Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, 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: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 3 of 10
Found at i:836890 original size:22 final size:21
Alignment explanation
Indices: 836851--836891 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
836841 TTACGTTCAA
* *
836851 TTAAATCTATAAATTTTTATT
1 TTAAATCAATAAACTTTTATT
836872 TTAAATCAAATAAACTTTTA
1 TTAAATC-AATAAACTTTTA
836892 AAATTAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAATCAATAAACTTTTATT
Found at i:837184 original size:26 final size:28
Alignment explanation
Indices: 837155--837222 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 28
837145 ATGATATCTT
837155 ATTTGATTAAAAATAA-AAA-T-ATAAAA
1 ATTT-ATTAAAAATAATAAATTAATAAAA
*
837181 ATTTAATTAAACATAATAAATTAATAAAA
1 ATTT-ATTAAAAATAATAAATTAATAAAA
*
837210 ATTTATTTAAAAT
1 ATTTATTAAAAAT
837223 TTTCTCGATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.40
27 3 0.09
28 8 0.23
29 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (28 bp):
ATTTATTAAAAATAATAAATTAATAAAA
Found at i:837208 original size:29 final size:26
Alignment explanation
Indices: 837155--837221 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 26
837145 ATGATATCTT
*
837155 ATTTGATTAAAAATAAAAATATAAAA
1 ATTTAATTAAAAATAAAAATATAAAA
*
837181 ATTTAATTAAACATAATAAATTAATAAAA
1 ATTTAATTAAAAATAA-AAA-T-ATAAAA
*
837210 ATTTATTTAAAA
1 ATTTAATTAAAA
837222 TTTTCTCGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.41
27 3 0.09
28 1 0.03
29 16 0.47
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (26 bp):
ATTTAATTAAAAATAAAAATATAAAA
Found at i:848168 original size:3 final size:3
Alignment explanation
Indices: 848162--848219 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
848152 GACTGCTCCC
* * *
848162 CAT CAT CAT CAT CAA CAT CAT CAT CAT AAT CAT CAT CCT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
848210 CAT CAT CAT C
1 CAT CAT CAT C
848220 CTCTACATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:849405 original size:29 final size:30
Alignment explanation
Indices: 849334--849406 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
849324 ATTGATAATC
*
849334 ATAAAAATTT-ATTTAATTTAAGATAAAAAT
1 ATAAAAATTTAATTTAATGT-AGATAAAAAT
* * *
849364 ACAAGTAA-CTAATTTAATGT-GATAAAAAT
1 ATAA-AAATTTAATTTAATGTAGATAAAAAT
849393 ATAAAAATTTAATT
1 ATAAAAATTTAATT
849407 AAAATTTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
28 2 0.06
29 17 0.52
30 4 0.12
31 10 0.30
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (30 bp):
ATAAAAATTTAATTTAATGTAGATAAAAAT
Found at i:850387 original size:17 final size:16
Alignment explanation
Indices: 850359--850394 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
850349 AACATATTCA
850359 TTAATAATATATACTT
1 TTAATAATATATACTT
*
850375 TTAATATATATATATTT
1 TTAATA-ATATATACTT
850392 TTA
1 TTA
850395 TATTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATAATATATACTT
Found at i:856133 original size:45 final size:45
Alignment explanation
Indices: 856044--856135 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
856034 TTATTGTTAG
* * * *
856044 GTTAACGTTCTTATATTGCGAAAAGTGTGGTTGCTATTCAATTTT
1 GTTAACGTTCTTATATTGCAAAAAGTATGGTTACCATTCAATTTT
* * **
856089 GTTAAGGTTCTTGTATTGCAAAAAGTATGGTTACCATTTGATTTT
1 GTTAACGTTCTTATATTGCAAAAAGTATGGTTACCATTCAATTTT
856134 GT
1 GT
856136 AGCAATTTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.45
Consensus pattern (45 bp):
GTTAACGTTCTTATATTGCAAAAAGTATGGTTACCATTCAATTTT
Found at i:862960 original size:152 final size:152
Alignment explanation
Indices: 862791--863100 Score: 505
Period size: 152 Copynumber: 2.0 Consensus size: 152
862781 GCTTAATATT
* * *
862791 TCATATGTATAAATATATATATATCTAGGCCCATCTAGGCATAATATATTCATATTTAAACATCT
1 TCATATATATAAATATATATATATCTAGGCCCATCTAGCCATAATATATTCATATTCAAACATCT
* *
862856 TAAATTCAAAAGTGCGAGGATCATCCTAATATCCTACATGCACAATTCATCGTAGTCAAACTC-G
66 TAAATTCAAAAGTGCGAGGATCATCCTAATATCCTACATGCACAATTCATCATAGTCAAACTCAC
862920 TCGAATCACATATCAACAGCGTA
131 T-GAATCACATATCAACAGCGTA
* *
862943 TCATATATATAGATATATATATATCTAGGCCCATCTAGCCATAATATATTCATATTCAAACATTT
1 TCATATATATAAATATATATATATCTAGGCCCATCTAGCCATAATATATTCATATTCAAACATCT
* *
863008 TAAATTCAAAAGTGCGAGGATCATCTTAATATCCTACATGCACAATTCTTCATAGTCAAACTCAC
66 TAAATTCAAAAGTGCGAGGATCATCCTAATATCCTACATGCACAATTCATCATAGTCAAACTCAC
* *
863073 TGGATCACATATCAGCAGCGTA
131 TGAATCACATATCAACAGCGTA
863095 TCATAT
1 TCATAT
863101 CCATAAATTT
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
152 145 0.99
153 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (152 bp):
TCATATATATAAATATATATATATCTAGGCCCATCTAGCCATAATATATTCATATTCAAACATCT
TAAATTCAAAAGTGCGAGGATCATCCTAATATCCTACATGCACAATTCATCATAGTCAAACTCAC
TGAATCACATATCAACAGCGTA
Found at i:864540 original size:18 final size:19
Alignment explanation
Indices: 864506--864541 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
864496 TATTTCCTAG
864506 TTTTCAAAAATATCCCAAC
1 TTTTCAAAAATATCCCAAC
864525 TTTTCAAAAATA-CCCAA
1 TTTTCAAAAATATCCCAA
864542 ATTCAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (19 bp):
TTTTCAAAAATATCCCAAC
Found at i:865298 original size:38 final size:38
Alignment explanation
Indices: 865256--865331 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
865246 AGGACCAGAC
* *
865256 TAGCCTAGTAACCAAAATGGGGAACCT-CTCAGATGCCA
1 TAGCCTAGTAACCAAAATAGAGAACCTCCT-AGATGCCA
*
865294 TAGCCTAGTGACCAAAATAGAGAACCTCCTAGATGCCA
1 TAGCCTAGTAACCAAAATAGAGAACCTCCTAGATGCCA
865332 AAATTCATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 32 0.94
39 2 0.06
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (38 bp):
TAGCCTAGTAACCAAAATAGAGAACCTCCTAGATGCCA
Found at i:869856 original size:37 final size:36
Alignment explanation
Indices: 869815--869887 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
869805 GGGCCATTAC
*
869815 ACCACACAACT-ATGAGGGCCATGGTGTGAGGTGTCAA
1 ACCACA-AACTAAT-AGGGCCATGATGTGAGGTGTCAA
*
869852 ACCACATACTCAATAGGGCCATGATGTGAGGTGTCA
1 ACCACAAACT-AATAGGGCCATGATGTGAGGTGTCA
869888 GACTATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 3 0.09
37 27 0.84
38 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (36 bp):
ACCACAAACTAATAGGGCCATGATGTGAGGTGTCAA
Found at i:872969 original size:36 final size:36
Alignment explanation
Indices: 872904--872972 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
872894 TTTCAAACTG
* *
872904 AGTAGCCCACTTTTTGTGATATGAATGTGGATGGTT
1 AGTAGCCCACCTATTGTGATATGAATGTGGATGGTT
872940 AGTAGCCCACCTATTGT-A-ATGGAAGTGTGGATG
1 AGTAGCCCACCTATTGTGATAT-GAA-TGTGGATG
872973 AATGATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 2 0.07
35 4 0.14
36 23 0.79
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (36 bp):
AGTAGCCCACCTATTGTGATATGAATGTGGATGGTT
Found at i:874535 original size:14 final size:14
Alignment explanation
Indices: 874516--874543 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
874506 CAAGGATTTG
874516 ATACATATATATAT
1 ATACATATATATAT
874530 ATACATATATATAT
1 ATACATATATATAT
874544 CAACAAGTGC
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATACATATATATAT
Found at i:888804 original size:18 final size:17
Alignment explanation
Indices: 888777--888811 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
888767 TTCACCATAA
*
888777 TTTTCAACAGTAATTTC
1 TTTTCAACAGCAATTTC
888794 TTTTCCAACAGCAATTTC
1 TTTT-CAACAGCAATTTC
888812 AACTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTTCAACAGCAATTTC
Found at i:889083 original size:21 final size:21
Alignment explanation
Indices: 889016--889084 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
889006 GATTTCTAGT
*
889016 TGAT-GCTGCTTGACTTTGAA
1 TGATGGCTACTTGACTTTGAA
*
889036 TGATAGCTACTTGACTTTGAA
1 TGATGGCTACTTGACTTTGAA
889057 TGATGGCTACTTGACTTTGAA
1 TGATGGCTACTTGACTTTGAA
889078 TGATGGC
1 TGATGGC
889085 ATCATTCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 4 0.09
21 42 0.91
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (21 bp):
TGATGGCTACTTGACTTTGAA
Found at i:912285 original size:36 final size:35
Alignment explanation
Indices: 912155--912327 Score: 181
Period size: 35 Copynumber: 4.9 Consensus size: 35
912145 TCTCAAGCAC
*
912155 TTGATTAAAATTATTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTATTTAATTAAGTTATTGGGCCTAA
* * *
912188 TTCATTAAATTGTTTAATTAAGTCATTGGGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
* ***
912223 TTAATTAAATTAAACAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
* * *
912258 TTGATTAAATTTGTTTAATTAAGTTATTAGGCTTAA
1 TTGATTAAA-TTATTTAATTAAGTTATTGGGCCTAA
**
912294 TTGATTAAATTAAATAATTAAGTTTATTGGGCCT
1 TTGATTAAATTATTTAATTAAG-TTATTGGGCCT
912328 CTTAAAGACT
Statistics
Matches: 114, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
32 15 0.13
33 5 0.04
35 56 0.49
36 38 0.33
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (35 bp):
TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
Found at i:912301 original size:71 final size:71
Alignment explanation
Indices: 912182--912327 Score: 222
Period size: 71 Copynumber: 2.1 Consensus size: 71
