Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 183 of 292
Found at i:54529041 original size:35 final size:35
Alignment explanation
Indices: 54528973--54529041 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
54528963 TAATTGTGTT
*
54528973 ATTAATTTCTTATTTTAAGTTCTAAATTTAAATTC
1 ATTAATTTCTTATTTTAAGTTCTAAATTAAAATTC
*
54529008 ATTAATTT-TTATATTT-AGTTTTAAAGTTAAAATT
1 ATTAATTTCTTAT-TTTAAGTTCTAAA-TTAAAATT
54529042 TTAATAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (35 bp):
ATTAATTTCTTATTTTAAGTTCTAAATTAAAATTC
Found at i:54529408 original size:43 final size:43
Alignment explanation
Indices: 54529174--54529411 Score: 343
Period size: 43 Copynumber: 5.6 Consensus size: 43
54529164 AAATATTTTT
**
54529174 TAAAGGTCATGTTCTTTAGCGATGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * * * *
54529217 TAAAGGT-ATGTTCTATAACAGCGTTTGTGGGAAAAGCACTGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
54529259 TAAAGGTCATGCTCTTTAGCAGCATTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* **
54529302 TAAAGGTCCTGTTCTTTAGCGGCGTTTGTGGGAAAAGTACCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
54529345 TAAAAGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
54529388 TAAAGGTCATGTTCTTTAGCGGCG
1 TAAAGGTCATGTTCTTTAGCGGCG
54529412 CTTTTAGGTC
Statistics
Matches: 170, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 35 0.21
43 135 0.79
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (43 bp):
TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:54529542 original size:12 final size:13
Alignment explanation
Indices: 54529507--54529557 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 13
54529497 CCGCAAAATA
54529507 TTAGCGGCGTTGTCT
1 TTAGCGGCGTT-T-T
54529522 TTAGCGGCGTTTT
1 TTAGCGGCGTTTT
*
54529535 TT-GCGGCGCTTT
1 TTAGCGGCGTTTT
*
54529547 TTAGCAGCGTT
1 TTAGCGGCGTT
54529558 ATATAGGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 11 0.34
13 9 0.28
14 1 0.03
15 11 0.34
ACGTcount: A:0.08, C:0.20, G:0.31, T:0.41
Consensus pattern (13 bp):
TTAGCGGCGTTTT
Found at i:54532438 original size:43 final size:41
Alignment explanation
Indices: 54532391--54532542 Score: 119
Period size: 42 Copynumber: 3.6 Consensus size: 41
54532381 CCTCGATTGA
54532391 GATTTACGTATAAGACCATGTCTGGAACATCAGCATTGTATTT
1 GATTT-CGTATAAGACCATGTCTGG-ACATCAGCATTGTATTT
* * * ** *
54532434 GATTTCGTGTAAGACCGTGTCTAGGACA-CATGC-CTCAATTGG
1 GATTTCGTATAAGACCATGTCT-GGACATCA-GCATTGTATT-T
* * * *
54532476 GATTTACGTATAAGACCATGTCTGGGAGATCGGCATCGTATCT
1 GATTT-CGTATAAGACCATGTCT-GGACATCAGCATTGTATTT
* *
54532519 GATTTCGTGTAAGACCCTGTCTGG
1 GATTTCGTATAAGACCATGTCTGG
54532543 GGCAGAGGCA
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
41 8 0.10
42 40 0.48
43 33 0.39
44 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (41 bp):
GATTTCGTATAAGACCATGTCTGGACATCAGCATTGTATTT
Found at i:54532498 original size:85 final size:85
Alignment explanation
Indices: 54532355--54532540 Score: 264
Period size: 85 Copynumber: 2.2 Consensus size: 85
54532345 CTAAGACATT
* * *
54532355 GTGTAAGACTATGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGAACA
1 GTGTAAGACCATGTCTAGGACACAGGCCTCAATTGAGATTTACGTATAAGACCATGTCTGGAACA
* *
54532420 TCAGCATTGTATTTGATTTC
66 TCAGCATCGTATCTGATTTC
* * * * *
54532440 GTGTAAGACCGTGTCTAGGACACATGCCTCAATTGGGATTTACGTATAAGACCATGTCTGGGAGA
1 GTGTAAGACCATGTCTAGGACACAGGCCTCAATTGAGATTTACGTATAAGACCATGTCTGGAACA
*
54532505 TCGGCATCGTATCTGATTTC
66 TCAGCATCGTATCTGATTTC
*
54532525 GTGTAAGACCCTGTCT
1 GTGTAAGACCATGTCT
54532541 GGGGCAGAGG
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (85 bp):
GTGTAAGACCATGTCTAGGACACAGGCCTCAATTGAGATTTACGTATAAGACCATGTCTGGAACA
TCAGCATCGTATCTGATTTC
Found at i:54532575 original size:85 final size:84
Alignment explanation
Indices: 54532355--54532578 Score: 216
Period size: 85 Copynumber: 2.6 Consensus size: 84
54532345 CTAAGACATT
** * * * * *
54532355 GTGTAAGACTATGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGAACA
1 GTGTAAGACCCTGTCTAGGACACAGGCATCAATTG-GAATTACATATAAGACCATGTCTGGAACA
* *
54532420 TCAGCATTGTATTTGATTTC
65 TCAGCATCGTATCTGATTTC
* * * * * * *
54532440 GTGTAAGACCGTGTCTAGGACACATGCCTCAATTGGGATTTACGTATAAGACCATGTCTGGGAGA
1 GTGTAAGACCCTGTCTAGGACACAGGCATCAATT-GGAATTACATATAAGACCATGTCTGGAACA
*
54532505 TCGGCATCGTATCTGATTTC
65 TCAGCATCGTATCTGATTTC
* * * *
54532525 GTGTAAGACCCTGTCTGGGGCAGAGGCATCGATATT-GAATTACATTTAAGACCA
1 GTGTAAGACCCTGTCTAGGACACAGGCATC-A-ATTGGAATTACATATAAGACCA
54532579 CATCCGGGAC
Statistics
Matches: 117, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
85 112 0.96
86 2 0.02
87 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCCTGTCTAGGACACAGGCATCAATTGGAATTACATATAAGACCATGTCTGGAACAT
CAGCATCGTATCTGATTTC
Found at i:54534461 original size:11 final size:12
Alignment explanation
Indices: 54534445--54534473 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
54534435 ACTCATAAAG
54534445 ATTTTTTCTA-A
1 ATTTTTTCTATA
54534456 ATTTTTTCTATA
1 ATTTTTTCTATA
54534468 ATTTTT
1 ATTTTT
54534474 GGTTCAGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTTTTCTATA
Found at i:54535321 original size:71 final size:71
Alignment explanation
Indices: 54535170--54535337 Score: 239
Period size: 71 Copynumber: 2.4 Consensus size: 71
54535160 CTAACCGATT
54535170 TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA
1 TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA
** *
54535235 TTTATC
66 TACAGC
* * *
54535241 TTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGTGACCTAGCTAC-
1 TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA
*
54535305 TACAGGG
66 TACA-GC
* *
54535312 TGTCTCGTAGCTTTCTTGTATACATG
1 TGTCTCGTAGCTCTCTTGTCTACATG
54535338 ATGTGCACTC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
70 2 0.02
71 83 0.98
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (71 bp):
TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA
TACAGC
Found at i:54542185 original size:26 final size:26
Alignment explanation
Indices: 54542154--54542205 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
54542144 GAAATGAATG
54542154 ATTGAATGGTTGAATTTGTATTGTAT
1 ATTGAATGGTTGAATTTGTATTGTAT
54542180 ATTGAATGGTTGAATTTGTATTGTAT
1 ATTGAATGGTTGAATTTGTATTGTAT
54542206 TAGATCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (26 bp):
ATTGAATGGTTGAATTTGTATTGTAT
Found at i:54542576 original size:42 final size:41
Alignment explanation
Indices: 54542474--54542626 Score: 157
Period size: 42 Copynumber: 3.6 Consensus size: 41
54542464 AGACATCGTG
* *
54542474 TAAGACCATGTCTGGGACA-CATGCCTCGATTGAGATTTACGTA
1 TAAGACCATGTCTGGGACATC-GGCATCGATT--GATTTACGTA
*
54542517 TAAGACCATGTCTGGGACATCGGCATCGTATCTGATTT-CGTG
1 TAAGACCATGTCTGGGACATCGGCATCG-AT-TGATTTACGTA
* * * *
54542559 TAAGACCGTGTCTGGGACATAGGCCTCGATGAGATTTACGTA
1 TAAGACCATGTCTGGGACATCGGCATCGAT-TGATTTACGTA
* *
54542601 TAAGACCATGACTGGGACATTGGCAT
1 TAAGACCATGTCTGGGACATCGGCAT
54542627 TGTACTTGTT
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
41 7 0.08
42 53 0.57
43 29 0.31
44 3 0.03
45 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (41 bp):
TAAGACCATGTCTGGGACATCGGCATCGATTGATTTACGTA
Found at i:54542619 original size:84 final size:85
Alignment explanation
Indices: 54542469--54542626 Score: 264
Period size: 84 Copynumber: 1.9 Consensus size: 85
54542459 GTCTGAGACA
* *
54542469 TCGTGTAAGACCATGTCTGGGACACATGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGA
1 TCGTGTAAGACCATGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGACTGGGA
54542534 CATCGGCATCGTATCTGATT
66 CATCGGCATCGTATCTGATT
* *
54542554 TCGTGTAAGACCGTGTCTGGGACATAGGCCTCGA-TGAGATTTACGTATAAGACCATGACTGGGA
1 TCGTGTAAGACCATGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGACTGGGA
*
54542618 CATTGGCAT
66 CATCGGCAT
54542627 TGTACTTGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 37 0.54
85 31 0.46
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (85 bp):
TCGTGTAAGACCATGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGACTGGGA
CATCGGCATCGTATCTGATT
Found at i:54547293 original size:28 final size:28
Alignment explanation
Indices: 54547239--54547293 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
54547229 AGATATAAAC
* *
54547239 TATTTAAATAATAAAATGATATTTTTAT
1 TATTTAAAAAATAAAATGATAATTTTAT
*
54547267 TATTATAAAAAATAAAAT-TTAATTTTA
1 TATT-TAAAAAATAAAATGATAATTTTA
54547294 GACCCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TATTTAAAAAATAAAATGATAATTTTAT
Found at i:54548382 original size:14 final size:14
Alignment explanation
Indices: 54548364--54548410 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
54548354 GGTTATATGT
*
54548364 TTTAATTATTGTTT
1 TTTAATTATTGTTA
*
54548378 TTTAATAATT-TTA
1 TTTAATTATTGTTA
*
54548391 TTTAATATATCGTTA
1 TTTAAT-TATTGTTA
54548406 TTTAA
1 TTTAA
54548411 ATAACAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 8 0.30
14 11 0.41
15 8 0.30
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (14 bp):
TTTAATTATTGTTA
