Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 139 of 352
Found at i:45166154 original size:27 final size:27
Alignment explanation
Indices: 45166122--45166360 Score: 185
Period size: 27 Copynumber: 8.6 Consensus size: 27
45166112 TATATTAGTC
* *
45166122 CGCACACTCAGTTCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
45166149 CGCACACTTAGTGTCATAATCGAATATAT-AAGGT
1 CGCACACTTAGTG-C-T-AT---ATA-ATCAA-CT
*
45166183 CCGCACACTCAGTGCTATATAATCAACT
1 -CGCACACTTAGTGCTATATAATCAACT
* *
45166211 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTATATAATCAACT
* *
45166238 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*** ** *
45166265 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATATAATCAACT
* **
45166292 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTAT-ATAATCAACT
* * * *
45166319 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTATATAATCAACT
45166346 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
45166361 GTACAATTTA
Statistics
Matches: 176, Mismatches: 24, Indels: 24
0.79 0.11 0.11
Matches are distributed among these distances:
27 139 0.79
28 5 0.03
29 6 0.03
30 2 0.01
32 2 0.01
33 6 0.03
34 4 0.02
35 12 0.07
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:45166189 original size:62 final size:63
Alignment explanation
Indices: 45166111--45166278 Score: 205
Period size: 62 Copynumber: 2.8 Consensus size: 63
45166101 ATTCAAGAAT
* *
45166111 ATATATTAGTCCGCACACTCAGTTCTATATAATCAACTCGCACACTTAGTG-T-CATAATCGA
1 ATATATAAGTCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCGA
45166172 ATATATAAGGTCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATC--
1 ATATATAA-GTCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCGA
* * *
45166234 ----A-AA-T-CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
1 ATATATAAGTCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGC
45166279 CGCATGGTCA
Statistics
Matches: 99, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
54 38 0.38
55 1 0.01
57 2 0.02
58 1 0.01
61 7 0.07
62 42 0.42
63 1 0.01
64 7 0.07
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (63 bp):
ATATATAAGTCCGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCGA
Found at i:45166266 original size:54 final size:54
Alignment explanation
Indices: 45166184--45166360 Score: 230
Period size: 54 Copynumber: 3.3 Consensus size: 54
45166174 ATATAAGGTC
* * * *
45166184 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
45166238 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
45166292 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
45166346 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
45166361 GTACAATTTA
Statistics
Matches: 106, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 105 0.99
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:45166322 original size:81 final size:81
Alignment explanation
Indices: 45166205--45166359 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 81
45166195 TGCTATATAA
* *
45166205 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
45166270 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* * **
45166286 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
45166350 CACTTAGTGC
65 CACTTAGTGC
45166360 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 66 0.99
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:45171887 original size:40 final size:40
Alignment explanation
Indices: 45171843--45172003 Score: 198
Period size: 40 Copynumber: 4.0 Consensus size: 40
45171833 GATTTAGTCA
*
45171843 GATATAACAACTCGCACAAATGCCATCGGGTCTTAGCCCG
1 GATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCG
*
45171883 GATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCG
1 GATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCG
* ** * *
45171923 GATATAATC-ACTAGCATGAATGCCTTCGGGACATAGCCCG
1 GATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCG
* * * * *
45171963 GATATAGCAACTCACACGAATGCCTTCGGATCTTAGTCCG
1 GATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCG
45172003 G
1 G
45172004 TTATCATCCG
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 101 0.98
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
GATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCG
Found at i:45177510 original size:18 final size:19
Alignment explanation
Indices: 45177469--45177517 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
45177459 CTTAGCCCAT
45177469 TGCAGTAACAGTAAAAAAA
1 TGCAGTAACAGTAAAAAAA
* *
45177488 AGCAGTAACAGT-AAAAAG
1 TGCAGTAACAGTAAAAAAA
45177506 TGCAGTAACAGT
1 TGCAGTAACAGT
45177518 TTAAACAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.16
Consensus pattern (19 bp):
TGCAGTAACAGTAAAAAAA
Found at i:45177940 original size:27 final size:27
Alignment explanation
Indices: 45177867--45178000 Score: 115
Period size: 27 Copynumber: 5.0 Consensus size: 27
45177857 ATAAATACCA
* *
