Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 92 of 141
Found at i:29791900 original size:9 final size:9
Alignment explanation
Indices: 29791882--29791979 Score: 84
Period size: 9 Copynumber: 11.7 Consensus size: 9
29791872 ATGTTTTCGA
29791882 TTAT-TAAG
1 TTATGTAAG
29791890 TTATGTAAG
1 TTATGTAAG
29791899 TTATGT-A-
1 TTATGTAAG
*
29791906 TTATATAAG
1 TTATGTAAG
*
29791915 CTATGTAAG
1 TTATGTAAG
*
29791924 TTATTTAAG
1 TTATGTAAG
29791933 TTATGTAAG
1 TTATGTAAG
*
29791942 TTGTGT-A-
1 TTATGTAAG
* *
29791949 TTATGTTAT
1 TTATGTAAG
29791958 TTATGT-A-
1 TTATGTAAG
*
29791965 CTATGTAAG
1 TTATGTAAG
29791974 TTATGT
1 TTATGT
29791980 GTATTATGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
7 15 0.21
8 10 0.14
9 48 0.66
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29791919 original size:25 final size:24
Alignment explanation
Indices: 29791881--29791927 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
29791871 GATGTTTTCG
*
29791881 ATTATTAAGTTATGTAAGTTATGT
1 ATTATTAAGCTATGTAAGTTATGT
29791905 ATTATATAAGCTATGTAAGTTAT
1 ATTAT-TAAGCTATGTAAGTTAT
29791928 TTAAGTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (24 bp):
ATTATTAAGCTATGTAAGTTATGT
Found at i:29791977 original size:25 final size:25
Alignment explanation
Indices: 29791891--29792003 Score: 76
Period size: 25 Copynumber: 4.5 Consensus size: 25
29791881 ATTATTAAGT
*
29791891 TATGTAAGTTATG-TATTATAT-AAGC
1 TATGTAAGTTATGTTATT-TATGTA-C
* *
29791916 TATGTAAGTTAT-TTAAGTTATGTAAG
1 TATGTAAGTTATGTT-ATTTATGT-AC
*
29791942 T-TGTGTA-TTATGTTATTTATGTAC
1 TATGT-AAGTTATGTTATTTATGTAC
*
29791966 TATGTAAGTTATGTGTA-TTATGTAT
1 TATGTAAGTTATGT-TATTTATGTAC
*
29791991 TATGTATGTTATG
1 TATGTAAGTTATG
29792004 CATAATATTA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
24 3 0.04
25 58 0.83
26 8 0.11
27 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (25 bp):
TATGTAAGTTATGTTATTTATGTAC
Found at i:29792003 original size:16 final size:16
Alignment explanation
Indices: 29791916--29791997 Score: 69
Period size: 16 Copynumber: 5.0 Consensus size: 16
29791906 TTATATAAGC
*
29791916 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
29791934 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
29791950 TATGTTATTTATGTAC
1 TATGTAAGTTATGTAT
29791966 TATGTAAGTTATGTGTAT
1 TATGTAAGTTA--TGTAT
29791984 TATGT-A-TTATGTAT
1 TATGTAAGTTATGTAT
29791998 GTTATGCATA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
14 5 0.09
16 25 0.47
17 2 0.04
18 21 0.40
ACGTcount: A:0.28, C:0.01, G:0.18, T:0.52
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:29792036 original size:44 final size:44
Alignment explanation
Indices: 29791977--29792220 Score: 295
Period size: 44 Copynumber: 5.5 Consensus size: 44
29791967 ATGTAAGTTA
*
29791977 TGTGTATTATGTATTATGTATGTTATGCATAATATTAATTAAGT
1 TGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGT
* *
29792021 TGTGTAATATGTATTATGTACGTTATGTATAATATTAATTAAGT
1 TGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGT
*
29792065 TGTGTATAATGTAAAAAATGTATTATGTATGTTATGTATAAAATTAATTAAG-
1 TGTG--T-AT-T-----ATGTATTATGTATGTTATGTATAATATTAATTAAGT
29792117 T-TG-----TGTATTATGTATGTTATGTATAATATTAATTAAGT
1 TGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGT
*
29792155 TGTGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGT
1 TGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGT
29792199 TGTGTATTATGTAAGTTATGTA
1 TGTGTATTATGT-A-TTATGTA
29792221 AGAAATGTAT
Statistics
Matches: 174, Mismatches: 8, Indels: 34
0.81 0.04 0.16
Matches are distributed among these distances:
37 33 0.19
38 1 0.01
39 2 0.01
44 91 0.52
45 1 0.01
46 8 0.05
47 1 0.01
48 1 0.01
51 2 0.01
52 1 0.01
53 33 0.19
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.48
Consensus pattern (44 bp):
TGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGT
Found at i:29792048 original size:53 final size:50
Alignment explanation
Indices: 29791979--29792140 Score: 158
Period size: 53 Copynumber: 3.2 Consensus size: 50
29791969 GTAAGTTATG
29791979 TGTATTATGTATTATGTATGTTATGCATAATATTAATTAAGTTGTGTAATA
1 TGTATTATGTATTATGTATGTTATG-ATAATATTAATTAAGTTGTGTAATA
**
29792030 TGTATTATGTA-CGT-TATG---T-ATAATATTAATTAAGTTGTGT-ATAA
1 TGTATTATGTATTATGTATGTTATGATAATATTAATTAAGTTGTGTAAT-A
** * *
29792074 TGTAAAAAATGTATTATGTATGTTATGTATAAAATTAATTAAGTTGTGTATTA
1 TGT--ATTATGTATTATGTATGTTATG-ATAATATTAATTAAGTTGTGTAATA
29792127 TGTATGTTATGTAT
1 TGTA--TTATGTAT
29792141 AATATTAATT
Statistics
Matches: 88, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
43 2 0.02
44 25 0.28
46 7 0.08
47 1 0.01
48 4 0.05
49 4 0.05
50 1 0.01
51 13 0.15
53 30 0.34
54 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.48
Consensus pattern (50 bp):
TGTATTATGTATTATGTATGTTATGATAATATTAATTAAGTTGTGTAATA
Found at i:29792133 original size:37 final size:37
Alignment explanation
Indices: 29792083--29792251 Score: 187
Period size: 37 Copynumber: 4.3 Consensus size: 37
29792073 ATGTAAAAAA
29792083 TGTATTATGTATGTTATGTATAAAATTAATTAAGTTG
1 TGTATTATGTATGTTATGTATAAAATTAATTAAGTTG
*
29792120 TGTATTATGTATGTTATGTATAATATTAATTAAGTTG
1 TGTATTATGTATGTTATGTATAAAATTAATTAAGTTG
*
29792157 TGTATTATGTATTATGTACGTTATGTATAATATTAATTAAGTTG
1 TGTATTATG---TA--T--GTTATGTATAAAATTAATTAAGTTG
*
29792201 TGTATTATGTAAGTTATGTA-AGAAATGTATTATGTAAGTTG
1 TGTATTATGTATGTTATGTATA-AAAT-TA--AT-TAAGTTG
*
29792242 TGTATAATGT
1 TGTATTATGT
29792252 TAGTTATCAA
Statistics
Matches: 116, Mismatches: 4, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
36 1 0.01
37 56 0.48
38 2 0.02
40 4 0.03
41 18 0.16
42 1 0.01
44 34 0.29
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.49
Consensus pattern (37 bp):
TGTATTATGTATGTTATGTATAAAATTAATTAAGTTG
Found at i:29792219 original size:9 final size:9
Alignment explanation
Indices: 29792205--29792347 Score: 61
Period size: 9 Copynumber: 16.2 Consensus size: 9
29792195 AAGTTGTGTA
29792205 TTATGTAAG
1 TTATGTAAG
29792214 TTATGTAAG
1 TTATGTAAG
**
29792223 AAATGT-A-
1 TTATGTAAG
29792230 TTATGTAAG
1 TTATGTAAG
*
29792239 TTGTGT-A-
1 TTATGTAAG
* *
29792246 TAATGTTAG
1 TTATGTAAG
**
29792255 TTATCAAAG
1 TTATGTAAG
29792264 TTATGT-A-
1 TTATGTAAG
*
29792271 CTATGTAATTAG
1 TTATGT-A--AG
*
29792283 TTATTTAAG
1 TTATGTAAG
29792292 TTATGTAAG
1 TTATGTAAG
*
29792301 TTGTGT-A-
1 TTATGTAAG
29792308 TTATGTAAG
1 TTATGTAAG
*
29792317 TTAT-TATG
1 TTATGTAAG
29792325 TTATTATGTAAG
1 ---TTATGTAAG
*
29792337 TTATGCAAG
1 TTATGTAAG
29792346 TT
1 TT
29792348 TATATATAAG
Statistics
Matches: 97, Mismatches: 22, Indels: 30
0.65 0.15 0.20
Matches are distributed among these distances:
7 18 0.19
8 10 0.10
9 56 0.58
11 6 0.06
12 7 0.07
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29792229 original size:25 final size:25
Alignment explanation
Indices: 29792201--29792320 Score: 102
Period size: 25 Copynumber: 4.7 Consensus size: 25
29792191 AATTAAGTTG
*
29792201 TGTATTATGTAAGTTATGTAAGAAA
1 TGTATTATGTAAGTTATGTAAGTAA
*
29792226 TGTATTATGTAAGTTGTGT-A-TAA
1 TGTATTATGTAAGTTATGTAAGTAA
**
29792249 TGTTAGTTATCAAAGTTATGTACTATGTAA
1 TG-TA-TTATGTAAGTTATGTA--A-GTAA
* **
29792279 T-TAGTTATTTAAGTTATGTAAGTTG
1 TGTA-TTATGTAAGTTATGTAAGTAA
29792304 TGTATTATGTAAGTTAT
1 TGTATTATGTAAGTTAT
29792321 TATGTTATTA
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
23 4 0.05
24 3 0.04
25 45 0.58
26 3 0.04
28 18 0.23
30 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (25 bp):
TGTATTATGTAAGTTATGTAAGTAA
Found at i:29792244 original size:41 final size:41
Alignment explanation
Indices: 29792194--29792347 Score: 138
Period size: 41 Copynumber: 3.8 Consensus size: 41
29792184 TAATATTAAT
**
29792194 TAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATG
1 TAAGTTGTGTATTATGTAAGTTATGTAAGTTATGTATTATG
* * ** *
29792235 TAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTACTATG
1 TAAGTTGTGTATTATGTAAGTTATGTAAGTTATGTATTATG
*
29792276 TAA-TTAGT-TA-T-T-TAAGTTATGTAAGTTGTGTATTATG
1 TAAGTT-GTGTATTATGTAAGTTATGTAAGTTATGTATTATG
* *
29792313 TAAGTTATTATGTTATTATGTAAGTTATGCAAGTT
1 TAAG---TTGTG-TATTATGTAAGTTATGTAAGTT
29792348 TATATATAAG
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
37 23 0.26
38 1 0.01
40 5 0.06
41 41 0.47
42 2 0.02
43 1 0.01
44 1 0.01
45 14 0.16
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (41 bp):
TAAGTTGTGTATTATGTAAGTTATGTAAGTTATGTATTATG
Found at i:29792313 original size:37 final size:36
Alignment explanation
Indices: 29792261--29792341 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
29792251 TTAGTTATCA
29792261 AAGTTATGTACTATGTAA-TTAGTTAT-TTAAGTTATGT
1 AAGTTATGTACTATGTAAGTTA-TTATGTT-A-TTATGT
* *
29792298 AAGTTGTGTATTATGTAAGTTATTATGTTATTATGT
1 AAGTTATGTACTATGTAAGTTATTATGTTATTATGT
29792334 AAGTTATG
1 AAGTTATG
29792342 CAAGTTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 13 0.33
37 21 0.54
38 5 0.13
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.49
Consensus pattern (36 bp):
AAGTTATGTACTATGTAAGTTATTATGTTATTATGT
Found at i:29792358 original size:12 final size:12
Alignment explanation
Indices: 29792343--29792370 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29792333 TAAGTTATGC
29792343 AAGTTTATATAT
1 AAGTTTATATAT
29792355 AAGTTTATATAT
1 AAGTTTATATAT
29792367 AAGT
1 AAGT
29792371 GTAAATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (12 bp):
AAGTTTATATAT
Found at i:29793605 original size:7 final size:7
Alignment explanation
Indices: 29793557--29793602 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
29793547 TAAAGTGATA
*
29793557 CCAAACT
1 CCAATCT
29793564 CCAATCT
1 CCAATCT
29793571 CCAATCT
1 CCAATCT
29793578 CCAATCT
1 CCAATCT
29793585 CCAATCT
1 CCAATCT
*
29793592 CCAACCT
1 CCAATCT
29793599 CCAA
1 CCAA
29793603 CCTACACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.22
Consensus pattern (7 bp):
CCAATCT
Found at i:29794621 original size:84 final size:84
Alignment explanation
Indices: 29794406--29794595 Score: 301
Period size: 84 Copynumber: 2.3 Consensus size: 84
29794396 TTCATGAAGC
* * *
29794406 GAAACGGTGCCGCATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAATGCCACTAG
1 GAAACGGTGCCGCTTTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTAT
* *
29794471 AAGATTTTATTCTAGTAGA
66 AAGATTTTATTCCAGTACA
**
29794490 GAAACGGCACCG-TATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTA
1 GAAACGGTGCCGCT-TTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTA
29794554 TAAGATTTTATTCCAGTACA
65 TAAGATTTTATTCCAGTACA
29794574 GAAACGGTGCCGCTTTGGCAAA
1 GAAACGGTGCCGCTTTGGCAAA
29794596 TTTTAATAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 94 0.99
85 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (84 bp):
GAAACGGTGCCGCTTTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTAT
AAGATTTTATTCCAGTACA
