Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 44 of 117
Found at i:10451680 original size:4 final size:4
Alignment explanation
Indices: 10451671--10451789 Score: 79
Period size: 4 Copynumber: 30.0 Consensus size: 4
10451661 TTATTTTTAC
* *
10451671 ATTT ATTT ATTT ATTT ATTT ATTTT ATTAAT GTTT AGTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT A-TTT ATT--T ATTT ATTT ATTT ATTT ATTT
* * * **
10451722 ATTT GTTT GTTT -TTC ATCTT -TTT -TGTT ATTT ATTT ATTT -TTT CCTT
1 ATTT ATTT ATTT ATTT AT-TT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
*
10451768 ATTT ATTT -GTT A-TT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT
10451790 GCAAATATTT
Statistics
Matches: 94, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
3 13 0.14
4 72 0.77
5 6 0.06
6 3 0.03
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:10451725 original size:39 final size:39
Alignment explanation
Indices: 10451671--10451760 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
10451661 TTATTTTTAC
*
10451671 ATTTATTTATTTATTTATTTATTTTATTA-ATGTTTAGTT
1 ATTTATTTATTTATTTATTTATTTT-TCATATGTTTAGTT
* * * * *
10451710 ATTTATTTATTTATTTGTTTGTTTTTCATCTTTTTTGTT
1 ATTTATTTATTTATTTATTTATTTTTCATATGTTTAGTT
10451749 ATTTATTTATTT
1 ATTTATTTATTT
10451761 TTTCCTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
38 2 0.05
39 42 0.95
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (39 bp):
ATTTATTTATTTATTTATTTATTTTTCATATGTTTAGTT
Found at i:10451849 original size:23 final size:22
Alignment explanation
Indices: 10451801--10451849 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
10451791 CAAATATTTT
* ** *
10451801 TTTTTAAAAAAGATAAAATTAT
1 TTTTTAAAAAAAATAAAAAGAA
10451823 TTTTTAAAATAAAATAAAAAGAA
1 TTTTTAAAA-AAAATAAAAAGAA
10451846 TTTT
1 TTTT
10451850 ACCAACATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTTTAAAAAAAATAAAAAGAA
Found at i:10453587 original size:15 final size:14
Alignment explanation
Indices: 10453563--10453596 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
10453553 AAGTGAGTCC
*
10453563 AATATTTTTTTTAA
1 AATATATTTTTTAA
10453577 ATATATATTTTTTAA
1 A-ATATATTTTTTAA
10453592 AATAT
1 AATAT
10453597 TGAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATATATTTTTTAA
Found at i:10454128 original size:52 final size:53
Alignment explanation
Indices: 10454014--10454145 Score: 196
Period size: 53 Copynumber: 2.5 Consensus size: 53
10454004 CACAGGATCG
* * **
10454014 AGATTTTTTTTTGTAATTATG-TTAAAAAAAGTATTATGTGAAGTAATAAATA
1 AGATATTTTTTTATAATTATGATTAAAAAAAGTATTATACGAAGTAATAAATA
10454066 AGATATTTTTTTATAATTATGATTAGAAAAAA-TATTATACGAAGTAATAAATA
1 AGATATTTTTTTATAATTATGATTA-AAAAAAGTATTATACGAAGTAATAAATA
*
10454119 AGATATTTTTTTATAATTATAATTAAA
1 AGATATTTTTTTATAATTATGATTAAA
10454146 CAGTATTAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
52 21 0.29
53 46 0.63
54 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (53 bp):
AGATATTTTTTTATAATTATGATTAAAAAAAGTATTATACGAAGTAATAAATA
Found at i:10455605 original size:24 final size:23
Alignment explanation
Indices: 10455586--10455661 Score: 102
Period size: 22 Copynumber: 3.3 Consensus size: 23
10455576 AAACAATAAT
*
10455586 AAAAATTATTATAATTACAATTGA
1 AAAAAATATTATAATTACAATT-A
*
10455610 AAAAAAAAGTT-TAATTACAATTA
1 AAAAAATA-TTATAATTACAATTA
10455633 AAAAAA-ATTATAATTACAATTA
1 AAAAAATATTATAATTACAATTA
10455655 AAAAAAT
1 AAAAAAT
10455662 TCAATAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.04
22 19 0.40
23 7 0.15
24 17 0.36
25 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (23 bp):
AAAAAATATTATAATTACAATTA
Found at i:10461831 original size:54 final size:53
Alignment explanation
Indices: 10461757--10461879 Score: 149
Period size: 54 Copynumber: 2.3 Consensus size: 53
10461747 TTGAGCCACA
* * * *
10461757 TTAGAAATATTTTCTCTTTTTGAATTTCTAAATTTTTCACAATTTGTG-CCTAT
1 TTAGAAATTTTTTTTATTTTTGAATCTCTAAATTTTTCACAATTTG-GACCTAT
** * *
10461810 TTAGAAATTCTTTTTTATTTTTTTATCTCTAAATTTTTCACCATTTGGATCTAT
1 TTAGAAATT-TTTTTTATTTTTGAATCTCTAAATTTTTCACAATTTGGACCTAT
10461864 TTAGAAATTTTTTTTA
1 TTAGAAATTTTTTTTA
10461880 AAAGAAAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 16 0.27
54 44 0.73
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (53 bp):
TTAGAAATTTTTTTTATTTTTGAATCTCTAAATTTTTCACAATTTGGACCTAT
Found at i:10462785 original size:9 final size:9
Alignment explanation
Indices: 10462770--10462801 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
10462760 CTCAACTACC
10462770 TATTTTTTT
1 TATTTTTTT
*
10462779 CATTTTTTT
1 TATTTTTTT
10462788 TATTTTTTT
1 TATTTTTTT
10462797 TATTT
1 TATTT
10462802 ACAAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (9 bp):
TATTTTTTT
Found at i:10463056 original size:40 final size:41
Alignment explanation
Indices: 10462959--10463207 Score: 223
Period size: 40 Copynumber: 6.0 Consensus size: 41
10462949 AAAAGTAAAC
* * * * * *
10462959 AATGCTCCTCTAATCAGAAGCTCAACAACTTTGAAAAAAAATA
1 AATGCTCATCTAAACAGAGGCACCACAACTTTG-AAAAATA-A
*
10463002 AATGTTCATCTAAACAGAGGCACCACAACTTTG-AAAATAA
1 AATGCTCATCTAAACAGAGGCACCACAACTTTGAAAAATAA
* * *
10463042 AATGCTCATCTAAACAAAGGCACCATAACTTTG-GAAATAA
1 AATGCTCATCTAAACAGAGGCACCACAACTTTGAAAAATAA
** * * *
10463082 CTTGCTCTTCTAAATAGAGGCACAACAACTTTTGAAAAATAA
1 AATGCTCATCTAAACAGAGGCACCACAAC-TTTGAAAAATAA
* * ** **
10463124 ATTGCTCATCTAAACGGAGATACCATGACTTTGAAAAAATAA
1 AATGCTCATCTAAACAGAGGCACCACAACTTTG-AAAAATAA
* * * *
10463166 AATGCTCCTCTAAATAAAGGCATCACAACTTTGAAAAATAA
1 AATGCTCATCTAAACAGAGGCACCACAACTTTGAAAAATAA
10463207 A
1 A
10463208 TTACTCCTTG
Statistics
Matches: 165, Mismatches: 38, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
40 59 0.36
41 22 0.13
42 57 0.35
43 27 0.16
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (41 bp):
AATGCTCATCTAAACAGAGGCACCACAACTTTGAAAAATAA
Found at i:10463136 original size:42 final size:41
Alignment explanation
Indices: 10462995--10463209 Score: 220
Period size: 42 Copynumber: 5.3 Consensus size: 41
10462985 AACTTTGAAA
*
10462995 AAAAATAAA-TGTTCATCTAAACAGAGGCACCACAACTTTG
1 AAAAATAAATTGCTCATCTAAACAGAGGCACCACAACTTTG
* * *
10463035 -AAAATAAAATGCTCATCTAAACAAAGGCACCATAACTTTG
1 AAAAATAAATTGCTCATCTAAACAGAGGCACCACAACTTTG
* * * * *
10463075 -GAAATAACTTGCTCTTCTAAATAGAGGCACAACAACTTTTG
1 AAAAATAAATTGCTCATCTAAACAGAGGCACCACAAC-TTTG
* ** **
10463116 AAAAATAAATTGCTCATCTAAACGGAGATACCATGACTTTG
1 AAAAATAAATTGCTCATCTAAACAGAGGCACCACAACTTTG
* * * * *
10463157 AAAAAATAAAATGCTCCTCTAAATAAAGGCATCACAACTTTG
1 -AAAAATAAATTGCTCATCTAAACAGAGGCACCACAACTTTG
10463199 AAAAATAAATT
1 AAAAATAAATT
10463210 ACTCCTTGAC
Statistics
Matches: 139, Mismatches: 32, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
39 8 0.06
40 56 0.40
41 18 0.13
42 57 0.41
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (41 bp):
AAAAATAAATTGCTCATCTAAACAGAGGCACCACAACTTTG
Found at i:10463149 original size:82 final size:81
Alignment explanation
Indices: 10462985--10463209 Score: 238
Period size: 82 Copynumber: 2.7 Consensus size: 81
10462975 GAAGCTCAAC
* * * * *
10462985 AACTTTGAAAAAAAATAAATGTTCATCTAAACAGAGGCACCACAACTTTG-AAAATAAAATGCTC
1 AACTTTG-AAAAATA-AAATGCTCCTCTAAATAGAGGCA-CACAACTTTGAAAAATAAATTGCTC
*
10463049 ATCTAAACAAAGGCACCAT
63 ATCTAAACAAAGACACCAT
* ** *
10463068 AACTTTG-GAAATAACTTGCTCTTCTAAATAGAGGCACAACAACTTTTGAAAAATAAATTGCTCA
1 AACTTTGAAAAATAAAATGCTCCTCTAAATAGAGGCAC-ACAAC-TTTGAAAAATAAATTGCTCA
** *
10463132 TCTAAACGGAGATACCAT
64 TCTAAACAAAGACACCAT
* *
10463150 GACTTTGAAAAAATAAAATGCTCCTCTAAATAAAGGCATCACAACTTTGAAAAATAAATT
1 AACTTTG-AAAAATAAAATGCTCCTCTAAATAGAGGCA-CACAACTTTGAAAAATAAATT
10463210 ACTCCTTGAC
Statistics
Matches: 118, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
79 1 0.01
80 23 0.19
81 8 0.07
82 34 0.29
83 22 0.19
84 29 0.25
85 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (81 bp):
AACTTTGAAAAATAAAATGCTCCTCTAAATAGAGGCACACAACTTTGAAAAATAAATTGCTCATC
TAAACAAAGACACCAT
Found at i:10463569 original size:21 final size:21
Alignment explanation
Indices: 10463545--10463584 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
10463535 GTTTCGCACC
10463545 TCAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTGAAAT
10463566 TCAAAGATTCTCATTTGAA
1 TCAAAGATTCTCATTTGAA
10463585 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
TCAAAGATTCTCATTTGAAAT
Found at i:10463595 original size:20 final size:21
Alignment explanation
Indices: 10463551--10463600 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
10463541 CACCTCAAAG
* *
10463551 ATTCTCATTTGAAATTCAAAG
1 ATTCTCATTTGAAATTAAAAA
10463572 ATTCTCATTTG-AATTAAAAA
1 ATTCTCATTTGAAATTAAAAA
*
10463592 ATTCACATT
1 ATTCTCATT
10463601 CGATAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (21 bp):
ATTCTCATTTGAAATTAAAAA
Found at i:10463637 original size:79 final size:79
Alignment explanation
Indices: 10463488--10463980 Score: 662
Period size: 79 Copynumber: 6.2 Consensus size: 79
10463478 CCAAAAGTTA
* * * ** * * * *
10463488 AAAGCTTCTCATTTGAGTCCAAAGGCTCACATTTGACAAATCTTAGGGTTTCGCACCTCAAAGAT
1 AAAGATTCTCATTTGAGTTCGAAGATTCACATTCGATAAATTTTA-GGTTTCACACCTCAAAGAT
10463553 TCTCATTTGAAATTC
65 TCTCATTTGAAATTC
* ** * *
10463568 AAAGATTCTCATTTGAATTAAAAAATTCACATTCGATAAATTTTAGGTTTCACACCTTAAAGATT
1 AAAGATTCTCATTTGAGTTCGAAGATTCACATTCGATAAATTTTAGGTTTCACACCTCAAAGATT
10463633 CTCATTTGAAATTC
66 CTCATTTGAAATTC
** * *
10463647 AAAGATTCTCATTTGAGTTTAAAGATTCACATTCGACAAAATTTAAGGTTTCACACCTCAAAGAT
1 AAAGATTCTCATTTGAGTTCGAAGATTCACATTCGA-TAAATTTTAGGTTTCACACCTCAAAGAT
10463712 TCTCATTTGAAATTC
65 TCTCATTTGAAATTC
* * *
10463727 AAAGATTCTCATTTGAGTTTGAAGATTCACATTCGATAAATTTTGGGTTTTACACCTCAAAGATT
1 AAAGATTCTCATTTGAGTTCGAAGATTCACATTCGATAAATTTTAGGTTTCACACCTCAAAGATT
10463792 CTCATTTGAAATTC
66 CTCATTTGAAATTC
* * * * * *
10463806 AAAGATTCTCATTTGAGTTCGAAGATTCATATTTGATGAATTTTGGGTTTCACACCCCAAACATT
1 AAAGATTCTCATTTGAGTTCGAAGATTCACATTCGATAAATTTTAGGTTTCACACCTCAAAGATT
10463871 CTCATTTGAAATTC
66 CTCATTTGAAATTC
* * * * * *
10463885 AAAGCTTCTCATTTGTGTTCGAAGATTCACATTCGACAAATTTTGGGTTTCATACCTCAAAGGTT
1 AAAGATTCTCATTTGAGTTCGAAGATTCACATTCGATAAATTTTAGGTTTCACACCTCAAAGATT
