Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000880.1 Hibiscus syriacus cultivar Beakdansim tig00001713_pilon, 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: 1459553
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:985706 original size:16 final size:16
Alignment explanation
Indices: 985685--985747 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
985675 TCATTTACAG
985685 GTCAGGTTAAAAACAA
1 GTCAGGTTAAAAACAA
* *
985701 GTCAGGTTAAAAATAG
1 GTCAGGTTAAAAACAA
* *
985717 GTCAGGTTGAAAACAT
1 GTCAGGTTAAAAACAA
*
985733 GTCAGGTTGAAAACA
1 GTCAGGTTAAAAACA
985748 GGTCGGGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GTCAGGTTAAAAACAA
Found at i:985719 original size:32 final size:32
Alignment explanation
Indices: 985681--985751 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
985671 TGGATCATTT
985681 ACAGGTCAGGTTAAAAACAAGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAAACAAGTCAGGTTAAAA
* * * *
985713 ATAGGTCAGGTTGAAAACATGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAAACAAGTCAGGTTAAAA
985745 ACAGGTC
1 ACAGGTC
985752 GGGTAATACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (32 bp):
ACAGGTCAGGTTAAAAACAAGTCAGGTTAAAA
Found at i:986722 original size:34 final size:35
Alignment explanation
Indices: 986668--986740 Score: 139
Period size: 34 Copynumber: 2.1 Consensus size: 35
986658 ATTAAAACCA
986668 AAATATTATTAAAAAAAAAAGAAAGAATCAGCTTT
1 AAATATTATTAAAAAAAAAAGAAAGAATCAGCTTT
986703 AAATATTATT-AAAAAAAAAGAAAGAATCAGCTTT
1 AAATATTATTAAAAAAAAAAGAAAGAATCAGCTTT
986737 AAAT
1 AAAT
986741 GGTCTTGACC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 28 0.74
35 10 0.26
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.26
Consensus pattern (35 bp):
AAATATTATTAAAAAAAAAAGAAAGAATCAGCTTT
Found at i:988716 original size:43 final size:43
Alignment explanation
Indices: 988555--988760 Score: 143
Period size: 43 Copynumber: 4.8 Consensus size: 43
988545 TTGGGACAAT
* * *
988555 AAACGCCGCAATAGGATTTGATATTTAGCGGCGTTTGTCCAAA
1 AAACGACGCAATAGGTTTTGATATTTAGCGGCGTTTGTCCAAC
* * * ** * *
988598 AAATG-CGTAATAGGTGTTGAGGTTTAGCGACGTTTTTCC-AC
1 AAACGACGCAATAGGTTTTGATATTTAGCGGCGTTTGTCCAAC
* * * * * * **
988639 AAA-TACCGCAATAGGTATTAAGATTTCGCAGCGTTTGTTTAAC
1 AAACGA-CGCAATAGGTTTTGATATTTAGCGGCGTTTGTCCAAC
* *
988682 AAACGACGCAATAGGTTTTGATATTTAGAGGCGTTTCTCTC-AC
1 AAACGACGCAATAGGTTTTGATATTTAGCGGCGTTTGTC-CAAC
* **
988725 AAACGCCATAATA-GTTTTCGATATTTAGCGGCGTTT
1 AAACGACGCAATAGGTTTT-GATATTTAGCGGCGTTT
988761 TTAACACAAA
Statistics
Matches: 123, Mismatches: 34, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
41 4 0.03
42 56 0.46
43 62 0.50
44 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (43 bp):
AAACGACGCAATAGGTTTTGATATTTAGCGGCGTTTGTCCAAC
Found at i:988769 original size:43 final size:43
Alignment explanation
Indices: 988691--988773 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
988681 CAAACGACGC
**
988691 AATAGGTTTTGATATTTAGAGGCGTTTCTCTCACAAACGCCAT
1 AATAGGTTTTGATATTTAGAGGCGTTTCTAACACAAACGCCAT
* *
988734 AATA-GTTTTCGATATTTAGCGGCGTTTTTAACACAAACGC
1 AATAGGTTTT-GATATTTAGAGGCGTTTCTAACACAAACGC
988774 TACAATAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 5 0.14
43 30 0.86
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (43 bp):
AATAGGTTTTGATATTTAGAGGCGTTTCTAACACAAACGCCAT
Found at i:996823 original size:169 final size:165
Alignment explanation
Indices: 996563--996964 Score: 436
Period size: 169 Copynumber: 2.4 Consensus size: 165
996553 AAAAAGTTGT
* *
996563 TAAAGTACAAATATTTTGCGGCG-TTTATTAAAAAAGCGACTATAGATTACACCTATTGTGGCGT
1 TAAAGTACAAATATTTTGCGGCGTTTTATTAAAAAAGCCACTATAGATTACACCTATTGCGGCGT
* * *
996627 TTGTACAAAAACACCGCTAAAGTATAAATATTTTGCGGCGTTT-GT-TGAAATAACACCACTATA
66 TTGTACAAAAACACCACTAAAGTATAAATATTTTACGGCATTTGGTAT-AAA-AACACCACTATA
* *
996690 TATATCAAACCTATTGCGGCGTTTGTACAAAAATGCCGC
129 GAT-T-AAACCTATTGCGGCGTTTGTACAAAAACGCCGC
* * *
996729 TAAAGTATAAATATTTTGCGGCGTTTTTTTATCCAAACA-CCACTATAGATTACACCTATTGCGG
1 TAAAGTACAAATATTTTGCGGCGTTTTATTA---AAAAAGCCACTATAGATTACACCTATTGCGG
* * * *** * *
996793 CGTTTTTATAAAAACACTACTTTTGTATAAATATTTTACGGCATTTGGTATTAAAACGCCACTAT
63 CGTTTGTACAAAAACACCACTAAAGTATAAATATTTTACGGCATTTGGTATAAAAACACCACTAT
* *
996858 AGATTACACCTATTGCGGCGTTTGTATAAAAACGCCGC
128 AGATTAAACCTATTGCGGCGTTTGTACAAAAACGCCGC
* * * * * * *
996896 TAAAGTACAAATATTTTTGCGACGTTTCT-TGAAAAAACGCAACTATATAGTAAACCTATTGCGA
1 TAAAGTACAAATA-TTTTGCGGCGTTT-TATTAAAAAA-GCCACTATAGATTACACCTATTGCGG
996960 CGTTT
63 CGTTT
996965 TTTATATAAA
Statistics
Matches: 197, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
165 4 0.02
166 22 0.11
167 73 0.37
168 15 0.08
169 74 0.38
170 8 0.04
171 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (165 bp):
TAAAGTACAAATATTTTGCGGCGTTTTATTAAAAAAGCCACTATAGATTACACCTATTGCGGCGT
TTGTACAAAAACACCACTAAAGTATAAATATTTTACGGCATTTGGTATAAAAACACCACTATAGA
TTAAACCTATTGCGGCGTTTGTACAAAAACGCCGC
Found at i:996886 original size:83 final size:82
Alignment explanation
Indices: 996563--996912 Score: 364
Period size: 83 Copynumber: 4.2 Consensus size: 82
996553 AAAAAGTTGT
* * * * *
996563 TAAAGTACAAATATTTTGCGGCGTTTAT-TAAAAA-AGCGACTATAGATTACACCTATTGTGGCG
1 TAAAGTATAAATATTTTGCGGCATTTGTATAAAAACA-CCACTATAGATTACACCTATTGCGGCG
996626 TTTGTACAAAAACACCGC
65 TTTGTACAAAAACACCGC
* * *
996644 TAAAGTATAAATATTTTGCGGCGTTTGT-TGAAATAACACCACTATATATATCAAACCTATTGCG
1 TAAAGTATAAATATTTTGCGGCATTTGTAT-AAA-AACACCACTATAGAT-T-ACACCTATTGCG
**
996708 GCGTTTGTACAAAAATGCCGC
62 GCGTTTGTACAAAAACACCGC
* * **
996729 TAAAGTATAAATATTTTGCGGCGTTTTTTTATCCAAACACCACTATAGATTACACCTATTGCGGC
1 TAAAGTATAAATATTTTGCGGC--ATTTGTATAAAAACACCACTATAGATTACACCTATTGCGGC
* * **
996794 GTTTTTATAAAAACACTAC
64 GTTTGTACAAAAACACCGC
*** * * *
996813 TTTTGTATAAATATTTTACGGCATTTGGTATTAAAACGCCACTATAGATTACACCTATTGCGGCG
1 TAAAGTATAAATATTTTGCGGCATTT-GTATAAAAACACCACTATAGATTACACCTATTGCGGCG
* *
996878 TTTGTATAAAAACGCCGC
65 TTTGTACAAAAACACCGC
*
996896 TAAAGTACAAATATTTT
1 TAAAGTATAAATATTTT
996913 TGCGACGTTT
Statistics
Matches: 223, Mismatches: 37, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
81 27 0.12
82 6 0.03
83 72 0.32
84 46 0.21
85 52 0.23
86 14 0.06
87 5 0.02
88 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (82 bp):
TAAAGTATAAATATTTTGCGGCATTTGTATAAAAACACCACTATAGATTACACCTATTGCGGCGT
TTGTACAAAAACACCGC
Found at i:996893 original size:41 final size:42
Alignment explanation
Indices: 996578--996890 Score: 185
Period size: 41 Copynumber: 7.5 Consensus size: 42
996568 TACAAATATT
* * *
996578 TTGCGGCGTTTAT-TAAAAA-AGCGACTATAGAT-TACACCTA
1 TTGCGGCGTTTGTATAAAAACA-CCACTATAGATATAAACCTA
* * * * ** *
996618 TTGTGGCGTTTGTACAAAAACACCGCTAAAG-TATAAATATT
1 TTGCGGCGTTTGTATAAAAACACCACTATAGATATAAACCTA
*
996659 TTGCGGCGTTTGT-TGAAATAACACCACTATATATATCAAACCTA
1 TTGCGGCGTTTGTAT-AAA-AACACCACTATAGATAT-AAACCTA
* ** * * ** *
996703 TTGCGGCGTTTGTACAAAAATGCCGCTAAAG-TATAAATATT
1 TTGCGGCGTTTGTATAAAAACACCACTATAGATATAAACCTA
* ** *
996744 TTGCGGCGTTTTTTTATCCAAACACCACTATAGAT-TACACCTA
1 TTGCGGCG--TTTGTATAAAAACACCACTATAGATATAAACCTA
* * * * ** *
996787 TTGCGGCGTTTTTATAAAAACACTACTTTTG-TATAAATATT
1 TTGCGGCGTTTGTATAAAAACACCACTATAGATATAAACCTA
* * * * *
996828 TTACGGCATTTGGTATTAAAACGCCACTATAGAT-TACACCTA
1 TTGCGGCGTTT-GTATAAAAACACCACTATAGATATAAACCTA
996870 TTGCGGCGTTTGTATAAAAAC
1 TTGCGGCGTTTGTATAAAAAC
996891 GCCGCTAAAG
Statistics
Matches: 196, Mismatches: 63, Indels: 27
0.69 0.22 0.09
Matches are distributed among these distances:
40 13 0.07
41 82 0.42
42 41 0.21
43 39 0.20
44 21 0.11
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (42 bp):
TTGCGGCGTTTGTATAAAAACACCACTATAGATATAAACCTA
Found at i:996958 original size:167 final size:167
Alignment explanation
Indices: 996563--996975 Score: 458
Period size: 167 Copynumber: 2.5 Consensus size: 167
996553 AAAAAGTTGT
* *
996563 TAAAGTACAAATATTTTGCGGCGTTTATTAAAAAA-GCGACTATAGATTACACCTATTGTGGCGT
1 TAAAGTACAAATATTTTGCGGCGTTTATTAAAAAACGCAACTATAGATTACACCTATTGCGGCGT
* * * * * *
996627 TTGTACAAAAACACCGCTAAAGTATAAATATTTTGCGGCGTTTGTTGAAATAACACCACTATATA
66 TTTTATAAAAACACCACTAAAGTATAAATATTTTACGGCATTTGTTGAAATAACACCACTATAGA
*
996692 TATCAAACCTATTGCGGCGTTTGTACAAAAATGCCGC
131 TATCAAACCTATTGCGGCGTTTGTACAAAAACGCCGC
* * ** * *
996729 TAAAGTATAAATATTTTGCGGCGTTTTTTTATCCAAACACCACTATAGATTACACCTATTGCGGC
1 TAAAGTACAAATATTTTGCGGCG-TTTATTA-AAAAACGCAACTATAGATTACACCTATTGCGGC
* *** * *
996794 GTTTTTATAAAAACACTACTTTTGTATAAATATTTTACGGCATTTGGTAT-TAA-AACGCCACTA
64 GTTTTTATAAAAACACCACTAAAGTATAAATATTTTACGGCATTT-GT-TGAAATAACACCACTA
* *
996857 TAGAT-T-ACACCTATTGCGGCGTTTGTATAAAAACGCCGC
127 TAGATATCAAACCTATTGCGGCGTTTGTACAAAAACGCCGC
* * * * * *
996896 TAAAGTACAAATATTTTTGCGACGTTTCTTGAAAAAACGCAACTATATAGTAAACCTATTGCGAC
1 TAAAGTACAAATA-TTTTGCGGCGTTTATT-AAAAAACGCAACTATAGATTACACCTATTGCGGC
*
996961 GTTTTTTATATAAAC
64 G-TTTTTATAAAAAC
996976 GCCGCAAAAT
Statistics
Matches: 205, Mismatches: 34, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
166 22 0.11
167 79 0.39
168 26 0.13
169 73 0.36
170 4 0.02
171 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (167 bp):
TAAAGTACAAATATTTTGCGGCGTTTATTAAAAAACGCAACTATAGATTACACCTATTGCGGCGT
TTTTATAAAAACACCACTAAAGTATAAATATTTTACGGCATTTGTTGAAATAACACCACTATAGA
TATCAAACCTATTGCGGCGTTTGTACAAAAACGCCGC
Found at i:996964 original size:84 final size:82
Alignment explanation
Indices: 996563--996980 Score: 415
Period size: 84 Copynumber: 5.0 Consensus size: 82
996553 AAAAAGTTGT
* * * *
996563 TAAAGTACAAATATTTTGCGGCGTTTATTAAAAAA-GCGACTATAGATTACACCTATTGTGGCGT
1 TAAAGTATAAATATTTTGCGGCGTTTGTTAAAAAACGCCACTATAGATTACACCTATTGCGGCGT
* *
996627 TTGTACAAAAACACCGC
66 TTGTATAAAAACGCCGC
* * * *
996644 TAAAGTATAAATATTTTGCGGCGTTTGTTGAAATAACACCACTATATATATCAAACCTATTGCGG
1 TAAAGTATAAATATTTTGCGGCGTTTGTT-AAAAAACGCCACTATAGAT-T-ACACCTATTGCGG
