Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 9 of 313
Found at i:2845529 original size:221 final size:221
Alignment explanation
Indices: 2845146--2845587 Score: 884
Period size: 221 Copynumber: 2.0 Consensus size: 221
2845136 TATCCAGGGA
2845146 TTTAAATAACGGTCTGATATCGTTATAGTGGACGCTATAAAGTGGTAGCGGCACCGTCCAAAACT
1 TTTAAATAACGGTCTGATATCGTTATAGTGGACGCTATAAAGTGGTAGCGGCACCGTCCAAAACT
2845211 GCTACTACTGAAAATAACAGTGTGAAGTGAAGTGACATCGATAGCAGTGGGTCGCAACCGCAATT
66 GCTACTACTGAAAATAACAGTGTGAAGTGAAGTGACATCGATAGCAGTGGGTCGCAACCGCAATT
2845276 TAACGCTTAACGGCCAATTGCGGCAATAATGGGCCGCTATTTCTATTATTTTCCATTACAGTAAA
131 TAACGCTTAACGGCCAATTGCGGCAATAATGGGCCGCTATTTCTATTATTTTCCATTACAGTAAA
2845341 TTAAAAAAAATACATCTCCCTCCGCT
196 TTAAAAAAAATACATCTCCCTCCGCT
2845367 TTTAAATAACGGTCTGATATCGTTATAGTGGACGCTATAAAGTGGTAGCGGCACCGTCCAAAACT
1 TTTAAATAACGGTCTGATATCGTTATAGTGGACGCTATAAAGTGGTAGCGGCACCGTCCAAAACT
2845432 GCTACTACTGAAAATAACAGTGTGAAGTGAAGTGACATCGATAGCAGTGGGTCGCAACCGCAATT
66 GCTACTACTGAAAATAACAGTGTGAAGTGAAGTGACATCGATAGCAGTGGGTCGCAACCGCAATT
2845497 TAACGCTTAACGGCCAATTGCGGCAATAATGGGCCGCTATTTCTATTATTTTCCATTACAGTAAA
131 TAACGCTTAACGGCCAATTGCGGCAATAATGGGCCGCTATTTCTATTATTTTCCATTACAGTAAA
2845562 TTAAAAAAAATACATCTCCCTCCGCT
196 TTAAAAAAAATACATCTCCCTCCGCT
2845588 AAACAAAAAT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 221 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (221 bp):
TTTAAATAACGGTCTGATATCGTTATAGTGGACGCTATAAAGTGGTAGCGGCACCGTCCAAAACT
GCTACTACTGAAAATAACAGTGTGAAGTGAAGTGACATCGATAGCAGTGGGTCGCAACCGCAATT
TAACGCTTAACGGCCAATTGCGGCAATAATGGGCCGCTATTTCTATTATTTTCCATTACAGTAAA
TTAAAAAAAATACATCTCCCTCCGCT
Found at i:2846005 original size:19 final size:19
Alignment explanation
Indices: 2845959--2846005 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 19
2845949 TCCAAGAATT
*
2845959 TGATAGGGTTTTGAGAGGA
1 TGATAGAGTTTTGAGAGGA
2845978 T-AT-GAGTTTTGAGAGGA
1 TGATAGAGTTTTGAGAGGA
2845995 TGATAGAGTTT
1 TGATAGAGTTT
2846006 AGGCCTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 14 0.56
18 4 0.16
19 7 0.28
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (19 bp):
TGATAGAGTTTTGAGAGGA
Found at i:2849814 original size:19 final size:18
Alignment explanation
Indices: 2849787--2849826 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2849777 TAAACAGTTA
2849787 ATTAAATTATTTAATTTAT
1 ATTAAATTATTTAA-TTAT
*
2849806 ATTATATTATTTAATTAT
1 ATTAAATTATTTAATTAT
2849824 ATT
1 ATT
2849827 GTACATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTAAATTATTTAATTAT
Found at i:2857419 original size:26 final size:26
Alignment explanation
Indices: 2857383--2857453 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
2857373 TAAGAGAAAG
*
2857383 TTAAAATTTTAATATTTTTATTTATT
1 TTAATATTTTAATATTTTTATTTATT
* *
2857409 TTAATATTTTAATATATTTATTTCTT
1 TTAATATTTTAATATTTTTATTTATT
* *
2857435 TTTAT-TTATTATTATTTTT
1 TTAATATT-TTAATATTTTT
2857454 GAAAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 2 0.05
26 36 0.95
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (26 bp):
TTAATATTTTAATATTTTTATTTATT
Found at i:2857426 original size:18 final size:18
Alignment explanation
Indices: 2857388--2857427 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2857378 GAAAGTTAAA
* *
2857388 ATTTTAATATTTTTATTT
1 ATTTTAATATTTTAATAT
2857406 ATTTTAATATTTTAATAT
1 ATTTTAATATTTTAATAT
2857424 ATTT
1 ATTT
2857428 ATTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTAATATTTTAATAT
Found at i:2865582 original size:90 final size:90
Alignment explanation
Indices: 2865455--2865622 Score: 266
Period size: 90 Copynumber: 1.9 Consensus size: 90
2865445 TCCTTTGACA
*
2865455 TAGATAGCCGCAAAAGCATCCAAACACATATACAAGATAGCCATAGA-GTCGTCCATATAGTTAG
1 TAGATAGCCGCAAAAGCATCCAAACACATATACAAGATAGCCATAGAGGT-GTCCATATAATTAG
2865519 ATAGCCACAAAGGCACCTACTCACAT
65 ATAGCCACAAAGGCACCTACTCACAT
** * *
2865545 TAGATAGCCGCAAGGGCATCCAAACTCATATAGAAGATAGCCATAGAGGTGTCCATATAATTAGA
1 TAGATAGCCGCAAAAGCATCCAAACACATATACAAGATAGCCATAGAGGTGTCCATATAATTAGA
*
2865610 TGGCCACAAAGGC
66 TAGCCACAAAGGC
2865623 GTCCACTTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
90 69 0.97
91 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (90 bp):
TAGATAGCCGCAAAAGCATCCAAACACATATACAAGATAGCCATAGAGGTGTCCATATAATTAGA
TAGCCACAAAGGCACCTACTCACAT
Found at i:2875405 original size:21 final size:21
Alignment explanation
Indices: 2875379--2875422 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2875369 TAGACATGTT
2875379 TCTAAAACGAATTTCCATCAA
1 TCTAAAACGAATTTCCATCAA
2875400 TCTAAAACGAATTTCCATCAA
1 TCTAAAACGAATTTCCATCAA
2875421 TC
1 TC
2875423 CCATGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (21 bp):
TCTAAAACGAATTTCCATCAA
Found at i:2878519 original size:6 final size:6
Alignment explanation
Indices: 2878499--2878538 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
2878489 AATAAAAGAC
* *
2878499 AAAAT- AAAATG AAAATA AAAATG AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
2878539 GTTAATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:2878519 original size:12 final size:12
Alignment explanation
Indices: 2878499--2878538 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
2878489 AATAAAAGAC
2878499 AAAAT-AAAATG
1 AAAATAAAAATG
2878510 AAAATAAAAATG
1 AAAATAAAAATG
*
2878522 AAAATAAAAATA
1 AAAATAAAAATG
2878534 AAAAT
1 AAAAT
2878539 GTTAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:2878547 original size:18 final size:18
Alignment explanation
Indices: 2878499--2878539 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2878489 AATAAAAGAC
*
2878499 AAAAT-AAAATGAAAATA
1 AAAATGAAAATAAAAATA
2878516 AAAATGAAAATAAAAATA
1 AAAATGAAAATAAAAATA
2878534 AAAATG
1 AAAATG
2878540 TTAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (18 bp):
AAAATGAAAATAAAAATA
Found at i:2880258 original size:9 final size:9
Alignment explanation
Indices: 2880241--2880277 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2880231 TGAGTTTTCG
2880241 AATTCGAAT
1 AATTCGAAT
*
2880250 AACTCGAAT
1 AATTCGAAT
*
2880259 AATTCAAAT
1 AATTCGAAT
2880268 AATTCGAAT
1 AATTCGAAT
2880277 A
1 A
2880278 TTAAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2883704 original size:26 final size:26
Alignment explanation
Indices: 2883666--2883723 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
2883656 GAGGAGGGGT
* * *
2883666 GAAAAGGAAGAGAGGAGGAAAGGGAAA
1 GAAAAGGAAGAGAGAAAGAAA-GAAAA
*
2883693 GAAAAGG-GGAGAGAAAGAAAGAAAA
1 GAAAAGGAAGAGAGAAAGAAAGAAAA
2883718 GAAAAG
1 GAAAAG
2883724 ATAAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.37
26 10 0.37
27 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (26 bp):
GAAAAGGAAGAGAGAAAGAAAGAAAA
Found at i:2883746 original size:22 final size:21
Alignment explanation
Indices: 2883690--2883764 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 21
2883680 GAGGAAAGGG
2883690 AAAGAAAAGGGGAGAGAAAGAAAGA
1 AAAGAAAA--GGA-AGAAA-AAAGA
*
2883715 AAAGAAAA-G-A-TAAAAAGA
1 AAAGAAAAGGAAGAAAAAAGA
*
2883733 AAAGAAAAGGAAGAAAAATGGA
1 AAAGAAAAGGAAGAAAAA-AGA
*
2883755 GAAGAAAAGG
1 AAAGAAAAGG
2883765 GTGGCTGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 13 0.31
19 3 0.07
20 2 0.05
21 4 0.10
22 12 0.29
25 8 0.19
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (21 bp):
AAAGAAAAGGAAGAAAAAAGA
Found at i:2889909 original size:79 final size:81
Alignment explanation
Indices: 2889773--2889957 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 81
2889763 TTGAATGATG
*
2889773 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
2889837 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * **
2889852 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
2889914 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
* *
2889932 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2889958 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
78 2 0.02
79 57 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:2889971 original size:40 final size:39
Alignment explanation
Indices: 2889774--2889957 Score: 189
Period size: 40 Copynumber: 4.6 Consensus size: 39
2889764 TGAATGATGT
* * *
2889774 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
* *
2889814 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATA-A
2889854 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
2889892 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAA
*
2889933 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
2889958 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
39 35 0.28
40 78 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:2889979 original size:79 final size:79
Alignment explanation
Indices: 2889774--2889990 Score: 194
Period size: 79 Copynumber: 2.7 Consensus size: 79
2889764 TGAATGATGT
** * * * **
2889774 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
2889837 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
2889854 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
2889919 GCGA-ATTACT-ATAA
66 GCGAGA-TACTAAT-A
* * *
2889933 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
2889991 TACGTGATTT
Statistics
Matches: 116, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
78 4 0.03
79 70 0.60
