Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 24 of 129
Found at i:4891688 original size:19 final size:20
Alignment explanation
Indices: 4891655--4891696 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4891645 ATAAACCCAA
* *
4891655 AAATAAATAAGTAAATAGAT
1 AAATAAATAAATAAATAAAT
4891675 AAAT-AATAAATAAATAAAT
1 AAATAAATAAATAAATAAAT
4891694 AAA
1 AAA
4891697 ACGTACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAATAAATAAATAAAT
Found at i:4891987 original size:43 final size:43
Alignment explanation
Indices: 4891939--4892387 Score: 424
Period size: 43 Copynumber: 10.3 Consensus size: 43
4891929 TAACTTTTAG
* * * * *
4891939 AAAATAAACAAGGTTCCTCTAAATAGAGGCTTAACGATTTTGA
1 AAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGACTTTGA
* * *
4891982 AAAATAAATAAAGCTCATCT-TATCAGAGGCTCAACTACTTTGAA
1 AAAATAAATAAAGCTCCTCTAAAT-AGAGGCTCAACGACTTTG-A
* *
4892026 AAAATAAAT-AAGACTCCTCTAAACAGAGGCTCAACGATTTTGA
1 AAAATAAATAAAG-CTCCTCTAAATAGAGGCTCAACGACTTTGA
* * *
4892069 AAAATAAATAAAGCT--TACTTATTAGAGGCTCAACCACTTTGAAA
1 AAAATAAATAAAGCTCCT-CTAAATAGAGGCTCAACGACTTTG--A
* * * *
4892113 AAAATAAATAAGGCTCCTCTAAATAGAGGTTCAATGACTTTTAA
1 AAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGAC-TTTGA
* *
4892157 AAAATAAATAATGCTCCTCTAAACAGAGGCTCAACGACTTTGA
1 AAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGACTTTGA
* * * * * * * *
4892200 AAAACAAATGAAGTTCATCTAATTAGAAGCTCAATGATTTTGA
1 AAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGACTTTGA
*** * *
4892243 AAAATAAATAAAAAACCTCTAAGTAGAGGCTTAACGACTTTGA
1 AAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGACTTTGA
* * * *
4892286 AAAATAAAAAAAACTCCTCT-AATCAGAAGTTCAACGACTTTGA
1 AAAATAAATAAAGCTCCTCTAAAT-AGAGGCTCAACGACTTTGA
* *
4892329 AAAAGTAAATAAAGCTCATCT-AATCAGAGGCTCAACAACTTTGA
1 AAAA-TAAATAAAGCTCCTCTAAAT-AGAGGCTCAACGACTTTGA
4892373 AAAATAAATAAAGCT
1 AAAATAAATAAAGCT
4892388 TATCGACAAT
Statistics
Matches: 329, Mismatches: 64, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.00
42 23 0.07
43 163 0.50
44 122 0.37
45 16 0.05
46 4 0.01
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (43 bp):
AAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGACTTTGA
Found at i:4892030 original size:87 final size:87
Alignment explanation
Indices: 4891939--4892383 Score: 449
Period size: 87 Copynumber: 5.1 Consensus size: 87
4891929 TAACTTTTAG
* * *
4891939 AAAATAAACAAGGTTCCTCTAAATAGAGGCTTAACGATTTTGAAAAATAAATAAAGCTCATCTTA
1 AAAATAAATAAGGCTCCTCTAAATAGAGGCTTAACGATTTTGAAAAATAAATAAAGCTCATCTAA
*
4892004 TCAGAGGCTCAACTACTTTGAA
66 TCAGAGGCTCAACGACTTTGAA
* * * * *
4892026 AAAATAAATAAGACTCCTCTAAACAGAGGCTCAACGATTTTGAAAAATAAATAAAGCTTA-CTTA
1 AAAATAAATAAGGCTCCTCTAAATAGAGGCTTAACGATTTTGAAAAATAAATAAAGCTCATCTAA
* *
4892090 TTAGAGGCTCAACCACTTTGAAA
66 TCAGAGGCTCAACGACTTTG-AA
* * * *
4892113 AAAATAAATAAGGCTCCTCTAAATAGAGG-TTCAATGACTTTTAAAAAATAAATAATGCTCCTCT
1 AAAATAAATAAGGCTCCTCTAAATAGAGGCTT-AACGA-TTTTGAAAAATAAATAAAGCTCATCT
*
4892177 AAACAGAGGCTCAACGACTTTG-A
64 AATCAGAGGCTCAACGACTTTGAA
* * * * * * * *** *
4892200 AAAACAAATGAA-GTTCATCTAATTAGAAGCTCAATGATTTTGAAAAATAAATAAAAAACCTCTA
1 AAAATAAAT-AAGGCTCCTCTAAATAGAGGCTTAACGATTTTGAAAAATAAATAAAGCTCATCTA
*
4892264 AGT-AGAGGCTTAACGACTTTG-A
65 A-TCAGAGGCTCAACGACTTTGAA
* ** * *
4892286 AAAATAAAAAAAACTCCTCT-AATCAGAAG-TTCAACGACTTTGAAAAAGTAAATAAAGCTCATC
1 AAAATAAATAAGGCTCCTCTAAAT-AGAGGCTT-AACGATTTTGAAAAA-TAAATAAAGCTCATC
*
4892349 TAATCAGAGGCTCAACAACTTTG-A
63 TAATCAGAGGCTCAACGACTTTGAA
4892373 AAAATAAATAA
1 AAAATAAATAA
4892384 AGCTTATCGA
Statistics
Matches: 297, Mismatches: 49, Indels: 24
0.80 0.13 0.06
Matches are distributed among these distances:
85 5 0.02
86 95 0.32
87 155 0.52
88 22 0.07
89 20 0.07
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (87 bp):
AAAATAAATAAGGCTCCTCTAAATAGAGGCTTAACGATTTTGAAAAATAAATAAAGCTCATCTAA
TCAGAGGCTCAACGACTTTGAA
Found at i:4893002 original size:22 final size:21
Alignment explanation
Indices: 4892974--4893061 Score: 122
Period size: 21 Copynumber: 4.1 Consensus size: 21
4892964 AAATTCTCAT
*
4892974 TCAAAGATTCTTATTTGAAAAC
1 TCAAAGATTCTCATTTG-AAAC
*
4892996 TCAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTGAAAC
* *
4893017 TTAAAAATTCTCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
*
4893038 TCAAATATTCTCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
4893059 TCA
1 TCA
4893062 CAATTTTATT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
21 43 0.73
22 16 0.27
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (21 bp):
TCAAAGATTCTCATTTGAAAC
Found at i:4893578 original size:79 final size:79
Alignment explanation
Indices: 4893452--4893637 Score: 232
Period size: 79 Copynumber: 2.4 Consensus size: 79
4893442 TTTTTCAACT
* * * *
4893452 GATCCATATCATTTGCATTATTTGATCGCAACTCACAGGTTACTCAGCACTAGCAATTTCAACAT
1 GATCCATATCATTTTCATCATTTGATCACAACTCACAGGCTACTCAGCACTAGCAATTTCAACAT
*
4893517 AAATTTCAT-TCACC
66 AAATTTCGTCT-ACC
* * * * *
4893531 GATCCATATCATTTTCATCATTTGATCACCATTCATAGGCTATTCAGCACTAGCAATTTTAACAT
1 GATCCATATCATTTTCATCATTTGATCACAACTCACAGGCTACTCAGCACTAGCAATTTCAACAT
*
4893596 AAATTTCGTCTACT
66 AAATTTCGTCTACC
*
4893610 AATCC-TCATCATTTTCATCATTTGATCA
1 GATCCAT-ATCATTTTCATCATTTGATCA
4893638 TAAACCCCAA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
78 1 0.01
79 91 0.98
80 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.37
Consensus pattern (79 bp):
GATCCATATCATTTTCATCATTTGATCACAACTCACAGGCTACTCAGCACTAGCAATTTCAACAT
AAATTTCGTCTACC
Found at i:4894241 original size:22 final size:20
Alignment explanation
Indices: 4894215--4894270 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
4894205 ATTTGAGTAT
4894215 TCATTTTTTCTCTTTTTTCATC
1 TCATTTTTTCTCTTTTTT--TC
*
4894237 TCATTTTTT-TCTTTGTTTC
1 TCATTTTTTCTCTTTTTTTC
4894256 TC-TTTTTTCT-TTTTT
1 TCATTTTTTCTCTTTTT
4894271 GTCCATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
21 7 0.23
22 9 0.29
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (20 bp):
TCATTTTTTCTCTTTTTTTC
Found at i:4897568 original size:58 final size:58
Alignment explanation
Indices: 4897504--4898129 Score: 690
Period size: 59 Copynumber: 10.6 Consensus size: 58
4897494 TTGTGCAGGA
* * *
4897504 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTCTTTT-AAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAA-TTTATTTTCAAGG
* * * *
4897562 AAAATTGATACTTTCAACTTTTCCTAAAAAATTTATTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCTCAAAAA--TATTTTTTTGAAAATTTATTTTCAAGG
* * * *
4897622 AAAATTGATACTTTCAATTTTTTCCCAAAAATATTTTTTTTGAAATTTTTATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTTGAAA-ATTTATTTTCAAGG
* ** *
4897682 AAAATTGATACTTTCAACTTTTCCTCAAAAA-CCTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTATTTTCAAGG
* * * *
4897739 AAAATTGATACTTTCAAC-TTTTCCCGAAAATATTTTTTTGAAACTTTAATTTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTT-ATTTTCAAGG
** *
4897797 AAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAA-TATTTTTTTGAAAATTTATTTTCAAGG
* * *
4897856 AAAATTGATACTTTCAAC-TTTTCTCCAAAAACATTTTTTTGAAACTTTGATTTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTTGAAAATTT-ATTTTCAAGG
* * * * *
4897915 AAAATTGATACTTTCAACTTTTCCTCAAAAAAAACCTTTTTTTTCTAAAATTTATTTTTAAAG
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAATA---TTTTTTT-GAAAATTTATTTTCAAGG
* * **
4897978 AAAATTGATACTTTCAACTTTTTCCCAAAAATA-TTTTTTGAAAACTTTGATTTTCGATA
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAA-TTT-ATTTTCAAGG
* *
4898037 AAAATTGATAATTTCAAC-TTTTCTTCAAAAA-ACCTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTC-TCAAAAATA--TTTTTTTGAAAATTTATTTTCAAGG
* *
4898096 AAAATTGATACTTTCAACTTTTCCCCAAAAATAT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATAT
4898130 ATATTTTTTA
Statistics
Matches: 477, Mismatches: 66, Indels: 50
0.80 0.11 0.08
Matches are distributed among these distances:
56 9 0.02
57 46 0.10
58 104 0.22
59 138 0.29
60 115 0.24
61 15 0.03
62 6 0.01
63 38 0.08
64 6 0.01
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTATTTTCAAGG
Found at i:4897608 original size:17 final size:17
Alignment explanation
Indices: 4897588--4897627 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4897578 ACTTTTCCTA
**
4897588 AAAAATTTATTTTTTTG
1 AAAAATTTATTTTTAAG
4897605 -AAAATTTATTTTTAAG
1 AAAAATTTATTTTTAAG
4897621 AAAAATT
1 AAAAATT
4897628 GATACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
AAAAATTTATTTTTAAG
Found at i:4897624 original size:118 final size:116
Alignment explanation
Indices: 4897502--4898129 Score: 841
Period size: 118 Copynumber: 5.3 Consensus size: 116
4897492 TCTTGTGCAG
* * *
4897502 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTCTTTTAAAACTTTAATTTCGAGGAAAAT
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAAAACTTTATTTTCGAGGAAAAT
**
4897567 TGATACTTTCAACTTTTCCTAAAAAATTTATTTTTTTGAAAATTTATTTTTAA
66 TGATACTTTCAACTTTTCCTAAAAAA--CCTTTTTTTGAAAATTTATTTTTAA
* ** * *
4897620 GAAAAATTGATACTTTCAATTTTTTCCCAAAAATATTTTTTTTGAAATTTTTATTTTCAAAGAAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATA-TTTTTTT-AAAACTTTATTTTCGAGGAAA
*
4897685 ATTGATACTTTCAACTTTTCCTCAAAAACC-TTTTTTGAAAATTTATTTTTAA
64 ATTGATACTTTCAACTTTTCCTAAAAAACCTTTTTTTGAAAATTTATTTTTAA
* * *
4897737 GGAAAATTGATACTTTCAAC-TTTTCCCGAAAATATTTTTTTGAAACTTTAATTTTCGAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAAAACTTT-ATTTTCGAGGAAAA
* *
4897801 TTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAA
65 TTGATACTTTCAACTTTTCCT-AAAAAACCTTTTTTTGAAAATTTATTTTTAA
* * *
4897854 GGAAAATTGATACTTTCAAC-TTTTCTCCAAAAACATTTTTTTGAAACTTTGATTTTCGAGGAAA
1 GAAAAATTGATACTTTCAACTTTTTC-CCAAAAATATTTTTTTAAAACTTT-ATTTTCGAGGAAA
*
4897918 ATTGATACTTTCAACTTTTCCTCAAAAAAAACCTTTTTTTTCTAAAATTTATTTTTAA
64 ATTGATACTTTCAACTTTTCCT---AAAAAACC-TTTTTTT-GAAAATTTATTTTTAA
* **
4897976 -AGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTGATTTTCGATAAAA
1 GA-AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAAAACTTT-ATTTTCGAGGAAA
* *
4898040 ATTGATAATTTCAACTTTTCTTCAAAAAACCTTTTTTTGAAAATTTATTTTTAA
64 ATTGATACTTTCAACTTTTCCT-AAAAAACCTTTTTTTGAAAATTTATTTTTAA
* *
4898094 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATAT
4898130 ATATTTTTTA
Statistics
Matches: 456, Mismatches: 41, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
114 5 0.01
115 39 0.09
116 19 0.04
117 87 0.19
118 137 0.30
119 13 0.03
120 58 0.13
121 7 0.02
122 86 0.19
123 5 0.01
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (116 bp):
GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAAAACTTTATTTTCGAGGAAAAT
TGATACTTTCAACTTTTCCTAAAAAACCTTTTTTTGAAAATTTATTTTTAA
