Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 161 of 163
Found at i:54308890 original size:11 final size:11
Alignment explanation
Indices: 54308876--54308924 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
54308866 GAGAAATTTA
*
54308876 AGAGCAAATTG
1 AGAGGAAATTG
*
54308887 AGAGTAAATTG
1 AGAGGAAATTG
54308898 AGAGGAAATTG
1 AGAGGAAATTG
54308909 AGAGGAAATTTG
1 AGAGGAAA-TTG
54308921 AGAG
1 AGAG
54308925 ATGATTAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
11 28 0.80
12 7 0.20
ACGTcount: A:0.45, C:0.02, G:0.33, T:0.20
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:54308901 original size:22 final size:23
Alignment explanation
Indices: 54308868--54308924 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
54308858 AGATTTCAGA
*
54308868 GAAATTTAAGAGCAAATTGAGAG
1 GAAATTTGAGAGCAAATTGAGAG
* *
54308891 TAAA-TTGAGAGGAAATTGAGAG
1 GAAATTTGAGAGCAAATTGAGAG
54308913 GAAATTTGAGAG
1 GAAATTTGAGAG
54308925 ATGATTAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.23
Consensus pattern (23 bp):
GAAATTTGAGAGCAAATTGAGAG
Found at i:54309301 original size:24 final size:24
Alignment explanation
Indices: 54309274--54309323 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
54309264 CGATTAACCG
54309274 ATTTTTAA-TATTTTATTTTAA-TAA
1 ATTTTTAATTA-TTTA-TTTAATTAA
54309298 ATTTTTAATTATTTATTTAATTAA
1 ATTTTTAATTATTTATTTAATTAA
54309322 AT
1 AT
54309324 CGATAGACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 17 0.71
25 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTTAATTATTTATTTAATTAA
Found at i:54313954 original size:43 final size:42
Alignment explanation
Indices: 54313870--54314031 Score: 137
Period size: 43 Copynumber: 3.8 Consensus size: 42
54313860 TACCGTAACA
* * * * * ***
54313870 ATGCCATATCCCAGATATGGTCTTACATGTAATCTTGTATCG
1 ATGCAATAGCCCAGACATGGTCTTACACGAAATCACATATCG
*
54313912 ATGCTAATAGCCCAGCCATGGTCTTACACGAAATCACATATCG
1 ATGC-AATAGCCCAGACATGGTCTTACACGAAATCACATATCG
* * * *
54313955 ATGCCAAT-GTCCTAGACATAGTCTTACACGAAGTCTCATATCG
1 ATG-CAATAG-CCCAGACATGGTCTTACACGAAATCACATATCG
* * * *
54313998 ATGCCATATCCCAGATATGGTCTTACACGTAATC
1 ATGCAATAGCCCAGACATGGTCTTACACGAAATC
54314032 TCGGTAACGC
Statistics
Matches: 95, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 28 0.29
43 66 0.69
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGCAATAGCCCAGACATGGTCTTACACGAAATCACATATCG
Found at i:54319104 original size:18 final size:18
Alignment explanation
Indices: 54319072--54319118 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
54319062 CGAAATTAAG
54319072 TTAT-ATAATTT-TATTAT
1 TTATAATAATTTATATT-T
54319089 TT-TAATAATTTATATTT
1 TTATAATAATTTATATTT
*
54319106 TTATAATATTTTA
1 TTATAATAATTTA
54319119 AATGGTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 12 0.46
18 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATAATAATTTATATTT
Found at i:54320194 original size:12 final size:11
Alignment explanation
Indices: 54320172--54320201 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
54320162 TTAACCACCC
54320172 TAATTATATTA
1 TAATTATATTA
54320183 TAATTCATATTA
1 TAATT-ATATTA
54320195 TAATTAT
1 TAATTAT
54320202 GTTGTATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTATATTA
Found at i:54325926 original size:62 final size:63
Alignment explanation
Indices: 54325829--54325955 Score: 229
Period size: 62 Copynumber: 2.0 Consensus size: 63
54325819 GACCTTTTTT
*
54325829 AAAAACCAGAATATACGAAAAAAGAAAAAAAAAAAAAAGGGGGGGGGGGTTCCCCTTGC-CAC
1 AAAAACCAGAATATACGAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGTTCCCCTTGCACAC
*
54325891 AAAAACCAGAATATACGAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGTTTCCCCTTGCACAC
1 AAAAACCAGAATATACGAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGTTCCCCTTGCACAC
54325954 AA
1 AA
54325956 CAATGCTCGT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 57 0.92
63 5 0.08
ACGTcount: A:0.52, C:0.16, G:0.22, T:0.10
Consensus pattern (63 bp):
AAAAACCAGAATATACGAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGTTCCCCTTGCACAC
Found at i:54329553 original size:21 final size:20
Alignment explanation
Indices: 54329515--54329553 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54329505 CCTAAAAAAA
*
54329515 TATTTTTTTTTTAGTTTTTT
1 TATTTTTTTTTTAATTTTTT
54329535 TATTTTTTTTTCTAATTTT
1 TATTTTTTTTT-TAATTTT
54329554 GTTTTATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (20 bp):
TATTTTTTTTTTAATTTTTT
Found at i:54330705 original size:236 final size:231
Alignment explanation
Indices: 54330290--54330955 Score: 765
Period size: 236 Copynumber: 2.8 Consensus size: 231
54330280 TGCAAGATGT
* * * * *
54330290 GCTTTATGCTTGAGATTCGGATACATAATCGTCATGGATAGTTAGGATTCTATCTACCTGCACTT
1 GCTTTATGCTCGAGATTAGGATACATAGTCATCATGGATA-TTA-GA-TC---CTACCTGCATTT
* * * *
54330355 TCTTGATTAGCAG-AGTAATTTCGGTTTAATGGCATACTTAGATTCTTTACTGTTGCTGTGTTTT
60 TCTTGATTAGCAGAAGTAATTTCGGTTTAATGGCATGCTCAGATTCTTTACTGTTACTCTGTTTT
* *
54330419 CTTTCTCTTTTGGCTTCATACTGCTCTAGGAGAAATAATTGATTTTCATGATCCATGACTTAGTT
125 CTTTCTCTTTTGGCTTCATACT--TCTAGGAGAAATAACTGGTTTTCATGATCCATGACTTAGTT
54330484 TCCTTTGTAGCATGTCGGGAATGCACGAAATAATTGTAACATGC
188 TCCTTTGTAGCATGTCGGGAATGCACGAAATAATTGTAACATGC
*
54330528 GCTTTATGCTCGAGATTAGGATACATAGTCATCATGGATGATTAAGATCCTATCTGCATTTTCTT
1 GCTTTATGCTCGAGATTAGGATACATAGTCATCATGGAT-ATT-AGATCCTACCTGCATTTTCTT
* *
54330593 GATTAGCAGATAGTAATTTCGGTTTAATGGCATGCTCGGATTCTTTACTGTTACTCTGTTTCCTT
64 GATTAGCAGA-AGTAATTTCGGTTTAATGGCATGCTCAGATTCTTTACTGTTACTCTGTTTTCTT
* * * *
54330658 TCTCTTTTGGCTTCATACCTATCTGGGAGGAATAACTGGTTTTCATGATCCATGACTTGGTTTTC
128 TCTCTTTTGGCTTCATA-CT-TCTAGGAGAAATAACTGGTTTTCATGATCCATGACTTAGTTTCC
* * * * * * *
54330723 TTTATATCATGTTGGGGATGCATGAAATAATTTTAACATGT
191 TTTGTAGCATGTCGGGAATGCACGAAATAATTGTAACATGC
* *** * ** *
54330764 GCTTTATGCTCGAGATTTGGAGGGAT-G--ATTA-GGATCCT-G-T-CTACCTGCATTTTCATGA
1 GCTTTATGCTCGAGATTAGGATACATAGTCATCATGGATATTAGATCCTACCTGCATTTTCTTGA
* *
54330822 TTATCAGAGAGTAATTTC-GTTTAATGGCATGCTCAGATTCTTTACTGTTACTCCGTTTTCTTTC
66 TTAGCAGA-AGTAATTTCGGTTTAATGGCATGCTCAGATTCTTTACTGTTACTCTGTTTTCTTTC
* * * *
54330886 TCTTTTGGCTCCATAAGGTTCTAGGAGAAATGACTGGTTTTCATGATCCATGTCTTAGTTTCCTT
130 TCTTTTGGCTTCAT-A-CTTCTAGGAGAAATAACTGGTTTTCATGATCCATGACTTAGTTTCCTT
54330951 ATGTA
193 -TGTA
54330956 TCGTGATGGG
Statistics
Matches: 371, Mismatches: 50, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
226 96 0.26
227 37 0.10
228 1 0.00
229 1 0.00
231 1 0.00
232 4 0.01
233 3 0.01
234 23 0.06
235 1 0.00
236 159 0.43
237 4 0.01
238 39 0.11
239 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (231 bp):
GCTTTATGCTCGAGATTAGGATACATAGTCATCATGGATATTAGATCCTACCTGCATTTTCTTGA
TTAGCAGAAGTAATTTCGGTTTAATGGCATGCTCAGATTCTTTACTGTTACTCTGTTTTCTTTCT
CTTTTGGCTTCATACTTCTAGGAGAAATAACTGGTTTTCATGATCCATGACTTAGTTTCCTTTGT
AGCATGTCGGGAATGCACGAAATAATTGTAACATGC
Found at i:54347547 original size:20 final size:20
Alignment explanation
Indices: 54347522--54347560 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54347512 GCATTGATGC
54347522 CTTGGGGCAAGTATCGATAT
1 CTTGGGGCAAGTATCGATAT
*
54347542 CTTGGGGCAAGTATTGATA
1 CTTGGGGCAAGTATCGATA
54347561 CTATAGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.31
Consensus pattern (20 bp):
CTTGGGGCAAGTATCGATAT
Found at i:54351863 original size:214 final size:215
Alignment explanation
Indices: 54351580--54352009 Score: 844
Period size: 214 Copynumber: 2.0 Consensus size: 215
54351570 TAGTTTGCTA
54351580 TTACCACATACTACTCATAAAAAAATTCAATAAATGGACTTAACGTGTTTTTTTTTTTTGTTTGT
1 TTACCACATAC-ACTCATAAAAAAATTCAATAAATGGACTTAACGTGTTTTTTTTTTTTGTTTGT
54351645 GAATACTAAAATTTTAAATTTTGAAAAATATAAGAATTAAGAATGATCAAATTGAAAAACGTGGA
65 GAATACTAAAATTTTAAATTTTGAAAAATATAAGAATTAAGAATGATCAAATTGAAAAACGTGGA
54351710 TTAAATCTAGAACGTTACGTGTAGTAGAAGACTAAGAATAGAATTTAACCAAATGTATTTAACTG
130 TTAAATCTAGAACGTTACGTGTAGTAGAAGACTAAGAATAGAATTTAACCAAATGTATTTAACTG
54351775 CTACTATTTGGATTAGAACTG
195 CTACTATTTGGATTAGAACTG
54351796 TTACCACATA-ACTCATAAAAAAATTCAATAAATGGACTTAACGTGTTTTTTTTTTTTGTTTGTG
1 TTACCACATACACTCATAAAAAAATTCAATAAATGGACTTAACGTGTTTTTTTTTTTTGTTTGTG
54351860 AATACTAAAATTTTAAATTTTGAAAAATATAAGAATTAAGAATGATCAAATTGAAAAACGTGGAT
66 AATACTAAAATTTTAAATTTTGAAAAATATAAGAATTAAGAATGATCAAATTGAAAAACGTGGAT
54351925 TAAATCTAGAACGTTACGTGTAGTAGAAGACTAAGAATAGAATTTAACCAAATGTATTTAACTGC
131 TAAATCTAGAACGTTACGTGTAGTAGAAGACTAAGAATAGAATTTAACCAAATGTATTTAACTGC
54351990 TACTATTTGGATTAGAACTG
196 TACTATTTGGATTAGAACTG
54352010 AAATTGACCA
Statistics
Matches: 214, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
214 204 0.95
216 10 0.05
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (215 bp):
TTACCACATACACTCATAAAAAAATTCAATAAATGGACTTAACGTGTTTTTTTTTTTTGTTTGTG
AATACTAAAATTTTAAATTTTGAAAAATATAAGAATTAAGAATGATCAAATTGAAAAACGTGGAT
TAAATCTAGAACGTTACGTGTAGTAGAAGACTAAGAATAGAATTTAACCAAATGTATTTAACTGC
TACTATTTGGATTAGAACTG
Found at i:54353550 original size:329 final size:329
Alignment explanation
Indices: 54352952--54353609 Score: 1300
Period size: 329 Copynumber: 2.0 Consensus size: 329
54352942 TCTTTTTGTT
54352952 TATTATTTTTGTTTCCGTTGGTGAAAATTTTGGATTCGAATCGTGATACGCATTAAGGGAGGGCT
1 TATTATTTTTGTTTCCGTTGGTGAAAATTTTGGATTCGAATCGTGATACGCATTAAGGGAGGGCT
54353017 AGTAGACGCTAAGGCTTCCCTAAAATGAAAAAATAGCGTTTTTTCCTTTTAGATTTTATAAAATT
66 AGTAGACGCTAAGGCTTCCCTAAAATGAAAAAATAGCGTTTTTTCCTTTTAGATTTTATAAAATT
54353082 ATAAGTTAATGAATAATTAAATTACATATTTTAATTTAATTTTTTAAAATTTATAAATATTAACA
131 ATAAGTTAATGAATAATTAAATTACATATTTTAATTTAATTTTTTAAAATTTATAAATATTAACA
54353147 TAATAATAAAATTATATAATTTAATTATTGTCTTTCCAACTTTACCTATCGGGGTGCTGATATTG
196 TAATAATAAAATTATATAATTTAATTATTGTCTTTCCAACTTTACCTATCGGGGTGCTGATATTG
54353212 TTTTTCGTGTATTTCGTTTTCAGGAAAATGAGTGCGGGATGCAATTATCTATTTCAATCCCACAT
261 TTTTTCGTGTATTTCGTTTTCAGGAAAATGAGTGCGGGATGCAATTATCTATTTCAATCCCACAT
54353277 CGGA
326 CGGA
54353281 TATTATTTTTGTTTCCGTTGGTGAAAATTTTGGATTCGAATCGTGATACGCATTAAGGGAGGGCT
1 TATTATTTTTGTTTCCGTTGGTGAAAATTTTGGATTCGAATCGTGATACGCATTAAGGGAGGGCT
54353346 AGTAGACGCTAAGGCTTCCCTAAAATGAAAAAATAGCGTTTTTTCCTTTTAGATTTTATAAAATT
66 AGTAGACGCTAAGGCTTCCCTAAAATGAAAAAATAGCGTTTTTTCCTTTTAGATTTTATAAAATT
54353411 ATAAGTTAATGAATAATTAAATTACATATTTTAATTTAATTTTTTAAAAATTTAT-AATATTAAC
131 ATAAGTTAATGAATAATTAAATTACATATTTTAATTTAATTTTTT-AAAATTTATAAATATTAAC
