Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 50 of 335
Found at i:17875456 original size:42 final size:44
Alignment explanation
Indices: 17875393--17875599 Score: 219
Period size: 42 Copynumber: 4.6 Consensus size: 44
17875383 TTTCGTTTTC
** *
17875393 TCGATGCCATAGTTCAACTATGGTCTTACACATATTCACATA-A
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATATA
17875436 T-GATGCCATAGCCCAGCTATGGTCTTACACATATT--CATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATATA
* *
17875477 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACACATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAT-AT-TCACAT---ATA
*
17875526 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATATC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATATA
* *
17875569 TCACTGATGCCATATCCCAGATATGGTCTTA
1 T--C-GATGCCATAGCCCAGCTATGGTCTTA
17875600 TACAGTAGCA
Statistics
Matches: 141, Mismatches: 10, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
40 4 0.03
41 2 0.01
42 61 0.43
43 6 0.04
45 1 0.01
46 32 0.23
48 1 0.01
49 34 0.24
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (44 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATATA
Found at i:17875537 original size:49 final size:48
Alignment explanation
Indices: 17875476--17875646 Score: 197
Period size: 47 Copynumber: 3.6 Consensus size: 48
17875466 ATATTCATAT
* *
17875476 ATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACACATCACA
1 ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
* *
17875524 TATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATATCTCA
1 -ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
* * * * *
17875572 CT-GATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC-
1 ATCGATGCCATAGCCCAGATATGGTCTTACAC-GTAATCACATATCACA
* *
17875618 ACCGATGCCATATCCCAGATATGGTCTTA
1 ATCGATGCCATAGCCCAGATATGGTCTTA
17875647 TACGGAAATC
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
46 26 0.24
47 37 0.34
48 12 0.11
49 33 0.31
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (48 bp):
ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
Found at i:17875708 original size:31 final size:31
Alignment explanation
Indices: 17875668--17875816 Score: 235
Period size: 31 Copynumber: 4.8 Consensus size: 31
17875658 CTTGTCACTT
*
17875668 GTAGCCGGAGCTACCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
17875699 GTAGTCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
17875730 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
** * *
17875761 GTAGTAGAAGCTACCACTTTTCACTGCTCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
17875792 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
17875817 TGTTATTTGT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:17875896 original size:50 final size:50
Alignment explanation
Indices: 17875792--17875968 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
17875782 CACTGCTCAG
* * *
17875792 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* * *
17875843 GTAGTCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAAT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
**
17875893 GTAGCCGAATATAAT-ACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCT-ATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
17875943 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
17875969 GTTGCCATGG
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
49 2 0.02
50 84 0.76
51 25 0.23
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:17879845 original size:30 final size:29
Alignment explanation
Indices: 17879809--17879869 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
17879799 AAACGGAAGT
17879809 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTT-AACTAGC
*
17879839 TTTGGCACTAAGTGTGTGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAACTAGC
17879868 TT
1 TT
17879870 CGACTACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAACTAGC
Found at i:17881768 original size:30 final size:30
Alignment explanation
Indices: 17881732--17881792 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
17881722 GAAAAGAGAA
17881732 AAAAAAAAACCTTAGCTCGATACCATGTAG
1 AAAAAAAAACCTTAGCTCGATACCATGTAG
17881762 AAAAAAAAACCTTAGCTCGATACCATGTAG
1 AAAAAAAAACCTTAGCTCGATACCATGTAG
17881792 A
1 A
17881793 GAAACGCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (30 bp):
AAAAAAAAACCTTAGCTCGATACCATGTAG
Found at i:17888647 original size:19 final size:19
Alignment explanation
Indices: 17888620--17888659 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17888610 AAGTTTTTTA
17888620 TATTATTAA-ATTATATTAT
1 TATTATTAATA-TATATTAT
*
17888639 TATTTTTAATATATATTAT
1 TATTATTAATATATATTAT
17888658 TA
1 TA
17888660 ACTCTAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTAATATATATTAT
Found at i:17891488 original size:14 final size:15
Alignment explanation
Indices: 17891469--17891498 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17891459 TACGCATTTA
17891469 ATTTTTAAATATTGT
1 ATTTTTAAATATTGT
*
17891484 ATTTTTAATTATTGT
1 ATTTTTAAATATTGT
17891499 TACTTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
ATTTTTAAATATTGT
Found at i:17892220 original size:15 final size:13
Alignment explanation
Indices: 17892190--17892225 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
17892180 TGTTTAACTA
17892190 ATAATTATAAATT
1 ATAATTATAAATT
17892203 ATAATTATAATTATT
1 ATAATTATAA--ATT
17892218 ATAATTAT
1 ATAATTAT
17892226 CACAATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
15 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATAATTATAAATT
Found at i:17892304 original size:117 final size:116
Alignment explanation
Indices: 17892102--17892333 Score: 310
Period size: 118 Copynumber: 2.0 Consensus size: 116
17892092 TAAAATTAAT
* * *
17892102 TAATTATCACAATTTATTTCTATATTTATGCTTAAAGTTCTATTTAAATAATAAATCTATTTTAA
1 TAATTATCACAATTTATTTCTATATTTATGATCAAAGTTCTATTCAAATAATAAATCTATTTTAA
* *
17892167 ATTTTAGCATATTTGTTTAACTAAT-AATTATAAATTATAATTATAATTATTA
66 ATATTAGCAAATTTGTTTAACTAATAAATT-TAAATTA-AATTATAATTATTA
* * *
17892219 TAATTATCACAATCTT-TTTCTATATTTTATGATCAATGTTCTATTCAAGTAATAAATTTATTTT
1 TAATTATCACAAT-TTATTTCTATA-TTTATGATCAAAGTTCTATTCAAATAATAAATCTATTTT
*
17892283 AAA-ATTAGCACAATTT-TTTAACTAATAAATTTAATTTAAATTATAATTATT
64 AAATATTAGCA-AATTTGTTTAACTAATAAATTTAAATTAAATTATAATTATT
17892334 TTTAAAGTTA
Statistics
Matches: 102, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
116 13 0.13
117 43 0.42
118 46 0.45
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (116 bp):
TAATTATCACAATTTATTTCTATATTTATGATCAAAGTTCTATTCAAATAATAAATCTATTTTAA
ATATTAGCAAATTTGTTTAACTAATAAATTTAAATTAAATTATAATTATTA
Found at i:17898394 original size:13 final size:14
Alignment explanation
Indices: 17898358--17898397 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
17898348 TTAAACAAAG
*
17898358 AAAGAAAGAAAATAA
1 AAAGAAAG-AAAGAA
17898373 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
17898387 AAAG-AAGAAAG
1 AAAGAAAGAAAG
17898398 GAATGCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.29
14 9 0.38
15 8 0.33
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:17923911 original size:40 final size:36
Alignment explanation
Indices: 17923826--17923994 Score: 188
Period size: 35 Copynumber: 4.7 Consensus size: 36
17923816 TTTTCCTCAT
**
17923826 TGAAATACCATACCTACATTTTTCAACTC-GTATGG
1 TGAAATACCATACCTACATTTCACAACTCAGTATGG
* **
17923861 -GAAATGCCATACCTACATTTCTTAACTCAGTATGG
1 TGAAATACCATACCTACATTTCACAACTCAGTATGG
*
17923896 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-G
1 ---TGA-AATACCATACCTACATTTCACAACTCAGTATGG
17923935 -GATAATACCATACCTACATTTCACAACTCAGTATGG
1 TGA-AATACCATACCTACATTTCACAACTCAGTATGG
17923971 ATG--ATACCATACCTACATTTCACA
1 -TGAAATACCATACCTACATTTCACA
17923995 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 8, Indels: 18
