Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 11 of 226
Found at i:5158552 original size:20 final size:20
Alignment explanation
Indices: 5158527--5158633 Score: 135
Period size: 20 Copynumber: 5.3 Consensus size: 20
5158517 TTTTGGTAAA
5158527 TGGTAAATCATTAGATATAT
1 TGGTAAATCATTAGATATAT
** *
5158547 TGGTAAATTGTTAGAAATAT
1 TGGTAAATCATTAGATATAT
* *
5158567 TGGAAAATCGTTAGATATAT
1 TGGTAAATCATTAGATATAT
5158587 TGGTAAATCATTAGATACT-T
1 TGGTAAATCATTAGATA-TAT
* *
5158607 TGGTAAATCATTATATATTT
1 TGGTAAATCATTAGATATAT
5158627 TGGTAAA
1 TGGTAAA
5158634 GTCGTAGAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 74 0.97
21 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (20 bp):
TGGTAAATCATTAGATATAT
Found at i:5158609 original size:87 final size:87
Alignment explanation
Indices: 5158450--5158614 Score: 204
Period size: 87 Copynumber: 1.9 Consensus size: 87
5158440 TGACAAATTG
* * * * *
5158450 TTAGATATATTGGTAAATCCTTAGAAATAGTAGTAAATTGTCAAATATTTTGGTAAGTCCTTAAA
1 TTAGATATATTGGTAAATCCTTAGAAATAGTAGAAAATCGTCAAATATATTGGTAAATCATTAAA
*
5158515 AATTTTGGTAAATGGTAAATCA
66 AACTTTGGTAAATGGTAAATCA
** * * * * *
5158537 TTAGATATATTGGTAAATTGTTAGAAATATTGGAAAATCGTTAGATATATTGGTAAATCATTAGA
1 TTAGATATATTGGTAAATCCTTAGAAATAGTAGAAAATCGTCAAATATATTGGTAAATCATTAAA
*
5158602 TACTTTGGTAAAT
66 AACTTTGGTAAAT
5158615 CATTATATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (87 bp):
TTAGATATATTGGTAAATCCTTAGAAATAGTAGAAAATCGTCAAATATATTGGTAAATCATTAAA
AACTTTGGTAAATGGTAAATCA
Found at i:5158615 original size:40 final size:40
Alignment explanation
Indices: 5158527--5158652 Score: 139
Period size: 40 Copynumber: 3.1 Consensus size: 40
5158517 TTTTGGTAAA
**
5158527 TGGTAAATCATTAGATATATTGGTAAATTGTTAGAAATAT
1 TGGTAAATCATTAGATATATTGGTAAATCATTAGAAATAT
* * *
5158567 TGGAAAATCGTTAGATATATTGGTAAATCATTAGATACT-T
1 TGGTAAATCATTAGATATATTGGTAAATCATTAGA-AATAT
* * * *
5158607 TGGTAAATCATTATATATTTTGGTAAAGTC-GTAGAAATTT
1 TGGTAAATCATTAGATATATTGGTAAA-TCATTAGAAATAT
5158647 TGGTAA
1 TGGTAA
5158653 TTGTTAAGAC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.03
40 66 0.92
41 4 0.06
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (40 bp):
TGGTAAATCATTAGATATATTGGTAAATCATTAGAAATAT
Found at i:5158650 original size:60 final size:60
Alignment explanation
Indices: 5158527--5158652 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
5158517 TTTTGGTAAA
** *
5158527 TGGTAAATCATTAGATATATTGGTAAATTGTTAGAAATATTGGAAAATCGTTAGATATAT
1 TGGTAAATCATTAGATATATTGGTAAATCATTAGAAATATTGGAAAATCGTTAGAAATAT
* * * * *
5158587 TGGTAAATCATTAGATACT-TTGGTAAATCATTATATATTTTGGTAAAGTCG-TAGAAATTT
1 TGGTAAATCATTAGATA-TATTGGTAAATCATTAGAAATATTGG-AAAATCGTTAGAAATAT
5158647 TGGTAA
1 TGGTAA
5158653 TTGTTAAGAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 49 0.88
61 7 0.12
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (60 bp):
TGGTAAATCATTAGATATATTGGTAAATCATTAGAAATATTGGAAAATCGTTAGAAATAT
Found at i:5158772 original size:20 final size:20
Alignment explanation
Indices: 5158749--5158920 Score: 107
Period size: 20 Copynumber: 8.7 Consensus size: 20
5158739 ATCCATAAAA
**
5158749 ATTTTGGTAAATTGTTAGAT
1 ATTTTGGTAAATCATTAGAT
* *
5158769 ATTTTGATAAAACATTACGA-
1 ATTTTGGTAAATCATTA-GAT
5158789 ATTTTGGTAAATCATTAGAT
1 ATTTTGGTAAATCATTAGAT
* * * *
5158809 GTTTTGGTAAA-CCTTATAA
1 ATTTTGGTAAATCATTAGAT
* ** *
5158828 ATTTTGGTAATTTGTTCGAT
1 ATTTTGGTAAATCATTAGAT
* **
5158848 ATATCAGTAAATCATTAGA-
1 ATTTTGGTAAATCATTAGAT
* * *
5158867 ATTTTTAGTGAACCATTAGAT
1 A-TTTTGGTAAATCATTAGAT
* * **
5158888 ATATAGGTAAATTGTTAGAT
1 ATTTTGGTAAATCATTAGAT
5158908 ATTTTGGTAAATC
1 ATTTTGGTAAATC
5158921 CTTGGAGATA
Statistics
Matches: 109, Mismatches: 38, Indels: 10
0.69 0.24 0.06
Matches are distributed among these distances:
19 17 0.16
20 89 0.82
21 3 0.03
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (20 bp):
ATTTTGGTAAATCATTAGAT
Found at i:5158792 original size:40 final size:39
Alignment explanation
Indices: 5158747--5158849 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
5158737 AAATCCATAA
5158747 AAATTTTGGTAAATTGTTAGATATTTTGATAAAACATTAC
1 AAATTTTGGTAAATTGTTAGATATTTTGAT-AAACATTAC
* ** * * * *
5158787 GAATTTTGGTAAATCATTAGATGTTTTGGTAAACCTTAT
1 AAATTTTGGTAAATTGTTAGATATTTTGATAAACATTAC
* *
5158826 AAATTTTGGTAATTTGTTCGATAT
1 AAATTTTGGTAAATTGTTAGATAT
5158850 ATCAGTAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
39 25 0.50
40 25 0.50
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.45
Consensus pattern (39 bp):
AAATTTTGGTAAATTGTTAGATATTTTGATAAACATTAC
Found at i:5158897 original size:79 final size:80
Alignment explanation
Indices: 5158729--5158899 Score: 186
Period size: 79 Copynumber: 2.1 Consensus size: 80
5158719 AGTAACATAA
**
5158729 ATATTGGTAAATCCATAAAAATTTTGGTAAATTGTTAGATATTTTGATAAAACATTACGAATTTT
1 ATATTGGTAAATCCATAAAAATTTTGGTAAATTGTTAGATATTCAGATAAAACATTACGAATTTT
* *
5158794 GGTAAATCATTAGAT
66 AGTAAACCATTAGAT
* * * * * * *
5158809 GTTTTGGTAAA-CCTTATAAATTTTGGTAATTTGTTCGATATATCAG-TAAATCATTA-GAATTT
1 ATATTGGTAAATCCATAAAAATTTTGGTAAATTGTTAGATAT-TCAGATAAAACATTACGAA-TT
*
5158871 TTAGTGAACCATTAGAT
64 TTAGTAAACCATTAGAT
*
5158888 ATATAGGTAAAT
1 ATATTGGTAAAT
5158900 TGTTAGATAT
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
78 3 0.04
79 59 0.81
80 11 0.15
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (80 bp):
ATATTGGTAAATCCATAAAAATTTTGGTAAATTGTTAGATATTCAGATAAAACATTACGAATTTT
AGTAAACCATTAGAT
Found at i:5158918 original size:60 final size:59
Alignment explanation
Indices: 5158789--5158920 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 59
5158779 AACATTACGA
* * * * * *
5158789 ATTTTGGTAAATCATTAGATGTTTTGGTAAACCTTATAAATTTTGGTAATTTGTTCGAT
1 ATTTTGGTAAATCATTAGATGTTTTAGTAAACCTTAGAAATATAGGTAAATTGTTAGAT
* ** * *
5158848 ATATCAGTAAATCATTAGAAT-TTTTAGTGAACCATTAGATATATAGGTAAATTGTTAGAT
1 ATTTTGGTAAATCATTAG-ATGTTTTAGTAAACC-TTAGAAATATAGGTAAATTGTTAGAT
5158908 ATTTTGGTAAATC
1 ATTTTGGTAAATC
5158921 CTTGGAGATA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
59 25 0.44
60 32 0.56
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (59 bp):
ATTTTGGTAAATCATTAGATGTTTTAGTAAACCTTAGAAATATAGGTAAATTGTTAGAT
Found at i:5159025 original size:20 final size:20
Alignment explanation
Indices: 5158977--5159027 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5158967 TGGAAATATT
* * * *
5158977 TAGAAATATTGTTAAATTGT
1 TAGAAATTTTGATAAAGTGA
*
5158997 TAGATATTTTGATAAAGTGA
1 TAGAAATTTTGATAAAGTGA
5159017 TAGAAATTTTG
1 TAGAAATTTTG
5159028 GTAATTGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (20 bp):
TAGAAATTTTGATAAAGTGA
Found at i:5159195 original size:20 final size:20
Alignment explanation
Indices: 5159143--5159183 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5159133 AAGTTCTTAA
*
5159143 AAATATTGGTAAATGGTTAG
1 AAATATTAGTAAATGGTTAG
5159163 AAATATTAGTAAATGGTTAG
1 AAATATTAGTAAATGGTTAG
5159183 A
1 A
5159184 TATTTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (20 bp):
AAATATTAGTAAATGGTTAG
Found at i:5159273 original size:20 final size:19
Alignment explanation
Indices: 5159250--5159302 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5159240 GAAATTTTGA
5159250 AAATATTGGTGAAATCTTAT
1 AAATATTGGT-AAATCTTAT
*
5159270 AAAT-TCTGGTAAAGTTTTAT
1 AAATAT-TGGTAAA-TCTTAT
5159290 AAATATTGGTAAA
1 AAATATTGGTAAA
5159303 ATGATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 24 0.83
21 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (19 bp):
AAATATTGGTAAATCTTAT
Found at i:5159318 original size:20 final size:20
Alignment explanation
Indices: 5159295--5159342 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
5159285 TTTATAAATA
*
5159295 TTGGTAAA-ATGATAGATGTT
1 TTGGTAAACAT-ATAGATATT
5159315 TTGGTAAACATATAGATATT
1 TTGGTAAACATATAGATATT
*
5159335 TTGATAAA
1 TTGGTAAA
5159343 TCCTTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGGTAAACATATAGATATT
Found at i:5159595 original size:20 final size:20
Alignment explanation
Indices: 5159572--5159690 Score: 107
Period size: 20 Copynumber: 6.0 Consensus size: 20
5159562 TAATAAATTG
* *
5159572 TTAGATATTTTGGTAAATCC
1 TTAGATATATTGGTAAATCA
* * *
5159592 TTAGAAATGTTGATAAA-CTA
1 TTAGATATATTGGTAAATC-A
*
5159612 TTAGATATATTGGTAAAACGA
1 TTAGATATATTGGTAAATC-A
* * *
5159633 -TAGAAATTTTGGTAAATCG
1 TTAGATATATTGGTAAATCA
* *
5159652 TTAGATATATTGATAAATAA
1 TTAGATATATTGGTAAATCA
5159672 TTAGATATATTGGTAAATC
1 TTAGATATATTGGTAAATC
5159691 CTTAAATATT
Statistics
Matches: 77, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.01
20 74 0.96
21 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (20 bp):
TTAGATATATTGGTAAATCA
Found at i:5159608 original size:40 final size:40
Alignment explanation
Indices: 5159564--5159669 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
5159554 AAAAAATTTA
* *
5159564 ATAAATTGTTAGATATTTTGGTAAATCCTTAGAAATGTTG
1 ATAAATTGTTAGATATATTGGTAAATCCATAGAAATGTTG
* * * * *
5159604 ATAAACTATTAGATATATTGGTAAAACGATAGAAATTTTG
1 ATAAATTGTTAGATATATTGGTAAATCCATAGAAATGTTG
* * *
5159644 GTAAATCGTTAGATATATTGATAAAT
1 ATAAATTGTTAGATATATTGGTAAAT
5159670 AATTAGATAT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (40 bp):
ATAAATTGTTAGATATATTGGTAAATCCATAGAAATGTTG
Found at i:5159647 original size:60 final size:60
Alignment explanation
Indices: 5159573--5159688 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
5159563 AATAAATTGT
* *
5159573 TAGATATTTTGGTAAATCCTTAGAAATGTTGATAAACT-ATTAGATATATTGGTAAAACGA
1 TAGAAATTTTGGTAAATCCTTAGAAATATTGATAAA-TAATTAGATATATTGGTAAAACGA
* *
5159633 TAGAAATTTTGGTAAATCGTTAGATATATTGATAAATAATTAGATATATTGGTAAA
1 TAGAAATTTTGGTAAATCCTTAGAAATATTGATAAATAATTAGATATATTGGTAAA
5159689 TCCTTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 50 0.98
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.38
Consensus pattern (60 bp):
TAGAAATTTTGGTAAATCCTTAGAAATATTGATAAATAATTAGATATATTGGTAAAACGA
Found at i:5159702 original size:60 final size:61
Alignment explanation
Indices: 5159576--5159708 Score: 173
Period size: 60 Copynumber: 2.2 Consensus size: 61
5159566 AAATTGTTAG
* *
5159576 ATATTTTGGTAAATCCTTAGAAATGTTGATAAACTATTAGATATATTGGTAAAACGATAGA