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:2894921 original size:18 final size:20
Alignment explanation
Indices: 2894879--2894921 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2894869 TCACTTCTCC
*
2894879 CACGCCCGTGTAGTATCCCA
1 CACGCCCGTGTAGTATCCAA
*
2894899 CACGCCCGTGT-GTA-CGAA
1 CACGCCCGTGTAGTATCCAA
2894917 CACGC
1 CACGC
2894922 GGCTGTGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 3 0.14
20 11 0.52
ACGTcount: A:0.21, C:0.40, G:0.23, T:0.16
Consensus pattern (20 bp):
CACGCCCGTGTAGTATCCAA
Found at i:2896811 original size:21 final size:18
Alignment explanation
Indices: 2896767--2896810 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2896757 TTGGTAAAAT
*
2896767 GGTTGTTTAAAGCCTGGG
1 GGTTGTTGAAAGCCTGGG
2896785 GGTTGTTGAAAGCCTGGG
1 GGTTGTTGAAAGCCTGGG
*
2896803 GGATGTTG
1 GGTTGTTG
2896811 TGGCCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.09, G:0.43, T:0.32
Consensus pattern (18 bp):
GGTTGTTGAAAGCCTGGG
Found at i:2903362 original size:21 final size:20
Alignment explanation
Indices: 2903316--2903362 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
2903306 GATTATAATT
*
2903316 CAACAATTTAAATATATATAT
1 CAAC-ATTTAAATATATATAG
2903337 CAACATTTAACATATAT-TAG
1 CAACATTTAA-ATATATATAG
2903357 CTAACA
1 C-AACA
2903363 AAATTATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (20 bp):
CAACATTTAAATATATATAG
Found at i:2905166 original size:14 final size:14
Alignment explanation
Indices: 2905127--2905167 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2905117 ATCCATGAGC
2905127 ATCTATTTTCCTTTAT
1 ATCTA-TTT-CTTTAT
2905143 -TCTA-TTCTTTAT
1 ATCTATTTCTTTAT
2905155 ATCTATTTCTTTA
1 ATCTATTTCTTTA
2905168 ACATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 7 0.30
15 4 0.17
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (14 bp):
ATCTATTTCTTTAT
Found at i:2906243 original size:27 final size:27
Alignment explanation
Indices: 2906205--2906261 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2906195 GATCAGAGTG
2906205 TTACAGAACCAAATAGAACAATTTATC
1 TTACAGAACCAAATAGAACAATTTATC
*
2906232 TTACAGAACCAAATAGAGCAATTTATC
1 TTACAGAACCAAATAGAACAATTTATC
2906259 TTA
1 TTA
2906262 ATTTAGAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.28
Consensus pattern (27 bp):
TTACAGAACCAAATAGAACAATTTATC
Found at i:2906284 original size:22 final size:22
Alignment explanation
Indices: 2906259--2906304 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2906249 GCAATTTATC
2906259 TTAATTTAGAACAAATAT-TCAA
1 TTAATTTAGAA-AAATATATCAA
*
2906281 TTAATTTAGAAACATATATCAA
1 TTAATTTAGAAAAATATATCAA
2906303 TT
1 TT
2906305 CATATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (22 bp):
TTAATTTAGAAAAATATATCAA
Found at i:2906859 original size:23 final size:23
Alignment explanation
Indices: 2906825--2906873 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
2906815 TCTCATGGCC
2906825 AAAACAATCAAAA-C-ATACACTT
1 AAAACAATCAAAATCAATA-ACTT
2906847 AAAACATATCAAAATCAATAACTT
1 AAAACA-ATCAAAATCAATAACTT
2906871 AAA
1 AAA
2906874 CTTCTAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 8 0.33
25 3 0.12
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAACAATCAAAATCAATAACTT
Found at i:2911354 original size:37 final size:37
Alignment explanation
Indices: 2911304--2911377 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2911294 TTTGGTAAGT
2911304 AGTTTTCAGGGATTAAGTGGATTATGTTTAGGTTAGG
1 AGTTTTCAGGGATTAAGTGGATTATGTTTAGGTTAGG
2911341 AGTTTTCAGGGATTAAGTGGATTATGTTTAGGTTAGG
1 AGTTTTCAGGGATTAAGTGGATTATGTTTAGGTTAGG
2911378 TAATAAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.03, G:0.32, T:0.41
Consensus pattern (37 bp):
AGTTTTCAGGGATTAAGTGGATTATGTTTAGGTTAGG
Found at i:2912318 original size:21 final size:22
Alignment explanation
Indices: 2912284--2912324 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2912274 ATCCCCACAA
*
2912284 GTGTGCTAGTTGG-TATGGGTT
1 GTGTGCTAGATGGTTATGGGTT
*
2912305 GTGTGCTGGATGGTTATGGG
1 GTGTGCTAGATGGTTATGGG
2912325 ATGGGTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.10, C:0.05, G:0.46, T:0.39
Consensus pattern (22 bp):
GTGTGCTAGATGGTTATGGGTT
Found at i:2912386 original size:33 final size:33
Alignment explanation
Indices: 2912341--2912421 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
2912331 TGCATTTTGC
*
2912341 ACTGTACCGATACTGAATAAGGCTTTGGCCCAA
1 ACTGTACTGATACTGAATAAGGCTTTGGCCCAA
* *
2912374 ACTGTACTGATACTGAATAAGGCTTTGGGCCAG
1 ACTGTACTGATACTGAATAAGGCTTTGGCCCAA
2912407 ACTGTACTGATACTG
1 ACTGTACTGATACTG
2912422 TGTTATTCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (33 bp):
ACTGTACTGATACTGAATAAGGCTTTGGCCCAA
Found at i:2920117 original size:33 final size:33
Alignment explanation
Indices: 2920071--2920151 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
2920061 TGCATTTTGC
*
2920071 ACTGTACCGATACTGAATAGGGCTTTGGCCCAA
1 ACTGTACTGATACTGAATAGGGCTTTGGCCCAA
* * *
2920104 ACTGTACTAATACTGAATAGGGCTTTGGGCCAG
1 ACTGTACTGATACTGAATAGGGCTTTGGCCCAA
2920137 ACTGTACTGATACTG
1 ACTGTACTGATACTG
2920152 TGTTATTAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (33 bp):
ACTGTACTGATACTGAATAGGGCTTTGGCCCAA
Found at i:2920962 original size:28 final size:28
Alignment explanation
Indices: 2920898--2920963 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
2920888 CTTCCATTTA
* *
2920898 TTTTTCAATTTAACCCCTCAATTTACAC
1 TTTTTCAAATTAACCCCTCAATTGACAC
* *
2920926 TTTTCTCAAATTAATCCCT-AATTGACAT
1 TTTT-TCAAATTAACCCCTCAATTGACAC
2920954 TTTTGTCAAA
1 TTTT-TCAAA
2920964 AATCTCTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (28 bp):
TTTTTCAAATTAACCCCTCAATTGACAC
Found at i:2942825 original size:46 final size:45
Alignment explanation
Indices: 2942733--2942837 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 45
2942723 CTCGTAGCCA
* *
2942733 ATGCATGTCTCAGACATGTCTTACACTAGCTTACGTCTCGAGGCTG
1 ATGCATGTCCCAGACATGTCTTACACTAGCTTAC-TCTCAAGGCTG
* *
2942779 ATGCATGTCCCAGACATGTCTTACATTAGCACTTA-TCTCAATGCTG
1 ATGCATGTCCCAGACATGTCTTACACTAG--CTTACTCTCAAGGCTG
2942825 ATGCCATGTCCCA
1 ATG-CATGTCCCA
2942838 AACACTGGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
46 39 0.75
47 9 0.17
48 4 0.08
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTTACTCTCAAGGCTG
Found at i:2944687 original size:28 final size:29
Alignment explanation
Indices: 2944623--2944688 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
2944613 CTTTCATTTA
* * *
2944623 TTTCACAATTTAACCCCTCAATTTACACT
1 TTTCTCAAATTAACCCCTCAATTGACACT
* *
2944652 TTTCTCAAATTAATCCCT-AATTGACATT
1 TTTCTCAAATTAACCCCTCAATTGACACT
*
2944680 TTTGTCAAA
1 TTTCTCAAA
2944689 AATCTCTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTCTCAAATTAACCCCTCAATTGACACT
Found at i:2956908 original size:21 final size:21
Alignment explanation
Indices: 2956864--2956930 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
2956854 TATAATGAGT
* **
2956864 ATATCATGTGCATCTCATAAC
1 ATATCATGTGCATATCATGTC
*
2956885 ATATCGTGTGCATATCATGTC
1 ATATCATGTGCATATCATGTC
*
2956906 ATATCTTGT-CATATCATGT-
1 ATATCATGTGCATATCATGTC
2956925 ATATCA
1 ATATCA
2956931 AAATCTTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.12
20 10 0.25
21 25 0.62
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (21 bp):
ATATCATGTGCATATCATGTC
Found at i:2956910 original size:10 final size:10
Alignment explanation
Indices: 2956864--2956930 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
2956854 TATAATGAGT
2956864 ATATCATGTGC
1 ATATCATGT-C
* **
2956875 ATCTCATAAC
1 ATATCATGTC
*
2956885 ATATCGTGTGC
1 ATATCATGT-C
2956896 ATATCATGTC
1 ATATCATGTC
*
2956906 ATATCTTGTC
1 ATATCATGTC
2956916 ATATCATGT-
1 ATATCATGTC
2956925 ATATCA
1 ATATCA
2956931 AAATCTTATG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
9 6 0.13
10 24 0.53
11 15 0.33
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (10 bp):
ATATCATGTC
Found at i:2958802 original size:19 final size:20
Alignment explanation
Indices: 2958778--2958816 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2958768 TCACAACCAA
*
2958778 TTACCAAATT-TTAAAAATT
1 TTACCAAATTCTCAAAAATT
2958797 TTACCAAATTCTCAAAAATT
1 TTACCAAATTCTCAAAAATT
2958817 ACGAAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (20 bp):
TTACCAAATTCTCAAAAATT
Found at i:2966261 original size:40 final size:40
Alignment explanation
Indices: 2966163--2966465 Score: 405
Period size: 40 Copynumber: 7.6 Consensus size: 40
2966153 TCCTCGTTCA
* * * * *
2966163 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
2966202 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2966242 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2966282 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2966322 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2966362 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
2966402 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
2966442 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2966466 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2975184 original size:27 final size:27
Alignment explanation
Indices: 2975145--2975313 Score: 196
Period size: 27 Copynumber: 6.2 Consensus size: 27
2975135 NNNNNNNNNC
* * *
2975145 AGTGCTATATAATCAACTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* *