45177867 CACATAAGGTCAAAACAGTCAATTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
** * ****
45177894 CATGTAGGGGCATTTTAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
45177921 CACATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * *
45177948 CTCATAATGGTAAAACAGTCACTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * *
45177975 CTCATAGGGGAAAAATAGTCATTTTA
1 CACATAAGGGCAAAACAGTCATTTTA
45178001 TCAAATTGGG
Statistics
Matches: 82, Mismatches: 25, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:45187354 original size:24 final size:24
Alignment explanation
Indices: 45187327--45187404 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
45187317 CTATCTAGAG
* *
45187327 CTTCCCAATATGGTTCTTTTTGAA
1 CTTCCCAATAAGGTTCTTTGTGAA
* *
45187351 CTTCCCAAAAAGGTTCTTCGTGAA
1 CTTCCCAATAAGGTTCTTTGTGAA
* *
45187375 CTTCCCGACAAGGTTCTTTGTGAA
1 CTTCCCAATAAGGTTCTTTGTGAA
45187399 CTTCCC
1 CTTCCC
45187405 GATTATGGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (24 bp):
CTTCCCAATAAGGTTCTTTGTGAA
Found at i:45187472 original size:23 final size:24
Alignment explanation
Indices: 45187446--45187499 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
45187436 AGCCCAGATA
* *
45187446 AGCTTCTCGATAT-GCTCTTTATG
1 AGCTTCTCGAAATGGCTCTATATG
* *
45187469 AGCTTCCCGAAATGGCTCTATGTG
1 AGCTTCTCGAAATGGCTCTATATG
45187493 AGCTTCT
1 AGCTTCT
45187500 AGTTACAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (24 bp):
AGCTTCTCGAAATGGCTCTATATG
Found at i:45190454 original size:25 final size:26
Alignment explanation
Indices: 45190426--45190476 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
45190416 GAGCATCTCG
*
45190426 ATTAAA-GGTTCTTTGTGAACTTCCC
1 ATTAAATGGCTCTTTGTGAACTTCCC
*
45190451 ATTAAATTGGCTCTTTGTGAGCTTCC
1 ATTAAA-TGGCTCTTTGTGAACTTCC
45190477 TGATAGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
27 16 0.73
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (26 bp):
ATTAAATGGCTCTTTGTGAACTTCCC
Found at i:45193925 original size:17 final size:18
Alignment explanation
Indices: 45193893--45193926 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45193883 AATTAACTCG
45193893 AATACCAAAAAGAAAAAA
1 AATACCAAAAAGAAAAAA
45193911 AATACCAAAAA-AAAAA
1 AATACCAAAAAGAAAAA
45193927 CTCTAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.79, C:0.12, G:0.03, T:0.06
Consensus pattern (18 bp):
AATACCAAAAAGAAAAAA
Found at i:45202371 original size:69 final size:69
Alignment explanation
Indices: 45202260--45202396 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
45202250 AAGTTTGTTT
* *
45202260 TGCATAAGAAAGAATTATAGCCGCTCATAATTATTTACCAATTTACACAAACATTAGAACAATAT
1 TGCATAAGAAAGAATCATAGCCACTCATAATTATTTACCAATTTACACAAACATTAGAACAATAT
45202325 ATGC
66 ATGC
45202329 TGCATAAGAAAGAATCATAGCCACTCATAATTATTTACCAATTTACACAAACATTAGAACAATAT
1 TGCATAAGAAAGAATCATAGCCACTCATAATTATTTACCAATTTACACAAACATTAGAACAATAT
45202394 ATG
66 ATG
45202397 TACATGTACC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (69 bp):
TGCATAAGAAAGAATCATAGCCACTCATAATTATTTACCAATTTACACAAACATTAGAACAATAT
ATGC
Found at i:45206015 original size:40 final size:40
Alignment explanation
Indices: 45205971--45206119 Score: 210
Period size: 40 Copynumber: 3.7 Consensus size: 40
45205961 GCTACTTGCT
45205971 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
45206011 CAAATACCTTCGGGACTTAGCCCGGATATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
45206051 CAAATGCCTTCGGAACTTAGCCCGGATT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
45206091 CAAATTCCTTCGGGACTTAGCCCGATTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
45206120 CATCCGAATA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
39 2 0.02
40 92 0.97
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:45214143 original size:40 final size:40
Alignment explanation
Indices: 45214099--45214247 Score: 237
Period size: 40 Copynumber: 3.7 Consensus size: 40
45214089 GCTACTTGCT
*
45214099 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
* *
45214139 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
*
45214179 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTAGCA
*
45214219 CAAATGCCTTCAGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
45214248 CATCTGAATA
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
39 2 0.02
40 98 0.97
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
Found at i:45214220 original size:80 final size:80
Alignment explanation
Indices: 45214076--45214243 Score: 261
Period size: 80 Copynumber: 2.1 Consensus size: 80
45214066 ACCTTGGAAT
* *
45214076 TTAG-CCGGATATAGCTACTTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
1 TTAGCCCGGATATAGCTACTTGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCAC
*
45214140 AAATGCCTTCGGGAC
66 AAATGCCTTCAGGAC
*
45214155 TTAGCCCGGATATAG-TAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTCACTAGC
1 TTAGCCCGGATATAGCT-ACTTGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTAGC
45214218 ACAAATGCCTTCAGGAC
64 ACAAATGCCTTCAGGAC
45214235 TTAGCCCGG
1 TTAGCCCGG
45214244 TTATCATCTG
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
79 5 0.06
80 75 0.91
81 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (80 bp):
TTAGCCCGGATATAGCTACTTGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCAC
AAATGCCTTCAGGAC
Found at i:45219898 original size:46 final size:46
Alignment explanation
Indices: 45219848--45220023 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 46
45219838 TGGTTGAGCA
45219848 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
45219894 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GA--CGTAACTAG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AA-T-G
*
45219938 ACATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 ---TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
45219987 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
45220024 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 3 0.03
44 1 0.01
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 1 0.01
50 2 0.02
51 2 0.02
52 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:45220005 original size:93 final size:93
Alignment explanation
Indices: 45219846--45220016 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
45219836 GATGGTTGAG
*
45219846 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
45219911 GAGTCCGAGTTCGTGAGACGTAACTAGA
66 GAGTCCGAGTTCGTGAGACGTAACTAGA
*
45219939 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAGT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAGT
45220003 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
45220017 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGACGTAACTAGA
Found at i:45221677 original size:33 final size:33
Alignment explanation
Indices: 45221635--45221697 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
45221625 TACTGGTACT
45221635 ATTGTCTTTGGTTTTAAATAAAATATTGTTACC
1 ATTGTCTTTGGTTTTAAATAAAATATTGTTACC
45221668 ATTGTCTTTGGTTTTAAATAAAATATTGTT
1 ATTGTCTTTGGTTTTAAATAAAATATTGTT
45221698 GTACTATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (33 bp):
ATTGTCTTTGGTTTTAAATAAAATATTGTTACC
Found at i:45223919 original size:46 final size:48
Alignment explanation
Indices: 45223815--45223928 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 48
45223805 TGTCTTCGAC
** * *
45223815 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATATAAT
* * *
45223863 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATATAAT
*
45223909 ATGGACTTACATAGCTCATT
1 ATGGACTTACATGGCTCATT
45223929 TCTGTCCTGT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
46 21 0.37
47 1 0.02
48 35 0.61
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATATAAT
Found at i:45238138 original size:17 final size:17
Alignment explanation
Indices: 45238116--45238148 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45238106 TTGAATTGGG
*
45238116 TTGAGAAATTTATTTAA
1 TTGAGAAATTAATTTAA
45238133 TTGAGAAATTAATTTA
1 TTGAGAAATTAATTTA
45238149 TCTAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:45240606 original size:48 final size:46
Alignment explanation
Indices: 45240440--45240614 Score: 178
Period size: 46 Copynumber: 3.7 Consensus size: 46
45240430 TGATATGTGT
45240440 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATT-ATG-AG--A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG---CATTGA-GAAGAAA
* * * *
45240486 GCCAGTGTAAGAAATGTCTGGGACATGCATCAGCATTGAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGAAGAAA
* * *
45240532 GCTAGTGTAAGACATGTCTGGCACATGCATCAGCCTTGAGAAATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAG-AAGA-AA
* *
45240580 GCTAGTGTAAGACCTGTTTGGGACATGGCATCAGC
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGC
45240615 TTGTTGAGTG
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
46 68 0.62
47 2 0.02
48 24 0.22
49 8 0.07
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGAAGAAA
Found at i:45240697 original size:49 final size:49
Alignment explanation
Indices: 45240445--45240798 Score: 197
Period size: 49 Copynumber: 7.5 Consensus size: 49
45240435 TGTGTGCTAG
* * * *
45240445 TGTAAGACATGTCTGGGACAT-GCATCAGCCAC-AT-TATGAGAGCCAG
1 TGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATGTATGAAAGCCAA
** * * * * * *
45240491 TGTAAGAAATGTCTGGGACAT-GCATCAGCATTGA-G-ACGAGAGCTAG
1 TGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATGTATGAAAGCCAA
* * * * * *
45240537 TGTAAGACATGTCTGGCACAT-GCATCAGCCTTGA-GAAAT-ACAAGCTAG
1 TGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATG-TATGA-AAGCCAA
* ** * *
45240585 TGTAAGACCTGTTTGGGACATGGCATCAG-CT---TGT-TGAGTGTCAG
1 TGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATGTATGAAAGCCAA
* *
45240629 TGGAAGACCTGTCTGGGACATGGCATCATCAC-CGATAG-ATGAAAGCCAA
1 TGTAAGACCTGTCTGGGACATGGCATCAGC-CTCGAT-GTATGAAAGCCAA
* * * * * *