912172 ATTAAGTTGT
*
912182 GCCTAATTCATTAAATTGTTTAATTAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAG-T
1 GCCTAATTCATTAAATTGTTTAATTAAGTCATTAGGCCTAATTAATTAAATTAAACAATTAAGTT
912246 TATTGG
66 TATTGG
* * * * *
912252 GCCTAATTGATTAAATTTGTTTAATTAAGTTATTAGGCTTAATTGATTAAATTAAATAATTAAGT
1 GCCTAATTCATTAAA-TTGTTTAATTAAGTCATTAGGCCTAATTAATTAAATTAAACAATTAAGT
912317 TTATTGG
65 TTATTGG
912324 GCCT
1 GCCT
912328 CTTAAAGACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 14 0.21
71 43 0.63
72 11 0.16
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (71 bp):
GCCTAATTCATTAAATTGTTTAATTAAGTCATTAGGCCTAATTAATTAAATTAAACAATTAAGTT
TATTGG
Found at i:922232 original size:14 final size:15
Alignment explanation
Indices: 922196--922237 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
922186 TTTAAAATAA
922196 AATAATATT-TTATT
1 AATAATATTATTATT
922210 AATAA-ATTATTATT
1 AATAATATTATTATT
*
922224 AA-AATATTAATATT
1 AATAATATTATTATT
922238 TTATCTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATTATTATT
Found at i:923052 original size:8 final size:8
Alignment explanation
Indices: 923032--923103 Score: 85
Period size: 8 Copynumber: 9.1 Consensus size: 8
923022 AAATTTGGCT
923032 AGGAAGCAA
1 AGGAAG-AA
923041 AGGAAGAA
1 AGGAAGAA
923049 AGGAAGAA
1 AGGAAGAA
*
923057 AGAAAGAA
1 AGGAAGAA
* *
923065 ATG-AGAG
1 AGGAAGAA
923072 AGGAAGAA
1 AGGAAGAA
923080 AGGAAGAA
1 AGGAAGAA
*
923088 AGGGAGAA
1 AGGAAGAA
923096 AGG-AGAA
1 AGGAAGAA
923103 A
1 A
923104 AAAAATAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
7 10 0.18
8 39 0.71
9 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.38, T:0.01
Consensus pattern (8 bp):
AGGAAGAA
Found at i:923096 original size:31 final size:31
Alignment explanation
Indices: 923041--923101 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
923031 TAGGAAGCAA
*
923041 AGGAAGAAAGGAAGAAAGAAAGAAATGAGAG
1 AGGAAGAAAGGAAGAAAGAAAGAAAGGAGAG
**
923072 AGGAAGAAAGGAAGAAAGGGAGAAAGGAGA
1 AGGAAGAAAGGAAGAAAGAAAGAAAGGAGA
923102 AAAAAAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (31 bp):
AGGAAGAAAGGAAGAAAGAAAGAAAGGAGAG
Found at i:923102 original size:23 final size:24
Alignment explanation
Indices: 923039--923103 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
923029 GCTAGGAAGC
*
923039 AAAGGAAGAAAGGAAGAAAGAAAG
1 AAAGGGAGAAAGGAAGAAAGAAAG
* * *
923063 AAA-TGAGAGAGGAAGAAAGGAAG
1 AAAGGGAGAAAGGAAGAAAGAAAG
923086 AAAGGGAGAAAGG-AGAAA
1 AAAGGGAGAAAGGAAGAAA
923104 AAAAATAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.02
Consensus pattern (24 bp):
AAAGGGAGAAAGGAAGAAAGAAAG
Found at i:929569 original size:28 final size:28
Alignment explanation
Indices: 929526--929634 Score: 132
Period size: 28 Copynumber: 3.9 Consensus size: 28
929516 ATGGTAACTT
*
929526 AACATGTTTGTCTTAATTTAGATAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* *
929554 AACATGTTTG-CTTTAATTCAAACAAGAA
1 AACATGTTTGTC-TTAATTTAGACAAGAA
* *
929582 AACATGTTTATCTTAATTTAGAGAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
929610 AACATGATTT-TCTTAATTAAGACAA
1 AACATG-TTTGTCTTAATTTAGACAA
929635 AAGTTGCTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.01
28 64 0.93
29 4 0.06
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:933179 original size:127 final size:128
Alignment explanation
Indices: 933023--933274 Score: 371
Period size: 127 Copynumber: 2.0 Consensus size: 128
933013 AAAATTATTA
* * *
933023 TTTTTGGAAAATTAAAATTTTTAATCTTGGATTGTAAAATGATTTTTATTTTGGTATTAATTAAT
1 TTTTTGGAAAATTAAAATTTTTAAGCTTGGATTGAAAAATAATTTTTATTTTGGTATTAATTAAT
* * * *
933088 GAGATTAATTACTTTTACAAAATTAAAATTATTTTCAAGCTGGGTTAAAT-TAAAAAGAATTT
66 GAGATTAATTAATTGTACAAAATTAAAATTACTTTCAAGCTGAGTTAAATATAAAAAGAATTT
* * *
933150 TTTTTGGAAAATTAAAATTTTTAGGCTTGGATTGAAAAATAATTTTTATTTTTGTATTGATTAAT
1 TTTTTGGAAAATTAAAATTTTTAAGCTTGGATTGAAAAATAATTTTTATTTTGGTATTAATTAAT
* * * *
933215 GAGATTAATTAATTGTACAAAGTTCAAATTACTTTCAAGTTGAGTTAAATATTAAAAGAA
66 GAGATTAATTAATTGTACAAAATTAAAATTACTTTCAAGCTGAGTTAAATATAAAAAGAA
933275 AAATTAGATT
Statistics
Matches: 110, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
127 102 0.93
128 8 0.07
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (128 bp):
TTTTTGGAAAATTAAAATTTTTAAGCTTGGATTGAAAAATAATTTTTATTTTGGTATTAATTAAT
GAGATTAATTAATTGTACAAAATTAAAATTACTTTCAAGCTGAGTTAAATATAAAAAGAATTT
Found at i:941539 original size:12 final size:13
Alignment explanation
Indices: 941513--941537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
941503 GACTCTGACT
941513 TTTTTTTTTGAAA
1 TTTTTTTTTGAAA
941526 TTTTTTTTTGAA
1 TTTTTTTTTGAA
941538 TTCAATTACC
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTGAAA
Found at i:949933 original size:29 final size:29
Alignment explanation
Indices: 949838--949939 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
949828 GTTCTTGAGT
*
949838 AAAAGGTA-ATAGAGAA-AAGTTATACATG
1 AAAAGGTATA-AGAGAAGAAGTTATGCATG
*
949866 AAAAGGTATAAGAGAAGAAGTTGTGCAT-
1 AAAAGGTATAAGAGAAGAAGTTATGCATG
*
949894 AAACAGATATAAGAGAAGAAGTTATGCATG
1 AAA-AGGTATAAGAGAAGAAGTTATGCATG
* *
949924 AATAGGTATAAAAGAA
1 AAAAGGTATAAGAGAA
949940 AAAGGTGCAT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 17 0.27
29 44 0.70
30 2 0.03
ACGTcount: A:0.52, C:0.04, G:0.24, T:0.21
Consensus pattern (29 bp):
AAAAGGTATAAGAGAAGAAGTTATGCATG
Found at i:959223 original size:21 final size:21
Alignment explanation
Indices: 959196--959267 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
959186 TCAAGACAAC
959196 GACTGATGCATTCATGATAAA
1 GACTGATGCATTCATGATAAA
* * * *
959217 GATTGATACATTCATAACAAA
1 GACTGATGCATTCATGATAAA
* * *
959238 TACTAATGCATTTATGATAAA
1 GACTGATGCATTCATGATAAA
*
959259 GACTAATGC
1 GACTGATGC
959268 CTCCATTCAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (21 bp):
GACTGATGCATTCATGATAAA
Found at i:961545 original size:3 final size:3
Alignment explanation
Indices: 961537--961576 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
961527 ACTTTATCTT
* *
961537 TAG TAG TAG TAG TAA TAG TAA TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
961577 GACTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:962856 original size:118 final size:119
Alignment explanation
Indices: 962632--962862 Score: 277
Period size: 118 Copynumber: 1.9 Consensus size: 119
962622 NNNNNNNNNN
* *
962632 TAACTCAGCCTAGAAAAGTTAGTTTTGGGGTTTTGGTTGATCTCAGAAAAAACCATTGTTGAAGA
1 TAACTCAGCCTAGAAAAGTTAGTTTTGGGATTTTAGTTGATCTCAGAAAAAACCATTGTTGAAGA
* **********
962697 TTGTGGCTGAGCTTGTGAAAAGCCATNNNNNNNNNNTGGTGAAAGCTTAGGTTC
66 TTGTGGCTGAGCCTGTGAAAAGCCATATGTAAAAGTTGGTGAAAGCTTAGGTTC
* * * * *
962751 TAACTCAGCTTGGAAAAGTTAGTTTTTGGATTTTAGTTGATC-CCGAAAAAACCATTGTTGAAGG
1 TAACTCAGCCTAGAAAAGTTAGTTTTGGGATTTTAGTTGATCTCAGAAAAAACCATTGTTGAAGA
962815 TTGTGGCTGAGCCTGTGAAAAGCCAT-TGTAAAAGTTGGGTGAAAGCTT
66 TTGTGGCTGAGCCTGTGAAAAGCCATATGTAAAAGTT-GGTGAAAGCTT
962863 CGAAATTTTA
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
117 1 0.01
118 56 0.60
119 37 0.39
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.31
Consensus pattern (119 bp):
TAACTCAGCCTAGAAAAGTTAGTTTTGGGATTTTAGTTGATCTCAGAAAAAACCATTGTTGAAGA
TTGTGGCTGAGCCTGTGAAAAGCCATATGTAAAAGTTGGTGAAAGCTTAGGTTC
Found at i:970456 original size:29 final size:28
Alignment explanation
Indices: 970386--970472 Score: 113
Period size: 27 Copynumber: 3.1 Consensus size: 28
970376 TTTCCAAAAT
*
970386 TTTTTAAAAATTTTATTTATTATATATA
1 TTTTTAAAATTTTTATTTATTATATATA
* * * *
970414 -TATTGAAATTTTTATTTTTTATTTATA
1 TTTTTAAAATTTTTATTTATTATATATA
970441 TTTTTAAAATTATTTATTTATTATATATA
1 TTTTTAAAATT-TTTATTTATTATATATA
970470 TTT
1 TTT
970473 CAAATGATCC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 22 0.46
28 8 0.17
29 18 0.38
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTTAAAATTTTTATTTATTATATATA
Found at i:981170 original size:336 final size:336
Alignment explanation
Indices: 980557--981219 Score: 1263
Period size: 336 Copynumber: 2.0 Consensus size: 336
980547 GATTCGTCGC
980557 GGTTCGCTACAAGTCCAGCCTCAAAATCCTCCCCAGTGCACTTTTTCTGGTGATGTACTGCTGAG
1 GGTTCGCTACAAGTCCAGCCTCAAAATCCTCCCCAGTGCACTTTTTCTGGTGATGTACTGCTGAG
*
980622 TCTGATGATGGGTGCGAGGAGGAAGGAGAGACAAAACCAAAAGAAAATGAAGAAGAAAAGAAAAA
66 TCTGATGATGGGTGCGAGGAGAAAGGAGAGACAAAACCAAAAGAAAATGAAGAAGAAAAGAAAAA
*
980687 GGGCATTGGAGTTCTACGTGTCAAAAAAATTAATTTTATTTGTTGAATAAAACAAAAAATAATGA
131 GGGCATGGGAGTTCTACGTGTCAAAAAAATTAATTTTATTTGTTGAATAAAACAAAAAATAATGA
980752 AATGTATAATTCATAAATTACATATATTAATTCTAAAGTAAAGAGTAAGGAATTAATTAAAAATG
196 AATGTATAATTCATAAATTACATATATTAATTCTAAAGTAAAGAGTAAGGAATTAATTAAAAATG
980817 ATAATTAATTATATAAATGTGTGATTATTTTTTAAAAAAAATTGATTTACTAATTGTCAAAGTCA
261 ATAATTAATTATATAAATGTGTGATTATTTTTTAAAAAAAATTGATTTACTAATTGTCAAAGTCA
980882 AAATGACTTGT
326 AAATGACTTGT
* *
980893 GGTTCGCTACAAGTCCAGCCTCAATATCCTCCCCAGTGCACTTTTTCTGTTGATGTACTGCTGAG
1 GGTTCGCTACAAGTCCAGCCTCAAAATCCTCCCCAGTGCACTTTTTCTGGTGATGTACTGCTGAG
980958 TCTGATGATGGGTGCGAGGAGAAAGGAGAGACAAAACCAAAAGAAAATGAAGAAGAAAAGAAAAA
66 TCTGATGATGGGTGCGAGGAGAAAGGAGAGACAAAACCAAAAGAAAATGAAGAAGAAAAGAAAAA
*
981023 GGGCGTGGGAGTTCTACGTGTCAAAAAAATTAATTTTATTTGTTGAATAAAACAAAAAATAATGA
