Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 70 of 325
Found at i:19144547 original size:35 final size:35
Alignment explanation
Indices: 19144485--19144553 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
19144475 TAGAAAAATG
*
19144485 ATCCATAAATAACGAAGCGTTCATGTTACGTTTTT
1 ATCCATAAATAACGAAGCGTTCATGTTACATTTTT
* * *
19144520 ATCCATAAATAATGAAGTG-TCTGTGTTACATTTT
1 ATCCATAAATAACGAAGCGTTC-ATGTTACATTTT
19144554 AAACAACCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (35 bp):
ATCCATAAATAACGAAGCGTTCATGTTACATTTTT
Found at i:19149158 original size:27 final size:27
Alignment explanation
Indices: 19149117--19149330 Score: 171
Period size: 27 Copynumber: 7.9 Consensus size: 27
19149107 AACATACATT
**
19149117 ACAT-AGGGCCAAAACTGTCATTTTACC
1 ACATAAGGG-CAAAACAATCATTTTACC
* *
19149144 ACACAAGGGCAAAACAGTCATTTTACC
1 ACATAAGGGCAAAACAATCATTTTACC
* *
19149171 ACATAAGGGCAAAACAATTATTTTTCC
1 ACATAAGGGCAAAACAATCATTTTACC
* *
19149198 ACATAAGGGAAAAATC-ATAATTTTACC
1 ACATAAGGGCAAAA-CAATCATTTTACC
* * * * * * *
19149225 ATACAAGGGAAAAATAATTATTTGATC
1 ACATAAGGGCAAAACAATCATTTTACC
* * *
19149252 ATATAAGGGCAAAACAGTCATTTTTCC
1 ACATAAGGGCAAAACAATCATTTTACC
* * * * *
19149279 ACAGAAAGGCTAAACAATTATTTTGCC
1 ACATAAGGGCAAAACAATCATTTTACC
* *
19149306 ACATAAGGGCAAAATAGTCATTTTA
1 ACATAAGGGCAAAACAATCATTTTA
19149331 TCAAATTGAG
Statistics
Matches: 147, Mismatches: 37, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
27 142 0.97
28 5 0.03
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (27 bp):
ACATAAGGGCAAAACAATCATTTTACC
Found at i:19149185 original size:54 final size:54
Alignment explanation
Indices: 19149136--19149330 Score: 221
Period size: 54 Copynumber: 3.6 Consensus size: 54
19149126 CAAAACTGTC
*
19149136 ATTTTACCACACAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAATT
1 ATTTTACCACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAATT
* * * * * * *
19149190 ATTTTTCCACATAAGGGAAAAATCA-TAATTTTACCATACAAGGGAAAAATAATT
1 ATTTTACCACATAAGGGCAAAA-CAGTCATTTTACCACATAAGGGCAAAACAATT
* * * * * * *
19149244 ATTTGATCATATAAGGGCAAAACAGTCATTTTTCCACAGAAAGGCTAAACAATT
1 ATTTTACCACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAATT
* *
19149298 ATTTTGCCACATAAGGGCAAAATAGTCATTTTA
1 ATTTTACCACATAAGGGCAAAACAGTCATTTTA
19149331 TCAAATTGAG
Statistics
Matches: 112, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
53 2 0.02
54 108 0.96
55 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (54 bp):
ATTTTACCACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAATT
Found at i:19149302 original size:81 final size:81
Alignment explanation
Indices: 19149136--19149328 Score: 208
Period size: 81 Copynumber: 2.4 Consensus size: 81
19149126 CAAAACTGTC
* * * *
19149136 ATTTTACCACACAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAATTATTTTTCCACA
1 ATTTTACCACACAAGGGCAAAATAATCATTTGACCACATAAGGGCAAAACAATCATTTTTCCACA
* *
19149201 TAAGGGAAAAATCATA
66 GAAAGGAAAAATCATA
* * * * * *
19149217 ATTTTACCATACAAGGGAAAAATAATTATTTGATCATATAAGGGCAAAACAGTCATTTTTCCACA
1 ATTTTACCACACAAGGGCAAAATAATCATTTGACCACATAAGGGCAAAACAATCATTTTTCCACA
** *
19149282 GAAAGGCTAAA-CAATT
66 GAAAGGAAAAATC-ATA
* * *
19149298 ATTTTGCCACATAAGGGCAAAATAGTCATTT
1 ATTTTACCACACAAGGGCAAAATAATCATTT
19149329 TATCAAATTG
Statistics
Matches: 90, Mismatches: 21, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
80 1 0.01
81 89 0.99
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (81 bp):
ATTTTACCACACAAGGGCAAAATAATCATTTGACCACATAAGGGCAAAACAATCATTTTTCCACA
GAAAGGAAAAATCATA
Found at i:19156953 original size:49 final size:49
Alignment explanation
Indices: 19156769--19156945 Score: 246
Period size: 49 Copynumber: 3.6 Consensus size: 49
19156759 TTGTGAGGTT
* *
19156769 ACATGTGTAGTATTAAGTGCAGGCTACTACATGTACCGGATAATTGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTC
* * * * * **
19156818 GCATGCGTAGTACTAAGTGCAGGCTACTACGTGGATCTGATGGTTTGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGAT-AATTGGTC
* *
19156868 ACGTGTGTAGTACTAAGTGCGGGCTACTACGTGTACCGGATAATTGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTC
19156917 ACATGTGTAGTACTAAGTGCAGGCTACTA
1 ACATGTGTAGTACTAAGTGCAGGCTACTA
19156946 TGCGTACCAG
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
49 67 0.63
50 40 0.37
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTC
Found at i:19161241 original size:19 final size:19
Alignment explanation
Indices: 19161213--19161252 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
19161203 AAAGCGAAAG
19161213 AAACGAG-AAACGGGCCAA
1 AAACGAGAAAACGGGCCAA
*
19161231 AAACAGAGAAAATGGGCCAA
1 AAAC-GAGAAAACGGGCCAA
19161251 AA
1 AA
19161253 TATGAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 3 0.16
20 12 0.63
ACGTcount: A:0.55, C:0.17, G:0.25, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAACGGGCCAA
Found at i:19165818 original size:27 final size:28
Alignment explanation
Indices: 19165782--19165921 Score: 184
Period size: 27 Copynumber: 5.2 Consensus size: 28
19165772 AGCATGGCTG
*
19165782 CCAGA-ACAGATA-ATGTGGCAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
19165808 CCAGATACAGATA-ATCGTGGCAGAGCTA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
19165836 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
19165863 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
19165890 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
19165917 CCAGA
1 CCAGA
19165922 ACGCTTCCTC
Statistics
Matches: 105, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
26 5 0.05
27 83 0.79
28 17 0.16
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:19167569 original size:26 final size:26
Alignment explanation
Indices: 19167533--19167642 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
19167523 CATGAAATTC
19167533 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
19167559 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
19167585 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
19167611 TTATCCTTG-AACATTTACCTAACCTA
1 TTAT-CATGAAACATTTACCTAACCCA
19167637 TTATCA
1 TTATCA
19167643 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
25 1 0.01
26 75 0.95
27 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:19183355 original size:47 final size:46
Alignment explanation
Indices: 19183241--19183370 Score: 124
Period size: 47 Copynumber: 2.8 Consensus size: 46
19183231 TCACTTGTGT
19183241 GAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCACATTATAA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGG-CACATTATAA
* * * * *
19183287 GAGCCATTGTAAGACCCTGTCTGGGACATGGCAT-TG-ACATTGAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCACATT---ATAA
* *
19183335 GTGCTAGTGTAAGACATGTCTGGGGCAT-GCATCGGC
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGC
19183371 CTCGAGACGT
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
45 5 0.08
46 16 0.24
47 27 0.41
48 18 0.27
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACATTATAA
Found at i:19187538 original size:105 final size:105
Alignment explanation
Indices: 19187356--19187568 Score: 390
Period size: 105 Copynumber: 2.0 Consensus size: 105
19187346 TTGGCACTCA
*
19187356 CAAGTAGGGATGATCATTTCCATAATAAAGACCCTATATACGGGCCACAATATTAGGACTCAAAA
1 CAAGTAGGGATGATCATTTCCATAATAAAGACCCTATATACAGGCCACAATATTAGGACTCAAAA
* *
19187421 TGAATATAATTGTACTGTTTCGATGATAGTATGATGTCTG
66 TGAACATAATTGTACTGTTTCGATGATAGTATGATGTCCG
*
19187461 CAAGTAGGGATGATCATTTCTATAATAAAGACCCTATATACAGGCCACAATATTAGGACTCAAAA
1 CAAGTAGGGATGATCATTTCCATAATAAAGACCCTATATACAGGCCACAATATTAGGACTCAAAA
19187526 TGAACATAATTGTACTGTTTCGATGATAGTATGATGTCCG
66 TGAACATAATTGTACTGTTTCGATGATAGTATGATGTCCG
19187566 CAA
1 CAA
19187569 TGATCTAGCT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (105 bp):
CAAGTAGGGATGATCATTTCCATAATAAAGACCCTATATACAGGCCACAATATTAGGACTCAAAA
TGAACATAATTGTACTGTTTCGATGATAGTATGATGTCCG
Found at i:19188244 original size:31 final size:31
Alignment explanation
Indices: 19188165--19188281 Score: 119
Period size: 31 Copynumber: 3.8 Consensus size: 31
19188155 GGCCATCAAC
* * **
19188165 CATTCATATTTGCAT-TTTCATACACTGCAAT
1 CATTCATAATTGCATATTT-ATACCCTATAAT
* *
19188196 CATTTATAATTGTATATTTATACCCTATAAT
1 CATTCATAATTGCATATTTATACCCTATAAT
* * *
19188227 CATTCATAACTGCATATTTATACTCTGTAAT
1 CATTCATAATTGCATATTTATACCCTATAAT
* *
19188258 CATTCATAATTGCAGATTTGTACC
1 CATTCATAATTGCATATTTATACC
19188282 ATGAACTATC
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
31 67 0.96
32 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.43
Consensus pattern (31 bp):
CATTCATAATTGCATATTTATACCCTATAAT
Found at i:19195500 original size:25 final size:24
Alignment explanation