Found at i:54548508 original size:18 final size:18
Alignment explanation
Indices: 54548487--54548521 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54548477 TTTCGAACAC
*
54548487 TTATTTATATTTTTTAAT
1 TTATTTATATCTTTTAAT
54548505 TTATTTATATCTTTTAA
1 TTATTTATATCTTTTAA
54548522 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATATCTTTTAAT
Found at i:54548567 original size:138 final size:140
Alignment explanation
Indices: 54548403--54548688 Score: 332
Period size: 138 Copynumber: 2.1 Consensus size: 140
54548393 TAATATATCG
* * ** *
54548403 TTATTTAAATAACAGTTTTATAAAACATACGAGCAATTCATACATCACATAG-GATAAAAAACTA
1 TTATTTAAATAACAGTTTTATAAAACACACAAGCAACCCATACAACACA-AGAGATAAAAAACTA
* * ** **
54548467 CCATATTATATTTCGAACACTTATTTATATTTTTTAAT-TT-ATTTATATCTTTTAAATATT-TT
65 CCATATTATATTTCAAAAACTTAAGTATA-TTTCAAATATTGA-TTATATCTTTTAAATATTGTT
*
54548529 TTATC-AATAAAT
128 TAATCAAATAAAT
* * *
54548541 TTATTTAAATAA-TGATTTTATAAAACACACAAGCAACCCGTACAACACACGAGATAAAAAACTA
1 TTATTTAAATAACAG-TTTTATAAAACACACAAGCAACCCATACAACACAAGAGATAAAAAACTA
**
54548605 GTATATTATATTTCAAAAACTTAAGTATATTTCAAATATTGATTATATCTTTTAAATATTGTTTA
65 CCATATTATATTTCAAAAACTTAAGTATATTTCAAATATTGATTATATCTTTTAAATATTGTTTA
*
54548670 ATCAAATAATT
130 ATCAAATAAAT
54548681 TTATTTAA
1 TTATTTAA
54548689 CATATAATTA
Statistics
Matches: 124, Mismatches: 18, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
137 8 0.06
138 95 0.77
139 7 0.06
140 14 0.11
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.41
Consensus pattern (140 bp):
TTATTTAAATAACAGTTTTATAAAACACACAAGCAACCCATACAACACAAGAGATAAAAAACTAC
CATATTATATTTCAAAAACTTAAGTATATTTCAAATATTGATTATATCTTTTAAATATTGTTTAA
TCAAATAAAT
Found at i:54551936 original size:136 final size:135
Alignment explanation
Indices: 54551727--54552111 Score: 554
Period size: 136 Copynumber: 2.8 Consensus size: 135
54551717 GAGCTGCTCG
*
54551727 AACTTAATCCAACTACTTTTAAGTTTATTTCCATCTTTCAAGTGCCAAATCATTTTGAAACTATT
1 AACTTAATCGAACTAC-TTTAAGTTTATTTCCATCTTTCAAGTGCCAAATCATTTTGAAACTATT
* * * * *
54551792 TGAGTCCAAGACTTTACTTCAGTAAGGCAGAGAAATAAATCATGTATTTGTAGACTATTGTGTTG
65 TGAGTCCAAGACTTTACTTCAATAAGGCAGTGAAATAAATTATGTATTTGCAAACTATTGTGTTG
54551857 CTTGTA
130 CTTGTA
* * * * *
54551863 AACTTAATTGAACTACTGTTAAGTTTATTTCTATTTTTCAAGTGTCAAATCATTTTGGAACTATT
1 AACTTAATCGAACTACT-TTAAGTTTATTTCCATCTTTCAAGTGCCAAATCATTTTGAAACTATT
* *
54551928 TGAGTCCAAGACTTTACTTCAACAAGGCAGTGAAATATATTATGTATTTGCAAACTATTGTGTTG
65 TGAGTCCAAGACTTTACTTCAATAAGGCAGTGAAATAAATTATGTATTTGCAAACTATTGTGTTG
54551993 CTTGTA
130 CTTGTA
*
54551999 AACTTAATCGAACTACTTTCAAATTTATTTCCATCTTTCAAGTGCCAAATCATTTTGAAACTATT
1 AACTTAATCGAACTACTTT-AAGTTTATTTCCATCTTTCAAGTGCCAAATCATTTTGAAACTATT
* * * * ** *
54552064 TGAATTCAAAATTTTACTTCAATAAATCAGTGAAATGAATTATGTATT
65 TGAGTCCAAGACTTTACTTCAATAAGGCAGTGAAATAAATTATGTATT
54552112 AATAGAATAT
Statistics
Matches: 219, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
135 3 0.01
136 216 0.99
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (135 bp):
AACTTAATCGAACTACTTTAAGTTTATTTCCATCTTTCAAGTGCCAAATCATTTTGAAACTATTT
GAGTCCAAGACTTTACTTCAATAAGGCAGTGAAATAAATTATGTATTTGCAAACTATTGTGTTGC
TTGTA
Found at i:54552853 original size:18 final size:18
Alignment explanation
Indices: 54552832--54552870 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
54552822 TGAATTTTCG
*
54552832 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCGAAT
*
54552850 AATTTGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
54552868 AAT
1 AAT
54552871 ATTTTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:54554068 original size:25 final size:25
Alignment explanation
Indices: 54554035--54554091 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
54554025 TATCAACAAA
54554035 TTAAATAGAATAATTAATAATAAAT
1 TTAAATAGAATAATTAATAATAAAT
54554060 TTAAATAGAATAATTAATAATAAAT
1 TTAAATAGAATAATTAATAATAAAT
54554085 TTAAATA
1 TTAAATA
54554092 TGTGTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
TTAAATAGAATAATTAATAATAAAT
Found at i:54555587 original size:23 final size:23
Alignment explanation
Indices: 54555561--54555604 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
54555551 TTAAAATAAA
*
54555561 TATTATGATATGAATT-TATTTTC
1 TATTATGACAT-AATTATATTTTC
*
54555584 TATTGTGACATAATTATATTT
1 TATTATGACATAATTATATTT
54555605 AGTACATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (23 bp):
TATTATGACATAATTATATTTTC
Found at i:54557984 original size:49 final size:49
Alignment explanation
Indices: 54557908--54558037 Score: 147
Period size: 49 Copynumber: 2.7 Consensus size: 49
54557898 TGTTGTGTGT
* * * *
54557908 CAGTGTAAGACTTGT-TGGGACATGGCATTGACAC-CGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTAGATAGATGAAAGC
* * * * *
54557956 CAGTGTAAGACCTGTCTAGGACATGGCATCGGCCTATATATATGAAAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTAGATAGATGAAAGC
*
54558005 CAGTGTAAGACCTGTCTGGGACACGGCATCGAC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC
54558038 TTTAATGTGC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 15 0.22
49 53 0.78
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTAGATAGATGAAAGC
Found at i:54561829 original size:35 final size:35
Alignment explanation
Indices: 54561790--54561860 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
54561780 AAATCCAAAA
*
54561790 ACCATAGTTTGTATAATCGCCTTACAAATAATCTT
1 ACCATAGTTTGTATAATCGACTTACAAATAATCTT
*
54561825 ACCATAGTTTGTATAATCGACTTAGAAATAATCTT
1 ACCATAGTTTGTATAATCGACTTACAAATAATCTT
54561860 A
1 A
54561861 AAACCAACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (35 bp):
ACCATAGTTTGTATAATCGACTTACAAATAATCTT
Found at i:54562396 original size:37 final size:38
Alignment explanation
Indices: 54562308--54562401 Score: 97
Period size: 37 Copynumber: 2.5 Consensus size: 38
54562298 CACCACTTCG
*
54562308 ACCACCCTACACACCACAAGAGACCCATGAAAAGCCCA
1 ACCACCCTATACACCACAAGAGACCCATGAAAAGCCCA
*
54562346 ACCACCCTGTACACCACATAG-GA-CCAT-AATAGAG-CCA
1 ACCACCCTATACACCACA-AGAGACCCATGAA-A-AGCCCA
* *
54562383 TCCACCCTATACACAACAA
1 ACCACCCTATACACCACAA
54562402 ATGTGGAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 3 0.06
37 23 0.48
38 20 0.42
39 2 0.04
ACGTcount: A:0.40, C:0.39, G:0.10, T:0.11
Consensus pattern (38 bp):
ACCACCCTATACACCACAAGAGACCCATGAAAAGCCCA
Found at i:54565091 original size:20 final size:21
Alignment explanation
Indices: 54565062--54565100 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
54565052 GGACTAAATC
54565062 AAAAACCTTAGAAAATTTTGG
1 AAAAACCTTAGAAAATTTTGG
54565083 AAAAA-CTTAGAAAATTTT
1 AAAAACCTTAGAAAATTTT
54565101 TCCATGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAACCTTAGAAAATTTTGG
Found at i:54567070 original size:47 final size:49
Alignment explanation
Indices: 54567000--54567122 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 49
54566990 GCCGACAACA
* *
54567000 TGTCCCAGACATGGTCTTACACTGGCTAGCACAT-T-AAGGTCAATACT-G
1 TGTCCCAAACA-GGTCTTACACTGGCTAGCACATATCAAGGCCAAT-CTCG
* ** * * *
54567048 TGTCCCAAATAGGTCTTACACTGGCTTTCATATATCGAGGCCAATGTCG
1 TGTCCCAAACAGGTCTTACACTGGCTAGCACATATCAAGGCCAATCTCG
54567097 TGTCCCAAACAGGTCTTACACTGGCT
1 TGTCCCAAACAGGTCTTACACTGGCT
54567123 CTCATCTATT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
47 19 0.30
48 11 0.17
49 33 0.52
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (49 bp):
TGTCCCAAACAGGTCTTACACTGGCTAGCACATATCAAGGCCAATCTCG
Found at i:54567150 original size:49 final size:49
Alignment explanation
Indices: 54567048--54567259 Score: 152
Period size: 49 Copynumber: 4.4 Consensus size: 49
54567038 GTCAATACTG
* * * *
54567048 TGTCCCAAATAGGTCTTACACTGGCTTTCATATATCGAGGCCAATGTCG
1 TGTCCCAAACAGGTCTTACACTGGCTCTCATATATCGAGGCCAATGCCA
* * * * *
54567097 TGTCCCAAACAGGTCTTACACTGGCTCTCATCTATTGATGTCGATGCCA
1 TGTCCCAAACAGGTCTTACACTGGCTCTCATATATCGAGGCCAATGCCA
* * * **
54567146 TGT-CCAAGACAAGTCTTACACTGGCACACA-ATA---A-GCTGATGCCA
1 TGTCCCAA-ACAGGTCTTACACTGGCTCTCATATATCGAGGCCAATGCCA
* * * * * *
54567190 TGTCTCAGACAGGTCTTATACTAGCT-TGCATATCTCGAGGCCGATG-CA
1 TGTCCCAAACAGGTCTTACACTGGCTCT-CATATATCGAGGCCAATGCCA
* *
54567238 TGTCCCAGACATGTCTTACACT
1 TGTCCCAAACAGGTCTTACACT
54567260 AGCACACATA
Statistics
Matches: 128, Mismatches: 27, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
44 27 0.21
45 5 0.04
48 28 0.22
49 68 0.53
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (49 bp):
TGTCCCAAACAGGTCTTACACTGGCTCTCATATATCGAGGCCAATGCCA
Found at i:54567270 original size:48 final size:47
Alignment explanation
Indices: 54567138--54567271 Score: 123
Period size: 48 Copynumber: 2.9 Consensus size: 47
54567128 CTATTGATGT
* *
54567138 CGATGCCATGTCCAAGACAAGTCTTACACTGGCACACA-A--TAAGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAGCACACATATCTAAGC
* * * * *** *
54567182 TGATGCCATGTCTCAGACAGGTCTTATACTAGCTTGCATATCTCGAGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAGCACACATATCT--AAGC
*
54567231 CGATG-CATGTCCCAGACATGTCTTACACTAGCACACATATC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAGCACACATATC
54567272 ACCCAATGTC
Statistics
Matches: 68, Mismatches: 17, Indels: 6
0.75 0.19 0.07
Matches are distributed among these distances:
44 29 0.43
45 1 0.01
47 1 0.01
48 30 0.44
49 7 0.10
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACAAGTCTTACACTAGCACACATATCTAAGC
Found at i:54569776 original size:46 final size:46
Alignment explanation
Indices: 54569601--54569776 Score: 164
Period size: 46 Copynumber: 3.8 Consensus size: 46
54569591 TGTAACCAGC
* * *
54569601 CCATAAGCGAACTCGGGCTCAACTCAACAAGCTCAGG-CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GGACGTTCGCAT
* * *
54569647 CCATAAGTGAATTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* *
54569697 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
54569740 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
54569777 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 4 0.04
46 58 0.55
47 27 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:54569776 original size:93 final size:93
Alignment explanation
Indices: 54569608--54569780 Score: 267
Period size: 93 Copynumber: 1.9 Consensus size: 93
54569598 AGCCCATAAG
* *
54569608 CGAACTCGGGCTCAACTCAACAAGCTCAGGCATTCGCATCCATAAGTGAATTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54569673 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * *
54569701 CGAACTCGGACTCAACTCAACGAGTTC-GGACGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACAAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTC
* *
54569765 AATGAGTTCGGATGCC
65 AACGAGCTCGGATGCC
54569781 CAAATATCTG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:54572560 original size:15 final size:15
Alignment explanation
Indices: 54572540--54572572 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54572530 AAATCCAAAA
54572540 CAAAATAAAAAGATC
1 CAAAATAAAAAGATC
*
54572555 CAAAATAAAGAGATC
1 CAAAATAAAAAGATC
54572570 CAA
1 CAA
54572573 GATTGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.15, G:0.09, T:0.12
Consensus pattern (15 bp):
CAAAATAAAAAGATC
Found at i:54577937 original size:39 final size:39
Alignment explanation
Indices: 54577883--54578123 Score: 365
Period size: 39 Copynumber: 6.2 Consensus size: 39
54577873 TGTGAATGAA
* *
54577883 TGTGCGAATTGTGATATCTGGGATAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
54577922 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
54577961 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
54578000 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* ** *
54578039 TGTGTGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
54578078 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
54578118 TGTGCG
1 TGTGCG
54578124 GGTTACCATA
Statistics
Matches: 184, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
39 167 0.91
40 17 0.09
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:54589337 original size:40 final size:39
Alignment explanation
Indices: 54589273--54589437 Score: 154
Period size: 40 Copynumber: 4.2 Consensus size: 39
54589263 TCTTCAGAAT
* **
54589273 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAA-TGCCTTCGGGTC
* * *** * *
54589312 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTTGGGTC
1 TTAGCCCGGATATAACAACTCGCAC-AATGCCTTCGGGTC
54589352 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCAC-AATGCCTTCGGGTC
* * *
54589392 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTCGCA-CAATGCCTTCGGGTC
54589432 TTAGCC
1 TTAGCC
54589438 TGGGTATCAT
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.03
40 96 0.94
41 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
TTAGCCCGGATATAACAACTCGCACAATGCCTTCGGGTC
Found at i:54589421 original size:80 final size:80
Alignment explanation
Indices: 54589273--54589437 Score: 199
Period size: 80 Copynumber: 2.1 Consensus size: 80
54589263 TCTTCAGAAT
* * ** *
54589273 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCAC
1 TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCAC
* *
54589337 AAATGCCTTTGGGTC
66 AAATGCCTTCGGGAC
** * *
54589352 TTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCA
1 TTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCA
*
54589416 TAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
54589432 TTAGCC
1 TTAGCC
54589438 TGGGTATCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 4 0.06
80 66 0.92
81 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCAC
AAATGCCTTCGGGAC
Found at i:54591505 original size:30 final size:30
Alignment explanation
Indices: 54591471--54591571 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 30
54591461 GCGTGTGTCT
* * *
54591471 CAGCCATGTTTGACACACGCCCAGGCAATA
1 CAGCCGTGTGTGACACACGCCCAGGCAACA
*
54591501 CAGCCGTGTGTGACACATGCCCAGGCAACA
1 CAGCCGTGTGTGACACACGCCCAGGCAACA
* * *
54591531 CAGTCGTGTGTGGCACACACCCAGGCAACA
1 CAGCCGTGTGTGACACACGCCCAGGCAACA
* *
54591561 CAACTGTGTGT
1 CAGCCGTGTGT
54591572 CCCTTGTAGC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.17
Consensus pattern (30 bp):
CAGCCGTGTGTGACACACGCCCAGGCAACA
Found at i:54593657 original size:53 final size:53
Alignment explanation
Indices: 54593574--54593679 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
54593564 TCATGCAGAC
*
54593574 ACAAACAAATGTCAACAATCAGACTTCACAAGATATCAATGAAATCAAAAGCA
1 ACAAACAAATGTCAACAATCAGACTCCACAAGATATCAATGAAATCAAAAGCA
*
54593627 ACAAACAAATGTCAACAATCAGACTCCACAAGATATCAATGAAATCAAGAGCA
1 ACAAACAAATGTCAACAATCAGACTCCACAAGATATCAATGAAATCAAAAGCA
54593680 TACTTTCTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.52, C:0.22, G:0.10, T:0.16
Consensus pattern (53 bp):
ACAAACAAATGTCAACAATCAGACTCCACAAGATATCAATGAAATCAAAAGCA
Found at i:54595333 original size:6 final size:6
Alignment explanation
Indices: 54595324--54595353 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
54595314 AGATTCAATA
*
54595324 TTATTA TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT
54595354 AACTTGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:54602776 original size:2 final size:2
Alignment explanation
Indices: 54602769--54602800 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54602759 AAATCGCTTA
54602769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54602801 CAATACTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54608259 original size:41 final size:40
Alignment explanation
Indices: 54608214--54608316 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 40
54608204 CAAAAAAATG
* *
54608214 CTTCCAGGTGGAAGCGTTTTCTTGCACAT-ACGCTGAAAACA
1 CTTCCAAGTGGAAGCATTTTC-TGCACATCAC-CTGAAAACA
* * **
54608255 CTTCCACGTGGATGCACTTTTCTGCATTTCACCTGAAAACA
1 CTTCCAAGTGGAAGCA-TTTTCTGCACATCACCTGAAAACA
*
54608296 CTTTCAAGTGGAAGCATTTTC
1 CTTCCAAGTGGAAGCATTTTC
54608317 GAAAATTGGC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 5 0.10
41 40 0.77
42 7 0.13
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (40 bp):
CTTCCAAGTGGAAGCATTTTCTGCACATCACCTGAAAACA
Found at i:54609349 original size:63 final size:61
Alignment explanation
Indices: 54609247--54609377 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 61
54609237 TTTGTGAACC
* *
54609247 ACACGGTTGTGTGGTAGGTCGTGCAACTCACTATTTGGAATTAAAGTCACACAGACCAGAG
1 ACACGGGTGTGTGGTAGGTAGTGCAACTCACTATTTGGAATTAAAGTCACACAGACCAGAG
* * * * * * * *
54609308 ACACGGGTGTGTGTTCAGGTAGTGTAACTCACTGTTTTGGAATTAGAGTCGCACGGGCTAGAG
1 ACACGGGTGTGTGGT-AGGTAGTGCAACTCACT-ATTTGGAATTAAAGTCACACAGACCAGAG
54609371 ACACGGG
1 ACACGGG
54609378 CATGTGCCAG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 13 0.22
62 15 0.26
63 30 0.52
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (61 bp):
ACACGGGTGTGTGGTAGGTAGTGCAACTCACTATTTGGAATTAAAGTCACACAGACCAGAG
Found at i:54621442 original size:2 final size:2
Alignment explanation
Indices: 54621435--54621466 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54621425 GCTCATGATC
54621435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54621467 TAAATAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54630270 original size:49 final size:49
Alignment explanation
Indices: 54630163--54630285 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 49
54630153 CTTGTTGTGT
** * * *
54630163 GCCAGTGTAAGACCTGTCTACGAGATGGCATCGACATTGATAGACGAGA
1 GCCAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGACGAAA
* * * * *
54630212 GCCAATGTAAGATCTGTCTGGGACATGGCATCGACCTCGATATATGAAA
1 GCCAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGACGAAA
*
54630261 GTCAGTGTAAGACCTGTCTGGGACA
1 GCCAGTGTAAGACCTGTCTGGGACA
54630286 CGACTTCGAC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (49 bp):
GCCAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGACGAAA
Found at i:54630277 original size:142 final size:138
Alignment explanation
Indices: 54630020--54630285 Score: 338
Period size: 142 Copynumber: 1.9 Consensus size: 138
54630010 TTGGGTGGTA
* * * * *
54630020 TGTGAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGACGTGAGCTAGTGTAAGAAA
1 TGTGAGCCAGTGTAAGACATGTCTACGACATGCATCGACATTGAGACGAGAGCCAATGTAAGAAA
