Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold21
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: 2821038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 98422 characters in sequence are not A, C, G, or T
File 13 of 15
Found at i:2085410 original size:14 final size:13
Alignment explanation
Indices: 2085391--2085419 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2085381 TAAATATTAT
2085391 ATTATA-AAAATA
1 ATTATATAAAATA
2085403 ATTATATAAAATA
1 ATTATATAAAATA
2085416 ATTA
1 ATTA
2085420 AATTAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTATATAAAATA
Found at i:2094082 original size:68 final size:68
Alignment explanation
Indices: 2093982--2094113 Score: 246
Period size: 68 Copynumber: 1.9 Consensus size: 68
2093972 CAGTTTTCAA
*
2093982 AAAAAAAAAAAAGTGCTTATTCATGGTGTTTTGAAGGTGAGGAAACAAAGTCCACCCCACAGTTT
1 AAAAAAAAAAAAGTGCTTATTCATGGTGTTTTGAAGGTGAGGAAACAAAGCCCACCCCACAGTTT
2094047 TTC
66 TTC
*
2094050 AAAAAAAAGAAAGTGCTTATTCATGGTGTTTTGAAGGTGAGGAAACAAAGCCCACCCCACAGTT
1 AAAAAAAAAAAAGTGCTTATTCATGGTGTTTTGAAGGTGAGGAAACAAAGCCCACCCCACAGTT
2094114 GTACCCCTCA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (68 bp):
AAAAAAAAAAAAGTGCTTATTCATGGTGTTTTGAAGGTGAGGAAACAAAGCCCACCCCACAGTTT
TTC
Found at i:2102482 original size:2 final size:2
Alignment explanation
Indices: 2102475--2102512 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2102465 CCAAAGTCTA
2102475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2102513 ATTATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2103741 original size:17 final size:17
Alignment explanation
Indices: 2103719--2103753 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2103709 TGTAGATTGT
2103719 AAAGTTTTAAAATTTTC
1 AAAGTTTTAAAATTTTC
**
2103736 AAAGTTTTGGAATTTTC
1 AAAGTTTTAAAATTTTC
2103753 A
1 A
2103754 GTTAGAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (17 bp):
AAAGTTTTAAAATTTTC
Found at i:2106934 original size:2 final size:2
Alignment explanation
Indices: 2106927--2106963 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2106917 TTTATAGTGG
*
2106927 AT AT AT AT AT AT AT AT AT AT AT AT A- AA 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
2106964 GGAAGATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2109679 original size:22 final size:23
Alignment explanation
Indices: 2109654--2109697 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2109644 AAATTTTAAT
*
2109654 TTTTATATT-TAAATTTTTTTAC
1 TTTTAAATTATAAATTTTTTTAC
*
2109676 TTTTAAATTATAATTTTTTTTA
1 TTTTAAATTATAAATTTTTTTA
2109698 AAAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTAAATTATAAATTTTTTTAC
Found at i:2109679 original size:23 final size:23
Alignment explanation
Indices: 2109647--2109698 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2109637 AAATTTAAAA
*
2109647 TTTTAATTTTTATATT-TAAATTT
1 TTTTAA-TTTTAAATTATAAATTT
* *
2109670 TTTTACTTTTAAATTATAATTTT
1 TTTTAATTTTAAATTATAAATTT
2109693 TTTTAA
1 TTTTAA
2109699 AAAATTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTAATTTTAAATTATAAATTT
Found at i:2110047 original size:2 final size:2
Alignment explanation
Indices: 2110040--2110070 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2110030 TAAGTTGGAT
2110040 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 T
2110071 TCAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2111521 original size:23 final size:24
Alignment explanation
Indices: 2111474--2111532 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
2111464 AGTTTCTTCC
*
2111474 AAATAATATATAATTAATTTGGAA
1 AAATAATATATAATTAATTTAGAA
*
2111498 AAA-AATATATAATT-TTTCTAGAA
1 AAATAATATATAATTAATT-TAGAA
2111521 AAATAATTATAT
1 AAATAA-TATAT
2111533 TATCCAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 2 0.07
23 18 0.60
24 5 0.17
25 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
AAATAATATATAATTAATTTAGAA
Found at i:2111980 original size:101 final size:101
Alignment explanation
Indices: 2111875--2112078 Score: 347
Period size: 101 Copynumber: 2.0 Consensus size: 101
2111865 ATCTTAAAGA
*
2111875 TACTTTCTGAAGTTAATATATGTAATAATATCTTTATTTTATATGCATTTAAAATGAT-AAAAAA
1 TACTTTCTGAAATTAATATATGTAATAATATCTTTATTTT-TATGCATTTAAAATGATAAAAAAA
* *
2111939 TTATCAATTATTATATTTAATATATTATTAATATTAT
65 TTACCAATTATTATATTTAATATATTATTAATACTAT
*
2111976 TACTTTTTGAAATTAATATATGTAATAATATCTTTATTTTTATGCATTTAAAATGATAAAAAAAT
1 TACTTTCTGAAATTAATATATGTAATAATATCTTTATTTTTATGCATTTAAAATGATAAAAAAAT
*
2112041 TACCAATTATTATATTTAATATATTATTATTACTAT
66 TACCAATTATTATATTTAATATATTATTAATACTAT
2112077 TA
1 TA
2112079 TTTTTATTAT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 17 0.18
101 80 0.82
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (101 bp):
TACTTTCTGAAATTAATATATGTAATAATATCTTTATTTTTATGCATTTAAAATGATAAAAAAAT
TACCAATTATTATATTTAATATATTATTAATACTAT
Found at i:2112364 original size:32 final size:33
Alignment explanation
Indices: 2112308--2112376 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
2112298 TAATTTATTT
*
2112308 TTTATATAAAATTAAAAATAAATATATT-TAAA
1 TTTATATAAAATTAAAAATAAATATATTAAAAA
* *
2112340 TTTATATAAAA-TAAATTATTAATATATTAAAAA
1 TTTATATAAAATTAAA-AATAAATATATTAAAAA
2112373 TTTA
1 TTTA
2112377 AAAATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 4 0.12
32 21 0.66
33 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TTTATATAAAATTAAAAATAAATATATTAAAAA
Found at i:2112399 original size:27 final size:27
Alignment explanation
Indices: 2112352--2112417 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
2112342 TATATAAAAT
**
2112352 AAATTAT-TAATATATTAAAAATTTAA
1 AAATTATATAATATATTAAAAAAATAA
* *
2112378 AAATTATATAATATTTTTAAAAAATAA
1 AAATTATATAATATATTAAAAAAATAA
2112405 AAATATAATATAA
1 AAAT-T-ATATAA
2112418 ATTCAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.21
27 19 0.58
28 1 0.03
29 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATTATATAATATATTAAAAAAATAA
Found at i:2112406 original size:26 final size:25
Alignment explanation
Indices: 2112321--2112415 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 25
2112311 ATATAAAATT
* *
2112321 AAAAATAAATATATTTAA-ATTTATA
1 AAAAATAAAT-TATATAATATTTTTA
* *
2112346 TAAAATAAATTAT-TAATA-TATTA
1 AAAAATAAATTATATAATATTTTTA
*
2112369 AAAATTTAAAAATTATATAATATTTTTA
1 AAAA---ATAAATTATATAATATTTTTA
*
2112397 AAAAATAAA-AATATAATAT
1 AAAAATAAATTATATAATAT
2112416 AAATTCAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
23 9 0.16
24 13 0.23
25 13 0.23
26 8 0.14
27 5 0.09
28 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATAAATTATATAATATTTTTA
Found at i:2112409 original size:19 final size:20
Alignment explanation
Indices: 2112373--2112410 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2112363 ATATTAAAAA
* *
2112373 TTTAAAAATTATATAATATT
1 TTTAAAAAATATAAAATATT
2112393 TTTAAAAAATA-AAAATAT
1 TTTAAAAAATATAAAATAT
2112411 AATATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAAAAATATAAAATATT
