Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_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: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 21
Found at i:1353131 original size:270 final size:270
Alignment explanation
Indices: 1352650--1353287 Score: 924
Period size: 270 Copynumber: 2.4 Consensus size: 270
1352640 TAAACCAATC
* * *
1352650 AACATTTCCAATGGAAAGTTTGTAATGAGAAGAACTCATCCAATAGAGGGAGAAGAAGTTTATAA
1 AACATTTCCAATGGAGAGTTTGTAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
* * * *
1352715 TGAGAATAACTTGTTCAACCTTTGCTCGATTCACAATATTTTGAATCAGCGACGCCTCACTTGAG
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAATATTTCGAATCAACAACGCCTCACTTGAG
* *
1352780 GGATTAATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAATAAGTT
131 GGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTT
** ** * * *
1352845 CATAATGTGAAGAACTTGTTCAACATTTGCTTGATTTAGAGCATTTTGAATCAGTGACAC-T-TT
196 CATAATAAGAAGAACTTGTTCAACATTTGCTTGATGCAAAGCATTTCGAATCAG-CA-ACGTCTT
1352908 ACTTGAGGGATT
259 ACTTGAGGGATT
* ** * *
1352920 AACATTTCCAACGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAAAAGTTCATAA
1 AACATTTCCAATGGAGAGTTTGTAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
* * *
1352985 TAAGAAGAACTTGTTCAGCCTTTGCTCGATTCACAATATTTCGAATCAACAACGTCTCACTTGAG
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAATATTTCGAATCAACAACGCCTCACTTGAG
* * *
1353050 GGATTAACATTTCCAATGGAGAGTTTC-TAATGAGAAGAACTCATTCGATA-AAGGGATAAGAAT
131 GGATTAACATTTCCAATGGAGAG-TTCATAATGAGAAGAACTCATCCGATAGAA-GGAGAAGAAG
* *
1353113 TTCATAATAAGAAGAACTTGTTCAACCTTTGGTTGATGCAAAGCATTTCGAATCAGCAACGTCTT
194 TTCATAATAAGAAGAACTTGTTCAACATTTGCTTGATGCAAAGCATTTCGAATCAGCAACGTCTT
1353178 ACTTGAGGGATT
259 ACTTGAGGGATT
*
1353190 AACATTTCCAATGGAGAGTTTGTAATGAGAAGAACTCATCCGATAGAGAGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTTGTAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
* *
1353255 TGAGAAGAACTTTTTCAACCTTTACTCGATTCA
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCA
1353288 TCGCACATGG
Statistics
Matches: 325, Mismatches: 39, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
268 2 0.01
269 4 0.01
270 316 0.97
271 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (270 bp):
AACATTTCCAATGGAGAGTTTGTAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAATATTTCGAATCAACAACGCCTCACTTGAG
GGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTT
CATAATAAGAAGAACTTGTTCAACATTTGCTTGATGCAAAGCATTTCGAATCAGCAACGTCTTAC
TTGAGGGATT
Found at i:1353665 original size:24 final size:23
Alignment explanation
Indices: 1353638--1353685 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1353628 AAACCAAGCT
1353638 CTGGAGCCCAAACCAAGACCCGAC
1 CTGGAGCCCAAACCAA-ACCCGAC
* *
1353662 CTGGGGCCCAAACCAAACCTGAC
1 CTGGAGCCCAAACCAAACCCGAC
1353685 C
1 C
1353686 CAGAACCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.31, C:0.42, G:0.21, T:0.06
Consensus pattern (23 bp):
CTGGAGCCCAAACCAAACCCGAC
Found at i:1354012 original size:35 final size:35
Alignment explanation
Indices: 1353958--1354068 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 35
1353948 CGCTAGCTCG
*
1353958 TTTA-TTTTATTGCTT-GAACTAACCCTCGAACTTT
1 TTTATTTTTATTG-TTCGAACTAACCCTCAAACTTT
*
1353992 TTTATTTTTATTGTTCGAACTAACCCGCTAAAC-TT
1 TTTATTTTTATTGTTCGAACTAACCCTC-AAACTTT
* ** * *
1354027 TTTATTTTTGTTGTTCGAGTTAACTCTCTAACTTT
1 TTTATTTTTATTGTTCGAACTAACCCTCAAACTTT
1354062 TATTATT
1 T-TTATT
1354069 CGATTATATT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
34 9 0.14
35 47 0.73
36 8 0.12
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (35 bp):
TTTATTTTTATTGTTCGAACTAACCCTCAAACTTT
Found at i:1354638 original size:2 final size:2
Alignment explanation
Indices: 1354631--1354676 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1354621 CCCCTTCATG
1354631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1354672 TA TA T
1 TA TA T
1354677 TTTTTGAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1354884 original size:15 final size:14
Alignment explanation
Indices: 1354854--1354907 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
1354844 TCATGTTGTC
*
1354854 TATTTTA-TTATCT
1 TATTTTATTTATTT
1354867 TATTTTACTTTATTT
1 TATTTTA-TTTATTT
*
1354882 TATTTCATTTATTAT
1 TATTTTATTTATT-T
1354897 TATTTTTATTT
1 TA-TTTTATTT
1354908 TACTTCATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 7 0.21
14 6 0.18
15 14 0.41
16 7 0.21
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:1355099 original size:2 final size:2
Alignment explanation
Indices: 1355094--1355133 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1355084 ACATTTTTTA
1355094 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
1355134 CAATAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1357192 original size:25 final size:27
Alignment explanation
Indices: 1357139--1357192 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
1357129 CAAGGTTTTT
**
1357139 TAAAAAAAATAATAATATAATAATGAA
1 TAAAAAAAATAATAATATAATAAAAAA
*
1357166 TAAAAAAAATGA-AA-ATAATAAAAAA
1 TAAAAAAAATAATAATATAATAAAAAA
1357191 TA
1 TA
1357193 TAAATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 2 0.08
27 11 0.46
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (27 bp):
TAAAAAAAATAATAATATAATAAAAAA
Found at i:1357203 original size:17 final size:16
Alignment explanation
Indices: 1357164--1357204 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1357154 TATAATAATG
1357164 AATAA-AAAAAATGAA
1 AATAATAAAAAATGAA
1357179 AATAATAAAAAAT-ATA
1 AATAATAAAAAATGA-A
1357195 AATATATAAA
1 AATA-ATAAA
1357205 GTTATAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
AATAATAAAAAATGAA
Found at i:1357389 original size:28 final size:27
Alignment explanation
Indices: 1357358--1357410 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1357348 ATATTAGACT
*
1357358 TATAAGTAA-AATATTAAAGAAATATATA
1 TATAA-TAATAATAATAAA-AAATATATA
1357386 TATAATAATAATAATAAAAAATATA
1 TATAATAATAATAATAAAAAATATA
1357411 GTAAAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (27 bp):
TATAATAATAATAATAAAAAATATATA
Found at i:1357474 original size:18 final size:17
Alignment explanation
Indices: 1357451--1357493 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1357441 ATATATACAT
1357451 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1357469 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1357486 ATAA-AATA
1 ATAATAATA
1357494 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1358826 original size:105 final size:105
Alignment explanation
Indices: 1358639--1358983 Score: 511
Period size: 105 Copynumber: 3.3 Consensus size: 105
1358629 GCATTGTTCA
* * ** *
1358639 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1358699 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1358739 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
1358804 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1358844 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
1358909 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1358949 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1358984 CGCGGATGGC
Statistics
Matches: 221, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
100 36 0.16
101 1 0.00
102 1 0.00
104 5 0.02
105 153 0.69
106 3 0.01
108 22 0.10
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1359934 original size:37 final size:36
Alignment explanation
Indices: 1359838--1359966 Score: 172
Period size: 36 Copynumber: 3.6 Consensus size: 36
1359828 AAAACATATT
* *
1359838 CAAATATTTGTTTCAAGGGAAACTGTCTCAAGAGATA
1 CAAA-ATTTATTTCAAGGGAAACTGTCTCAAGAGAGA
*
1359875 CAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGA
1 CAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGA
* *
1359911 CAAAATTTTGTTTCAAGGGAAACTATCTC-A-AGAGA
1 CAAAA-TTTATTTCAAGGGAAACTGTCTCAAGAGAGA
*
1359946 CGAAATTTATTTCAAGGGAAA
1 CAAAATTTATTTCAAGGGAAA
1359967 TGTTTTCAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
34 15 0.18
35 9 0.11
36 35 0.42
37 24 0.29
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (36 bp):
CAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:1360940 original size:22 final size:22
Alignment explanation
Indices: 1360915--1360958 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1360905 CATTTTTGTT
1360915 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
1360937 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
1360959 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:1361567 original size:22 final size:23
Alignment explanation
Indices: 1361539--1361588 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1361529 ATCTTTGTGT
1361539 TTTTTGTCCCTTTTT-CTTTTTC
1 TTTTTGTCCCTTTTTGCTTTTTC
* * *
1361561 TTTTTGTTCTTTTTTGCTTTTTT
1 TTTTTGTCCCTTTTTGCTTTTTC
1361584 TTTTT
1 TTTTT
1361589 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (23 bp):
TTTTTGTCCCTTTTTGCTTTTTC
Found at i:1361570 original size:9 final size:8
Alignment explanation
Indices: 1361555--1361598 Score: 56
Period size: 7 Copynumber: 5.6 Consensus size: 8
1361545 TCCCTTTTTC
1361555 TTTTTCTT
1 TTTTTCTT
1361563 TTTGTTCTT
1 TTT-TTCTT
*
1361572 TTTTGCTT
1 TTTTTCTT
1361580 TTTTT-TT
1 TTTTTCTT
1361587 TTTTT-TT
1 TTTTTCTT
1361594 TTTTT
1 TTTTT
1361599 TGCCCTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 14 0.42
8 11 0.33
9 8 0.24
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.89
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1361607 original size:24 final size:25
Alignment explanation
Indices: 1361554--1361608 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1361544 GTCCCTTTTT
1361554 CTTTTTCTTTTTGTTCTTTTTTG-C
1 CTTTTTCTTTTTGTTCTTTTTTGCC
* * * *
1361578 TTTTTTTTTTTTTTTTTTTTTTGCC
1 CTTTTTCTTTTTGTTCTTTTTTGCC