* * *
54630085 TGTTTGGGACATGCATCGGCCTCGGGATATACAAGCTAGTGTAAGACCTGTCTGGGACATGGCGT
66 TGTCTGGGACATGCATCGACCTCGAGATATACAAGCTAGTGTAAGACCTGTCTGGGACATGGCGT
54630150 CAGCTTGT
131 CAGCTTGT
* * *
54630158 TGTGTGCCAGTGTAAGACCTGTCTACGAGATGGCATCGACATTGATAGACGAGAGCCAATGTAAG
1 TGTGAGCCAGTGTAAGACATGTCTACGACAT-GCATCGACATTG--AGACGAGAGCCAATGTAAG
** *
54630223 ATCTGTCTGGGACATGGCATCGACCTCGATATATGA-AAG-TCAGTGTAAGACCTGTCTGGGACA
63 AAATGTCTGGGACAT-GCATCGACCTCGAGATAT-ACAAGCT-AGTGTAAGACCTGTCTGGGACA
54630286 CGACTTCGAC
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
138 27 0.25
139 11 0.10
141 29 0.27
142 40 0.37
143 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (138 bp):
TGTGAGCCAGTGTAAGACATGTCTACGACATGCATCGACATTGAGACGAGAGCCAATGTAAGAAA
TGTCTGGGACATGCATCGACCTCGAGATATACAAGCTAGTGTAAGACCTGTCTGGGACATGGCGT
CAGCTTGT
Found at i:54634754 original size:31 final size:31
Alignment explanation
Indices: 54634719--54634781 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
54634709 TGCTGACAAC
54634719 TTGTAAGTCTGTCGTCGTATCAACAAATCAT
1 TTGTAAGTCTGTCGTCGTATCAACAAATCAT
54634750 TTGTAAGTCTGTCGTCGTATCAACAAATCAT
1 TTGTAAGTCTGTCGTCGTATCAACAAATCAT
54634781 T
1 T
54634782 CTCACTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (31 bp):
TTGTAAGTCTGTCGTCGTATCAACAAATCAT
Found at i:54635770 original size:25 final size:26
Alignment explanation
Indices: 54635722--54635778 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
54635712 AAATTTATAC
*
54635722 ATAA-TATTAAAATTATATAGAAATGA
1 ATAATTATTAAAATTATATAAAAAT-A
*
54635748 A-AATTATT-AAATTATTTAAAAATA
1 ATAATTATTAAAATTATATAAAAATA
54635772 ATAATTA
1 ATAATTA
54635779 ATTTGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.07
25 20 0.74
26 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
ATAATTATTAAAATTATATAAAAATA
Found at i:54637664 original size:40 final size:40
Alignment explanation
Indices: 54637598--54637764 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
54637588 AAATTGAATG
* * *
54637598 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
54637637 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
54637677 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
54637717 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
54637757 ATATCCGG
1 ATATCCGG
54637765 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:54645665 original size:40 final size:40
Alignment explanation
Indices: 54645599--54645765 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
54645589 AAATTGAATG
* * *
54645599 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
54645638 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
54645678 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
54645718 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
54645758 ATATCCGG
1 ATATCCGG
54645766 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:54655186 original size:205 final size:205
Alignment explanation
Indices: 54654817--54655810 Score: 1692
Period size: 205 Copynumber: 4.9 Consensus size: 205
54654807 GTAATAGGCC
* *
54654817 ACACATAGCAGATCTCACCTTCAGACGATTTCA--CTGAAGCAGATCCAAGATGGTTTGGCATCC
1 ACACATAGCAGATCTCACCTTCAGATG-TTT-ATGCTGAAGCGGATCCAAGATGGTTTGGCATCC
54654880 TTGTGTTTACAAGGAACAAATCGAAGA-ATAGCTGATTTGGCTTTCATGTGATTACGATAAAGCA
64 TTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATAAAGCA
54654944 AATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTT
129 AATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTT
54655009 GATGGAGAGCAG
194 GATGGAGAGCAG
*
54655021 ACACATAGCAGATCTCACCTTCAGATGTTTATGTTGAAGCGGATCCAAGATGGTTTGGCATCCTT
1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT
*
54655086 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTATGATAAAGCAAA
66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATAAAGCAAA
54655151 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
54655216 TGGAGAGCAG
196 TGGAGAGCAG
* *
54655226 ACACATAGCAGATCTCACCTTCAGATGATTT-CGCTGAAGCAGATCCAAGATGGTTTGGCATCCT
1 ACACATAGCAGATCTCACCTTCAGATG-TTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCT
*
54655290 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAA
65 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATAAAGCAA
54655355 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
130 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG
54655420 ATGGAGAGCAG
195 ATGGAGAGCAG
54655431 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT
1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT
* * *
54655496 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTCGCTTTCATATGATTACGATGAAGCAAA
66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATAAAGCAAA
54655561 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
54655626 TGGAGAGCAG
196 TGGAGAGCAG
* *
54655636 ACACATAGCAGATCTCACCTTCGGATGTTTATGCTGAAGCGGATCCAAGATGGATTGGCATCCTT
1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT
* * * * ** * *
54655701 ATGCTTACAAGGAACAAATCGAA-TCATAGTTGATTTGGCTTTCGCGTGCTTACGTTAAAGCAAA
66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATAAAGCAAA
* * * * * *
54655765 TCTAAGATGATTTGGCATCTCTGTATTGTCAGGGATCAAATCGAAG
131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAG
54655811 AAATAAATCT
Statistics
Matches: 753, Mismatches: 32, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
202 1 0.00
203 3 0.00
204 156 0.21
205 590 0.78
206 3 0.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (205 bp):
ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT
GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATAAAGCAAA
TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA
TGGAGAGCAG
Found at i:54655942 original size:44 final size:43
Alignment explanation
Indices: 54655864--54655949 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
54655854 GATTTCAGCA
* *
54655864 TGGCATCCCTGTGTTTATAAGGAGCAAGTTGAAGACAGCAGATT
1 TGGCATCCCTGTGTTTATAAGGAACAAGTCGAAGA-AGCAGATT
**
54655908 TGGCATCCCTGTGTTTATGGGGAAC-AGATCGAAGAAGCAGAT
1 TGGCATCCCTGTGTTTATAAGGAACAAG-TCGAAGAAGCAGAT
54655950 CAAGAACTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 9 0.24
44 28 0.76
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (43 bp):
TGGCATCCCTGTGTTTATAAGGAACAAGTCGAAGAAGCAGATT
Found at i:54656182 original size:14 final size:13
Alignment explanation
Indices: 54656163--54656198 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
54656153 ACCCAACCCC
54656163 AAAAAAAAATCAA
1 AAAAAAAAATCAA
54656176 AAAAAAAAATCAA
1 AAAAAAAAATCAA
54656189 AAAAGAAAAA
1 AAAA-AAAAA
54656199 ACCTAATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.86, C:0.06, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAAAAAAATCAA
Found at i:54656412 original size:22 final size:24
Alignment explanation
Indices: 54656386--54656435 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
54656376 TATTTTGGAG
54656386 AGAAGA-A-ATTTTTTGAGATTCA
1 AGAAGAGATATTTTTTGAGATTCA
*
54656408 AGAAGAGATTTTTTTTTGAGATTCA
1 AGAAGAGA-TATTTTTTGAGATTCA
54656433 AGA
1 AGA
54656436 GGGGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
25 17 0.71
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (24 bp):
AGAAGAGATATTTTTTGAGATTCA
Found at i:54656428 original size:25 final size:25
Alignment explanation
Indices: 54656394--54656450 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
54656384 AGAGAAGAAA
54656394 TTTTTTGAGATTCAAGAAGAGATTT
1 TTTTTTGAGATTCAAGAAGAGATTT
* *
54656419 TTTTTTGAGATTCAAGAGGGGATTT
1 TTTTTTGAGATTCAAGAAGAGATTT
54656444 TTCTTTT
1 TT-TTTT
54656451 TTTTTGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.49
Consensus pattern (25 bp):
TTTTTTGAGATTCAAGAAGAGATTT
Found at i:54656444 original size:22 final size:22
Alignment explanation
Indices: 54656386--54656445 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 22
54656376 TATTTTGGAG
*
54656386 AGAAGAAATTTTTTGAGATTCA
1 AGAAGAGATTTTTTGAGATTCA
54656408 AGAAGAGATTTTTTTTTGAGATTCA
1 AGAAGAGA---TTTTTTGAGATTCA
* *
54656433 AGAGGGGATTTTT
1 AGAAGAGATTTTT
54656446 CTTTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 12 0.38
25 20 0.62
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.40
Consensus pattern (22 bp):
AGAAGAGATTTTTTGAGATTCA
Found at i:54656931 original size:3 final size:3
Alignment explanation
Indices: 54656923--54656969 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
54656913 TGCATTTTAA
54656923 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54656970 GTGTATATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54657070 original size:3 final size:3
Alignment explanation
Indices: 54657062--54657097 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
54657052 TGTATTTCTA
54657062 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54657098 ATGGTAGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54657223 original size:16 final size:15
Alignment explanation
Indices: 54657192--54657234 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
