCGAAAGA
* * * * * * *
5956458 CTTATAGATGGTCCGAAGGACTTACACATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGACT
1 CTTATGGATGGCCCGAAGGACTTA-TCATCTTGCTCGAAAGACTTA-TAGATGACCCGAAAGATT
* * * * **
5956522 TACA-CATCAAGCTCGAAAGACATACTGATGGCCCGAAGGACTTCAGCTGATTTGAAGTGTCGTG
64 TA-AGCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCAACTAATTCAAAGTGTCGTG
* * *
5956586 AATCGAGCAATATAAAATGTTAACCCCTTTGGTGAGGAGTTGTTGATTCGAAGTGTTGTGAATCG
128 AATCGAGCAATAGAAAATGTTAACCCCTCTGGTGAGGAGTTGCTGATTCGAAGTGTTGTGAATCG
*
5956651 AGCAAAGGAAATATTGAAAATATCCTGCCCGAAGGT
193 AGCAAAGGAAATATTGAAAACATCCTGCCCGAAGGT
* *
5956687 CTTATGGATGGCCCGAATGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAAGATTTA
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAAGATTTA
* *
5956752 AGCATCACGCTCGAAAGACTTACTGATTGCCCGAAGGACTT-ATACTAATTCAAAGTGTTGTGAA
66 AGCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCA-ACTAATTCAAAGTGTCGTGAA
* * * * * *
5956816 TTGAGCAATGGGAAATGTTATCCCCTCTGGTGGGGCGTTGCTGATTCGAAGTGTTGTGAATCGAG
130 TCGAGCAATAGAAAATGTTAACCCCTCTGGTGAGGAGTTGCTGATTCGAAGTGTTGTGAATCGAG
*
5956881 CAAAGGAAATGTTGAAAACATCCTGCCCGAAGGT
195 CAAAGGAAATATTGAAAACATCCTGCCCGAAGGT
* * *
5956915 CTTATGGATGTCCCGAAGGACTTATCATCTTGCTCGAAAAACTTATAGTTGACCC-AAAGGATTT
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAA-GATTT
5956979 AAGCATCACAG-TCGAAAGACTTACTGATGGC
65 AAGCATCAC-GCTCGAAAGACTTACTGATGGC
5957010 ATGAAAGACT
Statistics
Matches: 284, Mismatches: 34, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
227 6 0.02
228 256 0.90
229 22 0.08
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (228 bp):
CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAAGATTTA
AGCATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCAACTAATTCAAAGTGTCGTGAAT
CGAGCAATAGAAAATGTTAACCCCTCTGGTGAGGAGTTGCTGATTCGAAGTGTTGTGAATCGAGC
AAAGGAAATATTGAAAACATCCTGCCCGAAGGT
Found at i:5957028 original size:42 final size:42
Alignment explanation
Indices: 5956982--5957070 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
5956972 AGGATTTAAG
* *
5956982 CATCACAGTCGAAAGACTTACTGATGGCATGAAAGACTTACT
1 CATCACACTCGAAAGACTTACTGATGGCACGAAAGACTTACT
** * *
5957024 CATCATTCTCGAAAGACTTACTGATGGCCCGAACGACTTACT
1 CATCACACTCGAAAGACTTACTGATGGCACGAAAGACTTACT
5957066 CATCA
1 CATCA
5957071 AGAAACCCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
CATCACACTCGAAAGACTTACTGATGGCACGAAAGACTTACT
Found at i:5957387 original size:53 final size:53
Alignment explanation
Indices: 5957164--5957429 Score: 249
Period size: 54 Copynumber: 5.0 Consensus size: 53
5957154 TGGAGATAAT
* ** * *
5957164 CATCAAGAAACCCCT-GAAAATCAGGCTTAGTTTC-TAAAAACTCATTTAAAAAA
1 CATCAAGAAACCCCTAAAAAATCAGGCTTA-TTTCTTTCAAATTCATTT-GAAAA
* * *
5957217 CATCAAGAAATCCCTAAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAAATCAGGCTT-ATTTCTTTCAAATTCATTTGAAAA
* ** *
5957271 CATAAAGAAACCCCT-AAAAATCAAACTTAGTTTTTTTCCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAAATCAGGCTTA-TTTCTTT-CAAATTCATTTGAAAA
* * *
5957325 CATGAAGAAACCCCT-ACAAATTAGGCTTATCTTCTTTCAAATTCATTT-ATAAA
1 CATCAAGAAACCCCTAAAAAATCAGGCTTAT-TTCTTTCAAATTCATTTGA-AAA