Found at i:29794629 original size:84 final size:84
Alignment explanation
Indices: 29794419--29794640 Score: 243
Period size: 84 Copynumber: 2.6 Consensus size: 84
29794409 ACGGTGCCGC
* * * * * *
29794419 ATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAATGCCACTAGAAGATTTTATTCT
1 ATTGGCAAACATTAATTAAATCTTGCAGCGTTTTCCTAAAAAACGCCACTATAAGATTTTATTCC
*
29794484 AGTAGAGAAACGGCACCGT
66 AGTACAGAAACGGCACCGT
* * *
29794503 ATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTATAAGATTTTATTCC
1 ATTGGCAAACATTAATTAAATCTTGCAGCGTTTTCCTAAAAAACGCCACTATAAGATTTTATTCC
**
29794568 AGTACAGAAACGGTGCCGCT
66 AGTACAGAAACGGCACCG-T
** * * *
29794588 -TTGGCAAATTTTAA-TAAATATTTGCAGCGTTTTCAC-CAAAAACGCCACAATAA
1 ATTGGCAAACATTAATTAAAT-CTTGCAGCGTTTTC-CTAAAAAACGCCACTATAA
29794641 TTTTCATTCC
Statistics
Matches: 121, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
83 3 0.02
84 116 0.96
85 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (84 bp):
ATTGGCAAACATTAATTAAATCTTGCAGCGTTTTCCTAAAAAACGCCACTATAAGATTTTATTCC
AGTACAGAAACGGCACCGT
Found at i:29795146 original size:89 final size:89
Alignment explanation
Indices: 29795043--29795357 Score: 499
Period size: 89 Copynumber: 3.5 Consensus size: 89
29795033 TATAAAGAAC
** * * *
29795043 TTATTTAATATATAAATTAAAAAGTACTAATTAGTCTAAATCTTAAACCCTAACTTGACCTCAAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTTGACCTCAAA
* *
29795108 TTCCTAACCCCTAACCCCTAAACT
66 TCCCTAACCCTTAACCCCTAAACT
* *
29795132 TTATTTAATATATAAATT-AAAAACACTAATTAATCTAAACCCTAAACCCTAAACTCGACCCCAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCT-AACTTGACCTCAA
29795196 ATCCCTAACCCTTAACCCCTAAACT
65 ATCCCTAACCCTTAACCCCTAAACT
* *
29795221 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCTGATCCT-AA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTTGA-CCTCAA
29795285 ATCCCTAACCCTTAACCCCTAAACT
65 ATCCCTAACCCTTAACCCCTAAACT
29795310 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAAC
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAAC
29795358 TTTAACCTAA
Statistics
Matches: 210, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
88 27 0.13
89 150 0.71
90 33 0.16
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30
Consensus pattern (89 bp):
TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTTGACCTCAAA
TCCCTAACCCTTAACCCCTAAACT
Found at i:29795424 original size:12 final size:12
Alignment explanation
Indices: 29795407--29795431 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29795397 CTCTTAACAT
29795407 CTAACCCCTAAC
1 CTAACCCCTAAC
29795419 CTAACCCCTAAC
1 CTAACCCCTAAC
29795431 C
1 C
29795432 CTGACCTTTA
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:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:29795498 original size:14 final size:15
Alignment explanation
Indices: 29795479--29795511 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
29795469 CTTAAACCAG
29795479 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
29795493 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
29795508 AATC
1 AATC
29795512 TATAAACACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:29795970 original size:114 final size:114
Alignment explanation
Indices: 29795770--29796115 Score: 478
Period size: 114 Copynumber: 3.0 Consensus size: 114
29795760 GCGGCGCCTC
* * * * *
29795770 CTCAAAAACGCCGCTAAAGACTTGAGAATTAGC-AGCGCTTTATTAAAAACGTCGCTAAATCCCC
1 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGA-CGCTTTCTTAAAAACGCCGCTAAATCCCC
* * * * * * *
29795834 AAAAGCTAAGAAAATGACGTCGTTGAGCTTAGGTTCTTCTGCGGTGCTTT
65 GAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGTGCTTT
*
29795884 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACACTTTCTTAAAAACGCCGCTAAATCCCCG
1 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGCTAAATCCCCG
* *
29795949 AAAGCTCAGAAAACGGCGTCGTTGGGTTTAGGTTTTTTTGCGGCGCTTT
66 AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGTGCTTT
* * * *
29795998 CTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAGTCCCCG
1 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGCTAAATCCCCG
* * *
29796063 AAATCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTACGGTGCTTT
66 AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGTGCTTT
29796112 CTCA
1 CTCA
29796116 GGGCATTAGC
Statistics
Matches: 206, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
114 205 1.00
115 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (114 bp):
CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGCTAAATCCCCG
AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGTGCTTT
Found at i:29796194 original size:95 final size:95
Alignment explanation
Indices: 29796023--29796196 Score: 267
Period size: 95 Copynumber: 1.8 Consensus size: 95
29796013 AAAGCCCTAA
* * * *
29796023 GCATTAGCGGCGCTTACTTAAAAACGCCGCTAAGTCCCCGAAATCTCAAAAAACGGCGTCGTTGG
1 GCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACGGCATCGTTGG
*
29796088 GCTTAGGTTTTTTTACGGTGCTTTCTCAGG
66 GCTTAGATTTTTTTACGGTGCTTTCTCAGG
* **
29796118 GCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATTGCCAAAAGCTCAAAAAACGGCATCGTTGG
1 GCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACGGCATCGTTGG
*
29796183 GTTTAGATTTTTTT
66 GCTTAGATTTTTTT
29796197 TTGTGGCGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 70 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (95 bp):
GCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACGGCATCGTTGG
GCTTAGATTTTTTTACGGTGCTTTCTCAGG
Found at i:29807619 original size:29 final size:30
Alignment explanation
Indices: 29807577--29807633 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
29807567 TATACCACAT
* * *
29807577 TCAAACTTGTATGTGTATAATTGCACAAAA
1 TCAAAATTGTATGTATAGAATTGCACAAAA
*
29807607 TCAAAATT-TATGTATCGAATTGCACAA
1 TCAAAATTGTATGTATAGAATTGCACAA
29807634 TAAATTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (30 bp):
TCAAAATTGTATGTATAGAATTGCACAAAA
Found at i:29807732 original size:17 final size:17
Alignment explanation
Indices: 29807712--29807749 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
29807702 CAATTTAATT
*
29807712 ATAAATGTTTATGGATG
1 ATAAATGATTATGGATG
*
29807729 ATAAATGATTATGTATG
1 ATAAATGATTATGGATG
29807746 ATAA
1 ATAA
29807750 TAAACTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (17 bp):
ATAAATGATTATGGATG
Found at i:29813465 original size:33 final size:32
Alignment explanation
Indices: 29813408--29813469 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
29813398 TAATTTTTTG
29813408 TTTTATATTTTTAAATTTATTTTAACAAAATC
1 TTTTATATTTTTAAATTTATTTTAACAAAATC
*
29813440 TTTTATAATTTTTGAATATTA-TTTAACAAA
1 TTTTAT-ATTTTTAAAT-TTATTTTAACAAA
29813470 GTTTCAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 6 0.22
33 18 0.67
34 3 0.11
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (32 bp):
TTTTATATTTTTAAATTTATTTTAACAAAATC
Found at i:29813893 original size:17 final size:18
Alignment explanation
Indices: 29813871--29813911 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
29813861 ACGTATTTAG
29813871 ATATATTTAAA-AAT-AGA
1 ATATATTTAAATAATGA-A
29813888 ATATA-TTAAATAATGAA
1 ATATATTTAAATAATGAA
29813905 ATATATT
1 ATATATT
29813912 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.24
17 14 0.67
18 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATATTTAAATAATGAA
Found at i:29816736 original size:18 final size:18
Alignment explanation
Indices: 29816713--29816749 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29816703 AAACATTGAA
29816713 GCATTGTTTACCTTAACC
1 GCATTGTTTACCTTAACC
29816731 GCATTGTTTACCTTAACC
1 GCATTGTTTACCTTAACC
29816749 G
1 G
29816750 AAATAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.38
Consensus pattern (18 bp):
GCATTGTTTACCTTAACC
Found at i:29828927 original size:38 final size:38
Alignment explanation
Indices: 29828872--29828947 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
29828862 TCTTATTTTT
29828872 GATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAG
1 GATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAG
*
29828910 GATTAAAGAAGACTGCTCGAATGTTAGATTTAACGAAG
1 GATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAG
29828948 AAAATCGGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (38 bp):
GATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAG
Found at i:29830977 original size:44 final size:44
Alignment explanation
Indices: 29830929--29831113 Score: 132
Period size: 44 Copynumber: 4.2 Consensus size: 44
29830919 TATCTTGGAA
29830929 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
** * * *
29830973 AGATAAGA-TCTACAATCTTC-AACGTTCTCCACTACTGCTCAGGG
1 AGATAAGATTC-ACCGTCTTCGATC-TGCTCCACTACTGCTTAGGG
* * *** * * *
29831017 AGACAAGGCTT-GGTGGCTT-AAGTCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCACCGTCTTCGA-TCTGC-T-CCACTACTGCTTAGG-G
*
29831061 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
29831105 AGATAAGAT
1 AGATAAGAT
29831114 CTACAATCTT
Statistics
Matches: 104, Mismatches: 23, Indels: 28
0.67 0.15 0.18
Matches are distributed among these distances:
42 6 0.06
43 11 0.11
44 73 0.70
45 7 0.07
46 7 0.07
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
Found at i:29831116 original size:132 final size:132
Alignment explanation
Indices: 29830879--29831158 Score: 488
Period size: 132 Copynumber: 2.1 Consensus size: 132
29830869 CACTGCAATT
*
29830879 TCAGGGAGACAAGGCTTGTTGGCTTAAATCTGCATCCCACTATCTTGGAAAGATAAGATTCACCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCATCCCACTATCTTGGAAAGATAAGATTCACCG
*
29830944 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACGTTCTCCACTACT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
29831009 GC
131 GC
* * *
29831011 TCAGGGAGACAAGGCTTGGTGGCTTAAGTCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCATCCCACTATCTTGGAAAGATAAGATTCACCG
* **
29831076 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGTT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
29831141 GC
131 GC
29831143 TCAGGGAGACAAGGCT
1 TCAGGGAGACAAGGCT
29831159 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 140 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (132 bp):
TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCATCCCACTATCTTGGAAAGATAAGATTCACCG
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACT
GC
Found at i:29847506 original size:17 final size:18
Alignment explanation
Indices: 29847484--29847521 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
29847474 AATAATAATA
*
29847484 ATAATATGTT-TTACGAT
1 ATAATATGTTCTTAAGAT
29847501 ATAATATGTTCTTAAGAT
1 ATAATATGTTCTTAAGAT
29847519 ATA
1 ATA
29847522 GTACAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (18 bp):
ATAATATGTTCTTAAGAT
Found at i:29848960 original size:30 final size:30