Found at i:4898175 original size:6 final size:6
Alignment explanation
Indices: 4898160--4898214 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
4898150 AGAAAATAAC
*
4898160 AAAATA AAAATGA AAAA-A AAAGT- AAAATA AAAATA AAAAT- AAAATA
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
4898206 AAGATA AAA
1 AAAATA AAA
4898215 GAATATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 13 0.32
6 23 0.56
7 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:4898204 original size:17 final size:17
Alignment explanation
Indices: 4898160--4898214 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
4898150 AGAAAATAAC
4898160 AAAATAAAAATGAAAAA-A
1 AAAAT-AAAAT-AAAAATA
*
4898178 AAAGTAAAATAAAAATA
1 AAAATAAAATAAAAATA
*
4898195 AAAATAAAATAAAGATA
1 AAAATAAAATAAAAATA
4898212 AAA
1 AAA
4898215 GAATATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 5 0.15
17 24 0.73
18 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:4898212 original size:11 final size:11
Alignment explanation
Indices: 4898160--4898214 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
4898150 AGAAAATAAC
4898160 AAAATAAAAAT
1 AAAATAAAAAT
4898171 GAAAA-AAAAAGT
1 -AAAATAAAAA-T
4898183 AAAATAAAAAT
1 AAAATAAAAAT
4898194 AAAA-ATAAAAT
1 AAAATA-AAAAT
4898205 AAAGATAAAA
1 AAA-ATAAAA
4898215 GAATATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.03
11 22 0.58
12 14 0.37
13 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:4898809 original size:10 final size:11
Alignment explanation
Indices: 4898785--4898813 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
4898775 GTCACCGAAA
4898785 TCTAGAAATTT
1 TCTAGAAATTT
4898796 TCTAGAAA-TT
1 TCTAGAAATTT
4898806 TCTAGAAA
1 TCTAGAAA
4898814 AAAATTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (11 bp):
TCTAGAAATTT
Found at i:4899115 original size:9 final size:9
Alignment explanation
Indices: 4899101--4899154 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 9
4899091 CCAGTCGGAT
4899101 AAATAAAAA
1 AAATAAAAA
4899110 AAATAAAAA
1 AAATAAAAA
*
4899119 AATTAAATAA
1 AAATAAA-AA
4899129 AAATAAATCAGA
1 AAATAAA--A-A
4899141 TAAATAAAAA
1 -AAATAAAAA
4899151 AAAT
1 AAAT
4899155 TAACAGATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 19 0.50
10 9 0.24
11 2 0.05
12 1 0.03
13 7 0.18
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAATAAAAA
Found at i:4899152 original size:22 final size:21
Alignment explanation
Indices: 4899098--4899188 Score: 91
Period size: 22 Copynumber: 4.3 Consensus size: 21
4899088 TTTCCAGTCG
4899098 GATAAATAAAAAAAATAAA-A
1 GATAAATAAAAAAAATAAACA
*
4899118 -A-AATTAAATAAAAATAAATCA
1 GATAAATAAA-AAAAATAAA-CA
*
4899139 GATAAATAAAAAAAATTAACA
1 GATAAATAAAAAAAATAAACA
*
4899160 GATAAATTAAAATTAAAT-AACA
1 GATAAA-TAAAA-AAAATAAACA
4899182 GATAAAT
1 GATAAAT
4899189 TATAATATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
18 6 0.10
19 10 0.17
21 10 0.17
22 24 0.40
23 10 0.17
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.22
Consensus pattern (21 bp):
GATAAATAAAAAAAATAAACA
Found at i:4899168 original size:12 final size:12
Alignment explanation
Indices: 4899151--4899190 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
4899141 TAAATAAAAA
4899151 AAATTAACAGAT
1 AAATTAACAGAT
4899163 AAATTAA-A-ATT
1 AAATTAACAGA-T
4899174 AAA-TAACAGAT
1 AAATTAACAGAT
4899185 AAATTA
1 AAATTA
4899191 TAATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (12 bp):
AAATTAACAGAT
Found at i:4899171 original size:41 final size:42
Alignment explanation
Indices: 4899098--4899188 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 42
4899088 TTTCCAGTCG
4899098 GATAAATAAAAAAAATAAAAAAATTAAATAAAAATAAAT-CA
1 GATAAATAAAAAAAATAAAAAAATTAAATAAAAATAAATACA
* * * *
4899139 GATAAATAAAAAAAATTAACAGA-TAAATTAAAATTAAATAACA
1 GATAAATAAAAAAAATAAAAAAATTAAA-TAAAAATAAAT-ACA
4899182 GATAAAT
1 GATAAAT
4899189 TATAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 4 0.09
41 30 0.70
43 9 0.21
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.22
Consensus pattern (42 bp):
GATAAATAAAAAAAATAAAAAAATTAAATAAAAATAAATACA
Found at i:4899879 original size:158 final size:158
Alignment explanation
Indices: 4899496--4899953 Score: 748
Period size: 152 Copynumber: 2.9 Consensus size: 158
4899486 TAAAATTTTA
* * *
4899496 CCAAGTAATTAGTTGTTGGAAATGATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAA
1 CCAAGTAATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAA
*
4899561 AATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGG
66 AATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGG
* *
4899626 ATTTATTAAAG--AAAAATCAAAATCAT
131 ATTAATTAAAGAAAAAAATCAAAATCAG
*
4899652 CC----AATTAATTATTGGAAATTATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAGAA
1 CCAAGTAATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAA
* *
4899713 AATTCCCTCACCTCAAGAGTATACAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGG
66 AATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGG
4899778 ATTAATTAAAGAAAAAAATCAAAATCAG
131 ATTAATTAAAGAAAAAAATCAAAATCAG
* *
4899806 CCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAA
1 CCAAGTAATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAA
* *
4899871 AATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCG
66 AATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCG
4899936 GATTAATTAAAGAAAAAA
130 GATTAATTAAAGAAAAAA
4899954 GAAAAAAAAA
Statistics
Matches: 279, Mismatches: 16, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
152 127 0.46
154 16 0.06
156 2 0.01
158 92 0.33
159 42 0.15
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (158 bp):
CCAAGTAATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAA
AATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGG
ATTAATTAAAGAAAAAAATCAAAATCAG
Found at i:4900002 original size:1 final size:1
Alignment explanation
Indices: 4899998--4900030 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
4899988 TAAAAAATTC
4899998 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4900031 CCTGGAGCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4900396 original size:19 final size:19
Alignment explanation
Indices: 4900354--4900400 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
4900344 AGAACACCGG
*
4900354 TGCCGGATTCTGGAAATGT
1 TGCCGGAATCTGGAAATGT
* * *
4900373 CGCCGGAATCTGGAATTTT
1 TGCCGGAATCTGGAAATGT
4900392 TGCCGGAAT
1 TGCCGGAAT
4900401 ATGGCCGGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (19 bp):
TGCCGGAATCTGGAAATGT
Found at i:4901024 original size:3 final size:3
Alignment explanation
Indices: 4901016--4901041 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4901006 ATCTTACAAA
4901016 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4901042 ATATATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4901253 original size:19 final size:20
Alignment explanation
Indices: 4901204--4901261 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
4901194 CCCATTTGGC
* *
4901204 CAGGCCCAAATGATCTGGGT
1 CAGGCCCAATTGATCCGGGT
4901224 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
4901244 CAGG-CCAATTGATCCGGG
1 CAGGCCCAATTGATCCGGG
4901262 CCCGGACTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 14 0.39
20 22 0.61
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (20 bp):
CAGGCCCAATTGATCCGGGT
Found at i:4901333 original size:14 final size:14
Alignment explanation
Indices: 4901301--4901332 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
4901291 ATATTAATAG
4901301 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
4901315 AAAAAG-AAAAGAA
1 AAAAAGAAAAAGAA
4901328 AAAAA
1 AAAAA
4901333 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:4901421 original size:6 final size:5
Alignment explanation
Indices: 4901411--4901484 Score: 57
Period size: 5 Copynumber: 14.6 Consensus size: 5
4901401 ATATATATAT
*
4901411 AAATA ATAATA AAA-A ATA-A AAATA AAATAA AAATA AAATA AAATA CAAATGTA
1 AAATA A-AATA AAATA AAATA AAATA AAAT-A AAATA AAATA AAATA -AAA--TA
*
4901464 AAATA CAA-A AAA-A AAATA AAA
1 AAATA AAATA AAATA AAATA AAA
4901485 AGAAAAATAG
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
4 13 0.22
5 27 0.47
6 13 0.22
7 3 0.05
8 2 0.03
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:4901448 original size:11 final size:11
Alignment explanation
Indices: 4901423--4901504 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
4901413 ATAATAATAA
4901423 AAAATAAAAAT
1 AAAATAAAAAT
4901434 AAAATAAAAAT
1 AAAATAAAAAT
4901445 AAAAT-AAAAT
1 AAAATAAAAAT
*
4901455 ACAAATGTAAAAT
1 A-AAAT-AAAAAT
*
4901468 -ACA-AAAAA-
1 AAAATAAAAAT
*
4901476 AAAATAAAAAGA
1 AAAATAAAAA-T
* *
4901488 AAAATAGAAAG
1 AAAATAAAAAT
4901499 AAAATA
1 AAAATA
4901505 GACGCACCTA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.10
10 11 0.19
11 28 0.47
12 9 0.15
13 5 0.08
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:4901479 original size:13 final size:12
Alignment explanation
Indices: 4901411--4901493 Score: 51
Period size: 13 Copynumber: 6.4 Consensus size: 12
4901401 ATATATATAT
*
4901411 AAATAATAATAAA
1 AAATAA-AAAAAA
4901424 AAATAAAAATAAA
1 AAATAAAAA-AAA
4901437 ATAA-AAATAAAATA
1 A-AATAAA-AAAA-A
***
4901451 AAATACAAATGTA
1 AAATA-AAAAAAA
4901464 AAATACAAAAAAA
1 AAATA-AAAAAAA
*
4901477 AAATAAAAAGAA
1 AAATAAAAAAAA
4901489 AAATA
1 AAATA
4901494 GAAAGAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
12 13 0.23
13 33 0.59
14 8 0.14
15 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (12 bp):
AAATAAAAAAAA
Found at i:4901485 original size:6 final size:6
Alignment explanation
Indices: 4901411--4901493 Score: 73
Period size: 6 Copynumber: 13.8 Consensus size: 6
4901401 ATATATATAT
* *
4901411 AAATAA TAATAAA AAATAA AAAT-A AAATAA AAAT-A AAAT-A AAATAC
1 AAATAA AAAT-AA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * *
4901457 AAATGTA AAATACA AAAAAA AAATAA AAAGAA AAATA
1 AAAT-AA AAATA-A AAATAA AAATAA AAATAA AAATA
4901494 GAAAGAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
5 15 0.24
6 33 0.53
7 14 0.23
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:4901782 original size:41 final size:41
Alignment explanation
Indices: 4901689--4901859 Score: 189
Period size: 41 Copynumber: 4.1 Consensus size: 41
4901679 TTCGACCGAA
* * ** * *
4901689 GCTCCTCTAAGCAGAGGCTCAATGAGTTTGAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCACAACAACTTTG-GAAA-ATAAATT
* * *
4901732 GCTCCTCTAATCCGAGGCTCAACAACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAACAACTTTGGAAAATAAATT
* *