* * *
5957378 CATCGAGAAACTCCT-GAAAATCAGGCTTATGTT-TTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAAATCAGGCTTAT-TTCTTTCAAATTCATTTGAAAA
5957430 TTGTCGTAAC
Statistics
Matches: 178, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
52 19 0.11
53 72 0.40
54 76 0.43
55 11 0.06
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.31
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAAATCAGGCTTATTTCTTTCAAATTCATTTGAAAA
Found at i:5957413 original size:107 final size:106
Alignment explanation
Indices: 5957158--5957429 Score: 318
Period size: 107 Copynumber: 2.5 Consensus size: 106
5957148 AATGTTTGGA
* ** * *
5957158 GATAATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTAAAAAACATCAA
1 GATAAACATCAAGAAACCCCTGAAAATCAGGCTTAGTTT-TTCAAATTCATTT-GAAAACATCAA
* *
5957223 GAAATCCCTAAAAAATTAGGCTTAATTTCTTTGAAATTCATTT
64 GAAACCCCTAAAAAATTAGGCTTAATTTCTTTCAAATTCATTT
* * ** *
5957266 GA-AAACATAAAGAAACCCCTAAAAATCAAACTTAGTTTTTTTCCAAATTCATTTGAAAACATGA
1 GATAAACATCAAGAAACCCCTGAAAATCAGGCTTAG--TTTTT-CAAATTCATTTGAAAACATCA
*
5957330 AGAAACCCCT-ACAAATTAGGCTT-ATCTTCTTTCAAATTCATTT
63 AGAAACCCCTAAAAAATTAGGCTTAAT-TTCTTTCAAATTCATTT
* *
5957373 -ATAAACATCGAGAAACTCCTGAAAATCAGGCTTATGTTTTTCAAATTCATTTGAAAA
1 GATAAACATCAAGAAACCCCTGAAAATCAGGCTTA-GTTTTTCAAATTCATTTGAAAA
5957430 TTGTCGTAAC
Statistics
Matches: 139, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
105 16 0.12
106 8 0.06
107 82 0.59
108 21 0.15
109 12 0.09
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (106 bp):
GATAAACATCAAGAAACCCCTGAAAATCAGGCTTAGTTTTTCAAATTCATTTGAAAACATCAAGA
AACCCCTAAAAAATTAGGCTTAATTTCTTTCAAATTCATTT
Found at i:5958868 original size:22 final size:22
Alignment explanation
Indices: 5958843--5958886 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5958833 AGGTGATACT
5958843 GGCCACCGGCGA-CTACTATTCC
1 GGCCACCGGCGATC-ACTATTCC
*
5958865 GGCCACCGTCGATCACTATTCC
1 GGCCACCGGCGATCACTATTCC
5958887 AACCACCGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.41, G:0.20, T:0.20
Consensus pattern (22 bp):
GGCCACCGGCGATCACTATTCC
Found at i:5958892 original size:22 final size:22
Alignment explanation
Indices: 5958857--5958907 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5958847 ACCGGCGACT
** *
5958857 ACTATTCCGGCCACCGTCGATC
1 ACTATTCCAACCACCGTCGATA
*
5958879 ACTATTCCAACCACCGTCGGTA
1 ACTATTCCAACCACCGTCGATA
5958901 ACTATTC
1 ACTATTC
5958908 ACGGTGGCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.37, G:0.14, T:0.25
Consensus pattern (22 bp):
ACTATTCCAACCACCGTCGATA
Found at i:5959648 original size:3 final size:3
Alignment explanation
Indices: 5959640--5959703 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
5959630 TTATGGCCTG
*
5959640 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5959687 TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TA
5959704 CGAATGACGG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5959898 original size:16 final size:16
Alignment explanation
Indices: 5959846--5959900 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
5959836 TTAAACAAGT
5959846 TCTTCTTATTATGAAC