Alignment explanation
Indices: 29848926--29848984 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
29848916 ACCATGAAGG
29848926 CTCTTCTCACAAT-AGAACCAGCCAAAAAGC
1 CTCTTCTCAC-ATCAGAACCAGCCAAAAAGC
* * *
29848956 CTCTTCTTACATCAGAATCAGCCACAAAG
1 CTCTTCTCACATCAGAACCAGCCAAAAAG
29848985 GCTTCTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.20
Consensus pattern (30 bp):
CTCTTCTCACATCAGAACCAGCCAAAAAGC
Found at i:29849063 original size:29 final size:29
Alignment explanation
Indices: 29849024--29849157 Score: 142
Period size: 29 Copynumber: 4.6 Consensus size: 29
29849014 CTTCCACTTG
* *
29849024 TAACATATTCCGCCACTAGGGCTTACATA
1 TAACAGATTCCGCCACTAGGGCTCACATA
*
29849053 TAATAGATTCCGCCACTAGGGCTCACATA
1 TAACAGATTCCGCCACTAGGGCTCACATA
* * * *
29849082 TAACATATTCAGCCACAAAGGCCTCCACATA
1 TAACAGATTCCGCCAC-TAGGGCT-CACATA
** *
29849113 TAACAGATTTTGCCACTAGGACTCACATA
1 TAACAGATTCCGCCACTAGGGCTCACATA
* *
29849142 TAACATATTCAGCCAC
1 TAACAGATTCCGCCAC
29849158 AAACTATAAC
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 58 0.67
30 10 0.11
31 19 0.22
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (29 bp):
TAACAGATTCCGCCACTAGGGCTCACATA
Found at i:29849121 original size:60 final size:60
Alignment explanation
Indices: 29849048--29849160 Score: 190
Period size: 60 Copynumber: 1.9 Consensus size: 60
29849038 ACTAGGGCTT
* *
29849048 ACATATAATAGATTCCGCCACTAGGGCTCACATATAACATATTCAGCCACAAAGGCCTCC
1 ACATATAACAGATTCCGCCACTAGGACTCACATATAACATATTCAGCCACAAAGGCCTCC
**
29849108 ACATATAACAGATTTTGCCACTAGGACTCACATATAACATATTCAGCCACAAA
1 ACATATAACAGATTCCGCCACTAGGACTCACATATAACATATTCAGCCACAAA
29849161 CTATAACACC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (60 bp):
ACATATAACAGATTCCGCCACTAGGACTCACATATAACATATTCAGCCACAAAGGCCTCC
Found at i:29850914 original size:25 final size:25
Alignment explanation
Indices: 29850880--29850931 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29850870 AGAAAAAGTA
29850880 ACAAAAATTTGGAAACAGGGGTCAT
1 ACAAAAATTTGGAAACAGGGGTCAT
29850905 ACAAAAATTTGGAAACAGGGGTCAT
1 ACAAAAATTTGGAAACAGGGGTCAT
29850930 AC
1 AC
29850932 GGCCTTATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.19
Consensus pattern (25 bp):
ACAAAAATTTGGAAACAGGGGTCAT
Found at i:29859538 original size:35 final size:33
Alignment explanation
Indices: 29859476--29859545 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
29859466 TACATATTCA
29859476 TCAAACACCACTTGAAAACATCCTATATATATT
1 TCAAACACCACTTGAAAACATCCTATATATATT
29859509 TCAAACACCACTTGAAAACATCCTATATATATT
1 TCAAACACCACTTGAAAACATCCTATATATATT
29859542 TCAA
1 TCAA
29859546 CCACAAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (33 bp):
TCAAACACCACTTGAAAACATCCTATATATATT
Found at i:29859867 original size:41 final size:41
Alignment explanation
Indices: 29859815--29860083 Score: 279
Period size: 41 Copynumber: 6.6 Consensus size: 41
29859805 GCATTTAGGT
* *
29859815 GTACCGAAGTACAAATAGGGGCACATATGTGCAATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAAGG
* * * * * **
29859856 GTACCGTAGTACAAAGAGTGGTACGTATGTGCAATT-TGGAG
1 GTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAAG-G
* *
29859897 GTACCGAAGTACAAACAGGGGCACGTATGTGTAATTCAAGG
1 GTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAAGG
* * * *
29859938 GTACCAAAGTACAAACAGGAGCACGTATTTGCAATTCAAGG
1 GTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAAGG
* * * * * *
29859979 GTACCAAAGTACAAACACGAGCACATATGTGTAATTTAGGG
1 GTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAAGG
* * * *
29860020 GTACTGAAATACAAACAAGGGCACATATGTGCAATTTAAGG
1 GTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAAGG
* *
29860061 GTATCGAAGTACAAACAAGGGCA
1 GTACCGAAGTACAAACAGGGGCA
29860084 TGTTTGTGCA
Statistics
Matches: 193, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 2 0.01
41 190 0.98
42 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (41 bp):
GTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAAGG
Found at i:29859911 original size:82 final size:81
Alignment explanation
Indices: 29859803--29860083 Score: 307
Period size: 82 Copynumber: 3.4 Consensus size: 81
29859793 AGGCACAAAA
* * *
29859803 GTGC-ATTT-AGGTGTACCGAAGTACAAATAGGGGCACATATGTGCAATTCAGGGGTACCGTAGT
1 GTGCAATTTAAGG-GTACCGAAGTACAAACAGGGGCACATATGTGTAATTCAGGGGTACCGAAGT
* *
29859866 ACAAAGAGTGGTACGTAT
65 ACAAAAAG-GGCACGTAT
* * * *
29859884 GTGCAATTT-GGAGGTACCGAAGTACAAACAGGGGCACGTATGTGTAATTCAAGGGTACCAAAGT
1 GTGCAATTTAAG-GGTACCGAAGTACAAACAGGGGCACATATGTGTAATTCAGGGGTACCGAAGT
*
29859948 ACAAACAGGAGCACGTAT
65 ACAAAAAGG-GCACGTAT
* * * * * * * *
29859966 TTGCAATTCAAGGGTACCAAAGTACAAACACGAGCACATATGTGTAATTTAGGGGTACTGAAATA
1 GTGCAATTTAAGGGTACCGAAGTACAAACAGGGGCACATATGTGTAATTCAGGGGTACCGAAGTA
*
29860031 CAAACAAGGGCACATAT
66 CAAA-AAGGGCACGTAT
* *
29860048 GTGCAATTTAAGGGTATCGAAGTACAAACAAGGGCA
1 GTGCAATTTAAGGGTACCGAAGTACAAACAGGGGCA
29860084 TGTTTGTGCA
Statistics
Matches: 166, Mismatches: 29, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
81 5 0.03
82 156 0.94
83 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (81 bp):
GTGCAATTTAAGGGTACCGAAGTACAAACAGGGGCACATATGTGTAATTCAGGGGTACCGAAGTA
CAAAAAGGGCACGTAT
Found at i:29860094 original size:123 final size:123
Alignment explanation
Indices: 29859788--29860096 Score: 317
Period size: 123 Copynumber: 2.5 Consensus size: 123
29859778 ACCGGAGTCT
* * * * * *
29859788 AAACAA-GGCACAAAAGTGC-ATTT-AGGTGTACCGAAGTACAAATAGGGGCACATATGTGCAAT
1 AAACAAGGGCACATATGTGCAATTTAAGG-GTACCGAAGTACAAACAAGGGCACGTTTGTGCAAT
* ** * * * * *
29859850 TCAGGGGTACCGTAGTACAAAGAGTGGTACGTATGTGCAATTTGGAGGTACCGAAGTAC
65 TCAAGGGTACCAAAGTACAAACAGTAGCACATATGTGCAATTTGGAGGTACCGAAATAC
* * * * *
29859909 AAACAGGGGCACGTATGTGTAATTCAAGGGTACCAAAGTACAAAC-AGGAGCACGTATT-TGCAA
1 AAACAAGGGCACATATGTGCAATTTAAGGGTACCGAAGTACAAACAAGG-GCACGT-TTGTGCAA
* *
29859972 TTCAAGGGTACCAAAGTACAAACACG-AGCACATATGTGTAATTTAGG-GGTACTGAAATAC
64 TTCAAGGGTACCAAAGTACAAACA-GTAGCACATATGTGCAATTT-GGAGGTACCGAAATAC
* *
29860032 AAACAAGGGCACATATGTGCAATTTAAGGGTATCGAAGTACAAACAAGGGCATGTTTGTGCAATT
1 AAACAAGGGCACATATGTGCAATTTAAGGGTACCGAAGTACAAACAAGGGCACGTTTGTGCAATT
29860097 AAACAATAAT
Statistics
Matches: 151, Mismatches: 28, Indels: 16
0.77 0.14 0.08
Matches are distributed among these distances:
121 5 0.03
122 13 0.09
123 123 0.81
124 10 0.07
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.22
Consensus pattern (123 bp):
AAACAAGGGCACATATGTGCAATTTAAGGGTACCGAAGTACAAACAAGGGCACGTTTGTGCAATT
CAAGGGTACCAAAGTACAAACAGTAGCACATATGTGCAATTTGGAGGTACCGAAATAC
Found at i:29864955 original size:54 final size:54
Alignment explanation
Indices: 29864883--29865025 Score: 157
Period size: 54 Copynumber: 2.6 Consensus size: 54
29864873 CTCACATGAC
*
29864883 GCCATAGTCCCG-GACTAGGTCTTGCACTATGTGGTC-TTCATATCCCCATAGGAT
1 GCCATAGT-CCGAGACTAGGTCTTGCACTATATGGTCTTTC-TATCCCCATAGGAT
* * * *
29864937 GCCATAGTCCGAGTCTAGGTC-TGACACTATATGGTCTTTCTGTCCCTATATGAT
1 GCCATAGTCCGAGACTAGGTCTTG-CACTATATGGTCTTTCTATCCCCATAGGAT
* * * *
29864991 GCCATAATCCTAGACTAGGTCTTACACTTTATGGT
1 GCCATAGTCCGAGACTAGGTCTTGCACTATATGGT
29865026 ATTCTTGTCA
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
53 5 0.07
54 66 0.88
55 4 0.05
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (54 bp):
GCCATAGTCCGAGACTAGGTCTTGCACTATATGGTCTTTCTATCCCCATAGGAT
Found at i:29865157 original size:15 final size:16
Alignment explanation
Indices: 29865133--29865167 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
29865123 CATGCAACTT
29865133 ATGCACAGACTCT-TC
1 ATGCACAGACTCTATC
*
29865148 ATGCAGAGACTCTATC
1 ATGCACAGACTCTATC
29865164 ATGC
1 ATGC
29865168 TTTCAGACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (16 bp):
ATGCACAGACTCTATC
Found at i:29870800 original size:15 final size:16
Alignment explanation
Indices: 29870764--29870801 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
29870754 TTATATTGCA
29870764 TATATATATGTTAACT
1 TATATATATGTTAACT
*
29870780 TAATATATAT-TTAAGT
1 T-ATATATATGTTAACT
29870796 TATATA
1 TATATA
29870802 ATGATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
TATATATATGTTAACT
Found at i:29874510 original size:11 final size:11
Alignment explanation
Indices: 29874490--29874556 Score: 81
Period size: 11 Copynumber: 6.4 Consensus size: 11
29874480 TAAAAATTAA
29874490 AAAAAGTATTTT
1 AAAAA-TATTTT
29874502 AAAAATATTTT
1 AAAAATATTTT
29874513 --AAA-A--TT
1 AAAAATATTTT
29874519 AAAAATATTTT
1 AAAAATATTTT
29874530 AAAAAGTATTTT
1 AAAAA-TATTTT
29874542 AAAAATATTTT
1 AAAAATATTTT
29874553 AAAA
1 AAAA
29874557 TTATAAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
11 23 0.47
12 16 0.33
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:29874522 original size:17 final size:17
Alignment explanation
Indices: 29874500--29874533 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29874490 AAAAAGTATT
29874500 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
29874517 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
29874534 AGTATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:29874688 original size:32 final size:33
Alignment explanation
Indices: 29874652--29874722 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
29874642 ATTTTCTAAA
*
29874652 CGGGCCTCATTTTTTTACCC-AA-GCCCATATTT
1 CGGGCCT-ATATTTTTACCCAAACGCCCATATTT
*
29874684 CGGGCCTATATTTTTACCCAAACCTCCCATATTT
1 CGGGCCTATATTTTTACCCAAA-CGCCCATATTT
29874718 CGGGC
1 CGGGC
29874723 GGGCAGTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 11 0.32
32 9 0.26
34 14 0.41
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (33 bp):
CGGGCCTATATTTTTACCCAAACGCCCATATTT
Found at i:29877550 original size:27 final size:27
Alignment explanation
Indices: 29877484--29877568 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
29877474 GACTGAAATA
* * *
29877484 CCCTTGAAAGGTAAAATGAACGAAATA
1 CCCTTGTAAGGTAAAATGAACGTAATG
* * * *
29877511 CCCCTATATGGTAAAATGATCGTAATG
1 CCCTTGTAAGGTAAAATGAACGTAATG
* * *
29877538 CCCTTGTAGGGTAATATGACCGTAATG
1 CCCTTGTAAGGTAAAATGAACGTAATG
29877565 CCCT
1 CCCT
29877569 GGTGGGAATA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (27 bp):
CCCTTGTAAGGTAAAATGAACGTAATG
Found at i:29877679 original size:24 final size:23
Alignment explanation
Indices: 29877613--29877685 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
29877603 AAATGATTAT
* *
29877613 TTTGTCTGTGGTTAAATGAATGA
1 TTTGTCTGTGTTTGAATGAATGA
* *
29877636 TTTGTCTGTGTTTGGTATGACTGA
1 TTTGTCTGTGTTT-GAATGAATGA
*
29877660 TTTGTCTGTGATTTGAATGATTGA
1 TTTGTCTGTG-TTTGAATGAATGA
29877684 TT
1 TT
29877686 CTGAGCATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.29
24 27 0.64
25 3 0.07
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.49
Consensus pattern (23 bp):
TTTGTCTGTGTTTGAATGAATGA