45240678 TGTAAGACCTGTCTAGGACACGACATCGGCCTCGATGTATGAAAGTCAG
1 TGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATGTATGAAAGCCAA
* * ** *
45240727 TGTAAGACCTGTCTGGGACATGGCATC-GACTTTGATG--TGCTAGCCAG
1 TGTAAGACCTGTCTGGGACATGGCATCAG-CCTCGATGTATGAAAGCCAA
45240774 TGTAAGACCATGTCTGGGACATGGC
1 TGTAAGACC-TGTCTGGGACATGGC
45240799 GTCGACATTT
Statistics
Matches: 247, Mismatches: 42, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
44 30 0.12
45 1 0.00
46 71 0.29
47 18 0.07
48 46 0.19
49 81 0.33
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (49 bp):
TGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATGTATGAAAGCCAA
Found at i:45244085 original size:28 final size:28
Alignment explanation
Indices: 45244041--45244099 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
45244031 TTTGTTAATT
*
45244041 GTTAACTAATCTATCTTGGGGCAGTGGA
1 GTTAACTAATCTATCTTGGGGCAGTGAA
*
45244069 GTTAACTAATCTGTCTTGGGGCAGTGAA
1 GTTAACTAATCTATCTTGGGGCAGTGAA
45244097 GTT
1 GTT
45244100 TTTGTTGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.34
Consensus pattern (28 bp):
GTTAACTAATCTATCTTGGGGCAGTGAA
Found at i:45246837 original size:30 final size:30
Alignment explanation
Indices: 45246803--45246863 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
45246793 TCCTTAACTC
45246803 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
45246833 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
45246863 A
1 A
45246864 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:45253507 original size:40 final size:40
Alignment explanation
Indices: 45253357--45253647 Score: 424
Period size: 40 Copynumber: 7.5 Consensus size: 40
45253347 CAAACCAGTA
* *
45253357 CCTTCGGGATTTAG-CC-GATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
45253394 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
45253434 CCTTC-GGACTTA--CCGGATATA-TAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
45253470 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
45253510 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
45253549 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
45253589 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
45253629 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
45253648 TTATCATCCG
Statistics
Matches: 238, Mismatches: 6, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
35 1 0.00
36 17 0.07
37 29 0.12
38 2 0.01
39 73 0.31
40 116 0.49
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:45253570 original size:79 final size:79
Alignment explanation
Indices: 45253357--45253647 Score: 420
Period size: 76 Copynumber: 3.7 Consensus size: 79
45253347 CAAACCAGTA
* *
45253357 CCTTCGGGATTTAGCC-GATATAGCT-ACTCGCTC-AATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
45253419 CT-ACTCGCTCAAATG
65 -TAACTCGCACAAATG
45253434 CCTTC-GGACTTA-CCGGATATA-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
45253496 AACTCGCACAAATG
66 AACTCGCACAAATG
45253510 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
45253574 TAACTCGCACAAATG
65 TAACTCGCACAAATG
* * *
45253589 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAG-CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
45253648 TTATCATCCG
Statistics
Matches: 199, Mismatches: 6, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
74 1 0.01
75 10 0.05
76 65 0.33
77 5 0.03
78 9 0.05
79 61 0.31
80 48 0.24
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTCGCACAAATG
Found at i:45261532 original size:40 final size:40
Alignment explanation
Indices: 45261464--45261681 Score: 282
Period size: 40 Copynumber: 5.5 Consensus size: 40
45261454 AAACCATGTA
* *
45261464 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
45261503 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
45261543 CCTTGGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
45261583 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * * *
45261623 CTTTTGGGGCTTAGCCCGGA-ATTAGTCACTAGAACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
45261663 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
45261682 TTATCATCTG
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 15 0.09
40 149 0.91
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:45279213 original size:50 final size:50
Alignment explanation
Indices: 45279158--45279256 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
45279148 TATGGCATTG
* *
45279158 ATATGAGATCCCATGTAAAACCATGTATGGGACATGGTATTGGCATCGAC
1 ATATGAGATCCCATGTAAAACCATGTATGGAACATGGCATTGGCATCGAC
* * *
45279208 ATATGAGATTCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCGA
1 ATATGAGATCCCATGTAAAACCATGTATGGAACATGGCATTGGCATCGA
45279257 GTGGTGATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (50 bp):
ATATGAGATCCCATGTAAAACCATGTATGGAACATGGCATTGGCATCGAC
Found at i:45279293 original size:48 final size:48
Alignment explanation
Indices: 45279083--45279300 Score: 157