2975172 AGTGCTACGTAATCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
2975199 AGTGCTACATAGTCAAACTCGCACACTT
1 AGTGCTACATAGTCAAA-TCGCACACTT
** * *
2975227 AGTGCCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* **
2975254 AGTGC-ATCATATTCATTTCGCACACTT
1 AGTGCTA-CATAGTCAAATCGCACACTT
*
2975281 AGTGCAACATAGTCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
2975308 AGTGCT
1 AGTGCT
2975314 GTACAATTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 98 0.80
28 24 0.20
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
AGTGCTACATAGTCAAATCGCACACTT
Found at i:2975282 original size:82 final size:81
Alignment explanation
Indices: 2975157--2975312 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2975147 TGCTATATAA
* *
2975157 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
2975222 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
2975239 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
2975303 CACTTAGTGC
65 CACTTAGTGC
2975313 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:2980669 original size:22 final size:21
Alignment explanation
Indices: 2980640--2980686 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2980630 GTTGATCTAA
2980640 TGATGAAATTATGAGTTT-AAT
1 TGATGAAATTATGA-TTTAAAT
*
2980661 TGATAGAAATTTTGATTTAAAT
1 TGAT-GAAATTATGATTTAAAT
2980683 TGAT
1 TGAT
2980687 TAAAGGATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (21 bp):
TGATGAAATTATGATTTAAAT
Found at i:2981838 original size:60 final size:60
Alignment explanation
Indices: 2981745--2981863 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
2981735 ATCTCATATA
*
2981745 TGTGGCTAGATTTGGGCTAAAAGGGCCACACGAGGGAGTGGGCCCATTTGGGCCGAGAAC
1 TGTGGCTAGATTTGGGCTAAAAGGGCCACACGAGCGAGTGGGCCCATTTGGGCCGAGAAC
* *
2981805 TGTGGCTAGATTTGGGCTAAAAGGGCTACACGAGCGTGTGGGCCCATTTGGGCCGAGAA
1 TGTGGCTAGATTTGGGCTAAAAGGGCCACACGAGCGAGTGGGCCCATTTGGGCCGAGAA
2981864 TAGGCTTTAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (60 bp):
TGTGGCTAGATTTGGGCTAAAAGGGCCACACGAGCGAGTGGGCCCATTTGGGCCGAGAAC
Found at i:2981962 original size:27 final size:27
Alignment explanation
Indices: 2981932--2982032 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
2981922 TACTGAAATG
*
2981932 CCCTCGATTTGTAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
2981959 CCCTTGATTTATAGAATTACCGTTTCA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
2981986 CCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
2982013 CCCTCGATTTACAAAATTAC
1 CCCTCGATTTATAGAATTAC
2982033 TGAAATACCC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCGTTTTA
Found at i:2982041 original size:27 final size:27
Alignment explanation
Indices: 2981912--2982042 Score: 84
Period size: 27 Copynumber: 4.9 Consensus size: 27
2981902 AACACTTTAG
* * *
2981912 TTTACCAAATTACTGAAATGCCCTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
** * *** *
2981939 TTTGTAGAATTACCGTTTTACCCTTGA
1 TTTACAAAATTACCGAAATACCCTCGA
* * **
2981966 TTTATAGAATTACCG-TTTCACCCTCGA
1 TTTACAAAATTACCGAAAT-ACCCTCGA
***
2981993 TTTACAAAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
*
2982020 TTTACAAAATTACTGAAATACCC
1 TTTACAAAATTACCGAAATACCC
2982043 CTGTAGGGTA
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 3 0.04
27 78 0.93
28 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (27 bp):
TTTACAAAATTACCGAAATACCCTCGA
Found at i:2983060 original size:27 final size:27
Alignment explanation
Indices: 2982027--2983054 Score: 1413
Period size: 27 Copynumber: 38.3 Consensus size: 27
2982017 CGATTTACAA
*
2982027 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982054 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
2982081 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
2982108 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982135 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
2982162 AATTACTGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982189 AATTACCGGAATA-CCC-GTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
2982214 AATTACCGGAATATCCCAGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982241 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982268 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
2982295 AATTACCGGAATACCCCTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
2982322 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
2982349 AATTACCGAAATACCCCTGTAAAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
2982376 AATTACCGGGATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982403 AATTA-CGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
2982429 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
2982456 AATTATCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
2982483 AATTACC-AGAATACCCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
**
2982510 AATTACCGAAATACCCCCATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982537 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
2982564 AATTACCGGTATACCCCTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982591 AATTACCGAAATACCCCTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
2982618 AATTACAGAAATACCCCTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
2982645 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
2982672 AATTACCGAAATACCCCTACAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
2982699 AATTATCGGAATACCCCTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
2982726 AATTACCGAAATACCCCTGCT-GGGTAG
1 AATTACCGAAATACCCCTG-TAGGGTAG
* *
2982753 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
2982780 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
2982807 AATTACCGAAATACCCCTGTAAAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
2982834 AATTACCGGGATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982861 AATTA-CGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
2982887 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* **
2982914 AATTATCGAAATACCCCTGTAAAGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
2982941 AATTACCGGGATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
2982968 AATTA-CGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
2982994 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
2983021 AATTATCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
2983048 AATTACC
1 AATTACC
2983055 AGAATANNNN
Statistics
Matches: 890, Mismatches: 102, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
25 22 0.02
26 77 0.09
27 789 0.89
28 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:2983667 original size:6 final size:6
Alignment explanation
Indices: 2983637--2983722 Score: 63
Period size: 6 Copynumber: 14.2 Consensus size: 6
2983627 NNNNNNNNNN
* *
2983637 TTCTGA TTTTGA TTCTG- TTACCTGA TACTGA TTCTGA TTCTGA TTCTG-
1 TTCTGA TTCTGA TTCTGA TT--CTGA TTCTGA TTCTGA TTCTGA TTCTGA
* *
2983685 TCACCTAA TTCT-A TTCTGA TTCTGA TTCT-A GTTCTGA T
1 T--TCTGA TTCTGA TTCTGA TTCTGA TTCTGA -TTCTGA T
2983723 AATGTTTCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
5 9 0.14
6 47 0.73
7 6 0.09
8 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.49
Consensus pattern (6 bp):
TTCTGA
Found at i:2983675 original size:31 final size:30
Alignment explanation
Indices: 2983637--2983713 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
2983627 NNNNNNNNNN
* * *
2983637 TTCTGATTTTGATTCTGTTACCTGATACTGA
1 TTCTGATTCTGATTCTGTCACCTAATACT-A
*
2983668 TTCTGATTCTGATTCTGTCACCTAATTCTA
1 TTCTGATTCTGATTCTGTCACCTAATACTA
2983698 TTCTGATTCTGATTCT
1 TTCTGATTCTGATTCT
2983714 AGTTCTGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 17 0.40
31 25 0.60
ACGTcount: A:0.18, C:0.19, G:0.13, T:0.49
Consensus pattern (30 bp):
TTCTGATTCTGATTCTGTCACCTAATACTA
Found at i:2985002 original size:26 final size:24
Alignment explanation
Indices: 2984953--2985019 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 24
2984943 GAGAAAAATC
* *
2984953 AAATGAAATTGATAAATTGAATTATT
1 AAATGAAA-TGAGAAAGTGAATTA-T
*
2984979 GAATGAAATGAGAAAGTGATATTAT
1 AAATGAAATGAGAAAGTGA-ATTAT
2985004 AAGATGAAATGAGAAA
1 AA-ATGAAATGAGAAA
2985020 TACAATTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 11 0.31
26 24 0.69
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.28
Consensus pattern (24 bp):
AAATGAAATGAGAAAGTGAATTAT
Found at i:2993755 original size:42 final size:42
Alignment explanation
Indices: 2993672--2993757 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
2993662 GCCCAGGACG
* * *
2993672 TGTGACAAAGTCAGAATTGGCCACAGGTTAGTCCCACGGCCA
1 TGTGACAAAGTCAGAATTGCCCACAGGCTAGCCCCACGGCCA
* * *
2993714 TGTGAGAAAGTCAG-ATCTGCCCACGGGCTAGCCCCATGGCCA
1 TGTGACAAAGTCAGAAT-TGCCCACAGGCTAGCCCCACGGCCA
2993756 TG
1 TG
2993758 GGAGCCCCAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 35 0.95
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.19
Consensus pattern (42 bp):
TGTGACAAAGTCAGAATTGCCCACAGGCTAGCCCCACGGCCA
Found at i:2999050 original size:3 final size:3
Alignment explanation
Indices: 2999042--2999087 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2999032 TAAAAGATAT
2999042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2999088 CAATTAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3002318 original size:47 final size:47
