Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold155
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: 399999
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
File 1 of 2
Found at i:3470 original size:3 final size:3
Alignment explanation
Indices: 3462--3490 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3452 GTGAAATGGA
3462 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
3491 AAATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:4312 original size:101 final size:101
Alignment explanation
Indices: 4137--4332 Score: 275
Period size: 101 Copynumber: 1.9 Consensus size: 101
4127 GAATTGACGA
* * * * *
4137 ATAAGACCATGGTTGGACCATGGCAATTTTTATATGTAAGACCCTAACTAGGCTATGGCATTTTA
1 ATAAGACCATGGTTGGACCATGACAATATTTATAAGTAAGACCATAACTAGGCTATGGCATTCTA
4202 ATGAAAAGACCATAACTGGGTTATGGCACTTTGAAC
66 ATGAAAAGACCATAACTGGGTTATGGCACTTTGAAC
* * * ** * *
4238 ATAAGACCATGGTTGGACTATGATAGTATTTATAAGTAAGACCATAGTTGGGCTATGGCATTCTG
1 ATAAGACCATGGTTGGACCATGACAATATTTATAAGTAAGACCATAACTAGGCTATGGCATTCTA
*
4303 ATGATAAGACCATAACTGGGTTATGGCACT
66 ATGAAAAGACCATAACTGGGTTATGGCACT
4333 ACAAATCTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (101 bp):
ATAAGACCATGGTTGGACCATGACAATATTTATAAGTAAGACCATAACTAGGCTATGGCATTCTA
ATGAAAAGACCATAACTGGGTTATGGCACTTTGAAC
Found at i:4316 original size:33 final size:32
Alignment explanation
Indices: 4173--4330 Score: 102
Period size: 33 Copynumber: 4.8 Consensus size: 32
4163 TTTTTATATG
* * *
4173 TAAGACCCTAACTAGGCTATGGCATTTTAATGA
1 TAAGACCATAACTGGGCTATGGCA-TTTGATGA
* * **
4206 AAAGACCATAACTGGGTTATGGCACTTTGAACA
1 TAAGACCATAACTGGGCTATGGCA-TTTGATGA
*** * * *
4239 TAAGACCATGGTTGGACTATGATAGTATTT-ATAA
1 TAAGACCATAACTGGGCTATG---GCATTTGATGA
**
4273 GTAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 -TAAGACCATAACTGGGCTATGGCATT-TGATGA
*
4307 TAAGACCATAACTGGGTTATGGCA
1 TAAGACCATAACTGGGCTATGGCA
4331 CTACAAATCT
Statistics
Matches: 95, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
32 4 0.04
33 62 0.65
34 5 0.05
35 22 0.23
36 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (32 bp):
TAAGACCATAACTGGGCTATGGCATTTGATGA
Found at i:7975 original size:19 final size:20
Alignment explanation
Indices: 7929--7980 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
7919 GGGTTGGCAT
7929 TTTGGTGCCTCTGATTGCACA
1 TTTGGTG-CTCTGATTGCACA
7950 TTT-GTGCTCT-ATCTGCAC-
1 TTTGGTGCTCTGAT-TGCACA
7968 TTTGGTGCCTCTG
1 TTTGGTG-CTCTG
7981 TTACGCGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 7 0.26
21 3 0.11
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (20 bp):
TTTGGTGCTCTGATTGCACA
Found at i:9876 original size:9 final size:9
Alignment explanation
Indices: 9859--9889 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9849 TCGAGTTGAT
9859 TCGAATAAC
1 TCGAATAAC
*
9868 TCGATTAAC
1 TCGAATAAC
9877 TCGAATAAC
1 TCGAATAAC
9886 TCGA
1 TCGA
9890 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:12992 original size:29 final size:29
Alignment explanation
Indices: 12957--13023 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
12947 GTGAATGTCT
* *
12957 CAACATTGGGATCAAAATGCTCAATGCCG
1 CAACATTGGGATCAAAATGCCCAAGGCCG
* *
12986 CAACATTGAGATCAAAATGCCCAAGGTCG
1 CAACATTGGGATCAAAATGCCCAAGGCCG
13015 CAACATTGG
1 CAACATTGG
13024 CTAGGGAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (29 bp):
CAACATTGGGATCAAAATGCCCAAGGCCG
Found at i:15627 original size:4 final size:4
Alignment explanation
Indices: 15618--15685 Score: 127
Period size: 4 Copynumber: 17.0 Consensus size: 4
15608 TATTAAATCA
*
15618 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
15666 GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT
15686 ATCTATTGTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:16505 original size:14 final size:14
Alignment explanation
Indices: 16486--16515 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16476 GAGGTTTGAT
16486 TATATATATATTTA
1 TATATATATATTTA
*
16500 TATATATATGTTTA
1 TATATATATATTTA
16514 TA
1 TA
16516 AATTTATAAA
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:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TATATATATATTTA
Found at i:16710 original size:42 final size:41
Alignment explanation
Indices: 16656--16804 Score: 156
Period size: 42 Copynumber: 3.5 Consensus size: 41
16646 GATTTTAGGC
16656 TTACG-CCTAGCAGGCTTATCGCCAGTGAAACAATATCAGACT
1 TTACGTCC-AGCAGGCTTAT-GCCAGTGAAACAATATCAGACT
* * * *
16698 TTACGTCCAGCAGGCCTAATGCCAGTGAAATAATTTTAGACT
1 TTACGTCCAGCAGG-CTTATGCCAGTGAAACAATATCAGACT
* * * * *
16740 TTAAGTCTAGCAAGCTTAATGCCAGTGAAAGAATATCAAACT
1 TTACGTCCAGCAGGCTT-ATGCCAGTGAAACAATATCAGACT
*
16782 TTACGTCTAGCAGGCTTAATGCC
1 TTACGTCCAGCAGGCTT-ATGCC
16805 GGTCAAATAT
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.02
42 82 0.91
43 6 0.07
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (41 bp):
TTACGTCCAGCAGGCTTATGCCAGTGAAACAATATCAGACT
Found at i:16803 original size:84 final size:83
Alignment explanation
Indices: 16662--16838 Score: 239
Period size: 84 Copynumber: 2.1 Consensus size: 83
16652 AGGCTTACGC
* * *
16662 CTAGCAGGCTTATCGCCAGTGAAACAATATCAGACTTTACGTCCAGCAGGCCTAATGCCAGTGAA
1 CTAGCAAGCTTATCGCCAGTGAAACAATATCAAACTTTACGTCCAGCAGGCCTAATGCCAGTCAA
* *
16727 ATAATTTTAGACTTTAAGT
66 AT-ATTTCAGACTATAAGT
* * * *
16746 CTAGCAAGCTTAAT-GCCAGTGAAAGAATATCAAACTTTACGTCTAGCAGGCTTAATGCCGGTCA
1 CTAGCAAGCTT-ATCGCCAGTGAAACAATATCAAACTTTACGTCCAGCAGGCCTAATGCCAGTCA
*
16810 AATATTTCAGACTATATGT
65 AATATTTCAGACTATAAGT
16829 CTAGCAAGCT
1 CTAGCAAGCT
16839 AAGTGTCGAT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
83 23 0.28
84 57 0.70
85 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (83 bp):
CTAGCAAGCTTATCGCCAGTGAAACAATATCAAACTTTACGTCCAGCAGGCCTAATGCCAGTCAA
ATATTTCAGACTATAAGT
Found at i:23896 original size:42 final size:41
Alignment explanation
Indices: 23845--24033 Score: 172
Period size: 41 Copynumber: 4.6 Consensus size: 41
23835 GGCTTAGCGC
* *
23845 CTAGTAGGCTT-ATCGCCAGTGAAATAATTTCAGACTTTACGT
1 CTAGCAGGCTTAAT-GCCGGTGAAA-AATTTCAGACTTTACGT
* *
23887 CTAGCAGGCTTAATGCCGGTAAAACAATATCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAA-AATTTCAGACTTTACGT
* * *
23929 CTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGGTGAAAAATTTCAGACTTTACGT
* * * * *
23970 CTAGCAGG-ATAAGTGCCGGTGTACTAAA--TCAGGCTTTAAGC
1 CTAGCAGGCTTAA-TGCCGGTG-A-AAAATTTCAGACTTTACGT
24011 CTAGCAGGC-TAAGTGCCGGTGAA
1 CTAGCAGGCTTAA-TGCCGGTGAA
24034 TCTATTTAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
40 4 0.03
41 58 0.47
42 58 0.47
43 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAAAATTTCAGACTTTACGT
Found at i:24030 original size:82 final size:83
Alignment explanation
Indices: 23843--24033 Score: 203
Period size: 82 Copynumber: 2.3 Consensus size: 83
23833 CAGGCTTAGC
* * * * *
23843 GCCTAGTAGGCTT-ATCGCCAGTGAAATAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCGGT
1 GCCTAGCAGGCTTAAT-GCCGGTGAAA-CATTTCAGACTATACGTCTAGCAGGCATAATGCCGGT
*
23907 AAAACAATATCAGACTTTAC
64 AAAACAATATCAGACTTTAA
* *
23927 GTCTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTCTAGCAGG-ATAAGTGCCGGT-
1 GCCTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATACGTCTAGCAGGCATAA-TGCCGGTA
** *
23990 GTACTAA-ATCAGGCTTTAA
65 AAAC-AATATCAGACTTTAA
24009 GCCTAGCAGGC-TAAGTGCCGGTGAA
1 GCCTAGCAGGCTTAA-TGCCGGTGAA
24034 TCTATTTAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
81 3 0.03
82 35 0.38
83 31 0.34
84 20 0.22
85 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (83 bp):
GCCTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATACGTCTAGCAGGCATAATGCCGGTAA
AACAATATCAGACTTTAA
Found at i:32794 original size:539 final size:539
Alignment explanation
Indices: 31777--32842 Score: 1659
Period size: 539 Copynumber: 2.0 Consensus size: 539
31767 TTGACCTAAT
* * *
31777 CATCAGTAATAACTTTTGTACCTACAGAAGTGTTAACCTGAACATCTCCTATTCCCTTGGCTTCA
1 CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCCCCTATTCCCTTGGCTTCA
* * *
31842 ATGATCTGGCCATTTCAAACTCTGATTCTCGAACTGAATAATCTATCAATCTCCTTGAACATGCT
66 ATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGCT
* *
31907 TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACTAGTTTTTCTTGTCTTGGTTGT
131 TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTGGTTGT
*
31972 TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGCTTGATTTTCTTCAGCACTTGAG
196 TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTGAG
* * *
32037 CCTGATTAGACTACTATTGTTGTTACTGCACTTTGTTTTTATAAATTCTAAAATCGTGGCCGAAT
261 CCTGATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAAAT
* *** * * *
32102 TGCTTACAGTTTTTACACTGTGCACCAATTTTTATCCAACAAAACTTTTATGAATGACCCATCTT
326 TGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATCTT
* * * *
32167 TTTGCAATTCGATCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTTGCCTTTCTCTTGCTT
391 TTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTAGCCTTTCTCTTGCTT
* * * * *
32232 GATTCCTTTTCTTCTTGCCTTTGTTTCTTGAAGAGCATGGAGTTTCCTTGTTTCTCACTTGGTAA
456 GATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGTAA
32297 GCACCTTCTACGTGAAATA
521 GCACCTTCTACGTGAAATA
*
32316 CATCAGTAATAACTTTTGTACCTATAGAAGTGCTAACCTAAACATCCCC-ATTTCCCTTGGCTTC
1 CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCCCCTA-TTCCCTTGGCTTC
* * * *
32380 AATGATCTGGCCATTTCCAAGTCTGATTCTCAAACTGAAGGATATGTCAATCTCCTTGAACATGC
65 AATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGC
* * *
32445 TTTCATCTGAAACCATATGGTTTGTACAACCTCTGTCAATCAACCATTTTTTCTTATCTTGGTTG
130 TTTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTGGTTG
* * * *
32510 TTGATTTTGAAGCATGAAGTAGTGAAT-TCGAGCTCCTCCTGAGATTGATTTTCTTCAGCACTTG
195 TTGACTGTGAAGCATGAAGCAGTGAATGT-GAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTG
* * *
32574 AGCCTGATTAGACTGCTATTGTTGCTGCTGCACTTTGTTTTTACAAATTCTAAAATTGTGGCCAA
259 AGCCTGATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAA
* * * *
32639 ATTGCTTACAATTTTTACACTACACACCAGGTCTTGTCCAGCAAAACTTTTCTAAATGACCCATC
324 ATTGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATC
* *
32704 TTTTTGCAATCCAAGCGTGGTGGATACTTTTTCTTTTCACCATCTCTTTTTAGCCTTTCTCTTGC
389 TTTTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTAGCCTTTCTCTTGC
32769 TTGATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGT
454 TTGATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGT
32834 AAGCACCTT
519 AAGCACCTT
32843 TTGTGTGCCC
Statistics
Matches: 476, Mismatches: 49, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
538 2 0.00
539 474 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (539 bp):
CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCCCCTATTCCCTTGGCTTCA
ATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGCT
TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTGGTTGT
TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTGAG
CCTGATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAAAT
TGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATCTT
TTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTAGCCTTTCTCTTGCTT
GATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGTAA
GCACCTTCTACGTGAAATA
Found at i:40657 original size:2 final size:2
Alignment explanation
Indices: 40650--40674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40640 TAATAATGTT
40650 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 T
40675 TAGATACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50140 original size:18 final size:19
Alignment explanation
Indices: 50101--50144 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
50091 TACCATTTGA
50101 ATTAAATATTAATATTATT
1 ATTAAATATTAATATTATT
*
50120 ATTAAA-ATTAA-ATTGTAT