4901773 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACAACTTTGGAAAA-TAAATT
* * *
4901815 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACAACTTTGGAAAATAAATT
4901856 GCTC
1 GCTC
4901860 ATTGACAATC
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 46 0.41
42 42 0.37
43 25 0.22
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACAACAACTTTGGAAAATAAATT
Found at i:4902896 original size:24 final size:24
Alignment explanation
Indices: 4902868--4902915 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4902858 TTTCATTCAC
*
4902868 TTTTTTTTTTCATTTTCATTTTTTA
1 TTTTTTTATT-ATTTTCATTTTTTA
*
4902893 TTTTTTTATTTTTTTCATTTTTT
1 TTTTTTTATTATTTTCATTTTTT
4902916 TCAAGCATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTTTATTATTTTCATTTTTTA
Found at i:4902917 original size:9 final size:9
Alignment explanation
Indices: 4902880--4902918 Score: 57
Period size: 8 Copynumber: 4.7 Consensus size: 9
4902870 TTTTTTTTCA
4902880 TTTTCA-TT
1 TTTTCATTT
4902888 TTTT-ATTT
1 TTTTCATTT
4902896 TTTT-ATTT
1 TTTTCATTT
4902904 TTTTCATTT
1 TTTTCATTT
4902913 TTTTCA
1 TTTTCA
4902919 AGCATGGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 1 0.03
8 18 0.62
9 10 0.34
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCATTT
Found at i:4908953 original size:13 final size:13
Alignment explanation
Indices: 4908935--4908966 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
4908925 TAGAGGGATG
4908935 GAGCTCGGGTGTA
1 GAGCTCGGGTGTA
4908948 GAGCTCGGGTGTA
1 GAGCTCGGGTGTA
4908961 GAGCTC
1 GAGCTC
4908967 ATGTTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.44, T:0.22
Consensus pattern (13 bp):
GAGCTCGGGTGTA
Found at i:4909718 original size:17 final size:16
Alignment explanation
Indices: 4909683--4909721 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4909673 CTTTTCCTAA
**
4909683 AAAATTTATTTTTTTG
1 AAAATTTATTTTTAGG
4909699 AAAATTTATTTTTAAGG
1 AAAATTTATTTTT-AGG
4909716 AAAATT
1 AAAATT
4909722 GATACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
AAAATTTATTTTTAGG
Found at i:4909912 original size:58 final size:57
Alignment explanation
Indices: 4909598--4910169 Score: 655
Period size: 58 Copynumber: 9.7 Consensus size: 57
4909588 TTGTGCAAGA
* * * *
4909598 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGAAACTTTATTTTTGAGG
* * *
4909656 AAAATTGATACTTTCAACTTTTCCTAAAAAATTTATTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCC-CAAAAA--TATTTTTTTGAAACTTTATTTTTGAGG
* * *
4909716 AAAATTGATACTTTCAATTTTTTCCCAAAAATATTTTTTGGAAACTTTTATTTTCGAGG
1 AAAATTGATACTTTCAA-CTTTTCCCAAAAATATTTTTTTGAAAC-TTTATTTTTGAGG
** * *
4909775 AAAATTGATACTTTCAACTTTTCCTCAAAAA-CGTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTGAAACTTTATTTTTGAGG
* *
4909832 AAAATTGATACTTTCAACTTTTCCCAAAAAT-TTTTGTTTGAAACTTTGATTTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCCAAAAATATTTT-TTTGAAACTTT-ATTTTTGAGG
** * *
4909890 AAAATTGATACTTTCAACTTTTCCTGAAAATATTTTTTTAAAACTTTGATTTTTGAGA
1 AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAACTTT-ATTTTTGAGG
* * * *
4909948 AAAATTGATACTTTCAAATTTTTCTCAAAAACCT-TTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTC-AACTTTTCCCAAAAA--TATTTTTTTGAAACTTTATTTTTGAGG
*
4910007 AAAATTGATACTTTTAACTTTTCCCCAAAAATATTTTTTTTGAAACTTTGATTTTTGAGG
1 AAAATTGATACTTTCAACTTTT-CCCAAAAATA-TTTTTTTGAAACTTT-ATTTTTGAGG
* * * *
4910067 AAAATTGATACTTTCAACTTTTCCTAAAAAAAACCTTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCC---CAAAAA---TATTTTTTTGAAACTTTATTTTTGAGG
4910130 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTT
4910170 TTATTTTGTT
Statistics
Matches: 441, Mismatches: 49, Indels: 48
0.82 0.09 0.09
Matches are distributed among these distances:
56 9 0.02
57 51 0.12
58 135 0.31
59 94 0.21
60 87 0.20
61 12 0.03
62 5 0.01
63 31 0.07
64 16 0.04
65 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAACTTTATTTTTGAGG
Found at i:4910228 original size:20 final size:20
Alignment explanation
Indices: 4910185--4910254 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
4910175 TTGTTTAAAG
* * *
4910185 AAAATAACAAAATAAAAGTG
1 AAAATAAAAAAATAAAAATA
4910205 AAAATAAAAAAATAAAAAATA
1 AAAATAAAAAAAT-AAAAATA
* *
4910226 AAAA-AAGTAAAACAAAAATA
1 AAAATAA-AAAAATAAAAATA
4910246 AAAATAAAA
1 AAAATAAAA
4910255 TAAAGATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.80, C:0.03, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAATAAAAAAATAAAAATA
Found at i:4910242 original size:27 final size:28
Alignment explanation
Indices: 4910212--4910265 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
4910202 GTGAAAATAA
4910212 AAAAATAAAAAATAAAA-AAAG-TAAAAC
1 AAAAAT-AAAAATAAAATAAAGATAAAAC
4910239 AAAAATAAAAATAAAATAAAGATAAAA
1 AAAAATAAAAATAAAATAAAGATAAAA
4910266 GAATATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 10 0.40
27 10 0.40
28 5 0.20
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (28 bp):
AAAAATAAAAATAAAATAAAGATAAAAC
Found at i:4910263 original size:11 final size:11
Alignment explanation
Indices: 4910193--4910265 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 11
4910183 AGAAAATAAC
*
4910193 AAAATAAAAGTG
1 AAAATAAAA-TA
4910205 AAAATAAAA-A
1 AAAATAAAATA
4910215 AATAA-AAAAT-
1 AA-AATAAAATA
*
4910225 AAAA-AAAGTA
1 AAAATAAAATA
4910235 AAACA-AAAATA
1 AAA-ATAAAATA
4910246 AAAATAAAATA
1 AAAATAAAATA
*
4910257 AAGATAAAA
1 AAAATAAAA
4910266 GAATATTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
9 6 0.12
10 12 0.23
11 25 0.48
12 9 0.17
ACGTcount: A:0.79, C:0.01, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:4910863 original size:48 final size:48
Alignment explanation
Indices: 4910733--4910939 Score: 188
Period size: 48 Copynumber: 4.3 Consensus size: 48
4910723 TTTCGAGAAC
* * * *
4910733 AGATGAGATTTTTAAAGTTATTGA-ATCTCTGCTTATAAGAGCTTTTTCA
1 AGATGA-ATTTTTAAAATTATTGAGA-CTTTGCTTAGAGGAGCTTTTTCA
* * *
4910782 AGATGAA-TTTTAAAGA-TGTTGAG-CTTCTACTTAGAGGAGTTTTTTCA
1 AGATGAATTTTTAAA-ATTATTGAGACTT-TGCTTAGAGGAGCTTTTTCA
4910829 AGATGAATTTTTAAAATTATTGAGACTTTGCTTAGAGGAGCTTTTTCA
1 AGATGAATTTTTAAAATTATTGAGACTTTGCTTAGAGGAGCTTTTTCA
* * * * * * * * *
4910877 AAATGGATTTTTGAAGTTGTTGAGCCTATGCCTAGATGAGCTTTTTCA
1 AGATGAATTTTTAAAATTATTGAGACTTTGCTTAGAGGAGCTTTTTCA
* *
4910925 ATATGGATTTTTAAA
1 AGATGAATTTTTAAA
4910940 GTCGTTAAAC
Statistics
Matches: 131, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
46 2 0.02
47 36 0.27
48 84 0.64
49 9 0.07
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (48 bp):
AGATGAATTTTTAAAATTATTGAGACTTTGCTTAGAGGAGCTTTTTCA
Found at i:4910954 original size:96 final size:94
Alignment explanation
Indices: 4910733--4910965 Score: 241
Period size: 96 Copynumber: 2.4 Consensus size: 94
4910723 TTTCGAGAAC
* * * *
4910733 AGATGAGATTTTTAAAGTTATTGAATCTCTGCTTATAAGAGCTTTTTCAAGATGAATTTTAAAGA
1 AGATG-GATTTTTAAAGTTATT-AAACTTTGCTTAGAAGAGCTTTTTCAAAATGAATTTTAAAGA
* * * *
4910798 TGTTGAGCTTCTACTTAGAGGAGTTTTTTCA
64 TGTTGAGCCTATACCTAGAGGAGCTTTTTCA
* * * * * * *
4910829 AGATGAATTTTTAAAATTATTGAGACTTTGCTTAGAGGAGCTTTTTCAAAATGGATTTTTGAAGT
1 AGATGGATTTTTAAAGTTATT-AAACTTTGCTTAGAAGAGCTTTTTCAAAAT-GAATTTTAAAGA
* *
4910894 TGTTGAGCCTATGCCTAGATGAGCTTTTTCA
64 TGTTGAGCCTATACCTAGAGGAGCTTTTTCA
* **
4910925 ATATGGATTTTTAAAGTCGTTAAACCTTTGCTTAGAAGAGC
1 AGATGGATTTTTAAAGTTATTAAA-CTTTGCTTAGAAGAGC
4910966 CCTTTTAAAA
Statistics
Matches: 111, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
95 41 0.37
96 70 0.63
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (94 bp):
AGATGGATTTTTAAAGTTATTAAACTTTGCTTAGAAGAGCTTTTTCAAAATGAATTTTAAAGATG
TTGAGCCTATACCTAGAGGAGCTTTTTCA
Found at i:4913651 original size:71 final size:70
Alignment explanation
Indices: 4913517--4913720 Score: 346
Period size: 66 Copynumber: 3.0 Consensus size: 70
4913507 TGAGGGCCTG
* *
4913517 AAAGGTCAGATCAAGCTGGTCCATCGTGGTCAA-AATCAAATTATTGAAGCTGAGATAAGCAATG
1 AAAGGTCAGATCAAACTGGTCTATCGTGGTCAATAATCAAATTATTGAAGCTGAGATAAGCAATG
4913581 GCGTGA
66 GC-TGA
4913587 AAAGGTCAGATCAAACTGGTCTATCGTGGTCAATAATCAAATTATTGAAGCTGAGATAAGCAA--
1 AAAGGTCAGATCAAACTGGTCTATCGTGGTCAATAATCAAATTATTGAAGCTGAGATAAGCAATG
4913650 --TGA
66 GCTGA
4913653 AAAGGTCAGATCAAACTGGTCTATCGTGGTCAATAATCAAATTATTGAAGCTGAGATAAGCAATG
1 AAAGGTCAGATCAAACTGGTCTATCGTGGTCAATAATCAAATTATTGAAGCTGAGATAAGCAATG
4913718 GCT
66 GCT
4913721 TGCTACAATT
Statistics
Matches: 127, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
66 66 0.52
70 32 0.25
71 29 0.23
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (70 bp):
AAAGGTCAGATCAAACTGGTCTATCGTGGTCAATAATCAAATTATTGAAGCTGAGATAAGCAATG
GCTGA
Found at i:4913879 original size:33 final size:31
Alignment explanation
Indices: 4913821--4913884 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
4913811 TTATTTTTTA
4913821 ATTTAAATTTAATTTGAAATAAAAATTAAATT
1 ATTTAAATTTAATTTGAAATAAAAA-TAAATT
*
4913853 ATTTAAATTT-ATTTAATAAATAAAAATAAATT
1 ATTTAAATTTAATTT--GAAATAAAAATAAATT
4913885 TAATTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 16 0.55
33 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTTAAATTTAATTTGAAATAAAAATAAATT
Found at i:4913986 original size:21 final size:22
Alignment explanation
Indices: 4913946--4913994 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
4913936 TTATAAAATC
4913946 TGAATTAAACTCATAAATTATT
1 TGAATTAAACTCATAAATTATT
4913968 TGAATTAAA-T-ATAAAATTATT
1 TGAATTAAACTCAT-AAATTATT
*
4913989 TTAATT
1 TGAATT
4913995 TAATTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
TGAATTAAACTCATAAATTATT
Found at i:4914016 original size:31 final size:33
Alignment explanation
Indices: 4913981--4914042 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
4913971 ATTAAATATA
**
4913981 AAATTATTTTAATTT-AATTTAA-TTAATAAAT
1 AAATTATTCAAATTTAAATTTAATTTAATAAAT
4914012 AAATTATTCAAATTTAAATTTAATTTAATAA
1 AAATTATTCAAATTTAAATTTAATTTAATAA
4914043 TAATCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 13 0.48
32 7 0.26
33 7 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATTATTCAAATTTAAATTTAATTTAATAAAT
Found at i:4914049 original size:27 final size:28
Alignment explanation
Indices: 4914019--4914084 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
4914009 AATAAATTAT
4914019 TCAAATTTAAATTT-AATTTAATAATAA
1 TCAAATTTAAATTTAAATTTAATAATAA
* * **
4914046 TCAAA-TAAAATTTAAATTTTATTTTAA
1 TCAAATTTAAATTTAAATTTAATAATAA
4914073 TCAAATTTAAAT
1 TCAAATTTAAAT
4914085 AATTTATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.22
27 20 0.62
28 5 0.16
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
TCAAATTTAAATTTAAATTTAATAATAA
Found at i:4914057 original size:32 final size:35
Alignment explanation