1361603 CTTTTT
1 CTTTTT
1361609 ATTCTGATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (25 bp):
CTTTTTCTTTTTGTTCTTTTTTGCC
Found at i:1362772 original size:8 final size:8
Alignment explanation
Indices: 1362756--1362801 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
1362746 ATTGTAGATG
1362756 AAAATGCA
1 AAAATGCA
*
1362764 AAAAGGCA
1 AAAATGCA
1362772 AAAATGC-
1 AAAATGCA
1362779 AAAATGC-
1 AAAATGCA
1362786 AAAATGCA
1 AAAATGCA
*
1362794 AGAATGCA
1 AAAATGCA
1362802 TGAAATGTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
7 14 0.41
8 20 0.59
ACGTcount: A:0.59, C:0.13, G:0.17, T:0.11
Consensus pattern (8 bp):
AAAATGCA
Found at i:1362777 original size:16 final size:15
Alignment explanation
Indices: 1362756--1362794 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1362746 ATTGTAGATG
1362756 AAAATGCAAAAAGGC
1 AAAATGCAAAAAGGC
*
1362771 AAAAATGC-AAAATGC
1 -AAAATGCAAAAAGGC
1362786 AAAATGCAA
1 AAAATGCAA
1362795 GAATGCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
16 7 0.33
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAAGGC
Found at i:1362799 original size:15 final size:14
Alignment explanation
Indices: 1362756--1362801 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
1362746 ATTGTAGATG
*
1362756 AAAATGCAAAAAGGC
1 AAAATGC-AAAATGC
1362771 AAAAATGCAAAATGC
1 -AAAATGCAAAATGC
1362786 AAAATGCAAGAATGC
1 AAAATGCAA-AATGC
1362801 A
1 A
1362802 TGAAATGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 9 0.32
15 12 0.43
16 7 0.25
ACGTcount: A:0.59, C:0.13, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAATGCAAAATGC
Found at i:1365860 original size:45 final size:45
Alignment explanation
Indices: 1365768--1365857 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
1365758 ATAATTTAAT
* * ** * *
1365768 ATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGAA
1 ATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAAGAA
1365813 ATATATATATAATAATAATA-AAATAT-AGTAAAAAATCAAATGAA
1 ATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAA-GAA
1365857 A
1 A
1365858 ATAATTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 12 0.32
44 8 0.21
45 18 0.47
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (45 bp):
ATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAAGAA
Found at i:1365912 original size:17 final size:18
Alignment explanation
Indices: 1365879--1365914 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1365869 ATATATACAT
*
1365879 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1365897 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1365914 A
1 A
1365915 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1371713 original size:21 final size:21
Alignment explanation
Indices: 1371689--1371728 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1371679 TTTGCCATTA
1371689 CATTATGCATTTAGCACTTTT
1 CATTATGCATTTAGCACTTTT
* *
1371710 CATTTTGCATTTTGCACTT
1 CATTATGCATTTAGCACTT
1371729 GCATATTAAA
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:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (21 bp):
CATTATGCATTTAGCACTTTT
Found at i:1376296 original size:294 final size:295
Alignment explanation
Indices: 1375767--1376355 Score: 1153
Period size: 294 Copynumber: 2.0 Consensus size: 295
1375757 TGAGACCAGA
1375767 CATGTTGCTAAAAATAAAGGAGGAGGTGAAGAAACAGTTTGATGTCACATTCCTACAAGTATCCA
1 CATGTTGCTAAAAATAAAGGAGGAGGTGAAGAAACAGTTTGATGTCACATTCCTACAAGTATCCA
1375832 AATACCCTAAATGGGTAGCAAATATAGTGCCAATTCCAAAGAAATATGGAAAGGTCTAAATGTGT
66 AATACCCTAAATGGGTAGCAAATATAGTGCCAATTCCAAAGAAATATGGAAAGGTCTAAATGTGT
*
1375897 GTTGACTACCGAGATCTCAATCATACAAGTCCCAAAGATAACTTCACACTTCCTTGTATTGATAC
131 GTTGACTACCGAGATCTCAATCATACAAGTCCCAAAGATAACTTCACACTTCCTTATATTGATAC
1375962 AAGGTTCGATAATACAGCTAGACACGCTCTTTTCTCCTTCATGGATGGCTTCTTGTGGTACAATC
196 AAGGTTCGATAATACAGCTAGACACGCTCTTTTCTCCTTCATGGATGGCTTCTTGTGGTACAATC
1376027 -AATCAAAATAAATCCTGAAGATATAGAGAAGATG
261 AAATCAAAATAAATCCTGAAGATATAGAGAAGATG
1376061 CATGTTGCTAAAAATAAAGGAGGAGGTGAAGAAACAGTTTGATGTCACATTCCTACAAGTATCCA
1 CATGTTGCTAAAAATAAAGGAGGAGGTGAAGAAACAGTTTGATGTCACATTCCTACAAGTATCCA
*
1376126 AATACCCTAAATGGGTAGCAAATATAGTGCCAATTCCAAAGAAATATGGAAGGGTCTAAATGTGT
66 AATACCCTAAATGGGTAGCAAATATAGTGCCAATTCCAAAGAAATATGGAAAGGTCTAAATGTGT
1376191 GTTGACTACCGAGATCTCAATCATACAAGTCCCAAAGATAACTTCACACTTCCTTATATTGATAC
131 GTTGACTACCGAGATCTCAATCATACAAGTCCCAAAGATAACTTCACACTTCCTTATATTGATAC
1376256 AAGGTTCGATAATACAGCTAGACACGCTCTTTTCTCCTTCATGGATGGCTTCTTGTGGTACAATC
196 AAGGTTCGATAATACAGCTAGACACGCTCTTTTCTCCTTCATGGATGGCTTCTTGTGGTACAATC
1376321 AAATCAAAATAAATCCTGAAGATATAGAGAAGATG
261 AAATCAAAATAAATCCTGAAGATATAGAGAAGATG
1376356 GCGCTCGTGA
Statistics
Matches: 292, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
294 258 0.88
295 34 0.12
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (295 bp):
CATGTTGCTAAAAATAAAGGAGGAGGTGAAGAAACAGTTTGATGTCACATTCCTACAAGTATCCA
AATACCCTAAATGGGTAGCAAATATAGTGCCAATTCCAAAGAAATATGGAAAGGTCTAAATGTGT
GTTGACTACCGAGATCTCAATCATACAAGTCCCAAAGATAACTTCACACTTCCTTATATTGATAC
AAGGTTCGATAATACAGCTAGACACGCTCTTTTCTCCTTCATGGATGGCTTCTTGTGGTACAATC
AAATCAAAATAAATCCTGAAGATATAGAGAAGATG
Found at i:1382551 original size:36 final size:34
Alignment explanation
Indices: 1382500--1382604 Score: 115
Period size: 35 Copynumber: 3.0 Consensus size: 34
1382490 AACTCGTTTA
*
1382500 TTTTATTGCTTGAACTAACCCTCTTAACATTTTATT
1 TTTTATTG-TTGAACTAACCCGC-TAACATTTTATT
*
1382536 TTTTATTGTTCGAACTAACCAGCTAACATTTT-TAT
1 TTTTATTGTT-GAACTAACCCGCTAACATTTTAT-T
* *
1382571 TTTTGTTGTTAGAGCTAACCCGCTAAC-TTTTATT
1 TTTTATTGTT-GAACTAACCCGCTAACATTTTATT
1382605 GTTTGAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
34 6 0.10
35 36 0.60
36 18 0.30
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.48
Consensus pattern (34 bp):
TTTTATTGTTGAACTAACCCGCTAACATTTTATT
Found at i:1382574 original size:35 final size:33
Alignment explanation
Indices: 1382479--1382601 Score: 113
Period size: 35 Copynumber: 3.5 Consensus size: 33
1382469 AAATTATAAC
* *
1382479 ACTAACCTGCTAACTCGTTTA-TTTTATTGCTTGA
1 ACTAACCCGCTAACT-TTTTATTTTTATTG-TTGA
* *
1382513 ACTAACCCTCTTAACATTTTATTTTTTATTGTTCGA
1 ACTAACCCGC-TAACTTTTTA-TTTTTATTGTT-GA
* *
1382549 ACTAACCAGCTAACATTTTTATTTTTGTTGTTAGA
1 ACTAACCCGCTAAC-TTTTTATTTTTATTGTT-GA
*
1382584 GCTAACCCGCTAACTTTT
1 ACTAACCCGCTAACTTTT
1382602 ATTGTTTGAA
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
34 16 0.22
35 34 0.47
36 23 0.32
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (33 bp):
ACTAACCCGCTAACTTTTTATTTTTATTGTTGA
Found at i:1383457 original size:13 final size:12
Alignment explanation
Indices: 1383440--1383512 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 12
1383430 ATCATGTTGC
1383440 TTATTTTATTAT
1 TTATTTTATTAT
1383452 CTTATTTTA-T-T
1 -TTATTTTATTAT
*
1383463 TTATTTTTTTCAT
1 TTATTTTATT-AT
1383476 TTATTATTATTATT
1 TTATT-TTATTA-T
* *
1383490 TTATTTCATTTT
1 TTATTTTATTAT
1383502 TTATTTCTATT
1 TTATTT-TATT
1383513 TTCATTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 7 0.14
11 2 0.04
12 8 0.16
13 22 0.45
14 10 0.20
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:1383463 original size:18 final size:18
Alignment explanation
Indices: 1383440--1383520 Score: 85
Period size: 18 Copynumber: 4.4 Consensus size: 18
1383430 ATCATGTTGC
*
1383440 TTATTTTATTATCTTATT
1 TTATTTTATTATTTTATT
*
1383458 TTATTTTATTTTTTTCA-T
1 TTATTTTATTATTTT-ATT
1383476 TTATTATTATTATTTTATT
1 TTATT-TTATTATTTTATT
*
1383495 TCATTTT-TTATTTCTATT
1 TTATTTTATTATTT-TATT
1383513 TTCATTTT
1 TT-ATTTT
1383521 TAATGTTAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 6 0.11
18 27 0.51
19 20 0.38
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTATTATTTTATT
Found at i:1383466 original size:23 final size:22
Alignment explanation
Indices: 1383440--1383519 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 22
1383430 ATCATGTTGC
1383440 TTATTTTATTATC-TTATTTTATT
1 TTATTTTATT-TCATT-TTTTATT
*
1383463 TTATTTT-TTTCATTTATTATT
1 TTATTTTATTTCATTTTTTATT
1383484 ATTATTTTATTTCATTTTTTATT
1 -TTATTTTATTTCATTTTTTATT
1383507 TCTATTTTCATTT
1 T-TATTTT-ATTT
1383520 TTAATGTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.16
22 12 0.24
23 26 0.52
24 4 0.08
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTTTATTTCATTTTTTATT
Found at i:1383494 original size:32 final size:31
Alignment explanation
Indices: 1383444--1383503 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
1383434 TGTTGCTTAT
* *
1383444 TTTATTATCTTATTTTATTTTATTTTTTTCA
1 TTTATTATATTATTTTATTTCATTTTTTTCA
1383475 TTTATTATTATTATTTTATTTCATTTTTT
1 TTTATTA-TATTATTTTATTTCATTTTTT
1383504 ATTTCTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTATTATATTATTTTATTTCATTTTTTTCA
Found at i:1383517 original size:19 final size:17
Alignment explanation
Indices: 1383442--1383521 Score: 63
Period size: 19 Copynumber: 4.4 Consensus size: 17
1383432 CATGTTGCTT
* *
1383442 ATTTTATTATCTTATTTT
1 ATTTT-TTATTTTATTTC
*
1383460 ATTTTATTTTTTTCATTT-
1 ATTTT-TTATTTT-ATTTC
1383478 ATTATTATTATTTTATTTC
1 ATT-TT-TTATTTTATTTC
1383497 ATTTTTTATTTCTATTTTC
1 ATTTTTTATTT-TA-TTTC
1383516 ATTTTT
1 ATTTTT
1383522 AATGTTAAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
17 6 0.11
18 22 0.41
19 26 0.48
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTTTATTTTATTTC
Found at i:1383519 original size:12 final size:11
Alignment explanation
Indices: 1383441--1383519 Score: 58
Period size: 12 Copynumber: 6.9 Consensus size: 11
1383431 TCATGTTGCT
1383441 TATTTTATTATC
1 TATTTTATT-TC
1383453 TTATTTTATTT-
1 -TATTTTATTTC
1383464 TATTTT-TTTC
1 TATTTTATTTC
1383474 -ATTTATTATTAT-
1 TA-TT-TTATT-TC
1383486 TATTTTATTTC
1 TATTTTATTTC
*
1383497 ATTTTTTATTTC
1 -TATTTTATTTC
1383509 TATTTTCATTT
1 TATTTT-ATTT