Alignment explanation
Indices: 3002254--3002433 Score: 159
Period size: 47 Copynumber: 3.8 Consensus size: 47
3002244 GGATGTGACA
* * *
3002254 CACCTACTTCACCAGTGGTTTATCCACAACGTATCTTAGTTGACAAT
1 CACCTGCTTGACCAGTGGTTTATCCACAACGTATCTTAGTCGACAAT
* ** *
3002301 CATCTGCTCT-ACCAGTGGTTTATCCACAACGTA-CTTTAGTCGGTAGT
1 CACCTGCT-TGACCAGTGGTTTATCCACAACGTATC-TTAGTCGACAAT
* * * *
3002348 CACCTGCTTGACCACTGGTTTATCCATAACGTATTTTAGTGCG-CAGT
1 CACCTGCTTGACCAGTGGTTTATCCACAACGTATCTTAGT-CGACAAT
* * * * * *
3002395 CACCTTCTCGACCAGTGGTATATCTACAATGTATTTTAG
1 CACCTGCTTGACCAGTGGTTTATCCACAACGTATCTTAG
3002434 CAACGTCAGT
Statistics
Matches: 110, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
46 2 0.02
47 105 0.95
48 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.34
Consensus pattern (47 bp):
CACCTGCTTGACCAGTGGTTTATCCACAACGTATCTTAGTCGACAAT
Found at i:3002433 original size:94 final size:94
Alignment explanation
Indices: 3002254--3002433 Score: 218
Period size: 94 Copynumber: 1.9 Consensus size: 94
3002244 GGATGTGACA
* * *
3002254 CACCTACTTCACCAGTGGTTTATCCACAACGTATCTTAGTTGACAATCATCTGCTCTACCAGTGG
1 CACCTACTTCACCACTGGTTTATCCACAACGTATCTTAGTTGACAATCACCTGCTCGACCAGTGG
*
3002319 TTTATCCACAACGTACTTTAGTCGGTAGT
66 TATATCCACAACGTACTTTAGTCGGTAGT
* * * * * * *
3002348 CACCTGCTTGACCACTGGTTTATCCATAACGTATTTTAG-TGCGCAGTCACCTTCTCGACCAGTG
1 CACCTACTTCACCACTGGTTTATCCACAACGTATCTTAGTTG-ACAATCACCTGCTCGACCAGTG
* * *
3002412 GTATATCTACAATGTATTTTAG
65 GTATATCCACAACGTACTTTAG
3002434 CAACGTCAGT
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
93 2 0.03
94 69 0.97
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.34
Consensus pattern (94 bp):
CACCTACTTCACCACTGGTTTATCCACAACGTATCTTAGTTGACAATCACCTGCTCGACCAGTGG
TATATCCACAACGTACTTTAGTCGGTAGT
Found at i:3015784 original size:45 final size:45
Alignment explanation
Indices: 3015728--3015815 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
3015718 GAGCTATGTG
*
3015728 ATCTAAACTTATTGAGTTATGGTCTGAGTTCATGATATATGTGAC
1 ATCTAAACTTATTGAGTTATGGTCTGAATTCATGATATATGTGAC
* *
3015773 ATCTAAACTTATTGAGTTGTGGTCTGAATTCATGATGTATGTG
1 ATCTAAACTTATTGAGTTATGGTCTGAATTCATGATATATGTG
3015816 GCATATGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (45 bp):
ATCTAAACTTATTGAGTTATGGTCTGAATTCATGATATATGTGAC
Found at i:3017145 original size:111 final size:110
Alignment explanation
Indices: 3016974--3017200 Score: 375
Period size: 111 Copynumber: 2.1 Consensus size: 110
3016964 TATCTTGGCA
**
3016974 GTGTGTGACACACGGTTTGCCTAGGGGTGTATGATTCGATCGTGTGTCCCCTGCACCCTAATGAT
1 GTGTGTGACACACGGCCTGCCTAGGGGTGTATGATTCGATCGTGTGTCCCCTGCACCCTAATGAT
*
3017039 GCAAAATAGATTGCCAATAGTAAACACACAGGCAGA-GACACGGCC
66 GCAAAACAGATTGCCAATAGTAAACACACAGGCA-ACGACACGGCC
* *
3017084 GTGTGTGACACACGGCCTGCCCTAGGGGTGTGTGATTCGGTCGTGTGTCCCCTGCACCCTAATGA
1 GTGTGTGACACACGGCCTG-CCTAGGGGTGTATGATTCGATCGTGTGTCCCCTGCACCCTAATGA
*
3017149 TGCAAAACAGATTGCCAGTAGTAAACACACAGGCAACGACACGGCC
65 TGCAAAACAGATTGCCAATAGTAAACACACAGGCAACGACACGGCC
3017195 GTGTGT
1 GTGTGT
3017201 CTTAGCCGTG
Statistics
Matches: 109, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
110 18 0.17
111 91 0.83
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (110 bp):
GTGTGTGACACACGGCCTGCCTAGGGGTGTATGATTCGATCGTGTGTCCCCTGCACCCTAATGAT
GCAAAACAGATTGCCAATAGTAAACACACAGGCAACGACACGGCC
Found at i:3024984 original size:27 final size:27
Alignment explanation
Indices: 3024954--3025131 Score: 164
Period size: 27 Copynumber: 6.6 Consensus size: 27
3024944 ATATTGAGCC
* *
3024954 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
3024981 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
3025008 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
3025036 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
3025063 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
3025090 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
3025117 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3025132 GTACAATTTA
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.02
27 101 0.80
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:3025093 original size:82 final size:81
Alignment explanation
Indices: 3024975--3025130 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
3024965 TGCTATATAA
* * *
3024975 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCA-AACTCGC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACAAAGT-AGAA-TCGC
3025039 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * **
3025057 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACAAAGTAGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACAAAGTAGAATCGCA
3025121 CACTTAGTGC
65 CACTTAGTGC
3025131 TGTACAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACAAAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:3033172 original size:27 final size:27
Alignment explanation
Indices: 3033142--3033319 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
3033132 ATATTGAGCC
* *
3033142 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
3033169 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
3033196 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
3033224 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
3033251 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
3033278 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
3033305 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
3033320 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:3033281 original size:82 final size:81
Alignment explanation
Indices: 3033163--3033318 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
3033153 TGCTATATAA
* * * * *
3033163 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
3033228 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
3033245 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
3033309 CCCTTAGTGC
65 CACTTAGTGC
3033319 TGTACAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:3035121 original size:23 final size:23
Alignment explanation
Indices: 3035089--3035132 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3035079 GACTCACCAC
3035089 AGCTCGTATGAGCTTACCGTTTT
1 AGCTCGTATGAGCTTACCGTTTT
* *
3035112 AGCTCTTATGAGCTTATCGTT
1 AGCTCGTATGAGCTTACCGTT
3035133 CAACTCTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (23 bp):
AGCTCGTATGAGCTTACCGTTTT
Found at i:3043597 original size:20 final size:21
Alignment explanation
Indices: 3043572--3043611 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3043562 AGATTTACGT
3043572 CAAGAT-TCTGGAA-GAAATTA
1 CAAGATCT-TGGAACGAAATTA
3043592 CAAGATCTTGGAACGAAATT
1 CAAGATCTTGGAACGAAATT
3043612 GAATTTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
CAAGATCTTGGAACGAAATTA
Found at i:3045737 original size:22 final size:23
Alignment explanation
Indices: 3045692--3045754 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
3045682 CCACAGCTTG
*
3045692 TATGAGCTTATCGTTTTAGCTCT
1 TATGAGCTTATCGTTTCAGCTCT
3045715 TATGAGCTTATCG-TTCAGCTCT
1 TATGAGCTTATCGTTTCAGCTCT
**
3045737 TCGGAGCTTA-CTGTTTCA
1 TATGAGCTTATC-GTTTCA
3045755 ATCCTTAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 17 0.49
23 17 0.49
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (23 bp):
TATGAGCTTATCGTTTCAGCTCT
Found at i:3045791 original size:23 final size:23
Alignment explanation
Indices: 3045728--3045797 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
3045718 GAGCTTATCG
* *
3045728 TTCAGCTCTTCGGAGCTTACTGT
1 TTCAACTCTACGGAGCTTACTGT
*
3045751 TTCAA-TCCTTA-GGGGCTTACTGT
1 TTCAACT-C-TACGGAGCTTACTGT
3045774 TTCAACTCTACGGAGCTTACTGT
1 TTCAACTCTACGGAGCTTACTGT
3045797 T
1 T
3045798 CAGCTCAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.08
23 34 0.87
24 2 0.05
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (23 bp):
TTCAACTCTACGGAGCTTACTGT
Found at i:3050449 original size:33 final size:33
Alignment explanation
Indices: 3050412--3050481 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
3050402 AAACCCAAAA
3050412 TACCATCTACATTAATCTCAAAGTCTCTACTAC
1 TACCATCTACATTAATCTCAAAGTCTCTACTAC
3050445 TACCATCTACATTAATCTCAAAGTCTCTACTAC
1 TACCATCTACATTAATCTCAAAGTCTCTACTAC
3050478 TACC
1 TACC
3050482 TTTTTAAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (33 bp):
TACCATCTACATTAATCTCAAAGTCTCTACTAC
Found at i:3058912 original size:29 final size:30
Alignment explanation
Indices: 3058865--3058931 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
3058855 AAAGAAAATC
*
3058865 ATTTTTATAATAAAAAATTA-AAATTTTTT
1 ATTTTTATAATAAAAAATTATAAATTGTTT
* *
3058894 ATTTTTAT-TTAAAATAATTATTAATTGTTT
1 ATTTTTATAATAAAA-AATTATAAATTGTTT
3058924 ATTATTTA
1 ATT-TTTA
3058932 AAAAAACTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 5 0.16
29 13 0.41
30 10 0.31
31 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
ATTTTTATAATAAAAAATTATAAATTGTTT
Found at i:3061788 original size:24 final size:25
Alignment explanation
Indices: 3061756--3061819 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
3061746 ATATTTTTTG
3061756 TTATTTTTTTTATTT-CTCATATAT
1 TTATTTTTTTTATTTGCTCATATAT
* *
3061780 TTA-TTTTTTTATTTGCTTATATTT
1 TTATTTTTTTTATTTGCTCATATAT
*
3061804 TTAATATTTTTTATTT
1 TT-ATTTTTTTTATTT
3061820 ATTTTACCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.32