Indices: 4913986--4914069 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 35
4913976 ATATAAAATT
*
4913986 ATTTTAATTTAATTTAATTAATAAATAAATTATTCAA
1 ATTTAAATTTAATTTAATTAATAAATAAATTA-T-AA
4914023 ATTTAAATTTAATTTAA-TAAT-AATCAAA-TA-AA
1 ATTTAAATTTAATTTAATTAATAAAT-AAATTATAA
*
4914055 ATTTAAATTTTATTT
1 ATTTAAATTTAATTT
4914070 TAATCAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 16 0.36
35 5 0.11
36 7 0.16
37 16 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTTAAATTTAATTTAATTAATAAATAAATTATAA
Found at i:4918747 original size:23 final size:24
Alignment explanation
Indices: 4918702--4918747 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
4918692 TTAGCTGGAC
4918702 AAAATTTATATGAAATTTTTTAAAT
1 AAAATTTATA-GAAATTTTTTAAAT
*
4918727 AAAATTTATA-AATTTTTTTAA
1 AAAATTTATAGAAATTTTTTAA
4918748 GTGATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAAATTTATAGAAATTTTTTAAAT
Found at i:4918905 original size:14 final size:13
Alignment explanation
Indices: 4918886--4918939 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 13
4918876 AATATTTTTA
4918886 TTAAAAATATCTAT
1 TTAAAAATAT-TAT
4918900 TTAAAAATA-TAT
1 TTAAAAATATTAT
*
4918912 ATAAAAA-ATTAT
1 TTAAAAATATTAT
4918924 TTAAAAA-ATT-T
1 TTAAAAATATTAT
4918935 TTAAA
1 TTAAA
4918940 TTTACATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 7 0.19
12 21 0.57
14 9 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAAATATTAT
Found at i:4919165 original size:29 final size:30
Alignment explanation
Indices: 4919133--4919193 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
4919123 GCAAGTCCCT
*
4919133 TTTTTTTTTTGCC-ACTAAGTCCCTGGTAG
1 TTTTTTTTTGGCCAACTAAGTCCCTGGTAG
* *
4919162 TTTTTTTTTGGCCAATTAAGTCCCTTGTAG
1 TTTTTTTTTGGCCAACTAAGTCCCTGGTAG
4919192 TT
1 TT
4919194 GAATAAGGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.51
Consensus pattern (30 bp):
TTTTTTTTTGGCCAACTAAGTCCCTGGTAG
Found at i:4933424 original size:18 final size:18
Alignment explanation
Indices: 4933394--4933429 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4933384 AAAATTATCC
4933394 TTTTAATAATTTTAATTAA
1 TTTTAATAATTTT-ATTAA
4933413 TTTTAA-AATTTTATTAA
1 TTTTAATAATTTTATTAA
4933430 AAAGATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 6 0.35
19 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAATAATTTTATTAA
Found at i:4934046 original size:33 final size:31
Alignment explanation
Indices: 4933988--4934051 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
4933978 TTATTTTTTA
4933988 ATTTAAATTTAATTTGAAATAAAAATTAAATT
1 ATTTAAATTTAATTTGAAATAAAAA-TAAATT
*
4934020 ATTTAAATTT-ATTTAATAAATAAAAATAAATT
1 ATTTAAATTTAATTT--GAAATAAAAATAAATT
4934052 TAATTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 16 0.55
33 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTTAAATTTAATTTGAAATAAAAATAAATT
Found at i:4934153 original size:21 final size:22
Alignment explanation
Indices: 4934113--4934161 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
4934103 TTATAAAATC
4934113 TGAATTAAACTCATAAATTATT
1 TGAATTAAACTCATAAATTATT
4934135 TGAATTAAA-T-ATAAAATTATT
1 TGAATTAAACTCAT-AAATTATT
*
4934156 TTAATT
1 TGAATT
4934162 TAATTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
TGAATTAAACTCATAAATTATT
Found at i:4934183 original size:31 final size:33
Alignment explanation
Indices: 4934148--4934245 Score: 96
Period size: 32 Copynumber: 3.0 Consensus size: 33
4934138 ATTAAATATA
**
4934148 AAATTATTTTAATTT-AATTTAA-TTAATAAAT
1 AAATTATTCAAATTTAAATTTAATTTAATAAAT
4934179 AAATTATTCAAATTTAAATTTAATTTAAT-AAT
1 AAATTATTCAAATTTAAATTTAATTTAATAAAT
* * *
4934211 -AATTAAATAAAATTTAAATTTTATTTTAATCAAAT
1 AAATT-ATTCAAATTTAAA-TTTAATTTAAT-AAAT
4934246 TTAAATAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 17 0.30
32 21 0.38
33 15 0.27
35 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATTATTCAAATTTAAATTTAATTTAATAAAT
Found at i:4934239 original size:33 final size:32
Alignment explanation
Indices: 4934188--4934253 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
4934178 TAAATTATTC
4934188 AAATTTAAATTTAATTTAAT-AATAATTAAATA
1 AAATTTAAATTTAATTTAATCAA-AATTAAATA
* *
4934220 AAATTTAAATTTTATTTTAATCAAATTTAAATA
1 AAATTTAAA-TTTAATTTAATCAAAATTAAATA
4934253 A
1 A
4934254 TTTATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 9 0.30
33 19 0.63
34 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (32 bp):
AAATTTAAATTTAATTTAATCAAAATTAAATA
Found at i:4935609 original size:18 final size:19
Alignment explanation
Indices: 4935561--4935610 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
4935551 CATTTTTTAT
4935561 TATTTAATATTTATAATATC
1 TATTTAA-ATTTATAATATC
4935581 TAAATTT--ATTTA-AATATC
1 T--ATTTAAATTTATAATATC
4935599 TATTTAAATTTA
1 TATTTAAATTTA
4935611 GTATCACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
16 4 0.15
18 12 0.46
19 5 0.19
20 1 0.04
22 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTAAATTTATAATATC
Found at i:4940262 original size:2 final size:2
Alignment explanation
Indices: 4940255--4940284 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4940245 GATATCAAAT
*
4940255 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4940285 CACACTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4950977 original size:15 final size:15
Alignment explanation
Indices: 4950957--4950995 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
4950947 ATATAACAAA
4950957 AATTTTTAATTT-AT
1 AATTTTTAATTTAAT
4950971 CAA-TTTTAATTTAAT
1 -AATTTTTAATTTAAT
4950986 AATTTTTAAT
1 AATTTTTAAT
4950996 AATAAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTTAATTTAAT
Found at i:4951316 original size:28 final size:29
Alignment explanation
Indices: 4951280--4951334 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
4951270 CCTACATTTT
*
4951280 TTTTTGCC-ACGAAGTCCCTAGTAGTTTC
1 TTTTGGCCAACGAAGTCCCTAGTAGTTTC
** *
4951308 TTTTGGCCAATTAAGTCCCTTGTAGTT
1 TTTTGGCCAACGAAGTCCCTAGTAGTT
4951335 GAATAAACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 7 0.32
29 15 0.68
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (29 bp):
TTTTGGCCAACGAAGTCCCTAGTAGTTTC
Found at i:4951693 original size:15 final size:16
Alignment explanation
Indices: 4951673--4951702 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4951663 AATTCAAATT
4951673 ATTTTTTT-CTTTTTA
1 ATTTTTTTCCTTTTTA
4951688 ATTTTTTTCCTTTTT
1 ATTTTTTTCCTTTTT
4951703 TGTCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (16 bp):
ATTTTTTTCCTTTTTA
Found at i:4952459 original size:26 final size:26
Alignment explanation
Indices: 4952413--4952462 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4952403 ATTAGACTCA
*
4952413 CGAGCTACTCGACTCAATCGATAAGT
1 CGAGCTACTCAACTCAATCGATAAGT
*
4952439 CGAGCTACT-AACTCGATTCGATAA
1 CGAGCTACTCAACTC-AATCGATAA
4952463 TAATCGAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (26 bp):
CGAGCTACTCAACTCAATCGATAAGT
Found at i:4952583 original size:11 final size:11
Alignment explanation
Indices: 4952567--4952592 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4952557 CTCGAAGAAG
4952567 ATAATAATTTA
1 ATAATAATTTA
4952578 ATAATAATTTA
1 ATAATAATTTA
4952589 ATAA
1 ATAA
4952593 CATCAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAATAATTTA
Found at i:4955270 original size:28 final size:25
Alignment explanation
Indices: 4955241--4955291 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4955231 AATAATCAAT
*
4955241 TTTTAAATAATATAATTATATAATATA
1 TTTTAAATAA-A-AATAATATAATATA
*
4955268 TTTTAAATGAAAATAATATAATAT
1 TTTTAAATAAAAATAATATAATAT
4955292 TCATTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 1 0.05
27 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTTAAATAAAAATAATATAATATA
Found at i:4955732 original size:24 final size:21
Alignment explanation
Indices: 4955705--4955748 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
4955695 AAATGATATA
*
4955705 ATTTAAGATCTTAATAATAATTAT
1 ATTT-AGAT-TTAACAA-AATTAT
4955729 ATTTAGATTTAACAAAATTA
1 ATTTAGATTTAACAAAATTA
4955749 AAATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 4 0.21
24 4 0.21
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
ATTTAGATTTAACAAAATTAT
Found at i:4955947 original size:19 final size:18
Alignment explanation
Indices: 4955925--4955962 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
4955915 TAATTCGATT
4955925 TTTTTAATTTAAAATTTAA
1 TTTTTAATTT-AAATTTAA
4955944 TTTTTAATTTAAATTTAA
1 TTTTTAATTTAAATTTAA
4955962 T
1 T
4955963 ATATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTAATTTAAATTTAA
Found at i:4956719 original size:2 final size:2
Alignment explanation
Indices: 4956707--4956744 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4956697 GATATCAAAT
*
4956707 TA TA TA AA TA TA TA TA TA TA TA TA TA 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
4956745 CACACTAAAC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4956720 original size:10 final size:10
Alignment explanation
Indices: 4956698--4956742 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
4956688 CATTAAGAAG
4956698 ATATCAAAT-T
1 ATAT-AAATAT
4956708 ATATAAATAT
1 ATATAAATAT
*
4956718 ATATATATAT
1 ATATAAATAT
*
4956728 ATATATATAT
1 ATATAAATAT
4956738 ATATA
1 ATATA
4956743 TACACACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
9 4 0.12
10 29 0.88
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATAAATAT
Found at i:4958119 original size:2 final size:2
Alignment explanation
Indices: 4958114--4958139 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4958104 TTGCTGTGTG
4958114 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4958140 ATTTTTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4963853 original size:12 final size:14
Alignment explanation
Indices: 4963833--4963880 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 14
4963823 ATTATAGTTA
4963833 TTAT-TTAAAAAAT
1 TTATATTAAAAAAT
*
4963846 TTA-A-TAAAAATT
1 TTATATTAAAAAAT
4963858 TTATATTAAATAAAT
1 TTATATTAAA-AAAT
4963873 TT-TATTAA
1 TTATATTAA
4963881 TATTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 10 0.34
13 4 0.14
14 10 0.34
15 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATATTAAAAAAT
Found at i:4968927 original size:3 final size:3
Alignment explanation
Indices: 4968919--4968944 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4968909 GTTGTAAATC
4968919 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4968945 GGTTAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4971385 original size:3 final size:3
Alignment explanation