Period size: 48 Copynumber: 4.6 Consensus size: 48
45279073 AGATCCCGTA
** * * *
45279083 TAAGACCATATCTGGGATATGGCATCAGAATCAGTATGTG-TTATCATG
1 TAAGACCATATCTGGGATATGGCATTGGCATCAGTATGAGATCA-CATG
*
45279131 TAAGACCATATCTGGGATATGGCATT-G----A-TATGAGATCCCATG
1 TAAGACCATATCTGGGATATGGCATTGGCATCAGTATGAGATCACATG
* * * * * *
45279173 TAAAACCATGTATGGGACATGGTATTGGCATCGACATATGAGATTC-CATG
1 TAAGACCATATCTGGGATATGGCATTGGCATC-A-GTATGAGA-TCACATG
* * * * * *
45279223 TAAGACCATGTTTGGAACATGGCATTGGCATCGAGT-GGTGATCACATG
1 TAAGACCATATCTGGGATATGGCATTGGCATC-AGTATGAGATCACATG
*
45279271 TAAGACCATATCTGGGATATGGCGTTGGCA
1 TAAGACCATATCTGGGATATGGCATTGGCA
45279301 ACTTATTATG
Statistics
Matches: 138, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
42 30 0.22
43 3 0.02
47 3 0.02
48 58 0.42
49 1 0.01
50 41 0.30
51 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (48 bp):
TAAGACCATATCTGGGATATGGCATTGGCATCAGTATGAGATCACATG
Found at i:45286104 original size:15 final size:16
Alignment explanation
Indices: 45286081--45286115 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
45286071 ATTAGTTTAA
*
45286081 ATTTGATAA-TATTTT
1 ATTTAATAAGTATTTT
45286096 ATTTAATAAGTATTTT
1 ATTTAATAAGTATTTT
45286112 ATTT
1 ATTT
45286116 TTAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTTAATAAGTATTTT
Found at i:45286828 original size:25 final size:24
Alignment explanation
Indices: 45286780--45286837 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
45286770 ATTTTTCTCC
* * *
45286780 TAAATTTTTATTTTATTTAATTATT
1 TAAATTTTCAATTTATTGAATTA-T
*
45286805 TAAATTTTCAATTTATTGAGTTAT
1 TAAATTTTCAATTTATTGAATTAT
45286829 TAATATTTT
1 TAA-ATTTT
45286838 ATACTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (24 bp):
TAAATTTTCAATTTATTGAATTAT
Found at i:45291452 original size:10 final size:10
Alignment explanation
Indices: 45291439--45291471 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
45291429 ATTTAAAAGT
45291439 ATTAATTTAA
1 ATTAATTTAA
45291449 ATTAATTTAA
1 ATTAATTTAA
*
45291459 A-AAATTTAA
1 ATTAATTTAA
45291468 ATTA
1 ATTA
45291472 TAAAATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:45292212 original size:3 final size:3
Alignment explanation
Indices: 45292206--45292234 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
45292196 CTTTTTTTCT
45292206 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
45292235 AGCTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:45298345 original size:40 final size:40
Alignment explanation
Indices: 45298290--45298370 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
45298280 TGGTTTCAAA
45298290 CCACAAATCTGAGTTAGAAAAATATTTTAATATTAATTTC
1 CCACAAATCTGAGTTAGAAAAATATTTTAATATTAATTTC
45298330 CCACAAATCTGAGTTAGAAAAATATTTTAATATTAATTTC
1 CCACAAATCTGAGTTAGAAAAATATTTTAATATTAATTTC
45298370 C
1 C
45298371 ATGTATTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (40 bp):
CCACAAATCTGAGTTAGAAAAATATTTTAATATTAATTTC
Found at i:45301060 original size:23 final size:23
Alignment explanation
Indices: 45301002--45301061 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
45300992 CACTCATAAA
*
45301002 TTCTTTTACTTTTGAAGTTCTTT
1 TTCTTTTTCTTTTGAAGTTCTTT
* **
45301025 TTC-TATTCGTTTTGATTTTCTTT
1 TTCTTTTTC-TTTTGAAGTTCTTT
45301048 TTCTTTTTCTTTTG
1 TTCTTTTTCTTTTG
45301062 TTGCACATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.10
23 23 0.77
24 4 0.13
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.70
Consensus pattern (23 bp):
TTCTTTTTCTTTTGAAGTTCTTT
Found at i:45310233 original size:79 final size:81
Alignment explanation
Indices: 45310097--45310279 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
45310087 TCGAATGATG
* *
45310097 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
45310161 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
45310176 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
45310238 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
45310256 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
45310280 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:45310295 original size:40 final size:40
Alignment explanation
Indices: 45310098--45310281 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
45310088 CGAATGATGT
* * * *
45310098 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
45310138 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
45310178 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
45310216 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
45310257 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
45310282 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:45310303 original size:79 final size:79
Alignment explanation
Indices: 45310150--45310314 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
45310140 GGACTAAGAT
* **
45310150 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
45310215 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