1 ATATTTTGGTAAATCCTTAGAAATATTGATAAACTATTAGATATATTGGTAAAACCATAGA
* * * *
5159637 A-ATTTTGGTAAATCGTTAGATATATTGATAAA-TAATTAGATATATTGGTAAATCCTTA-A
1 ATATTTTGGTAAATCCTTAGAAATATTGATAAACT-ATTAGATATATTGGTAAAACCATAGA
*
5159696 ATATTTTGATAAA
1 ATATTTTGGTAAA
5159709 ACCACTGAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.05
60 59 0.94
61 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.39
Consensus pattern (61 bp):
ATATTTTGGTAAATCCTTAGAAATATTGATAAACTATTAGATATATTGGTAAAACCATAGA
Found at i:5159708 original size:20 final size:20
Alignment explanation
Indices: 5159572--5159708 Score: 98
Period size: 20 Copynumber: 6.8 Consensus size: 20
5159562 TAATAAATTG
* * *
5159572 TTAGATATTTTGGTAAATCC
1 TTAGATATATTGATAAATCA
* *
5159592 TTAGAAATGTTGATAAA-CTA
1 TTAGATATATTGATAAATC-A
* *
5159612 TTAGATATATTGGTAAAACGA
1 TTAGATATATTGATAAATC-A
* * * *
5159633 -TAGAAATTTTGGTAAATCG
1 TTAGATATATTGATAAATCA
*
5159652 TTAGATATATTGATAAATAA
1 TTAGATATATTGATAAATCA
* *
5159672 TTAGATATATTGGTAAATCC
1 TTAGATATATTGATAAATCA
* *
5159692 TTAAATATTTTGATAAA
1 TTAGATATATTGATAAA
5159709 ACCACTGAAC
Statistics
Matches: 91, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
19 1 0.01
20 88 0.97
21 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (20 bp):
TTAGATATATTGATAAATCA
Found at i:5160236 original size:22 final size:22
Alignment explanation
Indices: 5160196--5160241 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5160186 CATATATAAA
*
5160196 AAGAAAAAAAATTGAAATAATT
1 AAGAAAAAAAATAGAAATAATT
* * *
5160218 AAGATAAAAAATAGTAATAGTT
1 AAGAAAAAAAATAGAAATAATT
5160240 AA
1 AA
5160242 CATCCGTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (22 bp):
AAGAAAAAAAATAGAAATAATT
Found at i:5171392 original size:13 final size:13
Alignment explanation
Indices: 5171374--5171399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5171364 AATGTATTTG
5171374 TTTTTATTTTTAT
1 TTTTTATTTTTAT
5171387 TTTTTATTTTTAT
1 TTTTTATTTTTAT
5171400 GATTTCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:5173877 original size:4 final size:4
Alignment explanation
Indices: 5173870--5173929 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
5173860 CAATCGTTAC
5173870 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
5173918 ACAT ACAT ACAT
1 ACAT ACAT ACAT
5173930 GATACTTAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:5175577 original size:5 final size:5
Alignment explanation
Indices: 5175564--5175606 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
5175554 TGCAAGCTAG
* *
5175564 GTTTG GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTCT GTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTT
5175607 GGGTTTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.23, T:0.74
Consensus pattern (5 bp):
GTTTT
Found at i:5189834 original size:27 final size:24
Alignment explanation
Indices: 5189786--5189837 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5189776 AAACATTATT
*
5189786 CTCCTTACTATTACAATTCACCAC
1 CTCCTTACTACTACAATTCACCAC
* *
5189810 CTCCTTACTACTACAAGTCTCCAC
1 CTCCTTACTACTACAATTCACCAC
5189834 CTCC
1 CTCC
5189838 ACCATCTCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.42, G:0.02, T:0.31
Consensus pattern (24 bp):
CTCCTTACTACTACAATTCACCAC
Found at i:5189862 original size:48 final size:48
Alignment explanation
Indices: 5189804--5190710 Score: 685
Period size: 48 Copynumber: 18.9 Consensus size: 48
5189794 TATTACAATT
* * *
5189804 CACCACCTCCTTACTACTACAAGTCTCCACCTCCACCATCTCCCTCA-C
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * * * *
5189852 CACCTCCTCCTTACTATTACAAATCACCACCACC-CCCT-TCACCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTC-CCTAG-C
* * *
5189900 CCCCACCACCATACTACTACAACTCACCACCTCCACCATCTCCTTCA-C
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * * *
5189948 CACCTCCTCCTTACTATTACAAGTCTCCACCCCCACC--CTCACCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTC-CCTAG-C
* *
5189996 CCCCACCACCATACTACTACAAGTCACCACCTCCACCGTCTCCCTCA-C
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * * * *
5190044 CACCTCCTCCTTACTATTACAAATCACCACCACC-CCCT-TCACCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTC-CCTAG-C
* *
5190092 CCCCACCACCATACTACTACAACTCACCACCTCCACCATCTCCCTCA-C
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * *
5190140 CACCTCCTCCTTACTACTACAAATCACCACCACCACC-T-TCACCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTC-CCTAG-C
*
5190188 CTCCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCA-C
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * *
5190236 CACCTCCTCCTTACTACTACAAATCACCACCCCCACC-T-TCACCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTC-CCTAG-C
* * *
5190284 CTCCACCACCCTACTACTACAAGTCTCCACCTCCACCATC-CCCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTAG-C
* * *
5190332 CCCCACCACCATACTACTACAAATCACCACCCCCACCATCT-CCTAGCC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTAG-C
* * * *
5190380 CTCCACCACCATATTACTACAGGTCCCCACCTCCACCATCT-CCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTAG-C
* * * *
5190428 CACCATCACCGTACTACTACAAGTCACCACCACC-CCCT-TCACCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTC-CCTAG-C
* *
5190476 CCCCACCACCATACTACTACAAGTCACCGCCTCCACCATCT-CCTAGTC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTAG-C
* *
5190524 CCCCACCACCATACT-CTTACAAGTCACCACCACCACCATCTCCCTCA-C
1 CACCACCACCATACTAC-TACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * * *
5190572 CACCACCTCCATACTACTACAAATCTCCTCCTCCACCGTCTCCATCA-C
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * * * * * *
5190620 CCCCTCCTCCTTACTACTACAAATCACCACCACCTCCTTCTCCATCA-C
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCT-AGC
* * * * * * *
5190668 CCCCGCCACCTTACTATTATAAGTCACCTCCTCCACCACCTCC
1 CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCC
5190711 TTATCACTAC
Statistics
Matches: 694, Mismatches: 127, Indels: 76
0.77 0.14 0.08
Matches are distributed among these distances:
46 17 0.02
47 26 0.04
48 609 0.88
49 27 0.04
50 15 0.02
ACGTcount: A:0.25, C:0.51, G:0.03, T:0.21
Consensus pattern (48 bp):
CACCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTAGC
Found at i:5189917 original size:96 final size:96
Alignment explanation
Indices: 5189806--5190710 Score: 1061
Period size: 96 Copynumber: 9.4 Consensus size: 96
5189796 TTACAATTCA
* * * *
5189806 CCACCTCCTTACTACTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTATTA
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
5189871 CAAATCACCACCACCCCCTTCACCTAGTCCC
66 CAAATCACCACCACCCCCTTCACCTAGTCCC
* * *
5189902 CCACCACCATACTACTACAACTCACCACCTCCACCATCTCCTTCACCACCTCCTCCTTACTATTA
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
* * *
5189967 CAAGTCTCCACC-CCCACCCTCACCTAGTCCC
66 CAAATCACCACCACCC-CCTTCACCTAGTCCC
* *
5189998 CCACCACCATACTACTACAAGTCACCACCTCCACCGTCTCCCTCACCACCTCCTCCTTACTATTA
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
5190063 CAAATCACCACCACCCCCTTCACCTAGTCCC
66 CAAATCACCACCACCCCCTTCACCTAGTCCC
*
5190094 CCACCACCATACTACTACAACTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
* *
5190159 CAAATCACCACCACCACCTTCACCTAGTCCT
66 CAAATCACCACCACCCCCTTCACCTAGTCCC
5190190 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
*
5190255 CAAATCACCACC-CCCACCTTCACCTAGTCCT
66 CAAATCACCACCACCC-CCTTCACCTAGTCCC
* * * * * *
5190286 CCACCACCCTACTACTACAAGTCTCCACCTCCACCATC-CCCT-AGTCCCCCACCACCATACTAC
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCA--CCACCTCCTCCTTACTAC
* *
5190349 TACAAATCACCACC-CCCACCATCTCCTAG-CCC
64 TACAAATCACCACCACCC-CCTTCACCTAGTCCC
* * * * *
5190381 TCCACCACCATATTACTACAGGTCCCCACCTCCACCATCT-CCT-AGTCCACCAT-CACCGTACT
1 -CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCA--CCACC-TCCTCCTTACT
*
5190443 ACTACAAGTCACCACCACCCCCTTCACCTAGTCCC
62 ACTACAAATCACCACCACCCCCTTCACCTAGTCCC
* * * * *
5190478 CCACCACCATACTACTACAAGTCACCGCCTCCACCATCT-CCT-AGTCCCCCACCACCATACT-C
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCA--CCACCTCCTCCTTACTAC
* * *
5190540 TTACAAGTCACCACCACCACCATCTC-CCTCA--CCA
64 -TACAAATCACCACCACC-CCCT-TCACCT-AGTCCC
* * * * * * *
5190574 CCACCTCCATACTACTACAAATCTCCTCCTCCACCGTCTCCATCACCCCCTCCTCCTTACTACTA
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
* *
5190639 CAAATCACCACCACCTCCTTCTCC-A-TCACCC
66 CAAATCACCACCACCCCCTTCACCTAGT--CCC
* * * * * *
5190670 CCGCCACCTTACTATTATAAGTCACCTCCTCCACCACCTCC
1 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCC
5190711 TTATCACTAC
Statistics
Matches: 716, Mismatches: 71, Indels: 44
0.86 0.09 0.05
Matches are distributed among these distances:
93 1 0.00
94 3 0.00
95 16 0.02
96 674 0.94
97 18 0.03
98 4 0.01
ACGTcount: A:0.25, C:0.51, G:0.03, T:0.21
Consensus pattern (96 bp):
CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACTACTA
CAAATCACCACCACCCCCTTCACCTAGTCCC
Found at i:5190511 original size:27 final size:25
Alignment explanation
Indices: 5190286--5190562 Score: 94
Period size: 27 Copynumber: 11.4 Consensus size: 25
5190276 ACCTAGTCCT
* *
5190286 CCACCACCCTACTACTACAAGTCTCC
1 CCACCACCATACT-CTACAAGTCACC
* * *
5190312 ACCTCCACCAT-C-C-CCTAGTC-CC
1 -CCACCACCATACTCTACAAGTCACC
*
5190334 CCACCACCATACTACTACAAATCACC
1 CCACCACCATACT-CTACAAGTCACC
* *
5190360 ACCCCCACCAT-CTC--CTAG-C-CC
1 -CCACCACCATACTCTACAAGTCACC
* * *
5190381 TCCACCACCATATTACTACAGGTCCCC
1 -CCACCACCATACT-CTACAAGTCACC
* * *
5190408 ACCTCCACCAT-CTC--CTAGTC-CA
1 -CCACCACCATACTCTACAAGTCACC
* *
5190430 CCATCACCGTACTACTACAAGTCACC
1 CCACCACCATACT-CTACAAGTCACC
* *
5190456 ACCACC-CCCT--TC-ACCTAGTC-CC
1 -CCACCACCATACTCTA-CAAGTCACC
5190478 CCACCACCATACTACTACAAGTCACC
1 CCACCACCATACT-CTACAAGTCACC
* *
5190504 GCCTCCACCAT-CTC--CTAGTC-CC
1 -CCACCACCATACTCTACAAGTCACC
5190526 CCACCACCATACTCTTACAAGTCACC
1 CCACCACCATACTC-TACAAGTCACC
5190552 ACCACCACCAT
1 -CCACCACCAT
5190563 CTCCCTCACC
Statistics
Matches: 182, Mismatches: 36, Indels: 64
0.65 0.13 0.23
Matches are distributed among these distances:
21 41 0.23
22 19 0.10
23 24 0.13
24 4 0.02
25 25 0.14
26 18 0.10
27 51 0.28
ACGTcount: A:0.26, C:0.51, G:0.05, T:0.18
Consensus pattern (25 bp):
CCACCACCATACTCTACAAGTCACC