1383520 TTAATGTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
9 4 0.07
10 9 0.16
11 12 0.22
12 19 0.35
13 11 0.20
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTTATTTC
Found at i:1385126 original size:12 final size:12
Alignment explanation
Indices: 1385111--1385150 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1385101 CCAAAAAATG
1385111 CTTTTAAAAGTA
1 CTTTTAAAAGTA
*
1385123 C-TTTAAAAATA
1 CTTTTAAAAGTA
1385134 CTTTTAAAAGTA
1 CTTTTAAAAGTA
1385146 CTTTT
1 CTTTT
1385151 TCACAGTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (12 bp):
CTTTTAAAAGTA
Found at i:1385127 original size:11 final size:11
Alignment explanation
Indices: 1385113--1385149 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1385103 AAAAAATGCT
1385113 TTTAAAAGTAC
1 TTTAAAAGTAC
*
1385124 TTTAAAAATAC
1 TTTAAAAGTAC
1385135 TTTTAAAAGTAC
1 -TTTAAAAGTAC
1385147 TTT
1 TTT
1385150 TTCACAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (11 bp):
TTTAAAAGTAC
Found at i:1385137 original size:23 final size:23
Alignment explanation
Indices: 1385104--1385149 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1385094 ATACTTTCCA
*
1385104 AAAAATGCTTTTAAAAGTACTTT
1 AAAAATACTTTTAAAAGTACTTT
1385127 AAAAATACTTTTAAAAGTACTTT
1 AAAAATACTTTTAAAAGTACTTT
1385150 TTCACAGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
AAAAATACTTTTAAAAGTACTTT
Found at i:1391131 original size:14 final size:14
Alignment explanation
Indices: 1391112--1391140 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1391102 GTCAATCAAG
1391112 CCATTAATTTTTAT
1 CCATTAATTTTTAT
1391126 CCATTAATTTTTAT
1 CCATTAATTTTTAT
1391140 C
1 C
1391141 AGCTGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (14 bp):
CCATTAATTTTTAT
Found at i:1392695 original size:26 final size:26
Alignment explanation
Indices: 1392638--1392697 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
1392628 ATTTCAAAGG
*
1392638 TGAGTCTTGGTAAGCTGATTATTTCT
1 TGAGTTTTGGTAAGCTGATTATTTCT
1392664 TGAGTTTTGGTAAGCTGATTATTTCT
1 TGAGTTTTGGTAAGCTGATTATTTCT
1392690 TGAGTTTT
1 TGAGTTTT
1392698 AAGCTTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.50
Consensus pattern (26 bp):
TGAGTTTTGGTAAGCTGATTATTTCT
Found at i:1394940 original size:23 final size:21
Alignment explanation
Indices: 1394873--1394951 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
1394863 TCCTTAAGGA
1394873 GTGGTCCTTCGGGAC--ATAT
1 GTGGTCCTTCGGGACATATAT
*
1394892 GTGGTCCTTCGGTACATATAT
1 GTGGTCCTTCGGGACATATAT
* *
1394913 GTGGTCCTTTGGGACATTTCTAT
1 GTGGTCCTTCGGGACA--TATAT
*
1394936 GTGGTCCTTCAGGACA
1 GTGGTCCTTCGGGACA
1394952 CATTCTATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.28
21 18 0.36
23 18 0.36
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.35
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:1395170 original size:23 final size:21
Alignment explanation
Indices: 1395091--1395171 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
1395081 TCCTTAAGGA
*
1395091 GTGGTCATTCGGGACATCTAT
1 GTGGTCCTTCGGGACATCTAT
* *
1395112 GTGGTCCTTCGGTACATATAT
1 GTGGTCCTTCGGGACATCTAT
*
1395133 GTGGTCCTTTGGGACATTTCTAT
1 GTGGTCCTTCGGGACA--TCTAT
*
1395156 GTGGTCCTTCAGGACA
1 GTGGTCCTTCGGGACA
1395172 CATTCTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
21 32 0.64
23 18 0.36
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATCTAT
Found at i:1395170 original size:220 final size:218
Alignment explanation
Indices: 1394749--1395186 Score: 849
Period size: 218 Copynumber: 2.0 Consensus size: 218
1394739 GGGTATAGTT
1394749 GGCATGCAAAGAGTCGAGGGTTCTACGTGGCCCTTCGGGATATATATATAATACTTTGGAACATG
1 GGCATGCAAAGAGTCGAGGGTTCTACGTGGCCCTTCGGGATATATATATAATACTTTGGAACATG
1394814 TATGCGGTTCTTCGAAACACATATTTGGTCCTTTAGAATATATATGTGGTCCTTAAGGAGTGGTC
66 TATGCGGTTCTTCGAAACACATATTTGGTCCTTTAGAATATATATGTGGTCCTTAAGGAGTGGTC
*
1394879 CTTCGGGACATATGTGGTCCTTCGGTACATATATGTGGTCCTTTGGGACATTTCTATGTGGTCCT
131 ATTCGGGACATATGTGGTCCTTCGGTACATATATGTGGTCCTTTGGGACATTTCTATGTGGTCCT
1394944 TCAGGACACATTCTATATGGCCC
196 TCAGGACACATTCTATATGGCCC
1394967 GGCATGCAAAGAGTCGAGGGTTCTACGTGGCCCTTCGGGATATATATATAATACTTTGGAACATG
1 GGCATGCAAAGAGTCGAGGGTTCTACGTGGCCCTTCGGGATATATATATAATACTTTGGAACATG
1395032 TATGCGGTTCTTCGAAACACATATTTGGTCCTTTAGAATATATATGTGGTCCTTAAGGAGTGGTC
66 TATGCGGTTCTTCGAAACACATATTTGGTCCTTTAGAATATATATGTGGTCCTTAAGGAGTGGTC
1395097 ATTCGGGACATCTATGTGGTCCTTCGGTACATATATGTGGTCCTTTGGGACATTTCTATGTGGTC
131 ATTCGGGACA--TATGTGGTCCTTCGGTACATATATGTGGTCCTTTGGGACATTTCTATGTGGTC
1395162 CTTCAGGACACATTCTATATGGCCC
194 CTTCAGGACACATTCTATATGGCCC
1395187 TAGTGGGAAT
Statistics
Matches: 217, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
218 139 0.64
220 78 0.36
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (218 bp):
GGCATGCAAAGAGTCGAGGGTTCTACGTGGCCCTTCGGGATATATATATAATACTTTGGAACATG
TATGCGGTTCTTCGAAACACATATTTGGTCCTTTAGAATATATATGTGGTCCTTAAGGAGTGGTC
ATTCGGGACATATGTGGTCCTTCGGTACATATATGTGGTCCTTTGGGACATTTCTATGTGGTCCT
TCAGGACACATTCTATATGGCCC
Found at i:1397493 original size:23 final size:23
Alignment explanation
Indices: 1397429--1397485 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1397419 CTTATATGGA
*
1397429 ACTTCTGTGCAATTCTACGCGGC
1 ACTTCGGTGCAATTCTACGCGGC
* *
1397452 ACTTCGATGCAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGCGGC
1397475 ACTTCGGTGCA
1 ACTTCGGTGCA
1397486 TTTATACGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGGC
Found at i:1399384 original size:17 final size:17
Alignment explanation
Indices: 1399353--1399385 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1399343 AAATATTATT
1399353 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
1399370 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
1399386 TAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:1401878 original size:2 final size:2
Alignment explanation
Indices: 1401866--1401895 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1401856 TAGATTTTCA
1401866 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1401896 GTGATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1402704 original size:23 final size:23
Alignment explanation
Indices: 1402678--1402724 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1402668 AAATTAAGGG
1402678 TATATGATCCCTAATATTATCGA
1 TATATGATCCCTAATATTATCGA
*
1402701 TATATGATCTCTAATATTATCGA
1 TATATGATCCCTAATATTATCGA
1402724 T
1 T
1402725 CCTTTCGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (23 bp):
TATATGATCCCTAATATTATCGA
Found at i:1403265 original size:18 final size:18
Alignment explanation
Indices: 1403242--1403278 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1403232 ATTCATGGAT
*
1403242 GGTTAACCGTACCTTTTA
1 GGTTAACCGTACCGTTTA
1403260 GGTTAACCGTACCGTTTA
1 GGTTAACCGTACCGTTTA
1403278 G
1 G
1403279 CCTAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (18 bp):
GGTTAACCGTACCGTTTA
Found at i:1405432 original size:2 final size:2
Alignment explanation
Indices: 1405425--1405469 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1405415 AATTTATAAT
1405425 TA TA TA 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 TA TA TA
1405467 TA T
1 TA T
1405470 TGAGAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1406543 original size:24 final size:24
Alignment explanation
Indices: 1406511--1406611 Score: 88
Period size: 23 Copynumber: 4.3 Consensus size: 24
1406501 GTATAAATTA
1406511 CACCGAAGTGCCACATAGAATATG-
1 CACCGAAGTGCCACATAGAA-ATGT
*
1406535 CACCGAAGTGCCACGTAGAAATGT
1 CACCGAAGTGCCACATAGAAATGT
* *
1406559 C-CCGAAG-GACCACATATATATGT
1 CACCGAAGTG-CCACATAGAAATGT
* *
1406582 C-TCGAAG-GACAACATAGAAATGT
1 CACCGAAGTG-CCACATAGAAATGT
1406605 C-CCGAAG
1 CACCGAAG
1406612 GACCATGTAG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
22 1 0.02
23 45 0.68
24 20 0.30
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (24 bp):
CACCGAAGTGCCACATAGAAATGT
Found at i:1406571 original size:23 final size:23
Alignment explanation
Indices: 1406537--1406646 Score: 114
Period size: 23 Copynumber: 4.8 Consensus size: 23
1406527 AGAATATGCA
1406537 CCGAAGTG-CCACGTAGAAATGTC
1 CCGAAG-GACCACGTAGAAATGTC
* * *
1406560 CCGAAGGACCACATATATATGTC
1 CCGAAGGACCACGTAGAAATGTC
* * *
1406583 TCGAAGGACAACATAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
* *
1406606 CCGAAGGACCATGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTC
* *
1406629 CCGGAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
1406647 CCCTCGACTC
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
22 1 0.01
23 70 0.99
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:1406646 original size:46 final size:46
Alignment explanation
Indices: 1406513--1406616 Score: 115
Period size: 46 Copynumber: 2.2 Consensus size: 46
1406503 ATAAATTACA
*
1406513 CCGAAGTG-CCACATAGAATATG-CACCGAAGTG-CCACGTAGAAATGTC
1 CCGAAG-GACCACATA-AATATGTC-CCGAAG-GACAACGTAGAAATGTC
* * *
1406560 CCGAAGGACCACATATATATGTCTCGAAGGACAACATAGAAATGTC
1 CCGAAGGACCACATAAATATGTCCCGAAGGACAACGTAGAAATGTC
1406606 CCGAAGGACCA
1 CCGAAGGACCA
1406617 TGTAGAATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
45 1 0.02
46 35 0.70
47 14 0.28
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (46 bp):
CCGAAGGACCACATAAATATGTCCCGAAGGACAACGTAGAAATGTC
Found at i:1406842 original size:45 final size:45
Alignment explanation
Indices: 1406728--1406842 Score: 176
Period size: 45 Copynumber: 2.6 Consensus size: 45
1406718 CACTTCACAT
* *
1406728 ATCACATAGCTCATTGTCACATAGCTTATATCACATTTTCATGTA
1 ATCACATAGATCAATGTCACATAGCTTATATCACATTTTCATGTA
* *
1406773 ATCACATAGGTCAATGCCACATAGCTTATATCACATTTTCATGTA
1 ATCACATAGATCAATGTCACATAGCTTATATCACATTTTCATGTA
* *
1406818 ATCACATAGATCAATATCATATAGC
1 ATCACATAGATCAATGTCACATAGC
1406843 ATAAAATATA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.34