0.82 0.06 0.13
Matches are distributed among these distances:
34 25 0.21
35 60 0.51
36 1 0.01
38 1 0.01
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (36 bp):
TGAAATACCATACCTACATTTCACAACTCAGTATGG
Found at i:17923953 original size:75 final size:72
Alignment explanation
Indices: 17923824--17923994 Score: 224
Period size: 75 Copynumber: 2.4 Consensus size: 72
17923814 GGTTTTCCTC
** * **
17923824 ATTGAAATACCATACCTACATTTTTCAACTCGTATGGGAAATGCCATACCTACATTTCTTAACTC
1 ATTGAAATACCATACCTACATTTCACAACTCGTATGGGAAATACCATACCTACATTTCACAACTC
17923889 AGTATGG
66 AGTATGG
*
17923896 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACAACTC-GTATGGGA-AATACCATACCTACATTTCACA
17923960 ACTCAGTATGG
62 ACTCAGTATGG
17923971 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
17923995 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
70 21 0.24
72 1 0.01
73 6 0.07
74 26 0.29
75 35 0.39
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (72 bp):
ATTGAAATACCATACCTACATTTCACAACTCGTATGGGAAATACCATACCTACATTTCACAACTC
AGTATGG
Found at i:17931363 original size:35 final size:35
Alignment explanation
Indices: 17931319--17931485 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
17931309 TCCTCATTGA
** *
17931319 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
17931354 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
17931394 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
17931429 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
17931464 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
17931486 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:17931402 original size:75 final size:73
Alignment explanation
Indices: 17931314--17931485 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
17931304 GGTTTTCCTC
** * * **
17931314 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
17931378 TCAGTATGG
65 TCAGTATGG
*
17931387 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
17931452 CTCAGTATGG
64 CTCAGTATGG
17931462 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
17931486 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:17939007 original size:22 final size:21
Alignment explanation
Indices: 17938978--17939021 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
17938968 TCAGGTCAAA
*
17938978 TTAGGAAAG-CTGTTAACTGAG
1 TTAGGAAAGTATGTTAAC-GAG
17938999 TTAGAGAAAGTATGTTAACGAG
1 TTAG-GAAAGTATGTTAACGAG
17939021 T
1 T
17939022 CATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
23 7 0.35
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (21 bp):
TTAGGAAAGTATGTTAACGAG
Found at i:17941378 original size:5 final size:5
Alignment explanation
Indices: 17941368--17941400 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
17941358 AATAATTAAG
17941368 TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
17941401 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:17952050 original size:46 final size:45
Alignment explanation
Indices: 17951994--17952169 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
17951984 TGGTTGAGCA
*
17951994 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
17952040 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
17952087 TCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
17952133 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17952170 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.62
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:17952150 original size:93 final size:93
Alignment explanation
Indices: 17951991--17952161 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
17951981 GGATGGTTGA
* * *
17951991 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
17952056 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
17952084 GCATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
17952149 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
17952162 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:17953887 original size:21 final size:21
Alignment explanation
Indices: 17953850--17953903 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
17953840 TGCTATTCTG
*
17953850 TTGTTTTTCCATGTTTTG-CTA
1 TTGTTTTCCCATGTTTTGTC-A
17953871 TTGTTTTCCCACT-TTTTGTCA
1 TTGTTTTCCCA-TGTTTTGTCA
*
17953892 TTATTTTCCCAT
1 TTGTTTTCCCAT
17953904 CATTTCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.11, C:0.20, G:0.09, T:0.59
Consensus pattern (21 bp):
TTGTTTTCCCATGTTTTGTCA
Found at i:17958966 original size:44 final size:44
Alignment explanation
Indices: 17958889--17958983 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
17958879 TAAATTACTT
* * *
17958889 TTTAATATATAATTATCAATAATATTTAAAATTAATAGTTATTA
1 TTTAATATATAATTATAAATAATATTTAAAATTAATAATTAATA
*
17958933 TTTAATATA-AA-TATAAATATATATTTTATAATTAATAATTAATA
1 TTTAATATATAATTATAAATA-ATA-TTTAAAATTAATAATTAATA
*
17958977 ATTAATA
1 TTTAATA
17958984 ATTATATGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
42 7 0.16
43 5 0.11
44 32 0.73
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (44 bp):
TTTAATATATAATTATAAATAATATTTAAAATTAATAATTAATA
Found at i:17958970 original size:7 final size:7
Alignment explanation
Indices: 17958960--17958987 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
17958950 TATATATTTT
17958960 ATAATTA
1 ATAATTA
17958967 ATAATTA
1 ATAATTA
17958974 ATAATTA
1 ATAATTA
17958981 ATAATTA
1 ATAATTA
17958988 TATGTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATTA
Found at i:17959744 original size:10 final size:10
Alignment explanation
Indices: 17959729--17959765 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
17959719 TTAAGTATAT
17959729 TATATTATTA
1 TATATTATTA
17959739 TATATTATTA
1 TATATTATTA
17959749 TATTATATATTA
1 TA-TAT-TATTA
17959761 TATAT
1 TATAT
17959766 ATATAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 12 0.48
11 6 0.24
12 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATTATTA
Found at i:17959770 original size:15 final size:16
Alignment explanation
Indices: 17959724--17959767 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
17959714 AATAATTAAG
17959724 TATATTATAT-TATTA
1 TATATTATATATATTA
17959739 TATATTAT-TATATTA
1 TATATTATATATATTA
17959754 TATATTATATATAT
1 TATATTATATATAT
17959768 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.78
16 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTATATATATTA
Found at i:17960846 original size:6 final size:6
Alignment explanation
Indices: 17960835--17960875 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
17960825 ATGTGCCGAC
* * *
17960835 TACTGT TACTGT TACCGT TACTGT TACCGT TATTGT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG
17960876 ATTCGATACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (6 bp):
TACTGT
Found at i:17960856 original size:12 final size:12
Alignment explanation
Indices: 17960839--17960873 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
17960829 GCCGACTACT
17960839 GTTACTGTTACC
1 GTTACTGTTACC
17960851 GTTACTGTTACC
1 GTTACTGTTACC
*
17960863 GTTATTGTTAC
1 GTTACTGTTAC
17960874 TGATTCGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:17960924 original size:45 final size:45
Alignment explanation
Indices: 17960856--17961004 Score: 162
Period size: 45 Copynumber: 3.3 Consensus size: 45
17960846 TTACCGTTAC
* * * *
17960856 TGTTACCGTTATTGTTACT-GATTCGATACTTTGTGTGTCAAATAT
1 TGTTACTGTTACTGTTA-TCGATTCGACACTTTGTGTGTCGAATAT
17960901 TGTTACTGTTACTGTTATCGATTCGACACTTTGTGTGTCGAATAT
1 TGTTACTGTTACTGTTATCGATTCGACACTTTGTGTGTCGAATAT
* * * *
17960946 TGTTA-TCGTTATTGTTA-CAGATTC-AGCACTTTGTGTGTTGGATAC
1 TGTTACT-GTTACTGTTATC-GATTCGA-CACTTTGTGTGTCGAATAT
17960991 TGTTACTGTTACTG
1 TGTTACTGTTACTG
17961005 CTACTGCTAC
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
44 4 0.04
45 85 0.94