Found at i:5198703 original size:3 final size:3
Alignment explanation
Indices: 5198685--5198717 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5198675 GAACTACAGC
5198685 ATA AT- ATA ATTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
5198718 GTCATGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5202890 original size:26 final size:27
Alignment explanation
Indices: 5202861--5202928 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
5202851 AAAAATAAAA
* **
5202861 ATTTACCAAAATATAAT-CCCTTTTTT
1 ATTTACTAAAATATAATAAACTTTTTT
* * *
5202887 ATTTATTAAAATATTATAAATTTTTTT
1 ATTTACTAAAATATAATAAACTTTTTT
5202914 ATTTACTAAAATATA
1 ATTTACTAAAATATA
5202929 CCAAAAAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTACTAAAATATAATAAACTTTTTT
Found at i:5202945 original size:11 final size:11
Alignment explanation
Indices: 5202931--5202960 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5202921 AAAATATACC
*
5202931 AAAAAAACAGA
1 AAAAAAACAAA
5202942 AAAAAAACAAA
1 AAAAAAACAAA
5202953 AAAAAAAC
1 AAAAAAAC
5202961 TGACACAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:5203557 original size:19 final size:18
Alignment explanation
Indices: 5203533--5203598 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
5203523 CTGGTATTTC
5203533 TATTAATTTAAAATATAGT
1 TATTAA-TTAAAATATAGT
* * *
5203552 TATTAAATGAGA-ATAGTT
1 TATTAATTAAAATATAG-T
*
5203570 TATTAAATTAAAATAGAGT
1 TATT-AATTAAAATATAGT
*
5203589 TATTACTTAA
1 TATTAATTAA
5203599 TTAGAATTCT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
17 4 0.11
18 13 0.36
19 16 0.44
20 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (18 bp):
TATTAATTAAAATATAGT
Found at i:5203584 original size:18 final size:19
Alignment explanation
Indices: 5203533--5203585 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
5203523 CTGGTATTTC
*
5203533 TATTAATTTAAAATA-TAGT
1 TATTAAATTAAAATAGTA-T
* *
5203552 TATTAAATGAGAATAGT-T
1 TATTAAATTAAAATAGTAT
5203570 TATTAAATTAAAATAG
1 TATTAAATTAAAATAG
5203586 AGTTATTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 15 0.54
19 12 0.43
20 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (19 bp):
TATTAAATTAAAATAGTAT
Found at i:5206836 original size:25 final size:25
Alignment explanation
Indices: 5206763--5206829 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
5206753 TTCCGAGTTG
*
5206763 AATAACGGGAAGCTCATGCGAGCTA
1 AATAATGGGAAGCTCATGCGAGCTA
*
5206788 AATAATGGGAACCTCATGCGAGCTA
1 AATAATGGGAAGCTCATGCGAGCTA
* *
5206813 AGTATTGGGAAGCTCAT
1 AATAATGGGAAGCTCAT
5206830 AAGAGCTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (25 bp):
AATAATGGGAAGCTCATGCGAGCTA
Found at i:5207654 original size:5 final size:5
Alignment explanation
Indices: 5207644--5207668 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5207634 ATGATAATAG
5207644 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
5207669 ATCACTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:5210210 original size:51 final size:51
Alignment explanation
Indices: 5210140--5210385 Score: 146
Period size: 51 Copynumber: 5.0 Consensus size: 51
5210130 CCTGATCAGT
* * * *
5210140 AATCAGTAACGGTAGCAATAACAGTAACAGTATTCAACACACAAAGTGTTG
1 AATCTGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTG
* *
5210191 AATCTGTAACAGTAAC----A-A-TAACAGTATTCGACACACAAAGTGTCG
1 AATCTGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTG
* * * **
5210236 AAT-TGGTAACAGTAACAGTAGTC-G-ACACA-TAATGCCTAA-TCAGTAA-TCAG-T-
1 AATCT-GTAACAGTAACAGTA-ACAGTA-ACAGT-AT-TC-AACACACAAAGT--GTTG
* * *
5210287 AA-CGGTAGCAGTAACAGTAACTA-AAACAGTATTCAACACACAAAGTGTTG
1 AATCTGTAACAGTAACAGTAAC-AGTAACAGTATTCAACACACAAAGTGTTG
* * *
5210337 AATCTATAACAGTAACAGTAACAGTAATAGTATTCGACACACAAAGTGT
1 AATCTGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGT
5210386 CAAATCGGTA
Statistics
Matches: 145, Mismatches: 25, Indels: 50
0.66 0.11 0.23
Matches are distributed among these distances:
44 1 0.01
45 39 0.27
46 1 0.01
47 1 0.01
48 3 0.02
49 7 0.05
50 25 0.17
51 61 0.42
52 5 0.03
53 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.23
Consensus pattern (51 bp):
AATCTGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTG
Found at i:5210225 original size:45 final size:45
Alignment explanation
Indices: 5210158--5210252 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
5210148 ACGGTAGCAA
* *
5210158 TAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT-GTAACAG
1 TAACAATAACAGTATTCAACACACAAAGTGTCGAAT-TGGTAACAG
*
5210203 TAACAATAACAGTATTCGACACACAAAGTGTCGAATTGGTAACAG
1 TAACAATAACAGTATTCAACACACAAAGTGTCGAATTGGTAACAG
5210248 TAACA
1 TAACA
5210253 GTAGTCGACA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (45 bp):
TAACAATAACAGTATTCAACACACAAAGTGTCGAATTGGTAACAG
Found at i:5210245 original size:39 final size:41
Alignment explanation
Indices: 5210158--5210264 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 41
5210148 ACGGTAGCAA
* *
5210158 TAACAGTAACAGTATTCAACACACAAAGTGTTGAATCTGTAACAG
1 TAACAGTAACAGTATTCGACACACAAAGTGTCGAATCTG----AG
*
5210203 TAACAATAACAGTATTCGACACACAAAGTGTCGAAT-TG-G
1 TAACAGTAACAGTATTCGACACACAAAGTGTCGAATCTGAG
*
5210242 TAACAGTAACAGTAGTCGACACA
1 TAACAGTAACAGTATTCGACACA
5210265 TAATGCCTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
39 22 0.39
44 2 0.04
45 33 0.58
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (41 bp):
TAACAGTAACAGTATTCGACACACAAAGTGTCGAATCTGAG
Found at i:5210256 original size:141 final size:140
Alignment explanation
Indices: 5210002--5210434 Score: 571
Period size: 141 Copynumber: 3.0 Consensus size: 140
5209992 GTAACGGTAG
* * * * * *
5210002 CAGTAACAGTAACAATAATAGTAACAGTATTCAACACACAAAGTGTTGAATCTATAACAGCAACG
1 CAGTAACGGTAGCAATAACAGTAACAGTATTCAACACACAAAGTGTTGAATCTGTAACAGTAACA
* * *
5210067 GTAACAGTATTCGAAACATAAAGTGTCAAATTAGTAACAGTAACAGTAGTCAGCACATAAGTGCC
66 GTAACAGTATTCGACACACAAAGTGTCAAATTGGTAACAGTAACAGTAGTC-GCACATAAGTGCC
*
5210132 TGATCAGTAAT
130 TAATCAGTAAT
5210143 CAGTAACGGTAGCAATAACAGTAACAGTATTCAACACACAAAGTGTTGAATCTGTAACAGTAACA
1 CAGTAACGGTAGCAATAACAGTAACAGTATTCAACACACAAAGTGTTGAATCTGTAACAGTAACA
* *
5210208 ATAACAGTATTCGACACACAAAGTGTCGAATTGGTAACAGTAACAGTAGTCGACACATAA-TGCC
66 GTAACAGTATTCGACACACAAAGTGTCAAATTGGTAACAGTAACAGTAGTCG-CACATAAGTGCC
5210272 TAATCAGTAAT
130 TAATCAGTAAT
*
5210283 CAGTAACGGTAGCAGTAACAGTAACTAAAACAGTATTCAACACACAAAGTGTTGAATCTATAACA
1 CAGTAACGGTAGCAATAACAG----T--AACAGTATTCAACACACAAAGTGTTGAATC--T----
* * * *
5210348 GTAACAGTAACAGTAATAGTATTCGACACACAAAGTGTCAAATCGGTAACAATAATAGTAGTCGG
54 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGTCAAATTGGTAACAGTAACAGTAGTC-G
5210413 CACATAAGTGCCTAATCAGTAA
118 CACATAAGTGCCTAATCAGTAA
5210435 GCCGACAAAA
Statistics
Matches: 258, Mismatches: 19, Indels: 18
0.87 0.06 0.06
Matches are distributed among these distances:
140 35 0.14
141 112 0.43
144 1 0.00
146 30 0.12
148 1 0.00
152 64 0.25
153 15 0.06
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (140 bp):
CAGTAACGGTAGCAATAACAGTAACAGTATTCAACACACAAAGTGTTGAATCTGTAACAGTAACA
GTAACAGTATTCGACACACAAAGTGTCAAATTGGTAACAGTAACAGTAGTCGCACATAAGTGCCT
AATCAGTAAT
Found at i:5210398 original size:51 final size:51
Alignment explanation
Indices: 5210289--5210407 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
5210279 TAATCAGTAA
* **
5210289 CGGTAGCAGTAACAGTAACTAAAACAGTATTCAACACACAAAGTGTTGAAT
1 CGGTAACAGTAACAGTAACTAAAACAGTATTCAACACACAAAGTGTCAAAT
** * * *
5210340 CTATAACAGTAACAGTAAC-AGTAATAGTATTCGACACACAAAGTGTCAAAT
1 CGGTAACAGTAACAGTAACTA-AAACAGTATTCAACACACAAAGTGTCAAAT
* *
5210391 CGGTAACAATAATAGTA
1 CGGTAACAGTAACAGTA
5210408 GTCGGCACAT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 1 0.02
51 54 0.98
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.23
Consensus pattern (51 bp):
CGGTAACAGTAACAGTAACTAAAACAGTATTCAACACACAAAGTGTCAAAT
Found at i:5210651 original size:40 final size:40
Alignment explanation
Indices: 5210607--5210693 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
5210597 AATTTATTAC
* * *
5210607 TTCAGTAAATTCACAGTTCAA-TGCAATACACATAACAATA
1 TTCAGTAAATTCACAATTAAACT-CAATACACAAAACAATA
* * *
5210647 TTCAGTAACTTCACAATTAAACTCAGTACTCAAAACAATA
1 TTCAGTAAATTCACAATTAAACTCAATACACAAAACAATA
5210687 TTCAGTA
1 TTCAGTA
5210694 TTCCATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.29
Consensus pattern (40 bp):
TTCAGTAAATTCACAATTAAACTCAATACACAAAACAATA
Found at i:5212348 original size:26 final size:24
Alignment explanation
Indices: 5212310--5212358 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
5212300 ACTAAATAAA
*
5212310 TTAATAATAAAATAATAAAATATTAT
1 TTAAAAATAAAAT--TAAAATATTAT
*
5212336 TTAAAAATCAAATTAAAATATTA
1 TTAAAAATAAAATTAAAATATTA
5212359 ATAAACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
26 11 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TTAAAAATAAAATTAAAATATTAT
Found at i:5223422 original size:23 final size:23
Alignment explanation
Indices: 5223360--5223428 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 23
5223350 TACTTAGACA
* *
5223360 ATTTGCCGTCAATTTATCATTTAC
1 ATTT-CCGTCAATTCATCCTTTAC
5223384 ATTTTTCC-TCAATTCATCCTTTAC
1 A--TTTCCGTCAATTCATCCTTTAC
5223408 ATTTCCGTCAATTCATCCTTT
1 ATTTCCGTCAATTCATCCTTT
5223429 CCCAATAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.12
23 14 0.35
24 16 0.40
25 2 0.05
26 3 0.08
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
ATTTCCGTCAATTCATCCTTTAC
Found at i:5231187 original size:16 final size:17
Alignment explanation
Indices: 5231151--5231188 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
5231141 TTTTTAAAAA
*
5231151 AAAATTATTTTAATTTT
1 AAAATTATGTTAATTTT
5231168 -AAATTATGTT-ATTTT
1 AAAATTATGTTAATTTT
5231183 AAAATT
1 AAAATT
5231189 TTTTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AAAATTATGTTAATTTT
Found at i:5237133 original size:20 final size:18
Alignment explanation
Indices: 5237109--5237154 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
5237099 AAAATGAATA
*
5237109 AATTAATAATTACTTAAAT
1 AATTAATAAATA-TTAAAT
5237128 ATATT-ATAAATATTAAA-
1 A-ATTAATAAATATTAAAT
5237145 AATTAATAAA
1 AATTAATAAA