54353475 ATAATAATAAAATTATATAATTTAATTATTGTCTTTCCAACTTTACCTATCGGGGTGCTGATATT
195 ATAATAATAAAATTATATAATTTAATTATTGTCTTTCCAACTTTACCTATCGGGGTGCTGATATT
54353540 GTTTTTCGTGTATTTCGTTTTCAGGAAAATGAGTGCGGGATGCAATTATCTATTTCAATCCCACA
260 GTTTTTCGTGTATTTCGTTTTCAGGAAAATGAGTGCGGGATGCAATTATCTATTTCAATCCCACA
54353605 TCGGA
325 TCGGA
54353610 AGAGTGGAAA
Statistics
Matches: 328, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
329 319 0.97
330 9 0.03
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.41
Consensus pattern (329 bp):
TATTATTTTTGTTTCCGTTGGTGAAAATTTTGGATTCGAATCGTGATACGCATTAAGGGAGGGCT
AGTAGACGCTAAGGCTTCCCTAAAATGAAAAAATAGCGTTTTTTCCTTTTAGATTTTATAAAATT
ATAAGTTAATGAATAATTAAATTACATATTTTAATTTAATTTTTTAAAATTTATAAATATTAACA
TAATAATAAAATTATATAATTTAATTATTGTCTTTCCAACTTTACCTATCGGGGTGCTGATATTG
TTTTTCGTGTATTTCGTTTTCAGGAAAATGAGTGCGGGATGCAATTATCTATTTCAATCCCACAT
CGGA
Found at i:54354440 original size:28 final size:29
Alignment explanation
Indices: 54354408--54354462 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
54354398 TTTATAAGTA
* *
54354408 ATTTTATTTTTATAAT-ATAAAAATAAAT
1 ATTTTATATTTAAAATAATAAAAATAAAT
*
54354436 ATTTTATATTTAAAATAATGAAAATAA
1 ATTTTATATTTAAAATAATAAAAATAA
54354463 CTTAAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTTTATATTTAAAATAATAAAAATAAAT
Found at i:54354640 original size:20 final size:20
Alignment explanation
Indices: 54354604--54354641 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54354594 TCAAAAGTCA
*
54354604 TAAAATAAAATTTATTTTAT
1 TAAAATAAAATTAATTTTAT
54354624 TAAAAT-AAATCTAATTTT
1 TAAAATAAAAT-TAATTTT
54354642 TTTTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATAAAATTAATTTTAT
Found at i:54357509 original size:26 final size:27
Alignment explanation
Indices: 54357466--54357523 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
54357456 AGATTCAACA
54357466 AAGAAAAATGGGGAAAACAAACTTGGC
1 AAGAAAAATGGGGAAAACAAACTTGGC
*
54357493 AAGAAAAATGGGG-AAACAAACTTTGC
1 AAGAAAAATGGGGAAAACAAACTTGGC
54357519 AAGAA
1 AAGAA
54357524 CCTGTTAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 17 0.57
27 13 0.43
ACGTcount: A:0.53, C:0.10, G:0.24, T:0.12
Consensus pattern (27 bp):
AAGAAAAATGGGGAAAACAAACTTGGC
Found at i:54362189 original size:82 final size:83
Alignment explanation
Indices: 54362051--54362218 Score: 329
Period size: 82 Copynumber: 2.0 Consensus size: 83
54362041 TTTTTATTTT
54362051 TGAATTTTTTAAAATTATTTTGATTTTTTTTTTGTAATTTTTGTTGAGAGAGAGACTAATTTGCT
1 TGAATTTTTTAAAATTATTTTGATTTTTTTTTTGTAATTTTTGTTGAGAGAGAGACTAATTTGCT
54362116 TGTTTTCAAAGTTGGCAA
66 TGTTTTCAAAGTTGGCAA
54362134 TGAATTTTTT-AAATTATTTTGATTTTTTTTTTGTAATTTTTGTTGAGAGAGAGACTAATTTGCT
1 TGAATTTTTTAAAATTATTTTGATTTTTTTTTTGTAATTTTTGTTGAGAGAGAGACTAATTTGCT
54362198 TGTTTTCAAAGTTGGCAA
66 TGTTTTCAAAGTTGGCAA
54362216 TGA
1 TGA
54362219 CCAAAAAGGT
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 75 0.88
83 10 0.12
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (83 bp):
TGAATTTTTTAAAATTATTTTGATTTTTTTTTTGTAATTTTTGTTGAGAGAGAGACTAATTTGCT
TGTTTTCAAAGTTGGCAA
Found at i:54365292 original size:12 final size:12
Alignment explanation
Indices: 54365275--54365300 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54365265 TTTAACGGGC
54365275 TTAAATGAAAAA
1 TTAAATGAAAAA
54365287 TTAAATGAAAAA
1 TTAAATGAAAAA
54365299 TT
1 TT
54365301 TTAGGAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
TTAAATGAAAAA
Found at i:54368526 original size:113 final size:113
Alignment explanation
Indices: 54368323--54368530 Score: 330
Period size: 113 Copynumber: 1.8 Consensus size: 113
54368313 AGTTGCCTTA
* * *
54368323 AGGGTTTGGTTTACAGAATTGAGAGTACCTTGACCGTACATGAGCACACACCACCCACCAAGGGG
1 AGGGCTTGGTTTACAAAATTGAGAGTACCTCGACCGTACATGAGCACACACCACCCACCAAGGGG
*
54368388 ACATGAGCATCTCGCCCCTGGTGGGGTTCTCGCCCACATCCCTTTGTG
66 ACATGAGCATCTCGCCCCTAGTGGGGTTCTCGCCCACATCCCTTTGTG
*
54368436 AGGGCTTGGTTTACAAAATTGAGAGTACCTCGACCGTACATTG-GCACACAACCACCCATCAAGG
1 AGGGCTTGGTTTACAAAATTGAGAGTACCTCGACCGTACA-TGAGCACAC-ACCACCCACCAAGG
*
54368500 GGACATGAGCGTCTCG-CCCTAGTGGGGTTCT
64 GGACATGAGCATCTCGCCCCTAGTGGGGTTCT
54368531 AGCTCACGTC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
113 57 0.66
114 30 0.34
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.23
Consensus pattern (113 bp):
AGGGCTTGGTTTACAAAATTGAGAGTACCTCGACCGTACATGAGCACACACCACCCACCAAGGGG
ACATGAGCATCTCGCCCCTAGTGGGGTTCTCGCCCACATCCCTTTGTG
Found at i:54369191 original size:54 final size:53
Alignment explanation
Indices: 54369132--54369238 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 53
54369122 CCGTCCATAT
*
54369132 TATAAAAGTATAAAACAGGCCTAACATAAGTCTTAAATGTTGAAGCCTAACAAG
1 TATAAAAGTATAAAACAGGCCTAACATAAGTCTAAAATGTT-AAGCCTAACAAG
54369186 TATAAAAGTATAAAACAGGCCTAACATAAGTCTAAAATGTTAAGCCTAACAAG
1 TATAAAAGTATAAAACAGGCCTAACATAAGTCTAAAATGTTAAGCCTAACAAG
54369239 GAAGAAGCCA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 12 0.23
54 40 0.77
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (53 bp):
TATAAAAGTATAAAACAGGCCTAACATAAGTCTAAAATGTTAAGCCTAACAAG
Found at i:54372640 original size:14 final size:15
Alignment explanation
Indices: 54372564--54372640 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
54372554 TATTGCCAGT
*
54372564 AAAATG-TTTTCTGT
1 AAAATGATTTTCTGG
*
54372578 AAAATGATTTT-TAG
1 AAAATGATTTTCTGG
*
54372592 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
54372612 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
54372627 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
54372641 TGTTTGATTG
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 21 0.43
15 15 0.31
16 1 0.02
18 1 0.02
19 4 0.08
20 7 0.14
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.45
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:54375344 original size:17 final size:17
Alignment explanation
Indices: 54375302--54375346 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
54375292 CAATTTTGTG
*
54375302 TTTTATA-ATACTTGAT
1 TTTTATATATATTTGAT
*
54375318 TTTGAT-TATATTTGAT
1 TTTTATATATATTTGAT
54375334 TTTTATATATATT
1 TTTTATATATATT
54375347 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (17 bp):
TTTTATATATATTTGAT
Found at i:54393588 original size:98 final size:99
Alignment explanation
Indices: 54393388--54393675 Score: 325
Period size: 98 Copynumber: 2.9 Consensus size: 99
54393378 ACAAAAAATT
* *
54393388 AAAAAAAAATTTG-GGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAAAATTTGGG
1 AAAAAAAAATTTGCGCTCCTGGCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAAAATTTGGG
* * * *
54393452 TGCT-GACCTATCAATGTTCGACACCAGCAGTACG
66 TGCTAG-CCTGTCAATGGTCGGCACCACCAGTACG
* * * *
54393486 AAAAAAATATTTTCTCTACCT-GTCTGTCAATGGTCGGCACCACCAGTTA-GAAAAAAAAATTT-
1 AAAAAAAAATTTGCGCT-CCTGGCCTGTCAATGGTCGGCACCACCAG-TACGAAAAAAAAATTTG
* *
54393548 GGTGCTAGCCTGTCAATGGTCGGCACCACCTGTATG
64 GGTGCTAGCCTGTCAATGGTCGGCACCACCAGTACG
* * * * * * *
54393584 AAAAAAAAATTTGGGGTGCTGGCCTGTCAATCGCCAGCACCAGCAGTACGAAAAAAAAAATTTGG
1 AAAAAAAAATTTGCGCTCCTGGCCTGTCAATGGTCGGCACCACCAGTACG-AAAAAAAAATTTGG
*
54393649 GTGCTAGCCTGTCAATGGGCGGCACCA
65 GTGCTAGCCTGTCAATGGTCGGCACCA
54393676 GTCTACGAAA
Statistics
Matches: 158, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
97 4 0.03
98 72 0.46
99 51 0.32
100 31 0.20
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (99 bp):
AAAAAAAAATTTGCGCTCCTGGCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAAAATTTGGG
TGCTAGCCTGTCAATGGTCGGCACCACCAGTACG
Found at i:54393611 original size:50 final size:49
Alignment explanation
Indices: 54393388--54393702 Score: 334
Period size: 50 Copynumber: 6.4 Consensus size: 49
54393378 ACAAAAAATT
54393388 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACG
* * * * *
54393437 AAAAAAAAATTTGGGTGCTGACCTATCAATGTTCGACACCAGCAGTACG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACG
* *** * *
54393486 AAAAAAATATTTTCTCTACCT-GTCTGTCAATGGTCGGCACCACCAGTTA-G
1 AAAAAAA-AATTTGGGT-GCTGGCCTGTCAATGGTCGGCACCACCAG-TACG
* * *
54393536 AAAAAAAAATTT-GGTGCTAGCCTGTCAATGGTCGGCACCACCTGTATG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACG
* * * *
54393584 AAAAAAAAATTTGGGGTGCTGGCCTGTCAATCGCCAGCACCAGCAGTACG
1 AAAAAAAAATTT-GGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACG
* * *
54393634 AAAAAAAAAATTTGGGTGCTAGCCTGTCAATGGGCGGCACCAGTC--TACG
1 -AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCA-CCAGTACG
*
54393683 AAAAAAAATTTTGGGGTGCT
1 AAAAAAAAATTT-GGGTGCT
54393703 AGTTTGTCAA
Statistics
Matches: 221, Mismatches: 35, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.02
48 48 0.22
49 66 0.30
50 86 0.39
51 17 0.08
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (49 bp):
AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACG
Found at i:54393661 original size:148 final size:148
Alignment explanation
Indices: 54393388--54393713 Score: 387
Period size: 148 Copynumber: 2.2 Consensus size: 148
54393378 ACAAAAAATT
*
54393388 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAAAATTTGGGT
1 AAAAAAAAATTTGGGTGCTAGCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAAAATTTGGGT
* * * * *
54393453 GCTGACCTATCAATGTTCGACACCAGCAGTACGAAAAAAATATTTTCTCTACCTGTCTGTCAATG
66 GCTGACCTATCAATGTCCGACACCAGCAGTACGAAAAAAAAAATTTCGCTACCTGCCTGTCAATG
*
54393518 GTCGGCACCACCAGTTAG
131 GGCGGCACCACCAGTTAG
* *
54393536 AAAAAAAAATTT-GGTGCTAGCCTGTCAATGGTCGGCACCACCTGTATGAAAAAAAAATTTGGGG
1 AAAAAAAAATTTGGGTGCTAGCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAAAATTT-GGG
* * * * *
54393600 TGCTGGCCTGTCAATCG-CC-AGCACCAGCAGTACGAAAAAAAAAATTTGGGT-GCTAGCCTGTC
65 TGCTGACCTATCAAT-GTCCGA-CACCAGCAGTACGAAAAAAAAAATTTCGCTACCT-GCCTGTC
54393662 AATGGGCGG---CACCAGTCTACG
127 AATGGGCGGCACCACCAGT-TA-G
* **
54393683 AAAAAAAATTTTGGGGTGCTAGTTTGTCAAT
1 AAAAAAAAATTT-GGGTGCTAGCCTGTCAAT
54393714 TGTAATATCC
Statistics
Matches: 153, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
145 7 0.05
146 2 0.01
147 60 0.39
148 68 0.44
149 16 0.10
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (148 bp):
AAAAAAAAATTTGGGTGCTAGCCTGTCAATGGTCGGCACCACCAGTACGAAAAAAAAATTTGGGT
GCTGACCTATCAATGTCCGACACCAGCAGTACGAAAAAAAAAATTTCGCTACCTGCCTGTCAATG
GGCGGCACCACCAGTTAG
Found at i:54396141 original size:47 final size:46
Alignment explanation
Indices: 54396089--54396228 Score: 133