1 ATTAAATATTAATATTAT-T
50138 ATTAAAT
1 ATTAAAT
50145 GATTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTAAATATTAATATTATT
Found at i:58190 original size:22 final size:22
Alignment explanation
Indices: 58165--58244 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 22
58155 TTTACCTTTG
58165 ATTTTAATATTAAAATAAAAAT
1 ATTTTAATATTAAAATAAAAAT
* * * *
58187 ATTTTAAATTTTAAATTTAATTTGCATT
1 ATTTT-AATATTAAA-ATAA----AAAT
58215 GATTTTAATATTAAAATAAAAAT
1 -ATTTTAATATTAAAATAAAAAT
58238 ATTTTAA
1 ATTTTAA
58245 ATTTTAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
22 12 0.28
23 10 0.23
24 3 0.07
27 3 0.07
28 10 0.23
29 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTTTAATATTAAAATAAAAAT
Found at i:58197 original size:29 final size:28
Alignment explanation
Indices: 58165--58266 Score: 81
Period size: 28 Copynumber: 3.8 Consensus size: 28
58155 TTTACCTTTG
58165 ATTTTAATATTAAAATAAAAATATTTTAA
1 ATTTTAA-ATTAAAATAAAAATATTTTAA
* * *** *
58194 ATTTTAAATTTAATTTGCATTGATTTT-A
1 ATTTTAAATTAAAATAAAAAT-ATTTTAA
58222 A---T--ATTAAAATAAAAATATTTTAA
1 ATTTTAAATTAAAATAAAAATATTTTAA
*
58245 ATTTTAAATTTAAATAAAAATA
1 ATTTTAAATTAAAATAAAAATA
58267 AAATAATATA
Statistics
Matches: 53, Mismatches: 13, Indels: 15
0.65 0.16 0.19
Matches are distributed among these distances:
22 5 0.09
23 10 0.19
25 1 0.02
26 1 0.02
28 24 0.45
29 12 0.23
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (28 bp):
ATTTTAAATTAAAATAAAAATATTTTAA
Found at i:58784 original size:3 final size:3
Alignment explanation
Indices: 58776--58821 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
58766 CATGGTTGCT
58776 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
58822 AAGAGTCGTA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:69664 original size:43 final size:43
Alignment explanation
Indices: 69539--69665 Score: 161
Period size: 41 Copynumber: 3.0 Consensus size: 43
69529 ATAGGATCTC
* *
69539 CGATATGTGTTTACGTGTAAGACCAAGTCTGGGACATTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
* *
69582 CG-TATTTGATT-CGTGTAAGACC-CTGTCTGGGACAATGGCAT
1 CGATATGTGATTACGTGTAAGACCAC-GTCTGGGACATTGGCAT
* * *
69623 CGATATGTGATTACATGTAAGACCACGTATGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
69666 TGTACGAGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
41 29 0.41
42 15 0.21
43 26 0.37
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
CGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
Found at i:78438 original size:27 final size:27
Alignment explanation
Indices: 78402--78456 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
78392 ACTTAGATTT
**
78402 TACATTGGTTAAATACTTAGTGTGAGA
1 TACATTGGTTAAATACCAAGTGTGAGA
78429 TACATTGGTTAAATACCAAGTGTGAGA
1 TACATTGGTTAAATACCAAGTGTGAGA
78456 T
1 T
78457 TTGCATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (27 bp):
TACATTGGTTAAATACCAAGTGTGAGA
Found at i:86854 original size:18 final size:20
Alignment explanation
Indices: 86819--86860 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
86809 CAGATTCAAA
86819 AAAATAAAAAAATCAAAATC
1 AAAATAAAAAAATCAAAATC
86839 AAAAT-AAAAAAT-AAAATC
1 AAAATAAAAAAATCAAAATC
86857 AAAA
1 AAAA
86861 ATGAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAATAAAAAAATCAAAATC
Found at i:86859 original size:24 final size:23
Alignment explanation
Indices: 86814--86860 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
86804 GAGTTCAGAT
86814 TCAAAAAAATAAAAAAATCAAAA
1 TCAAAAAAATAAAAAAATCAAAA
86837 TCAAAATAAA-AAATAAAATCAAAA
1 TCAAAA-AAATAAA-AAAATCAAAA
86861 ATGAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.15
Consensus pattern (23 bp):
TCAAAAAAATAAAAAAATCAAAA
Found at i:86875 original size:6 final size:6
Alignment explanation
Indices: 86866--86909 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
86856 CAAAAATGAG
86866 AGAAAA AGAAAGA AGAAAAAA AGAAAA AGAAAA AG-AAA AGAAAA
1 AGAAAA AGAAA-A AG--AAAA AGAAAA AGAAAA AGAAAA AGAAAA
86910 TAAGAGGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.15
6 20 0.59
7 3 0.09
8 3 0.09
9 3 0.09
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:86892 original size:21 final size:20
Alignment explanation
Indices: 86866--86904 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
86856 CAAAAATGAG
86866 AGAAAAAGAAAGAAGAAAAAA
1 AGAAAAAGAAA-AAGAAAAAA
86887 AGAAAAAGAAAAAGAAAA
1 AGAAAAAGAAAAAGAAAA
86905 GAAAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AGAAAAAGAAAAAGAAAAAA
Found at i:86895 original size:14 final size:15
Alignment explanation
Indices: 86868--86899 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
86858 AAAATGAGAG
86868 AAAAAGAAAGAAGAA
1 AAAAAGAAAGAAGAA
86883 AAAAAGAAA-AAGAA
1 AAAAAGAAAGAAGAA
86897 AAA
1 AAA
86900 GAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAGAA
Found at i:86896 original size:17 final size:17
Alignment explanation
Indices: 86874--86909 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
86864 AGAGAAAAAG
86874 AAAGAAGAAA-AAAAGAA
1 AAAGAA-AAAGAAAAGAA
86891 AAAGAAAAAGAAAAGAA
1 AAAGAAAAAGAAAAGAA
86908 AA
1 AA
86910 TAAGAGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAGAA
Found at i:86904 original size:11 final size:11
Alignment explanation
Indices: 86869--86909 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
86859 AAATGAGAGA
86869 AAAAGAAAGAAG
1 AAAAGAAA-AAG
*
86881 AAAA-AAAGA-
1 AAAAGAAAAAG
86890 AAAAGAAAAAG
1 AAAAGAAAAAG
86901 AAAAGAAAA
1 AAAAGAAAA
86910 TAAGAGGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 4 0.16
10 5 0.20
11 12 0.48
12 4 0.16
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:89161 original size:44 final size:44
Alignment explanation
Indices: 89111--89420 Score: 439
Period size: 44 Copynumber: 7.0 Consensus size: 44
89101 ACAGATCGGT
* *
89111 AAGATTGTGAA-TCCTATCTCCCTAGACAGCAGTGGAATAGGTTA
1 AAGATTGT-AAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTG
*
89155 AAGATTGTAAGTCCTATCTCCTTGGACAGCAGTGGAATAGGTTG
1 AAGATTGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTG
*
89199 AAGATTGTAAGTCCTATCTCCCTGGACAACAGTGGAATAGGTTG
1 AAGATTGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTG
** * *
89243 AAGATTGTAAGTCCTATCTCTTTAGACAACAGTGGAATAGGTTG
1 AAGATTGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTG
* * *
89287 AAGATTGTAAGTCCTATCTTCCTGGACAACAGTGGAATAGGTTA
1 AAGATTGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTG
* *
89331 AAGATTGTAAGTCCTATCTTCCTGGATAGCAGTGGAATAGGTTG
1 AAGATTGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTG
89375 AAGATTGTGAA-TCCTATCTCCCT-GAGCAGCAGT-GAAGTAGGTTG
1 AAGATTGT-AAGTCCTATCTCCCTGGA-CAGCAGTGGAA-TAGGTTG
89419 AA
1 AA
89421 AATAACAGAT
Statistics
Matches: 244, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
43 7 0.03
44 235 0.96
45 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
AAGATTGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTG
Found at i:89439 original size:88 final size:89
Alignment explanation
Indices: 89345--90492 Score: 722
Period size: 88 Copynumber: 13.1 Consensus size: 89
89335 TTGTAAGTCC
* * * * *
89345 TATCTTCCTGGA-TAGCAGTGGAA-TAGGTTGAAGATTGTGAATCC-TATCTCCCTGAGCAGCAG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGA-TCT-AATCCTTATCTCCCTGAGCAGCAG
*
89407 TGAAGTAGGTTGAAAATAACAGATAT
64 TGAAGTAGGTTGAAAATAACAGATCT
* * * * *
89433 TGTCTTCCTGTACTGGCTGT-GAAGTAGATCGAAGATCTCATCCTTATCTCCCTGAACAGCAGCG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* * *
89497 GAGTAGGTTAAAAATAGCAGATCT
66 AAGTAGGTTGAAAATAACAGATCT
* * * * *
89521 TATCTTCCTGTATTGGCAG-GGAAGTAGATCGAAGACCCCAA-CCTTGTCTCCCTGAGCAGCAAT
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGA-TCTAATCCTTATCTCCCTGAGCAGCAGT
* *
89584 GGAGTAGGTTGAAAATAGCAGATCT
65 GAAGTAGGTTGAAAATAACAGATCT
* * * * * * ** * *
89609 TGTCTTCTTGTATTGGCAG-CGAAGTAGATTGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* * *
89673 GAGTAGGTTAAAAATAGCAGATCT
66 AAGTAGGTTGAAAATAACAGATCT
** * * * * * * *
89697 CGTCTTCCTGTATTGGTAGT-GAAGTAGATCGAAGACCCCAA-CCTTATCTCTCTTAGCAGTAGT
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGA-TCTAATCCTTATCTCCCTGAGCAGCAGT
* *
89760 GGAGTAGGTTGAAAATAACAGATAT
65 GAAGTAGGTTGAAAATAACAGATCT
* * * * ** * * *
89785 TATCTTCCTATATTGGCAG-CGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAACAGCAGTG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* *
89849 GAGTAGGTTGAAAATAGCAGATCT
66 AAGTAGGTTGAAAATAACAGATCT
* * * * * * * ** *
89873 TGTTTTCTTGTATTGGCAG-CGAAGTAGATCAAAGACCCCAGCCTTATCTCCCTGAGCAGCAGTG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* * * *
89937 GAGTAGGTTAAAAATGACAAATCT
66 AAGTAGGTTGAAAATAACAGATCT
* * * * * * * * *
89961 TGT-TTTCTAGTATTGGCAG-CGAAGTAGATCGAA-AACTCCAGCCTTGTCTCCTTGAGCAGCAG
1 TATCTTCCT-GTACTGGCAGTGGAAGTAGATCGAAGATCT-AATCCTTATCTCCCTGAGCAGCAG
* * *
90023 TGGAGTAGGTTAAAAATATCAGATCT
64 TGAAGTAGGTTGAAAATAACAGATCT
* * * * * * * **
90049 TGTATTCC-GTTATTGGCAG-CGAAGTAGATCGAAGACCCT-AGCCTTATCTCCCTAAGCAATAG
1 TATCTTCCTG-TACTGGCAGTGGAAGTAGATCGAAGA-TCTAATCCTTATCTCCCTGAGCAGCAG
* **
90111 TGGAGTAGGTTGAAAATAGTAGATCT
64 TGAAGTAGGTTGAAAATAACAGATCT
* * * * * ** * * * *
90137 TGTCTTCTTGTATTGGCAG-CGAAGTAGATCGAAGACCCCATCCTTGTCTCTCTAAGCAGCAATG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* *
90201 GAGTAGGTTAAAAATGAA-AGATCT
66 AAGTAGGTTGAAAAT-AACAGATCT
* * * ** * * * ** * * *
90225 TGTCTTCCAGTATTGGCAG-CAAAGTAGATTGAAAACCCCAGCCTTGTCTCCTTGAGCAGCAGTG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* * *
90289 AAGTAGGTTAAAAATAGCAGATAT
66 AAGTAGGTTGAAAATAACAGATCT
* * * * * ** * * * **
90313 TGTCTTCCTGTATTGGCAG-CGAAGTAGATAGAAGACCCCAGCCTTGTCTCCCTGAGTAATAGTG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* *
90377 GAGTAGGTTGAAAATAGCAGATCT
66 AAGTAGGTTGAAAATAACAGATCT
* * * * ** * * *
90401 TGTCTTCCTGTATTGGCAG-CGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAGTAGCAGTG
1 TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
* *
90465 GAGTAGGTTGAAAAT-ATAGATCT
66 AAGTAGGTTGAAAATAACAGATCT
90488 TATCT
1 TATCT
90493 ATCTGAAGTT
Statistics
Matches: 912, Mismatches: 128, Indels: 41
0.84 0.12 0.04
Matches are distributed among these distances:
87 31 0.03
88 853 0.94
89 26 0.03
90 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (89 bp):
TATCTTCCTGTACTGGCAGTGGAAGTAGATCGAAGATCTAATCCTTATCTCCCTGAGCAGCAGTG
AAGTAGGTTGAAAATAACAGATCT
Found at i:89506 original size:176 final size:177
Alignment explanation
Indices: 89301--90480 Score: 1058
Period size: 176 Copynumber: 6.7 Consensus size: 177
89291 TTGTAAGTCC
* * * * * *
89301 TATCTTCCTGGACAACAGTGGAATAGGTTAAAGATTGTAAG-TCCTATCTTCCTGGA-TAGCAGT
1 TATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAG-AAGATCCTATCTTCCTGGATTAGCAGT
* * ****
89364 GGAA-TAGGTTGAAGATTGTGAATCC-TATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAAC
65 GGAAGTAGATCGAAGA-CCCCAA-CCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAAC
* * * *
89427 AGATATTGTCTTCCTGTACTGGCTGTGAAGTAGATCGAAGATCTCATCCT
128 AGATATTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACCCCATCCT
* * * * *
89477 TATCTCCCTGAACAGCAGCGGAGTAGGTTAAAAATAGCAGATCTTATCTTCCTGTATTGGCAG-G
1 TATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGAAGATCCTATCTTCCTGGATTAGCAGTG
* * * *
89541 GAAGTAGATCGAAGACCCCAACCTTGTCTCCCTGAGCAGCAATGGAGTAGGTTGAAAATAGCAGA
66 GAAGTAGATCGAAGACCCCAACCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAACAGA
* * * * *
89606 TCTTGTCTTCTTGTATTGGCAGCGAAGTAGATTGAAGACCCCAGCCT
131 TATTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACCCCATCCT
* * * * * * *
89653 TGTCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGAT-CTCGTCTTCCTGTATTGGTAGT