24 12 0.35
25 1 0.03
26 10 0.29
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (25 bp):
TTATTTTTTTTATTTGCTCATATAT
Found at i:3061800 original size:22 final size:22
Alignment explanation
Indices: 3061760--3061819 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 22
3061750 TTTTTGTTAT
3061760 TTTTTTTATTTCTCATATATTTA
1 TTTTTTTATTTCT-ATATATTTA
*
3061783 TTTTTTTATTTGCTTATATTTTTAA
1 TTTTTTTATTT-C-TATATATTT-A
3061808 TATTTTTTATTT
1 T-TTTTTTATTT
3061820 ATTTTACCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.34
24 8 0.25
25 3 0.09
26 10 0.31
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTTTATTTCTATATATTTA
Found at i:3062445 original size:8 final size:8
Alignment explanation
Indices: 3062415--3062459 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
3062405 TCATGATCTT
3062415 TTTTTAATA
1 TTTTT-ATA
*
3062424 GTTTTATA
1 TTTTTATA
3062432 -TTTTATA
1 TTTTTATA
3062439 TTTTTATA
1 TTTTTATA
*
3062447 TTTTCATA
1 TTTTTATA
3062455 TTTTT
1 TTTTT
3062460 TAAATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 7 0.22
8 21 0.66
9 4 0.12
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:3062445 original size:15 final size:16
Alignment explanation
Indices: 3062425--3062459 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
3062415 TTTTTAATAG
3062425 TTTTATATTTT-ATAT
1 TTTTATATTTTCATAT
3062440 TTTTATATTTTCATAT
1 TTTTATATTTTCATAT
3062456 TTTT
1 TTTT
3062460 TAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATATTTTCATAT
Found at i:3063812 original size:18 final size:19
Alignment explanation
Indices: 3063791--3063834 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3063781 CAGATACAGT
**
3063791 TTCAGATTC-AAATTTGGA
1 TTCAGATTCTAAATTCAGA
3063809 TTCAGA-TCTAAATTCAGA
1 TTCAGATTCTAAATTCAGA
3063827 TTCAGATT
1 TTCAGATT
3063835 ACAGAAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 19 0.86
19 1 0.05
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (19 bp):
TTCAGATTCTAAATTCAGA
Found at i:3064396 original size:17 final size:18
Alignment explanation
Indices: 3064364--3064402 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3064354 CGTGTGACAT
3064364 ACCCGTGTAGGCCCACAC
1 ACCCGTGTAGGCCCACAC
*
3064382 ACCCGTGTA-GCCCACAT
1 ACCCGTGTAGGCCCACAC
3064399 ACCC
1 ACCC
3064403 AACTTGGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.23, C:0.46, G:0.18, T:0.13
Consensus pattern (18 bp):
ACCCGTGTAGGCCCACAC
Found at i:3075734 original size:30 final size:31
Alignment explanation
Indices: 3075698--3075761 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
3075688 ACTTATTTTA
3075698 TTGTTAA-TTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTTCTTATTATTTTAAAGGCAT
* *
3075728 TTGTTAATTTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTCTTATTATTTTAAAGGCAT
3075759 TTG
1 TTG
3075762 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTCTTATTATTTTAAAGGCAT
Found at i:3080667 original size:135 final size:134
Alignment explanation
Indices: 3080472--3080841 Score: 535
Period size: 135 Copynumber: 2.7 Consensus size: 134
3080462 CCTCGATTAG
* * * *
3080472 CAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAAAATACCCCTAGTTTGTGAAATTACCA
1 CAAAATTACCAAAATA-CCCTGGTTTGTAAAATTACCAAAATACCCTTAGTTTATAAAATTACCA
*
3080537 AAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAAGACCCTTG
65 AAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAAGACCCCTG
*
3080602 GTTTA
130 ATTTA
3080607 CAAAATTACCAAAATACTCCTGGTTTGTAAAATTACCAAAATACCCTTAGTTTATAAAATTACCA
1 CAAAATTACCAAAATAC-CCTGGTTTGTAAAATTACCAAAATACCCTTAGTTTATAAAATTACCA
*
3080672 AAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAATACCCCTG
65 AAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAAGACCCCTG
*
3080737 ATTTG
130 ATTTA
** ** ** *
3080742 TGAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAATACCCTTAGTTTACAAAATTACCA
1 CAAAATTACCAAAATACCCT-GGTTTGTAAAATTACCAAAATACCCTTAGTTTATAAAATTACCA
* **
3080807 AAATACCCCT-AGTTTGTAAAATTACCAAAATACCC
65 AAATACCCCTGA-TTTGTGAAATTACTGAAATACCC
3080842 CTGTAGGGTA
Statistics
Matches: 214, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
134 5 0.02
135 209 0.98
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.29
Consensus pattern (134 bp):
CAAAATTACCAAAATACCCTGGTTTGTAAAATTACCAAAATACCCTTAGTTTATAAAATTACCAA
AATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAAGACCCCTGA
TTTA
Found at i:3080842 original size:27 final size:26
Alignment explanation
Indices: 3080473--3080872 Score: 374
Period size: 27 Copynumber: 14.8 Consensus size: 26
3080463 CTCGATTAGC
3080473 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
*
3080500 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
*
3080527 GAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTG-TTTGT
* ** *
3080554 GAAATTACTGAAATA-CCCTCGACTTGT
1 AAAATTACCAAAATACCCCT-G-TTTGT
* * **
3080581 AAAATTACCAAAAGACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCT-GTTTGT
*
3080608 AAAATTACCAAAATACTCCTGGTTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
* *
3080635 AAAATTACCAAAATACCCTTAGTTTAT
1 AAAATTACCAAAATACCCCT-GTTTGT
3080662 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTG-TTTGT
* ** *
3080689 GAAATTACTGAAATA-CCCTCGACTTGT
1 AAAATTACCAAAATACCCCT-G-TTTGT
3080716 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTG-TTTGT
* ** *
3080743 GAAATTACTGAAATA-CCCTCGACTTGT
1 AAAATTACCAAAATACCCCT-G-TTTGT
* **
3080770 AAAATTACCAAAATACCCTTAGTTTAC
1 AAAATTACCAAAATACCCCT-GTTTGT
3080797 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
**
3080824 AAAATTACCAAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTGT-TTGT
* *
3080851 AGAATTACTAAAATACCCCTGT
1 AAAATTACCAAAATACCCCTGT
3080873 AGGGTAGAGT
Statistics
Matches: 310, Mismatches: 54, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
26 16 0.05
27 282 0.91
28 12 0.04
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (26 bp):
AAAATTACCAAAATACCCCTGTTTGT
Found at i:3080857 original size:54 final size:53
Alignment explanation
Indices: 3080475--3080980 Score: 316
Period size: 54 Copynumber: 9.4 Consensus size: 53
3080465 CGATTAGCAA
*
3080475 AATTACCAAAATACCCCTGGTTTGTAAAATTATCAAAATACCCCTAGT-TTGT-G
1 AATTACCAAAATACCCCT-GTTTGTAAAATTACCAAAATACCCCT-GTATTGTAG
* ** *
3080528 AAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATA-CCCTCG-ACTTGTAA
1 -AATTACCAAAATACCCCTG-TTTGTAAAATTACCAAAATACCCCT-GTA-TTGTAG
* * ** * *
3080583 AATTACCAAAAGACCCTTGGTTTACAAAATTACCAAAATACTCCTGGT-TTGTAA
1 AATTACCAAAATACCCCT-GTTTGTAAAATTACCAAAATACCCCT-GTATTGTAG
* *
3080637 AATTACCAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTG-ATTTGT-G
1 AATTACCAAAATACCCCT-GTTTGTAAAATTACCAAAATACCCCTGTA-TTGTAG
** *
3080690 AAATTACTGAAATA-CCCTCGACTTGTAAAATTACCAAAATACCCCTG-ATTTGT-G
1 -AATTACCAAAATACCCCT-G-TTTGTAAAATTACCAAAATACCCCTGTA-TTGTAG
** * * ** *
3080744 AAATTACTGAAATA-CCCTCGACTTGTAAAATTACCAAAATACCCTTAGT-TTACAA
1 -AATTACCAAAATACCCCT-G-TTTGTAAAATTACCAAAATACCCCT-GTATTGTAG
**
3080799 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCT-GTTTGTAAAATTACCAAAATACCCCTGTATTGTAG
* ** * * * * **
3080853 AATTACTAAAATACCCCTGTAGGGTAGAGTTACCGAAATACCCTTGTAAGGTAG
1 AATTACCAAAATACCCCTGT-TTGTAAAATTACCAAAATACCCCTGTATTGTAG
* *** ** * * * * **
3080907 AAATATTGAAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCAAAATACCCCTGT-TTGTAAAATTACCAAAATACCCCTGTATTGTAG
*
3080961 AAATACCAAAATACCCCTGT
1 AATTACCAAAATACCCCTGT
3080981 AGGGTAGAAT
Statistics
Matches: 378, Mismatches: 57, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
53 15 0.04
54 352 0.93
55 11 0.03
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (53 bp):
AATTACCAAAATACCCCTGTTTGTAAAATTACCAAAATACCCCTGTATTGTAG
Found at i:3080873 original size:27 final size:27
Alignment explanation
Indices: 3080799--3081022 Score: 234
Period size: 27 Copynumber: 8.3 Consensus size: 27
3080789 TAGTTTACAA
** *
3080799 AATTACCAAAATACCCCTAGT-TTGTAA
1 AATTACCAAAATACCCCT-GTAGGGTAG
3080826 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
*
3080853 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * * *
3080880 AGTTACCGAAATACCCTTGTAAGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* ***
3080907 AAATATTGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * *
3080934 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
*
3080961 AAATACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * ** * *
3080988 AATTACCGAGATACCTTTGTGGGGTAA
1 AATTACCAAAATACCCCTGTAGGGTAG
3081015 AATTACCA
1 AATTACCA
3081023 TTTTGCCCCT
Statistics
Matches: 166, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
26 2 0.01
27 164 0.99
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGTAGGGTAG
Found at i:3080886 original size:81 final size:80
Alignment explanation
Indices: 3080473--3080978 Score: 240
Period size: 81 Copynumber: 6.2 Consensus size: 80
3080463 CTCGATTAGC
* * *
3080473 AAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAAAATACCCCT-A-GTTTGT-GAAATTAC
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGACG--GGTAG-AATTAC
* **
3080535 CAAAATACCCCTG-ATTTGT
63 TAAAATA-CCCTGTA-GGGT
* ** * * * * ** *
3080554 GAAATTACTGAAATA-CCCTCGACTTGTAAAATTACCAAAAGACCCTTG--GTTTACAAAATTAC
1 AAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCCTGACGGGT--AGAATTAC