Period size: 51 Copynumber: 2.9 Consensus size: 46
54396079 CGAGTGCTAG
*
54396089 CCTGTCAATGGATGGCACCAGCAGTACGAAAAAAATTTTGGTGCCGG
1 CCTGTCAATGG-TGGCACCAGCAGTACGAAAAAAATTTTGGTGCCGA
* * * *
54396136 TCTGTCAATGGTCTGCACCAGTAG-ACGAAAAAATTAATTTTTGGGTGCTGA
1 CCTGTCAATGGT-GGCACCAGCAGTACG-AAAAA--AA-TTTT-GGTGCCGA
*
54396187 CCTGTCAATGGCCGGCACCAGC-GTACGAAAAAAA-TTTGGTGC
1 CCTGTCAATGG-TGGCACCAGCAGTACGAAAAAAATTTTGGTGC
54396229 AGGCTTGTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
45 5 0.07
46 7 0.09
47 24 0.32
48 2 0.03
49 2 0.03
50 10 0.13
51 26 0.34
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (46 bp):
CCTGTCAATGGTGGCACCAGCAGTACGAAAAAAATTTTGGTGCCGA
Found at i:54396215 original size:51 final size:47
Alignment explanation
Indices: 54396089--54396251 Score: 127
Period size: 51 Copynumber: 3.4 Consensus size: 47
54396079 CGAGTGCTAG
* *
54396089 CCTGTCAATGGATGGCACCAGCAGTACG-AAAAAAATTTTGGTGCCGG
1 CCTGTCAATGGACGGCACCAGC-GTACGAAAAAAAATTTTGGTGCCGA
* * * * *
54396136 TCTGTCAATGGTCTGCACCAGTAG-ACGAAAAAATTAATTTTTGGGTGCTGA
1 CCTGTCAATGGACGGCACCAG-CGTACGAAAAAA--AA-TTTT-GGTGCCGA
* * *
54396187 CCTGTCAATGGCCGGCACCAGCGTACG-AAAAAAA-TTTGGTGCAGG
1 CCTGTCAATGGACGGCACCAGCGTACGAAAAAAAATTTTGGTGCCGA
* * *
54396232 CTTGTTAATGGCCGGCACCA
1 CCTGTCAATGGACGGCACCA
54396252 AATTTATCAA
Statistics
Matches: 94, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
45 24 0.26
46 6 0.06
47 23 0.24
48 2 0.02
49 2 0.02
50 10 0.11
51 27 0.29
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24
Consensus pattern (47 bp):
CCTGTCAATGGACGGCACCAGCGTACGAAAAAAAATTTTGGTGCCGA
Found at i:54399125 original size:27 final size:26
Alignment explanation
Indices: 54399099--54399178 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
54399089 TGAGAAAAAT
54399099 TTTGAATTGAAAATAGAAAATTTAAA
1 TTTGAATTGAAAATAGAAAATTTAAA
* * * **
54399125 TATAAAATG-AAATGAGAAAAAAATAAA
1 TTTGAATTGAAAAT-AG-AAAATTTAAA
* *
54399152 ATTGCATTGAAAATAGAAAATTTAAA
1 TTTGAATTGAAAATAGAAAATTTAAA
54399178 T
1 T
54399179 GAAATTCGGA
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
25 4 0.11
26 16 0.42
27 14 0.37
28 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.11, T:0.29
Consensus pattern (26 bp):
TTTGAATTGAAAATAGAAAATTTAAA
Found at i:54399139 original size:48 final size:50
Alignment explanation
Indices: 54399081--54399178 Score: 128
Period size: 53 Copynumber: 1.9 Consensus size: 50
54399071 TAGATAATTT
* *
54399081 AAATGTAATGAG-AAAAAT-TTTGAATTGAAAATAGAAAATTTAAATATA
1 AAATGAAATGAGAAAAAATAATTGAATTGAAAATAGAAAATTTAAATATA
*
54399129 AAATGAAATGAGAAAAAAATAAAATTGCATTGAAAATAGAAAATTTAAAT
1 AAATGAAATGAG-AAAAAAT--AATTGAATTGAAAATAGAAAATTTAAAT
54399179 GAAATTCGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 11 0.26
50 6 0.14
53 25 0.60
ACGTcount: A:0.59, C:0.01, G:0.12, T:0.28
Consensus pattern (50 bp):
AAATGAAATGAGAAAAAATAATTGAATTGAAAATAGAAAATTTAAATATA
Found at i:54399304 original size:11 final size:10
Alignment explanation
Indices: 54399268--54399360 Score: 89
Period size: 11 Copynumber: 8.8 Consensus size: 10
54399258 TATATTTTTT
54399268 AAATGAAATG
1 AAATGAAATG
*
54399278 AAAGGGAAATGG
1 AAA-TGAAAT-G
54399290 AAATGGAAATG
1 AAAT-GAAATG
*
54399301 AAATTAGAATG
1 AAATGA-AATG
*
54399312 AAATGAAATAA
1 AAATGAAAT-G
*
54399323 AAATAAAATG
1 AAATGAAATG
54399333 AAATGAAAATG
1 AAATG-AAATG
54399344 AAATG-AATG
1 AAATGAAATG
54399353 AAATGAAA
1 AAATGAAA
54399361 AAAAAAAAGA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
9 9 0.13
10 13 0.19
11 37 0.54
12 9 0.13
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.18
Consensus pattern (10 bp):
AAATGAAATG
Found at i:54399316 original size:16 final size:16
Alignment explanation
Indices: 54399290--54399350 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
54399280 AGGGAAATGG
*
54399290 AAATGGAAATGAAATTA
1 AAAT-GAAATGAAATAA
*
54399307 GAATGAAATGAAATAA
1 AAATGAAATGAAATAA
* *
54399323 AAATAAAATGAAATGA
1 AAATGAAATGAAATAA
54399339 AAATGAAATGAA
1 AAATGAAATGAA
54399351 TGAAATGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
16 35 0.92
17 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (16 bp):
AAATGAAATGAAATAA
Found at i:54399354 original size:4 final size:5
Alignment explanation
Indices: 54399268--54399360 Score: 89
Period size: 5 Copynumber: 17.6 Consensus size: 5
54399258 TATATTTTTT
* *
54399268 AAATG AAATG AAAGGG AAATGG AAATGG AAATG AAATT AGAATG AAATG
1 AAATG AAATG AAA-TG AAAT-G AAAT-G AAATG AAATG A-AATG AAATG
* *
54399317 AAATAA AAATA AAATG AAATG AAAATG AAATG -AATG AAATG AAA
1 AAAT-G AAATG AAATG AAATG -AAATG AAATG AAATG AAATG AAA
54399361 AAAAAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
4 4 0.05
5 44 0.58
6 28 0.37
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:54399624 original size:14 final size:14
Alignment explanation
Indices: 54399588--54399623 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
54399578 AAATAATAAA
54399588 TAAATGAAAATATT
1 TAAATGAAAATATT
54399602 TAAAT-AAAATA-T
1 TAAATGAAAATATT
54399614 TAAATGAAAA
1 TAAATGAAAA
54399624 AAAGAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (14 bp):
TAAATGAAAATATT
Found at i:54399765 original size:22 final size:21
Alignment explanation
Indices: 54399707--54399765 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
54399697 AAATTAGCTT
54399707 TAAATTTTAAATGAAACTAAAA
1 TAAATTTT-AATGAAACTAAAA
*** *
54399729 TAAAAAGTAATGAAATTAAAA
1 TAAATTTTAATGAAACTAAAA
54399750 TAAATTTTGAATGAAA
1 TAAATTTT-AATGAAA
54399766 AAAAGGGTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (21 bp):
TAAATTTTAATGAAACTAAAA
Found at i:54399954 original size:33 final size:33
Alignment explanation
Indices: 54399917--54400025 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 33
54399907 ATAGGCAACC
* * * *
54399917 CCGACGACCACCGCGGTTCACTCTCAACCACCG
1 CCGACGACCGCCGCTGTTCACCCTCAACCACCA
* * *
54399950 CCGACGACTGCCACTGTTCACCCTTAACCACCA
1 CCGACGACCGCCGCTGTTCACCCTCAACCACCA
* *
54399983 CCGACGACTGCCGCTATTCACCCTCAACCACCA
1 CCGACGACCGCCGCTGTTCACCCTCAACCACCA
*
54400016 ACGACGACCG
1 CCGACGACCG
54400026 TCGATCACTC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.24, C:0.47, G:0.16, T:0.14
Consensus pattern (33 bp):
CCGACGACCGCCGCTGTTCACCCTCAACCACCA
Found at i:54403014 original size:48 final size:48
Alignment explanation
Indices: 54402945--54403146 Score: 239
Period size: 48 Copynumber: 4.2 Consensus size: 48
54402935 TCTCAAAATT
* * * **
54402945 ATTTTTTTTCGTATATTGGTGCTGGTCATTGACAGGCCAACA-CTTAA
1 ATTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAACACCCAAA
**
54402992 ATTTTTTTTCGTATTGTTGGTGCCGGCCATTGACAGGCCAACAGCCCAAA
1 ATTTTTTTTCGTA-TACTGGTGCCGGCCATTGACAGGCCAACA-CCCAAA
* *
54403042 TTTTTTTTTCGTATACTGGTGCCGGCCATTGACAAGG-CAGCA-CCAAA
1 ATTTTTTTTCGTATACTGGTGCCGGCCATTGAC-AGGCCAACACCCAAA
* * *
54403089 ATTTTTTTTTCGTATACTGGTGCTGGCCATTGACAAGCCAGCACCCAAA
1 A-TTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAACACCCAAA
54403138 ATTTTTTTT
1 ATTTTTTTT
54403147 TAAAATTTTT
Statistics
Matches: 136, Mismatches: 12, Indels: 13
0.84 0.07 0.08
Matches are distributed among these distances:
47 20 0.15
48 70 0.51
49 28 0.21
50 18 0.13
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (48 bp):
ATTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAACACCCAAA
Found at i:54403110 original size:97 final size:97
Alignment explanation
Indices: 54402946--54403147 Score: 257
Period size: 97 Copynumber: 2.1 Consensus size: 97
54402936 CTCAAAATTA
* * * ** **
54402946 TTTTTTTTCGTATATTGGTGCTGGTCATTGACAGGCCAACACTTAAATTTTTTTTCGTATTGTTG
1 TTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAACACCAAAATTTTTTTTCGTATTACTG
*
54403011 GTGCCGGCCATTGACAGGCCAACAGCCC-AAAT
66 GTGCCGGCCATTGACAAGCCAACA-CCCAAAAT
*
54403043 TTTTTTTTCGTATACTGGTGCCGGCCATTGACAAGG-CAGCACCAAAATTTTTTTTTCGTA-TAC
1 TTTTTTTTCGTATACTGGTGCCGGCCATTGAC-AGGCCAACACCAAAA-TTTTTTTTCGTATTAC
* *
54403106 TGGTGCTGGCCATTGACAAGCCAGCACCCAAAAT
64 TGGTGCCGGCCATTGACAAGCCAACACCCAAAAT
54403140 TTTTTTTT
1 TTTTTTTT
54403148 AAAATTTTTA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 3 0.03
97 73 0.80
98 15 0.16
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (97 bp):
TTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAACACCAAAATTTTTTTTCGTATTACTG
GTGCCGGCCATTGACAAGCCAACACCCAAAAT
Found at i:54410666 original size:25 final size:25
Alignment explanation
Indices: 54410638--54410695 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
54410628 ACCTTAGCGC
*
54410638 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACATTAGT
* *
54410663 GCTCTATGATTATTAGCACATTTGT
1 GCTCTCTGATTATTAGCACATTAGT
54410688 GCTCTCTG
1 GCTCTCTG
54410696 TATAGAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATTAGT
Found at i:54416826 original size:39 final size:40
Alignment explanation
Indices: 54416744--54416830 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
54416734 TTTAATTGTA
* *
54416744 TTAAAAATAAATTTTTATAAATTTTAATGTTTTTTAAGTT
1 TTAAAAATAAATTTTTATAAATTTTAACGTTTTTTAAGAT
*
54416784 TTAAAAATAAA-TTTTATAATTTTTTAAACG-TTTTTAA-AT
1 TTAAAAATAAATTTTTATAA-ATTTT-AACGTTTTTTAAGAT
54416823 TTAAAAAT
1 TTAAAAAT
54416831 TGAAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 17 0.40
40 22 0.52
41 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (40 bp):
TTAAAAATAAATTTTTATAAATTTTAACGTTTTTTAAGAT
Found at i:54417307 original size:14 final size:15
Alignment explanation
Indices: 54417280--54417308 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54417270 TGAATTTAAT
54417280 TTTTTAATATATTTA
1 TTTTTAATATATTTA
54417295 TTTTTAATA-ATTTA
1 TTTTTAATATATTTA
54417309 ATAATCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATATATTTA
Found at i:54419107 original size:24 final size:24
Alignment explanation
Indices: 54419057--54419107 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
54419047 AAATTTTTAA
* *
54419057 TTTTTATTTTTAAGAATTTAAATT
1 TTTTTATATTTAAGAATTTAAAAT
*
54419081 TTTTTATATTTCAG-ATTTGAAAAT
1 TTTTTATATTTAAGAATTT-AAAAT
54419105 TTT
1 TTT
54419108 CATCTTGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTTTATATTTAAGAATTTAAAAT
Found at i:54430347 original size:237 final size:238
Alignment explanation
Indices: 54429913--54430360 Score: 760
Period size: 237 Copynumber: 1.9 Consensus size: 238