Indices: 4971377--4971425 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
4971367 GGGATGTATA
4971377 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4971425 T
1 T
4971426 TTGGTTTACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4971611 original size:13 final size:13
Alignment explanation
Indices: 4971593--4971627 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4971583 TATATTTTTT
4971593 TAAAAAACAAAAA
1 TAAAAAACAAAAA
*
4971606 TAAAAAATAAAAA
1 TAAAAAACAAAAA
4971619 TAAAAAACA
1 TAAAAAACA
4971628 TTTTCTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (13 bp):
TAAAAAACAAAAA
Found at i:4979689 original size:27 final size:26
Alignment explanation
Indices: 4979654--4979706 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
4979644 TAACAAGTTA
* *
4979654 AAATTTTTAACATTTATAAAATTATT
1 AAATTTTTAAAAATTATAAAATTATT
*
4979680 AAATTATTTAAAAATTATTAAATTATT
1 AAATT-TTTAAAAATTATAAAATTATT
4979707 TTAATGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATTTTTAAAAATTATAAAATTATT
Found at i:4979695 original size:19 final size:20
Alignment explanation
Indices: 4979665--4979707 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
4979655 AATTTTTAAC
4979665 ATTTATAAAATTATTAAATT
1 ATTTATAAAATTATTAAATT
4979685 ATTTA-AAAATTATTAAATT
1 ATTTATAAAATTATTAAATT
4979704 ATTT
1 ATTT
4979708 TAATGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATAAAATTATTAAATT
Found at i:4979824 original size:29 final size:28
Alignment explanation
Indices: 4979746--4979824 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 28
4979736 TAATTAAAAC
*
4979746 TTAATAAAATACATCAAATAATATTTTTTATT
1 TTAATAAAA-A-ATC-AA-AATATTTCTTATT
* *
4979778 ATATTAAATAAA-CAAAATATTTCTTATTT
1 TTAATAAA-AAATCAAAATATTTCTTA-TT
4979807 TTAATAAAAAATCAAAAT
1 TTAATAAAAAATCAAAAT
4979825 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
28 13 0.33
29 16 0.41
30 1 0.03
31 1 0.03
32 7 0.18
33 1 0.03
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAATAAAAAATCAAAATATTTCTTATT
Found at i:4979832 original size:17 final size:17
Alignment explanation
Indices: 4979807--4979845 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4979797 TTTCTTATTT
* *
4979807 TTAATAAAAAATCAAAA
1 TTAAAAAAAAAACAAAA
*
4979824 TTAAAAAAAAAAGAAAA
1 TTAAAAAAAAAACAAAA
4979841 TTAAA
1 TTAAA
4979846 TTATGAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
TTAAAAAAAAAACAAAA
Found at i:4986145 original size:132 final size:131
Alignment explanation
Indices: 4986000--4986252 Score: 314
Period size: 132 Copynumber: 1.9 Consensus size: 131
4985990 CAAAAATGTC
* * ** * *
4986000 TTTATGATTGTTTCATAAAAAATTGACATGTACTATTTTATTTGAATATTATTATAATACCCATT
1 TTTATCATAGTTTCATAAAAAATTGACATGTAAAATTTTATTTGAAAATTACTATAATA-CCATT
* *
4986065 -TTAATTTATGTA-ATAAATTTTAACATAATAATATAAAATTAA-TCACATATTAAATTACTAAA
65 ATTAAATTACGTATATAAATTTTAA-AT-ATAATATAAAATTAACT-ACATATTAAATTACTAAA
4986127 ATACT
127 ATACT
* * **
4986132 TTTATCATAGTTTCATAGAAATTTGACATGTAAAATTTTATTTGAAAATTACTATAATACTTTTA
1 TTTATCATAGTTTCATAAAAAATTGACATGTAAAATTTTATTTGAAAATTACTATAATACCATTA
* * *
4986197 TTAAATTACGTATTTTAATTTTTAATATAATATAAAATTAACTACATATTAAATTA
66 TTAAATTACGTATATAAATTTTAAATATAATATAAAATTAACTACATATTAAATTA
4986253 TTAATCTCAT
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
131 31 0.30
132 64 0.62
133 8 0.08
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (131 bp):
TTTATCATAGTTTCATAAAAAATTGACATGTAAAATTTTATTTGAAAATTACTATAATACCATTA
TTAAATTACGTATATAAATTTTAAATATAATATAAAATTAACTACATATTAAATTACTAAAATAC
T
Found at i:4986550 original size:22 final size:26
Alignment explanation
Indices: 4986478--4986542 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
4986468 AATTTTTTAA
* * * *
4986478 AATTATTATAATACTCTTCATATCAT
1 AATTATAAAAATACTCTTCCTACCAT
4986504 AATTATAAAAATACTCTTCCTACCAT
1 AATTATAAAAATACTCTTCCTACCAT
4986530 AATTATAAAAATA
1 AATTATAAAAATA
4986543 TCTCACCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTATAAAAATACTCTTCCTACCAT
Found at i:4986555 original size:22 final size:26
Alignment explanation
Indices: 4986476--4986556 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 26
4986466 ATAATTTTTT
* * * *
4986476 AAAATTATTATAATACTCTTCATATC
1 AAAATTATAAAAATACTCTTCCTACC
*
4986502 ATAATTATAAAAATACTCTTCCTACC
1 AAAATTATAAAAATACTCTTCCTACC
*
4986528 ATAATTATAAAAATA-TC-T-C-ACC
1 AAAATTATAAAAATACTCTTCCTACC
4986550 AAAATTA
1 AAAATTA
4986557 CATTAATACC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.18
23 1 0.02
24 1 0.02
25 2 0.04
26 36 0.73
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (26 bp):
AAAATTATAAAAATACTCTTCCTACC
Found at i:4989307 original size:39 final size:39
Alignment explanation
Indices: 4989253--4989327 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
4989243 TTGTTTAACC
4989253 AGCCCAATAACTATCCAA-TCCATTAACATTTCTCCATCT
1 AGCCCAATAACTATCCAACT-CATTAACATTTCTCCATCT
*
4989292 AGCCCAATAACTATCCGACTCATTAACATTTCTCCA
1 AGCCCAATAACTATCCAACTCATTAACATTTCTCCA
4989328 ACTCTTAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.29
Consensus pattern (39 bp):
AGCCCAATAACTATCCAACTCATTAACATTTCTCCATCT
Found at i:4989552 original size:162 final size:165
Alignment explanation
Indices: 4989279--4989605 Score: 489
Period size: 162 Copynumber: 2.0 Consensus size: 165
4989269 AATCCATTAA
* * *
4989279 CATTTCTCCATCTAGCCCAATAACTATCCGACTCATTAACATTTCTCCAACTCTTAGGTAGGGAT
1 CATTTCTCCATCTAGCCCAATAACTATCCAACCCATTAACATTTCTCCAACTCTTAGATAGGGAT
*
4989344 GACGATCCAAACCGTACCTGATAGATTCTGATTCAACACGACTTTTTAAGAT-T-TTCTTTTT-A
66 GACGATCCAAACCGTACCTGATAGATTCTGATTCAACACAACTTTTTAAGATATATTCTTTTTAA
* * *
4989406 GTTAAGTTTTGGGTTGAATGATAGTAAAACAAAGT
131 ATTAAGTTTTGGGTTGAATAATAATAAAACAAAGT
*
4989441 CATTTCTCCATCTAGCCCAATAACTATCCAACCCATTAACATTTTTCCAACTCTTAGATAGGGAT
1 CATTTCTCCATCTAGCCCAATAACTATCCAACCCATTAACATTTCTCCAACTCTTAGATAGGGAT
* * * * *
4989506 GACGATCCAAATCGTACTTGATAGATTCTGATTTAACGCAACTTTTTAAGATATATTTTTTTTAA
66 GACGATCCAAACCGTACCTGATAGATTCTGATTCAACACAACTTTTTAAGATATATTCTTTTTAA
* * *
4989571 ATTAAGTTTTTGGTTGGATAATAATAGAACAAAGT
131 ATTAAGTTTTGGGTTGAATAATAATAAAACAAAGT
4989606 TAAGATTAGA
Statistics
Matches: 146, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 108 0.74
163 1 0.01
164 7 0.05
165 30 0.21
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (165 bp):
CATTTCTCCATCTAGCCCAATAACTATCCAACCCATTAACATTTCTCCAACTCTTAGATAGGGAT
GACGATCCAAACCGTACCTGATAGATTCTGATTCAACACAACTTTTTAAGATATATTCTTTTTAA
ATTAAGTTTTGGGTTGAATAATAATAAAACAAAGT
Found at i:4992017 original size:3 final size:3
Alignment explanation
Indices: 4992011--4992035 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4992001 TAAATTTTTT
4992011 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
4992036 TAATTGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4992237 original size:15 final size:14
Alignment explanation
Indices: 4992217--4992274 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
4992207 TTTTCTAAGC
4992217 CCCTAAAATCGAAAA
1 CCCTAAAATC-AAAA
*
4992232 CCCTAAAATCCAAA
1 CCCTAAAATCAAAA
* *
4992246 CCTTTAAATTCAAAA
1 CC-CTAAAATCAAAA
4992261 CCCTAAAATTCAAA
1 CCCTAAAA-TCAAA
4992275 CCCCAAAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.50, C:0.28, G:0.02, T:0.21
Consensus pattern (14 bp):
CCCTAAAATCAAAA
Found at i:4992267 original size:14 final size:14
Alignment explanation
Indices: 4992217--4992297 Score: 56
Period size: 15 Copynumber: 5.5 Consensus size: 14
4992207 TTTTCTAAGC
*
4992217 CCCTAAAATCGAAAA
1 CCCTAAATTC-AAAA
* *
4992232 CCCTAAAATCCAAA
1 CCCTAAATTCAAAA
*
4992246 CCTTTAAATTCAAAA
1 CC-CTAAATTCAAAA
*
4992261 CCCTAAAATTCAAAC
1 CCCT-AAATTCAAAA
*
4992276 CCCAAAACTTTCAAAA
1 CCCTAAA--TTCAAAA
4992292 -CCTAAA
1 CCCTAAA
4992298 CCCAAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
14 9 0.17
15 38 0.72
16 6 0.11
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.20
Consensus pattern (14 bp):
CCCTAAATTCAAAA
Found at i:4992301 original size:22 final size:22
Alignment explanation
Indices: 4992276--4992319 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4992266 AAATTCAAAC
4992276 CCCAAAACTTTC-AAAACCTAAA
1 CCCAAAA-TTTCTAAAACCTAAA
*
4992298 CCCAAAATTTCTAAACCCTAAA
1 CCCAAAATTTCTAAAACCTAAA
4992320 ATCAAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (22 bp):
CCCAAAATTTCTAAAACCTAAA
Found at i:4992325 original size:22 final size:22
Alignment explanation
Indices: 4992277--4992327 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4992267 AATTCAAACC
*
4992277 CCAAAACTTTCAAAACCTAAAC
1 CCAAAACTTTCAAAACCTAAAA
*
4992299 CCAAAA-TTTCTAAACCCTAAAA
1 CCAAAACTTTC-AAAACCTAAAA
*
4992321 TCAAAAC
1 CCAAAAC
4992328 CCCAAATCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (22 bp):
CCAAAACTTTCAAAACCTAAAA
Found at i:4992329 original size:14 final size:14
Alignment explanation
Indices: 4992310--4992391 Score: 51
Period size: 14 Copynumber: 5.7 Consensus size: 14
4992300 CAAAATTTCT
4992310 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* *
4992324 AAACCC-CAAATCTC
1 AAACCCTAAAATC-A
* ** *
4992338 GAACTTTAAAACCA
1 AAACCCTAAAATCA
4992352 AAACCCTAAAATTTTC-
1 AAACCCTAAAA---TCA
*
4992368 AAACCTTAAAATCA
1 AAACCCTAAAATCA
4992382 AAACCCTAAA
1 AAACCCTAAA
4992392 CCTTCCATAC
Statistics
Matches: 48, Mismatches: 14, Indels: 12
0.65 0.19 0.16
Matches are distributed among these distances:
13 7 0.15
14 26 0.54
15 4 0.08
16 10 0.21
17 1 0.02
ACGTcount: A:0.51, C:0.28, G:0.01, T:0.20
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:4992391 original size:30 final size:28
Alignment explanation
Indices: 4992295--4992387 Score: 105
Period size: 30 Copynumber: 3.2 Consensus size: 28
4992285 TTCAAAACCT
*
4992295 AAACCCAAAATTTCTAAACCCTAAAATCA
1 AAACCCAAAATTTC-AAACCTTAAAATCA
* * * * *
4992324 AAACCCCAAATCTCGAACTTTAAAACCA
1 AAACCCAAAATTTCAAACCTTAAAATCA
4992352 AAACCCTAAAATTTTCAAACCTTAAAATCA
1 AAACCC-AAAA-TTTCAAACCTTAAAATCA
4992382 AAACCC
1 AAACCC
4992388 TAAACCTTCC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
28 16 0.31
29 15 0.29
30 20 0.39
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.20
Consensus pattern (28 bp):
AAACCCAAAATTTCAAACCTTAAAATCA
Found at i:4992408 original size:30 final size:30
Alignment explanation
Indices: 4992310--4992444 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 30
4992300 CAAAATTTCT
* *
4992310 AAACCCTAAAATCAAAACCCCAAATC-T-C
1 AAACCCTAAAATCAAAACCCTAAACCTTCC
* ** * ** *
4992338 GAACTTTAAAACCAAAACCCTAAAATTTTC
1 AAACCCTAAAATCAAAACCCTAAACCTTCC
*
4992368 AAACCTTAAAATCAAAACCCTAAACCTTCC
1 AAACCCTAAAATCAAAACCCTAAACCTTCC
* * * *
4992398 ATACCCTAAAATTC-AAGCCCTAAGACCCTCT