46 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (45 bp):
TGTTACTGTTACTGTTATCGATTCGACACTTTGTGTGTCGAATAT
Found at i:17968462 original size:18 final size:17
Alignment explanation
Indices: 17968427--17968459 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17968417 CTTTTTATTC
17968427 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
17968444 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
17968460 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:17970040 original size:13 final size:13
Alignment explanation
Indices: 17970022--17970046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17970012 TTTTATTGAT
17970022 TAAAATATATATA
1 TAAAATATATATA
17970035 TAAAATATATAT
1 TAAAATATATAT
17970047 TTGTTTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATATATATA
Found at i:17971168 original size:12 final size:12
Alignment explanation
Indices: 17971151--17971175 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17971141 GCCGACTACT
17971151 GTTACTGTTACC
1 GTTACTGTTACC
17971163 GTTACTGTTACC
1 GTTACTGTTACC
17971175 G
1 G
17971176 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:17971206 original size:45 final size:45
Alignment explanation
Indices: 17971156--17971296 Score: 230
Period size: 45 Copynumber: 3.1 Consensus size: 45
17971146 CTACTGTTAC
17971156 TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
1 TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
17971201 TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
1 TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
* * * *
17971246 TGTTACTGTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATAC
1 TGTTACCGTTACTGTTACCGATTCGA-CACTTTGTGTGTCGAATAT
17971291 TGTTAC
1 TGTTAC
17971297 TATTACTGCT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
44 1 0.01
45 90 0.99
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (45 bp):
TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
Found at i:17978886 original size:2 final size:2
Alignment explanation
Indices: 17978879--17978905 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17978869 CATATTAATT
17978879 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 T
17978906 TGAACTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17979102 original size:18 final size:18
Alignment explanation
Indices: 17979074--17979118 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
17979064 CAGTCGGTAA
*
17979074 CAATCAATTATTCAATAAT
1 CAATCAGTTATTCAAT-AT
*
17979093 -AATCAGTTATTCAGTAT
1 CAATCAGTTATTCAATAT
17979110 CAATCAGTT
1 CAATCAGTT
17979119 GATCGGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (18 bp):
CAATCAGTTATTCAATAT
Found at i:17981812 original size:25 final size:26
Alignment explanation
Indices: 17981772--17981868 Score: 126
Period size: 26 Copynumber: 3.8 Consensus size: 26
17981762 TGAAATGCCC
17981772 ATCATGGAACATTTACCTAAATCATT
1 ATCATGGAACATTTACCTAAATCATT
**
17981798 ATCAT-GAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAATCATT
*
17981823 ATCATGGAATATTTACCT-AATCCATT
1 ATCATGGAACATTTACCTAAAT-CATT
* *
17981849 TTCATGGAATATTTACCTAA
1 ATCATGGAACATTTACCTAA
17981869 CCTATTATCA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
25 24 0.39
26 37 0.60
27 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAATCATT
Found at i:17981842 original size:51 final size:52
Alignment explanation
Indices: 17981772--17981878 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 52
17981762 TGAAATGCCC
17981772 ATCATGGAACATTTACCTAAAT-CATTATCAT-GAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCT-AATCCATTATCATGGAACATTTACCTAACCCATT
* * * *
17981823 ATCATGGAATATTTACCTAATCCATTTTCATGGAATATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
17981875 ATCA
1 ATCA
17981879 ATTTGTACCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
50 3 0.06
51 25 0.50
52 22 0.44
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
Found at i:17984754 original size:53 final size:53
Alignment explanation
Indices: 17984613--17984763 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
17984603 ACAAGTGTGC
* **
17984613 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
17984666 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
17984719 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
17984764 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:17992267 original size:53 final size:53
Alignment explanation
Indices: 17992126--17992276 Score: 207
Period size: 53 Copynumber: 2.8 Consensus size: 53
17992116 GACAAGTGTG
* *
17992126 CCGTTTAAGACCATAGCTGGGGCTATGGCATCGGT-CAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCT-GGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
17992179 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
17992232 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
17992277 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
52 17 0.19
53 65 0.73
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:17996921 original size:25 final size:26
Alignment explanation
Indices: 17996884--17996932 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
17996874 TCAAACATGC
*
17996884 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACACTAGGGGT
* *
17996910 ATTTCGGT-AATTTATCACTAGGG
1 ATTTAGGTCAATTTAACACTAGGG
17996933 TTAAAACTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACACTAGGGGT
Found at i:17998336 original size:26 final size:26
Alignment explanation
Indices: 17998300--17998434 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
17998290 CATGAAATTC
*
17998300 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
17998326 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
17998352 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
17998378 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
17998404 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
17998429 TTATCA
1 TTATCA
17998435 ATTTGTATCA
Statistics
Matches: 107, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
25 23 0.21
26 84 0.79
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:18002376 original size:135 final size:136
Alignment explanation
Indices: 18002134--18002417 Score: 509
Period size: 135 Copynumber: 2.1 Consensus size: 136
18002124 CATTGGGCCT
** *
18002134 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAACTGGGCCTTA
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAACTGGGCCTTA
18002199 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AAC
66 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
18002263 ATATGC
131 ATATGC
18002269 AAGCCCATTTGGGTAACAGT-GTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAAT-AACTGGGCCTT
*
18002333 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
65 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
18002398 CATATGC
130 CATATGC
18002405 AAGCCCATTTGGG
1 AAGCCCATTTGGG
18002418 GAGACTACTC
Statistics
Matches: 143, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
134 31 0.22
135 90 0.63
136 22 0.15
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAACTGGGCCTTA
GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
ATATGC
Found at i:18004233 original size:26 final size:26
Alignment explanation
Indices: 18004197--18004311 Score: 185
Period size: 26 Copynumber: 4.4 Consensus size: 26
18004187 CATGAAATTC
*
18004197 TTATCATGAAACATTTATCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
18004223 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
18004249 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
18004275 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
18004301 TTATCATGAAA
1 TTATCATGAAA
18004312 TTATCAATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 85 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:18006528 original size:13 final size:14