Indices: 19195429--19195498 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
19195419 ATATTTTTTT
*
19195429 AAAATTTTACTAGGGCCGAAATCATC
1 AAAATTTTACTAGGG--TAAATCATC
*
19195455 AAAATTTTATCAAGGGTAAATCATC
1 AAAATTTTA-CTAGGGTAAATCATC
*
19195480 AAAATTTTGCTAGGGTAAA
1 AAAATTTTACTAGGGTAAA
19195499 ATAGGGATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.23
25 16 0.41
26 9 0.23
27 5 0.13
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (24 bp):
AAAATTTTACTAGGGTAAATCATC
Found at i:19198289 original size:27 final size:27
Alignment explanation
Indices: 19198259--19198337 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
19198249 GACTACCTTG
19198259 TGTTTAACGTCCCATCGGACTATGC-CA
1 TGTTTAACGTCCCATCGGACTAT-CTCA
* *** ** *
19198286 TGTTTAACTTCTTGTCAAACTATCTCG
1 TGTTTAACGTCCCATCGGACTATCTCA
19198313 TGTTTAACGTCCCATCGGACTATCT
1 TGTTTAACGTCCCATCGGACTATCT
19198338 ATGATGTCGT
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.37
Consensus pattern (27 bp):
TGTTTAACGTCCCATCGGACTATCTCA
Found at i:19211152 original size:27 final size:26
Alignment explanation
Indices: 19211121--19211193 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
19211111 AACATCTTAT
* *
19211121 CAGACTATCCTGTGTTTAATGTCCCAT
1 CAGACTATCC-ATGTTTAATGTCCCAA
* * *
19211148 TAGACTATGCCCTATTTAATGTCCCAA
1 CAGACTAT-CCATGTTTAATGTCCCAA
19211175 CAGACTATCCCATGTTTAA
1 CAGACTAT-CCATGTTTAA
19211194 CGTCTCGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (26 bp):
CAGACTATCCATGTTTAATGTCCCAA
Found at i:19211419 original size:45 final size:45
Alignment explanation
Indices: 19211345--19211430 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
19211335 TATACTTTCA
* * *
19211345 CATGATGTCATAGCATCTTTCAACCATGGTCTTACTTATTTATAT
1 CATGATGTCAAAGCATCTTTCAACCATGGTATTACTCATTTATAT
* * * *
19211390 CATGATGTCAAATCATCTTTTAGCTATGGTATTACTCATTT
1 CATGATGTCAAAGCATCTTTCAACCATGGTATTACTCATTT
19211431 TAGGCGTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.43
Consensus pattern (45 bp):
CATGATGTCAAAGCATCTTTCAACCATGGTATTACTCATTTATAT
Found at i:19219658 original size:80 final size:80
Alignment explanation
Indices: 19219574--19219722 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
19219564 TATGGTAACC
* * * *
19219574 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
19219638 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
19219654 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
19219719 CCGG
66 CCGG
19219723 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:19219664 original size:40 final size:38
Alignment explanation
Indices: 19219615--19219722 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
19219605 ATCACGATTT
*
19219615 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
19219655 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
19219695 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
19219723 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:19227759 original size:80 final size:80
Alignment explanation
Indices: 19227675--19227823 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
19227665 TATGGTAACC
* * * *
19227675 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
19227739 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
19227755 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
19227820 CCGG
66 CCGG
19227824 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:19227765 original size:40 final size:38
Alignment explanation
Indices: 19227716--19227823 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
19227706 ATCACGATTT
*
19227716 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
19227756 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
19227796 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
19227824 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:19235833 original size:80 final size:80
Alignment explanation
Indices: 19235749--19235897 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
19235739 TATGGTAACC
* * * *
19235749 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
19235813 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
19235829 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
19235894 CCGG
66 CCGG
19235898 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:19235839 original size:40 final size:38
Alignment explanation
Indices: 19235790--19235897 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
19235780 ATCACGATTT
*
19235790 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
19235830 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
19235870 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
19235898 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:19246619 original size:31 final size:31
Alignment explanation
Indices: 19246581--19246644 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
19246571 TAATTTTAAA
19246581 TGTATCGCATAGTTCCAAGAAGTTCGCTAAG
1 TGTATCGCATAGTTCCAAGAAGTTCGCTAAG
19246612 TGTATCGCATAGTTCCAAGAAGTTCGCTAAG
1 TGTATCGCATAGTTCCAAGAAGTTCGCTAAG
19246643 TG
1 TG
19246645 AACGTTGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (31 bp):
TGTATCGCATAGTTCCAAGAAGTTCGCTAAG
Found at i:19258386 original size:45 final size:44
Alignment explanation
Indices: 19258279--19258388 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 44
19258269 TCCAGGATAA
19258279 GCACATAGTGCTTCATCGGAACAAATCGGAACTTTAACATTATAGT
1 GCACATAGTGCTTCATC-GAACAAATCGGAACTTTAACA-TATAGT
* * * *
19258325 ACACAAAGTACTTCATCGAACAAATCCGGAACTTTAACA-GTAGT
1 GCACATAGTGCTTCATCGAACAAAT-CGGAACTTTAACATATAGT
19258369 CGCACATAGTG-TCTCATCGA
1 -GCACATAGTGCT-TCATCGA
19258389 CTCAATGTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
44 5 0.09
45 22 0.41
46 27 0.50
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (44 bp):
GCACATAGTGCTTCATCGAACAAATCGGAACTTTAACATATAGT
Found at i:19259158 original size:4 final size:4
Alignment explanation
Indices: 19259149--19259177 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
19259139 CCCTTTTCTA
19259149 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
19259178 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:19265616 original size:47 final size:47
Alignment explanation
Indices: 19265507--19265617 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
19265497 CCGGGATAAG
*
19265507 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
19265554 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
19265601 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
19265618 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:19266389 original size:4 final size:4
Alignment explanation
Indices: 19266380--19266408 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
19266370 CCCTTTTCTA
19266380 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
19266409 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:19268340 original size:42 final size:43
Alignment explanation
Indices: 19268270--19268395 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 43
19268260 TCATACATGT
*
19268270 AATCAAACATCGATGCCACTGTCCCAGAC-TGGGTCTTACACGA
1 AATCAAACATCGATGCCAATGTCCCAGACAT-GGTCTTACACGA
* * *
19268313 AATCAAATA-CGATGCCAATGTCTCAGACATGGTCTTACACAAA
1 AATCAAACATCGATGCCAATGTCCCAGACATGGTCTTACAC-GA
* * * **
19268356 AAACAGAA-GTCGATGCCAACGTCATAGACATGGTCTTACA
1 AATCA-AACATCGATGCCAATGTCCCAGACATGGTCTTACA
19268396 TGCAGAACAG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
42 27 0.39
43 14 0.20
44 29 0.41
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (43 bp):
AATCAAACATCGATGCCAATGTCCCAGACATGGTCTTACACGA
Found at i:19271218 original size:39 final size:39
Alignment explanation
Indices: 19271137--19271325 Score: 319
Period size: 39 Copynumber: 4.9 Consensus size: 39
19271127 TATGGTAACC
* * * *
19271137 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
19271177 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
19271216 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
19271255 CGCACAATTGCCTTC-GGCTTAGCCCGG-TATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
19271292 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
19271326 CTCGAACATT
Statistics
Matches: 143, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
37 25 0.17
38 24 0.17
39 77 0.54
40 17 0.12
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:19271311 original size:76 final size:78
Alignment explanation
Indices: 19271137--19271326 Score: 321
Period size: 76 Copynumber: 2.4 Consensus size: 78
19271127 TATGGTAACC
* *
19271137 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
19271202 CGGATATCATAGCT
65 CGGATATCATAGCT
* *