131 GGGCATGGGAGTTCTACGTGTCAAAAAAATTAATTTTATTTGTTGAATAAAACAAAAAATAATGA
*
981088 AATGTATAATTCATAAATTACATATATTAATTCTAAAGTAAAGAGTAATGAATTAATTAAAAATG
196 AATGTATAATTCATAAATTACATATATTAATTCTAAAGTAAAGAGTAAGGAATTAATTAAAAATG
*
981153 ATAATTAATTATATAAATGTGTGATTATTTTTTTAAAAAAATTGATTTACTAATTGTCAAAGTCA
261 ATAATTAATTATATAAATGTGTGATTATTTTTTAAAAAAAATTGATTTACTAATTGTCAAAGTCA
981218 AA
326 AA
981220 CGAGTACCAA
Statistics
Matches: 320, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
336 320 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (336 bp):
GGTTCGCTACAAGTCCAGCCTCAAAATCCTCCCCAGTGCACTTTTTCTGGTGATGTACTGCTGAG
TCTGATGATGGGTGCGAGGAGAAAGGAGAGACAAAACCAAAAGAAAATGAAGAAGAAAAGAAAAA
GGGCATGGGAGTTCTACGTGTCAAAAAAATTAATTTTATTTGTTGAATAAAACAAAAAATAATGA
AATGTATAATTCATAAATTACATATATTAATTCTAAAGTAAAGAGTAAGGAATTAATTAAAAATG
ATAATTAATTATATAAATGTGTGATTATTTTTTAAAAAAAATTGATTTACTAATTGTCAAAGTCA
AAATGACTTGT
Found at i:984593 original size:43 final size:43
Alignment explanation
Indices: 984545--984631 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
984535 TAACATACTC
* *
984545 TCTCAAATTTCCCTAGTAACTTCTAATTCTTTATCTACATTTG
1 TCTCAAATTTCCCTAGTAACTTCTAATTCATCATCTACATTTG
*
984588 TCTCAAATTTCCCTAGTAACTTCTAATTCATCATCTGCATTTG
1 TCTCAAATTTCCCTAGTAACTTCTAATTCATCATCTACATTTG
984631 T
1 T
984632 ATCTTCATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.25, C:0.24, G:0.06, T:0.45
Consensus pattern (43 bp):
TCTCAAATTTCCCTAGTAACTTCTAATTCATCATCTACATTTG
Found at i:988063 original size:19 final size:19
Alignment explanation
Indices: 988039--988080 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
988029 AATAAGATTC
988039 TTCTTTCCC-CTTAAATACT
1 TTCTTTCCCTC-TAAATACT
988058 TTCTTTCCCTCTAAATACT
1 TTCTTTCCCTCTAAATACT
988077 TTCT
1 TTCT
988081 CTTATATNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCTTTCCCTCTAAATACT
Found at i:988478 original size:53 final size:55
Alignment explanation
Indices: 988382--988525 Score: 175
Period size: 53 Copynumber: 2.6 Consensus size: 55
988372 ATAAAAAACC
** **
988382 ATAAATGTCCATTCCCTGAAGTGAATGTGACAAATGAGCTAC-TAAT-AAAATTT
1 ATAAATGTCCATTCCCTGAAGTGAATGTGACAAACAAAATACATAATAAAAATTT
* *
988435 ATGAATGTTCATTCCCTGAAGTGAATGTGACAAACAAAATACTAATAATAAAAATTT
1 ATAAATGTCCATTCCCTGAAGTGAATGTGACAAACAAAATAC--ATAATAAAAATTT
*
988492 ATAAATTCGTCCATTCTCTGAAGTGAATGTGACA
1 ATAAA-T-GTCCATTCCCTGAAGTGAATGTGACA
988526 TCATTTAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
53 36 0.47
56 4 0.05
57 11 0.14
58 1 0.01
59 24 0.32
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (55 bp):
ATAAATGTCCATTCCCTGAAGTGAATGTGACAAACAAAATACATAATAAAAATTT
Found at i:988558 original size:59 final size:59
Alignment explanation
Indices: 988495--988607 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
988485 AAAATTTATA
* * * *
988495 AATTCGTCCATTC-TCTGAAGTGAATGTGACATCATTTAATAATTATGGTCATAATCATG
1 AATTCATCCATTCAT-TGAAGTGAATGTAACATCATTTAATAATGATGGCCATAATCATG
* * *
988554 AATTCATCTATTCATTGAAGTGAATGTAATATCATTTAATTATGATGGCCATAA
1 AATTCATCCATTCATTGAAGTGAATGTAACATCATTTAATAATGATGGCCATAA
988608 CAATTTACAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (59 bp):
AATTCATCCATTCATTGAAGTGAATGTAACATCATTTAATAATGATGGCCATAATCATG
Found at i:988732 original size:26 final size:26
Alignment explanation
Indices: 988684--988735 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
988674 GAATTTAAGA
* *
988684 ATAATTTTACCACTAGAAGTGGATAG
1 ATAATTTTACCACTAAAAATGGATAG
988710 ATAATTTTACC-CTAAAAAATGGATAG
1 ATAATTTTACCACT-AAAAATGGATAG
988736 GTGCCTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (26 bp):
ATAATTTTACCACTAAAAATGGATAG
Found at i:988795 original size:18 final size:18
Alignment explanation
Indices: 988748--988797 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
988738 GCCTATAATC
988748 CACCAAAAGTGGATAACT
1 CACCAAAAGTGGATAACT
* * * *
988766 CATCATATGTGGATCACT
1 CACCAAAAGTGGATAACT
988784 CACCAAAAGTGGAT
1 CACCAAAAGTGGAT
988798 GTATACTTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (18 bp):
CACCAAAAGTGGATAACT
Found at i:993175 original size:19 final size:20
Alignment explanation
Indices: 993153--993197 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
993143 ATAAGATTTC
993153 TTCTCTTCCCT-TAAATACT
1 TTCTCTTCCCTCTAAATACT
*
993172 TTCT-TTTCCTCTAAATACT
1 TTCTCTTCCCTCTAAATACT
*
993191 TTTTCTT
1 TTCTCTT
993198 ATATTTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.56
Consensus pattern (20 bp):
TTCTCTTCCCTCTAAATACT
Found at i:996638 original size:22 final size:19
Alignment explanation
Indices: 996613--996658 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
996603 TTCAATAAGA
996613 TTTCTTATCTTCCCTTAAATAC
1 TTTCTTATCTT--C-TAAATAC
*
996635 TTTCTTTTCTTCTAAATAC
1 TTTCTTATCTTCTAAATAC
996654 TTTCT
1 TTTCT
996659 CTTATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 12 0.52
20 1 0.04
22 10 0.43
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTCTTATCTTCTAAATAC
Found at i:997799 original size:26 final size:26
Alignment explanation
Indices: 997758--997810 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
997748 AGGTTTATTA
*
997758 TATTTCTATCTTGTTTTTTTATTTTTT
1 TATTTCTATCTTG-TTTTTCATTTTTT
*
997785 TATTT-TATTTTGTTTTTCATTTTTT
1 TATTTCTATCTTGTTTTTCATTTTTT
997810 T
1 T
997811 TCTCTTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
26 6 0.25
27 5 0.21
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (26 bp):
TATTTCTATCTTGTTTTTCATTTTTT
Found at i:1002307 original size:18 final size:17
Alignment explanation
Indices: 1002286--1002319 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1002276 ATATATATAT
*
1002286 ATATATATACACACACAC
1 ATATATAGAC-CACACAC
1002304 ATATATAGACCACACA
1 ATATATAGACCACACA
1002320 GAGAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.26, G:0.03, T:0.21
Consensus pattern (17 bp):
ATATATAGACCACACAC
Found at i:1002310 original size:2 final size:2
Alignment explanation
Indices: 1002259--1002294 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1002249 ATTATAAAAT
1002259 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1002295 CACACACACA
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):
TA
Found at i:1003039 original size:2 final size:2
Alignment explanation
Indices: 1003032--1003062 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1003022 TTCACAAACC
*
1003032 AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1003063 CAAAATCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1004315 original size:18 final size:19
Alignment explanation
Indices: 1004288--1004334 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1004278 GCGATAGGTG
*
1004288 AAAA-AATATTTT-TGAAT
1 AAAATAATATTTTATAAAT
1004305 AAAATAATATTTTATAAAT
1 AAAATAATATTTTATAAAT
1004324 AAAATAATATT
1 AAAATAATATT
1004335 AAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 8 0.30
19 15 0.56
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:1006075 original size:25 final size:25
Alignment explanation
Indices: 1006041--1006129 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
1006031 AAGAAAATAA
* *
1006041 AATCCCTATAATTATGGTGATTCTC
1 AATCTCTATAATTATGGTGATTCCC
1006066 AATCGT-TATAATTATGGTGATTCCC
1 AATC-TCTATAATTATGGTGATTCCC
* * * *
1006091 AATCTCTATAATTTTGGTAATTTCT
1 AATCTCTATAATTATGGTGATTCCC
*
1006116 AATTTCTATAATTA
1 AATCTCTATAATTA
1006130 CGTTTATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.02
25 53 0.98
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (25 bp):
AATCTCTATAATTATGGTGATTCCC
Found at i:1007444 original size:23 final size:23
Alignment explanation
Indices: 1007393--1007445 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1007383 AACAATAAGA
*
1007393 TGAAAATGCATTCTTTTTTTTTC
1 TGAAATTGCATTCTTTTTTTTTC
*
1007416 TAAAATTGACATT-TTTTTTGTTT-
1 TGAAATTG-CATTCTTTTTT-TTTC
1007439 TGAAATT
1 TGAAATT
1007446 TCTTCCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.57
Consensus pattern (23 bp):
TGAAATTGCATTCTTTTTTTTTC
Found at i:1013961 original size:29 final size:31
Alignment explanation
Indices: 1013923--1013980 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1013913 TTTTTTTACT
*
1013923 TTAATAAATTTTTA-TAAAAGAAATGTAAAC
1 TTAATAAATTTATATTAAAAGAAATGTAAAC
*
1013953 TTAA-AAATTTATATTAAAAGGAATGTAA
1 TTAATAAATTTATATTAAAAGAAATGTAA
1013981 GTATTCAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (31 bp):
TTAATAAATTTATATTAAAAGAAATGTAAAC
Found at i:1014933 original size:63 final size:63
Alignment explanation
Indices: 1014834--1014953 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
1014824 ATCTTTCTCT
* * *
1014834 CTCAACTCTCTGAACTGTATCAACTCTGTTAACTCTCTGTTAAGCACCATTATCATCAGCTCG
1 CTCAACTCTCTGAACTGTATCAACCCTGTAAACTCTCTGTTAAGCACCATCATCATCAGCTCG
* * * *
1014897 CTCAACTCTCTGAATTGTATGAGCCCTGTAAACTCTCTGTTGAGCACCATCATCATC
1 CTCAACTCTCTGAACTGTATCAACCCTGTAAACTCTCTGTTAAGCACCATCATCATC
1014954 GTGTTATGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (63 bp):
CTCAACTCTCTGAACTGTATCAACCCTGTAAACTCTCTGTTAAGCACCATCATCATCAGCTCG
Found at i:1020984 original size:31 final size:31
Alignment explanation