1 TATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGAAGATCCT-ATCTTCCTGGATTAGCAGT
* * * *
89717 -GAAGTAGATCGAAGACCCCAACCTTATCTCTCTTAGCAGTAGTGGAGTAGGTTGAAAATAACAG
65 GGAAGTAGATCGAAGACCCCAACCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAACAG
* * * *
89781 ATATTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCCT
130 ATATTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACCCCATCCT
* * * * * * * * * *
89829 TGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTTTTCTTGTATTGGCAG-C
1 TATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGAAGATCCTATCTTCCTGGATTAGCAGTG
* * * * * *
89893 GAAGTAGATCAAAGACCCCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATGACAAA
66 GAAGTAGATCGAAGACCCCAACCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAACAGA
* * * * * *
89958 TCTTGT-TTTCTAGTATTGGCAGCGAAGTAGATCGAAAACTCCAGCCT
131 TATTGTCTTCCT-GTACTGGCAGCGAAGTAGATCGAAGACCCCATCCT
* * * ** * * * * *
90005 TGTCTCCTTGAGCAGCAGTGGAGTAGGTTAAAAATATCAGATCTTGTATTCC-GTTATTGGCAG-
1 TATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGAAGATCCTATCTTCCTG-GATTAGCAGT
* * * * ** * **
90068 CGAAGTAGATCGAAGACCCTAGCCTTATCTCCCTAAGCAATAGTGGAGTAGGTTGAAAATAGTAG
65 GGAAGTAGATCGAAGACCCCAACCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAACAG
* * *
90133 ATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACCCCATCCT
130 ATATTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACCCCATCCT
* * * * * * * *
90181 TGTCTCTCT-AAGCAGCAATGGAGTAGGTTAAAAAT-GAAAGATCTTGTCTTCCAGTATTGGCAG
1 TATCTCCCTGAA-CAGCAGTGGAGTAGGTTAAAAATAG-AAGATCCTATCTTCCTGGATTAGCAG
** * * * * * * *
90244 -CAAAGTAGATTGAAAACCCCAGCCTTGTCTCCTTGAGCAGCAGTGAAGTAGGTTAAAAATAGCA
64 TGGAAGTAGATCGAAGACCCCAACCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAACA
* * *
90308 GATATTGTCTTCCTGTATTGGCAGCGAAGTAGATAGAAGACCCCAGCCT
129 GATATTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACCCCATCCT
* ** ** * * * * * * *
90357 TGTCTCCCTGAGTAATAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAG-C
1 TATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGAAGATCCTATCTTCCTGGATTAGCAGTG
* * * *
90421 GAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATA
66 GAAGTAGATCGAAGACCCCAACCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATA
90481 TAGATCTTAT
Statistics
Matches: 861, Mismatches: 127, Indels: 32
0.84 0.12 0.03
Matches are distributed among these distances:
175 11 0.01
176 829 0.96
177 21 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (177 bp):
TATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGAAGATCCTATCTTCCTGGATTAGCAGTG
GAAGTAGATCGAAGACCCCAACCTTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAACAGA
TATTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGACCCCATCCT
Found at i:89613 original size:44 final size:44
Alignment explanation
Indices: 89391--89875 Score: 131
Period size: 44 Copynumber: 11.0 Consensus size: 44
89381 GTGAATCCTA
* * *
89391 TCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATAACAGATATTG
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* * * * * * * ** *
89435 TCTTCCTGTA-CTGGCTGTGAAGTAGATCGAAGAT--CTCATCCTTA
1 TCTCCCTG-AGC-AGCAGTGGAGTAGGTTGAAAATAGCAGAT-CTTG
* * * *
89479 TCTCCCTGAACAGCAGCGGAGTAGGTTAAAAATAGCAGATCTTA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* *** * * * *** *
89523 TCTTCCTGTATTGGCAG-GGAAGTAGATCGAAGACCCCA-ACCTTG
1 TCTCCCTG-AGCAGCAGTGG-AGTAGGTTGAAAATAGCAGATCTTG
*
89567 TCTCCCTGAGCAGCAATGGAGTAGGTTGAAAATAGCAGATCTTG
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* * *** * * * * *** *
89611 TCTTCTTGTATTGGCAGCGAAGTAGATTGAAGACCCCAG-CCTTG
1 TCTCCCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* *
89655 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTCG
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* *** * * * * * *** * *
89699 TCTTCCTGTATTGGTAGTGAAGTAGATCGAAGACCCCA-ACCTTA
1 TCTCCCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* * * * * *
89743 TCTCTCTTAGCAGTAGTGGAGTAGGTTGAAAATAACAGATATTA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* * *** * * * * * *** *
89787 TCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAG-CCTTG
1 TCTCCCT-GAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
*
89831 TCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
89875 T
1 T
89876 TTTCTTGTAT
Statistics
Matches: 288, Mismatches: 137, Indels: 32
0.63 0.30 0.07
Matches are distributed among these distances:
43 91 0.32
44 105 0.36
45 92 0.32
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
Found at i:89861 original size:264 final size:265
Alignment explanation
Indices: 89391--90480 Score: 1521
Period size: 264 Copynumber: 4.1 Consensus size: 265
89381 GTGAATCCTA
* * * * * *
89391 TCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAATA-ACAGATATTGTCTTCCTGTACTGGCTGTGA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGACAGATCTTGTCTTCCTGTATTGGCAGCGA
* * * * * * * *
89455 AGTAGATCGAAGATCTCATCCTTATCTCCCTGAACAGCAGCGGAGTAGGTTAAAAATAGCAGATC
66 AGTAGATCGAAAACCCCAGCCTTATCTCCTTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATA
* * * * *
89520 TTATCTTCCTGTATTGGCAGGGAAGTAGATCGAAGACCCCAACCTTGTCTCCCTGAGCAGCAATG
131 TTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAACAACAGTG
*
89585 GAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATTGAAGACCCCAG
196 GAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACCCCAG
89650 CCTTG
261 CCTTG
* * *
89655 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAG-CAGATCTCGTCTTCCTGTATTGGTAGTGA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGACAGATCTTGTCTTCCTGTATTGGCAGCGA
* * * * *
89719 AGTAGATCGAAGACCCCAACCTTATCTCTCTT-AGCAGTAGTGGAGTAGGTTGAAAATAACAGAT
66 AGTAGATCGAAAACCCCAGCCTTATCTC-CTTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGAT
* *
89783 ATTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAACAGCAGT
130 ATTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAACAACAGT
* *
89848 GGAGTAGGTTGAAAATAGCAGATCTTGTTTTCTTGTATTGGCAGCGAAGTAGATCAAAGACCCCA
195 GGAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACCCCA
*
89913 GCCTTA
260 GCCTTG
* *
89919 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAAT-GACAAATCTTGT-TTTCTAGTATTGGCAGCG
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGACAGATCTTGTCTTCCT-GTATTGGCAGCG
* * *
89982 AAGTAGATCGAAAACTCCAGCCTTGTCTCCTTGAGCAGCAGTGGAGTAGGTTAAAAATATCAGAT
65 AAGTAGATCGAAAACCCCAGCCTTATCTCCTTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGAT
* * * * * *
90047 CTTGTATTCC-GTTATTGGCAGCGAAGTAGATCGAAGACCCTAGCCTTATCTCCCT-AAGCAATA
130 ATTATCTTCCTG-TATTGGCAGCGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAA-CAACA
*
90110 GTGGAGTAGGTTGAAAATAGTAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACCC
193 GTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACCC
*
90175 CATCCTTG
258 CAGCCTTG
* * * * * *
90183 TCTCTCTAAGCAGCAATGGAGTAGGTTAAAAAT-GAAAGATCTTGTCTTCCAGTATTGGCAGCAA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGACAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
90247 AGTAGATTGAAAACCCCAGCCTTGTCTCCTTGAGCAGCAGTGAAGTAGGTTAAAAATAGCAGATA
66 AGTAGATCGAAAACCCCAGCCTTATCTCCTTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATA
* * ** *
90312 TTGTCTTCCTGTATTGGCAGCGAAGTAGATAGAAGACCCCAGCCTTGTCTCCCTGAGTAATAGTG
131 TTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAACAACAGTG
*
90377 GAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAG
196 GAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACCCCAG
90442 CCTTG
261 CCTTG
* *
90447 TCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATA
90481 TAGATCTTAT
Statistics
Matches: 737, Mismatches: 78, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
263 10 0.01
264 720 0.98
265 7 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (265 bp):
TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGACAGATCTTGTCTTCCTGTATTGGCAGCGA
AGTAGATCGAAAACCCCAGCCTTATCTCCTTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATA
TTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAGCCTTGTCTCCCTGAACAACAGTG
GAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACCCCAG
CCTTG
Found at i:90338 original size:45 final size:45
Alignment explanation
Indices: 90202--90427 Score: 124
Period size: 45 Copynumber: 5.1 Consensus size: 45
90192 GCAGCAATGG
* * *
90202 AGTAGGTTAAAAAT-GAAAGATCTTGTCTTCCAGTATTGGCAGCAA
1 AGTAGGTTAAAAATAG-CAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *** * *** *
90247 AGTAGATTGAAAACCCCAG-CCTTGTC-TCCT-TGAGCAGCAGTGA
1 AGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGT-ATTGGCAGCGA
*
90290 AGTAGGTTAAAAATAGCAGATATTGTCTTCCTGTATTGGCAGCGA
1 AGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *** * * * *** * *
90335 AGTA-GATAGAAGACCCCAG-CCTTGTCTCCCTG-AGTAATAGTGG
1 AGTAGGTTA-AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
*
90378 AGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
90423 AGTAG
1 AGTAG
90428 ATCGAAGACC
Statistics
Matches: 121, Mismatches: 51, Indels: 18
0.64 0.27 0.09
Matches are distributed among these distances:
42 1 0.01
43 38 0.31
44 37 0.31
45 44 0.36
46 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (45 bp):
AGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
Found at i:90360 original size:44 final size:44
Alignment explanation
Indices: 90312--90454 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 44
90302 ATAGCAGATA
*
90312 TTGTCTTCCTGTATTGGCAGCGAAGTAGATAGAAGACCCCAGCC
1 TTGTCTCCCTGTATTGGCAGCGAAGTAGATAGAAGACCCCAGCC
* *** * * * * * *** *
90356 TTGTCTCCCTG-AGTAATAGTGGAGTAGGTTGAAAATAGCAGATC
1 TTGTCTCCCTGTATTGGCAGCGAAGTAGATAGAAGACCCCAG-CC
* *
90400 TTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
1 TTGTCTCCCTGTATTGGCAGCGAAGTAGATAGAAGACCCCAGCC
90444 TTGTCTCCCTG
1 TTGTCTCCCTG
90455 AGTAGCAGTG
Statistics
Matches: 68, Mismatches: 29, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
43 18 0.26
44 32 0.47
45 18 0.26
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (44 bp):
TTGTCTCCCTGTATTGGCAGCGAAGTAGATAGAAGACCCCAGCC
Found at i:92056 original size:3 final size:3
Alignment explanation
Indices: 92048--92105 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
92038 ATTACTTAAC
* * * * * * *
92048 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAA TGT TAC TAT AAC TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
92096 TAT TAT TAT T
1 TAT TAT TAT T
92106 TATATTAGTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:106117 original size:63 final size:61
Alignment explanation
Indices: 106008--106126 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 61
105998 CATCAAGTAC
* ** *
106008 CATAATAAAACACATATTGATAGTTCATGTACCACATTGGACATTTTATGAAAGTACACATAT
1 CATAATAAAACACATATTAATAGTTCAAATACCACATTAGACATTTT-T-AAAGTACACATAT
* * *
106071 CATAATAAAATACATATTAATAGTTCAAATACCTCATTAGATATTTTTAAAGTACA
1 CATAATAAAACACATATTAATAGTTCAAATACCACATTAGACATTTTTAAAGTACA
106127 TGTACTACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 8 0.16
62 1 0.02
63 40 0.82
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (61 bp):
CATAATAAAACACATATTAATAGTTCAAATACCACATTAGACATTTTTAAAGTACACATAT
Found at i:108657 original size:15 final size:16
Alignment explanation
Indices: 108627--108658 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
108617 TCAAACATGC
108627 TTTAACACATTATCAA
1 TTTAACACATTATCAA
108643 TTTAACACA-TATCAA
1 TTTAACACATTATCAA
108658 T
1 T
108659 AAGGCACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAACACATTATCAA
Found at i:119698 original size:914 final size:917
Alignment explanation
Indices: 117926--119720 Score: 3229
Period size: 914 Copynumber: 2.0 Consensus size: 917