1 AAACCCTAAAA-TCAAAACCCTAA-ACCTTCC
*
4992429 AAACCCTAAAACCAAA
1 AAACCCTAAAATCAAA
4992445 TCCTAAAACC
Statistics
Matches: 82, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
28 19 0.23
29 1 0.01
30 43 0.52
31 19 0.23
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.19
Consensus pattern (30 bp):
AAACCCTAAAATCAAAACCCTAAACCTTCC
Found at i:4994555 original size:14 final size:13
Alignment explanation
Indices: 4994536--4994580 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
4994526 TAGGAGAAAC
4994536 AAAAAGAGATAAAA
1 AAAAAGAGA-AAAA
4994550 AAAAAGA-AAAAA
1 AAAAAGAGAAAAA
4994562 CAAAAA-AGAAAAA
1 -AAAAAGAGAAAAA
4994575 AAAAAG
1 AAAAAG
4994581 GATTTGGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 10 0.36
13 11 0.39
14 7 0.25
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:4995973 original size:28 final size:28
Alignment explanation
Indices: 4995916--4995978 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
4995906 GTGCATTCAC
* * **
4995916 TCATTCATTCATTTATTCATTTGTGCAT
1 TCATTCATTCATTCATCCATTTACGCAT
*
4995944 TCATTCATTCATTCATCCATTTACGTAT
1 TCATTCATTCATTCATCCATTTACGCAT
4995972 TCATTCA
1 TCATTCA
4995979 ATATTATACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (28 bp):
TCATTCATTCATTCATCCATTTACGCAT
Found at i:4995978 original size:4 final size:4
Alignment explanation
Indices: 4995909--4995964 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
4995899 GTCAGTTGTG
* * ** *
4995909 CATT CACT CATT CATT CATT TATT CATT TGTG CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
*
4995957 CATC CATT
1 CATT CATT
4995965 TACGTATTCA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.23, C:0.25, G:0.04, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:4999403 original size:91 final size:92
Alignment explanation
Indices: 4999283--4999464 Score: 357
Period size: 91 Copynumber: 2.0 Consensus size: 92
4999273 GTGAAAGAAT
4999283 GTAAAAAAAAAACAAAAGAGAAAAATGAAAGGAAATGAAGAATAAAAGAAGGAAAAA-AAAATAA
1 GTAAAAAAAAAACAAAAGAGAAAAATGAAAGGAAATGAAGAATAAAAGAAGGAAAAAGAAAATAA
4999347 ATGAATGGGTGGAAAGTATAAAAGGGG
66 ATGAATGGGTGGAAAGTATAAAAGGGG
4999374 GTAAAAAAAAAACAAAAGAGAAAAATGAAAGGAAATGAAGAATAAAAGAAGGAAAAAGAAAATAA
1 GTAAAAAAAAAACAAAAGAGAAAAATGAAAGGAAATGAAGAATAAAAGAAGGAAAAAGAAAATAA
4999439 ATGAATGGGTGGAAAGTATAAAAGGG
66 ATGAATGGGTGGAAAGTATAAAAGGG
4999465 AATATACCTC
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 57 0.63
92 33 0.37
ACGTcount: A:0.64, C:0.01, G:0.24, T:0.11
Consensus pattern (92 bp):
GTAAAAAAAAAACAAAAGAGAAAAATGAAAGGAAATGAAGAATAAAAGAAGGAAAAAGAAAATAA
ATGAATGGGTGGAAAGTATAAAAGGGG
Found at i:5000366 original size:33 final size:32
Alignment explanation
Indices: 5000324--5000669 Score: 133
Period size: 33 Copynumber: 10.8 Consensus size: 32
5000314 AGCTAGCATC
* *
5000324 AATGAAGTTTTAAGCTCAATTTATCTGGCCATT
1 AATGAAATTTTAAGC-CAGTTTATCTGGCCATT
* * * **
5000357 AATGAAGTTTTAAGCCCAATTTAGCTGGCCCCT
1 AATGAAATTTTAAG-CCAGTTTATCTGGCCATT
* * *
5000390 AAGGAAATCTTAAGCCTAGTTTATCTGACC-TT
1 AATGAAATTTTAAGCC-AGTTTATCTGGCCATT
* * ***
5000422 CAAT----TTTAAACCCAGTTTATCTGGCCCCC
1 -AATGAAATTTTAAGCCAGTTTATCTGGCCATT
* * * *
5000451 AAGGAAATCTTAAGCCCATTTTATTTGGCC-TCT
1 AATGAAATTTTAAG-CCAGTTTATCTGGCCAT-T
* *
5000484 AAT---A-TTTAAGCCTAGTTTATCTGACCATC
1 AATGAAATTTTAAGCC-AGTTTATCTGGCCATT
* * *
5000513 AATGAAATTTTAAACCTAATTTATCTGGCCATC
1 AATGAAATTTTAAGCC-AGTTTATCTGGCCATT
* * * **
5000546 AATGAAGTTTTAAGCTCAGTTTACCTGACTTTT
1 AATGAAATTTTAAGC-CAGTTTATCTGGCCATT
* * *
5000579 AA-GAAAAATTTAAGCTCAGTTTATCTGGCCCTA
1 AATG-AAATTTTAAGC-CAGTTTATCTGGCCATT
** * *
5000612 AATGAGGTTTTAAGCCCAGCTTAGCTGGCC-TT
1 AATGAAATTTTAAG-CCAGTTTATCTGGCCATT
* *
5000644 CAAT-AAAATTTAAGCCTAATTTATCT
1 -AATGAAATTTTAAGCC-AGTTTATCT
5000670 AGCCCCAAAA
Statistics
Matches: 230, Mismatches: 61, Indels: 45
0.68 0.18 0.13
Matches are distributed among these distances:
28 16 0.07
29 24 0.10
30 2 0.01
31 2 0.01
32 23 0.10
33 159 0.69
34 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (32 bp):
AATGAAATTTTAAGCCAGTTTATCTGGCCATT
Found at i:5000414 original size:66 final size:65
Alignment explanation
Indices: 5000343--5000641 Score: 206
Period size: 66 Copynumber: 4.7 Consensus size: 65
5000333 TTAAGCTCAA
*
5000343 TTTATCTGGCCATTAATGAAGTTTTAAGCCCAATTTAGCTGGCCCCTAAGGAAATCTTAAGCCTA
1 TTTATCTGGCC-TTAATGAAGTTTTAAGCCCAGTTTAGCTGGCCCCTAAGGAAATCTTAAGCCTA
5000408 G
65 G
* * * * * * *
5000409 TTTATCTGACC-T--TCAA-TTTTAAACCCAGTTTATCTGGCCCCCAAGGAAATCTTAAGCCCAT
1 TTTATCTGGCCTTAATGAAGTTTTAAGCCCAGTTTAGCTGGCCCCTAAGGAAATCTTAAGCCTAG
* * * * * * * *
5000470 TTTATTTGGCCTCTAAT--A--TTTAAGCCTAGTTTATCT-GACCATCAATGAAATTTTAAACCT
1 TTTATCTGGCCT-TAATGAAGTTTTAAGCCCAGTTTAGCTGGCCCCT-AAGGAAATCTTAAGCCT
*
5000530 AA
64 AG
* * * * *** *
5000532 TTTATCTGGCCATCAATGAAGTTTTAAGCTCAGTTTACCTGACTTTTAAGAAAAAT-TTAAG-CT
1 TTTATCTGGCC-TTAATGAAGTTTTAAGCCCAGTTTAGCTGGCCCCTAAG-GAAATCTTAAGCCT
5000595 CAG
64 -AG
* * *
5000598 TTTATCTGGCCCTAAATGAGGTTTTAAGCCCAGCTTAGCTGGCC
1 TTTATCTGG-CCTTAATGAAGTTTTAAGCCCAGTTTAGCTGGCC
5000642 TTCAATAAAA
Statistics
Matches: 178, Mismatches: 41, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
61 51 0.29
62 46 0.26
63 3 0.02
64 2 0.01
65 3 0.02
66 66 0.37
67 7 0.04
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (65 bp):
TTTATCTGGCCTTAATGAAGTTTTAAGCCCAGTTTAGCTGGCCCCTAAGGAAATCTTAAGCCTAG
Found at i:5000449 original size:61 final size:61
Alignment explanation
Indices: 5000364--5000506 Score: 180
Period size: 61 Copynumber: 2.3 Consensus size: 61
5000354 ATTAATGAAG
* * * *
5000364 TTTTAAGCCCAATTTAGCTGGCCCCTAAGGAAATCTTAAGCCTAGTTTATCTGACCT-TCAA
1 TTTTAAGCCCAGTTTATCTGGCCCCCAAGGAAATCTTAAGCCCAGTTTATCTGACCTCT-AA
* * * *
5000425 TTTTAAACCCAGTTTATCTGGCCCCCAAGGAAATCTTAAGCCCATTTTATTTGGCCTCTAA
1 TTTTAAGCCCAGTTTATCTGGCCCCCAAGGAAATCTTAAGCCCAGTTTATCTGACCTCTAA
*
5000486 TATTTAAGCCTAGTTTATCTG
1 T-TTTAAGCCCAGTTTATCTG
5000507 ACCATCAATG
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 52 0.74
62 18 0.26
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (61 bp):
TTTTAAGCCCAGTTTATCTGGCCCCCAAGGAAATCTTAAGCCCAGTTTATCTGACCTCTAA
Found at i:5001402 original size:22 final size:22
Alignment explanation
Indices: 5001360--5001402 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5001350 ATCAATTCTA
*
5001360 TAAGACCTCCGGGCATGATTTT
1 TAAGACCTCCGGGCATAATTTT
* *
5001382 TAAGACCTCTGGGCTTAATTT
1 TAAGACCTCCGGGCATAATTT
5001403 CGACCCGCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (22 bp):
TAAGACCTCCGGGCATAATTTT
Found at i:5001459 original size:37 final size:37
Alignment explanation
Indices: 5001412--5001518 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 37
5001402 TCGACCCGCA
* *
5001412 GTATTGTCCCGATCAATTCTTTACTTCTCGACTTAAG
1 GTATTATCCCGATCAATTCTTTACTTTTCGACTTAAG
* * * * **
5001449 GTGTTATCCCGATCATTTTTTTACTTTTCAACTTGCG
1 GTATTATCCCGATCAATTCTTTACTTTTCGACTTAAG
* *
5001486 GTATTATCCCAATCGATTCTTTACTTTTCGACT
1 GTATTATCCCGATCAATTCTTTACTTTTCGACT
5001519 CGCGGTGTTG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (37 bp):
GTATTATCCCGATCAATTCTTTACTTTTCGACTTAAG
Found at i:5001524 original size:37 final size:36
Alignment explanation
Indices: 5001400--5001539 Score: 118
Period size: 37 Copynumber: 3.8 Consensus size: 36
5001390 CTGGGCTTAA
* * *
5001400 TTTCGACCCGCAGTATTGTCCCGATCAATTCTTTACT
1 TTTCGACTCGCGGTATTATCCCGATC-ATTCTTTACT
* *** * *
5001437 TCTCGACTTAAGGTGTTATCCCGATCATTTTTTTACT
1 TTTCGACTCGCGGTATTATCCCGATCA-TTCTTTACT
* * *
5001474 TTTCAACTTGCGGTATTATCCCAATCGATTCTTTACT
1 TTTCGACTCGCGGTATTATCCCGATC-ATTCTTTACT
* * *
5001511 TTTCGACTCGCGGTGTTGTCTCGATCATT
1 TTTCGACTCGCGGTATTATCCCGATCATT
5001540 TTTTTTTACT
Statistics
Matches: 79, Mismatches: 22, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
36 4 0.05
37 74 0.94
38 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTCGACTCGCGGTATTATCCCGATCATTCTTTACT
Found at i:5001698 original size:112 final size:111
Alignment explanation
Indices: 5001492--5001756 Score: 293
Period size: 112 Copynumber: 2.4 Consensus size: 111
5001482 TGCGGTATTA
* * * * * *
5001492 TCCCAATCGATTCTTTACTTTTCGACTCGCGGTGTTGTCTCGATCATTTTTTTTTACTTTTTGAC
1 TCCCAGTCG-TTCTTTACTTTTTGACTCGCGGTGTTATCCCGAT-ATATTTTTTTACTTTTTAAC
* **
5001557 TTGTGGTGTTGTCCTGGTCGATTATTTACTTCTCAACCCACGATGTTG
64 TTGGGGTGTTGTCCCAGTCGATTATTTACTTCTCAACCCACGATGTTG
* * *
5001605 TCCCAGTTGTTTTCTTTACTTTTTGACTCACAGTGTTATCCCGAT-TATTTTTTTACTTTTTAAC
1 TCCCAGTCG--TTCTTTACTTTTTGACTCGCGGTGTTATCCCGATATATTTTTTTACTTTTTAAC
* * * * *
5001669 TTGGGGTGTTGTCCCAGTC-ATTTTCTTACTTTTCGACTCGCGATGTTG
64 TTGGGGTGTTGTCCCAGTCGATTAT-TTACTTCTCAACCCACGATGTTG
*
5001717 TCCCGGTCGTTCTTTA-TTTCTTGACTCGCGGTGTTATCCC
1 TCCCAGTCGTTCTTTACTTT-TTGACTCGCGGTGTTATCCC
5001757 TATCGTTTTC
Statistics
Matches: 127, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
109 3 0.02
110 25 0.20
111 4 0.03
112 59 0.46
113 7 0.06
114 29 0.23
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (111 bp):
TCCCAGTCGTTCTTTACTTTTTGACTCGCGGTGTTATCCCGATATATTTTTTTACTTTTTAACTT
GGGGTGTTGTCCCAGTCGATTATTTACTTCTCAACCCACGATGTTG
Found at i:5001716 original size:37 final size:37
Alignment explanation
Indices: 5001448--5001756 Score: 155
Period size: 37 Copynumber: 8.3 Consensus size: 37
5001438 CTCGACTTAA
* * *
5001448 GGTGTTATCCC-GATCATTTTTTTACTTTTCAACTTGC
1 GGTGTTGTCCCAG-TCATTTTTTTACTTTTCGACTCGC
* * * *
5001485 GGTATTATCCCAATCGA-TTCTTTACTTTTCGACTCGC
1 GGTGTTGTCCCAGTC-ATTTTTTTACTTTTCGACTCGC
* * * *
5001522 GGTGTTGTCTC-GATCATTTTTTTTTACTTTTTGACTTGT
1 GGTGTTGTCCCAG-TCA--TTTTTTTACTTTTCGACTCGC
** * * * * *
5001561 GGTGTTGTCCTGGTCGA-TTATTTACTTCTCAACCCAC
1 GGTGTTGTCCCAGTC-ATTTTTTTACTTTTCGACTCGC
* ** * *
5001598 GATGTTGTCCCAGTTGTTTTCTTTACTTTTTGACTCAC
1 GGTGTTGTCCCAGTCATTTT-TTTACTTTTCGACTCGC
* * * ** * *
5001636 AGTGTTATCCC-GATTATTTTTTTACTTTTTAACTTGG
1 GGTGTTGTCCCAG-TCATTTTTTTACTTTTCGACTCGC
*
5001673 GGTGTTGTCCCAGTCATTTTCTTACTTTTCGACTCGC
1 GGTGTTGTCCCAGTCATTTTTTTACTTTTCGACTCGC
* * * * *
5001710 GATGTTGTCCCGGTC-GTTCTTTA-TTTCTTGACTCGC
1 GGTGTTGTCCCAGTCATTTTTTTACTTT-TCGACTCGC
*
5001746 GGTGTTATCCC
1 GGTGTTGTCCC
5001757 TATCGTTTTC
Statistics
Matches: 202, Mismatches: 57, Indels: 27
0.71 0.20 0.09
Matches are distributed among these distances:
35 3 0.01
36 23 0.11
37 118 0.58
38 29 0.14
39 27 0.13
40 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (37 bp):
GGTGTTGTCCCAGTCATTTTTTTACTTTTCGACTCGC
Found at i:5001763 original size:36 final size:37
Alignment explanation
Indices: 5001703--5001798 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 37