10463950 CTCATTTGAAATTC
66 CTCATTTGAAATTC
*
10463964 AAAGATTTTCATTTGAG
1 AAAGATTCTCATTTGAG
10463981 AACTCAAAAA
Statistics
Matches: 369, Mismatches: 43, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
79 259 0.70
80 110 0.30
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (79 bp):
AAAGATTCTCATTTGAGTTCGAAGATTCACATTCGATAAATTTTAGGTTTCACACCTCAAAGATT
CTCATTTGAAATTC
Found at i:10463652 original size:21 final size:21
Alignment explanation
Indices: 10463626--10463742 Score: 86
Period size: 21 Copynumber: 5.8 Consensus size: 21
10463616 TTCACACCTT
10463626 AAAGATTCTCATTTGAAATTC
1 AAAGATTCTCATTTGAAATTC
* *
10463647 AAAGATTCTCATTTG-AGTTT
1 AAAGATTCTCATTTGAAATTC
* *
10463667 AAAGATTCACATTCG--A--C
1 AAAGATTCTCATTTGAAATTC
* * **
10463684 AAA-ATT-TAAGGTTTCACACCTC
1 AAAGATTCTCA--TTTGA-AATTC
10463706 AAAGATTCTCATTTGAAATTC
1 AAAGATTCTCATTTGAAATTC
10463727 AAAGATTCTCATTTGA
1 AAAGATTCTCATTTGA
10463743 GTTTGAAGAT
Statistics
Matches: 72, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
15 1 0.01
16 3 0.04
17 5 0.07
20 16 0.22
21 34 0.47
22 8 0.11
23 3 0.04
24 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
AAAGATTCTCATTTGAAATTC
Found at i:10463782 original size:159 final size:158
Alignment explanation
Indices: 10463488--10463980 Score: 707
Period size: 159 Copynumber: 3.1 Consensus size: 158
10463478 CCAAAAGTTA
* * ** *
10463488 AAAGCTTCTCATTTGAGTCCAAAGGCTCACATTTGACAAATCTTAGGGTTTCGCACCTCAAAGAT
1 AAAGATTCTCATTTGAGTTCAAAGATTCACATTTGACAAAT-TTAGGGTTTCACACCTCAAAGAT
* * * *
10463553 TCTCATTTGAAATTCAAAGATTCTCATTTGAATTAAAAAATTCACATTCGATAAATTTTAGGTTT
65 TCTCATTTGAAATTCAAAGATTCTCATTTGAGTTAGAAGATTCACATTCGATAAATTTTGGGTTT
*
10463618 CACACCTTAAAGATTCTCATTTGAAATTC
130 CACACCTCAAAGATTCTCATTTGAAATTC
* * *
10463647 AAAGATTCTCATTTGAGTTTAAAGATTCACATTCGACAAAATTTAAGGTTTCACACCTCAAAGAT
1 AAAGATTCTCATTTGAGTTCAAAGATTCACATTTGAC-AAATTTAGGGTTTCACACCTCAAAGAT
*
10463712 TCTCATTTGAAATTCAAAGATTCTCATTTGAGTTTGAAGATTCACATTCGATAAATTTTGGGTTT
65 TCTCATTTGAAATTCAAAGATTCTCATTTGAGTTAGAAGATTCACATTCGATAAATTTTGGGTTT
*
10463777 TACACCTCAAAGATTCTCATTTGAAATTC
130 CACACCTCAAAGATTCTCATTTGAAATTC
* * ** * * *
10463806 AAAGATTCTCATTTGAGTTCGAAGATTCATATTTGATGAATTTTGGGTTTCACACCCCAAACATT
1 AAAGATTCTCATTTGAGTTCAAAGATTCACATTTGACAAATTTAGGGTTTCACACCTCAAAGATT
* * * *
10463871 CTCATTTGAAATTCAAAGCTTCTCATTTGTGTTCGAAGATTCACATTCGACAAATTTTGGGTTTC
66 CTCATTTGAAATTCAAAGATTCTCATTTGAGTTAGAAGATTCACATTCGATAAATTTTGGGTTTC
* *
10463936 ATACCTCAAAGGTTCTCATTTGAAATTC
131 ACACCTCAAAGATTCTCATTTGAAATTC
*
10463964 AAAGATTTTCATTTGAG
1 AAAGATTCTCATTTGAG
10463981 AACTCAAAAA
Statistics
Matches: 300, Mismatches: 33, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
158 125 0.42
159 171 0.57
160 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (158 bp):
AAAGATTCTCATTTGAGTTCAAAGATTCACATTTGACAAATTTAGGGTTTCACACCTCAAAGATT
CTCATTTGAAATTCAAAGATTCTCATTTGAGTTAGAAGATTCACATTCGATAAATTTTGGGTTTC
ACACCTCAAAGATTCTCATTTGAAATTC
Found at i:10463965 original size:21 final size:22
Alignment explanation
Indices: 10463940--10463994 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
10463930 GGTTTCATAC
*
10463940 CTCAAAGGTTCTCATTTGA-AA
1 CTCAAAGATTCTCATTTGAGAA
* *
10463961 TTCAAAGATTTTCATTTGAGAA
1 CTCAAAGATTCTCATTTGAGAA
*
10463983 CTCAAAAATTCT
1 CTCAAAGATTCT
10463995 TATCAAAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
CTCAAAGATTCTCATTTGAGAA
Found at i:10465302 original size:10 final size:10
Alignment explanation
Indices: 10465284--10465325 Score: 61
Period size: 9 Copynumber: 4.4 Consensus size: 10
10465274 TTTATCATTC
*
10465284 TTTCATTTTT
1 TTTCTTTTTT
10465294 TTTCTTTTTT
1 TTTCTTTTTT
10465304 TTT-TTTTTT
1 TTTCTTTTTT
10465313 TTT-TTTTTT
1 TTTCTTTTTT
10465322 TTTC
1 TTTC
10465326 ATCTTTTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 18 0.60
10 12 0.40
ACGTcount: A:0.02, C:0.07, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:10465332 original size:19 final size:19
Alignment explanation
Indices: 10465265--10465333 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
10465255 TTTCTCTCAC
* ** *
10465265 TTTCATCTTTTTATCATTC
1 TTTCATCTTTTTTTTTTTT
10465284 TTTCAT-TTTTTTTCTTTTT
1 TTTCATCTTTTTTT-TTTTT
** *
10465303 TTTTTTTTTTTTTTTTTTT
1 TTTCATCTTTTTTTTTTTT
10465322 TTTCATCTTTTT
1 TTTCATCTTTTT
10465334 CCATCTGCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 6 0.15
19 26 0.67
20 7 0.18
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTCATCTTTTTTTTTTTT
Found at i:10465333 original size:1 final size:1
Alignment explanation
Indices: 10465289--10465324 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
10465279 CATTCTTTCA
*
10465289 TTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10465325 CATCTTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:10465731 original size:24 final size:24
Alignment explanation
Indices: 10465686--10465732 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
10465676 TGTTTATGGT
* *
10465686 ATTTTTCTTTTATCTCTTTCTTTC
1 ATTTTGCTTTTATCTCTCTCTTTC
* *
10465710 ATTTTGCTTTTCTTTCTCTCTTT
1 ATTTTGCTTTTATCTCTCTCTTT
10465733 GAAACCTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTTGCTTTTATCTCTCTCTTTC
Found at i:10470030 original size:22 final size:21
Alignment explanation
Indices: 10469979--10470030 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
10469969 TATTTATTCT
10469979 TAAAATTTATTTTATTTTTTA
1 TAAAATTTATTTTATTTTTTA
*****
10470000 CCTTTTTTATTTTTATTTTTTA
1 TAAAATTTA-TTTTATTTTTTA
10470022 TAAAATTTA
1 TAAAATTTA
10470031 ATCACGTAAA
Statistics
Matches: 20, Mismatches: 10, Indels: 1
0.65 0.32 0.03
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TAAAATTTATTTTATTTTTTA
Found at i:10478582 original size:14 final size:14
Alignment explanation
Indices: 10478563--10478595 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
10478553 ACATAGTAAT
10478563 AAATAAAATATTTA
1 AAATAAAATATTTA
10478577 AAATAAAATATTTA
1 AAATAAAATATTTA
*
10478591 TAATA
1 AAATA
10478596 TTTTTAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAAAATATTTA
Found at i:10478829 original size:22 final size:22
Alignment explanation
Indices: 10478799--10478842 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10478789 TTTTAAAATA
10478799 ATAACAAAATAAATTTGATATT
1 ATAACAAAATAAATTTGATATT
*
10478821 ATAATAAAATAAATTTGATATT
1 ATAACAAAATAAATTTGATATT
10478843 TTTATTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (22 bp):
ATAACAAAATAAATTTGATATT
Found at i:10479543 original size:56 final size:55
Alignment explanation
Indices: 10479447--10479555 Score: 137
Period size: 56 Copynumber: 2.0 Consensus size: 55
10479437 ATCATACTTA
** * * * *
10479447 TTCTTGCTATTTGTTATTTGTTCGATTTGGCTTAGTTCTTGATCTACTCAAATGTT
1 TTCTTGCTATTTGTTATTCATTAGATGTGACTTAGATCTTGATCTAC-CAAATGTT
* *
10479503 TTCTTGCTATTTGTTATTCATTAGATGTGATTTAGATCTTGATTTACCAAATG
1 TTCTTGCTATTTGTTATTCATTAGATGTGACTTAGATCTTGATCTACCAAATG
10479556 CACATTGTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
55 6 0.13
56 39 0.87
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (55 bp):
TTCTTGCTATTTGTTATTCATTAGATGTGACTTAGATCTTGATCTACCAAATGTT
Found at i:10480561 original size:30 final size:30
Alignment explanation
Indices: 10480525--10480584 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
10480515 ACATTTGAAA
10480525 TGTATATAAATATTATGACACTAAACTTAG
1 TGTATATAAATATTATGACACTAAACTTAG
*
10480555 TGTATATTAATATTATGACACTAAACTTAG
1 TGTATATAAATATTATGACACTAAACTTAG
10480585 GTTCTTACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (30 bp):
TGTATATAAATATTATGACACTAAACTTAG
Found at i:10482763 original size:126 final size:128
Alignment explanation
Indices: 10482505--10482839 Score: 365
Period size: 128 Copynumber: 2.6 Consensus size: 128
10482495 AAATTAGGAT
* * * **
10482505 AAAAATATCGTCATTATTAAGTTAATATAAAATTGATAACGTTCAATTTAAAATTTGATAAA-TA
1 AAAAAAATCGTCATTATTTAGTTAATATAAAATTGACAAAATTCAATTTAAAATTTGATAAACT-
* * * * * *
10482569 AACAAAAACTGT-GTTTTTAACGTAAAAACGTCATTTTTGTATACAAATACTGCATTTTTAACC
65 AACAAAAACTATATTTTTTAACATAAAAACGTCATCTTTGGATACAAATACTACATTTTTAACC
* * *
10482632 AAAAAAGTTGTCATTATTTA-TTAATATAAAATTGACAAAATTCAATTTAAAATTTGATAAACTG
1 AAAAAAATCGTCATTATTTAGTTAATATAAAATTGACAAAATTCAATTTAAAATTTGATAAACTA
* * * * * * *
10482696 ACAAAAATTATATTTTTTTATATAAAAATGTCATCTTTGGCTACAAATATTACATTTCTTAACA
66 ACAAAAACTATATTTTTTAACATAAAAACGTCATCTTTGGATACAAATACTACATTT-TTAACC
* * * * *
10482760 AAAAAAATCGTCATT-GTTAGTTAACATGAAATT-ACCAAGATTCAATTTAAAATTTAATAAACT
1 AAAAAAATCGTCATTATTTAGTTAATATAAAATTGA-CAAAATTCAATTTAAAATTTGATAAACT
*
10482823 AACAAAGACTATATTTT
65 AACAAAAACTATATTTT
10482840 AAAAAAAAAT
Statistics
Matches: 172, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
126 47 0.27
127 56 0.33
128 69 0.40
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.37
Consensus pattern (128 bp):
AAAAAAATCGTCATTATTTAGTTAATATAAAATTGACAAAATTCAATTTAAAATTTGATAAACTA
ACAAAAACTATATTTTTTAACATAAAAACGTCATCTTTGGATACAAATACTACATTTTTAACC
Found at i:10482808 original size:128 final size:127
Alignment explanation
Indices: 10482505--10482896 Score: 344
Period size: 128 Copynumber: 3.1 Consensus size: 127
10482495 AAATTAGGAT
* * * **
10482505 AAAAATATCGTCATTA-TTAAGTTAATATAAAATTGATAACGTTCAATTTAAAATTTGATAAA-T
1 AAAAAAATCGTCATTAGTT-A-TTAACATAAAATTGACAAAATTCAATTTAAAATTTGATAAACT
* * * * * * *
10482568 AAACAAAAACTGT-GTTTTTAACGTAAAAACGTCATTTTTGTATACAAATACTGCATTTTTAACC
64 -AACAAAAACTATATTTTTTAACATAAAAACGTCATCTTTGGATACAAATACTACATTTTTAACA
* * * * *
10482632 AAAAAAGTTGTCATTATTTATTAATATAAAATTGACAAAATTCAATTTAAAATTTGATAAACTGA
1 AAAAAAATCGTCATTAGTTATTAACATAAAATTGACAAAATTCAATTTAAAATTTGATAAACTAA
* * * * * *
10482697 CAAAAATTATATTTTTTTATATAAAAATGTCATCTTTGGCTACAAATATTACATTTCTTAACA
66 CAAAAACTATATTTTTTAACATAAAAACGTCATCTTTGGATACAAATACTACATTT-TTAACA
* * *
10482760 AAAAAAATCGTCATT-GTTAGTTAACATGAAATT-ACCAAGATTCAATTTAAAATTTAATAAACT
1 AAAAAAATCGTCATTAGTTA-TTAACATAAAATTGA-CAAAATTCAATTTAAAATTTGATAAACT
* ** * * * * * **
10482823 AACAAAGACTATATTTTAAAAAAAAATAAAAACATCATCTTTTGAGACAAAGACTATGTTTTTAA