Found at i:2113141 original size:18 final size:18
Alignment explanation
Indices: 2113087--2113141 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
2113077 TAGCAACATT
*
2113087 AAAA-ATTTAGATTTTAA
1 AAAATATTTAAATTTTAA
* *
2113104 AATATATTT-AATGTTAAA
1 AAAATATTTAAAT-TTTAA
2113122 AAAATATTTAAATTTTAA
1 AAAATATTTAAATTTTAA
2113140 AA
1 AA
2113142 TTTATAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 5 0.17
18 22 0.73
19 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
AAAATATTTAAATTTTAA
Found at i:2116324 original size:2 final size:2
Alignment explanation
Indices: 2116319--2116344 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2116309 GCACACACTC
2116319 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
2116345 TAATTAGTTT
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:2116589 original size:2 final size:2
Alignment explanation
Indices: 2116582--2116613 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2116572 AAAGATTTTA
2116582 CT 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 CT
2116614 TAGGACAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2117787 original size:3 final size:3
Alignment explanation
Indices: 2117779--2117804 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2117769 GTGGAAGTAG
2117779 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
2117805 GGAACAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2118072 original size:6 final size:6
Alignment explanation
Indices: 2118061--2118091 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2118051 AAATAATATT
*
2118061 TTAATA TTAATA TTAATA TTAATA TTCATA T
1 TTAATA TTAATA TTAATA TTAATA TTAATA T
2118092 AGTTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:2118915 original size:2 final size:2
Alignment explanation
Indices: 2118908--2118943 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2118898 GGTCCCTACA
2118908 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
2118944 GTTAGTGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2118972 original size:19 final size:19
Alignment explanation
Indices: 2118948--2118985 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2118938 ATATATGTTA
2118948 GTGCATCGATGGTTAGAGC
1 GTGCATCGATGGTTAGAGC
*
2118967 GTGCATTGATGGTTAGAGC
1 GTGCATCGATGGTTAGAGC
2118986 AAGATTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.37, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGGTTAGAGC
Found at i:2119258 original size:50 final size:50
Alignment explanation
Indices: 2119175--2119330 Score: 195
Period size: 50 Copynumber: 3.1 Consensus size: 50
2119165 AGTTGCTTAG
** * * *
2119175 AGTCAACAATTACGGTCACTTCTCTCAACTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACAATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* ** *
2119225 AGTTATTAATTACAATCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACAATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*** *
2119275 AGTCAACAATTATGGTCACCTCTTTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACAATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
2119325 AGTCAA
1 AGTCAA
2119331 TAATGGCAAC
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACAATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:2123789 original size:50 final size:50
Alignment explanation
Indices: 2123714--2123912 Score: 217
Period size: 50 Copynumber: 4.0 Consensus size: 50
2123704 AGTTGCTTAG
* * * *
2123714 AGTCAACAATTATG-GCTACCTCTCTCTATTGTCAAAAATTAGTGAAGAAT
1 AGTCAACAATTACGATC-ACCTCTCTCTATTGTCAAAAGTTGGTGAAGAAT
* * *
2123764 AGTCAACAATTATGATCA--TCTCTCTCTTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAAT
* * * * *
2123812 AGTCAATAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAAT
* * *
2123862 AGTCAACAATTACGATCACCTCT-TTTGATTGTCAAAAGTTGATGAAAAAT
1 AGTCAACAATTACGATCACCTCTCTCT-ATTGTCAAAAGTTGGTGAAGAAT
2123912 A
1 A
2123913 ATTAATAATG
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
48 41 0.32
49 1 0.01
50 85 0.66
51 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (50 bp):
AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAAT
Found at i:2123807 original size:48 final size:48
Alignment explanation
Indices: 2123735--2123884 Score: 201
Period size: 48 Copynumber: 3.1 Consensus size: 48
2123725 ATGGCTACCT
* ** * * *
2123735 CTCTCTATTGTCAAAAATTAGTGAAGAATAGTCAACAATTATGATCAT
1 CTCTCTCTTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGATCAC
* *
2123783 CTCTCTCTTGTCAAAGGTTGGTGAAGAATAGTCAATAATTACGGTCAC
1 CTCTCTCTTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGATCAC
*
2123831 CTCTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAACAATTACGATCAC
1 CTCTCTC--TTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGATCAC
2123881 CTCT
1 CTCT
2123885 TTTGATTGTC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
48 47 0.53
50 42 0.47
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (48 bp):
CTCTCTCTTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGATCAC
Found at i:2129409 original size:21 final size:21
Alignment explanation
Indices: 2129383--2129451 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
2129373 GAATTTTTGC
2129383 TGGTTGATAACCCTCGAAAGA
1 TGGTTGATAACCCTCGAAAGA
*** * ** *
2129404 TGGTTG-TAAATTTAGAGTTGC
1 TGGTTGATAACCCTCGA-AAGA
2129425 TGGTTGATAACCCTCGAAAGA
1 TGGTTGATAACCCTCGAAAGA
2129446 TGGTTG
1 TGGTTG
2129452 TAAATTTAGA
Statistics
Matches: 32, Mismatches: 14, Indels: 4
0.64 0.28 0.08
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (21 bp):
TGGTTGATAACCCTCGAAAGA
Found at i:2129429 original size:42 final size:42
Alignment explanation
Indices: 2129379--2129478 Score: 200
Period size: 42 Copynumber: 2.4 Consensus size: 42
2129369 TTATGAATTT
2129379 TTGCTGGTTGATAACCCTCGAAAGATGGTTGTAAATTTAGAG
1 TTGCTGGTTGATAACCCTCGAAAGATGGTTGTAAATTTAGAG
2129421 TTGCTGGTTGATAACCCTCGAAAGATGGTTGTAAATTTAGAG
1 TTGCTGGTTGATAACCCTCGAAAGATGGTTGTAAATTTAGAG
2129463 TTGCTGGTTGATAACC
1 TTGCTGGTTGATAACC
2129479 ATCATCATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (42 bp):
TTGCTGGTTGATAACCCTCGAAAGATGGTTGTAAATTTAGAG
Found at i:2129470 original size:21 final size:21
Alignment explanation
Indices: 2129404--2129472 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
2129394 CCTCGAAAGA
2129404 TGGTTGTAAATTTAGAGTTGC
1 TGGTTGTAAATTTAGAGTTGC
*** * ** *
2129425 TGGTTGATAACCCTCGA-AAGA
1 TGGTTG-TAAATTTAGAGTTGC
2129446 TGGTTGTAAATTTAGAGTTGC
1 TGGTTGTAAATTTAGAGTTGC
2129467 TGGTTG
1 TGGTTG
2129473 ATAACCATCA
Statistics
Matches: 32, Mismatches: 14, Indels: 4
0.64 0.28 0.08
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.38
Consensus pattern (21 bp):
TGGTTGTAAATTTAGAGTTGC
Found at i:2136061 original size:19 final size:20
Alignment explanation
Indices: 2136021--2136061 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2136011 TCTAGCTCAT
*
2136021 ATATTACAAGAAAGAGAGAC