* *
996709 CGTTTGTACAAAAATGCCGC
63 CGTTTGTATAAAAACGCCGC
* ** *
996729 TAAAGTATAAATATTTTGCGGCGTTTTTTTATCCAAACACCACTATAGATTACACCTATTGCGGC
1 TAAAGTATAAATATTTTGCGGCG-TTTGTTA-AAAAACGCCACTATAGATTACACCTATTGCGGC
* * **
996794 GTTTTTATAAAAACACTAC
64 GTTTGTATAAAAACGCCGC
*** * * * *
996813 TTTTGTATAAATATTTTACGGCATTTGGTATTAAAACGCCACTATAGATTACACCTATTGCGGCG
1 TAAAGTATAAATATTTTGCGGCGTTTGTTA-AAAAACGCCACTATAGATTACACCTATTGCGGCG
996878 TTTGTATAAAAACGCCGC
65 TTTGTATAAAAACGCCGC
* * * * * * * *
996896 TAAAGTACAAATATTTTTGCGACGTTTCTTGAAAAAACGCAACTATATAGTAAACCTATTGCGAC
1 TAAAGTATAAATA-TTTTGCGGCGTTTGTT-AAAAAACGCCACTATAGATTACACCTATTGCGGC
* *
996961 GTTTTTTATATAAACGCCGC
64 G-TTTGTATAAAAACGCCGC
996981 AAAATTCTGG
Statistics
Matches: 275, Mismatches: 53, Indels: 14
0.80 0.15 0.04
Matches are distributed among these distances:
81 27 0.10
82 5 0.02
83 69 0.25
84 84 0.31
85 71 0.26
86 19 0.07
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (82 bp):
TAAAGTATAAATATTTTGCGGCGTTTGTTAAAAAACGCCACTATAGATTACACCTATTGCGGCGT
TTGTATAAAAACGCCGC
Found at i:997241 original size:73 final size:73
Alignment explanation
Indices: 997154--997299 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 73
997144 GTTATGCATT
* * *
997154 AAATTAATACTTAACAACAGAATACATTAAAATTTAGAAACATTAAAGTTATGCATAGACACTCT
1 AAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAAAACTCT
997219 TCACCATA
66 TCACCATA
*
997227 AAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAAAAGTCT
1 AAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAAAACTCT
997292 TCACCATA
66 TCACCATA
997300 TTGTTCACTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (73 bp):
AAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAAAACTCT
TCACCATA
Found at i:1002528 original size:16 final size:16
Alignment explanation
Indices: 1002507--1002539 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1002497 TCTTGCAGTA
1002507 CGTAAT-TATATTATTT
1 CGTAATCTA-ATTATTT
1002523 CGTAATCTAATTATTT
1 CGTAATCTAATTATTT
1002539 C
1 C
1002540 ATCATACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (16 bp):
CGTAATCTAATTATTT
Found at i:1002841 original size:18 final size:18
Alignment explanation
Indices: 1002807--1002841 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1002797 ATATTTGCAT
**
1002807 TATCGATACCACTATGAG
1 TATCGATACCAAAATGAG
1002825 TATCGATACCAAAATGA
1 TATCGATACCAAAATGA
1002842 CTTCTGTTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (18 bp):
TATCGATACCAAAATGAG
Found at i:1003523 original size:15 final size:17
Alignment explanation
Indices: 1003505--1003549 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
1003495 AAAAATGAGA
1003505 AAGA-AATAAAAA-ATG
1 AAGAGAATAAAAAGATG
1003520 AAGAGAATAAAAAGATG
1 AAGAGAATAAAAAGATG
*
1003537 AATAGATATAAAA
1 AAGAGA-ATAAAA
1003550 GCCTTCATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 8 0.31
18 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (17 bp):
AAGAGAATAAAAAGATG
Found at i:1003526 original size:17 final size:17
Alignment explanation
Indices: 1003495--1003549 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
1003485 GAAGAAGAGT
1003495 AAAAATGAGAAAGAAATA
1 AAAAATGA-AAAGAAATA
*
1003513 AAAAATGAAGAG-AATA
1 AAAAATGAAAAGAAATA
* *
1003529 AAAAGATGAATAGATATA
1 AAAA-ATGAAAAGAAATA
1003547 AAA
1 AAA
1003550 GCCTTCATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 8 0.25
17 10 0.31
18 14 0.44
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.15
Consensus pattern (17 bp):
AAAAATGAAAAGAAATA
Found at i:1003548 original size:34 final size:34
Alignment explanation
Indices: 1003485--1003549 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1003475 GCTTGAAGAA
*
1003485 GAAGAAGAGTAAAAATGAGAAAGAAATAAAAAAT
1 GAAGAAGAATAAAAATGAGAAAGAAATAAAAAAT
*
1003519 GAAG-AGAATAAAAA-GATGAATAGATATAAAA
1 GAAGAAGAATAAAAATGA-GAA-AGAAATAAAA
1003550 GCCTTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.07
33 12 0.44
34 13 0.48
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (34 bp):
GAAGAAGAATAAAAATGAGAAAGAAATAAAAAAT
Found at i:1004838 original size:23 final size:23
Alignment explanation
Indices: 1004795--1004838 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1004785 TTTAAAATGG
*
1004795 AAACATCAACCATTCATTAAAAA
1 AAACATCAACCATTCAGTAAAAA
*
1004818 AAACAT-AATCATTCAAGTAAA
1 AAACATCAACCATTC-AGTAAA
1004839 CCCACACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.57, C:0.18, G:0.02, T:0.23
Consensus pattern (23 bp):
AAACATCAACCATTCAGTAAAAA
Found at i:1014043 original size:77 final size:77
Alignment explanation
Indices: 1013911--1014066 Score: 249
Period size: 77 Copynumber: 2.0 Consensus size: 77
1013901 ATACTACCAC
1013911 TAAAAAGGAACTTTTAACAATAGTATTTGCATTCGATAAGTTTAGGAAATACCTATAAGCACTAA
1 TAAAAAGGAACTTTTAACAATAGTATTTGCATTCGATAAGTTTAGGAAATACCTATAAGCACTAA
*
1013976 GGTAATTGTGCA
66 AGTAATTGTGCA
** * * * *
1013988 TAAAAAGGAACTTTTAACCGTAGTATTTGTATTCGATAAGTTTAGGCAATCCCTATAGGCACTAA
1 TAAAAAGGAACTTTTAACAATAGTATTTGCATTCGATAAGTTTAGGAAATACCTATAAGCACTAA
1014053 AGTAATTGTGCA
66 AGTAATTGTGCA
1014065 TA
1 TA
1014067 CAGATCACTC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (77 bp):
TAAAAAGGAACTTTTAACAATAGTATTTGCATTCGATAAGTTTAGGAAATACCTATAAGCACTAA
AGTAATTGTGCA
Found at i:1035262 original size:20 final size:20
Alignment explanation
Indices: 1035226--1035263 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1035216 TGGCATTCTG
*
1035226 AAATGTTTTCAAGCCTGGAT
1 AAATGTTTGCAAGCCTGGAT
1035246 AAATGATTTGCAA-CCTGG
1 AAATG-TTTGCAAGCCTGG
1035264 TTCTCAGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (20 bp):
AAATGTTTGCAAGCCTGGAT
Found at i:1046302 original size:23 final size:23
Alignment explanation
Indices: 1046262--1046305 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1046252 CTCACATAAA
*
1046262 CTATGTGGTCCTTCGGGACAATC
1 CTATGTGGTCATTCGGGACAATC
* *
1046285 CTATGTGGTTATTTGGGACAA
1 CTATGTGGTCATTCGGGACAA
1046306 ATATGTGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAATC
Found at i:1051284 original size:51 final size:51
Alignment explanation
Indices: 1051221--1051335 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
1051211 AGTATTCAAT
* * *
1051221 TTATTATTTTATT-AGAGAT-TGAGATAGATTTAAAACATTATCTTTAGTTTA
1 TTATTATTTTATTAAGAAATAT--GATAGAATTAAAAAATTATCTTTAGTTTA
1051272 TTATTATTTTATTAAGAAATATGATAGAATTAAAAAATTATCTTTAGTTTA
1 TTATTATTTTATTAAGAAATATGATAGAATTAAAAAATTATCTTTAGTTTA
1051323 TTATTATTTTATT
1 TTATTATTTTATT
1051336 CAGCAGTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
51 53 0.90
52 5 0.08
53 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (51 bp):
TTATTATTTTATTAAGAAATATGATAGAATTAAAAAATTATCTTTAGTTTA
Found at i:1060239 original size:2 final size:2
Alignment explanation
Indices: 1060174--1060223 Score: 82
Period size: 2 Copynumber: 24.0 Consensus size: 2
1060164 TTTATTACAT
1060174 TA TA TA GTA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1060218 TA TA TA
1 TA TA TA
1060224 ATTTCAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 42 0.91
3 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1060294 original size:14 final size:14
Alignment explanation
Indices: 1060275--1060302 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1060265 ATAGTATAGC
1060275 TTTTGAAAACATAT
1 TTTTGAAAACATAT
1060289 TTTTGAAAACATAT
1 TTTTGAAAACATAT
1060303 ATATATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTTGAAAACATAT
Found at i:1060315 original size:17 final size:17
Alignment explanation
Indices: 1060293--1060326 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1060283 ACATATTTTT
1060293 GAAAACATATATATATA
1 GAAAACATATATATATA
1060310 GAAAACATATATATATA
1 GAAAACATATATATATA
1060327 TATATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
GAAAACATATATATATA
Found at i:1060321 original size:2 final size:2
Alignment explanation
Indices: 1060316--1060352 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1060306 TATAGAAAAC
1060316 AT AT AT AT AT AT AT AT AT A- 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
1060353 ATTAGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1060323 original size:19 final size:19
Alignment explanation
Indices: 1060294--1060347 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1060284 CATATTTTTG
*
1060294 AAAACATATATATATAGA-
1 AAAATATATATATATAGAT
*
1060312 AAACATATATATATATATAT
1 AAA-ATATATATATATAGAT
*
1060332 ATAATATATATATATA
1 AAAATATATATATATA
1060348 TTATAATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.10
19 26 0.84
20 2 0.06
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATATATATATATAGAT
Found at i:1064439 original size:24 final size:24
Alignment explanation
Indices: 1064407--1064454 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1064397 AGTCTTCCTG
1064407 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1064431 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1064455 CGTGTTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:1079279 original size:199 final size:199
Alignment explanation
Indices: 1078938--1079485 Score: 672
Period size: 199 Copynumber: 2.7 Consensus size: 199
1078928 GGTGAGAAGG
* * * *
1078938 GTTATCTGTCAACAAAAACTTTCGAGTTCGATTCCATTAAGCTCAAGGCATATCAAACACATGGT
1 GTTATCTGTCAATAAAAACTTTCGAGTTTGATTCCATTAAGCTCGAGGCGTATC-AACACATGGT
* * * * **
1079003 AGCAGCGAGGACCTACTTTTTGGTTGAAGTTTAAACTGAGGTCTTTAA-ACCAAGAAGAATAATT
65 AGCAGCGAGGAACTACTTTTTGATTGAAGTTTAAACCGAGGTCTTTAAGA-CAAGAAGAAGACCT
** *
1079067 AGGTTGGCTGCGATTTAGCAACAAAGAACTATCTCTCAACCTAATTTACAGTATAGTTTAAGTCG
129 AGGTTGGCTGCGATTTAGCAACAAAGAACTATCTCTCAACCTAATTTACAACATAGTTTAAGTCA
1079132 AGAAAA
194 AGAAAA
* * * *
1079138 GTTATCTGTCAATAAAAACTTT-TAGGTTTGATTCCATTCAGCTCGAGG-GTATCAACCGCGTGG
