Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 181 of 335
Found at i:54326945 original size:19 final size:19
Alignment explanation
Indices: 54326910--54326947 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54326900 GTGTGGGGCC
*
54326910 CATGAGCCCATTGGGCCCA
1 CATGAGCCCATTAGGCCCA
54326929 CATG-GCCCATCTAGGCCCA
1 CATGAGCCCAT-TAGGCCCA
54326948 ACGAGGCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.21, C:0.39, G:0.24, T:0.16
Consensus pattern (19 bp):
CATGAGCCCATTAGGCCCA
Found at i:54329750 original size:30 final size:30
Alignment explanation
Indices: 54329714--54329782 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
54329704 CACATGGATA
54329714 GACACACGGGTATGTGTCTAGGCCGTGTGT
1 GACACACGGGTATGTGTCTAGGCCGTGTGT
*
54329744 GACACACGAGTATGTGTCTAGGCCGTGTGT
1 GACACACGGGTATGTGTCTAGGCCGTGTGT
54329774 GACACACGG
1 GACACACGG
54329783 TCTATCCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.23
Consensus pattern (30 bp):
GACACACGGGTATGTGTCTAGGCCGTGTGT
Found at i:54330601 original size:42 final size:42
Alignment explanation
Indices: 54330486--54330649 Score: 166
Period size: 42 Copynumber: 3.9 Consensus size: 42
54330476 TAATATACCA
* ** *
54330486 ATGCCATATCCCAGATATGGTCTTACATAGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCACATCG
** * * *
54330528 ATGGAAATAGCCCAGTTATGGTCTTACACAAAATCTCACATTG
1 AT-GCCATATCCCAGATATGGTCTTACACAAAATCTCACATCG
* * * * *
54330571 ATTCCATATCCCAGATATGGTCTTATACAAAGTGTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCACATCG
* **
54330613 ATGCCATATCTCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCA
54330650 GTAACTCTAA
Statistics
Matches: 95, Mismatches: 26, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 62 0.65
43 33 0.35
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACAAAATCTCACATCG
Found at i:54333049 original size:16 final size:16
Alignment explanation
Indices: 54333010--54333052 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
54333000 ATGAATCGGT
* *
54333010 AAAAGCCAAAATGCCA
1 AAAAGCCGAAATACCA
54333026 AAAAGCCGAAATACCA
1 AAAAGCCGAAATACCA
54333042 AAAAGCCGAAA
1 AAAAGCCGAAA
54333053 GTTGGGCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.58, C:0.23, G:0.14, T:0.05
Consensus pattern (16 bp):
AAAAGCCGAAATACCA
Found at i:54333308 original size:29 final size:29
Alignment explanation
Indices: 54333263--54333381 Score: 109
Period size: 29 Copynumber: 4.2 Consensus size: 29
54333253 GTAAGCATGA
*
54333263 ATAT-AATATGATTTGGGCCTAATGGGCC
1 ATATGAATATGAATTGGGCCTAATGGGCC
* *
54333291 ATATGAATGTGAATTGGGCCTAGTGGGCC
1 ATATGAATATGAATTGGGCCTAATGGGCC
** * *
54333320 ATAAAAATATGAACTAGGCC-AGATGGGCC
1 ATATGAATATGAATTGGGCCTA-ATGGGCC
* * * *
54333349 ATTTGAATAAG-ATTGGGCATAGTGGGCC
1 ATATGAATATGAATTGGGCCTAATGGGCC
54333377 ATATG
1 ATATG
54333382 CATGTATGTA
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
28 20 0.29
29 50 0.71
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (29 bp):
ATATGAATATGAATTGGGCCTAATGGGCC
Found at i:54351369 original size:6 final size:6
Alignment explanation
Indices: 54351351--54351416 Score: 75
Period size: 6 Copynumber: 11.5 Consensus size: 6
54351341 ATCCTCCTTT
*
54351351 TTTTTA TTCTTA TTTTTA -TTTTA -TTTTA -TTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * *
54351396 TTTTGA TTTTTG TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTT
54351417 CAATTTTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
5 15 0.29
6 37 0.71
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:54351374 original size:5 final size:5
Alignment explanation
Indices: 54351348--54351436 Score: 67
Period size: 5 Copynumber: 16.8 Consensus size: 5
54351338 TAAATCCTCC
54351348 TTTT- TTTTA TTCTTA TTTTTA TTTTA TTTTA TTTTA TTTTTA TTTTTA
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA
* *
54351396 TTTTGA TTTTTG TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 TTTT-A -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
54351437 GAAAGGCATA
Statistics
Matches: 71, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.04
4 4 0.06
5 33 0.46
6 25 0.35
7 6 0.08
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:54351385 original size:27 final size:27
Alignment explanation
Indices: 54351348--54351406 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
54351338 TAAATCCTCC
54351348 TTTTTTTTATTCTTATTTTTATTTT-A
1 TTTTTTTTATTCTTATTTTTATTTTGA
*
54351374 TTTTATTTTATTTTTATTTTTATTTTGA
1 TTTT-TTTTATTCTTATTTTTATTTTGA
54351402 TTTTT
1 TTTTT
54351407 GTTTTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 4 0.13
27 21 0.70
28 5 0.17
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTTTTTTATTCTTATTTTTATTTTGA
Found at i:54351404 original size:12 final size:11
Alignment explanation
Indices: 54351351--54351436 Score: 77
Period size: 12 Copynumber: 7.4 Consensus size: 11
54351341 ATCCTCCTTT
54351351 TTTTTATTCTTA
1 TTTTTATT-TTA
54351363 TTTTTATTTTA
1 TTTTTATTTTA
54351374 -TTTTATTTTA
1 TTTTTATTTTA
54351384 TTTTTATTTTTA
1 TTTTTA-TTTTA
*
54351396 TTTTGATTTT-
1 TTTTTATTTTA
*
54351406 TGTTTTCATTTCAA
1 T-TTTT-ATTT-TA
54351420 TTTTATTATTTTA
1 -TTT-TTATTTTA
54351433 TTTT
1 TTTT
54351437 GAAAGGCATA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
10 11 0.18
11 16 0.26
12 25 0.40
13 1 0.02
14 6 0.10
15 3 0.05
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:54353889 original size:20 final size:20
Alignment explanation
Indices: 54353864--54353903 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54353854 GATAAAACTT
54353864 GATTTGTTCTTAATTATGTG
1 GATTTGTTCTTAATTATGTG
54353884 GATTTGTTCTTAATTATGTG
1 GATTTGTTCTTAATTATGTG
54353904 TTATTAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (20 bp):
GATTTGTTCTTAATTATGTG
Found at i:54354356 original size:13 final size:13
Alignment explanation
Indices: 54354340--54354372 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54354330 TTTAATTAAA
*
54354340 TTAGTTAATTAGT
1 TTAGATAATTAGT
54354353 TTAGATAATTAGT
1 TTAGATAATTAGT
54354366 TTA-ATAA
1 TTAGATAA
54354373 ACAAACCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:54356019 original size:25 final size:25
Alignment explanation
Indices: 54355985--54356036 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
54355975 GAACTCCTGC
54355985 TTCCAATATC-TCTT-CCAAATTTATG
1 TTCCAATATCTTCTTGCC--ATTTATG
54356010 TTCCAATATCTTCTTGCCATTTATG
1 TTCCAATATCTTCTTGCCATTTATG
54356035 TT
1 TT
54356037 TGCACTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 19 0.76
26 4 0.16
27 2 0.08
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (25 bp):
TTCCAATATCTTCTTGCCATTTATG
Found at i:54357628 original size:31 final size:31
Alignment explanation
Indices: 54357590--54357648 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
54357580 TCACACTTCG
54357590 TATTTCATAACACTGGGCCGAAACCTTTTCA
1 TATTTCATAACACTGGGCCGAAACCTTTTCA
** *
54357621 TATTTCATATTACTGGGCCGAAGCCTTT
1 TATTTCATAACACTGGGCCGAAACCTTT
54357649 ACTGTAAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (31 bp):
TATTTCATAACACTGGGCCGAAACCTTTTCA
Found at i:54357948 original size:25 final size:24
Alignment explanation
Indices: 54357842--54357987 Score: 215
Period size: 25 Copynumber: 6.0 Consensus size: 24
54357832 GCTTTATCAT
*
54357842 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
54357867 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54357890 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
54357914 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
*
54357939 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
54357964 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54357988 CACTTCCTCC
Statistics
Matches: 115, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
23 18 0.16
24 41 0.36
25 56 0.49
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:54358061 original size:20 final size:20
Alignment explanation
Indices: 54358036--54358102 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
54358026 TTATGAATAC
54358036 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54358056 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54358076 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54358096 ACCATGT
1 ATCATGT
54358103 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54358067 original size:11 final size:11
Alignment explanation
Indices: 54358036--54358091 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54358026 TTATGAATAC
54358036 ATCATGTGCAT
1 ATCATGTGCAT
*
54358047 ATCA--TACAT
1 ATCATGTGCAT
54358056 ATCATGTGCAT
1 ATCATGTGCAT
*
54358067 ATCA--TACAT
1 ATCATGTGCAT
*
54358076 GTCATGTGCAT
1 ATCATGTGCAT
54358087 ATCAT
1 ATCAT
54358092 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:54364634 original size:16 final size:16
Alignment explanation
Indices: 54364613--54364643 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54364603 TGTAAAACAG
54364613 ATGAAATGAGGTTTAC
1 ATGAAATGAGGTTTAC
54364629 ATGAAATGAGGTTTA
1 ATGAAATGAGGTTTA
54364644 TTAAGGCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (16 bp):
ATGAAATGAGGTTTAC
Found at i:54370590 original size:49 final size:49
Alignment explanation
Indices: 54370517--54370698 Score: 213
Period size: 49 Copynumber: 3.7 Consensus size: 49
54370507 AAGCTATCTG
* * *
54370517 GTACACATAGTAGCCTGCAGTTAGTACTATACATGCGACCAATTATCCA
1 GTACACATAGTAGCCAGCACTTAGTACTACACATGCGACCAATTATCCA
* * * * **
54370566 GTACACGTAGTAGCCAGCACTTAGTACTACACAAGTGATCAAAGTTATCGG