Alignment explanation
Indices: 18006506--18006538 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
18006496 TAACTAATTT
*
18006506 AATAATAAAAT-AA
1 AATAAAAAAATAAA
18006519 AATAAAAAAATAAA
1 AATAAAAAAATAAA
18006533 AATAAA
1 AATAAA
18006539 TAATGCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:18011479 original size:39 final size:39
Alignment explanation
Indices: 18011424--18011520 Score: 140
Period size: 39 Copynumber: 2.5 Consensus size: 39
18011414 TGATTTGAAA
* * * *
18011424 CCCGAAGTCTAGCTAAAGCACATAAGTGCTAAATGGAAG
1 CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
*
18011463 CCCGAAGGCTAACTAAAGCACACAAGTGTTAAACGGAAG
1 CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
*
18011502 CCCGAAGGCTAACTGAAGC
1 CCCGAAGGCTAACTAAAGC
18011521 TCATCAGAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (39 bp):
CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
Found at i:18021984 original size:26 final size:26
Alignment explanation
Indices: 18021955--18022014 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
18021945 TCCCTTTGAA
* * *
18021955 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
18021981 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
18022009 CCATTC
1 TCATTC
18022015 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:18022000 original size:28 final size:28
Alignment explanation
Indices: 18021969--18022040 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
18021959 TCGATATTTT
18021969 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
* *
18021997 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
* * *
18022025 GTACACTGAGTATCAT
1 GCACACTAAGTGTCAT
18022041 ATTTGATTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:18025525 original size:7 final size:7
Alignment explanation
Indices: 18025513--18025541 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
18025503 TTACATATTA
18025513 TAAATTT
1 TAAATTT
18025520 TAAATTT
1 TAAATTT
18025527 TAAATTT
1 TAAATTT
18025534 TAAATTT
1 TAAATTT
18025541 T
1 T
18025542 CGTATATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:18025527 original size:27 final size:27
Alignment explanation
Indices: 18025474--18025527 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
18025464 ACATTGTTTA
* * *
18025474 TTTTACACATTATTACTTTGAATTTTT
1 TTTTACACATTATAAATTTGAAATTTT
* *
18025501 TTTTACATATTATAAATTTTAAATTTT
1 TTTTACACATTATAAATTTGAAATTTT
18025528 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTACACATTATAAATTTGAAATTTT
Found at i:18034301 original size:64 final size:64
Alignment explanation
Indices: 18034228--18034352 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 64
18034218 TCATTCATAA
* * * * **
18034228 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATATCATCCTAATTATTTGACATAAGTAT
1 CACATCTAGTTAAGAACATTTGATTCATGTCAATCATAGAATCCTAATTATTTGACATAAGTAT
*
18034292 CACATCTAGTTAAGAACATTTTATTCATGTCAATCATAGAATCCTAATTATTTGACATAAG
1 CACATCTAGTTAAGAACATTTGATTCATGTCAATCATAGAATCCTAATTATTTGACATAAG
18034353 CATAGGCCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAAGAACATTTGATTCATGTCAATCATAGAATCCTAATTATTTGACATAAGTAT
Found at i:18034607 original size:133 final size:133
Alignment explanation
Indices: 18034369--18034815 Score: 637
Period size: 133 Copynumber: 3.4 Consensus size: 133
18034359 CCTATGAAAC
* * *
18034369 AGATTGTA-AATCTTGTCTCCCTGAAGTTGCAATGGAGCAAAGCAAAGATGACGAATCTTAGCTT
1 AGATTGTAGAA-CTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCAAAGATGACGAATCTTGGCTT
*
18034433 CCTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
65 CTTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
*
18034498 ATAA
130 CTAA
* * * *
18034502 AGATTGTAGAACTTGTCTCCTTAAAATTGCAGTGGGGCAAATCAAAGATGACGAATCTTGGCTTC
1 AGATTGTAGAACTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCAAAGATGACGAATCTTGGCTTC
* * * * *
18034567 TTAAAGTTGCAGTTAAAAAGATTTAAGCCACCATCCTAGCTCTCTAGAGTTGTAGTGGAGTAGGC
66 TTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
18034632 TAA
131 TAA
* *
18034635 AGATTGTAGATCTTGTCTCCCTGAAGTTGCAGCGGAGCAAAT-AGAAGATGACGAATCTTGGCTT
1 AGATTGTAGAACTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCA-AAGATGACGAATCTTGGCTT
* *
18034699 CTTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAATGTTGTAGTGGAGTAGG
65 CTTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
*
18034764 CTGA
130 CTAA
* * * ** *
18034768 AGATTATAGATCTTGTCTCCCTGAAGTTGTAGCAGAGCAAATCGAAGA
1 AGATTGTAGAACTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCAAAGA
18034816 CGGCAAGCCT
Statistics
Matches: 279, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
132 1 0.00
133 276 0.99
134 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (133 bp):
AGATTGTAGAACTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCAAAGATGACGAATCTTGGCTTC
TTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
TAA
Found at i:18034867 original size:89 final size:88
Alignment explanation
Indices: 18034761--18034976 Score: 288
Period size: 88 Copynumber: 2.4 Consensus size: 88
18034751 GTAGTGGAGT
* * * * **
18034761 AGGCTGAAGATTATAGATCTTGTCTCCCTGAAGTTGTAGCAGAGCAAATCGAAGACGGCAAGCCT
1 AGGCTGAAGATTGTAGATCTTGTCTCTCTGAAGTTGTAGCAGAGCAAAT-AAAAAAAGCAAGCCT
* *
18034826 TAACTCCCTAAGTCGTAGGGTGAC
65 TAACCCCCTAAGTCGTAGGGTAAC
* * *
18034850 AGGCTGAAGATTGTAGATCTTGTCTCTCTGAAGTCGCAGCGGAGCAAATAAAAAAAGCAAGCCTT
1 AGGCTGAAGATTGTAGATCTTGTCTCTCTGAAGTTGTAGCAGAGCAAATAAAAAAAGCAAGCCTT
18034915 AACCCCCTAAGTCGTAGGGTAAC
66 AACCCCCTAAGTCGTAGGGTAAC
* * * *
18034938 AGGCTAAAGTTTGCAGATCTCGTCTCTCTGAAGTTGTAG
1 AGGCTGAAGATTGTAGATCTTGTCTCTCTGAAGTTGTAG
18034977 TGGAACAAAT
Statistics
Matches: 110, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 66 0.60
89 44 0.40
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (88 bp):
AGGCTGAAGATTGTAGATCTTGTCTCTCTGAAGTTGTAGCAGAGCAAATAAAAAAAGCAAGCCTT
AACCCCCTAAGTCGTAGGGTAAC
Found at i:18037126 original size:2 final size:2
Alignment explanation
Indices: 18037114--18037156 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
18037104 TAAACTAATT
*
18037114 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18037156 T
1 T
18037157 CTCCTTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18037752 original size:3 final size:3
Alignment explanation
Indices: 18037738--18037784 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
18037728 TAATTTGTTT
* *
18037738 TTA TTA TT- TTA TTA TTA TTA TTA TTT TTA -TA TTA TTT TTA TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
18037782 TTA
1 TTA
18037785 ATAGAGTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:18037760 original size:17 final size:17
Alignment explanation
Indices: 18037738--18037779 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
18037728 TAATTTGTTT
18037738 TTATTA-TTTTATTATTA
1 TTATTATTTTTA-TATTA
18037755 TTATTATTTTTATATTA
1 TTATTATTTTTATATTA
*
18037772 TTTTTATT
1 TTATTATT
18037780 CATTAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTATTTTTATATTA
Found at i:18038292 original size:131 final size:131
Alignment explanation
Indices: 18037946--18038304 Score: 450
Period size: 130 Copynumber: 2.7 Consensus size: 131
18037936 AACAAAAGCG
* * * * *
18037946 ATGTTTGACGTTTAGAAATTCGAGGAATTGTGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGT
1 ATGTTCGACGTTTGGCAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCCCGTTTGT
* * *
18038011 TCAAAATGATCGAATATTTCTTTAGAATTTCACACATGTCTTTAAAAATTCTTCTAAACGAAGGC
66 TCAAAATAATCGAATATTCCTTTAGAATTTCACACATGTCTTTAAAAATTCTTCAAAACGAAGGC
18038076 A
131 A
** * * * *
18038077 ATACTCGATGCTTGTCAATTC-AGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCCCGTTTGC
1 ATGTTCGACGTTTGGCAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCCCGTTTGT
* * *** * *