1 ATATTACAAGAAAAAGAGAC
2136041 ATATT-CAAGTAAAAAGA-AC
1 ATATTACAAG-AAAAAGAGAC
2136060 AT
1 AT
2136062 GGATTTTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (20 bp):
ATATTACAAGAAAAAGAGAC
Found at i:2144017 original size:2 final size:2
Alignment explanation
Indices: 2144012--2144036 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2144002 TCCTACACAC
2144012 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 A
2144037 ATGCCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2144255 original size:21 final size:21
Alignment explanation
Indices: 2144229--2144269 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2144219 ATAATTAAAT
2144229 TAATATGATAATTCACATATA
1 TAATATGATAATTCACATATA
* * *
2144250 TAATATTATATTTCATATAT
1 TAATATGATAATTCACATAT
2144270 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATATGATAATTCACATATA
Found at i:2146462 original size:46 final size:45
Alignment explanation
Indices: 2146406--2146557 Score: 137
Period size: 46 Copynumber: 3.3 Consensus size: 45
2146396 ATTATACTTA
*
2146406 TTTATAAAATTTAAAATTAGATAAATTTAAATTTTATTATTTTATT
1 TTTATAAAATTTAAAATTAAATAAATTTAAATTTTATTATTTTA-T
* * ** **
2146452 TTTATAAAATTTTAAA-TAAATTAATAGACAATTAGAATTATATTTA-
1 TTTATAAAATTTAAAATTAAATAAATTTA-AATT-TTATTAT-TTTAT
* *
2146498 TCTATAAAATTTAAAATCTTAAATAAATTTAAATTTTATTAATTTAT
1 TTTATAAAATTTAAAA--TTAAATAAATTTAAATTTTATTATTTTAT
*
2146545 CTTTATATAATTT
1 -TTTATAAAATTT
2146558 TAAGTAAATT
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
45 8 0.10
46 37 0.46
47 9 0.11
48 18 0.22
49 9 0.11
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (45 bp):
TTTATAAAATTTAAAATTAAATAAATTTAAATTTTATTATTTTAT
Found at i:2146544 original size:94 final size:92
Alignment explanation
Indices: 2146395--2146569 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 92
2146385 GAACAGTTAA
* * * *
2146395 AATTATACTTATTTATAAAATTTAAAATTAGATAAATTTAAATTTTATTATTTTATTTTTATAAA
1 AATTATACTTATCTATAAAATTTAAAATTAAATAAATTTAAATTTTATTAATTTATCTTTATAAA
2146460 ATTTTAAATAAATTAATAGACAATTAG
66 ATTTTAAATAAATTAATAGACAATTAG
*
2146487 AATTATATTTATCTATAAAATTTAAAATCTTAAATAAATTTAAATTTTATTAATTTATCTTTATA
1 AATTATACTTATCTATAAAATTTAAAA--TTAAATAAATTTAAATTTTATTAATTTATCTTTATA
* *
2146552 TAATTTTAAGTAAATTAA
64 AAATTTTAAATAAATTAA
2146570 ACTGAACTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
92 25 0.34
94 49 0.66
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (92 bp):
AATTATACTTATCTATAAAATTTAAAATTAAATAAATTTAAATTTTATTAATTTATCTTTATAAA
ATTTTAAATAAATTAATAGACAATTAG
Found at i:2148493 original size:22 final size:22
Alignment explanation
Indices: 2148468--2148510 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2148458 TTAAGATTGA
2148468 TTGTGAGAGCTTTTCTGTCACT
1 TTGTGAGAGCTTTTCTGTCACT
2148490 TTGTGAGAGCTTTTCTGTCAC
1 TTGTGAGAGCTTTTCTGTCAC
2148511 AGCTTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (22 bp):
TTGTGAGAGCTTTTCTGTCACT
Found at i:2155789 original size:9 final size:9
Alignment explanation
Indices: 2155775--2155810 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2155765 ATGCTTATCC
2155775 TTTTCTTTT
1 TTTTCTTTT
2155784 TTTTCTTTT
1 TTTTCTTTT
2155793 TTTT-TTTT
1 TTTTCTTTT
*
2155801 TTTCCTTTT
1 TTTTCTTTT
2155810 T
1 T
2155811 CCATGGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:2155797 original size:14 final size:14
Alignment explanation
Indices: 2155774--2155810 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2155764 TATGCTTATC
2155774 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
2155788 CTTTT-TTTTTTTT
1 CTTTTCTTTTTTTT
*
2155801 -TTTCCTTTTT
1 CTTTTCTTTTT
2155811 CCATGGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 13 0.62
14 5 0.24
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:2155799 original size:16 final size:17
Alignment explanation
Indices: 2155775--2155810 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2155765 ATGCTTATCC
2155775 TTTTCTTTTTTTT-CTT
1 TTTTCTTTTTTTTCCTT
*
2155791 TTTTTTTTTTTTTCCTT
1 TTTTCTTTTTTTTCCTT
2155808 TTT
1 TTT
2155811 CCATGGGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTCTTTTTTTTCCTT
Found at i:2155800 original size:17 final size:17
Alignment explanation
Indices: 2155775--2155810 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2155765 ATGCTTATCC
*
2155775 TTTTCTTTTTTTTCTTT
1 TTTTCTTTTTTTCCTTT
*
2155792 TTTTTTTTTTTTCCTTT
1 TTTTCTTTTTTTCCTTT
2155809 TT
1 TT
2155811 CCATGGGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTCTTTTTTTCCTTT
Found at i:2159795 original size:28 final size:29
Alignment explanation
Indices: 2159742--2159801 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
2159732 AATAAATTAA
*
2159742 TAAGTATTTTTCTATCATATTAATTTT-T
1 TAAGTATTTTTCCATCATATTAATTTTGT
**
2159770 TAAGTATTTTTTCCATTTTATT-ATTTTGT
1 TAAGTA-TTTTTCCATCATATTAATTTTGT
2159799 TAA
1 TAA
2159802 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.62
Consensus pattern (29 bp):
TAAGTATTTTTCCATCATATTAATTTTGT
Found at i:2164411 original size:15 final size:17
Alignment explanation
Indices: 2164391--2164426 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2164381 TCGATTTTCG
2164391 TTAAATA-TTA-TTTTT
1 TTAAATATTTAGTTTTT
2164406 TTAAATATTTAGTTTTT
1 TTAAATATTTAGTTTTT
2164423 TTAA
1 TTAA
2164427 GTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 3 0.16
17 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTAAATATTTAGTTTTT
Found at i:2165228 original size:20 final size:20
Alignment explanation
Indices: 2165203--2165240 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2165193 TACTTTACCT
* *
2165203 AGCTTGTCTTTGTCTTTTCG
1 AGCTTGTCATTATCTTTTCG
2165223 AGCTTGTCATTATCTTTT
1 AGCTTGTCATTATCTTTT
2165241 GAGATTCGCT
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:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
AGCTTGTCATTATCTTTTCG
Found at i:2176426 original size:18 final size:18
Alignment explanation
Indices: 2176403--2176460 Score: 116
Period size: 18 Copynumber: 3.2 Consensus size: 18
2176393 ACAGCATTTC
2176403 CTGAATTTGTACCCAAAT
1 CTGAATTTGTACCCAAAT
2176421 CTGAATTTGTACCCAAAT
1 CTGAATTTGTACCCAAAT
2176439 CTGAATTTGTACCCAAAT
1 CTGAATTTGTACCCAAAT
2176457 CTGA
1 CTGA
2176461 GGCAGCAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (18 bp):
CTGAATTTGTACCCAAAT
Found at i:2187856 original size:16 final size:16
Alignment explanation
Indices: 2187835--2187896 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
2187825 GTTATACGCT
2187835 GAGTTGAAATGATTTA
1 GAGTTGAAATGATTTA
*
2187851 GAGTTGAAATGTTTTA
1 GAGTTGAAATGATTTA
* *
2187867 AATTTTG-AATGATTTA
1 GA-GTTGAAATGATTTA
*
2187883 -AATTGGAAATGATT
1 GAGTT-GAAATGATT
2187897 GAATTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 2 0.05
15 2 0.05
16 31 0.82
17 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (16 bp):
GAGTTGAAATGATTTA
Found at i:2187944 original size:14 final size:15