1 GTTATCTGTCAATAAAAACTTTCGA-GTTTGATTCCATTAAGCTCGAGGCGTATCAA-CACATGG
* *** * *
1079201 TAGCAGCGAGGAAATACTTTCCAATTGAAGTTTAAACCAAGGTCTTTAAGACAAGGAGAAGACCT
64 TAGCAGCGAGGAACTACTTTTTGATTGAAGTTTAAACCGAGGTCTTTAAGACAAGAAGAAGACCT
*
1079266 AGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCTCAACCTAATTTACAACATAGTTTAAGTCA
129 AGGTTGGCTGCGATTTAGCAACAAAGAACTATCTCTCAACCTAATTTACAACATAGTTTAAGTCA
1079331 AGAAAA
194 AGAAAA
* * * ** * * *
1079337 GATGTTTGTCAATGGAAACTTTCGAGTTTGATTCCATTTAGCTTGAGGGTGTATCAACACATGGT
1 GTTATCTGTCAATAAAAACTTTCGAGTTTGATTCCATTAAGCTCGA-GGCGTATCAACACATGGT
* * * *
1079402 AGCAACGAGGAACTACTTTTTGATTGAATTTTAAATCGAGGTCTTTAAG-CAAGAAGAAGACCAA
65 AGCAGCGAGGAACTACTTTTTGATTGAAGTTTAAACCGAGGTCTTTAAGACAAGAAGAAGACCTA
* * *
1079466 GGTTGACTACGATTTGGCAA
130 GGTTGGCTGCGATTTAGCAA
1079486 TAATAAGCCA
Statistics
Matches: 295, Mismatches: 47, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
198 2 0.01
199 194 0.66
200 92 0.31
201 7 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (199 bp):
GTTATCTGTCAATAAAAACTTTCGAGTTTGATTCCATTAAGCTCGAGGCGTATCAACACATGGTA
GCAGCGAGGAACTACTTTTTGATTGAAGTTTAAACCGAGGTCTTTAAGACAAGAAGAAGACCTAG
GTTGGCTGCGATTTAGCAACAAAGAACTATCTCTCAACCTAATTTACAACATAGTTTAAGTCAAG
AAAA
Found at i:1079804 original size:150 final size:151
Alignment explanation
Indices: 1079521--1079846 Score: 503
Period size: 150 Copynumber: 2.2 Consensus size: 151
1079511 TTCGAATTAG
*
1079521 ATTTCAACTTCAC-AGCGAATGATATCATGCTCGAAACATCCAAGATTGAATCAACTTCATGAAG
1 ATTTCAACTTCACGA-CGAAGGATATCATGCTCGAAACATCCAAGATTGAATCAACTTCATGAAG
* * *
1079585 AATAAGTCACCTATGACTCAACTTTACATAGAATGAGTCATCCACAAAATAGTTCAACTCAACGA
65 AATAAGTAACCTAAGACTCAACTTTACATAGAATGAGTCATCCACAAAATAGTTCAAATCAACGA
*
1079650 CGGACTAAGGTCATTTAGTCAA
130 CGGACTAAGGTCATCTAGTCAA
* * * *
1079672 ATTTCAACTTCACGATGAAGGATATCATGCTCGAAACATCCAAGATTGACTCATCTTCATGACGA
1 ATTTCAACTTCACGACGAAGGATATCATGCTCGAAACATCCAAGATTGAATCAACTTCATGAAGA
* * * **
1079737 ATGAGTAACC-AAGACTCAACTTTACATCGAATGAGTCATCCATAGCATAGTTCAAATCAACGAC
66 ATAAGTAACCTAAGACTCAACTTTACATAGAATGAGTCATCCACAAAATAGTTCAAATCAACGAC
1079801 GGACTAAGGTCATCTAGTCAA
131 GGACTAAGGTCATCTAGTCAA
1079822 ATTTCAACTTCACGACGAAGGATAT
1 ATTTCAACTTCACGACGAAGGATAT
1079847 GGACTATAAG
Statistics
Matches: 159, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
150 92 0.58
151 66 0.42
152 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (151 bp):
ATTTCAACTTCACGACGAAGGATATCATGCTCGAAACATCCAAGATTGAATCAACTTCATGAAGA
ATAAGTAACCTAAGACTCAACTTTACATAGAATGAGTCATCCACAAAATAGTTCAAATCAACGAC
GGACTAAGGTCATCTAGTCAA
Found at i:1080310 original size:30 final size:31
Alignment explanation
Indices: 1080274--1080478 Score: 122
Period size: 30 Copynumber: 6.5 Consensus size: 31
1080264 CCAGACACAT
*
1080274 TTAATATATTAT-TATTTAGTATATTTTATA
1 TTAATATATTATATATTTAGTATATATTATA
* *
1080304 TTAATATATTATATGATATAAGTATATTATTATT
1 TTAATATATTATAT-AT-TTAGTATA-TATTATA
* * *
1080338 TTACGTATGTTATATATATATGTATATATTATA
1 TTA-ATATATTATATATTTA-GTATATATTATA
* *
1080371 TT--TATAATATATA-TTAGTTTATA-TATA
1 TTAATATATTATATATTTAGTATATATTATA
*
1080398 TT-ATAT-TTATAT-TATAGTACATATATTATA
1 TTAATATATTATATATTTAGT--ATATATTATA
* * * *
1080428 TTTATAT-TTTTATGTTATATTATATATTATTA
1 TTAATATATTATATATT-TAGTATATATTA-TA
*
1080460 TTATTTATTATTATATATT
1 TTA-ATA-TATTATATATT
1080479 CAATATATCA
Statistics
Matches: 135, Mismatches: 22, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
27 15 0.11
28 9 0.07
29 6 0.04
30 27 0.20
31 18 0.13
32 7 0.05
33 21 0.16
34 16 0.12
35 16 0.12
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (31 bp):
TTAATATATTATATATTTAGTATATATTATA
Found at i:1080329 original size:18 final size:16
Alignment explanation
Indices: 1080274--1080400 Score: 74
Period size: 17 Copynumber: 8.2 Consensus size: 16
1080264 CCAGACACAT
1080274 TTAA-TATATTAT-TA
1 TTAAGTATATTATATA
* *
1080288 TTTAGTATATTTTATA
1 TTAAGTATATTATATA
1080304 TTAA-TATATTATATGA
1 TTAAGTATATTATAT-A
*
1080320 TATAAGTATATTATTATT
1 T-TAAGTATATTA-TATA
* *
1080338 TTACGTATGTTATATA
1 TTAAGTATATTATATA
*
1080354 TATATGTATA-TATTATA
1 T-TAAGTATATTA-TATA
*
1080371 TT---TATAATATATA
1 TTAAGTATATTATATA
*
1080384 TT-AGTTTA-TATATA
1 TTAAGTATATTATATA
1080398 TTA
1 TTA
1080401 TATTTATATT
Statistics
Matches: 90, Mismatches: 11, Indels: 23
0.73 0.09 0.19
Matches are distributed among these distances:
13 10 0.11
14 13 0.14
15 19 0.21
16 14 0.16
17 23 0.26
18 8 0.09
19 3 0.03
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.55
Consensus pattern (16 bp):
TTAAGTATATTATATA
Found at i:1080365 original size:8 final size:7
Alignment explanation
Indices: 1080348--1080475 Score: 79
Period size: 6 Copynumber: 19.7 Consensus size: 7
1080338 TTACGTATGT
1080348 TATA-TA
1 TATATTA
1080354 TATATGTA
1 TATAT-TA
1080362 TATATTA
1 TATATTA
1080369 TAT-TTA
1 TATATTA
1080375 TA-A-TA
1 TATATTA
1080380 TATATTA
1 TATATTA
*
1080387 -GT-TTA
1 TATATTA
1080392 TATA-TA
1 TATATTA
1080398 TTATATT-
1 -TATATTA
1080405 TATATTA
1 TATATTA
*
1080412 TAGTA-CA
1 TA-TATTA
1080419 TATATTA
1 TATATTA
1080426 TAT-TTA
1 TATATTA
1080432 TAT-TT-
1 TATATTA
1080437 T-TATGT-
1 TATAT-TA
1080443 TATATTA
1 TATATTA
1080450 TATATTA
1 TATATTA
1080457 T-TATTA
1 TATATTA
*
1080463 TTTATTA
1 TATATTA
1080470 TTATAT
1 -TATAT
1080476 ATTCAATATA
Statistics
Matches: 99, Mismatches: 5, Indels: 34
0.72 0.04 0.25
Matches are distributed among these distances:
4 1 0.01
5 9 0.09
6 39 0.39
7 36 0.36
8 14 0.14
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:1080486 original size:2 final size:2
Alignment explanation
Indices: 1080348--1080477 Score: 61
Period size: 2 Copynumber: 70.5 Consensus size: 2
1080338 TTACGTATGT
* *
1080348 TA TA TA TA TA TG TA TA TA T- TA TA TT TA TA -A TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1080387 GTT TA TA TA TA T- TA TA TT TA TA T- TA TA GTA CA TA TA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
1080428 TT TA TA TT TT TA TG T- TA TA T- TA TA TA T- TA T- TA T- TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1080465 TA T- TA T- TA TA TA T
1 TA TA TA TA TA TA TA T
1080478 TCAATATATC
Statistics
Matches: 96, Mismatches: 17, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
1 13 0.14
2 80 0.83
3 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (2 bp):
TA
Found at i:1080754 original size:40 final size:41
Alignment explanation
Indices: 1080702--1080780 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 41
1080692 CGCTCCAATG
*
1080702 TCGAACCAAAAAACCAAGGAG-AAATTAGAGGAAATCTCCA
1 TCGAACCAAAAAACCAAGGAGCAAATTAGAAGAAATCTCCA
* * *
1080742 TCGAACCGAAAAACCAGGGAGCAAATTGGAAGAAATCTC
1 TCGAACCAAAAAACCAAGGAGCAAATTAGAAGAAATCTC
1080781 TCATGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 19 0.56
41 15 0.44
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (41 bp):
TCGAACCAAAAAACCAAGGAGCAAATTAGAAGAAATCTCCA
Found at i:1081587 original size:14 final size:15
Alignment explanation
Indices: 1081555--1081588 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1081545 ATTCTTGATT
*
1081555 TTTAATTCTTTTCAA
1 TTTAATCCTTTTCAA
1081570 TTTAATCCTTTT-AA
1 TTTAATCCTTTTCAA
1081584 TTTAA
1 TTTAA
1081589 ATTTTCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATCCTTTTCAA
Found at i:1083611 original size:3 final size:3
Alignment explanation
Indices: 1083603--1083692 Score: 84
Period size: 3 Copynumber: 31.7 Consensus size: 3
1083593 CCATTTGTTT
* * * *
1083603 TTA TTA TTA -TA TTA TTA CTG TTA TTA TTA -TC TTA TTTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
1083647 TTA TTA TT- TTA TAA TTA -TA TTA TTA TT- TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1083691 TT
1 TT
1083693 TACATTACAG
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
2 11 0.15
3 57 0.80
4 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1083643 original size:32 final size:30
Alignment explanation
Indices: 1083603--1083692 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 30
1083593 CCATTTGTTT
* *
1083603 TTATTATTATATTATTACTGTTATTATTATC
1 TTATTATTATATTATTA-TATTATTATTATA
* *
1083634 TTATTTATTACTATTATTATTTTATAATTATA
1 TTA-TTATTA-TATTATTATATTATTATTATA
*
1083666 TTATTATT-TTTTATTATTATTATTATT
1 TTATTATTATATTATTA-TATTATTATT
1083693 TACATTACAG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 7 0.14
30 8 0.16
31 8 0.16
32 19 0.38
33 8 0.16
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (30 bp):
TTATTATTATATTATTATATTATTATTATA
Found at i:1084912 original size:31 final size:28
Alignment explanation
Indices: 1084840--1084915 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 28
1084830 CTAATTTTAA
*
1084840 TATTTTCATTTATTTTTAATTACAAGTTT
1 TATTTT-ATTTATTTTTAAATACAAGTTT
* *
1084869 TATTTCTTTTTATATTTTAAATATATAGTTT
1 TATTT-TATTTAT-TTTTAAATACA-AGTTT
1084900 TAATTTTATTTATTTT
1 T-ATTTTATTTATTTT
1084916 AGTCACTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 10 0.26
30 13 0.33
31 12 0.31
32 4 0.10
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (28 bp):
TATTTTATTTATTTTTAAATACAAGTTT
Found at i:1084976 original size:3 final size:3
Alignment explanation
Indices: 1084968--1085002 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1084958 AATATATTTA
1084968 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1085003 ATATAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1092049 original size:23 final size:22
Alignment explanation
Indices: 1092005--1092049 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1091995 AATGTCATGG
*
1092005 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
1092027 GGGAACCGGTTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1092050 AGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.29, C:0.33, G:0.29, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1093644 original size:23 final size:23