1 TCTTCTTATTATGAAC
* **
5959862 TTCTTCTTCA-GATGAGT
1 -TCTTCTT-ATTATGAAC
5959879 TCTTCTTATTATGAAC
1 TCTTCTTATTATGAAC
5959895 TCTTCT
1 TCTTCT
5959901 ACTGGGAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 1 0.03
16 17 0.57
17 11 0.37
18 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.51
Consensus pattern (16 bp):
TCTTCTTATTATGAAC
Found at i:5960070 original size:123 final size:123
Alignment explanation
Indices: 5959943--5960398 Score: 603
Period size: 123 Copynumber: 3.7 Consensus size: 123
5959933 GAAATATATT
* * * ** * *
5959943 AAAAGTTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTATACGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
* * *
5960008 ACGAACTCCTTATGGAAATATTGATGTTGCTCTATCTCATTCTGCGATAGAGTCAAGC
66 ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
*
5960066 AAAAGGTTGAATAAGTTCTTCAGATTATGAACATCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
* * * ** *
5960131 ACAAACTCCTTCTGAAAATGTTGATACTGCTTTATCTCCTTCTGCGATAGAGTCGAGC
66 ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
*
5960189 AAAAGGTTGAATAAGTTCTTCAGATTATGAA---CTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
* * * * **
5960251 ACGAACTCTTTCTAGAAATATTGATGTTGCTCTATCTCCTTCCGTGATAGAGTCGATT
66 ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
* * ** * *
5960309 AAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCATCTTTGGATGAGTTATTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
* *
5960374 ACGACCTCCTTCTGGAAATGTTGAT
66 ACGAACTCCTTCTGGAAATATTGAT
5960399 CTATCGAGTG
Statistics
Matches: 291, Mismatches: 39, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
120 106 0.36
123 185 0.64
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (123 bp):
AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
Found at i:5967630 original size:23 final size:25
Alignment explanation
Indices: 5967591--5967646 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
5967581 ATGTAATGAA
5967591 AATTAAAAATTAATAGA-AA-AATC
1 AATTAAAAATTAATAGACAATAATC
*
5967614 AATTAATAA-TAATTAGACAATAATC
1 AATTAAAAATTAA-TAGACAATAATC
5967639 -A-TAAAAAT
1 AATTAAAAAT
5967647 CCTGGCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 3 0.11
25 4 0.15
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (25 bp):
AATTAAAAATTAATAGACAATAATC
Found at i:5970597 original size:9 final size:9
Alignment explanation
Indices: 5970532--5970601 Score: 56
Period size: 9 Copynumber: 7.9 Consensus size: 9
5970522 TTATGGCATG
*
5970532 TAATAATAA
1 TAATAATAT
*
5970541 TAATATTAT
1 TAATAATAT
*
5970550 TATTAATAT
1 TAATAATAT
5970559 TAATAA-A-
1 TAATAATAT
5970566 -AATAATAT
1 TAATAATAT
* *
5970574 TGACAAAATAG
1 T-A-ATAATAT
5970585 TAATAATAT
1 TAATAATAT
5970594 TAATAATA
1 TAATAATA
5970602 CGAATGACAG
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
6 5 0.11
7 1 0.02
8 1 0.02
9 32 0.68
10 2 0.04
11 6 0.13
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (9 bp):
TAATAATAT
Found at i:5970918 original size:55 final size:55
Alignment explanation
Indices: 5970786--5970928 Score: 189
Period size: 55 Copynumber: 2.6 Consensus size: 55