* **
3080616 CAAAATACTCCTGGT-TTGT
63 TAAAATAC-CCT-GTAGGGT
* * *** *
3080635 AAAATTACCAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGATTTGT-GAAATTACTG
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGACGGGTAG-AATTACTA
**
3080699 AAATACCCTCG-ACTTGT
65 AAATACCCT-GTA-GGGT
* ** ** * *
3080716 AAAATTACCAAAATACCCCT-GATTTGTGAAATTACTGAAATA-CCCTCGACTTGTAAAATTACC
1 AAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCCT-GACGGGTAGAATTACT
**
3080779 AAAATACCCT-TAGTTT
64 AAAATACCCTGTAGGGT
3080795 ACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGTA-GGGTAGAATTAC
1 --AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTG-ACGGGTAGAATTAC
3080859 TAAAATACCCCTGTAGGGT
63 TAAAATA-CCCTGTAGGGT
* * * * ** ***
3080878 AGAGTTACCGAAATA-CCCTTGTAAGGTAGAAA-TATTGAAATACCCCTGTA-GGGTAGAATTA-
1 AAAATTACCAAAATACCCCTAGT-TTGTA-AAATTACCAAAATACCCCTG-ACGGGTAGAATTAC
*
3080939 TCGAAATACCCTTGTAGGGT
63 T-AAAATACCC-TGTAGGGT
3080959 AGAAA-TACCAAAATACCCCT
1 A-AAATTACCAAAATACCCCT
3080979 GTAGGGTAGA
Statistics
Matches: 336, Mismatches: 58, Indels: 61
0.74 0.13 0.13
Matches are distributed among these distances:
79 4 0.01
80 26 0.08
81 277 0.82
82 23 0.07
83 6 0.02
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGACGGGTAGAATTACTAA
AATACCCTGTAGGGT
Found at i:3081032 original size:54 final size:54
Alignment explanation
Indices: 3080802--3081022 Score: 266
Period size: 54 Copynumber: 4.1 Consensus size: 54
3080792 TTTACAAAAT
** * * * *
3080802 TACCAAAATACCCCTAGT-TTGTAAAATTACCAAAATACCCCTGTAGGGTAGAAT
1 TACCAAAATACCCCT-GTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAA
* * *
3080856 TACTAAAATACCCCTGTAGGGTAGAGTTACCGAAATACCCTTGTAAGGTAGAAA
1 TACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAA
*** *
3080910 TATTGAAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAAA
1 TACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAA
* * *
3080964 TACCAAAATACCCCTGTAGGGTAGAATTACCGAGATACCTTTGTGGGGTA-AAA
1 TACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAA
3081017 TTACCA
1 -TACCA
3081023 TTTTGCCCCT
Statistics
Matches: 144, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
53 5 0.03
54 139 0.97
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (54 bp):
TACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAA
Found at i:3081283 original size:24 final size:24
Alignment explanation
Indices: 3081251--3081297 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3081241 CAGTTTACCA
* *
3081251 AAAAGGGCTTTGCC-CTAGTTATT
1 AAAAGGGCTATGCCTCCAGTTATT
3081274 AAAAGAGGCTATGCCTCCAGTTAT
1 AAAAG-GGCTATGCCTCCAGTTAT
3081298 ATGATAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTATGCCTCCAGTTATT
Found at i:3081591 original size:29 final size:28
Alignment explanation
Indices: 3081557--3081611 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
3081547 AGACTGAATT
* *
3081557 AGGGCTTAGGCCCATACTGCTACTGTTGA
1 AGGGCTAAGGCCCAGACTG-TACTGTTGA
3081586 AGGGCTAAGGCCCAGACTGTACTGTT
1 AGGGCTAAGGCCCAGACTGTACTGTT
3081612 ACTGAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (28 bp):
AGGGCTAAGGCCCAGACTGTACTGTTGA
Found at i:3081631 original size:33 final size:32
Alignment explanation
Indices: 3081549--3081642 Score: 97
Period size: 33 Copynumber: 3.0 Consensus size: 32
3081539 ATATGTCGAG
*
3081549 ACTGAATTAGGGCTTAGGCCCATACTGCTACTGT
1 ACTGAA-TAGGGCTTAGGCCCAGACTG-TACTGT
*
3081583 --TG-A-AGGGCTAAGGCCCAGACTGTACTGTT
1 ACTGAATAGGGCTTAGGCCCAGACTGTACTG-T
* *
3081612 ACTGAATAGGGCTTTGGCCCAGATTGTACTG
1 ACTGAATAGGGCTTAGGCCCAGACTGTACTG
3081643 ACACTGTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
28 5 0.10
29 18 0.36
31 3 0.06
32 3 0.06
33 21 0.42
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (32 bp):
ACTGAATAGGGCTTAGGCCCAGACTGTACTGT
Found at i:3085302 original size:12 final size:12
Alignment explanation
Indices: 3085285--3085311 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3085275 TCCGAAGTGT
3085285 ATATATATATAC
1 ATATATATATAC
3085297 ATATATATATAC
1 ATATATATATAC
3085309 ATA
1 ATA
3085312 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:3085872 original size:27 final size:28
Alignment explanation
Indices: 3085760--3085885 Score: 191
Period size: 28 Copynumber: 4.5 Consensus size: 28
3085750 CATGAGATTG
* * * *
3085760 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
3085789 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
3085817 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
3085845 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
3085872 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
3085886 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 24 0.26
28 50 0.54
29 18 0.20
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:3085882 original size:55 final size:57
Alignment explanation
Indices: 3085760--3085885 Score: 193
Period size: 55 Copynumber: 2.2 Consensus size: 57
3085750 CATGAGATTG
* *
3085760 GCACTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTTGATTATATA
* *
3085817 GCACTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTTGATTATATA
*
3085872 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
3085886 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 24 0.38
56 22 0.34
57 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTTGATTATATA
Found at i:3085896 original size:27 final size:27
Alignment explanation
Indices: 3085788--3085898 Score: 143
Period size: 28 Copynumber: 4.0 Consensus size: 27
3085778 TAAATTGTAC
*
3085788 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGATTATAT
*
3085816 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGATTATAT
*
3085844 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGATTATAT
* *
3085871 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGATTATAT
3085898 A
1 A
3085899 CTTTTGAATC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
27 30 0.38
28 48 0.62
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGATTATAT
Found at i:3089689 original size:12 final size:12
Alignment explanation
Indices: 3089674--3089746 Score: 58
Period size: 12 Copynumber: 6.2 Consensus size: 12
3089664 ATAGCAACAA
3089674 TAATATTATTAT
1 TAATATTATTAT
3089686 TAATA-TATTAT
1 TAATATTATTAT
* *
3089697 TAATATCAATAT
1 TAATATTATTAT
* *
3089709 TAATAATAATAT
1 TAATATTATTAT
* * *
3089721 TACTATTCTTCT
1 TAATATTATTAT
**
3089733 TCTTATTATTAT
1 TAATATTATTAT
3089745 TA
1 TA
3089747 TAACTACACA
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
11 11 0.24
12 35 0.76
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:3089713 original size:6 final size:6
Alignment explanation
Indices: 3089674--3089727 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
3089664 ATAGCAACAA
* * * *
3089674 TAATAT TATTAT TAATA- TATTAT TAATAT CAATAT TAATAA TAATAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
*
3089721 TACTAT T
1 TAATAT T
3089728 CTTCTTCTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATAT
Found at i:3090063 original size:10 final size:10
Alignment explanation
Indices: 3090044--3090086 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
3090034 TCGCTTCTTC
3090044 TTCTTCTTTCT
1 TTCTT-TTTCT
3090055 TTCTTTTTCT
1 TTCTTTTTCT
3090065 TTC-TTTTCT
1 TTCTTTTTCT
* *
3090074 TTTTTTTTTT
1 TTCTTTTTCT
3090084 TTC
1 TTC
3090087 AAAATTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 8 0.29
10 15 0.54
11 5 0.18
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:3090064 original size:14 final size:15
Alignment explanation
Indices: 3090041--3090086 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
3090031 TTTTCGCTTC
*
3090041 TTCTTCTTCTTTC-T
1 TTCTTTTTCTTTCTT
3090055 TTCTTTTTCTTTCTT
1 TTCTTTTTCTTTCTT
*
3090070 TTCTTTTT-TTTTTT
1 TTCTTTTTCTTTCTT
3090084 TTC
1 TTC
3090087 AAAATTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTCTTTTTCTTTCTT
Found at i:3090064 original size:23 final size:23
Alignment explanation
Indices: 3090041--3090086 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3090031 TTTTCGCTTC
3090041 TTCTTCTTCTTTCTTTCTTTTTCT
1 TTCTT-TTCTTTCTTTCTTTTTCT
* *
3090065 TTCTTTTCTTTTTTTTTTTTTC
1 TTCTTTTCTTTCTTTCTTTTTC
3090087 AAAATTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTCTTTTCTTTCTTTCTTTTTCT
Found at i:3095734 original size:13 final size:13
Alignment explanation
Indices: 3095718--3095755 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
3095708 TTAAATCCGT
3095718 TAATTAGTTTAAA
1 TAATTAGTTTAAA
3095731 TAATTAGTTTAAA
1 TAATTAGTTTAAA
3095744 TAATTAGTTTAA
1 TAATTAGTTTAA
3095756 TAAACAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:3101095 original size:6 final size:6
Alignment explanation
Indices: 3101072--3101129 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
3101062 TGAATCCTCC
* * * *
3101072 TATTTT T-TATT TAGTTT TATTTT TATTTT TATTTT TCTTTT GATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
*
3101119 TATTTT CATTT
1 TATTTT TATTT
3101130 CAATTTTATT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
5 4 0.10
6 38 0.90
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:3101102 original size:18 final size:17
Alignment explanation
Indices: 3101072--3101149 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 17