Alignment explanation
Indices: 1093589--1093645 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1093579 TTTATATGGT
* *
1093589 ACTTCGGTTCAATTCTACGTGGC
1 ACTTAGGTGCAATTCTACGTGGC
*
1093612 ACGTCA-GTGCAATTCTACGTGGC
1 AC-TTAGGTGCAATTCTACGTGGC
1093635 ACTTAGGTGCA
1 ACTTAGGTGCA
1093646 TTTATACGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 25 0.89
24 1 0.04
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
ACTTAGGTGCAATTCTACGTGGC
Found at i:1093653 original size:23 final size:23
Alignment explanation
Indices: 1093598--1093653 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1093588 TACTTCGGTT
*
1093598 CAATTCTACGTGGCACGTCAGTG
1 CAATTATACGTGGCACGTCAGTG
* *
1093621 CAATTCTACGTGGCAC-TTAGGTG
1 CAATTATACGTGGCACGTCA-GTG
*
1093644 CATTTATACG
1 CAATTATACG
1093654 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
CAATTATACGTGGCACGTCAGTG
Found at i:1097189 original size:23 final size:22
Alignment explanation
Indices: 1097145--1097189 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1097135 AATGTCATGG
*
1097145 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1097167 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1097190 AGAAATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1098794 original size:23 final size:23
Alignment explanation
Indices: 1098726--1098786 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1098716 ACATTTTATA
1098726 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1098749 CGGCACGTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1098772 TGGCACTTAGGTGCA
1 TGGCACTTCGGTGCA
1098787 TTTATACGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1104863 original size:16 final size:17
Alignment explanation
Indices: 1104842--1104880 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1104832 CTTGAAGAAG
*
1104842 AAAAAAATTA-AATGAA
1 AAAAAAATGATAATGAA
*
1104858 AAAAAAATGATGATGAA
1 AAAAAAATGATAATGAA
1104875 AAAAAA
1 AAAAAA
1104881 TATAGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (17 bp):
AAAAAAATGATAATGAA
Found at i:1105561 original size:20 final size:20
Alignment explanation
Indices: 1105532--1105576 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1105522 AAATGTTTTG
*
1105532 TGAACTAGTAATTATGGTGC
1 TGAACAAGTAATTATGGTGC
*
1105552 TGAACAAGTAATTATGGTGT
1 TGAACAAGTAATTATGGTGC
1105572 TGAAC
1 TGAAC
1105577 CAATGTTGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (20 bp):
TGAACAAGTAATTATGGTGC
Found at i:1105974 original size:25 final size:22
Alignment explanation
Indices: 1105921--1105980 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1105911 TCTACATTCC
*
1105921 TCAAAGATGATAGATTCTCTCT
1 TCAAAGAAGATAGATTCTCTCT
*
1105943 TCAAAGAAGATAGATTCTCTTT
1 TCAAAGAAGATAGATTCTCTCT
*
1105965 TCAAAGAAGAAAGATT
1 TCAAAGAAGATAGATT
1105981 TATTGGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (22 bp):
TCAAAGAAGATAGATTCTCTCT
Found at i:1106426 original size:122 final size:122
Alignment explanation
Indices: 1106298--1106733 Score: 653
Period size: 121 Copynumber: 3.6 Consensus size: 122
1106288 TTTCCCATAG
* *
1106298 GAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTTATAATAAGAAGAACTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
* * * *
1106363 CAACCTTTGTATGACTCTATCACAGAAGGAGATAGATCAATATCAATATTTCTAGAG
66 CAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCTAGAA
*
1106420 GAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
* *
1106485 CAACCTTTGCATGACTCTATCACTGAAGGAGATAGATCAGCATCAACATTTCTAGAA
66 CAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCTAGAA
* * * * *
1106542 G-TGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCGTAATGAGAAGAACTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
* * * *
1106606 CAACCCTTGCATGACTCTATCGCAGAAGAAGATAGATCAACATCAACATTTCCAGAA
66 CAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCTAGAA
* * *
1106663 GTA-TTCATAATGAGAAGAACTCATATGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
1106726 TCAACCTT
65 TCAACCTT
1106734 GCCTTAATTC
Statistics
Matches: 287, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
121 169 0.59
122 118 0.41
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (122 bp):
GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
CAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCTAGAA
Found at i:1106607 original size:243 final size:233
Alignment explanation
Indices: 1106171--1106748 Score: 708
Period size: 243 Copynumber: 2.5 Consensus size: 233
1106161 CATTCAATGG
*
1106171 ATCAACATTT-CGGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
1106234 AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTCCCATAGG
66 AATGAGAAGAACTTGTTCAACC-TTTGCATGAATTCATCACTAGATGGATCAACTTT-CCATAGG
* * * *
1106299 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTTATAATAAGAAGAACTTGTTC
129 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATAAGAAGAACTTGTTC
* * * *
1106364 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCAAT
194 AACCCTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
* * * *
1106404 ATCAATATTTCTAGAGGAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
1106468 AATAAGAAGAACTTGTTCAACCTTTGCATG-ACTCTATCACTGAAGGAGATAGATCAGCATCAAC
66 AATGAGAAGAACTTGTTCAACCTTTGCATGAATTC-ATCACT-----AGAT-G----G-ATCAAC
* *
1106532 ATTT-C-TA-GAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCGTAATGA
119 -TTTCCATAGGAA--GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATAA
*
1106594 GAAGAACTTGTTCAACCCTTGCATGACTCTATCGCAGAAGAAGATAGATCAAC
181 GAAGAACTTGTTCAACCCTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
* *
1106647 ATCAACATTTCCAGAAGTA-TTCATAATGAGAAGAACTCATATGAAGAAGG-AGAAGAAGTTCAT
1 ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
1106710 AATGAGAAGAACTTGTTCAACC-TTGCCTTAATTCATCAC
66 AATGAGAAGAACTTGTTCAACCTTTGCATGAATTCATCAC
1106749 ATATGAAGCC
Statistics
Matches: 295, Mismatches: 31, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
232 3 0.01
233 22 0.07
234 40 0.14
235 28 0.09
238 3 0.01
239 1 0.00
241 13 0.04
242 64 0.22
243 112 0.38
244 6 0.02
245 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (233 bp):
ATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTGCATGAATTCATCACTAGATGGATCAACTTTCCATAGGAA
GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATAAGAAGAACTTGTTCAA
CCCTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
Found at i:1107103 original size:3 final size:3
Alignment explanation
Indices: 1107097--1107198 Score: 117
Period size: 3 Copynumber: 35.7 Consensus size: 3
1107087 CCATTTGTTT
* *
1107097 TTA TTA TTA -TA TTA TTA TTG TTA TTA TTA TT- TTA TTTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
1107141 TTA TTA TT- TTA TAA TTA -TA TTA TTA TTA TT- TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1107185 ATA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
1107199 TACATTACAG
Statistics
Matches: 85, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
2 12 0.14
3 70 0.82
4 3 0.04
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1107158 original size:44 final size:44
Alignment explanation
Indices: 1107097--1107197 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
1107087 CCATTTGTTT
* * *
1107097 TTATTATTATATTATTATTGTTATTATTATTTTAT-TTATTACTA
1 TTATTATTTTATAATTA-TATTATTATTATTTTATATTATTACTA
* *
1107141 TTATTATTTTATAATTATATTATTATTATTTTTTATTATTATTA
1 TTATTATTTTATAATTATATTATTATTATTTTATATTATTACTA
*
1107185 ATATTATTATTAT
1 TTATTATT-TTAT
1107198 TTACATTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
43 15 0.31
44 30 0.61
45 4 0.08
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (44 bp):
TTATTATTTTATAATTATATTATTATTATTTTATATTATTACTA
Found at i:1108322 original size:13 final size:13
Alignment explanation
Indices: 1108304--1108328 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1108294 TAATTTATTT
1108304 TAATTTGATATAC
1 TAATTTGATATAC
1108317 TAATTTGATATA
1 TAATTTGATATA
1108329 ATTTTATTTT
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTTGATATAC
Found at i:1108526 original size:31 final size:28
Alignment explanation
Indices: 1108454--1108529 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 28
1108444 CTAATTTTAA
*
1108454 TATTTTCATTTATTTTTAATTACAAGTTT
1 TATTTT-ATTTATTTTTAAATACAAGTTT
* *
1108483 TATTTCTTTTTATATTTTAAATATATAGTTT
1 TATTT-TATTTAT-TTTTAAATACA-AGTTT
1108514 TAATTTTATTTATTTT
1 T-ATTTTATTTATTTT
1108530 AGTCACTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 10 0.26
30 13 0.33
31 12 0.31
32 4 0.10
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (28 bp):
TATTTTATTTATTTTTAAATACAAGTTT
Found at i:1114742 original size:4 final size:4
Alignment explanation
Indices: 1114725--1114868 Score: 261
Period size: 4 Copynumber: 36.0 Consensus size: 4
1114715 GAAATTAAAT
* * *
1114725 ATAC ATAT ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1114773 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1114821 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1114869 CCCATGGGCC
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 136 1.00
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1119147 original size:3 final size:3
Alignment explanation
Indices: 1119134--1119184 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
1119124 CAGGATATAA
*
1119134 TAT TA- TAT TAT TAT TAT TAA TA- TAT TA- TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
1119177 TAA TAT TA
1 TAT TAT TA
1119185 ATACAAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1119150 original size:11 final size:10
Alignment explanation
Indices: 1119134--1119183 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
1119124 CAGGATATAA
1119134 TATTATATTAT
1 TATTAT-TTAT
*
1119145 TATTATTAAT
1 TATTATTTAT
1119155 ATATTATATTAT