Alignment explanation
Indices: 2187918--2187967 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2187908 ATTTAAAATG
2187918 ATTT-AAATAATT-A
1 ATTTAAAATAATTAA
*
2187931 ATTTAAAATGATTAA
1 ATTTAAAATAATTAA
*
2187946 ATTTAATA-AATATAA
1 ATTTAAAATAAT-TAA
2187961 ATTTAAA
1 ATTTAAA
2187968 TAGTAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 4 0.13
14 9 0.30
15 17 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
ATTTAAAATAATTAA
Found at i:2188076 original size:21 final size:20
Alignment explanation
Indices: 2188035--2188076 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2188025 GAATATAAAA
*
2188035 TAATTTAAATTTAGTTAATT
1 TAATTTAAATTTAATTAATT
*
2188055 TAATATTAAATTTAATTGATT
1 TAAT-TTAAATTTAATTAATT
2188076 T
1 T
2188077 GAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TAATTTAAATTTAATTAATT
Found at i:2188103 original size:16 final size:17
Alignment explanation
Indices: 2188084--2188128 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
2188074 TTTGAAATAA
2188084 AAAAT-ATTTGAAAATT
1 AAAATAATTTGAAAATT
2188100 AAAATAATTT-AAAATT
1 AAAATAATTTGAAAATT
*
2188116 AAAATGATTTGAA
1 AAAATAATTTGAA
2188129 TTTAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
AAAATAATTTGAAAATT
Found at i:2188133 original size:16 final size:15
Alignment explanation
Indices: 2188073--2188141 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
2188063 AATTTAATTG
*
2188073 ATTTGAAATAAAAAAT
1 ATTTGAAAT-TAAAAT
2188089 ATTTGAAAATTAAAAT
1 ATTTG-AAATTAAAAT
*
2188105 AATTTAAAATTAAAAT
1 -ATTTGAAATTAAAAT
*
2188121 GATTTGAATTTAATAAT
1 -ATTTGAAATTAA-AAT
2188138 ATTT
1 ATTT
2188142 AAAAATTTGC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 34 0.76
17 11 0.24
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
ATTTGAAATTAAAAT
Found at i:2188148 original size:33 final size:32
Alignment explanation
Indices: 2188084--2188145 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
2188074 TTTGAAATAA
2188084 AAAATATTTGAAAATTAAAATAATTTAAAATT
1 AAAATATTTGAAAATTAAAATAATTTAAAATT
*
2188116 AAAATGATTTG-AATTTAATAAT-ATTTAAAA
1 AAAAT-ATTTGAAAATTAA-AATAATTTAAAA
2188146 ATTTGCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (32 bp):
AAAATATTTGAAAATTAAAATAATTTAAAATT
Found at i:2188886 original size:3 final size:3
Alignment explanation
Indices: 2188880--2188922 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2188870 TCATCACCCA
2188880 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2188923 ATAGTAGTCA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2189706 original size:20 final size:20
Alignment explanation
Indices: 2189669--2189706 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2189659 AGAGCAGACC
*
2189669 TTTCTTGTTGTTGCTTTCCA
1 TTTCTTGTTCTTGCTTTCCA
*
2189689 TTTCTTGTTCTTGTTTTC
1 TTTCTTGTTCTTGCTTTC
2189707 GACACACTCT
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:0.03, C:0.18, G:0.13, T:0.66
Consensus pattern (20 bp):
TTTCTTGTTCTTGCTTTCCA
Found at i:2190203 original size:3 final size:3
Alignment explanation
Indices: 2190195--2190228 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2190185 CGTGTTTGGC
2190195 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2190229 ACAACTAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2191744 original size:29 final size:28
Alignment explanation
Indices: 2191707--2191776 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
2191697 TTATTATTTA
* *
2191707 TTAATAATAAAAATTA-TTTAAAATTAAT
1 TTAAAAATAAAAAATATTTTAAAATT-AT
*
2191735 TATAAAAATATAAAAATATTTTAATATTAT
1 T-TAAAAATA-AAAAATATTTTAAAATTAT
2191765 TTAAAAATAAAA
1 TTAAAAATAAAA
2191777 TAAATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.11
29 15 0.42
30 9 0.25
31 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TTAAAAATAAAAAATATTTTAAAATTAT
Found at i:2191782 original size:30 final size:30
Alignment explanation
Indices: 2191698--2191786 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 30
2191688 TAATTTAAAT
**
2191698 TATTATTTATTAATAATAAAAAT-TATTTAA
1 TATTATTTAAAAATAA-AAAAATATATTTAA
* *
2191728 AATTAATTATAAAAATATAAAAATAT-TTTAA
1 TATT-ATT-TAAAAATAAAAAAATATATTTAA
2191759 TATTATTTAAAAATAAAATAAATA-ATTT
1 TATTATTTAAAAATAAAA-AAATATATTT
2191787 GATCAACTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
29 10 0.21
30 14 0.29
31 17 0.35
32 7 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TATTATTTAAAAATAAAAAAATATATTTAA
Found at i:2194490 original size:23 final size:23
Alignment explanation
Indices: 2194464--2194508 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2194454 AAAATTTAGT
*
2194464 TTAA-AAAAAAACTAGTATTTTTC
1 TTAATAAAAAAACAAG-ATTTTTC
*
2194487 TTAATAACAAAACAAGATTTTT
1 TTAATAAAAAAACAAGATTTTT
2194509 TTATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAATAAAAAAACAAGATTTTTC
Found at i:2196086 original size:17 final size:16
Alignment explanation
Indices: 2196040--2196080 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2196030 ATAAAAAAAA
2196040 TAAAATTATAAA--TAT
1 TAAAATTA-AAATTTAT
2196055 TAAAATTAAAATTTAT
1 TAAAATTAAAATTTAT
2196071 TAAAAATTAA
1 T-AAAATTAA
2196081 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.13
15 8 0.35
16 4 0.17
17 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATTAAAATTTAT
Found at i:2197202 original size:17 final size:18
Alignment explanation
Indices: 2197180--2197220 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2197170 AAAAAAGTTA
2197180 TTTTATTATTA-AAATAT
1 TTTTATTATTATAAATAT
*
2197197 TTTTA-TATTATTAATAT
1 TTTTATTATTATAAATAT
*
2197214 TTATATT
1 TTTTATT
2197221 TAAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATTATTATAAATAT
Found at i:2197367 original size:18 final size:20
Alignment explanation
Indices: 2197334--2197371 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2197324 AATCGAAAAT
2197334 TTAAATTTTGATATTTTTAA
1 TTAAATTTTGATATTTTTAA
2197354 TTAAA-TTT-ATATTTTTAA
1 TTAAATTTTGATATTTTTAA
2197372 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TTAAATTTTGATATTTTTAA
Found at i:2198800 original size:2 final size:2
Alignment explanation
Indices: 2198795--2198827 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2198785 GTGTGTGTGT
2198795 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2198828 TCGTGAGGAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2199234 original size:28 final size:28
Alignment explanation
Indices: 2199203--2199256 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2199193 AGAATATTAC
*
2199203 ATATGCAGACAACATAACAATAGATTTA
1 ATATGCAGACAACAAAACAATAGATTTA
*
2199231 ATATGCAGACAACAAAATAATAGATT
1 ATATGCAGACAACAAAACAATAGATT
2199257 ATCAATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
ATATGCAGACAACAAAACAATAGATTTA
Found at i:2199633 original size:24 final size:24
Alignment explanation
Indices: 2199591--2199638 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2199581 CTTAACCATT
*