Consensus pattern (45 bp):
ATCACATAGATCAATGTCACATAGCTTATATCACATTTTCATGTA
Found at i:1414602 original size:17 final size:18
Alignment explanation
Indices: 1414558--1414604 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1414548 ACATATATAT
*
1414558 TTATATATTATATACATA
1 TTATATATTATATAAATA
*
1414576 TATATATATTGTATAAATA
1 T-TATATATTATATAAATA
1414595 TTAT-TATTAT
1 TTATATATTAT
1414605 TTTATTAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 5 0.20
18 4 0.16
19 16 0.64
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATATATTATATAAATA
Found at i:1415929 original size:8 final size:8
Alignment explanation
Indices: 1415928--1415958 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1415918 TTTTTTTGTT
1415928 TTTGTTTA
1 TTTGTTTA
1415936 TTTGTTTA
1 TTTGTTTA
1415944 TTTGTTTA
1 TTTGTTTA
1415952 TTTGTTT
1 TTTGTTT
1415959 TTGTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (8 bp):
TTTGTTTA
Found at i:1415973 original size:14 final size:14
Alignment explanation
Indices: 1415926--1415973 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1415916 CCTTTTTTTG
*
1415926 TTTTTGTTTATTTGT
1 TTTTTGTTTATTT-A
*
1415941 TTATTTGTTTATTTG
1 TT-TTTGTTTATTTA
*
1415956 TTTTTGTTTCTTTA
1 TTTTTGTTTATTTA
1415970 TTTT
1 TTTT
1415974 CATTTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 14 0.48
15 4 0.14
16 11 0.38
ACGTcount: A:0.08, C:0.02, G:0.10, T:0.79
Consensus pattern (14 bp):
TTTTTGTTTATTTA
Found at i:1416022 original size:23 final size:22
Alignment explanation
Indices: 1415996--1416076 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
1415986 TGCACTTACC
*
1415996 TTTTTATCTTTATTTTGTTTATT
1 TTTTTAT-TTTATTTTCTTTATT
* *
1416019 TTTTT-CTTTATCTTCCTTTATT
1 TTTTTATTTTAT-TTTCTTTATT
* *
1416041 CTTTTATTTTATCTTCTTTATT
1 TTTTTATTTTATTTTCTTTATT
*
1416063 CTATTTATTTTATT
1 -TTTTTATTTTATT
1416077 ATTGGCTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
21 5 0.11
22 20 0.44
23 20 0.44
ACGTcount: A:0.14, C:0.11, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTTTATTTTATTTTCTTTATT
Found at i:1416038 original size:22 final size:21
Alignment explanation
Indices: 1415996--1416062 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
1415986 TGCACTTACC
* * *
1415996 TTTTTATCTTTATTTTGTTTA
1 TTTTTTTCTTTATCTTCTTTA
1416017 TTTTTTTCTTTATCTTCCTTTA
1 TTTTTTTCTTTATCTT-CTTTA
1416039 TTCTTTTAT-TTTATCTTCTTTA
1 TT-TTTT-TCTTTATCTTCTTTA
1416061 TT
1 TT
1416063 CTATTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 14 0.35
22 13 0.32
23 12 0.30
24 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.01, T:0.75
Consensus pattern (21 bp):
TTTTTTTCTTTATCTTCTTTA
Found at i:1416063 original size:22 final size:23
Alignment explanation
Indices: 1415997--1416075 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
1415987 GCACTTACCT
* *
1415997 TTTTATCTTTATTTTGTTTATT-
1 TTTTATCTTTATCTTCTTTATTC
1416019 TTTT-TCTTTATCTTCCTTTATTC
1 TTTTATCTTTATCTT-CTTTATTC
1416042 TTTTAT-TTTATCTTCTTTATTC
1 TTTTATCTTTATCTTCTTTATTC
1416064 TATTTAT-TTTAT
1 T-TTTATCTTTAT
1416076 TATTGGCTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.18
22 19 0.37
23 22 0.43
24 1 0.02
ACGTcount: A:0.14, C:0.11, G:0.01, T:0.73
Consensus pattern (23 bp):
TTTTATCTTTATCTTCTTTATTC
Found at i:1418855 original size:22 final size:22
Alignment explanation
Indices: 1418827--1418870 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1418817 CTTCGGGCAC
1418827 CTGGTGGCAATCACATCAGGAA
1 CTGGTGGCAATCACATCAGGAA
*
1418849 CTGGTGGCAATCACATCGGGAA
1 CTGGTGGCAATCACATCAGGAA
1418871 GTTTCTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.18
Consensus pattern (22 bp):
CTGGTGGCAATCACATCAGGAA
Found at i:1419204 original size:24 final size:24
Alignment explanation
Indices: 1419177--1419231 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1419167 CAATGACATA
1419177 TGAGGAGTTGCTCCAAACGCTAGT
1 TGAGGAGTTGCTCCAAACGCTAGT
* *
1419201 TGAGGAGTTGCTCCCAATGCTAGT
1 TGAGGAGTTGCTCCAAACGCTAGT
1419225 TGAGGAG
1 TGAGGAG
1419232 AATCTCGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (24 bp):
TGAGGAGTTGCTCCAAACGCTAGT
Found at i:1420110 original size:95 final size:94
Alignment explanation
Indices: 1419942--1420137 Score: 252
Period size: 95 Copynumber: 2.1 Consensus size: 94
1419932 TATAATATTA
* * ** *
1419942 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAATTTGGTTAAATTCCCTGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGAATTTGGTTAAACGCCCCGGCTTTATGGA
* *
1420007 TAATATTCAGCTAGCCTGATAAAGGTAAT
66 TAAGATTCAGCTAACCTGATAAAGGTAAT
1420036 TATACTATACAATAAAGCTTGAGCTATCCCTCTA-AGGCAA-TTGGTTAAACGCCCCGGCTTTAT
1 TATA-TATACAATAAAGCTTGAGCTATCCCTCTAGA-G-AATTTGGTTAAACGCCCCGGCTTTAT
* * *
1420099 GGATAAGATTCAGCTAATCTTATAAAGGTATT
63 GGATAAGATTCAGCTAACCTGATAAAGGTAAT
*
1420131 TACATAT
1 TATATAT
1420138 TGAGCTGTCC
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
94 8 0.09
95 78 0.89
96 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGAATTTGGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTAAT
Found at i:1421528 original size:36 final size:36
Alignment explanation
Indices: 1421476--1421592 Score: 198
Period size: 36 Copynumber: 3.2 Consensus size: 36
1421466 TAATTTACTC
1421476 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
1421513 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
1421549 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
1421585 GAAACAAA
1 AAAACAAA
1421593 ATCTTTGAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 68 0.89
37 8 0.11
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:1421689 original size:101 final size:101
Alignment explanation
Indices: 1421505--1421782 Score: 421
Period size: 101 Copynumber: 2.7 Consensus size: 101
1421495 CTTGAGACAG
* * * * * * *
1421505 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTT
1 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAAAAAAAAATTTGTCTCTCTT
*
1421570 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGT
65 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
* *
1421607 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGGCAATTTCTTTTAAAAAAAAATTTGTCTATCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAAAAAAAAATTTGTCTCTCTTG
1421672 AGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
66 AGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
* * *
1421708 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAATAAAGTTTGTCTCTCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAAAAAAAAATTTGTCTCTCTTG
*
1421773 AGACATTTTC
66 AGACAGTTTC
1421783 TCTTAAAAAT
Statistics
Matches: 160, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 156 0.98
102 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (101 bp):
TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAAAAAAAAATTTGTCTCTCTTG
AGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
Found at i:1421695 original size:36 final size:37
Alignment explanation
Indices: 1421605--1421695 Score: 87
Period size: 36 Copynumber: 2.5 Consensus size: 37
1421595 CTTTGAATTT
* * *
1421605 GTTTTCCTTGAAAC-AAATTTCGTCTCCCTTGAGGCA
1 GTTTCCCTTGAAACAAAATTTCGTCTACCTTGAGACA
* ** * * *
1421641 ATTTCTTTTAAAAAAAAATTT-GTCTATCTTGAGACA
1 GTTTCCCTTGAAACAAAATTTCGTCTACCTTGAGACA
1421677 GTTTCCCTTGAAACAAAAT
1 GTTTCCCTTGAAACAAAAT
1421696 CTTTGAATCT
Statistics
Matches: 40, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
36 34 0.85
37 6 0.15
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (37 bp):
GTTTCCCTTGAAACAAAATTTCGTCTACCTTGAGACA
Found at i:1421774 original size:36 final size:33
Alignment explanation
Indices: 1421727--1421815 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 33
1421717 AACAAATTTC
* *
1421727 GTCTCCCTTGAGACAGTTTCTTTTAAAATAAAGTTT
1 GTCTCTCTTGAGACAGTTTCTCTT--AA-AAAGTTT
* *
1421763 GTCTCTCTTGAGACATTTTCTCTTAAAAATTTT
1 GTCTCTCTTGAGACAGTTTCTCTTAAAAAGTTT
1421796 GTCTCTCTTGAGACAGTTTC
1 GTCTCTCTTGAGACAGTTTC
1421816 CCTTGAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 25 0.52
34 2 0.04
36 21 0.44
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (33 bp):
GTCTCTCTTGAGACAGTTTCTCTTAAAAAGTTT
Found at i:1421802 original size:33 final size:35
Alignment explanation
Indices: 1421720--1421815 Score: 124
Period size: 36 Copynumber: 2.8 Consensus size: 35
1421710 TCCTTGAAAC
* * *
1421720 AAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAAT
1 AAATTTTGTCTCTCTTGAGACAGTTTCTCTT-AAAT
* *
1421756 AAAGTTTGTCTCTCTTGAGACATTTTCTCTT-AA-
1 AAATTTTGTCTCTCTTGAGACAGTTTCTCTTAAAT
1421789 AAATTTTGTCTCTCTTGAGACAGTTTC
1 AAATTTTGTCTCTCTTGAGACAGTTTC
1421816 CCTTGAAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.47
34 2 0.04
36 26 0.49
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (35 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCTCTTAAAT
Found at i:1421818 original size:134 final size:135
Alignment explanation
Indices: 1421615--1421990 Score: 540
Period size: 134 Copynumber: 2.8 Consensus size: 135
1421605 GTTTTCCTTG
* * * * * *
1421615 AAACAAA-TTTCGTCTCCCTTGAGGCAATTTCTTTTAAAAAAAAATTTGTCTATCTTGAGACAGT
1 AAACAAAGTTT-GTCTCTCTTGAGACATTTTCTCTT--AAAAAATTTTGTCTCTCTTGAGACAGT
* * *
1421679 TTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGT
63 TTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTCGTATCCATTGAGACAAT
1421744 TTCTTTTA
128 TTCTTTTA
*
1421752 AAATAAAGTTTGTCTCTCTTGAGACATTTTCTCTT-AAAAATTTTGTCTCTCTTGAGACAGTTTC
1 AAACAAAGTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAATTTTGTCTCTCTTGAGACAGTTTC
* *
1421816 CCTTGAAACAAAATCTTTGAATCTATTTTCCTTGAAATAAATTTCGTATCCATTGAGACAATTTC
66 CCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTCGTATCCATTGAGACAATTTC
1421881 TTTTA
131 TTTTA
*