Found at i:29877787 original size:27 final size:27
Alignment explanation
Indices: 29877749--29877813 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
29877739 ATGGAGGAAG
29877749 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
*
29877774 TCACTGTTACTGGTGGCTTGGGCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
29877802 TACTGTTACTGG
1 TACTGTTACTGG
29877814 CAGCTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:29877839 original size:26 final size:26
Alignment explanation
Indices: 29877801--29877866 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
29877791 TTGGGCACAT
* *
29877801 ATACTGTTACTGGCAGCTTTGCTGTG
1 ATACTGTTGCTGGCAGCTTTGCTGCG
29877827 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTGTTGCTGGCAGCTTTGCTGCG
* *
29877853 ATACTATTGATGGC
1 ATACTGTTGCTGGC
29877867 TTTGTGCCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (26 bp):
ATACTGTTGCTGGCAGCTTTGCTGCG
Found at i:29877992 original size:96 final size:96
Alignment explanation
Indices: 29877854--29878044 Score: 285
Period size: 96 Copynumber: 2.0 Consensus size: 96
29877844 TTTGCTGCGA
* *
29877854 TACTATTGATGGCTTTGTGCCGATCATATAATCATTATTGATGGTTGTGTGCTGATCATATTACC
1 TACTACTGATGGCTTTGTGCCGATCATATAATCATTACTGATGGTTGTGTGCTGATCATATTACC
* * *
29877919 ATTACTGATGGCTGTGTGCCTATTATATTAC
66 ACTACTGATGGCTGTGTGCCAATCATATTAC
* *
29877950 TACTACTGATGGCTTTGTGCTGATCATACTACT-ATTACTGATGGTTGTGTGCTGATCATATTAC
1 TACTACTGATGGCTTTGTGCCGATCATA-TAATCATTACTGATGGTTGTGTGCTGATCATATTAC
* *
29878014 TACTACTGATGGCTTTGTGCCAATCATATTA
65 CACTACTGATGGCTGTGTGCCAATCATATTA
29878045 TTGTACTTGT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 82 0.96
97 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (96 bp):
TACTACTGATGGCTTTGTGCCGATCATATAATCATTACTGATGGTTGTGTGCTGATCATATTACC
ACTACTGATGGCTGTGTGCCAATCATATTAC
Found at i:29878015 original size:32 final size:32
Alignment explanation
Indices: 29877860--29878044 Score: 207
Period size: 32 Copynumber: 5.8 Consensus size: 32
29877850 GCGATACTAT
* * *
29877860 TGATGGCTTTGTGCCGATCATA-TAATCATTAT
1 TGATGGCTTTGTGCTGATCATATTACT-ATTAC
*
29877892 TGATGG-TTGTGTGCTGATCATATTACCATTAC
1 TGATGGCTT-TGTGCTGATCATATTACTATTAC
* * *
29877924 TGATGGCTGTGTGCCT-ATTATATTACTACTAC
1 TGATGGCTTTGTG-CTGATCATATTACTATTAC
*
29877956 TGATGGCTTTGTGCTGATCATACTACTATTAC
1 TGATGGCTTTGTGCTGATCATATTACTATTAC
*
29877988 TGATGG-TTGTGTGCTGATCATATTACTACTAC
1 TGATGGCTT-TGTGCTGATCATATTACTATTAC
**
29878020 TGATGGCTTTGTGCCAATCATATTA
1 TGATGGCTTTGTGCTGATCATATTA
29878045 TTGTACTTGT
Statistics
Matches: 130, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
31 6 0.05
32 117 0.90
33 7 0.05
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (32 bp):
TGATGGCTTTGTGCTGATCATATTACTATTAC
Found at i:29879207 original size:19 final size:19
Alignment explanation
Indices: 29879185--29879222 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29879175 TCAATCATCC
29879185 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
29879204 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
29879223 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:29880860 original size:18 final size:18
Alignment explanation
Indices: 29880837--29880878 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
29880827 TGGGATATTA
*
29880837 AGTGAAAATATCT-TAGAG
1 AGTGAAAATAGCTCTAG-G
29880855 AGTG-AAATAGCTCTAGG
1 AGTGAAAATAGCTCTAGG
29880872 AGTGAAA
1 AGTGAAA
29880879 CTTGGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (18 bp):
AGTGAAAATAGCTCTAGG
Found at i:29888136 original size:56 final size:51
Alignment explanation
Indices: 29888045--29888188 Score: 173
Period size: 50 Copynumber: 2.7 Consensus size: 51
29888035 GGTAAAAAGA
* *
29888045 TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC----AG-TGATGAGAGG
* * * *
29888101 TCTCATGTAAGAGCATGTCTGGGACATGGCGTTGGCA-CCGTGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGTGATGAGAGG
*
29888151 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
29888189 GTTATTATCA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
50 43 0.55
51 1 0.01
55 1 0.01
56 33 0.42
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGTGATGAGAGG
Found at i:29892675 original size:25 final size:25
Alignment explanation
Indices: 29892622--29892681 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
29892612 GTGGTCCACC
* *
29892622 TTTTTTAAAAATATATTTTTTTTTA
1 TTTTTTAAAAATATATTTCTTCTTA
*
29892647 TTTTTTAATAAATCTATTTCTTCTT-
1 TTTTTTAA-AAATATATTTCTTCTTA
*
29892672 TTTTTCAAAA
1 TTTTTTAAAA
29892682 TTTTTAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.07
25 15 0.50
26 13 0.43
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTTTAAAAATATATTTCTTCTTA
Found at i:29892676 original size:26 final size:25
Alignment explanation
Indices: 29892622--29892676 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
29892612 GTGGTCCACC
*
29892622 TTTTTTAAAAATATATTTTTTTTTA
1 TTTTTTAAAAATATATTTTTCTTTA
*
29892647 TTTTTTAATAAATCTATTTCTTCTTT-
1 TTTTTTAA-AAATATATTT-TTCTTTA
29892673 TTTT
1 TTTT
29892677 CAAAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 13 0.50
27 5 0.19
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTAAAAATATATTTTTCTTTA
Found at i:29898573 original size:47 final size:47
Alignment explanation
Indices: 29898504--29898599 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
29898494 CACACTTTGT
29898504 AAAATGATCCACTATCACCCAAACTGAATCCTTCTTGAGATGGAGTC
1 AAAATGATCCACTATCACCCAAACTGAATCCTTCTTGAGATGGAGTC
29898551 AAAATGATCCACTATCACCCAAACTGAATCCTTCTTGAGATGGAGTC
1 AAAATGATCCACTATCACCCAAACTGAATCCTTCTTGAGATGGAGTC
29898598 AA
1 AA
29898600 TGACAAATCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (47 bp):
AAAATGATCCACTATCACCCAAACTGAATCCTTCTTGAGATGGAGTC
Found at i:29905432 original size:28 final size:27
Alignment explanation
Indices: 29905381--29905434 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
29905371 CTGATACTGA
*
29905381 TTCTGTAATGGGCTTAGGTCCACCTGG
1 TTCTGTAATGGGCTAAGGTCCACCTGG
29905408 TTCTGTTAATGGGCTAAGG-CTCACCTG
1 TTCTG-TAATGGGCTAAGGTC-CACCTG
29905435 ATACTATGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (27 bp):
TTCTGTAATGGGCTAAGGTCCACCTGG
Found at i:29910612 original size:75 final size:75
Alignment explanation
Indices: 29910501--29911147 Score: 1269
Period size: 75 Copynumber: 8.6 Consensus size: 75
29910491 GTGGATTTCA
29910501 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29910566 GTGGAATCAG
66 GTGGAATCAG
29910576 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29910641 GTGGAATCAG
66 GTGGAATCAG
29910651 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29910716 GTGGAATCAG
66 GTGGAATCAG
29910726 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29910791 GTGGAATCAG
66 GTGGAATCAG
29910801 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29910866 GTGGAATCAG
66 GTGGAATCAG
29910876 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29910941 GTGGAATCAG
66 GTGGAATCAG
29910951 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29911016 GTGGAATCAG
66 GTGGAATCAG
29911026 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
29911091 GTGGAATCAG
66 GTGGAATCAG
*
29911101 CAAC-TAGCAACCACCAATGAATTGGGGAATCAGCACACAGCAACCCC
1 C-ACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCC
29911148 TTTATATGCA
Statistics
Matches: 570, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
75 568 1.00
76 2 0.00
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.17
Consensus pattern (75 bp):
CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCCTTCACATTTCAGATGCG
GTGGAATCAG
Found at i:29914993 original size:19 final size:19
Alignment explanation
Indices: 29914943--29914999 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
29914933 AAATGTAACA
* *
29914943 ACTAAATTAAAAACAAAATT
1 ACTAAATTAATAA-AAAATG
* **
29914963 ATTAAAAAAATAAAAAATG
1 ACTAAATTAATAAAAAATG
29914982 ACTAAATTAATAGAAAAA
1 ACTAAATTAATA-AAAAA
29915000 AAAGTTTTCC
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.23
Consensus pattern (19 bp):
ACTAAATTAATAAAAAATG
Found at i:29921995 original size:61 final size:61
Alignment explanation
Indices: 29921900--29922046 Score: 188
Period size: 61 Copynumber: 2.4 Consensus size: 61
29921890 AAGAGAAGTA
* * * *
29921900 TACTAAATGTTAATGAATGCCTTTGTGGTAAAACTCTGGACAGGAAAACATTTGTGGT-GAG
1 TACTAAATGTTAAGGAACGCCTTTGGGGTAAAACTATGGACAGGAAAACATTTGT-GTCGAG
* * * *
29921961 TACTAAATGTTACGGAACGCCTTTGGGGTAAAACTATGGACATGAAAGCCTTTGTGTCGAG
1 TACTAAATGTTAAGGAACGCCTTTGGGGTAAAACTATGGACAGGAAAACATTTGTGTCGAG
* *
29922022 TATTAAATGTTAAGGAACGTCTTTG
1 TACTAAATGTTAAGGAACGCCTTTG
29922047 TGGAAAGAGT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 2 0.03
61 72 0.97
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (61 bp):
TACTAAATGTTAAGGAACGCCTTTGGGGTAAAACTATGGACAGGAAAACATTTGTGTCGAG
Found at i:29923880 original size:7 final size:7
Alignment explanation
Indices: 29923796--29923879 Score: 114
Period size: 7 Copynumber: 12.0 Consensus size: 7
29923786 TAAAATTAAT
*
29923796 AATTGGG
1 AATTGAG
*
29923803 AATTGGG
1 AATTGAG
29923810 AATTGAG
1 AATTGAG
29923817 AATTGAG
1 AATTGAG
29923824 AATTGAG
1 AATTGAG
29923831 AATTGAG
1 AATTGAG
29923838 AATTGAG
1 AATTGAG
29923845 AATTGAG
1 AATTGAG
29923852 AATTGAG
1 AATTGAG
* *
29923859 GAGTGAG
1 AATTGAG
*
29923866 GATTGAG
1 AATTGAG
*
29923873 TATTGAG
1 AATTGAG
29923880 TTGAAAAGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 72 1.00
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.29
Consensus pattern (7 bp):
AATTGAG
Found at i:29924758 original size:13 final size:13
Alignment explanation
Indices: 29924740--29924764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29924730 AAATTTTTAT
29924740 TATTTATTATTTC
1 TATTTATTATTTC
29924753 TATTTATTATTT
1 TATTTATTATTT
29924765 ATCTTAATTT
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTATTATTTC
Found at i:29934446 original size:18 final size:18
Alignment explanation
Indices: 29934420--29934481 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 18
29934410 TTATTATAAA
*
29934420 TTATGATAATTCCTATTT
1 TTATTATAATTCCTATTT
*
29934438 TTATTATAATT--TATATA
1 TTATTATAATTCCTAT-TT
*
29934455 TTGTTA-AATTCCTA-TT
1 TTATTATAATTCCTATTT
29934471 TTATTATAATT
1 TTATTATAATT
29934482 TACATACTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
16 13 0.37
17 10 0.29
18 12 0.34
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATTATAATTCCTATTT
Found at i:29937283 original size:57 final size:58
Alignment explanation
Indices: 29937190--29937304 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 58
29937180 GGTAAAATGG
29937190 GATTTTTAGCTCATATGTGTTCAGAATTTCGTTAACATTGTATTCGAAAATGTTTTTT
1 GATTTTTAGCTCATATGTGTTCAGAATTTCGTTAACATTGTATTCGAAAATGTTTTTT