64 AACAAAAACTATATTTT---TTAACATAAAAACGTCATCTTTGGATACAAATACTACATTTTTAA
10482888 CA
126 CA
10482890 AAAAAAA
1 AAAAAAA
10482897 AAAAATCTAA
Statistics
Matches: 213, Mismatches: 43, Indels: 15
0.79 0.16 0.06
Matches are distributed among these distances:
126 47 0.22
127 54 0.25
128 71 0.33
130 13 0.06
131 28 0.13
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (127 bp):
AAAAAAATCGTCATTAGTTATTAACATAAAATTGACAAAATTCAATTTAAAATTTGATAAACTAA
CAAAAACTATATTTTTTAACATAAAAACGTCATCTTTGGATACAAATACTACATTTTTAACA
Found at i:10486971 original size:21 final size:20
Alignment explanation
Indices: 10486947--10487005 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
10486937 GAAAAAATAA
*
10486947 TAAATAAAATAATAATATTAT
1 TAAATAAAATAATAATA-AAT
*
10486968 TAAATACAATAATAA-AAAT
1 TAAATAAAATAATAATAAAT
10486987 TAAATAAAAATACATAATA
1 TAAAT-AAAATA-ATAATA
10487006 CAAAAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.22
20 6 0.19
21 18 0.56
22 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAATAAAATAATAATAAAT
Found at i:10487003 original size:10 final size:9
Alignment explanation
Indices: 10486975--10487070 Score: 54
Period size: 10 Copynumber: 10.1 Consensus size: 9
10486965 TATTAAATAC
10486975 AATAATAAA
1 AATAATAAA
10486984 AATTAAATAAA
1 AA-T-AATAAA
10486995 AATACATAATA
1 AATA-ATAA-A
*
10487006 CAAAAATACAA
1 -AATAATA-AA
*
10487017 AATATAAAAA
1 AATA-ATAAA
10487027 AATAA-AAA
1 AATAATAAA
10487035 ATATAATAAA
1 A-ATAATAAA
*
10487045 AACAA-AAA
1 AATAATAAA
* *
10487053 AACAAAAAA
1 AATAATAAA
10487062 AATAA-AAA
1 AATAATAAA
10487070 A
1 A
10487071 GGGGCTGGCA
Statistics
Matches: 72, Mismatches: 5, Indels: 21
0.73 0.05 0.21
Matches are distributed among these distances:
8 16 0.22
9 18 0.25
10 19 0.26
11 15 0.21
12 4 0.06
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (9 bp):
AATAATAAA
Found at i:10487012 original size:15 final size:15
Alignment explanation
Indices: 10486992--10487026 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10486982 AAAATTAAAT
*
10486992 AAAAATACATAATAC
1 AAAAATACAAAATAC
*
10487007 AAAAATACAAAATAT
1 AAAAATACAAAATAC
10487022 AAAAA
1 AAAAA
10487027 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATACAAAATAC
Found at i:10487015 original size:8 final size:8
Alignment explanation
Indices: 10486992--10487060 Score: 61
Period size: 8 Copynumber: 8.6 Consensus size: 8
10486982 AAAATTAAAT
10486992 AAAAATAC
1 AAAAATAC
*
10487000 -ATAATAC
1 AAAAATAC
10487007 AAAAATAC
1 AAAAATAC
*
10487015 AAAATATAA
1 AAAA-ATAC
10487024 AAAAATA-
1 AAAAATAC
*
10487031 AAAAATAT
1 AAAAATAC
*
10487039 AATAAAAAC
1 AA-AAATAC
*
10487048 AAAAAAAC
1 AAAAATAC
10487056 AAAAA
1 AAAAA
10487061 AAATAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
7 13 0.25
8 26 0.50
9 13 0.25
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAATAC
Found at i:10487052 original size:17 final size:17
Alignment explanation
Indices: 10487007--10487070 Score: 76
Period size: 17 Copynumber: 3.7 Consensus size: 17
10486997 TACATAATAC
*
10487007 AAAAATACAAAATATAA
1 AAAAATAAAAAATATAA
10487024 AAAAATAAAAAATATAA
1 AAAAATAAAAAATATAA
* *
10487041 TAAAAACAAAAAA-ACAAA
1 -AAAAATAAAAAATA-TAA
10487059 AAAAATAAAAAA
1 AAAAATAAAAAA
10487071 GGGGCTGGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 28 0.68
18 13 0.32
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAAATATAA
Found at i:10487059 original size:26 final size:25
Alignment explanation
Indices: 10487007--10487070 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
10486997 TACATAATAC
* * *
10487007 AAAAATACAAAATATAAAAAAATAAA
1 AAAAATA-AAAAAACAAAAAAACAAA
*
10487033 AAATATAATAAAAACAAAAAAACAAA
1 AAAAATAA-AAAAACAAAAAAACAAA
10487059 AAAAATAAAAAA
1 AAAAATAAAAAA
10487071 GGGGCTGGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 5 0.16
26 27 0.84
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (25 bp):
AAAAATAAAAAAACAAAAAAACAAA
Found at i:10487068 original size:8 final size:8
Alignment explanation
Indices: 10487002--10487070 Score: 66
Period size: 8 Copynumber: 8.1 Consensus size: 8
10486992 AAAAATACAT
*
10487002 AATACAAA
1 AATAAAAA
10487010 AATACAAAA
1 AATA-AAAA
*
10487019 TATAAAAA
1 AATAAAAA
10487027 AATAAAAA
1 AATAAAAA
10487035 ATATAATAAA
1 A-ATAA-AAA
*
10487045 AACAAAAA
1 AATAAAAA
*
10487053 AACAAAAAA
1 AA-TAAAAA
10487062 AATAAAAA
1 AATAAAAA
10487070 A
1 A
10487071 GGGGCTGGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
8 27 0.53
9 20 0.39
10 4 0.08
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:10487069 original size:41 final size:44
Alignment explanation
Indices: 10486978--10487069 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 44
10486968 TAAATACAAT
* * *
10486978 AATAAAAATTAAATAAAAATACATAATACAAAAATACAAAATAT
1 AATAAAAATTAAATAAAAATACATAAAACAAAAAAACAAAATAA
*
10487022 AA-AAAAA-TAAA-AAATATA-ATAAAAACAAAAAAACAAAA-AA
1 AATAAAAATTAAATAAAAATACAT-AAAACAAAAAAACAAAATAA
10487062 AATAAAAA
1 AATAAAAA
10487070 AGGGGCTGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
40 5 0.12
41 26 0.62
42 4 0.10
43 5 0.12
44 2 0.05
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (44 bp):
AATAAAAATTAAATAAAAATACATAAAACAAAAAAACAAAATAA
Found at i:10488404 original size:18 final size:18
Alignment explanation
Indices: 10488361--10488408 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
10488351 TTGGGTTATA
*
10488361 AAATGATAATAATAAAATT
1 AAATAATAA-AATAAAATT
*
10488380 AACTAATAAAATAAGAA-T
1 AAATAATAAAATAA-AATT
10488398 AAATAATAAAA
1 AAATAATAAAA
10488409 AATGAGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (18 bp):
AAATAATAAAATAAAATT
Found at i:10488601 original size:14 final size:14
Alignment explanation
Indices: 10488582--10488608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10488572 TTTCAATTGA
10488582 AAATAAAAAAATTT
1 AAATAAAAAAATTT
10488596 AAATAAAAAAATT
1 AAATAAAAAAATT
10488609 AATAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAAAAAATTT
Found at i:10488603 original size:13 final size:13
Alignment explanation
Indices: 10488582--10488615 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
10488572 TTTCAATTGA
10488582 AAATAAAAAAATTT
1 AAATAAAAAAA-TT
10488596 AAATAAAAAAATT
1 AAATAAAAAAATT
10488609 -AATAAAA
1 AAATAAAA
10488616 TTACCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 2 0.10
14 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAAAAATT
Found at i:10500437 original size:47 final size:46
Alignment explanation
Indices: 10500371--10501008 Score: 492
Period size: 47 Copynumber: 13.2 Consensus size: 46
10500361 GAACGGATGA
*
10500371 GATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAT
1 GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAA-AT
* ** *
10500418 GATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAAATTTTCCAAAT
1 GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAAT
* * * *
10500464 AAATTTTTAAAGTTATTGAGCCTCTGCTGAAAAGAGCCTTTTTCAAGAT
1 -GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAA-AT
* * *
10500513 GAAAATTTTTAAAGTTGTTGAGCCTCTGCTAAAAAGAGCCATTTTT-AAGAT
1 G---ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-C-TTTTTCAA-AT
* * * *
10500564 GATAATTTTTAAAGTTGTTAAGCTTCTGTTGAGAGAAG-TTTTTCCAAAT
1 G---ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-CAAAT
* * * *
10500613 GAGATTTTAAAGTTGTTGAGCTTCTGCTAAGAGGAGCCTTTTCAAGAT
1 GA-TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAA-AT
* * ** *
10500661 GAGATTTTTAAAGTTGTTGAACCTCTGCTGAAAATAGCTTTTTTAAAT
1 --GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAAT
* *
10500709 AAGA-TTTTAAAGTTGATGAGCCTCTGTTGAGAGGAGCTTTTTCAAAT
1 --GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAAT
* * * * * * * *
10500756 GAGATTTTAAAGTTATTGAGCTTTTGTTAAGAGAAACTTTTTCAAGAT
1 GA-TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAA-AT
* *
10500804 GAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGTTTTTTCAAAT
1 --GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAAT
* * * * *
10500852 GAGATTTTAAAGTTATTGAGCTTTTGCTGAGATGAGC-TTTTCAAAT
1 GA-TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAAT
* * * *
10500898 GAGATTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAACCATTTTCAAGAT
1 GA-TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTTTCAA-AT
* * * *
10500947 GAGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAGCCCTTTTAAAAT
1 --G-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAAT
10500997 GAGATTTTTAAA
1 --GATTTTTAAA
10501009 TAGGAGCTCT
Statistics
Matches: 486, Mismatches: 78, Indels: 52
0.79 0.13 0.08
Matches are distributed among these distances:
45 2 0.00
46 43 0.09
47 200 0.41
48 34 0.07
49 83 0.17
50 12 0.02
51 106 0.22
52 6 0.01
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (46 bp):
GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAAT
Found at i:10500742 original size:96 final size:97
Alignment explanation
Indices: 10500366--10500978 Score: 578
Period size: 96 Copynumber: 6.4 Consensus size: 97
10500356 TTGAAGAACG
* **
10500366 GATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAT--GATTTTTAAAG
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGA-AAAAGCTTTTTCAAGATGAGATTTTTAAAG
* **
10500429 TTGTTGAGCCTCTGTTGAGAGGA-AATTTTCCAA
65 TTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-CAA
* * *
10500462 -AT-AAATTTTTAAAGTTATTGAGCCTCTGCTGAAAAGAGCCTTTTTCAAGATGAAAATTTTTAA
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAA-AG-CTTTTTCAAGATG-AGATTTTTAA
* * * *
10500525 AGTTGTTGAGCCTCTGCTAAAAAGAGCCATTTTTAA
63 AGTTGTTGAGCCTCTGCTGAGAGGAGCC-TTTTCAA
* * * * *
10500561 GATGATAATTTTTAAAGTTGTTAAGCTTCTGTTGAGAGAAG-TTTTTCCAA-ATGAGA-TTTTAA
1 GATGA-GATTTTTAAAGTTGTTGAGCCTCTGCTGA-AAAAGCTTTTT-CAAGATGAGATTTTTAA
* *
10500623 AGTTGTTGAGCTTCTGCTAAGAGGAGCCTTTTCAA
63 AGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAA
* * *
10500658 GATGAGATTTTTAAAGTTGTTGAACCTCTGCTGAAAATAGCTTTTTTAA-ATAAGA-TTTTAAAG
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAA-AGCTTTTTCAAGATGAGATTTTTAAAG
* * *
10500721 TTGATGAGCCTCTGTTGAGAGGAGCTTTTTCAA
65 TTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAA
* * * * *
10500754 -ATGAGA-TTTTAAAGTTATTGAGCTTTTG-TTAAGAGAAACTTTTTCAAGATGAGATTTTTAAA
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAA-A-AAGCTTTTTCAAGATGAGATTTTTAAA
* **
10500816 GTTGTTGAGCCTTTGCTGAGAGGAGTTTTTTCAA
64 GTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAA
* * * **
10500850 -ATGAGA-TTTTAAAGTTATTGAGCTTTTGCTGAGATGAGC-TTTTCAA-ATGAGA-TTTTAAAG
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGA-AAAAGCTTTTTCAAGATGAGATTTTTAAAG
* *
10500910 TTGTTAAGCCTCTGCTGAGAGGAACCATTTTCAA
65 TTGTTGAGCCTCTGCTGAGAGGAGCC-TTTTCAA
* *
10500944 GATGAGAATTTTTAAAGTTGTTAAGCCTCTACTGA
1 GATGAG-ATTTTTAAAGTTGTTGAGCCTCTGCTGA
10500979 GAGGAGCCCT
Statistics
Matches: 431, Mismatches: 62, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
93 33 0.08
94 70 0.16
95 40 0.09
96 137 0.32
97 39 0.09
98 61 0.14
99 4 0.01
100 14 0.03
101 4 0.01
102 27 0.06
103 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (97 bp):
GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAAAGCTTTTTCAAGATGAGATTTTTAAAGT
TGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAA
Found at i:10500761 original size:143 final size:146
Alignment explanation
Indices: 10500366--10501008 Score: 659
Period size: 143 Copynumber: 4.4 Consensus size: 146
10500356 TTGAAGAACG
* * * *
10500366 GATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAT--GATTTTTAAAG
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAAGAGCTTTTTTAAGATAAGATTTTTAAAG
* ** * *
10500429 TTGTTGAGCCTCTGTTGAGAGGAAATTTTCCAAAT-AAATTTTTAAAGTTATTGAGCCTCTGCTG
66 TTGATGAGCCTCTGTTGAGAGGAGCTTTTTCAAATGAGA-TTTTAAAGTTATTGAGCCTCTGCT-
* * *
10500493 AA-AAGAGCCTTTTTCAA
129 AAGAGGAACCATTTTCAA
* * *
10500510 GATGAAAATTTTTAAAGTTGTTGAGCCTCTGCTAAAAAGAGCCATTTTTAAGATGATA-ATTTTT
1 GATG-AGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAAGAG-CTTTTTTAAGAT-A-AGATTTTT
* * * * * *
10500574 AAAGTTGTTAAGCTTCTGTTGAGAGAAG-TTTTTCCAAATGAGATTTTAAAGTTGTTGAGCTTCT
62 AAAGTTGATGAGCCTCTGTTGAGAGGAGCTTTTT-CAAATGAGATTTTAAAGTTATTGAGCCTCT
*
10500638 GCTAAGAGGAGCC-TTTTCAA
126 GCTAAGAGGAACCATTTTCAA
* *
10500658 GATGAGATTTTTAAAGTTGTTGAACCTCTGCTGAAAATAGCTTTTTTAA-ATAAGA-TTTTAAAG
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAAGAGCTTTTTTAAGATAAGATTTTTAAAG
* * *
10500721 TTGATGAGCCTCTGTTGAGAGGAGCTTTTTCAAATGAGATTTTAAAGTTATTGAGCTTTTGTTAA
66 TTGATGAGCCTCTGTTGAGAGGAGCTTTTTCAAATGAGATTTTAAAGTTATTGAGCCTCTGCTAA
* *
10500786 GA-GAAACTTTTTCAA
131 GAGGAACCATTTTCAA
* * * *
10500801 GATGAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAG-TTTTTTCAA-ATGAGA-TTTTAAA
1 GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAAGAGCTTTTTT-AAGATAAGATTTTTAAA
* * * * * *
10500863 GTT-ATTGAGCTTTTGCTGAGATGAGC-TTTTCAAATGAGATTTTAAAGTTGTTAAGCCTCTGCT
65 GTTGA-TGAGCCTCTGTTGAGAGGAGCTTTTTCAAATGAGATTTTAAAGTTATTGAGCCTCTGCT
*
10500926 GAGAGGAACCATTTTCAA
129 AAGAGGAACCATTTTCAA
* * * * ** * *
10500944 GATGAGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAGCCCTTTTAAAATGAGATTTTTAAA
1 GATGAG-ATTTTTAAAGTTGTTGAGCCTCTGCTGAAAAGAGCTTTTTTAAGATAAGATTTTTAAA
10501009 TAGGAGCTCT
Statistics
Matches: 427, Mismatches: 53, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
142 45 0.11
143 156 0.37
144 44 0.10
145 43 0.10
146 25 0.06
147 32 0.07
148 17 0.04
149 63 0.15
150 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (146 bp):
GATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAAGAGCTTTTTTAAGATAAGATTTTTAAAG
TTGATGAGCCTCTGTTGAGAGGAGCTTTTTCAAATGAGATTTTAAAGTTATTGAGCCTCTGCTAA
GAGGAACCATTTTCAA
Found at i:10501007 original size:14 final size:14
Alignment explanation
Indices: 10500988--10501039 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
10500978 AGAGGAGCCC
10500988 TTTTAAAATGAGAT
1 TTTTAAAATGAGAT
* *
10501002 TTTTAAATAGGAGCTCT
1 TTTTAAA-ATGAG--AT
*
10501019 TTTTAAGATGAGAT
1 TTTTAAAATGAGAT
10501033 TTTTAAA
1 TTTTAAA
10501040 GTTGTTGAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 14 0.48
15 4 0.14
16 4 0.14
17 7 0.24
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TTTTAAAATGAGAT
Found at i:10501021 original size:30 final size:31
Alignment explanation
Indices: 10500980--10501039 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
10500970 CTCTACTGAG
10500980 AGGAGCCC-TTTTAAAATGAGATTTTTAAAT
1 AGGAGCCCTTTTTAAAATGAGATTTTTAAAT
* *
10501010 AGGAGCTCTTTTTAAGATGAGATTTTTAAA
1 AGGAGCCCTTTTTAAAATGAGATTTTTAAA
10501040 GTTGTTGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
AGGAGCCCTTTTTAAAATGAGATTTTTAAAT
Found at i:10501043 original size:80 final size:82
Alignment explanation
Indices: 10500937--10501089 Score: 220
Period size: 80 Copynumber: 1.9 Consensus size: 82
10500927 AGAGGAACCA
* *
10500937 TTTTCAAGATGAGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAGCCCTTTT-AAAATGAGA
1 TTTTCAAGATGAGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAGCCCTTTTCAAAATAAAA
10501001 TTTTTAAATAGGAGCTC
66 TTTTTAAATAGGAGCTC
* * * * * *
10501018 TTTTTAAGATGAG-ATTTTTAAAGTTGTTGAGCCTTTACTGAGATGAGCCTTTTTCAAGATAAAA
1 TTTTCAAGATGAGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAGCCCTTTTCAAAATAAAA
10501082 TTTTTAAA
66 TTTTTAAA
10501090 GTTGTTGAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 37 0.59
81 26 0.41
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (82 bp):
TTTTCAAGATGAGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAGCCCTTTTCAAAATAAAA
TTTTTAAATAGGAGCTC
Found at i:10501155 original size:46 final size:49
Alignment explanation
Indices: 10501033--10501183 Score: 195
Period size: 46 Copynumber: 3.1 Consensus size: 49
10501023 AAGATGAGAT
*
10501033 TTTTAAAGTTGTTGAGCCTTTACTGAGATGAGCCTTTTTCAAGATAAAA
1 TTTTAAAGTTGTTGAGCCTTTACTGAGATGAGACTTTTTCAAGATAAAA
*
10501082 TTTTTAAAGTTGTTGAGCCTTTACTGAGA-GCA-ACTTTTTTAA-ATAAAA
1 -TTTTAAAGTTGTTGAGCCTTTACTGAGATG-AGACTTTTTCAAGATAAAA
* * * *
10501130 -TTTAACGTTGTTGAGCCTCTGCTGAGATGAG-CTTTTTCAAGATAAGA
1 TTTTAAAGTTGTTGAGCCTTTACTGAGATGAGACTTTTTCAAGATAAAA
10501177 TTTTAAA
1 TTTTAAA
10501184 AATTATTGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
46 33 0.38
47 6 0.07
48 11 0.12
49 9 0.10
50 29 0.33
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (49 bp):
TTTTAAAGTTGTTGAGCCTTTACTGAGATGAGACTTTTTCAAGATAAAA
Found at i:10501203 original size:49 final size:49
Alignment explanation
Indices: 10501017--10501194 Score: 204
Period size: 50 Copynumber: 3.7 Consensus size: 49
10501007 AATAGGAGCT
*
10501017 CTTTTT-AAGATGAGATTTTTAAAGTTGTTGAGCCTTTACTGAGATGAG
1 CTTTTTCAAGATAAGATTTTTAAAGTTGTTGAGCCTTTACTGAGATGAG
* *
10501065 CCTTTTTCAAGATAAAATTTTTAAAGTTGTTGAGCCTTTACTGAGA-GCAA
1 -CTTTTTCAAGATAAGATTTTTAAAGTTGTTGAGCCTTTACTGAGATG-AG
* * * * *
10501115 CTTTTTTAA-ATAA-A-ATTTAACGTTGTTGAGCCTCTGCTGAGATGAG
1 CTTTTTCAAGATAAGATTTTTAAAGTTGTTGAGCCTTTACTGAGATGAG
* * *
10501161 CTTTTTCAAGATAAGATTTTAAAAATTATTGAGC
1 CTTTTTCAAGATAAGATTTTTAAAGTTGTTGAGC
10501195 TTCTGCTGAA
Statistics
Matches: 108, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
46 33 0.31
47 6 0.06
48 5 0.05
49 27 0.25
50 37 0.34
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (49 bp):
CTTTTTCAAGATAAGATTTTTAAAGTTGTTGAGCCTTTACTGAGATGAG
Found at i:10501528 original size:17 final size:17
Alignment explanation
Indices: 10501473--10501522 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
10501463 AATATTATTA
*
10501473 AAAACAATAATAAAAAT
1 AAAACAAAAATAAAAAT
*
10501490 TAAACAAAAATACAAAAT
1 AAAACAAAAATA-AAAAT
*
10501508 AAAATAAAAATAAAA
1 AAAACAAAAATAAAA
10501523 CAAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAACAAAAATAAAAAT
Found at i:10503029 original size:12 final size:13
Alignment explanation
Indices: 10503001--10503033 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10502991 TTTCAATTGA
10503001 AAATAAAAAAATC
1 AAATAAAAAAATC
*
10503014 AAATAAAACAAT-
1 AAATAAAAAAATC
10503026 AAATAAAA
1 AAATAAAA
10503034 TTACCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAAAAATC
Found at i:10506276 original size:19 final size:19
Alignment explanation
Indices: 10506230--10506267 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
10506220 TAAAAGAAAT
10506230 TTCAA-AAAAATCTAAAAA
1 TTCAATAAAAATCTAAAAA
10506248 TTCAATAAAAATCTAAAAA
1 TTCAATAAAAATCTAAAAA
10506267 T
1 T
10506268 AACTTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (19 bp):
TTCAATAAAAATCTAAAAA
Found at i:10506388 original size:35 final size:36
Alignment explanation
Indices: 10506340--10506407 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
10506330 AAATTATAAA
***
10506340 AAAATTATTAT-AAATTTTAAAAATTAAAAAATCTC
1 AAAATTATTATAAAATCCAAAAAATTAAAAAATCTC
10506375 AAAATT-TTAATAAAATCCAAAAAATTAAAAAAT
1 AAAATTATT-ATAAAATCCAAAAAATTAAAAAAT
10506408 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 2 0.07
35 8 0.29
36 18 0.64
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (36 bp):
AAAATTATTATAAAATCCAAAAAATTAAAAAATCTC
Found at i:10506578 original size:18 final size:19
Alignment explanation
Indices: 10506547--10506593 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
10506537 TTTTTTTTTT
10506547 TTTTAA-TTTCAG-AAAAG
1 TTTTAATTTTCAGAAAAAG
*
10506564 TTTTAATTTTTAGAAAAAG
1 TTTTAATTTTCAGAAAAAG
10506583 TTTTATATTTT
1 TTTTA-ATTTT
10506594 ATTTTTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 10 0.38
20 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTAATTTTCAGAAAAAG
Found at i:10506654 original size:10 final size:10
Alignment explanation
Indices: 10506641--10506674 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
10506631 GATTTTTTAA
10506641 TTTTCATAAT
1 TTTTCATAAT
*
10506651 TTTTCAAAAT
1 TTTTCATAAT
*
10506661 TTTTTATAAT
1 TTTTCATAAT
10506671 TTTT
1 TTTT
10506675 AAAAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTCATAAT
Found at i:10506679 original size:20 final size:20
Alignment explanation
Indices: 10506641--10506679 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10506631 GATTTTTTAA
*
10506641 TTTTCATAATTTTTCAAAAT
1 TTTTCATAATTTTTAAAAAT
*
10506661 TTTTTATAATTTTTAAAAA
1 TTTTCATAATTTTTAAAAA
10506680 ATATTTGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTCATAATTTTTAAAAAT
Found at i:10506687 original size:57 final size:56
Alignment explanation
Indices: 10506612--10506741 Score: 131
Period size: 57 Copynumber: 2.3 Consensus size: 56
10506602 AATTTTTTGG
* *
10506612 ATTTTTATTAAAATTTTGAGATT-TTTTAATTTTCATAATT-TTTCAAAATT-TTTTATA
1 ATTTTTA-AAAAATTTTGAGATTATTATAATTTTCA-AATTATTTC-AAATTATTTT-TA
* * *
10506669 ATTTTTAAAAAATATTTGAGGTTATTATAATTTTTAAATTATTTCAGATTATTTTTA
1 ATTTTTAAAAAAT-TTTGAGATTATTATAATTTTCAAATTATTTCAAATTATTTTTA
* *
10506726 ATTTTTTAAAATTTTT
1 ATTTTTAAAAAATTTT
10506742 TTAAAATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
56 8 0.13
57 36 0.58
58 18 0.29
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (56 bp):
ATTTTTAAAAAATTTTGAGATTATTATAATTTTCAAATTATTTCAAATTATTTTTA
Found at i:10506720 original size:27 final size:29
Alignment explanation
Indices: 10506663--10506737 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
10506653 TTCAAAATTT
* *
10506663 TTTATAATTTTTAAAAAATATTTGAGGTTA
1 TTTATAATTTTT-AAAAATATTTCAGATTA
*
10506693 -TTATAATTTTT-AAATTATTTCAGATTA
1 TTTATAATTTTTAAAAATATTTCAGATTA
* *
10506720 TTTTTAATTTTTTAAAAT
1 TTTATAATTTTTAAAAAT
10506738 TTTTTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 13 0.34
28 10 0.26
29 15 0.39
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTATAATTTTTAAAAATATTTCAGATTA
Found at i:10506743 original size:11 final size:11
Alignment explanation
Indices: 10506727--10506752 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10506717 TTATTTTTAA
10506727 TTTTTTAAAAT
1 TTTTTTAAAAT
10506738 TTTTTTAAAAT
1 TTTTTTAAAAT
10506749 TTTT
1 TTTT
10506753 AGAATTTTCA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:10506759 original size:30 final size:31
Alignment explanation
Indices: 10506725--10506791 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
10506715 GATTATTTTT
*
10506725 AATTTTTTAAAATTT-TTTTAAAATTTTTAG
1 AATTTTTCAAAATTTGTTTTAAAATTTTTAG
* *
10506755 AA-TTTTCAGAATTTGTTTTAAAATTTTTTG
1 AATTTTTCAAAATTTGTTTTAAAATTTTTAG
10506785 AATTTTT
1 AATTTTT
10506792 AGCATCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.31
30 18 0.56
31 4 0.12
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (31 bp):
AATTTTTCAAAATTTGTTTTAAAATTTTTAG
Found at i:10506978 original size:25 final size:26
Alignment explanation
Indices: 10506936--10506990 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
10506926 TAATCCTTAA
* * *
10506936 TTTGATTCAAATTTAAATTAAATATTT
1 TTTGATT-AAATTCAAATAAAAAATTT
10506963 TTTGATT-AATTCAAATAAAAAATTT
1 TTTGATTAAATTCAAATAAAAAATTT
10506988 TTT
1 TTT
10506991 AATGTGAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 18 0.72
27 7 0.28
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
TTTGATTAAATTCAAATAAAAAATTT
Found at i:10507379 original size:34 final size:33
Alignment explanation
Indices: 10507310--10507390 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 33
10507300 CATAACTGTA
**
10507310 AAATTTTAAAAATTCACAAAAATGCATATTCAT
1 AAATTTTAAAAATTCACAAAAATAAATATTCAT
*
10507343 AAATATTTAAATATTCACAAAAATAAATA-TCTAT
1 AAAT-TTTAAAAATTCACAAAAATAAATATTC-AT
*
10507377 AAATTTTTAAAATT
1 AAATTTTAAAAATT
10507391 TACGAACTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 14 0.34
34 27 0.66
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (33 bp):
AAATTTTAAAAATTCACAAAAATAAATATTCAT
Found at i:10512213 original size:14 final size:14
Alignment explanation
Indices: 10512196--10512238 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
10512186 ACTCACTTAG
10512196 ATATACTTAATATA
1 ATATACTTAATATA
**
10512210 ATATACGAAATATA
1 ATATACTTAATATA
* *
10512224 ATATAATTATTATA
1 ATATACTTAATATA
10512238 A
1 A
10512239 GATATATTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (14 bp):
ATATACTTAATATA
Found at i:10515052 original size:22 final size:22
Alignment explanation
Indices: 10515027--10515095 Score: 52
Period size: 25 Copynumber: 3.0 Consensus size: 22
10515017 TCTGATAATT
10515027 ATAATTTATTTTTAAAATTTTA
1 ATAATTTATTTTTAAAATTTTA
**
10515049 ATAAAGTATTATTTTTATATTTTTTA
1 AT-AA-T-TTATTTTTA-AAATTTTA
* *
10515075 ATGA-TT-TTTTTATAATTTTA
1 ATAATTTATTTTTAAAATTTTA
10515095 A
1 A
10515096 AAAAAGTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 6 0.16
21 6 0.16
22 4 0.11
23 2 0.05
24 1 0.03
25 10 0.27
26 8 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (22 bp):
ATAATTTATTTTTAAAATTTTA
Found at i:10516519 original size:19 final size:18
Alignment explanation
Indices: 10516495--10516546 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
10516485 ACCAATACAT
10516495 AAATAAATAAATAAAGTA-A
1 AAATAAA-AAATAAAG-AGA
10516514 AAATAAAAACATAAAGAGA
1 AAATAAAAA-ATAAAGAGA
*
10516533 AAGTAAAAAATAAA
1 AAATAAAAAATAAA
10516547 TGAACATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (18 bp):
AAATAAAAAATAAAGAGA
Found at i:10517077 original size:18 final size:18
Alignment explanation
Indices: 10517030--10517078 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
10517020 GGATTTCATG
10517030 TTCGTAAGAATTTTCAAA
1 TTCGTAAGAATTTTCAAA
* * * *
10517048 TTCATAAAAATTTTTAGA
1 TTCGTAAGAATTTTCAAA
*
10517066 TTTGTAAGAATTT
1 TTCGTAAGAATTT
10517079 GATTCTCAGG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (18 bp):
TTCGTAAGAATTTTCAAA
Found at i:10517431 original size:43 final size:43
Alignment explanation
Indices: 10517384--10517468 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
10517374 GGGTTTCATC
* *
10517384 CAAAATTTCAAAGATTTGGATTC-AAAAACTTTAGAGATTCACA
1 CAAAATTT-AAAGATTTGCATTCGAAAAACTTTAGAAATTCACA
* *
10517427 CAAAATTTTAAGATTTTCATTCGAAAAACTTTAGAAATTCAC
1 CAAAATTTAAAGATTTGCATTCGAAAAACTTTAGAAATTCAC
10517469 GTCTAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 11 0.30
43 26 0.70
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (43 bp):
CAAAATTTAAAGATTTGCATTCGAAAAACTTTAGAAATTCACA
Found at i:10518605 original size:16 final size:17
Alignment explanation
Indices: 10518572--10518615 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
10518562 CAATTAAGTG
* *
10518572 TTCTTTTTATCTC-TTT
1 TTCTTTTTTTCACATTT
10518588 TTCTTTTTTTCACATTT
1 TTCTTTTTTTCACATTT
10518605 TTCATTTTTTT
1 TTC-TTTTTTT
10518616 TGCTTCATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 6 0.25
18 7 0.29
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTCACATTT
Found at i:10518964 original size:23 final size:24
Alignment explanation
Indices: 10518938--10518986 Score: 57
Period size: 23 Copynumber: 2.0 Consensus size: 24
10518928 CAACCAATAC
*
10518938 ATAAATAA-ATAAAGAGAG-TAAAA
1 ATAAA-AATATAAAGAGAAGTAAAA
10518961 ATAAAAATATAAAGAGAAAGTAAAA
1 ATAAAAATATAAAGAG-AAGTAAAA
10518986 A
1 A
10518987 AATAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 2 0.09
23 13 0.59
24 1 0.05
25 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.16
Consensus pattern (24 bp):
ATAAAAATATAAAGAGAAGTAAAA
Found at i:10537613 original size:11 final size:11
Alignment explanation
Indices: 10537597--10537621 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10537587 TGGATGAAAG
10537597 ATGCATTAAAC
1 ATGCATTAAAC
10537608 ATGCATTAAAC
1 ATGCATTAAAC
10537619 ATG
1 ATG
10537622 AATACTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (11 bp):
ATGCATTAAAC
Found at i:10539160 original size:21 final size:20
Alignment explanation
Indices: 10539134--10539220 Score: 74
Period size: 21 Copynumber: 4.4 Consensus size: 20
10539124 TAGGGTTTGA
10539134 GGTTTGAGATTTTGATTTTAG
1 GGTTTG-GATTTTGATTTTAG
10539155 GGTTTGGA---TG-TTTTAG
1 GGTTTGGATTTTGATTTTAG
* *
10539171 GGTTTTGATTTTAATGTTTAG
1 GGTTTGGATTTTGAT-TTTAG
** *
10539192 TTTTTGGGATTTCGATTTTAG
1 GGTTT-GGATTTTGATTTTAG
10539213 GGTTTGGA
1 GGTTTGGA
10539221 GGATTTGATG
Statistics
Matches: 51, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
16 13 0.25
17 2 0.04
19 1 0.02
20 6 0.12
21 22 0.43
22 7 0.14
ACGTcount: A:0.16, C:0.01, G:0.30, T:0.53
Consensus pattern (20 bp):
GGTTTGGATTTTGATTTTAG
Found at i:10539239 original size:44 final size:42
Alignment explanation
Indices: 10539113--10539243 Score: 124
Period size: 44 Copynumber: 3.0 Consensus size: 42
10539103 AATGGTTTAA
*
10539113 GATTTCGATTTTAGGGTTTGAGGTTTGA-GATTTTGATTTTAGG
1 GATTTCGATTTTAGGGTTTGAGGTTTGATG--TTTGGTTTTAGG
* * * * *
10539156 G-TTTGGATGTTTTAGGGTTTTGA-TTTTAATGTTTAGTTTTTGG
1 GATTTCGA--TTTTAGGG-TTTGAGGTTTGATGTTTGGTTTTAGG
10539199 GATTTCGATTTTAGGGTTTGGAGGATTTGATGTTTGGTTTTAGG
1 GATTTCGATTTTAGGGTTT-GAGG-TTTGATGTTTGGTTTTAGG
10539243 G
1 G
10539244 TTTAGAGGGT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
41 3 0.04
42 15 0.22
43 11 0.16
44 34 0.49
45 6 0.09
ACGTcount: A:0.16, C:0.02, G:0.31, T:0.51
Consensus pattern (42 bp):
GATTTCGATTTTAGGGTTTGAGGTTTGATGTTTGGTTTTAGG
Found at i:10539251 original size:29 final size:28
Alignment explanation
Indices: 10539207--10539473 Score: 214
Period size: 29 Copynumber: 9.2 Consensus size: 28
10539197 GGGATTTCGA
* *
10539207 TTTTAGGGTTTGGAGGATTTGATGTTTGG
1 TTTTAGGGTTTGGAGGGTTT-ATGTTTAG
* *
10539236 TTTTAGGGTTTAGAGGGTTTATGGTTTAA
1 TTTTAGGGTTTGGAGGGTTTAT-GTTTAG
*
10539265 TTTTAGGGTTTGGAGGGTTTAAGATTTAG
1 TTTTAGGGTTTGGAGGGTTTATG-TTTAG
* * *
10539294 TTTTAGAGATTT-GAGGGTTTAAGGTTTTG
1 TTTTAG-GGTTTGGAGGGTTT-ATGTTTAG
*
10539323 TTTTAGGGTTTGGAGGGTTTAGGGTTTAG
1 TTTTAGGGTTTGGAGGGTTTA-TGTTTAG
* * * *
10539352 TTTTAGAGTTTCGAGGGTTTAAAGTTCAG
1 TTTTAGGGTTTGGAGGGTTT-ATGTTTAG
* *
10539381 TGTTTAGGGTTTGGAGGGTTTAGGGTTTAT
1 T-TTTAGGGTTTGGAGGGTTTA-TGTTTAG
* ** * *
10539411 TTTTAGAGTTTTCAGGATTTAGAGTTTAG
1 TTTTAGGGTTTGGAGGGTTTA-TGTTTAG
* *
10539440 TGTTTAGGGTTTTGAGGGTTTGTGATTTA-
1 T-TTTAGGGTTTGGAGGGTTTATG-TTTAG
10539469 TTTTA
1 TTTTA
10539474 TTATTATTAT
Statistics
Matches: 195, Mismatches: 32, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
28 12 0.06
29 134 0.69
30 49 0.25
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.48
Consensus pattern (28 bp):
TTTTAGGGTTTGGAGGGTTTATGTTTAG
Found at i:10539345 original size:16 final size:15
Alignment explanation
Indices: 10539237--10539460 Score: 85
Period size: 16 Copynumber: 15.2 Consensus size: 15
10539227 GATGTTTGGT