2199591 ATTTATTTATATATATATATATAA
1 ATTTATTTATATATATATAAATAA
*
2199615 ATTTAATTTATA-ATTTATAAATAA
1 ATTT-ATTTATATATATATAAATAA
2199639 TTTTTAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTATTTATATATATATAAATAA
Found at i:2212515 original size:14 final size:16
Alignment explanation
Indices: 2212498--2212535 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2212488 AAAAATTTCA
2212498 TAAATATTAAATTT-T
1 TAAATATTAAATTTAT
*
2212513 AAAAT-TTAAATTTAT
1 TAAATATTAAATTTAT
2212528 TAAATATT
1 TAAATATT
2212536 TTTTATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 8 0.42
15 9 0.47
16 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATATTAAATTTAT
Found at i:2213250 original size:14 final size:16
Alignment explanation
Indices: 2213220--2213266 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
2213210 TTTAAAAAAA
2213220 TAATATTTA-ATAATTT
1 TAATATTTATA-AATTT
2213236 TAA-ATTT-TAAATTT
1 TAATATTTATAAATTT
2213250 TAATATTTATAAATTT
1 TAATATTTATAAATTT
2213266 T
1 T
2213267 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.29
15 9 0.32
16 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATATTTATAAATTT
Found at i:2213265 original size:8 final size:7
Alignment explanation
Indices: 2213231--2213266 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
2213221 AATATTTAAT
2213231 AATTTTA
1 AATTTTA
2213238 AATTTTA
1 AATTTTA
2213245 AATTTTA
1 AATTTTA
2213252 ATATTTATA
1 A-ATTT-TA
2213261 AATTTT
1 AATTTT
2213267 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 16 0.59
8 8 0.30
9 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:2215024 original size:20 final size:20
Alignment explanation
Indices: 2215001--2215046 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2214991 TAAATACTTT
2215001 AATTTTATTTTAATATTATA
1 AATTTTATTTTAATATTATA
* *
2215021 AATTTTATTTTATTTTTATA
1 AATTTTATTTTAATATTATA
*
2215041 TATTTT
1 AATTTT
2215047 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTATTTTAATATTATA
Found at i:2215117 original size:19 final size:17
Alignment explanation
Indices: 2215090--2215133 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2215080 TATTAGTTAA
2215090 AAATATTATCACA-ATTAT
1 AAATATTAT-ACATA-TAT
2215108 AAATTATTATACATATAT
1 AAA-TATTATACATATAT
2215126 AAATATTA
1 AAATATTA
2215134 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 12 0.50
19 7 0.29
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTATACATATAT
Found at i:2216426 original size:6 final size:6
Alignment explanation
Indices: 2216415--2216447 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2216405 TGCAGTGAAG
2216415 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
2216448 GAGTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:2217093 original size:31 final size:32
Alignment explanation
Indices: 2217058--2217118 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
2217048 ATTTAAATTT
*
2217058 AAATATAATTTTT-TATTATTAAAAATATTAA
1 AAATATAATTTTTATATTAATAAAAATATTAA
*
2217089 AAATATTATTTTTATATTAATAAAAATATT
1 AAATATAATTTTTATATTAATAAAAATATT
2217119 TTTTATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
AAATATAATTTTTATATTAATAAAAATATTAA
Found at i:2217107 original size:20 final size:21
Alignment explanation
Indices: 2217082--2217141 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
2217072 ATTATTAAAA
2217082 ATATTAA-AAATATTATTTTT
1 ATATTAATAAATATTATTTTT
*
2217102 ATATTAATAAA-AATATTTTT
1 ATATTAATAAATATTATTTTT
2217122 -TATTAATTAAATAATTATTT
1 ATATTAA-TAAAT-ATTATTT
2217142 AAATTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 6 0.18
20 19 0.56
21 3 0.09
22 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTAATAAATATTATTTTT
Found at i:2217135 original size:24 final size:23
Alignment explanation
Indices: 2217086--2217131 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2217076 TTAAAAATAT
2217086 TAAAAATATTATTTTTATATTAA
1 TAAAAATATTATTTTTATATTAA
*
2217109 TAAAAATATTTTTTATTA-ATTAA
1 TAAAAATATTATTT-TTATATTAA
2217132 ATAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAAAATATTATTTTTATATTAA
Found at i:2217148 original size:21 final size:21
Alignment explanation
Indices: 2217123--2217177 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
2217113 AATATTTTTT
2217123 ATTAATTAAATAATTATTTAA
1 ATTAATTAAATAATTATTTAA
2217144 ATTAAATTAAAT-A-TATTTAA
1 ATT-AATTAAATAATTATTTAA
*
2217164 A-TAA-AAAATAATTA
1 ATTAATTAAATAATTA
2217178 AATATTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
19 3 0.10
20 8 0.27
21 4 0.13
22 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAATTAAATAATTATTTAA
Found at i:2217165 original size:15 final size:15
Alignment explanation
Indices: 2217143--2217181 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2217133 TAATTATTTA
* *
2217143 AATTAAATTAAATAT
1 AATTAAATAAAAAAT
*
2217158 ATTTAAATAAAAAAT
1 AATTAAATAAAAAAT
2217173 AATTAAATA
1 AATTAAATA
2217182 TTATATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTAAATAAAAAAT
Found at i:2218252 original size:9 final size:9
Alignment explanation
Indices: 2218240--2218301 Score: 56
Period size: 9 Copynumber: 6.7 Consensus size: 9
2218230 ATATGATAAG
2218240 ATATATTTA
1 ATATATTTA
2218249 ATATATATTA
1 ATATAT-TTA
2218259 CATTTATATTTA
1 -A--TATATTTA
*
2218271 AAAT-TTTA
1 ATATATTTA
2218279 ATATATTTA
1 ATATATTTA
2218288 ATA-ATTTA
1 ATATATTTA
*
2218296 TTATAT
1 ATATAT
2218302 GTTTAATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 14 0.32
9 17 0.39
10 3 0.07
11 2 0.05
12 3 0.07
13 5 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
ATATATTTA
Found at i:2218295 original size:17 final size:17
Alignment explanation
Indices: 2218240--2218301 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
2218230 ATATGATAAG
2218240 ATATATTTAATATATATTA
1 ATATATTTAATA-AT-TTA
2218259 CATTTATATTTAA-AATTTTA
1 -A--TATATTTAATAA-TTTA
2218279 ATATATTTAATAATTTA
1 ATATATTTAATAATTTA
*
2218296 TTATAT
1 ATATAT
2218302 GTTTAATTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 18 0.49
18 2 0.05
19 1 0.03
20 5 0.14
21 2 0.05
22 9 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTTAATAATTTA
Found at i:2218306 original size:19 final size:18
Alignment explanation
Indices: 2218240--2218308 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
2218230 ATATGATAAG
*
2218240 ATATATTTAATATATATTA
1 ATATATTTAATA-ATTTTA
2218259 CATTTATATTTAA-AATTTTA
1 -A--TATATTTAATAATTTTA
*
2218279 ATATATTTAATAATTTATT
1 ATATATTTAATAATTT-TA
*
2218298 ATATGTTTAAT
1 ATATATTTAAT
2218309 TCAAATAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.21
18 5 0.12
19 12 0.29
20 6 0.14
21 1 0.02
22 9 0.21
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (18 bp):
ATATATTTAATAATTTTA
Found at i:2219631 original size:17 final size:18
Alignment explanation
Indices: 2219598--2219633 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2219588 AGAATATTAT
*
2219598 ATATTTTATATAAATTTG
