Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 34 of 117
Found at i:5594942 original size:20 final size:19
Alignment explanation
Indices: 5594919--5594982 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
5594909 TAAAAAAATT
*
5594919 AAAAAATTTAAAAAACAAAG
1 AAAAAATTTAAAAAA-AAAC
**
5594939 AAAAAAAAT-AAAAAAAAC
1 AAAAAATTTAAAAAAAAAC
*
5594957 AAAAACTTTAAAAAATAAAC
1 AAAAAATTTAAAAAA-AAAC
5594977 AAAAAA
1 AAAAAA
5594983 GAAAGGAGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
18 9 0.26
19 10 0.29
20 16 0.46
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAAAATTTAAAAAAAAAC
Found at i:5594951 original size:38 final size:38
Alignment explanation
Indices: 5594907--5594982 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
5594897 AAATTTATCC
** *
5594907 AATAAAAAAATTAAAAAATTTAAAAAACAAAGAAAAAA
1 AATAAAAAAAACAAAAAATTTAAAAAACAAACAAAAAA
* *
5594945 AATAAAAAAAACAAAAACTTTAAAAAATAAACAAAAAA
1 AATAAAAAAAACAAAAAATTTAAAAAACAAACAAAAAA
5594983 GAAAGGAGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.79, C:0.05, G:0.01, T:0.14
Consensus pattern (38 bp):
AATAAAAAAAACAAAAAATTTAAAAAACAAACAAAAAA
Found at i:5595200 original size:13 final size:12
Alignment explanation
Indices: 5595184--5595227 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
5595174 AAATTTATTT
5595184 AATAAAAAATTAA
1 AATAAAAAA-TAA
*
5595197 AATACAAAATAA
1 AATAAAAAATAA
5595209 AATAGAAAAATAA
1 AATA-AAAAATAA
5595222 AA-AAAA
1 AATAAAA
5595228 GAATGGAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.11
12 8 0.29
13 17 0.61
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:5597848 original size:68 final size:67
Alignment explanation
Indices: 5597765--5597900 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 67
5597755 ATTTGAAAGA
*
5597765 TACATGTGTTAGTTTATAAATAATGATCCATTTATATCAATATAAATTTTATATTTTATATTTTA
1 TACATGTGTTAGTTTATAAATAATGATCCATTTATATCAATATAAAATTTATATTTTATA-TTTA
5597830 TAT
65 TAT
5597833 TACATGTGTTAGTTTATAAATAATGATCCATTTATATCAATATAAAATTTATATTTTATATTTAT
1 TACATGTGTTAGTTTATAAATAATGATCCATTTATATCAATATAAAATTTATATTTTATATTTAT
5597898 AT
66 AT
5597900 T
1 T
5597901 TTAAAATTAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 8 0.12
68 59 0.88
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.51
Consensus pattern (67 bp):
TACATGTGTTAGTTTATAAATAATGATCCATTTATATCAATATAAAATTTATATTTTATATTTAT
AT
Found at i:5597897 original size:13 final size:13
Alignment explanation
Indices: 5597879--5597903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5597869 TCAATATAAA
5597879 ATTTATATTTTAT
1 ATTTATATTTTAT
5597892 ATTTATATTTTA
1 ATTTATATTTTA
5597904 AAATTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTATATTTTAT
Found at i:5598701 original size:2 final size:2
Alignment explanation
Indices: 5598694--5598720 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5598684 ATTGGTGTGC
5598694 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5598721 AAACAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5601451 original size:141 final size:141
Alignment explanation
Indices: 5601180--5601440 Score: 328
Period size: 141 Copynumber: 1.9 Consensus size: 141
5601170 CTTCCGGCAC
* * * * *
5601180 AAGTAAACAAATATCATGAAGTAGATTTTCTACTATCATGATCACCTACCATGTTAGTATCAATA
1 AAGTAAACAAATACCATGAAATAAATTTTCTACCATCAAGATCACCTACCATGTTAGTATCAATA
* * * *
5601245 AACCCTTCTAGAATTAGTTGTGAAACTCTATAACTCAAGTACATTTTTGAGGTGCTCCTCAAATA
66 AACCCTTCTAGAATTAGTTATGAAACTCCATAACTCAAGCACATTTTTGAGGTACTCCTCAAATA
5601310 TCCTCATGCAA
131 TCCTCATGCAA
* * * * *
5601321 AAGTGAACAAATACCTTGAAATAAATTTTTTACCATCAAGATCACTTGCCATGTTAGTATCAATA
1 AAGTAAACAAATACCATGAAATAAATTTTCTACCATCAAGATCACCTACCATGTTAGTATCAATA
* * * *
5601386 GATCTTTCTATAATT-GATTATGAAACTCCATAACT-AAGGCACATTTTTGAGGTAC
66 AACCCTTCTAGAATTAG-TTATGAAACTCCATAACTCAA-GCACATTTTTGAGGTAC
5601441 CCTTTAAATA
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
140 3 0.03
141 97 0.97
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (141 bp):
AAGTAAACAAATACCATGAAATAAATTTTCTACCATCAAGATCACCTACCATGTTAGTATCAATA
AACCCTTCTAGAATTAGTTATGAAACTCCATAACTCAAGCACATTTTTGAGGTACTCCTCAAATA
TCCTCATGCAA
Found at i:5604224 original size:12 final size:12
Alignment explanation
Indices: 5604209--5604284 Score: 61
Period size: 12 Copynumber: 6.3 Consensus size: 12
5604199 AGGTACCAGA
5604209 AAAAGAAGAAAG
1 AAAAGAAGAAAG
5604221 AAAA-AAGAAAAG
1 AAAAGAAG-AAAG
5604233 AAAAAGAA-AAAG
1 -AAAAGAAGAAAG
*
5604245 AAAAAGAAAAAAGG
1 -AAAAGAAGAAA-G
*
5604259 AAAA-AAAAAAG
1 AAAAGAAGAAAG
*
5604270 -AAAGATGAAAG
1 AAAAGAAGAAAG
5604281 AAAA
1 AAAA
5604285 AATATATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
10 3 0.05
11 9 0.16
12 29 0.53
13 11 0.20
14 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.01
Consensus pattern (12 bp):
AAAAGAAGAAAG
Found at i:5604233 original size:5 final size:6
Alignment explanation
Indices: 5604206--5604272 Score: 84
Period size: 6 Copynumber: 10.8 Consensus size: 6
5604196 AAAAGGTACC
5604206 AGAAAA AGAAGAA AGAAAA A-AGAAA AGAAAA AGAAAA AGAAAA AGAAAAA
1 AGAAAA AGAA-AA AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA AG-AAAA
5604256 AGGAAAA A-AAAA AGAAA
1 A-GAAAA AGAAAA AGAAA
5604273 GATGAAAGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
5 6 0.11
6 31 0.56
7 17 0.31
8 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:5604243 original size:31 final size:31
Alignment explanation
Indices: 5604207--5604286 Score: 112
Period size: 30 Copynumber: 2.6 Consensus size: 31
5604197 AAAGGTACCA
5604207 GAAAAAGAAGAAAGAAAAAA-GAAAAGAAAAA
1 GAAAAAGAAGAAAGAAAAAAGGAAAA-AAAAA
5604238 GAAAAAGAA-AAAGAAAAAAGGAAAAAAAAA
1 GAAAAAGAAGAAAGAAAAAAGGAAAAAAAAA
* *
5604268 -AGAAAGATGAAAGAAAAAA
1 GAAAAAGAAGAAAGAAAAAA
5604287 TATATAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
29 6 0.13
30 25 0.56
31 14 0.31
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (31 bp):
GAAAAAGAAGAAAGAAAAAAGGAAAAAAAAA
Found at i:5604261 original size:8 final size:7
Alignment explanation
Indices: 5604208--5604286 Score: 69
Period size: 7 Copynumber: 11.7 Consensus size: 7
5604198 AAGGTACCAG
5604208 AAAAAGA
1 AAAAAGA
*
5604215 AGAAAGA
1 AAAAAGA
5604222 AAAAAG-
1 AAAAAGA
5604228 -AAAAG-
1 AAAAAGA
5604233 AAAAAG-
1 AAAAAGA
5604239 AAAAAG-
1 AAAAAGA
5604245 AAAAAGA
1 AAAAAGA
5604252 AAAAAGGA
1 AAAAA-GA
*
5604260 AAAAAAA
1 AAAAAGA
5604267 AAGAAAGA
1 AA-AAAGA
**
5604275 TGAAAGA
1 AAAAAGA
5604282 AAAAA
1 AAAAA
5604287 TATATAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
5 5 0.08
6 17 0.28
7 27 0.45
8 11 0.18
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:5606225 original size:25 final size:25
Alignment explanation
Indices: 5606197--5606246 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5606187 GTGACTTTTG
5606197 AAAGAAATAAGGTAAAAAAATTTAT
1 AAAGAAATAAGGTAAAAAAATTTAT
5606222 AAAGAAATAAGGTAAAAAAATTTAT
1 AAAGAAATAAGGTAAAAAAATTTAT
5606247 TCTTTGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (25 bp):
AAAGAAATAAGGTAAAAAAATTTAT
Found at i:5610843 original size:2 final size:2
Alignment explanation
Indices: 5610836--5610861 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5610826 CATATTCATG
5610836 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
5610862 TCTAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5613963 original size:52 final size:51
Alignment explanation
Indices: 5613877--5614033 Score: 188
Period size: 52 Copynumber: 3.0 Consensus size: 51
5613867 TATAACCATA
* * * *
5613877 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAAT-CCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
* * *
5613929 CAAACTTGCCTATTAAGAATCAATTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATC-CTTTCCTTTTAGAATTCTTCTCCTGCAAGT
* * **
5613981 CAAACTTACCTATTAAGAATCCTCTTTCTTTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATCCT-TTCCTTTTAGAATTCTTCTCCTGCAAGT
5614033 C
1 C
5614034 TTCTTGTCCA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (51 bp):
CAAACTTACCTATTAAGAATCCTTTCCTTTTAGAATTCTTCTCCTGCAAGT