29937248 GATTTTTAGCTCATATGT-TTCAGAATTTCGTTAACATTGTATTCGAAAATGTTTTTT
1 GATTTTTAGCTCATATGTGTTCAGAATTTCGTTAACATTGTATTCGAAAATGTTTTTT
29937305 ACTATGGTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 39 0.68
58 18 0.32
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (58 bp):
GATTTTTAGCTCATATGTGTTCAGAATTTCGTTAACATTGTATTCGAAAATGTTTTTT
Found at i:29945946 original size:25 final size:25
Alignment explanation
Indices: 29945910--29945993 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 25
29945900 ATCTGGAAAT
*
29945910 CCTTTGTAGTGAATTCTCTAAAAAG
1 CCTTTGTGGTGAATTCTCTAAAAAG
* *
29945935 CCTTTGTGGTGAATTCTCTAGAAAT
1 CCTTTGTGGTGAATTCTCTAAAAAG
** *
29945960 CCTTTGTGGCAAATCCTCTAAAAAG
1 CCTTTGTGGTGAATTCTCTAAAAAG
*
29945985 CCTATGTGG
1 CCTTTGTGG
29945994 CTACCTCTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (25 bp):
CCTTTGTGGTGAATTCTCTAAAAAG
Found at i:29948698 original size:6 final size:6
Alignment explanation
Indices: 29948687--29948713 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29948677 GTTGACAAAG
29948687 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
29948714 TAGAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:29949745 original size:30 final size:32
Alignment explanation
Indices: 29949711--29949771 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
29949701 TTCTGTAACT
* *
29949711 TTTCAATTTGGCCC-ATTTTCTTGTT-TTTTG
1 TTTCAATTTAGCCCAATTTGCTTGTTCTTTTG
29949741 TTTCAATTTAGCCCAATTTGCTTGTTCTTTT
1 TTTCAATTTAGCCCAATTTGCTTGTTCTTTT
29949772 TTTGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 13 0.48
31 10 0.37
32 4 0.15
ACGTcount: A:0.13, C:0.18, G:0.11, T:0.57
Consensus pattern (32 bp):
TTTCAATTTAGCCCAATTTGCTTGTTCTTTTG
Found at i:29951952 original size:20 final size:20
Alignment explanation
Indices: 29951927--29952012 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
29951917 TTGTACGGGA
29951927 TTGCACTTCTGTGCCTCTGT
1 TTGCACTTCTGTGCCTCTGT
29951947 TTGCACTT-TAGTGCCTCTGT
1 TTGCACTTCT-GTGCCTCTGT
** * *
29951967 TTATACTTC-GATGTCTCTAT
1 TTGCACTTCTG-TGCCTCTGT
* * *
29951987 TTGCACTACGGTGCCTCTGA
1 TTGCACTTCTGTGCCTCTGT
29952007 TTGCAC
1 TTGCAC
29952013 AATCGTGCCT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.04
20 49 0.94
21 1 0.02
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGCACTTCTGTGCCTCTGT
Found at i:29956292 original size:70 final size:70
Alignment explanation
Indices: 29956174--29956313 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
29956164 CAAACATACT
*
29956174 TGATTAAATTTCATATCAAAACATTCCCTAAATGATCACTTTGCAAACATGGC-AACACATACCA
1 TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGCAAACAT-GCTAACACATACCA
29956238 CTTTGG
65 CTTTGG
* *
29956244 TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGTAAACATGCTAGCACATACCAC
1 TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGCAAACATGCTAACACATACCAC
29956309 TTTGG
66 TTTGG
29956314 CCATAAAACC
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 2 0.03
70 64 0.97
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (70 bp):
TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGCAAACATGCTAACACATACCAC
TTTGG
Found at i:29957802 original size:29 final size:29
Alignment explanation
Indices: 29957740--29957863 Score: 176
Period size: 29 Copynumber: 4.2 Consensus size: 29
29957730 GTGTGCTAAA
** *
29957740 CGATGGTCGAAACCATCTCTCTTTTTTTAAT
1 CGATGGTCGAAACCATC-C-CTTTTCATATT
29957771 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
29957800 CGATGGTCGAAGCCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
**
29957829 CGATGGTCGTCACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
29957858 CGATGG
1 CGATGG
29957864 GCGTCAATAC
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
29 68 0.79
30 1 0.01
31 17 0.20
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:29967499 original size:45 final size:45
Alignment explanation
Indices: 29967435--29967522 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
29967425 ACAGATACTC
* *
29967435 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAAGGATGTCA
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAAGGATGTCA
*
29967480 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAAGGATGT
29967523 TCGGTTCACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAAGGATGTCA
Found at i:29967637 original size:51 final size:51
Alignment explanation
Indices: 29967533--29967639 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
29967523 TCGGTTCACA
* * * ** *
29967533 TAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATCCGATGCACG
1 TAGTAGCCTGCACATAATACTACACACGTGACCAAAACCATCCGATACACG
* * * *
29967584 TAGTAGCCTGCACATAATACTACACACGTGATCAAAACTATTCGATACGCG
1 TAGTAGCCTGCACATAATACTACACACGTGACCAAAACCATCCGATACACG
29967635 TAGTA
1 TAGTA
29967640 CACATGCGAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAATACTACACACGTGACCAAAACCATCCGATACACG
Found at i:29970178 original size:20 final size:20
Alignment explanation
Indices: 29970136--29970178 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
29970126 GGGCACAAAT
* * *
29970136 GTGCAAACAGGGGCACTGTA
1 GTGCAAACAGGGACACCGAA
*
29970156 GTGCGAACAGGGACACCGAA
1 GTGCAAACAGGGACACCGAA
29970176 GTG
1 GTG
29970179 TATTCAAAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.37, T:0.12
Consensus pattern (20 bp):
GTGCAAACAGGGACACCGAA
Found at i:29975482 original size:51 final size:51
Alignment explanation
Indices: 29975408--29975518 Score: 186
Period size: 51 Copynumber: 2.2 Consensus size: 51
29975398 AGAAAGAAAG
*
29975408 AAAATTGAAGAGAAAAAAGGAGAGGAAGAGGGCGAACGGCTAGGGTAGGGA
1 AAAATTGAAGAGAAAAAAGGAGAGGAAGAGGACGAACGGCTAGGGTAGGGA
* * *
29975459 AAAATTGAAGAGAAAAGAGGAGAGGAAGAGGATGAATGGCTAGGGTAGGGA
1 AAAATTGAAGAGAAAAAAGGAGAGGAAGAGGACGAACGGCTAGGGTAGGGA
29975510 AAAATTGAA
1 AAAATTGAA
29975519 TTAAAGGCTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.47, C:0.04, G:0.39, T:0.11
Consensus pattern (51 bp):
AAAATTGAAGAGAAAAAAGGAGAGGAAGAGGACGAACGGCTAGGGTAGGGA
Found at i:29976957 original size:27 final size:27
Alignment explanation
Indices: 29976935--29977378 Score: 461
Period size: 27 Copynumber: 16.4 Consensus size: 27
29976925 GAGGTATAAC
29976935 AGTCATTTTACCCTATAGGGGTATTTT
1 AGTCATTTTACCCTATAGGGGTATTTT
* * * *
29976962 GGTCATTTTAACCTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTT
* *
29976989 AGTCATTTTATCCTATGGGGGTATTTT
1 AGTCATTTTACCCTATAGGGGTATTTT
*
29977016 AGTCATTTTATCCTAT-GGAGGTATTTT
1 AGTCATTTTACCCTATAGG-GGTATTTT
* *
29977043 GGTCATTTTACCCTATAGGGATATTTT
1 AGTCATTTTACCCTATAGGGGTATTTT
* * *
29977070 GGTCATTTTACCCTATAAGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTT
* * * *
29977097 AGTTATTTTACCTTATGGGGGTGTTTT
1 AGTCATTTTACCCTATAGGGGTATTTT
*
29977124 AGTCATTTTACCCTATAGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTT
* * * *
29977151 AGTCATTCTATCTTAT-GAGGGCATTTT
1 AGTCATTTTACCCTATAG-GGGTATTTT
*
29977178 AGTCATTTTACCCTATAGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTT
29977205 AGTCATTTTACCCTAT-GGGGCTATTTT
1 AGTCATTTTACCCTATAGGGG-TATTTT
*
29977232 -GATCATTTTACCCTATGGGGGTATTTT
1 AG-TCATTTTACCCTATAGGGGTATTTT
* * * *
29977259 GGTCATTTTACCTTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTT
* * *
29977286 AATAATTTTACCTTAT-GGAGGTA-TTT
1 AGTCATTTTACCCTATAGG-GGTATTTT
* *
29977312 CGATCATTTTACCCTGT-GGAGGTATTTT
1 AG-TCATTTTACCCTATAGG-GGTATTTT
* *
29977340 GGTCATTTTACCCTATAGAGGTATTTT
1 AGTCATTTTACCCTATAGGGGTATTTT
*
29977367 GGTCATTTTACC
1 AGTCATTTTACC
29977379 TATTTTGGGG
Statistics
Matches: 355, Mismatches: 50, Indels: 24
0.83 0.12 0.06
Matches are distributed among these distances:
26 12 0.03
27 330 0.93
28 13 0.04
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (27 bp):
AGTCATTTTACCCTATAGGGGTATTTT
Found at i:29988930 original size:2 final size:2
Alignment explanation
Indices: 29988923--29988955 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29988913 TTTGAATAAA
29988923 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29988956 TTTAAAACAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:29993531 original size:44 final size:44
Alignment explanation
Indices: 29993474--29993807 Score: 166
Period size: 44 Copynumber: 7.7 Consensus size: 44
29993464 ATGTGATCTA
* ** *
29993474 CTCCACTGTAACTTCAGATAGATAAGATCT-GCGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TAGCGGCTTTAATCCG
* ** *
29993518 CTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCGGCTTTAATCCG
** ** * * *
29993562 CTCCACTGCAACTTCAGGGAGATAAGATTCTCAATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGC-GGCTTTAATCCG
** * *** * *
29993607 C-CTCACTGCAACTTCA-AAAGGATAGGACTT-GATTAC-TTACTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGA-TTAG-CGGCTTTAATCCG
* * ** * *
29993651 CCCCACTGCAACTTCAGGGAGATAAGACTAGATGC---CATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCGGCTTTAATCCG
* * * * **
29993692 CT-CTCTACAACTTCAGAGAGATAAGATCT-GTGATTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TAGCGGCTTTAATCCG
* ** * *
29993735 CTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTATTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCGGCTTTAATCCG
*
29993779 CTCCACTACAACTTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
29993808 CGCCATCTTC
Statistics
Matches: 221, Mismatches: 54, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
40 22 0.10
41 6 0.03
43 11 0.05
44 149 0.67
45 31 0.14
46 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTAGCGGCTTTAATCCG
Found at i:29993622 original size:45 final size:44
Alignment explanation
Indices: 29993512--29993807 Score: 196
Period size: 44 Copynumber: 6.8 Consensus size: 44
29993502 CTGCGGTTTT
* * ** *
29993512 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATAAGCTTC
* *
29993556 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCAATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-AAGCTTC
* ** * *
29993601 AGTCTGC-CTCACTGCAACTTCA-AAAGGATAGGACTTGATTA-CTT-
1 AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TT-ATAAGCTTC
* * * * *
29993645 ACTCTGCCCCACTGCAACTTCAGGGAGATAAGACTAGATGC--C
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATAAGCTTC
* * * * * * *
29993687 -ATCTGCT-CTCTACAACTTCAGAGAGATAAGATCTGTGA-TTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATAAGCTTC
* * ** *
29993729 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATAAGCTTC
* *
29993773 ATTCTGCTCCACTACAACTTCAGGGAGATAAGATT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
29993808 CGCCATCTTC
Statistics
Matches: 191, Mismatches: 46, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
40 21 0.11
41 6 0.03
42 1 0.01
43 10 0.05
44 116 0.61
45 33 0.17
46 3 0.02
47 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATAAGCTTC
Found at i:29993753 original size:84 final size:85
Alignment explanation
Indices: 29993553--29993758 Score: 226
Period size: 84 Copynumber: 2.4 Consensus size: 85
29993543 GATTATTGGC
*
29993553 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCAATCTTCAGTCTGCCTCACTGCAA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TCTCAATC-TCAGTCTGCCTCACTACAA
*
29993618 CTTCAAAAGGATAGGACTTGAT
64 CTTCAAAAGGATAAGACTTGAT
* * *
29993640 TACTTACTCTGCCCCACTGCAACTTCAGGGAGATAAGA-CT-AGATGC-CA-TCTG-CTCTCTAC
1 T--TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCA-AT-CTCAGTCTGCCTCACTAC
*
29993700 AACTTC-AGAGAGATAAGATCTGTGAT
62 AACTTCAAAAG-GATAAGA-CT-TGAT
*
29993726 TTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATA
29993759 GGATTATTGG
Statistics
Matches: 103, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
83 3 0.03
84 47 0.46
85 6 0.06
86 8 0.08
87 5 0.05
88 1 0.01
89 33 0.32
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (85 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCAATCTCAGTCTGCCTCACTACAACT
TCAAAAGGATAAGACTTGAT
Found at i:29993893 original size:95 final size:97
Alignment explanation
Indices: 29993766--29994003 Score: 223
Period size: 100 Copynumber: 2.4 Consensus size: 97
29993756 ATAGGATTAT
* * * * ** *
29993766 TGGCTTTATTCTGCTCCACTACAACTTCAGGGAGATAAGATTC-GCCAT-CTTCAGTATTTTAAA
1 TGGCTTCAATCTGTTCCACTACACCGCCAGGGAGATAAGATTCTGCCATGCTTCAATATTTTAAA
* *
29993829 TTGCAATGTTGGGGAAACAAGATTCTCTGTCG
66 TTGCAATGTTGGGGAAACAAGATTCACCGTCG
*** *
29993861 TGGCTTCAATCTGTTCCACTACACCGCCAGGGA-AGTAAGATTCACTGTTGTGGCTTCAATCTTT
1 TGGCTTCAATCTGTTCCACTACACCGCCAGGGAGA-TAAGATT--CTGCCAT-GCTTCAATATTT
* * **
29993925 TTAATTGCAATGTTGGGGAAATAAGATTCACCGTTT
62 TAAATTGCAATGTTGGGGAAACAAGATTCACCGTCG
* * *
29993961 TAGCTTCAATCTGTTTCATTACACCGCCAGAGGAG-TAAGATTC
1 TGGCTTCAATCTGTTCCACTACACCGCCAG-GGAGATAAGATTC
29994004 ACTGTCGTGG
Statistics
Matches: 115, Mismatches: 20, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
94 1 0.01
95 34 0.30
97 1 0.01
98 3 0.03
100 73 0.63
101 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (97 bp):
TGGCTTCAATCTGTTCCACTACACCGCCAGGGAGATAAGATTCTGCCATGCTTCAATATTTTAAA
TTGCAATGTTGGGGAAACAAGATTCACCGTCG
Found at i:29993944 original size:50 final size:50
Alignment explanation
Indices: 29993822--29993972 Score: 140
Period size: 50 Copynumber: 3.0 Consensus size: 50
29993812 ATCTTCAGTA
* * *
29993822 TTTTAAATTGCAATGTTGGGGAAACAAGATTCTCTGTCGTGGCTTCAATC
1 TTTTAAATTGCAATGTTGGGGAAATAAGATTCACTGTTGTGGCTTCAATC
* ** * * ** *** *
29993872 TGTTCCACTACACCGCCAGGGAAGTAAGATTCACTGTTGTGGCTTCAATC
1 TTTTAAATTGCAATGTTGGGGAAATAAGATTCACTGTTGTGGCTTCAATC
* * * *
29993922 TTTTTAATTGCAATGTTGGGGAAATAAGATTCACCGTTTTAGCTTCAATC
1 TTTTAAATTGCAATGTTGGGGAAATAAGATTCACTGTTGTGGCTTCAATC
29993972 T
1 T
29993973 GTTTCATTAC
Statistics
Matches: 73, Mismatches: 28, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (50 bp):
TTTTAAATTGCAATGTTGGGGAAATAAGATTCACTGTTGTGGCTTCAATC
Found at i:29993951 original size:100 final size:100
Alignment explanation
Indices: 29993822--29994020 Score: 283
Period size: 100 Copynumber: 2.0 Consensus size: 100
29993812 ATCTTCAGTA
* * *
29993822 TTTTAAATTGCAATGTTGGGGAAACAAGATTCTCTGTCGTGGCTTCAATCTGTTCCACTACACCG
1 TTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCG
*
29993887 CCAG-GGAAGTAAGATTCACTGTTGTGGCTTCAATC
66 CCAGAGG-AGTAAGATTCACTGTCGTGGCTTCAATC
* * ** * *
29993922 TTTTTAATTGCAATGTTGGGGAAATAAGATTCACCGTTTTAGCTTCAATCTGTTTCATTACACCG
1 TTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCG
*
29993987 CCAGAGGAGTAAGATTCACTGTCGTGGTTTCAAT
66 CCAGAGGAGTAAGATTCACTGTCGTGGCTTCAAT
29994021 TTGCTCCACT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 85 0.98
101 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (100 bp):
TTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCG
CCAGAGGAGTAAGATTCACTGTCGTGGCTTCAATC
Found at i:29994019 original size:50 final size:50
Alignment explanation
Indices: 29993847--29994020 Score: 170
Period size: 50 Copynumber: 3.5 Consensus size: 50
29993837 TTGGGGAAAC
* * *
29993847 AAGATTCTCTGTCGTGGCTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATTCACTGTCGTGGCTTCAATCTGTTTCATTACACCGCCAGGGAAGT
* * * * ** *** *
29993897 AAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAT
1 AAGATTCACTGTCGTGGCTTCAATCTGTTTCATTACACCGCCAGGGAAGT
* ** *
29993947 AAGATTCACCGTTTTAGCTTCAATCTGTTTCATTACACCGCCAGAGG-AGT
1 AAGATTCACTGTCGTGGCTTCAATCTGTTTCATTACACCGCCAG-GGAAGT
*
29993997 AAGATTCACTGTCGTGGTTTCAAT
1 AAGATTCACTGTCGTGGCTTCAAT
29994021 TTGCTCCACT
Statistics
Matches: 93, Mismatches: 30, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
50 91 0.98
51 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (50 bp):
AAGATTCACTGTCGTGGCTTCAATCTGTTTCATTACACCGCCAGGGAAGT
Found at i:29994093 original size:45 final size:45
Alignment explanation
Indices: 29994042--29994183 Score: 180
Period size: 45 Copynumber: 3.2 Consensus size: 45
29994032 TAATGCTAAA
*
29994042 GAGATAGGACTTTGTGATTTTCAGCCTATTCTACTGCTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCTACTGCTGACCAGG
**** *
29994087 GAGATAGGA-TTCACAATCTTCAACCTATT-TCACTGCTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCT-ACTGCTGACCAGG
* * *
29994131 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTTCTGACTAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCTACTGCTGACCAGG
29994176 GAGATAGG
1 GAGATAGG
29994184 GCTGGGGTAA
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
43 1 0.01
44 36 0.45
45 43 0.54
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (45 bp):
GAGATAGGACTTTGTGATTTTCAACCTATTCTACTGCTGACCAGG
Found at i:29994296 original size:88 final size:88
Alignment explanation
Indices: 29994194--29994591 Score: 597
Period size: 88 Copynumber: 4.5 Consensus size: 88
29994184 GCTGGGGTAA
* * * * * *
29994194 TCGATCTGTTTCACTGTCGGTGTAGGAAGGCAAGATCTACTATTTCTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
29994259 CCAAGGG-GGCAAGGCTGGTGTCT
66 CC-AGGGAGGCAAGGCTGGTGTCT
*
29994282 TCGATCTGCTTCACTGTCGGCT-CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAA
1 TCGATCTGCTTCGCTGTCGG-TGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAA
29994346 CCCA-GGAGGC-AGGCTGGTGTCT
65 CCCAGGGAGGCAAGGCTGGTGTCT
* * * * * *
29994368 TTGAACTACTTCGCTGTCGGTACAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCTGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
29994433 CAAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
29994456 TCGATATGCTTCGCTGTCGGTGCAGGAAGGCAATATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
29994521 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
29994544 TCGATATGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
29994592 CTGATCTGCT
Statistics
Matches: 283, Mismatches: 22, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
85 1 0.00
86 73 0.26
87 10 0.04
88 198 0.70
89 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:29994497 original size:174 final size:176
Alignment explanation
Indices: 29994207--29994591 Score: 600
Period size: 174 Copynumber: 2.2 Consensus size: 176
29994197 ATCTGTTTCA
* * * *
29994207 CTGTCGGTGTAGGAAGGCAAGATCTACTATTTCTAACCTGCTCCGCTGCAACCCAAGGGGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAAGGGGGCAAG
*
29994272 GCTGGTGTCTTCGATCTGCTTCACTGTCGGCTCAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
66 GCTGGTGTCTTCGATATGCTTCACTGTCGGCTCAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
*
29994337 CCGCTACAACCCA-GGAGGC-AGGCTGGTGTCTTTGA-ACTACTTCG
131 CCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATA-TACTTCG
* * *
29994381 CTGTCGGTACAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCTGCTACAA-CCAAGGGAGGCAA
1 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAAGGG-GGCAA
* *
29994445 GGCTGGTGTCTTCGATATGCTTCGCTGTCGG-TGCAGGAAGGCAATATCTGCTATTTTTAACCTG
65 GGCTGGTGTCTTCGATATGCTTCACTGTCGGCT-CAGGAAGGCAAGATCTGCTATTTTTAACCTG
*
29994509 CTCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATATGCTTCG
129 CTCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATATACTTCG
29994557 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
29994592 CTGATCTGCT
Statistics
Matches: 192, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
173 8 0.04
174 123 0.64
175 6 0.03
176 54 0.28
177 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (176 bp):
CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAAGGGGGCAAG
GCTGGTGTCTTCGATATGCTTCACTGTCGGCTCAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
CCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATATACTTCG
Found at i:30001119 original size:21 final size:21
Alignment explanation
Indices: 30001082--30001136 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
30001072 AATCATATCT
30001082 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
30001101 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
30001122 TCTAAGATTACATAT
1 TCTAAGATTGCATAT
30001137 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 11 0.33
21 22 0.67
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:30015867 original size:35 final size:35
Alignment explanation
Indices: 30015813--30016003 Score: 95
Period size: 35 Copynumber: 5.4 Consensus size: 35
30015803 ATAGATGTGT
* **
30015813 GCCCAACACTAGTCAGATAAACTGACGAAAGTTGC
1 GCCCAACGCTAGTTGGATAAACTGACGAAAGTTGC
* * *
30015848 GCCCAACGCTAGTTGGATAAA-TCGACAAATAATTAGTGA
1 GCCCAACGCTAGTTGGATAAACT-GAC-GA-AAGT--TGC
* * ** * * *
30015887 GCCCAGCTCTAGTTGGATAAACAAACGATATTTGT
1 GCCCAACGCTAGTTGGATAAACTGACGAAAGTTGC
* * * *
30015922 GCCCTACGCTAGTTGGACAAA-TCGACGAATG-TGT
1 GCCCAACGCTAGTTGGATAAACT-GACGAAAGTTGC
* * *
30015956 GCCCAACACTA-TT-CATATAATCTGACAAAAGTTGC
1 GCCCAACGCTAGTTGGATA-AA-CTGACGAAAGTTGC
30015991 GCCCAACGCTAGT
1 GCCCAACGCTAGT
30016004 CGAATGAACC
Statistics
Matches: 114, Mismatches: 30, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
32 2 0.02
33 4 0.04
34 19 0.17
35 57 0.50
36 2 0.02
37 6 0.05
38 1 0.01
39 23 0.20
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (35 bp):
GCCCAACGCTAGTTGGATAAACTGACGAAAGTTGC
Found at i:30016088 original size:20 final size:21
Alignment explanation
Indices: 30016048--30016092 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
30016038 AATCCATAAA
30016048 ATCACATTTCATAATCTCAAT
1 ATCACATTTCATAATCTCAAT
30016069 ATCACATTTCATAA-CTCAAT
1 ATCACATTTCATAATCTCAAT
30016089 ATCA
1 ATCA
30016093 AATTCACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (21 bp):
ATCACATTTCATAATCTCAAT
Found at i:30016105 original size:37 final size:36
Alignment explanation
Indices: 30016064--30016155 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
30016054 TTTCATAATC
*
30016064 TCAATATCACATTTCAT-AACTCAATATCAAATTCACT