1 -TATTAT-TTAT
1119167 TATTATTTAT
1 TATTATTTAT
*
1119177 TAATATT
1 TATTATT
1119184 AATACAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 13 0.38
11 18 0.53
12 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTTAT
Found at i:1119166 original size:19 final size:19
Alignment explanation
Indices: 1119142--1119184 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1119132 AATATTATAT
1119142 TATTATTATTAATATATT-A
1 TATTATTATT-ATATATTAA
*
1119161 TATTATTATTATTTATTAA
1 TATTATTATTATATATTAA
1119180 TATTA
1 TATTA
1119185 ATACAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTATTATATATTAA
Found at i:1123193 original size:14 final size:14
Alignment explanation
Indices: 1123174--1123201 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1123164 TATTTCCTTC
1123174 TATAACATAATCTG
1 TATAACATAATCTG
1123188 TATAACATAATCTG
1 TATAACATAATCTG
1123202 AGTGTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TATAACATAATCTG
Found at i:1132248 original size:20 final size:21
Alignment explanation
Indices: 1132225--1132265 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1132215 TGAGAAATTG
1132225 TTTTT-AAAATAT-AAAAATGA
1 TTTTTCAAAAT-TGAAAAATGA
1132245 TTTTTCAAAATTGAAAAATGA
1 TTTTTCAAAATTGAAAAATGA
1132266 AAATAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTTCAAAATTGAAAAATGA
Found at i:1134077 original size:12 final size:12
Alignment explanation
Indices: 1134060--1134094 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1134050 ATAAATACAA
1134060 ATGACGTTAGAC
1 ATGACGTTAGAC
1134072 ATGACGTTAGAC
1 ATGACGTTAGAC
*
1134084 TTGACGTTAGA
1 ATGACGTTAGA
1134095 GAACCATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (12 bp):
ATGACGTTAGAC
Found at i:1137732 original size:21 final size:21
Alignment explanation
Indices: 1137690--1137733 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1137680 ACTCCGGGAG
* *
1137690 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1137711 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1137732 CT
1 CT
1137734 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1138897 original size:19 final size:19
Alignment explanation
Indices: 1138873--1138915 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1138863 TTATGTATCG
1138873 ATGCATATACCATGCATCA
1 ATGCATATACCATGCATCA
*
1138892 ATGCATATACCATGCATCG
1 ATGCATATACCATGCATCA
1138911 ATGCA
1 ATGCA
1138916 CTTAGTGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (19 bp):
ATGCATATACCATGCATCA
Found at i:1145112 original size:16 final size:16
Alignment explanation
Indices: 1145091--1145121 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1145081 TAATAGGCAT
1145091 AGTGGTACCATTTGAG
1 AGTGGTACCATTTGAG
1145107 AGTGGTACCATTTGA
1 AGTGGTACCATTTGA
1145122 AAGATGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (16 bp):
AGTGGTACCATTTGAG
Found at i:1147402 original size:24 final size:24
Alignment explanation
Indices: 1147338--1147405 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
1147328 TATAATTCAG
* *
1147338 GTCAGATATCATAACAAAATCCAT
1 GTCAGGTATCATAACAGAATCCAT
* *
1147362 GTCAGGTATTAGAACAGAATCCAT
1 GTCAGGTATCATAACAGAATCCAT
1147386 GTCAGGTATCATAACAGAAT
1 GTCAGGTATCATAACAGAAT
1147406 TCAATTCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAGGTATCATAACAGAATCCAT
Found at i:1151587 original size:24 final size:24
Alignment explanation
Indices: 1151555--1151651 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 24
1151545 TATATCAAAA
* * *
1151555 ATCAAAACATAATTCAAGTCAGAT
1 ATCATAACAGAATCCAAGTCAGAT
* * *
1151579 ATCATAACATAATCCAGGTCAGGT
1 ATCATAACAGAATCCAAGTCAGAT
* * *
1151603 ATTAGAACAGAATCCATGTCACG-T
1 ATCATAACAGAATCCAAGTCA-GAT
* *
1151627 ATCATAACAGAATTCAAATCAGAT
1 ATCATAACAGAATCCAAGTCAGAT
1151651 A
1 A
1151652 AAATATTCAT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCATAACAGAATCCAAGTCAGAT
Found at i:1155165 original size:22 final size:22
Alignment explanation
Indices: 1155139--1155187 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1155129 AGGTTAAGAA
* *
1155139 ATAAATTT-TAAAAATTTTAAGG
1 ATAAATTTAT-AAAACTGTAAGG
1155161 ATAAATTTATAAAACTGTAAGG
1 ATAAATTTATAAAACTGTAAGG
1155183 ATAAA
1 ATAAA
1155188 AGTAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (22 bp):
ATAAATTTATAAAACTGTAAGG
Found at i:1161850 original size:12 final size:12
Alignment explanation
Indices: 1161833--1161874 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1161823 TTATAAAAAT
1161833 ATATTAATTATA
1 ATATTAATTATA
1161845 ATATTAATTAT-
1 ATATTAATTATA
1161856 -TATT-ATTATA
1 ATATTAATTATA
1161866 AT-TTAATTA
1 ATATTAATTA
1161875 AGTTTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.19
10 6 0.22
11 5 0.19
12 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATTAATTATA
Found at i:1163500 original size:33 final size:35
Alignment explanation
Indices: 1163462--1163561 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 35
1163452 CCCGAACCCA
*
1163462 AAAAATATTTTATATATAATTAATA-AACAAATAT
1 AAAAATATTTTATATATAATTAATATAAAAAATAT
1163496 AAAATATTATATATATATATATAATTAATATAAAAAATAT
1 AAAA-A-TAT-T-T-TATATATAATTAATATAAAAAATAT
* *
1163536 -AAAATATTATATATATAAAT-ATATAA
1 AAAAATATTTTATATATAATTAATATAA
1163562 TCGGGGCAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
33 6 0.11
34 14 0.25
35 1 0.02
36 4 0.07
37 4 0.07
38 2 0.04
39 18 0.32
40 8 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (35 bp):
AAAAATATTTTATATATAATTAATATAAAAAATAT
Found at i:1163544 original size:40 final size:39
Alignment explanation
Indices: 1163472--1163558 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 39
1163462 AAAAATATTT
*
1163472 TATATATAATTAATAAACAAATATAAAATATTATATATA
1 TATATATAATTAATAAAAAAATATAAAATATTATATATA
1163511 TATATATAATTAATATAAAAAATATAAAATATTATATATA
1 TATATATAATTAATA-AAAAAATATAAAATATTATATATA
*
1163551 TAAATATA
1 TATATATA
1163559 TAATCGGGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 15 0.33
40 30 0.67
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (39 bp):
TATATATAATTAATAAAAAAATATAAAATATTATATATA
Found at i:1176849 original size:2 final size:2
Alignment explanation
Indices: 1176842--1176875 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1176832 CAACATTCAC
1176842 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
1176876 CAATAAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1177598 original size:20 final size:20
Alignment explanation
Indices: 1177573--1177615 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1177563 TCTAAAGGCC
1177573 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
1177593 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
1177613 CAT
1 CAT
1177616 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:1211035 original size:20 final size:20
Alignment explanation
Indices: 1211006--1211044 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1210996 AAAGCTCATA
*
1211006 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1211026 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1211045 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1215241 original size:20 final size:19
Alignment explanation
Indices: 1215180--1215244 Score: 91
Period size: 18 Copynumber: 3.5 Consensus size: 19
1215170 GTGTATATTA
1215180 TGGCACTTC-AGTGCA-TTG
1 TGGCACTTCGA-TGCATTTG
1215198 TGGCACTTCGATGCATTT-
1 TGGCACTTCGATGCATTTG
1215216 TGGCACTTCGATGCATTTTG
1 TGGCACTTCGATGCA-TTTG
1215236 TGGCACTTC
1 TGGCACTTC
1215245 AGTGCACCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 28 0.65
19 6 0.14
20 9 0.21
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (19 bp):
TGGCACTTCGATGCATTTG
Found at i:1215905 original size:104 final size:101
Alignment explanation
Indices: 1215711--1215913 Score: 253
Period size: 103 Copynumber: 2.0 Consensus size: 101
1215701 TCTATTCAAT
* * * * * *
1215711 AATTATAATAATTTTTTTGACACTAAAATATATTTTGTGACCATCAATATTGCCACACTAGGTAT
1 AATTATAATAATTTATTCGACACTAAAATATATTTTGTGACCACCAATATTACCACAATAAGTAT
* *
1215776 TTTTGTGACCAAATGTTTGATACTATTATCAATAGA
66 TTTTGTGACCAAATGTTCGATACTATTAACAATAGA
* * * *
1215812 AATTGTAATAAATTTATTCGACACTGAAAGTATATTTTGTGACCACCAATGTTATCACAATAAGT
1 AATTATAAT-AATTTATTCGACACT-AAAATATATTTTGTGACCACCAATATTACCACAATAAGT
* *
1215877 GTTTTTAGTGACTAAATGTTCGATACTATTAACAATA
64 ATTTTT-GTGACCAAATGTTCGATACTATTAACAATA
1215914 ACTATGTCAC
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
101 8 0.09
102 13 0.15
103 37 0.44
104 27 0.32
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (101 bp):
AATTATAATAATTTATTCGACACTAAAATATATTTTGTGACCACCAATATTACCACAATAAGTAT
TTTTGTGACCAAATGTTCGATACTATTAACAATAGA
Found at i:1216486 original size:20 final size:22
Alignment explanation
Indices: 1216452--1216496 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
1216442 TTTTAATATA
1216452 TATATATAATATTAATTATTAT
1 TATATATAATATTAATTATTAT
*
1216474 TATA-ATAAT-TTAATTATTTT
1 TATATATAATATTAATTATTAT
1216494 TAT
1 TAT
1216497 GATTTCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 5 0.23
22 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATATAATATTAATTATTAT
Found at i:1224937 original size:9 final size:9
Alignment explanation
Indices: 1224923--1224956 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1224913 CATAACTTCA
1224923 TTTTTTTCT
1 TTTTTTTCT
*
1224932 TTTTTTCCT
1 TTTTTTTCT
*
1224941 TTTTTCTCT
1 TTTTTTTCT
1224950 TTTTTTT
1 TTTTTTT
1224957 ACAAAGTGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1239284 original size:21 final size:21
Alignment explanation
Indices: 1239258--1239297 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1239248 AAACAATTGG
1239258 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
1239279 TAACAATTGGTATCGTTTT
1 TAACAATTGATATCATTTT
1239298 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1239548 original size:21 final size:21