Found at i:5614074 original size:11 final size:11
Alignment explanation
Indices: 5614058--5614099 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
5614048 GCAATATCTG
*
5614058 ACAAATCCCAA
1 ACAAATCTCAA
* *
5614069 ACAAATTTCTA
1 ACAAATCTCAA
5614080 ACAAATCTCAA
1 ACAAATCTCAA
5614091 ACAAATCTC
1 ACAAATCTC
5614100 TTAAGAGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:5614982 original size:10 final size:10
Alignment explanation
Indices: 5614967--5614992 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5614957 TCAGGTAATT
5614967 TTTTTTTGAA
1 TTTTTTTGAA
5614977 TTTTTTTGAA
1 TTTTTTTGAA
5614987 TTTTTT
1 TTTTTT
5614993 AATATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:5616615 original size:16 final size:16
Alignment explanation
Indices: 5616566--5616636 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 16
5616556 TGTAGTTTTT
5616566 TATTAA-ATAA-A-AA
1 TATTAATATAATATAA
**
5616579 TATTAA-ATAATATCT
1 TATTAATATAATATAA
*
5616594 TTTTAATATAATATAA
1 TATTAATATAATATAA
*
5616610 TATTAATA-CATATATA
1 TATTAATATAATATA-A
*
5616626 TATAAATATAA
1 TATTAATATAA
5616637 ATTAAATAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
15 10 0.23
16 22 0.50
17 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAATATAATATAA
Found at i:5619571 original size:2 final size:2
Alignment explanation
Indices: 5619564--5619589 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5619554 TAAATAATAA
5619564 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
5619590 CAATGCCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5619764 original size:8 final size:8
Alignment explanation
Indices: 5619751--5619784 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
5619741 AAATTTATCT
5619751 AATAAAAA
1 AATAAAAA
5619759 AATAAAAA
1 AATAAAAA
*
5619767 ATTAAAAA
1 AATAAAAA
5619775 AATAAAAA
1 AATAAAAA
5619783 AA
1 AA
5619785 AGCAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:5619766 original size:9 final size:9
Alignment explanation
Indices: 5619754--5619814 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
5619744 TTTATCTAAT
5619754 AAAAAAAT-
1 AAAAAAATA
*
5619762 -AAAAAATT
1 AAAAAAATA
5619770 AAAAAAATA
1 AAAAAAATA
*
5619779 AAAAAAAGCA
1 AAAAAAA-TA
**
5619789 AAAACTATA
1 AAAAAAATA
5619798 AAAAAAATTA
1 AAAAAAA-TA
5619808 AAAAAAA
1 AAAAAAA
5619815 GAGAAAAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 7 0.17
9 20 0.48
10 15 0.36
ACGTcount: A:0.82, C:0.03, G:0.02, T:0.13
Consensus pattern (9 bp):
AAAAAAATA
Found at i:5632872 original size:16 final size:15
Alignment explanation
Indices: 5632853--5632895 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
5632843 TTAAAAAAAA
5632853 CAAATGATAAAAATTT
1 CAAAT-ATAAAAATTT
5632869 CAAAT-TAAAAATTT
1 CAAATATAAAAATTT
*
5632883 TAAACTATAAAAA
1 CAAA-TATAAAAA
5632896 AATATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 1 0.04
16 11 0.46
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (15 bp):
CAAATATAAAAATTT
Found at i:5648720 original size:8 final size:8
Alignment explanation
Indices: 5648707--5648776 Score: 70
Period size: 8 Copynumber: 8.4 Consensus size: 8
5648697 ATCCTCTATA
5648707 ATTTTTTT
1 ATTTTTTT
5648715 A-TTTTTT
1 ATTTTTTT
5648722 ATTTTTTT
1 ATTTTTTT
5648730 ATTTTTATT
1 ATTTTT-TT
*
5648739 TTTTGGTTTT
1 ATTT--TTTT
* *
5648749 GTATTTTTC
1 AT-TTTTTT
5648758 ATTTTTTT
1 ATTTTTTT
5648766 ATTTTTTT
1 ATTTTTTT
5648774 ATT
1 ATT
5648777 AAATAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
7 7 0.13
8 29 0.56
9 9 0.17
10 3 0.06
11 4 0.08
ACGTcount: A:0.13, C:0.01, G:0.04, T:0.81
Consensus pattern (8 bp):
ATTTTTTT
Found at i:5648721 original size:7 final size:7
Alignment explanation
Indices: 5648709--5648772 Score: 67
Period size: 7 Copynumber: 8.9 Consensus size: 7
5648699 CCTCTATAAT
5648709 TTTTTTA
1 TTTTTTA
5648716 TTTTTTA
1 TTTTTTA
5648723 TTTTTT-
1 TTTTTTA
5648729 TATTTTTA
1 T-TTTTTA
*
5648737 TTTTTTGG
1 TTTTTT-A
*
5648745 TTTTGTA
1 TTTTTTA
*
5648752 TTTTTCA
1 TTTTTTA
5648759 TTTTTTTA
1 -TTTTTTA
5648767 TTTTTT
1 TTTTTT
5648773 TATTAAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 1 0.02
7 34 0.72
8 12 0.26
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:5648727 original size:15 final size:15
Alignment explanation
Indices: 5648707--5648776 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
5648697 ATCCTCTATA
5648707 ATTTTTTTATTTTTT
1 ATTTTTTTATTTTTT
5648722 ATTTTTTTA-TTTTT
1 ATTTTTTTATTTTTT
** *
5648736 ATTTTTTGGTTTTGT
1 ATTTTTTTATTTTTT
*
5648751 A-TTTTTCATTTTTTT
1 ATTTTTTTA-TTTTTT
5648766 ATTTTTTTATT
1 ATTTTTTTATT
5648777 AAATAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 17 0.38
15 22 0.49
16 6 0.13
ACGTcount: A:0.13, C:0.01, G:0.04, T:0.81
Consensus pattern (15 bp):
ATTTTTTTATTTTTT
Found at i:5650305 original size:30 final size:30
Alignment explanation
Indices: 5650265--5650332 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
5650255 GACATGATAT
* *
5650265 ATCAAGTTAATTTGACAAATTCAGGGTCAC
1 ATCAACTTAATTTGACAAATTCAAGGTCAC
*
5650295 ATCAACTTAATTTGACAAATTCAATGTCAC
1 ATCAACTTAATTTGACAAATTCAAGGTCAC
5650325 ATCAACTT
1 ATCAACTT
5650333 GACACTATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (30 bp):
ATCAACTTAATTTGACAAATTCAAGGTCAC
Found at i:5659316 original size:23 final size:21
Alignment explanation
Indices: 5659275--5659330 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
5659265 GAACACATAG
*
5659275 CTCTTTTGTGCTCACTATTCGTT
1 CTCTTTT-TGCTCACTATT-GTC
*
5659298 CTCTTTTTGCTCGAGTATTGTC
1 CTCTTTTTGCTC-ACTATTGTC
*
5659320 CTCATTTTGCT
1 CTCTTTTTGCT
5659331 GATGTCCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.09, C:0.25, G:0.14, T:0.52
Consensus pattern (21 bp):
CTCTTTTTGCTCACTATTGTC
Found at i:5661250 original size:31 final size:31
Alignment explanation
Indices: 5661215--5661278 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
5661205 AAATGCATGC
*
5661215 AAAAATGAATAAATAACTAATGAGTGAGTTG
1 AAAAATGAATAAATAACTAATGAGTGAATTG
5661246 AAAAATGAATAAATAACTAATGAGTGAATTG
1 AAAAATGAATAAATAACTAATGAGTGAATTG
5661277 AA
1 AA
5661279 TTTACTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAAATGAATAAATAACTAATGAGTGAATTG
Found at i:5663351 original size:3 final size:3
Alignment explanation
Indices: 5663345--5663373 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5663335 TTTTTTTGCT
5663345 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5663374 TCTATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5664116 original size:35 final size:33
Alignment explanation
Indices: 5664051--5664118 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
5664041 GATAACACAG
** *
5664051 ATAATTTTTATTTTTAAAAATTTATTTTAATAA
1 ATAATTTTTATTTTTAAAAATAAATATTAATAA
*
5664084 ATAATTTTTTATATTTTAATAATAAATATTAATAA
1 ATAA-TTTTTAT-TTTTAAAAATAAATATTAATAA
5664119 TTTTATTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 4 0.14
34 7 0.24
35 18 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
ATAATTTTTATTTTTAAAAATAAATATTAATAA
Found at i:5664121 original size:22 final size:22
Alignment explanation
Indices: 5664073--5664123 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5664063 TTTAAAAATT
* * *
5664073 TATTTTAATAAATAATTTTTTA
1 TATTTTAATAAATAAATATTAA
5664095 TATTTTAAT-AATAAATATTAA
1 TATTTTAATAAATAAATATTAA
5664116 TAATTTTA
1 T-ATTTTA
5664124 TTTTGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAATAAATAAATATTAA
Found at i:5664143 original size:31 final size:31
Alignment explanation
Indices: 5664080--5664149 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
5664070 ATTTATTTTA
5664080 ATAAATAATTTTTTATATTTTAATAATAAAT
1 ATAAATAATTTTTTATATTTTAATAATAAAT
* * *
5664111 ATTAATAATTTTATTTTGATTTTGAT-AT-AAT
1 ATAAATAATTTT-TTAT-ATTTTAATAATAAAT
5664142 ATAAATAA
1 ATAAATAA
5664150 AATTTGATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 21 0.64
32 5 0.15
33 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
ATAAATAATTTTTTATATTTTAATAATAAAT
Found at i:5664359 original size:19 final size:20
Alignment explanation