19271216 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTGCCTTC-GGCTTAGCCC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCC
19271280 GG-TATCATAGCT
66 GGATATCATAGCT
19271292 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
19271327 TCGAACATTC
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
76 44 0.42
77 12 0.11
78 33 0.31
79 17 0.16
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (78 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCC
GGATATCATAGCT
Found at i:19283301 original size:40 final size:39
Alignment explanation
Indices: 19283257--19283437 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
19283247 GTTCAAAACA
* * ** * *
19283257 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
19283297 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
19283337 CCTTCGGGCTTAGCCCGG-TATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
19283375 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
19283414 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
19283438 CTCGAACATT
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 36 0.28
39 53 0.41
40 40 0.31
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:19283407 original size:77 final size:79
Alignment explanation
Indices: 19283287--19283437 Score: 252
Period size: 77 Copynumber: 1.9 Consensus size: 79
19283277 TATGGTAACC
19283287 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
19283352 CGG-TATCATAGCT
66 CGGATATCATAGCT
* * * *
19283365 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
19283429 CGGATATCA
66 CGGATATCA
19283438 CTCGAACATT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
77 46 0.68
78 22 0.32
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.24
Consensus pattern (79 bp):
CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
CGGATATCATAGCT
Found at i:19283409 original size:39 final size:39
Alignment explanation
Indices: 19283287--19283437 Score: 250
Period size: 39 Copynumber: 3.9 Consensus size: 39
19283277 TATGGTAACC
* * * *
19283287 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
19283327 CGCACAATTGCCTTCGGGCTTAGCCCGG-TATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
19283365 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
19283404 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
19283438 CTCGAACATT
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
38 36 0.34
39 53 0.50
40 17 0.16
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:19287089 original size:48 final size:48
Alignment explanation
Indices: 19286805--19287085 Score: 508
Period size: 48 Copynumber: 5.9 Consensus size: 48
19286795 TATATATGTG
* *
19286805 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
19286853 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
19286901 TGTGGTAAAGCTGAATGGCTAGTGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
19286949 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
19286997 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATGTGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
19287045 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
19287086 GTGTGTATAT
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 225 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
Found at i:19287278 original size:37 final size:37
Alignment explanation
Indices: 19287228--19287328 Score: 184
Period size: 37 Copynumber: 2.7 Consensus size: 37
19287218 AAATATATTT
19287228 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
*
19287265 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
*
19287302 CGGGTAAGACCCGATAACTACGTGTGG
1 CGGGTAAGACCCGATGACTACGTGTGG
19287329 GGACTATTCG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.24
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
Found at i:19289462 original size:43 final size:44
Alignment explanation
Indices: 19289395--19289498 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
19289385 CCTGAATTCA
* *
19289395 TTCACCAGCATT-TCGCCTGCTAGGCTC-AAAGCCCT-ATA-TCAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAG-CCTAATAGT-AT
19289437 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCTGAATAGTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCT-AATAGTAT
*
19289482 CTCACCGGCATTATAGC
1 TTCACCGGCATTATAGC
19289499 TTGCATTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
42 11 0.20
43 17 0.31
44 4 0.07
45 21 0.39
46 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGCCTAATAGTAT
Found at i:19290961 original size:28 final size:28
Alignment explanation
Indices: 19290863--19290961 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 28
19290853 GTGTTAATTA
* * *
19290863 GGCCTTAGCCCATATCAATATTAATCTG
1 GGCCATAGCCCATATCAGTATCAATCTG
* * *
19290891 GGCCATAACCCCT-TACAGTATCAGAGTATATTG
1 GGCCATAGCCCATAT-CAGTATC--A--AT-CTG
19290924 GGCC-TAGCCCATATCAGTATCAATCTG
1 GGCCATAGCCCATATCAGTATCAATCTG
19290951 GGCCATAGCCC
1 GGCCATAGCCC
19290962 TATTACTAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
27 7 0.13
28 23 0.43
30 2 0.04
32 15 0.28
33 7 0.13
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (28 bp):
GGCCATAGCCCATATCAGTATCAATCTG
Found at i:19290981 original size:60 final size:59
Alignment explanation
Indices: 19290863--19290997 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 59
19290853 GTGTTAATTA
* *
19290863 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAACCCCTTACAGTATCAGAGTATATTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAACCCATTACAG-ATCAGAGTATATTG
* *
19290924 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCTATTACTAG-TC-GAGATATATTG
1 GGCCTAGCCCATATCAATATCAATCTGGGCCATAACCC-ATTAC-AGATCAGAG-TATATTG
* *
19290984 GGCCTTGGCCATAT
1 GGCCTAGCCCATAT
19290998 TAACACAGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 3 0.05
60 52 0.80
61 8 0.12
62 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (59 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAACCCATTACAGATCAGAGTATATTG
Found at i:19293474 original size:47 final size:46
Alignment explanation
Indices: 19293418--19293512 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 46
19293408 AAAATTTTCT
* *
19293418 TTAACTAAGTAACTTATCTGGAAATAATAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATAATAAGAGC-AATTTAACAAGC
*
19293465 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATAATAAGAGCAATTTAACAAGC
19293511 TT
1 TT
19293513 TAAATTCAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 14 0.31
47 31 0.69
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (46 bp):
TTAACTAAGTAACTTATCCGGAAATAATAAGAGCAATTTAACAAGC
Found at i:19297198 original size:29 final size:29
Alignment explanation
Indices: 19297165--19297224 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
19297155 TAAAGCTTAC
*
19297165 TTTGTTTATTTTTCTATGTTTTATAGTGA
1 TTTGTTTATTTTTCTATGTTCTATAGTGA
19297194 TTTGTTTATTTTTCTATGTTCTATAGTGA
1 TTTGTTTATTTTTCTATGTTCTATAGTGA
19297223 TT
1 TT
19297225 ACAAAACTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.05, G:0.13, T:0.65
Consensus pattern (29 bp):
TTTGTTTATTTTTCTATGTTCTATAGTGA
Found at i:19297732 original size:13 final size:13
Alignment explanation
Indices: 19297714--19297738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19297704 GGTTTATTTA
19297714 TTAAACTAATTAT
1 TTAAACTAATTAT
19297727 TTAAACTAATTA
1 TTAAACTAATTA
19297739 ACTGATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:19300685 original size:6 final size:5
Alignment explanation
Indices: 19300656--19300734 Score: 65
Period size: 5 Copynumber: 15.2 Consensus size: 5
19300646 TATGTCTTTC
*
19300656 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT AAAAT
*
19300703 AAAAT AAAAT AAAACT -AAAT AATAAA AAAAT A
1 AAAAT AAAAT AAAA-T AAAAT AA-AAT AAAAT A
19300735 GGAGGATTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
3 3 0.05
4 1 0.02
5 34 0.55
6 24 0.39
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:19300688 original size:17 final size:16
Alignment explanation
Indices: 19300656--19300729 Score: 73
Period size: 17 Copynumber: 4.6 Consensus size: 16
19300646 TATGTCTTTC
19300656 AAAATAAAAT--AATA
1 AAAATAAAATAAAATA
* *
19300670 AAATTGAAATGAAAATA
1 AAAATAAAAT-AAAATA
19300687 AAAATAAAAATAAAAT-
1 AAAAT-AAAATAAAATA
19300703 AAAATAAAATAAAACTA
1 AAAATAAAATAAAA-TA
19300720 AATAATAAAA
1 AA-AATAAAA
19300730 AAATAGGAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 8 0.16
15 9 0.18
16 6 0.12
17 15 0.31
18 11 0.22
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:19320126 original size:13 final size:13
Alignment explanation
Indices: 19320108--19320137 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19320098 AATAAACCAA
19320108 AATATCATCAATG