117916 CTTGTGGATT
* * *
117926 TCCCTTCGTTTCGATTTATCCACCAGGAAAGCAAACTTGTTCCCTTTCTTTACAGCCGAACAGCC
1 TCCCTTCATTTCGATTTATCCACCAGCAAAGCAAACTTGTTCCCTTTATTTACAGCCGAACAGCC
* *
117991 ATGCAAACTAGTAAAGAAATTATGGCAATCAAACCAGCCGCACATCTGACATCAGCAATTAGCAA
66 ATGCAAACCAGTAAAGAAATTATGGCAATCAAACCAGCCGCACATCCGACATCAGCAATTAGCAA
118056 GCTTCTCTTCTTGGATTTTTCACCTGCAGAATTGGACGAATACGAAGGTGGCCGTGGAGCCACCT
131 GCTTCTCTTCTTGGATTTTTCACCTGCAGAATTGGACGAATACGAAGGTGGCCGTGGAG-CACCT
*
118121 GTAGTTCTAGGTTTGGTTTGCCCAAATTGTCATCAGAGTTGCTTAATTTGAACACTTGAATCCCA
195 GTAGTTCTAGGTTTGGTTTGCCCAAATTGCCATCAGAGTTGCTTAATTTGAACACTTGAATCCCA
118186 TTTAAGATTACATCATAGTACTTTGCATGAATGGTGATGTACTCCTTTGATACTAACACGACATA
260 TTTAAGATTACATCATAGTACTTTGCATGAATGGTGATGTACTCCTTTGATACTAACACGACATA
*
118251 ATCCTTAAATATCGGAACTTTGCCTTGCACAGTCCACACAATCACATCAGCGTTTTGTTTAGCCG
325 ATCCTTAAATATCGAAACTTTGCCTTGCACAGTCCACACAATCACATCAGCGTTTTGTTTAGCCG
*
118316 TCTGACTGTTTATAAAGACCTTAAACTTTTGGTCTCCCAGAGAGTTTACCAGATCTTGTGGTTCT
390 TCTGACTGTTTATAAAGACCTTAAACTTTTGGTCTCCCAGAGAGTTTACCAGATCTTGTGGTTCA
*
118381 CAAAAATGAAGCCTCACCATATACCTAAATCCCGAACCCATGGGCAATCTCCATGATAAGTTATG
455 CAAAAATGAAGCCTCACCATATACCTAAATCCCGAACACATGGGCAATCTCCATGATAAGTTATG
*
118446 CTTCTCGTTGTACGCAAGGCTAGGCCCCATTGTCTGTGTAGTTTGATAAACCATCTCCGGTGCCG
520 CTTCTCGTTGTACGCAAGGCTAGGCCCCATTGTCTGTGTAGTCTGATAAACCATCTCCGGTGCCG
118511 TGTATCTCAGAATCATTGTGTAGTTGATTAGCATGGAGGTGTTGACAGTGACATAATTATTTTTT
585 TGTATCTCAGAATCATTGTGTAGTTGATTAGCATGGAGGTGTTGACAGTGACATAATTATTTTTT
*
118576 GTCATGTAAAAATAGTCATCGGACGAAAGCCGGAAAAGGCCAGTGTCATCCTTGAGGGAAATGGG
650 GTCATGTAAAAATAGTCATCGGACGAAAGCCGGAAAAGGCCAGTATCATCCTTGAGGGAAATGGG
*
118641 TTTGCCCTCAACATTTAATCGATACGCCATCTCAAGTACCGTGTCATTATCAACGAGGAATGGAT
715 TTTGCCCTCAACATTCAATCGATACGCCATCTCAAGTACCGTGTCATTATCAACGAGGAATGGAT
* *
118706 AATTCTGACCAATGAAAGGTACATACGTTGAGTCAGGCGGTGTGTAGTAAAGATCGGTAGGCATC
780 AATTCTGACCAACGAAAGGTACATACGTTGAGTCAGGCAGTGTGTAGTAAAGATCGGTAGGCATC
118771 GACACGATCTCGATTCCATTGATGAAAGCGTAAGTAAAGATTGGTAGGCATCAACACGATCACGA
845 GACACGATCTCGATTCCATTGATGAAAGCGTAAGTAAAGATTGGTAGGCATCAACACGATCACGA
118836 TCTCGATC
910 TCTCGATC
* *
118844 TCCCTTCATTTCGATTTATCCACCAGCAAAGCAAACTTGTTCCCTTTATTTGCAGCCGAATAGCC
1 TCCCTTCATTTCGATTTATCCACCAGCAAAGCAAACTTGTTCCCTTTATTTACAGCCGAACAGCC
118909 ATGCAAACCAGTAAAGAAATTATGGCAATCAAACCAGCCGCACATCCGACATCAGCAATTAGCAA
66 ATGCAAACCAGTAAAGAAATTATGGCAATCAAACCAGCCGCACATCCGACATCAGCAATTAGCAA
* *
118974 GCTTCTCTTCTTGGATTTTTCACCTGCAGAATTGGACGAATCCGAAGGTGGTCGT-G-G-ACCTG
131 GCTTCTCTTCTTGGATTTTTCACCTGCAGAATTGGACGAATACGAAGGTGGCCGTGGAGCACCTG
*
119036 TAGTTCTAGGTTTGGTTTGCCCAAATTGCCATTAGAGTTGCTTAATTTGAACACTTGAATCCCAT
196 TAGTTCTAGGTTTGGTTTGCCCAAATTGCCATCAGAGTTGCTTAATTTGAACACTTGAATCCCAT
119101 TTAAGATTACATCATAGTACTTTGCATGAATGGTGATGTACTCCTTTGATACTAACACGACATAA
261 TTAAGATTACATCATAGTACTTTGCATGAATGGTGATGTACTCCTTTGATACTAACACGACATAA
119166 TCCTTAAATATCGAAACTTTGCCTTGCACAGTCCACACAATCACATCAGCGTTTTGTTTAGCCGT
326 TCCTTAAATATCGAAACTTTGCCTTGCACAGTCCACACAATCACATCAGCGTTTTGTTTAGCCGT
119231 CTGACTGTTTATAAAGACCTTAAACTTTTGGTCTCCCAGAGAGTTTACCAGATCTTGTGGTTCAC
391 CTGACTGTTTATAAAGACCTTAAACTTTTGGTCTCCCAGAGAGTTTACCAGATCTTGTGGTTCAC
119296 AAAAATGAAGCCTCACCATATACCTAAATCCCGAACACATGGGCAATCTCCATGATAAGTTATGC
456 AAAAATGAAGCCTCACCATATACCTAAATCCCGAACACATGGGCAATCTCCATGATAAGTTATGC
*
119361 TTCTCGTTGTATGCAAGGCTAGGCCCCATTGTCTGTGTAGTCTGATAAACCATCTCCGGTGCCGT
521 TTCTCGTTGTACGCAAGGCTAGGCCCCATTGTCTGTGTAGTCTGATAAACCATCTCCGGTGCCGT
119426 GTATCTCAGAATCATTGTGTAGTTGATTAGCATGGAGGTGTTGACAGTGACATAATTATTTTTTG
586 GTATCTCAGAATCATTGTGTAGTTGATTAGCATGGAGGTGTTGACAGTGACATAATTATTTTTTG
* * *** *
119491 TCATGTAAAAATAGTCATTGGATGAATTTCGGAAAAGGCCAGTATCATCCTTGTGGGAAATGGGT
651 TCATGTAAAAATAGTCATCGGACGAAAGCCGGAAAAGGCCAGTATCATCCTTGAGGGAAATGGGT
* * * * *
119556 TTGGCCC-CAACATTCAATTGATACGCCATCTCAATTATCGTGTCATTCTTAACGAGGAATGGAT
716 TT-GCCCTCAACATTCAATCGATACGCCATCTCAAGTACCGTGTCATTATCAACGAGGAATGGAT
* *
119620 AATTCTGGCCAACGAAAGGTACATACGTTGAGTCAGGCAGTGTGTAGTAAAGATTGGTAGGCATC
780 AATTCTGACCAACGAAAGGTACATACGTTGAGTCAGGCAGTGTGTAGTAAAGATCGGTAGGCATC
* *
119685 GACACGTTCTCGATTCCATTGTTGAAAGCGTAAGTA
845 GACACGATCTCGATTCCATTGATGAAAGCGTAAGTA
119721 TCGTTAGAAG
Statistics
Matches: 841, Mismatches: 35, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
914 659 0.78
915 4 0.00
916 1 0.00
917 1 0.00
918 176 0.21
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (917 bp):
TCCCTTCATTTCGATTTATCCACCAGCAAAGCAAACTTGTTCCCTTTATTTACAGCCGAACAGCC
ATGCAAACCAGTAAAGAAATTATGGCAATCAAACCAGCCGCACATCCGACATCAGCAATTAGCAA
GCTTCTCTTCTTGGATTTTTCACCTGCAGAATTGGACGAATACGAAGGTGGCCGTGGAGCACCTG
TAGTTCTAGGTTTGGTTTGCCCAAATTGCCATCAGAGTTGCTTAATTTGAACACTTGAATCCCAT
TTAAGATTACATCATAGTACTTTGCATGAATGGTGATGTACTCCTTTGATACTAACACGACATAA
TCCTTAAATATCGAAACTTTGCCTTGCACAGTCCACACAATCACATCAGCGTTTTGTTTAGCCGT
CTGACTGTTTATAAAGACCTTAAACTTTTGGTCTCCCAGAGAGTTTACCAGATCTTGTGGTTCAC
AAAAATGAAGCCTCACCATATACCTAAATCCCGAACACATGGGCAATCTCCATGATAAGTTATGC
TTCTCGTTGTACGCAAGGCTAGGCCCCATTGTCTGTGTAGTCTGATAAACCATCTCCGGTGCCGT
GTATCTCAGAATCATTGTGTAGTTGATTAGCATGGAGGTGTTGACAGTGACATAATTATTTTTTG
TCATGTAAAAATAGTCATCGGACGAAAGCCGGAAAAGGCCAGTATCATCCTTGAGGGAAATGGGT
TTGCCCTCAACATTCAATCGATACGCCATCTCAAGTACCGTGTCATTATCAACGAGGAATGGATA
ATTCTGACCAACGAAAGGTACATACGTTGAGTCAGGCAGTGTGTAGTAAAGATCGGTAGGCATCG
ACACGATCTCGATTCCATTGATGAAAGCGTAAGTAAAGATTGGTAGGCATCAACACGATCACGAT
CTCGATC
Found at i:122645 original size:50 final size:50
Alignment explanation
Indices: 122570--122813 Score: 337
Period size: 50 Copynumber: 4.8 Consensus size: 50
122560 TTTCCTGAAC
* * * ** *
122570 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
122620 TGCCCAA-GCCATGTCTCAAACATGGTCTTACAGGGGACCTCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAAACATGGTCTTACATGGGA-C-CTCTCATCTCGG
* *
122672 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
*
122722 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
122772 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
122814 TTACCCAAAT
Statistics
Matches: 172, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
50 125 0.73
51 9 0.05
52 38 0.22
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:122702 original size:102 final size:100
Alignment explanation
Indices: 122570--122813 Score: 391
Period size: 102 Copynumber: 2.4 Consensus size: 100
122560 TTTCCTGAAC
**
122570 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAA-GCCATGT
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTG-CCAACGCCATGT
*
122634 CTCAAACATGGTCTTACAGGGGACCTCTCTCATCTCGG
65 CCCAAACATGGTCTTACAGGGGA-C-CTCTCATCTCGG
* *
122672 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTC
*
122737 CCAAACATGGTCTTACATGGGACCTCTCATCTCGG
66 CCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
*
122772 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGACCTCT
122814 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
100 52 0.39
101 5 0.04
102 76 0.57
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (100 bp):
TGCCAATGCCATATCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTC
CCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:127659 original size:43 final size:43
Alignment explanation
Indices: 127589--127670 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
127579 GAGTTTAGCG
* *
127589 TGCTATCTGATTATTAGCATGTCAGTGCTCTCTGATTATGACA
1 TGCTATCTAATTATTAGCACGTCAGTGCTCTCTGATTATGACA
* *
127632 TGCTCTCTAATTATTAGCACGTTAGTGCTCTCTGATTAT
1 TGCTATCTAATTATTAGCACGTCAGTGCTCTCTGATTAT
127671 TAGTCCATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (43 bp):
TGCTATCTAATTATTAGCACGTCAGTGCTCTCTGATTATGACA
Found at i:127669 original size:25 final size:25
Alignment explanation
Indices: 127632--127734 Score: 94
Period size: 25 Copynumber: 4.4 Consensus size: 25
127622 GATTATGACA
* *
127632 TGCTCTCTAATTATTAGCACGTTAG
1 TGCTCTCTGATTATTAGCACATTAG
*
127657 TGCTCTCTGATTATTAGTC-CATCAG
1 TGCTCTCTGATTATTAG-CACATTAG
* *
127682 TTCTCTCTGATTACTA--AC---A-
1 TGCTCTCTGATTATTAGCACATTAG
*
127701 CGCTCTCTGATTATTAGCACATTAG
1 TGCTCTCTGATTATTAGCACATTAG
127726 TGCTCTCTG
1 TGCTCTCTG
127735 TTTAGACAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
19 13 0.21
20 1 0.02
21 2 0.03
23 1 0.02
24 1 0.02
25 42 0.69
26 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (25 bp):
TGCTCTCTGATTATTAGCACATTAG
Found at i:127731 original size:69 final size:67
Alignment explanation
Indices: 127588--127734 Score: 197
Period size: 69 Copynumber: 2.1 Consensus size: 67
127578 GGAGTTTAGC
* * * *
127588 GTGCTATCTGATTATTAGCATGTCAGTGCTCTCTGATTATGACATGCTCTCTAATTATTAGCACG
1 GTGCTCTCTGATTATTAGCA-GTCAGTGCTCTCTGATTATAACACGCTCTCTAATTATTAGCACA
127653 TTA
65 TTA
* *
127656 GTGCTCTCTGATTATTAGTCCA-TCAGTTCTCTCTGATTACTAACACGCTCTCTGATTATTAGCA
1 GTGCTCTCTGATTATTAG--CAGTCAGTGCTCTCTGATTA-TAACACGCTCTCTAATTATTAGCA
127720 CATTA
63 CATTA
127725 GTGCTCTCTG
1 GTGCTCTCTG
127735 TTTAGACAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
68 33 0.47
69 35 0.50
70 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (67 bp):
GTGCTCTCTGATTATTAGCAGTCAGTGCTCTCTGATTATAACACGCTCTCTAATTATTAGCACAT
TA
Found at i:129718 original size:45 final size:45
Alignment explanation
Indices: 129662--129756 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
129652 TACTATGTGA
*
129662 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCCGATTCC
1 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCCGAATCC
* * *
129707 ACCGGACATCATTGATTATTAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCCGAATCC
129752 ACCGA
1 ACCGA
129757 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCCGAATCC
Found at i:139496 original size:12 final size:12
Alignment explanation
Indices: 139479--139503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
139469 TTCATAAGTG
139479 AGATAAGATGAA
1 AGATAAGATGAA
139491 AGATAAGATGAA
1 AGATAAGATGAA
139503 A
1 A
139504 AAGAAAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AGATAAGATGAA
Found at i:144553 original size:27 final size:28
Alignment explanation
Indices: 144424--144553 Score: 113
Period size: 28 Copynumber: 4.7 Consensus size: 28
144414 AACACGTCAG
* * *
144424 GAAATAATAAACCTTTCTGGTGAACTAT
1 GAAAGAATAAGCCTTTGTGGTGAACTAT
* *
144452 GAAAGAATAAGCCTTTGCGGTGAAGTAT
1 GAAAGAATAAGCCTTTGTGGTGAACTAT
* * * * ** *
144480 -AAATCAGT-AGCCTTTATTGCAAACTAC
1 GAAA-GAATAAGCCTTTGTGGTGAACTAT
144507 GAAAGAATAAGCCTTTGTGGTGAACTAT
1 GAAAGAATAAGCCTTTGTGGTGAACTAT
*
144535 GAAAG-ATTAGCCTTTGTGG
1 GAAAGAATAAGCCTTTGTGG
144554 CGGACTTTGT
Statistics
Matches: 77, Mismatches: 22, Indels: 7
0.73 0.21 0.07
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (28 bp):
GAAAGAATAAGCCTTTGTGGTGAACTAT
Found at i:146975 original size:37 final size:37
Alignment explanation
Indices: 146830--147006 Score: 196
Period size: 37 Copynumber: 4.8 Consensus size: 37
146820 ATCCAACTGA
* *
146830 AACACGCC-AATCGATCATAAGACCTAATCCA-CCTGAT
1 AACACGCCAAAT-GCTCATAAGAGCTAATCCACCCT-AT
* *
146867 AATACGCCAAATGCTCATAAGAGCTAATCCACCCGAT
1 AACACGCCAAATGCTCATAAGAGCTAATCCACCCTAT
* * * *
146904 AACATGTCAAATGCTCATAAGAGGTAATCTACCCTAT
1 AACACGCCAAATGCTCATAAGAGCTAATCCACCCTAT
* *
146941 AACAGGCCAAATGCTCATATGAGCTAATCCACCCTAT
1 AACACGCCAAATGCTCATAAGAGCTAATCCACCCTAT
** **
146978 GGCACGCCAAACACTCATAAGAGCTAATC
1 AACACGCCAAATGCTCATAAGAGCTAATC
147007 ATCCACCCTC
Statistics
Matches: 117, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
37 112 0.96
38 5 0.04
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (37 bp):
AACACGCCAAATGCTCATAAGAGCTAATCCACCCTAT
Found at i:151439 original size:189 final size:189
Alignment explanation
Indices: 151116--151494 Score: 713