1 GTACACATAGTAGCCAGCACTTAGTACTACACATGCGA-CCAA-TTATCCA
* * * *
54370617 GTACACATAGTAGCCTGCATTTAATACTACACATGCGACCAATAATCCA
1 GTACACATAGTAGCCAGCACTTAGTACTACACATGCGACCAATTATCCA
54370666 GTACACATAGTAGCCTA-CACTTAGTACTACACA
1 GTACACATAGTAGCC-AGCACTTAGTACTACACA
54370699 CGTGACATCA
Statistics
Matches: 108, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
49 65 0.60
50 6 0.06
51 37 0.34
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (49 bp):
GTACACATAGTAGCCAGCACTTAGTACTACACATGCGACCAATTATCCA
Found at i:54370678 original size:100 final size:100
Alignment explanation
Indices: 54370505--54370703 Score: 310
Period size: 100 Copynumber: 2.0 Consensus size: 100
54370495 CACTTGTAGC
* * * *
54370505 CAAAGCTATCTGGTACACATAGTAGCCTGCAGTTAGTACTATACATGCGACCAATTATCCAGTAC
1 CAAAGCTATCGGGTACACATAGTAGCCTGCAGTTAATACTACACATGCGACCAATAATCCAGTAC
*
54370570 ACGTAGTAGCC-AGCACTTAGTACTACACAAGTGAT
66 ACATAGTAGCCTA-CACTTAGTACTACACAAGTGAT
* *
54370605 CAAAGTTATCGGGTACACATAGTAGCCTGCATTTAATACTACACATGCGACCAATAATCCAGTAC
1 CAAAGCTATCGGGTACACATAGTAGCCTGCAGTTAATACTACACATGCGACCAATAATCCAGTAC
*
54370670 ACATAGTAGCCTACACTTAGTACTACACACGTGA
66 ACATAGTAGCCTACACTTAGTACTACACAAGTGA
54370704 CATCACAATA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 89 0.99
101 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (100 bp):
CAAAGCTATCGGGTACACATAGTAGCCTGCAGTTAATACTACACATGCGACCAATAATCCAGTAC
ACATAGTAGCCTACACTTAGTACTACACAAGTGAT
Found at i:54373207 original size:26 final size:25
Alignment explanation
Indices: 54373178--54373248 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 25
54373168 AGTCATGGTC
*
54373178 AGTAAGCTCCT-CCTGAGCTGATAAAT
1 AGTAAGCTCCTATC-GAGCTGA-AAAT
54373204 AGTAAGCT-CTATCGAGCTGAAAAT
1 AGTAAGCTCCTATCGAGCTGAAAAT
*
54373228 GGTAAGCT-CTATCGAGCTGAA
1 AGTAAGCTCCTATCGAGCTGAA
54373249 TTGTAAGCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 24 0.57
25 9 0.21
26 9 0.21
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (25 bp):
AGTAAGCTCCTATCGAGCTGAAAAT
Found at i:54373232 original size:24 final size:24
Alignment explanation
Indices: 54373192--54373248 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
54373182 AGCTCCTCCT
54373192 GAGCTGATAAATAGTAAGCTCTATC
1 GAGCTGA-AAATAGTAAGCTCTATC
*
54373217 GAGCTGAAAATGGTAAGCTCTATC
1 GAGCTGAAAATAGTAAGCTCTATC
54373241 GAGCTGAA
1 GAGCTGAA
54373249 TTGTAAGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.25
Consensus pattern (24 bp):
GAGCTGAAAATAGTAAGCTCTATC
Found at i:54373257 original size:22 final size:23
Alignment explanation
Indices: 54373200--54373257 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
54373190 CTGAGCTGAT
*
54373200 AAATAGTAAGCTCTATCGAGCTG
1 AAATGGTAAGCTCTATCGAGCTG
54373223 AAAATGGTAAGCTCTATCGAGCTG
1 -AAATGGTAAGCTCTATCGAGCTG
*
54373247 -AATTGTAAGCT
1 AAATGGTAAGCT
54373258 TTTTCAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 10 0.31
24 22 0.69
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (23 bp):
AAATGGTAAGCTCTATCGAGCTG
Found at i:54373311 original size:23 final size:24
Alignment explanation
Indices: 54373204--54373308 Score: 80
Period size: 23 Copynumber: 4.5 Consensus size: 24
54373194 GCTGATAAAT
54373204 AGTAAGC-TCTATCGAGCTGAAA-
1 AGTAAGCTTCTATCGAGCTGAAAC
*
54373226 ATGGTAAGC-TCTATCGAGCTG-AAT
1 A--GTAAGCTTCTATCGAGCTGAAAC
* * *
54373250 TGTAAGCTT-TTTCAAGCT-AAATC
1 AGTAAGCTTCTATCGAGCTGAAA-C
* *
54373273 AGTAAGCTCCAAT-GAGCTGAAAC
1 AGTAAGCTTCTATCGAGCTGAAAC
54373296 AGTAAGCTTCTAT
1 AGTAAGCTTCTAT
54373309 GAGTTGTGGA
Statistics
Matches: 64, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
22 16 0.25
23 26 0.41
24 22 0.34
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (24 bp):
AGTAAGCTTCTATCGAGCTGAAAC
Found at i:54377646 original size:40 final size:40
Alignment explanation
Indices: 54377601--54377767 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
54377591 CGGAATATAA
54377601 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
54377641 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
54377681 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
54377721 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
54377760 CCGGATAT
1 CCGGATAT
54377768 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54385397 original size:40 final size:39
Alignment explanation
Indices: 54385352--54385478 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 39
54385342 CGGAATATAA
*
54385352 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TGCACAATTGCCTTCGGGTCTTAGC
** *
54385392 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACT-GCACAATTGCCTTCGGGTCTTAGC
* * *
54385432 CCGGATATAATTTC-CAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAA--TCACTGCACAATTGCCTTCGGGTCTTAGC
54385471 CCGGATAT
1 CCGGATAT
54385479 CATTCAATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
39 14 0.19
40 58 0.78
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (39 bp):
CCGGATATAATCACTGCACAATTGCCTTCGGGTCTTAGC
Found at i:54395421 original size:17 final size:17
Alignment explanation
Indices: 54395399--54395454 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
54395389 TCCCTCAGAA
54395399 GTTTTGGGTTTTCTTAT
1 GTTTTGGGTTTTCTTAT
* *
54395416 GTTTT--GTTATTTTTAA
1 GTTTTGGGTT-TTCTTAT
54395432 GTTTTGGGTTTTCTTAT
1 GTTTTGGGTTTTCTTAT
54395449 GTTTTG
1 GTTTTG
54395455 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.09
16 10 0.31
17 16 0.50
18 3 0.09
ACGTcount: A:0.09, C:0.04, G:0.21, T:0.66
Consensus pattern (17 bp):
GTTTTGGGTTTTCTTAT
Found at i:54395437 original size:16 final size:16
Alignment explanation
Indices: 54395416--54395463 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
54395406 GTTTTCTTAT
54395416 GTTTTGTTATTTTTAA
1 GTTTTGTTATTTTTAA
* *
54395432 GTTTTGGGTT-TTCTTAT
1 GTTTT--GTTATTTTTAA
54395449 GTTTTGTTATTTTTA
1 GTTTTGTTATTTTTA
54395464 TTCTTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 10 0.38
18 3 0.12
ACGTcount: A:0.12, C:0.02, G:0.17, T:0.69
Consensus pattern (16 bp):
GTTTTGTTATTTTTAA
Found at i:54395439 original size:33 final size:33
Alignment explanation
Indices: 54395397--54395463 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
54395387 ATTCCCTCAG
54395397 AAGTTTTGGGTTTTCTTATGTTTTGTTATTTTT
1 AAGTTTTGGGTTTTCTTATGTTTTGTTATTTTT
54395430 AAGTTTTGGGTTTTCTTATGTTTTGTTATTTTT
1 AAGTTTTGGGTTTTCTTATGTTTTGTTATTTTT
54395463 A
1 A
54395464 TTCTTTTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.66
Consensus pattern (33 bp):
AAGTTTTGGGTTTTCTTATGTTTTGTTATTTTT
Found at i:54399289 original size:17 final size:18
Alignment explanation
Indices: 54399264--54399297 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54399254 AAAGTCATTC
54399264 TCTTGTAAAACATTATTA
1 TCTTGTAAAACATTATTA
*
54399282 TCTT-TAAAACTTTATT
1 TCTTGTAAAACATTATT
54399298 TGCTCCGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (18 bp):
TCTTGTAAAACATTATTA
Found at i:54400144 original size:21 final size:22
Alignment explanation
Indices: 54400120--54400171 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
54400110 GGCACACAAT
* *
54400120 CATAATCAGGTT-GGACAGAGC
1 CATAATCAGGTTAGCACAAAGC
*
54400141 CAT-ATGTAGGTTAGCACAAAGC
1 CATAAT-CAGGTTAGCACAAAGC
54400163 CATAATCAG
1 CATAATCAG
54400172 AAAATTGGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.08
21 8 0.33
22 12 0.50
23 2 0.08
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
CATAATCAGGTTAGCACAAAGC
Found at i:54400674 original size:27 final size:27
Alignment explanation
Indices: 54400629--54401144 Score: 453
Period size: 27 Copynumber: 19.1 Consensus size: 27
54400619 TTTTAGTCAT
* *
54400629 TTTTGGTAAATTTACAAACCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * * * *
54400656 TTTCGATAATTTTGCAAACCAATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* **
54400683 TTTCT-ATAATTTTTGAAAGTCAAGGGTA
1 TTT-TGGTAATTTTACAAA-TCAAGGGTA
* ** *
54400711 TTTTTGTAATTTTGTAAATCAGGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
*
54400738 TTTAT-GTAATTTTCCAAATCAAGGGTA
1 TTT-TGGTAATTTTACAAATCAAGGGTA
* * * * * *
54400765 TTTCGATAATTTTCCAAATTAGGGGTG
1 TTTTGGTAATTTTACAAATCAAGGGTA
* *
54400792 TTTTGGTAATTTTACAAATTAAAGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * *
54400819 TTTTAGTAATTTTACAAGTCAATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * ** * *
54400846 TTTCGGTAATTTTATAGGTCGAGCGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
*
54400873 TTTTGGTAATTTCACAAATCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
*
54400900 TTTTGGTAATTTTACAAACCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* *
54400927 TTTTGGTAATTTTACAAACCAGGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* *
54400954 TTTTGGTAATTTTACAAGTCGAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
** *
54400981 TTTAAGTAATTTTACAAGTCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * * * *
54401008 TTTCGATAATTTCACAAATTATGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
*
54401035 TTTTGGTAATTTTACAAACCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * * *
54401062 TTTTGGTAATTTTGCTAATCGATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* ** *
54401089 TTTTAGTAATTTTGTAAACCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* ** *
54401116 -TTTAGTAATTTTGTAAACCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
54401142 TTT
1 TTT
54401145 CAGTAATTCT
Statistics
Matches: 403, Mismatches: 80, Indels: 12