1 ATATGTTATATAAATTTG
2219616 ATATGTTATA-AAATTTG
1 ATATGTTATATAAATTTG
2219633 A
1 A
2219634 GATATTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
ATATGTTATATAAATTTG
Found at i:2226481 original size:33 final size:33
Alignment explanation
Indices: 2226439--2226514 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
2226429 TTCTGGAATT
2226439 ACTAAAGTTCACATTGTGGAGAAAGGACAGACC
1 ACTAAAGTTCACATTGTGGAGAAAGGACAGACC
2226472 ACTAAAGTTCACATTGTGGAGAAAGGACAGACC
1 ACTAAAGTTCACATTGTGGAGAAAGGACAGACC
2226505 ACTAAAGTTC
1 ACTAAAGTTC
2226515 TTAAACCTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (33 bp):
ACTAAAGTTCACATTGTGGAGAAAGGACAGACC
Found at i:2230418 original size:14 final size:14
Alignment explanation
Indices: 2230399--2230430 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2230389 GTGTATGCCT
2230399 ACATTAAATATGAC
1 ACATTAAATATGAC
2230413 ACATTAAATATGAC
1 ACATTAAATATGAC
2230427 ACAT
1 ACAT
2230431 ATGGATCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (14 bp):
ACATTAAATATGAC
Found at i:2233373 original size:20 final size:20
Alignment explanation
Indices: 2233351--2233389 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2233341 TAATTAAAAA
2233351 TTTTAAATTATAATATTATAT
1 TTTTAAA-TATAATATTATAT
*
2233372 TTTTAAATATAATTTTAT
1 TTTTAAATATAATATTAT
2233390 GTATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAATATAATATTATAT
Found at i:2240772 original size:24 final size:24
Alignment explanation
Indices: 2240736--2240785 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2240726 TTAGCACTAT
*
2240736 CAATCCACTTTGCAATGAATCAGA
1 CAATCCACCTTGCAATGAATCAGA
*
2240760 CAATCCGCCTTGCAATGAATCAGA
1 CAATCCACCTTGCAATGAATCAGA
2240784 CA
1 CA
2240786 TGAATCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (24 bp):
CAATCCACCTTGCAATGAATCAGA
Found at i:2251379 original size:27 final size:27
Alignment explanation
Indices: 2251349--2251401 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2251339 GGTAATTCAT
2251349 GTAATGCATGAACAACAAAGAAGCAGG
1 GTAATGCATGAACAACAAAGAAGCAGG
*
2251376 GTAATGCATGAACACCAAAGAAGCAG
1 GTAATGCATGAACAACAAAGAAGCAG
2251402 TCGGTAAATG
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:0.47, C:0.17, G:0.25, T:0.11
Consensus pattern (27 bp):
GTAATGCATGAACAACAAAGAAGCAGG
Found at i:2251627 original size:17 final size:17
Alignment explanation
Indices: 2251607--2251655 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 17
2251597 ATATATAAAT
2251607 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
*
2251624 ATA-T-AAA-TTATTAAA
1 ATATTAAAATTTA-TATA
2251639 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
2251656 TAATATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 2 0.08
17 9 0.35
18 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:2251635 original size:24 final size:24
Alignment explanation
Indices: 2251595--2251640 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2251585 TAATGATATG
2251595 ATATATATAAATATATTAAAATTT
1 ATATATATAAATATATTAAAATTT
2251619 ATATAATATAAAT-TATTAAAAT
1 ATAT-ATATAAATATATTAAAAT
2251641 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATATAAATATATTAAAATTT
Found at i:2251653 original size:25 final size:25
Alignment explanation
Indices: 2251599--2251646 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2251589 GATATGATAT
*
2251599 ATATAAATATATTAAAATTTATATA
1 ATATAAATATATTAAAATTTAAATA
2251624 ATATAAAT-TATTAAAATATTAAA
1 ATATAAATATATTAAAAT-TTAAA
2251647 ATTTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATAAATATATTAAAATTTAAATA
Found at i:2255114 original size:2 final size:2
Alignment explanation
Indices: 2255107--2255139 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2255097 CCACTACTTT
*
2255107 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2255140 TCAAGTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2269310 original size:32 final size:32
Alignment explanation
Indices: 2269254--2269333 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
2269244 TATTTTAAAT
* *
2269254 TTAATTTATTAACTTATAAGATTTAAATTAATG
1 TTAATTT-TTAAATTATAAGATTTAAATCAATG
* *
2269287 TTAATTTTTAAATTATATA-ATTTAAGTCAATT
1 TTAATTTTTAAATTATA-AGATTTAAATCAATG
*
2269319 TTAA-ATTTAAATTAT
1 TTAATTTTTAAATTAT
2269334 TTTTATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 10 0.24
32 23 0.56
33 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (32 bp):
TTAATTTTTAAATTATAAGATTTAAATCAATG
Found at i:2269692 original size:17 final size:17
Alignment explanation
Indices: 2269665--2269704 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2269655 ATTAAAATTT
*
2269665 TATTTATTTAATTTTTA
1 TATTTAATTAATTTTTA
*
2269682 TTTTTAATTAATTTTTA
1 TATTTAATTAATTTTTA
2269699 TATTTA
1 TATTTA
2269705 TAAAATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTAATTAATTTTTA
Found at i:2270214 original size:12 final size:13
Alignment explanation
Indices: 2270197--2270230 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2270187 AATTTGTCAG
2270197 ATTAAATTTAAA-
1 ATTAAATTTAAAT
*
2270209 ATTAAATATAAAT
1 ATTAAATTTAAAT
2270222 ATTAAATTT
1 ATTAAATTT
2270231 TTTATTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:2285108 original size:2 final size:2
Alignment explanation
Indices: 2285101--2285133 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2285091 GCATGCATCA
2285101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2285134 GAAATAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2285664 original size:11 final size:10
Alignment explanation
Indices: 2285622--2285667 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
2285612 TGAATATCAA
2285622 TATATATTTT
1 TATATATTTT
*
2285632 TA-ATTTTTT
1 TATATATTTT
*
2285641 TA-AAATTTT
1 TATATATTTT
2285650 TATATA-TTT
1 TATATATTTT
2285659 TATATATTT
1 TATATATTT
2285668 AAAAATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 24 0.80
10 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATATATTTT
Found at i:2285668 original size:26 final size:25
Alignment explanation
Indices: 2285639--2285694 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
2285629 TTTTAATTTT
* * *
2285639 TTTAAAATTTTTATATATTTTATATA
1 TTTAAAAATTATATATATATT-TATA
*
2285665 TTTAAAAATTATATTTATATTTATA
1 TTTAAAAATTATATATATATTTATA
2285690 TTTAA
1 TTTAA
2285695 TATAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTAAAAATTATATATATATTTATA
Found at i:2289366 original size:187 final size:186
Alignment explanation
Indices: 2289051--2289394 Score: 634
Period size: 187 Copynumber: 1.8 Consensus size: 186
2289041 TTGAATGATG
*
2289051 AATTACAATACTTGTATCTACTACAATTTGCTTTGTAATTAAGGTCGAGTAACTCAAGTGAGTCT
1 AATTACAATACTTGTATCTACTACAACTTGCTTTGTAATTAAGGTCGAGTAACTCAAGTGAGTCT
2289116 CCTGTCAACTTCATAATAGTAAATGAGGAAGGCCACAGTTGCAGTAACAAGAACTCCCACAGCTA
66 CCTGTCAACTTCATAATAGTAAATGAGGAAGGCCACAGTTGCAGTAACAAGAACTCCCACAGCTA
2289181 CCTTCAAAAGCTAACCTTGAAGGCGAAACTCAGAGAGTTTCTTGTGGGAGCCTGCAT