Indices: 1020951--1021246 Score: 294
Period size: 31 Copynumber: 9.6 Consensus size: 31
1020941 AGAAAGAAAT
* *
1020951 AAATGTTGTTACACGTCGTGCATATCAAGAT-
1 AAATGTTGTTACACGCCATGCATATCAAG-TC
** *
1020982 AAATGTTGTTACGTGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTC
* * ** *
1021013 AAATGTTATTACATGTAATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTC
* * ** *
1021044 AAATGTTGTTACATGCCATACATAT-ACCCTA
1 AAATGTTGTTACACGCCATGCATATCA-AGTC
* * ** *
1021075 AAATATT-ATAGCACGTAATGCATAACAAGTC
1 AAATGTTGTTA-CACGCCATGCATATCAAGTC
*
1021106 AAATGTTGTTACACGCCATGCATATCAAGCC
1 AAATGTTGTTACACGCCATGCATATCAAGTC
* *
1021137 AAATGTTGTTACACACCATGCATACCAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTC
* *
1021168 AAATGTTGTTACATGCCATGCATA-AAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTC
* *
1021198 AAATGTTGTTTCATGCCATGCATATCAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTC
1021229 AAATGTTGTTACACGCCA
1 AAATGTTGTTACACGCCA
1021247 ATGCTGACAC
Statistics
Matches: 219, Mismatches: 40, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
30 32 0.15
31 184 0.84
32 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.30
Consensus pattern (31 bp):
AAATGTTGTTACACGCCATGCATATCAAGTC
Found at i:1022104 original size:92 final size:92
Alignment explanation
Indices: 1021938--1022143 Score: 272
Period size: 92 Copynumber: 2.2 Consensus size: 92
1021928 CCATGATGTA
*
1021938 TCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACCCTAGTGTGTCACAAATTCCCTTAATG
1 TCACAGATTCCCTCCATGGCGTGT-ACAAACTCTGAACCCTAGTGTG-CACAAATTCCCTCAATG
* * *
1022003 GCGTGTCACAAACTCTTATCACTAGCATG
64 GCATGTCACAAACTCTGAACACTAGCATG
* * *
1022032 TCACAGATTCCCTCCATGGCGTGT-CAAACTCTGAACTCTGACGTGTG-ACAGATTCCCTCCATG
1 TCACAGATTCCCTCCATGGCGTGTACAAACTCTGAACCCT-A-GTGTGCACAAATTCCCTCAATG
* * *
1022095 GCATGTCACAAACTCTGAACTCTGGCGTG
64 GCATGTCACAAACTCTGAACACTAGCATG
1022124 TCACAGATTCCCTCCATGGC
1 TCACAGATTCCCTCCATGGC
1022144 ATGTGGCAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
92 70 0.70
93 1 0.01
94 29 0.29
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (92 bp):
TCACAGATTCCCTCCATGGCGTGTACAAACTCTGAACCCTAGTGTGCACAAATTCCCTCAATGGC
ATGTCACAAACTCTGAACACTAGCATG
Found at i:1022147 original size:47 final size:47
Alignment explanation
Indices: 1021938--1022143 Score: 274
Period size: 47 Copynumber: 4.4 Consensus size: 47
1021928 CCATGATGTA
* *
1021938 TCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACCCTAGTGTG
1 TCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACTCTAGCGTG
* ** * * * *
1021985 TCACAAATTCCCTTAATGGCGTGTCACAAACTCTTATCACTAGCATG
1 TCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACTCTAGCGTG
1022032 TCACAGATTCCCTCCATGGCGTGT--CAAACTCTGAACTCT-GACGTG
1 TCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACTCTAG-CGTG
* * *
1022077 TGACAGATTCCCTCCATGGCATGTCACAAACTCTGAACTCTGGCGTG
1 TCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACTCTAGCGTG
1022124 TCACAGATTCCCTCCATGGC
1 TCACAGATTCCCTCCATGGC
1022144 ATGTGGCAAA
Statistics
Matches: 137, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.01
45 37 0.27
47 98 0.72
48 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (47 bp):
TCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACTCTAGCGTG
Found at i:1029274 original size:19 final size:19
Alignment explanation
Indices: 1029250--1029287 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1029240 GTTTAACCTT
1029250 TGTTTT-GATTTTCTTTTTC
1 TGTTTTGGATTTT-TTTTTC
1029269 TGTTTTGGATTTTTTTTTC
1 TGTTTTGGATTTTTTTTTC
1029288 ACTGTTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.05, C:0.08, G:0.13, T:0.74
Consensus pattern (19 bp):
TGTTTTGGATTTTTTTTTC
Found at i:1031376 original size:46 final size:43
Alignment explanation
Indices: 1031319--1031408 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 43
1031309 AACCATAATT
1031319 AAAATTTCAAGAGCATTAAAACGCACACGGCA-GGAAATACATGGC
1 AAAATTTCAAGAGCATTAAAACGCACA---CATGGAAATACATGGC
1031364 AAAATTTTCAAGAGCATTAAAACGCACACATGGAAATACATGGC
1 AAAA-TTTCAAGAGCATTAAAACGCACACATGGAAATACATGGC
1031408 A
1 A
1031409 GGAAATACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
43 2 0.05
44 14 0.33
45 4 0.09
46 23 0.53
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.18
Consensus pattern (43 bp):
AAAATTTCAAGAGCATTAAAACGCACACATGGAAATACATGGC
Found at i:1031414 original size:14 final size:14
Alignment explanation
Indices: 1031395--1031431 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1031385 ACGCACACAT
* *
1031395 GGAAATACATGGCA
1 GGAAATACACGCCA
1031409 GGAAATACACGCCA
1 GGAAATACACGCCA
1031423 GGAAATACA
1 GGAAATACA
1031432 GATGTAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (14 bp):
GGAAATACACGCCA
Found at i:1035430 original size:21 final size:21
Alignment explanation
Indices: 1035397--1035445 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1035387 TATTTAAAGG
*
1035397 TAATATACTTAACATGAATGT
1 TAATATACATAACATGAATGT
* * *
1035418 TAATTTACATAACGTTAATGT
1 TAATATACATAACATGAATGT
1035439 TATATAT
1 TA-ATAT
1035446 TAATGTCAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (21 bp):
TAATATACATAACATGAATGT
Found at i:1038762 original size:152 final size:152
Alignment explanation
Indices: 1038564--1038867 Score: 572
Period size: 152 Copynumber: 2.0 Consensus size: 152
1038554 TTGTCATTAG
*
1038564 ATGGTTATGAAAGTTCACAGTATAAGGTTTACAATTGGAAAACTAATACTTAATATCAAGTATTG
1 ATGGTTATGAAAGTTCACAGTATAAGGTTTACAATTGGAAAACTAATAATTAATATCAAGTATTG
* *
1038629 AATTGTTTCTTGTAATAAAAATTAATCCATGAGTGCAACCATGAATCTATGGTGGAGTGATTTCA
66 AATTGTTTCTTGTAATAAAAATTAATCCATGAGTGCAAACATGAATCTATGGTGGAGTGACTTCA
1038694 TGGTTAATAAGCTTGAATTATT
131 TGGTTAATAAGCTTGAATTATT
1038716 ATGGTTATGAAAGTTCACAGTATAAGGTTTACAATTGGAAAACTAATAATTAATATCAAGTATTG
1 ATGGTTATGAAAGTTCACAGTATAAGGTTTACAATTGGAAAACTAATAATTAATATCAAGTATTG
*
1038781 AATTGTTTCTTGTAATTAAAATTAATCCATGAGTGCAAACATGAATCTATGGTGGAGTGACTTCA
66 AATTGTTTCTTGTAATAAAAATTAATCCATGAGTGCAAACATGAATCTATGGTGGAGTGACTTCA
1038846 TGGTTAATAAGCTTGAATTATT
131 TGGTTAATAAGCTTGAATTATT
1038868 TTTAATGATA
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 148 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (152 bp):
ATGGTTATGAAAGTTCACAGTATAAGGTTTACAATTGGAAAACTAATAATTAATATCAAGTATTG
AATTGTTTCTTGTAATAAAAATTAATCCATGAGTGCAAACATGAATCTATGGTGGAGTGACTTCA
TGGTTAATAAGCTTGAATTATT
Found at i:1039054 original size:28 final size:29
Alignment explanation
Indices: 1039022--1039157 Score: 150
Period size: 29 Copynumber: 4.7 Consensus size: 29
1039012 TGACAGCTTT
1039022 AATATATTTGTCTTAATTTAGACAAG-AA
1 AATATATTTGTCTTAATTTAGACAAGAAA
* * * *
1039050 AATATGTTTATCTTAATTAAGATAAGAAA
1 AATATATTTGTCTTAATTTAGACAAGAAA
* * *
1039079 AATATGTTTGTCTTAATTAAGATAAGAAA
1 AATATATTTGTCTTAATTTAGACAAGAAA
* *
1039108 AATATTTTTTGTCTTAATCTAGACAAG-AA
1 AATA-TATTTGTCTTAATTTAGACAAGAAA
* *
1039137 AACATATTTGTCTCAATTTAG
1 AATATATTTGTCTTAATTTAG
1039158 GAAAAATAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
28 36 0.39
29 39 0.42
30 18 0.19
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (29 bp):
AATATATTTGTCTTAATTTAGACAAGAAA
Found at i:1039092 original size:29 final size:29
Alignment explanation
Indices: 1039022--1039192 Score: 149
Period size: 29 Copynumber: 5.9 Consensus size: 29
1039012 TGACAGCTTT
* *
1039022 AATATATTTGTCTTAATTTAGACAAG-AA
1 AATATGTTTGTCTTAATTAAGACAAGAAA
* *
1039050 AATATGTTTATCTTAATTAAGATAAGAAA
1 AATATGTTTGTCTTAATTAAGACAAGAAA
*
1039079 AATATGTTTGTCTTAATTAAGATAAGAAA
1 AATATGTTTGTCTTAATTAAGACAAGAAA
*
1039108 AATATTTTTTGTCTTAATCT-AGACAAGAAA
1 AATA-TGTTTGTCTTAAT-TAAGACAAGAAA
* * *
1039138 ACATA--TTTGTCTCAATTTAGGA-AAAATAA
1 A-ATATGTTTGTCTTAA-TTAAGACAAGA-AA
*
1039167 AATAT-TTT-TTTTAATTAAAGACAAGA
1 AATATGTTTGTCTTAATT-AAGACAAGA
1039193 GTTGTTTTAA
Statistics
Matches: 119, Mismatches: 14, Indels: 19
0.78 0.09 0.12
Matches are distributed among these distances:
27 2 0.02
28 45 0.38
29 46 0.39
30 22 0.18
31 4 0.03
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (29 bp):
AATATGTTTGTCTTAATTAAGACAAGAAA
Found at i:1039353 original size:17 final size:17
Alignment explanation
Indices: 1039331--1039363 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1039321 ATAATAATGA
1039331 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
1039348 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
1039364 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:1044531 original size:22 final size:22
Alignment explanation
Indices: 1044505--1044549 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1044495 AAAAGAAGTT
1044505 TCATAAGTCTCTATAAAAGTAA
1 TCATAAGTCTCTATAAAAGTAA
1044527 TCATAAGTCTCTATAAAAGTAA
1 TCATAAGTCTCTATAAAAGTAA
1044549 T
1 T
1044550 GATCTAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (22 bp):
TCATAAGTCTCTATAAAAGTAA
Found at i:1064946 original size:29 final size:28
Alignment explanation
Indices: 1064900--1065053 Score: 134
Period size: 29 Copynumber: 5.3 Consensus size: 28
1064890 TGACAGCTTT
*
1064900 AACATGTTTGT-TCTAATTTAGACAAGAA
1 AACATATTTGTCT-TAATTTAGACAAGAA
*
1064928 AACATGTTTAGTCTTAATTTAGACAAGAA