54657182 CCTTCATTCC
*
54657192 ATTATTATTATTACT
1 ATTATTATTTTTACT
54657207 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
54657223 ATCATTATTTTT
1 ATTATTATTTTT
54657235 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:54657359 original size:16 final size:16
Alignment explanation
Indices: 54657338--54657369 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54657328 CTATTGTTAC
54657338 TGTTATTATCATCACT
1 TGTTATTATCATCACT
*
54657354 TGTTATTCTCATCACT
1 TGTTATTATCATCACT
54657370 ATTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTATCATCACT
Found at i:54657411 original size:11 final size:13
Alignment explanation
Indices: 54657381--54657412 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54657371 TTATTATAAT
54657381 TTATTATTGTTAC
1 TTATTATTGTTAC
54657394 TTATTATT-TTAC
1 TTATTATTGTTAC
54657406 -TATTATT
1 TTATTATT
54657413 ATCTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 4 0.21
13 8 0.42
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATTATTGTTAC
Found at i:54657610 original size:22 final size:22
Alignment explanation
Indices: 54657580--54657640 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
54657570 TTATTATATC
*
54657580 TTTTACTATTATTATTGTTGTA
1 TTTTACTATTATTATTGTTATA
* * *
54657602 TTTTTCTATTATTGTTATTATA
1 TTTTACTATTATTATTGTTATA
* *
54657624 TTTTCCT-TTATTTTTGT
1 TTTTACTATTATTATTGT
54657641 ATTTACTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTACTATTATTATTGTTATA
Found at i:54657614 original size:3 final size:3
Alignment explanation
Indices: 54657369--54657595 Score: 60
Period size: 3 Copynumber: 76.3 Consensus size: 3
54657359 TTCTCATCAC
* * *
54657369 TAT TAT TAT AATT TAT TAT TGT TACT TAT TAT T-T TAC TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
54657415 CTAA TA- TAT CAT CAT TAT CAT TAT T-T TCAT TAT AACT TAA TA- GAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
* * * * * *
54657460 CAT CAT TAT TAT TAT TAT TAT TAT TAT TAG CAC TACT T-T TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * ** * * *
54657505 TAT TAT T-T AAT ATAT TAT TTT TAC TAT TAT CGT CA- TAT TGT TAC
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
54657549 TAT TAC TAT TA- TAT TAT TA- TGT TAT TA- TAT CTTT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
54657592 TAT T
1 TAT T
54657596 GTTGTATTTT
Statistics
Matches: 160, Mismatches: 46, Indels: 36
0.66 0.19 0.15
Matches are distributed among these distances:
2 16 0.10
3 128 0.80
4 16 0.10
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:54658952 original size:2 final size:2
Alignment explanation
Indices: 54658945--54658982 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
54658935 ATGATGCTTT
*
54658945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54658983 TCAATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54660588 original size:24 final size:25
Alignment explanation
Indices: 54660555--54660602 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
54660545 TAAGAAAGTG
54660555 GTTACAAGAAGATAAAAGGTGAAAT
1 GTTACAAGAAGATAAAAGGTGAAAT
*
54660580 GTTA-AAGAAGTTAAAAGGTGAAA
1 GTTACAAGAAGATAAAAGGTGAAA
54660603 GGTAGAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.52, C:0.02, G:0.25, T:0.21
Consensus pattern (25 bp):
GTTACAAGAAGATAAAAGGTGAAAT
Found at i:54662287 original size:17 final size:18
Alignment explanation
Indices: 54662255--54662292 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
54662245 GAAGTGTTTA
54662255 TGAACAAAAGTT-AAAAT
1 TGAACAAAAGTTAAAAAT
54662272 TGAACAAAA-TTGAAAAAT
1 TGAACAAAAGTT-AAAAAT
54662290 TGA
1 TGA
54662293 TTCTTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (18 bp):
TGAACAAAAGTTAAAAAT
Found at i:54668429 original size:2 final size:2
Alignment explanation
Indices: 54668422--54668458 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54668412 TAAATTAATG
54668422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54668459 AATTAAAGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54668592 original size:21 final size:21
Alignment explanation
Indices: 54668520--54668593 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
54668510 CATACAATTG
* *
54668520 TAATT-TATTTAAGTAAATAAA
1 TAATTATATTT-ATTAATTAAA
* *
54668541 TATTTATTATTTATT-ATTAAG
1 TAATTA-TATTTATTAATTAAA
**
54668562 TAAAAAATATTTATTAATTAAA
1 T-AATTATATTTATTAATTAAA
54668584 TAATTATATT
1 TAATTATATT
54668594 ATAAAATTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
21 24 0.62
22 10 0.26
23 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TAATTATATTTATTAATTAAA
Found at i:54669577 original size:18 final size:18
Alignment explanation
Indices: 54669545--54669580 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54669535 ATTTGTGATC
*
54669545 AAAATTGAAGGTGAAAGT
1 AAAATTGAAAGTGAAAGT
*
54669563 AAAATTGAAATTGAAAGT
1 AAAATTGAAAGTGAAAGT
54669581 GATATGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (18 bp):
AAAATTGAAAGTGAAAGT
Found at i:54669777 original size:37 final size:38
Alignment explanation
Indices: 54669736--54669819 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 38
54669726 TCAATGAGGT
*
54669736 ACTGGGTACCACTTTA-CTTCG-GCTAAGCCGATGAGAC
1 ACTGGGTACCACTTTATCTTCGAACT-AGCCGATGAGAC
** *
54669773 ACTGGGTGTCACTTTATTTCTTCGAACTAGCCGATGAGGC
1 ACTGGGTACCACTTTA--TCTTCGAACTAGCCGATGAGAC
54669813 ACTGGGT
1 ACTGGGT
54669820 GCCATTCTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 14 0.36
40 23 0.59
41 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (38 bp):
ACTGGGTACCACTTTATCTTCGAACTAGCCGATGAGAC
Found at i:54673382 original size:70 final size:71
Alignment explanation
Indices: 54673231--54673393 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
54673221 GAGATGTATC
54673231 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54673296 AGGACA
66 AGGACA
54673302 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
54673366 CGGACA
66 AGGACA
54673372 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54673394 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54680390 original size:71 final size:71
Alignment explanation
Indices: 54680302--54680465 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
54680292 GAGATGTATC
54680302 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54680367 AGGACA
66 AGGACA
*
54680373 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTGGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
54680438 CGGACA
66 AGGACA
54680444 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54680466 AGACAAATCG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54689644 original size:42 final size:42
Alignment explanation
Indices: 54689529--54689675 Score: 174
Period size: 44 Copynumber: 3.4 Consensus size: 42
54689519 ATATGTGTTA
*
54689529 TCGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTATGATT
1 TCGTGTAAGACCACGTCTGGGATGTTGGCATCGTA-TT-TGATT
*
54689572 TACGTGTAAGACCACGTCTGAGATGTTGGCATCGTATTTGATT
1 T-CGTGTAAGACCACGTCTGGGATGTTGGCATCGTATTTGATT
*
54689615 TCGTGTAAGACC-CTGTTTGGGATAG-TGGCATCGATATTTGATT
1 TCGTGTAAGACCAC-GTCTGGGAT-GTTGGCATCG-TATTTGATT
* *
54689658 ACATGTAAGACCACGTCT
1 TCGTGTAAGACCACGTCT
54689676 AGGACGTTTG
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
41 1 0.01
42 26 0.29
43 30 0.33
44 33 0.36
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (42 bp):
TCGTGTAAGACCACGTCTGGGATGTTGGCATCGTATTTGATT
Found at i:54696389 original size:13 final size:13
Alignment explanation
Indices: 54696371--54696405 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
54696361 ATCTCACACG
54696371 CCCGTATGGTTTA
1 CCCGTATGGTTTA
54696384 CCCGTATGGTTTA
1 CCCGTATGGTTTA
54696397 CCCGTATGG
1 CCCGTATGG
54696406 GCCCACATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.26, T:0.34
Consensus pattern (13 bp):
CCCGTATGGTTTA
Found at i:54696435 original size:18 final size:18
Alignment explanation
Indices: 54696397--54696431 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54696387 GTATGGTTTA
*
54696397 CCCGTATGGGCCCACATG
1 CCCGTATGGGCCCACAGG
54696415 CCCGTAT-GGCCCACAGG
1 CCCGTATGGGCCCACAGG
54696432 GCCCAATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (18 bp):
CCCGTATGGGCCCACAGG
Found at i:54704544 original size:47 final size:46
Alignment explanation
Indices: 54704490--54704651 Score: 200
Period size: 47 Copynumber: 3.5 Consensus size: 46
54704480 CTAAGTTGCC
* * * * * *
54704490 TAAACTTAGGACACATTAAGTAGCT-ATATTAACTAAAACATATTAAA
1 TAAACTTAAGACA-ATTAAATAGCTGA-ACTAATTAGAACACATTAAA
*
54704537 TAAACTTAGGACATATTAAATAGCTGAACTAATTAGAACACATTAAA
1 TAAACTTAAGACA-ATTAAATAGCTGAACTAATTAGAACACATTAAA
* *
54704584 TAAAATTAAGACAATTTAAATTGCTGAACTAATTAGAACACATTAAA
1 TAAACTTAAGACAA-TTAAATAGCTGAACTAATTAGAACACATTAAA
54704631 TAAACTTAAGACAATTAAATA
1 TAAACTTAAGACAATTAAATA
54704652 CTTAAACTAA
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
46 7 0.07
47 94 0.92
48 1 0.01
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.29