1421886 AAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAATTTTTGTCTCTCTTGAGACAGTT
1 AAACAAAGTTTGTCTCTCTTGAGACATTTTCTCTTAAAA-AA-TTTTGTCTCTCTTGAGACAGTT
* * **
1421951 TCCCTTGAAACAAAATATTTGAATCAGTTCCCCTTGAAAC
64 TCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAAC
1421991 GAGTTTTGAG
Statistics
Matches: 215, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
134 125 0.58
135 3 0.01
136 2 0.01
137 82 0.38
138 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (135 bp):
AAACAAAGTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAATTTTGTCTCTCTTGAGACAGTTTC
CCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTCGTATCCATTGAGACAATTTC
TTTTA
Found at i:1421908 original size:36 final size:36
Alignment explanation
Indices: 1421868--1421964 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
1421858 TTCGTATCCA
*
1421868 TTGAGACAATTTCTTTTAAAACAAATTTTGTCTCTC
1 TTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTC
* *
1421904 TTGAGACATTTTCTCTTAAAACAATTTTTGTCTCTC
1 TTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTC
* * *
1421940 TTGAGACAGTTTCCCTTGAAACAAA
1 TTGAGACAATTTCTCTTAAAACAAA
1421965 ATATTTGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (36 bp):
TTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTC
Found at i:1422006 original size:27 final size:29
Alignment explanation
Indices: 1421940--1422018 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 29
1421930 TTTGTCTCTC
1421940 TTGAGACAGTTTCCCTTGAAACAAAATAT
1 TTGAGACAGTTTCCCTTGAAACAAAATAT
* * *
1421969 TTGA-ATCAGTTCCCCTTGAAAC-GAGT-T
1 TTGAGA-CAGTTTCCCTTGAAACAAAATAT
*
1421996 TTGAGACAGTTTCCCATGAAACA
1 TTGAGACAGTTTCCCTTGAAACA
1422019 TCGTAACTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 19 0.45
28 4 0.10
29 19 0.45
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (29 bp):
TTGAGACAGTTTCCCTTGAAACAAAATAT
Found at i:1423612 original size:15 final size:14
Alignment explanation
Indices: 1423592--1423687 Score: 61
Period size: 15 Copynumber: 6.6 Consensus size: 14
1423582 TTCACATATA
1423592 TATTTTTATATTTAT
1 TATTTTTAT-TTTAT
*
1423607 TATTTTTTTCTTTATT
1 TATTTTTAT-TTTA-T
1423623 TATTTTTATTTTAT
1 TATTTTTATTTTAT
* *
1423637 TA--TCTATTTTTT
1 TATTTTTATTTTAT
* **
1423649 TCTTTTGCTTTTATT
1 TATTTTTATTTTA-T
*
1423664 TATTTATTATGTATAT
1 TATTT-TTAT-TTTAT
1423680 TATTTTTA
1 TATTTTTA
1423688 CCATTATTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
12 9 0.15
14 8 0.13
15 24 0.39
16 17 0.28
17 3 0.05
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (14 bp):
TATTTTTATTTTAT
Found at i:1423624 original size:19 final size:18
Alignment explanation
Indices: 1423603--1423653 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 18
1423593 ATTTTTATAT
1423603 TTATTATTTTTTTCTTTA
1 TTATTATTTTTTTCTTTA
*
1423621 -T-TTATTTTTAT-TTTA
1 TTATTATTTTTTTCTTTA
1423636 TTATCTATTTTTTTCTTT
1 TTAT-TATTTTTTTCTTT
1423654 TGCTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 2 0.07
18 8 0.30
19 3 0.11
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATTATTTTTTTCTTTA
Found at i:1423807 original size:14 final size:14
Alignment explanation
Indices: 1423788--1423835 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
1423778 TGCACTTACC
1423788 TTTTTATCTTTTTA
1 TTTTTATCTTTTTA
1423802 TTTTTAT-TTTTT-
1 TTTTTATCTTTTTA
1423814 TTCTTTATCTTCTTTTA
1 TT-TTTATC-T-TTTTA
1423831 TTTTT
1 TTTTT
1423836 TTATTTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.07
13 10 0.34
14 7 0.24
15 1 0.03
16 7 0.24
17 2 0.07
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATCTTTTTA
Found at i:1423829 original size:23 final size:23
Alignment explanation
Indices: 1423803--1423867 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 23
1423793 ATCTTTTTAT
1423803 TTTTATTTTTTT-TCTTTATCTTC
1 TTTTATTTTTTTAT-TTTATCTTC
1423826 TTTTATTTTTTTATTTTATCTTC
1 TTTTATTTTTTTATTTTATCTTC
*
1423849 -TTTATTCTATTTATTTTAT
1 TTTTATT-TTTTTATTTTAT
1423868 TATTGGTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 6 0.15
23 32 0.82
24 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTATTTTTTTATTTTATCTTC
Found at i:1423837 original size:31 final size:30
Alignment explanation
Indices: 1423790--1423871 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
1423780 CACTTACCTT
* *
1423790 TTTA-TCTTTT-TATTTTTATTTT-TTTTC
1 TTTATTCTTTTATTTTTTTATTTTATCTTC
1423817 TTTATCTTCTTTTATTTTTTTATTTTATCTTC
1 TTTA--TTCTTTTATTTTTTTATTTTATCTTC
*
1423849 TTTATTCTATTTATTTTATTATT
1 TTTATTCT-TTTATTTTTTTATT
1423872 GGTTTTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.09
30 10 0.22
31 24 0.52
32 8 0.17
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTATTCTTTTATTTTTTTATTTTATCTTC
Found at i:1424682 original size:24 final size:24
Alignment explanation
Indices: 1424650--1424695 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1424640 TCGTATAAAT
*
1424650 TGCACCGAAGTGTCACATAGAATA
1 TGCACCGAAGTGCCACATAGAATA
*
1424674 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACATAGAA
1424696 ATGTCCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (24 bp):
TGCACCGAAGTGCCACATAGAATA
Found at i:1424722 original size:23 final size:23
Alignment explanation
Indices: 1424691--1424778 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
1424681 AAGTGCCACG
1424691 TAGAAATGTCCCGAAGGACCGCA
1 TAGAAATGTCCCGAAGGACCGCA
* * * *
1424714 TATATATGTCACGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCGCA
* * *
1424737 TAGAAATGTCCCGAAAGACCACG
1 TAGAAATGTCCCGAAGGACCGCA
* *
1424760 TAGAATTGTCTCGAAGGAC
1 TAGAAATGTCCCGAAGGAC
1424779 TCGAGTCTTG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCGCA
Found at i:1424775 original size:46 final size:46
Alignment explanation
Indices: 1424663--1424778 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 46
1424653 ACCGAAGTGT
* *
1424663 CACATAGAATATG-CACCGAAGTG-CCACGTAGAAATGTCCCGAAGGAC
1 CACATA-AATATGTCA-CGAAG-GACCGCGTAGAAATGTCCCGAAAGAC
* *
1424710 CGCATATATATGTCACGAAGGACCGCGTAGAAATGTCCCGAAAGAC
1 CACATAAATATGTCACGAAGGACCGCGTAGAAATGTCCCGAAAGAC
* *
1424756 CACGTAGAAT-TGTCTCGAAGGAC
1 CACATA-AATATGTCACGAAGGAC
1424779 TCGAGTCTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
45 1 0.02
46 48 0.83
47 9 0.16
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (46 bp):
CACATAAATATGTCACGAAGGACCGCGTAGAAATGTCCCGAAAGAC
Found at i:1424932 original size:45 final size:45
Alignment explanation
Indices: 1424883--1424970 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
1424873 ACATATAATT
* *
1424883 ACATAGCTCATTGTCACATAACTTATATCACATTTTCATGTAAAC
1 ACATAGCTCAATGCCACATAACTTATATCACATTTTCATGTAAAC
* * * *
1424928 ACATAGGTCAATGCCACATAGCTTATATCGCCTTTTCATGTAA
1 ACATAGCTCAATGCCACATAACTTATATCACATTTTCATGTAA
1424971 TGACCTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (45 bp):
ACATAGCTCAATGCCACATAACTTATATCACATTTTCATGTAAAC
Found at i:1424984 original size:45 final size:45
Alignment explanation
Indices: 1424897--1424984 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 45
1424887 AGCTCATTGT
**
1424897 CACATAACTTATATCACATTTTCATGTAAACACATAGGTCAATGC
1 CACATAACTTATATCACATTTTCATGTAAACACATAAATCAATGC
* * * ** *
1424942 CACATAGCTTATATCGCCTTTTCATGTAATGACCTAAATCAAT
1 CACATAACTTATATCACATTTTCATGTAAACACATAAATCAAT
1424985 ATCATATAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (45 bp):
CACATAACTTATATCACATTTTCATGTAAACACATAAATCAATGC
Found at i:1431978 original size:200 final size:203
Alignment explanation
Indices: 1431635--1432034 Score: 743
Period size: 200 Copynumber: 2.0 Consensus size: 203
1431625 AGATTGCGTA
*
1431635 GCTTATCCTACAATAACAGAAAGACAAGAGTCATTTATTCATACTGCAACTACCACTTTTTTCCT
1 GCTTATCCTACAATAACAGAAAGACAAGAGTCATTTATTCATACTGCAACTACCACTTTTTTCAT
1431700 TGTGCCTAGTATGGCAGCAACTCACAGTGTTCCAAAACACTCTAATGCTTTGTCGTATCCAGACA
66 TGTGCCTAGTATGGCAGCAACTCACAGTGTTCCAAAACACTCTAATGCTTTGTCGTATCCAGACA
1431765 CGGGTGCCACTCAT-C-A-CGAATGATCTTGCACCATTCAATTCAGGTATGGCATATAAAGGTAA
131 CGGGTGCCACTCATACGATCGAATGATCTTGCACCATTCAATTCAGGTATGGCATATAAAGGTAA
1431827 CAAACATC
196 CAAACATC
*
1431835 GCTTATCCTACAATAACAGAAAGACAAGAGTCATTTATTCATACTGCACCTACCACTTTTTTCAT
1 GCTTATCCTACAATAACAGAAAGACAAGAGTCATTTATTCATACTGCAACTACCACTTTTTTCAT
1431900 TGTGCCTAGTATGGCAGCAACTCACAGTGTTCCAAAACACTCTAATGCTTTGTCGTATCCAGACA
66 TGTGCCTAGTATGGCAGCAACTCACAGTGTTCCAAAACACTCTAATGCTTTGTCGTATCCAGACA
1431965 CGGGTGCCACTCATCACGTATCGAATGATCTTGCACCATTCAATTCAGGTATGGCATATAAAGGT
131 CGGGTGCCACTCAT-ACG-ATCGAATGATCTTGCACCATTCAATTCAGGTATGGCATATAAAGGT
1432030 AACAA
194 AACAA
1432035 CACTCTTGTA
Statistics
Matches: 193, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
200 142 0.74
202 1 0.01
204 1 0.01
205 49 0.25
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (203 bp):
GCTTATCCTACAATAACAGAAAGACAAGAGTCATTTATTCATACTGCAACTACCACTTTTTTCAT
TGTGCCTAGTATGGCAGCAACTCACAGTGTTCCAAAACACTCTAATGCTTTGTCGTATCCAGACA
CGGGTGCCACTCATACGATCGAATGATCTTGCACCATTCAATTCAGGTATGGCATATAAAGGTAA
CAAACATC
Found at i:1433667 original size:39 final size:39
Alignment explanation
Indices: 1433600--1433725 Score: 146
Period size: 39 Copynumber: 3.2 Consensus size: 39
1433590 GGGAGTAATG
* ** * *
1433600 GTCATGGTGCACATTCGTATGGGGTCCAAGAAGAAAATT
1 GTCATGGTGCACACTCACATGAGATCCAAGAAGAAAATT
* *
1433639 GTCATGGTGCACACTCACGTGAGATCCAAGAAGGAAATT
1 GTCATGGTGCACACTCACATGAGATCCAAGAAGAAAATT
* * *
1433678 GGCATGGTGCACACTCACATGGGGTCCAAGAA-AGAAATT
1 GTCATGGTGCACACTCACATGAGATCCAAGAAGA-AAATT
1433717 GTCATGGTG
1 GTCATGGTG
1433726 TGGCAAATAC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (39 bp):
GTCATGGTGCACACTCACATGAGATCCAAGAAGAAAATT
Found at i:1433902 original size:63 final size:66
Alignment explanation
Indices: 1433819--1433970 Score: 167
Period size: 63 Copynumber: 2.4 Consensus size: 66
1433809 ACTATGAATA
*
1433819 ATAGTAATAATAATAGCAATTATGATGG-AA-A-C-TCATATGGGATCCAAGAA-AAAAGTCACG