1 TCAATATC-CA-TTAATCAACTCAATATCAAATTCACT
* * *
30016101 TCAATTATCTATTAATCAACTCAGTATCACATTCACT
1 TCAA-TATCCATTAATCAACTCAATATCAAATTCACT
*
30016138 TCAATTATCTATTAATCA
1 TCAA-TATCCATTAATCA
30016156 TTCATTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 4 0.08
37 41 0.84
38 4 0.08
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (36 bp):
TCAATATCCATTAATCAACTCAATATCAAATTCACT
Found at i:30029041 original size:37 final size:37
Alignment explanation
Indices: 30028991--30029063 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
30028981 TATCATTCAA
30028991 CATCATTTTAACAAATCAATTTATAAAGAGCAATCAC
1 CATCATTTTAACAAATCAATTTATAAAGAGCAATCAC
*
30029028 CATCATTTTAACAAGTCAATTTATAAAGAGCAATCA
1 CATCATTTTAACAAATCAATTTATAAAGAGCAATCA
30029064 AGAAATAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (37 bp):
CATCATTTTAACAAATCAATTTATAAAGAGCAATCAC
Found at i:30037074 original size:81 final size:81
Alignment explanation
Indices: 30036935--30037091 Score: 296
Period size: 81 Copynumber: 1.9 Consensus size: 81
30036925 GTAAATTTTT
*
30036935 AAGCAACCTATGTACATGCTCCTAACCAATCACTTGTATATCTACAAGCTCAATCACACAAAAGA
1 AAGCAACCTATGTACATGCTCCTAACCAATCACTTGTATATCTACAAGCTCAAGCACACAAAAGA
30037000 AAAAAAATCAACTTTC
66 AAAAAAATCAACTTTC
*
30037016 AAGCAACCTATGTACATGCTCCTAACCAATCACTTGTATATTTACAAGCTCAAGCACACAAAAGA
1 AAGCAACCTATGTACATGCTCCTAACCAATCACTTGTATATCTACAAGCTCAAGCACACAAAAGA
30037081 AAAAAAATCAA
66 AAAAAAATCAA
30037092 TGAAAAAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (81 bp):
AAGCAACCTATGTACATGCTCCTAACCAATCACTTGTATATCTACAAGCTCAAGCACACAAAAGA
AAAAAAATCAACTTTC
Found at i:30038410 original size:16 final size:16
Alignment explanation
Indices: 30038386--30038422 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
30038376 GAATCATATG
*
30038386 GGGTCGAAAACATGTA
1 GGGTTGAAAACATGTA
*
30038402 GGGTTGAAAACATGTG
1 GGGTTGAAAACATGTA
30038418 GGGTT
1 GGGTT
30038423 TCTGGAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.08, G:0.38, T:0.24
Consensus pattern (16 bp):
GGGTTGAAAACATGTA
Found at i:30045694 original size:187 final size:180
Alignment explanation
Indices: 30045369--30045787 Score: 630
Period size: 187 Copynumber: 2.3 Consensus size: 180
30045359 TGTAACAAAA
* *
30045369 TTTTT-TCTCTCATTTTCTCTCTTGCCAAACACCACTTTTT-TTCTTCAAAACATATGGTTGGTT
1 TTTTTCTCTCTCATTTTCTCTCTTGCCAAACACCA-TTTTTCTTCTTCAAAACACATGGTTGGCT
* *
30045432 CATTTCATCTACAAGAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAAC
65 CATTTCATCTACAAGAATTTCCATCACCATGATTATAATCATGCTTTTGTGCAATTTTTGTAAAC
* * * * *
30045497 CCACACCACACTTTCAGCTTAAAATTATTGGTTTTTTCCCTCCATTGTCGGCTGCCAT
130 CCACACCACACTTGCAACTTAAAATCA-----TTTTT-CC-CCATTGTCAGCTACCAT
30045555 TTTTTCTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTC
1 TTTTTCTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTC
30045620 ATTTCATCTACAAGAATTTCCATCACCATGATTATAATCATGCTTTTGTGCAATTTTTGTAAACC
66 ATTTCATCTACAAGAATTTCCATCACCATGATTATAATCATGCTTTTGTGCAATTTTTGTAAACC
*
30045685 CATACCACACTTGCAACTTAAAATCATTTTTCCCCATTGTCAGCTACCAT
131 CACACCACACTTGCAACTTAAAATCATTTTTCCCCATTGTCAGCTACCAT
* *
30045735 TTTTTCTCT-T-ATTTTCTCTCTTGTCAAACACCATTTTTCTTCTTCTAAACACA
1 TTTTTCTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACA
30045788 ACATCTGGTT
Statistics
Matches: 219, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
178 41 0.19
179 1 0.00
180 24 0.11
181 2 0.01
182 5 0.02
186 10 0.05
187 136 0.62
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.42
Consensus pattern (180 bp):
TTTTTCTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTC
ATTTCATCTACAAGAATTTCCATCACCATGATTATAATCATGCTTTTGTGCAATTTTTGTAAACC
CACACCACACTTGCAACTTAAAATCATTTTTCCCCATTGTCAGCTACCAT
Found at i:30046106 original size:14 final size:15
Alignment explanation
Indices: 30046077--30046109 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
30046067 ATCAACAATT
30046077 AAAG-GGGAAGAGAG
1 AAAGAGGGAAGAGAG
30046091 AAAGAGGGAAGA-AG
1 AAAGAGGGAAGAGAG
30046105 AAAGA
1 AAAGA
30046110 AAATGGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (15 bp):
AAAGAGGGAAGAGAG
Found at i:30047949 original size:3 final size:3
Alignment explanation
Indices: 30047941--30047973 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
30047931 TAAATCATCG
30047941 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
30047974 GCGACAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:30049387 original size:315 final size:315
Alignment explanation
Indices: 30048809--30049883 Score: 1583
Period size: 315 Copynumber: 3.4 Consensus size: 315
30048799 GATGATAAGT
* ** *
30048809 ATCAATAGTTAGTGGATAGACTCAATTGTATCGAATCTGCTTCTACACCATCTATGCAT-GGGGG
1 ATCAATACTTAGTGGATAGACTCAACCGTATCGAATCTGCTTCTACACCATCTATGCATAGGGTG
* * * *
30048873 AGACAAGCCGCTTTCCCACTATATCAATAATCTGAATGAGGATATAAATTATGTC-AGGAATAGG
66 AGACAAACCG-TTTTCCACTATATCAATAATCTGGATGAGGATGTAAATTATGTCGA-GAATA-G
** * *
30048937 GGTGGAAACCCTTATTTGAATACATATAATCCCAGCTAGAGACATCACCCAAATCTGAGGTGGGG
128 GGTGGAAACCCTTATTCAAATACATATAATCCCAGCTAGAGAGATCACCCAAATCTGAGATGGGG
* * * * * * *
30049002 GAAATAATGAGAAGGTACTAATTTAAATCAAGTTAAAAACAATAATTAACAACCTTCTTATTTTC
193 GAAACAAGGAGCAGGTAGTAATTTAAATCAAGTTGAAAACAATAATTACCAACCTTCTTATTTGC
* *
30049067 AGAAAACCCAAGATAGATTCAACCCAAATGACCATAATGTATGTAGTCAACCCAAATG
258 AGAAAACCCAAGATAGGTTCAACCTAAATGACCATAATGTATGTAGTCAACCCAAATG
*
30049125 ATCAATACTTAGTGGATAGACTCAACCGTATCGAATCTGCTTCTACACCATCTATGCAT-GGGTT
1 ATCAATACTTAGTGGATAGACTCAACCGTATCGAATCTGCTTCTACACCATCTATGCATAGGGTG
* *
30049189 A-ACAAACTCATTTTCCACTATATCAATAATCTGGCTGAGGATGTAAATTATGTC-AGGAATAGG
66 AGACAAAC-CGTTTTCCACTATATCAATAATCTGGATGAGGATGTAAATTATGTCGA-GAATAGG
* *
30049252 TGTGGAAACCCTTATTCAAATACATATAATCCTAGCTAGAGAGATCACCCAAATTTGAGATGGGG
129 -GTGGAAACCCTTATTCAAATACATATAATCCCAGCTAGAGAGATCACCCAAATCTGAGATGGGG
* *
30049317 GAAACAAGGAGCAGGTAGTAATTTAAATCAAGTTGAAAATAACAATTACCAACCTTCTTATTTGC
193 GAAACAAGGAGCAGGTAGTAATTTAAATCAAGTTGAAAACAATAATTACCAACCTTCTTATTTGC
*
30049382 AGAAAACCC-AGTATAGGTTCAACCTAAATGACCATAATGTATCTAGTCAACCCAAATG
258 AGAAAACCCAAG-ATAGGTTCAACCTAAATGACCATAATGTATGTAGTCAACCCAAATG
* * *
30049440 ATCAGTACTTAGTGGATAGACTCAACCGTACCGAATCTGCTTCTACACCATCTATGCATGGGGT-
1 ATCAATACTTAGTGGATAGACTCAACCGTATCGAATCTGCTTCTACACCATCTATGCATAGGGTG
* * * * *
30049504 TGACAAACTGCTTTTCCACTATATCAATAATTTGGCTGAGGATGTAAATTATGTCGAGAGTAAGG
66 AGACAAACCG-TTTTCCACTATATCAATAATCTGGATGAGGATGTAAATTATGTCGAGAAT-AGG
**
30049569 GTGGAAACCCTTATTCAAATACATATAATCCCAGCTAGAGAGATCACCCAAATCTGAGATAAGGG
129 GTGGAAACCCTTATTCAAATACATATAATCCCAGCTAGAGAGATCACCCAAATCTGAGATGGGGG
* *
30049634 AAACAAGAAGCAGGTAGTAATTTAAATCAAGTTGAAAACAGTAATTACCAACCTTCTTATTTGCA
194 AAACAAGGAGCAGGTAGTAATTTAAATCAAGTTGAAAACAATAATTACCAACCTTCTTATTTGCA
* *
30049699 GAAAACCCAATATAGGTTCAACCTAAATGACCATAATGTACGTAGTCAACCCAAATG
259 GAAAACCCAAGATAGGTTCAACCTAAATGACCATAATGTATGTAGTCAACCCAAATG
*
30049756 ATCAATAGTT-GTGGATAGACTCAACCGTATCGAATCTGCTTCTACACCATCTATGCATAGGG-G
1 ATCAATACTTAGTGGATAGACTCAACCGTATCGAATCTGCTTCTACACCATCTATGCATAGGGTG
* *
30049819 AGACAAACCGGTTTTCCACTATATCAATAATTTGGATGATGATGTAAATTATGTCGAGAATAGGG
66 AGACAAACC-GTTTTCCACTATATCAATAATCTGGATGAGGATGTAAATTATGTCGAGAATAGGG
30049884 ATGAGGATGA
Statistics
Matches: 692, Mismatches: 56, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
314 8 0.01
315 379 0.55
316 300 0.43
317 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (315 bp):
ATCAATACTTAGTGGATAGACTCAACCGTATCGAATCTGCTTCTACACCATCTATGCATAGGGTG
AGACAAACCGTTTTCCACTATATCAATAATCTGGATGAGGATGTAAATTATGTCGAGAATAGGGT
GGAAACCCTTATTCAAATACATATAATCCCAGCTAGAGAGATCACCCAAATCTGAGATGGGGGAA
ACAAGGAGCAGGTAGTAATTTAAATCAAGTTGAAAACAATAATTACCAACCTTCTTATTTGCAGA
AAACCCAAGATAGGTTCAACCTAAATGACCATAATGTATGTAGTCAACCCAAATG
Found at i:30058117 original size:16 final size:17
Alignment explanation
Indices: 30058098--30058135 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
30058088 CTCTTGAAAT
30058098 TTATTTT-TCTTTTA-TG
1 TTATTTTGT-TTTTATTG
30058114 TTATTTTGTTTTTATTG
1 TTATTTTGTTTTTATTG
30058131 TTATT
1 TTATT
30058136 ACTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (17 bp):
TTATTTTGTTTTTATTG
Found at i:30062990 original size:12 final size:12
Alignment explanation
Indices: 30062952--30062993 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
30062942 GAGATGACCA
30062952 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
30062964 GAGGGATATT-TG
1 GAGAGAT-TTGAG
30062976 GAGAGATTTGAG
1 GAGAGATTTGAG
30062988 GAGAGA
1 GAGAGA
30062994 ATATTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:30063000 original size:24 final size:24
Alignment explanation
Indices: 30062952--30062998 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
30062942 GAGATGACCA
*
30062952 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
30062976 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
30062999 GGGATTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:30063745 original size:27 final size:27
Alignment explanation
Indices: 30063668--30064099 Score: 496
Period size: 27 Copynumber: 16.1 Consensus size: 27
30063658 CGATTTATAC
*
30063668 ACCGAAATACCCCCATAGGGTAAAATA
1 ACCGAAATACCCCCATAGGGTAAAATG
**
30063695 ATTGAAATA-CCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* **
30063721 ACCGAAATACACTTATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
30063748 ACCAAAATACCCTCCATAGGGTAAAATA
1 ACCGAAATACCC-CCATAGGGTAAAATG
* *
30063776 ACCGGAATACCCCCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
30063803 ACCGAAATACCCCCATAGGGTAGAATA
1 ACCGAAATACCCCCATAGGGTAAAATG
* * *
30063830 ACTGAAATGCCCCCATAGGGTAAAATA
1 ACCGAAATACCCCCATAGGGTAAAATG
** *
30063857 ACTAAAATACCCTCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
** *
30063884 ATTGAAATAACCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
30063911 ACCGAAATACCCCTATAGGATAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
*
30063938 ACCGAAATACCCCTCATAAGGTAAAATG
1 ACCGAAATACCCC-CATAGGGTAAAATG
** *
30063966 A-C--AATACCCTTATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* * *
30063990 ATCAAAATA-CCCCATAGGGTAACATG
1 ACCGAAATACCCCCATAGGGTAAAATG
** *
30064016 ACCGAAATACCCAAATAGGGTGAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
30064043 ACCGAAATGACCCCCATAGGGTAAAATG
1 ACCGAAAT-ACCCCCATAGGGTAAAATG
*
30064071 ACCGAAATACCCCTATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
30064098 AC
1 AC
30064100 TATTATACCC
Statistics
Matches: 341, Mismatches: 56, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
24 12 0.04
25 8 0.02
26 43 0.13
27 220 0.65
28 58 0.17
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.19
Consensus pattern (27 bp):
ACCGAAATACCCCCATAGGGTAAAATG
Found at i:30064384 original size:26 final size:26
Alignment explanation