5237155 AAAATTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 6 0.25
18 5 0.21
19 7 0.29
20 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTAATAAATATTAAAT
Found at i:5237975 original size:31 final size:31
Alignment explanation
Indices: 5237940--5238009 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
5237930 TTATCCAAGA
* * **
5237940 GTAAATACTCAAAAATTTGAGGGGTTAA-AGT
1 GTAAATA-TCAAAAAGTTGAAGGACTAATAGT
*
5237971 GTAAATATGAAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAAGTTGAAGGACTAATAGT
5238002 GTAAATAT
1 GTAAATAT
5238010 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (31 bp):
GTAAATATCAAAAAGTTGAAGGACTAATAGT
Found at i:5240154 original size:44 final size:44
Alignment explanation
Indices: 5240091--5240200 Score: 202
Period size: 44 Copynumber: 2.5 Consensus size: 44
5240081 TTTGAGTACT
*
5240091 TCTGATCAGTGACAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
5240135 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
5240179 TCTGATCAGTGATAAGTGATAA
1 TCTGATCAGTGACAAGTGATAA
5240201 ATGTGATCCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:5258722 original size:23 final size:23
Alignment explanation
Indices: 5258695--5258750 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
5258685 AATTTAGTAT
5258695 ATTGAACAAAATAAACTAATTAA
1 ATTGAACAAAATAAACTAATTAA
** *
5258718 ATTGAACATGA-AAACTGATTAA
1 ATTGAACAAAATAAACTAATTAA
*
5258740 ATCGAA-AAAAT
1 ATTGAACAAAAT
5258751 TTGGTTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 9 0.35
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (23 bp):
ATTGAACAAAATAAACTAATTAA
Found at i:5265386 original size:15 final size:16
Alignment explanation
Indices: 5265366--5265406 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
5265356 TTTCAATCGC
5265366 TTTGTTTCATTTC-AT
1 TTTGTTTCATTTCGAT
*
5265381 TTTGTTTTATTTCTGAT
1 TTTGTTTCATTTC-GAT
5265398 TTT-TTTCAT
1 TTTGTTTCAT
5265407 GTTAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (16 bp):
TTTGTTTCATTTCGAT
Found at i:5283653 original size:17 final size:18
Alignment explanation
Indices: 5283631--5283665 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5283621 ATTTTCATTT
5283631 TATTA-TTAAAAAAATTA
1 TATTATTTAAAAAAATTA
*
5283648 TATTATTTAATAAAATTA
1 TATTATTTAAAAAAATTA
5283666 AAAAAAACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTATTTAAAAAAATTA
Found at i:5285448 original size:34 final size:35
Alignment explanation
Indices: 5285390--5285456 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5285380 CAAACACCAG
5285390 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
5285425 AAAATATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
5285457 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5291079 original size:18 final size:19
Alignment explanation
Indices: 5291056--5291095 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5291046 ATCGTTTCTC
*
5291056 ATTATCCATTAAT-TAAAT
1 ATTATCAATTAATCTAAAT
*
5291074 ATTATCAATTCATCTAAAT
1 ATTATCAATTAATCTAAAT
5291093 ATT
1 ATT
5291096 TAATCTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATCAATTAATCTAAAT
Found at i:5301323 original size:60 final size:60
Alignment explanation
Indices: 5301221--5301339 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
5301211 ATATTAAACT
* * *
5301221 AAACACAATAATTTATAACTTAATCCTAAATTATTAATAAATTAATTTTAAAATAATTAC
1 AAACACAATAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
5301281 AAACACAA-AAGTTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAATAA-TTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
5301340 TAAAAAACAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 2 0.04
60 53 0.96
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (60 bp):
AAACACAATAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:5301476 original size:20 final size:23
Alignment explanation
Indices: 5301453--5301501 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
5301443 TTCTTTCTTA
5301453 TTCTTA-TTCT-TCTTTT-TTTC
1 TTCTTATTTCTCTCTTTTCTTTC
*
5301473 TTCTCATTTCTCTCTTTTCTTTC
1 TTCTTATTTCTCTCTTTTCTTTC
5301496 TCTCTT
1 T-TCTT
5301502 CCGGATGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 6 0.26
23 5 0.22
24 3 0.13
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (23 bp):
TTCTTATTTCTCTCTTTTCTTTC
Found at i:5301672 original size:27 final size:27
Alignment explanation
Indices: 5301628--5301731 Score: 154
Period size: 27 Copynumber: 3.9 Consensus size: 27
5301618 ACAGCACCAT
* * **
5301628 TCGCGCCTACCTGTCAGGAGCGATTAG
1 TCGCGCCTATCTGACAGGCTCGATTAG
*
5301655 TCGCGCCTATTTGACAGGCTCGATTAG
1 TCGCGCCTATCTGACAGGCTCGATTAG
*
5301682 TCACGCCTATCTGACAGGCTCGATTAG
1 TCGCGCCTATCTGACAGGCTCGATTAG
5301709 TCGCGCCTATCTGACAGGCTCGA
1 TCGCGCCTATCTGACAGGCTCGA
5301732 CCCATTTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.25
Consensus pattern (27 bp):
TCGCGCCTATCTGACAGGCTCGATTAG
Found at i:5305712 original size:5 final size:5
Alignment explanation
Indices: 5305702--5305732 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5305692 TTAAACTATA
*
5305702 CTCTC CTCTC CTCTC CCCTC CTCTC CTCTC C
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC C
5305733 AAATAAGGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (5 bp):
CTCTC
Found at i:5330870 original size:2 final size:2
Alignment explanation
Indices: 5330863--5330900 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5330853 GTTCAAAAGA
5330863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5330901 TAATTTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5340266 original size:36 final size:36
Alignment explanation
Indices: 5340226--5340299 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
5340216 AGAGACATAA
*
5340226 GTTGTCAATGCAGGATGTTTATGTCCTTGGATCATT
1 GTTGTCAATGCAGGATATTTATGTCCTTGGATCATT
*
5340262 GTTGTCAATGCAGGATATTTATGTCCTTGGTTCATT
1 GTTGTCAATGCAGGATATTTATGTCCTTGGATCATT
5340298 GT
1 GT
5340300 CTGGGTATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (36 bp):
GTTGTCAATGCAGGATATTTATGTCCTTGGATCATT
Found at i:5349281 original size:33 final size:35
Alignment explanation
Indices: 5349204--5349281 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 35
5349194 CAAAATAAAT
* *
5349204 AAAGAATAAATAAGAAAAGAAAGATAGATAGAAACT
1 AAAGAA-AAATAAGAAAAGAAAGATAGAAAGAAACA
* *
5349240 AAACAAAAAT-A-AAAAGAAAGA-ACGAAAGAAAGA
1 AAAGAAAAATAAGAAAAGAAAGATA-GAAAGAAACA
5349273 AAAGAAAAA
1 AAAGAAAAA
5349282 GGAAAGAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
32 1 0.03
33 25 0.69
34 1 0.03
35 4 0.11
36 5 0.14
ACGTcount: A:0.73, C:0.04, G:0.15, T:0.08
Consensus pattern (35 bp):
AAAGAAAAATAAGAAAAGAAAGATAGAAAGAAACA
Found at i:5349302 original size:20 final size:20
Alignment explanation
Indices: 5349251--5349291 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5349241 AACAAAAATA
*
5349251 AAAAGAAAGAACGAAAGAAAG
1 AAAAGAAA-AAGGAAAGAAAG
5349272 AAAAGAAAAAGGAAAGAAAG
1 AAAAGAAAAAGGAAAGAAAG
5349292 TAAGGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAGGAAAGAAAG
Found at i:5349812 original size:37 final size:38
Alignment explanation
Indices: 5349719--5349824 Score: 133
Period size: 37 Copynumber: 2.7 Consensus size: 38
5349709 TTCGACTTTG
5349719 AGTCGATGAGACACTGGGTGTCAATCTACTACTTCGGATTA
1 AGTCGATGAGACACTGGGTGTCAAT-T--TACTTCGGATTA
* * * *
5349760 ATTCGATGAGGCACTGGATGTCAATTTACTTCGG-TTT
1 AGTCGATGAGACACTGGGTGTCAATTTACTTCGGATTA
*
5349797 AGTCGATGAGACACTGGGTGTTAATTTA
1 AGTCGATGAGACACTGGGTGTCAATTTA
5349825 TTACTTCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
37 26 0.46
38 8 0.14
40 1 0.02
41 22 0.39
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (38 bp):
AGTCGATGAGACACTGGGTGTCAATTTACTTCGGATTA
Found at i:5355628 original size:24 final size:24
Alignment explanation
Indices: 5355453--5355640 Score: 91
Period size: 25 Copynumber: 7.7 Consensus size: 24
5355443 ACACACCATC
* * *
5355453 GCTCTTATGAGCGTCCCAATTCTTG
1 GCTCTCATGAGCTTCCCAATT-ATG
* *
5355478 GCTCTCATGAGCTTCCC-GTTATTTA
1 GCTCTCATGAGCTTCCCAATTA--TG
* * ** *
5355503 GCTCTTATGAGCATATCGATATATG
1 GCTCTCATGAGCTTCCCAAT-TATG
* * *
5355528 GCTCTCATAAGCTTCTCGATTAGTG
1 GCTCTCATGAGCTTCCCAATTA-TG
*
5355553 GCTCTTC-GGAGCTTCCCAA-TATTG
1 GCTC-TCATGAGCTTCCCAATTA-TG
* *
5355577 G-TTTGCATGAGCTTCCCAAATT-TA
1 GCTCT-CATGAGCTTCCC-AATTATG
*
5355601 GCTCTCTTGAGCTTCCCAATTATG
1 GCTCTCATGAGCTTCCCAATTATG
5355625 GCTCGT-ATGAGCTTCC
1 GCTC-TCATGAGCTTCC
5355641 GGATAATTGG
Statistics
Matches: 123, Mismatches: 27, Indels: 27
0.69 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 6 0.05
24 45 0.37
25 65 0.53
26 4 0.03
27 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (24 bp):
GCTCTCATGAGCTTCCCAATTATG
Found at i:5380914 original size:13 final size:13
Alignment explanation
Indices: 5380896--5380923 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5380886 TTGCTTAACT
5380896 CTTAGACCAAATA
1 CTTAGACCAAATA
5380909 CTTAGACCAAATA
1 CTTAGACCAAATA
5380922 CT
1 CT
5380924 GTATGAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (13 bp):
CTTAGACCAAATA
Found at i:5383796 original size:17 final size:17
Alignment explanation
Indices: 5383774--5383807 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5383764 GATTATATTA
5383774 TGTTAAA-ATAATCATAT
1 TGTTAAATATAAT-ATAT
5383791 TGTTAAATATAATATAT
1 TGTTAAATATAATATAT
5383808 ATTTCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
TGTTAAATATAATATAT
Found at i:5397482 original size:11 final size:11
Alignment explanation
Indices: 5397466--5397500 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5397456 AGCAGAAGAT
5397466 AAAAAAACAAA
1 AAAAAAACAAA
5397477 AAAAAAACAAA
1 AAAAAAACAAA
5397488 AAAACAAA-AAA
1 AAAA-AAACAAA
5397499 AA
1 AA
5397501 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.87
12 3 0.13
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:5399123 original size:14 final size:13
Alignment explanation
Indices: 5399083--5399133 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
5399073 TTAAGTATAT
*
5399083 TATTATTTTATTA
1 TATTATTATATTA
* *
5399096 TATT-GTAAATTA
1 TATTATTATATTA
5399108 TATTAATTATATTA
1 TATT-ATTATATTA
5399122 TATTATTATATT
1 TATTATTATATT