1 AATATCATCAATG
19320121 AATATCATCAATG
1 AATATCATCAATG
19320134 AATA
1 AATA
19320138 CTACCACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (13 bp):
AATATCATCAATG
Found at i:19327966 original size:25 final size:26
Alignment explanation
Indices: 19327917--19327970 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 26
19327907 TTAATCACAT
19327917 TTAGTGGAAAAGTCATCATCATTCACTA
1 TTAGTGGAAAAG--ATCATCATTCACTA
19327945 TTAGTGGAAAAG-TCATCATTCACTA
1 TTAGTGGAAAAGATCATCATTCACTA
19327970 T
1 T
19327971 CTCCTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 14 0.54
28 12 0.46
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (26 bp):
TTAGTGGAAAAGATCATCATTCACTA
Found at i:19334441 original size:29 final size:29
Alignment explanation
Indices: 19334409--19334511 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
19334399 GTGACGAGAT
* *
19334409 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
19334438 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
19334467 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
19334496 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
19334512 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:19339781 original size:40 final size:40
Alignment explanation
Indices: 19339737--19339822 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
19339727 AAAAAGGGAT
*
19339737 TAAATTATAATGTTTAATTGTTCGTTTTGTTCATAAGCAC
1 TAAATTATAATGTTTAATTGTTAGTTTTGTTCATAAGCAC
*
19339777 TAAATTATAATGTTTAATTGTTAGTTTTGTTCATAAGGAC
1 TAAATTATAATGTTTAATTGTTAGTTTTGTTCATAAGCAC
19339817 TAAATT
1 TAAATT
19339823 GAATAAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (40 bp):
TAAATTATAATGTTTAATTGTTAGTTTTGTTCATAAGCAC
Found at i:19343682 original size:18 final size:18
Alignment explanation
Indices: 19343631--19343716 Score: 77
Period size: 18 Copynumber: 4.8 Consensus size: 18
19343621 GGCGAATTAT
*
19343631 CAAATGTGGCAGACAATC
1 CAAATATGGCAGACAATC
* *
19343649 CAAATATTGCAAACAATC
1 CAAATATGGCAGACAATC
*
19343667 CAAATATGGTAGACAATC
1 CAAATATGGCAGACAATC
* * *
19343685 TAAGA-GTGGCAGACAAGC
1 CAA-ATATGGCAGACAATC
*
19343703 C-AATATCGCAGACA
1 CAAATATGGCAGACA
19343717 TTTGGAGTGT
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
16 1 0.02
17 9 0.17
18 42 0.79
19 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (18 bp):
CAAATATGGCAGACAATC
Found at i:19346264 original size:13 final size:13
Alignment explanation
Indices: 19346246--19346270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19346236 CTAACTTGTG
19346246 CACACGGCCATGC
1 CACACGGCCATGC
19346259 CACACGGCCATG
1 CACACGGCCATG
19346271 TGCTAGGCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.44, G:0.24, T:0.08
Consensus pattern (13 bp):
CACACGGCCATGC
Found at i:19348783 original size:19 final size:19
Alignment explanation
Indices: 19348737--19348784 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
19348727 GTATATATTT
19348737 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
19348755 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
19348774 TAAATTTTATT
1 TAAATTTTATT
19348785 CATATTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:19352720 original size:19 final size:19
Alignment explanation
Indices: 19352674--19352721 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
19352664 GTATATATTT
19352674 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
19352692 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
19352711 TAAATTTTATT
1 TAAATTTTATT
19352722 CATATTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:19352802 original size:42 final size:42
Alignment explanation
Indices: 19352745--19352827 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
19352735 TATTTTTATT
19352745 TTATCTTTTACTAGTTTATTAGAACAAGGGAACTAGTTTCCC
1 TTATCTTTTACTAGTTTATTAGAACAAGGGAACTAGTTTCCC
* * * *
19352787 TTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCC
1 TTATCTTTTACTAGTTTATTAGAACAAGGGAACTAGTTTCC
19352828 AATTAGGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (42 bp):
TTATCTTTTACTAGTTTATTAGAACAAGGGAACTAGTTTCCC
Found at i:19353494 original size:17 final size:18
Alignment explanation
Indices: 19353464--19353520 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
19353454 CTTACACTCA
**
19353464 GACTGTTCATCATA-TTG
1 GACTGTTCGCCATATTTG
19353481 GACTGTTCGCCATATTTG
1 GACTGTTCGCCATATTTG
* * *
19353499 GATTGCTCGCCACATTTG
1 GACTGTTCGCCATATTTG
19353517 GACT
1 GACT
19353521 ATCCTCCACA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (18 bp):
GACTGTTCGCCATATTTG
Found at i:19362016 original size:12 final size:13
Alignment explanation
Indices: 19361994--19362022 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
19361984 AGACGAAGGA
19361994 AAAATTAAAAATT
1 AAAATTAAAAATT
19362007 AAAA-TAAAAATT
1 AAAATTAAAAATT
19362019 AAAA
1 AAAA
19362023 AAGACCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:19367375 original size:29 final size:28
Alignment explanation
Indices: 19367332--19367426 Score: 118
Period size: 29 Copynumber: 3.3 Consensus size: 28
19367322 TTCTATTGAT
*
19367332 GTCACACAGCCGTGTGGCAGACCGTGTGG
1 GTCACACA-ACGTGTGGCAGACCGTGTGG
19367361 GTCACACAACAGTGTGGCAGACCGTGTGG
1 GTCACACAAC-GTGTGGCAGACCGTGTGG
* * * *
19367390 GTCACATGATCGTGTGGCAAACCATGTGG
1 GTCACA-CAACGTGTGGCAGACCGTGTGG
19367419 GTCACACA
1 GTCACACA
19367427 GTCATGTGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.03
29 54 0.93
30 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (28 bp):
GTCACACAACGTGTGGCAGACCGTGTGG
Found at i:19367452 original size:20 final size:20
Alignment explanation
Indices: 19367429--19367466 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19367419 GTCACACAGT
*
19367429 CATGTGGTTGGTCGTGTGAC
1 CATGTGGTTGGCCGTGTGAC
19367449 CATGTGGTTGGCCGTGTG
1 CATGTGGTTGGCCGTGTG
19367467 GGTCAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.16, G:0.42, T:0.34
Consensus pattern (20 bp):
CATGTGGTTGGCCGTGTGAC
Found at i:19368839 original size:18 final size:19
Alignment explanation
Indices: 19368801--19368839 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19368791 TGTATTTTGA
*
19368801 TTAAATTATGATGTGAATG
1 TTAAATGATGATGTGAATG
*
19368820 TTAAATGATTATGT-AATG
1 TTAAATGATGATGTGAATG
19368838 TT
1 TT
19368840 TGTATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (19 bp):
TTAAATGATGATGTGAATG
Found at i:19375794 original size:47 final size:46
Alignment explanation
Indices: 19375491--19375797 Score: 280
Period size: 47 Copynumber: 6.6 Consensus size: 46
19375481 TTTGTGTACT
19375491 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACATTAT-GA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G--AC-TTATGGATGAGCC
*
19375537 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGAGGA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TT-A-TGGATGAGCC
* *
19375585 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTT-CGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTATG-GATG--AGCC
* * * *
19375631 AGTGTAAGA-CATATCTGGGACAT-ACATC-AGC-TACGAGATG-GTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTATG-GATGAGCC
* * *
19375674 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGATGTGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTATGGATGAGCC
*
19375722 AGTGTAAGACCATGTCTGAGACATGGCATCGACTTGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTT-ATGGATGAGCC
*
19375769 AGTGTAAGACCATGTTTGGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
19375798 TGGTATTATA
Statistics
Matches: 224, Mismatches: 18, Indels: 37
0.80 0.06 0.13
Matches are distributed among these distances:
42 1 0.00
43 13 0.06
44 14 0.06
45 12 0.05
46 58 0.26
47 71 0.32
48 55 0.25
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTTATGGATGAGCC
Found at i:19376947 original size:21 final size:22
Alignment explanation
Indices: 19376921--19376965 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
19376911 CGCACAAGCA
*
19376921 TGTTGCCCTCTTACATGGG-TG
1 TGTTGCCCTCTTACACGGGCTG
19376942 TGTTGCCCTCTTACACGGGCTG
1 TGTTGCCCTCTTACACGGGCTG
19376964 TG
1 TG
19376966 CCCTGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.09, C:0.27, G:0.29, T:0.36
Consensus pattern (22 bp):
TGTTGCCCTCTTACACGGGCTG
Found at i:19393255 original size:79 final size:81
Alignment explanation
Indices: 19393146--19393328 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
19393136 TACTCGTTCA
* *
19393146 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
19393209 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
19393226 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
19393289 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