Alignment explanation
Indices: 1239522--1239579 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1239512 AGGGTGTCAA
*
1239522 AGTGCATCCATGCACCCCTCC
1 AGTGCATCCATGAACCCCTCC
*
1239543 AGTGCATCCATGAACCCCTGC
1 AGTGCATCCATGAACCCCTCC
*
1239564 AATGCATCCATGAACC
1 AGTGCATCCATGAACC
1239580 TGCCACTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.40, G:0.16, T:0.19
Consensus pattern (21 bp):
AGTGCATCCATGAACCCCTCC
Found at i:1239957 original size:21 final size:21
Alignment explanation
Indices: 1239933--1239972 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1239923 ATGTTTAATG
1239933 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
1239954 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
1239973 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:1241124 original size:20 final size:20
Alignment explanation
Indices: 1241087--1241123 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1241077 TCTAAATCCT
*
1241087 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
1241107 TTTTCAAAA-TCCATTTT
1 TTTTCAAAATTCCATTTT
1241124 TACTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:1242488 original size:21 final size:21
Alignment explanation
Indices: 1242462--1242519 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1242452 ACTAGTGGCA
*
1242462 GGTGCATGGATGCATTGCAAG
1 GGTGCATGGATGCACTGCAAG
* *
1242483 GGTGCATGGATGCACTGGAGG
1 GGTGCATGGATGCACTGCAAG
1242504 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
1242520 TTGACACCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.41, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAAG
Found at i:1253663 original size:32 final size:32
Alignment explanation
Indices: 1253585--1253663 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
1253575 CTTTTGGTAT
* *
1253585 TCGGGTCAGATTTTTTTTAAAAAAATTCAGAA
1 TCGGGTCAGGTTTTTTTAAAAAAAATTCAGAA
* * **
1253617 TCGGGTC-GGATTTTTTAAAAAAAATTCGGGG
1 TCGGGTCAGGTTTTTTTAAAAAAAATTCAGAA
1253648 TCGGGTCAGGTTTTTT
1 TCGGGTCAGGTTTTTT
1253664 AGGTTTGATA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 25 0.64
32 14 0.36
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (32 bp):
TCGGGTCAGGTTTTTTTAAAAAAAATTCAGAA
Found at i:1253700 original size:28 final size:28
Alignment explanation
Indices: 1253648--1253714 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1253638 AAATTCGGGG
* * *
1253648 TCGGGTCAGG-TTTTTTAGGTTTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1253675 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1253703 TCGGGTCGGGTT
1 TCGGGTCGGGTT
1253715 CGGGTTGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.12, C:0.09, G:0.34, T:0.45
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:1260967 original size:67 final size:66
Alignment explanation
Indices: 1260869--1260999 Score: 172
Period size: 67 Copynumber: 2.0 Consensus size: 66
1260859 GTTTTCCTAA
* * ** *
1260869 AAACAAATTTCGTCTCACTTGAGTCAGTTTCTCTTGAAACATAAATTTTTGAGATTGTTTCTCTC
1 AAACAAATTTCGTCTCACTTGAGACAATTTCTCTTGAAACATAAACCTTCGAGATTGTTTCTCTC
1260934 C
66 C
* * * *
1260935 AAACAAAGTTTTGTCTCGCTTGAGACAATTTCTTTTGAAACATAAGCCTTCGAGATTGTTTCTCT
1 AAACAAA-TTTCGTCTCACTTGAGACAATTTCTCTTGAAACATAAACCTTCGAGATTGTTTCTCT
1261000 AAAAAAATCA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 7 0.13
67 48 0.87
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (66 bp):
AAACAAATTTCGTCTCACTTGAGACAATTTCTCTTGAAACATAAACCTTCGAGATTGTTTCTCTC
C
Found at i:1261142 original size:102 final size:102
Alignment explanation
Indices: 1261015--1261292 Score: 360
Period size: 102 Copynumber: 2.7 Consensus size: 102
1261005 AATCATCTTG
* *
1261015 CTTGAGACAGTTTTCTCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTT
1 CTTGAGACAGTTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTC
* *
1261080 ACTTGAGATTGTTTTTCTAAAAATAAATTTCGTCTCA
66 ACTTGAGAGTGTTTTTCTAAAAACAAATTTCGTCTCA
* *
1261117 CTTGAGACAGCTTTCCCTCGGAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTC
1 CTTGAGACAGTTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTC
* * * *
1261182 ACTTGAGAGTGTTTTTCTCATAACAAATTTTGTCTCG
66 ACTTGAGAGTGTTTTTCTAAAAACAAATTTCGTCTCA
* * ** * * * *
1261219 CTTGAGA-TGATTTTCCCTTGAAACGTAAATTTTGAAATTGTTTCACTCGACAGAAAATTTTATC
1 CTTGAGACAG-TTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAA-TTGATC
*
1261283 TCACCTGAGA
64 TCACTTGAGA
1261293 TAGCTTCTCT
Statistics
Matches: 153, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
101 1 0.01
102 138 0.90
103 14 0.09
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (102 bp):
CTTGAGACAGTTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTC
ACTTGAGAGTGTTTTTCTAAAAACAAATTTCGTCTCA
Found at i:1262196 original size:104 final size:103
Alignment explanation
Indices: 1261945--1262196 Score: 283
Period size: 104 Copynumber: 2.4 Consensus size: 103
1261935 CTTTAAATTA
* * **
1261945 TCCAGATTGACCAGACTTCCTCAATGAAAAGGAACAACGTCATATGAAAGCAGCCAGAACTCTTC
1 TCCAGATTGACTAGACTTCCTCAA-CAAAAGGAACAACGTCATCCGAAAGCAGCCAGAACTCTTC
* * *
1262010 GATATGGATAAGCATTGTCATCTTCAACACCAAATTATC
65 AACATGGATAAGCAGTGTCATCTTCAACACCAAATTATC
* * ** *
1262049 TTCA-ACTTGACTCGACTTCCTCAACAAGAAGGAA-AACCGTCATCCGAAAGTGGCTAGAACTCT
1 TCCAGA-TTGACTAGACTTCCTCAACAA-AAGGAACAA-CGTCATCCGAAAGCAGCCAGAACTCT
* * *
1262112 TTAACATGGATGAGCAGTGTCATCTTCAACTCCAAATTATC
63 TCAACATGGATAAGCAGTGTCATCTTCAACACCAAATTATC
* * *
1262153 TCCAGATTGACTAGATTTCCTCGACAATAAGGAACAACATCATC
1 TCCAGATTGACTAGACTTCCTCAACAA-AAGGAACAACGTCATC
1262197 TTCAGTAAAC
Statistics
Matches: 122, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
103 5 0.04
104 114 0.93
105 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (103 bp):
TCCAGATTGACTAGACTTCCTCAACAAAAGGAACAACGTCATCCGAAAGCAGCCAGAACTCTTCA
ACATGGATAAGCAGTGTCATCTTCAACACCAAATTATC
Found at i:1263891 original size:2 final size:2
Alignment explanation
Indices: 1263884--1263950 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
1263874 CATTTTTACC
1263884 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
* *
1263926 AT AT AT AT AT AT GT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1263951 TATTATCCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1264766 original size:17 final size:17
Alignment explanation
Indices: 1264735--1264768 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1264725 AACGCAGACC
1264735 AATGTTTTTCTTTAAAA
1 AATGTTTTTCTTTAAAA
1264752 AATGATTTTTC-TTAAAA
1 AATG-TTTTTCTTTAAAA
1264769 TTATTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
AATGTTTTTCTTTAAAA
Found at i:1269650 original size:81 final size:81
Alignment explanation
Indices: 1269537--1270434 Score: 1418
Period size: 81 Copynumber: 11.1 Consensus size: 81
1269527 ATTCCTTTGG
* * * * * * * *
1269537 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCGTGATTAACACTTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1269602 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* ** * **
1269618 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGATTCGTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1269683 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
1269699 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1269764 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
1269780 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1269845 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
1269861 TCTTTTACTCAAAGGTATTTAACCTTTCATCAAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
1269926 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
1269942 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
1270007 ATAGCTAGGTCATTAA
66 ACAGCTAGGCCATTAA
* *
1270023 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCACAATTGACACCTTTCTACCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1270088 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
1270104 TCTTTTACTCAAAGGTATTTAACCTTTAATTTAACTGGCATAATTGATACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
**
1270169 ACAGCTAAACCATTAA
66 ACAGCTAGGCCATTAA
*
1270185 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* * *
1270250 ACGGCTAGTCCTTTAA
66 ACAGCTAGGCCATTAA
* * *
1270266 TCTTTTACTGAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1270331 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
1270347 TCTTTTACTCATAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
1270412 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
1270428 TCTTTTA
1 TCTTTTA
1270435 TTTTAGAACA
Statistics
Matches: 748, Mismatches: 69, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 748 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:1270823 original size:46 final size:46
Alignment explanation
Indices: 1270771--1270866 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
1270761 TTATTCGTTA
*
1270771 ATTTCATTTATGACATCATTTCATGCCTTAATGCATCCTCTCATGC
1 ATTTCATTTATGACATCATTTCATGCCTTAATGCATCATCTCATGC
* * *
1270817 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGACATCATTTCATGCCTTAATGCATCATCTCATGC
1270863 ATTT
1 ATTT
1270867 TTAGTTATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (46 bp):
ATTTCATTTATGACATCATTTCATGCCTTAATGCATCATCTCATGC
Found at i:1270858 original size:20 final size:20
Alignment explanation
Indices: 1270784--1270862 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
1270774 TCATTTATGA
1270784 CATCATTTCATGCCTTAATG
1 CATCATTTCATGCCTTAATG
* * *
1270804 CATCCTCTCATGCATTTCATTTATGG
1 CATCATTTCATGC----C-TTAAT-G
*
1270830 CATCCTTTCATGCCTTAATG
1 CATCATTTCATGCCTTAATG
1270850 CATCATTTCATGC
1 CATCATTTCATGC
1270863 ATTTTTAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
20 24 0.51
21 4 0.09
22 1 0.02
24 1 0.02
25 4 0.09
26 13 0.28
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.41