5399134 TCAAATAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:5407076 original size:18 final size:18
Alignment explanation
Indices: 5407055--5407099 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5407045 ACCAATATTT
* *
5407055 GGCCCAATACCATCCTTC
1 GGCCCAACACCATCATTC
5407073 GGCCCAACACCATCATTC
1 GGCCCAACACCATCATTC
5407091 GGCCCAACA
1 GGCCCAACA
5407100 GCACTATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.16
Consensus pattern (18 bp):
GGCCCAACACCATCATTC
Found at i:5407285 original size:18 final size:18
Alignment explanation
Indices: 5407262--5407306 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5407252 AGCAAGCCAC
*
5407262 TTTTGACCA-GAATTATAA
1 TTTTGACCAGGAA-CATAA
*
5407280 TTTTGACTAGGAACATAA
1 TTTTGACCAGGAACATAA
5407298 TTTTGACCA
1 TTTTGACCA
5407307 TTTTCAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTTGACCAGGAACATAA
Found at i:5410538 original size:12 final size:11
Alignment explanation
Indices: 5410516--5410559 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
5410506 CAAATGCCTC
5410516 TAAAATAATAA
1 TAAAATAATAA
5410527 TAAAATTAATAA
1 TAAAA-TAATAA
5410539 TAAAATAATAA
1 TAAAATAATAA
* *
5410550 CAACATAATA
1 TAAAATAATA
5410560 GTACCAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:5411021 original size:2 final size:2
Alignment explanation
Indices: 5411014--5411048 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5411004 CAATTTATCT
5411014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5411049 TAAGTTGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5416851 original size:11 final size:11
Alignment explanation
Indices: 5416835--5416861 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5416825 TAGAAATTAG
5416835 TTTGTGAAACT
1 TTTGTGAAACT
5416846 TTTGTGAAACT
1 TTTGTGAAACT
5416857 TTTGT
1 TTTGT
5416862 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:5418398 original size:91 final size:92
Alignment explanation
Indices: 5418273--5418449 Score: 295
Period size: 91 Copynumber: 1.9 Consensus size: 92
5418263 TTAATTTTAG
*
5418273 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTA-AATTA
1 TAAATTCATATAAGAACAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTATAA-TA
* *
5418337 TATTTAATATTAATTATTTTAAATTGTA
65 TATTTAATAATAATTATGTTAAATTGTA
*
5418365 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATTATTATTATAATAT
1 TAAATTCATATAAGAACAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTATAATAT
5418429 ATTTAATAATAATTATGTTAA
66 ATTTAATAATAATTATGTTAA
5418450 TTTATATTTG
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
91 62 0.77
92 18 0.22
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (92 bp):
TAAATTCATATAAGAACAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTATAATAT
ATTTAATAATAATTATGTTAAATTGTA
Found at i:5418400 original size:44 final size:44
Alignment explanation
Indices: 5418273--5418411 Score: 122
Period size: 47 Copynumber: 3.0 Consensus size: 44
5418263 TTAATTTTAG
*
5418273 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTA-GAAATTA
* * * ** *
5418319 TATA-TCATTATTAA-ATTATATTTAATATTAATTATTTTA-AATTGTA
1 TAAATTCA-TA-TAAGA--AAATTTATTATTAAGAATTTTAGAAAT-TA
5418365 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTA-GAAATTA
5418410 TA
1 TA
5418412 TATTATTATT
Statistics
Matches: 71, Mismatches: 13, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
44 18 0.25
45 13 0.18
46 17 0.24
47 22 0.31
48 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (44 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTAGAAATTA
Found at i:5418554 original size:15 final size:15
Alignment explanation
Indices: 5418520--5418561 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5418510 TTAAGAATTT
*
5418520 TATTAAATTAT-ATA
1 TATTTAATTATAATA
5418534 -ATTTAATTATAATA
1 TATTTAATTATAATA
*
5418548 TATTTAATAATAAT
1 TATTTAATTATAAT
5418562 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
15 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:5418699 original size:18 final size:17
Alignment explanation
Indices: 5418671--5418705 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5418661 ATTATTAAGA
*
5418671 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5418688 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5418706 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5418710 original size:155 final size:157
Alignment explanation
Indices: 5418504--5418818 Score: 553
Period size: 155 Copynumber: 2.0 Consensus size: 157
5418494 GTAAGAATAT
*
5418504 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
*
5418569 AAATATGATTAAATTATTTATTATTGATATTAACAATCTTATTAAAATTTAAATAACAATAAC-A
66 AAATATGATTAAATTATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
*
5418633 -AATAATTTACCAAAACAAATTTTTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
5418659 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
*
5418724 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
* *
5418789 TAATCATTTACCAAAATAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
5418816 TAA
1 TAA
5418819 GGGTATTCTA
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
155 124 0.82
156 1 0.01
157 26 0.17
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:5418955 original size:45 final size:44
Alignment explanation
Indices: 5418866--5418960 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 44
5418856 TTACACCTCT
*
5418866 ATTACATTCAACCAAACATAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACATAGGATTACTATTACACCTCTATTCC
* *
5418910 ATTACATTCAACCAAACAGT-TGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACA-TAGGA-TTACTATTACACCTCTATTCC
5418955 ATTACA
1 ATTACA
5418961 CCTCTAATCC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 20 0.43
45 26 0.57
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (44 bp):
ATTACATTCAACCAAACATAGGATTACTATTACACCTCTATTCC
Found at i:5418960 original size:16 final size:16
Alignment explanation
Indices: 5418939--5418992 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5418929 TTGATTTGCT
*
5418939 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
5418955 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* * *
5418971 AATACAACTTTAATCC
1 ATTACACCTCTAATCC
*
5418987 AATACA
1 ATTACA
5418993 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:5422908 original size:25 final size:25
Alignment explanation
Indices: 5422861--5422908 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5422851 TTTGGTGGTC
* * *
5422861 AAATCATGCTTTTAACGCCAAAAGG
1 AAATCACGCTTTTAACACAAAAAGG
*
5422886 AAATCACGTTTTTAACACAAAAA
1 AAATCACGCTTTTAACACAAAAA
5422909 CCCTCGTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (25 bp):
AAATCACGCTTTTAACACAAAAAGG
Found at i:5435272 original size:62 final size:62
Alignment explanation
Indices: 5435182--5435324 Score: 250
Period size: 62 Copynumber: 2.3 Consensus size: 62
5435172 ACGGTAAAAA
*
5435182 GGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTAAATT
1 GGATTTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTAAATT
* *
5435244 GGATTTAGCCTGGACGGGTGGTCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTAAATT
1 GGATTTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTAAATT
*
5435306 AGATTTAGCCCGGACGGGT
1 GGATTTAGCCCGGACGGGT
5435325 AATCTGAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 76 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (62 bp):
GGATTTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTAAATT
Found at i:5437364 original size:67 final size:67
Alignment explanation
Indices: 5437256--5437387 Score: 212
Period size: 67 Copynumber: 2.0 Consensus size: 67
5437246 TTTTCAATTC
*
5437256 AGAGAGCACACTCCCGCGAACCTCATTTATTACAGCAGGATTACTAG-TCTAGGCTAAATCCCCT
1 AGAGAGCACACTCCCGCGAACCTCATTTATTACAGCAGGATTACCAGTTC-AGGCTAAATCCCCT
5437320 GCA
65 GCA
* * *
5437323 AGAGAGCACACTCCCGCGAGCCTCATTTCTTACAGCGGGATTACCAGTTCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTATTACAGCAGGATTACCAGTTCAGGCTAAATCCCCTG
5437388 TAATATAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 58 0.97
68 2 0.03
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTATTACAGCAGGATTACCAGTTCAGGCTAAATCCCCTG
CA
Found at i:5439741 original size:2 final size:2
Alignment explanation
Indices: 5439734--5439807 Score: 121
Period size: 2 Copynumber: 37.0 Consensus size: 2
5439724 GAGGAGGAAG
*
5439734 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5439776 AT AT AT AA AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5439808 GGATATTCAG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5443264 original size:17 final size:17
Alignment explanation
Indices: 5443227--5443274 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
5443217 GAATTTAGAA
*
5443227 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
5443243 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
5443260 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
5443275 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:5444569 original size:46 final size:46
Alignment explanation
Indices: 5444498--5444636 Score: 183
Period size: 46 Copynumber: 3.0 Consensus size: 46
5444488 CTTGGCAAAG
* *
5444498 TGTGAAACA-TAGGTATGGTATTTCAGCGAAGAAAACCATACTGAGT
1 TGTGAAA-AGTAGATATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
5444544 TGTGAAAAGTAGATATGTTGTTTCAGTGAAGAAAACCATA-TAGAGT
1 TGTGAAAAGTAGATATGGTATTTCAGTGAAGAAAACCATACT-GAGT
* * *
5444590 TGTGAATAGTAGGTATGGTATTTCTGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGATATGGTATTTCAGTGAAGAAAACCATACTGAGT
5444636 T
1 T
5444637 ATAGCAATGT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
45 2 0.02
46 78 0.96
47 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGATATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:5464947 original size:21 final size:22
Alignment explanation
Indices: 5464901--5464947 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
5464891 TCAAGCAAAA
* *
5464901 AAAATCCTAAAAAGGAATAATG
1 AAAATCCTAAAAAAGAAAAATG
*
5464923 -AAATCC-AAAAAATAAAAATG
1 AAAATCCTAAAAAAGAAAAATG
5464943 AAAAT
1 AAAAT
5464948 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAATCCTAAAAAAGAAAAATG
Found at i:5465332 original size:25 final size:25
Alignment explanation
Indices: 5465287--5465343 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
5465277 TTTCTTTTTC
* *
5465287 CCATTTTATATTTTTAATATTATAT
1 CCATTTTATATTATTAATATTACAT
*
5465312 CCATTTTAT-TATATTATTATTACAT
1 CCATTTTATAT-TATTAATATTACAT
*
5465337 ACATTTT
1 CCATTTT
5465344 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (25 bp):
CCATTTTATATTATTAATATTACAT
Found at i:5465447 original size:15 final size:16
Alignment explanation
Indices: 5465416--5465449 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5465406 ACTAGTAATT
5465416 TTTATTTATCGTAAAA
1 TTTATTTATCGTAAAA
*
5465432 TTTATTTAT-TTAAAA
1 TTTATTTATCGTAAAA
5465447 TTT
1 TTT
5465450 TAAAGTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTATTTATCGTAAAA
Found at i:5467683 original size:7 final size:7
Alignment explanation
Indices: 5467671--5467697 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5467661 TCATTAATTT
5467671 AAATATA
1 AAATATA
5467678 AAATATA
1 AAATATA
5467685 AAATATA
1 AAATATA
5467692 AAATAT
1 AAATAT
5467698 TTATTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATATA
Found at i:5472221 original size:101 final size:101
Alignment explanation
Indices: 5472033--5472439 Score: 584
Period size: 101 Copynumber: 4.0 Consensus size: 101
5472023 AATTTATCCA
* * * *
5472033 TTACATTCGTAGTGCCATAACCCAGTTATGATCTTATTATCAAAATGTCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAGCTATGGT
*
5472098 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGTCATGGTCCAACCATGGTC
*
5472134 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATG-CTATAGCCCAGCTATGG
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTC-ATAGCCCAGCTATGG
* *
5472198 TCTTACATATAAACACTGTCATGGTCTAACCATGGTT
65 TCTTACATATAAACACTGTCATGGTCCAACCATGGTC
* * * * * *
5472235 TTAAGTTCACAGTTCCATAACCCAGTTATGGTCTTATCATCAGAATGCCAAAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAGCTATGGT
*
5472300 CTTACATATAAACACTGTCATAGTCCAACCATGGTC
66 CTTACATATAAACACTGTCATGGTCCAACCATGGTC
* * * *
5472336 TTACGTTCATAGTGCTATAACTCAGTTATGGTCTTTTCATTAAAATGTCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAGCTATGGT
* * *
5472401 CTTACATTTAAACA-TTTCCATGGTCCAATCATGGTC
66 CTTACATATAAACACTGT-CATGGTCCAACCATGGTC
5472437 TTA
1 TTA
5472440 TCCATCAATT
Statistics
Matches: 274, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
100 3 0.01
101 270 0.99
102 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAGCTATGGT
CTTACATATAAACACTGTCATGGTCCAACCATGGTC
Found at i:5472412 original size:33 final size:33
Alignment explanation
Indices: 5472074--5472412 Score: 125
Period size: 33 Copynumber: 10.1 Consensus size: 33
5472064 TCTTATTATC
*
5472074 AAAATGTCATAGCCCAGCTATGGTCTTACATAT
1 AAAATGTCATAGCCCAGCTATGGTCTTACATTT
* * * * * * *
5472107 AAACACTGCCATGGTCCAACCATGGTCTTACGTTC
1 AAA-A-TGTCATAGCCCAGCTATGGTCTTACATTT
* * * * * *
5472142 ATAGTGCCATAACCCAGTTATGGTCTTATCA-TC
1 AAAATGTCATAGCCCAGCTATGGTCTTA-CATTT
* *
5472175 AGAATG-CTATAGCCCAGCTATGGTCTTACATAT
1 AAAATGTC-ATAGCCCAGCTATGGTCTTACATTT
* * * * * * *
5472208 AAACACTGTCATGGTCTAACCATGGTTTTA-AGTT
1 AAA-A-TGTCATAGCCCAGCTATGGTCTTACATTT
* * * * *
5472242 CACA-GTTCCATAACCCAGTTATGGTCTTATCA-TC
1 AAAATG-T-CATAGCCCAGCTATGGTCTTA-CATTT
* * * *
5472276 AGAATGCCAAAGCCCAGCTATGGTCTTACATAT
1 AAAATGTCATAGCCCAGCTATGGTCTTACATTT
* * * * *
5472309 AAACACTGTCATAGTCCAACCATGGTCTTACGTTC
1 AAA-A-TGTCATAGCCCAGCTATGGTCTTACATTT
* * * * * *
5472344 ATAGTG-CTATAACTCAGTTATGGTCTTTTCA-TT
1 AAAATGTC-ATAGCCCAGCTATGGTC-TTACATTT
5472377 AAAATGTCATAGCCCAGCTATGGTCTTACATTT
1 AAAATGTCATAGCCCAGCTATGGTCTTACATTT
5472410 AAA
1 AAA
5472413 CATTTCCATG
Statistics
Matches: 208, Mismatches: 78, Indels: 40
0.64 0.24 0.12
Matches are distributed among these distances:
31 1 0.00
32 11 0.05
33 118 0.57
34 13 0.06
35 64 0.31
36 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (33 bp):
AAAATGTCATAGCCCAGCTATGGTCTTACATTT
Found at i:5475869 original size:25 final size:24
Alignment explanation
Indices: 5475826--5475878 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
5475816 AAATTCAAAC
5475826 GAGCCATATCAGGAAGCTCATAAA
1 GAGCCATATCAGGAAGCTCATAAA
* *
5475850 GAGCCTATATCGGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
5475875 GAGC
1 GAGC
5475879 TGCGGTCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:5476226 original size:23 final size:22
Alignment explanation
Indices: 5476180--5476259 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
5476170 GACATTTATA
*
5476180 CAATTCACACATATACAACATT
1 CAATTCAAACATATACAACATT
*
5476202 CAATTCGAACATATACGAACATT
1 CAATTCAAACATATAC-AACATT
5476225 CAATTCAAACATATACAACATT
1 CAATTCAAACATATACAACATT
5476247 CAATTCAAACATA
1 CAATTCAAACATA
5476260 ATTTAGTTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 33 0.61
23 21 0.39
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (22 bp):
CAATTCAAACATATACAACATT
Found at i:5479526 original size:31 final size:29
Alignment explanation
Indices: 5479462--5479544 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
5479452 TATAATCCAT
* *
5479462 ATTTTTATAAT-TTTTAGAGAATTAAATTAA
1 ATTTTTATTATATTTTA-A-AATTAAAATAA
5479492 ATTTTTATTATATTTTAAAATCTAAAATATA
1 ATTTTTATTATATTTTAAAAT-TAAAATA-A
*
5479523 A-TTTTATTATTAATTTAAAATT
1 ATTTTTATTA-TATTTTAAAATT
5479545 TTATAAAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 3 0.07
30 26 0.57
31 17 0.37
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (29 bp):
ATTTTTATTATATTTTAAAATTAAAATAA
Found at i:5493244 original size:30 final size:30
Alignment explanation
Indices: 5493208--5493270 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
5493198 ACTTAACAAG
5493208 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
5493238 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
5493268 CAA
1 CAA
5493271 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:5495621 original size:19 final size:20
Alignment explanation
Indices: 5495577--5495621 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5495567 TACAATTTTG
5495577 TTTTAATAATAAAATTTTAA
1 TTTTAATAATAAAATTTTAA
** *
5495597 CATTAAT-ATTAAATTTTAA
1 TTTTAATAATAAAATTTTAA
5495616 TTTTAA
1 TTTTAA
5495622 ATGATTTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAATAATAAAATTTTAA
Found at i:5501967 original size:20 final size:20
Alignment explanation
Indices: 5501942--5501981 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5501932 AGTAACAATC
5501942 ACTCACTGGAGACACAGACT
1 ACTCACTGGAGACACAGACT
5501962 ACTCACTGGAGACACAGACT
1 ACTCACTGGAGACACAGACT
5501982 GTGATGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (20 bp):
ACTCACTGGAGACACAGACT
Found at i:5517784 original size:26 final size:25
Alignment explanation
Indices: 5517755--5517817 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
5517745 TTTGAATTTT
*
5517755 TTCGAATC-AAGTTGAGTGAAATTAAA
1 TTCGAATCGAA-TTGAGT-AAATGAAA
*
5517781 TTCGAGTCGAATTGAGTAAATGAAA
1 TTCGAATCGAATTGAGTAAATGAAA
* *
5517806 TTTGAGTCGAAT
1 TTCGAATCGAAT
5517818 CGAATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.55
26 13 0.39
27 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (25 bp):
TTCGAATCGAATTGAGTAAATGAAA
Found at i:5517801 original size:25 final size:26
Alignment explanation
Indices: 5517766--5517817 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
5517756 TCGAATCAAG
*
5517766 TTGAGTGAAATTAAATTCGAGTCGAA
1 TTGAGTGAAATGAAATTCGAGTCGAA
*
5517792 TTGAGT-AAATGAAATTTGAGTCGAA
1 TTGAGTGAAATGAAATTCGAGTCGAA
5517817 T
1 T
5517818 CGAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (26 bp):
TTGAGTGAAATGAAATTCGAGTCGAA
Found at i:5519598 original size:29 final size:29
Alignment explanation
Indices: 5519565--5519634 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
5519555 ATGCTGTACC
*
5519565 AAATAATAATAATTCATATTT-GTCCTCTT
1 AAATAATAATAATTC-TATTTAATCCTCTT
* * *
5519594 AAATATAAAAAAATTCTATTTAATCCTTTT
1 AAATA-ATAATAATTCTATTTAATCCTCTT
5519624 AAA-AATAATAA
1 AAATAATAATAA
5519635 AATTATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.15
29 11 0.33
30 17 0.52
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (29 bp):
AAATAATAATAATTCTATTTAATCCTCTT
Found at i:5521225 original size:12 final size:12
Alignment explanation
Indices: 5521210--5521234 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5521200 TGTTAAATTA
5521210 TAATTTAATTTT
1 TAATTTAATTTT
5521222 TAATTTAATTTT
1 TAATTTAATTTT
5521234 T
1 T
5521235 TGTATATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTAATTTT
Found at i:5522204 original size:26 final size:26
Alignment explanation
Indices: 5522157--5522209 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
5522147 TTGAAAGGAA
* *
5522157 ATTTTAAAAATGTTCTAAATATATTTT
1 ATTTAAAAAATATTCTAAATAT-TTTT
*
5522184 ATTTAAAAAATATTC-ATATATTTTT
1 ATTTAAAAAATATTCTAAATATTTTT
5522209 A
1 A
5522210 GTAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 5 0.22
27 13 0.57
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTAAAAAATATTCTAAATATTTTT
Found at i:5523861 original size:13 final size:13
Alignment explanation
Indices: 5523843--5523885 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
5523833 TCATTTTATT
5523843 AAAATAAATATAA
1 AAAATAAATATAA
*
5523856 AAAATAAAAAT-A
1 AAAATAAATATAA
*
5523868 AAAAT-TATATAA
1 AAAATAAATATAA
5523880 AAAATA
1 AAAATA
5523886 GATAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 3 0.12
12 12 0.48
13 10 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:5527678 original size:2 final size:2
Alignment explanation
Indices: 5527673--5527700 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5527663 GTGTGGAATA
5527673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5527701 TGTCTTAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5552351 original size:13 final size:13
Alignment explanation
Indices: 5552333--5552370 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5552323 TTCTTCATTA
5552333 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
5552346 CTTTTGAGAATTG
1 CTTTTGAAAAGTG
5552359 CTTTTGAAAAGT
1 CTTTTGAAAAGT