1 AACATATTT-GTCTTAATTTAGACAAGAA
* *
1064957 AATATATTTGTCTTAATTGAAGACAAGAAA
1 AACATATTTGTCTTAATT-TAGACAAG-AA
* * *
1064987 AAAAGTTTTTGGTCTTAATATAGACAAGAA
1 AACA-TATTT-GTCTTAATTTAGACAAGAA
* *
1065017 AATATATTTGTCTCAA-TTAGGACAAGATA
1 AACATATTTGTCTTAATTTA-GACAAGA-A
1065046 AA-ATATTT
1 AACATATTT
1065054 TTTGTCTTAA
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.02
28 37 0.35
29 38 0.36
30 11 0.10
31 11 0.10
32 8 0.07
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:1065011 original size:60 final size:59
Alignment explanation
Indices: 1064938--1065064 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 59
1064928 AACATGTTTA
* *
1064938 GTCTTAATTTAGACAAGAAAATATATTTGTCTTAATTGAAGACAAGA-AAAAAAGTTTTTG
1 GTCTTAATATAGACAAGAAAATATATTTGTCTCAATT-AAGACAAGATAAAAAA-TTTTTG
* * *
1064998 GTCTTAATATAGACAAGAAAATATATTTGTCTCAATTAGGACAAGATAAAATATTTTTT
1 GTCTTAATATAGACAAGAAAATATATTTGTCTCAATTAAGACAAGATAAAAAATTTTTG
1065057 GTCTTAAT
1 GTCTTAAT
1065065 TACATACAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 21 0.34
60 40 0.66
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (59 bp):
GTCTTAATATAGACAAGAAAATATATTTGTCTCAATTAAGACAAGATAAAAAATTTTTG
Found at i:1065066 original size:31 final size:27
Alignment explanation
Indices: 1064917--1065066 Score: 138
Period size: 29 Copynumber: 5.1 Consensus size: 27
1064907 TTGTTCTAAT
* *
1064917 TTAGACAAGAAAACATGTTTAGTCTTAA
1 TTAGACAAGAAAATATATTT-GTCTTAA
1064945 TTTAGACAAGAAAATATATTTGTCTTAA
1 -TTAGACAAGAAAATATATTTGTCTTAA
* *
1064973 TTGAAGACAAGAAAAAAAGTTTTTGGTCTTAA
1 TT--AGACAAG-AAAATA-TATTT-GTCTTAA
*
1065005 TATAGACAAGAAAATATATTTGTCTCAA
1 T-TAGACAAGAAAATATATTTGTCTTAA
*
1065033 TTAGGACAAGATAAAATATTTTTTGTCTTAA
1 TTA-GACAAG--AAAATA-TATTTGTCTTAA
1065064 TTA
1 TTA
1065067 CATACAAGAG
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.04
28 20 0.20
29 29 0.28
30 16 0.16
31 24 0.24
32 8 0.08
33 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (27 bp):
TTAGACAAGAAAATATATTTGTCTTAA
Found at i:1065368 original size:36 final size:36
Alignment explanation
Indices: 1065316--1065388 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1065306 ATTTTGATAA
1065316 GTATGGAGCATGTTTGATGCTTTCATAACTCTAAAT
1 GTATGGAGCATGTTTGATGCTTTCATAACTCTAAAT
*
1065352 GTATTGAGCATGTTTGATGCTTTCATAACTCTAAAT
1 GTATGGAGCATGTTTGATGCTTTCATAACTCTAAAT
1065388 G
1 G
1065389 GATGATCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (36 bp):
GTATGGAGCATGTTTGATGCTTTCATAACTCTAAAT
Found at i:1067623 original size:72 final size:72
Alignment explanation
Indices: 1067542--1067685 Score: 198
Period size: 72 Copynumber: 2.0 Consensus size: 72
1067532 AATTTATTGA
* ** *
1067542 TACATAGGCACATATATTAATACATGCAAGAATGTGTATCGATAGATCGCCAAATCTATTGATAC
1 TACATAGGCACATATATTAACACATGCAAGAACATGTATCGATAGATCACCAAATCTATTGATAC
1067607 ATTTCAT
66 ATTTCAT
* * * * * *
1067614 TACATAGGCATATGTATTGACACATGCACGAACATGTATCGATAGATCATCAAATTTATTGATAC
1 TACATAGGCACATATATTAACACATGCAAGAACATGTATCGATAGATCACCAAATCTATTGATAC
1067679 ATTTCAT
66 ATTTCAT
1067686 CCAGTAGCCA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (72 bp):
TACATAGGCACATATATTAACACATGCAAGAACATGTATCGATAGATCACCAAATCTATTGATAC
ATTTCAT
Found at i:1084703 original size:29 final size:27
Alignment explanation
Indices: 1084670--1084736 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
1084660 TAGAAATCAA
* *
1084670 GTTACATGCTATGTTTAAAAAGTAATATT
1 GTTACATGCCATATTT--AAAGTAATATT
*
1084699 GTTACATACCATATTTAAAGTAATATT
1 GTTACATGCCATATTTAAAGTAATATT
1084726 GTTACATGCCA
1 GTTACATGCCA
1084737 CGTTAGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.62
29 13 0.38
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (27 bp):
GTTACATGCCATATTTAAAGTAATATT
Found at i:1084990 original size:28 final size:29
Alignment explanation
Indices: 1084929--1084991 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
1084919 TAGAGAACAA
* * *
1084929 ATTACATGCTATGTTTTAAAAATATTATT
1 ATTACATGCTATGTTTCAAAAAAAATATT
*
1084958 ATTACATGTTATG-TTCAAAAAAAATATT
1 ATTACATGCTATGTTTCAAAAAAAATATT
*
1084986 GTTACA
1 ATTACA
1084992 ATTGAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (29 bp):
ATTACATGCTATGTTTCAAAAAAAATATT
Found at i:1095234 original size:2 final size:2
Alignment explanation
Indices: 1095229--1095260 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1095219 TAACCTTCGG
1095229 AT AT AT A- AT AT A- 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
1095261 GTACGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1096874 original size:46 final size:46
Alignment explanation
Indices: 1096821--1096913 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
1096811 ATTCTTCCTT
*
1096821 AACCTTGTTAATTTAATTGTATACTTATAAGAAATAAAGAAACCCC
1 AACCTTGTTAATTTAATTGTACACTTATAAGAAATAAAGAAACCCC
*
1096867 AACCTTGTTAATTTAATTGTACACTTATAAGGAATAAAGAAACCCC
1 AACCTTGTTAATTTAATTGTACACTTATAAGAAATAAAGAAACCCC
1096913 A
1 A
1096914 TTATATTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (46 bp):
AACCTTGTTAATTTAATTGTACACTTATAAGAAATAAAGAAACCCC
Found at i:1099187 original size:13 final size:13
Alignment explanation
Indices: 1099134--1099179 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
1099124 ACTAAACAAT
1099134 ATTTTCCATTTCG
1 ATTTTCCATTTCG
*
1099147 AATTTT-CATTTCC
1 -ATTTTCCATTTCG
1099160 A-TTTCCATTTCG
1 ATTTTCCATTTCG
1099172 ATTTTCCA
1 ATTTTCCA
1099180 GTTTGATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 3 0.11
12 8 0.29
13 12 0.43
14 5 0.18
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (13 bp):
ATTTTCCATTTCG
Found at i:1099447 original size:20 final size:20
Alignment explanation
Indices: 1099404--1099447 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1099394 TTCATTCTTG
* *
1099404 AATGTCACATCATTAAATTT
1 AATGCCACATCATTAAATTC
*
1099424 AATGCCACATCATTAGATTC
1 AATGCCACATCATTAAATTC
1099444 AATG
1 AATG
1099448 TCTTTTCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (20 bp):
AATGCCACATCATTAAATTC
Found at i:1100108 original size:17 final size:17
Alignment explanation
Indices: 1100086--1100126 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1100076 TATTTGTTCA
*
1100086 TTTTTAATC-ATAATTAT
1 TTTTTAATCTAT-ACTAT
1100103 TTTTT-ATCTATACTAT
1 TTTTTAATCTATACTAT
1100119 TTTTTAAT
1 TTTTTAAT
1100127 TCCAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAATCTATACTAT
Found at i:1101017 original size:72 final size:72
Alignment explanation
Indices: 1100935--1101078 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
1100925 ACATTTGATG
* * *
1100935 TCAACGTTGTAATGC-ACCCTAGGTGCTCGTATGGGGCTCTCAGGCCATTATCTTTTACA-TTTA
1 TCAACGTTGTAATGCAACCC-AGGTGCTCATAT-GGGCTCTCAGGCCATCATCTTTCACATTTTA
1100998 CACATTTCC
64 CACATTTCC
* * * *
1101007 TCAACTTTGTAATGCAACCCATGTGCTCATATGGGCTTTTAGGCCATCATCTTTCACATTTTACA
1 TCAACGTTGTAATGCAACCCAGGTGCTCATATGGGCTCTCAGGCCATCATCTTTCACATTTTACA
1101072 CATTTCC
66 CATTTCC
1101079 ATATAAATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
71 22 0.35
72 37 0.59
73 4 0.06
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.36
Consensus pattern (72 bp):
TCAACGTTGTAATGCAACCCAGGTGCTCATATGGGCTCTCAGGCCATCATCTTTCACATTTTACA
CATTTCC
Found at i:1102319 original size:60 final size:64
Alignment explanation
Indices: 1102210--1102447 Score: 169
Period size: 68 Copynumber: 3.7 Consensus size: 64
1102200 CTTTTACATA
* * * ** *
1102210 ACTCTTATAGTATATGGAAACAAAATCACATACATGACAAAATAACATATATCATG-T-G-CTC
1 ACTCATATAGTATGTGGAAACAAAATCACATACATGTCATCATAGCATATATCATGCTCGTCTC
* * * *
1102271 A-TCATATAGTATGTGGAAACCATATCACATACATGTCATCGTAGCATATAACTTATGCTCGTTC
1 ACTCATATAGTATGTGGAAACAAAATCACATACATGTCATCATAGCATAT-A-TCATGCTCG-TC
*
1102335 TT
63 TC
* * * * **
1102337 ATCTCATATAGTATGTGGAAACAACATCACATACATATCATCTTAGCATTTATCTTATGCCTATT
1 A-CTCATATAGTATGTGGAAACAAAATCACATACATGTCATCATAGCATATATC--ATG-CTCGT
* *
1102402 TTT
62 CTC
* * * *
1102405 ATCTCATATGGTAAGTGGAAACAACATCACATACATGGCATCA
1 A-CTCATATAGTATGTGGAAACAAAATCACATACATGTCATCA
1102448 CAACATTTAT
Statistics
Matches: 141, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
60 39 0.28
61 2 0.01
62 4 0.03
63 1 0.01
64 1 0.01
66 4 0.03
67 1 0.01
68 87 0.62
69 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (64 bp):
ACTCATATAGTATGTGGAAACAAAATCACATACATGTCATCATAGCATATATCATGCTCGTCTC
Found at i:1102455 original size:68 final size:68
Alignment explanation
Indices: 1102272--1102520 Score: 243
Period size: 68 Copynumber: 3.7 Consensus size: 68
1102262 CATGTGCTCA
* * * * * *
1102272 TCATATAGTATGTGGAAACCATATCACATACATGTCATCGTAGCATATAACTTATGCTCGTTCTT
1 TCATATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATTTATCTTATGCTCATTCTT
1102337 ATC
66 ATC
* * *
1102340 TCATATAGTATGTGGAAACAACATCACATACATATCATCTTAGCATTTATCTTATGC-CTATTTT
1 TCATATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATTTATCTTATGCTC-ATTCT
1102404 TATC
65 TATC
* * * * * ** * *
1102408 TCATATGGTAAGTGGAAACAACATCACATACATGGCATCACAACATTTATCACATGTTCATTCCT
1 TCATATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATTTATCTTATGCTCATTCTT
*
1102473 ATT
66 ATC
* ** * *
1102476 TCAGATAACATGTGG-AACAACATCAGATACAT-TGCAACATAGCAT