19393305 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
19393329 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:19393328 original size:40 final size:40
Alignment explanation
Indices: 19393125--19393328 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
19393115 CGGAATTTAA
** *
19393125 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19393165 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19393205 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
19393244 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
19393284 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
19393324 CCGGA
1 CCGGA
19393329 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:19394811 original size:14 final size:14
Alignment explanation
Indices: 19394792--19394820 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19394782 CATATTAGGG
19394792 GGGAAAATTGACAT
1 GGGAAAATTGACAT
19394806 GGGAAAATTGACAT
1 GGGAAAATTGACAT
19394820 G
1 G
19394821 CAAGTCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (14 bp):
GGGAAAATTGACAT
Found at i:19408343 original size:29 final size:29
Alignment explanation
Indices: 19408253--19408440 Score: 229
Period size: 29 Copynumber: 6.5 Consensus size: 29
19408243 ACTCGATTTC
* * **
19408253 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
19408282 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
19408310 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
19408340 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
19408369 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
19408398 GCACACTTAGTGCCATATA-TTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
19408426 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
19408441 ATCTCGTCAC
Statistics
Matches: 139, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
28 26 0.19
29 112 0.81
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:19423893 original size:32 final size:32
Alignment explanation
Indices: 19423855--19423950 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 32
19423845 CAAACGACTC
*
19423855 TAATTTCCCCTTCAAGAAAGAAAACATGGTAA
1 TAATTTCCCCTTCAAGAAAGAAAACATGGCAA
19423887 TAATTT-CCCTTCTAAGAAAGAAAACATGGCAA
1 TAATTTCCCCTTC-AAGAAAGAAAACATGGCAA
* * *
19423919 TAACTTCCCCTCCAAGAAAGAAAACTTGGCAA
1 TAATTTCCCCTTCAAGAAAGAAAACATGGCAA
19423951 AAAAAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
31 6 0.10
32 47 0.81
33 5 0.09
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (32 bp):
TAATTTCCCCTTCAAGAAAGAAAACATGGCAA
Found at i:19433735 original size:2 final size:2
Alignment explanation
Indices: 19433730--19433758 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19433720 TATAAACTGC
19433730 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19433759 TCTCCCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19439720 original size:22 final size:22
Alignment explanation
Indices: 19439695--19439736 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19439685 ATCGACAACT
*
19439695 TTTCTTCTTATTTCCATATTCC
1 TTTCTTCTTAGTTCCATATTCC
*
19439717 TTTCTTTTTAGTTCCATATT
1 TTTCTTCTTAGTTCCATATT
19439737 TTCTTGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.21, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTCTTCTTAGTTCCATATTCC
Found at i:19458775 original size:60 final size:60
Alignment explanation
Indices: 19458634--19458779 Score: 177
Period size: 61 Copynumber: 2.4 Consensus size: 60
19458624 AAGGACAGCC
* *
19458634 TTGTGGCACAACTCTGAACATGAAAGCCTTTGTAGCGAGTACTAGATATAAAGGATGACAT
1 TTGTGGCACAACTCTG-ACAGGAAAACCTTTGTAGCGAGTACTAGATATAAAGGATGACAT
* * ** * * *
19458695 TTGTGGCACAACTCTGGACAGGAAAACCTTTGTGGTGAGTTTTGGATATAAATGATG-CCT
1 TTGTGGCACAACTCT-GACAGGAAAACCTTTGTAGCGAGTACTAGATATAAAGGATGACAT
19458755 TTGTGGCACAACTCTAGACAGGAAA
1 TTGTGGCACAACTCT-GACAGGAAA
19458780 GCTTTTATGG
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
60 26 0.35
61 47 0.64
62 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (60 bp):
TTGTGGCACAACTCTGACAGGAAAACCTTTGTAGCGAGTACTAGATATAAAGGATGACAT
Found at i:19462537 original size:50 final size:50
Alignment explanation
Indices: 19462432--19462538 Score: 128
Period size: 50 Copynumber: 2.1 Consensus size: 50
19462422 AAGCTCCTCC
* * * **
19462432 GAGCTGAATAATGGGAAGCTCATGAGAGCTGAATATCGGGAAGCTTATGT
1 GAGCTGTATAATGGGAAGCTCATAAAAGCTGAATATCGGGAAGCTTATAA
*
19462482 TAGCTGTATAATGGGAAGCTCATAAAAGCTGTAA-ATCGGGAAG-TTCATAA
1 GAGCTGTATAATGGGAAGCTCATAAAAGCTG-AATATCGGGAAGCTT-ATAA
19462532 GAGCTGT
1 GAGCTGT
19462539 GGTGTGTCCG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 2 0.04
50 44 0.92
51 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (50 bp):
GAGCTGTATAATGGGAAGCTCATAAAAGCTGAATATCGGGAAGCTTATAA
Found at i:19462538 original size:25 final size:25
Alignment explanation
Indices: 19462400--19462538 Score: 106
Period size: 25 Copynumber: 5.6 Consensus size: 25
19462390 ATTCATATAT
* *
19462400 GCTCATACGAGCTGTAAATC-GAAA
1 GCTCATAAGAGCTGTAAATCGGGAA
* ** *
19462424 GCTCCTCCGAGCTGAATAAT-GGGAA
1 GCTCATAAGAGCTGTA-AATCGGGAA
*
19462449 GCTCATGAGAGCTG-AATATCGGGAA
1 GCTCATAAGAGCTGTAA-ATCGGGAA
* ***
19462474 GCTTATGTTAGCTGTATAAT-GGGAA
1 GCTCATAAGAGCTGTA-AATCGGGAA
*
19462499 GCTCATAAAAGCTGTAAATCGGGAA
1 GCTCATAAGAGCTGTAAATCGGGAA
*
19462524 GTTCATAAGAGCTGT
1 GCTCATAAGAGCTGT
19462539 GGTGTGTCCG
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
23 1 0.01
24 19 0.21
25 68 0.74
26 3 0.03
27 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (25 bp):
GCTCATAAGAGCTGTAAATCGGGAA
Found at i:19467112 original size:40 final size:34
Alignment explanation
Indices: 19467039--19467107 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
19467029 GGCAACCTCT
19467039 TTGGCGATTATTATAATTACACCTACCGCGTCCA
1 TTGGCGATTATTATAATTACACCTACCGCGTCCA
*
19467073 TTGGCGATTATTATAATTACACCTACCACGTCCA
1 TTGGCGATTATTATAATTACACCTACCGCGTCCA
19467107 T
1 T
19467108 GTCCACGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (34 bp):
TTGGCGATTATTATAATTACACCTACCGCGTCCA
Found at i:19467557 original size:51 final size:51
Alignment explanation
Indices: 19467488--19467591 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 51
19467478 TCATAAATTA
* *
19467488 TAATTAAATCACAAATATATATAAATTCTCAATGTTTTATTGACAAGCACC
1 TAATTAAATCACAAATATATATAAATTCTCAATGCTTTAGTGACAAGCACC
* * *
19467539 TAATTCAAATCA-TAATATATATAACTTTTCAATGCTTTAGTGACAAGCACC
1 TAATT-AAATCACAAATATATATAAATTCTCAATGCTTTAGTGACAAGCACC
19467590 TA
1 TA
19467592 CTTTAAACTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 41 0.87
52 6 0.13
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (51 bp):
TAATTAAATCACAAATATATATAAATTCTCAATGCTTTAGTGACAAGCACC
Found at i:19473396 original size:47 final size:46
Alignment explanation
Indices: 19473327--19473639 Score: 266
Period size: 47 Copynumber: 6.7 Consensus size: 46
19473317 GGTATAGTGT
19473327 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-T-CATCAATGC
* * *
19473374 CGATGCCATGTCCCAGACATGGTCTTTA-ACTGACTTTCACATATCTATGC
1 CGATGCCATGTCCCAGACATGGTC-TTACACTGGC--TCTC--ATCAATGC
** * * ** **
19473424 TAATGCCATGTCCCAGACATGGTCTTACACTGACACATTTTGTA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATCAATGC
19473470 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCAT-AATGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCAA--T-GC
* * * *
19473517 CAATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--ATCAATGC
*
19473563 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATCGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCA-AT-GC
* *
19473611 CAAT-ACATGTCCCAGACAT-GTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
19473640 ACCACACAAA
Statistics
Matches: 219, Mismatches: 28, Indels: 39
0.77 0.10 0.14
Matches are distributed among these distances:
43 1 0.00
44 2 0.01
45 28 0.13
46 39 0.18
47 82 0.37
48 26 0.12
49 11 0.05
50 30 0.14
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (46 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCAATGC
Found at i:19473588 original size:94 final size:94
Alignment explanation
Indices: 19473333--19473640 Score: 355
Period size: 94 Copynumber: 3.3 Consensus size: 94
19473323 GTGTCGATGC
*
19473333 CATGTCCCAGACATGGTCTTACACTGGCTCATC-CATCAAGCCGATGCCATGTCCCAGACATGGT
1 CATGTCCCAGACATGGTCTTACACTAGCTCATCTC-TCAAGCCGATGCCATGTCCCAGACATGGT
* * * *
19473397 CTTTA-ACTGACTTTCA-CATATCTATGCTAATG
65 C-TTACACTGGCTCTCATAATATC---GCCAATG
* * **
19473429 CCATGTCCCAGACATGGTCTTACACT-GACACAT-TTTGTAGCCGATG-CATGTCCCAGACATGG
1 -CATGTCCCAGACATGGTCTTACACTAG-CTCATCTCTCAAGCCGATGCCATGTCCCAGACATGG
* *
19473491 TCTTACACTGGCTCTCATAATGTGGCCAATG
64 TCTTACACTGGCTCTCATAATATCGCCAATG
*