Indices: 30064333--30064413 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
30064323 TTTGTCACAT
* * * *
30064333 ATACTGTTACTGGCAACTTTGTTGCG
1 ATACTATTACTGGCAGCTCTGCTGCG
*
30064359 ATACTGA-TGCTGGCAGCTCTGCTGCG
1 ATACT-ATTACTGGCAGCTCTGCTGCG
* * *
30064385 ATGCTATTATTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTCTGCTGCG
30064411 ATA
1 ATA
30064414 TTGGTGTGTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.02
26 42 0.98
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTCTGCTGCG
Found at i:30064634 original size:27 final size:28
Alignment explanation
Indices: 30064515--30064636 Score: 160
Period size: 28 Copynumber: 4.4 Consensus size: 28
30064505 TATTGCACTG
* *
30064515 CACTGTTACTGTATTGGGCTAAGGCTCG
1 CACTGTTACTGTATTGGGCTAAGGCCCA
30064543 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
* *
30064571 CACTATTACTG-CTTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
30064598 TACTGTTACTGTATTAGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
30064626 CACTG-TACTGT
1 CACTGTTACTGT
30064637 CACTGAATAG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 32 0.39
28 48 0.59
29 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:30070383 original size:93 final size:94
Alignment explanation
Indices: 30070170--30070438 Score: 468
Period size: 93 Copynumber: 2.9 Consensus size: 94
30070160 ACGAGATAAA
* * * * * *
30070170 AAAAGGATTTGATATATTCCTTATCAGATGAGGAGATAAAATTTAATTATTATTTAAAAGAGTTT
1 AAAAGGATTTGATATATTCCTTATCATATAAGTAAATAGAATTTAGTTATTATTTAAAAGAGTTT
30070235 TAGATAAAGAATAATTAAAATTCAAAAGC
66 TAGATAAAGAATAATTAAAATTCAAAAGC
30070264 AAAAGGATTTGATATATTCCTTATCATATAAGTAAATAGAATTTAGTTATTATTTAAAAGAGTTT
1 AAAAGGATTTGATATATTCCTTATCATATAAGTAAATAGAATTTAGTTATTATTTAAAAGAGTTT
30070329 TAGA-AAAGAATAATTAAAATTCAAAAGC
66 TAGATAAAGAATAATTAAAATTCAAAAGC
30070357 AAAAGGATTTGATATATTCCTTATCATATAAGTAAATAGAATTTAGTTATTATTTAAAAGAGTTT
1 AAAAGGATTTGATATATTCCTTATCATATAAGTAAATAGAATTTAGTTATTATTTAAAAGAGTTT
*
30070422 TAGATAAATAATAATTA
66 TAGATAAAGAATAATTA
30070439 TATTATTTAA
Statistics
Matches: 167, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
93 93 0.56
94 74 0.44
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.36
Consensus pattern (94 bp):
AAAAGGATTTGATATATTCCTTATCATATAAGTAAATAGAATTTAGTTATTATTTAAAAGAGTTT
TAGATAAAGAATAATTAAAATTCAAAAGC
Found at i:30070444 original size:35 final size:35
Alignment explanation
Indices: 30070404--30070472 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
30070394 AGAATTTAGT
30070404 TATTATTTAAAAGAGTTTTAGATAAATAATAATTA
1 TATTATTTAAAAGAGTTTTAGATAAATAATAATTA
* *
30070439 TATTATTTAAAATATTTTTAGATAAATAATAATT
1 TATTATTTAAAAGAGTTTTAGATAAATAATAATT
30070473 GAAATAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (35 bp):
TATTATTTAAAAGAGTTTTAGATAAATAATAATTA
Found at i:30070485 original size:38 final size:35
Alignment explanation
Indices: 30070408--30070486 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
30070398 TTTAGTTATT
**
30070408 ATTTAAAAGAGTTTTAGATAAATAATAATTATATT
1 ATTTAAAAGAGTTTTAGATAAATAATAATTATAGA
* *
30070443 ATTTAAAATATTTTTAGATAAATAATAATTGAAATAGA
1 ATTTAAAAGAGTTTTAGATAAATAATAATT---ATAGA
30070481 ATTTAA
1 ATTTAA
30070487 TTATCATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 28 0.76
38 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (35 bp):
ATTTAAAAGAGTTTTAGATAAATAATAATTATAGA
Found at i:30070501 original size:52 final size:50
Alignment explanation
Indices: 30070433--30070550 Score: 145
Period size: 52 Copynumber: 2.4 Consensus size: 50
30070423 AGATAAATAA
* *
30070433 TAATTATATTATTTAAAA-TATTTTTAGAT-AAATAATAATTGAAATAGAATT
1 TAATTATATTATTTAAAAGT-GTTTTAAATAAAAT-ATAATT-AAATAGAATT
30070484 TAATTATCATTATTTAAAAGTGTTTTAAATAAAATATAATTAAATAGAATT
1 TAATTAT-ATTATTTAAAAGTGTTTTAAATAAAATATAATTAAATAGAATT
*
30070535 TAAAT-TATTA-TTAAAA
1 TAATTATATTATTTAAAA
30070551 CGAGTTTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
48 6 0.10
49 4 0.07
50 1 0.02
51 21 0.34
52 24 0.39
53 5 0.08
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (50 bp):
TAATTATATTATTTAAAAGTGTTTTAAATAAAATATAATTAAATAGAATT
Found at i:30071607 original size:16 final size:16
Alignment explanation
Indices: 30071581--30071634 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
30071571 TTTAGTTCGC
*
30071581 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
*
30071597 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
30071613 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
30071629 TGTAAT
1 TGTAAT
30071635 AGCAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:30074746 original size:16 final size:16
Alignment explanation
Indices: 30074725--30074756 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30074715 TCAAATCTAT
*
30074725 TTGAAGTGATTTAAAA
1 TTGAAGTGATGTAAAA
30074741 TTGAAGTGATGTAAAA
1 TTGAAGTGATGTAAAA
30074757 GGCATGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAAGTGATGTAAAA
Found at i:30083807 original size:16 final size:16
Alignment explanation
Indices: 30083786--30083817 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30083776 TCAACTCTAT
*
30083786 TTGAAGTGATTTAAAA
1 TTGAAGTGATGTAAAA
30083802 TTGAAGTGATGTAAAA
1 TTGAAGTGATGTAAAA
30083818 GGCATGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAAGTGATGTAAAA
Found at i:30088312 original size:15 final size:16
Alignment explanation
Indices: 30088280--30088312 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30088270 TCAAGATGGA
*
30088280 ATTTTGAATTCATTTG
1 ATTTTGAATTCATATG
30088296 ATTTTGAA-TCATATG
1 ATTTTGAATTCATATG
30088311 AT
1 AT
30088313 ACTTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTTTGAATTCATATG
Found at i:30091997 original size:34 final size:33
Alignment explanation
Indices: 30091959--30092024 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
30091949 ATAGAATTTA
*
30091959 GTTATT-ATTTAAAAGAGTTTTATATTAAATAATT
1 GTTATTAATTT-AAAGAGTTTTAGA-TAAATAATT
30091993 GTTATTAATTTAAAGAGTTTTAGATAAATAAT
1 GTTATTAATTTAAAGAGTTTTAGATAAATAAT
30092025 AATTAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 8 0.27
34 18 0.60
35 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (33 bp):
GTTATTAATTTAAAGAGTTTTAGATAAATAATT
Found at i:30092053 original size:48 final size:48
Alignment explanation
Indices: 30092000--30092109 Score: 127
Period size: 47 Copynumber: 2.3 Consensus size: 48
30091990 ATTGTTATTA
* * * **
30092000 ATTT-AAAGAGTTTTAGATAAATA-ATAATTAAAACAGAATTTCATTAAT
1 ATTTAAAAGAGTTTTA-AAAAAAAGATAATTAAAA-AAAATTAAATTAAT
*
30092048 ATTTAAAAGAG-TTTAAAAAAAAGATAATTAAAAAAAATTAAATTATT
1 ATTTAAAAGAGTTTTAAAAAAAAGATAATTAAAAAAAATTAAATTAAT
30092095 ATTTAAAAGAGTTTT
1 ATTTAAAAGAGTTTT
30092110 TCAAATTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
47 26 0.49
48 21 0.40
49 6 0.11
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (48 bp):
ATTTAAAAGAGTTTTAAAAAAAAGATAATTAAAAAAAATTAAATTAAT
Found at i:30094807 original size:26 final size:27
Alignment explanation
Indices: 30094778--30094830 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
30094768 ATGATCGTAA
30094778 TTCCCCTAGAAGGTAAATGACT-ATTT
1 TTCCCCTAGAAGGTAAATGACTGATTT
* *
30094804 TTCCCCTCGAGGGTAAATGACTGATTT
1 TTCCCCTAGAAGGTAAATGACTGATTT
30094831 GTGCTATGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
TTCCCCTAGAAGGTAAATGACTGATTT
Found at i:30100411 original size:16 final size:16
Alignment explanation
Indices: 30100370--30100413 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
30100360 CAACCACATC
30100370 AGGTTCCATATGAGTA
1 AGGTTCCATATGAGTA
**
30100386 AGAG-AGCATATGAGTA
1 AG-GTTCCATATGAGTA
30100402 AGGTTCCATATG
1 AGGTTCCATATG
30100414 CTTCAATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.27
Consensus pattern (16 bp):
AGGTTCCATATGAGTA
Found at i:30102737 original size:29 final size:29
Alignment explanation
Indices: 30102695--30102752 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
30102685 GGAAGTCATG
30102695 ATTCGACATAACCTCTCTGTGACTAACCC
1 ATTCGACATAACCTCTCTGTGACTAACCC
30102724 ATTCGACATAACCTCTCTGTGACTAACCC
1 ATTCGACATAACCTCTCTGTGACTAACCC
30102753 TTCATGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.34, G:0.10, T:0.28
Consensus pattern (29 bp):
ATTCGACATAACCTCTCTGTGACTAACCC
Found at i:30104294 original size:6 final size:6
Alignment explanation
Indices: 30104278--30104314 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
30104268 ACTAAAATGT
30104278 ATTAT- ATTATA ATTATA ATTAT- ATTATA ATGTATA AT
1 ATTATA ATTATA ATTATA ATTATA ATTATA AT-TATA AT
30104315 AGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 13 0.45
7 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
ATTATA
Found at i:30104300 original size:17 final size:18
Alignment explanation
Indices: 30104278--30104314 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
30104268 ACTAAAATGT
30104278 ATTATATTATAAT-TATA
1 ATTATATTATAATGTATA
30104295 ATTATATTATAATGTATA
1 ATTATATTATAATGTATA
30104313 AT
1 AT
30104315 AGTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTATATTATAATGTATA
Found at i:30109075 original size:43 final size:42
Alignment explanation
Indices: 30109027--30109141 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 42
30109017 CCCAAATATG
* * *
30109027 GTCTTACATGTAATCTCGTATCGATGCCAATAG-CCCAGCCATA
1 GTCTTACACG-AATCTCATATCGATGCCAAT-GTCCCAGACATA
* ** *
30109070 GTCTTACACAAAATAACATATCGATGCCAATGTCCCAGACATG
1 GTCTTACAC-GAATCTCATATCGATGCCAATGTCCCAGACATA
30109113 GTCTTACACGAAGTCTCATATCGATGCCA
1 GTCTTACACGAA-TCTCATATCGATGCCA
30109142 TATCACAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
42 3 0.05
43 56 0.95
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (42 bp):
GTCTTACACGAATCTCATATCGATGCCAATGTCCCAGACATA
Found at i:30114958 original size:21 final size:21
Alignment explanation
Indices: 30114934--30114974 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30114924 GTACCCCTAT
*
30114934 CACACGGGCGTGTCCCTCAGC
1 CACACAGGCGTGTCCCTCAGC
*
30114955 CACACAGGTGTGTCCCTCAG
1 CACACAGGCGTGTCCCTCAG
30114975 TTACATGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.27, T:0.17
Consensus pattern (21 bp):
CACACAGGCGTGTCCCTCAGC
Found at i:30133738 original size:27 final size:27
Alignment explanation
Indices: 30133680--30133765 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
30133670 ATGGGGTCAA
30133680 TAAAATGACCGAAATA-CCCCAAAGGG
1 TAAAATGACCGAAATACCCCCAAAGGG
*
30133706 TGAAATGACCGAAATACCCCCAAAGGG
1 TAAAATGACCGAAATACCCCCAAAGGG
* * *
30133733 TTAAATGGCCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCAAAGGG
30133760 TAAAAT
1 TAAAAT
30133766 ATCTATTATA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 15 0.28
27 39 0.72
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCAAAGGG
Done.