Consensus pattern (20 bp):
CATCATTTCATGCCTTAATG
Found at i:1271412 original size:19 final size:20
Alignment explanation
Indices: 1271367--1271418 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1271357 TCTATTAACA
*
1271367 ATGGTATCAATACCATCCTC
1 ATGGTATCAATACCACCCTC
*
1271387 ATAGTATCAATACC-CCCTC
1 ATGGTATCAATACCACCCTC
* *
1271406 TTGGTATCGATAC
1 ATGGTATCAATAC
1271419 TACTCAGCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGGTATCAATACCACCCTC
Found at i:1273085 original size:2 final size:2
Alignment explanation
Indices: 1273078--1273107 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1273068 CCTAATATCA
1273078 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
1273108 TAAAATTTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1278913 original size:24 final size:24
Alignment explanation
Indices: 1278881--1278926 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1278871 AAAAAGAAAG
1278881 AAAAAAAAGGAACGTTGATGCAGA
1 AAAAAAAAGGAACGTTGATGCAGA
1278905 AAAAAAAAGGAACGTTGATGCA
1 AAAAAAAAGGAACGTTGATGCA
1278927 ATAAGAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.24, T:0.13
Consensus pattern (24 bp):
AAAAAAAAGGAACGTTGATGCAGA
Found at i:1280893 original size:17 final size:17
Alignment explanation
Indices: 1280860--1280893 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1280850 TTCTCTAACT
* *
1280860 AATTAAAAACAAGCCTA
1 AATTAAAAAAAAACCTA
1280877 AATTAAAAAAAAACCTA
1 AATTAAAAAAAAACCTA
1280894 GGTGCTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.15, G:0.03, T:0.18
Consensus pattern (17 bp):
AATTAAAAAAAAACCTA
Found at i:1282230 original size:21 final size:21
Alignment explanation
Indices: 1282204--1282245 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1282194 CCAAAATGGG
*
1282204 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1282225 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1282246 ATATTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1282379 original size:15 final size:15
Alignment explanation
Indices: 1282359--1282415 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1282349 AACCATGCAG
1282359 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
1282374 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
1282390 TGAGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
1282408 GGGGAATC
1 GGGGAATC
1282416 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:1282425 original size:35 final size:34
Alignment explanation
Indices: 1282359--1282442 Score: 141
Period size: 34 Copynumber: 2.4 Consensus size: 34
1282349 AACCATGCAG
*
1282359 GGGGAATCTGTACCCGGGGAATCGATACCCCTGA
1 GGGGAATCTGTTCCCGGGGAATCGATACCCCTGA
*
1282393 GGGGAATCTGTTCCCGGGGAATCGATACCCCCTGG
1 GGGGAATCTGTTCCCGGGGAATCGATA-CCCCTGA
1282428 GGGGAATCTGTTCCC
1 GGGGAATCTGTTCCC
1282443 TCTGGGCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 26 0.55
35 21 0.45
ACGTcount: A:0.19, C:0.27, G:0.33, T:0.20
Consensus pattern (34 bp):
GGGGAATCTGTTCCCGGGGAATCGATACCCCTGA
Found at i:1283866 original size:19 final size:20
Alignment explanation
Indices: 1283821--1283868 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1283811 TCTAAATCCT
* *
1283821 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTAATTTTGG
*
1283841 CTTTCAAAATCTAATTTT-G
1 TTTTCAAAATCTAATTTTGG
1283860 TTTTCAAAA
1 TTTTCAAAA
1283869 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATCTAATTTTGG
Found at i:1285106 original size:21 final size:21
Alignment explanation
Indices: 1285080--1285121 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1285070 CCAGAATGGG
*
1285080 GGGAATCGGTAACCCTTCATA
1 GGGAATCGATAACCCTTCATA
*
1285101 GGGAATCGATACCCCTTCATA
1 GGGAATCGATAACCCTTCATA
1285122 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATAACCCTTCATA
Found at i:1285311 original size:35 final size:34
Alignment explanation
Indices: 1285234--1285318 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
1285224 AAACCATGCA
* * *
1285234 GGGGGAATATGTACCCGGGGAATTGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
*
1285268 GGGAGAATCTGTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
1285303 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
1285319 TCTGGGCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 24 0.53
35 21 0.47
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.21
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:1286120 original size:31 final size:31
Alignment explanation
Indices: 1286085--1286193 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
1286075 TAGATCCCGA
* * *
1286085 AGAACCTAGGTAAACTGGCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCAT
* * * *
1286116 AGAACATATGTATACTGTCCATATGTCTCGAA
1 AGAACATAGGTAAACTGTCCATATGT-TCCAT
1286148 AG-ACATAGGTAATTA-TGTCCATATGTTCCAT
1 AGAACATAGGTAA--ACTGTCCATATGTTCCAT
1286179 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
1286194 CCTCGACTCT
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
30 1 0.02
31 35 0.56
32 25 0.40
33 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCAT
Found at i:1286172 original size:32 final size:32
Alignment explanation
Indices: 1286103--1286191 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
1286093 GGTAAACTGG
** *
1286103 CCATATGTTCCTTAGAACATATGT-A-TACTGT
1 CCATATGTTCCAAAGAACATAGGTAATTA-TGT
*
1286134 CCATATGTCTCGAAAG-ACATAGGTAATTATGT
1 CCATATGT-TCCAAAGAACATAGGTAATTATGT
*
1286166 CCATATGTTCCATAGAACATAGGTAA
1 CCATATGTTCCAAAGAACATAGGTAA
1286192 ACCCTCGACT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
31 20 0.42
32 26 0.54
33 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (32 bp):
CCATATGTTCCAAAGAACATAGGTAATTATGT
Found at i:1287152 original size:24 final size:20
Alignment explanation
Indices: 1287095--1287152 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1287085 TTTCCCTTGA
*
1287095 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
1287115 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1287138 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1287153 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1288037 original size:35 final size:35
Alignment explanation
Indices: 1287998--1288065 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
1287988 AATATAGTCC
1287998 TCAA-TATCATTATAAACCCTAAATTCTAAAATAAT
1 TCAATTAT-ATTATAAACCCTAAATTCTAAAATAAT
*
1288033 TCAATTATATTTTAAACCCTAAATTCTAAAATA
1 TCAATTATATTATAAACCCTAAATTCTAAAATA
1288066 CTTTAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTATATTATAAACCCTAAATTCTAAAATAAT
Found at i:1288141 original size:33 final size:35
Alignment explanation
Indices: 1288077--1288142 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
1288067 TTTAATTTAA
1288077 GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
1 GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
* *
1288112 GGTTTAGAATGTAA-T-AAGTGTTTTGGAATTT
1 GGTTTAGAATATAATTAAAGTATTTTGGAATTT
1288143 TGAACATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 15 0.52
34 1 0.03
35 13 0.45
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
Found at i:1292124 original size:87 final size:87
Alignment explanation
Indices: 1291975--1292164 Score: 294
Period size: 87 Copynumber: 2.2 Consensus size: 87
1291965 AACCAAACAC
*
1291975 GGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCTAGTAATTCTATTCC
1 GGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCTAGTAATCCTATT-C
*
1292040 CCAG-TAATCTTTTATTCCCACT
65 CCAGATAATATTTTATTCCCACT
* *
1292062 GGTAATCTTACATTCCTGCTAAACTAATCAAACACAAAATACAACATT-CTCAGTAATCCTATTC
1 GGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCT-AGTAATCCTATTC
* *
1292126 CCTGATAATATTTTATTCTCACT
65 CCAGATAATATTTTATTCCCACT
1292149 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
1292165 GTGAACCAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
86 6 0.06
87 89 0.94
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.33
Consensus pattern (87 bp):
GGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCTAGTAATCCTATTCC
CAGATAATATTTTATTCCCACT
Found at i:1294485 original size:135 final size:136
Alignment explanation
Indices: 1294105--1294485 Score: 364
Period size: 135 Copynumber: 2.8 Consensus size: 136
1294095 GTTAAACGGT
* * * * * *
1294105 TAGGATAATAT-CCTTCCAAACAATAGAACTGGATTCGACTCTTGGCAAACGCAATTCTTTTTAA
1 TAGGATAAT-TGCCTTCCAAGCAATAGACCTGGATTAGACTCCTGGAAAACGCAATTATTTTTAA
* *
1294169 ATTACTGATCGAATTAAACTTAAACAACAAAGATTAGTGTTAGCTCATTGACAAACAAAGCGTTT
65 ATTACTGATCGAATTAAA-TTAAACAACAAA-ATTA-TATTAGCTCAATGACAAACAAAGCGTTT
1294234 GTAGTCTAACGA
127 GTAGTCT-AC-A
* ** * * *
1294246 TTAGGATAATTGTCTTTTAAGCAATAGACCTGGCTTTGACTCCTGGAAAACGCAATTTTTTTTAA
1 -TAGGATAATTGCCTTCCAAGCAATAGACCTGGATTAGACTCCTGGAAAACGCAATTATTTTTAA
* * * * * * *
1294311 ACTATTGAGCGAATTAAA-TGAACAACAAACTTAAAATTAGCTCAGAATGACCAACAAAGCGTTT
65 ATTACTGATCGAATTAAATTAAACAACAAAATT-ATATTAGCTC--AATGACAAACAAAGCGTTT
1294375 GTAGT-T-C-
127 GTAGTCTACA
* * **
1294382 TAGGATAATTGCCTTCCAAGGAATAGA-CTCGGATTAGACTCCCT-GCAAGTGCAATTATTTTTA
1 TAGGATAATTGCCTTCCAAGCAATAGACCT-GGATTAGACT-CCTGGAAAACGCAATTATTTTTA
1294445 AATTACTGATCGAATTAAATTTAAACAACAAAATT-TATTAG
64 AATTACTGATCGAATTAAA-TTAAACAACAAAATTATATTAG
1294486 TAGCTCAAAA
Statistics
Matches: 196, Mismatches: 35, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
134 2 0.01
135 67 0.34
136 3 0.02
137 12 0.06
138 1 0.01
139 9 0.05
140 12 0.06
141 23 0.12
142 67 0.34
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (136 bp):
TAGGATAATTGCCTTCCAAGCAATAGACCTGGATTAGACTCCTGGAAAACGCAATTATTTTTAAA
TTACTGATCGAATTAAATTAAACAACAAAATTATATTAGCTCAATGACAAACAAAGCGTTTGTAG
TCTACA
Found at i:1294729 original size:142 final size:145
Alignment explanation
Indices: 1294507--1294808 Score: 409