3101062 TGAATCCTCC
*
3101072 TATTTTT-TATTTAGTTT
1 TATTTTTATTTTTA-TTT
3101089 TATTTTTATTTTTATTT
1 TATTTTTATTTTTATTT
3101106 T-TCTTTTGATTTTTATTT
1 TAT-TTTT-ATTTTTATTT
**
3101124 TCATTTCAATTTTATTATTT
1 T-ATTTTTA-TTT-TTATTT
3101144 TATTTT
1 TATTTT
3101150 GAAAGACATA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.02
17 15 0.30
18 17 0.34
19 9 0.18
20 8 0.16
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTATTTTTATTT
Found at i:3101713 original size:18 final size:18
Alignment explanation
Indices: 3101690--3101726 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3101680 TTATGCATGA
3101690 TTATTGATTATAGGACCT
1 TTATTGATTATAGGACCT
3101708 TTATTGATTATAGGACCT
1 TTATTGATTATAGGACCT
3101726 T
1 T
3101727 AAAGAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (18 bp):
TTATTGATTATAGGACCT
Found at i:3104093 original size:13 final size:13
Alignment explanation
Indices: 3104077--3104101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3104067 TTAAATCCAT
3104077 TAATTAGTTTAAA
1 TAATTAGTTTAAA
3104090 TAATTAGTTTAA
1 TAATTAGTTTAA
3104102 TAAACAAACC
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:3130023 original size:94 final size:94
Alignment explanation
Indices: 3129690--3130427 Score: 1012
Period size: 94 Copynumber: 7.8 Consensus size: 94
3129680 CCATCAAATA
* * * *
3129690 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCA-AATTCGAGGCCGACGCCATGTCCCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAA-T-GTGGCCGATG-CATGTCCCAG
* * **
3129754 ACATGGTCTTACACTAGCTCTCACATATCTGTGCC
63 ACAT-GTCTTACACTA--TCTCTCATTTCAATGCC
* * * * * * * *
3129789 GATGCCATTTCCCAGACATGGTCTTACATTGACAC-CACTACAGGT-ACTGATTCCATGTCCCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-TA-ATGTGGCCGA-TGCATGTCCCAG
* ** *
3129852 ACATGGTCTTATACTGGCACATC-TTGT--A-GCC
63 ACAT-GTCTTACACTATCTC-TCATT-TCAATGCC
* * *
3129883 GATG-CATGTCCCAGACAT-GTCGTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAGA
3129944 CATGTCTTACACTATCTCTCATTTCAATGCC
64 CATGTCTTACACTATCTCTCATTTCAATGCC
* *
3129975 GATGCCATGTCCCAGGCATGGTCTTACACTGGCTCTCATAATTTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
3130040 TGTCTTACACTATCTCTCATTTCAATGCC
66 TGTCTTACACTATCTCTCATTTCAATGCC
* *
3130069 GATGCCATGTCCCAGGCATGGTCTTACACTGGCTCTCATAATTTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
3130134 TGTCTTACACTATCTCTCATTTCAATGCC
66 TGTCTTACACTATCTCTCATTTCAATGCC
* *
3130163 GATGCCATGTCCCAGGCATGGTCTTACACTGGCTCTCATAATTTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
3130228 TGTCTTACACTATCTCTCATTTCAATGCC
66 TGTCTTACACTATCTCTCATTTCAATGCC
3130257 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
3130322 TGTCTTACACTATCTCTCATTTCAATGCC
66 TGTCTTACACTATCTCTCATTTCAATGCC
3130351 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
3130416 TGTCTTACACTA
66 TGTCTTACACTA
3130428 GCACACTAAT
Statistics
Matches: 582, Mismatches: 39, Indels: 41
0.88 0.06 0.06
Matches are distributed among these distances:
89 3 0.01
90 13 0.02
91 17 0.03
92 21 0.04
93 28 0.05
94 430 0.74
95 2 0.00
96 3 0.01
97 2 0.00
98 29 0.05
99 32 0.05
100 1 0.00
101 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (94 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACA
TGTCTTACACTATCTCTCATTTCAATGCC
Found at i:3134280 original size:62 final size:64
Alignment explanation
Indices: 3134202--3134384 Score: 165
Period size: 67 Copynumber: 2.8 Consensus size: 64
3134192 ATATAGTTCG
** * * *
3134202 GCTCTCTTGTAAACATGGTAACAC-TCAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGTA
1 GCTCTCTTGTCTACATGGTAACACATCAGTACCACCCATGCGACCTAGCCACATATATCCCGTA
** * * * * * *
3134264 GCTCTCTTGTCTACATGGTGTCCTTCATCTGGAACCACGCATGCGACCTAACTACATATATCCCG
1 GCTCTCTTGTCTACATGGT-AAC-ACATC-AGTACCACCCATGCGACCTAGCCACATATATCCCG
3134329 TA
63 TA
* * *
3134331 GCTCTCTTGTCTACATGGTGTACACAT-AGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGT-AACACATCAGTACCACCCATGCGACCTAGCCACAT
3134385 CATAATGTCT
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
62 17 0.18
63 1 0.01
64 23 0.24
65 2 0.02
66 21 0.22
67 32 0.33
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTAACACATCAGTACCACCCATGCGACCTAGCCACATATATCCCGTA
Found at i:3135152 original size:30 final size:30
Alignment explanation
Indices: 3135118--3135178 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3135108 TCCTTAACTC
3135118 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
3135148 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
3135178 A
1 A
3135179 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:3156411 original size:40 final size:40
Alignment explanation
Indices: 3156327--3156418 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
3156317 CTCGGTATCG
*
3156327 CACACTTAGTGCATCATATAGCCAAAGCTATTCCAATCCG
1 CACACTTAGTGCATCATATAGCCAAAGCTATTCCAATCCA
** * **
3156367 CACACTTAGTGCATTTTATAGCCGAAGCTATTTTACAT-CA
1 CACACTTAGTGCATCATATAGCCAAAGCTATTCCA-ATCCA
3156407 CACACTTAGTGC
1 CACACTTAGTGC
3156419 CTAACATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 43 0.96
41 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.29
Consensus pattern (40 bp):
CACACTTAGTGCATCATATAGCCAAAGCTATTCCAATCCA
Found at i:3158947 original size:28 final size:27
Alignment explanation
Indices: 3158913--3158982 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
3158903 AACTTACATG
*
3158913 GCGAACCACCAGTTCGCCAAACAAACTA
1 GCGAACC-CCAGCTCGCCAAACAAACTA
* * *
3158941 GCGAACCCTAGCTCGCCAAATAGACTA
1 GCGAACCCCAGCTCGCCAAACAAACTA
*
3158968 GAGAACCCCTAGCTC
1 GCGAACCCC-AGCTC
3158983 ACTAAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.66
28 12 0.34
ACGTcount: A:0.34, C:0.36, G:0.17, T:0.13
Consensus pattern (27 bp):
GCGAACCCCAGCTCGCCAAACAAACTA
Found at i:3158959 original size:27 final size:28
Alignment explanation
Indices: 3158926--3158982 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
3158916 AACCACCAGT
*
3158926 TCGCCAAACAAACTAGCGAA-CCCTAGC
1 TCGCCAAACAAACTAGAGAACCCCTAGC
* *
3158953 TCGCCAAATAGACTAGAGAACCCCTAGC
1 TCGCCAAACAAACTAGAGAACCCCTAGC
3158981 TC
1 TC
3158983 ACTAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.14
Consensus pattern (28 bp):
TCGCCAAACAAACTAGAGAACCCCTAGC
Found at i:3159001 original size:28 final size:29
Alignment explanation
Indices: 3158929--3159001 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
3158919 CACCAGTTCG
* *
3158929 CCAAACAAACTAG-CGAA-CCCTAGCTCG
1 CCAAATAAACTAGACGAACCCCTAGCTCA
*
3158956 CCAAATAGACTAGA-GAACCCCTAGCTCA
1 CCAAATAAACTAGACGAACCCCTAGCTCA
*
3158984 CTAAATAAACT-GACGAAC
1 CCAAATAAACTAGACGAAC
3159002 ATGACTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.41, C:0.32, G:0.14, T:0.14
Consensus pattern (29 bp):
CCAAATAAACTAGACGAACCCCTAGCTCA
Found at i:3159691 original size:18 final size:18
Alignment explanation
Indices: 3159670--3159705 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3159660 AAACTAAACT
3159670 TTCTTATTTAACTAAGAA
1 TTCTTATTTAACTAAGAA
* *
3159688 TTCTTGTTTGACTAAGAA
1 TTCTTATTTAACTAAGAA
3159706 ACAAATACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
TTCTTATTTAACTAAGAA
Found at i:3168272 original size:123 final size:123
Alignment explanation
Indices: 3168113--3168473 Score: 677
Period size: 123 Copynumber: 2.9 Consensus size: 123
3168103 TAGAATCCAG
* *
3168113 CTTCCTCTTATTTGAAGAAAAGTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
1 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
*
3168178 CACTATGTGTGTATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
66 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
3168236 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
1 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
*
3168301 CACAATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
66 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
*
3168359 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATAAT
1 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
3168424 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
66 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
3168474 TTCACCTCAT
Statistics
Matches: 232, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 232 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (123 bp):
CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
Found at i:3172526 original size:18 final size:18
Alignment explanation
Indices: 3172503--3172552 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
3172493 AACTCTATAT
3172503 CCTTCTAGGATTTTAAAC
1 CCTTCTAGGATTTTAAAC
3172521 CCTTCTAGGATTTTAAAC
1 CCTTCTAGGATTTTAAAC
3172539 CCTTCTAGGATTTT
1 CCTTCTAGGATTTT
3172553 CATATAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (18 bp):
CCTTCTAGGATTTTAAAC
Found at i:3174968 original size:64 final size:65
Alignment explanation
Indices: 3174900--3175020 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
3174890 ATGTATAATT
* *
3174900 TGCAAGAAAA-TAAACATACTT-AAAATATCATAAAAATGCCAAAATAACACCAACTTATTATTT
1 TGCAAGAAAACGAAACATACTTAAAAATAACAT-AAAATGCCAAAATAACACCAACTTATTATTT
3174963 A
65 A
*
3174964 TGCAAGAAAACGAAACATACTTAAAAATAACATAAAATGCTAAAATAACACCAACTT
1 TGCAAGAAAACGAAACATACTTAAAAATAACATAAAATGCCAAAATAACACCAACTT
3175021 TTCTAATGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 10 0.19