0.81 0.16 0.02
Matches are distributed among these distances:
26 26 0.06
27 356 0.88
28 21 0.05
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
TTTTGGTAATTTTACAAATCAAGGGTA
Found at i:54401410 original size:8 final size:8
Alignment explanation
Indices: 54401397--54401427 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
54401387 CCGTGTGACT
54401397 GGCATTTC
1 GGCATTTC
54401405 GGCATTTC
1 GGCATTTC
54401413 GGCATTTC
1 GGCATTTC
*
54401421 GACATTT
1 GGCATTT
54401428 GCCGTTCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (8 bp):
GGCATTTC
Found at i:54406594 original size:31 final size:31
Alignment explanation
Indices: 54406552--54406610 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
54406542 TCACATATTG
* *
54406552 ATGCCACTGTCCTAGACAGGGTCTTACAAAC
1 ATGCCAATGTCCCAGACAGGGTCTTACAAAC
* *
54406583 ATGCCAATGTCCCAGATATGGTCTTACA
1 ATGCCAATGTCCCAGACAGGGTCTTACA
54406611 TGTAATCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (31 bp):
ATGCCAATGTCCCAGACAGGGTCTTACAAAC
Found at i:54412124 original size:40 final size:40
Alignment explanation
Indices: 54412078--54412243 Score: 192
Period size: 40 Copynumber: 4.2 Consensus size: 40
54412068 GAATACAACT
* **
54412078 GGATATAACCACATGCACGAATATCTTCGGGTCTTAGCCC
1 GGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGCCC
** * *
54412118 GGATATAACGTCTTGCACAAATGCCTTCGGGTATTAGCCC
1 GGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGCCC
* *
54412158 GGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCC
1 GGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGCCC
* * *
54412198 GGATA-AAGTCACTAGCAC-AATTGCCTTCGGGTCTTAACCC
1 GGATATAA-CCACTTGCACGAA-TGCCTTCGGGTCTTAGCCC
54412238 GGATAT
1 GGATAT
54412244 CATTCAATTG
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.04
40 102 0.96
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
GGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGCCC
Found at i:54412224 original size:80 final size:80
Alignment explanation
Indices: 54412091--54412241 Score: 216
Period size: 80 Copynumber: 1.9 Consensus size: 80
54412081 TATAACCACA
* * *
54412091 TGCACGAATATCTTCGGGTCTTAGCCCGGATATAACGTCTTGCACAAATGCCTTCGGGTATTAGC
1 TGCACGAATACCTTCGGGTCTTAGCCCGGATATAACGTCTAGCACAAATGCCTTCGGGTATTAAC
54412156 CCGGATTTAACAACT
66 CCGGATTTAACAACT
* * *
54412171 TGCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAATTGCCTTCGGGTCTTA
1 TGCACGAATACCTTCGGGTCTTAGCCCGGATATAACGT--CTAGCACAAATGCCTTCGGGTATTA
54412234 ACCCGGAT
64 ACCCGGAT
54412242 ATCATTCAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
78 2 0.03
79 2 0.03
80 59 0.94
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (80 bp):
TGCACGAATACCTTCGGGTCTTAGCCCGGATATAACGTCTAGCACAAATGCCTTCGGGTATTAAC
CCGGATTTAACAACT
Found at i:54420167 original size:40 final size:40
Alignment explanation
Indices: 54420122--54420290 Score: 193
Period size: 40 Copynumber: 4.2 Consensus size: 40
54420112 CGGAATACAA
54420122 CCGGATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTA-GCACGAATGCCTTCGGGTCTTAGC
* * * *
54420162 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
54420202 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
*
54420242 CCGGATA-AAGTCACTAGCAC-AATTGCCTTC-GGTGCTTAGAC
1 CCGGATATAA-CCACTAGCACGAA-TGCCTTCGGGT-CTTAG-C
54420283 CCGGATAT
1 CCGGATAT
54420291 CATTCAATGT
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
39 7 0.06
40 95 0.86
41 8 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:54420262 original size:80 final size:80
Alignment explanation
Indices: 54420122--54420290 Score: 227
Period size: 80 Copynumber: 2.1 Consensus size: 80
54420112 CGGAATACAA
* *
54420122 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
54420187 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAGC
* * *
54420202 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAA
*
54420265 TGCCTTC-GGTGCTTAGAC
64 TGCCTTCGGGT-ATTAG-C
54420283 CCGGATAT
1 CCGGATAT
54420291 CATTCAATGT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 5 0.06
80 64 0.82
81 8 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAGC
Found at i:54422936 original size:27 final size:24
Alignment explanation
Indices: 54422906--54422969 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 24
54422896 TCGTGGCGTA
54422906 GCCACTAATGTCAGAATGCGTGGCAAG
1 GCCACTAATGT-AGAAT--GTGGCAAG
*
54422933 GCCACTAGAACGGTAGAATGTGGCAAG
1 GCCACT--AA-TGTAGAATGTGGCAAG
54422960 GCCACTAATG
1 GCCACTAATG
54422970 CAGTACATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 1 0.03
25 2 0.06
27 20 0.62
29 7 0.22
30 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.30, T:0.17
Consensus pattern (24 bp):
GCCACTAATGTAGAATGTGGCAAG
Found at i:54430478 original size:49 final size:50
Alignment explanation
Indices: 54430296--54430493 Score: 227
Period size: 49 Copynumber: 3.9 Consensus size: 50
54430286 ATCTATTGTG
* * *
54430296 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TT
* * * * * **
54430347 CGATCACGTGTTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATG-TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* *
54430398 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * **
54430448 -GGTCTCATGTGTAGTACTATGTGCAGGCTACTATGCATACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
54430494 GCTTTGGCTA
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 40 0.33
50 35 0.28
51 16 0.13
52 32 0.26
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
Found at i:54430511 original size:102 final size:102
Alignment explanation
Indices: 54430304--54430511 Score: 251
Period size: 102 Copynumber: 2.0 Consensus size: 102
54430294 TGAGGTCGCA
*
54430304 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTTGTAGTACTAA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACATGTTGTAGTACTAA
** * * *
54430369 GTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
66 GTGCAGGCTACTACGCATACCAGATGCTTAGGTCAAG
* * * * *
54430406 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAA-TT-GGTCTCATG-TGTAGTACTAT
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACATGTTGTAGTACTAA
* *
54430468 GTGCAGGCTACTATGCATACCAGATAGCTTTGGCTACAAG
66 GTGCAGGCTACTACGCATACCAGAT-GCTTAGG-T-CAAG
54430508 TGTG
1 TGTG
54430512 AAAATATGTG
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
99 31 0.34
100 11 0.12
101 3 0.03
102 45 0.50
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACATGTTGTAGTACTAA
GTGCAGGCTACTACGCATACCAGATGCTTAGGTCAAG
Found at i:54442330 original size:69 final size:69
Alignment explanation
Indices: 54442244--54442380 Score: 247
Period size: 69 Copynumber: 2.0 Consensus size: 69
54442234 AAAGCTTTTC
* * *
54442244 TGACACTTTTCAGACCATTCAAATTTCACATCTTTCTGAAGCAATTTCGTCAACGAAGTAGCAAT
1 TGACACTTTTCAGACCATTCAAATTTCACATCTTTCTAAAGCAATTTCATCAACAAAGTAGCAAT
54442309 CATT
66 CATT
54442313 TGACACTTTTCAGACCATTCAAATTTCACATCTTTCTAAAGCAATTTCATCAACAAAGTAGCAAT
1 TGACACTTTTCAGACCATTCAAATTTCACATCTTTCTAAAGCAATTTCATCAACAAAGTAGCAAT
54442378 CAT
66 CAT
54442381 GGAAAAGCCT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.33
Consensus pattern (69 bp):
TGACACTTTTCAGACCATTCAAATTTCACATCTTTCTAAAGCAATTTCATCAACAAAGTAGCAAT
CATT
Found at i:54448353 original size:3 final size:3
Alignment explanation
Indices: 54448347--54448410 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
54448337 TGTATTGAAG
54448347 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54448395 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
54448411 TTTGTTTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54451765 original size:40 final size:40
Alignment explanation
Indices: 54451710--54451932 Score: 344
Period size: 40 Copynumber: 5.6 Consensus size: 40
54451700 GATGATAACG
*
54451710 GGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
54451750 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
54451790 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
54451830 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-TCC
* *
54451870 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-TAGTGACTAAT-TCC
*
54451910 GAGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
54451933 AGCGAGTAGC
Statistics
Matches: 175, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
39 2 0.01
40 171 0.98
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
Found at i:54451843 original size:80 final size:80
Alignment explanation
Indices: 54451710--54451965 Score: 360
Period size: 80 Copynumber: 3.2 Consensus size: 80
54451700 GATGATAACG
*
54451710 GGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
*
54451775 CTAGTGACTA-ATTCC
66 CGAGTGACTATA-TCC
*
54451790 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
*
54451855 CGAGTTACTATATCC
66 CGAGTGACTATATCC
* *
54451870 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCCGAGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTGTGC-TACTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTG
*
54451933 AGCGAGT-AGCTATATCC
64 TGCGAGTGA-CTATATCC
* *
54451950 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
54451966 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
79 17 0.10
80 143 0.88
81 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAGTGACTATATCC
Found at i:54451946 original size:40 final size:41
Alignment explanation
Indices: 54451710--54451965 Score: 309
Period size: 40 Copynumber: 6.4 Consensus size: 41
54451700 GATGATAACG