1 ATAGCAATAATAATAGCAATTATGATGGTAATAGCAT-ATATGGGATCCAAGAAGAAAA-TCACG
1433879 ATG
64 ATG
* * * * *
1433882 ATGGCAATAATAATAGCAA-T-TG-TGGTAATAGCATGTGTGGGGTCCAAGAAGAAAATCACGTT
1 ATAGCAATAATAATAGCAATTATGATGGTAATAGCATATATGGGATCCAAGAAGAAAATCACGAT
1433944 G
66 G
*
1433945 GTAGCAATAATAATAGCAATTATGAT
1 ATAGCAATAATAATAGCAATTATGAT
1433971 AGCTCGCGTG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
60 3 0.04
61 4 0.05
62 2 0.03
63 55 0.75
64 6 0.08
65 2 0.03
66 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (66 bp):
ATAGCAATAATAATAGCAATTATGATGGTAATAGCATATATGGGATCCAAGAAGAAAATCACGAT
G
Found at i:1433984 original size:60 final size:60
Alignment explanation
Indices: 1433819--1433989 Score: 166
Period size: 63 Copynumber: 2.8 Consensus size: 60
1433809 ACTATGAATA
* * * * *
1433819 ATAGTAATAATAATAGCAATTATGATGGAAACTCATATGGGATCCAAGAAAAAAGTCACGATG
1 ATAGCAATAATAATAGCAATTATGAT---AGCTCGTGTGGGGTCCAAGAAAAAAGTCACGATG
* * *
1433882 ATGGCAATAATAATAGCAATTGTGGTAATAGCAT-GTGTGGGGTCCAAGAAGAAAA-TCACGTTG
1 ATAGCAATAATAATAGCAATTAT-G--ATAGC-TCGTGTGGGGTCCAAGAA-AAAAGTCACGATG
* *
1433945 GTAGCAATAATAATAGCAATTATGATAGCTCGCGTGGGGTCCAAG
1 ATAGCAATAATAATAGCAATTATGATAGCTCGTGTGGGGTCCAAG
1433990 GAGAGAATAG
Statistics
Matches: 90, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
59 1 0.01
60 18 0.20
62 1 0.01
63 62 0.69
64 6 0.07
66 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (60 bp):
ATAGCAATAATAATAGCAATTATGATAGCTCGTGTGGGGTCCAAGAAAAAAGTCACGATG
Found at i:1436851 original size:24 final size:21
Alignment explanation
Indices: 1436816--1436858 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
1436806 GGCATATTCT
*
1436816 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
1436839 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
1436859 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:1438147 original size:24 final size:24
Alignment explanation
Indices: 1438120--1438174 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1438110 TCAACTTTTC
1438120 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
1438143 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
1438167 CTTCTTTT
1 TTTCTTTT
1438175 CTGATTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:1443595 original size:35 final size:35
Alignment explanation
Indices: 1443516--1443595 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
1443506 ACCGAATTAA
* *
1443516 ACGGGGACAGGGGAAAATCGTTTATACTAAACGGGG
1 ACGGGGAC-GGGGAAAACCATTTATACTAAACGGGG
* ** *
1443552 ACGAGGACGGGGAAAACCATTTATGTTCAACGGGG
1 ACGGGGACGGGGAAAACCATTTATACTAAACGGGG
*
1443587 ATGGGGACG
1 ACGGGGACG
1443596 AGTTTAGTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
35 29 0.81
36 7 0.19
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.16
Consensus pattern (35 bp):
ACGGGGACGGGGAAAACCATTTATACTAAACGGGG
Found at i:1443647 original size:12 final size:12
Alignment explanation
Indices: 1443621--1443664 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1443611 GCCCCAATTA
*
1443621 CCCGATTACCTGG
1 CCCGA-TACCCGG
1443634 CCCGATACCCGG
1 CCCGATACCCGG
*
1443646 CCCGATACCCGA
1 CCCGATACCCGG
1443658 CCCGATA
1 CCCGATA
1443665 AATATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 24 0.83
13 5 0.17
ACGTcount: A:0.20, C:0.45, G:0.20, T:0.14
Consensus pattern (12 bp):
CCCGATACCCGG
Found at i:1443756 original size:15 final size:15
Alignment explanation
Indices: 1443682--1443775 Score: 55
Period size: 13 Copynumber: 6.9 Consensus size: 15
1443672 AAAATAATTA
1443682 TTAT-TATATAT-AT
1 TTATATATATATAAT
*
1443695 ATATATATATATAAT
1 TTATATATATATAAT
* *
1443710 ATTA-ATAAATTTAAT
1 -TTATATATATATAAT
*
1443725 TTA-A-AT-TAAAAT
1 TTATATATATATAAT
*
1443737 ATATATATA-AT-AT
1 TTATATATATATAAT
1443750 TTATATAT-T-TAAT
1 TTATATATATATAAT
*
1443763 TTAAATATATATA
1 TTATATATATATA
1443776 CCCGGCCCGA
Statistics
Matches: 60, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
12 7 0.12
13 23 0.38
14 15 0.25
15 13 0.22
16 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATATATATAAT
Found at i:1443790 original size:12 final size:12
Alignment explanation
Indices: 1443773--1443803 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1443763 TTAAATATAT
*
1443773 ATACCCGGCCCG
1 ATACCCGACCCG
1443785 ATACCCGACCCG
1 ATACCCGACCCG
1443797 ATACCCG
1 ATACCCG
1443804 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (12 bp):
ATACCCGACCCG
Found at i:1444337 original size:53 final size:53
Alignment explanation
Indices: 1444273--1444486 Score: 338
Period size: 53 Copynumber: 4.0 Consensus size: 53
1444263 CCTAAGTGTC
* *
1444273 GAAATGGTAATTCACAAACTCATTTTGAATTCCATGGTTGCACACATAGTGCC
1 GAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGCT
* * *
1444326 AAAATGATAATTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGTT
1 GAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGCT
1444379 GAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGCT
1 GAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGCT
* * * * *
1444432 GAAATGGTAATTTACAAACTCATTATGAATTTCAGGGTTGTACACATAGTACT
1 GAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGCT
1444485 GA
1 GA
1444487 TAGTACTGAT
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 148 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (53 bp):
GAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGCT
Found at i:1445208 original size:22 final size:22
Alignment explanation
Indices: 1445157--1445208 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1445147 CCTACACTTA
*
1445157 GTATCGAGACTTCTTTAAATCG
1 GTATCGATACTTCTTTAAATCG
1445179 GTATCGATACTTCTTTAAATCG
1 GTATCGATACTTCTTTAAATCG
1445201 GTATCGAT
1 GTATCGAT
1445209 TATGTTCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (22 bp):
GTATCGATACTTCTTTAAATCG
Found at i:1447371 original size:20 final size:20
Alignment explanation
Indices: 1447335--1447372 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1447325 ATCCTATTCC
**
1447335 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1447355 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1447373 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1455371 original size:20 final size:20
Alignment explanation
Indices: 1455346--1455388 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1455336 CTAACCCTTG
1455346 TTCTGAAATTCTCAATCTCC
1 TTCTGAAATTCTCAATCTCC
1455366 TTCTGAAATTCTCAATCTCC
1 TTCTGAAATTCTCAATCTCC
1455386 TTC
1 TTC
1455389 CCTCTCGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.30, G:0.05, T:0.42
Consensus pattern (20 bp):
TTCTGAAATTCTCAATCTCC
Found at i:1460792 original size:131 final size:130
Alignment explanation
Indices: 1460565--1460854 Score: 375
Period size: 131 Copynumber: 2.2 Consensus size: 130
1460555 ATTCCCATGT
* * *
1460565 GATGAGGACGGTAGACCATCTTTAAGGATGATAATACAATTCTTACGTGATGAGGACGACTGGTT
1 GATGAGGACGGTAGACCATCTTTAGGGATGATAACACAATTCCTACGTGATGAGGACGACTGGTT
* * * *
1460630 ATCTATGGGTGACACAGCTCATACGTTATGAGAAGGAT-TGGTCGGGGGATGACACGGTTCCTAC
66 ATCTATGGGTGACACAGCTCATACATGATGAGAAGG-TCTGGTC-AGGGATGACACAGTTCCTAC
1460694 GC
129 GC
* * * * **
1460696 GATGAGGATGGCATACCATCTTTAGGGATGATAACACAGTTCCTACGTGATGAGGACGGTTGGTT
1 GATGAGGACGGTAGACCATCTTTAGGGATGATAACACAATTCCTACGTGATGAGGACGACTGGTT
* * * * *
1460761 ATCTATGGGTGACACATCTCCTACATGATGAGGAGGTCTGGTCAGGGATGATACAGTTCCTACGT
66 ATCTATGGGTGACACAGCTCATACATGATGAGAAGGTCTGGTCAGGGATGACACAGTTCCTACGC
* *
1460826 GATGATGACGGTAGGCCATCTTTAGGGAT
1 GATGAGGACGGTAGACCATCTTTAGGGAT
1460855 AATGGTTTCA
Statistics
Matches: 135, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
130 43 0.32
131 92 0.68
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (130 bp):
GATGAGGACGGTAGACCATCTTTAGGGATGATAACACAATTCCTACGTGATGAGGACGACTGGTT
ATCTATGGGTGACACAGCTCATACATGATGAGAAGGTCTGGTCAGGGATGACACAGTTCCTACGC
Found at i:1460829 original size:39 final size:41
Alignment explanation
Indices: 1460729--1460837 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 41
1460719 AGGGATGATA
1460729 ACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTATGGGTG
1 ACACAGTTCCTACGTGATGAGGACGGTTGG-T-TCTATGGGTG
*
1460772 ACACA-TCTCCTACATGATGAGGA-GGTCTGG-TC-A-GGGATG
1 ACACAGT-TCCTACGTGATGAGGACGGT-TGGTTCTATGGG-TG
* *
1460811 ATACAGTTCCTACGTGATGATGACGGT
1 ACACAGTTCCTACGTGATGAGGACGGT
1460838 AGGCCATCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
38 3 0.05
39 21 0.37
40 6 0.11
42 4 0.07
43 23 0.40
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (41 bp):
ACACAGTTCCTACGTGATGAGGACGGTTGGTTCTATGGGTG
Found at i:1461034 original size:98 final size:97
Alignment explanation
Indices: 1460889--1461065 Score: 250
Period size: 98 Copynumber: 1.8 Consensus size: 97
1460879 AAAGATGATG
* * ** *
1460889 TTTCAAAAGAAACTGTCTCAAAGAGACAAAATTCGTTTCAAGGGAAAC-GATCTCAAAGA-TGTT
1 TTTCAAAAGAAACTGTCTCAAAGAGACAAAACTAGTTTCAAAAGAAACAAAT-TCAAAGACT-TT
1460952 TGTTTCAAGAGAAATAGACTCAAAGACTTTTTTT
64 TGTTTCAAGAGAAATAGACTCAAAGACTTTTTTT
*
1460986 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTAGTTTCAAAAGAAACAAATTCCAAGACTTTT
1 TTTCAAAAGAAACTGTCTCAA-AGAGACAAAACTAGTTTCAAAAGAAACAAATTCAAAGACTTTT
*
1461051 GTTTCAAGTGAAATA
65 GTTTCAAGAGAAATA
1461066 ATTTCCAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
97 21 0.30
98 46 0.66
99 3 0.04
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (97 bp):
TTTCAAAAGAAACTGTCTCAAAGAGACAAAACTAGTTTCAAAAGAAACAAATTCAAAGACTTTTG
TTTCAAGAGAAATAGACTCAAAGACTTTTTTT
Found at i:1461036 original size:21 final size:20
Alignment explanation
Indices: 1460995--1461037 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1460985 TTTTCAAAAG
* *
1460995 AAACTGTCTCAAGAGAGACA
1 AAACTGTCTCAAAAGAAACA
*
1461015 AAACTAGTTTCAAAAGAAACA
1 AAACT-GTCTCAAAAGAAACA