18038141 TCAAAACAATCGAATATTCCTTTGGAATTTCGTTCATGTCTTTAAAAATTCTTCAAAACGAATGT
66 TCAAAATAATCGAATATTCCTTTAGAATTTCACACATGTCTTTAAAAATTCTTCAAAACGAAGGC
18038206 A
131 A
* * * * * **
18038207 ATGTTCGACGTTTGGCAATTCGGGGAATCGTGCCCTATCATGCTAGGTTGTGATCTCTTGTTTGT
1 ATGTTCGACGTTTGGCAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCCCGTTTGT
*
18038272 TCCAAATAATCGAATATTCCTTTAGAATTTCAC
66 TCAAAATAATCGAATATTCCTTTAGAATTTCAC
18038305 TCATTCTAAG
Statistics
Matches: 188, Mismatches: 39, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
130 112 0.60
131 76 0.40
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (131 bp):
ATGTTCGACGTTTGGCAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCCCGTTTGT
TCAAAATAATCGAATATTCCTTTAGAATTTCACACATGTCTTTAAAAATTCTTCAAAACGAAGGC
A
Found at i:18039257 original size:24 final size:24
Alignment explanation
Indices: 18039228--18039274 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
18039218 CCATAAAAAA
18039228 ATTAATGATTAATAACCAATCACC
1 ATTAATGATTAATAACCAATCACC
* * *
18039252 ATTAATTATTAATTATCAATCAC
1 ATTAATGATTAATAACCAATCAC
18039275 GTTTTAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (24 bp):
ATTAATGATTAATAACCAATCACC
Found at i:18045238 original size:16 final size:16
Alignment explanation
Indices: 18045199--18045238 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
18045189 ATTATATTCT
*
18045199 TTAATTTAATTTAATC
1 TTAATTTAATTTAACC
18045215 -TAATTTTAATTTAACC
1 TTAA-TTTAATTTAACC
18045231 TTAATTTA
1 TTAATTTA
18045239 TAGAAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 15 0.71
17 3 0.14
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTTAATTTAACC
Found at i:18063843 original size:27 final size:26
Alignment explanation
Indices: 18063812--18063889 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
18063802 CAAACTCCCA
18063812 AATAAAAAAATAAATAAATAGAAAAGC-
1 AATAAAAAAA-AAATAAATA-AAAAGCG
*
18063839 TATAAGAAAACAAAA-AAATAAAAAGCG
1 AATAA-AAAA-AAAATAAATAAAAAGCG
*
18063866 AATAAAAAAAAAACTAAACAAAAA
1 AATAAAAAAAAAA-TAAATAAAAA
18063890 TGATTCTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
25 4 0.09
26 10 0.23
27 21 0.49
28 7 0.16
29 1 0.02
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (26 bp):
AATAAAAAAAAAATAAATAAAAAGCG
Found at i:18064552 original size:21 final size:23
Alignment explanation
Indices: 18064528--18064570 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
18064518 TTGATAGTAT
18064528 AATTATATTATT-TAA-TATTTG
1 AATTATATTATTATAATTATTTG
*
18064549 AATTATTTTATTATAATTATTT
1 AATTATATTATTATAATTATTT
18064571 TTAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AATTATATTATTATAATTATTTG
Found at i:18072030 original size:2 final size:2
Alignment explanation
Indices: 18072025--18072057 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18072015 TCAAACTGTT
18072025 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 T
18072058 TGTAGGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18087067 original size:2 final size:2
Alignment explanation
Indices: 18087060--18087088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18087050 CATTATTTGT
18087060 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 T
18087089 GACAATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18087189 original size:15 final size:15
Alignment explanation
Indices: 18087166--18087215 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
18087156 TTTATTTAAT
18087166 TTATATTGATTGAAA
1 TTATATTGATTGAAA
*
18087181 TTATTTTGATTGAAA
1 TTATATTGATTGAAA
18087196 TTATATTGATTG-AA
1 TTATATTGATTGAAA
18087210 TTATAT
1 TTATAT
18087216 AATATATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
14 8 0.24
15 25 0.76
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:18087870 original size:19 final size:20
Alignment explanation
Indices: 18087846--18087887 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
18087836 ATGAAACGAG
18087846 AAATTGA-AT-TGAGAATTGA
1 AAATTGAGATATGAG-ATTGA
18087865 AAATTGAGATATGAGATTGA
1 AAATTGAGATATGAGATTGA
18087885 AAA
1 AAA
18087888 CATGAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (20 bp):
AAATTGAGATATGAGATTGA
Found at i:18117186 original size:18 final size:20
Alignment explanation
Indices: 18117139--18117186 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
18117129 CTCTAACTTA
18117139 ATTTAAATT-TAATTAAATT
1 ATTTAAATTATAATTAAATT
*
18117158 ACTTAAA--ATAATT-AATT
1 ATTTAAATTATAATTAAATT
18117175 -TTTAAATTATAA
1 ATTTAAATTATAA
18117187 ACAAACGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.21
17 4 0.17
18 9 0.38
19 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAATTATAATTAAATT
Found at i:18117830 original size:26 final size:26
Alignment explanation
Indices: 18117796--18117849 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
18117786 ATTCTTATAT
* * * *
18117796 AAATTATTTCCTATTTCTTTTATTAA
1 AAATGATTTCATATATCTTCTATTAA
*
18117822 AAATGATTTGATATATCTTCTATTAA
1 AAATGATTTCATATATCTTCTATTAA
18117848 AA
1 AA
18117850 TACAGATCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (26 bp):
AAATGATTTCATATATCTTCTATTAA
Found at i:18120286 original size:7 final size:7
Alignment explanation
Indices: 18120274--18120301 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
18120264 AGGCCATTAC
18120274 ATGTTCA
1 ATGTTCA
18120281 ATGTTCA
1 ATGTTCA
18120288 ATGTTCA
1 ATGTTCA
18120295 ATGTTCA
1 ATGTTCA
18120302 CTATTCACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
ATGTTCA
Found at i:18121065 original size:15 final size:15
Alignment explanation
Indices: 18121047--18121081 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18121037 TAATGATATT
18121047 TTATAAAAAATTAAA
1 TTATAAAAAATTAAA
*
18121062 TTATATAAAATTAAA
1 TTATAAAAAATTAAA
*
18121077 ATATA
1 TTATA
18121082 GATACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTATAAAAAATTAAA
Found at i:18125556 original size:2 final size:2
Alignment explanation
Indices: 18125551--18125581 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18125541 GCTTCTTTAA
18125551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18125582 ACATTTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18134256 original size:18 final size:18
Alignment explanation
Indices: 18134233--18134275 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
18134223 GAATAGGTTT
*
18134233 TTAATTAAACCATTTT-AA
1 TTAATTAAA-AATTTTAAA
18134251 TTAATTAAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
18134269 TTAATTA
1 TTAATTA
18134276 CACGTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:18134711 original size:2 final size:2
Alignment explanation
Indices: 18134704--18134732 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18134694 CCTAAAAATT
18134704 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 T
18134733 TAATTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18138275 original size:15 final size:15
Alignment explanation
Indices: 18138255--18138284 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18138245 CATGAAAATT
18138255 ATTTTTTTATAATAA
1 ATTTTTTTATAATAA
*
18138270 ATTTTTTTATTATAA
1 ATTTTTTTATAATAA
18138285 CTTTAGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTTTATAATAA
Found at i:18138277 original size:18 final size:18
Alignment explanation
Indices: 18138250--18138284 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18138240 TATAACATGA
*
18138250 AAATTATTTTTTTATAAT
1 AAATTATTTTATTATAAT
*
18138268 AAATTTTTTTATTATAA
1 AAATTATTTTATTATAA
18138285 CTTTAGAAAT
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:0.00, T:0.60
Consensus pattern (18 bp):
AAATTATTTTATTATAAT
Found at i:18149856 original size:126 final size:127
Alignment explanation
Indices: 18149608--18149964 Score: 500
Period size: 126 Copynumber: 2.8 Consensus size: 127
18149598 GAGAGGTCTG
* * *
18149608 TTTTAGGTCAGACGCACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAATGAAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATT-A-GAAGAGGAAG
* * * * *
18149673 TTGGCTGGCATGCCTCAAACTTAAAGTCGGCTGTATCGTAGGTAATCCGATTCTCTTCACCCTC
64 TTGGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATCGTAGATAATCAGATTCTCTTCACCCTC
* *
18149737 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTTCTCCAAATCATCCATTA-AAGAGGATGTT
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
* * * *
18149801 GGCTGGCAAGCCTCGAACTTAAAGTCAGTTGCGTTGTAGATAATCAGATTCTCTTCACCCTC
66 GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATCGTAGATAATCAGATTCTCTTCACCCTC
*
18149863 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTACTGTAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTA--GAAGAGGAAG
* * **
18149928 TTGTCTGGCATGCCTCGAACTTAGAGTTGGCTGCATC
64 TTGGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATC
18149965 ATGGGCGATC
Statistics
Matches: 200, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
126 115 0.57
128 1 0.00
129 84 0.42
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (127 bp):
TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATCGTAGATAATCAGATTCTCTTCACCCTC
Found at i:18156422 original size:31 final size:32
Alignment explanation
Indices: 18156387--18156461 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
18156377 CGTATAATTA
18156387 AATTAAAATTAAAATTTTATGTAT-TTATAT-C
1 AATTAAAATTAAAATTTTATGTATATTA-ATGC
* *
18156418 AATTACAATTTAAATTTTATGTATATTAATGC
1 AATTAAAATTAAAATTTTATGTATATTAATGC
18156450 AA-TAAAATTAAA
1 AATTAAAATTAAA
18156462 GTTTATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 32 0.84
32 6 0.16
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (32 bp):
AATTAAAATTAAAATTTTATGTATATTAATGC
Found at i:18164802 original size:2 final size:2
Alignment explanation
Indices: 18164795--18164823 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18164785 GATTATTCTG
18164795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18164824 ATTATATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18176157 original size:21 final size:20
Alignment explanation
Indices: 18176127--18176166 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
18176117 CCGCCACTCT
18176127 TTCTCCCCCTTAC-CCTCCCC
1 TTCTCCCCCTT-CTCCTCCCC
18176147 TTCTCGCCCCTTCTCCTCCC
1 TTCTC-CCCCTTCTCCTCCC
18176167 GAACGCCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.03, C:0.62, G:0.03, T:0.33
Consensus pattern (20 bp):
TTCTCCCCCTTCTCCTCCCC
Found at i:18176576 original size:10 final size:10
Alignment explanation
Indices: 18176549--18176578 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
18176539 TTTTATCTTC
*
18176549 TTCTTTTCTT
1 TTCTTTTTTT
18176559 TTCTTTTTTT
1 TTCTTTTTTT
18176569 TTCTTTTTTT
1 TTCTTTTTTT
18176579 AATTTGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:18185242 original size:25 final size:26
Alignment explanation
Indices: 18185213--18185277 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
18185203 TTTTTCAATA
18185213 AAAAAAAACCAAAATCAATT-TTTTT
1 AAAAAAAACCAAAATCAATTCTTTTT
**
18185238 AAAAAACCCCAAAATCAATTGCTTTTT
1 AAAAAAAACCAAAATCAATT-CTTTTT
*
18185265 AAAAAAAAACAAA
1 AAAAAAAACCAAA
18185278 GTTGTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 18 0.55
27 15 0.45
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAAAAACCAAAATCAATTCTTTTT
Found at i:18194490 original size:21 final size:21
Alignment explanation
Indices: 18194466--18194528 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
18194456 ATTAAATATT
18194466 TATTTTAATTTTTTTAATAAA
1 TATTTTAATTTTTTTAATAAA
* **
18194487 TATTTTCA-TAATTTAATAATA
1 TATTTTAATTTTTTTAATAA-A
*
18194508 TATTTTTATTTTTGTT-ATAAA
1 TATTTTAATTTTT-TTAATAAA
18194529 ATTATCAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 9 0.27
21 16 0.48
22 6 0.18
23 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTAATTTTTTTAATAAA
Found at i:18195070 original size:2 final size:2
Alignment explanation
Indices: 18195065--18195101 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
18195055 CCCCCAACAA
* *
18195065 TC TC TC TC TC TC TC TC TC TG TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
18195102 GCGTCGGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.43, G:0.03, T:0.54
Consensus pattern (2 bp):
TC
Found at i:18201601 original size:12 final size:12
Alignment explanation
Indices: 18201580--18201656 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
18201570 ATGGGGATGG
18201580 GGTGGAGGAGGT
1 GGTGGAGGAGGT
* *
18201592 GGTGGGGGAGGA
1 GGTGGAGGAGGT
* *
18201604 GGAGGAGGAGGG
1 GGTGGAGGAGGT
* * *
18201616 GGAGGAGGCGGGG
1 GGTGGAGG-AGGT
18201629 GGTGG-GGATGG-
1 GGTGGAGGA-GGT
*
18201640 GGAGGAGGAGGT
1 GGTGGAGGAGGT
18201652 GGTGG
1 GGTGG
18201657 TTGGTATAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
11 6 0.12
12 38 0.75
13 7 0.14
ACGTcount: A:0.17, C:0.01, G:0.73, T:0.09
Consensus pattern (12 bp):
GGTGGAGGAGGT
Found at i:18201602 original size:60 final size:60
Alignment explanation
Indices: 18201529--18201656 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
18201519 TGGCGGCGGG
* * * * * *
18201529 GGTGGAGGTGGAGGAGGAGGAGGTGGCGGTGGCGG-GTACGGATGGGGATGGGGTGGAGGA
1 GGTGGTGGGGGAGGAGGAGGAGGAGGCGGAGGAGGCG-ACGGATGGGGATGGGGAGGAGGA
* ** *
18201589 GGTGGTGGGGGAGGAGGAGGAGGAGGGGGAGGAGGCGGGGGGTGGGGATGGGGAGGAGGA
1 GGTGGTGGGGGAGGAGGAGGAGGAGGCGGAGGAGGCGACGGATGGGGATGGGGAGGAGGA
18201649 GGTGGTGG
1 GGTGGTGG
18201657 TTGGTATAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 56 0.98
61 1 0.02
ACGTcount: A:0.16, C:0.03, G:0.70, T:0.11
Consensus pattern (60 bp):
GGTGGTGGGGGAGGAGGAGGAGGAGGCGGAGGAGGCGACGGATGGGGATGGGGAGGAGGA
Found at i:18201621 original size:18 final size:18
Alignment explanation
Indices: 18201578--18201650 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 18
18201568 GGATGGGGAT
* * *
18201578 GGGGTGGAGGAGGTGGTG
1 GGGGAGGAGGAGGAGGAG
18201596 GGGGAGGAGGAGGAGGAG
1 GGGGAGGAGGAGGAGGAG
* *
18201614 GGGGAGGAGGCGG-GGGG
1 GGGGAGGAGGAGGAGGAG
18201631 TGGGGATGG-GGAGGAGGAG
1 -GGGGA-GGAGGAGGAGGAG
18201650 G
1 G
18201651 TGGTGGTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 3 0.07
18 37 0.82
19 5 0.11
ACGTcount: A:0.18, C:0.01, G:0.74, T:0.07
Consensus pattern (18 bp):
GGGGAGGAGGAGGAGGAG
Found at i:18201623 original size:36 final size:36
Alignment explanation
Indices: 18201502--18201650 Score: 99
Period size: 36 Copynumber: 4.1 Consensus size: 36
18201492 TGTTGGTCGT
* * * * * *
18201502 GGGGGAGGTGGAGGTGGTGGCGGCGGGGGTGGAGGT
1 GGGGGAGGAGGAGGTGGTGGGGGAGGAGGAGGAGGA
* *
18201538 GGAGGAGGAGGAGGTGGCGGTGGCG-GGTACGGATGG-GGA
1 GGGGGAGGAGGAGGTGGTGG-GG-GAGG-A-GGA-GGAGGA
* *
18201577 TGGGGTGGAGGAGGTGGTGGGGGAGGAGGAGGAGGA
1 GGGGGAGGAGGAGGTGGTGGGGGAGGAGGAGGAGGA
* *
18201613 GGGGGAGGAGGCGG-GGGGTGGGGATGG-GGAGGAGGA
1 GGGGGAGGAGGAGGTGGTG-GGGGA-GGAGGAGGAGGA
18201649 GG
1 GG
18201651 TGGTGGTTGG
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
35 5 0.06
36 50 0.56
37 7 0.08
38 5 0.06
39 20 0.22
40 2 0.02
ACGTcount: A:0.15, C:0.04, G:0.70, T:0.10
Consensus pattern (36 bp):
GGGGGAGGAGGAGGTGGTGGGGGAGGAGGAGGAGGA
Found at i:18202935 original size:15 final size:16
Alignment explanation
Indices: 18202915--18202948 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18202905 GATATCAATT
*
18202915 TATATAA-ATATTTAA
1 TATATAATATATTAAA
18202930 TATATAATATATTAAA
1 TATATAATATATTAAA
18202946 TAT
1 TAT
18202949 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATAATATATTAAA
Found at i:18203477 original size:22 final size:21
Alignment explanation
Indices: 18203435--18203478 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
18203425 AGACTCATTC
18203435 ATATTATTTTTTTAAATATTT
1 ATATTATTTTTTTAAATATTT
18203456 ATATTATTTTAATTT-AATATTT