65 33 0.63
66 9 0.17
ACGTcount: A:0.55, C:0.17, G:0.06, T:0.23
Consensus pattern (65 bp):
TGCAAGAAAACGAAACATACTTAAAAATAACATAAAATGCCAAAATAACACCAACTTATTATTTA
Found at i:3175404 original size:43 final size:43
Alignment explanation
Indices: 3175343--3175430 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
3175333 TACTATGAAC
3175343 ATCATGATAACAATTACTAGTATGTCCTCGACCATGTCCACCA
1 ATCATGATAACAATTACTAGTATGTCCTCGACCATGTCCACCA
3175386 ATCATGATAACAATTACTAGTATGTCCTCGACCATGTCCACCA
1 ATCATGATAACAATTACTAGTATGTCCTCGACCATGTCCACCA
3175429 AT
1 AT
3175431 ATGTCCAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (43 bp):
ATCATGATAACAATTACTAGTATGTCCTCGACCATGTCCACCA
Found at i:3185310 original size:93 final size:93
Alignment explanation
Indices: 3185200--3185370 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
3185190 GCCCCTAAGT
* *
3185200 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
3185265 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
3185293 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
3185358 CGAGTTCGGATGC
66 CGAGTTCGGATGC
3185371 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:3185367 original size:46 final size:46
Alignment explanation
Indices: 3185195--3185367 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
3185185 AACCCGCCCC
* * *
3185195 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
3185241 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
3185289 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
3185334 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3185368 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:3195648 original size:101 final size:101
Alignment explanation
Indices: 3195493--3195674 Score: 303
Period size: 101 Copynumber: 1.8 Consensus size: 101
3195483 ATTTCACGAT
* * *
3195493 TAAAAATCAGCATATCATATAATTAACATTAATAACTTAAATATAACATTTATGCTACATTATTT
1 TAAAAATCAGCATAACATATAATTAACATCAATAACTTAAAAATAACATTTATGCTACATTATTT
*
3195558 TCACATGAACTTACCTACAAAGCATACATTTCATAA
66 ACACATGAACTTACCTACAAAGCATACATTTCATAA
*
3195594 TAAAATTCAGCATAACATATAATTAACATCAATAACTTAAAAATAACCA-TTATGCTACATTATT
1 TAAAAATCAGCATAACATATAATTAACATCAATAACTTAAAAATAA-CATTTATGCTACATTATT
3195658 TACACATGAACTTACCT
65 TACACATGAACTTACCT
3195675 TGGTACCAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
101 73 0.97
102 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (101 bp):
TAAAAATCAGCATAACATATAATTAACATCAATAACTTAAAAATAACATTTATGCTACATTATTT
ACACATGAACTTACCTACAAAGCATACATTTCATAA
Found at i:3197939 original size:32 final size:32
Alignment explanation
Indices: 3197898--3197961 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3197888 AGAGATTTTC
3197898 TTATTTCTTAATTCTTTAACCTCACTATCTAA
1 TTATTTCTTAATTCTTTAACCTCACTATCTAA
3197930 TTATTTCTTAATTCTTTAACCTCACTATCTAA
1 TTATTTCTTAATTCTTTAACCTCACTATCTAA
3197962 AATTCAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (32 bp):
TTATTTCTTAATTCTTTAACCTCACTATCTAA
Found at i:3204400 original size:44 final size:43
Alignment explanation
Indices: 3204299--3204413 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 43
3204289 AACGCAAACA
* *
3204299 TCCCAGACGTGGTCTTACATGTAATCACATATCAATGCCACTG
1 TCCCAGACGTGGTCTTACACGTAATCACAAATCAATGCCACTG
* * * *
3204342 TCCCAAATAG-GGTCTTACACGTAAATTACAAATCGATGCCAAC-G
1 TCCCAGA-CGTGGTCTTACACGT-AATCACAAATCAATGCC-ACTG
3204386 TCCCAGACGTGGTCTTACACG-AATCACA
1 TCCCAGACGTGGTCTTACACGTAATCACA
3204414 TATCGGAATC
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 6 0.10
43 18 0.31
44 33 0.56
45 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
TCCCAGACGTGGTCTTACACGTAATCACAAATCAATGCCACTG
Found at i:3205538 original size:13 final size:13
Alignment explanation
Indices: 3205520--3205544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3205510 TCAAACGATA
3205520 AAATTTTCACACG
1 AAATTTTCACACG
3205533 AAATTTTCACAC
1 AAATTTTCACAC
3205545 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:3206626 original size:29 final size:27
Alignment explanation
Indices: 3206608--3206677 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
3206598 ATATTAAGTC
3206608 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
3206635 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
3206663 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
3206678 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:3206671 original size:28 final size:28
Alignment explanation
Indices: 3206608--3206705 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
3206598 ATATTAAGTC
*
3206608 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
3206635 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
3206663 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
3206692 CGCACACTTAGTGC
1 CGCACACTTAGTGC
3206706 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:3209105 original size:29 final size:29
Alignment explanation
Indices: 3209064--3209123 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
3209054 ACTAATTAAA
*
3209064 TTAATTAATCTAAAATAACCTAACGAAAT
1 TTAATTAACCTAAAATAACCTAACGAAAT
* * *
3209093 TTAATTAACCTAAGATATCCTAATGAAAT
1 TTAATTAACCTAAAATAACCTAACGAAAT
3209122 TT
1 TT
3209124 CCTGTTCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (29 bp):
TTAATTAACCTAAAATAACCTAACGAAAT
Found at i:3209728 original size:17 final size:16
Alignment explanation
Indices: 3209702--3209733 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3209692 AAGAAATGAT
3209702 AAAATAAAAATTAAAG
1 AAAATAAAAATTAAAG
3209718 AAAACTAAAAATTAAA
1 AAAA-TAAAAATTAAA
3209734 AGTATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATTAAAG
Found at i:3213866 original size:29 final size:29
Alignment explanation
Indices: 3213824--3213905 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
3213814 TATATATATG
3213824 AATTATCGAGCACTAAGTGTGCGAAGTAA
1 AATTATCGAGCACTAAGTGTGCGAAGTAA
3213853 AATTATCGAGCACTAAGTGTGCGAAGTAA
1 AATTATCGAGCACTAAGTGTGCGAAGTAA
*
3213882 AACTATCGAGCACTAAGTGTGCGA
1 AATTATCGAGCACTAAGTGTGCGA
3213906 TTTCATTGCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (29 bp):
AATTATCGAGCACTAAGTGTGCGAAGTAA
Found at i:3225116 original size:28 final size:29
Alignment explanation
Indices: 3225075--3225137 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
3225065 AGGAAGCGTC
* *
3225075 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCCATGCCACAAAATATCTGTAT
*
3225103 CTGGTGGCCCTGCCACAAAATATCTGTAT
1 CTGGTGGCCATGCCACAAAATATCTGTAT
3225132 CTGGTG
1 CTGGTG
3225138 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCCATGCCACAAAATATCTGTAT
Found at i:3225148 original size:29 final size:28
Alignment explanation
Indices: 3225085--3225148 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
3225075 CTGGTGGCTA
* *
3225085 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACCC
*
3225113 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACCC
*
3225142 TGTCACA
1 TGCCACA
3225149 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACCC
Found at i:3226922 original size:6 final size:6
Alignment explanation
Indices: 3226911--3226939 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3226901 GCCATGTTCA
3226911 TATATC TATATC TATATC TATATC TATAT
1 TATATC TATATC TATATC TATATC TATAT
3226940 ATTTAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATC
Found at i:3229592 original size:13 final size:14
Alignment explanation
Indices: 3229563--3229593 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3229553 TTTGGTTTTC
3229563 TTTATTTTACTTAA
1 TTTATTTTACTTAA
3229577 TTTATTTTAC-TAA
1 TTTATTTTACTTAA
3229590 TTTA
1 TTTA
3229594 CAATTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTTTACTTAA
Found at i:3237798 original size:38 final size:39
Alignment explanation
Indices: 3237734--3237808 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
3237724 TCAAACATGT
* *
3237734 ACTGGGCCATAGCCCTTTTCATATTTCATATTTCATAAC
1 ACTGGGCCAAAGCCCTTTTCAAATTTCATATTTCATAAC
3237773 ACTGGGCCAAAG-CCTTTTCAAATTTCATATTTCATA
1 ACTGGGCCAAAGCCCTTTTCAAATTTCATATTTCATA
3237809 TTTCATAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 23 0.68
39 11 0.32
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (39 bp):
ACTGGGCCAAAGCCCTTTTCAAATTTCATATTTCATAAC
Found at i:3237814 original size:45 final size:45
Alignment explanation
Indices: 3237750--3237848 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 45
3237740 CCATAGCCCT
3237750 TTTCATATTTCATATTTCATAACACTGGGCCAAAGCCTTTTCAAA
1 TTTCATATTTCATATTTCATAACACTGGGCCAAAGCCTTTTCAAA
* *
3237795 TTTCATATTTCATATTTCATAACACTGGGCCGAAGCCTTTTCATA
1 TTTCATATTTCATATTTCATAACACTGGGCCAAAGCCTTTTCAAA
3237840 TTTCATATT
1 TTTCATATT
3237849 ACTAGGCCGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.41
Consensus pattern (45 bp):
TTTCATATTTCATATTTCATAACACTGGGCCAAAGCCTTTTCAAA
Found at i:3237840 original size:31 final size:31
Alignment explanation
Indices: 3237802--3237865 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3237792 AAATTTCATA
*
3237802 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
**
3237833 TTTCATATTTCATATTACTAGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
3237864 TT
1 TT
3237866 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCGAAGCCT
Done.