Consensus pattern (46 bp):
TAAACTTAAGACAATTAAATAGCTGAACTAATTAGAACACATTAAA
Found at i:54704581 original size:27 final size:27
Alignment explanation
Indices: 54704542--54704632 Score: 74
Period size: 27 Copynumber: 3.6 Consensus size: 27
54704532 TTAAATAAAC
* *
54704542 TTAGGACATATTAAATAGCTGAACTAA
1 TTAGAACACATTAAATAGCTGAACTAA
54704569 TTAGAACACATT-AA-A--T-AA--AA
1 TTAGAACACATTAAATAGCTGAACTAA
*
54704589 TTA-AGACA-ATTTAAATTGCTGAACTAA
1 TTAGA-ACACA-TTAAATAGCTGAACTAA
54704616 TTAGAACACATTAAATA
1 TTAGAACACATTAAATA
54704633 AACTTAAGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 22
0.65 0.05 0.29
Matches are distributed among these distances:
19 2 0.04
20 10 0.20
21 2 0.04
22 2 0.04
23 1 0.02
24 1 0.02
25 3 0.06
26 2 0.04
27 24 0.49
28 2 0.04
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (27 bp):
TTAGAACACATTAAATAGCTGAACTAA
Found at i:54706007 original size:15 final size:15
Alignment explanation
Indices: 54705966--54706012 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
54705956 GTTAAAATTT
*
54705966 AAAAATATAGAAACTA
1 AAAAAT-TATAAACTA
* *
54705982 AAAAAAT-TAAATTA
1 AAAAATTATAAACTA
54705996 AAAAATTATAAACTA
1 AAAAATTATAAACTA
54706011 AA
1 AA
54706013 TCCACATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAAATTATAAACTA
Found at i:54706855 original size:88 final size:88
Alignment explanation
Indices: 54706753--54706925 Score: 224
Period size: 88 Copynumber: 2.0 Consensus size: 88
54706743 CTCTCCCTTT
* * * * * *
54706753 TTTTTTTTTGCACTCAATT-GAGCACTTGAACTTTTAAAATGCATCAAAAAGGCCCTCAAACTTC
1 TTTTTTTTTGCACTCAATTAG-GCACTTAAACTGTCAAAATGCATAAAAAAGACCCTCAAAATTC
*
54706817 TTCAATAAAAGCAATTAAGCCCCTG
65 TTCAA-AAAAACAATTAAGCCCCTG
* * *
54706842 TTTTTTTTT-CACTCAATTAGGTACTTAAACTGTCAAATTGCATAAAAAAGACCCTCAAAATTTT
1 TTTTTTTTTGCACTCAATTAGGCACTTAAACTGTCAAAATGCATAAAAAAGACCCTCAAAATTCT
54706906 TCAAAAAAACAATTAAGCCC
66 TCAAAAAAACAATTAAGCCC
54706926 TTGCTTTTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 15 0.21
88 48 0.66
89 10 0.14
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (88 bp):
TTTTTTTTTGCACTCAATTAGGCACTTAAACTGTCAAAATGCATAAAAAAGACCCTCAAAATTCT
TCAAAAAAACAATTAAGCCCCTG
Found at i:54706977 original size:10 final size:9
Alignment explanation
Indices: 54706936--54707016 Score: 56
Period size: 10 Copynumber: 8.7 Consensus size: 9
54706926 TTGCTTTTAT
54706936 TAAAAATTA
1 TAAAAATTA
*
54706945 TAAAAAATAA
1 T-AAAAATTA
**
54706955 TAAATTTTA
1 TAAAAATTA
54706964 TAAAAATTA
1 TAAAAATTA
**
54706973 TTAAATTTTAA
1 -TAAAAATT-A
54706984 TAAAAATTA
1 TAAAAATTA
*
54706993 -AAAAATTG
1 TAAAAATTA
*
54707001 TAAAATTTTA
1 TAAAA-ATTA
54707011 TAAAAA
1 TAAAAA
54707017 CAAAATTTAT
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
8 7 0.13
9 18 0.34
10 27 0.51
11 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (9 bp):
TAAAAATTA
Found at i:54706986 original size:20 final size:19
Alignment explanation
Indices: 54706942--54706999 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
54706932 TTATTAAAAA
*
54706942 TTATAAAAAATAATAAATT
1 TTATAAAAATTAATAAATT
*
54706961 TTATAAAAATTATTAAATT
1 TTATAAAAATTAATAAATT
*
54706980 TTAATAAAAATTAAAAAATT
1 TT-ATAAAAATTAATAAATT
54707000 GTAAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTATAAAAATTAATAAATT
Found at i:54707131 original size:30 final size:29
Alignment explanation
Indices: 54707043--54707181 Score: 113
Period size: 30 Copynumber: 4.7 Consensus size: 29
54707033 TTACATTTTG
* *
54707043 TATAATTTTCTTAGGA-CTTTATAAAATTT
1 TATAATTTTTTTA-GATTTTTATAAAATTT
* * *
54707072 TATAAATTTTTTTATATTTCTAT-ATATTT
1 TAT-AATTTTTTTAGATTTTTATAAAATTT
*
54707101 TCTAATTTTTTTACGATTTTTATAAAATTT
1 TATAATTTTTTTA-GATTTTTATAAAATTT
* * * *
54707131 TATAATTTTTTTATATTTTTTTACGATTTT
1 TATAATTTTTTTAGATTTTTATA-AAATTT
*
54707161 TATATTTTTTTCTA-ATTTTTA
1 TATAATTTTTT-TAGATTTTTA
54707182 ATATTTTAAT
Statistics
Matches: 88, Mismatches: 16, Indels: 11
0.77 0.14 0.10
Matches are distributed among these distances:
28 10 0.11
29 26 0.30
30 50 0.57
31 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (29 bp):
TATAATTTTTTTAGATTTTTATAAAATTT
Found at i:54707169 original size:58 final size:58
Alignment explanation
Indices: 54707022--54707170 Score: 178
Period size: 58 Copynumber: 2.5 Consensus size: 58
54707012 AAAAACAAAA
* *
54707022 TTTATATTTCTTTACATTTTGTATAATTTTCTTAGGACTTTATAAAATTTTATAAATTTT
1 TTTATATTTCTTTACATTTTCTAT-ATTTT-TTACGACTTTATAAAATTTTATAAATTTT
* * *
54707082 TTTATATTTCTATATATTTTCTA-ATTTTTTTACGATTTTTATAAAATTTTAT-AATTTT
1 TTTATATTTCTTTACATTTTCTATA-TTTTTTACGA-CTTTATAAAATTTTATAAATTTT
*
54707140 TTTATATTTTTTTACGATTTT-TATATTTTTT
1 TTTATATTTCTTTAC-ATTTTCTATATTTTTT
54707171 TCTAATTTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
58 32 0.42
59 25 0.32
60 20 0.26
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (58 bp):
TTTATATTTCTTTACATTTTCTATATTTTTTACGACTTTATAAAATTTTATAAATTTT
Found at i:54707171 original size:11 final size:11
Alignment explanation
Indices: 54707128--54707180 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
54707118 TTTTATAAAA
54707128 TTTTATAATTT
1 TTTTATAATTT
54707139 TTTTAT-ATTT
1 TTTTATAATTT
**
54707149 TTTTACGA--T
1 TTTTATAATTT
54707158 TTTTAT-ATTT
1 TTTTATAATTT
*
54707168 TTTTCTAATTT
1 TTTTATAATTT
54707179 TT
1 TT
54707181 AATATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.03
9 6 0.17
10 15 0.43
11 13 0.37
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:54707177 original size:40 final size:40
Alignment explanation
Indices: 54707088--54707188 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
54707078 TTTTTTTATA
*
54707088 TTTCTATATATTTTCTA-ATTTTTTTACGATTTTTATAAAAT
1 TTTCTA-AT-TTTTTTATATTTTTTTACGATTTTTATAAAAT
* ***
54707129 TTTATAATTTTTTTATATTTTTTTACGATTTTTATATTTT
1 TTTCTAATTTTTTTATATTTTTTTACGATTTTTATAAAAT
*
54707169 TTTCTAA-TTTTTAATATTTT
1 TTTCTAATTTTTTTATATTTT
54707189 AATATTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 18 0.35
40 29 0.56
41 5 0.10
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (40 bp):
TTTCTAATTTTTTTATATTTTTTTACGATTTTTATAAAAT
Found at i:54707178 original size:19 final size:19
Alignment explanation
Indices: 54707105--54707188 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
54707095 ATATTTTCTA
*
54707105 ATTTTTTTACGATTTTTAT
1 ATTTTTTTACAATTTTTAT
*** *
54707124 AAAATTTTATAATTTTTTTAT
1 ATTTTTTTACAA--TTTTTAT
*
54707145 ATTTTTTTACGATTTTTAT
1 ATTTTTTTACAATTTTTAT
54707164 ATTTTTTT-CTAATTTTTAAT
1 ATTTTTTTAC-AATTTTT-AT
54707184 ATTTT
1 ATTTT
54707189 AATATTTTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.02
19 28 0.56
20 7 0.14
21 14 0.28
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTTTACAATTTTTAT
Found at i:54707179 original size:59 final size:59
Alignment explanation
Indices: 54707060--54707181 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
54707050 TTCTTAGGAC
* *
54707060 TTTATAAAATTTTATAAATTTTTTTATATTTCTATATATTTTCTAATTTTTTTACGATT
1 TTTATAAAATTTTATAAATTTTTTTATATTTCTATAGATTTTCTAATTTTTTTACAATT
* *
54707119 TTTATAAAATTTTAT-AATTTTTTTATATTTTTTTACGATTTT-TATATTTTTTT-CTAATT
1 TTTATAAAATTTTATAAATTTTTTTATATTTCTATA-GATTTTCTA-ATTTTTTTAC-AATT
54707178 TTTA
1 TTTA
54707182 ATATTTTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
58 21 0.38
59 35 0.62
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (59 bp):
TTTATAAAATTTTATAAATTTTTTTATATTTCTATAGATTTTCTAATTTTTTTACAATT
Found at i:54711145 original size:22 final size:23
Alignment explanation
Indices: 54711101--54711145 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54711091 ATTTCGGGTT
* *
54711101 TTTTTACCCGTATTTTAACTATA
1 TTTTTACCCGTATTATAAATATA
54711124 TTTTTACCCGTA-TATAAATATA
1 TTTTTACCCGTATTATAAATATA
54711146 AATATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTTTACCCGTATTATAAATATA
Found at i:54711523 original size:15 final size:15
Alignment explanation
Indices: 54711503--54711550 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
54711493 TGATAAACTA
*
54711503 AAAAAATTAAGTGTT
1 AAAAAATTAAGTATT
*
54711518 AAAAAATTAAATATT
1 AAAAAATTAAGTATT
*
54711533 AAAAAATTAAGTACT
1 AAAAAATTAAGTATT
54711548 AAA
1 AAA
54711551 TTAAAGTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (15 bp):
AAAAAATTAAGTATT
Found at i:54712926 original size:34 final size:34
Alignment explanation
Indices: 54712883--54712954 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
54712873 ATGTCCCAGA
54712883 CATGGTCTTACACTGACACATCTCGTAGCCGATG
1 CATGGTCTTACACTGACACATCTCGTAGCCGATG
54712917 CATGGTCTTACACTGACACATCTCGTAGCCGATG
1 CATGGTCTTACACTGACACATCTCGTAGCCGATG
54712951 CATG
1 CATG
54712955 TCCCAGACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (34 bp):
CATGGTCTTACACTGACACATCTCGTAGCCGATG
Found at i:54713002 original size:46 final size:46
Alignment explanation
Indices: 54712951--54713073 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 46
54712941 GTAGCCGATG
* *
54712951 CATGTCCCAGACATGTCTTACACTGGCTTAGGTCTCGA-GACCGA-AA