Indices: 5664322--5664369 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
5664312 CATAGACTCA
*
5664322 TTTTTAGTATAAGATAATT-T
1 TTTTTA-TATAAGAAAATTAT
*
5664342 TTTTTATATAATAAAATTAT
1 TTTTTATATAAGAAAATTAT
5664362 TGTTTTAT
1 T-TTTTAT
5664370 TCAAATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTTTATATAAGAAAATTAT
Found at i:5664978 original size:23 final size:23
Alignment explanation
Indices: 5664952--5664998 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5664942 CAAATATTGT
*
5664952 TTTCATAAATATTATAT-AAATCA
1 TTTCAAAAATATT-TATCAAATCA
5664975 TTTCAAAAATATTTATCAAATCA
1 TTTCAAAAATATTTATCAAATCA
5664998 T
1 T
5664999 AATGTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTCAAAAATATTTATCAAATCA
Found at i:5670672 original size:52 final size:51
Alignment explanation
Indices: 5670554--5670847 Score: 252
Period size: 51 Copynumber: 5.9 Consensus size: 51
5670544 TTAAAATCTG
* * *
5670554 AAAAAGGCTTCTCTTAGCAAATG-CTCAACAACTTTAAAAGTTCTCATATTG
1 AAAAAGGCTTCTCTCAGCAAA-GACTCAACAACTTTAAAAATTCTCATATTA
* *
5670605 AAAAAGG-TTCATCTCAGCAAAGACTTAATAACTTTAAAAAATTCTCATATTA
1 AAAAAGGCTTC-TCTCAGCAAAGACTCAACAACTTT-AAAAATTCTCATATTA
* *
5670657 AAAAAGGCTTCTCTCAG-AGAGACTCAATAACTTTAAAAATTCTCATATTGA
1 AAAAAGGCTTCTCTCAGCAAAGACTCAACAACTTTAAAAATTCTCATATT-A
* * * * *
5670708 AAAAA-GCTCCTCTTAGTAGAAG-CTCAACAACTTTAAAAATTCTTATCTT-
1 AAAAAGGCTTCTCTCAGCA-AAGACTCAACAACTTTAAAAATTCTCATATTA
* * * *
5670757 AACAA-GCTCCTCTCAGCAAA-AGCTCAACAACTTT-AAAATT-TTATCTTGA
1 AAAAAGGCTTCTCTCAGCAAAGA-CTCAACAACTTTAAAAATTCTCATATT-A
* * * * *
5670806 AAAAA-GCTTATCTAAGCAGAGGCTCAACAA-TTTTAAAATTCT
1 AAAAAGGCTTCTCTCAGCAAAGACTCAACAACTTTAAAAATTCT
5670848 ATCTTGAAAA
Statistics
Matches: 207, Mismatches: 22, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
47 7 0.03
48 11 0.05
49 56 0.27
50 29 0.14
51 72 0.35
52 29 0.14
53 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (51 bp):
AAAAAGGCTTCTCTCAGCAAAGACTCAACAACTTTAAAAATTCTCATATTA
Found at i:5670783 original size:49 final size:50
Alignment explanation
Indices: 5670552--5671091 Score: 282
Period size: 48 Copynumber: 10.8 Consensus size: 50
5670542 ATTTAAAATC
* * * *
5670552 TGAAAAAGGCTTCTCTTAGCAAATGCTCAACAACTTTAAAAGTTCTCATAT
1 TGAAAAA-GCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATAT
* * * *
5670603 TGAAAAAGGTTCATCTCAGC-AAAGACTTAATAACTTTAAAAAATTCTCATAT
1 TGAAAAA-GCTCCTCTCAGCAAAAG-CTCAACAACTTT-AAAAATTCTCATAT
* * * *
5670655 TAAAAAAGGCTTCTCTCAG--AGAGACTCAATAACTTTAAAAATTCTCATAT
1 TGAAAAA-GCTCCTCTCAGCAAAAG-CTCAACAACTTTAAAAATTCTCATAT
* * * * *
5670705 TGAAAAAAGCTCCTCTTAGTAGAAGCTCAACAACTTTAAAAATTCTTATCT
1 TG-AAAAAGCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATAT
* * *
5670756 T-AACAAGCTCCTCTCAGCAAAAGCTCAACAACTTT-AAAATT-TTATCT
1 TGAAAAAGCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATAT
** * * * * *
5670803 TGAAAAAAGCTTATCTAAGCAGAGGCTCAACAA-TTTTAAAATTCT-ATCT
1 TG-AAAAAGCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATAT
* * * * * * * * *
5670852 TGAAAAAGCTCATTTAAACAGAGGCTCAATAA-TTTTAAAA-TCTCATCT
1 TGAAAAAGCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATAT
** * * * * * * *
5670900 TGAAAAAGCTTTTCTAAGCATAGGCTCGATAACTTT-AAAATT-TTATCT
1 TGAAAAAGCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATAT
* * * ** * *
5670948 TGAAAAAGCTCTTCTAAG-TAGGGCTCAACAACTTTAAAGAAATACTCATCT
1 TGAAAAAGCTCCTCTCAGCAAAAGCTCAACAACTTT-AA-AAATTCTCATAT
** * ** *
5670999 TGAAAAAAGCTATTCTCAGCAAAAGTTCAGTAACTTAAAAAAAATTCTCATCA-
1 TG-AAAAAGCTCCTCTCAGCAAAAGCTCAACAACTT--TAAAAATTCTCAT-AT
* * * *
5671052 TAAAAAAACTTCTCTAAAG-AAAAGCTCAACAACTTTAAAA
1 TGAAAAAGCTCCTCT-CAGCAAAAGCTCAACAACTTTAAAA
5671092 TGCTAATCTT
Statistics
Matches: 396, Mismatches: 71, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
47 22 0.06
48 99 0.25
49 71 0.18
50 36 0.09
51 77 0.19
52 67 0.17
53 22 0.06
54 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (50 bp):
TGAAAAAGCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATAT
Found at i:5679223 original size:12 final size:12
Alignment explanation
Indices: 5679206--5679238 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5679196 TTTGTCAAAA
5679206 ATTTTATTTTTC
1 ATTTTATTTTTC
*
5679218 ATTTTATTTTTG
1 ATTTTATTTTTC
5679230 ATTTT-TTTT
1 ATTTTATTTT
5679239 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (12 bp):
ATTTTATTTTTC
Found at i:5680836 original size:20 final size:20
Alignment explanation
Indices: 5680786--5680837 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
5680776 AAATTTTTCA
*
5680786 TTTAAAAAT-TTGAAAATTT
1 TTTATAAATATTGAAAATTT
* * *
5680805 TTTTTATTATATTGAAGATTT
1 TTTATA-AATATTGAAAATTT
5680826 TTTATAAATATT
1 TTTATAAATATT
5680838 CTAATACACT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 4 0.16
20 7 0.28
21 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTATAAATATTGAAAATTT
Found at i:5682335 original size:21 final size:22
Alignment explanation
Indices: 5682309--5682349 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5682299 TTAATTTAAC
*
5682309 AAAAATAGAATAAAA-AAAACT
1 AAAAATAAAATAAAATAAAACT
5682330 AAAAATAAAATAAAATAAAA
1 AAAAATAAAATAAAATAAAA
5682350 AGTAAGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (22 bp):
AAAAATAAAATAAAATAAAACT
Found at i:5682338 original size:16 final size:16
Alignment explanation
Indices: 5682317--5682350 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5682307 ACAAAAATAG
5682317 AATAAAA-AAAACTAAA
1 AATAAAATAAAA-TAAA
5682333 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
5682349 AA
1 AA
5682351 GTAAGCTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AATAAAATAAAATAAA
Found at i:5687684 original size:31 final size:30
Alignment explanation
Indices: 5687620--5687700 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 30
5687610 TAATAAATAT
* * *
5687620 TTTTTAA-TTTTAATTTACATTTAAATAAT
1 TTTTTAATTTTTAATTTATATTCAAATAAA
*
5687649 TTTTTAATTTTTAATTATATATTCGAATAAA
1 TTTTTAATTTTTAATT-TATATTCAAATAAA
5687680 TTTTTAATTTTTTAATTTATA
1 TTTTTAA-TTTTTAATTTATA
5687701 CGTAAATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 7 0.16
30 8 0.18
31 21 0.47
32 9 0.20
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (30 bp):
TTTTTAATTTTTAATTTATATTCAAATAAA
Found at i:5687709 original size:31 final size:30
Alignment explanation
Indices: 5687620--5687715 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 30
5687610 TAATAAATAT
* ** *
5687620 TTTTTAA-TTTTAATTTACATTTAAATAAT
1 TTTTTAATTTTTAATTTATACGTAAATAAA
5687649 TTTTTAATTTTTAATTATATATTCG--AATAAA
1 TTTTTAATTTTTAATT-TATA--CGTAAATAAA
5687680 TTTTTAATTTTTTAATTTATACGTAAATAATA
1 TTTTTAA-TTTTTAATTTATACGTAAATAA-A
5687712 TTTT
1 TTTT
5687716 AATATAAATC
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
29 9 0.16
30 8 0.15
31 24 0.44
32 14 0.25
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTTAATTTTTAATTTATACGTAAATAAA
Found at i:5688119 original size:24 final size:22
Alignment explanation
Indices: 5688092--5688151 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
5688082 TTTATAAAAT
5688092 AATTTTTATAAAAAAAAATTATAA
1 AATTTTTATAAAAAAAAA-TAT-A
* *
5688116 AATTTTCGTATCAAAATAAATATA
1 AATTTT--TATAAAAAAAAATATA
5688140 AATTTTTATAAA
1 AATTTTTATAAA
5688152 TATTATCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.16
24 13 0.42
25 3 0.10
26 10 0.32
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTTTTATAAAAAAAAATATA
Found at i:5694620 original size:2 final size:2
Alignment explanation
Indices: 5694613--5694649 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5694603 ATAAAACTGA
*
5694613 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5694650 GAAATAGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5710927 original size:18 final size:19
Alignment explanation
Indices: 5710906--5710949 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
5710896 CTTTTTTTGC
*
5710906 TTTTTTTCC-CTTTTTAAT
1 TTTTTTTCCAATTTTTAAT
5710924 TTTTTTTCCAAATTTTTAAT
1 TTTTTTTCC-AATTTTTAAT
5710944 TTTTTT
1 TTTTTT