Period size: 189 Copynumber: 2.0 Consensus size: 189
151106 TGATTCTGGG
151116 TATAGACTGGTTAACTTTACATGATGCTATTGTAAACTGTAGACGAAAGCATATTGTATTGAAAT
1 TATAGACTGGTTAACTTTACATGATGCTATTGTAAACTGTAGACGAAAGCATATTGTATTGAAAT
151181 GTCAAAATGGTGAAAGGATTCGAATTGAATAAGACATATTGGATGGTACATCTAATGTTATCCCA
66 GTCAAAATGGTGAAAGGATTCGAATTGAATAAGACATATTGGATGGTACATCTAATGTTATCCCA
*
151246 GCTATGATGACACAATAATATATTCGAAAGGGTTATGAAGCGTATCTAGCTTACATATT
131 GCTATGATGACACAACAATATATTCGAAAGGGTTATGAAGCGTATCTAGCTTACATATT
* *
151305 TATAGACTGGTTAACTTTGCATGATGCTGTTGTAAACTGTAGACGAAAGCATATTGTATTGAAAT
1 TATAGACTGGTTAACTTTACATGATGCTATTGTAAACTGTAGACGAAAGCATATTGTATTGAAAT
*
151370 GTCAAAATGGTGAAAGGATTCGAATTGAATAAGACATATTGGATGGTACATCTAATGTTATCTCA
66 GTCAAAATGGTGAAAGGATTCGAATTGAATAAGACATATTGGATGGTACATCTAATGTTATCCCA
*
151435 GCTATGATGACACAACAATATATTCGAAAGGGTTATGAAGCTTATCTAGCTTACATATT
131 GCTATGATGACACAACAATATATTCGAAAGGGTTATGAAGCGTATCTAGCTTACATATT
151494 T
1 T
151495 GATTCCAGAG
Statistics
Matches: 185, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 185 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (189 bp):
TATAGACTGGTTAACTTTACATGATGCTATTGTAAACTGTAGACGAAAGCATATTGTATTGAAAT
GTCAAAATGGTGAAAGGATTCGAATTGAATAAGACATATTGGATGGTACATCTAATGTTATCCCA
GCTATGATGACACAACAATATATTCGAAAGGGTTATGAAGCGTATCTAGCTTACATATT
Found at i:153116 original size:40 final size:40
Alignment explanation
Indices: 153058--153142 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
153048 GGATCAACTG
*
153058 AACACGCCAAACAGAAGCTAACAAGAGCTAATCCAACCGA
1 AACACGCCAAACAAAAGCTAACAAGAGCTAATCCAACCGA
* * *
153098 AACACGCCAAACAAAAGCTTATAAGAGGTAATCCAACCGA
1 AACACGCCAAACAAAAGCTAACAAGAGCTAATCCAACCGA
153138 AACAC
1 AACAC
153143 ACCAGACAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.48, C:0.28, G:0.14, T:0.09
Consensus pattern (40 bp):
AACACGCCAAACAAAAGCTAACAAGAGCTAATCCAACCGA
Found at i:166537 original size:9 final size:9
Alignment explanation
Indices: 166523--166554 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
166513 TAGAAACCTT
166523 ATATTTTAC
1 ATATTTTAC
166532 ATATTTTAC
1 ATATTTTAC
166541 ATATTTTAC
1 ATATTTTAC
166550 A-ATTT
1 ATATTT
166555 AATCCATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTTTAC
Found at i:169174 original size:26 final size:26
Alignment explanation
Indices: 169144--169219 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
169134 ACACCAATAT
*
169144 CGCAGCAAAGCTGCCAATAATAGTAA
1 CGCAGCAAAGCTGCCAATAACAGTAA
* *
169170 CGCAGCAAGGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAATAACAGTAA
* * * *
169196 CGTAGCAAAACCGCCAGTAACAGT
1 CGCAGCAAAGCTGCCAATAACAGT
169220 GTATGTGGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.13
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAATAACAGTAA
Found at i:169427 original size:27 final size:26
Alignment explanation
Indices: 169395--169722 Score: 408
Period size: 27 Copynumber: 12.2 Consensus size: 26
169385 GGTATAATAG
* * *
169395 TCATTTTACCTTTCAGGGGTATTTTGG
1 TCATTTTACCCTTC-GGGGTATTTCGA
* *
169422 TTATTTTACCCATCGGGGGTATTTCGA
1 TCATTTTACCCTTC-GGGGTATTTCGA
*
169449 TCATTTTACCCTTCGAGGGTATTTTGA
1 TCATTTTACCCTTCG-GGGTATTTCGA
169476 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTC-GGGGTATTTCGA
* *
169503 TCATTTTACCATTCCGGGTATTTCGA
1 TCATTTTACCCTTCGGGGTATTTCGA
*
169529 TCATTTTACCCTTCGAGGCTATTTC-A
1 TCATTTTACCCTTCG-GGGTATTTCGA
169555 GTCATTTTACCCTTCAGGGGTATTTCGA
1 -TCATTTTACCCTTC-GGGGTATTTCGA
*
169583 TCATTTTACCCTTCTGGGGTATTTTGA
1 TCATTTTACCCTTC-GGGGTATTTCGA
*
169610 TTATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCG-GGGTATTTCGA
*
169637 TCATTTTACCATTCGTGGGTATTTCGA
1 TCATTTTACCCTTCG-GGGTATTTCGA
* *
169664 TTATTTTACCCTTCGGGGTATTTCGG
1 TCATTTTACCCTTCGGGGTATTTCGA
169690 TCATTTTACCCTTCGAGGGTATTTC-A
1 TCATTTTACCCTTCG-GGGTATTTCGA
169716 GTCATTT
1 -TCATTT
169723 GGGAACGAAT
Statistics
Matches: 264, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
26 51 0.19
27 210 0.80
28 3 0.01
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (26 bp):
TCATTTTACCCTTCGGGGTATTTCGA
Found at i:169577 original size:161 final size:161
Alignment explanation
Indices: 169393--169722 Score: 516
Period size: 161 Copynumber: 2.0 Consensus size: 161
169383 GGGGTATAAT
* * * *
169393 AGTCATTTTACCTTTCAGGGGTATTTTGGTTATTTTACCCATCGGGGGTATTTCGATCATTTTAC
1 AGTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCATCGGGGGTATTTCGATCATTTTAC
* *
169458 CCTTCGAGGGTATTTTGATCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCATTCCGGGTA
66 CCTTCGAGGGTATTTCGATCATTTTACCATTCGGGGGTATTTCGATCATTTTACCATTCCGGGTA
169523 TTTCGATCATTTTACCCTTCGAGGCTATTTC
131 TTTCGATCATTTTACCCTTCGAGGCTATTTC
* * * *
169554 AGTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCTGGGGTATTTTGATTATTTTAC
1 AGTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCATCGGGGGTATTTCGATCATTTTAC
* * * *
169619 CCTTCGAGGGTATTTCGATCATTTTACCATTCGTGGGTATTTCGATTATTTTACCCTTCGGGGTA
66 CCTTCGAGGGTATTTCGATCATTTTACCATTCGGGGGTATTTCGATCATTTTACCATTCCGGGTA
* *
169684 TTTCGGTCATTTTACCCTTCGAGGGTATTTC
131 TTTCGATCATTTTACCCTTCGAGGCTATTTC
169715 AGTCATTT
1 AGTCATTT
169723 GGGAACGAAT
Statistics
Matches: 153, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
161 153 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (161 bp):
AGTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCATCGGGGGTATTTCGATCATTTTAC
CCTTCGAGGGTATTTCGATCATTTTACCATTCGGGGGTATTTCGATCATTTTACCATTCCGGGTA
TTTCGATCATTTTACCCTTCGAGGCTATTTC
Found at i:169624 original size:134 final size:133
Alignment explanation
Indices: 169395--169722 Score: 464
Period size: 134 Copynumber: 2.4 Consensus size: 133
169385 GGTATAATAG
* * ** * *
169395 TCATTTTACCTTTCAGGGGTATTTTGGTTATTTTACCCATCGGGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTTC-GGGCTATTTCAGTCATTTTACCCTTC-GGGGTATTTCGATCATTTTACCC
*
169460 TTCGAGGGTATTTTGATCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCATTC-CGGGTAT
64 TTCGAGGGTATTTTGATCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCATTCGCGGGTAT
169524 TTCGA
129 TTCGA
169529 TCATTTTACCCTTCGAGGCTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTTCG-GGCTATTTCAGTCATTTTACCCTTC-GGGGTATTTCGATCATTTTACCC
* *
169594 TTCTG-GGGTATTTTGATTATTTTACCCTTCGAGGGTATTTCGATCATTTTACCATTCGTGGGTA
64 TTC-GAGGGTATTTTGATCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCATTCGCGGGTA
169658 TTTCGA
128 TTTCGA
* * *
169664 TTATTTTACCCTTCGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTC-AGTCATTT
1 TCATTTTACCCTTCGGGCTATTTCAGTCATTTTACCCTTCG-GGGTATTTCGA-TCATTT
169723 GGGAACGAAT
Statistics
Matches: 176, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
133 3 0.02
134 147 0.84
135 26 0.15
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (133 bp):
TCATTTTACCCTTCGGGCTATTTCAGTCATTTTACCCTTCGGGGTATTTCGATCATTTTACCCTT
CGAGGGTATTTTGATCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCATTCGCGGGTATTT
CGA
Found at i:174462 original size:21 final size:19
Alignment explanation
Indices: 174438--174479 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
174428 TGTTAGCATT
*
174438 TTATTTATTAAATTGTTTCTA
1 TTATGTATTAAA-TG-TTCTA
174459 TTATGTATTAAATGTTCTA
1 TTATGTATTAAATGTTCTA
174478 TT
1 TT
174480 TTGCTCGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
TTATGTATTAAATGTTCTA
Found at i:175571 original size:2 final size:2
Alignment explanation
Indices: 175564--175602 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
175554 TACGCGGGCG
175564 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 T
175603 GTTAAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:175748 original size:23 final size:22
Alignment explanation
Indices: 175721--175763 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
175711 TTTAAAATTT
*
175721 TTTAAGTTATTTCATGTCTTTTG
1 TTTAAATTATTT-ATGTCTTTTG
*
175744 TTTAAATTATTTATTTCTTT
1 TTTAAATTATTTATGTCTTT
175764 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (22 bp):
TTTAAATTATTTATGTCTTTTG
Found at i:175769 original size:22 final size:22
Alignment explanation
Indices: 175718--175770 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
175708 TCTTTTAAAA
*
175718 TTTTTTAAGTTATTTCATGTCT
1 TTTTTTAAATTATTTCATGTCT
*
175740 TTTGTTTAAATTATTT-ATTTCT
1 TTT-TTTAAATTATTTCATGTCT
175762 TTATTTTAA
1 TT-TTTTAA
175771 TATCTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (22 bp):
TTTTTTAAATTATTTCATGTCT
Found at i:178792 original size:29 final size:29
Alignment explanation
Indices: 178732--178797 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
178722 GTGAATGTCA
** * *
178732 CAACATTGAGATCGGAATGCTCAATGCCG
1 CAACATTGAGATCAAAATGCCCAAGGCCG
**
178761 CAACATTGAGATCAAAATGCCCAAGGTTG
1 CAACATTGAGATCAAAATGCCCAAGGCCG
178790 CAACATTG
1 CAACATTG
178798 GCTAGGGAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (29 bp):
CAACATTGAGATCAAAATGCCCAAGGCCG
Found at i:188119 original size:29 final size:29
Alignment explanation
Indices: 188082--188141 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
188072 TACCTATGTT
*
188082 AAATTAATATATGTATATTATTTGCTTCA
1 AAATTAATATATCTATATTATTTGCTTCA
188111 AAATTAATATATCTATATTATTTGCTTCA
1 AAATTAATATATCTATATTATTTGCTTCA
188140 AA
1 AA
188142 TTTATTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (29 bp):
AAATTAATATATCTATATTATTTGCTTCA
Found at i:193010 original size:160 final size:160
Alignment explanation
Indices: 192741--193053 Score: 545
Period size: 160 Copynumber: 2.0 Consensus size: 160
192731 TTTTACGAAC
*
192741 GACCTATCTTTTTGCAATTTGATCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTTGCCTT
1 GACCCATCTTTTTGCAATTTGATCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTTGCCTT
*
192806 TCTCTTGCTTGATTCCATTTCTTCTTGCCTTTGTTTCTTGAAGAGCATGGAGCTTCCTTGTTTCT
66 TCTCTTGCTTGATTCCATTTCTCCTTGCCTTTGTTTCTTGAAGAGCATGGAGCTTCCTTGTTTCT
* * *
192871 CATTTGGTAGGCACCTTTTACGTTATGAAT
131 CACTTGGTAAGCACCTTCTACGTTATGAAT
* * *
192901 GACCCATCTTTTTGCAATTTGATCATTGTGGATACTTTTTCTTTCCAGCATCTCTTTTTTTCCTT
1 GACCCATCTTTTTGCAATTTGATCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTTGCCTT
*
192966 TCTCTTGCTTGATTCCATTTCTCCTTGCCTTTGTTTCTTGAAGAGCATGGAGTTTCCTTGTTTCT
66 TCTCTTGCTTGATTCCATTTCTCCTTGCCTTTGTTTCTTGAAGAGCATGGAGCTTCCTTGTTTCT
193031 CACTTGGTAAGCACCTTCTACGT
131 CACTTGGTAAGCACCTTCTACGT
193054 GAAGGACATC
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
160 144 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (160 bp):
GACCCATCTTTTTGCAATTTGATCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTTGCCTT
TCTCTTGCTTGATTCCATTTCTCCTTGCCTTTGTTTCTTGAAGAGCATGGAGCTTCCTTGTTTCT
CACTTGGTAAGCACCTTCTACGTTATGAAT
Found at i:199079 original size:59 final size:57
Alignment explanation
Indices: 199006--199324 Score: 241
Period size: 59 Copynumber: 5.3 Consensus size: 57
198996 AATATTAAGA
*
199006 ATTTTATTAAATTATATATTTTTATCTAATTATATTTAATAATAATAATTTTAAATTAT
1 ATTTTA-TATATTATATATTTTTAT-TAATTATATTTAATAATAATAATTTTAAATTAT
* * * * * * * * *
199065 ATTTTGTAGTATTATATATTATGATTTTAGTAAATTCATATAATAAT-ATTTTATATTAAGA
1 ATTTTATA-TATTATATATTTTTA-TTAATTATATTTA-ATAATAATAATTTTAAATT-A-T
* * *
199126 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAAAAATTATTTTAAATTAT
1 ATTTTA-TATATTATATATTTTTATT-AATTATATTTAATAATAATAATTTTAAATTAT
* * * * * * *
199185 ATTTTAAATTATTATATATTATGATT--TTAGTAAATTCAT-ATAAGAATATTTAATATTAAGA
1 ATTTTATA-TATTATATATTTTTATTAATTA-T-ATTTAATAATAATAAT-TTTAA-ATT-A-T
* *
199246 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATAACTTTAAATTAT
1 ATTTTA-TATATTATATATTTTTATT-AATTATATTTAATAATAATAATTTTAAATTAT
199305 ATTTTATAGTATTATATATT
1 ATTTTATA-TATTATATATT
199325 ATGATTTTAG
Statistics