54429903 TTTGCACTAC
* * *
54429913 TACGGTCCGCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTCTTGAAACTTTTCCATCAAGT
1 TACGGTCCGCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTCTTAAAACCTTGCCATCAAGT
*
54429978 AAAATAGGGAAATAGTTGCATGGAGTTCATAAACATATCACTCATTCACTCCATTTCTTTTTCTC
66 AAAACAGGGAAATAGTTGCATGGAGTTCATAAACA-ATCACTCATTCACTCCATTTCTTTTTCTC
*
54430043 CTTACGTTTTTCTCGCAACCAAACAACGTTCTTCACCGTATTGCTACTAACATTTTCTAAACGTA
130 CTTACGTTTTTCTCGCAACCAAACAACGTTCTTAACCGTATTGCTACTAACATTTTCTAAACGTA
54430108 TATAACGAAAAAAAGTCAGACAAATCATTACTGCTTATAGACTT
195 TATAACGAAAAAAAGTCAGACAAATCATTACTGCTTATAGACTT
*
54430152 TACGGTCCTCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTC-TAAAACCTTGCCATCAAGT
1 TACGGTCCGCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTCTTAAAACCTTGCCATCAAGT
*
54430216 AAAACAGGGAAGTAGTTGCATGGAGTTCATAAAC-ATCACTCATTCACT-CATTTTCTTTTTCTC
66 AAAACAGGGAAATAGTTGCATGGAGTTCATAAACAATCACTCATTCACTCCA-TTTCTTTTTCTC
54430279 CTTACGTTTTTCTCGGCAACCAAACAACGTTCTTAACCGTATTGCTACTAACATTTTC-AAATCG
130 CTTACGTTTTTCTC-GCAACCAAACAACGTTCTTAACCGTATTGCTACTAACATTTTCTAAA-CG
*
54430343 TATATAACTAAAAAAAGT
193 TATATAACGAAAAAAAGT
54430361 GCAAAAAAAA
Statistics
Matches: 198, Mismatches: 8, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
235 2 0.01
236 43 0.22
237 61 0.31
238 48 0.24
239 44 0.22
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (238 bp):
TACGGTCCGCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTCTTAAAACCTTGCCATCAAGT
AAAACAGGGAAATAGTTGCATGGAGTTCATAAACAATCACTCATTCACTCCATTTCTTTTTCTCC
TTACGTTTTTCTCGCAACCAAACAACGTTCTTAACCGTATTGCTACTAACATTTTCTAAACGTAT
ATAACGAAAAAAAGTCAGACAAATCATTACTGCTTATAGACTT
Found at i:54432114 original size:29 final size:29
Alignment explanation
Indices: 54432051--54432115 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
54432041 ATGCTTTAGT
** * *
54432051 AAAAAAAAAAAGGTACTTAATTGGGATAA
1 AAAAAAAAAAAGGTACCAAATTGGAACAA
54432080 AGAAAAAAAAAAGGTACCAAATTGGAACAA
1 A-AAAAAAAAAAGGTACCAAATTGGAACAA
54432110 AAAAAA
1 AAAAAA
54432116 CCTCAAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.14
Consensus pattern (29 bp):
AAAAAAAAAAAGGTACCAAATTGGAACAA
Found at i:54440158 original size:128 final size:132
Alignment explanation
Indices: 54439974--54440223 Score: 337
Period size: 130 Copynumber: 1.9 Consensus size: 132
54439964 TCATCGGTTT
* * *
54439974 CAACTAAAAACTTATTTATTTCTTACGTTAATTTTTTATAAATATATTTATTAAAT-AAAA-GTA
1 CAACCAAAAACTCATTTATTTCTTA-G-TAAATTTTTATAAATATATTTATTAAATAAAAATGTA
* *
54440037 TCCATAATTTTTTTTATAAATAACAAGATTTATATCTATTCATCAACCAAAAATCAATTTTTCTA
64 TCCATAATTTTTTTAATAAATAACAAGATTTACATCTATTCATCAACCAAAAATCAATTTTTCTA
54440102 TTAC
129 TTAC
* * *
54440106 CAACCAAAAACTCATTTATTTCTT-G-AAATTTTTATGAATATATTTATTAAATAAAAATTTATT
1 CAACCAAAAACTCATTTATTTCTTAGTAAATTTTTATAAATATATTTATTAAATAAAAATGTATC
* * * * *
54440169 CATAATTTTTTTAATAATTAATAAGATTTACATCTATTTATCCACCGAAAATCAA
66 CATAATTTTTTTAATAAATAACAAGATTTACATCTATTCATCAACCAAAAATCAA
54440224 CAGTAATGTG
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
128 25 0.24
129 4 0.04
130 52 0.50
132 22 0.21
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.44
Consensus pattern (132 bp):
CAACCAAAAACTCATTTATTTCTTAGTAAATTTTTATAAATATATTTATTAAATAAAAATGTATC
CATAATTTTTTTAATAAATAACAAGATTTACATCTATTCATCAACCAAAAATCAATTTTTCTATT
AC
Found at i:54442301 original size:152 final size:152
Alignment explanation
Indices: 54442127--54442421 Score: 590
Period size: 152 Copynumber: 1.9 Consensus size: 152
54442117 TAAAATTTTC
54442127 TCGTTAAATTTATTAGTTCGACATTTTAAAATAAAAAGGTAAACTCACTCAATAACAATGCATCT
1 TCGTTAAATTTATTAGTTCGACATTTTAAAATAAAAAGGTAAACTCACTCAATAACAATGCATCT
54442192 AAAAAGTTAAAATTATATTAAGCTTAACTTTAATAAAATAATTTAATATTTTTAACAATTAAACT
66 AAAAAGTTAAAATTATATTAAGCTTAACTTTAATAAAATAATTTAATATTTTTAACAATTAAACT
54442257 TAAATTTTAAAATCATGAGGTA
131 TAAATTTTAAAATCATGAGGTA
54442279 TCGTTAAATTTATTAGTTCGACATTTTAAAATAAAAAGGTAAACTCACTCAATAACAATGCATCT
1 TCGTTAAATTTATTAGTTCGACATTTTAAAATAAAAAGGTAAACTCACTCAATAACAATGCATCT
54442344 AAAAAGTTAAAATTATATTAAGCTTAACTTTAATAAAATAATTTAATATTTTTAACAATTAAACT
66 AAAAAGTTAAAATTATATTAAGCTTAACTTTAATAAAATAATTTAATATTTTTAACAATTAAACT
54442409 TAAATTTTAAAAT
131 TAAATTTTAAAAT
54442422 TTTAAAAATA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 143 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.37
Consensus pattern (152 bp):
TCGTTAAATTTATTAGTTCGACATTTTAAAATAAAAAGGTAAACTCACTCAATAACAATGCATCT
AAAAAGTTAAAATTATATTAAGCTTAACTTTAATAAAATAATTTAATATTTTTAACAATTAAACT
TAAATTTTAAAATCATGAGGTA
Found at i:54454716 original size:13 final size:13
Alignment explanation
Indices: 54454698--54454723 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54454688 ATGATGTTGG
54454698 CCTTACTTTTCCA
1 CCTTACTTTTCCA
54454711 CCTTACTTTTCCA
1 CCTTACTTTTCCA
54454724 TTTTAATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (13 bp):
CCTTACTTTTCCA
Found at i:54465878 original size:34 final size:35
Alignment explanation
Indices: 54465840--54465906 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
54465830 CAGTAAAATA
*
54465840 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
54465874 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
54465907 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:54465880 original size:20 final size:20
Alignment explanation
Indices: 54465855--54465894 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54465845 CGTAAAATGA
*
54465855 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
54465875 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
54465895 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:54465910 original size:14 final size:15
Alignment explanation
Indices: 54465834--54465910 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
54465824 GATTGTCAGT
* *
54465834 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
54465848 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
54465862 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
54465882 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
54465897 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
54465911 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:54476434 original size:16 final size:17
Alignment explanation
Indices: 54476399--54476436 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
54476389 TTTGGTTGAC
54476399 AAAATATAAAATTACTT
1 AAAATATAAAATTACTT
54476416 AAAA-ATAAAATTTAC-T
1 AAAATATAAAA-TTACTT
54476432 AAAAT
1 AAAAT
54476437 TAGCCGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATAAAATTACTT
Found at i:54477551 original size:26 final size:26
Alignment explanation
Indices: 54477496--54477551 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
54477486 TTATCCATGT
*
54477496 TTTAATTTTATTATAATTTAAAAAAT
1 TTTAATTTTATTATAATTTAAAAAAC
*
54477522 TTTAA-TTTATT-TGAATATTAAAATAC
1 TTTAATTTTATTAT-AAT-TTAAAAAAC
54477548 TTTA
1 TTTA
54477552 TCCCAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 9 0.35
26 16 0.62
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTAATTTTATTATAATTTAAAAAAC
Found at i:54483120 original size:3 final size:3
Alignment explanation
Indices: 54483112--54483139 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54483102 TTTTCAGATT
54483112 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
54483140 TTTCCTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:54483375 original size:21 final size:20
Alignment explanation
Indices: 54483351--54483389 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54483341 TTTTAAACTT
*
54483351 ATTTTAAGTGTTTTTTCAGAG
1 ATTTTAAG-CTTTTTTCAGAG
*
54483372 ATTTTTAGCTTTTTTCAG
1 ATTTTAAGCTTTTTTCAG
54483390 CCCAAAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (20 bp):
ATTTTAAGCTTTTTTCAGAG
Found at i:54484473 original size:29 final size:30
Alignment explanation
Indices: 54484424--54484481 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
54484414 AAAATTATAC
54484424 ATGAACTTTGATTTAATGTATAATTTTATGT
1 ATGAACTTTGATTT-ATGTATAATTTTATGT
*
54484455 ATGAACTTTGCTTT-TGTATAATTTTAT
1 ATGAACTTTGATTTATGTATAATTTTAT
54484482 AAAAATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.53
Consensus pattern (30 bp):
ATGAACTTTGATTTATGTATAATTTTATGT
Found at i:54490622 original size:74 final size:75
Alignment explanation
Indices: 54490533--54490674 Score: 259
Period size: 75 Copynumber: 1.9 Consensus size: 75
54490523 TTCAGATGCA
*
54490533 AGTATTGAAAACGGATGTGTTAGCTTAT-GAGAAATAAAAAAGGATTGCAAGAACTAGCACAAAC
1 AGTATTGAAAACGGATGTGTTAGCTTATCAAGAAATAAAAAAGGATTGCAAGAACTAGCACAAAC
54490597 ATGGATGACG
66 ATGGATGACG
*
54490607 AGTATTGATAACGGATGTGTTAGCTTATCAAGAAATAAAAAAGGATTGCAAGAACTAGCACAAAC
1 AGTATTGAAAACGGATGTGTTAGCTTATCAAGAAATAAAAAAGGATTGCAAGAACTAGCACAAAC
54490672 ATG
66 ATG
54490675 AGAAGTCAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 27 0.42
75 38 0.58
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (75 bp):
AGTATTGAAAACGGATGTGTTAGCTTATCAAGAAATAAAAAAGGATTGCAAGAACTAGCACAAAC
ATGGATGACG
Found at i:54491090 original size:218 final size:218
Alignment explanation
Indices: 54490828--54491252 Score: 715
Period size: 218 Copynumber: 1.9 Consensus size: 218
54490818 TAGAGGATTG
* *
54490828 AAGAATGAATGAAGAAACACATTTTTTATACTTCCATACAAACCAAATTTGTGAACTATGTAAAA
1 AAGAAAGAATGAAGAAACACATTTTTTATACTTCCATACAAACCAAATTTGTGAACTACGTAAAA
*
54490893 TTGATCACTTAATGTTTCCACCAGAAACTCAAGTTAGCATCACCCATGATGTCTTGAAGAGGAAT
66 TTGATCACTTAATGTTTCCACCAGAAACTCAAGTTAGCATCACCCATGAAGTCTTGAAGAGGAAT
** ** *
54490958 CCAAGTAGAGTTCATTGTATGCGTATAATAGGAAGGAAAAACAACCAAAACCAATGCAAATAGGA
131 CCAAGTAGAGTTCATCATATGCAAATAATAGGAAGCAAAAACAACCAAAACCAATGCAAATAGGA
54491023 AGGCAAATCAACAAACCAAATTA
196 AGGCAAATCAACAAACCAAATTA
*
54491046 AAGAAAGAATGAAGAAACACATTTTTTATACTTTCATACAAACCAAATTTGTGAACTACGTAAAA
1 AAGAAAGAATGAAGAAACACATTTTTTATACTTCCATACAAACCAAATTTGTGAACTACGTAAAA
* * * * *
54491111 TTTATCACTTAATGTTTGCATCAGAAACTCGAGTTAGCATCACCCATGAAGTCTTGAAGGGGAAT
66 TTGATCACTTAATGTTTCCACCAGAAACTCAAGTTAGCATCACCCATGAAGTCTTGAAGAGGAAT
*
54491176 CCGAGTAGAGTTCATCATATGCAAATAATAGGAAGCAAAAACAACCAAAACCAATGCAAATAGGA
131 CCAAGTAGAGTTCATCATATGCAAATAATAGGAAGCAAAAACAACCAAAACCAATGCAAATAGGA
54491241 AGGCAAATCAAC
196 AGGCAAATCAAC
54491253 CAAAAGCAAT
Statistics