10539237 TTTAGGGTTTAGAGGG
1 TTTAGGGTTT-GAGGG
* **
10539253 TTTATGGTTT-A-AT
1 TTTAGGGTTTGAGGG
10539266 TTTAGGGTTTGGAGGG
1 TTTAGGGTTT-GAGGG
* * *
10539282 TTTAAGATTT-A-GT
1 TTTAGGGTTTGAGGG
*
10539295 TTTAGAGATTTGAGGG
1 TTTAG-GGTTTGAGGG
* * *
10539311 TTTAAGGTTT--TGT
1 TTTAGGGTTTGAGGG
10539324 TTTAGGGTTTGGAGGG
1 TTTAGGGTTT-GAGGG
*
10539340 TTTAGGGTTT-A-GT
1 TTTAGGGTTTGAGGG
*
10539353 TTTAGAGTTTCGAGGG
1 TTTAGGGTTT-GAGGG
** * *
10539369 TTTAAAG-TTCAGTG
1 TTTAGGGTTTGAGGG
10539383 TTTAGGGTTTGGAGGG
1 TTTAGGGTTT-GAGGG
**
10539399 TTTAGGGTTT-A-TT
1 TTTAGGGTTTGAGGG
* * *
10539412 TTTAGAGTTTTCAGGA
1 TTTAG-GGTTTGAGGG
* *
10539428 TTTAGAGTTT-AGTG
1 TTTAGGGTTTGAGGG
10539442 TTTAGGGTTTTGAGGG
1 TTTAGGG-TTTGAGGG
10539458 TTT
1 TTT
10539461 GTGATTTATT
Statistics
Matches: 150, Mismatches: 39, Indels: 38
0.66 0.17 0.17
Matches are distributed among these distances:
13 39 0.26
14 29 0.19
15 18 0.12
16 64 0.43
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.46
Consensus pattern (15 bp):
TTTAGGGTTTGAGGG
Found at i:10539405 original size:59 final size:59
Alignment explanation
Indices: 10539207--10539460 Score: 284
Period size: 58 Copynumber: 4.3 Consensus size: 59
10539197 GGGATTTCGA
* * * * * ** *
10539207 TTTTAGGGTTTGGAGGATTT-GATGTTTGGTTTTAG-GGTTTAGAGGGTTTATGGTTTAA
1 TTTTAGGGTTTGGAGGGTTTAG-GGTTTAGTTTTAGAGATTTCGAGGGTTTAAAGTTTAG
* * * *
10539265 TTTTAGGGTTTGGAGGGTTTAAGATTTAGTTTTAGAGATTT-GAGGGTTTAAGGTTTTG
1 TTTTAGGGTTTGGAGGGTTTAGGGTTTAGTTTTAGAGATTTCGAGGGTTTAAAGTTTAG
*
10539323 TTTTAGGGTTTGGAGGGTTTAGGGTTTAGTTTTAGAG-TTTCGAGGGTTTAAAGTTCAG
1 TTTTAGGGTTTGGAGGGTTTAGGGTTTAGTTTTAGAGATTTCGAGGGTTTAAAGTTTAG
* * * *
10539381 TGTTTAGGGTTTGGAGGGTTTAGGGTTTATTTTTAGAGTTTTC-AGGATTTAGAGTTTAG
1 T-TTTAGGGTTTGGAGGGTTTAGGGTTTAGTTTTAGAGATTTCGAGGGTTTAAAGTTTAG
*
10539440 TGTTTAGGGTTTTGAGGGTTT
1 T-TTTAGGGTTTGGAGGGTTT
10539461 GTGATTTATT
Statistics
Matches: 172, Mismatches: 19, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
57 3 0.02
58 93 0.54
59 72 0.42
60 4 0.02
ACGTcount: A:0.18, C:0.01, G:0.34, T:0.47
Consensus pattern (59 bp):
TTTTAGGGTTTGGAGGGTTTAGGGTTTAGTTTTAGAGATTTCGAGGGTTTAAAGTTTAG
Found at i:10539781 original size:7 final size:7
Alignment explanation
Indices: 10539766--10539801 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
10539756 ATTTTATATT
10539766 TTATATTA
1 TTAT-TTA
10539774 TTATTTA
1 TTATTTA
*
10539781 TTACTTA
1 TTATTTA
10539788 TTATTTA
1 TTATTTA
10539795 TTATTTA
1 TTATTTA
10539802 ACACTTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:10539807 original size:21 final size:22
Alignment explanation
Indices: 10539766--10539807 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10539756 ATTTTATATT
**
10539766 TTATATTATTATTTATTACTTA
1 TTATATTATTATTTAACACTTA
10539788 TTAT-TTATTATTTAACACTT
1 TTATATTATTATTTAACACTT
10539808 GGGTTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATTATTATTTAACACTTA
Found at i:10541174 original size:28 final size:28
Alignment explanation
Indices: 10541143--10541201 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
10541133 GATTGAATTG
*
10541143 AATTGGG-CTTGAAGCTTAGTTGAATCAA
1 AATTGGGTC-TGAAGCTCAGTTGAATCAA
* *
10541171 AATTGGGTCTGGAGCTCAGTTGAATCGA
1 AATTGGGTCTGAAGCTCAGTTGAATCAA
10541199 AAT
1 AAT
10541202 CAGGCTTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (28 bp):
AATTGGGTCTGAAGCTCAGTTGAATCAA
Found at i:10541607 original size:36 final size:36
Alignment explanation
Indices: 10541542--10541724 Score: 128
Period size: 36 Copynumber: 5.1 Consensus size: 36
10541532 TTGACTCGTA
*
10541542 AGTCAAAAAAATA-AAGAGTGATC-GAGATTAAATTGCG
1 AGTCAAGAAAATAGAA-A-TGATCAG-GATTAAATTGCG
* ***
10541579 AATCAAGAAAATAGAAATGATCAGGATTAAATAATG
1 AGTCAAGAAAATAGAAATGATCAGGATTAAATTGCG
* * ** **
10541615 AGTCAAAGATTAAT-GACAT--TTGGGATTAAACCGCG
1 AGTC-AAGA-AAATAGAAATGATCAGGATTAAATTGCG
* *
10541650 AGTCAAGAAAATAGAAATGATCA-GAGCTAAATTGTG
1 AGTCAAGAAAATAGAAATGATCAGGA-TTAAATTGCG
*
10541686 AGTTAAGAAAATAGAAATGATC-GAGATTAAATTGCG
1 AGTCAAGAAAATAGAAATGATCAG-GATTAAATTGCG
10541722 AGT
1 AGT
10541725 GAAAAATTAA
Statistics
Matches: 111, Mismatches: 25, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
33 3 0.03
34 8 0.07
35 16 0.14
36 56 0.50
37 23 0.21
38 5 0.05
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.23
Consensus pattern (36 bp):
AGTCAAGAAAATAGAAATGATCAGGATTAAATTGCG
Found at i:10541703 original size:107 final size:106
Alignment explanation
Indices: 10541481--10541717 Score: 254
Period size: 107 Copynumber: 2.2 Consensus size: 106
10541471 CATGAGTCGA
* * * * *
10541481 AAAATA-AAAAGATCAAGATTAAATCATGAGTAAGATTAACGACTTTCGGGATTGACTCGTAAGT
1 AAAATAGAAATGATCAGGATTAAATAATGAGTAAGATTAACGACTTTCGGGATTAACTCGCAAGT
*
10541545 CAAAAAAATAAAGAGTGATCGAGATTAAATTGCGAATCAAG
66 CAAAAAAATAAAGAGTGATCGAGACTAAATTGCGAATCAAG
*
10541586 AAAATAGAAATGATCAGGATTAAATAATGAGTCAAAGATTAATGACATTT-GGGATTAAAC-CGC
1 AAAATAGAAATGATCAGGATTAAATAATGAGT--AAGATTAACGAC-TTTCGGGATT-AACTCGC
* * * * *
10541649 GAGTCAAGAAAATAGAA-A-TGATC-AGAGCTAAATTGTGAGTTAAG
62 AAGTCAAAAAAATA-AAGAGTGATCGAGA-CTAAATTGCGAATCAAG
10541693 AAAATAGAAATGATC-GAGATTAAAT
1 AAAATAGAAATGATCAG-GATTAAAT
10541718 TGCGAGTGAA
Statistics
Matches: 112, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
105 6 0.05
106 26 0.23
107 41 0.37
108 32 0.29
109 7 0.06
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (106 bp):
AAAATAGAAATGATCAGGATTAAATAATGAGTAAGATTAACGACTTTCGGGATTAACTCGCAAGT
CAAAAAAATAAAGAGTGATCGAGACTAAATTGCGAATCAAG
Found at i:10541849 original size:107 final size:106
Alignment explanation
Indices: 10541745--10542072 Score: 308
Period size: 107 Copynumber: 3.1 Consensus size: 106
10541735 CGATGATTGG
* * * * *
10541745 GATTAAATCGTAAGTTAGAGATTAACGACAATTAAGATTGAATTGCATGTTAGAAAAATAAAAGC
1 GATTAAATCGTAAGTAAGAGATTAACGAC-ATTAAGATTGAATTGTAAGTTAGAAAAACAAAAGT
* *
10541810 GATTGGAATTAAAGCACAAGTCAAAAAAATAAAAATGATTGA
65 GATTGGAATTAAAGCGCAAGTCAAAAAAATAAAAATGATCGA
** * * * * * *
10541852 GATTAAATCGCGAGTCAGAGATTAATGACGACTAAGATCGAACTGTAAGTCA-AAAAACAAAAGT
1 GATTAAATCGTAAGTAAGAGATTAACGAC-ATTAAGATTGAATTGTAAGTTAGAAAAACAAAAGT
* * *
10541916 GATT-GAGATTAAATCGCGAGTCAAAAAAATTAAAATGATCGA
65 GATTGGA-ATTAAAGCGCAAGTCAAAAAAATAAAAATGATCGA
** * * * *
10541958 GATTAAACTTTTAAGTAAAAAATTAACG--ATTAGGATTGAATCGTAAGTTAGAAAAACAAAAGT
1 GATTAAA-TCGTAAGTAAGAGATTAACGACATTAAGATTGAATTGTAAGTTAGAAAAACAAAAGT
* * * *
10542021 GACTAGG-ATT-AAGCTGTAAGTCAAGAAAATAAAAATGATCGG
65 GA-TTGGAATTAAAGC-GCAAGTCAAAAAAATAAAAATGATCGA
10542063 GATTAAATCG
1 GATTAAATCG
10542073 CGATTTAAAA
Statistics
Matches: 174, Mismatches: 41, Indels: 15
0.76 0.18 0.07
Matches are distributed among these distances:
104 20 0.11
105 48 0.28
106 52 0.30
107 54 0.31
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (106 bp):
GATTAAATCGTAAGTAAGAGATTAACGACATTAAGATTGAATTGTAAGTTAGAAAAACAAAAGTG
ATTGGAATTAAAGCGCAAGTCAAAAAAATAAAAATGATCGA
Found at i:10542660 original size:21 final size:21
Alignment explanation
Indices: 10542635--10542703 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
10542625 TCATTTAATT
10542635 TTTTCTTGTCTTGTATTGTTA
1 TTTTCTTGTCTTGTATTGTTA
** * *
10542656 TTTTCGTCATCCT-TATT-TAATT
1 TTTTC-TTGTCTTGTATTGT--TA
10542678 TTTTCTTGTCTTGTATTGTTA
1 TTTTCTTGTCTTGTATTGTTA
10542699 TTTTC
1 TTTTC
10542704 GTCATCCTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 1 0.03
21 19 0.54
22 14 0.40
23 1 0.03
ACGTcount: A:0.12, C:0.13, G:0.10, T:0.65
Consensus pattern (21 bp):
TTTTCTTGTCTTGTATTGTTA
Found at i:10542675 original size:43 final size:43
Alignment explanation
Indices: 10542627--10542713 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
10542617 AATCCATTTC
10542627 ATTTAATTTTTTCTTGTCTTGTATTGTTATTTTCGTCATCCTT
1 ATTTAATTTTTTCTTGTCTTGTATTGTTATTTTCGTCATCCTT
10542670 ATTTAATTTTTTCTTGTCTTGTATTGTTATTTTCGTCATCCTT
1 ATTTAATTTTTTCTTGTCTTGTATTGTTATTTTCGTCATCCTT
10542713 A
1 A
10542714 CATTCTCCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.15, C:0.14, G:0.09, T:0.62
Consensus pattern (43 bp):
ATTTAATTTTTTCTTGTCTTGTATTGTTATTTTCGTCATCCTT
Found at i:10542702 original size:22 final size:22
Alignment explanation
Indices: 10542634--10542702 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
10542624 TTCATTTAAT
10542634 TTTTTCTTGTCTTGTATTGTTA
1 TTTTTCTTGTCTTGTATTGTTA
** * *
10542656 -TTTTCGTCATCCT-TATT-TAA
1 TTTTTC-TTGTCTTGTATTGTTA
10542676 TTTTTTCTTGTCTTGTATTGTTA
1 -TTTTTCTTGTCTTGTATTGTTA
10542699 TTTT
1 TTTT
10542703 CGTCATCCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
20 2 0.06
21 13 0.38
22 17 0.50
23 2 0.06
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.67
Consensus pattern (22 bp):
TTTTTCTTGTCTTGTATTGTTA
Found at i:10554879 original size:58 final size:58
Alignment explanation
Indices: 10554783--10554967 Score: 214
Period size: 58 Copynumber: 3.2 Consensus size: 58
10554773 TGGTTTAAGA
* *
10554783 TTTTGATTTTAAGGTTTGAGGTTTTGGGATTTCGATTTTAAGATTTGAAGGTTTTAGGG
1 TTTTGATTTTAAGGTTTGAGG-TTTGGGATTTCAATTTTAAGATTTGGAGGTTTTAGGG
* * * *
10554842 TTTTGATTTTAGGGTTTGAGGTTTGGTATTTCAATTTTAAGGTTTGGATGTTTTAGGG
1 TTTTGATTTTAAGGTTTGAGGTTTGGGATTTCAATTTTAAGATTTGGAGGTTTTAGGG
* * * ** *
10554900 TTTTAATCTTAAGGTTT-AGTTCTTGGGATTTCAATTTTTGGATTTGGAGGGTTT-GAGG
1 TTTTGATTTTAAGGTTTGAGGT-TTGGGATTTCAATTTTAAGATTTGGAGGTTTTAG-GG
10554958 -TTTGATTTTA
1 TTTTGATTTTA
10554968 GGATTTAGAG
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
57 12 0.11
58 74 0.70
59 20 0.19
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.51
Consensus pattern (58 bp):
TTTTGATTTTAAGGTTTGAGGTTTGGGATTTCAATTTTAAGATTTGGAGGTTTTAGGG
Found at i:10554978 original size:29 final size:28
Alignment explanation
Indices: 10554933--10555024 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
10554923 TGGGATTTCA
* *
10554933 ATTTTTGGATTTGGAGGGTTT-GAGGTTT
1 ATTTTAGGATTTAGAGGGTTTAG-GGTTT
10554961 GATTTTAGGATTTAGAGGGTTTAGGGTTT
1 -ATTTTAGGATTTAGAGGGTTTAGGGTTT
* *
10554990 AGTTTTAGGGTTT-GAAAGGTTTAGGGTTT
1 A-TTTTAGGATTTAG-AGGGTTTAGGGTTT
10555019 ATTTTA
1 ATTTTA
10555025 TTATTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.12