5552371 TTGGTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:5554040 original size:2 final size:2
Alignment explanation
Indices: 5554033--5554077 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
5554023 TATTTTATTT
* *
5554033 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5554075 TA T
1 TA T
5554078 TTTTGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5565289 original size:115 final size:115
Alignment explanation
Indices: 5564945--5565900 Score: 1048
Period size: 115 Copynumber: 8.4 Consensus size: 115
5564935 TTACCATCCT
* * * *
5564945 GCGCCGCAAAATCTC-AAGACCAAAACGCATCGTTTTGGTTTTGATGTATACTAGAATTAGTGGC
1 GCGCCGCAAAATATCTTA-ACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * *
5565009 GATT-ATGAGAAAACGCCGCTAAAGCA-AGTATTAGCGGCGCATTGTG-GAAA
65 G-TTCAAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAG-AA
* * * * * *
5565059 GCGCCTCAAAA-ATCTTAACGAAAACGCATCGTTTTGGTCTCGCTGTATATTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * *
5565123 CTT-ACGA-AAAACGCCGCTAAAGCATACTATTAGCGGCGCATTTTGAGAA
66 -TTCAAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* ** *
5565172 GCGCCGCAAAATATATTAACCAAAACGCAGCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * *
5565237 TTCAAGAGAAAACGTCGCTAAAGCATAGTATTAGTGGCGCTTTTTTAGAA
66 TTCAAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* * * * *
5565287 GCGCCGCAAAATATCCTAACCAAAACGCACCGTTTTGGTCTTGGTGTATATTACAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * * *
5565352 CTT-ACGGGAAAACGCCGCTAAAGCATAATATTAGAGGCG-TTTTGTGAGAA
66 -TTCAAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTT-TGAGAA
* * * *
5565402 GCGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTATAATTAGTAGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * * * *
5565466 --CAAAGGGAAAACGCCGCTAACGCATACTATTAGCGGCGCGTTTGGAGAA
66 TTC-AAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* * *
5565515 GCGCCGCAAAATTTCTTAACCAAAACGTAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* *** *
5565580 --CATACTG-GAAAACGCCGCTAAATCATAGTATTAGCGGCGCTTTGCAAAAA
66 TTCA-A--GAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* ** * *
5565630 GCGCCGCAAAATATGC-TCACCAAAACGCAAAG-TTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 GCGCCGCAAAATAT-CTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * * * * * *
5565693 -TCTTATGGGAACACGCCGCTAAAGCATACTATTAGCGGCACATTTTGAGAA
65 GT-TCAAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* ** * *
5565744 GCGCCGCAAAATATATTAACCAAAACGCAGCGTTTAAGTATTGATGTATACTGGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
*
5565809 TTCACGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
66 TTCAAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* * *
5565859 GCGCCGGAAAATATCTTAACCAAAACGCAGAGTTGTGGTCTT
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTT
5565901 AACCATGCAT
Statistics
Matches: 706, Mismatches: 113, Indels: 45
0.82 0.13 0.05
Matches are distributed among these distances:
112 17 0.02
113 149 0.21
114 214 0.30
115 320 0.45
116 6 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (115 bp):
GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
TTCAAGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
Found at i:5565452 original size:229 final size:228
Alignment explanation
Indices: 5564945--5565900 Score: 1117
Period size: 229 Copynumber: 4.2 Consensus size: 228
5564935 TTACCATCCT
* * ** * *
5564945 GCGCCGCAAAATCTC-AAGACCAAAACGCATCGTTTTGGTTTTGATGTATACTAGAATTAGTGGC
1 GCGCCGCAAAATATCTTA-ACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTGGC
* * *
5565009 GATT-ATGAGAAAACGCCGCTAAAGCA-AGTATTAGCGGCGCATTGTGGA-AAGCGCCTCAAAA-
64 G-TTCAAGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TT-TGGAGAAGCGCCGCAAAAT
* * * * * *
5565070 ATCTTAACGAAAACGCATCGTTTTGGTCTCGCTGTATATTAGAATTAGTGGCGCTTAC-GAAAAA
126 ATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAAA
* *
5565134 CGCCGCTAAAGCATACTATTAGCGGCGCATTTTGAGAA
191 CGCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* * * * *
5565172 GCGCCGCAAAATATATTAACCAAAACGCAGCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAATTAGTGGCG
* * * **
5565237 TTCAAGAGAAAACGTCGCTAAAGCATAGTATTAGTGGCGCTTTTTTAGAAGCGCCGCAAAATATC
65 TTCAAGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTGGAGAAGCGCCGCAAAATATC
* * * * *
5565302 CTAACCAAAACGCACCGTTTTGGTCTTGGTGTATATTACAATTAGTGGCGCTTACGGGAAAACGC
129 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAAACGC
* *
5565367 CGCTAAAGCATAATATTAGAGGCG-TTTTGTGAGAA
194 CGCTAAAGCATAGTATTAGCGGCGCTTTT-TGAGAA
* *
5565402 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTATAATTAGTAGCG-
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGT
* * *
5565466 -CAAAGGGAAAACGCCGCTAACGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAAATTTC
66 TC-AAGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTGGAGAAGCGCCGCAAAATATC
* * * *
5565530 TTAACCAAAACGTAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGCATACTGGAAAACGC
129 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAAACGC
* *** *
5565595 CGCTAAATCATAGTATTAGCGGCGCTTTGCAAAAA
194 CGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
* * *
5565630 GCGCCGCAAAATATGC-TCACCAAAACGCAAAGTTTGGTCTTGAGGTATATTAGAATTAGTGGC-
1 GCGCCGCAAAATAT-CTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCG
* * * * * *
5565693 TCTTATGGGAACACGCCGCTAAAGCATACTATTAGCGGCACATTTTGAGAAGCGCCGCAAAATAT
65 T-TCAAGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTGGAGAAGCGCCGCAAAATAT
* ** * * *
5565758 ATTAACCAAAACGCAGCGTTTAAGTATTGATGTATACTGGAATTAGTGGCG-TTCACGAGAAAAC
128 CTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTT-ACGGGAAAAC
5565822 GCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
192 GCCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
*
5565859 GCGCCGGAAAATATCTTAACCAAAACGCAGAGTTGTGGTCTT
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTT-TGGTCTT
5565901 AACCATGCAT
Statistics
Matches: 626, Mismatches: 86, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
226 5 0.01
227 75 0.12
228 220 0.35
229 250 0.40
230 76 0.12
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (228 bp):
GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGT
TCAAGAGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTGGAGAAGCGCCGCAAAATATCTT
AACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAAACGCCG
CTAAAGCATAGTATTAGCGGCGCTTTTTGAGAA
Found at i:5565757 original size:457 final size:454
Alignment explanation
Indices: 5564945--5565900 Score: 1181
Period size: 457 Copynumber: 2.1 Consensus size: 454
5564935 TTACCATCCT
* * ** * * *
5564945 GCGCCGCAAAATCTC-AAGACCAAAACGCATCGTTTTGGTTTTGATGTATACTAGAATTAGTGGC
1 GCGCCGCAAAATATCTTA-ACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTAGC
* * *
5565009 GATTATGAGAAAACGCCGCTAAAGCAAGTATTAGCGGCGCATTGTGGAAAGCGCCTCAAAAATCT
64 GA-TAAGAGAAAACGCCGCTAAAGCAACTATTAGCGGCGCATTGTGGAAAGCGCCGCAAAAATCT
* * * * *
5565074 TAACGAAAACGCATCGTTTTGGTCTCGCTGTATATTAGAATTAGTGGCGCTTACGAAAAACGCCG
128 TAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAGAATTAGTGGCGCATACGAAAAACGCCG
* * **
5565139 CTAAAGCATACTATTAGCGGCGCATTTTGAGAAGCGCCGCAAAATATATTAACCAAAACGCAGCG
193 CTAAAGCATACTATTAGCGGCGCA-TTTGAAAAGCGCCGCAAAATATACTAACCAAAACGCAAAG
* * * *
5565204 TTTAAGTCTTGATGTATACTGGAATTAGTGGCGTTCAAGAGAAAACGTCGCTAAAGCATAGTATT
257 TTTAAGTCTTGAGGTATACTAGAATTAGTGGCGTTCAAGAGAAAACGCCGCTAAAGCATACTATT
* * * * * ** * *
5565269 AGTGGCGCTTTTTTAGAAGCGCCGCAAAATATCCTAACCAAAACGCACCGTTTTGGTCTTGGTGT
322 AGCGGCACATTTTGAGAAGCGCCGCAAAATATACTAACCAAAACGCACCGTTTAAGTATTGATGT
* *
5565334 ATATTACAATTAGTGGCGCTT-ACGGGAAAACGCCGCTAAAGCATAATATTAGAGGCG-TTTTGT
387 ATACTACAATTAGTGGCG-TTCACGAGAAAACGCCGCTAAAGCATAATATTAGAGGCGCTTTT-T
5565397 GAGAA
450 GAGAA
*
5565402 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTATAATTAGTAGCGC
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTAGCG-
* * * *
5565467 A-AAGGGAAAACGCCGCTAACGCATACTATTAGCGGCGCGTT-TGGAGAAGCGCCGCAAAATTTC
65 ATAAGAGAAAACGCCGCTAAAGCA-ACTATTAGCGGCGCATTGTGGA-AAGCGCCGCAAAA-ATC
* * * *
5565530 TTAACCAAAACGTAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGCATACTGGAAAACGC
127 TTAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAGAATTAGTGGCGCATAC-GAAAAACGC
* * * *
5565595 CGCTAAATCATAGTATTAGCGGCGC-TTTGCAAAAAGCGCCGCAAAATATGCTCACCAAAACGCA
191 CGCTAAAGCATACTATTAGCGGCGCATTTG--AAAAGCGCCGCAAAATATACTAACCAAAACGCA
* * * * * *
5565659 AAGTTT-GGTCTTGAGGTATATTAGAATTAGTGGC-TCTTATGGGAACACGCCGCTAAAGCATAC
254 AAGTTTAAGTCTTGAGGTATACTAGAATTAGTGGCGT-TCAAGAGAAAACGCCGCTAAAGCATAC
* *
5565722 TATTAGCGGCACATTTTGAGAAGCGCCGCAAAATATATTAACCAAAACGCAGCGTTTAAGTATTG
318 TATTAGCGGCACATTTTGAGAAGCGCCGCAAAATATACTAACCAAAACGCACCGTTTAAGTATTG
** * *
5565787 ATGTATACTGGAATTAGTGGCGTTCACGAGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTT
383 ATGTATACTACAATTAGTGGCGTTCACGAGAAAACGCCGCTAAAGCATAATATTAGAGGCGCTTT
5565852 TTGAGAA
448 TTGAGAA
*
5565859 GCGCCGGAAAATATCTTAACCAAAACGCAGAGTTGTGGTCTT
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTT-TGGTCTT
5565901 AACCATGCAT
Statistics
Matches: 427, Mismatches: 60, Indels: 23
0.84 0.12 0.05
Matches are distributed among these distances:
455 23 0.05
456 62 0.15
457 266 0.62
458 76 0.18
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (454 bp):
GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTAGCGA
TAAGAGAAAACGCCGCTAAAGCAACTATTAGCGGCGCATTGTGGAAAGCGCCGCAAAAATCTTAA
CCAAAACGCAGCGTTTTGGTCTCGATGTATACTAGAATTAGTGGCGCATACGAAAAACGCCGCTA
AAGCATACTATTAGCGGCGCATTTGAAAAGCGCCGCAAAATATACTAACCAAAACGCAAAGTTTA
AGTCTTGAGGTATACTAGAATTAGTGGCGTTCAAGAGAAAACGCCGCTAAAGCATACTATTAGCG
GCACATTTTGAGAAGCGCCGCAAAATATACTAACCAAAACGCACCGTTTAAGTATTGATGTATAC
TACAATTAGTGGCGTTCACGAGAAAACGCCGCTAAAGCATAATATTAGAGGCGCTTTTTGAGAA
Found at i:5566243 original size:14 final size:14
Alignment explanation
Indices: 5566211--5566253 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5566201 TGGTTTTTTA
*
5566211 GTTTAAGAGTTTGGG
1 GTTTAAGA-TTTAGG
5566226 GTTTAAGATTTAGG
1 GTTTAAGATTTAGG
**
5566240 GTTTGGGATTTAGG
1 GTTTAAGATTTAGG
5566254 CCGCTGTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (14 bp):