131 CCTTC-AAAGCTAACCTTGAAGGCGAAACTCAGAGAGTTTCTTGTGGGAGCCTGCAT
2289238 AATTACAATACTTGTATCTACTACAACTTGCTTTGTAATTAAGGTCGAGTAACTCAAGTGAGTCT
1 AATTACAATACTTGTATCTACTACAACTTGCTTTGTAATTAAGGTCGAGTAACTCAAGTGAGTCT
* * *
2289303 CCTTTCAACTTCATAATAGTAACTGAGGAAGGCCATAGTTGCAGTAACAAGAACTCCCACAGCTA
66 CCTGTCAACTTCATAATAGTAAATGAGGAAGGCCACAGTTGCAGTAACAAGAACTCCCACAGCTA
*
2289368 TCTTCAAAGCTAACCTTGAAGGCGAAA
131 CCTTCAAAGCTAACCTTGAAGGCGAAA
2289395 TGAAGCCTAG
Statistics
Matches: 152, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
186 22 0.14
187 130 0.86
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (186 bp):
AATTACAATACTTGTATCTACTACAACTTGCTTTGTAATTAAGGTCGAGTAACTCAAGTGAGTCT
CCTGTCAACTTCATAATAGTAAATGAGGAAGGCCACAGTTGCAGTAACAAGAACTCCCACAGCTA
CCTTCAAAGCTAACCTTGAAGGCGAAACTCAGAGAGTTTCTTGTGGGAGCCTGCAT
Found at i:2297376 original size:2 final size:2
Alignment explanation
Indices: 2297369--2297395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2297359 TTTGAGCTAC
2297369 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
2297396 TTAATTAACA
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:2298262 original size:26 final size:28
Alignment explanation
Indices: 2298214--2298280 Score: 93
Period size: 26 Copynumber: 2.5 Consensus size: 28
2298204 TCAAAATGTT
*
2298214 TAATTTTATTTTTTAAAATTATATGTAA
1 TAATTTTATTTTTCAAAATTATATGTAA
*
2298242 TAATTTT-TTTTTCATAA-TATATGTAA
1 TAATTTTATTTTTCAAAATTATATGTAA
*
2298268 TAATTTTACTTTT
1 TAATTTTATTTTT
2298281 AAATAAATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 16 0.46
27 12 0.34
28 7 0.20
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (28 bp):
TAATTTTATTTTTCAAAATTATATGTAA
Found at i:2298289 original size:29 final size:28
Alignment explanation
Indices: 2298214--2298289 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 28
2298204 TCAAAATGTT
*
2298214 TAATTTTATTTTTTAA-AATTATATGTAA
1 TAATTTTA-TTTTTAATAAATATATGTAA
*
2298242 TAATTTT-TTTTTCAT-AATATATGTAA
1 TAATTTTATTTTTAATAAATATATGTAA
*
2298268 TAATTTTACTTTTAAATAAATA
1 TAATTTTA-TTTTTAATAAATA
2298290 CTCACTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 23 0.57
28 13 0.32
29 4 0.10
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (28 bp):
TAATTTTATTTTTAATAAATATATGTAA
Found at i:2300626 original size:17 final size:17
Alignment explanation
Indices: 2300604--2300640 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2300594 GCAGTTATAC
2300604 TCTTTTTCTTTTTTTT-T
1 TCTTTTT-TTTTTTTTGT
2300621 TCTTTTTTTTTTTTTGT
1 TCTTTTTTTTTTTTTGT
2300638 TCT
1 TCT
2300641 CTCGGGGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (17 bp):
TCTTTTTTTTTTTTTGT
Found at i:2300633 original size:12 final size:11
Alignment explanation
Indices: 2300606--2300632 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2300596 AGTTATACTC
2300606 TTTTTCTTTTT
1 TTTTTCTTTTT
2300617 TTTTTCTTTTT
1 TTTTTCTTTTT
2300628 TTTTT
1 TTTTT
2300633 TTTGTTCTCT
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:2303655 original size:3 final size:3
Alignment explanation
Indices: 2303647--2303677 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2303637 GTGGCTAATT
2303647 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2303678 GAGTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2309933 original size:18 final size:17
Alignment explanation
Indices: 2309848--2309934 Score: 52
Period size: 18 Copynumber: 4.9 Consensus size: 17
2309838 TAATTTGATA
*
2309848 ATATTTATATTATATTAT
1 ATATTTATA-TATTTTAT
* *
2309866 ATATTTTTATATTATAATT
1 ATATTTATATATT-TTA-T
* * *
2309885 ATATTTA-AAATATTAA
1 ATATTTATATATTTTAT
*
2309901 ATA-TTATAAATTTTTCAT
1 ATATTTATATA-TTTT-AT
2309919 ATATTTATATATTTTA
1 ATATTTATATATTTTA
2309935 ATTATAATCA
Statistics
Matches: 52, Mismatches: 11, Indels: 13
0.68 0.14 0.17
Matches are distributed among these distances:
15 3 0.06
16 6 0.12
17 9 0.17
18 21 0.40
19 13 0.25
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTATATATTTTAT
Found at i:2309947 original size:19 final size:18
Alignment explanation
Indices: 2309925--2309976 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
2309915 TCATATATTT
2309925 ATATATTTTAATTATAATC
1 ATATATTTTAATTATAA-C
*
2309944 ATATTATTTT-TTTATAAC
1 ATA-TATTTTAATTATAAC
*
2309962 ATAT-TTTAAATTATA
1 ATATATTTTAATTATA
2309977 TTTTAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.11
17 6 0.21
18 4 0.14
19 9 0.32
20 6 0.21
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATATTTTAATTATAAC
Found at i:2311163 original size:2 final size:2
Alignment explanation
Indices: 2311156--2311199 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2311146 TAGTTCAACA
2311156 AT AT 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 AT AT
2311198 AT
1 AT
2311200 TAACACCTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2312085 original size:2 final size:2
Alignment explanation
Indices: 2312078--2312102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2312068 ACATCCATAA
2312078 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 A
2312103 AGGTAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2313970 original size:19 final size:22
Alignment explanation
Indices: 2313946--2313993 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
2313936 TTGTCACGCC
2313946 AATTAA-TA-TAATAATA-ATT
1 AATTAATTATTAATAATATATT
2313965 AATTAATTATTAATAATATTATT
1 AATTAATTATTAATAATA-TATT
2313988 AATTAA
1 AATTAA
2313994 ATTTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 8 0.32
23 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTAATTATTAATAATATATT
Found at i:2313972 original size:23 final size:20
Alignment explanation
Indices: 2313946--2313993 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 20
2313936 TTGTCACGCC
2313946 AATTAATATAATAATAATTAATT
1 AATTAAT-TAATAAT-ATT-ATT
2313969 AATT-ATTAATAATATTATT
1 AATTAATTAATAATATTATT
2313988 AATTAA
1 AATTAA
2313994 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 7 0.29
22 2 0.08
23 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTAATTAATAATATTATT
Found at i:2321697 original size:16 final size:16
Alignment explanation
Indices: 2321676--2321720 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2321666 TTATGTTGAT
2321676 ATTTTATAATTTT-ATA
1 ATTTTA-AATTTTAATA
2321692 ATTTTAAATTTTAATA
1 ATTTTAAATTTTAATA
*
2321708 ATTATAATATTTT
1 ATTTTAA-ATTTT
2321721 TTATTCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.23
16 15 0.58
17 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAAATTTTAATA
Found at i:2321703 original size:7 final size:8
Alignment explanation
Indices: 2321676--2321710 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
2321666 TTATGTTGAT
2321676 ATTTTATA
1 ATTTTATA
2321684 ATTTTATA
1 ATTTTATA
2321692 ATTTTA-A
1 ATTTTATA
2321699 ATTTTAATA
1 ATTTT-ATA
2321708 ATT
1 ATT
2321711 ATAATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.24