45310229 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
45310292 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
45310308 CCGAAGG
1 CCGAAGG
45310315 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:45318247 original size:40 final size:41
Alignment explanation
Indices: 45318164--45318269 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 41
45318154 TCGAATGATG
*
45318164 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAA
* * * *
45318204 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGTGACCAAA
*
45318244 TCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
45318270 AACGAGTAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.02
40 47 0.84
41 8 0.14
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAA
Found at i:45318302 original size:39 final size:40
Alignment explanation
Indices: 45318216--45318302 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
45318206 CGGACTAAGA
** *
45318216 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGT
1 TCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAAT
* *
45318256 CCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAAT
1 TCCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAAT
45318295 TCCGAAGG
1 TCCGAAGG
45318303 TACGTGATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 16 0.40
40 24 0.60
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAAT
Found at i:45332655 original size:30 final size:30
Alignment explanation
Indices: 45332621--45332681 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
45332611 TCCTTAACTC
45332621 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
45332651 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
45332681 A
1 A
45332682 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:45334093 original size:14 final size:14
Alignment explanation
Indices: 45334056--45334096 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
45334046 TGTATGAGCT
45334056 TATATGTTGAAATTA
1 TATATG-TGAAATTA
*
45334071 AATTATGTGAAATTA
1 TA-TATGTGAAATTA
45334086 TATATGTGAAA
1 TATATGTGAAA
45334097 GTCGAATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 10 0.43
16 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (14 bp):
TATATGTGAAATTA
Found at i:45335449 original size:82 final size:82
Alignment explanation
Indices: 45335359--45335563 Score: 299
Period size: 87 Copynumber: 2.5 Consensus size: 82
45335349 TAAATATGTA
*
45335359 TGTTATATATATATGCTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAGCTTATGACC
1 TGTTATATATATATGCTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTATGACC
45335424 ATTCATTTTGGCAAGGT
66 ATTCATTTTGGCAAGGT
45335441 TGTTATATATATATGTTTGCGTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTA
1 TGTTATATATATA----TGC-TTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTA
45335506 TGACCATTCATTTTGGCAAGGT
61 TGACCATTCATTTTGGCAAGGT
* * *
45335528 TGTTATA-ATGGTATG-TTTTGTATATGCATATT-TTTA
1 TGTTATATAT-ATATGCTTTGGTATATGCTTATTATTTA
45335564 TGAATTAGCT
Statistics
Matches: 113, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
80 4 0.04
81 15 0.13
82 13 0.12
83 2 0.02
86 5 0.04
87 74 0.65
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.47
Consensus pattern (82 bp):
TGTTATATATATATGCTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTATGACC
ATTCATTTTGGCAAGGT
Found at i:45335545 original size:87 final size:87
Alignment explanation
Indices: 45335362--45335534 Score: 312
Period size: 87 Copynumber: 2.0 Consensus size: 87
45335352 ATATGTATGT
* * *
45335362 TATATATATATGC-TTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAGCTTATGACCAT
1 TATATATGTTTGCGTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTATGACCAT
45335426 TCATTTTGGCAAGGTTGTTATA
66 TCATTTTGGCAAGGTTGTTATA
45335448 TATATATGTTTGCGTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTATGACCAT
1 TATATATGTTTGCGTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTATGACCAT
45335513 TCATTTTGGCAAGGTTGTTATA
66 TCATTTTGGCAAGGTTGTTATA
45335535 ATGGTATGTT
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
86 11 0.13
87 72 0.87
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (87 bp):
TATATATGTTTGCGTTTGGTATATGCTTATTATTTACAGTAATAATATGGTTAACTTATGACCAT
TCATTTTGGCAAGGTTGTTATA
Found at i:45346444 original size:57 final size:56
Alignment explanation
Indices: 45346370--45346512 Score: 137
Period size: 57 Copynumber: 2.5 Consensus size: 56
45346360 GCTTAGTCAA
* * * * *
45346370 GATTACCAGTCCAGGCTAAATCCTTTTTATGACATATACTCTAAAGAGTT-TGATCT-G
1 GATTA-CAGTCCGGGCTAAATCCTTTTCATAACATATACTCGAAAGACTTAT-AT-TAG
* * * *
45346427 GATTACATGTCCGGGCTAAATCCATTCCATAACATATGCTCGAAATACTTATATTAG
1 GATTACA-GTCCGGGCTAAATCCTTTTCATAACATATACTCGAAAGACTTATATTAG
*
45346484 GATTACCCGTCCGGGCTAAATCCTTTTCA
1 GATTA-CAGTCCGGGCTAAATCCTTTTCA
45346513 AAATGAGGTC
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
56 3 0.04