* *
54451710 GGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGACTAATTCC
*
54451750 GGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGACTAATTCC
*
54451790 GGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGACTAATTCC
*
54451830 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT-TACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGACTAAT-TCC
*
54451870 GGGCTAAGTCCCGAAGGCATTTGTGCGA--ACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-GACTAAT-TCC
* *
54451910 GAGCTAAGTCCCGAAGGCATTTGAGCGAGTAG-CT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGACTAAT-TCC
* *
54451950 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
54451966 TACTTGGTTT
Statistics
Matches: 202, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
39 15 0.07
40 185 0.92
41 1 0.00
42 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (41 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGACTAATTCC
Found at i:54454226 original size:93 final size:93
Alignment explanation
Indices: 54454114--54454284 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54454104 GCCCATAAGT
* *
54454114 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54454179 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
54454207 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54454272 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54454285 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54454281 original size:46 final size:46
Alignment explanation
Indices: 54454106--54454281 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
54454096 TGTAACCCGC
* * *
54454106 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54454152 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
54454202 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
54454245 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54454282 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54456683 original size:29 final size:29
Alignment explanation
Indices: 54456644--54456731 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
54456634 CAAAGATAAC
*
54456644 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
54456673 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
54456702 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
54456732 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:54456702 original size:15 final size:15
Alignment explanation
Indices: 54456644--54456722 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
54456634 CAAAGATAAC
*
54456644 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
54456658 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
54456673 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
54456687 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
54456702 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
54456717 AAGAAA
1 AAGAAA
54456723 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54456731 original size:15 final size:15
Alignment explanation
Indices: 54456655--54456731 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
54456645 AGAAAACCGA
54456655 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
54456670 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
54456684 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
54456698 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
54456714 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
54456729 ATA
1 ATA
54456732 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:54459796 original size:93 final size:93
Alignment explanation
Indices: 54459684--54459854 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54459674 GCCCATAAGT
* *
54459684 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54459749 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
54459777 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54459842 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54459855 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54459851 original size:46 final size:46
Alignment explanation
Indices: 54459676--54459851 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
54459666 TGTAACCCGC
* * *
54459676 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54459722 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
54459772 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
54459815 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54459852 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54464586 original size:29 final size:29
Alignment explanation
Indices: 54464524--54464626 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
54464514 GTGACGAGAT
* * *
54464524 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
54464553 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
54464582 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
54464611 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54464627 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:54471560 original size:29 final size:29
Alignment explanation
Indices: 54471498--54471600 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
54471488 GTGACGAGAT
* * *
54471498 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
54471527 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
54471556 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
54471585 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54471601 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:54477366 original size:40 final size:40
Alignment explanation
Indices: 54477311--54477480 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
54477301 AACATTGGAA
54477311 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
54477351 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
54477391 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
54477430 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
54477471 CTATATCCGG
1 ATATATCCGG
54477481 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:54479755 original size:3 final size:3
Alignment explanation
Indices: 54479749--54479800 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
54479739 TGTATTGAAG
54479749 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54479797 TAT T
1 TAT T
54479801 TTGTTTAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54483152 original size:40 final size:40
Alignment explanation
Indices: 54483097--54483359 Score: 390
Period size: 40 Copynumber: 6.6 Consensus size: 40
54483087 GATGATAACG
*
54483097 GGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
*
54483137 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
54483177 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* * *
54483217 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
54483257 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-TCC
*
54483297 GGGCTAAGTCCCGAAGGCATTTGTG-T-G-AACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA--AT-TCC
54483337 GGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
54483360 AGCGAGTAGC
Statistics
Matches: 210, Mismatches: 9, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
37 3 0.01
38 1 0.00
39 2 0.01
40 204 0.97
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
Found at i:54483204 original size:22 final size:22
Alignment explanation
Indices: 54483139--54483204 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
54483129 CTAATTCCGG
54483139 GCTAAGTCCCGAAGGCATTTGT
1 GCTAAGTCCCGAAGGCATTTGT
*** *
54483161 GCT-AGT---G-ACTAATTTCGG
1 GCTAAGTCCCGAAGGCATTT-GT
54483179 GCTAAGTCCCGAAGGCATTTGT
1 GCTAAGTCCCGAAGGCATTTGT
54483201 GCTA
1 GCTA
54483205 GTGACTAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 3 0.10
21 3 0.10
22 9 0.30
23 5 0.17
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (22 bp):
GCTAAGTCCCGAAGGCATTTGT
Found at i:54483373 original size:40 final size:40
Alignment explanation
Indices: 54483097--54483392 Score: 342
Period size: 40 Copynumber: 7.4 Consensus size: 40
54483087 GATGATAACG
* *
54483097 GGGCTAAGTCCCGAAGGAATTTGTGCTAGT-GACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CTAATTCC
* *
54483137 GGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTAATTTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CTAATTCC
*
54483177 GGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CTAATTCC
*
54483217 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTAATTCC
54483257 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTAAT-TCC
* *
54483297 GGGCTAAGTCCCGAAGGCATTTGTGTGAACTA-CT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCG-AGTAGCTAAT-TCC
*
54483337 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTAAT-TCC
* *
54483377 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
54483393 TACTTGGTTT
Statistics
Matches: 238, Mismatches: 13, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
39 19 0.08
40 217 0.91
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTAATTCC
Found at i:54489110 original size:28 final size:29
Alignment explanation
Indices: 54489010--54489111 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
54489000 TAATCAGCCG
** *
54489010 CGCACACTTAGTGCCATATACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAGCT
54489039 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
54489068 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
*
54489097 C-CACACTCAGTGCCA