5710950 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
20 14 0.61
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTTCCAATTTTTAAT
Found at i:5714952 original size:10 final size:11
Alignment explanation
Indices: 5714925--5714951 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5714915 TAAGTAAACG
5714925 ATTTTTATATA
1 ATTTTTATATA
5714936 ATTTTTATATA
1 ATTTTTATATA
5714947 ATTTT
1 ATTTT
5714952 AATTAATTAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTATATA
Found at i:5715211 original size:2 final size:2
Alignment explanation
Indices: 5715204--5715236 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5715194 ATAAAAATGA
5715204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5715237 CACACACAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5720569 original size:3 final size:3
Alignment explanation
Indices: 5720561--5720603 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5720551 TGAAGCAATC
5720561 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5720604 CAGTTTATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5721024 original size:23 final size:21
Alignment explanation
Indices: 5720977--5721019 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5720967 TAATATGTAA
*
5720977 ATTAAAATTTTATTTATTTTT
1 ATTAAAATTTTATATATTTTT
5720998 ATTATAAATTTT-TATATTTTT
1 ATTA-AAATTTTATATATTTTT
5721019 A
1 A
5721020 GATTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTAAAATTTTATATATTTTT
Found at i:5722704 original size:15 final size:14
Alignment explanation
Indices: 5722679--5722716 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
5722669 ATATTACTTA
5722679 TAATTATTATAATT
1 TAATTATTATAATT
5722693 TAATTAATTATAATT
1 TAATT-ATTATAATT
5722708 TAA-TATTAT
1 TAATTATTAT
5722717 GTTGAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 6 0.26
15 12 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTATTATAATT
Found at i:5733913 original size:31 final size:31
Alignment explanation
Indices: 5733829--5733917 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 31
5733819 TTATTACATT
* * *
5733829 CAAATAAAT-TTTTAATTTTTAATTTGAATT
1 CAAATAAATCCTTTAATTTTTAATTTGTATG
* * *
5733859 CATATCAA-CCCTTAATTTTTAATTTGTATG
1 CAAATAAATCCTTTAATTTTTAATTTGTATG
*
5733889 CAAATAAATCCTTTAACTTTTAATTTGTA
1 CAAATAAATCCTTTAATTTTTAATTTGTA
5733918 CTTAAATAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
30 29 0.62
31 18 0.38
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.48
Consensus pattern (31 bp):
CAAATAAATCCTTTAATTTTTAATTTGTATG
Found at i:5734031 original size:18 final size:19
Alignment explanation
Indices: 5733983--5734032 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
5733973 GATGTAAATC
* *
5733983 AAAATATAAAAATTTATTT
1 AAAAAATAAAAATATATTT
5734002 AAATACAATAAAAATAT-TTT
1 AAA-A-AATAAAAATATATTT
5734022 AAAAAATAAAA
1 AAAAAATAAAA
5734033 TAATATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 7 0.26
21 9 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATAAAAATATATTT
Found at i:5742062 original size:29 final size:30
Alignment explanation
Indices: 5741987--5742094 Score: 79
Period size: 29 Copynumber: 3.7 Consensus size: 30
5741977 ACTTTTTAAT
5741987 TATATATAAATATAATATTTTTATTAA-ATTAA
1 TATATATAAATAT-ATA-TTTTATTAATA-TAA
* *
5742019 GATA-CTAAATA-ATAATTTTATTAATATAA
1 TATATATAAATATAT-ATTTTATTAATATAA
** *
5742048 TATATATAAATATA-AAATTA-AAATA-AA
1 TATATATAAATATATATTTTATTAATATAA
5742075 TA-ATA-AAATATATATTTTAT
1 TATATATAAATATATATTTTAT
5742095 ATATACCTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
25 7 0.11
26 7 0.11
27 4 0.07
28 4 0.07
29 21 0.34
30 8 0.13
31 7 0.11
32 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TATATATAAATATATATTTTATTAATATAA
Found at i:5744820 original size:22 final size:22
Alignment explanation
Indices: 5744772--5744818 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5744762 AATAAATATT
5744772 TAAATGTTTAATAGAATTAAAA
1 TAAATGTTTAATAGAATTAAAA
*
5744794 TAAATG-TTAA-AGAAATTATAA
1 TAAATGTTTAATAG-AATTAAAA
5744815 TAAA
1 TAAA
5744819 ATAATAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 2 0.09
21 15 0.65
22 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (22 bp):
TAAATGTTTAATAGAATTAAAA
Found at i:5751865 original size:24 final size:25
Alignment explanation
Indices: 5751832--5751894 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
5751822 ACAAACAATT
*
5751832 AAAAACAAAAAAAGAGCCCAAG-AA
1 AAAAAAAAAAAAAGAGCCCAAGCAA
* * *
5751856 AAAAAAAAAAAAGGGGCCCCAGCAA
1 AAAAAAAAAAAAAGAGCCCAAGCAA
*
5751881 AATAGAAAAAAAAA
1 AA-AAAAAAAAAAA
5751895 TGAAGAGCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 18 0.58
25 4 0.13
26 9 0.29
ACGTcount: A:0.70, C:0.14, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAAAAGAGCCCAAGCAA
Found at i:5755508 original size:2 final size:2
Alignment explanation
Indices: 5755501--5755533 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5755491 ATTAAATCTT
5755501 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 T
5755534 CATAACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5758431 original size:56 final size:56
Alignment explanation
Indices: 5758361--5758476 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 56
5758351 GGTCGTTATC
* * * *
5758361 CATATGCAATAAAAGAAATTGACTGGACAATGCATTATGAAATTCCTTCGGAGTCT
1 CATATGCAACAAAAGAAATTGACTGGACAATGCATTAAGAAATTCCTCCGAAGTCT
* *
5758417 CATATGCAACAAAAGAAATTGATTGGACAATGCATTAAGAAATTTCTCCGAAGTCT
1 CATATGCAACAAAAGAAATTGACTGGACAATGCATTAAGAAATTCCTCCGAAGTCT
5758473 CATA
1 CATA
5758477 AACGCAATTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (56 bp):
CATATGCAACAAAAGAAATTGACTGGACAATGCATTAAGAAATTCCTCCGAAGTCT
Found at i:5765146 original size:20 final size:20
Alignment explanation
Indices: 5765123--5765167 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5765113 TTGGTCGGTG
*
5765123 TTTTTACTTTTTGTTATTTA
1 TTTTTACTTTTTATTATTTA
* *
5765143 TTTTTATTTTTTATTTTTTA
1 TTTTTACTTTTTATTATTTA
5765163 TTTTT
1 TTTTT
5765168 TCACCTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTACTTTTTATTATTTA
Found at i:5765153 original size:7 final size:7
Alignment explanation
Indices: 5765123--5765168 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
5765113 TTGGTCGGTG
*
5765123 TTTTTAC
1 TTTTTAT
*
5765130 TTTTTGT
1 TTTTTAT
*
5765137 TATTTA-
1 TTTTTAT
5765143 TTTTTAT
1 TTTTTAT
5765150 TTTTTAT
1 TTTTTAT
5765157 TTTTTAT
1 TTTTTAT
5765164 TTTTT
1 TTTTT
5765169 CACCTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTAT
Found at i:5773907 original size:21 final size:21
Alignment explanation
Indices: 5773881--5773955 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
5773871 GAAGAAAACA
*
5773881 GGATCGATCCCTTTTGCTAGG
1 GGATCGATCCCTTATGCTAGG
*** * *
5773902 GGATCGATCTGGTAAG-GAGG
1 GGATCGATCCCTTATGCTAGG
*
5773922 GGATCGATCCCTTCT-CTTAGG
1 GGATCGATCCCTTATGC-TAGG
5773943 GGATCGATCCCTT
1 GGATCGATCCCTT
5773956 CCATCACAGC
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
20 13 0.32
21 27 0.68
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (21 bp):
GGATCGATCCCTTATGCTAGG
Found at i:5774539 original size:13 final size:13
Alignment explanation
Indices: 5774521--5774548 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5774511 ATACCCCGAT
5774521 CCACCATGGGATA
1 CCACCATGGGATA
5774534 CCACCATGGGATA
1 CCACCATGGGATA
5774547 CC
1 CC
5774549 GCTAGACCCC
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:0.29, C:0.36, G:0.21, T:0.14
Consensus pattern (13 bp):
CCACCATGGGATA
Found at i:5774828 original size:65 final size:65
Alignment explanation
Indices: 5774736--5774866 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
5774726 TGGGATACCG
*
5774736 CTGGACCCCATAATCCAACAATCTCCCCGCTTCGCAATTCTTCGCAATTCATGGGATACCTCACC
1 CTGGACCCCATAATCCAACAATATCCCCGCTTCGCAATTCTTCGCAATTCATGGGATACCTCACC
*
5774801 CTGGACCCCATAATCCAACAATATCCCCGCTTCGCAATTCTTCGCAATTCGTGGGATACCTCACC
1 CTGGACCCCATAATCCAACAATATCCCCGCTTCGCAATTCTTCGCAATTCATGGGATACCTCACC
5774866 C
1 C