19473522 CATGTCCCAAACAT-GTCTTACACTAGCTC-TCGTCTCAATGCCGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACATGGTCTTACACTAGCTCATC-TCTCAA-GCCGATGCCATGTCCCAGACATGG
*
19473585 TCTTACACTGGCTCTCATAATATCGCCAATA
64 TCTTACACTGGCTCTCATAATATCGCCAATG
19473616 CATGTCCCAGACAT-GTCTTACACTA
1 CATGTCCCAGACATGGTCTTACACTA
19473641 CCACACAAAT
Statistics
Matches: 183, Mismatches: 19, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
90 1 0.01
91 12 0.07
92 17 0.09
93 13 0.07
94 71 0.39
95 27 0.15
96 13 0.07
97 29 0.16
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (94 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCATCTCTCAAGCCGATGCCATGTCCCAGACATGGTC
TTACACTGGCTCTCATAATATCGCCAATG
Found at i:19475950 original size:18 final size:18
Alignment explanation
Indices: 19475927--19475962 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19475917 TTCCCGGGTG
19475927 ATAGTCTATTATCAACTC
1 ATAGTCTATTATCAACTC
*
19475945 ATAGTCTTTTATCAACTC
1 ATAGTCTATTATCAACTC
19475963 CAACCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
ATAGTCTATTATCAACTC
Found at i:19482738 original size:50 final size:47
Alignment explanation
Indices: 19482626--19482801 Score: 155
Period size: 50 Copynumber: 3.7 Consensus size: 47
19482616 ATAGGGTATA
* * * *
19482626 ATGTCAATGCCATGTCCCAGACATAGTCTTACACTGGCTCATCCATC
1 ATGTCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCCATC
* *
19482673 AAGTCGATACCATGTCCCAAACATGGTCTTACACTGACTC-TCACGTATTC
1 ATGTCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATC-C--A-TC
* * * * *
19482723 GTGTCGATGCCATGTCCCAAACATGGTCTTAGACTGACACAT--TTT
1 ATGTCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCCATC
* *
19482768 GTAGCCGATG-CATGTCCCAAACAT-GTCTTACACT
1 AT-GTCGATGCCATGTCCCAAACATGGTCTTACACT
19482802 AGCTTACAAC
Statistics
Matches: 108, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
44 9 0.08
45 17 0.16
46 8 0.07
47 35 0.32
49 1 0.01
50 37 0.34
51 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (47 bp):
ATGTCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCCATC
Found at i:19482842 original size:46 final size:46
Alignment explanation
Indices: 19482771--19482944 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
19482761 ACATTTTGTA
*
19482771 GCCGATGCATGTCCCAAACATGTCTTACACTAGCT-TACAACTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CAACTCGAG
* * * ** * *
19482817 GCTGATGCATGTCCCAGACACGTCTTACAATAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCAACTCGAG
* * * *
19482863 GCCGATGCCATGTCCCAGACGTGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCA-ACTCGAG
19482911 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
19482945 ATACAAATGA
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
46 54 0.52
47 26 0.25
48 22 0.21
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCAACTCGAG
Found at i:19482890 original size:94 final size:92
Alignment explanation
Indices: 19482771--19482944 Score: 226
Period size: 94 Copynumber: 1.9 Consensus size: 92
19482761 ACATTTTGTA
* *
19482771 GCCGATGCATGTCCCAAACATGTCTTACACTAGCT-TACA-ACTCGAGGCTGATGCATGTCCCAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCT-CATAAT-GAGGCCGATGCATGTCCCAG
19482834 ACACGTCTTACAATAGCTCTCGTCTCAAT
64 ACACGTCTTACAATAGCTCTCGTCTCAAT
* * * *
19482863 GCCGATGCCATGTCCCAGACGTGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAG
1 GCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCATAATGAGGCCGATGCATGTCCCAG
* *
19482928 ACATGTCTTACACTAGC
64 ACACGTCTTACAATAGC
19482945 ATACAAATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
92 7 0.10
93 12 0.17
94 48 0.69
95 3 0.04
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (92 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATAATGAGGCCGATGCATGTCCCAGAC
ACGTCTTACAATAGCTCTCGTCTCAAT
Found at i:19489955 original size:46 final size:44
Alignment explanation
Indices: 19489851--19489958 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
19489841 TGTCTTTGAC
** * * *
19489851 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
19489895 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
19489941 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
19489959 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:19491102 original size:2 final size:2
Alignment explanation
Indices: 19491095--19491132 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19491085 AATAATAGTA
19491095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19491133 TTTACCCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19495029 original size:27 final size:28
Alignment explanation
Indices: 19494986--19495048 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
19494976 TTTAATCATT
* *
19494986 TTAATATTTTTATAATTACATT-TAAAA
1 TTAATATTATTATAATTAAATTATAAAA
*
19495013 TTAATAGTTATTA-AATTAAATTATAGAA
1 TTAATA-TTATTATAATTAAATTATAAAA
19495041 TTAA-ATTA
1 TTAATATTA
19495049 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 3 0.10
27 15 0.48
28 13 0.42
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
TTAATATTATTATAATTAAATTATAAAA
Found at i:19501698 original size:12 final size:12
Alignment explanation
Indices: 19501663--19501700 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
19501653 GTTTATATAT
*
19501663 ATATTAAAATT-
1 ATATAAAAATTA
19501674 ATATAAAAA-TA
1 ATATAAAAATTA
19501685 ATATAAAAATTA
1 ATATAAAAATTA
19501697 ATAT
1 ATAT
19501701 GGACGGGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
12 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATAAAAATTA
Found at i:19501980 original size:21 final size:21
Alignment explanation
Indices: 19501956--19501996 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
19501946 TAGTTACTTT
19501956 TTTGAGATGGAAGTAAGTAGG
1 TTTGAGATGGAAGTAAGTAGG
19501977 TTTGAGATGGAAGTAAGTAG
1 TTTGAGATGGAAGTAAGTAG
19501997 TTTCATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (21 bp):
TTTGAGATGGAAGTAAGTAGG
Found at i:19510953 original size:13 final size:15
Alignment explanation
Indices: 19510926--19510957 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
19510916 AATTAAGTTT
19510926 AAAAATTCATAATAA
1 AAAAATTCATAATAA
19510941 AAAAATT-AT-ATAA
1 AAAAATTCATAATAA
19510954 AAAA
1 AAAA
19510958 CGAAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAATTCATAATAA
Found at i:19511105 original size:48 final size:51
Alignment explanation
Indices: 19511038--19511142 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 51
19511028 ATGCCACCCC
*
19511038 TAACTATAAGAGGGCGGTAAGGTT-A-AGCATTAAATTGGATAA-TTTATA
1 TAACTATAAAAGGGCGGTAAGGTTAACAGCATTAAATTGGATAATTTTATA
*
19511086 TAACTATAAAAGGGTGGTAAGGTTAAAGCTAGCATTAAATTGGATAATTTTATA
1 TAACTATAAAAGGGCGGTAAGGTT-AA-C-AGCATTAAATTGGATAATTTTATA
19511140 TAA
1 TAA
19511143 ATTAGTAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
48 22 0.45
50 1 0.02
53 17 0.35
54 9 0.18
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (51 bp):
TAACTATAAAAGGGCGGTAAGGTTAACAGCATTAAATTGGATAATTTTATA
Found at i:19511246 original size:2 final size:2
Alignment explanation
Indices: 19511241--19511276 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19511231 TGGTAATTTC
19511241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19511277 AAACCTGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19513108 original size:29 final size:30
Alignment explanation
Indices: 19513052--19513108 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
19513042 ACTTTTGAAA
**
19513052 TTGACAGAGATTAAATTACTTTTATTTTTG
1 TTGACAGAGATTAAATTACTTCAATTTTTG
* *
19513082 TTGAGAGAGATTAATTTAC-TCAATTTT
1 TTGACAGAGATTAAATTACTTCAATTTT
19513109 GACTGAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 6 0.26
30 17 0.74
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TTGACAGAGATTAAATTACTTCAATTTTTG
Found at i:19514085 original size:6 final size:6
Alignment explanation
Indices: 19514076--19514101 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19514066 CCGCCACCGC
19514076 AGGGTT AGGGTT AGGGTT AGGGTT AG
1 AGGGTT AGGGTT AGGGTT AGGGTT AG
19514102 AGCTAGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.50, T:0.31
Consensus pattern (6 bp):
AGGGTT
Found at i:19514108 original size:18 final size:18
Alignment explanation
Indices: 19514076--19514110 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19514066 CCGCCACCGC
* *
19514076 AGGGTTAGGGTTAGGGTT
1 AGGGTTAGAGCTAGGGTT
19514094 AGGGTTAGAGCTAGGGT
1 AGGGTTAGAGCTAGGGT
19514111 CAGGTGGTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.49, T:0.29
Consensus pattern (18 bp):
AGGGTTAGAGCTAGGGTT
Found at i:19518808 original size:16 final size:17
Alignment explanation
Indices: 19518779--19518824 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