1 CGCACACTTAGTGCCA
54489112 ATCTCTCAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
28 16 0.24
29 52 0.76
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAGCT
Found at i:54492487 original size:16 final size:18
Alignment explanation
Indices: 54492458--54492491 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
54492448 GAAGAATTAG
54492458 AAAAGAAAATTAAAAATT
1 AAAAGAAAATTAAAAATT
54492476 AAAA-AAAA-TAAAAATT
1 AAAAGAAAATTAAAAATT
54492492 TGAATTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAGAAAATTAAAAATT
Found at i:54494612 original size:24 final size:23
Alignment explanation
Indices: 54494560--54494621 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
54494550 GTAAGCTGAT
* *
54494560 GAACAGTAAGCTCTATCGAGCTG
1 GAACAGTAAGCTCTATCAAGATG
54494583 GAAACAGTAAGCTCTGA-CAAGATG
1 G-AACAGTAAGCTCT-ATCAAGATG
*
54494607 AGAACAATAAGCTCT
1 -GAACAGTAAGCTCT
54494622 TACGAGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 1 0.03
24 30 0.91
25 2 0.06
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (23 bp):
GAACAGTAAGCTCTATCAAGATG
Found at i:54504055 original size:50 final size:50
Alignment explanation
Indices: 54503989--54504087 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
54503979 TCCACAGTCG
*
54503989 TCTCGTACGACACGTGCGACATTAACAAATCAATACTGGATCCAAAATCA
1 TCTCGTACGACACGTGCAACATTAACAAATCAATACTGGATCCAAAATCA
* * * * * *
54504039 TCTCGTACGACCCGTGCAACCTTAATAGATCAATACTGTATCCACAATC
1 TCTCGTACGACACGTGCAACATTAACAAATCAATACTGGATCCAAAATC
54504088 GTCTTGTGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.24
Consensus pattern (50 bp):
TCTCGTACGACACGTGCAACATTAACAAATCAATACTGGATCCAAAATCA
Found at i:54504414 original size:27 final size:27
Alignment explanation
Indices: 54504349--54504449 Score: 118
Period size: 26 Copynumber: 3.9 Consensus size: 27
54504339 TCATTTTTCC
* *
54504349 CTACAGGGGT-TTTCAGTAATTTTACA
1 CTACAAGGGTATTTCAATAATTTTACA
54504375 C-ACAAGGGTATTTCAATAATTTTACA
1 CTACAAGGGTATTTCAATAATTTTACA
*** *
54504401 CTACAAGGGTATTTTGGTAATTATA-A
1 CTACAAGGGTATTTCAATAATTTTACA
*
54504427 CTACAATGGTATTTCAATAATTT
1 CTACAAGGGTATTTCAATAATTT
54504450 CACAAATCGG
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
25 7 0.11
26 36 0.58
27 19 0.31
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (27 bp):
CTACAAGGGTATTTCAATAATTTTACA
Found at i:54508610 original size:27 final size:27
Alignment explanation
Indices: 54508544--54508612 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
54508534 ATCAGCACAC
* *
54508544 AGCCACCGGTAAATATGATCGACATAG
1 AGCCACAGGTAAATATGATAGACATAG
* * *
54508571 AGTCATCA-ATAAATATGATAGACATAT
1 AGCCA-CAGGTAAATATGATAGACATAG
54508598 AGCCACAGGTAAATA
1 AGCCACAGGTAAATA
54508613 CGATTGGCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
26 2 0.06
27 30 0.91
28 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (27 bp):
AGCCACAGGTAAATATGATAGACATAG
Found at i:54509062 original size:27 final size:28
Alignment explanation
Indices: 54509032--54509129 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 28
54509022 TGCCCTACTG
*
54509032 GGGTATTTCGA-TAATTTTACATTACAA
1 GGGTATTTCGAGTAATTTTACACTACAA
*
54509059 GGGTA-TTCTAGTAATTTTACACTACAA
1 GGGTATTTCGAGTAATTTTACACTACAA
* * ** *
54509086 GGGTATTTTG-GTAAGTGCACACTACAT
1 GGGTATTTCGAGTAATTTTACACTACAA
*
54509113 GGGTATTT-TAGTAATTT
1 GGGTATTTCGAGTAATTT
54509130 CACAAATTGG
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.07
27 51 0.89
28 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (28 bp):
GGGTATTTCGAGTAATTTTACACTACAA
Found at i:54509133 original size:27 final size:27
Alignment explanation
Indices: 54509043--54509133 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 27
54509033 GGTATTTCGA
* * *
54509043 TAATTTTACATTACAAGGGTATTCTAG
1 TAATTTCACACTACAAGGGTATTTTAG
* *
54509070 TAATTTTACACTACAAGGGTATTTTGG
1 TAATTTCACACTACAAGGGTATTTTAG
* * *
54509097 TAAGTGCACACTACATGGGTATTTTAG
1 TAATTTCACACTACAAGGGTATTTTAG
54509124 TAATTTCACA
1 TAATTTCACA
54509134 AATTGGGGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (27 bp):
TAATTTCACACTACAAGGGTATTTTAG
Found at i:54528213 original size:21 final size:22
Alignment explanation
Indices: 54528180--54528227 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
54528170 TTTTCATTGA
**
54528180 AAACCCTTCTTAAAAT-AAAAG
1 AAACCCTAATTAAAATAAAAAG
**
54528201 AAACCCTAATTAACTTAAAAAG
1 AAACCCTAATTAAAATAAAAAG
54528223 AAACC
1 AAACC
54528228 TTTCAGTTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.21
Consensus pattern (22 bp):
AAACCCTAATTAAAATAAAAAG
Found at i:54529267 original size:28 final size:29
Alignment explanation
Indices: 54529235--54529349 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
54529225 TACCTGTATC
* *
54529235 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
54529263 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* *
54529292 TGGCCTATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
54529321 TGGCCCGTTAGGCCC-AATCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
54529349 T
1 T
54529350 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 28 0.37
29 47 0.62
30 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:54529289 original size:57 final size:57
Alignment explanation
Indices: 54529226--54529341 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
54529216 AATTTCACAT
* *
54529226 ACCTGTATCTGGCCCATTAAGCCC-AATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCC-AATC
* * * *
54529283 ACCTGTATATGGCCTATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCAATC
1 ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAATC
54529340 AC
1 AC
54529342 ATTCATATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 27 0.52
58 25 0.48
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (57 bp):
ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAATC
Found at i:54529573 original size:8 final size:8
Alignment explanation
Indices: 54529560--54529610 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
54529550 GTAGCCAAAC
54529560 TTTCGGCT
1 TTTCGGCT
54529568 TTTCGGCAT
1 TTTCGGC-T
*
54529577 TTT-AGCT
1 TTTCGGCT
54529584 TTTCGGCT
1 TTTCGGCT
54529592 TTTCGGCAT
1 TTTCGGC-T
54529601 TTT-GGCT
1 TTTCGGCT
54529608 TTT
1 TTT
54529611 GCCGATACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
7 8 0.21
8 22 0.58
9 8 0.21
ACGTcount: A:0.06, C:0.20, G:0.22, T:0.53
Consensus pattern (8 bp):
TTTCGGCT
Found at i:54529590 original size:24 final size:24
Alignment explanation
Indices: 54529560--54529610 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
54529550 GTAGCCAAAC
54529560 TTTCGGCTTTTCGGCATTTTAGCT
1 TTTCGGCTTTTCGGCATTTTAGCT
*
54529584 TTTCGGCTTTTCGGCATTTTGGCT
1 TTTCGGCTTTTCGGCATTTTAGCT
54529608 TTT
1 TTT
54529611 GCCGATACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.06, C:0.20, G:0.22, T:0.53
Consensus pattern (24 bp):
TTTCGGCTTTTCGGCATTTTAGCT
Found at i:54530712 original size:16 final size:16
Alignment explanation
Indices: 54530687--54530718 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54530677 AAGTTCGGGA
*
54530687 TTTCAGGATTTTTGGG
1 TTTCAAGATTTTTGGG
54530703 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
54530719 CCGTTACAAC
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:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTCAAGATTTTTGGG
Found at i:54533335 original size:30 final size:30
Alignment explanation
Indices: 54533279--54533337 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
54533269 TACGAGCCTT
**
54533279 GGGGCAAAAGTGCAAATATGTGAAAGTTTA
1 GGGGCAAAAGTGCAAATATGCCAAAGTTTA
* *
54533309 GGGGCAAAAGTGCAATTTTGCCAAAGTTT
1 GGGGCAAAAGTGCAAATATGCCAAAGTTT
54533338 GGGTTAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.29, T:0.25
Consensus pattern (30 bp):
GGGGCAAAAGTGCAAATATGCCAAAGTTTA
Found at i:54536230 original size:29 final size:28
Alignment explanation
Indices: 54536198--54536255 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
54536188 TACCTGTATC
*
54536198 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
* *
54536227 TGGCCCGTTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
54536255 T
1 T
54536256 TATGCTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:54537612 original size:16 final size:16
Alignment explanation
Indices: 54537591--54537622 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54537581 AAGTTCAGGA
54537591 TTTCGGGATTTTTGGG
1 TTTCGGGATTTTTGGG
54537607 TTTCGGGATTTTTGGG
1 TTTCGGGATTTTTGGG
54537623 GCATTACACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.38, T:0.50
Consensus pattern (16 bp):
TTTCGGGATTTTTGGG
Found at i:54538303 original size:7 final size:7
Alignment explanation
Indices: 54538293--54538324 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
54538283 TTATATACAT
54538293 AATACTA
1 AATACTA
54538300 AATACTA
1 AATACTA
54538307 AATACTA
1 AATACTA
*
54538314 AGTACTA
1 AATACTA
54538321 AATA
1 AATA
54538325 TGAAACGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:54544587 original size:805 final size:803
Alignment explanation
Indices: 54542994--54544600 Score: 3018
Period size: 805 Copynumber: 2.0 Consensus size: 803
54542984 CAAGGCACAG
54542994 AAGTACTACAATATGCTATTCAATTTCATACCAAATTCACATTCAAATCAACTAAATGGTCACAT
1 AAGTACTACAATATGCTATTCAATTTCATACCAAATTCACATTCAAATCAACTAAATGGTCACAT
*
54543059 TCAATTATGCACTATTTTACTTAAAGCCACAAGCATATCAACTTCAAATTTCAACCATTTGACAT