57 65 0.93
58 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (56 bp):
GATTACAGTCCGGGCTAAATCCTTTTCATAACATATACTCGAAAGACTTATATTAG
Found at i:45375334 original size:46 final size:45
Alignment explanation
Indices: 45375281--45375453 Score: 197
Period size: 46 Copynumber: 3.8 Consensus size: 45
45375271 TTGGGCATCT
*
45375281 GAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
*** * *
45375327 GAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCC
* *
45375374 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
*
45375420 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
45375454 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCC
Found at i:45375433 original size:93 final size:93
Alignment explanation
Indices: 45375274--45375445 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
45375264 AGGATATTTG
* * * *
45375274 GGCATCTGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
45375339 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
45375367 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
45375432 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
45375446 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:45382664 original size:21 final size:21
Alignment explanation
Indices: 45382638--45382681 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
45382628 TTACAAAGTG
*
45382638 AGATCCTTCATCATTAATTAT
1 AGATCCTTCATCACTAATTAT
*
45382659 AGATCCTTCATCGCTAATTAT
1 AGATCCTTCATCACTAATTAT
45382680 AG
1 AG
45382682 CTCTCGAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (21 bp):
AGATCCTTCATCACTAATTAT
Found at i:45390371 original size:21 final size:20
Alignment explanation
Indices: 45390341--45390384 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
45390331 TAAACACCTA
*
45390341 AAAAATAAATCACA-AAAAAT
1 AAAAATAAAT-AAATAAAAAT
45390361 AAAAATAAAATAAATAAAAAT
1 AAAAAT-AAATAAATAAAAAT
45390382 AAA
1 AAA
45390385 TAAACCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAATAAATAAATAAAAAT
Found at i:45390375 original size:15 final size:14
Alignment explanation
Indices: 45390357--45390388 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
45390347 AAATCACAAA
45390357 AAATAAAAATAAAAT
1 AAATAAAAAT-AAAT
45390372 AAATAAAAATAAAT
1 AAATAAAAATAAAT
45390386 AAA
1 AAA
45390389 CCAATTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:45390382 original size:10 final size:10
Alignment explanation
Indices: 45390355--45390388 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
45390345 ATAAATCACA
*
45390355 AAAAATAAAA
1 AAAAATAAAT
45390365 ATAAAATAAAT
1 A-AAAATAAAT
45390376 AAAAATAAAT
1 AAAAATAAAT
45390386 AAA
1 AAA
45390389 CCAATTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:45390576 original size:18 final size:18
Alignment explanation
Indices: 45390553--45390588 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45390543 TATGTTAATC
45390553 AATATTTTGCAAAATTAA
1 AATATTTTGCAAAATTAA
45390571 AATATTTTGCAAAATTAA
1 AATATTTTGCAAAATTAA
45390589 CGTTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
AATATTTTGCAAAATTAA
Found at i:45390676 original size:17 final size:17
Alignment explanation
Indices: 45390654--45390693 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
45390644 TAATAACTAG
45390654 ATGCAAAATTATCCTAA
1 ATGCAAAATTATCCTAA
45390671 ATGCAAAATTATCCTAA
1 ATGCAAAATTATCCTAA
45390688 ATGCAA
1 ATGCAA
45390694 CTTAACCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.28
Consensus pattern (17 bp):
ATGCAAAATTATCCTAA
Found at i:45392084 original size:27 final size:25
Alignment explanation
Indices: 45392034--45392083 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
45392024 ATATGTAAAA
45392034 TATATATATAGTGTTAGAAATATAT
1 TATATATATAGTGTTAGAAATATAT
* *
45392059 TATATATATAGTGTTTGAAGTATAT
1 TATATATATAGTGTTAGAAATATAT
45392084 ACATGAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (25 bp):
TATATATATAGTGTTAGAAATATAT
Found at i:45394537 original size:55 final size:55
Alignment explanation
Indices: 45394433--45394573 Score: 203
Period size: 55 Copynumber: 2.5 Consensus size: 55
45394423 TGAATTGACT
* *
45394433 CTCTCGTAATATGAGTTGATTTTTTTGAAA-AACAGAAATCAAAAGGCTTAACTCAC
1 CTCTCGCAACATGAGTTGA--TTTTTGAAACAACAGAAATCAAAAGGCTTAACTCAC
* * *
45394489 CTCTCGCAACATGAGTTGATTTTTGAAACAATAGAAATTAACAGGCTTAACTCAC
1 CTCTCGCAACATGAGTTGATTTTTGAAACAACAGAAATCAAAAGGCTTAACTCAC
*
45394544 CTCTTGCAACATGAGTTGATTTTTGAAACA
1 CTCTCGCAACATGAGTTGATTTTTGAAACA
45394574 TAAACTAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
54 9 0.12
55 52 0.67
56 17 0.22
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (55 bp):
CTCTCGCAACATGAGTTGATTTTTGAAACAACAGAAATCAAAAGGCTTAACTCAC
Found at i:45394720 original size:88 final size:89
Alignment explanation
Indices: 45394602--45394812 Score: 293
Period size: 88 Copynumber: 2.4 Consensus size: 89
45394592 GCGCGTGGCT
* *