1 ATATTATTTT--TTTAAATATTT
18203478 A
1 A
18203479 CTAGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 8 0.38
23 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTATTTTTTTAAATATTT
Found at i:18210904 original size:24 final size:24
Alignment explanation
Indices: 18210877--18210925 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
18210867 ATTTGAATGT
18210877 ACTAAATCATATTAGAATTATTTA
1 ACTAAATCATATTAGAATTATTTA
*
18210901 ACTAAATCGTATTAGAATTATTTA
1 ACTAAATCATATTAGAATTATTTA
18210925 A
1 A
18210926 TTATTACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (24 bp):
ACTAAATCATATTAGAATTATTTA
Found at i:18214160 original size:51 final size:50
Alignment explanation
Indices: 18214089--18214248 Score: 239
Period size: 51 Copynumber: 3.2 Consensus size: 50
18214079 CTGATCACAT
*
18214089 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* *
18214140 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * *
18214190 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
18214241 TTGTCACT
1 TTATCACT
18214249 GATCAGAAGT
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 45 0.45
51 55 0.55
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:18216779 original size:46 final size:44
Alignment explanation
Indices: 18216675--18216782 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
18216665 TGTCTTTGAC
** * * *
18216675 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
18216719 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
18216765 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
18216783 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:18225171 original size:46 final size:44
Alignment explanation
Indices: 18225067--18225174 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
18225057 TGTCTTTGAC
** * * *
18225067 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
18225111 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
18225157 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
18225175 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:18226188 original size:84 final size:84
Alignment explanation
Indices: 18226090--18226257 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
18226080 TTCCTTCCAT
18226090 GTCCTAATTTTGTCCATGAACTTAAAATTGGTCAAATTACCATTTAAGATCTCCTAATTAATATT
1 GTCCTAATTTTGTCCATGAACTTAAAATTGGTCAAATTACCATTTAAGATCTCCTAATTAATATT
18226155 CCAAAATAATTTCATACTA
66 CCAAAATAATTTCATACTA
18226174 GTCCTAATTTTGTCCATGAACTTAAAATTGGTCAAATTACCATTTAAGATCTCCTAATTAATATT
1 GTCCTAATTTTGTCCATGAACTTAAAATTGGTCAAATTACCATTTAAGATCTCCTAATTAATATT
18226239 CCAAAATAATTTCATACTA
66 CCAAAATAATTTCATACTA
18226258 AAAACTTCTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (84 bp):
GTCCTAATTTTGTCCATGAACTTAAAATTGGTCAAATTACCATTTAAGATCTCCTAATTAATATT
CCAAAATAATTTCATACTA
Found at i:18231933 original size:51 final size:50
Alignment explanation
Indices: 18231862--18232021 Score: 248
Period size: 51 Copynumber: 3.2 Consensus size: 50
18231852 CTGATCACAT
18231862 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* *
18231913 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * *
18231963 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
18232014 TTGTCACT
1 TTATCACT
18232022 GATCAGAAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 46 0.46
51 55 0.54
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:18245111 original size:37 final size:37
Alignment explanation
Indices: 18245039--18245111 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
18245029 ATGACTAAAC
* ** *
18245039 AATTTAATAATATAAATAATATAAATATGTGAAATTT
1 AATTTAATAATATAAATAATAGAAATAAATAAAATTT
* *
18245076 AATTTAATAATATAAATAGTAGATATAAATAAAATT
1 AATTTAATAATATAAATAATAGAAATAAATAAAATT
18245112 ATTTTTTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (37 bp):
AATTTAATAATATAAATAATAGAAATAAATAAAATTT
Found at i:18245268 original size:18 final size:17
Alignment explanation
Indices: 18245209--18245268 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
18245199 AATGAGTGAG
*
18245209 AAGTAAAAATTTAGGGGA
1 AAGTAAAAGTTTA-GGGA
* *
18245227 AAATAAAAAGTTT-TGGA
1 AAGT-AAAAGTTTAGGGA
*
18245244 GAGTAAAAGTTTAAGGGA
1 AAGTAAAAGTTT-AGGGA
18245262 AAGTAAA
1 AAGTAAA
18245269 TGGGGGAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 12 0.38
19 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (17 bp):
AAGTAAAAGTTTAGGGA
Found at i:18245388 original size:30 final size:30
Alignment explanation
Indices: 18245343--18245401 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
18245333 GGGGCTGGGA
18245343 TGGGAAGGAAGTAAAAGTTTTAAGGGGAAAG
1 TGGGAAGGAAGTAAAA-TTTTAAGGGGAAAG
*
18245374 TGGGAAGG-AGTAAAATTTTAGGGGGAAA
1 TGGGAAGGAAGTAAAATTTTAAGGGGAAA
18245402 ATAAAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.44
30 7 0.26
31 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (30 bp):
TGGGAAGGAAGTAAAATTTTAAGGGGAAAG
Found at i:18245562 original size:30 final size:30
Alignment explanation
Indices: 18245501--18245562 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
18245491 AGATAGGAGG
* **
18245501 GGAGTAAAAGTTTTGGGGAGAAAGTGGAAA
1 GGAGTAAAAGTTTTGGGGAGAAAATAAAAA
18245531 GGAGTAAAAGTTTTGAGGGA-AAAATAAAAA
1 GGAGTAAAAGTTTTG-GGGAGAAAATAAAAA
18245561 GG
1 GG
18245563 TTTGGAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGGGGAGAAAATAAAAA
Found at i:18254520 original size:20 final size:20
Alignment explanation
Indices: 18254480--18254520 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18254470 TATTATCACG
* *
18254480 TATATTTTATTTTTTTATAT
1 TATATTATATTTTCTTATAT
*
18254500 TATATTATATTTTCTTGTAT
1 TATATTATATTTTCTTATAT
18254520 T
1 T
18254521 CATTTTCCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TATATTATATTTTCTTATAT
Found at i:18255291 original size:2 final size:2
Alignment explanation
Indices: 18255278--18255311 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
18255268 TAAAGAGATA
* *
18255278 AT AT AT AG AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18255312 TTCTGTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18264592 original size:19 final size:19
Alignment explanation
Indices: 18264565--18264601 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18264555 ATACATATTC
*
18264565 TTTTGTTTTTTAATTTTAA
1 TTTTGTTTTTTAAATTTAA
*
18264584 TTTTTTTTTTTAAATTTA
1 TTTTGTTTTTTAAATTTA
18264602 CGGTGGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTGTTTTTTAAATTTAA
Found at i:18268515 original size:2 final size:2
Alignment explanation
Indices: 18268508--18268537 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18268498 GTTTGATTGA
18268508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18268538 TTGTAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18271101 original size:5 final size:5
Alignment explanation
Indices: 18271059--18271087 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
18271049 AGATGAAGTG
18271059 GGGTA GGGTA GGGTA GGGTA GGGTA GGGT
1 GGGTA GGGTA GGGTA GGGTA GGGTA GGGT
18271088 GAGGTGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.62, T:0.21
Consensus pattern (5 bp):
GGGTA
Found at i:18280236 original size:2 final size:2
Alignment explanation
Indices: 18280229--18280259 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18280219 TTTTAGTTCC
18280229 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 T
18280260 TTCATCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18281961 original size:19 final size:19
Alignment explanation
Indices: 18281937--18281975 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18281927 TAGTTGGGTT
18281937 AATATTGTTTGATGATACA
1 AATATTGTTTGATGATACA
18281956 AATATTGTTTGATGATACA
1 AATATTGTTTGATGATACA
18281975 A
1 A
18281976 CTGAAGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
AATATTGTTTGATGATACA