29 48 0.86
30 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (28 bp):
ATTTTAGGATTTAGAGGGTTTAGGGTTT
Found at i:10555329 original size:7 final size:7
Alignment explanation
Indices: 10555310--10555349 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
10555300 AATCATATTA
*
10555310 TATTTTT
1 TATTTAT
10555317 TA-TTAT
1 TATTTAT
10555323 TATTTAT
1 TATTTAT
10555330 TATTTAT
1 TATTTAT
10555337 TATTTAT
1 TATTTAT
10555344 TATTTA
1 TATTTA
10555350 ACACTTGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:10557382 original size:21 final size:20
Alignment explanation
Indices: 10557344--10557382 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10557334 GTTTTTTCTT
10557344 TATTTTTTTAAAAATATATA
1 TATTTTTTTAAAAATATATA
*
10557364 TATTTTTTTACAAAT-TATA
1 TATTTTTTTAAAAATATATA
10557383 ATAGAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTTTTTAAAAATATATA
Found at i:10559009 original size:2 final size:2
Alignment explanation
Indices: 10559004--10559033 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10558994 TCTGATCTAA
10559004 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10559034 AGGACCTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:10559892 original size:3 final size:3
Alignment explanation
Indices: 10559867--10559911 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
10559857 GTCTTTGCTT
* * * *
10559867 GAA GAT GAA GAA GAT GAA CAA GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
10559912 AATAATAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.02, G:0.29, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:10563993 original size:19 final size:18
Alignment explanation
Indices: 10563969--10564004 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10563959 AGAGTCAATT
10563969 GGTAAAAAAATAAAAAAGA
1 GGTAAAAAAA-AAAAAAGA
*
10563988 GGTAAAAAGAAAAAAAG
1 GGTAAAAAAAAAAAAAG
10564005 GAAAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.08
Consensus pattern (18 bp):
GGTAAAAAAAAAAAAAGA
Found at i:10564599 original size:20 final size:20
Alignment explanation
Indices: 10564565--10564656 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
10564555 TTTTACATGA
* *
10564565 ATTTGCATGACTATTAATAT
1 ATTTGCATGATTATTAATTT
* * *
10564585 GTTTACATGATTATTAGTTT
1 ATTTGCATGATTATTAATTT
*
10564605 ATCTGCATGATTATTAATTT
1 ATTTGCATGATTATTAATTT
10564625 ATTTGCATGATTA-TATATTT
1 ATTTGCATGATTATTA-ATTT
*
10564645 AATTGCATGATT
1 ATTTGCATGATT
10564657 TATATATTAC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 2 0.03
20 58 0.97
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (20 bp):
ATTTGCATGATTATTAATTT
Found at i:10564612 original size:40 final size:40
Alignment explanation
Indices: 10564567--10564694 Score: 118
Period size: 40 Copynumber: 3.1 Consensus size: 40
10564557 TTACATGAAT
*
10564567 TTGCATGACTATTAATATGTTTACATGATTAT-TAGTTT-A
1 TTGCATGACTATTAATATATTTACATGATTATATA-TTTAA
* * *
10564606 TCTGCATGATTATTAATTTATTTGCATGATTATATATTTAA
1 T-TGCATGACTATTAATATATTTACATGATTATATATTTAA
* * **
10564647 TTGCATGATTTATATATTACTATTTGTATGATTATAT-TTTAA
1 TTGCATGA-CTAT-TAATA-TATTTACATGATTATATATTTAA
10564689 TTGCAT
1 TTGCAT
10564695 ATTTATTTGC
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
39 1 0.01
40 37 0.49
41 8 0.11
42 14 0.18
43 16 0.21
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (40 bp):
TTGCATGACTATTAATATATTTACATGATTATATATTTAA
Found at i:10564757 original size:56 final size:52
Alignment explanation
Indices: 10564647--10564810 Score: 168
Period size: 52 Copynumber: 3.0 Consensus size: 52
10564637 ATATATTTAA
* * *
10564647 TTGCATGATTTATATATTACTATTTGTATGATTATAT-TTTAATTGCATATTTAT
1 TTGCATGA-TT-TACATTATTATTTGTATGATTATATATTTAATTGCAT-GTTAT
* * * * *
10564701 TTGCATGGTTTGTATATATATATTTTTGCATGACTATATATTTAATTGCATGTTAT
1 TTGCAT-GATT-TACAT-TAT-TATTTGTATGATTATATATTTAATTGCATGTTAT
*
10564757 TTGCATGATTTACATTATTAATTGTATGATTATATATTTAATTGCATGATTAT
1 TTGCATGATTTACATTATTATTTGTATGATTATATATTTAATTGCATG-TTAT
10564810 T
1 T
10564811 AATTTATTTA
Statistics
Matches: 92, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
52 26 0.28
53 8 0.09
54 17 0.18
55 6 0.07
56 24 0.26
57 11 0.12
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (52 bp):
TTGCATGATTTACATTATTATTTGTATGATTATATATTTAATTGCATGTTAT
Found at i:10564816 original size:20 final size:20
Alignment explanation
Indices: 10564590--10564809 Score: 118
Period size: 20 Copynumber: 11.4 Consensus size: 20
10564580 AATATGTTTA
10564590 CATGATTAT-TAGTTT-ATCTG
1 CATGATTATATA-TTTAAT-TG
*
10564610 CATGATTAT-TAATTTATTTG
1 CATGATTATAT-ATTTAATTG
10564630 CATGATTATATATTTAATTG
1 CATGATTATATATTTAATTG
*
10564650 CATGATTTATATATTACTATTTG
1 CATGA-TTATATATT--TAATTG
*
10564673 TATGATTATAT-TTTAATTG
1 CATGATTATATATTTAATTG
** *
10564692 CAT-ATT-TAT-TTGCATGG
1 CATGATTATATATTTAATTG
**
10564709 TTTGTATATATATATTT--TTG
1 CATG-AT-TATATATTTAATTG
*
10564729 CATGACTATATATTTAATTG
1 CATGATTATATATTTAATTG
10564749 CATG----T-TA--T--TTG
1 CATGATTATATATTTAATTG
*
10564760 CATGATT-TACATTATTAATTG
1 CATGATTATATA-T-TTAATTG
*
10564781 TATGATTATATATTTAATTG
1 CATGATTATATATTTAATTG
10564801 CATGATTAT
1 CATGATTAT
10564810 TAATTTATTT
Statistics
Matches: 156, Mismatches: 20, Indels: 48
0.70 0.09 0.21
Matches are distributed among these distances:
11 7 0.04
13 1 0.01
14 1 0.01
15 3 0.02
16 1 0.01
17 9 0.06
18 12 0.08
19 11 0.07
20 64 0.41
21 27 0.17
22 11 0.07
23 9 0.06
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.52
Consensus pattern (20 bp):
CATGATTATATATTTAATTG
Found at i:10564915 original size:24 final size:24
Alignment explanation
Indices: 10564883--10564946 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
10564873 TATTATTGCA
* **
10564883 TAATTTTATAT-TTATTGTATGAT
1 TAATATTATATATTATTACATGAT
* *
10564906 ATGATATTATATGTTATTACATGAT
1 -TAATATTATATATTATTACATGAT
10564931 TAATATTATATATTAT
1 TAATATTATATATTAT
10564947 ATGTTATTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.55
Consensus pattern (24 bp):
TAATATTATATATTATTACATGAT
Found at i:10564947 original size:31 final size:31
Alignment explanation
Indices: 10564909--10564972 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
10564899 GTATGATATG
10564909 ATATTATATGTTATTACATGATTAATATTAT
1 ATATTATATGTTATTACATGATTAATATTAT
*
10564940 ATATTATATGTTATTGCATGATTAATATTAT
1 ATATTATATGTTATTACATGATTAATATTAT
10564971 AT
1 AT
10564973 TTGAATAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.52
Consensus pattern (31 bp):
ATATTATATGTTATTACATGATTAATATTAT
Found at i:10565040 original size:14 final size:14
Alignment explanation
Indices: 10565023--10565049 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10565013 GTATAATTGC
10565023 GTGATTATATTTGT
1 GTGATTATATTTGT
10565037 GTGATTATATTTG
1 GTGATTATATTTG
10565050 GTTGCATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (14 bp):
GTGATTATATTTGT
Found at i:10565061 original size:18 final size:16
Alignment explanation
Indices: 10565019--10565064 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 16
10565009 GTGTGTATAA
10565019 TTGCGTGATTATATTTG
1 TTGC-TGATTATATTTG
10565036 -TG-TGATTATATTTGG
1 TTGCTGATTATATTT-G
10565051 TTGCATGATTATAT
1 TTGC-TGATTATAT
10565065 ATTTGAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 4 0.16
18 9 0.36
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (16 bp):
TTGCTGATTATATTTG
Found at i:10565109 original size:18 final size:18
Alignment explanation
Indices: 10565080--10565171 Score: 89
Period size: 18 Copynumber: 5.0 Consensus size: 18
10565070 AATGAATGGT
* *
10565080 TATTAATATATTTGTATGG
1 TATT-ATATATTTGCATGA
*
10565099 TATTTTATATTTGCATGA
1 TATTATATATTTGCATGA
*
10565117 TATTATATATTTACATGA
1 TATTATATATTTGCATGA
10565135 TTATTAT-TA-TTGCATGA
1 -TATTATATATTTGCATGA
*
10565152 TAATTAATGTATTTGCATGA
1 T-ATT-ATATATTTGCATGA
10565172 GGTTCTTGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.02
17 10 0.16
18 31 0.50
19 12 0.19
20 8 0.13
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (18 bp):
TATTATATATTTGCATGA
Found at i:10570956 original size:41 final size:41
Alignment explanation
Indices: 10570899--10570976 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
10570889 ATAAAAATAT
*
10570899 ATTAAGATAAAAACAAAGAAATGAAAAAGAA-AATAACATAA
1 ATTAACATAAAAACAAAGAAATGAAAAA-AAGAATAACATAA
*
10570940 ATTAACATAAAAACAAAGATATGAAAAAAAGAATAAC
1 ATTAACATAAAAACAAAGAAATGAAAAAAAGAATAAC
10570977 CTTGGTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.15
Consensus pattern (41 bp):
ATTAACATAAAAACAAAGAAATGAAAAAAAGAATAACATAA
Found at i:10571967 original size:30 final size:29
Alignment explanation
Indices: 10571933--10571990 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
10571923 TAAGGGTCCA
10571933 ATTGAGTCGAAATAAAA-GATTAAGGGCTTG
1 ATTGA-TCGAAATAAAATG-TTAAGGGCTTG
* *
10571963 ATTGATTGCAATAAAATGTTAAGGGCTT
1 ATTGATCGAAATAAAATGTTAAGGGCTT
10571991 AAAAGATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (29 bp):
ATTGATCGAAATAAAATGTTAAGGGCTTG
Found at i:10571998 original size:29 final size:29
Alignment explanation
Indices: 10571943--10571998 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
10571933 ATTGAGTCGA
* **
10571943 AATAAAAGATTAAGGGCTTGATTGATTGC
1 AATAAAAGATTAAGGGCTTAAAAGATTGC
10571972 AATAAAATG-TTAAGGGCTTAAAAGATT
1 AATAAAA-GATTAAGGGCTTAAAAGATT
10571999 ATTGAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.30
Consensus pattern (29 bp):
AATAAAAGATTAAGGGCTTAAAAGATTGC
Found at i:10573181 original size:6 final size:6
Alignment explanation
Indices: 10573167--10573202 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
10573157 TTCTCATGTC
*
10573167 TATATA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA
10573203 CAGTAATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:10577048 original size:23 final size:22
Alignment explanation
Indices: 10577022--10577142 Score: 94
Period size: 23 Copynumber: 5.5 Consensus size: 22
10577012 GTCCAATTTT
*
10577022 TTATATTTTATTCATATTTATCA
1 TTATATTTTATTTATATTTAT-A
10577045 TTAT-TTTATATTTATATTTATA
1 TTATATTT-TATTTATATTTATA