5001693 CTTACTTTTC
* *
5001703 GACTCGCGATGTTGTCCCGGTCG-TTCTTTATTTCTT
1 GACTCGCGATGTTATCCCGATCGTTTCTTTATTTCTT
* *
5001739 GACTCGCGGTGTTATCCCTATCGTTTTCTTTATTTCTT
1 GACTCGCGATGTTATCCCGATCG-TTTCTTTATTTCTT
* *
5001777 GACTCGCGATATTATCTCGATC
1 GACTCGCGATGTTATCCCGATC
5001799 ATGTTTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
36 19 0.38
38 31 0.62
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (37 bp):
GACTCGCGATGTTATCCCGATCGTTTCTTTATTTCTT
Found at i:5001988 original size:38 final size:36
Alignment explanation
Indices: 5001946--5002232 Score: 105
Period size: 36 Copynumber: 8.0 Consensus size: 36
5001936 TCTTGGTTAT
*
5001946 TTTTATAGTTTTCTGACTTGCGATTTAATCTCAGTCA
1 TTTTATA-TTTTCTGACTTGCGATTTAATCCCAGTCA
* * * *
5001983 CTTTTAT-TTTTCGGACTCGC-AGTTCAATCCCAGTCG
1 -TTTTATATTTTCTGACTTGCGA-TTTAATCCCAGTCA
* * * * *
5002019 TCGTTA-ATCTT-TGACTTGTGGTTTAATCTC-GATCA
1 T-TTTATATTTTCTGACTTGCGATTTAATCCCAG-TCA
* *
5002054 TTTCTATAGTTTTCTGACTGGCAATTTAATCCCAGTCA
1 TTT-TATA-TTTTCTGACTTGCGATTTAATCCCAGTCA
* * * * * *
5002092 TTTT-TATTTT-TCGAGCTTGCGGTTCAGTTCTAGTCG
1 TTTTATATTTTCT-GA-CTTGCGATTTAATCCCAGTCA
* * * * *
5002128 TTGTCA-ATCTT-TGACTCGC-AGTTAATCCCTGTCA
1 TT-TTATATTTTCTGACTTGCGATTTAATCCCAGTCA
* * *
5002162 TTCTATATTTTCTTGACTTGTGGTTTAAT-CCAGTCA
1 TTTTATATTTTC-TGACTTGCGATTTAATCCCAGTCA
* * *
5002198 CTTTTAT-TTTT-TGGACTCGCGGTTTAGTCCCAGTC
1 -TTTTATATTTTCT-GACTTGCGATTTAATCCCAGTC
5002233 GTCGTTAGTC
Statistics
Matches: 176, Mismatches: 52, Indels: 44
0.65 0.19 0.16
Matches are distributed among these distances:
33 1 0.01
34 17 0.10
35 41 0.23
36 70 0.40
37 20 0.11
38 26 0.15
39 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (36 bp):
TTTTATATTTTCTGACTTGCGATTTAATCCCAGTCA
Found at i:5001988 original size:109 final size:108
Alignment explanation
Indices: 5001845--5002992 Score: 779
Period size: 109 Copynumber: 10.6 Consensus size: 108
5001835 TCATTTTCAT
** * * * * *
5001845 TTTTCTGACTCACAATTTAATCTCAGTCATTTTTATTTTTTAGGCTTACGATTCAATCCCAATCG
1 TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATTTTTT-GGCTTACGGTTCAGTCCCAGTCG
* * *
5001910 TCGTTAATCTTTGACTCGTGGTTTAATCTTGGTTATTTTTATAG
65 TCGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
* ** * *
5001954 TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATTTTTCGGACTCGCAGTTCAATCCCAGTCG
1 TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATTTTTTGG-CTTACGGTTCAGTCCCAGTCG
* *
5002019 TCGTTAATCTTTGACTTGTGGTTTAATCTCGATCATTTCTATAG
65 TCGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
* * * * * * * *
5002063 TTTTCTGACTGGCAATTTAATCCCAGTCATTTTTATTTTTCGAGCTTGCGGTTCAGTTCTAGTCG
1 TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATTTTTTG-GCTTACGGTTCAGTCCCAGTCG
* * ** *
5002128 TTGTCAATCTTTGACTCGCAG-TTAATCCCTG-TCA-TTCTATA-
65 TCGTTAATCTTTGACTCGTGGTTTAAT-CTTGATCATTTCTATAG
* * ** *
5002169 TTTTCTTGACTTGTGGTTTAATC-CAGTCACTTTTATTTTTTGGACTCGCGGTTTAGTCCCAGTC
1 TTTTC-TGACTTGCGATTTAATCTCAGTCACTTTTATTTTTTGG-CTTACGGTTCAGTCCCAGTC
* * * * *
5002233 GTCGTTAGTCTTTGACTCGTGATTTAATTTTGGTCATTTCTGTAG
64 GTCGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
* * **
5002278 -TTTCTTTACTTGCGATTTAATCTCAATCGTTTTTATTTTTTGGAC-T-CGTTGTTCAGTCCCAG
1 TTTTC-TGACTTGCGATTTAATCTCAGTCACTTTTATTTTTTGG-CTTACG--GTTCAGTCCCAG
* * * * * *
5002340 TCGTCATTAATCTTTGACTCATGGTTTAATCTCGATTATTTTTATAA
62 TCGTCGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
* ** * * * * * ** *
5002387 TTTCCCAACTTGTGGTTTAAT-TCCAATCATTTTTATTGTTCTAACTTACGGTTCAGTCCTAGTC
1 TTTTCTGACTTGCGATTTAATCT-CAGTCACTTTTATT-TTTTGGCTTACGGTTCAGTCCCAGTC
* * ***
5002451 ATCGTTAATCTTTGACTCGTGATTTAATCCCAATCATTTCTATAG
64 GTCGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
* * * * ** * * * *
5002496 TTTCCTGACTTGCGGTTTAATCTCAATCCCTTTTATTTTTTGGACTCGCGGTTTAGTCTCAATTG
1 TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATTTTTTGG-CTTACGGTTCAGTCCCAGTCG
* ** * *
5002561 TTGTTAATCTTTGACTCGTGGTTTAATCTCCATTATTTTTATA-
65 TCGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
* ** * * * * *
5002604 ATTT-TGACTTATGATTTAATCCCAATCGCTTTTATTATTTTGACTTACGGTTCAGT-CCAGTCA
1 TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATT-TTTTGGCTTACGGTTCAGTCCCAGTCG
* * * *
5002667 TCGTTAATCTTTGACTTGTGATTTAATCCTGGTCATTTCTATAG
65 TCGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
* * * * * * * * * * * *
5002711 TTTCCCGACTTGCGGTTTAATCCCAATCACTTTTATTGTTCTGACTTGCTGTTTAGTTCCAATCG
1 TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATT-TTTTGGCTTACGGTTCAGTCCCAGTCG
* * * *
5002776 TTGTTAATTTTTGACTCGTGGTTTAAT-TCTGATTATTTTTATAG
65 TCGTTAATCTTTGACTCGTGGTTTAATCT-TGATCATTTCTATAG
* * * ** * * **
5002820 TTTT-TCGACTTGCGGTTTAATCTCAGTCGCTTTTATTTTCTAACTTACAGTTCAAT-CTTGATC
1 TTTTCT-GACTTGCGATTTAATCTCAGTCACTTTTATTTTTTGGCTTACGGTTCAGTCCCAG-TC
* * * ** * * *
5002883 ATCATTAATCTTTGGCTCACGATTTAAT-TCAGGTCATTTC--TA-
64 GTCGTTAATCTTTGACTCGTGGTTTAATCT-TGATCATTTCTATAG
* * * * *
5002925 TTTTCTTGACTTGCGATTTAATCTCAGTCGCCTTTTATTTTTCTGACTTGCGGTTTAAT-CCAGT
1 TTTTC-TGACTTGCGATTTAATCTCAGTC-ACTTTTATTTTT-TGGCTTACGGTTCAGTCCCAGT
5002989 CGTC
63 CGTC
5002993 ATTATTTTCT
Statistics
Matches: 818, Mismatches: 191, Indels: 62
0.76 0.18 0.06
Matches are distributed among these distances:
105 5 0.01
106 116 0.14
107 85 0.10
108 146 0.18
109 455 0.56
110 9 0.01
111 2 0.00
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.47
Consensus pattern (108 bp):
TTTTCTGACTTGCGATTTAATCTCAGTCACTTTTATTTTTTGGCTTACGGTTCAGTCCCAGTCGT
CGTTAATCTTTGACTCGTGGTTTAATCTTGATCATTTCTATAG
Found at i:5002573 original size:433 final size:431
Alignment explanation
Indices: 5001896--5002981 Score: 1192
Period size: 433 Copynumber: 2.5 Consensus size: 431
5001886 AGGCTTACGA
* * * *
5001896 TTCAATCCCAATCGTCGTTAATCTTTGACTCGTGGTTTAATCTTGGTTATTTTTATAGTTTTCTG
1 TTCAGTCCCAATCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGATTATTTTTATAGTTTTCCG
* ** ** * *
5001961 ACTTGCGATTTAATCTCAGTCACTTTTATTTTTCGGACTCGCAGTTCAATCCCAGTCGTCGTTAA
66 ACTTGCGGTTTAATCTCAGTCACTTTTA-TTTTCTAACTTACAGTTCAATCCTAGTCATCGTTAA
* * * * * * *
5002026 TCTTTGACTTGTGGTTTAATCTCGATCATTTCTATAGTTTTCTGACTGGCAATTTAATCCCAGTC
130 TCTTTGACTCGTGATTTAATCTCAATCATTTCTATAGTTTCCTGACTTGCGATTTAATCTCAGTC
** * * *
5002091 ATTTTTATTTTTCGAGCTTGCGGTTCAGTTCTAGTCGTTGTCAATCTTTGACTCGCAG-TTAATC
195 CCTTTTATTTTTTGA-CTTGCGGTTTAGTTCTAATCGTTGTCAATCTTTGACTCGCAGTTTAATC
* * * *
5002155 -CC-TGTCATTCTATAT-TTTCTTGACTTGTGGTTTAAT-CCAGTCACTTTTATT-TTTTGGACT
259 TCCAT-T-ATT-TATATAATT-TTGACTTATGATTTAATCCCAATCACTTTTATTATTTT-GACT
* * * * ** *
5002215 CGCGGTTTAGTCCCAGTCGTCGTTAGTCTTTGACTCGTGATTTAATTTTGGTCATTTCTGTAGTT
319 CACGGTTCAGT-CCAGTCATCGTTAATCTTTGACTCGTGATTTAATCCTGGTCATTTCTATAGTT
*** * ** * *
5002280 TCTTTACTTGCGATTTAATCTCAATCGTTTTTATT-TTTTGGACTCGTTG
383 TCCCGACTTGCGATTTAATCCCAATCACTTTTATTGTTCT-GACTCGCTG
* * * * * *
5002329 TTCAGTCCCAGTCGTCATTAATCTTTGACTCATGGTTTAATCTCGATTATTTTTATAATTTCCCA
1 TTCAGTCCCAATCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGATTATTTTTATAGTTTTCCG
* * * * *
5002394 ACTTGTGGTTTAAT-TCCAATCATTTTTATTGTTCTAACTTACGGTTCAGTCCTAGTCATCGTTA
66 ACTTGCGGTTTAATCT-CAGTCACTTTTATT-TTCTAACTTACAGTTCAATCCTAGTCATCGTTA
* * *
5002458 ATCTTTGACTCGTGATTTAATCCCAATCATTTCTATAGTTTCCTGACTTGCGGTTTAATCTCAAT
129 ATCTTTGACTCGTGATTTAATCTCAATCATTTCTATAGTTTCCTGACTTGCGATTTAATCTCAGT
* * * **
5002523 CCCTTTTATTTTTTGGACTCGCGGTTTAG-TCTCAATTGTTGTTAATCTTTGACTCGTGGTTTAA
194 CCCTTTTATTTTTT-GACTTGCGGTTTAGTTCT-AATCGTTGTCAATCTTTGACTCGCAGTTTAA
* * *
5002587 TCTCCATTATTTTTATAATTTTGACTTATGATTTAATCCCAATCGCTTTTATTATTTTGACTTAC
257 TCTCCATTATTTATATAATTTTGACTTATGATTTAATCCCAATCACTTTTATTATTTTGACTCAC
*
5002652 GGTTCAGTCCAGTCATCGTTAATCTTTGACTTGTGATTTAATCCTGGTCATTTCTATAGTTTCCC
322 GGTTCAGTCCAGTCATCGTTAATCTTTGACTCGTGATTTAATCCTGGTCATTTCTATAGTTTCCC
* *
5002717 GACTTGCGGTTTAATCCCAATCACTTTTATTGTTCTGACTTGCTG
387 GACTTGCGATTTAATCCCAATCACTTTTATTGTTCTGACTCGCTG
* * * * *
5002762 TTTAGTTCCAATCGTTGTTAATTTTTGACTCGTGGTTTAAT-TCTGATTATTTTTATAGTTTTTC
1 TTCAGTCCCAATCGTCGTTAATCTTTGACTCGTGGTTTAATCTC-GATTATTTTTATAGTTTTCC
* * *
5002826 GACTTGCGGTTTAATCTCAGTCGCTTTTATTTTCTAACTTACAGTTCAAT-CTTGATCATCATTA
65 GACTTGCGGTTTAATCTCAGTCACTTTTATTTTCTAACTTACAGTTCAATCCTAG-TCATCGTTA
* ** * *
5002890 ATCTTTGGCTCACGATTTAAT-TCAGGTCATTTCTAT--TTTCTTGACTTGCGATTTAATCTCAG
129 ATCTTTGACTCGTGATTTAATCTCA-ATCATTTCTATAGTTTCCTGACTTGCGATTTAATCTCAG
5002952 TCGCCTTTTATTTTTCTGACTTGCGGTTTA
193 TC-CCTTTTATTTTT-TGACTTGCGGTTTA
5002982 ATCCAGTCGT
Statistics
Matches: 541, Mismatches: 95, Indels: 36
0.81 0.14 0.05
Matches are distributed among these distances:
430 25 0.05
431 29 0.05
432 62 0.11
433 375 0.69
434 42 0.08
435 7 0.01
436 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (431 bp):
TTCAGTCCCAATCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGATTATTTTTATAGTTTTCCG
ACTTGCGGTTTAATCTCAGTCACTTTTATTTTCTAACTTACAGTTCAATCCTAGTCATCGTTAAT
CTTTGACTCGTGATTTAATCTCAATCATTTCTATAGTTTCCTGACTTGCGATTTAATCTCAGTCC
CTTTTATTTTTTGACTTGCGGTTTAGTTCTAATCGTTGTCAATCTTTGACTCGCAGTTTAATCTC
CATTATTTATATAATTTTGACTTATGATTTAATCCCAATCACTTTTATTATTTTGACTCACGGTT
CAGTCCAGTCATCGTTAATCTTTGACTCGTGATTTAATCCTGGTCATTTCTATAGTTTCCCGACT
TGCGATTTAATCCCAATCACTTTTATTGTTCTGACTCGCTG
Found at i:5002962 original size:324 final size:325
Alignment explanation
Indices: 5001860--5002992 Score: 1064
Period size: 324 Copynumber: 3.5 Consensus size: 325
5001850 TGACTCACAA
* ** * * * *
5001860 TTTAATCTCAGTCATTTTTATTTTTTAGG-CTTACGATTCAATCCCAATCGTCGTTAATCTTTGA
1 TTTAATCTCAGTCACTTTTATTTTTT-GGACTCGCGGTTTAGTCTCAATCGTCGTTAATCTTTGA
* * * * * *
5001924 CTCGTGGTTTAA-TCTTGGTTATTTTTATAGTTT-TCTGACTTGCGATTTAATCTCAGTCACTTT
65 CTCGTGATTTAATTC-AGGTCATTTCTAT--TTTCT-TGACTTGCGATTTAATCTCAATCGCTTT
* * *
5001987 TATTTTTCGGACTCGCAGTTCAATCCCAGTCGTCGTTAATCTTTGACTTGTGGTTTAATCTCGAT
126 TATTTTTCTGACTTGCGGTTCAATCCCAGTCGTCGTTAATCTTTGACTTGTGGTTTAATCTCGAT
* * * ** * *
5002052 CATTTCTATAGTTTTCTGACTGGCAATTTAATCCCAGTCATTTTTATTTTTC-GAGCTTGCGGTT
191 CATTTCTATAGTTTCCCGACTTGCGGTTTAATCCCAATCATTTTTATTGTTCTGA-CTTGCGGTT
* * ** *
5002116 CAGTTCTAGTCGTTGTCAATCTTTGACTCGCAG-TTAATCCCTG-TCA-TTCTATA-TTTTCTTG
255 CAGTTCCAGTCGTTGTTAATCTTTGACTCGTGGTTTAAT-CCTGATCATTTCTATAGTTTT-TCG
*
5002177 ACTTGTGG
318 ACTTGCGG
* * *
5002185 TTTAATC-CAGTCACTTTTATTTTTTGGACTCGCGGTTTAGTCCCAGTCGTCGTTAGTCTTTGAC
1 TTTAATCTCAGTCACTTTTATTTTTTGGACTCGCGGTTTAGTCTCAATCGTCGTTAATCTTTGAC
** * * *
5002249 TCGTGATTTAATTTTGGTCATTTCTGTAGTTTCTTTACTTGCGATTTAATCTCAATCGTTTTTAT
66 TCGTGATTTAATTCAGGTCATTTC--TATTTTCTTGACTTGCGATTTAATCTCAATCGCTTTTAT
* ** * * ** *
5002314 TTTT-TGGACTCGTTGTTCAGTCCCAGTCGTCATTAATCTTTGACTCATGGTTTAATCTCGATTA