1461036 AA
1 AA
1461038 TTCCAAGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.16
Consensus pattern (20 bp):
AAACTGTCTCAAAAGAAACA
Found at i:1461140 original size:37 final size:38
Alignment explanation
Indices: 1461080--1461167 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 38
1461070 CCAAATTTTG
* *
1461080 TGTTTTAAG-GAAAACTGTCTTAAGTGAGATGAA-A-TT
1 TGTTTTGAGAGAAAAATGTCTTAAGTGAGAT-AACATTT
*
1461116 TGTTTTGAGAGAAAAATGTGTTAAGTGAGATAACATTT
1 TGTTTTGAGAGAAAAATGTCTTAAGTGAGATAACATTT
*
1461154 TGTTTCGAGAGAAA
1 TGTTTTGAGAGAAA
1461168 CAACATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 10 0.22
37 20 0.44
38 15 0.33
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (38 bp):
TGTTTTGAGAGAAAAATGTCTTAAGTGAGATAACATTT
Found at i:1461296 original size:32 final size:32
Alignment explanation
Indices: 1461248--1461343 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
1461238 TTCACATCAA
* * *
1461248 GATGTTTAATCCCCAAAGATGCACCAACATTC
1 GATGTTGAATCTCCAAAGATGCACCATCATTC
* *
1461280 GATGTTGAATCTCCAAAGAGGCTCCATCATTC
1 GATGTTGAATCTCCAAAGATGCACCATCATTC
*
1461312 GATGTTGAATCTCCAAAGATGCCCCATCATTC
1 GATGTTGAATCTCCAAAGATGCACCATCATTC
1461344 ATCGTTTCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCACCATCATTC
Found at i:1462424 original size:25 final size:24
Alignment explanation
Indices: 1462390--1462472 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 24
1462380 GTACTTCTCA
1462390 TCTTT-TTTTTTCTTTTGCTCTTTT
1 TCTTTATTTTTTC-TTTGCTCTTTT
*
1462414 TCTTTGATTTTTTCTTTACT-TTTT
1 TCTTT-ATTTTTTCTTTGCTCTTTT
1462438 TCTTTA-TTTTT-TTT-CTCTTCTT
1 TCTTTATTTTTTCTTTGCTCTT-TT
1462460 TCTTT-TTTTTTCT
1 TCTTTATTTTTTCT
1462473 CTTTGTTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
20 2 0.04
21 5 0.10
22 17 0.33
23 2 0.04
24 14 0.27
25 5 0.10
26 7 0.13
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (24 bp):
TCTTTATTTTTTCTTTGCTCTTTT
Found at i:1462427 original size:12 final size:11
Alignment explanation
Indices: 1462410--1462483 Score: 69
Period size: 12 Copynumber: 6.5 Consensus size: 11
1462400 TCTTTTGCTC
1462410 TTTTTCTTTGAT
1 TTTTTCTTT-AT
1462422 TTTTTCTTTACT
1 TTTTTCTTTA-T
1462434 TTTTTCTTTAT
1 TTTTTCTTTAT
*
1462445 TTTTT-TTCTCT
1 TTTTTCTT-TAT
* *
1462456 TCTTTCTTTTT
1 TTTTTCTTTAT
*
1462467 TTTTCTCTTTGT
1 TTTT-TCTTTAT
1462479 TTTTT
1 TTTTT
1462484 ATTTTCTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
10 2 0.04
11 19 0.36
12 32 0.60
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTCTTTAT
Found at i:1462453 original size:13 final size:12
Alignment explanation
Indices: 1462395--1462449 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
1462385 TCTCATCTTT
*
1462395 TTTTTTCTTTTGC
1 TTTTTTC-TTTAC
1462408 TCTTTTTCTTTGA-
1 T-TTTTTCTTT-AC
1462421 TTTTTTCTTTAC
1 TTTTTTCTTTAC
1462433 TTTTTTCTTTA-
1 TTTTTTCTTTAC
1462444 TTTTTT
1 TTTTTT
1462450 TTCTCTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 7 0.18
12 20 0.53
13 5 0.13
14 6 0.16
ACGTcount: A:0.05, C:0.13, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTTCTTTAC
Found at i:1462460 original size:18 final size:17
Alignment explanation
Indices: 1462433--1462483 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
1462423 TTTTCTTTAC
1462433 TTTT-TTCTTTATTTTT
1 TTTTCTTCTTTATTTTT
*
1462449 TTTCTCTTCTTTCTTTTT
1 TTT-TCTTCTTTATTTTT
*
1462467 TTTTC-TCTTTGTTTTT
1 TTTTCTTCTTTATTTTT
1462483 T
1 T
1462484 ATTTTCTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 14 0.45
17 3 0.10
18 14 0.45
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTCTTCTTTATTTTT
Found at i:1462491 original size:18 final size:18
Alignment explanation
Indices: 1462437--1462483 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1462427 CTTTACTTTT
*
1462437 TTCTTTATTTTTTTTCTC
1 TTCTTTCTTTTTTTTCTC
1462455 TTCTTTCTTTTTTTT-TC
1 TTCTTTCTTTTTTTTCTC
*
1462472 -TCTTTGTTTTTT
1 TTCTTTCTTTTTT
1462484 ATTTTCTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 14 0.52
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (18 bp):
TTCTTTCTTTTTTTTCTC
Found at i:1469603 original size:23 final size:23
Alignment explanation
Indices: 1469572--1469647 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
1469562 TACACTAAAT
*
1469572 AATGTATCGATGCACATTCAAGG
1 AATGCATCGATGCACATTCAAGG
* *
1469595 AATGCATCGGTGCACCTTCATA-G
1 AATGCATCGATGCACATTCA-AGG
* *
1469618 --TGTATCGATGCATATTCAAGG
1 AATGCATCGATGCACATTCAAGG
*
1469639 GATGCATCG
1 AATGCATCG
1469648 GTACAGTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.02
21 15 0.37
23 24 0.59
24 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (23 bp):
AATGCATCGATGCACATTCAAGG
Found at i:1469637 original size:44 final size:44
Alignment explanation
Indices: 1469574--1469675 Score: 159
Period size: 44 Copynumber: 2.3 Consensus size: 44
1469564 CACTAAATAA
*
1469574 TGTATCGATGCACATTCAAGGAATGCATCGGTGCACCTTCATAG
1 TGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCATAG
* * **
1469618 TGTATCGATGCATATTCAAGGGATGCATCGGTACAGTTTCATAG
1 TGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCATAG
1469662 TGTATCGATGCACA
1 TGTATCGATGCACA
1469676 GAGCACAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (44 bp):
TGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCATAG
Found at i:1473767 original size:117 final size:117
Alignment explanation
Indices: 1473546--1473767 Score: 268
Period size: 117 Copynumber: 1.9 Consensus size: 117
1473536 CTTTCAAATC
* * *
1473546 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAATCTCTAAATCCTTCTTCAAGATTG
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTG
* **
1473611 CATTTTGATTTTCAAAATCCATTTTTGTTTCTAGGAGAAGTTTGCTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTTCTTTCTAAAAGAAGTTTGCTTAATTT
* * * * * *
1473663 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCTTTTTTCAACATT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATT
* * * *
1473727 TCATTTTGATTTTCCAAGTCTATTTTATCTTTC-AAAAGAAG
65 GCATTTTGATTTTCAAAATCCATTTT-TCTTTCTAAAAGAAG
1473768 ATCATTTTTA
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
116 1 0.01
117 81 0.93
118 5 0.06
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTG
CATTTTGATTTTCAAAATCCATTTTTCTTTCTAAAAGAAGTTTGCTTAATTT
Found at i:1475650 original size:33 final size:32
Alignment explanation
Indices: 1475613--1475692 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 32
1475603 TTAGTTTGTG
1475613 CAATAAAATAAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAA-GTTAGTAAGTTAGTAAGAA
* * *
1475646 CAAT-AAA-AAAA-TCAGTACGTTAGTATGAA
1 CAATAAAATAAAAGTTAGTAAGTTAGTAAGAA
1475675 CAATAAAATAAAAGTTAG
1 CAATAAAATAAAAGTTAG
1475693 AATGTTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 19 0.47
30 3 0.08
31 8 0.20
32 6 0.15
33 4 0.10
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.25
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTAAGTTAGTAAGAA
Found at i:1475830 original size:15 final size:14
Alignment explanation
Indices: 1475806--1475841 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1475796 TAATGTAAAC
*
1475806 AAATATATAAAATTA
1 AAATAAATAAAA-TA
1475821 AAATAAATAAAATA
1 AAATAAATAAAATA
1475835 AAATAAA
1 AAATAAA
1475842 AAAGTTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:1475866 original size:125 final size:125
Alignment explanation
Indices: 1475720--1475962 Score: 371
Period size: 125 Copynumber: 1.9 Consensus size: 125
1475710 AAAGTTAACG
* * *
1475720 GTTAATGGTTAGTAGAGTCCGAACCATAATAATGTGGGCCTTACCCCGGAAT-AGGTCACCACAA
1 GTTAACGGTTAGCAGAGTCCGAACCATAATAATGTAGGCCTTACCCCGG-ATCAGGTCACCACAA
* *
1475784 GATCGAATAGAATAATGTAAACAAATATATAAAATTAAAATAAATAAAATAAAATAAAAAA
65 GATCGAATAGAATAATGTAAACAAATATATAAAAATAAAATAAAAAAAATAAAATAAAAAA
* * * *
1475845 GTTAACGGTTAGCAGAGTCCGAACCATAATAATGTAGGTCTTACTCTGGATCGGGTCACCACAAG
1 GTTAACGGTTAGCAGAGTCCGAACCATAATAATGTAGGCCTTACCCCGGATCAGGTCACCACAAG
* *
1475910 GTCGAATCGAATAATGTAAACAAATATATAAAAATAAAATAAAAAAAATAAAA
66 ATCGAATAGAATAATGTAAACAAATATATAAAAATAAAATAAAAAAAATAAAA
1475963 AGGTTAGTAA
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 2 0.02
125 104 0.98
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (125 bp):
GTTAACGGTTAGCAGAGTCCGAACCATAATAATGTAGGCCTTACCCCGGATCAGGTCACCACAAG
ATCGAATAGAATAATGTAAACAAATATATAAAAATAAAATAAAAAAAATAAAATAAAAAA
Found at i:1476952 original size:56 final size:56
Alignment explanation
Indices: 1476794--1476943 Score: 223
Period size: 56 Copynumber: 2.7 Consensus size: 56
1476784 AAATAGTAAT
* *
1476794 ATTACAAGTT-AGTCCTTACA-TTTGTTCCCTCTTTAATTTTTGGACAATGATACA
1 ATTACAAGTTCGGTCCTTACACTTTATTCCCTCTTTAATTTTTGGACAATGATACA
* *
1476848 ATTGCAAGTTCGGTCCTTACACTTTATTCCCTCTTTAATTTTTGGACAATGGTACA
1 ATTACAAGTTCGGTCCTTACACTTTATTCCCTCTTTAATTTTTGGACAATGATACA
* * *
1476904 ATTATAAGTTTGGTCCTTACACTTTATTCCTTCTTTAATT
1 ATTACAAGTTCGGTCCTTACACTTTATTCCCTCTTTAATT
1476944 CCCGGACAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 9 0.10
55 9 0.10
56 68 0.79
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (56 bp):
ATTACAAGTTCGGTCCTTACACTTTATTCCCTCTTTAATTTTTGGACAATGATACA
Found at i:1480972 original size:80 final size:80
Alignment explanation
Indices: 1480732--1480974 Score: 253
Period size: 80 Copynumber: 3.0 Consensus size: 80
1480722 TCCCTCTATG
* * *
1480732 TAGTCATGAAAACTTTGAGAATTGAGCATGTTTGCACACCAAATCAAGCAAGATATTCAAAGTTT
1 TAGTCATGAAAACTTTGATAA-TAAGCATGTTTGCATACCAAATCAAGCAAGATATTCAAAGTTT
1480797 TAAAGTCTGAT-T-TA
65 TAAAGTCTGATATATA
* * * *
1480811 TAATCATGAAATACTTTGATAATTAAG-TTGTTTGTATAAACACAAATCAAGCAAGATATTCCAA
1 TAGTCATGAAA-ACTTTGATAA-TAAGCATGTTTGCAT--AC-CAAATCAAGCAAGATATTCAAA
*
1480875 GTATTGAAA-TCTAGATATATA
61 GT-TTTAAAGTCT-GATATATA
* * * **
1480896 TAGTCATGAAAACTTTGATAA-AAGCATGTTTGCATACCGAATCGAGCAAGATGTTTGAAGTTTT