Period size: 143 Copynumber: 2.1 Consensus size: 145
1294497 GATCAGCAAA
*
1294507 CCTTCCAAGCAATAGATCCGGGTTCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGATAGA
1 CCTTCCAAGCAATAGATCCGGGTTCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGAGAGA
*
1294572 ATTAAAATTAAAACAACAAATAG-TAGTGTTAGCTCAGAA-AACCAAACA-AGCGTTTGTAGTCC
66 ATTAAAATTAAAACAACAAA-AGTTAGAGTTAGCTCAGAATAACC-AACAGAGCGTTTGTAGTCC
*
1294634 AACGGTTAGGATAATTG
129 AACGGTTAGGAAAATTG
* * *
1294651 CCTTCCAAGCAATAGA-CCGGGTTCGACTCCCGGCAAACGCAGTT-CTTTTAAATTACTGAGCGA
1 CCTTCCAAGCAATAGATCCGGGTTCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGAGAGA
* * * * * *
1294714 ATTACACTTAAAACAACAAAGGTTAGAGTTAGCTCAGAATGACCAACAGAGCGTTTGTGGTTCAA
66 ATTAAAATTAAAACAACAAAAGTTAGAGTTAGCTCAGAATAACCAACAGAGCGTTTGTAGTCCAA
*
1294779 TGGTTAGGAAAATTG
131 CGGTTAGGAAAATTG
*
1294794 TCTT-CAATGCAATAG
1 CCTTCCAA-GCAATAG
1294809 GGTTGTGACT
Statistics
Matches: 140, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
141 1 0.01
142 57 0.41
143 66 0.47
144 16 0.11
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (145 bp):
CCTTCCAAGCAATAGATCCGGGTTCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGAGAGA
ATTAAAATTAAAACAACAAAAGTTAGAGTTAGCTCAGAATAACCAACAGAGCGTTTGTAGTCCAA
CGGTTAGGAAAATTG
Found at i:1297546 original size:74 final size:73
Alignment explanation
Indices: 1297327--1297821 Score: 519
Period size: 74 Copynumber: 6.7 Consensus size: 73
1297317 AAATAGGCTA
** * **
1297327 GTAAACGGTAAAATAAAATAGGTGTTATATATTATATTAAAATACCTACCGATTTTTTTAAGGTT
1 GTAAACGGTAAAA-AAAATAGACGCTACCTATTATATTAAAATACCTACCGATTTTTTTAAGGTT
* *
1297392 ACTAATGAT
65 GCTAATAAT
* * * **
1297401 ATAAACGGT-AAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGGGTTTTTTAAGGTT
1 GTAAACGGTAAAAAAAATAGACGCTACCTATTATATTAAAATACCTACC-GATTTTTTTAAGGTT
1297465 GCTAATAAT
65 GCTAATAAT
* * * * *
1297474 ATAAACAGTAAAAAAAAATAGACGCTGCCTATTATATTAAACTACATACCGATTTTTTTAAGGTT
1 GTAAACGGT-AAAAAAAATAGACGCTACCTATTATATTAAAATACCTACCGATTTTTTTAAGGTT
*
1297539 GTTAATAAT
65 GCTAATAAT
* * * ** * * *
1297548 GTAAACGGTAAAACAAATAGACGCTACTTATTAGATTAAAATACCTATTGGTTTGTTTAAAGATT
1 GTAAACGGTAAAAAAAATAGACGCTACCTATTATATTAAAATACCTACCGATTT-TTTTAAGGTT
1297613 GCTAATAAT
65 GCTAATAAT
* * * * * * * **
1297622 GTAAATGATAAAATAAAATAGGCGTTACCTATTACATTAAAATACATACCGGTTTTTTTTAACAT
1 GTAAACGGTAAAA-AAAATAGACGCTACCTATTATATTAAAATACCTACC-GATTTTTTTAAGGT
*
1297687 TGTTAATAAT
64 TGCTAATAAT
* *
1297697 CTAAACGGTAAAAAAAATAAGA-GCTACCTATTATATTAAAATACCTACCGGTTTTTTTTAAGGT
1 GTAAACGGTAAAAAAAAT-AGACGCTACCTATTATATTAAAATACCTACC-GATTTTTTTAAGGT
1297761 TGCTAATAAT
64 TGCTAATAAT
* * *
1297771 GTAAACGGTAAAAAAAATA-AGTGCTACCTATTATATTAAACTACATACCGA
1 GTAAACGGTAAAAAAAATAGA-CGCTACCTATTATATTAAAATACCTACCGA
1297822 ACATGTTGAA
Statistics
Matches: 351, Mismatches: 61, Indels: 19
0.81 0.14 0.04
Matches are distributed among these distances:
72 32 0.09
73 69 0.20
74 156 0.44
75 90 0.26
76 4 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (73 bp):
GTAAACGGTAAAAAAAATAGACGCTACCTATTATATTAAAATACCTACCGATTTTTTTAAGGTTG
CTAATAAT
Found at i:1298138 original size:111 final size:112
Alignment explanation
Indices: 1297901--1298157 Score: 335
Period size: 111 Copynumber: 2.3 Consensus size: 112
1297891 TAGCACCTAT
* * * *
1297901 AAAGTATCGA-ATCTTTATAAAAATATATCGATTCATAACAATATAACATGTTAAAATATGACAA
1 AAAGTATCGATA-CTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAA
* *
1297965 AACCAGTTTCATTATGACAAAACCAGTAAAGAGCTACCAGATATGTTG
65 AACCAGTTTCATTATGACAAAACCAGCAAAGAACTACCAGATATGTTG
1298013 AAAGTATC-ATTACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGA-AA
1 AAAGTATCGA-TACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAA
* *
1298076 AACCAGTTTCATTATGACAAAATCGGCAATA-AACTACC-GAATATGTTG
65 AACCAGTTTCATTATGACAAAACCAGCAA-AGAACTACCAG-ATATGTTG
* ** *
1298124 AAAGTATCGATACTTTTTGTACATGTATCGATAC
1 AAAGTATCGATACTTTATAAAAATGTATCGATAC
1298158 TTTGTTGAAA
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
110 1 0.01
111 71 0.55
112 55 0.43
113 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAACCAGCAAAGAACTACCAGATATGTTG
Found at i:1299168 original size:46 final size:45
Alignment explanation
Indices: 1299098--1299242 Score: 218
Period size: 45 Copynumber: 3.2 Consensus size: 45
1299088 TATAAAATCT
* *
1299098 CTTACTATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
1299143 CTTACCATTTAATACCATAAACTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
1299189 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
1299234 CTTGCCATT
1 CTTACCATT
1299243 ATTTCCATAA
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 48 0.53
46 43 0.47
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:1299183 original size:24 final size:24
Alignment explanation
Indices: 1299155--1299228 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 24
1299145 TACCATTTAA
1299155 TACCATAAACTCGTAAGCTTATTT
1 TACCATAAACTCGTAAGCTTATTT
* *
1299179 TACCAATATACT--T-A-C-CATTT
1 TACC-ATAAACTCGTAAGCTTATTT
* *
1299199 GTTCCATAAGCTCGTAAGCTTATTT
1 -TACCATAAACTCGTAAGCTTATTT
1299224 TACCA
1 TACCA
1299229 ATACACTTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
20 9 0.25
21 4 0.11
22 2 0.06
23 2 0.06
24 9 0.25
25 10 0.28
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (24 bp):
TACCATAAACTCGTAAGCTTATTT
Found at i:1300312 original size:20 final size:20
Alignment explanation
Indices: 1300287--1300379 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 20
1300277 TCTGTCAGTT
1300287 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
* *
1300307 ATTAGATAGAATCAATTTT-
1 ATTAGATAGGATCAGTTTTA
* ** *
1300326 -TTA-TTCTG-TTAG--TT-
1 ATTAGATAGGATCAGTTTTA
1300340 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
*
1300360 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
1300380 TTCTGTTGCT
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
14 2 0.04
15 3 0.06
16 4 0.07
17 4 0.07
18 3 0.06
19 2 0.04
20 36 0.67
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (20 bp):
ATTAGATAGGATCAGTTTTA
Found at i:1300334 original size:53 final size:51
Alignment explanation
Indices: 1300271--1300385 Score: 194
Period size: 53 Copynumber: 2.2 Consensus size: 51
1300261 TAACTAGATA
*
1300271 TTTTATTCTGTCAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAATT
1 TTTTATTCTGTCAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATC-A-G
*
1300324 TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
1 TTTTATTCTGTCAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
1300375 TTTTATTCTGT
1 TTTTATTCTGT
1300386 TGCTAATTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 11 0.18
52 1 0.02
53 48 0.80
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.48
Consensus pattern (51 bp):
TTTTATTCTGTCAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
Found at i:1305392 original size:20 final size:20
Alignment explanation
Indices: 1305367--1305459 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 20
1305357 TCTGTCAGTT
1305367 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
*
1305387 ATTAGATAGAATCAGTTTT-
1 ATTAGATAGGATCAGTTTTA
* ** *
1305406 -TTA-TTCTG-TTAG--TT-
1 ATTAGATAGGATCAGTTTTA
*
1305420 ATTAGATAGGATCATTTTTA
1 ATTAGATAGGATCAGTTTTA
*
1305440 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
1305460 TTCTGTTGCT
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
14 2 0.04
15 3 0.06
16 5 0.09
17 3 0.06
18 3 0.06
19 2 0.04
20 36 0.67
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.45
Consensus pattern (20 bp):
ATTAGATAGGATCAGTTTTA
Found at i:1305431 original size:53 final size:51
Alignment explanation
Indices: 1305351--1305466 Score: 196
Period size: 53 Copynumber: 2.2 Consensus size: 51
1305341 TAACTAGATA
*
1305351 TTTTATTCTGTCAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
1 TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
*
1305402 TTTTTTATTCTGTTAGTTATTAGATAGGATCATTTTTAATTAGATAGAATCAG
1 --TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
1305455 TTTTATTCTGTT
1 TTTTATTCTGTT
1305467 GCTAATTTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 12 0.20
53 49 0.80
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (51 bp):
TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
Found at i:1312586 original size:16 final size:16
Alignment explanation
Indices: 1312561--1312602 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1312551 TGAAAAATTA
*
1312561 GCAAATTTGAAAGTTG
1 GCAAAATTGAAAGTTG
1312577 GCAAAATTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
1312593 GCAAAGTTGA
1 GCAAAATTGA
1312603 CATCTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (16 bp):
GCAAAATTGAAAGTTG
Found at i:1317290 original size:16 final size:16
Alignment explanation
Indices: 1317265--1317338 Score: 103
Period size: 16 Copynumber: 4.6 Consensus size: 16
1317255 TGAAAAATTA
*
1317265 GCAAAGTTGAAAGTTG
1 GCAAAATTGAAAGTTG
1317281 GCAAAATTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
1317297 GCAAATTTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
1317313 GTAAAATTGAAAGTTG
1 GCAAAATTGAAAGTTG
* *
1317329 ACAAAGTTGA
1 GCAAAATTGA
1317339 CATCTTTGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.27
Consensus pattern (16 bp):
GCAAAATTGAAAGTTG
Found at i:1317307 original size:32 final size:32
Alignment explanation
Indices: 1317265--1317338 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
1317255 TGAAAAATTA
1317265 GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
* *
1317297 GCAAATTTGAAAGTTGGTAAAATTGAAAGTTG
1 GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
*
1317329 ACAAAGTTGA
1 GCAAAGTTGA
1317339 CATCTTTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.27
Consensus pattern (32 bp):
GCAAAGTTGAAAGTTGGCAAAATTGAAAGTTG
Done.