129 TTTTCT-GACTTGCGGTTCAATCCCAGTCGTCGTTAATCTTTGACTTGTGGTTTAATCTCGATCA
* * * * * * *
5002378 TTTTTATAATTTCCCAACTTGTGGTTTAATTCCAATCATTTTTATTGTTCTAACTTACGGTTCAG
193 TTTCTATAGTTTCCCGACTTGCGGTTTAATCCCAATCATTTTTATTGTTCTGACTTGCGGTTCAG
* * * ** *
5002443 -TCCTAGTCATCGTTAATCTTTGACTCGTGATTTAATCCCAATCATTTCTATAG-TTTCCTGACT
258 TTCC-AGTCGTTGTTAATCTTTGACTCGTGGTTTAATCCTGATCATTTCTATAGTTTTTC-GACT
5002506 TGCGG
321 TGCGG
* * * *
5002511 TTTAATCTCAATCCCTTTTATTTTTTGGACTCGCGGTTTAGTCTCAATTGTTGTTAATCTTTGAC
1 TTTAATCTCAGTCACTTTTATTTTTTGGACTCGCGGTTTAGTCTCAATCGTCGTTAATCTTTGAC
* * * * ** *
5002576 TCGTGGTTTAATCTCCA--TTATTTTTATAATT-TTGACTTATGATTTAATCCCAATCGCTTTTA
66 TCGTGATTTAAT-T-CAGGTCATTTCTAT-TTTCTTGACTTGCGATTTAATCTCAATCGCTTTTA
* * * * *
5002638 TTATTT-TGACTTACGGTTCAGT-CCAGTCATCGTTAATCTTTGACTTGTGATTTAATC-CTGGT
128 TT-TTTCTGACTTGCGGTTCAATCCCAGTCGTCGTTAATCTTTGACTTGTGGTTTAATCTC-GAT
* * *
5002700 CATTTCTATAGTTTCCCGACTTGCGGTTTAATCCCAATCACTTTTATTGTTCTGACTTGCTGTTT
191 CATTTCTATAGTTTCCCGACTTGCGGTTTAATCCCAATCATTTTTATTGTTCTGACTTGCGGTTC
* * * * *
5002765 AGTTCCAATCGTTGTTAATTTTTGACTCGTGGTTTAATTCTGATTATTTTTATAGTTTTTCGACT
256 AGTTCCAGTCGTTGTTAATCTTTGACTCGTGGTTTAATCCTGATCATTTCTATAGTTTTTCGACT
5002830 TGCGG
321 TGCGG
* * * ** * * * ** * * *
5002835 TTTAATCTCAGTCGCTTTTATTTTCT-AACTTACAGTTCAATCTTGATCATCATTAATCTTTGGC
1 TTTAATCTCAGTCACTTTTATTTTTTGGACTCGCGGTTTAGTCTCAATCGTCGTTAATCTTTGAC
** *
5002899 TCACGATTTAATTCAGGTCATTTCTATTTTCTTGACTTGCGATTTAATCTCAGTCGCCTTTTATT
66 TCGTGATTTAATTCAGGTCATTTCTATTTTCTTGACTTGCGATTTAATCTCAATCG-CTTTTATT
*
5002964 TTTCTGACTTGCGGTTTAAT-CCAGTCGTC
130 TTTCTGACTTGCGGTTCAATCCCAGTCGTC
5002993 ATTATTTTCT
Statistics
Matches: 650, Mismatches: 132, Indels: 53
0.78 0.16 0.06
Matches are distributed among these distances:
321 2 0.00
322 3 0.00
323 71 0.11
324 408 0.63
325 66 0.10
326 33 0.05
327 66 0.10
328 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (325 bp):
TTTAATCTCAGTCACTTTTATTTTTTGGACTCGCGGTTTAGTCTCAATCGTCGTTAATCTTTGAC
TCGTGATTTAATTCAGGTCATTTCTATTTTCTTGACTTGCGATTTAATCTCAATCGCTTTTATTT
TTCTGACTTGCGGTTCAATCCCAGTCGTCGTTAATCTTTGACTTGTGGTTTAATCTCGATCATTT
CTATAGTTTCCCGACTTGCGGTTTAATCCCAATCATTTTTATTGTTCTGACTTGCGGTTCAGTTC
CAGTCGTTGTTAATCTTTGACTCGTGGTTTAATCCTGATCATTTCTATAGTTTTTCGACTTGCGG
Found at i:5003006 original size:34 final size:36
Alignment explanation
Indices: 5002923--5003006 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 36
5002913 AGGTCATTTC
*
5002923 TATTTTCTTGACTTGCGATTTAATCTCAGTCGCCTTT
1 TATTTTC-TGACTTGCGATTTAATCTCAGTCGCCTAT
* *
5002960 TATTTTTCTGACTTGCGGTTTAATC-CAGTCGTC-AT
1 TA-TTTTCTGACTTGCGATTTAATCTCAGTCGCCTAT
5002995 TATTTTCTGACT
1 TATTTTCTGACT
5003007 CACATTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 10 0.23
35 3 0.07
36 7 0.16
37 18 0.42
38 5 0.12
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (36 bp):
TATTTTCTGACTTGCGATTTAATCTCAGTCGCCTAT
Found at i:5003285 original size:3 final size:3
Alignment explanation
Indices: 5003277--5003311 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5003267 AGTTCTTGTT
5003277 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5003312 TTGGTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5003840 original size:9 final size:9
Alignment explanation
Indices: 5003828--5003879 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
5003818 GATTCAAGTT
5003828 TTTTTTTTA
1 TTTTTTTTA
5003837 TTTTTTTCTAA
1 TTTTTTT-T-A
5003848 TTTTTTTATA
1 TTTTTTT-TA
* *
5003858 TGTTATTTA
1 TTTTTTTTA
*
5003867 TTTTTATTA
1 TTTTTTTTA
5003876 TTTT
1 TTTT
5003880 AAGCTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 19 0.54
10 7 0.20
11 9 0.26
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:5003956 original size:3 final size:3
Alignment explanation
Indices: 5003948--5004015 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
5003938 TGATTGTTTT
* * * *
5003948 TAA TAA TAA TAA AAA TGAA AAA AAA TAA -AA AAA GTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* *
5003994 AAA TAA AAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
5004016 TTTTTAGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.85
4 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (3 bp):
TAA
Found at i:5003989 original size:15 final size:15
Alignment explanation
Indices: 5003952--5004008 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
5003942 TGTTTTTAAT
5003952 AATAATAAAAATGAAA
1 AATAATAAAAAT-AAA
* *
5003968 AAAAATAAAAAAAGTAAT
1 AATAAT--AAAAA-TAAA
5003986 AATAATAAAAATAAA
1 AATAATAAAAATAAA
5004001 AATAATAA
1 AATAATAA
5004009 TATAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 11 0.32
16 10 0.29
18 12 0.35
19 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AATAATAAAAATAAA
Found at i:5004307 original size:15 final size:15
Alignment explanation
Indices: 5004287--5004344 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
5004277 ATTTCTAAGC
5004287 CCTTAAAATCCAAAA
1 CCTTAAAATCCAAAA
5004302 CCTTAAAATCC-AAA
1 CCTTAAAATCCAAAA
* *
5004316 CCTTTAAATTCAAAA
1 CCTTAAAATCCAAAA
5004331 TCC-TAAAATCCAAA
1 -CCTTAAAATCCAAA
5004345 CCTCAAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.32
15 23 0.62
16 2 0.05
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (15 bp):
CCTTAAAATCCAAAA
Found at i:5004318 original size:14 final size:14
Alignment explanation
Indices: 5004287--5004352 Score: 71
Period size: 15 Copynumber: 4.6 Consensus size: 14
5004277 ATTTCTAAGC
5004287 CCTTAAAATCCAAAA
1 CCTTAAAATCC-AAA
5004302 CCTTAAAATCCAAA
1 CCTTAAAATCCAAA
* *
5004316 CCTTTAAATTCAAAA
1 CC-TTAAAATCCAAA
5004331 TCC-TAAAATCCAAA
1 -CCTTAAAATCCAAA
*
5004345 CCTCAAAA
1 CCTTAAAA
5004353 CTTTCAAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 2 0.05
14 18 0.42
15 21 0.49
16 2 0.05
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (14 bp):
CCTTAAAATCCAAA
Found at i:5004329 original size:29 final size:29
Alignment explanation
Indices: 5004287--5004352 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
5004277 ATTTCTAAGC
5004287 CCTTAAAATCCAAAA-CCTTAAAATCCAAA
1 CCTTAAAATCCAAAATCC-TAAAATCCAAA
* *
5004316 CCTTTAAATTCAAAATCCTAAAATCCAAA
1 CCTTAAAATCCAAAATCCTAAAATCCAAA
*
5004345 CCTCAAAA
1 CCTTAAAA
5004353 CTTTCAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 30 0.94
30 2 0.06
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (29 bp):
CCTTAAAATCCAAAATCCTAAAATCCAAA
Found at i:5004389 original size:22 final size:23
Alignment explanation
Indices: 5004342--5004385 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
5004332 CCTAAAATCC
5004342 AAACCTCAAAACTTTCAAAACCT
1 AAACCTCAAAACTTTCAAAACCT
*
5004365 AAACC-CAAAA-TTTCTAAACCT
1 AAACCTCAAAACTTTCAAAACCT
5004386 TAAAATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 5 0.25
23 5 0.25
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (23 bp):
AAACCTCAAAACTTTCAAAACCT
Found at i:5004395 original size:22 final size:22
Alignment explanation
Indices: 5004347--5004397 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5004337 AATCCAAACC
*
5004347 TCAAAACTTTCAAAACCTAAAC
1 TCAAAACTTTCAAAACCTAAAA
* *
5004369 CCAAAA-TTTCTAAACCTTAAAA
1 TCAAAACTTTCAAAACC-TAAAA
5004391 TCAAAAC
1 TCAAAAC
5004398 CTCAAACCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (22 bp):
TCAAAACTTTCAAAACCTAAAA
Found at i:5005205 original size:36 final size:36
Alignment explanation
Indices: 5005158--5005229 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
5005148 AAGAATATCA
5005158 TAGTAAATATCAGTTAAAAACATTATTTTCAAAGTT
1 TAGTAAATATCAGTTAAAAACATTATTTTCAAAGTT
*
5005194 TAGTAAATATCAGTTAAAAATATTATTTTCAAAGTT
1 TAGTAAATATCAGTTAAAAACATTATTTTCAAAGTT
5005230 CTGTCTAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.40
Consensus pattern (36 bp):
TAGTAAATATCAGTTAAAAACATTATTTTCAAAGTT
Found at i:5024177 original size:1 final size:1
Alignment explanation
Indices: 5024171--5024198 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
5024161 AGTGGACAAG
5024171 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
5024199 CGATTCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5027734 original size:111 final size:110
Alignment explanation
Indices: 5027541--5027755 Score: 340
Period size: 111 Copynumber: 1.9 Consensus size: 110
5027531 TCTTTTTCTC
* * * *
5027541 TTGGTTTAAGGGTTTTGTATATAAAAATTAAAATGTTATAAATTTGTTGATACTTGTGATTGAAT
1 TTGGTTTAAGGGTTTTGTATATAAAAAGTAAAATGTTATAAATTTGTCGATACTTCTGATTAAAT
5027606 ATGGAATTGTTATGTAATAAAGGCTGATTGTGTCTTTTTCTTTTT
66 ATGGAATTGTTATGTAATAAAGGCTGATTGTGTCTTTTTCTTTTT
* * *
5027651 TTGGTTTAAGGGTTTTGTGTATAAAAAAGTAAAATTTTCTAAATTTGTCGATACTTCTGATTAAA
1 TTGGTTTAAGGGTTTTGTATAT-AAAAAGTAAAATGTTATAAATTTGTCGATACTTCTGATTAAA
* *
5027716 TATGGAATTGTTGTGTAATAAAGGTTGATTGTGTCTTTTT
65 TATGGAATTGTTATGTAATAAAGGCTGATTGTGTCTTTTT
5027756 TCCTTTTTGG
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 21 0.22
111 74 0.78
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (110 bp):
TTGGTTTAAGGGTTTTGTATATAAAAAGTAAAATGTTATAAATTTGTCGATACTTCTGATTAAAT
ATGGAATTGTTATGTAATAAAGGCTGATTGTGTCTTTTTCTTTTT
Found at i:5030587 original size:2 final size:2
Alignment explanation
Indices: 5030582--5030614 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5030572 ATATATATAT
5030582 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5030615 ATGAAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5032942 original size:12 final size:12
Alignment explanation
Indices: 5032927--5032966 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5032917 ATATACACAC
5032927 ATATTTATATGT
1 ATATTTATATGT
*
5032939 ATATTTATACGT
1 ATATTTATATGT
* *
5032951 ATAATTATATAT
1 ATATTTATATGT
5032963 ATAT
1 ATAT
5032967 ACATATATAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (12 bp):
ATATTTATATGT
Found at i:5033463 original size:33 final size:33
Alignment explanation
Indices: 5033397--5033467 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
5033387 TCAAGATTTT
* *
5033397 TTTTTAATATACCATAAATTCATTTCCGTAAAC
1 TTTTTAATATACCAAAAATTCATTTCCGAAAAC
* **
5033430 TTTTTAATATACCAAAAATTTATTTTTGAAAAC
1 TTTTTAATATACCAAAAATTCATTTCCGAAAAC
5033463 TTTTT
1 TTTTT
5033468 CATTGTATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTTTAATATACCAAAAATTCATTTCCGAAAAC
Found at i:5035761 original size:5 final size:5
Alignment explanation
Indices: 5035746--5035775 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5035736 TAAAAGAAAG
5035746 AAAAT -AAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
5035776 TAAGGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Done.