5774867 ATTGGGCCTG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.24, C:0.38, G:0.13, T:0.24
Consensus pattern (65 bp):
CTGGACCCCATAATCCAACAATATCCCCGCTTCGCAATTCTTCGCAATTCATGGGATACCTCACC
Found at i:5774990 original size:76 final size:76
Alignment explanation
Indices: 5774864--5775016 Score: 252
Period size: 76 Copynumber: 2.0 Consensus size: 76
5774854 GGATACCTCA
** *
5774864 CCCATTGGGCCTGGACACAAGGGGCTTCGCAATTCACGGGATACCTCACCCATTGGGCCTCGACA
1 CCCATTGGGCCTAAACACAAGGGGCTTCGCAATTCACGGGATACCTCACCCATTAGGCCTCGACA
5774929 AGTTGAGTTGC
66 AGTTGAGTTGC
* *
5774940 CCCATTGGGCCTAAACATAAGGGGCTTCGCAATTCATGGGATACCTCACCCATTAGGCCTCGACA
1 CCCATTGGGCCTAAACACAAGGGGCTTCGCAATTCACGGGATACCTCACCCATTAGGCCTCGACA
*
5775005 AGTTGGGTTGC
66 AGTTGAGTTGC
5775016 C
1 C
5775017 ATACACCCAG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.22
Consensus pattern (76 bp):
CCCATTGGGCCTAAACACAAGGGGCTTCGCAATTCACGGGATACCTCACCCATTAGGCCTCGACA
AGTTGAGTTGC
Found at i:5778633 original size:63 final size:63
Alignment explanation
Indices: 5778546--5778670 Score: 196
Period size: 63 Copynumber: 2.0 Consensus size: 63
5778536 CAGACTGACT
* *
5778546 CTGTGGGGAGTGAACCGGGAAGGGGCAAGGTTGTGTTCCAGATTCATCTTCCATATTGTCATC
1 CTGTGGGGAGCGAACCGGGAAGGGGCAAGGTAGTGTTCCAGATTCATCTTCCATATTGTCATC
* * * *
5778609 CTGTGGGGAGCGAACTGGGGAGGGGCCAGGTAGTGTTCCAGGTTCATCTTCCATATTGTCAT
1 CTGTGGGGAGCGAACCGGGAAGGGGCAAGGTAGTGTTCCAGATTCATCTTCCATATTGTCAT
5778671 TCTGCCAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (63 bp):
CTGTGGGGAGCGAACCGGGAAGGGGCAAGGTAGTGTTCCAGATTCATCTTCCATATTGTCATC
Found at i:5781734 original size:23 final size:24
Alignment explanation
Indices: 5781689--5781742 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
5781679 ATTTTTTTAT
*
5781689 TTTTAAATATTATTTTAATAAATA
1 TTTTAAATATTATTTAAATAAATA
5781713 TTTT-AATA-TATTTAAATAAA-A
1 TTTTAAATATTATTTAAATAAATA
*
5781734 TTATAAATA
1 TTTTAAATA
5781743 AATAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 15 0.56
23 4 0.15
24 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTAAATATTATTTAAATAAATA
Found at i:5781753 original size:38 final size:34
Alignment explanation
Indices: 5781705--5781776 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 34
5781695 ATATTATTTT
5781705 AATAAATATTTTAATATATTTA-AATAAAATTATAAATA
1 AATAAATATTTT--TAT-TTTATAA-AAAATTA-AAATA
*
5781743 AATAATTATTTTTATTTTATAAAAAATTAAAATA
1 AATAAATATTTTTATTTTATAAAAAATTAAAATA
5781777 TATATAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 5 0.16
35 11 0.34
36 5 0.16
38 11 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AATAAATATTTTTATTTTATAAAAAATTAAAATA
Found at i:5783008 original size:2 final size:2
Alignment explanation
Indices: 5783001--5783030 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5782991 ATGATCATGA
5783001 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5783031 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5783035 original size:2 final size:2
Alignment explanation
Indices: 5783030--5783064 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5783020 TCTCTCTCTC
5783030 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
5783065 GATGAAACAA
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:5783429 original size:27 final size:27
Alignment explanation
Indices: 5783399--5783451 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5783389 TCAATGGGGA
5783399 AGCTAGCCAATGTACAAACCATGTGAC
1 AGCTAGCCAATGTACAAACCATGTGAC
*
5783426 AGCTAGCCAATGTCCAAACCATGTGA
1 AGCTAGCCAATGTACAAACCATGTGA
5783452 AGAAATACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (27 bp):
AGCTAGCCAATGTACAAACCATGTGAC
Found at i:5788565 original size:16 final size:16
Alignment explanation
Indices: 5788544--5788575 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5788534 CTCATTGATC
5788544 AATATGTTACAGTCAA
1 AATATGTTACAGTCAA
5788560 AATATGTTACAGTCAA
1 AATATGTTACAGTCAA
5788576 GTGAAGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
AATATGTTACAGTCAA
Found at i:5788771 original size:18 final size:19
Alignment explanation
Indices: 5788741--5788777 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
5788731 AAAGAATCAA
5788741 ATTAAATTATATAT-TTTT
1 ATTAAATTATATATATTTT
5788759 ATTAATATT-TATATATTTT
1 ATTAA-ATTATATATATTTT
5788778 TAAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAAATTATATATATTTT
Found at i:5790317 original size:34 final size:34
Alignment explanation
Indices: 5790274--5790345 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
5790264 AATGTTGCTT
5790274 ATTATTCATTATTATGGTATGCATGCAAGAGAGA
1 ATTATTCATTATTATGGTATGCATGCAAGAGAGA
5790308 ATTATTCATTATTATGGTATGCATGCAAGAGAGA
1 ATTATTCATTATTATGGTATGCATGCAAGAGAGA
5790342 ATTA
1 ATTA
5790346 ATCTCTGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (34 bp):
ATTATTCATTATTATGGTATGCATGCAAGAGAGA
Found at i:5798401 original size:102 final size:104
Alignment explanation
Indices: 5798224--5798860 Score: 931
Period size: 102 Copynumber: 6.0 Consensus size: 104
5798214 CCTCTTTGCC
* * * *
5798224 ACTGCAAGAATTACATTAAAAACATCAAACATAATAATATTTCAAAAATCCCATTTCAAAATAAA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
5798289 TCTGATTCTTCCTT-AAAAAAAACATTTATTCAATATTT
66 TCTGATTCTTCCTTAAAAAAAAACATTTATTCAATATTT
5798327 ACTGCAAAAATTACATT-AAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
5798391 TCTGATTCTTCCTTAAAAAAAAAAAAAACTATTTATTCAATATTT
66 TCTGATTCTTCCTT-----AAAAAAAAAC-ATTTATTCAATATTT
* *
5798436 ACCGCAAAAATTACATAAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
5798501 TCTGATTCTTCCTTAAAAAAAAAACCATTTATTCAATATTT
66 TCTGATTCTTCCTT-AAAAAAAAA-CATTTATTCAATATTT
* *
5798542 ACTGCAAAAATTACATTAAAAACATCAAAGATAATAATATTTCAAAAATCCCATTTCAAAATTAA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
*
5798607 TCTGATTCTTCCTTAAAAAAAAAAAAAAAACCATTTTTTCAATATTT
66 TCTGATTCTTCCTT-------AAAAAAAAA-CATTTATTCAATATTT
5798654 ACTGCAAAAATTACATTAAAAACATCAAATATAACAAATATTTCAAAAATCCCATTTCAAAATTA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAAC-AATATTTCAAAAATCCCATTTCAAAATTA
*
5798719 ATCTGATTCTTCCTT-AAAAAAACCATTTATTCAATATTT
65 ATCTGATTCTTCCTTAAAAAAAAACATTTATTCAATATTT
* * *
5798758 ACAGC-AAAATTACATTAAAAACATCGAATATAACAATATTTGAAAAATCCCATTTCAAAATTAA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
* * * **
5798822 TCTGATTCTTGCTTAAAAAGAACCATTTACCCAATATTT
66 TCTGATTCTTCCTTAAAAAAAAACATTTATTCAATATTT
5798861 TAAATTTAAC
Statistics
Matches: 495, Mismatches: 22, Indels: 34
0.90 0.04 0.06
Matches are distributed among these distances:
102 100 0.20
103 65 0.13
104 19 0.04
105 7 0.01
106 100 0.20
107 1 0.00
108 9 0.02
109 30 0.06
110 61 0.12
112 59 0.12
113 44 0.09
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (104 bp):
ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
TCTGATTCTTCCTTAAAAAAAAACATTTATTCAATATTT
Found at i:5798775 original size:215 final size:215
Alignment explanation
Indices: 5798224--5798840 Score: 1035
Period size: 215 Copynumber: 2.9 Consensus size: 215
5798214 CCTCTTTGCC
* * * *
5798224 ACTGCAAGAATTACATTAAAAACATCAAACATAATAATATTTCAAAAATCCCATTTCAAAATAAA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
*
5798289 TCTGATTCTTCCTTAAAAAAAACATTTATTCAATATTTACTGCAAAAATTACATT-AAAACATCA
66 TCTGATTCTTCCTTAAAAAAACCATTTATTCAATATTTACTGCAAAAATTACATTAAAAACATCA
5798353 AATATAACAATATTTCAAAAATCCCATTTCAAAATTAATCTGATTCTTCCTT--AAAAAAAAAAA
131 AATATAACAATATTTCAAAAATCCCATTTCAAAATTAATCTGATTCTTCCTTAAAAAAAAAAAAA
*
5798416 AAACTATTTATTCAATATTT
196 AAACCATTTATTCAATATTT
* *
5798436 ACCGCAAAAATTACATAAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
5798501 TCTGATTCTTCCTTAAAAAAAAAACCATTTATTCAATATTTACTGCAAAAATTACATTAAAAACA
66 TCTGATTCTTCCTT---AAAAAAACCATTTATTCAATATTTACTGCAAAAATTACATTAAAAACA
* *
5798566 TCAAAGATAATAATATTTCAAAAATCCCATTTCAAAATTAATCTGATTCTTCCTTAAAAAAAAAA
128 TCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAATCTGATTCTTCCTTAAAAAAAAAA
*
5798631 AAAAAACCATTTTTTCAATATTT
193 AAAAAACCATTTATTCAATATTT
5798654 ACTGCAAAAATTACATTAAAAACATCAAATATAACAAATATTTCAAAAATCCCATTTCAAAATTA
1 ACTGCAAAAATTACATTAAAAACATCAAATATAAC-AATATTTCAAAAATCCCATTTCAAAATTA