8 15 0.60
9 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTATA
Found at i:2321719 original size:24 final size:23
Alignment explanation
Indices: 2321676--2321721 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
2321666 TTATGTTGAT
*
2321676 ATTTTATAATTTTATAATTTTAA
1 ATTTTATAATTTAATAATTTTAA
*
2321699 ATTTTAATAATTATAATATTTTT
1 ATTTT-ATAATT-TAATAATTTT
2321722 TATTCTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 6 0.32
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTATAATTTAATAATTTTAA
Found at i:2323872 original size:21 final size:22
Alignment explanation
Indices: 2323827--2323873 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2323817 AAAATTATAA
* *
2323827 AATTTTTATATATTTAACAACT
1 AATTTTTATATATTAAACAAAT
*
2323849 AATTTTT-TATATTAAATAAAT
1 AATTTTTATATATTAAACAAAT
2323870 AATT
1 AATT
2323874 AAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTTATATATTAAACAAAT
Found at i:2324205 original size:14 final size:14
Alignment explanation
Indices: 2324163--2324207 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2324153 TTTTTATTAA
2324163 TATAATAATTAAATT
1 TATAAT-ATTAAATT
*
2324178 TATATTACTT-AATT
1 TATAATA-TTAAATT
2324192 TATAATATTAAATT
1 TATAATATTAAATT
2324206 TA
1 TA
2324208 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.08
14 17 0.65
15 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TATAATATTAAATT
Found at i:2324461 original size:26 final size:26
Alignment explanation
Indices: 2324419--2324470 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2324409 CGTGCTTAGA
*
2324419 AAAAGACAAAATATAATGTATTAAAG
1 AAAAGACAAAATATAATGGATTAAAG
*
2324445 AAAAGACACGAAT-TAATGGATTAAAG
1 AAAAGACA-AAATATAATGGATTAAAG
2324471 TGAGTAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (26 bp):
AAAAGACAAAATATAATGGATTAAAG
Found at i:2324864 original size:21 final size:21
Alignment explanation
Indices: 2324840--2324882 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2324830 TCAAATTATC
2324840 ATTTAAAATT-TAATTTATTAA
1 ATTT-AAATTATAATTTATTAA
*
2324861 ATTTAAATTATATTTTATTAA
1 ATTTAAATTATAATTTATTAA
2324882 A
1 A
2324883 ATATATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAAATTATAATTTATTAA
Found at i:2325415 original size:21 final size:21
Alignment explanation
Indices: 2325377--2325422 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
2325367 AACTTATATT
2325377 TAAATATTTATGAAATAATAATA
1 TAAATATTTA-GAAATAATAA-A
2325400 TAAATATTTA-AAATAATAAA
1 TAAATATTTAGAAATAATAAA
2325420 TAA
1 TAA
2325423 CTCAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 9 0.39
23 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAATATTTAGAAATAATAAA
Found at i:2326819 original size:3 final size:3
Alignment explanation
Indices: 2326811--2326850 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
2326801 GTTTTCTAGA
* *
2326811 AAG AAG AAG AAG AAG AAG AAG ACG ACG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2326851 GCGGAGAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.05, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2332048 original size:26 final size:26
Alignment explanation
Indices: 2332001--2332050 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2331991 ATTATTCAAA
**
2332001 TTTAAATAAAAATACTCTTATTTTAC
1 TTTAAATAAAAATACTAATATTTTAC
2332027 TTTAAATAAAAATTA-TAATATTTT
1 TTTAAATAAAAA-TACTAATATTTT
2332051 TTTATGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTAAATAAAAATACTAATATTTTAC
Found at i:2332131 original size:22 final size:21
Alignment explanation
Indices: 2332089--2332130 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2332079 AAAGTAATAT
2332089 TTTTTTTCATCTTACTTAAAA
1 TTTTTTTCATCTTACTTAAAA
2332110 TTTTTTTCATCTTGA-TTAAAA
1 TTTTTTTCATCTT-ACTTAAAA
2332131 AAGTTAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTTTTCATCTTACTTAAAA
Found at i:2333126 original size:13 final size:13
Alignment explanation
Indices: 2333108--2333133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2333098 TTGATATGAT
2333108 TGGGCATCTTAAA
1 TGGGCATCTTAAA
2333121 TGGGCATCTTAAA
1 TGGGCATCTTAAA
2333134 CTATGTTTCA
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
TGGGCATCTTAAA
Found at i:2337368 original size:2 final size:2
Alignment explanation
Indices: 2337361--2337395 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2337351 TAATACACAT
2337361 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
2337396 TAGACTAATA
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:2342131 original size:25 final size:26
Alignment explanation
Indices: 2342080--2342180 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 26
2342070 ACACCATATA
* *
2342080 TACA-TATATATATATATAA-TCAATT
1 TACATTATATAAATAT-TAATTAAATT
*
2342105 TACATTATATAAA-ATTAATTAATTT
1 TACATTATATAAATATTAATTAAATT
*
2342130 TACATTTTAATAAATTATTAATTAAATT
1 TACATTAT-ATAAA-TATTAATTAAATT
*
2342158 TA-ATAATATAATTATATTAATTA
1 TACATTATATAA--ATATTAATTA
2342181 TGTAAATAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
24 3 0.05
25 17 0.27
26 16 0.26
27 12 0.19
28 14 0.23
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TACATTATATAAATATTAATTAAATT
Found at i:2342150 original size:28 final size:25
Alignment explanation
Indices: 2342101--2342168 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 25
2342091 ATATATAATC
2342101 AATTTACATTATATAAAATTAATTA
1 AATTTACATTATATAAAATTAATTA
* *
2342126 ATTTTACATTTTAATAAATTATTAATTA
1 AATTTACATTAT-ATAAA--ATTAATTA
*
2342154 AATTTA-ATAATATAA
1 AATTTACATTATATAA
2342169 TTATATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 10 0.29
26 9 0.26
27 3 0.09
28 13 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTACATTATATAAAATTAATTA
Found at i:2342159 original size:21 final size:23
Alignment explanation
Indices: 2342135--2342177 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2342125 AATTTTACAT
*
2342135 TTTAATAA-ATTATTA-ATTAAA
1 TTTAATAATATAATTATATTAAA
2342156 TTTAATAATATAATTATATTAA
1 TTTAATAATATAATTATATTAA
2342178 TTATGTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAATAATATAATTATATTAAA
Found at i:2345581 original size:3 final size:3
Alignment explanation
Indices: 2345575--2345611 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2345565 CTACTACTTA
2345575 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 T
2345612 CTCAGTGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2350155 original size:40 final size:40
Alignment explanation
Indices: 2350100--2350182 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
2350090 AACATGCATT
2350100 TTTCAATATTACTAAATTAATTTATTAATGTACATATTTA
1 TTTCAATATTACTAAATTAATTTATTAATGTACATATTTA
*
2350140 TTTCATTATTACTAAATTAATTTATTAATGTACATATTTA
1 TTTCAATATTACTAAATTAATTTATTAATGTACATATTTA
2350180 TTT
1 TTT
2350183 TGCTTCTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (40 bp):
TTTCAATATTACTAAATTAATTTATTAATGTACATATTTA
Done.