Matches: 192, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
218 192 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (218 bp):
AAGAAAGAATGAAGAAACACATTTTTTATACTTCCATACAAACCAAATTTGTGAACTACGTAAAA
TTGATCACTTAATGTTTCCACCAGAAACTCAAGTTAGCATCACCCATGAAGTCTTGAAGAGGAAT
CCAAGTAGAGTTCATCATATGCAAATAATAGGAAGCAAAAACAACCAAAACCAATGCAAATAGGA
AGGCAAATCAACAAACCAAATTA
Found at i:54491242 original size:32 final size:32
Alignment explanation
Indices: 54491202--54491265 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
54491192 ATATGCAAAT
54491202 AATAGGAA-GCAAAAACAACCAAAACCAATGCA
1 AATAGGAAGGC-AAAACAACCAAAACCAATGCA
* *
54491234 AATAGGAAGGCAAATCAACCAAAAGCAATGCA
1 AATAGGAAGGCAAAACAACCAAAACCAATGCA
54491266 GGCAAGCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.56, C:0.20, G:0.16, T:0.08
Consensus pattern (32 bp):
AATAGGAAGGCAAAACAACCAAAACCAATGCA
Found at i:54493744 original size:34 final size:35
Alignment explanation
Indices: 54493706--54493772 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
54493696 CAGTAAAATA
54493706 TTTTCTGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCTGTAAAATGATTTACGGGAAAATATTTTAC
*
54493740 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACGGGAAAATATTTT
54493773 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:54497423 original size:24 final size:23
Alignment explanation
Indices: 54497396--54497449 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
54497386 AATACCTTCA
* * *
54497396 TACGGGCATCCTCAATCGGCTCCT
1 TACGGGC-CCCTCAACCGGCACCT
54497420 TACGGAGCCCCTCAACCGGCACCT
1 TACGG-GCCCCTCAACCGGCACCT
54497444 TACGGG
1 TACGGG
54497450 GCTCATCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 23 0.88
25 2 0.08
ACGTcount: A:0.19, C:0.39, G:0.24, T:0.19
Consensus pattern (23 bp):
TACGGGCCCCTCAACCGGCACCT
Found at i:54512266 original size:15 final size:15
Alignment explanation
Indices: 54512246--54512277 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54512236 TGATATGTAC
54512246 CTAATTTGAAAATGA
1 CTAATTTGAAAATGA
*
54512261 CTAATTTGGAAATGA
1 CTAATTTGAAAATGA
54512276 CT
1 CT
54512278 TTTGTAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (15 bp):
CTAATTTGAAAATGA
Found at i:54512611 original size:81 final size:82
Alignment explanation
Indices: 54512509--54512672 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
54512499 ATTTTTAAAA
54512509 TATAATAAATAGGAATTTTGAGTATTAAATTAGGAAGTATATAGTCTAATAAGAAATTAGAAAAA
1 TATAATAAATAGGAATTTTGAGTATTAAATTAGGAAGTATATAGTCTAATAAGAAATTAGAAAAA
54512574 AAATAAAAAAAATACTC
66 AAATAAAAAAAATACTC
54512591 TATAATAAAT-GGAATTTTGAGTATTAAATTAGGAAGTATATAGTCTAATAAGAAATTAGAAAAA
1 TATAATAAATAGGAATTTTGAGTATTAAATTAGGAAGTATATAGTCTAATAAGAAATTAGAAAAA
54512655 AAATAAAAAAAATACTC
66 AAATAAAAAAAATACTC
54512672 T
1 T
54512673 TTAGATAGGA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 72 0.88
82 10 0.12
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (82 bp):
TATAATAAATAGGAATTTTGAGTATTAAATTAGGAAGTATATAGTCTAATAAGAAATTAGAAAAA
AAATAAAAAAAATACTC
Found at i:54513772 original size:22 final size:22
Alignment explanation
Indices: 54513745--54513807 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
54513735 TCTTCGATTA
54513745 TTAGCATATTAGTGCTCTCCGT
1 TTAGCATATTAGTGCTCTCCGT
* * *
54513767 TTAGCACATTTGTGCTCTCTGT
1 TTAGCATATTAGTGCTCTCCGT
*
54513789 ATAGCACT-TTAGTGCTCTC
1 TTAGCA-TATTAGTGCTCTC
54513808 TGTTCAATAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (22 bp):
TTAGCATATTAGTGCTCTCCGT
Found at i:54513808 original size:22 final size:23
Alignment explanation
Indices: 54513753--54513810 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
54513743 TATTAGCATA
* *
54513753 TTAGTGCTCTCCGTTTAGCACAT
1 TTAGTGCTCTCTGTATAGCACAT
54513776 TT-GTGCTCTCTGTATAGCAC-T
1 TTAGTGCTCTCTGTATAGCACAT
54513797 TTAGTGCTCTCTGT
1 TTAGTGCTCTCTGT
54513811 TCAATAGTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 27 0.84
23 2 0.06
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (23 bp):
TTAGTGCTCTCTGTATAGCACAT
Found at i:54531843 original size:47 final size:47
Alignment explanation
Indices: 54531782--54531873 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
54531772 CGACACTAAC
*
54531782 TGTCGAATTGACTTATGATTGTTCTACTTTTTTATGGATACTAACAG
1 TGTCGAATTGACTTAGGATTGTTCTACTTTTTTATGGATACTAACAG
* *
54531829 TGTCGAATTGACTTAGGATTTTTCTACTTTTTTATGGGTACTAAC
1 TGTCGAATTGACTTAGGATTGTTCTACTTTTTTATGGATACTAAC
54531874 TCACCAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (47 bp):
TGTCGAATTGACTTAGGATTGTTCTACTTTTTTATGGATACTAACAG
Found at i:54532303 original size:9 final size:8
Alignment explanation
Indices: 54532275--54532301 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
54532265 TGCATGATCG
54532275 AAAGAAAA
1 AAAGAAAA
54532283 AAAGAAAA
1 AAAGAAAA
54532291 AAAGAAAA
1 AAAGAAAA
54532299 AAA
1 AAA
54532302 AGTTGAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:54539597 original size:41 final size:42
Alignment explanation
Indices: 54539522--54539601 Score: 137
Period size: 41 Copynumber: 1.9 Consensus size: 42
54539512 GAAGTATTGG
54539522 TACAAAGAAAGTAGCTTATAATTTCTCAAAAAATTATTAAAAT
1 TACAAAGAAAGTAGCTTATAATTTCTCAAAAAATT-TTAAAAT
54539565 TACAAAGAAAGTAGC-T-TAATTTCTCAAAAAATTTTAA
1 TACAAAGAAAGTAGCTTATAATTTCTCAAAAAATTTTAA
54539602 TGCAATTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
40 4 0.11
41 17 0.46
42 1 0.03
43 15 0.41
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (42 bp):
TACAAAGAAAGTAGCTTATAATTTCTCAAAAAATTTTAAAAT
Found at i:54539782 original size:20 final size:20
Alignment explanation
Indices: 54539757--54539794 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
54539747 ATAATTTAAA
54539757 ATATAAATTTATTAATATGT
1 ATATAAATTTATTAATATGT
54539777 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
54539795 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:54541194 original size:9 final size:9
Alignment explanation
Indices: 54541180--54541206 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54541170 AGAGTTGATT
54541180 GATTCAAAA
1 GATTCAAAA
54541189 GATTCAAAA
1 GATTCAAAA
54541198 GATTCAAAA
1 GATTCAAAA
54541207 TTGTTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
GATTCAAAA
Found at i:54541426 original size:9 final size:9
Alignment explanation
Indices: 54541412--54541438 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54541402 TTAGTAACAA
54541412 TTTTGAATC
1 TTTTGAATC
54541421 TTTTGAATC
1 TTTTGAATC
54541430 TTTTGAATC
1 TTTTGAATC
54541439 AATCAACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
TTTTGAATC
Found at i:54549057 original size:14 final size:15
Alignment explanation
Indices: 54549028--54549059 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54549018 AAAAACATCA
54549028 TAATTTTATCTATTT
1 TAATTTTATCTATTT
54549043 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
54549057 TAA
1 TAA
54549060 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:54556533 original size:18 final size:19
Alignment explanation
Indices: 54556511--54556553 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
54556501 TCAAATATAG
54556511 TTTTTTTAAAAT-TT-TGT
1 TTTTTTTAAAATATTATGT
54556528 TATTTTTTAAAATATTATGT
1 T-TTTTTTAAAATATTATGT
54556548 TTTTTT
1 TTTTTT
54556554 CCTGGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 7 0.30
20 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTTTTAAAATATTATGT
Found at i:54565631 original size:156 final size:154
Alignment explanation
Indices: 54565407--54565808 Score: 406
Period size: 156 Copynumber: 2.6 Consensus size: 154
54565397 GATACCTTGA
* * * * * *
54565407 TAAATAAAAAATCATGTAAAATTTTAAAATTCA-CCGTTAAACATTAAAAAATGCATATTTTGTA
1 TAAATTAAAATTCATGTATAATTTTAAAATTTATCC-TTAAATATTAAAAAATGTATATTTTGT-
* * * *
54565471 AAAATTCTAAATCAGAGTGAAAAACTAACTCTTGTTGAAATATCTATACTA-TAATA-AATTTAT
64 AAAATTCTAAATCAGAGTGAGAAACTAACTCTTCTTGAAATATCTATACTATTAATAGAACTCA-
*
54565534 TAACCGAGTTGGTATATAAAATTATATAT
128 TAACCGAGTTGG--TATAAAATTACATAT
* *
54565563 TAAATTAAAATTCATGTATAATTTTAAAATTTATCTTTAAATATT-AAAAATGTATCATTTTATG
1 TAAATTAAAATTCATGTATAATTTTAAAATTTATCCTTAAATATTAAAAAATGTAT-ATTTTGT-
* * *
54565627 AAAATTCTAAAT-TGACATGAGAAAC---CTTTTCTTGAAATATCTATACTATTAATAGAACTCA
64 AAAATTCTAAATCAGA-GTGAGAAACTAACTCTTCTTGAAATATCTATACTATTAATAGAACTCA
* **
54565688 TGATTGAGTTGGTATAAAATTACATAT
128 TAACCGAGTTGGTATAAAATTACATAT
* * * * *
54565715 TAAATTAAAATTAATATATAACTTTAAAACTTGTCCTTAAATATTAAAAAAATGTATTATTTTGT
1 TAAATTAAAATTCATGTATAATTTTAAAATTTATCCTTAAATATT-AAAAAATGTA-TATTTTGT
** *
54565780 AAAAGTTGAAAATCAAAGTGAGAAACTAA
64 AAAA-TTCTAAATCAGAGTGAGAAACTAA
54565809 TTCCTATCAA
Statistics
Matches: 201, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
152 53 0.26
153 25 0.12
154 43 0.21
155 17 0.08
156 62 0.31
157 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (154 bp):
TAAATTAAAATTCATGTATAATTTTAAAATTTATCCTTAAATATTAAAAAATGTATATTTTGTAA
AATTCTAAATCAGAGTGAGAAACTAACTCTTCTTGAAATATCTATACTATTAATAGAACTCATAA
CCGAGTTGGTATAAAATTACATAT
Found at i:54568719 original size:4 final size:4
Alignment explanation
Indices: 54568710--54568734 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
54568700 TTACTTGAGA
54568710 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
54568735 GTACTGGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:54585090 original size:22 final size:22
Alignment explanation
Indices: 54585055--54585097 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
54585045 AAATAAATTT
54585055 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
54585077 TAAATGTTAA-TATAAAAATAT
1 TAAAT-TTAATTATAAAAATAT
54585098 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:54593006 original size:152 final size:149
Alignment explanation
Indices: 54592595--54593212 Score: 827
Period size: 152 Copynumber: 4.1 Consensus size: 149
54592585 AACATGTTCC
* *
54592595 TATTTCAGCCCTTTGTTCGTATTTTTTTCCCCGATTTTATTAC-TTAAAAAAATACTATTTTCTA
1 TATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTTAAAAAAATA-TATTTTCTA
*
54592659 TTTTTATTATTTTACATTATTTTAGTACATTATGTTT-AAATGTATTCATTTAGTGTGTTTTTTA
64 GTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTA
54592723 TTGAAATTAAAAAAAAAACCCT
129 TTGAAATT-AAAAAAAAACCCT
* * * *
54592745 CATTTCAGCCCTTTATTCGTATTTTTTCCCCGAATTTTATTACTTTTAAAAAATATTATATTTTC