GTTTAAGATTTAGG
Found at i:5570655 original size:8 final size:8
Alignment explanation
Indices: 5570642--5570667 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5570632 GATATGTGGC
5570642 AAAAAATA
1 AAAAAATA
5570650 AAAAAATA
1 AAAAAATA
5570658 AAAAAATA
1 AAAAAATA
5570666 AA
1 AA
5570668 TTAAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:5570811 original size:9 final size:9
Alignment explanation
Indices: 5570782--5570960 Score: 70
Period size: 9 Copynumber: 19.6 Consensus size: 9
5570772 CTTTATAAAA
5570782 TTTTAT-AT
1 TTTTATAAT
*
5570790 TTCTAT-AT
1 TTTTATAAT
5570798 ATTTTATAAT
1 -TTTTATAAT
5570808 TTTTAATAAT
1 TTTT-ATAAT
*
5570818 ATTTTACGAA-
1 -TTTTA-TAAT
*
5570828 TTTTATAAAA
1 TTTTAT-AAT
5570838 TTTTATAAT
1 TTTTATAAT
5570847 TTTTATATAT
1 TTTTATA-AT
*
5570857 ATTTTTTACGAT
1 -TTTTATA--AT
*
5570869 TTATATATAT
1 TTTTATA-AT
5570879 TTTTAT-AT
1 TTTTATAAT
5570887 TTTTAT-AT
1 TTTTATAAT
5570895 TTTTA-AA-
1 TTTTATAAT
* *
5570902 ATTT-GAAT
1 TTTTATAAT
*
5570910 TTTTATTAAA
1 TTTTA-TAAT
* *
5570920 ATTTATAGT
1 TTTTATAAT
*
5570929 TTTTATTGAT
1 TTTTA-TAAT
* *
5570939 TTTAAT-TT
1 TTTTATAAT
5570947 TTTTATAAT
1 TTTTATAAT
5570956 TTTTA
1 TTTTA
5570961 ATAAAAGCAG
Statistics
Matches: 129, Mismatches: 25, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
7 5 0.04
8 32 0.25
9 38 0.29
10 35 0.27
11 17 0.13
12 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:5570842 original size:39 final size:41
Alignment explanation
Indices: 5570798--5570894 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 41
5570788 ATTTCTATAT
5570798 ATTTTATAATTTTTA-ATA-ATATTTTACGAATTT-TATAAA
1 ATTTTATAATTTTTATATATATATTTTACG-ATTTATATAAA
* *
5570837 ATTTTATAATTTTTATATATATTTTTTACGATTTATATATA
1 ATTTTATAATTTTTATATATATATTTTACGATTTATATAAA
*
5570878 TTTTTAT-ATTTTTATAT
1 ATTTTATAATTTTTATAT
5570895 TTTTAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
39 15 0.29
40 17 0.33
41 20 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (41 bp):
ATTTTATAATTTTTATATATATATTTTACGATTTATATAAA
Found at i:5570887 original size:8 final size:8
Alignment explanation
Indices: 5570874--5570899 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5570864 ACGATTTATA
5570874 TATATTTT
1 TATATTTT
5570882 TATATTTT
1 TATATTTT
5570890 TATATTTT
1 TATATTTT
5570898 TA
1 TA
5570900 AAATTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TATATTTT
Found at i:5570891 original size:20 final size:20
Alignment explanation
Indices: 5570782--5570894 Score: 78
Period size: 20 Copynumber: 5.8 Consensus size: 20
5570772 CTTTATAAAA
*
5570782 TTTTATATTTCTATATAT-T
1 TTTTATATTTTTATATATAT
*
5570801 TTATA-ATTTTTA-ATA-AT
1 TTTTATATTTTTATATATAT
* * *
5570818 ATTTTACGAATTTTATA-A-AA
1 -TTTTA-TATTTTTATATATAT
5570838 TTTTATAATTTTTATATATAT
1 TTTTAT-ATTTTTATATATAT
**
5570859 TTTT-TACGATTTATATATAT
1 TTTTATA-TTTTTATATATAT
5570879 TTTTATATTTTTATAT
1 TTTTATATTTTTATAT
5570895 TTTTAAAATT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
17 4 0.06
18 10 0.14
19 18 0.25
20 32 0.44
21 8 0.11
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTATATTTTTATATATAT
Found at i:5570959 original size:18 final size:18
Alignment explanation
Indices: 5570838--5570962 Score: 55
Period size: 16 Copynumber: 6.9 Consensus size: 18
5570828 TTTTATAAAA
5570838 TTTTATAATTTTTATATATAT
1 TTTTATAATTTTTA-AT-T-T
* *
5570859 TTTT-TACGATTTATATATAT
1 TTTTATA--ATTTTTA-ATTT
*
5570879 TTTTAT-ATTTTT-ATAT
1 TTTTATAATTTTTAATTT
* *
5570895 TTTTA-AAATTTGAATTT
1 TTTTATAATTTTTAATTT
* * *
5570912 TTATTAAAATTTATAGTTT
1 TT-TTATAATTTTTAATTT
* *
5570931 TTAT-TGA-TTTTAATTT
1 TTTTATAATTTTTAATTT
5570947 TTTTATAATTTTTAAT
1 TTTTATAATTTTTAAT
5570963 AAAAGCAGGG
Statistics
Matches: 78, Mismatches: 17, Indels: 21
0.67 0.15 0.18
Matches are distributed among these distances:
16 23 0.29
17 8 0.10
18 16 0.21
19 10 0.13
20 7 0.09
21 5 0.06
22 9 0.12
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTATAATTTTTAATTT
Found at i:5571122 original size:88 final size:88
Alignment explanation
Indices: 5570969--5571143 Score: 221
Period size: 88 Copynumber: 2.0 Consensus size: 88
5570959 TAATAAAAGC
* * *
5570969 AGGGGTTTAATTACTTTTATTTGAAAAAGTTTCAGAGTCTTTTTATGCATTTTGAAAGTTCAAGT
1 AGGGATTTAATTACTTTTATTTGAAAAAGTTTAAGAGTCTTTTTATGAATTTTGAAAGTTCAAGT
* *
5571034 ACCCAATTAAGTG-AAAAAAAAT
66 ACCCAAATAAATGTAAAAAAAAT
* * *
5571056 AGGGATTTAATTA-TTTTTTTTG-AAAAGATTTAAGAGACTTTTTTTATGAATTTTGAAAGTTTA
1 AGGGATTTAATTACTTTTATTTGAAAAAG-TTTAAGAG--TCTTTTTATGAATTTTGAAAGTTCA
*
5571119 AGTACCTAAATAAATGTAAAAAAAA
63 AGTACCCAAATAAATGTAAAAAAAA
5571144 GACTTAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
85 5 0.07
86 15 0.20
87 12 0.16
88 35 0.47
89 8 0.11
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (88 bp):
AGGGATTTAATTACTTTTATTTGAAAAAGTTTAAGAGTCTTTTTATGAATTTTGAAAGTTCAAGT
ACCCAAATAAATGTAAAAAAAAT
Found at i:5571973 original size:12 final size:12
Alignment explanation
Indices: 5571966--5571992 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5571956 TCTTTTTTCT
5571966 TTTATTTTTTAG
1 TTTATTTTTTAG
5571978 TTTATTTTTTAG
1 TTTATTTTTTAG
5571990 TTT
1 TTT
5571993 TTGTTTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTATTTTTTAG
Found at i:5576548 original size:21 final size:21
Alignment explanation
Indices: 5576524--5576587 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
5576514 CATTATATTA
5576524 AGCATAAAGTTCTGTCCCCAT
1 AGCATAAAGTTCTGTCCCCAT
* * *
5576545 AGCAT-TAGTTAACTGT--CAAA
1 AGCATAAAGTT--CTGTCCCCAT
5576565 AGCATAAAGTTCTGTCCCCAT
1 AGCATAAAGTTCTGTCCCCAT
5576586 AG
1 AG
5576588 TACTTTGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
19 4 0.12
20 11 0.34
21 13 0.41
22 4 0.12
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (21 bp):
AGCATAAAGTTCTGTCCCCAT
Found at i:5580071 original size:294 final size:297
Alignment explanation
Indices: 5579647--5580201 Score: 758
Period size: 295 Copynumber: 1.9 Consensus size: 297
5579637 AGAAAAACGC
* * * *
5579647 TTTATTGTTCTTGCATCATTGCTTTGTGCTCCATTGCTGCATTCTAGGATTTTCCATCACACAAG
1 TTTATTGTTCTAGCATCATCGCTTTGTGCTCCAGTGCTGCATTCTAGGATTTTCCATCACACAAC
*** * * * * *
5579712 TCATGGTTTAGTTTCTTTCATTTTCTTTTATCGTTTTTTATAAACCCTGCTTACAGAGGTTAACA
66 TCACAATTTAGTTTCTTTCATTTTCTTTTATCGTTTTTGACAAACCCTGCATACAAAGCTTAACA
5579777 AACAAACAT-GCACCTACAACT-TCAAGGCCATAAGTATTCCATCATTCAATAGATAAAGCTCCA
131 AACAAACATAGCACCTACAA-TGTCAAGGCCATAAGTATTCCATCATTCAATAGATAAAGCTCCA
* * *
5579840 AACTATCCAGACATTGCATTTATTGTTCTCAG-AATGTTTGTGGGTCATTTAGGTTCAACACATA
195 AACCATCCAGACATTGCATTTATTGTTCTCAGTAATGTTTGGGGGTCATTTAGCTTCAACACATA
5579904 ATGAAGGAGACAAGAAAAAATTATTTTTGAAGAAGTGT
260 ATGAAGGAGACAAGAAAAAATTATTTTTGAAGAAGTGT
** * * **
5579942 TTTATTGTTCTAGTTTCATCGCTTTGTGTTTCAGTGCTGCATTCTAGGA-TTTCCATCACATGAC
1 TTTATTGTTCTAGCATCATCGCTTTGTGCTCCAGTGCTGCATTCTAGGATTTTCCATCACACAAC
* * * *
5580006 TCACAATTTATTTTCTTTCCTTTTCTTTTATTGTTTTTGACAAACCCTGCATGCAAAGCTTAACA
66 TCACAATTTAGTTTCTTTCATTTTCTTTTATCGTTTTTGACAAACCCTGCATACAAAGCTTAACA
* * *
5580071 AACAAACATAGCGCTTACAATGTCGAGGCCATAAGTATTCCATCATTCAATAGATAAAGCTCCAA
131 AACAAACATAGCACCTACAATGTCAAGGCCATAAGTATTCCATCATTCAATAGATAAAGCTCCAA
* * * **
5580136 ACCATTCAGACATTGCGTTTATTGTTCTCGGTTTAATGTTTGGGGGTGGTTTAGCTTCAACACAT
196 ACCATCCAGACATTGCATTTATTGTTCTCAG--TAATGTTTGGGGGTCATTTAGCTTCAACACAT
5580201 A
259 A
5580202 TCAAACTCAG
Statistics
Matches: 222, Mismatches: 33, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
294 75 0.34
295 119 0.54
298 28 0.13
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (297 bp):
TTTATTGTTCTAGCATCATCGCTTTGTGCTCCAGTGCTGCATTCTAGGATTTTCCATCACACAAC
TCACAATTTAGTTTCTTTCATTTTCTTTTATCGTTTTTGACAAACCCTGCATACAAAGCTTAACA
AACAAACATAGCACCTACAATGTCAAGGCCATAAGTATTCCATCATTCAATAGATAAAGCTCCAA
ACCATCCAGACATTGCATTTATTGTTCTCAGTAATGTTTGGGGGTCATTTAGCTTCAACACATAA
TGAAGGAGACAAGAAAAAATTATTTTTGAAGAAGTGT
Found at i:5583234 original size:134 final size:134
Alignment explanation
Indices: 5582994--5583265 Score: 517
Period size: 134 Copynumber: 2.0 Consensus size: 134
5582984 TGTCTGCTGA
*
5582994 AGAGTTGAAACTCAATAATTTTAGTATGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTTTG
1 AGAGTTGAAACTCAATAATTTTAGTACGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTTTG
*
5583059 TAGGAGGTTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
66 TAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
5583124 GAAC
131 GAAC
*
5583128 AGAGTTGAAACTCAATAATTTTATTACGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTTTG
1 AGAGTTGAAACTCAATAATTTTAGTACGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTTTG
5583193 TAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
66 TAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
5583258 GAAC
131 GAAC
5583262 AGAG
1 AGAG
5583266 GTACGCCTTC
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 135 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (134 bp):
AGAGTTGAAACTCAATAATTTTAGTACGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTTTG
TAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
GAAC
Found at i:5612923 original size:7 final size:8
Alignment explanation
Indices: 5612906--5612930 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5612896 CAACCCACAA
5612906 TTTTTCTT
1 TTTTTCTT
5612914 TTTTTCTT
1 TTTTTCTT
5612922 TTTTTCTT
1 TTTTTCTT
5612930 T
1 T
5612931 AAGCAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:5615485 original size:18 final size:17
Alignment explanation
Indices: 5615462--5615496 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
5615452 GAATTGATTT
5615462 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
5615480 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
5615497 ACCCTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:5616332 original size:18 final size:17
Alignment explanation
Indices: 5616301--5616335 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
5616291 GATTTAGGGT
5616301 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
5616318 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
5616336 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Done.