1 CATGTCCCAAACATGTCTTACACTGGCTT-CGTCTCGATG-CCGATAA
* * * * **
54712997 CATGTCCTAAACATGTCTTATACTAGCACTCGTCTCGATGCCGATGT
1 CATGTCCCAAACATGTCTTACACTGGC-TTCGTCTCGATGCCGATAA
54713044 CATGTCCCAAACATGGTCTTACACTGGCTT
1 CATGTCCCAAACAT-GTCTTACACTGGCTT
54713074 TCAAAATGTG
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
46 34 0.56
47 16 0.26
48 11 0.18
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGTCCCAAACATGTCTTACACTGGCTTCGTCTCGATGCCGATAA
Found at i:54720083 original size:35 final size:35
Alignment explanation
Indices: 54720037--54720153 Score: 171
Period size: 35 Copynumber: 3.3 Consensus size: 35
54720027 TACTCTCTCT
*
54720037 TTGGTGTGTTTCGATTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
*
54720072 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGTA
1 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
* * *
54720107 TTGGCGTGTTACGGTTGGACTAGCTCTTATAAGCA
1 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
*
54720142 TTTGATGTGTTT
1 -TTGGTGTGTTT
54720154 TAGAAGGATT
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 64 0.89
36 8 0.11
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (35 bp):
TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
Found at i:54720289 original size:36 final size:36
Alignment explanation
Indices: 54720248--54720322 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
54720238 GAAAGAATAT
* *
54720248 TTGTGAAATGTTATTGAATTTGATGTTCAGTTTAGA
1 TTGTGAAATGTTATTGAATTTAATGTTCAGATTAGA
54720284 TTGTGAAATGTTATTGAATTTAATGTTCAGATTAGA
1 TTGTGAAATGTTATTGAATTTAATGTTCAGATTAGA
54720320 TTG
1 TTG
54720323 AACGAGGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (36 bp):
TTGTGAAATGTTATTGAATTTAATGTTCAGATTAGA
Found at i:54720515 original size:35 final size:36
Alignment explanation
Indices: 54720464--54720542 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
54720454 CTCTCTCTTG
* *
54720464 GGTGTGTTTCGATTGGACTAGCTCTTATGAGTA-TT
1 GGTGTGTTACGATTGGACTAGCTCTTATAAGTATTT
* *
54720499 GGTGTGTTACGGTTGGACTAGCTCTTGTAAGTATTT
1 GGTGTGTTACGATTGGACTAGCTCTTATAAGTATTT
*
54720535 GATGTGTT
1 GGTGTGTT
54720543 TTAGAGGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
35 29 0.76
36 9 0.24
ACGTcount: A:0.16, C:0.10, G:0.30, T:0.43
Consensus pattern (36 bp):
GGTGTGTTACGATTGGACTAGCTCTTATAAGTATTT
Found at i:54722393 original size:30 final size:30
Alignment explanation
Indices: 54722359--54722425 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
54722349 GTGTTTCAGT
54722359 CGTGTGAGGCACATGGCCTGGCCACACGGC
1 CGTGTGAGGCACATGGCCTGGCCACACGGC
54722389 CGTGTGAGGCACATGGCCTGGCCACACGGC
1 CGTGTGAGGCACATGGCCTGGCCACACGGC
54722419 CGTGTGA
1 CGTGTGA
54722426 CCCTTGCAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.31, G:0.37, T:0.15
Consensus pattern (30 bp):
CGTGTGAGGCACATGGCCTGGCCACACGGC
Found at i:54722406 original size:17 final size:17
Alignment explanation
Indices: 54722359--54722406 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
54722349 GTGTTTCAGT
54722359 CGTGTGAGGCACATGGC
1 CGTGTGAGGCACATGGC
* *
54722376 C---TG-GCCACACGGC
1 CGTGTGAGGCACATGGC
54722389 CGTGTGAGGCACATGGC
1 CGTGTGAGGCACATGGC
54722406 C
1 C
54722407 TGGCCACACG
Statistics
Matches: 23, Mismatches: 4, Indels: 8
0.66 0.11 0.23
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
16 2 0.09
17 10 0.43
ACGTcount: A:0.17, C:0.31, G:0.38, T:0.15
Consensus pattern (17 bp):
CGTGTGAGGCACATGGC
Found at i:54723219 original size:17 final size:18
Alignment explanation
Indices: 54723197--54723230 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
54723187 TATGCTTCAA
54723197 TTGTTTGTG-AATTGTGT
1 TTGTTTGTGAAATTGTGT
54723214 TTGTTTGTGAAATTGTG
1 TTGTTTGTGAAATTGTG
54723231 AACCTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (18 bp):
TTGTTTGTGAAATTGTGT
Found at i:54728129 original size:2 final size:2
Alignment explanation
Indices: 54728122--54728155 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54728112 TCTTTTGTAC
*
54728122 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54728156 TGTAAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:54728482 original size:19 final size:21
Alignment explanation
Indices: 54728458--54728497 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
54728448 AAGAAACGGC
54728458 TCTCATGCT-AA-TCTCTCAA
1 TCTCATGCTCAATTCTCTCAA
*
54728477 TCTCATGTTCAATTCTCTCAA
1 TCTCATGCTCAATTCTCTCAA
54728498 ACCAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 2 0.11
21 8 0.44
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (21 bp):
TCTCATGCTCAATTCTCTCAA
Found at i:54745132 original size:43 final size:43
Alignment explanation
Indices: 54745084--54745253 Score: 193
Period size: 43 Copynumber: 4.0 Consensus size: 43
54745074 ATTACCGAGA
*
54745084 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
* *
54745127 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTAT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTG-TAT
* * * * * *
54745171 T-CGATTTCGTGTAAGACCCTATCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
* * *
54745212 AAGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTA
1 -TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTA
54745254 CGAGCTTTAT
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
41 2 0.02
42 7 0.06
43 95 0.88
44 4 0.04
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT
Found at i:54747492 original size:41 final size:41
Alignment explanation
Indices: 54747435--54747517 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
54747425 TGTTGAATTA
54747435 TTCCTGACGTTAAGTTCGTTAATCCATCCACTTTCCCAAAT
1 TTCCTGACGTTAAGTTCGTTAATCCATCCACTTTCCCAAAT
54747476 TTCCTGACGTTAAGTTCGTTAATCCATCCACTTTCCCAAAT
1 TTCCTGACGTTAAGTTCGTTAATCCATCCACTTTCCCAAAT
54747517 T
1 T
54747518 CTTTCTTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (41 bp):
TTCCTGACGTTAAGTTCGTTAATCCATCCACTTTCCCAAAT
Found at i:54747629 original size:17 final size:19
Alignment explanation
Indices: 54747600--54747634 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
54747590 ATTCTTACAT
54747600 TTATTTGAAACCT-TCCAC
1 TTATTTGAAACCTATCCAC
54747618 TTATTT-AAACCTATCCA
1 TTATTTGAAACCTATCCA
54747635 TTCACTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (19 bp):
TTATTTGAAACCTATCCAC
Found at i:54754473 original size:49 final size:49
Alignment explanation
Indices: 54754368--54754489 Score: 129
Period size: 49 Copynumber: 2.5 Consensus size: 49
54754358 TGTTGTGTGT
* * * * *
54754368 CAGTGTAAGACCTGTTTGGCACATGGCATCGACACCGATAGATGAGAGC
1 CAGTGTAAGACCTGTTTGGGACACGACATCGACACCGATAGAAGAAAGC
* * * *
54754417 TATTGTAAGACCTGTTTGGGACACGACATCGAC-CTCGATATAAGAAATC
1 CAGTGTAAGACCTGTTTGGGACACGACATCGACAC-CGATAGAAGAAAGC
*
54754466 CAGTGTAAGACCATGTCTGGGACA
1 CAGTGTAAGACC-TGTTTGGGACA
54754490 TGGCGTCGGT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
48 1 0.02
49 48 0.81
50 10 0.17
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (49 bp):
CAGTGTAAGACCTGTTTGGGACACGACATCGACACCGATAGAAGAAAGC
Found at i:54760936 original size:28 final size:28
Alignment explanation
Indices: 54760901--54760959 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
54760891 CTAGGGTATA
54760901 TCGGTAATTTTGCTCTTTAGGGGTAATT
1 TCGGTAATTTTGCTCTTTAGGGGTAATT
54760929 TCGGTAATTTTGCTCTTTAGGGGTAATT
1 TCGGTAATTTTGCTCTTTAGGGGTAATT
54760957 TCG
1 TCG
54760960 TGATCTACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (28 bp):
TCGGTAATTTTGCTCTTTAGGGGTAATT
Found at i:54762608 original size:20 final size:20
Alignment explanation
Indices: 54762585--54762622 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54762575 CACATCCAAA
*
54762585 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
54762605 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
54762623 ACGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:54768923 original size:27 final size:26
Alignment explanation
Indices: 54768893--54768954 Score: 97
Period size: 28 Copynumber: 2.3 Consensus size: 26
54768883 TTTAAAACCC
54768893 TAGGGGTATATCGGTAATTTTGCTCTT
1 TAGGGGTATATCGGTAATTTTGCTC-T
*
54768920 TAGGGGTAATTTCGGTAATTTTGCTCT
1 TAGGGGT-ATATCGGTAATTTTGCTCT
54768947 TAGGGGTA
1 TAGGGGTA
54768955 ATTTCGTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 15 0.45
28 17 0.52
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (26 bp):
TAGGGGTATATCGGTAATTTTGCTCT
Found at i:54768957 original size:27 final size:28
Alignment explanation
Indices: 54768893--54768960 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
54768883 TTTAAAACCC
*
54768893 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
54768920 TAGGGGTAATTTCGGTAATTTTGCTC-T
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
54768947 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
54768961 TGATCTACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:54770405 original size:93 final size:93
Alignment explanation
Indices: 54770293--54770464 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54770283 CGCCCATAAG