Matches: 198, Mismatches: 41, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
56 3 0.02
57 6 0.03
58 15 0.08
59 73 0.37
60 22 0.11
61 56 0.28
62 13 0.07
63 7 0.04
64 3 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
ATTTTATATATTATATATTTTTATTAATTATATTTAATAATAATAATTTTAAATTAT
Found at i:199101 original size:120 final size:120
Alignment explanation
Indices: 198957--199420 Score: 786
Period size: 120 Copynumber: 3.9 Consensus size: 120
198947 AATTAAATTA
*
198957 TATATATTATGATTTTAGTAAATTCATATAAGAATATGTAATATTAAGAATTTTATTAAATTATA
1 TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATA
*
199022 TATTTTTATCT-AATTATATTTAATAATAATAATTTTAAATTATATTTTGTAGTAT
66 TATTTTTAT-TAAATTATATTTAATAATAATAATTTTAAATTATATTTTATAGTAT
* *
199077 TATATATTATGATTTTAGTAAATTCATATAATAATATTTTATATTAAGAATTTTATTAAATTATA
1 TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATA
* * * *
199142 TATTTTTATTAAATTATATTTAATAAAAATTATTTTAAATTATATTTTAAATTAT
66 TATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTATAGTAT
199197 TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATA
1 TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATA
*
199262 TATTTTTATTAAATTATATTTAATAATAATAACTTTAAATTATATTTTATAGTAT
66 TATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTATAGTAT
199317 TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATA
1 TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATA
* * * * *
199382 TATTTTGATTAAAATATATGTAATAATAATTATGTTAAA
66 TATTTTTATTAAATTATATTTAATAATAATAATTTTAAA
199421 ATATGATTAA
Statistics
Matches: 322, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
119 1 0.00
120 321 1.00
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATA
TATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTATAGTAT
Found at i:199187 original size:12 final size:12
Alignment explanation
Indices: 199150--199196 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
199140 TATATTTTTA
199150 TTAAATTATATT
1 TTAAATTATATT
*
199162 TAATAAA-AATTATT
1 T--TAAATTA-TATT
199176 TTAAATTATATT
1 TTAAATTATATT
199188 TTAAATTAT
1 TTAAATTAT
199197 TATATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 18 0.62
13 2 0.07
14 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATTATATT
Found at i:199219 original size:64 final size:62
Alignment explanation
Indices: 199145--199345 Score: 170
Period size: 64 Copynumber: 3.3 Consensus size: 62
199135 AATTATATAT
*
199145 TTTTATTAAATTATATTTAATAAAAATTATTTTAAATTATATTTTAAATTATTATATATTATGA
1 TTTTAGTAAATTATATTTAATAAAAATTA-TTTAAATTATATTTT-AATTATTATATATTATGA
* * * *
199209 TTTTAGTAAATT-CA--T-ATAAGAA-TATTTAATATTAAGAATTTT-ATTA-AAT-TA-TAT-A
1 TTTTAGTAAATTATATTTAATAAAAATTATTTAA-ATT-A-TATTTTAATTATTATATATTATGA
* * * *
199264 TTTTTATTAAATTATATTTAATAATAATAACTTTAAATTATATTTTATAGTATTATATATTATGA
1 -TTTTAGTAAATTATATTTAATAAAAATTA-TTTAAATTATATTTTA-ATTATTATATATTATGA
199329 TTTTAGTAAATTCATAT
1 TTTTAGTAAATT-ATAT
199346 AAGAATATTT
Statistics
Matches: 107, Mismatches: 13, Indels: 33
0.70 0.08 0.22
Matches are distributed among these distances:
55 1 0.01
56 14 0.13
57 3 0.03
58 7 0.07
59 15 0.14
60 14 0.13
61 13 0.12
62 7 0.07
63 3 0.03
64 25 0.23
65 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (62 bp):
TTTTAGTAAATTATATTTAATAAAAATTATTTAAATTATATTTTAATTATTATATATTATGA
Found at i:199392 original size:18 final size:17
Alignment explanation
Indices: 199366--199400 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
199356 AATATTAAGA
*
199366 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
199383 ATTTTGATTAAAATATAT
1 ATTTT-ATTAAAATATAT
199401 GTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:199620 original size:44 final size:46
Alignment explanation
Indices: 199557--199654 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
199547 CTATTTCACC
* * *
199557 TCCATTTCATTCAACCAAACCCA-AG-AA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAA-CAATAGAAATTACTATTACGCATCTAT
*
199601 TCCATTACATTCAACCAAACAATAGAAATTCCTATTACGCATCTAT
1 TCCATTACATTCAACCAAACAATAGAAATTACTATTACGCATCTAT
199647 TCCATTAC
1 TCCATTAC
199655 GCCTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 2 0.04
44 20 0.43
45 2 0.04
46 23 0.49
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.31
Consensus pattern (46 bp):
TCCATTACATTCAACCAAACAATAGAAATTACTATTACGCATCTAT
Found at i:199655 original size:16 final size:15
Alignment explanation
Indices: 199628--199682 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 15
199618 AACAATAGAA
199628 ATTCCTATTACGCATCT
1 ATTCC-ATTACGC-TCT
199645 ATTCCATTACGCCTCT
1 ATTCCATTACG-CTCT
199661 ATTCCATTACGTCTCT
1 ATTCCATTACG-CTCT
199677 ATTCCA
1 ATTCCA
199683 ATACAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 30 0.83
17 6 0.17
ACGTcount: A:0.22, C:0.33, G:0.05, T:0.40
Consensus pattern (15 bp):
ATTCCATTACGCTCT
Found at i:206283 original size:48 final size:48
Alignment explanation
Indices: 206212--206306 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
206202 TTCTTTGCTT
*
206212 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
1 AAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAGC
** * *
206260 AAAAACGCCTAAGTTGGCCTAACTTGCAAAGATAAATGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAG
206307 AATTCCCTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAGC
Found at i:206570 original size:36 final size:36
Alignment explanation
Indices: 206511--206579 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
206501 ATCAAAGGCT
* *
206511 ACAATTAAAAGTTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGCATACAATTAGAACTCTAAGAC
* *
206547 ACAATTAGAAGCTGCATATAATTAGAACTCTAA
1 ACAATTAAAAGCTGCATACAATTAGAACTCTAA
206580 AATTACATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (36 bp):
ACAATTAAAAGCTGCATACAATTAGAACTCTAAGAC
Found at i:209833 original size:41 final size:41
Alignment explanation
Indices: 209772--209872 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
209762 AAGTAAGATG
* *
209772 ATTT-AGACTTTACATCTAGCAGGCTTGATGCCTGTGAAAT
1 ATTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAAT
*
209812 ATTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAAT
1 ATTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAAT
209853 ATTTCAGACTTTACGTCTAG
1 ATTTCAGACTTTACGTCTAG
209873 TAGACTAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 4 0.07
41 52 0.93
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (41 bp):
ATTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAAT
Found at i:217784 original size:41 final size:41
Alignment explanation
Indices: 217733--217878 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 41
217723 AGTAAAATGA
217733 TTCAGACTTTACGTCTAGCAGGCTTGATGCCTGTTAAATGA-
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCTGTTAAAT-AT
* * * *
217774 TTCAGACTTTACGTCAAGCAGGCTTGAT-ACTGATGAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCTGTTAAATAT
* * *
217814 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCTGTTAAATAT
*
217855 TTCAGACTTTACATCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
217879 ATTTGTCGGT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 33 0.37
41 56 0.62
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCTGTTAAATAT
Found at i:220177 original size:14 final size:14
Alignment explanation
Indices: 220158--220205 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
220148 TAGTATTCTC
220158 TTTTCCTCTCTTTT
1 TTTTCCTCTCTTTT
220172 TTTTCCTCTTTTCTTCTT
1 TTTTCCTC---TCTT-TT
220190 TTCTTCCTCTCTTTT
1 TT-TTCCTCTCTTTT
220205 T
1 T
220206 CTTAGCCGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 8 0.28
15 3 0.10
16 4 0.14
17 4 0.14
18 4 0.14
19 6 0.21
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCCTCTCTTTT
Found at i:220183 original size:22 final size:19
Alignment explanation
Indices: 220155--220208 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
220145 CACTAGTATT
*
220155 CTCTTTTCCTCTCTTTTTTTTC
1 CTCTTTT-CT-TC-TTTTCTTC
220177 CTCTTTTCTTCTTTTCTTC
1 CTCTTTTCTTCTTTTCTTC
220196 CTCTCTTT-TTCTT
1 CTCT-TTTCTTCTT
220209 AGCCGTCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 16 0.53
20 5 0.17
21 2 0.07
22 7 0.23
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
CTCTTTTCTTCTTTTCTTC
Found at i:225745 original size:28 final size:28
Alignment explanation
Indices: 225713--225792 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
225703 CCATTTTTAA
225713 TGAAAGGATAACCATTGTGGTGAACCTC
1 TGAAAGGATAACCATTGTGGTGAACCTC
* *
225741 TGAAAGGAT-AGCATTTGTGGCGAACCTC
1 TGAAAGGATAACCA-TTGTGGTGAACCTC
* * *
225769 TAAAAAGGA-AGCCATTGTGTTGAA
1 T-GAAAGGATAACCATTGTGGTGAA
225793 ATCTGAAGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.07
28 31 0.74
29 8 0.19
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (28 bp):
TGAAAGGATAACCATTGTGGTGAACCTC
Found at i:225845 original size:23 final size:23
Alignment explanation
Indices: 225791--225836 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
225781 CATTGTGTTG
225791 AAATCTGAAGGAAAGAAATGGCA
1 AAATCTGAAGGAAAGAAATGGCA
225814 AAATCTGAAGGAAAGAAATGGCA
1 AAATCTGAAGGAAAGAAATGGCA
225837 GACACTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.26, T:0.13
Consensus pattern (23 bp):
AAATCTGAAGGAAAGAAATGGCA
Found at i:227625 original size:14 final size:14
Alignment explanation
Indices: 227606--227635 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
227596 AGAGTCTTCC
227606 AATTTCCAAGTTCA
1 AATTTCCAAGTTCA
227620 AATTTCCAAGTTCA
1 AATTTCCAAGTTCA
227634 AA
1 AA
227636 CATTGTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (14 bp):
AATTTCCAAGTTCA
Found at i:230348 original size:15 final size:15
Alignment explanation
Indices: 230328--230367 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
230318 TTCTGTCCGG
230328 CCCAATACCCACAAA
1 CCCAATACCCACAAA
230343 CCCAATACCCACAAA
1 CCCAATACCCACAAA
230358 CCCAATACCC
1 CCCAATACCC
230368 TCAGCCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.50, G:0.00, T:0.07
Consensus pattern (15 bp):
CCCAATACCCACAAA
Found at i:243911 original size:44 final size:46
Alignment explanation
Indices: 243797--243911 Score: 137
Period size: 46 Copynumber: 2.5 Consensus size: 46
243787 ATGCAGGTCT
* * *
243797 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATGTCAGATCC
* *
243843 TATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-ATAGT-A-ATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAT-GTCAGATCC
* *
243887 TATCTCCTTGAGATTACAATGGAGC
1 TATCTCCCTGAGATTACAGTGGAGC
243912 GGATTAAAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 25 0.42
45 3 0.05
46 32 0.53
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (46 bp):
TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATGTCAGATCC
Found at i:244087 original size:128 final size:127
Alignment explanation
Indices: 243840--244234 Score: 496
Period size: 129 Copynumber: 3.1 Consensus size: 127
243830 GAATTTCAGA
* * * *
243840 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTG-AGATTAC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAAACT-ATCCTATCTCCCTGAAG-TTAC
* * **
243904 AATGGAGCGGATT---A-AAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCTGG
64 AGTGGAGCGGATTAAAATAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
*
243964 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAAACTATCCTATCTCCCTGAAGTTACAG
*
244029 TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAG
66 TGGAGCGGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
* * * * *
244092 TCTTATCTCCCTGA-AGTTGCAGCGGAGCAGATAGAAGAAACCAATCCTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGAAA-CTATCCTATCTCCCTGAAGTTAC
* * * * * *
244156 AGTAGAGCGGATTAAAATCACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCGCATCAAG
64 AGTGGAGCGGATTAAAAT-AAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
*
244221 TCTTATTTCCCTGA
1 TCTTATCTCCCTGA
244235 AGTACAATGG
Statistics
Matches: 239, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
123 29 0.12
124 41 0.17
126 1 0.00
127 4 0.02
128 74 0.31
129 88 0.37
130 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (127 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAAACTATCCTATCTCCCTGAAGTTACAG
TGGAGCGGATTAAAATAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
Found at i:244187 original size:44 final size:44
Alignment explanation
Indices: 244010--244211 Score: 155
Period size: 44 Copynumber: 4.7 Consensus size: 44
244000 GACACTATCC
* * * * *
244010 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT-AAAGGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAATCACA-GATCT
* * * * ***
244054 TATCTCTCTGAGGTTACAGCAGAGTAGA-TCGCATCA-AG-TCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAATCACAGATCT
* ** * * *
244095 TATCTCCCTGAAGTTGCAGCGGAGCAGATAGAAGAAAC-CA-ATCC
1 TATCTCTCTGAAGTTGCAGTAGAGCAGAT-TAA-AATCACAGATCT
*
244139 TATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAATCACAGATCT
*
244183 TATCTCTTTGAAGTTGCAGTAGAGCAGAT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGAT
244212 CGCATCAAGT
Statistics
Matches: 121, Mismatches: 29, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
41 26 0.21
42 4 0.03
43 8 0.07
44 83 0.69
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAATCACAGATCT
Found at i:244237 original size:41 final size:41
Alignment explanation
Indices: 244051--244237 Score: 142
Period size: 44 Copynumber: 4.4 Consensus size: 41
244041 AAATAAAGGA
* * * * *
244051 TCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAG
1 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATAGAATCAAG
* * *
244092 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGATAGAAGAAACCAA-
1 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGAT---AG-AATCAAG
* * * *
244136 TCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCACAG
1 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGA-TAGAATCA-AG
* * * *
244179 ATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCGCATCAAG
1 -TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATAGAATCAAG
* *
244221 TCTTATTTCCCTGAAGT
1 TCTTATCTCTCTGAAGT
244238 ACAATGGATT
Statistics
Matches: 114, Mismatches: 24, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
41 45 0.39
42 4 0.04
43 5 0.04
44 55 0.48
45 5 0.04
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATAGAATCAAG
Found at i:244437 original size:15 final size:15
Alignment explanation
Indices: 244417--244456 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
244407 TTCTGTCCGG
244417 CCCAATACCCACAAA
1 CCCAATACCCACAAA
244432 CCCAATACCCACAAA
1 CCCAATACCCACAAA
244447 CCCAATACCC
1 CCCAATACCC
244457 TCAGCCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.50, G:0.00, T:0.07
Consensus pattern (15 bp):
CCCAATACCCACAAA
Found at i:254825 original size:3 final size:3
Alignment explanation
Indices: 254817--254846 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
254807 GGCATGGTTG
254817 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
254847 AGGAGTCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:259618 original size:32 final size:32
Alignment explanation
Indices: 259579--259640 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
259569 ATTAAAGAAA
259579 GGGGATATTTGGTCAAGCTAACATTGAGTGAG
1 GGGGATATTTGGTCAAGCTAACATTGAGTGAG
259611 GGGGATATTTGGTCAAGCTAACATTGAGTG
1 GGGGATATTTGGTCAAGCTAACATTGAGTG
259641 CATGGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (32 bp):
GGGGATATTTGGTCAAGCTAACATTGAGTGAG
Found at i:271429 original size:24 final size:24
Alignment explanation
Indices: 271395--271440 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
271385 TATATGAAAT
* *
271395 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
271419 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
271441 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:271678 original size:13 final size:13
Alignment explanation
Indices: 271660--271693 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
271650 CTTCCCCTCT
271660 TGAAAAGCACTTC
1 TGAAAAGCACTTC
* *
271673 TGAAAAGTACTTT
1 TGAAAAGCACTTC
271686 TGAAAAGC
1 TGAAAAGC
271694 TAAAAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (13 bp):
TGAAAAGCACTTC
Found at i:282841 original size:23 final size:23
Alignment explanation
Indices: 282796--282841 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
282786 ATGTCTTTTC
*
282796 TAATTTTAATCTAAAAATGTAAA
1 TAATTTTAATCTAAAAATATAAA
*
282819 TAATTTTAAATTTAAAAA-ATAAA
1 TAATTTT-AATCTAAAAATATAAA
282842 AACTTCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATTTTAATCTAAAAATATAAA
Found at i:284325 original size:7 final size:7
Alignment explanation
Indices: 284315--284341 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
284305 AGTTTTTAGT
284315 TTCTAGA
1 TTCTAGA
284322 TTCTAGA
1 TTCTAGA
284329 TTCTAGA
1 TTCTAGA
284336 TTCTAG
1 TTCTAG
284342 TTGTATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (7 bp):
TTCTAGA
Found at i:292117 original size:40 final size:41
Alignment explanation
Indices: 292062--292139 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
292052 GCTTTTAGGG
*
292062 TTTTAGCGGCGTTTTTC-ATAAAGTGCCACTAATGCTCTAT
1 TTTTAGCGGCGTTTTTCTAAAAAGTGCCACTAATGCTCTAT
**
292102 TTTTAGCGGCGTTTTTCTAAAAAGTGCTGCTAATGCTC
1 TTTTAGCGGCGTTTTTCTAAAAAGTGCCACTAATGCTC
292140 AGGGATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 17 0.50
41 17 0.50
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCTAAAAAGTGCCACTAATGCTCTAT
Found at i:293359 original size:16 final size:16
Alignment explanation
Indices: 293330--293362 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
293320 GTTTTTGAAG
293330 TATTTTAAATAAATAT
1 TATTTTAAATAAATAT
293346 TATTGTTAAA-AAATAT
1 TATT-TTAAATAAATAT
293362 T
1 T
293363 TTTGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TATTTTAAATAAATAT
Found at i:294036 original size:14 final size:15
Alignment explanation
Indices: 294011--294039 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
294001 AAATTGTAAA
294011 ATAAATATAAAATAT
1 ATAAATATAAAATAT
294026 ATAAA-ATAAAATAT
1 ATAAATATAAAATAT
294040 TTTTACTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAATATAAAATAT
Found at i:296877 original size:24 final size:24
Alignment explanation
Indices: 296849--296894 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
296839 CTTTTTCCCA
*
296849 GAAAATATAAGGCTTTTATGGTGG
1 GAAAATATAAGGCTTCTATGGTGG
296873 GAAAATATAAGGCTTCTATGGT
1 GAAAATATAAGGCTTCTATGGT
296895 TATTTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (24 bp):
GAAAATATAAGGCTTCTATGGTGG
Found at i:305136 original size:18 final size:18
Alignment explanation
Indices: 305113--305147 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
305103 TAATTGAGAA
* *
305113 ATTAATTTAGTTAATTTG
1 ATTAATTAAATTAATTTG
305131 ATTAATTAAATTAATTT
1 ATTAATTAAATTAATTT
305148 TTATTTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTAATTAAATTAATTTG
Found at i:307078 original size:18 final size:18
Alignment explanation
Indices: 307055--307090 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
307045 AAGAAATAGC
*
307055 AGCAAAATAATACATAAA
1 AGCAAAACAATACATAAA
307073 AGCAAAACAATACATAAA
1 AGCAAAACAATACATAAA
307091 TGCTGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.67, C:0.14, G:0.06, T:0.14
Consensus pattern (18 bp):
AGCAAAACAATACATAAA
Found at i:307456 original size:20 final size:20
Alignment explanation
Indices: 307431--307485 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
307421 TGTGGTTCAA
*
307431 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
307451 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
307471 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
307486 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:309296 original size:12 final size:12
Alignment explanation
Indices: 309281--309326 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
309271 TAAAAAAAAG
309281 GAAAAAAAATTT
1 GAAAAAAAATTT
309293 GAAAAAAAA-TT
1 GAAAAAAAATTT
* *
309304 CAAAAAAAATTC
1 GAAAAAAAATTT
*
309316 AAAAAAAAATT
1 GAAAAAAAATT
309327 GTATTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (12 bp):
GAAAAAAAATTT
Found at i:309308 original size:10 final size:11
Alignment explanation
Indices: 309282--309323 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
309272 AAAAAAAAGG
*
309282 AAAAAAAATTTG
1 AAAAAAAA-TTC
309294 AAAAAAAATTC
1 AAAAAAAATTC
309305 AAAAAAAATTC
1 AAAAAAAATTC
309316 AAAAAAAA
1 AAAAAAAA
309324 ATTGTATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:309308 original size:23 final size:23
Alignment explanation
Indices: 309282--309326 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
309272 AAAAAAAAGG
**
309282 AAAAAAAATTTGAAAAAAAATTC
1 AAAAAAAATTCAAAAAAAAATTC
309305 AAAAAAAATTCAAAAAAAAATT
1 AAAAAAAATTCAAAAAAAAATT
309327 GTATTCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAAAAAATTCAAAAAAAAATTC
Found at i:310346 original size:17 final size:15
Alignment explanation
Indices: 310326--310364 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
310316 GCGAGCGAGA
310326 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
310343 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
310358 AAGATGA
1 AA-ATGA
310365 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:311870 original size:20 final size:20
Alignment explanation
Indices: 311840--311901 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
311830 TTTCGTGTGG
*
311840 TTCAACTCATTCGAGCTCAA
1 TTCAGCTCATTCGAGCTCAA
*
311860 GTT-AGCTCATTCGTGCTCAA
1 -TTCAGCTCATTCGAGCTCAA
*
311880 TTCAGCTCATTCAAGCTCAA
1 TTCAGCTCATTCGAGCTCAA
311900 TT
1 TT
311902 TAACTCGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (20 bp):
TTCAGCTCATTCGAGCTCAA
Found at i:315982 original size:26 final size:27
Alignment explanation
Indices: 315946--316017 Score: 112
Period size: 26 Copynumber: 2.7 Consensus size: 27
315936 AAAAATAAAA
315946 ATTTACCAAAATATTATAA-CTTTTTT
1 ATTTACCAAAATATTATAATCTTTTTT
*
315972 ATTTACCAAAATATATATAATTTTTTTT
1 ATTTACCAAAATAT-TATAATCTTTTTT
316000 ATTTACCAAAATA-TATAA
1 ATTTACCAAAATATTATAA
316018 AAAAACAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 19 0.44
27 5 0.12
28 19 0.44
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTACCAAAATATTATAATCTTTTTT
Found at i:315998 original size:28 final size:27
Alignment explanation
Indices: 315946--316016 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 27
315936 AAAAATAAAA
315946 ATTTACCAAAATAT-TATAACTTTTTT
1 ATTTACCAAAATATATATAACTTTTTT
*
315972 ATTTACCAAAATATATATAATTTTTTTT
1 ATTTACCAAAATATATATAA-CTTTTTT
316000 ATTTACCAAAATATATA
1 ATTTACCAAAATATATA
316017 AAAAAACAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
26 14 0.33
27 5 0.12
28 23 0.55
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTACCAAAATATATATAACTTTTTT
Found at i:316114 original size:27 final size:27
Alignment explanation
Indices: 316084--316150 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
316074 CGCCAATGGG
316084 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* * *
316111 ATTGGCGGCACCAATGGTGCTAATACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
316138 ATTGGCGGCACCA
1 ATTGGCGGCACCA
316151 GTTAATAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:316202 original size:4 final size:4