66 TCAATTATGCACTATTTTACTTAAAGCCACAAGCATATCAACTTCAAATTTCAACCATTTGAAAT
54543124 CCATAATTCCAACTCACAACAAACATATAAATGGCAATATTACACAACATATCAAAAGGCCTTTC
131 CCATAATTCCAACTCACAACAAACATATAAATGGCAATATTACACAACATATCAAAAGGCCTTTC
* *
54543189 TAACATATATACATATATCACCAAACATACCAAAATAAGCCAAAATCACATGGCTATACACATAA
196 TAACAGATATACATATATCACCAAACATACCAAAATAAGCCAAAATCACATAGCTATACACATAA
* *
54543254 CAAACCATTCATCATTTACAAACCAACTCAAATGGTTGAATCCATTACTAACATATACCAAAATG
261 CAAACCATTCATCATTTACAAACCAACTCAAATGGCTAAATCCATTACTAACATATACCAAAATG
54543319 ACCATAAATCCTATACATGCCATATAACCAAATACATAAGCTCAAAAGTACCAAAGTGGAAGCTC
326 ACCATAAATCCTATACATGCCATATAACCAAATACATAAGCTCAAAAGTACCAAAGTGGAAGCTC
** *
54543384 GATAGTGTGATGCAATCTCCGATGACTCCCAATCTGAGCTAGCTTCAATATTCACTATAAAACAC
391 GATAGTGCAATGCAATCTCCGACGACTCCCAATCTGAGCTAGCTTCAATATTCACTATAAAACAC
* *
54543449 GGAAAAGTAAACAAAGTAAGCTATAAAGCTTAGTAAGCTCATATACTAAGTAAGTAAAACTTACC
456 GAAAAAGTAAACAAAGTAAGCTATAAAGCTTAGTAAGATCATATACTAAGTAAGTAAAACTTACC
54543514 AACCAACAATTCAATAACATAAACATCATATAATGGAATTCAAATTTGAAGCATAACTTAACACA
521 AACCAACAATTCAATAACATAAACATCATATAATGGAATTCAAATTTGAAGCATAACTTAACACA
54543579 TATATTCAATTCAAGGATTAAACACAATTTCCATCAACTTCTTCGATTTGATGATTGTATAGTTC
586 TATATTCAATTCAAGGATTAAACACAATTTCCATCAACTTCTTCGATTTGATGATTGTATAGTTC
54543644 ACGTACATACCTGTACAAGCTCGTATCAATTTCATACTCATCCATATCCTTGATATACCCGTTGA
651 ACGTACATACCTGTACAAGCTCGTATCAATTTCATACTCATCCATATCCTTGATATACCCGTTGA
*
54543709 ACCATTTGAAATACTATTGGATACTCAGGAATCTCACACCCTAAGTGTCAATACATAGCCGAAGC
716 ACCATTTGAAATACTATTGGATACTCAGGAATCTCACACCCTAAGTGCCAATACATAGCCGAAGC
54543774 TATCTCAATCTCATATCACATAC
781 TATCTCAATCTCATATCACATAC
*
54543797 AAGTACTACAATATGCTATTCAATTTCATACCAAATTCACATTCTCAAATCACCTAAATGGTCAC
1 AAGTACTACAATATGCTATTCAATTTCATACCAAATTCACA-T-TCAAATCAACTAAATGGTCAC
54543862 ATTCAATTATGCACTATTTTACTTAAAGCCACAAGCATATCAACTTCAAATTTCAACCATTTGAA
64 ATTCAATTATGCACTATTTTACTTAAAGCCACAAGCATATCAACTTCAAATTTCAACCATTTGAA
*
54543927 ATCCATAATTCCAACTCACAACAAGCATATAAATGGCAATATTACACAACATATCAAAAGGCCTT
129 ATCCATAATTCCAACTCACAACAAACATATAAATGGCAATATTACACAACATATCAAAAGGCCTT
* *
54543992 TCTCACAGATATACATATATCACCAAACATACCAAAATAAGCCAAAATCACCTAGCTATACACAT
194 TCTAACAGATATACATATATCACCAAACATACCAAAATAAGCCAAAATCACATAGCTATACACAT
54544057 AACAAACCATTCATCATTTACAAACCAACTCAAATGGCTAAATCCATTACTAACATATACCAAAA
259 AACAAACCATTCATCATTTACAAACCAACTCAAATGGCTAAATCCATTACTAACATATACCAAAA
54544122 TGACCATAAATCCTATACATGCCATATAACCAAATACATAAGCTCAAAAGTACCAAAGTGGAAGC
324 TGACCATAAATCCTATACATGCCATATAACCAAATACATAAGCTCAAAAGTACCAAAGTGGAAGC
* *
54544187 TCGATAGTGCAATGCAATCTCCGACGACTCCTAATCTGAGCTAGCTTCGATATTCACTATAAAAC
389 TCGATAGTGCAATGCAATCTCCGACGACTCCCAATCTGAGCTAGCTTCAATATTCACTATAAAAC
*
54544252 ACGAAAAAGTAAACAAAGTAAGCTATAAAGCTTAGTAAGATCGTATACTAAGTAAGTAAAACTTA
454 ACGAAAAAGTAAACAAAGTAAGCTATAAAGCTTAGTAAGATCATATACTAAGTAAGTAAAACTTA
54544317 CCAACCAACAATTCAATAACATAAACATCATATAATGGAATTCAAATTTGAAGCATAACTTAACA
519 CCAACCAACAATTCAATAACATAAACATCATATAATGGAATTCAAATTTGAAGCATAACTTAACA
54544382 CATATATTC-ATTCCAAGGATTAAACACAATTTCCATCAACTTCTTCGATTTGATGATTGTATAG
584 CATATATTCAATT-CAAGGATTAAACACAATTTCCATCAACTTCTTCGATTTGATGATTGTATAG
54544446 TTCACGTACATACCTGTACAAGCTCGTATCAATTTCATACTCATCCATATCCTTGATATACCCGT
648 TTCACGTACATACCTGTACAAGCTCGTATCAATTTCATACTCATCCATATCCTTGATATACCCGT
54544511 TGAACCATTTGAAATACTATTGGATACTCAGGAATCTCACACCCTAAGTGCCAATACATAGCCGA
713 TGAACCATTTGAAATACTATTGGATACTCAGGAATCTCACACCCTAAGTGCCAATACATAGCCGA
54544576 AGCTATCTCAATCTCATATCACATA
778 AGCTATCTCAATCTCATATCACATA
54544601 TAATGCTCAC
Statistics
Matches: 783, Mismatches: 18, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
803 41 0.05
804 4 0.01
805 738 0.94
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (803 bp):
AAGTACTACAATATGCTATTCAATTTCATACCAAATTCACATTCAAATCAACTAAATGGTCACAT
TCAATTATGCACTATTTTACTTAAAGCCACAAGCATATCAACTTCAAATTTCAACCATTTGAAAT
CCATAATTCCAACTCACAACAAACATATAAATGGCAATATTACACAACATATCAAAAGGCCTTTC
TAACAGATATACATATATCACCAAACATACCAAAATAAGCCAAAATCACATAGCTATACACATAA
CAAACCATTCATCATTTACAAACCAACTCAAATGGCTAAATCCATTACTAACATATACCAAAATG
ACCATAAATCCTATACATGCCATATAACCAAATACATAAGCTCAAAAGTACCAAAGTGGAAGCTC
GATAGTGCAATGCAATCTCCGACGACTCCCAATCTGAGCTAGCTTCAATATTCACTATAAAACAC
GAAAAAGTAAACAAAGTAAGCTATAAAGCTTAGTAAGATCATATACTAAGTAAGTAAAACTTACC
AACCAACAATTCAATAACATAAACATCATATAATGGAATTCAAATTTGAAGCATAACTTAACACA
TATATTCAATTCAAGGATTAAACACAATTTCCATCAACTTCTTCGATTTGATGATTGTATAGTTC
ACGTACATACCTGTACAAGCTCGTATCAATTTCATACTCATCCATATCCTTGATATACCCGTTGA
ACCATTTGAAATACTATTGGATACTCAGGAATCTCACACCCTAAGTGCCAATACATAGCCGAAGC
TATCTCAATCTCATATCACATAC
Found at i:54546813 original size:42 final size:42
Alignment explanation
Indices: 54546754--54546877 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 42
54546744 TTAGGGTTAC
*
54546754 TGAGATTATGTGTAAGACCATATTTGGGATATGGCATTGATA
1 TGAGATTACGTGTAAGACCATATTTGGGATATGGCATTGATA
** * *
54546796 TGAGACTT-CGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGA-TTACGTGTAAGACCATATTTGGGATA-TGGCATTGATA
*
54546839 TGAGATTACATGTAAGACCATATTTGGGATATGGCATTG
1 TGAGATTACGTGTAAGACCATATTTGGGATATGGCATTG
54546878 GTATAATACT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 33 0.48
43 36 0.52
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATTTGGGATATGGCATTGATA
Found at i:54553316 original size:21 final size:20
Alignment explanation
Indices: 54553282--54553321 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
54553272 CCCTTGAAAT
*
54553282 AGGGCACACGCCCGTGTGGA
1 AGGGCACACACCCGTGTGGA
54553302 AGGGCAACACACCCGTGTGG
1 AGGGC-ACACACCCGTGTGG
54553322 CCATTATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.10
Consensus pattern (20 bp):
AGGGCACACACCCGTGTGGA
Found at i:54554969 original size:34 final size:34
Alignment explanation
Indices: 54554918--54555002 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
54554908 CAATGCTGAA
* *
54554918 CAGTCTGGGCCTAAGCCC-ATATCAGTAGCAATAT
1 CAGTGTGGGCCTTAGCCCTATA-CAGTAGCAATAT
* * * * *
54554952 CGGTGTGGGCCTTAGCCCTTTACAGTTGCAGTGT
1 CAGTGTGGGCCTTAGCCCTATACAGTAGCAATAT
54554986 CAGTGTGGGCCTTAGCC
1 CAGTGTGGGCCTTAGCC
54555003 TAATTCAGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 40 0.95
35 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.27
Consensus pattern (34 bp):
CAGTGTGGGCCTTAGCCCTATACAGTAGCAATAT
Found at i:54563913 original size:29 final size:29
Alignment explanation
Indices: 54563864--54563919 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
54563854 CCACACTTAC
* *
54563864 TATTACTGGCAGCTATGCTGCGTTATTAT
1 TATTACTGGCAGCTATACTGCGATATTAT
* *
54563893 TATTACTGGCAGTTCTACTGCGATATT
1 TATTACTGGCAGCTATACTGCGATATT
54563920 GGTGTGCTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (29 bp):
TATTACTGGCAGCTATACTGCGATATTAT
Found at i:54564063 original size:28 final size:28
Alignment explanation
Indices: 54563999--54564066 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
54563989 ATGCAGTTAT
* *
54563999 ACTGATACTGTATAAGGCTTAGGCCCAC
1 ACTGATACTGTTTAAGGCTAAGGCCCAC
* * *
54564027 ATTGCTACTGTTTAAGGGCTAAGGCCCAG
1 ACTGATACTGTTTAA-GGCTAAGGCCCAC
54564056 ACTG-TACTGTT
1 ACTGATACTGTT
54564067 ACTGAATAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (28 bp):
ACTGATACTGTTTAAGGCTAAGGCCCAC
Found at i:54566673 original size:28 final size:29
Alignment explanation
Indices: 54566606--54566706 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
54566596 ATCGTGAATC
*
54566606 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
54566635 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
54566663 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
54566693 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54566707 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:54569942 original size:29 final size:28
Alignment explanation
Indices: 54569851--54569957 Score: 92
Period size: 29 Copynumber: 3.8 Consensus size: 28
54569841 TACATACATG
* *
54569851 CATATAGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGGCCCAATTC-AATT
* * *
54569879 CAAATGGCCCATCT-GGCCCAGTTTATATT
1 CATATGGCCCA-CTAGGCCCAATTCA-ATT
*
54569908 CTTATGGCCCACTAGGCCCAATTCAACTT
1 CATATGGCCCACTAGGCCCAATTCAA-TT
* *
54569937 CATATGGCCCATTAGTCCCAA
1 CATATGGCCCACTAGGCCCAA
54569958 ATCATATTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 18 0.29
29 44 0.71
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (28 bp):
CATATGGCCCACTAGGCCCAATTCAATT
Found at i:54572575 original size:80 final size:80
Alignment explanation
Indices: 54572491--54572639 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
54572481 TATGGTAACC
* * * *
54572491 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
54572555 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
54572571 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
54572636 CCGG
66 CCGG
54572640 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:54572581 original size:40 final size:38
Alignment explanation
Indices: 54572532--54572639 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
54572522 ATCACGATTT
*
54572532 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
54572572 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
54572612 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
54572640 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:54580676 original size:80 final size:80
Alignment explanation
Indices: 54580592--54580740 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