*
5798719 ATCTGATTCTTCCTTAAAAAAACCATTTATTCAATATTTACAGC-AAAATTACATTAAAAACATC
65 ATCTGATTCTTCCTTAAAAAAACCATTTATTCAATATTTACTGCAAAAATTACATTAAAAACATC
* * *
5798783 GAATATAACAATATTTGAAAAATCCCATTTCAAAATTAATCTGATTCTTGCTTAAAAA
130 AAATATAACAATATTTCAAAAATCCCATTTCAAAATTAATCTGATTCTTCCTTAAAAA
5798841 GAACCATTTA
Statistics
Matches: 379, Mismatches: 19, Indels: 11
0.93 0.05 0.03
Matches are distributed among these distances:
212 73 0.19
215 113 0.30
216 87 0.23
218 62 0.16
219 44 0.12
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (215 bp):
ACTGCAAAAATTACATTAAAAACATCAAATATAACAATATTTCAAAAATCCCATTTCAAAATTAA
TCTGATTCTTCCTTAAAAAAACCATTTATTCAATATTTACTGCAAAAATTACATTAAAAACATCA
AATATAACAATATTTCAAAAATCCCATTTCAAAATTAATCTGATTCTTCCTTAAAAAAAAAAAAA
AAACCATTTATTCAATATTT
Found at i:5799732 original size:13 final size:12
Alignment explanation
Indices: 5799697--5799749 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
5799687 TTTTAAATTA
5799697 TATATTTTATAT
1 TATATTTTATAT
5799709 T-TAATTTTTATAT
1 TAT-A-TTTTATAT
5799722 TATATTATTATAT
1 TATATT-TTATAT
* *
5799735 CATATTTTAAAT
1 TATATTTTATAT
5799747 TAT
1 TAT
5799750 CGAATTATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 1 0.03
12 11 0.32
13 21 0.62
14 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:5801266 original size:18 final size:18
Alignment explanation
Indices: 5801223--5801266 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
5801213 TTGAAGGAAA
* **
5801223 GCTCACTCTTTGCTATGG
1 GCTCATTCTTTGCTACCG
5801241 GACTCATTCTTTGCTACCG
1 G-CTCATTCTTTGCTACCG
5801260 GCTCATT
1 GCTCATT
5801267 GAATAGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.14, C:0.30, G:0.18, T:0.39
Consensus pattern (18 bp):
GCTCATTCTTTGCTACCG
Found at i:5802297 original size:27 final size:27
Alignment explanation
Indices: 5802259--5802311 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5802249 TTGCAGTTGC
*
5802259 TGCTGCCCCTGTTGCTGCTGATGCCGG
1 TGCTGCACCTGTTGCTGCTGATGCCGG
*
5802286 TGCTGCACCTGTTGCTGCTGCTGCCG
1 TGCTGCACCTGTTGCTGCTGATGCCG
5802312 AAGAGGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.04, C:0.34, G:0.32, T:0.30
Consensus pattern (27 bp):
TGCTGCACCTGTTGCTGCTGATGCCGG
Found at i:5803491 original size:28 final size:28
Alignment explanation
Indices: 5803456--5803517 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
5803446 TTATATTAAA
*
5803456 AATA-TTATTT-ATAATTTAAATTTGATT
1 AATATTTATTTAATAA-TAAAATTTGATT
* *
5803483 GATATTTATTTAATAATAAAATTTTATT
1 AATATTTATTTAATAATAAAATTTGATT
5803511 AATATTT
1 AATATTT
5803518 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 22 0.76
29 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
AATATTTATTTAATAATAAAATTTGATT
Found at i:5805477 original size:30 final size:29
Alignment explanation
Indices: 5805380--5805487 Score: 103
Period size: 30 Copynumber: 3.7 Consensus size: 29
5805370 TTTATCACTT
* **
5805380 TATTTAAATAAATTTTTAT-ATTTTTATTA
1 TATTTAAATAAATTTTAATCATTAAT-TTA
* *
5805409 TATTTAAACAAATATTTAA-CTTTTAATTTA
1 TATTTAAATAAAT-TTTAATC-ATTAATTTA
*
5805439 CATTTAAATAAATTATTAATCATTAATTTA
1 TATTTAAATAAATT-TTAATCATTAATTTA
*
5805469 TATTTAAATATATTTTAAT
1 TATTTAAATAAATTTTAAT
5805488 ATAAACCAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
29 18 0.28
30 42 0.66
31 4 0.06
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTTAAATAAATTTTAATCATTAATTTA
Found at i:5811830 original size:15 final size:15
Alignment explanation
Indices: 5811810--5811842 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5811800 AGAATCTAGT
5811810 TTTGATTTGAATTT-A
1 TTTGA-TTGAATTTGA
5811825 TTTGATTGAATTTGA
1 TTTGATTGAATTTGA
5811840 TTT
1 TTT
5811843 AATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (15 bp):
TTTGATTGAATTTGA
Found at i:5815106 original size:43 final size:43
Alignment explanation
Indices: 5815045--5815130 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
5815035 TAGTTTGGTA
5815045 TAAAATATATTACAGAAATGAAAAAGAAAAAAGATTAATTATT
1 TAAAATATATTACAGAAATGAAAAAGAAAAAAGATTAATTATT
5815088 TAAAATATATTACAGAAATGAAAAAGAAAAAAGATTAATTATT
1 TAAAATATATTACAGAAATGAAAAAGAAAAAAGATTAATTATT
5815131 CTTTGTAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.28
Consensus pattern (43 bp):
TAAAATATATTACAGAAATGAAAAAGAAAAAAGATTAATTATT
Found at i:5819431 original size:13 final size:13
Alignment explanation
Indices: 5819397--5819432 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
5819387 AAATTTAAAT
5819397 TATATTATTTTTA
1 TATATTATTTTTA
*
5819410 TATTTTATTTTTA
1 TATATTATTTTTA
*
5819423 TATAATATTT
1 TATATTATTT
5819433 AAAATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATTATTTTTA
Found at i:5825715 original size:26 final size:25
Alignment explanation
Indices: 5825702--5825754 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
5825692 TTTATCATTA
5825702 AATTTTTTTTAATAATAATTATAAT
1 AATTTTTTTTAATAATAATTATAAT
* * *
5825727 AATTTTTTTT-ATCACAATTATATT
1 AATTTTTTTTAATAATAATTATAAT
5825751 AATT
1 AATT
5825755 ATTATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTTTTTTAATAATAATTATAAT
Found at i:5827104 original size:14 final size:14
Alignment explanation
Indices: 5827070--5827108 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
5827060 CGATAATATC
*
5827070 TTAAATATATGATTT
1 TTAAAT-TATTATTT
5827085 TT-AATTATTATTT
1 TTAAATTATTATTT
5827098 TTAAATTATTA
1 TTAAATTATTA
5827109 AATATCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 9 0.41
14 11 0.50
15 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TTAAATTATTATTT
Found at i:5827964 original size:22 final size:22
Alignment explanation
Indices: 5827925--5827981 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
5827915 AATTAATTTA
*
5827925 ATAAAAATTAA-AAAATTTGAT
1 ATAAAAATTAATAAAATTTAAT
*
5827946 -TGATAAATTAATAAAATTTAAT
1 AT-AAAAATTAATAAAATTTAAT
5827968 ATAAAAATTAATAA
1 ATAAAAATTAATAA
5827982 TATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 8 0.27
22 20 0.67
23 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
ATAAAAATTAATAAAATTTAAT
Found at i:5828069 original size:13 final size:13
Alignment explanation
Indices: 5828051--5828105 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 13
5828041 TAATAAACAT
5828051 TTTATTAAAAATA
1 TTTATTAAAAATA
5828064 TTTATTTAAAAAATA
1 TTTA-TT-AAAAATA
*
5828079 TATATT--AAA-A
1 TTTATTAAAAATA
*
5828089 TTTATTAAAAATT
1 TTTATTAAAAATA
5828102 TTTA
1 TTTA
5828106 AAATTTATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
12 3 0.09
13 8 0.24
14 4 0.12
15 10 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTATTAAAAATA
Found at i:5828096 original size:10 final size:10
Alignment explanation
Indices: 5828081--5828113 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
5828071 AAAAAATATA
5828081 TATTAAAATT
1 TATTAAAATT
5828091 TATTAAAAATT
1 TATT-AAAATT
5828102 T-TTAAAATT
1 TATTAAAATT
5828111 TAT
1 TAT
5828114 ACACTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 7 0.33
10 7 0.33
11 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATTAAAATT
Found at i:5829085 original size:5 final size:5
Alignment explanation
Indices: 5829077--5829106 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5829067 AATTTTAACG
*
5829077 ATTCA ATTCG ATTCA ATTCA ATTCA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA
5829107 TCAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:5829168 original size:22 final size:23
Alignment explanation
Indices: 5829134--5829176 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5829124 AATTTTTTAT
* *
5829134 TTTTTATATTATTTTAATAAAAA
1 TTTTAATATTATTTAAATAAAAA
5829157 TTTTAATA-TATTTAAATAAA
1 TTTTAATATTATTTAAATAAA
5829177 TGTATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAATATTATTTAAATAAAAA
Found at i:5829242 original size:16 final size:17
Alignment explanation
Indices: 5829214--5829250 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
5829204 TTATAAAAAT
5829214 TTAA-AAAATATATAAA
1 TTAATAAAATATATAAA
5829230 TTAATAAAA-ATATAAA
1 TTAATAAAATATATAAA