* *
54770293 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54770358 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54770386 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54770451 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54770465 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54770461 original size:46 final size:46
Alignment explanation
Indices: 54770286--54770461 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54770276 TGTAACCCGC
* * *
54770286 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
54770332 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54770382 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54770425 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54770462 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54777959 original size:93 final size:93
Alignment explanation
Indices: 54777847--54778018 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54777837 CGCCCATAAG
* *
54777847 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54777912 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54777940 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54778005 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54778019 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54778015 original size:46 final size:46
Alignment explanation
Indices: 54777840--54778015 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54777830 TGTAACCCGC
* * *
54777840 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
54777886 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54777936 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54777979 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54778016 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54786807 original size:28 final size:28
Alignment explanation
Indices: 54786772--54786830 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
54786762 CTAGGGTATA
54786772 TCGGTAATTTTGCTCTTTAGGGGTAATT
1 TCGGTAATTTTGCTCTTTAGGGGTAATT
54786800 TCGGTAATTTTGCTCTTTAGGGGTAATT
1 TCGGTAATTTTGCTCTTTAGGGGTAATT
54786828 TCG
1 TCG
54786831 TGATCTACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (28 bp):
TCGGTAATTTTGCTCTTTAGGGGTAATT
Found at i:54788272 original size:93 final size:93
Alignment explanation
Indices: 54788160--54788331 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54788150 CGCCCATAAG
* *
54788160 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54788225 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54788253 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54788318 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54788332 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54788328 original size:46 final size:46
Alignment explanation
Indices: 54788153--54788328 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54788143 TGTAACCCGC
* * *
54788153 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
54788199 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54788249 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54788292 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54788329 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54795842 original size:93 final size:93
Alignment explanation
Indices: 54795730--54795901 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54795720 CGCCCATAAG
* *
54795730 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54795795 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54795823 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54795888 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54795902 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54795898 original size:46 final size:46
Alignment explanation
Indices: 54795723--54795898 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54795713 TGTAACCCGC
* * *
54795723 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
54795769 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54795819 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54795862 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54795899 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54798821 original size:20 final size:20
Alignment explanation
Indices: 54798798--54798835 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54798788 CACATCCAAA
*
54798798 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
54798818 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
54798836 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:54800356 original size:16 final size:16
Alignment explanation
Indices: 54800300--54800361 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
54800290 TCTTCACCAA
54800300 AAGTTTTAGAAATAGT
1 AAGTTTTAGAAATAGT
*
54800316 AAGGGTTTT-GAAGAT-TT
1 AA--GTTTTAGAA-ATAGT
*
54800333 AAAATTTTAGAAATAGT
1 -AAGTTTTAGAAATAGT
54800350 AAGTTTTAGAAA
1 AAGTTTTAGAAA
54800362 GTTTTAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
16 19 0.53
17 8 0.22
18 9 0.25
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (16 bp):
AAGTTTTAGAAATAGT
Found at i:54801275 original size:49 final size:49
Alignment explanation
Indices: 54801216--54801325 Score: 150
Period size: 49 Copynumber: 2.2 Consensus size: 49
54801206 TATTGTGTGT
* * *
54801216 CAGTGTAAGACCTGTTTGGGACATGGCATCGACAC-CGATAGATGAAAGC
1 CAGTGTAAGACCTGTTTGGGACACGACATCGAC-CTCGATAGAAGAAAGC
* *
54801265 CAGTGTAAGACCTGTTTGGGACACGACATCGACCTCGATATAAGAAATC
1 CAGTGTAAGACCTGTTTGGGACACGACATCGACCTCGATAGAAGAAAGC
*
54801314 CAATGTAAGACC
1 CAGTGTAAGACC
54801326 ATATCTGGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 1 0.02
49 53 0.98
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGTTTGGGACACGACATCGACCTCGATAGAAGAAAGC
Found at i:54804562 original size:43 final size:43
Alignment explanation
Indices: 54804463--54804586 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 43
54804453 TACCGAGATA
*
54804463 TGATTACGA-GTAAGACCATGTCTGGGACATTGGCATTGTATTG
1 TGATTAC-ACGTAAGACCATGTCTGGGACATTGGCATCGTATTG
* * * *
54804506 TGGTTACGCGTAAGACTATGTTTGGGACATTGGCATCGTTATT-
1 TGATTACACGTAAGACCATGTCTGGGACATTGGCATCG-TATTG
* * * * *
54804549 TGATTTCATGTAAGACCCTGTCTGAGACAGTGGCATCG
1 TGATTACACGTAAGACCATGTCTGGGACATTGGCATCG
54804587 ATAAGTGATA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
43 61 0.94
44 4 0.06
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
TGATTACACGTAAGACCATGTCTGGGACATTGGCATCGTATTG
Found at i:54811848 original size:42 final size:42
Alignment explanation
Indices: 54811799--54811910 Score: 152
Period size: 43 Copynumber: 2.6 Consensus size: 42
54811789 TGAGATTATG
**
54811799 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCACA
* * * * *
54811841 TGTAAGACCATAGCTAGGCTCTTGGAATCGATATGAGATCACA
1 TGTAAGACCATATCTGGGAT-ATGGCATCGATATGAGATCACA
54811884 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
54811911 TGGTATGGTA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 22 0.39
43 35 0.61
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCACA
Found at i:54812024 original size:20 final size:20
Alignment explanation
Indices: 54811996--54812033 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54811986 CAATGTTACA
54811996 GTTGGGAAAGACTATGGTAT
1 GTTGGGAAAGACTATGGTAT
* *
54812016 GTTGTGAAAGATTATGGT
1 GTTGGGAAAGACTATGGT
54812034 GATTTGCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (20 bp):
GTTGGGAAAGACTATGGTAT
Found at i:54812692 original size:15 final size:15
Alignment explanation
Indices: 54812664--54812697 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54812654 GTAATTGATG
*
54812664 TGTGGATGACTTGGT
1 TGTGGATGAATTGGT
*
54812679 TGTGGTTGAATTGGT
1 TGTGGATGAATTGGT
54812694 TGTG
1 TGTG
54812698 TGTATATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.41, T:0.44
Consensus pattern (15 bp):
TGTGGATGAATTGGT
Found at i:54813095 original size:21 final size:22
Alignment explanation
Indices: 54813069--54813109 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
54813059 TGCTAGACAC
54813069 AGGGGC-ACACACCCGTGTGGG
1 AGGGGCAACACACCCGTGTGGG
54813090 AGGGGCAACACACCCGTGTG
1 AGGGGCAACACACCCGTGTG
54813110 ACCAATACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.22, C:0.29, G:0.39, T:0.10
Consensus pattern (22 bp):
AGGGGCAACACACCCGTGTGGG
Found at i:54816090 original size:19 final size:19
Alignment explanation
Indices: 54816068--54816129 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
54816058 ATTTTTTAAT
54816068 TATTGAATGATTTTAGCTC
1 TATTGAATGATTTTAGCTC
* *
54816087 TATTTGCATCTG-TTTCA-CTC
1 TA-TTG-A-ATGATTTTAGCTC
*
54816107 TATTGAATGATTTTCGCTC
1 TATTGAATGATTTTAGCTC
54816126 TATT
1 TATT
54816130 TTCCTTCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 2 0.06
18 4 0.12
19 12 0.36
20 8 0.24
21 5 0.15
22 2 0.06
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (19 bp):
TATTGAATGATTTTAGCTC
Done.