54580582 TATGGTAACC
* * * *
54580592 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
54580656 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
54580672 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
54580737 CCGG
66 CCGG
54580741 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:54580682 original size:40 final size:38
Alignment explanation
Indices: 54580633--54580740 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
54580623 ATCACGATTT
*
54580633 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
54580673 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
54580713 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
54580741 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:54584975 original size:3 final size:3
Alignment explanation
Indices: 54584963--54584994 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
54584953 AAAATATCTT
54584963 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
54584995 CAAAATATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:54585503 original size:14 final size:14
Alignment explanation
Indices: 54585484--54585527 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
54585474 CATCAACAAC
54585484 TAACTACTAACTGT
1 TAACTACTAACTGT
54585498 TAACTACTCAA-TGT
1 TAACTACT-AACTGT
54585512 TAACTACTAACTGT
1 TAACTACTAACTGT
54585526 TA
1 TA
54585528 CAACCGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (14 bp):
TAACTACTAACTGT
Found at i:54588334 original size:40 final size:40
Alignment explanation
Indices: 54588276--54588652 Score: 546
Period size: 40 Copynumber: 9.4 Consensus size: 40
54588266 GGATGATAAT
* * * *
54588276 CGGGCTAAGTCCTGAAGGCATTTGCGCTAGTGACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATC
* * *
54588316 TGAGCTAAGTTCCGAAGGCATTTGTGCGAGTTACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATC
*
54588356 CGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
54588396 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
54588436 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
54588476 CGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
54588516 CGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
54588556 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* * *
54588596 CGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
54588636 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
54588653 TACTTGGCTT
Statistics
Matches: 312, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
39 16 0.05
40 296 0.95
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:54594783 original size:40 final size:40
Alignment explanation
Indices: 54594717--54594866 Score: 187
Period size: 40 Copynumber: 3.8 Consensus size: 40
54594707 GTTATAATAG
*
54594717 CTCGCACAAATG-CTTCGGGACTTAACCCGGATTTGGTAA
1 CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
*
54594756 CTCGCACAATTGCCTTCGGGAATTAACCCGGATTTGGTAA
1 CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
* * * *
54594796 CTCGCACAAATGCCTTCGAGAATTGACCCGGATTTAGTCA
1 CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
* * *
54594836 CTTAGCACAAGA-GCCTTCGGGACTTAGCCCG
1 C-TCGCACAA-ATGCCTTCGGGAATTAACCCG
54594867 AATACCATTC
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
39 11 0.11
40 62 0.65
41 22 0.23
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAA
Found at i:54602823 original size:40 final size:40
Alignment explanation
Indices: 54602779--54602928 Score: 160
Period size: 40 Copynumber: 3.8 Consensus size: 40
54602769 TATAATAGCC
* * *
54602779 CGCACAAATGCCTTCAGGACTTAACACGGATTTGGTAACT
1 CGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAACT
* * *
54602819 CGCACAATTACCTTTGGGAATTAACCCGGATTTGGTAACT
1 CGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAACT
* * * *
54602859 TGCACAAATGCCTTC-GGAATTGACCCGGATTTAGTCACTT
1 CGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAAC-T
* * *
54602899 AGCACAAA-GCCTTCGGGACTTAGCCCGGAT
1 CGCACAAATGCCTTCGGGAATTAACCCGGAT
54602929 ACCATTCGAA
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 26 0.29
40 65 0.71
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (40 bp):
CGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAACT
Found at i:54608025 original size:40 final size:40
Alignment explanation
Indices: 54607970--54608347 Score: 611
Period size: 40 Copynumber: 9.5 Consensus size: 40
54607960 TGGATGATAA
** * *
54607970 CCGGGCTAAGTCCCGAAGGCATTTGCACTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
54608010 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
54608050 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54608090 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54608130 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54608170 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54608210 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54608250 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
54608290 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
54608330 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
54608348 TACTTGGCTT
Statistics
Matches: 325, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
39 16 0.05
40 309 0.95
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54613289 original size:15 final size:14
Alignment explanation
Indices: 54613258--54613298 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
54613248 AACAACTAAT
*
54613258 TACTAACTATTAGC
1 TACTAACTATTAAC
*
54613272 TACTCAACTGTTAAC
1 TACT-AACTATTAAC
54613287 TACTAACTATTA
1 TACTAACTATTA
54613299 CAATTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (14 bp):
TACTAACTATTAAC
Found at i:54614147 original size:76 final size:76
Alignment explanation
Indices: 54614034--54614175 Score: 239
Period size: 76 Copynumber: 1.9 Consensus size: 76
54614024 TAATCAATCG
* *
54614034 GTTAACTGAATTTTTTTAGTCCGGGGTCAATTAATTATTTTTTGATTTTTCGGTTAACGGTTAAT
1 GTTAACCGAATTTTTTCAGTCCGGGGTCAATTAATTATTTTTTGATTTTTCGGTTAACGGTTAAT
54614099 TCGATCGATCA
66 TCGATCGATCA
* **
54614110 GTTAACCGAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAT
1 GTTAACCGAATTTTTTCAGTCCGGGGTCAATTAATTATTTTTTGATTTTTCGGTTAACGGTTAAT
54614175 T
66 T
54614176 TGGTTTGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.46
Consensus pattern (76 bp):
GTTAACCGAATTTTTTCAGTCCGGGGTCAATTAATTATTTTTTGATTTTTCGGTTAACGGTTAAT
TCGATCGATCA
Found at i:54614836 original size:12 final size:12
Alignment explanation
Indices: 54614801--54614839 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54614791 ACTGTCCAAC
*
54614801 AAAACATAAATA
1 AAAACAAAAATA
54614813 ATAAACAAAAATA
1 A-AAACAAAAATA
*
54614826 AAAATAAAAATA
1 AAAACAAAAATA
54614838 AA
1 AA
54614840 TGATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACAAAAATA
Found at i:54615227 original size:56 final size:57
Alignment explanation
Indices: 54615134--54615384 Score: 242
Period size: 56 Copynumber: 4.5 Consensus size: 57
54615124 TGTTTGCATG
* *
54615134 CTATCATAAATTGAATTAAAGTTGTTGTTTGAGTGTTTCAAATTGAGCATATTCATA
1 CTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTTCATA
* * * *
54615191 CTATCTTAAATTGAA-TCAAGCTGTTGTTTTAGTGTTTCAAATTGAGCATTTTCATG
1 CTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTTCATA
* * * ** * *
54615247 TTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTAACAAATTAAGCATTTTCATT
1 CTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTTCATA
* * ** * * * *
54615304 CTGTCTTAAATTTCATT-AAGTTGTTG-TTTAATGTTTCAAACTGAGTATTATT-ATG
1 CTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATT-TTCATA
* * *
54615359 CTGTCCTAAATTAAATTAAAG-TGTTG
1 CTATCATAAATTGAATTAAAGTTGTTG
54615385 CTTCATGTCT
Statistics
Matches: 160, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
55 38 0.24
56 61 0.38
57 61 0.38
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.44
Consensus pattern (57 bp):
CTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTTCATA
Found at i:54618188 original size:9 final size:9
Alignment explanation
Indices: 54618171--54618201 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54618161 GTAGTGATTC
54618171 AATTCGGTT
1 AATTCGGTT
*
54618180 AATTTGGTT
1 AATTCGGTT
54618189 AATTCGGTT
1 AATTCGGTT
54618198 AATT
1 AATT
54618202 TTTAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (9 bp):
AATTCGGTT
Found at i:54629270 original size:40 final size:40
Alignment explanation
Indices: 54629225--54629354 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
54629215 CGGAATACAA
54629225 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
54629265 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
54629305 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
54629345 CCGGATATAA
1 CCGGATATAA
54629355 TTTCCAGCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:54637317 original size:40 final size:40
Alignment explanation
Indices: 54637272--54637401 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
54637262 CGGAATACAA
54637272 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
54637312 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
54637352 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
54637392 CCGGATATAA
1 CCGGATATAA
54637402 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:54639814 original size:5 final size:5
Alignment explanation
Indices: 54639804--54639828 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54639794 GATACCAACC