5829246 TTAAT
1 TTAAT
5829251 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAATAAAATATATAAA
Found at i:5829243 original size:57 final size:57
Alignment explanation
Indices: 5829142--5829251 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
5829132 ATTTTTTATA
* * * ** *
5829142 TTATTTTAATAAAAATTTTAATATATTTAAATAAATGTATATATAAAATAATTGTTT
1 TTATTTTAATAAAAATTTAAAAATATATAAATAAATAAAAATATAAAATAATTGTTT
* *
5829199 TTATTTT-ATAAAAATTTAAAAAATATATAAATTAATAAAAATATAAATTAATT
1 TTATTTTAATAAAAATTT-AAAAATATATAAATAAATAAAAATATAAAATAATT
5829252 TATTTAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 10 0.23
57 34 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (57 bp):
TTATTTTAATAAAAATTTAAAAATATATAAATAAATAAAAATATAAAATAATTGTTT
Found at i:5834129 original size:2 final size:2
Alignment explanation
Indices: 5834122--5834148 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5834112 AACATCATCC
5834122 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 T
5834149 TGTTAATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5836885 original size:23 final size:22
Alignment explanation
Indices: 5836833--5836890 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5836823 AATCGATCAA
* *
5836833 ATTTAAATTATAAATAATTTTTT
1 ATTTAAATT-TTAATAATTTTTG
*
5836856 ATATTAAATTTTATTAATTTATTG
1 AT-TTAAATTTTAATAATTT-TTG
5836880 ATTTAAATTTT
1 ATTTAAATTTT
5836891 TTATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTAAATTTTAATAATTTTTG
Found at i:5845256 original size:12 final size:12
Alignment explanation
Indices: 5845238--5845268 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5845228 TTTTTAAGTG
5845238 ATGTGCTCTGAA
1 ATGTGCTCTGAA
*
5845250 GTGTGCTCTGAA
1 ATGTGCTCTGAA
5845262 ATGTGCT
1 ATGTGCT
5845269 AAGTAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.35
Consensus pattern (12 bp):
ATGTGCTCTGAA
Found at i:5845928 original size:2 final size:2
Alignment explanation
Indices: 5845921--5845953 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5845911 CATTGTCTAT
5845921 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5845954 AAAAACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5848193 original size:3 final size:3
Alignment explanation
Indices: 5848185--5848224 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5848175 GACTAAGTGC
5848185 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5848225 CTCTATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5848910 original size:10 final size:10
Alignment explanation
Indices: 5848895--5848924 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5848885 ATTGAGCTTT
5848895 TATATTTTAA
1 TATATTTTAA
5848905 TATATTTTAA
1 TATATTTTAA
5848915 T-TATTTTAA
1 TATATTTTAA
5848924 T
1 T
5848925 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:5848921 original size:9 final size:9
Alignment explanation
Indices: 5848897--5848926 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5848887 TGAGCTTTTA
5848897 TATTTTAAT
1 TATTTTAAT
5848906 ATATTTTAAT
1 -TATTTTAAT
5848916 TATTTTAAT
1 TATTTTAAT
5848925 TA
1 TA
5848927 ATAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:5859451 original size:338 final size:341
Alignment explanation
Indices: 5858819--5859497 Score: 1303
Period size: 338 Copynumber: 2.0 Consensus size: 341
5858809 TTGTTTTTAG
5858819 AAGATTTTTTCTTCTTTTTAACAACAAACTTACCTTTTTTAGGTTTGAAATTTGTGGGTTTCCAC
1 AAGATTTTTTCTTCTTTTTAACAACAAACTTACCTTTTTTAGGTTTGAAATTTGTGGGTTTCCAC
5858884 TTTTTCCAAAAATGTTTTTATTTTTTCTTAAAACGAGATTTCTTTGAAAAAGATTGTTTATTACA
66 TTTTTCCAAAAATGTTTTTATTTTTTCTTAAAACGAGATTTCTTTGAAAAAGATTGTTTATTACA
5858949 ACCAAATTCAAATTCATTTTCCAAAATCTTTGTACATTGTTTATACGAAAGTTTGAATTTTACCT
131 ACCAAATTCAAATTCATTTTCCAAAATCTTTGTACATTGTTTATACGAAAGTTTGAATTTTACCT
5859014 GCTTTGTAGCTTTTTGCTTGAGGCAGTATTCTGTTACCTGATTCTGAATGTAGTGTATTCTACAT
196 GCTTTGTAGCTTTTTGCTTGAGGCAGTATTCTGTTACCTGATTCTGAATGTAGTGTATTCTACAT
5859079 CCAAGAGTATCATAAAATTCTCTGTACAGTGCCCGTTACAATATACAGTAGAATTTTTATCTATA
261 CCAAGAGTATCATAAAATTCTCTGTACAGTGCCCGTTACAATATACAGTAGAATTTTTATCTATA
5859144 GTACCGCTACAGTGAC
326 GTACCGCTACAGTGAC
*
5859160 AAGA-TTTTT-TTCTTTTTTAACAACAAATTTACCTTTTTTAGGTTTGAAATTTGTGGGTTTCCA
1 AAGATTTTTTCTTC-TTTTTAACAACAAACTTACCTTTTTTAGGTTTGAAATTTGTGGGTTTCCA
*
5859223 CTTTTTCCAAAAATGTTTTTA-TTTTTCTTAAAACGAGATTT-TTTTAAAAAGATTGTTTATTAC
65 CTTTTTCCAAAAATGTTTTTATTTTTTCTTAAAACGAGATTTCTTTGAAAAAGATTGTTTATTAC
5859286 AACCAAATTCAAATTCATTTTCCAAAATCTTTGTACATTGTTTATACGAAAGTTTGAATTTTACC
130 AACCAAATTCAAATTCATTTTCCAAAATCTTTGTACATTGTTTATACGAAAGTTTGAATTTTACC
5859351 TGCTTTGTAGCTTTTTGCTTGAGGCAGTATTCTGTTACCTGATTCTGAATGTAGTGTATTCTACA
195 TGCTTTGTAGCTTTTTGCTTGAGGCAGTATTCTGTTACCTGATTCTGAATGTAGTGTATTCTACA
5859416 TCCAAGAGTATCATAAAATTCTCTGTACAGTGCCCGTTACAATATACAGTAGAATTTTTATCTAT
260 TCCAAGAGTATCATAAAATTCTCTGTACAGTGCCCGTTACAATATACAGTAGAATTTTTATCTAT
5859481 AGTACCGCTACAGTGAC
325 AGTACCGCTACAGTGAC
5859498 TTGCTATAGT
Statistics
Matches: 335, Mismatches: 2, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
338 233 0.70
339 23 0.07
340 75 0.22
341 4 0.01
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (341 bp):
AAGATTTTTTCTTCTTTTTAACAACAAACTTACCTTTTTTAGGTTTGAAATTTGTGGGTTTCCAC
TTTTTCCAAAAATGTTTTTATTTTTTCTTAAAACGAGATTTCTTTGAAAAAGATTGTTTATTACA
ACCAAATTCAAATTCATTTTCCAAAATCTTTGTACATTGTTTATACGAAAGTTTGAATTTTACCT
GCTTTGTAGCTTTTTGCTTGAGGCAGTATTCTGTTACCTGATTCTGAATGTAGTGTATTCTACAT
CCAAGAGTATCATAAAATTCTCTGTACAGTGCCCGTTACAATATACAGTAGAATTTTTATCTATA
GTACCGCTACAGTGAC
Found at i:5860758 original size:3 final size:3
Alignment explanation
Indices: 5860750--5860780 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5860740 ATTTCCAGAG
*
5860750 ACA ACA ACA ACA ACA ACA ACA TCA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
5860781 GATTTCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.32, G:0.00, T:0.03
Consensus pattern (3 bp):
ACA
Found at i:5865738 original size:20 final size:20
Alignment explanation
Indices: 5865713--5865750 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5865703 ATATTTGTAA
5865713 TTTTTTATAATTAGTGAAAT
1 TTTTTTATAATTAGTGAAAT
* *
5865733 TTTTTTATCATTCGTGAA
1 TTTTTTATAATTAGTGAA
5865751 TATAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTTTATAATTAGTGAAAT
Found at i:5871238 original size:3 final size:3
Alignment explanation
Indices: 5871230--5871275 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5871220 TAATATTTTC
5871230 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5871276 TATTTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5871311 original size:26 final size:24
Alignment explanation
Indices: 5871236--5871310 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
5871226 TTTCAATAAT
* *
5871236 AATAATAATAATAATA-ATAATAAT
1 AATAATAATAATAATATAT-TTAAA
5871260 AATAATAATAATAATATATTTAAA
1 AATAATAATAATAATATATTTAAA
*
5871284 AATACATATATAATAAT-TTTTTAAA
1 AATA-ATA-ATAATAATATATTTAAA
5871309 AA
1 AA
5871311 AAGAAAAACA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 23 0.51
25 14 0.31
26 8 0.18
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (24 bp):
AATAATAATAATAATATATTTAAA
Found at i:5871641 original size:14 final size:14
Alignment explanation
Indices: 5871611--5871641 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5871601 ACCCATACCC
*
5871611 AAACAGAAACACAA
1 AAACAGAAACAAAA
5871625 AAACAGAAACAAAA
1 AAACAGAAACAAAA
5871639 AAA
1 AAA
5871642 TAAAGACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.16, G:0.06, T:0.00
Consensus pattern (14 bp):
AAACAGAAACAAAA
Found at i:5872309 original size:10 final size:9
Alignment explanation
Indices: 5872281--5872307 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5872271 GGTAAAAAAA
5872281 AATTTTTTT
1 AATTTTTTT
5872290 AATTTTTTT
1 AATTTTTTT
5872299 AATTTTTTT
1 AATTTTTTT
5872308 TATATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
AATTTTTTT
Found at i:5872573 original size:15 final size:15
Alignment explanation
Indices: 5872555--5872584 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5872545 TTTAATTTAC