5970776 CAAATTCATT
* * *
5970786 TTGTCAAGAAATCTCTGAAAAT-AAGACTTAATTTCTTTGAAAGCTCATTTAAAAA
1 TTGTCAAGAAATTTCTGAAAATCAA-ACTTAGTTTCTTTAAAAGCTCATTTAAAAA
* * * *
5970841 TCGTCAAGAAACTTCTGAAAATCATACTTAGTTTCTTTAAAAGCTCATTTGAAAA
1 TTGTCAAGAAATTTCTGAAAATCAAACTTAGTTTCTTTAAAAGCTCATTTAAAAA
* *
5970896 TTGTCAAGAAATTTATGAAAATCAAACGTAGTT
1 TTGTCAAGAAATTTCTGAAAATCAAACTTAGTT
5970929 CCTAAAAACA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
55 74 0.99
56 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (55 bp):
TTGTCAAGAAATTTCTGAAAATCAAACTTAGTTTCTTTAAAAGCTCATTTAAAAA
Found at i:5971296 original size:29 final size:29
Alignment explanation
Indices: 5971249--5971335 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
5971239 TAGGCTGACT
*
5971249 TGGGTAGGTAATGCGTTTCAAGTTAATTTG
1 TGGG-AGGTAATGTGTTTCAAGTTAATTTG
5971279 TGGGAGGTAATGTGTTTCAAGTTAATTTG
1 TGGGAGGTAATGTGTTTCAAGTTAATTTG
* * *
5971308 GGGGAGGTAATATGTTTCAGGTTAATTT
1 TGGGAGGTAATGTGTTTCAAGTTAATTT
5971336 CTTGCGTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 49 0.92
30 4 0.08
ACGTcount: A:0.24, C:0.05, G:0.31, T:0.40
Consensus pattern (29 bp):
TGGGAGGTAATGTGTTTCAAGTTAATTTG
Found at i:5971968 original size:4 final size:4
Alignment explanation
Indices: 5971959--5972073 Score: 80
Period size: 4 Copynumber: 28.2 Consensus size: 4
5971949 TTTGATCGGT
5971959 TTTC TTTC -TTC TTTC TTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC -TTTC -TTTC -TTTC -TTTC -TTTC TTTC
* * * *
5972007 TTTTT TTTC TTT- TTTT TTTC TTTT TTTC TATT- TTTA TGTT- TTTC TTTC
1 -TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC T-TTC TTTC TTTC
5972055 TTTC TTTC -TT- TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC T
5972074 GTGTGTTTTT
Statistics
Matches: 96, Mismatches: 5, Indels: 20
0.79 0.04 0.17
Matches are distributed among these distances:
3 14 0.15
4 51 0.53
5 31 0.32
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:5971983 original size:20 final size:19
Alignment explanation
Indices: 5971958--5972073 Score: 116
Period size: 20 Copynumber: 6.1 Consensus size: 19
5971948 GTTTGATCGG
5971958 TTTTCTTTCTTCTTTCTTTC
1 TTTTCTTTCTT-TTTCTTTC
5971978 TTTTCTTT-TCTTTTCTTTTC
1 TTTTCTTTCT-TTTTC-TTTC
5971998 TTTTCTTTCTTTTT-TTTC
1 TTTTCTTTCTTTTTCTTTC
* *
5972016 TTTT-TTTTTTCTTTTTTTC
1 TTTTCTTTCTT-TTTCTTTC
*
5972035 TATTT-TTATGTTTTTCTTTC
1 T-TTTCTT-TCTTTTTCTTTC
5972055 -TTTCTTTCTTTTTCTTTC
1 TTTTCTTTCTTTTTCTTTC
5972073 T
1 T
5972074 GTGTGTTTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 19
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.06
18 25 0.30
19 12 0.14
20 37 0.45
21 4 0.05
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (19 bp):
TTTTCTTTCTTTTTCTTTC
Found at i:5971984 original size:5 final size:5
Alignment explanation
Indices: 5971970--5972030 Score: 83
Period size: 5 Copynumber: 12.6 Consensus size: 5
5971960 TTCTTTCTTC
5971970 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT TTTC- TTTCT TTT-T TTTCTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC-T
*
5972018 TTTTT TTTCT TTT
1 TTTCT TTTCT TTT