19518769 ATCTTTATTG
*
19518779 AATCCCTAAAATCTT-TA
1 AATCCCT-AAATCTTAAA
*
19518796 AATTCCTAAATCTTAAA
1 AATCCCTAAATCTTAAA
19518813 AATCCCTAAATC
1 AATCCCTAAATC
19518825 GTTAGCATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (17 bp):
AATCCCTAAATCTTAAA
Found at i:19518835 original size:34 final size:35
Alignment explanation
Indices: 19518779--19518858 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
19518769 ATCTTTATTG
* *
19518779 AATCCCTAAAATCTTTAAATTCC-TAA-A-TCTTAAA
1 AATCCCT-AAATCGTTAAATTCCAAAATATTCTT-AA
*
19518813 AATCCCTAAATCGTTAGCATTCCAAAATATTCTTAA
1 AATCCCTAAATCGTTA-AATTCCAAAATATTCTTAA
19518849 AATCCCTAAA
1 AATCCCTAAA
19518859 ACTTTTACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
33 8 0.21
34 12 0.31
35 2 0.05
36 13 0.33
37 4 0.10
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.33
Consensus pattern (35 bp):
AATCCCTAAATCGTTAAATTCCAAAATATTCTTAA
Found at i:19520389 original size:16 final size:16
Alignment explanation
Indices: 19520352--19520390 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
19520342 ATATGATTAG
*
19520352 TCTATACACCATTCAC
1 TCTATACACCATCCAC
19520368 -CATATACACCATCCAC
1 TC-TATACACCATCCAC
19520384 TCTATAC
1 TCTATAC
19520391 CAACCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.33, C:0.38, G:0.00, T:0.28
Consensus pattern (16 bp):
TCTATACACCATCCAC
Found at i:19527310 original size:117 final size:117
Alignment explanation
Indices: 19527139--19527349 Score: 318
Period size: 117 Copynumber: 1.8 Consensus size: 117
19527129 GGTAACAGAA
* *
19527139 ATCAACATCACCGGGACCATTGTCGCATCACAAATAGACAAAACAAACCTTACATTGTGGCACTG
1 ATCAACAACACCGGGACCATTGTCGCATCACAAATAGACAAAACAAACCTTACATTGTGACACTG
**
19527204 AAATTGCAATAATAAATTACAAATAACCATCTACAATTTTAACAATAGCTTT
66 AAATTGCAATAATAAACCACAAATAACCATCTACAATTTTAACAATAGCTTT
* * * *
19527256 ATCAACAACATCGGGACCACTT-TTGCATCACAAATCGACAAAACAAATCC-TACATTGTGACAT
1 ATCAACAACACCGGGACCA-TTGTCGCATCACAAATAGACAAAACAAA-CCTTACATTGTGACAC
19527319 TGAAATTGCAATAATAAACCACAAATAACCA
64 TGAAATTGCAATAATAAACCACAAATAACCA
19527350 ACAAATCAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
117 80 0.95
118 4 0.05
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (117 bp):
ATCAACAACACCGGGACCATTGTCGCATCACAAATAGACAAAACAAACCTTACATTGTGACACTG
AAATTGCAATAATAAACCACAAATAACCATCTACAATTTTAACAATAGCTTT
Found at i:19529911 original size:15 final size:16
Alignment explanation
Indices: 19529879--19529914 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
19529869 TGATTCAATC
*
19529879 AAATAAATTATTAAAA
1 AAATAAATTATAAAAA
19529895 AAATAAATT-TAAAAA
1 AAATAAATTATAAAAA
19529910 AAATA
1 AAATA
19529915 GAGGAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAAATTATAAAAA
Found at i:19530118 original size:2 final size:2
Alignment explanation
Indices: 19530111--19530137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19530101 TAATGAAATT
19530111 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19530138 TTGCCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19530419 original size:19 final size:20
Alignment explanation
Indices: 19530395--19530436 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
19530385 GAAAATATAT
*
19530395 AAATAATAT-TTATTTTTAA
1 AAATAATATAATATTTTTAA
19530414 AAATAATATGAATATTTTTAA
1 AAATAATAT-AATATTTTTAA
19530435 AA
1 AA
19530437 TAAACGCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATAATATAATATTTTTAA
Found at i:19532650 original size:16 final size:17
Alignment explanation
Indices: 19532629--19532666 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19532619 ATGAAAATTT
*
19532629 TTAAATAAT-TTAGTGA
1 TTAAATAATAATAGTGA
*
19532645 TTAAATTATAATAGTGA
1 TTAAATAATAATAGTGA
19532662 TTAAA
1 TTAAA
19532667 ACAAAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
TTAAATAATAATAGTGA
Found at i:19550553 original size:35 final size:36
Alignment explanation
Indices: 19550431--19550628 Score: 155
Period size: 40 Copynumber: 5.3 Consensus size: 36
19550421 TAAATGTGTA
* * **
19550431 CCCAGCACTAGTCGGATTAACTGTCAAAGATTTACG
1 CCCAACACTAGTCGGATTAACTGACAAAGATTTGTG
* * * * * *
19550467 CCCAGCATTAGTCGGATAAACCGACGATATTAAATGTGTG
1 CCCAACACTAGTCGGATTAACTGAC-A-A--AGATTTGTG
19550507 CCCAACACTAGTCGGATTAACTG-CAAAGATTTGTG
1 CCCAACACTAGTCGGATTAACTGACAAAGATTTGTG
* * * *
19550542 CCCAACGCTAGTCGGATAAACTGACGATATTAAATATGTG
1 CCCAACACTAGTCGGATTAACTGAC-A-A--AGATTTGTG
* *
19550582 CCCAACACTAGTCGAATTAACCGACAAAGATTTGTG
1 CCCAACACTAGTCGGATTAACTGACAAAGATTTGTG
* *
19550618 CCTAACGCTAG
1 CCCAACACTAG
19550629 CCGAAACTGA
Statistics
Matches: 127, Mismatches: 26, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
35 28 0.22
36 38 0.30
37 3 0.02
38 4 0.03
39 2 0.02
40 52 0.41
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (36 bp):
CCCAACACTAGTCGGATTAACTGACAAAGATTTGTG
Found at i:19550569 original size:75 final size:76
Alignment explanation
Indices: 19550414--19550654 Score: 310
Period size: 75 Copynumber: 3.2 Consensus size: 76
19550404 GGATAAATCA
* * * * ** * **
19550414 ACGATACTAAATGTGTACCCAGCACTAGTCGGATTAACTGTCAAAGATTTACGCCCAGCATTAGT
1 ACGATATTAAATGTGTGCCCAACACTAGTCGGATTAACTGACAAAGATTTGTGCCCAACGCTAGT
*
19550479 CGGATAAACCG
66 CGGATAAACTG
19550490 ACGATATTAAATGTGTGCCCAACACTAGTCGGATTAACTG-CAAAGATTTGTGCCCAACGCTAGT
1 ACGATATTAAATGTGTGCCCAACACTAGTCGGATTAACTGACAAAGATTTGTGCCCAACGCTAGT
19550554 CGGATAAACTG
66 CGGATAAACTG
* * * *
19550565 ACGATATTAAATATGTGCCCAACACTAGTCGAATTAACCGACAAAGATTTGTGCCTAACGCTAG-
1 ACGATATTAAATGTGTGCCCAACACTAGTCGGATTAACTGACAAAGATTTGTGCCCAACGCTAGT
*
19550629 CCG--AAACTG
66 CGGATAAACTG
*
19550638 ACAATATTAAATGTGTG
1 ACGATATTAAATGTGTG
19550655 TATACGTCCT
Statistics
Matches: 148, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
73 21 0.14
75 68 0.46
76 59 0.40
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (76 bp):
ACGATATTAAATGTGTGCCCAACACTAGTCGGATTAACTGACAAAGATTTGTGCCCAACGCTAGT
CGGATAAACTG
Found at i:19550790 original size:13 final size:13
Alignment explanation
Indices: 19550772--19550808 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
19550762 TTGGCAATGC
19550772 TTTTGAAAAGTGA
1 TTTTGAAAAGTGA
*
19550785 TTTTGAAAAGTGC
1 TTTTGAAAAGTGA
19550798 TTTTGAAAAGT
1 TTTTGAAAAGT
19550809 TTGATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:19551573 original size:2 final size:2
Alignment explanation
Indices: 19551566--19551612 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
19551556 TAGAATTATC
19551566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19551608 AT AT A
1 AT AT A
19551613 ATTCCATGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19554963 original size:26 final size:26
Alignment explanation
Indices: 19554934--19555015 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
19554924 TGATACAAAT
*
19554934 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
19554960 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19554986 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19555012 TGAT
1 TGAT
19555016 GGGAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:19559055 original size:48 final size:46
Alignment explanation
Indices: 19558940--19559057 Score: 112
Period size: 46 Copynumber: 2.5 Consensus size: 46
19558930 TATTAGAGCC
* * * *
19558940 AGTGTAAGA-CAAGTCTGGGACATGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCTA-TCTGGGACATGCATCGGCATCGAGAAGAAAGCT
* * * * * *
19558986 AATGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATACAAGCT
1 AGTGTAAGACCTATCTGGGACATGCATCGGCATCGAGA-AGA-AAGCT
19559034 AGTGTAAGACCTATCTGGGACATG
1 AGTGTAAGACCTATCTGGGACATG
19559058 GCGTCAGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
46 30 0.55
47 1 0.02
48 24 0.44
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACCTATCTGGGACATGCATCGGCATCGAGAAGAAAGCT
Found at i:19559593 original size:35 final size:35
Alignment explanation
Indices: 19559554--19559625 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
19559544 GTCTAAGATC
19559554 GCATATCTTTGAAGATCT-CCTTCCATATTTACCAA
1 GCATATCTTTGAAGAT-TACCTTCCATATTTACCAA
* *
19559589 GCATATCTTTGAAGATTACTTTCCATATTTGCCAA
1 GCATATCTTTGAAGATTACCTTCCATATTTACCAA
19559624 GC
1 GC
19559626 TCCGGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (35 bp):
GCATATCTTTGAAGATTACCTTCCATATTTACCAA
Found at i:19564822 original size:35 final size:35
Alignment explanation
Indices: 19564783--19564854 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
19564773 GTCTAAGATC
19564783 GCATATCTTTGAAGATCT-CCTTCCATATTTACCAA
1 GCATATCTTTGAAGAT-TACCTTCCATATTTACCAA
* *
19564818 GCATATCTTTGAAGATTACTTTCCATATTTGCCAA
1 GCATATCTTTGAAGATTACCTTCCATATTTACCAA
19564853 GC
1 GC