5872555 TATTTAATAATAAAA
1 TATTTAATAATAAAA
*
5872570 TATTTTATAATAAAA
1 TATTTAATAATAAAA
5872585 AAAGAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTTAATAATAAAA
Found at i:5884146 original size:18 final size:18
Alignment explanation
Indices: 5884110--5884148 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5884100 ATTGATTACT
*
5884110 AAAGACAAAGAAGAGAAA
1 AAAGACAAAGAAGAAAAA
* *
5884128 AAAGATAAAGAATAAAAA
1 AAAGACAAAGAAGAAAAA
5884146 AAA
1 AAA
5884149 AAAAGATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAGACAAAGAAGAAAAA
Found at i:5884714 original size:36 final size:35
Alignment explanation
Indices: 5884666--5884774 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 35
5884656 TTAATCTTTG
5884666 ACTCGTGATTTAATCCCAGTCGTTTTTATTTTTCTC
1 ACTCGTGATTTAATCCCAGTC-TTTTTATTTTTCTC
* * * *
5884702 ACTCGTGGTTTAATCCCAATCATTTTATAGTTTTCCTG
1 ACTCGTGATTTAATCCCAGTC-TTTT-TA-TTTTTCTC
* * *
5884740 ACTTGCGATTTAATCCCAGTCTCTTTTATCTTTCT
1 ACTCGTGATTTAATCCCAGTCT-TTTTATTTTTCT
5884775 AACTTACGGT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
36 28 0.47
37 5 0.08
38 26 0.44
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (35 bp):
ACTCGTGATTTAATCCCAGTCTTTTTATTTTTCTC
Found at i:5885112 original size:134 final size:134
Alignment explanation
Indices: 5884944--5885212 Score: 353
Period size: 134 Copynumber: 2.0 Consensus size: 134
5884934 TCGATCTTTT
* * * *
5884944 TATTCTCTGATTCACGGTTCAGTCCTGATTTCTTTAAATCAAAATCATAGTTTAATCTTGATTAT
1 TATTCTCTAATTCACGGTTCAATCCTGATCTCTTTAAATCAAAATCATAGTTTAATCTCGATTAT
* * ** * *
5885009 TGTTATCCTCTGACTCGT-AGTTTAATCCCGGTCTCTTTATTTTTTTACTTATGATTCAATCTAA
66 TGTTATCATCTAACTCGTGA-TTTAATCCCGACCTCTTTATTTTTTGACTTATGATTCAATCCAA
5885073 GTTAA
130 GTTAA
* * * *
5885078 TATTCTCTAATTCATGGTTCAAT-CTCGATCTCTTTAAGTCAAAATCGTAGTTTAATCTCGATTG
1 TATTCTCTAATTCACGGTTCAATCCT-GATCTCTTTAAATCAAAATCATAGTTTAATCTCGATTA
* * *
5885142 TTGTTATCATTTAACTCGTGATTTAATCCCGACCTCTTTATTTTTTGGCTTATGATTCGATCCAA
65 TTGTTATCATCTAACTCGTGATTTAATCCCGACCTCTTTATTTTTTGACTTATGATTCAATCCAA
5885207 GTTAA
130 GTTAA
5885212 T
1 T
5885213 GTCACTTTCT
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
133 2 0.02
134 113 0.97
135 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (134 bp):
TATTCTCTAATTCACGGTTCAATCCTGATCTCTTTAAATCAAAATCATAGTTTAATCTCGATTAT
TGTTATCATCTAACTCGTGATTTAATCCCGACCTCTTTATTTTTTGACTTATGATTCAATCCAAG
TTAA
Found at i:5885477 original size:139 final size:139
Alignment explanation
Indices: 5885222--5885478 Score: 381
Period size: 139 Copynumber: 1.8 Consensus size: 139
5885212 TGTCACTTTC
*
5885222 TAACTAGCGATTTAATCCCGGTCTCTTTATTCTCTGATTCACGATTCAATCTCAATCTTTTTAAT
1 TAACTAGCGATTTAATCCCGGTCTCTTTATTCTCTGATTCACGATTCAATCTCAATCTCTTTAAT
** ** *
5885287 TTAAAATCGTAGTTTAATCTCGATTGTTGTTAACCTCTGACTCGTGGTTTAATTCCAATCATTTT
66 TTAAAATCACAGTTTAATCTCGATTGTTGTTAACCTCTGACTCACGATTTAATTCCAATCATTTT
5885352 TTTATTTTT
131 TTTATTTTT
* * * *
5885361 TAACTTGCGATTTAATCCTGGTCTCTTTATTCT-TCGATTCACGATTTAATCTCGATCTCTTTAA
1 TAACTAGCGATTTAATCCCGGTCTCTTTATTCTCT-GATTCACGATTCAATCTCAATCTCTTTAA
* * *
5885425 TTTAAAATCACAGTTTAATCTTGATTGTTGTTGACCTCTGATTCACGATTTAAT
65 TTTAAAATCACAGTTTAATCTCGATTGTTGTTAACCTCTGACTCACGATTTAAT
5885479 CCTGGTTTTC
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
138 1 0.01
139 103 0.99
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (139 bp):
TAACTAGCGATTTAATCCCGGTCTCTTTATTCTCTGATTCACGATTCAATCTCAATCTCTTTAAT
TTAAAATCACAGTTTAATCTCGATTGTTGTTAACCTCTGACTCACGATTTAATTCCAATCATTTT
TTTATTTTT
Found at i:5885826 original size:3 final size:3
Alignment explanation
Indices: 5885818--5885853 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5885808 ATTAATATTT
5885818 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5885854 ATATATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5886201 original size:14 final size:14
Alignment explanation
Indices: 5886171--5886201 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5886161 ACCCATACCC
*
5886171 AAACAGAAACACAA
1 AAACAGAAACAAAA
5886185 AAACAGAAACAAAA
1 AAACAGAAACAAAA
5886199 AAA
1 AAA
5886202 TAAGACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.16, G:0.06, T:0.00
Consensus pattern (14 bp):
AAACAGAAACAAAA
Found at i:5889319 original size:28 final size:28
Alignment explanation
Indices: 5889266--5889321 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5889256 CATTTAATCA
* **
5889266 AAAAATTAATAAATTTAATTTGATTAAT
1 AAAAATTAATAAATATAATTCAATTAAT
5889294 AAAAA-TAATATAATATAATTCAATTAAT
1 AAAAATTAATA-AATATAATTCAATTAAT
5889322 TTAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
AAAAATTAATAAATATAATTCAATTAAT
Found at i:5889348 original size:15 final size:14
Alignment explanation
Indices: 5889303--5889346 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5889293 TAAAAATAAT
5889303 ATAATATAATTCAA
1 ATAATATAATTCAA
* * *
5889317 TTAATTTAATTTTAA
1 ATAATATAA-TTCAA
5889332 ATAATATAATTCAA
1 ATAATATAATTCAA
5889346 A
1 A
5889347 ATTAATTGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATATAATTCAA
Found at i:5890071 original size:20 final size:20
Alignment explanation
Indices: 5890023--5890071 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5890013 TATTTATATA
5890023 ATATAAAT-TATTAAAATTT
1 ATATAAATATATTAAAATTT
* * * *
5890042 ATGTATATATATTATATTTT
1 ATATAAATATATTAAAATTT
5890062 ATATAAATAT
1 ATATAAATAT
5890072 TATGTATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATAAATATATTAAAATTT
Found at i:5892757 original size:2 final size:2
Alignment explanation
Indices: 5892750--5892777 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5892740 GAACCAAGCA
5892750 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5892778 GGTTACATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5892990 original size:28 final size:25
Alignment explanation
Indices: 5892936--5892988 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
5892926 TTTAATAATC
*
5892936 AAGTAA-TATAATTTTATAAATATA
1 AAGTAAGTATAATTTTAGAAATATA
*
5892960 AAGTAAGTATTAACTTTTAGAATTATA
1 AAGTAAGTA-TAA-TTTTAGAAATATA
5892987 AA
1 AA
5892989 AGAAAGTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 2 0.08
26 3 0.12
27 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (25 bp):
AAGTAAGTATAATTTTAGAAATATA
Found at i:5897536 original size:24 final size:24
Alignment explanation
Indices: 5897508--5897554 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5897498 TGTTTAGGTA
*
5897508 ATTTTTT-ATAAACATATATTAAT
1 ATTTTTTAATAAAAATATATTAAT
5897531 ATTTTTTAATAAAAATATATTAAT
1 ATTTTTTAATAAAAATATATTAAT
5897555 TTTAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTTTTAATAAAAATATATTAAT
Found at i:5897563 original size:24 final size:24
Alignment explanation
Indices: 5897515--5897564 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5897505 GTAATTTTTT
* *
5897515 ATAAACATATATTAATATTTTTTA
1 ATAAAAATATATTAATATTTATTA
5897539 ATAAAAATATATTAAT-TTTAATTA
1 ATAAAAATATATTAATATTT-ATTA
5897563 AT
1 AT
5897565 CTAAAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATAAAAATATATTAATATTTATTA
Found at i:5897598 original size:27 final size:26
Alignment explanation
Indices: 5897529--5897605 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
5897519 ACATATATTA
*
5897529 ATATTTTTTAATAAAAATATATTAATTT
1 ATATTATTTAATAAAAA-AT-TTAATTT
**
5897557 -TA--A-TTAATCTAAAATGTTAATTT
1 ATATTATTTAATAAAAAAT-TTAATTT
5897580 ATATTATTTAATAAAAAATTT-ATTT
1 ATATTATTTAATAAAAAATTTAATTT
5897605 A
1 A
5897606 CTAAATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
23 9 0.23
24 10 0.26
25 5 0.13
26 3 0.08
27 12 0.31
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
ATATTATTTAATAAAAAATTTAATTT
Found at i:5902687 original size:3 final size:3
Alignment explanation
Indices: 5902679--5902730 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
5902669 ATTTAGTTTT
5902679 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5902727 TTA T
1 TTA T
5902731 ATCGGACATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.