54639804 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
54639829 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:54647666 original size:43 final size:42
Alignment explanation
Indices: 54647589--54647725 Score: 123
Period size: 43 Copynumber: 3.2 Consensus size: 42
54647579 GATTACAACC
* * *
54647589 AAGACCATCTCTGGGACATTGGCATTGTATTATGATTACGTGT
1 AAGACCATGTCTAGGACATTGGCATCGTA-TATGATTACGTGT
* * * *
54647632 ATGACCATGTGTTGGACATTGGCATCGTTATATGAATT-CGTAT
1 AAGACCATGTCTAGGACATTGGCATCG-TATATG-ATTACGTGT
* * * * *
54647675 AAGACCCTGTCTAGGACAGTGGCATCGATATGTGATAACATGT
1 AAGACCATGTCTAGGACATTGGCATCG-TATATGATTACGTGT
54647718 AAGACCAT
1 AAGACCAT
54647726 ATCTGGGATA
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
42 2 0.03
43 67 0.91
44 5 0.07
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (42 bp):
AAGACCATGTCTAGGACATTGGCATCGTATATGATTACGTGT
Found at i:54653280 original size:15 final size:15
Alignment explanation
Indices: 54653250--54653303 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
54653240 CTGAGACGGA
*
54653250 AAATCCCAGAATAAAG
1 AAATCCAAG-ATAAAG
54653266 AAATCCAAGATAAAG
1 AAATCCAAGATAAAG
* *
54653281 AAATCCATGATAAGG
1 AAATCCAAGATAAAG
54653296 AAATCCAA
1 AAATCCAA
54653304 ATTACAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 26 0.76
16 8 0.24
ACGTcount: A:0.56, C:0.17, G:0.13, T:0.15
Consensus pattern (15 bp):
AAATCCAAGATAAAG
Found at i:54670104 original size:40 final size:39
Alignment explanation
Indices: 54669939--54670122 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
54669929 AAATTGAATG
* * *
54669939 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
54669979 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
54670019 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
54670059 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
54670098 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
54670123 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:54670147 original size:80 final size:81
Alignment explanation
Indices: 54669979--54670167 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
54669969 GCTGGAAATT
* * * *
54669979 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
54670044 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
54670060 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
54670123 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
54670139 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
54670168 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:54672080 original size:40 final size:40
Alignment explanation
Indices: 54672035--54672238 Score: 322
Period size: 40 Copynumber: 5.1 Consensus size: 40
54672025 CGAGATTTAA
* * *
54672035 CCGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
54672075 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
54672115 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
54672155 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
54672195 CCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
54672235 CCGG
1 CCGG
54672239 TTATCATCCA
Statistics
Matches: 156, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
39 2 0.01
40 154 0.99
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54673500 original size:7 final size:7
Alignment explanation
Indices: 54673488--54673535 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
54673478 AACATGAGAG
54673488 CTTTTTT
1 CTTTTTT
54673495 CTTTTTT
1 CTTTTTT
54673502 CTTTTTT
1 CTTTTTT
*
54673509 -TTCTTT
1 CTTTTTT
*
54673515 -TTCTTT
1 CTTTTTT
*
54673521 CTCTTTT
1 CTTTTTT
54673528 CTTTTTT
1 CTTTTTT
54673535 C
1 C
54673536 ATCATCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
6 11 0.31
7 25 0.69
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:54676080 original size:19 final size:20
Alignment explanation
Indices: 54676056--54676099 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
54676046 AATGTTTCAA
*
54676056 TGAAT-AAAAGAGTTAATTT
1 TGAATAAAAAAAGTTAATTT
*
54676075 TGAATAAAAAAATTTAATTT
1 TGAATAAAAAAAGTTAATTT
54676095 TGAAT
1 TGAAT
54676100 GTATATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
TGAATAAAAAAAGTTAATTT
Found at i:54676518 original size:43 final size:43
Alignment explanation
Indices: 54676374--54676530 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 43
54676364 GGTTACCGAG
* *
54676374 ATGTGATTACATGTAAGACCATGTCTGGAACATTGGCAT-TATC
1 ATGTGATTACATGTAAGACCATGTCTGG-ACATTGGCATCGATA
* ** * *
54676417 TTGTGATTATGTGTAAGACCATGTTTGGGACATTGGCATCGTTA
1 ATGTGATTACATGTAAGACCATGTCT-GGACATTGGCATCGATA
* * * * * *
54676461 AT-CGATTTCGTGTAAGACCCTGTCTAGGACAGTGACATCGAT-
1 ATGTGATTACATGTAAGACCATGTCT-GGACATTGGCATCGATA
*
54676503 ATGTGATTACATGTAAGACCATATCTGG
1 ATGTGATTACATGTAAGACCATGTCTGG
54676531 GATATGACAT
Statistics
Matches: 89, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
42 4 0.04
43 81 0.91
44 4 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGACATTGGCATCGATA
Found at i:54684084 original size:10 final size:10
Alignment explanation
Indices: 54684069--54684149 Score: 67
Period size: 10 Copynumber: 7.9 Consensus size: 10
54684059 AATTTTAGCT
54684069 TTTATCTTTA
1 TTTATCTTTA
*
54684079 TTTATC-CTA
1 TTTATCTTTA
54684088 GCTTTTATCTTTA
1 ---TTTATCTTTA
*
54684101 TTTATCCTTA
1 TTTATCTTTA
*
54684111 TTTATCGTTA
1 TTTATCTTTA
*
54684121 ATTATCTTTA
1 TTTATCTTTA
*
54684131 TATAT-TTGTA
1 TTTATCTT-TA
54684141 TTTATCTTT
1 TTTATCTTT
54684150 TAGAATTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
9 4 0.07
10 42 0.75
11 2 0.04
12 6 0.11
13 2 0.04
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.63
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:54684092 original size:22 final size:22
Alignment explanation
Indices: 54684064--54684108 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
54684054 GATTTAATTT
54684064 TAGCTTTTATCTTTATTTATCC
1 TAGCTTTTATCTTTATTTATCC
54684086 TAGCTTTTATCTTTATTTATCC
1 TAGCTTTTATCTTTATTTATCC
54684108 T
1 T
54684109 TATTTATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.60
Consensus pattern (22 bp):
TAGCTTTTATCTTTATTTATCC
Found at i:54692435 original size:2 final size:2
Alignment explanation
Indices: 54692428--54692461 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54692418 AATTTGACAA
54692428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54692462 CTAAAAGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54693433 original size:21 final size:21
Alignment explanation
Indices: 54693409--54693449 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
54693399 CATATAAGAG
54693409 TATAATTAAATATTAAAAATA
1 TATAATTAAATATTAAAAATA
54693430 TATAATTAAATATTAAAAAT
1 TATAATTAAATATTAAAAAT
54693450 TAATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAATTAAATATTAAAAATA
Found at i:54693450 original size:14 final size:15
Alignment explanation
Indices: 54693413--54693474 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
54693403 TAAGAGTATA
54693413 ATTAAAT-ATTAAA-
1 ATTAAATAATTAAAT
* *
54693426 AATATATAATTAAAT
1 ATTAAATAATTAAAT
*
54693441 ATTAAA-AATTAATT
1 ATTAAATAATTAAAT
*
54693455 ATATAAATAA-TAACT
1 AT-TAAATAATTAAAT
54693470 ATTAA
1 ATTAA
54693475 TAAAATATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
13 5 0.13
14 18 0.46
15 14 0.36
16 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATAATTAAAT
Found at i:54694109 original size:3 final size:3
Alignment explanation
Indices: 54694101--54694151 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
54694091 CCCAATTTGG
54694101 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
54694149 CTT
1 CTT
54694152 GCCTTCTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:54694588 original size:18 final size:19
Alignment explanation
Indices: 54694565--54694604 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
54694555 TTCTTTCTAA
54694565 TCTCTTAACTCTCTCAA-T
1 TCTCTTAACTCTCTCAAGT
* *
54694583 TCTCTTAATTTTCTCAAGT
1 TCTCTTAACTCTCTCAAGT
54694602 TCT
1 TCT
54694605 TGTTCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.50
Consensus pattern (19 bp):
TCTCTTAACTCTCTCAAGT
Found at i:54701601 original size:31 final size:32
Alignment explanation
Indices: 54701541--54701614 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
54701531 AATAGTTTAA
* *
54701541 TATTTTATTTTATTTAATACTTATCTTAATAC
1 TATTTTATTTAATTTAATACTTAACTTAATAC
54701573 TATTTTA-TTAATTTAATA-TTAACTTTAAT-C
1 TATTTTATTTAATTTAATACTTAAC-TTAATAC
54701603 TAATATTTATTT
1 T-AT-TTTATTT
54701615 TGTTAACTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
30 6 0.17
31 17 0.47
32 11 0.31
33 2 0.06
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTTTATTTAATTTAATACTTAACTTAATAC
Found at i:54701607 original size:48 final size:47
Alignment explanation
Indices: 54701520--54701643 Score: 122
Period size: 48 Copynumber: 2.6 Consensus size: 47
54701510 ATTCCACAAA
* * * * * *
54701520 AATATTATTTTAATAGTTTAATATTTTATTTTATTTAATACTTATCTT
1 AATACTATTTTATTAATTTAATA-TTAATTTAATCTAATACTTATCTT
* *
54701568 AATACTATTTTATTAATTTAATATTAACTTTAATCTAATATTTATTTT
1 AATACTATTTTATTAATTTAATATTAA-TTTAATCTAATACTTATCTT
** *
54701616 GTTAACTATTATATTAATTTAATATTAA
1 AAT-ACTATTTTATTAATTTAATATTAA
54701644 AGTGATTATG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
47 3 0.05
48 37 0.59
49 23 0.37
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (47 bp):
AATACTATTTTATTAATTTAATATTAATTTAATCTAATACTTATCTT
Done.