5972031 TTTCTATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
4 12 0.24
5 35 0.69
6 4 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:5972014 original size:28 final size:28
Alignment explanation
Indices: 5971970--5972073 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 28
5971960 TTCTTTCTTC
5971970 TTTCTTTCTTTTCTTTTCTTTTCTTTTCT
1 TTTCTTTCTTTT-TTTTCTTTTCTTTTCT
*
5971999 TTTCTTTCTTTTTTTTCTTTTTTTTTTCT
1 TTTCTTTCTTTTTTTTC-TTTTCTTTTCT
5972028 TTT-TTTCTATTTTTATGT-TTTTC-TTTC-
1 TTTCTTTCT-TTTTT-T-TCTTTTCTTTTCT
5972055 TTTCTTTCTTTTTCTTTCT
1 TTTCTTTCTTTTT-TTTCT
5972074 GTGTGTTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
26 1 0.02
27 9 0.14
28 20 0.30
29 34 0.52
30 1 0.02
31 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTCTTTCTTTTTTTTCTTTTCTTTTCT
Found at i:5972072 original size:10 final size:10
Alignment explanation
Indices: 5971958--5972073 Score: 97
Period size: 10 Copynumber: 12.0 Consensus size: 10
5971948 GTTTGATCGG
5971958 TTTTCTTTCT
1 TTTTCTTTCT
5971968 TCTTTCTTTC-
1 T-TTTCTTTCT
5971978 TTTTCTTT-T
1 TTTTCTTTCT
5971987 CTTTTCTTT-T
1 -TTTTCTTTCT
5971997 CTTTTCTTTCT
1 -TTTTCTTTCT
5972008 TTTT-TTTCT
1 TTTTCTTTCT
5972017 TTTT-TTT-T
1 TTTTCTTTCT
*
5972025 TCTTTTTTTCT
1 T-TTTCTTTCT
* *
5972036 ATTTT-TATGT
1 -TTTTCTTTCT
5972046 TTTTCTTTC-
1 TTTTCTTTCT
5972055 -TTTCTTTCT
1 TTTTCTTTCT
5972064 TTTTCTTTCT
1 TTTTCTTTCT
5972074 GTGTGTTTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 22
0.78 0.03 0.19
Matches are distributed among these distances:
8 10 0.11
9 26 0.29
10 41 0.45
11 13 0.14
12 1 0.01
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:5972084 original size:18 final size:18
Alignment explanation
Indices: 5971958--5972075 Score: 61
Period size: 18 Copynumber: 6.7 Consensus size: 18
5971948 GTTTGATCGG
5971958 TTTTCTTTCT-TCTTTCT
1 TTTTCTTTCTGTCTTTCT
* *
5971975 TTCT-TTTCTTTTCTTT-T
1 TTTTCTTTC-TGTCTTTCT
*
5971992 CTTTTCTTTTCTTTCTTT-T
1 -TTTTC-TTTCTGTCTTTCT
* *
5972011 TTTTCTTT-TTTTTTTC-
1 TTTTCTTTCTGTCTTTCT
* * *
5972027 TTTT-TTTCTATTTTTATGT
1 TTTTCTTTCT-GTCTT-TCT
*
5972046 TTTTCTTTCTTTCTTTCT
1 TTTTCTTTCTGTCTTTCT
5972064 TTTTCTTTCTGT
1 TTTTCTTTCTGT
5972076 GTGTTTTTTA
Statistics
Matches: 83, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.04
16 15 0.18
17 13 0.16
18 27 0.33
19 16 0.19
20 9 0.11
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTCTGTCTTTCT
Found at i:5972334 original size:2 final size:2
Alignment explanation
Indices: 5972327--5972364 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5972317 AAAACAAGGG
* *
5972327 AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5972365 TTAAAGGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5981714 original size:22 final size:22
Alignment explanation
Indices: 5981688--5981734 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5981678 ACCCGAAATA
*
5981688 ATATTCACAATAAACATCATAT
1 ATATTCACAATAAAAATCATAT
**
5981710 ATATTCATGATAAAAATCATAT
1 ATATTCACAATAAAAATCATAT
5981732 ATA
1 ATA
5981735 ATAATCAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (22 bp):
ATATTCACAATAAAAATCATAT
Done.