Alignment explanation
Indices: 316193--316341 Score: 141
Period size: 4 Copynumber: 37.0 Consensus size: 4
316183 GAAGGAGAGG
316193 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* * *
316240 -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAGA GAAA AAAA GAAA
1 GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAA-A GAAA GAAA GAAA
316286 GAAA G-AA G-AA G-AA GAAAA GGAAAA GAGAA GAAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAAA G-AAA -G-AAA GA-AA GAAA GAAA GAAA GAAA
*
316330 GAAG GAAA GAAA
1 GAAA GAAA GAAA
316342 AGGAAAGGAG
Statistics
Matches: 126, Mismatches: 8, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
3 18 0.14
4 80 0.63
5 22 0.17
6 6 0.05
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:316348 original size:87 final size:83
Alignment explanation
Indices: 316194--316369 Score: 252
Period size: 87 Copynumber: 2.1 Consensus size: 83
316184 AAGGAGAGGG
316194 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGA
1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGA
316259 AAGGAGAAGAGAAGAGAAAA
66 AAGGAGAAGAGAA-A-AAAA
316279 AAAGAAAGAAAG-AAG-AAG-AAGAAAAGGAAAAGAGAAGAAA-AAAGAAAGAAAGAAGGAAAGA
1 AAAGAAAGAAAGAAAGAAAGAAAG-AAA-G-AAAGA-AAGAAAGAAAG-AA-AAAGAAGGAAAGA
316340 AAAGGAAAGGAGAAGAGAAAAAAA
60 AAAGGAAAGGAGAAGAGAAAAAAA
316364 AAAGAA
1 AAAGAA
316370 GAGGGAATGA
Statistics
Matches: 85, Mismatches: 0, Indels: 12
0.88 0.00 0.12
Matches are distributed among these distances:
82 3 0.04
83 6 0.07
84 4 0.05
85 31 0.36
86 9 0.11
87 32 0.38
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (83 bp):
AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGA
AAGGAGAAGAGAAAAAAA
Found at i:316366 original size:24 final size:26
Alignment explanation
Indices: 316339--316393 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
316329 AGAAGGAAAG
316339 AAAAGGAA-AGGAGAA-G-AGAAAAAA
1 AAAAGGAAGAGG-GAATGAAGAAAAAA
*
316363 AAAA-GAAGAGGGAATGAAGGAAAAA
1 AAAAGGAAGAGGGAATGAAGAAAAAA
316388 AAAAGG
1 AAAAGG
316394 TAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 6 0.23
24 8 0.31
25 11 0.42
26 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (26 bp):
AAAAGGAAGAGGGAATGAAGAAAAAA
Found at i:316369 original size:16 final size:17
Alignment explanation
Indices: 316194--316372 Score: 108
Period size: 16 Copynumber: 10.5 Consensus size: 17
316184 AAGGAGAGGG
*
316194 AAAGAA-AGAAAGAAAG
1 AAAGAAGAGAAAGAAAA
*
316210 AAAGAA-AGAAAGAAAG
1 AAAGAAGAGAAAGAAAA
316226 AAAGAA-AGAAAGAAAA
1 AAAGAAGAGAAAGAAAA
*
316242 AGAAGGAA-AGAAAAGGAAA
1 A-AA-GAAGAG-AAAGAAAA
**
316261 GGAGAAGAGAAGAGAAAA
1 AAAGAAGAGAA-AGAAAA
316279 AAAGAA-AGAAAG--AA
1 AAAGAAGAGAAAGAAAA
* *
316293 GAAGAAGA-AAAGGAAA
1 AAAGAAGAGAAAGAAAA
* * *
316309 AGAGAAGAAAAAAGAAAG
1 AAAGAAG-AGAAAGAAAA
316327 AAAGAAG-GAAAGAAAAGGA
1 AAAGAAGAGAAAG-AAA--A
316346 AAGGAGAAGAGAAA-AAAA
1 AA--AGAAGAGAAAGAAAA
316364 AAAGAAGAG
1 AAAGAAGAG
316373 GGAATGAAGG
Statistics
Matches: 132, Mismatches: 15, Indels: 32
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.08
15 1 0.01
16 52 0.39
17 15 0.11
18 32 0.24
19 9 0.07
20 3 0.02
21 5 0.04
22 4 0.03
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAGAAGAGAAAGAAAA
Found at i:316384 original size:48 final size:47
Alignment explanation
Indices: 316192--316390 Score: 197
Period size: 48 Copynumber: 4.4 Consensus size: 47
316182 AGAAGGAGAG
* * *
316192 GGAAAGAAAGAAAG-AAA-GAAAGAAAGAA-AGAAAGAAAGAAAGAAA
1 GGAAAGAAGGAAAGAAAAGGAAAG-GAGAAGAGAAAGAAAAAAAGAAA
*
316237 GAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAAAAAGAAA
1 G-GAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAA-AGAAAAAAAGAAA
* *
316286 -GAAAGAA-G-AAG--AAGAAAAGGAAAAGAG-AAG-AAAAAAGAAA
1 GGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAGAAAAAAAGAAA
316326 -GAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA-AAAAAAAGAAGA
1 GGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAGAAAAAAAGAA-A
* *
316372 GGGAATGAAGGAAAAAAAA
1 -GGAAAGAAGGAAAGAAAA
316391 AGGTAATTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
40 17 0.13
41 3 0.02
42 4 0.03
43 14 0.11
44 14 0.11
45 15 0.12
46 13 0.10
47 13 0.10
48 24 0.19
49 12 0.09
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (47 bp):
GGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAGAAAAAAAGAAA
Found at i:316386 original size:44 final size:41
Alignment explanation
Indices: 316228--316386 Score: 129
Period size: 41 Copynumber: 3.8 Consensus size: 41
316218 AAAGAAAGAA
316228 AGAA-AGAAAGAAAAAGAAGGAA-AGAA-AAGG-AAAGGAGAA-G
1 AGAAGAGAAA-AAAAA-AA-GAAGAGAAGAAGGAAAAGGA-AAGG
*
316268 AGAAGAGAAAAAAAGAAAGAA-AGAAGAAGAAGAAAAGGAAAAG
1 AGAAGAGAAAAAAA-AAAGAAGAGAAGAAG--GAAAAGGAAAGG
* *
316311 AG-A-AGAAAAAAGAAAGAA-AGAAGGAAAGAAAAGGAAAGG
1 AGAAGAGAAAAAAAAAAGAAGAGAA-GAAGGAAAAGGAAAGG
316350 AGAAGAGAAAAAAAAAAGAAGAGGGAATGAAGGAAAA
1 AGAAGAGAAAAAAAAAAGAAGA--GAA-GAAGGAAAA
316387 AAAAAGGTAA
Statistics
Matches: 100, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
39 20 0.20
40 24 0.24
41 31 0.31
42 5 0.05
43 9 0.09
44 11 0.11
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (41 bp):
AGAAGAGAAAAAAAAAAGAAGAGAAGAAGGAAAAGGAAAGG
Found at i:316393 original size:44 final size:41
Alignment explanation
Indices: 316194--316372 Score: 136
Period size: 44 Copynumber: 4.2 Consensus size: 41
316184 AAGGAGAGGG
* *
316194 AAAGAA-AGAAAGAA-AGAAAG-AAAGAAAGAA-AGAAAGAAAG
1 AAAGAAGAGAAAGAAGA-AAAGAAAAG-GAGAAGAGAAA-AAAA
* * *
316234 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAA
1 AAAG-AAGAGAAAG-AAGAAAAGAAAAGGAGAAGAGAA-A-AAAA
*
316279 AAAGAA-AGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAA
1 AAAGAAGAGAAAGAAGAA-AAGAAAAGGAGAAGAG-A-AAAAAA
* *
316322 GAAAGAA-AGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAA
1 -AAAGAAGAGAAAG-AAGAAAAGAAAAGGAGAAGAGAAAAAAA
316364 AAAGAAGAG
1 AAAGAAGAG
316373 GGAATGAAGG
Statistics
Matches: 117, Mismatches: 9, Indels: 24
0.78 0.06 0.16
Matches are distributed among these distances:
40 4 0.03
41 8 0.07
42 18 0.15
43 34 0.29
44 38 0.32
45 15 0.13
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (41 bp):
AAAGAAGAGAAAGAAGAAAAGAAAAGGAGAAGAGAAAAAAA
Found at i:322744 original size:15 final size:12
Alignment explanation
Indices: 322707--322737 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
322697 AAAAAATTTT
*
322707 ATACTCAAAATA
1 ATACACAAAATA
322719 ATACACAAAATA
1 ATACACAAAATA
322731 ATACACA
1 ATACACA
322738 CTAAAATTAT
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:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:322777 original size:26 final size:26
Alignment explanation
Indices: 322743--322821 Score: 149
Period size: 26 Copynumber: 3.0 Consensus size: 26
322733 ACACACTAAA
*
322743 ATTATTAATTTTATACTCAAAATAAT
1 ATTAATAATTTTATACTCAAAATAAT
322769 ATTAATAATTTTATACTCAAAATAAT
1 ATTAATAATTTTATACTCAAAATAAT
322795 ATTAATAATTTTATACTCAAAATAAT
1 ATTAATAATTTTATACTCAAAATAAT
322821 A
1 A
322822 CACACTAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTCAAAATAAT
Found at i:323117 original size:19 final size:21
Alignment explanation
Indices: 323093--323131 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
323083 ACTAAAACAA
*
323093 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
323112 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
323132 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:323308 original size:27 final size:27
Alignment explanation
Indices: 323270--323347 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
323260 ATAATACGAA
*
323270 TAGTACCGCCAATGGTTTTGACACCAT
1 TAGTGCCGCCAATGGTTTTGACACCAT
** *
323297 TAGTGCCGCCAATGGCATTGGCACCAT
1 TAGTGCCGCCAATGGTTTTGACACCAT
* *
323324 TGGTGCCGCCAATGATTTTGACAC
1 TAGTGCCGCCAATGGTTTTGACAC
323348 AAAAATTATA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (27 bp):
TAGTGCCGCCAATGGTTTTGACACCAT
Found at i:325858 original size:31 final size:31
Alignment explanation
Indices: 325817--325887 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
325807 TTAAAATTAA
325817 AAAAATATTTTTATA-ATTTTAAT-AATTTTT
1 AAAAATATTTTTATATATTTT-ATGAATTTTT
*
325847 AAAAATAATTTTTATATATTTTTTGAATTTTT
1 AAAAAT-ATTTTTATATATTTTATGAATTTTT
325879 AAAAA-ATTT
1 AAAAATATTT
325888 AAAAATTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 10 0.27
31 10 0.27
32 17 0.46
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
AAAAATATTTTTATATATTTTATGAATTTTT
Found at i:328129 original size:176 final size:176
Alignment explanation
Indices: 327835--328187 Score: 706
Period size: 176 Copynumber: 2.0 Consensus size: 176
327825 TTAAAAATGA
327835 AAGGTATAAGCTTCTAAACTTTGGTAAACAAATTAATTACGTTCTTCGCTTAAATTATATTAATT
1 AAGGTATAAGCTTCTAAACTTTGGTAAACAAATTAATTACGTTCTTCGCTTAAATTATATTAATT
327900 AAATTATTTGACCAACATTTTTCATCTTTGAACATTAGAGTAATGATATGGTCGTCTTAACTGTA
66 AAATTATTTGACCAACATTTTTCATCTTTGAACATTAGAGTAATGATATGGTCGTCTTAACTGTA
327965 CTGACATGGTGCTCCATGTCAACAAAAAATATAAATAAATCTAAAT
131 CTGACATGGTGCTCCATGTCAACAAAAAATATAAATAAATCTAAAT
328011 AAGGTATAAGCTTCTAAACTTTGGTAAACAAATTAATTACGTTCTTCGCTTAAATTATATTAATT
1 AAGGTATAAGCTTCTAAACTTTGGTAAACAAATTAATTACGTTCTTCGCTTAAATTATATTAATT
328076 AAATTATTTGACCAACATTTTTCATCTTTGAACATTAGAGTAATGATATGGTCGTCTTAACTGTA
66 AAATTATTTGACCAACATTTTTCATCTTTGAACATTAGAGTAATGATATGGTCGTCTTAACTGTA
328141 CTGACATGGTGCTCCATGTCAACAAAAAATATAAATAAATCTAAAT
131 CTGACATGGTGCTCCATGTCAACAAAAAATATAAATAAATCTAAAT
328187 A
1 A
328188 TTTATTTAAG
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 177 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (176 bp):
AAGGTATAAGCTTCTAAACTTTGGTAAACAAATTAATTACGTTCTTCGCTTAAATTATATTAATT
AAATTATTTGACCAACATTTTTCATCTTTGAACATTAGAGTAATGATATGGTCGTCTTAACTGTA
CTGACATGGTGCTCCATGTCAACAAAAAATATAAATAAATCTAAAT
Found at i:328266 original size:20 final size:20
Alignment explanation
Indices: 328240--328288 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
328230 TAAAATTTTT
328240 AATTATTAAAAATTT-TAAA
1 AATTATTAAAAATTTATAAA
328259 ATATTATT-AAAATTTATAAA
1 A-ATTATTAAAAATTTATAAA
328279 AA-TATTAAAA
1 AATTATTAAAA
328289 TTAATATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTATTAAAAATTTATAAA
Found at i:328284 original size:18 final size:19
Alignment explanation
Indices: 328229--328290 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 19
328219 GGACAAATAG
* *
328229 TTAAAATTTTTAATTATTA
1 TTAAAATTTTAAAATATTA
328248 --AAAATTTTAAAATATTA
1 TTAAAATTTTAAAATATTA
328265 TTAAAATTTATAAAA-A-TA
1 TTAAAATTT-TAAAATATTA
328283 TTAAAATT
1 TTAAAATT
328291 AATATTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 15 0.39
18 10 0.26
19 8 0.21
20 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATTTTAAAATATTA
Found at i:332755 original size:27 final size:25
Alignment explanation
Indices: 332725--332911 Score: 87
Period size: 27 Copynumber: 7.7 Consensus size: 25
332715 ATATTTGAAA
*
332725 CAAGTTCATGCAAATATACATGCCCAT
1 CAAGTTCATGCAAATATACAT--CTAT
* *
332752 CAAGTTCATTCAAA-AT---TTTA-
1 CAAGTTCATGCAAATATACATCTAT
*
332772 CAAGTTCATGCAAATATACATACCCAT
1 CAAGTTCATGCAAATATACAT--CTAT
* * *
332799 CAAGTTTATTCAAATAT---TTTA-
1 CAAGTTCATGCAAATATACATCTAT
*
332820 CAAGTTCATGCAAATATACATGACAAT
1 CAAGTTCATGCAAATATACAT--CTAT
* *
332847 CAAGTTCGTTCAAATAT---T-TA-
1 CAAGTTCATGCAAATATACATCTAT
*
332867 CAAGTTCATGCAAATATACATGACAAT
1 CAAGTTCATGCAAATATACAT--CTAT
* *
332894 AAAGTTCATACAAATATA
1 CAAGTTCATGCAAATATA
332912 TGTAAATAAA
Statistics
Matches: 118, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
20 28 0.24
21 19 0.16
22 1 0.01
23 2 0.02
24 4 0.03
26 5 0.04
27 59 0.50
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (25 bp):
CAAGTTCATGCAAATATACATCTAT
Done.