Found at i:18288951 original size:5 final size:5
Alignment explanation
Indices: 18288941--18288968 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
18288931 AAAACGTAAA
18288941 AAAAC AAAAC AAAAC AAAAC AAAAC AAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAA
18288969 CCCCTTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:18297080 original size:16 final size:18
Alignment explanation
Indices: 18297041--18297074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18297031 TAAGTTTATA
18297041 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
18297058 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
18297075 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:18298600 original size:21 final size:21
Alignment explanation
Indices: 18298576--18298615 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
18298566 GCTTTCAAAA
18298576 TTTAGGGGTGACATTGCGATG
1 TTTAGGGGTGACATTGCGATG
18298597 TTTAGGGGTGACATTGCGA
1 TTTAGGGGTGACATTGCGA
18298616 CGACTTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.38, T:0.33
Consensus pattern (21 bp):
TTTAGGGGTGACATTGCGATG
Found at i:18299378 original size:30 final size:30
Alignment explanation
Indices: 18299342--18299406 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
18299332 ACATATTTTA
* *
18299342 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAAACAT
18299372 TTGTTAATTTTATTATTATTTTAAAAACAT
1 TTGTTAATTTTATTATTATTTTAAAAACAT
18299402 TTGTT
1 TTGTT
18299407 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAAACAT
Found at i:18300779 original size:11 final size:11
Alignment explanation
Indices: 18300763--18300804 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
18300753 TAGCTATTTA
18300763 TAATAAAATAT
1 TAATAAAATAT
18300774 TAATAAAATATCT
1 TAATAAAATA--T
*
18300787 TATTAAAATAT
1 TAATAAAATAT
18300798 TAATAAA
1 TAATAAA
18300805 GTAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:18305344 original size:93 final size:93
Alignment explanation
Indices: 18305232--18305402 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
18305222 GCCCATAAGT
* * *
18305232 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
18305297 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
18305325 GAACTCGGACTCAACTCAACGAGTTCAGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
18305390 CGAGTTCGGATGC
66 CGAGTTCGGATGC
18305403 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:18305418 original size:46 final size:46
Alignment explanation
Indices: 18305224--18305404 Score: 224
Period size: 46 Copynumber: 3.9 Consensus size: 46
18305214 TGTAACCCGC
* * *
18305224 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
18305270 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* * *
18305320 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
18305363 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
18305405 AACCATCCTA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 71 0.62
47 31 0.27
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:18317539 original size:47 final size:47
Alignment explanation
Indices: 18317430--18317540 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
18317420 TCGGGATAAG
*
18317430 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
18317477 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
18317524 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
18317541 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:18322379 original size:53 final size:53
Alignment explanation
Indices: 18322298--18322448 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
18322288 CTTACACGGT
* *
18322298 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
18322353 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
18322406 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
18322449 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:18329894 original size:53 final size:53
Alignment explanation
Indices: 18329813--18329963 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
18329803 CTTACACGGT
* *
18329813 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
18329868 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
18329921 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
18329964 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:18342303 original size:18 final size:18
Alignment explanation
Indices: 18342280--18342315 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18342270 TTTACTTACA
18342280 CAAAAAACACCAACAACC
1 CAAAAAACACCAACAACC
* *
18342298 CAAAAATCACCGACAACC
1 CAAAAAACACCAACAACC
18342316 ATGTAAAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.39, G:0.03, T:0.03
Consensus pattern (18 bp):
CAAAAAACACCAACAACC
Found at i:18350312 original size:17 final size:18
Alignment explanation
Indices: 18350290--18350323 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18350280 TTTCTTCTTC
18350290 TTTTTTG-TTTTACTTTA
1 TTTTTTGTTTTTACTTTA
18350307 TTTTTTGTTTTTACTTT
1 TTTTTTGTTTTTACTTT
18350324 TAAAAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTTGTTTTTACTTTA
Found at i:18350752 original size:2 final size:2
Alignment explanation
Indices: 18350745--18350769 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18350735 ATACTAATCT
18350745 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
18350770 GGATATTTGA
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:18351573 original size:6 final size:6
Alignment explanation
Indices: 18351555--18351605 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
18351545 AATGAATGAA
*
18351555 ATGAGC ATAAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
1 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
18351603 ATG
1 ATG
18351606 TAAAGGGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (6 bp):
ATGAGC
Found at i:18364084 original size:17 final size:17
Alignment explanation
Indices: 18364047--18364080 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18364037 AATTGATCTA
18364047 ATTTAAATTATATTATT
1 ATTTAAATTATATTATT
18364064 ATTTAAA-TATATT-TT
1 ATTTAAATTATATTATT
18364079 AT
1 AT
18364081 ATTTTGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAAATTATATTATT
Found at i:18364222 original size:22 final size:20
Alignment explanation
Indices: 18364182--18364220 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18364172 AATATTTAAA
18364182 TTATTAAAAAATATAAAATG
1 TTATTAAAAAATATAAAATG
*
18364202 TTATATAAAAAATTTAAAA
1 TTAT-TAAAAAATATAAAA
18364221 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TTATTAAAAAATATAAAATG
Found at i:18368431 original size:6 final size:6
Alignment explanation
Indices: 18368420--18368460 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
18368410 ATAATTTAAT
*
18368420 AAATAA AAATAAA AAACTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAAT-AA AAA-TAA AAATAA AAATAA AAATAA AAA
18368461 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 21 0.68
7 9 0.29
8 1 0.03
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:18368494 original size:9 final size:9
Alignment explanation
Indices: 18368480--18368592 Score: 86
Period size: 9 Copynumber: 12.6 Consensus size: 9
18368470 TTTATACAAA
18368480 TAATTCGGT
1 TAATTCGGT
**
18368489 TAATTCAAT
1 TAATTCGGT
18368498 TAATTCGGT
1 TAATTCGGT
***
18368507 TAATTTAAT
1 TAATTCGGT
* *
18368516 TAA-TCTAGA
1 TAATTC-GGT
*
18368525 TAATTTGAG-
1 TAATTCG-GT
18368534 TAATTCGGT
1 TAATTCGGT
*
18368543 TAATTCGAT
1 TAATTCGGT
*
18368552 TAATTAGGT
1 TAATTCGGT
*
18368561 TAATTCGAT
1 TAATTCGGT
18368570 TAATTCGGT
1 TAATTCGGT
*
18368579 TAATTCGTT
1 TAATTCGGT
18368588 TAATT
1 TAATT
18368593 TTATACTTAT
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
8 2 0.03
9 76 0.95
10 2 0.03
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Done.