19564855 TCCGGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (35 bp):
GCATATCTTTGAAGATTACCTTCCATATTTACCAA
Found at i:19569468 original size:15 final size:17
Alignment explanation
Indices: 19569448--19569479 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19569438 TAAAGGGTTC
19569448 TCGATGA-TA-GCTACT
1 TCGATGACTAGGCTACT
19569463 TCGATGACTAGGCTACT
1 TCGATGACTAGGCTACT
19569480 ACAAAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (17 bp):
TCGATGACTAGGCTACT
Found at i:19572818 original size:48 final size:46
Alignment explanation
Indices: 19572702--19572821 Score: 141
Period size: 46 Copynumber: 2.6 Consensus size: 46
19572692 TGATATGTGT
* * *
19572702 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGCCGAGA
1 GCTAGTGTAAGACATGTCTGGGACATACATCGACATTGAGCAGAAA
* * * * *
19572748 GCTAATGTAAGACATGTCTGGGACATACATCGGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATACATCGACATTGAG-CAGA-AA
*
19572796 GCTAGTGTAAGACCTGTCTGGGACAT
1 GCTAGTGTAAGACATGTCTGGGACAT
19572822 GGCGTCAGCT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 36 0.58
47 1 0.02
48 25 0.40
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATACATCGACATTGAGCAGAAA
Found at i:19572911 original size:49 final size:49
Alignment explanation
Indices: 19572858--19572971 Score: 122
Period size: 49 Copynumber: 2.3 Consensus size: 49
19572848 AAGACCTACT
* * *
19572858 TGGGACATGGCATCGACAC-CGATAGATGAGAGCCAGTACAAGACCTGTC
1 TGGGACATGGCATCGAC-CTCAATAGATAAAAGCCAGTACAAGACCTGTC
* * * * **
19572907 TGGGACACGGCATCGGCCTCAATATATAAAAGTCAGTGTAAGACCTGTC
1 TGGGACATGGCATCGACCTCAATAGATAAAAGCCAGTACAAGACCTGTC
*
19572956 AGGGACATGGCATCGA
1 TGGGACATGGCATCGA
19572972 ATTTGACGTG
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
48 1 0.02
49 51 0.98
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (49 bp):
TGGGACATGGCATCGACCTCAATAGATAAAAGCCAGTACAAGACCTGTC
Found at i:19575486 original size:46 final size:46
Alignment explanation
Indices: 19575419--19575639 Score: 306
Period size: 46 Copynumber: 4.8 Consensus size: 46
19575409 TGTAACCCGC
* *
19575419 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
*
19575465 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
*
19575511 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCAT
* * *
19575561 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
19575604 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
19575640 ATGCTCAACC
Statistics
Matches: 157, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 2 0.01
45 2 0.01
46 108 0.69
47 28 0.18
48 3 0.02
49 2 0.01
50 4 0.03
51 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
Found at i:19575601 original size:93 final size:93
Alignment explanation
Indices: 19575473--19575643 Score: 324
Period size: 93 Copynumber: 1.8 Consensus size: 93
19575463 ATCCATAAGT
*
19575473 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
19575538 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
19575566 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
19575631 CGAGTTCGGATGC
66 CGAGTTCGGATGC
19575644 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19578060 original size:30 final size:30
Alignment explanation
Indices: 19578016--19578104 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
19578006 CAAAGATAAC
*
19578016 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
19578045 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
19578075 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
19578105 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:19578064 original size:15 final size:14
Alignment explanation
Indices: 19578016--19578098 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
19578006 CAAAGATAAC
*
19578016 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
19578030 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
19578045 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
19578060 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
19578075 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
19578090 AAGAAACCC
1 AAGAAACCC
19578099 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:19578104 original size:15 final size:15
Alignment explanation
Indices: 19578027--19578104 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
19578017 AGAAAACCGA
19578027 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
19578042 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
19578056 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
19578071 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
19578087 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
19578102 ATA
1 ATA
19578105 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:19581164 original size:93 final size:93
Alignment explanation
Indices: 19581052--19581222 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
19581042 GCCCATAAGT
* *
19581052 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
19581117 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
19581145 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
19581210 CGAGTTCGGATGC
66 CGAGTTCGGATGC
19581223 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19581219 original size:46 final size:46
Alignment explanation
Indices: 19581044--19581219 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
19581034 TGTAACCCGC
* * *
19581044 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
19581090 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
19581140 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
19581183 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
19581220 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:19583680 original size:5 final size:5
Alignment explanation
Indices: 19583670--19583696 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19583660 ATAATTAAGT
19583670 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
19583697 AATCATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:19587089 original size:4 final size:4
Alignment explanation
Indices: 19587082--19587137 Score: 58
Period size: 4 Copynumber: 13.5 Consensus size: 4
19587072 TTTCCTTTCT
* * * *
19587082 TTTA TTTA TTTG TTTA TTTT TTTA TTTT TTTA TTTCT TTTA TTTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA -TTTA
19587132 TTTA TT
1 TTTA TT
19587138 ATAATAATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 35 0.83
5 7 0.17
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:19593528 original size:26 final size:25
Alignment explanation
Indices: 19593483--19593554 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
19593473 TATTTTCTTG
* *
19593483 AAATTTTACCAATGGCAAAATCGTC
1 AAATTTTACCAAGGGTAAAATCGTC
*
19593508 AAGATTTTACCAAGGGTAAAATTGTC
1 AA-ATTTTACCAAGGGTAAAATCGTC
* * *
19593534 AAATTTTGCTAGGGGTAAAAT
1 AAATTTTACCAAGGGTAAAAT
19593555 AAGGATTAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
25 18 0.45
26 22 0.55
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (25 bp):
AAATTTTACCAAGGGTAAAATCGTC
Found at i:19593921 original size:21 final size:22
Alignment explanation
Indices: 19593895--19593940 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
19593885 GCCTCTACTA
* *
19593895 TTTTGCTGTTGTTTTTCCA-TG
1 TTTTGCTATTGTTTTCCCACTG
19593916 TTTTGCTATTGTTTTCCCACTG
1 TTTTGCTATTGTTTTCCCACTG
19593938 TTT
1 TTT
19593941 GCTCTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.07, C:0.17, G:0.15, T:0.61
Consensus pattern (22 bp):
TTTTGCTATTGTTTTCCCACTG
Found at i:19599448 original size:20 final size:19
Alignment explanation
Indices: 19599401--19599449 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
19599391 AATATTTTTA
*
19599401 TAAAATTTGTTTATAATTTT
1 TAAAATTT-TTTATAAATTT
**
19599421 TATGATTTTTTATATAATTT
1 TAAAATTTTTTATA-AATTT
19599441 TAAAATTTT
1 TAAAATTTT
19599450 AAAAAGGGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TAAAATTTTTTATAAATTT
Found at i:19603673 original size:15 final size:15
Alignment explanation
Indices: 19603655--19603685 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19603645 GAAATGTGAT
19603655 GACTTAAAATATTTA
1 GACTTAAAATATTTA
19603670 GACTTAAAATATTTA
1 GACTTAAAATATTTA
19603685 G
1 G
19603686 GGGTTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (15 bp):
GACTTAAAATATTTA
Found at i:19603941 original size:17 final size:16
Alignment explanation
Indices: 19603912--19603948 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
19603902 AATAAATTTT
19603912 ATTATTTTTAAAAAAA
1 ATTATTTTTAAAAAAA
*
19603928 ATTATTTTT-CAAAAA
1 ATTATTTTTAAAAAAA
19603943 ATTATT
1 ATTATT
19603949 CGAATTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTATTTTTAAAAAAA
Done.