10577067 TT-TATTTTATCTTTATATTTATA
1 TTATATTTTA--TTTATATTTATA
10577090 TT-TATATTTATTT-TATCTT-TA
1 TTATAT-TTTATTTATAT-TTATA
* ** *
10577111 TTTTATTTTAACT-TATTTATC
1 TTATATTTTATTTATATTTATA
10577132 TTA-ATTTTATT
1 TTATATTTTATT
10577143 GTTTATCTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 19
0.76 0.06 0.17
Matches are distributed among these distances:
20 8 0.10
21 21 0.25
22 17 0.20
23 33 0.40
24 4 0.05
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATATTTTATTTATATTTATA
Found at i:10577058 original size:6 final size:6
Alignment explanation
Indices: 10577021--10577120 Score: 115
Period size: 6 Copynumber: 17.7 Consensus size: 6
10577011 TGTCCAATTT
*
10577021 TTTATA TTT-TA TTCATA TTTATCA -TTAT- TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTAT-A TTTATA TTTATA TTTATA TTTATA
* *
10577067 TTTAT- TTTATC TTTATA TTTATA TTTATA TTTAT- TTTATC TTTAT-
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
10577112 TTTAT- TTTA
1 TTTATA TTTA
10577121 ACTTATTTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
5 27 0.32
6 57 0.67
7 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:10577067 original size:29 final size:28
Alignment explanation
Indices: 10577020--10577128 Score: 136
Period size: 29 Copynumber: 3.9 Consensus size: 28
10577010 ATGTCCAATT
* *
10577020 TTTTATATTT-TATTCATATTTATCATTA
1 TTTTATATTTATATTTATATTTAT-TTTA
10577048 TTTTATATTTATATTTATATTTATTTTA
1 TTTTATATTTATATTTATATTTATTTTA
10577076 TCTTTATATTTATATTTATATTTATTTTA
1 T-TTTATATTTATATTTATATTTATTTTA
*
10577105 TCTTTAT-TTTAT-TTTA-ACTTATTT
1 T-TTTATATTTATATTTATATTTATTT
10577129 ATCTTAATTT
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.09
27 4 0.05
28 19 0.25
29 46 0.61
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTATATTTATATTTATATTTATTTTA
Found at i:10577936 original size:3 final size:3
Alignment explanation
Indices: 10577928--10577988 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
10577918 TTTTCAAAGT
10577928 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10577976 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
10577989 ACTTTATAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10578269 original size:16 final size:17
Alignment explanation
Indices: 10578248--10578279 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10578238 TTGAATTTCT
10578248 AGGAA-TTTTCTAAATG
1 AGGAATTTTTCTAAATG
10578264 AGGAATTTTTCTAAAT
1 AGGAATTTTTCTAAAT
10578280 TTAACCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (17 bp):
AGGAATTTTTCTAAATG
Found at i:10592475 original size:28 final size:27
Alignment explanation
Indices: 10592435--10592496 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
10592425 TATCAAATAC
*
10592435 ATTTTTTAAAAAACAAAAAATAAAAACA-
1 ATTTTCTAAAAAA-AAAAAATAAAAA-AT
*
10592463 ATTTTCTAAAAAATAAAAATAAAAAAT
1 ATTTTCTAAAAAAAAAAAATAAAAAAT
10592490 ATTTTCT
1 ATTTTCT
10592497 CAAGCCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 1 0.03
27 18 0.58
28 12 0.39
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (27 bp):
ATTTTCTAAAAAAAAAAAATAAAAAAT
Found at i:10592737 original size:18 final size:17
Alignment explanation
Indices: 10592696--10592741 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
10592686 TCAACTTAAT
*
10592696 TTTAATTAT-TTAAAAA
1 TTTAATTTTATTAAAAA
10592712 TTTAATTTCTATTAAAAA
1 TTTAATTT-TATTAAAAA
10592730 TATT-ATTTTATT
1 T-TTAATTTTATT
10592742 GATAAATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 7 0.27
17 5 0.19
18 12 0.46
19 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTTTATTAAAAA
Found at i:10595511 original size:14 final size:14
Alignment explanation
Indices: 10595488--10595519 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10595478 ATTTTAAATT
*
10595488 ATTAATTTTTATTA
1 ATTAATTTTTATCA
10595502 ATTAATTTTTATCA
1 ATTAATTTTTATCA
10595516 ATTA
1 ATTA
10595520 TTGTATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAATTTTTATCA
Found at i:10596108 original size:18 final size:19
Alignment explanation
Indices: 10596061--10596109 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
10596051 GCAATCCTGT
*
10596061 TGCCACTGTCGATCACCGG
1 TGCCACTGTCGGTCACCGG
*
10596080 TGCCACCGTCGGTCACC-G
1 TGCCACTGTCGGTCACCGG
*
10596098 TGCCATTGTCGG
1 TGCCACTGTCGG
10596110 CCACGGTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.12, C:0.37, G:0.29, T:0.22
Consensus pattern (19 bp):
TGCCACTGTCGGTCACCGG
Found at i:10596595 original size:6 final size:6
Alignment explanation
Indices: 10596575--10596616 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
10596565 AAAAGTTGCC
*
10596575 AAAA-A AAAAGC AAAAGA AAAAGGA AAAA-A AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA A
10596617 GAAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 9 0.28
6 17 0.53
7 6 0.19
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:10596607 original size:18 final size:18
Alignment explanation
Indices: 10596586--10596623 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
10596576 AAAAAAAAGC
10596586 AAAAGAAAAAGGAA-AAAA
1 AAAAGAAAAA-GAAGAAAA
10596604 AAAAGAAAAAGAAGAAAA
1 AAAAGAAAAAGAAGAAAA
10596622 AA
1 AA
10596624 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAGAAAA
Found at i:10607480 original size:21 final size:20
Alignment explanation
Indices: 10607455--10607501 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
10607445 GTGAAAGTAT
10607455 GATTAATTACTATAACGATAA
1 GATTAATTACTATAACGA-AA
* * *
10607476 GATTAATTATTGTAACGAGA
1 GATTAATTACTATAACGAAA
10607496 GATTAA
1 GATTAA
10607502 AATAAGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (20 bp):
GATTAATTACTATAACGAAA
Found at i:10607790 original size:17 final size:18
Alignment explanation
Indices: 10607747--10607803 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
10607737 ATTTATTTAT
* *
10607747 TAGTTTATTATATAATAA
1 TAGTTTATTATATAACAG
*
10607765 TAAGATTTATT-TATTACAG
1 T-AG-TTTATTATATAACAG
10607784 TAGTTTATTATATAACAG
1 TAGTTTATTATATAACAG
10607802 TA
1 TA
10607804 AAATTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.19
18 12 0.38
19 8 0.25
20 6 0.19
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (18 bp):
TAGTTTATTATATAACAG
Found at i:10607792 original size:37 final size:37
Alignment explanation
Indices: 10607747--10607817 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
10607737 ATTTATTTAT
* * *
10607747 TAGTTTATTATATAATAATAAGATTTATTTATTACAG
1 TAGTTTATTATATAACAATAAAATTAATTTATTACAG
*
10607784 TAGTTTATTATATAACAGTAAAATTAATTTATTA
1 TAGTTTATTATATAACAATAAAATTAATTTATTA
10607818 TATTAAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (37 bp):
TAGTTTATTATATAACAATAAAATTAATTTATTACAG
Found at i:10617642 original size:11 final size:11
Alignment explanation
Indices: 10617628--10617666 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
10617618 TTAGTAAATT
10617628 ATTTAAATTTA
1 ATTTAAATTTA
**
10617639 ATTTAAATAAA
1 ATTTAAATTTA
10617650 ATTTAAATTTA
1 ATTTAAATTTA
10617661 ATTTAA
1 ATTTAA
10617667 TTGTTATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:10618326 original size:28 final size:28
Alignment explanation
Indices: 10618290--10618353 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
10618280 AATAGCTAGT
* * *
10618290 ATAATTAAATAAA-TTATTAAATAATTTA
1 ATAAATAAA-AAAGTTAATAAATAATTGA
*
10618318 ATACATAAAAAAGTTAATAAATAATTGA
1 ATAAATAAAAAAGTTAATAAATAATTGA
10618346 ATAAATAA
1 ATAAATAA
10618354 TTCAATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 3 0.10
28 27 0.90
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (28 bp):
ATAAATAAAAAAGTTAATAAATAATTGA
Found at i:10623051 original size:186 final size:181
Alignment explanation
Indices: 10622724--10623287 Score: 654
Period size: 186 Copynumber: 3.1 Consensus size: 181
10622714 TTTTTCATGT
** * *
10622724 AATTATTCTAGGTTTTTTTGGGAGAAAATACCTTCAATAATTTTTTCTTAAAATTTTTTAGATTA
1 AATTATTGAAGGTTTTTTTGAGAGAAAACA-CTTCAATAA-TTTTTCTTAAAATTTTTTAGATTA
* * * * *
10622789 TTAAAGCATCTTCCAACGAAAAAATACCTTTAATATTCTAGTACTCAGATTTTAATATAGTTAGT
64 TTAAAGCATCTTTCAATGAAAAAAT-CCTTCAATATTCTAATACTCAGATTTTAAGATAGTTAG-
10622854 TAAGGCATTTATTCTAGAAAAACACCTTCACTAATTTCTTTTAATTTATGTACAA
127 TAAGGCATTTATTCTAGAAAAACACCTTCACTAATTTCTTTTAATTTATGTACAA
10622909 AATTATTGAAGGTATTTTTTGAGAGAAAACATCTTCAATAATTTTCTCTTAAAATTTTTTAGATT
1 AATTATTGAAGGT-TTTTTTGAGAGAAAACA-CTTCAATAATTTT-TCTTAAAATTTTTTAGATT
* *
10622974 ATTAAAGACATCTTTCAGTGAAAAAATGCCTTCAATATTCTAATACTTAGATTTTAAGATAGTTA
63 ATTAAAG-CATCTTTCAATGAAAAAAT-CCTTCAATATTCTAATACTCAGATTTTAAGATAGTTA
* ** *
10623039 GTGAGGCATTTATTCTAGAAAAATGCCTTCACTAATTTCTTTTAATTTACGTACAA
126 GTAAGGCATTTATTCTAGAAAAACACCTTCACTAATTTCTTTTAATTTATGTACAA
* * * * *
10623095 AATTATTGAATGTGTTTTTTGAGAAAAAACACATTCAATAATTTTTTTTAAAA-ATTTGAGATTA
1 AATTATTGAAGGT-TTTTTTGAGAGAAAACAC-TTCAATAATTTTTCTTAAAATTTTTTAGATTA
* * * * *
10623159 TTAAAGGCATC-TTCTAAT-AAAAACA-CCTTCAGTAATCCACTACTCAAATTCTT-AGATAGTT
64 TTAAA-GCATCTTTC-AATGAAAAA-ATCCTTCAATATTCTAATACTCAGATT-TTAAGATAGTT
* * * * * *
10623220 AGTAAGGGCATTTATTTTTGAAAAACTCCTTTACTAA-TTCTTTTTAATTTTTGTACAT
125 AGTAA-GGCATTTATTCTAGAAAAACACCTTCACTAATTTC-TTTTAATTTATGTACAA
10623278 AATTATTGAA
1 AATTATTGAA
10623288 ACCGATTTTT
Statistics
Matches: 330, Mismatches: 39, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
182 34 0.10
183 60 0.18
184 21 0.06
185 24 0.07
186 141 0.43
187 50 0.15
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (181 bp):
AATTATTGAAGGTTTTTTTGAGAGAAAACACTTCAATAATTTTTCTTAAAATTTTTTAGATTATT
AAAGCATCTTTCAATGAAAAAATCCTTCAATATTCTAATACTCAGATTTTAAGATAGTTAGTAAG
GCATTTATTCTAGAAAAACACCTTCACTAATTTCTTTTAATTTATGTACAA
Found at i:10623916 original size:28 final size:28
Alignment explanation
Indices: 10623863--10623921 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
10623853 TGTTGAACCT
* * * * *
10623863 TATTGTGTGATATTGTTTTGCTAAATGG
1 TATTGTATGATATTGGTATGCCAAATCG
10623891 TATTGTATGATATTGGTATGCCAAATCG
1 TATTGTATGATATTGGTATGCCAAATCG
10623919 TAT
1 TAT
10623922 ACTGAATGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (28 bp):
TATTGTATGATATTGGTATGCCAAATCG
Done.