1 TCATATAGTATGTGGAAACAACATCACATACATGT-CATCATAGCAT
1102521 ACTTCATGCA
Statistics
Matches: 147, Mismatches: 31, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
67 25 0.17
68 121 0.82
69 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (68 bp):
TCATATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATTTATCTTATGCTCATTCTT
ATC
Found at i:1107026 original size:8 final size:8
Alignment explanation
Indices: 1107006--1107097 Score: 66
Period size: 8 Copynumber: 11.8 Consensus size: 8
1106996 AGATTTGGCT
1107006 AGGAAGCAA
1 AGGAAG-AA
1107015 AGGAAGAA
1 AGGAAGAA
1107023 AGGAAGAA
1 AGGAAGAA
* *
1107031 AGAAATAA
1 AGGAAGAA
*
1107039 A-AAAGAA
1 AGGAAGAA
1107046 AGGAAGAA
1 AGGAAGAA
*
1107054 AGAAAGAA
1 AGGAAGAA
* * *
1107062 GGGGAGAG
1 AGGAAGAA
1107070 AGG-AGAA
1 AGGAAGAA
1107077 A-GAAGAA
1 AGGAAGAA
*
1107084 AAG-AGAA
1 AGGAAGAA
1107091 AGTGAAG
1 AG-GAAG
1107098 GTTTGGGCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
6 1 0.02
7 20 0.30
8 37 0.56
9 8 0.12
ACGTcount: A:0.62, C:0.01, G:0.35, T:0.02
Consensus pattern (8 bp):
AGGAAGAA
Found at i:1107080 original size:4 final size:4
Alignment explanation
Indices: 1107013--1107061 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
1107003 GCTAGGAAGC
* * * *
1107013 AAAG GAAG AAAG GAAG AAAG AAAT AAA- AAAG AAAG GAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1107060 AA
1 AA
1107062 GGGGAGAGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:1114189 original size:6 final size:6
Alignment explanation
Indices: 1114178--1114204 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1114168 CAGTCTGTGC
1114178 TATGTT TATGTT TATGTT TATGTT TAT
1 TATGTT TATGTT TATGTT TATGTT TAT
1114205 AGACTATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
TATGTT
Found at i:1116649 original size:27 final size:27
Alignment explanation
Indices: 1116618--1116673 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1116608 AATGTATGAG
1116618 ATATTGATAAAGTAATGCCAATATCAA
1 ATATTGATAAAGTAATGCCAATATCAA
1116645 ATATTGATAAAGTAATGCCAATATCAA
1 ATATTGATAAAGTAATGCCAATATCAA
1116672 AT
1 AT
1116674 GATGAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (27 bp):
ATATTGATAAAGTAATGCCAATATCAA
Found at i:1124316 original size:17 final size:18
Alignment explanation
Indices: 1124285--1124329 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1124275 CAAGGAGAAA
*
1124285 AGAGAAAGGAGAGGAAAGG
1 AGAGAAA-GACAGGAAAGG
*
1124304 A-AGAAAGACAGGAGAGG
1 AGAGAAAGACAGGAAAGG
1124321 AGAGAAAGA
1 AGAGAAAGA
1124330 AAGGGGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
18 12 0.52
19 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (18 bp):
AGAGAAAGACAGGAAAGG
Found at i:1124319 original size:22 final size:22
Alignment explanation
Indices: 1124291--1124332 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1124281 GAAAAGAGAA
*
1124291 AGGAGAGGAAAGGAAGAAAGAC
1 AGGAGAGGAAAGAAAGAAAGAC
*
1124313 AGGAGAGGAGAGAAAGAAAG
1 AGGAGAGGAAAGAAAGAAAG
1124333 GGGGAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00
Consensus pattern (22 bp):
AGGAGAGGAAAGAAAGAAAGAC
Found at i:1124344 original size:16 final size:18
Alignment explanation
Indices: 1124304--1124362 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 18
1124294 AGAGGAAAGG
*
1124304 AAGAAAGACAGGAGAGGA
1 AAGAAAGAAAGGAGAGGA
*
1124322 GAGAAAGAAAGG-G-GGA
1 AAGAAAGAAAGGAGAGGA
1124338 AAGAAAGAAAGGA-A-GA
1 AAGAAAGAAAGGAGAGGA
*
1124354 AAGGAAGAA
1 AAGAAAGAA
1124363 GAAGAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 24 0.69
17 1 0.03
18 10 0.29
ACGTcount: A:0.59, C:0.02, G:0.39, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAAGGAGAGGA
Found at i:1137452 original size:35 final size:35
Alignment explanation
Indices: 1137421--1137635 Score: 160
Period size: 35 Copynumber: 5.9 Consensus size: 35
1137411 ATTTAATTGT
*
1137421 TTAATTTAATTAATTAAGCCCAATAACTTAATTAA
1 TTAATTTAATCAATTAAGCCCAATAACTTAATTAA
* * * **
1137456 ATAATTTAATCAATTAGGCCCAATAATTTAATTGT
1 TTAATTTAATCAATTAAGCCCAATAACTTAATTAA
** * *
1137491 TTAATTTAATCAATTAAATCCAATAGCTTGATTAAA
1 TTAATTTAATCAATTAAGCCCAATAACTTAATT-AA
** *
1137527 CAAATTTAATCAATTAGGCCCAATAACTTAATTAAAGAA
1 TTAATTTAATCAATTAAGCCCAATAACTTAATT----AA
* * * *
1137566 TTAAACAATTTAATTAATTAGGCCCAATAACTTGATCACA
1 TT----AATTTAATCAATTAAGCCCAATAACTTAATTA-A
** *
1137606 CAAATTTAATCAATTAGGCCCAATAACTTA
1 TTAATTTAATCAATTAAGCCCAATAACTTA
1137636 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 32, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
35 55 0.40
36 52 0.37
39 3 0.02
40 1 0.01
43 28 0.20
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (35 bp):
TTAATTTAATCAATTAAGCCCAATAACTTAATTAA
Found at i:1140896 original size:50 final size:53
Alignment explanation
Indices: 1140842--1140942 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 53
1140832 AGGTTACCGG
* *
1140842 TTGATCCCATG-AAAAGCAAGAATCCTT-TTATGGA-T-TGTAAGGGTTATTAC
1 TTGATCCCATGAAAAAGCAAAAAT-CTTAGTATGGATTATGTAAGGGTTATTAC
* *
1140892 TTGATCTCATGAAAAAGTAAAAATCTTAGTATGGATTATGTAAGGGTTATT
1 TTGATCCCATGAAAAAGCAAAAATCTTAGTATGGATTATGTAAGGGTTATT
1140943 TATTCCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
50 13 0.30
51 16 0.37
52 1 0.02
53 13 0.30
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (53 bp):
TTGATCCCATGAAAAAGCAAAAATCTTAGTATGGATTATGTAAGGGTTATTAC
Found at i:1141430 original size:47 final size:47
Alignment explanation
Indices: 1141376--1141469 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1141366 TTTGAAAGAT
1141376 ACTTTACAGAAACTCAAGCAATGAAAATAGAGGTAATGGCAATTGTC
1 ACTTTACAGAAACTCAAGCAATGAAAATAGAGGTAATGGCAATTGTC
1141423 ACTTTACAGAAACTCAAGCAATGAAAATAGAGGTAATGGCAATTGTC
1 ACTTTACAGAAACTCAAGCAATGAAAATAGAGGTAATGGCAATTGTC
1141470 CTTACTAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (47 bp):
ACTTTACAGAAACTCAAGCAATGAAAATAGAGGTAATGGCAATTGTC
Found at i:1143152 original size:21 final size:22
Alignment explanation
Indices: 1143112--1143154 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1143102 AAATACTGCA
*
1143112 AAGAAATTATGATCAATTAAAAG
1 AAGAAAATATGA-CAATTAAAAG
1143135 AAGAAAATATGA-AATTAAAA
1 AAGAAAATATGACAATTAAAA
1143155 AGAATCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (22 bp):
AAGAAAATATGACAATTAAAAG
Found at i:1171015 original size:17 final size:18
Alignment explanation
Indices: 1170993--1171026 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1170983 TATTTATTTC
1170993 CTAGC-TTTCAAAAATAT
1 CTAGCTTTTCAAAAATAT
1171010 CTAGCTTTTCAAAAATA
1 CTAGCTTTTCAAAAATA
1171027 ACTAAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (18 bp):
CTAGCTTTTCAAAAATAT
Found at i:1176170 original size:18 final size:19
Alignment explanation
Indices: 1176144--1176192 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1176134 GTGATAGGTA
*
1176144 AAAAAAATATTTTTA-AAT
1 AAAATAATATTTTTAGAAT
1176162 AAAATAATATTTTTATGAAT
1 AAAATAATATTTTTA-GAAT
*
1176182 AAAATATTATT
1 AAAATAATATT
1176193 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATAATATTTTTAGAAT
Found at i:1179632 original size:330 final size:329
Alignment explanation
Indices: 1179014--1179678 Score: 1057
Period size: 330 Copynumber: 2.0 Consensus size: 329
1179004 AGAAATTTGC
* *
1179014 TGCTATTGATGATGTCCTGGTTCGCATCACTCTTGAACATTTGCTTGACTATTTAATTAAATCGG
1 TGCTATCGATGATGTCATGGTTCGCATCACTCTTGAACATTTGCTTGACTATTTAATTAAATCGG
*
1179079 TTGCCAAATCCATTTACCCTTATTTCTTCATCCCACAACTTGGACTTATTGCATATTTATTTGCT
66 TTGCCAAATCCATTTACCCTTATTTCTTCATCCCACAACTTGGACTTATTGCATATTTATTCGCT
** *
1179144 TTCCTCAATCAATTGAATGTTAATAATGTTTCTCATGTGGAAAATGCATTACTTGAGCAGGATGC
131 TTCCTCAATCAATTGAATGTTAATAATGTTTCTCATGAAGAAAATGCATTACTTGAGCAAGATGC
* *
1179209 TTTTAAGCCTTTTGCTTTATCTGCTAGTCTTCCTACAAGCATTCTACTCATGACAATGATTCTTT
196 TTTTAAGCCTTTTGCTCTATCTGCTAGTCTTCCTACAAGCATTCTACTAATGACAATGATTCTTT
* * *
1179274 TTCATGCATTTGTTGATTCTTATCTAGACAACTATCACTTATCTTCTTCATTGGAAAGGCAGCTT
261 TTCATGCATTTGTTGATTCATATCTAGACAACTATCACTTATCTTCTTCATTAGAAA-GAAGCTT
1179339 ATGTT
325 ATGTT
* * *
1179344 TGCTATCGATGATGTCATGGTTTGCATCACTCTTGAACTTTTGCTTGACTATTTAATTAAATTGA
1 TGCTATCGATGATGTCATGGTTCGCATCACTCTTGAACATTTGCTTGACTATTTAATTAAATCG-
*
1179409 G-TGCCAAATCCATTTACCTTTATTTCTTCATCCCACAACTTGGACTTATTGCATATTTATTCGC
65 GTTGCCAAATCCATTTACCCTTATTTCTTCATCCCACAACTTGGACTTATTGCATATTTATTCGC
* *
1179473 TTTCCTCAATCTATTGAATGTTAATAATGTTTTTCATGAAGAAAATGCATTACTTGAGCAAGATG
130 TTTCCTCAATCAATTGAATGTTAATAATGTTTCTCATGAAGAAAATGCATTACTTGAGCAAGATG
* * * *
1179538 CTTTTAAGCCTTTTGCTCTATCTGCTAGTCTTCCTATAGGCATTTTACTAATGGCAATGATTCTT
195 CTTTTAAGCCTTTTGCTCTATCTGCTAGTCTTCCTACAAGCATTCTACTAATGACAATGATTCTT
* *
1179603 TGTT-ATTCATTTGTTGCTTCGAT-TCTAGACAACTATCACTTATCTTCTTCATTAGAAAGAAGC
260 T-TTCATGCATTTGTTGATTC-ATATCTAGACAACTATCACTTATCTTCTTCATTAGAAAGAAGC
1179666 TTATGTT
323 TTATGTT
*
1179673 TCCTAT
1 TGCTAT
1179679 TTATGGATTT
Statistics
Matches: 308, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
329 16 0.05
330 288 0.94
331 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (329 bp):
TGCTATCGATGATGTCATGGTTCGCATCACTCTTGAACATTTGCTTGACTATTTAATTAAATCGG