1 TATTTCGGCCCTTTGTTCGTATTTTTT-CCCGGATTTTATTAC-TTTAAAAAA-A-TATATTTTC
*
54592810 TAGTTTTATTATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTT
62 TAGTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTG--TTT
54592875 TTTATTGAAATTAAAAAAAAACCCT
125 TTTATTGAAATTAAAAAAAAACCCT
***
54592900 TATTTCGGCAAATTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATATCATTTTCTAG
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATAT-ATTTTCTAG
*
54592965 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCGTTTAGTGTGTTTTTTAT
65 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAT
*
54593030 TGAAATT-AAAAAAAACCAT
130 TGAAATTAAAAAAAAACCCT
** *
54593049 TATTTCGGCCCTTTGTTCGTATTTTTT-TTGGATTTTATTACTTTCAATAAAAATATATTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTT-AA-AAAAATATATT-TTCT
* * * *
54593113 TGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCATTAATTTATTGTGTTTT
63 AG--TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
* * * *
54593178 TAAAT-AAATT--TAAAAAATCCT
126 TTATTGAAATTAAAAAAAAACCCT
*
54593199 TATTTCGGCTCTTT
1 TATTTCGGCCCTTT
54593213 AATTTAGTGT
Statistics
Matches: 421, Mismatches: 33, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
148 15 0.04
149 46 0.11
150 80 0.19
151 8 0.02
152 133 0.32
153 54 0.13
154 36 0.09
155 34 0.08
156 15 0.04
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (149 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATATATTTTCTAGT
TTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTATT
GAAATTAAAAAAAAACCCT
Found at i:54593286 original size:187 final size:187
Alignment explanation
Indices: 54593036--54593376 Score: 551
Period size: 187 Copynumber: 1.8 Consensus size: 187
54593026 TTATTGAAAT
* * ** * *
54593036 TAAAAAAAACCATTATTTCGGCCCTTTGTTCGTATTTTTTTTGGATTTTATTACTTTCAATAAAA
1 TAAAAAAAACCATTATTCCGGCCCTTTGCTCGTATTTTTTCCGAATTTTATTACTTCCAATAAAA
* *
54593101 ATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCATTAAT
66 ATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGCATTAAT
*
54593166 TTATTGTG-TTTTTAAATAAATTTAAAAAATCCTTATTTCGGCTCTTTAATTTAGTG
131 TTACTGTGTTTTTTAAATAAATTTAAAAAATCCTTATTTCGGCTCTTTAATTTAGTG
*
54593222 TAAAAAAAACC-TTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAATAA
1 TAAAAAAAACCATTATTCCGGCCCTTTGCTCGTATT-TTTT-CCGAATTTTATTACTTCCAATAA
*
54593286 AAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTA
64 AAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGCATTA
54593351 ATTTACTGTGTTTTTTAAATAAATTT
129 ATTTACTGTGTTTTTTAAATAAATTT
54593377 TTAAAAAACT
Statistics
Matches: 141, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
185 21 0.15
186 15 0.11
187 90 0.64
188 15 0.11
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (187 bp):
TAAAAAAAACCATTATTCCGGCCCTTTGCTCGTATTTTTTCCGAATTTTATTACTTCCAATAAAA
ATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGCATTAAT
TTACTGTGTTTTTTAAATAAATTTAAAAAATCCTTATTTCGGCTCTTTAATTTAGTG
Found at i:54593532 original size:340 final size:334
Alignment explanation
Indices: 54592916--54593545 Score: 806
Period size: 340 Copynumber: 1.9 Consensus size: 334
54592906 GGCAAATTGT
*
54592916 TCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATATCATTTTCTAGTTTTATTATTTTACAT
1 TCGTATTTTTTCCCGAATTTTATTACTTTAAAAAAATATCATTTTCTAGTTTTATTATTTTACAT
* ** * *
54592981 TATTTTAGTACATTATGTTTGAAATGTATTCGTTTAGTGTGTTTTTTATTGAAATTAAAAAAAAC
66 TATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGTTTTTTAATGAAATTAAAAAAAAC
* * **** *
54593046 CATTATTTCGGCCCTTTGTTCGTATTTTTTTTGGATTTTATTACTTTCAATAAAAATATATTATT
131 CATTATTTCGGCCATTTATTCGTATTTTTTCCAAATTTTATTACTTTCAATAAAAATATAATATT
* * * * * * *
54593111 TTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCATTAATTTATTGTGTT
196 TTTGAATCTTATTATTTTACATTATTTTAATACATTATATTTAAAATACATTAATTTA-TGTGTG
* *
54593176 TTTAAATAAATTT-AAAAAATCCTTATTTCGGCTCTTTAATTTAGTGTAAAAAAAACCTTATTCC
260 CTTAAATAAATTTAAAAAAACCCTTATTTCGGCTCTTTAATTTAGTGTAAAAAAAACCTTATTCC
54593240 TGCCCTTTGC
325 TGCCCTTTGC
* *
54593250 TCGTATTATTTTCCCGAATTTTATTACTTCCAATAAAAATATATTATTTTCGTA-TTTTATTATT
1 TCGTATT-TTTTCCCGAATTTTATTACTT----TAAAAAAATATCATTTTC-TAGTTTTATTATT
*
54593314 TTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGTTTTTTAAAT-AAATTTT
60 TTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGTTTTTT-AATGAAA-TTA
* * *
54593378 TAAAAAACTATTATTTCGGCCATTTATTCGTATTTTTTCCCCAAATTTTATTACTTT-TA-AAAA
123 AAAAAAACCATTATTTCGGCCATTTATTCGTATTTTTT--CCAAATTTTATTACTTTCAATAAAA
** *
54593441 ATATAATATTTTCT-AATCTTATTATTTTACATTATTTTAATACATTATATTTAAAATATTTTCA
186 ATATAATATTTT-TGAATCTTATTATTTTACATTATTTTAATACATTATATTTAAAATACATTAA
54593505 TTTA-GTGTGCTTAAATAAATTTTTAAAAAAACCCTTATTTC
250 TTTATGTGTGCTTAAATAAA--TTTAAAAAAACCCTTATTTC
54593546 AACTATTTTT
Statistics
Matches: 251, Mismatches: 31, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
334 7 0.03
335 20 0.08
338 13 0.05
339 78 0.31
340 103 0.41
341 17 0.07
342 13 0.05
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.51
Consensus pattern (334 bp):
TCGTATTTTTTCCCGAATTTTATTACTTTAAAAAAATATCATTTTCTAGTTTTATTATTTTACAT
TATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGTTTTTTAATGAAATTAAAAAAAAC
CATTATTTCGGCCATTTATTCGTATTTTTTCCAAATTTTATTACTTTCAATAAAAATATAATATT
TTTGAATCTTATTATTTTACATTATTTTAATACATTATATTTAAAATACATTAATTTATGTGTGC
TTAAATAAATTTAAAAAAACCCTTATTTCGGCTCTTTAATTTAGTGTAAAAAAAACCTTATTCCT
GCCCTTTGC
Found at i:54593594 original size:153 final size:155
Alignment explanation
Indices: 54593250--54593594 Score: 411
Period size: 153 Copynumber: 2.3 Consensus size: 155
54593240 TGCCCTTTGC
* *
54593250 TCGTATTATTTTC-CCGAATTTTATTACTTCCAAT-AAAAATATATTATTTTCGTATTTTATTAT
1 TCGTATT-TTTTCACCGAATTTTATTACTTCCAATAAAAAATATAATATTTTCGTATCTTATTAT
* * * **
54593313 TTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTT
65 TTTACATTATTTTAATACATTATATTTAAAATATATTAATTTAC-GTGTTGCTTAAATAAATTTT
* **
54593378 TAAAAAACTATTATTTCGGCCATTTAT
129 TAAAAAACCATTATTTCAACCATTTAT
* * *
54593405 TCGTATTTTTTCCCCAAATTTTATTACTT---TTAAAAAATATAATATTTTC-TAATCTTATTAT
1 TCGTATTTTTTCACCGAATTTTATTACTTCCAATAAAAAATATAATATTTTCGT-ATCTTATTAT
* *
54593466 TTTACATTATTTTAATACATTATATTTAAAATATTTTCATTTA-GTG-TGCTTAAATAAATTTTT
65 TTTACATTATTTTAATACATTATATTTAAAATATATTAATTTACGTGTTGCTTAAATAAATTTTT
* * *
54593529 AAAAAAACCCTTATTTCAACTATTTTT
130 -AAAAAACCATTATTTCAACCATTTAT
* *
54593556 TTGTATTTTTT-ACTGAATTTTATTACTTCCAATAAAAAA
1 TCGTATTTTTTCACCGAATTTTATTACTTCCAATAAAAAA
54593595 CACACTAACT
Statistics
Matches: 161, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
150 29 0.18
151 33 0.20
152 2 0.01
153 70 0.43
154 5 0.03
155 22 0.14
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (155 bp):
TCGTATTTTTTCACCGAATTTTATTACTTCCAATAAAAAATATAATATTTTCGTATCTTATTATT
TTACATTATTTTAATACATTATATTTAAAATATATTAATTTACGTGTTGCTTAAATAAATTTTTA
AAAAACCATTATTTCAACCATTTAT
Found at i:54593834 original size:20 final size:21
Alignment explanation
Indices: 54593797--54593836 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
54593787 TAGTAAATAA
*
54593797 TTTTTTTTATGTATTATTTTGG
1 TTTTTTTTA-GTAATATTTTGG
54593819 TTTTTTTTA-TAATATTTT
1 TTTTTTTTAGTAATATTTT
54593837 AGTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTTTTTTAGTAATATTTTGG
Found at i:54595793 original size:173 final size:168
Alignment explanation
Indices: 54595577--54596324 Score: 802
Period size: 178 Copynumber: 4.3 Consensus size: 168
54595567 CTTAATTTAC
* *
54595577 TTTAATCATCGCTGCAATTACCACAAAACAACACTCAAAAACCAAACATTTGTTTAAAAATTTTG
1 TTTAATCATCGCTGCACTTACTACAAAACAACACTC-AAAACCAAACATTTGTTTAAAAA--TTG
* * **
54595642 AACATT-CGGTCGGAAAAACGTTGTAAAAAAGAT-ACGGCAGCTCATTAGAGATTATATTGTAAT
63 AACATTAC--CCGGAAAAACGTCGTAAAAAAGATAAAAGCAGCTCATTAGAGATTATATTGTAAT
* * *
54595705 CATAGCTTAGGCAAAACCTTGGCTCATTACAACCCTAAACCTCAT
126 CATAGCTAAGGCAAAGCCTTGCCTCATT--AACCCTAAACCTCAT
* *
54595750 TTTAATCATCGCTGCAAC-TACTACAAAACAACACTCGAAAACCAAACATTTATTTATAAATCTT
1 TTTAATCATCGCTGC-ACTTACTACAAAACAACACTC-AAAACCAAACATTTGTTTA-AAA-ATT
* * * * *
54595814 GAACATTCAGCCGGAAAAACGTCGTTAGAAAGATAAAAGAAGCTCATTAAAGATTATATTGTAAT
62 GAACATT-ACCCGGAAAAACGTCGTAAAAAAGATAAAAGCAGCTCATTAGAGATTATATTGTAAT
54595879 CATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAACCTCAT
126 CATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAACCTCAT
* * ** * *
54595922 TTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACCTTTGCTGGAAGAACT-A
1 TTTAATCATCGCTGCACTTACTACAAAACAACACTCA-AAACCAAACATTTG-TTTAAAAATTGA
* * * *
54595986 AGCTTTACCCGGAAAAAAGTCATAAAACAGATAATAGCATAAAAGCAGCTCATTAGAGATTATAC
64 A-CATTACCCGGAAAAACGTCGT---A-A-A-AA-AG-ATAAAAGCAGCTCATTAGAGATTATAT
*
54596051 TGTAATCATAGCTAAGGCAAAGCCTTGCCTCGTTAACCCTAAACCTCAT
120 TGTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAACCTCAT
* * ** * * *
54596100 TTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACTTTTGCTGGAAGAACTCA
1 TTTAATCATCGCTGCACTTACTACAAAACAACACTCA-AAACCAAACATTTG-TTTAAAAATTGA
* * * *
54596165 GCTTTACCCGGAAAAAAGTCGTAAAACAGATAATAGCATAAAAGCAACTCATTAGAGATTATATT
64 ACATTACCCGGAAAAACGTCGT---A-A-A-AA-AG-ATAAAAGCAGCTCATTAGAGATTATATT
54596230 GTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAACCTCAT
121 GTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAACCTCAT
* *
54596278 TTTAATCATCGCTGCACTTACTACAAAACAACATTCATAATCCAAAC
1 TTTAATCATCGCTGCACTTACTACAAAACAACACTCA-AAACCAAAC
54596325 CATTGCTGGA
Statistics
Matches: 514, Mismatches: 42, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
170 16 0.03
171 7 0.01
172 61 0.12
173 81 0.16
174 56 0.11
176 2 0.00
177 2 0.00
178 288 0.56
179 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (168 bp):
TTTAATCATCGCTGCACTTACTACAAAACAACACTCAAAACCAAACATTTGTTTAAAAATTGAAC
ATTACCCGGAAAAACGTCGTAAAAAAGATAAAAGCAGCTCATTAGAGATTATATTGTAATCATAG
CTAAGGCAAAGCCTTGCCTCATTAACCCTAAACCTCAT
Found at i:54596075 original size:178 final size:178
Alignment explanation
Indices: 54595678--54596380 Score: 1018
Period size: 178 Copynumber: 4.0 Consensus size: 178
54595668 AAAAGATACG
* * *
54595678 GCAGCTCATTAGAGATTATATTGTAATCATAGCTTAGGCAAAACCTTGGCTCATTACAACCCTAA
1 GCAGCTCATTAGAGATTATATTGTAATCATAGCTAAGGCAAAGCCTTGCCTCATT--AACCCTAA
* * * **
54595743 ACCTCATTTTAATCATCGCTGCAAC-TACTACAAAACAACACTCGA-AAACCAAACATTT-ATTT
64 ACCTCATTTTAATCATCGCTGC-ACTTACTACAAAACAACACTC-ATAATCCAAACCTTTGCTGG