1 TAGTCATGAAAACTTTGATAATAAGCATGTTTGCATACCAAATCAAGCAAGATATTCAAAGTTTT
1480960 AAAGTCTCGATATAT
66 AAAGTCT-GATATAT
1480975 CACTCTGGCC
Statistics
Matches: 136, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
79 22 0.16
80 42 0.31
81 4 0.03
82 29 0.21
83 16 0.12
84 11 0.08
85 12 0.09
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (80 bp):
TAGTCATGAAAACTTTGATAATAAGCATGTTTGCATACCAAATCAAGCAAGATATTCAAAGTTTT
AAAGTCTGATATATA
Found at i:1482285 original size:18 final size:18
Alignment explanation
Indices: 1482262--1482305 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
1482252 AACTCTCCTT
1482262 CACAACAAGAGCAAAATA
1 CACAACAAGAGCAAAATA
1482280 CACAACAAGAGCAAAATA
1 CACAACAAGAGCAAAATA
1482298 CACAACAA
1 CACAACAA
1482306 TTTTGATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.61, C:0.25, G:0.09, T:0.05
Consensus pattern (18 bp):
CACAACAAGAGCAAAATA
Found at i:1484956 original size:14 final size:14
Alignment explanation
Indices: 1484937--1484966 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1484927 GGATCAAATG
1484937 AATTATTATTTATT
1 AATTATTATTTATT
*
1484951 AATTATTATTTTTT
1 AATTATTATTTATT
1484965 AA
1 AA
1484967 CAACAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTATTATTTATT
Found at i:1485013 original size:329 final size:325
Alignment explanation
Indices: 1484409--1485067 Score: 1095
Period size: 329 Copynumber: 2.0 Consensus size: 325
1484399 TTAAAATATG
* * *
1484409 AATAATTTTATAAAAATTTTATAATTAATATTTCTTTTTCAAAATGATGATGATGATAATAATAA
1 AATAACTTTATAAAAATTTTATAACTAATATTTCTTTTTAAAAATGATGATGATGATAATAATAA
1484474 TAAAAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAAATTTTCTTAACTTT
66 TAAAAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAAATTTTCTTAACTTT
* *
1484539 TAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAAATTTTAATTATAATTGAGGGATCA
131 TAAAATTAATTATTTAAAAATATAAAAAATATTAAAATAAAATTTTAATTACAATTGAGGGATCA
*
1484604 AATAAATTATTATTCATTAATTATTATTTTTAAACAACAATTAATAATGTGTATTCATTTTTAAA
196 AATAAATTATTATTCATTAATTATTATTTTTAAACAACAATTAATAATGTATATTCATTTTTAAA
* * * *
1484669 ATTAAGTACTATGACCATAAATTATCAAAATTATTAATTGTTTTTAAAAATACTAATTAATGAAT
261 ATTAAATACTATGACCACAAATTATCAAAATTATTAATTGTTGTTAAAAATAATAATTAATGAAT
*
1484734 AATAACTTTATAAAAATTTTATAACTAGTATTTCTTTTTTAAAATGATGATGATGATGATAATAA
1 AATAACTTTATAAAAATTTTATAACTAATATTTC-TTTTTAAAA--ATGATGATGATGATAATAA
* *
1484799 TAATAAGAAATATTTTATAATTTAAAAATTTATAAATTTCATATATTTTTGAAAAA-TTTCTTAA
63 TAATAAAAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTT-AAAAATTTTCTTAA
*
1484863 CTTTTAAAATTAATTATTTAAAATTATAAAAAAATATTAAAATAAAATTTTAATTACAATTGAGG
127 CTTTTAAAATTAATTATTTAAAAATAT-AAAAAATATTAAAATAAAATTTTAATTACAATTGAGG
* * *
1484928 GATCAAATGAATTATTATTTATTAATTATTATTTTTTAACAACAATTAATAATGTATATTCATTT
191 GATCAAATAAATTATTATTCATTAATTATTATTTTTAAACAACAATTAATAATGTATATTCATTT
* *
1484993 TTAAAATTAAATATTATGACCACAAATTATCAAAATTATTAATTGTTGTTAGAAATAATAATTAA
256 TTAAAATTAAATACTATGACCACAAATTATCAAAATTATTAATTGTTGTTAAAAATAATAATTAA
1485058 TGAAT
321 TGAAT
1485063 AATAA
1 AATAA
1485068 TTCATTTGAT
Statistics
Matches: 310, Mismatches: 19, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
325 31 0.10
326 8 0.03
328 100 0.32
329 171 0.55
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (325 bp):
AATAACTTTATAAAAATTTTATAACTAATATTTCTTTTTAAAAATGATGATGATGATAATAATAA
TAAAAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTAAAAATTTTCTTAACTTT
TAAAATTAATTATTTAAAAATATAAAAAATATTAAAATAAAATTTTAATTACAATTGAGGGATCA
AATAAATTATTATTCATTAATTATTATTTTTAAACAACAATTAATAATGTATATTCATTTTTAAA
ATTAAATACTATGACCACAAATTATCAAAATTATTAATTGTTGTTAAAAATAATAATTAATGAAT
Found at i:1489032 original size:24 final size:23
Alignment explanation
Indices: 1488975--1489034 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
1488965 AATCAAAACG
1488975 AGGGGTATTGGTACCTTTGGAAT
1 AGGGGTATTGGTACCTTTGGAAT
* * * *
1488998 A--AGTATCGGTACCTCTTTGTAT
1 AGGGGTATTGGTACCT-TTGGAAT
1489020 AGGGGTATTGGTACC
1 AGGGGTATTGGTACC
1489035 CTGTAAGGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
21 11 0.39
22 6 0.21
23 1 0.04
24 10 0.36
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (23 bp):
AGGGGTATTGGTACCTTTGGAAT
Found at i:1490955 original size:18 final size:18
Alignment explanation
Indices: 1490928--1490962 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1490918 TTGGGTTCAT
* *
1490928 GTGGATTAGGATTTGGAG
1 GTGGAATAGGATATGGAG
1490946 GTGGAATAGGATATGGA
1 GTGGAATAGGATATGGA
1490963 TTCTATCGAC
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:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (18 bp):
GTGGAATAGGATATGGAG
Found at i:1494314 original size:22 final size:22
Alignment explanation
Indices: 1494283--1494425 Score: 170
Period size: 22 Copynumber: 6.7 Consensus size: 22
1494273 GGACCATTAC
*
1494283 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
*
1494305 GTCCCGAAGGACCACT--ACA-
1 GTCCCGAAGGACCACTGGATAT
1494324 -TCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* * *
1494345 GTCCCGAAGGACCATTAGATAC
1 GTCCCGAAGGACCACTGGATAT
** *
1494367 GTTTCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAT
1494389 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
*
1494411 GT-CTGAAGGACCACT
1 GTCCCGAAGGACCACT
1494426 ATAAACCCTC
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.15
20 4 0.04
21 12 0.12
22 72 0.70
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAT
Found at i:1494333 original size:40 final size:40
Alignment explanation
Indices: 1494264--1494404 Score: 174
Period size: 40 Copynumber: 3.4 Consensus size: 40
1494254 AGTGAATATT
* * * *
1494264 TGTCCCGACGGACCATTACGTCCCTAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
1494304 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
* * *
1494344 TGTCCCGAAGGACCATTAGATACGTTTCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACAT-C---CCGAAGGACCACTGGATA
*
1494388 CGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1494405 GGATATGTCT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 55 0.62
41 1 0.01
44 32 0.36
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.18
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
Found at i:1497770 original size:21 final size:21
Alignment explanation
Indices: 1497733--1497772 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1497723 TTTGTTTTTC
*
1497733 AATTTTGAAATATATTTCTTG
1 AATTTTGAAATAAATTTCTTG
1497754 AATTTTGAAA-ACAATTTCT
1 AATTTTGAAATA-AATTTCT
1497773 CATAATCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
AATTTTGAAATAAATTTCTTG
Found at i:1499744 original size:45 final size:45
Alignment explanation
Indices: 1499676--1499777 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
1499666 CAAGACCATG
1499676 GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
1 GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
* *
1499721 GGTATCGGTACCTCTTAATGGGGTATCGATACTTATATGTAAATA
1 GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
1499766 GGTATCGGTACC
1 GGTATCGGTACC
1499778 CATTTTGTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (45 bp):
GGTATCGGTACCTCTCAAGGGGGTATCGATACTTATATGTAAATA
Found at i:1508321 original size:96 final size:98
Alignment explanation
Indices: 1508079--1508407 Score: 331
Period size: 96 Copynumber: 3.3 Consensus size: 98
1508069 TTTAAGATCG
* * * * * *
1508079 TCTCAATTGAGATTGCTTTTCTTAAAACCAATTTCGTTTCTCTTGAGACAGTTTCCCTTGAAACG
1 TCTCACTTGAGATTG-ATTTCTTAAAA--AATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACA
* * **
1508144 TAGATTTTGAAATTGTTTCACTCGAAACAAAAAACAAATTA
63 CAAATTTTGAAATTGTTTCACTCGAAAC----AA-ATTTTA
* * * * * *
1508185 TCTCACTCGAGATTGTTTTTCTTAAACCAATTTTGTCTCGCTTGAGATATTTTTCCTTGAAACAC
1 TCTCACTTGAGATTG-ATTTCTTAAA-AAATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAC
*
1508250 AAATTTTGAAATTGTTTCACTCGAAA-ATA-TTTA
64 AAATTTTGAAATTGTTTCACTCGAAACAAATTTTA
* *
1508283 TCTCACTTGAGATTGATTT-TTAAAAATATTTTGTCTCGCTTGAGACAGTTTCCCTTGGAGCACA
1 TCTCACTTGAGATTGATTTCTTAAAAA-ATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACACA
*
1508347 AATTTTGAAATTGTTTCACTTGAAACAAATTTTA
65 AATTTTGAAATTGTTTCACTCGAAACAAATTTTA
* *
1508381 TCTCACCTGAGATAGATTCTCTTAAAA
1 TCTCACTTGAGATTGATT-TCTTAAAA
1508408 TAAATTTCAA
Statistics
Matches: 190, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
95 1 0.01
96 61 0.32
97 5 0.03
98 37 0.19
99 2 0.01
100 7 0.04
105 54 0.28
106 23 0.12
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (98 bp):
TCTCACTTGAGATTGATTTCTTAAAAAATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACACAA
ATTTTGAAATTGTTTCACTCGAAACAAATTTTA
Found at i:1508781 original size:119 final size:118
Alignment explanation
Indices: 1508583--1508825 Score: 355
Period size: 119 Copynumber: 2.1 Consensus size: 118
1508573 TCCATTGCGG
* * * *
1508583 AAGGAGGTGGTTCAACTTTTCTAATGAAAGGTTTCATAATGAGAAGAACTCATCCAAAGAGGGAG
1 AAGGAGGTGGATCAACATTTCCAATGAAAGGTTTCATAATGAGAAGAACTCATCCAAAGAGGAAG
*
1508648 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA-AATCCATCACAA
66 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-CT-AGAATCCATCACAA
* *
1508702 ATGGAGGTGGATCAACATTTCCAATGGAAAGG-TTCATAATGAGAATAACTCATCCAAAGAGGAA
1 AAGGAGGTGGATCAACATTTCCAAT-GAAAGGTTTCATAATGAGAAGAACTCATCCAAAGAGGAA
* * *
1508766 GAAGAAGTTTATAATGAGAAGAACTTGTTCACCCTTTTCTAGATTCCATCACAA
65 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCTAGAATCCATCACAA
1508820 AAGGAG
1 AAGGAG
1508826 ATAGATTAAC
Statistics
Matches: 111, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
117 1 0.01
118 18 0.16
119 86 0.77
120 6 0.05
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (118 bp):
AAGGAGGTGGATCAACATTTCCAATGAAAGGTTTCATAATGAGAAGAACTCATCCAAAGAGGAAG
AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCTAGAATCCATCACAA
Done.