TTGCCAAATCCATTTACCCTTATTTCTTCATCCCACAACTTGGACTTATTGCATATTTATTCGCT
TTCCTCAATCAATTGAATGTTAATAATGTTTCTCATGAAGAAAATGCATTACTTGAGCAAGATGC
TTTTAAGCCTTTTGCTCTATCTGCTAGTCTTCCTACAAGCATTCTACTAATGACAATGATTCTTT
TTCATGCATTTGTTGATTCATATCTAGACAACTATCACTTATCTTCTTCATTAGAAAGAAGCTTA
TGTT
Found at i:1181985 original size:238 final size:238
Alignment explanation
Indices: 1181563--1182042 Score: 861
Period size: 238 Copynumber: 2.0 Consensus size: 238
1181553 ACTGGGATAC
* *
1181563 CAAAATTGATTAAAGTGAAAACTTTCTTTCGTGGAAAATAAAAATTAAAAGAAGAAACTTGCAAG
1 CAAAATTGATTAAAATGAAAACTTTCTTTCATGGAAAATAAAAATTAAAAGAAGAAACTTGCAAG
* *
1181628 TTGCAATAAAATTTGTGTAAAACTAAGCTCAACAACTAACATGGAAATAAGTAATGAAGTTTGGC
66 TTGCAATAAAATTTGTGCAAAACTAAGCTCAACAACTAACATGGAAATAAGTAATGAAGTTTGGA
*
1181693 CATAAAAATTTGCATCAATTGAAAAATGGAATAGAAAGTTAGAGGAGCTGGAAAAAGAGTTAACA
131 CATAAAAATTTGCATCAATTGAAAAATGGAATAAAAAGTTAGAGGAGCTGGAAAAAGAGTTAACA
* *
1181758 AATGTCAGGCATATGAAAGAGGGTTATAATCTCAATTGAATAG
196 AATGTCAGGCATATGAAAGAAGGTTATAATCTCAATCGAATAG
*
1181801 CAAAATTGATTAAAATGAAAACTTTCTTTCATGGAAAATAAAAATTAAAGGAAGAAACTTGCAAG
1 CAAAATTGATTAAAATGAAAACTTTCTTTCATGGAAAATAAAAATTAAAAGAAGAAACTTGCAAG
1181866 TTGCAATAAAATTTGTGCAAAACTAAGCTCAACAACTAACATGGAAATAAGTAATGAAGTTTGGA
66 TTGCAATAAAATTTGTGCAAAACTAAGCTCAACAACTAACATGGAAATAAGTAATGAAGTTTGGA
* *
1181931 CATAAAAATTTGCATCAATTGAAAAATGGAATAAAAAGTTAGAGGAGTTGGAAAAAGAGTTAACG
131 CATAAAAATTTGCATCAATTGAAAAATGGAATAAAAAGTTAGAGGAGCTGGAAAAAGAGTTAACA
*
1181996 AATGTCAGGCATATGATAGAAGGTTATAATCTCAATCGAATAG
196 AATGTCAGGCATATGAAAGAAGGTTATAATCTCAATCGAATAG
1182039 CAAA
1 CAAA
1182043 GTGGTGGAAA
Statistics
Matches: 231, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
238 231 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (238 bp):
CAAAATTGATTAAAATGAAAACTTTCTTTCATGGAAAATAAAAATTAAAAGAAGAAACTTGCAAG
TTGCAATAAAATTTGTGCAAAACTAAGCTCAACAACTAACATGGAAATAAGTAATGAAGTTTGGA
CATAAAAATTTGCATCAATTGAAAAATGGAATAAAAAGTTAGAGGAGCTGGAAAAAGAGTTAACA
AATGTCAGGCATATGAAAGAAGGTTATAATCTCAATCGAATAG
Found at i:1185389 original size:77 final size:76
Alignment explanation
Indices: 1185293--1185441 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 76
1185283 ATAAATTGAA
* * * *
1185293 TAAATCTTACTATAATTATAATAAAAAATATTTCAATAATCGTCATTTGATGAATATACATTTAC
1 TAAACCTTACTATAATTATAATAAAAAATATTTCAATAACCGTCATTTAATGAATACACATTTAC
1185358 AAGTATAGATT
66 AAGTATAGATT
* * * * *
1185369 TAAACCTTACTAATAGTTATAATAAAAAATATTTTAATGACCGTCATTTAATGGATACATATTTA
1 TAAACCTTACT-ATAATTATAATAAAAAATATTTCAATAACCGTCATTTAATGAATACACATTTA
*
1185434 TAAGTATA
65 CAAGTATA
1185442 CGTTTTGGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
76 10 0.16
77 52 0.84
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (76 bp):
TAAACCTTACTATAATTATAATAAAAAATATTTCAATAACCGTCATTTAATGAATACACATTTAC
AAGTATAGATT
Found at i:1186011 original size:20 final size:20
Alignment explanation
Indices: 1185986--1186062 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1185976 AAATCCAATG
1185986 AATATTAATATTTAACTTAA
1 AATATTAATATTTAACTTAA
1186006 AATATTAAAAATATAGTTAACTTAA
1 AATATT---AATAT--TTAACTTAA
*
1186031 AA-A--AATTTTTAACTTAA
1 AATATTAATATTTAACTTAA
1186048 AATATTAATATTTAA
1 AATATTAATATTTAA
1186063 ATTATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
17 11 0.23
18 1 0.02
19 4 0.09
20 14 0.30
23 5 0.11
24 1 0.02
25 11 0.23
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (20 bp):
AATATTAATATTTAACTTAA
Found at i:1186032 original size:17 final size:17
Alignment explanation
Indices: 1186010--1186049 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1186000 ACTTAAAATA
*
1186010 TTAAAAATATAGTTAAC
1 TTAAAAAAATAGTTAAC
**
1186027 TTAAAAAAATTTTTAAC
1 TTAAAAAAATAGTTAAC
1186044 TTAAAA
1 TTAAAA
1186050 TATTAATATT
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:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
TTAAAAAAATAGTTAAC
Found at i:1186295 original size:62 final size:64
Alignment explanation
Indices: 1186184--1186375 Score: 289
Period size: 64 Copynumber: 3.0 Consensus size: 64
1186174 CATCATTTGA
* *
1186184 TGAATACATATAACTATAGATTTTGGATGTCTTACACAATTGATAAATATTGATATTTTTATAG
1 TGAATACACATAAATATAGATTTTGGATGTCTTACACAATTGATAAATATTGATATTTTTATAG
* * * * * *
1186248 T-AA-ACACATAAATATAGGTTTTAGATGTCTTATACTATTGATAAATATTAATATTTTTATAA
1 TGAATACACATAAATATAGATTTTGGATGTCTTACACAATTGATAAATATTGATATTTTTATAG
*
1186310 TGAATACACATAAATATAGATTTTGGATGTTTTACACAATTGATAAATATTGATATTTTTATAG
1 TGAATACACATAAATATAGATTTTGGATGTCTTACACAATTGATAAATATTGATATTTTTATAG
1186374 TG
1 TG
1186376 TTATGGTAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
62 52 0.47
63 4 0.04
64 55 0.50
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (64 bp):
TGAATACACATAAATATAGATTTTGGATGTCTTACACAATTGATAAATATTGATATTTTTATAG
Found at i:1186563 original size:19 final size:19
Alignment explanation
Indices: 1186536--1186575 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1186526 AGTCATAAAC
*
1186536 ACCCATTAATTAGATCCAA
1 ACCCATTAATCAGATCCAA
* *
1186555 ACCCGTTAATCGGATCCAA
1 ACCCATTAATCAGATCCAA
1186574 AC
1 AC
1186576 AACTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.23
Consensus pattern (19 bp):
ACCCATTAATCAGATCCAA
Found at i:1187931 original size:36 final size:36
Alignment explanation
Indices: 1187884--1187956 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1187874 AAATTAAAAT
1187884 CCAATTCCTATCCCTTACTCTATTACTCATAAGACC
1 CCAATTCCTATCCCTTACTCTATTACTCATAAGACC
*
1187920 CCAATTCCTATCCCTTACTCTATTACTCCTAAGACC
1 CCAATTCCTATCCCTTACTCTATTACTCATAAGACC
1187956 C
1 C
1187957 AAATAGTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.38, G:0.03, T:0.33
Consensus pattern (36 bp):
CCAATTCCTATCCCTTACTCTATTACTCATAAGACC
Found at i:1199232 original size:33 final size:33
Alignment explanation
Indices: 1199194--1199267 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
1199184 TTTATAATGT
1199194 TATAAT-TAA-AATAAAAAAGATTAAAATAAAATA
1 TATAATATAAGAAT-AAAAA-ATTAAAATAAAATA
1199227 TATAATATAAGAATAAAAAATTAAAATAAAATA
1 TATAATATAAGAATAAAAAATTAAAATAAAATA
1199260 -A-AATATAA
1 TATAATATAA
1199268 AAAATTAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
31 7 0.18
32 1 0.03
33 20 0.51
34 8 0.21
35 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (33 bp):
TATAATATAAGAATAAAAAATTAAAATAAAATA
Found at i:1199326 original size:14 final size:14
Alignment explanation
Indices: 1199299--1199359 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 14
1199289 TAGGTAAAAC
1199299 AAAT-TAAAATAAA
1 AAATATAAAATAAA
* *
1199312 ACATATAATATAAA
1 AAATATAAAATAAA
**
1199326 AAATATATTA-AAA
1 AAATATAAAATAAA
1199339 AAATA-AAAATAAA
1 AAATATAAAATAAA
*
1199352 ATATATAA
1 AAATATAA
1199360 GATTATAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.05
13 18 0.47
14 18 0.47
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATAAAATAAA
Found at i:1199349 original size:40 final size:40
Alignment explanation
Indices: 1199205--1199359 Score: 123
Period size: 44 Copynumber: 3.6 Consensus size: 40
1199195 ATAATTAAAA
* * *
1199205 TAAAAAAGATTAAAATAAAATATATAATATAAGAATAAAAAAT
1 TAAAAAA-ATAAAAATAAAATATATAATATAA-AA-AATATAT
* * * * *
1199248 TAAAATAAAATAAAATATAAAAAAT-TAACATTTATATAATATAGG
1 T-AAA-AAAATAAAA-ATAAAATATAT-A-ATATAAAAAATATA-T
* *
1199293 TAAAACAAATTAAAATAAAACATATAATATAAAAAATATAT
1 TAAAA-AAATAAAAATAAAATATATAATATAAAAAATATAT
1199334 TAAAAAAATAAAAATAAAATATATAA
1 TAAAAAAATAAAAATAAAATATATAA
1199360 GATTATAATA
Statistics
Matches: 88, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
40 19 0.22
41 5 0.06
42 11 0.12
43 11 0.12
44 24 0.27
45 14 0.16
46 4 0.05
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (40 bp):
TAAAAAAATAAAAATAAAATATATAATATAAAAAATATAT
Found at i:1199355 original size:33 final size:32
Alignment explanation
Indices: 1199304--1199389 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
1199294 AAAACAAATT
*
1199304 AAAATAAAACATATAATATAAAAAATATATTAA-A
1 AAAATAAAA-ATAAAATATAAAAAAT-TA-TAATA
* *
1199338 AAAATAAAAATAAAATATATAAGATTATAATA
1 AAAATAAAAATAAAATATAAAAAATTATAATA
*
1199370 ATAAATGAAAATAAAATATA
1 A-AAATAAAAATAAAATATA
1199390 TGACATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 3 0.07
32 4 0.09
33 30 0.65
34 9 0.20
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (32 bp):
AAAATAAAAATAAAATATAAAAAATTATAATA
Found at i:1200725 original size:28 final size:28
Alignment explanation
Indices: 1200691--1200745 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1200681 GATTGAAATT
* *
1200691 TTATTTATGTTTGGTGTAATATATTTGC
1 TTATTTATATATGGTGTAATATATTTGC
* *
1200719 TTATTTATATATGGTGTATTTTATTTG
1 TTATTTATATATGGTGTAATATATTTG
1200746 TTTGTAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (28 bp):
TTATTTATATATGGTGTAATATATTTGC
Found at i:1204144 original size:7 final size:7
Alignment explanation
Indices: 1204132--1204157 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1204122 TCAAAACATG
1204132 AATTATA
1 AATTATA
1204139 AATTATA
1 AATTATA
1204146 AATTATA
1 AATTATA
1204153 AATTA
1 AATTA
1204158 ATAATTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTATA
Found at i:1204163 original size:14 final size:15
Alignment explanation
Indices: 1204132--1204201 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 15
1204122 TCAAAACATG
*
1204132 AATTATAAATTATA-
1 AATTATAAATTAAAT
1204146 AATTATAAATT-AAT
1 AATTATAAATTAAAT
*
1204160 AATT-TCAAATTCAAT
1 AATTAT-AAATTAAAT
*
1204175 AATGATATAAAATTAAAA
1 AAT--TAT-AAATTAAAT
1204193 AATTATAAA
1 AATTATAAA
1204202 AATAACATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
13 2 0.04
14 20 0.43
15 9 0.20
16 3 0.07
17 1 0.02
18 11 0.24
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (15 bp):
AATTATAAATTAAAT
Found at i:1204915 original size:6 final size:6
Alignment explanation
Indices: 1204906--1204949 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
1204896 CATGTATATT
* *
1204906 TATACA TATACA TATACA TAT--A TATACA CATACA TATATA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
1204950 ACAACAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 4 0.12
6 29 0.88
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:1204920 original size:16 final size:16
Alignment explanation
Indices: 1204911--1204947 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1204901 ATATTTATAC
*
1204911 ATATACATATACATAT
1 ATATACACATACATAT
1204927 ATATACACATACATAT
1 ATATACACATACATAT
1204943 ATATA
1 ATATA
1204948 TAACAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATACACATACATAT
Found at i:1205002 original size:15 final size:15
Alignment explanation
Indices: 1204984--1205052 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 15
1204974 AATTAATTTG
1204984 TATATATATTATTA-A
1 TATATATATTA-TACA
1204999 TATATCAT-TTATACA
1 TATAT-ATATTATACA
1205014 TAT-TATATTA-AC-
1 TATATATATTATACA
* * *
1205026 CAGATACATTATACA
1 TATATATATTATACA
1205041 TA-ATATATTATA
1 TATATATATTATA
1205053 TATGTATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
12 1 0.02
13 10 0.23
14 17 0.40
15 13 0.30
16 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (15 bp):
TATATATATTATACA
Found at i:1205060 original size:22 final size:21
Alignment explanation
Indices: 1205035--1205084 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1205025 CCAGATACAT
*
1205035 TATACATAATATATTATATATG
1 TATAAATAATATATTA-ATATG
*
1205057 TATAAATAATTTATTAATAT-
1 TATAAATAATATATTAATATG
1205077 TACTAAAT
1 TA-TAAAT
1205085 TATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 9 0.36
22 14 0.56
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
TATAAATAATATATTAATATG
Found at i:1217057 original size:16 final size:18
Alignment explanation
Indices: 1217031--1217067 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1217021 AAAAAAGAAG
1217031 AAAAATGTTTT-TTTCCT
1 AAAAATGTTTTATTTCCT
*
1217048 AAAAAT-TTTTATTTCTT
1 AAAAATGTTTTATTTCCT
1217065 AAA
1 AAA
1217068 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
AAAAATGTTTTATTTCCT
Found at i:1217173 original size:22 final size:23
Alignment explanation
Indices: 1217130--1217174 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1217120 TACAAATTTT
*
1217130 ATTTTTCAAATTTAAAATAAAAG
1 ATTTTTCAAATTGAAAATAAAAG
*
1217153 ATTTTT-AAATGTGAAAAAAAAA
1 ATTTTTCAAAT-TGAAAATAAAA
1217175 ACAAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTTTTCAAATTGAAAATAAAAG
Found at i:1227246 original size:14 final size:14
Alignment explanation
Indices: 1227227--1227254 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1227217 TGGCATTTGT
1227227 TTGTTGTGAGATTA
1 TTGTTGTGAGATTA
1227241 TTGTTGTGAGATTA
1 TTGTTGTGAGATTA
1227255 AATTATGCCT
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:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
TTGTTGTGAGATTA
Found at i:1227872 original size:69 final size:68
Alignment explanation
Indices: 1227828--1227969 Score: 185
Period size: 69 Copynumber: 2.0 Consensus size: 68
1227818 TCCTTAAGAA
*
1227828 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACATTTAATCA
1 GCCCAA-TAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAAC-TAATTAAACATTAAATCA
1227893 ATTAG
64 ATTAG
* * * * * *
1227898 GCCCAATAACTTAATTGTTTAATTTAATTAATTAAGCCTAATGACTTAATTAAACAATTTAATGA
1 GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAAC-TAATTAAAC-ATTAAATCA
1227963 ATTAG
64 ATTAG
1227968 GC
1 GC
1227970 ACAACTTAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 45 0.68
70 21 0.32
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (68 bp):
GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTAATTAAACATTAAATCAAT
TAG
Found at i:1227876 original size:35 final size:35
Alignment explanation
Indices: 1227828--1227948 Score: 156
Period size: 35 Copynumber: 3.5 Consensus size: 35
1227818 TCCTTAAGAA
1227828 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTGTTTAATTTAATCAATTAG
**
1227864 GCCCAATAACTTAA-T-TAAACATTTAATCAATTAG
1 GCCCAATAACTTAATTGTTTA-ATTTAATCAATTAG
* *
1227898 GCCCAATAACTTAATTGTTTAATTTAATTAATTAA
1 GCCCAATAACTTAATTGTTTAATTTAATCAATTAG
* *
1227933 GCCTAATGACTTAATT
1 GCCCAATAACTTAATT
1227949 AAACAATTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
33 2 0.03
34 29 0.39
35 35 0.47
36 8 0.11
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (35 bp):
GCCCAATAACTTAATTGTTTAATTTAATCAATTAG
Found at i:1227957 original size:35 final size:35
Alignment explanation
Indices: 1227849--1227969 Score: 154
Period size: 35 Copynumber: 3.5 Consensus size: 35
1227839 TTAATTGTTT
1227849 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
****
1227884 -ATTTAATCAATTAGGCCCAATAACTTAATTGTTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
1227918 AATTTAATTAATTAAGCCTAATGACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
*
1227953 AATTTAATGAATTAGGC
1 AATTTAATCAATTAGGC
1227970 ACAACTTAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
34 30 0.42
35 41 0.58
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.36
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:1233536 original size:15 final size:14
Alignment explanation
Indices: 1233516--1233550 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1233506 TGTTGGAGGG
1233516 TTAAAAGTAAAAAAA
1 TTAAAA-TAAAAAAA
*
1233531 TTAAAATTAAAAAA
1 TTAAAATAAAAAAA
1233545 TTAAAA
1 TTAAAA
1233551 ATTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
TTAAAATAAAAAAA
Found at i:1233544 original size:14 final size:15
Alignment explanation
Indices: 1233525--1233555 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1233515 GTTAAAAGTA
1233525 AAAAAATT-AAAATT
1 AAAAAATTAAAAATT
1233539 AAAAAATTAAAAATT
1 AAAAAATTAAAAATT
1233554 AA
1 AA
1233556 TATATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAATTAAAAATT
Found at i:1234330 original size:18 final size:18
Alignment explanation
Indices: 1234305--1234344 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1234295 ATATAAATAG
1234305 AATAAAAATAAAAAATATA
1 AATAAAAAT-AAAAATATA
*
1234324 AATAAAAATAATAATATA
1 AATAAAAATAAAAATATA
1234342 AAT
1 AAT
1234345 TACAAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAAAAATAAAAATATA
Found at i:1236803 original size:17 final size:17
Alignment explanation
Indices: 1236762--1236804 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1236752 AAATATTTAT
1236762 ATATATTTTTTAACATA
1 ATATATTTTTTAACATA
* *
1236779 ATAAATTTTTTACACTTA
1 ATATATTTTTTA-ACATA
1236797 A-ATATTTT
1 ATATATTTT
1236805 GTTTATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTTTTTAACATA
Found at i:1238289 original size:12 final size:12
Alignment explanation
Indices: 1238274--1238299 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1238264 CCTTCTTGAT
1238274 CTCTCTCTCTCC
1 CTCTCTCTCTCC
1238286 CTCTCTCTCTCC
1 CTCTCTCTCTCC
1238298 CT
1 CT
1238300 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:1244831 original size:34 final size:34
Alignment explanation
Indices: 1244750--1244831 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
1244740 CATAACAAAT
* *
1244750 ACAACCCTTACAATGCCTTTTCACAAGAGCAAGC
1 ACAACCCTTACAATACCTTTTCACAAGAACAAGC
* ** *
1244784 ATAACCCACACAATACCTTTTTACAAGAACAAGC
1 ACAACCCTTACAATACCTTTTCACAAGAACAAGC
*
1244818 ACAATCCTTACAAT
1 ACAACCCTTACAAT
1244832 GTTACCTTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.22
Consensus pattern (34 bp):
ACAACCCTTACAATACCTTTTCACAAGAACAAGC
Found at i:1248782 original size:11 final size:11
Alignment explanation
Indices: 1248756--1248785 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1248746 TACATAATAC
1248756 ATAAATTTTTT
1 ATAAATTTTTT
1248767 A-AAATTTTTT
1 ATAAATTTTTT
1248777 ATAAATTTT
1 ATAAATTTT
1248786 CTTAATGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATAAATTTTTT
Found at i:1248921 original size:12 final size:13
Alignment explanation
Indices: 1248899--1248948 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
1248889 TGTTCTTTCA
1248899 ATTTA-TATTATT
1 ATTTATTATTATT
1248911 A-TTATTATTATTT
1 ATTTATTATTA-TT
*
1248924 ATTTATT-TAATT
1 ATTTATTATTATT
*
1248936 ATTTATTTTTATT
1 ATTTATTATTATT
1248949 TTATTTACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 3 0.09
12 15 0.47
13 9 0.28
14 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTATTATT
Done.