* * * *
54595805 ATA-AATCTTGAA-CATTCAGCCGGAAAAACGTCGT----TAG--AA-AG-ATAAAA
127 A-AGAA-C-T-AAGC-TTTACCCGGAAAAAAGTCGTAAAACAGATAATAGCATAAAA
* *
54595852 GAAGCTCATTAAAGATTATATTGTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAAC
1 GCAGCTCATTAGAGATTATATTGTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAAC
54595917 CTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACCTTTGCTGGAAGA
66 CTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACCTTTGCTGGAAGA
*
54595982 ACTAAGCTTTACCCGGAAAAAAGTCATAAAACAGATAATAGCATAAAA
131 ACTAAGCTTTACCCGGAAAAAAGTCGTAAAACAGATAATAGCATAAAA
* *
54596030 GCAGCTCATTAGAGATTATACTGTAATCATAGCTAAGGCAAAGCCTTGCCTCGTTAACCCTAAAC
1 GCAGCTCATTAGAGATTATATTGTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAAC
*
54596095 CTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACTTTTGCTGGAAGA
66 CTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACCTTTGCTGGAAGA
*
54596160 ACTCAGCTTTACCCGGAAAAAAGTCGTAAAACAGATAATAGCATAAAA
131 ACTAAGCTTTACCCGGAAAAAAGTCGTAAAACAGATAATAGCATAAAA
*
54596208 GCAACTCATTAGAGATTATATTGTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAAC
1 GCAGCTCATTAGAGATTATATTGTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAAC
* *
54596273 CTCATTTTAATCATCGCTGCACTTACTACAAAACAACATTCATAATCCAAACCATTGCTGGAAGA
66 CTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACCTTTGCTGGAAGA
* *
54596338 ACTCAGCTTTACCCGGTAAAAAGTCGTAAAACAGATAATAGCA
131 ACTAAGCTTTACCCGGAAAAAAGTCGTAAAACAGATAATAGCA
54596381 GCTTGAAAAA
Statistics
Matches: 487, Mismatches: 29, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
170 18 0.04
171 5 0.01
172 61 0.13
173 4 0.01
174 52 0.11
176 2 0.00
177 2 0.00
178 343 0.70
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (178 bp):
GCAGCTCATTAGAGATTATATTGTAATCATAGCTAAGGCAAAGCCTTGCCTCATTAACCCTAAAC
CTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCATAATCCAAACCTTTGCTGGAAGA
ACTAAGCTTTACCCGGAAAAAAGTCGTAAAACAGATAATAGCATAAAA
Found at i:54600115 original size:3 final size:3
Alignment explanation
Indices: 54600107--54600131 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54600097 TCGTTTGCAG
54600107 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
54600132 TTCGAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:54608071 original size:15 final size:14
Alignment explanation
Indices: 54608051--54608079 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54608041 ACATCTTTCC
54608051 ATATATA-AAATAT
1 ATATATATAAATAT
54608064 ATATATATAAATAT
1 ATATATATAAATAT
54608078 AT
1 AT
54608080 CTCTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATAAATAT
Found at i:54608900 original size:11 final size:11
Alignment explanation
Indices: 54608877--54608933 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
54608867 AATTGTTCTT
*
54608877 TTTTGTTACTA
1 TTTTGTTATTA
*
54608888 TTTTGTTGTTA
1 TTTTGTTATTA
***
54608899 TTTCACTATTA
1 TTTTGTTATTA
*
54608910 TATTGTTATTA
1 TTTTGTTATTA
54608921 TTTTGTTATTA
1 TTTTGTTATTA
54608932 TT
1 TT
54608934 ATTTGAATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:54608930 original size:22 final size:22
Alignment explanation
Indices: 54608868--54608932 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
54608858 GCAAACAAAA
* *
54608868 ATTGTTCTT-TTTTGTTACTAT
1 ATTGTTATTATTTTGTTATTAT
* * ***
54608889 TTTGTTGTTATTTCACTATTAT
1 ATTGTTATTATTTTGTTATTAT
54608911 ATTGTTATTATTTTGTTATTAT
1 ATTGTTATTATTTTGTTATTAT
54608933 TATTTGAATA
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.66
Consensus pattern (22 bp):
ATTGTTATTATTTTGTTATTAT
Found at i:54611614 original size:32 final size:32
Alignment explanation
Indices: 54611543--54611614 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
54611533 TGTTTTTTTT
** *
54611543 AGTTAAATTTGGTCTTCAATCTTTTAAAAAGA
1 AGTTAAATTTGACCATCAATCTTTTAAAAAGA
*
54611575 A-TCAAATTTGACCATCAATCTTTTGAAAAA-A
1 AGTTAAATTTGACCATCAATCTTTT-AAAAAGA
54611606 AGTTAAATT
1 AGTTAAATT
54611615 ATTGTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.38
Consensus pattern (32 bp):
AGTTAAATTTGACCATCAATCTTTTAAAAAGA
Found at i:54623929 original size:39 final size:39
Alignment explanation
Indices: 54623875--54624034 Score: 320
Period size: 39 Copynumber: 4.1 Consensus size: 39
54623865 ACGGACTGCT
54623875 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
1 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
54623914 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
1 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
54623953 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
1 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
54623992 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
1 GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
54624031 GTTG
1 GTTG
54624035 TTGGATCATT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 121 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (39 bp):
GTTGAACTCCCGTGTTGTTATTAGACATCTCCTGGAGAA
Found at i:54631345 original size:16 final size:18
Alignment explanation
Indices: 54631310--54631346 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
54631300 TATTAAAAAT
*
54631310 ATATTTTATCAATATGAA
1 ATATTTTATCAATATAAA
54631328 ATATTTT-T-AATATAAA
1 ATATTTTATCAATATAAA
54631344 ATA
1 ATA
54631347 GTGGGTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATTTTATCAATATAAA
Found at i:54646651 original size:23 final size:22
Alignment explanation
Indices: 54646609--54646651 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
54646599 CTTAAATTCC
*
54646609 TTAAAGATAATATAATTATAAA
1 TTAAAGATAACATAATTATAAA
54646631 TTAATAGATAACA-AATATATA
1 TTAA-AGATAACATAAT-TATA
54646652 TTTTTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (22 bp):
TTAAAGATAACATAATTATAAA
Found at i:54648037 original size:22 final size:21
Alignment explanation
Indices: 54648023--54648064 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
54648013 TAAATTCAAT
*
54648023 ATATACAT-TTTTTAAAATGA
1 ATATACATATTTTTAAAATAA
54648043 ATATACATATTTTTAAAA-AA
1 ATATACATATTTTTAAAATAA
54648063 AT
1 AT
54648065 CAAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATACATATTTTTAAAATAA
Found at i:54661143 original size:7 final size:7
Alignment explanation
Indices: 54661131--54661159 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
54661121 AATAATCACA
54661131 CCCATTG
1 CCCATTG
54661138 CCCATTG
1 CCCATTG
54661145 CCCATTG
1 CCCATTG
54661152 CCCATTG
1 CCCATTG
54661159 C
1 C
54661160 TGAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.45, G:0.14, T:0.28
Consensus pattern (7 bp):
CCCATTG
Found at i:54663761 original size:29 final size:29
Alignment explanation
Indices: 54663702--54663760 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
54663692 TTTAGTTTAA
* *
54663702 TGTGTAATTTTATACATGAACTTTGATTT
1 TGTGCAATTTTATACATAAACTTTGATTT
*
54663731 TGTGCAATTTTATACATTAAATTTTGATTT
1 TGTGCAATTTTATACA-TAAACTTTGATTT
54663761 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.53
Consensus pattern (29 bp):
TGTGCAATTTTATACATAAACTTTGATTT
Found at i:54663769 original size:30 final size:29
Alignment explanation
Indices: 54663707--54663769 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
54663697 TTTAATGTGT
* *
54663707 AATTTTATACATGAACTTTGATTTTGTGC
1 AATTTTATACATAAACTTTGATTTTGTCC
*
54663736 AATTTTATACATTAAATTTTGA-TTTGATCC
1 AATTTTATACA-TAAACTTTGATTTTG-TCC
54663766 AATT
1 AATT
54663770 CTCACAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (29 bp):
AATTTTATACATAAACTTTGATTTTGTCC
Found at i:54667876 original size:15 final size:15
Alignment explanation
Indices: 54667856--54667886 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54667846 ACTGATATTC
54667856 GTGCCGCCGCTGCTA
1 GTGCCGCCGCTGCTA
*
54667871 GTGCCGCCGCTTCTA
1 GTGCCGCCGCTGCTA
54667886 G
1 G
54667887 ACTACTACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.39, G:0.32, T:0.23
Consensus pattern (15 bp):
GTGCCGCCGCTGCTA
Found at i:54671001 original size:6 final size:7
Alignment explanation
Indices: 54670984--54671008 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54670974 GTTGTCTCGT
54670984 AAAAAAG
1 AAAAAAG
54670991 AAAAAAG
1 AAAAAAG
54670998 AAAAAAG
1 AAAAAAG
54671005 AAAA
1 AAAA
54671009 CGGTCAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:54673117 original size:21 final size:20
Alignment explanation
Indices: 54673093--54673133 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
54673083 ATGTTATATA
54673093 TTATAAAATTTATATTATTAT
1 TTATAAAATTTATA-TATTAT
**
54673114 TTATTTAATTTATATATTAT
1 TTATAAAATTTATATATTAT
54673134 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATAAAATTTATATATTAT
Found at i:54675412 original size:2 final size:2
Alignment explanation
Indices: 54675405--54675437 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
54675395 TACTTTGTAT
*
54675405 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54675438 TTAAGTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54677262 original size:17 final size:19
Alignment explanation
Indices: 54677240--54677285 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
54677230 AAAGAAAAAA
54677240 AAAGAA-AAAA-AAAGTTG
1 AAAGAATAAAATAAAGTTG
54677257 AAAGAATATAAAATAAAGTTG
1 AAAG-A-ATAAAATAAAGTTG
54677278 AAAGAATA
1 AAAGAATA
54677286 TAAAAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.16
18 1 0.04
19 4 0.16
20 5 0.20
21 11 0.44
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.17
Consensus pattern (19 bp):
AAAGAATAAAATAAAGTTG
Found at i:54677274 original size:21 final size:21
Alignment explanation
Indices: 54677245--54677295 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
54677235 AAAAAAAAGA
54677245 AAAAAAAAGTTGAAAGAATAT
1 AAAAAAAAGTTGAAAGAATAT
*
54677266 AAAATAAAGTTGAAAGAATAT
1 AAAAAAAAGTTGAAAGAATAT
54677287 AAAAGAAAA
1 AAAA-AAAA
54677296 AAAATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (21 bp):
AAAAAAAAGTTGAAAGAATAT
Found at i:54686303 original size:22 final size:21
Alignment explanation
Indices: 54686258--54686315 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
54686248 AATTTTAAAA
* *
54686258 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
54686278 TATTTTTAAAATAAATTTTTGG
1 TATTTTTAAAATAAATTTTT-G
54686300 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
54686316 GGGTCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.36
21 6 0.18
22 9 0.27
23 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:54686459 original size:20 final size:20
Alignment explanation
Indices: 54686420--54686460 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54686410 TTATTTTAAC
**
54686420 TTATTTTTAAAATACTTTTT
1 TTATTTTTAAAATAAATTTT
54686440 TTATTTTTAAAATAAATTTT
1 TTATTTTTAAAATAAATTTT
54686460 T
1 T
54686461 GGTGTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTTTTAAAATAAATTTT
Found at i:54692123 original size:31 final size:30
Alignment explanation
Indices: 54692085--54692147 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 30
54692075 ATATTTTTTA
54692085 ATTTTTTTTA-ATTTTAAAATATTTTGAAAAT
1 ATTTTTTTTACATTTTAAAAT-TTTT-AAAAT
*
54692116 ATTTTTTTTACTTTTTTAAAATTTTTAAAAT
1 ATTTTTTTTAC-ATTTTAAAATTTTTAAAAT
54692147 A
1 A
54692148 AATATGGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 16 0.55
32 4 0.14
33 9 0.31
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTTTTTTACATTTTAAAATTTTTAAAAT
Found at i:54698521 original size:14 final size:14
Alignment explanation
Indices: 54698502--54698528 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54698492 TAGATTGCAT
54698502 TTTGTTCTCATTAC
1 TTTGTTCTCATTAC
54698516 TTTGTTCTCATTA
1 TTTGTTCTCATTA
54698529 TTAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTGTTCTCATTAC
Found at i:54700064 original size:2 final size:2
Alignment explanation
Indices: 54700057--54700081 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54700047 TGTATGTATG
54700057 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54700082 CCTCGACGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54703339 original size:23 final size:22
Alignment explanation
Indices: 54703313--54703388 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 22
54703303 ATAAGTGCCA
54703313 CACTGATATGTAGCGGAAGCTAC
1 CACTGATATGTAGC-GAAGCTAC
*
54703336 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAG-CGAAGCTAC
*
54703359 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAG-CGAAGCTAC
54703382 CACTGAT
1 CACTGAT
54703389 CAAAAACACT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 46 0.98
24 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
CACTGATATGTAGCGAAGCTAC
Found at i:54703640 original size:18 final size:17
Alignment explanation
Indices: 54703614--54703652 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54703604 ATTTTCCTTC
54703614 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
54703631 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
54703649 CACA
1 CACA
54703653 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:54707317 original size:92 final size:88
Alignment explanation
Indices: 54707144--54707468 Score: 397
Period size: 90 Copynumber: 3.6 Consensus size: 88
54707134 ATAAATCAAA
*
54707144 TTCGTGTATTAATTCTT-TAGAATGTTTGTATTTT-TTGTATCTGTAAATTTAATTTAGTAGGTA
1 TTCGTGTATTAATT-TTCTAGAATGTTTGTATTTTGTTGTATCTGTAAATTTAATTTAGT-CGTA
*
54707207 TTATTTGTTGTTTCAATTTTATATT
64 TTATTTGTTGTTTGAATTTTATATT
* *
54707232 TTCGTGTATTAATTTTTTAGAATGTTTGTATTTTTTTGTTGTATCTATAAATTTAATTTAGCTCG
1 TTCGTGTATTAATTTTCTAGAATGTTTGTA---TTTTGTTGTATCTGTAAATTTAATTTAG-TCG
* *
54707297 TATTATTTGTAGTTTGAATTTTAAATT
62 TATTATTTGTTGTTTGAATTTTATATT
* ** * **
54707324 TTCTTGTATTAATTTTACCTA-TCTATTTGTATTTTGTTGGGTCTGTAAATTTAATTTAGTTCGT
1 TTCGTGTATTAATTTT--CTAGAATGTTTGTATTTTGTTGTATCTGTAAATTTAATTTAG-TCGT
54707388 ATTATTTGTTGTTTGAATTTTATATT
63 ATTATTTGTTGTTTGAATTTTATATT
* * * *
54707414 TTCGTGTATTAATCTTCAAAAATGTTTGTATTTTCTTGTAT-TGTAAATTTAATTT
1 TTCGTGTATTAATTTTCTAGAATGTTTGTATTTTGTTGTATCTGTAAATTTAATTT
54707469 GTTGTGTATT
Statistics
Matches: 203, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
87 2 0.01
88 43 0.21
89 15 0.07
90 67 0.33
91 4 0.02
92 62 0.31
93 8 0.04
94 2 0.01
ACGTcount: A:0.24, C:0.06, G:0.13, T:0.58
Consensus pattern (88 bp):
TTCGTGTATTAATTTTCTAGAATGTTTGTATTTTGTTGTATCTGTAAATTTAATTTAGTCGTATT
ATTTGTTGTTTGAATTTTATATT
Found at i:54707584 original size:21 final size:21
Alignment explanation
Indices: 54707532--54707584 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
54707522 TCATTTATCC
*
54707532 AAACAAATAA-TTATTTTAGA
1 AAACAAATAATTTATATTAGA
54707552 AAA-AAATAAATTTATATTA-A
1 AAACAAAT-AATTTATATTAGA
54707572 AAACAGAATAATT
1 AAACA-AATAATT
54707585 ACAAAGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 4 0.14
20 9 0.32
21 12 0.43
22 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (21 bp):
AAACAAATAATTTATATTAGA
Found at i:54708262 original size:20 final size:20
Alignment explanation
Indices: 54708237--54708275 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54708227 CTTTTTAAAT
* *
54708237 TTCATTTGAATTTCATTTTC
1 TTCATTTCAATCTCATTTTC
54708257 TTCATTTCAATCTCATTTT
1 TTCATTTCAATCTCATTTT
54708276 ACTTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (20 bp):
TTCATTTCAATCTCATTTTC
Found at i:54708434 original size:16 final size:16
Alignment explanation
Indices: 54708413--54708449 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
54708403 TTGGTTGGCT
*
54708413 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
54708429 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
54708445 GTAAT
1 GTAAT
54708450 AGGTAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:54708493 original size:45 final size:44
Alignment explanation
Indices: 54708429--54708518 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
54708419 GAATAGATGC
*
54708429 GTAATGGAATAGAGGCGTAATAGGTAATCTTTTATTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAAT-GGTAATCTTGTATTTGGTTGAAT
* *
54708474 GTAATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATGGTAATCTTGTATTTGGTTGAAT
54708518 G
1 G
54708519 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 21 0.50
45 21 0.50
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.38
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATGGTAATCTTGTATTTGGTTGAAT
Found at i:54708519 original size:39 final size:43
Alignment explanation
Indices: 54708429--54708535 Score: 132
Period size: 45 Copynumber: 2.5 Consensus size: 43
54708419 GAATAGATGC
*
54708429 GTAATGGAATAGAGGCGTAATAGGTAATCTTTTATTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATCTTGTATTTGGTT--AT
* *
54708474 GTAATGGAATAGAGGCGTAAT-GGTATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATCTTGTATTTGGTTAT
*
54708514 G-AATGGAATAGAGGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
54708536 CATAAGGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 18 0.32
40 3 0.05
43 1 0.02
44 14 0.25
45 21 0.37
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.36
Consensus pattern (43 bp):
GTAATGGAATAGAGGCGTAATAGGTAATCTTGTATTTGGTTAT
Found at i:54712571 original size:17 final size:17
Alignment explanation
Indices: 54712549--54712599 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
54712539 GACTAATCCC
*
54712549 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
*
54712566 TATACATTACCTAGGTA
1 TATACATTACTTAGGTA
*
54712583 TGTACATTACTTAGGTA
1 TATACATTACTTAGGTA
54712600 CATGCCACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:54715640 original size:21 final size:21
Alignment explanation
Indices: 54715616--54715655 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54715606 TTAAATTGTG
*
54715616 CTACATATTCAATTTAGTCCC
1 CTACATATTCAATTAAGTCCC
* *
54715637 CTACTTATTTAATTAAGTC
1 CTACATATTCAATTAAGTC
54715656 TCTGTACTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (21 bp):
CTACATATTCAATTAAGTCCC
Found at i:54717406 original size:22 final size:20
Alignment explanation
Indices: 54717376--54717419 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
54717366 TAATATGGTG
* *
54717376 TTTGATAATCATATTTAACAA
1 TTTGATAAT-AAATTTAAAAA
54717397 TTTGAATAATAAATTTAAAAA
1 TTTG-ATAATAAATTTAAAAA
54717418 TT
1 TT
54717420 AATTACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
TTTGATAATAAATTTAAAAA
Found at i:54717987 original size:21 final size:20
Alignment explanation
Indices: 54717956--54717999 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
54717946 GATGAAATGA
*
54717956 AAATTTATTTAT-TTAAAAT
1 AAATTTATTTATATAAAAAT
54717975 AAATTATATTTTATATAAAAAT
1 AAATT-TA-TTTATATAAAAAT
54717997 AAA
1 AAA
54718000 AATATCTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 5 0.24
22 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTATTTATATAAAAAT
Found at i:54721299 original size:14 final size:14
Alignment explanation
Indices: 54721280--54721306 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54721270 TAACAACTTT
54721280 CTAACTGCTTAATA
1 CTAACTGCTTAATA
54721294 CTAACTGCTTAAT
1 CTAACTGCTTAAT
54721307 TGCTTGATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (14 bp):
CTAACTGCTTAATA
Found at i:54721310 original size:22 final size:22
Alignment explanation
Indices: 54721285--54721328 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54721275 ACTTTCTAAC
54721285 TGCTTAATACTAACTGCTTAAT
1 TGCTTAATACTAACTGCTTAAT
*
54721307 TGCTTGATACTAACTGCTTAAT
1 TGCTTAATACTAACTGCTTAAT
54721329 AATATGCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (22 bp):
TGCTTAATACTAACTGCTTAAT
Found at i:54722353 original size:2 final size:2
Alignment explanation
Indices: 54722346--54722376 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54722336 AATTAAGTTT
54722346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54722377 CATTATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54730503 original size:6 final size:6
Alignment explanation
Indices: 54730492--54730516 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54730482 CTTTTCCCTT
54730492 CATCTC CATCTC CATCTC CATCTC C
1 CATCTC CATCTC CATCTC CATCTC C
54730517 TTCTTCCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CATCTC
Found at i:54747901 original size:20 final size:20
Alignment explanation
Indices: 54747865--54747906 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54747855 AACCTTGGTC
*
54747865 TTTTTAATATATTATTATTA
1 TTTTTAATATATTATTAATA
*
54747885 TTTTTAAT-TTTTAATTAATA
1 TTTTTAATATATT-ATTAATA
54747905 TT
1 TT
54747907 AAAAATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAATATATTATTAATA
Done.