45394602 TGAGGCTCGACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACATAATAATGAAA-ACAGA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACAGAA-AATGAAAGACAGA
45394666 ATTGGAAAATACCTC-G-GTGTGACC
65 ATT-GAAAATACCTCGGCGTGTGACC
* * * * * * **
45394690 TGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAAGGCTTAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACAGAAAATGAAAGACAGAA
45394755 TTGAAAATACCTCGGCGTGTGACC
66 TTGAAAATACCTCGGCGTGTGACC
45394779 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
45394813 AATTAAAACA
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
87 17 0.16
88 51 0.47
89 41 0.38
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (89 bp):
TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACAGAAAATGAAAGACAGAA
TTGAAAATACCTCGGCGTGTGACC
Found at i:45395240 original size:71 final size:70
Alignment explanation
Indices: 45395097--45395272 Score: 223
Period size: 71 Copynumber: 2.5 Consensus size: 70
45395087 ACAAATTAAA
* * * * *
45395097 AGGCTTAACTCACCTCTCGCAATATGAGTC-AATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTAAAACAAAAACTAAAAATACCTCAGCGTG
45395161 CTCCG
66 CTCCG
* *
45395166 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTGAAAACAAAAATTAAAAATACCTCATCGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTT-AAAACAAAAACTAAAAATACCTCAGCGT
*
45395231 G-TCTTG
65 GCTC-CG
*
45395237 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTCGATTTT
45395273 CCTTGAAAAG
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
69 28 0.30
70 7 0.07
71 59 0.63
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTCGATTTTAAAACAAAAACTAAAAATACCTCAGCGTG
CTCCG
Found at i:45405249 original size:27 final size:25
Alignment explanation
Indices: 45405199--45405248 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
45405189 ATATGTAAAA
45405199 TATATATATAGTGTTAGAAATATAT
1 TATATATATAGTGTTAGAAATATAT
* *
45405224 TATATATATAGTGTTTGAAGTATAT
1 TATATATATAGTGTTAGAAATATAT
45405249 ACATGAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (25 bp):
TATATATATAGTGTTAGAAATATAT
Found at i:45411933 original size:15 final size:14
Alignment explanation
Indices: 45411913--45411946 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
45411903 ATCTAAAGCA
45411913 TCTTTTTTTTCTTTT
1 TCTTTTTTTT-TTTT
45411928 TCTTTTTTTTTTTT
1 TCTTTTTTTTTTTT
*
45411942 GCTTT
1 TCTTT
45411947 CAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (14 bp):
TCTTTTTTTTTTTT
Found at i:45412071 original size:26 final size:26
Alignment explanation
Indices: 45412015--45412084 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 26
45412005 GTTTAATTTT
* *
45412015 TTAATTTAACTCGAAT--AATTTTAC
1 TTAATTTGACTCGACTCGAATTTTAC
* *
45412039 TTAATTTGACTTGACTCGAATTTTAT
1 TTAATTTGACTCGACTCGAATTTTAC
* *
45412065 TTCATTTGACTCGATTCGAA
1 TTAATTTGACTCGACTCGAA
45412085 AAATTTTCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 13 0.35
26 24 0.65
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (26 bp):
TTAATTTGACTCGACTCGAATTTTAC
Found at i:45412559 original size:21 final size:21
Alignment explanation
Indices: 45412533--45412578 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
45412523 TTAAAATTAA
45412533 AAAATTTTAAAATAATATAAT
1 AAAATTTTAAAATAATATAAT
*
45412554 AAAATTTTAAAATAATATATT
1 AAAATTTTAAAATAATATAAT
45412575 AAAA
1 AAAA
45412579 ATAGTTAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATTTTAAAATAATATAAT
Found at i:45413915 original size:48 final size:48
Alignment explanation
Indices: 45413824--45413915 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
45413814 GACTTGACCT
* * * *
45413824 TTTGTGCGTCATTGTGGTAGGTCTCTTGGGACTTTTCGTAGTTTACCA
1 TTTGCGCGTCATTGTGGTAAGTCTCTTGGGACTCTTCGCAGTTTACCA
* *
45413872 TTTGCGCGTCATTGTGGTAAGTCTTTTGGGACTCTTGGCAGTTT
1 TTTGCGCGTCATTGTGGTAAGTCTCTTGGGACTCTTCGCAGTTT
45413916 TCTTGATTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.43
Consensus pattern (48 bp):
TTTGCGCGTCATTGTGGTAAGTCTCTTGGGACTCTTCGCAGTTTACCA
Found at i:45420762 original size:22 final size:22
Alignment explanation
Indices: 45420697--45420784 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
45420687 CTTGTACGGG
* *
45420697 TTTAGCACTTCTG-TGCTCTTTG
1 TTTAGCACTT-TGATGCTCTCTA
*
45420719 TTTAGCACTTCGATGCTCTCTA
1 TTTAGCACTTTGATGCTCTCTA
*
45420741 TTTAGCACTTTGATGCTATCTA
1 TTTAGCACTTTGATGCTCTCTA
* * * *
45420763 ATCATCACTTTGGTGCTCTCTA
1 TTTAGCACTTTGATGCTCTCTA
45420785 ATCAACACTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 1 0.02
22 54 0.98
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (22 bp):
TTTAGCACTTTGATGCTCTCTA
Found at i:45420785 original size:22 final size:22
Alignment explanation
Indices: 45420724--45420794 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
45420714 CTTTGTTTAG
* * * *
45420724 CACTTCGATGCTCTCTATTTAG
1 CACTTTGATGCTCTCTAATCAA
* *
45420746 CACTTTGATGCTATCTAATCAT
1 CACTTTGATGCTCTCTAATCAA
*
45420768 CACTTTGGTGCTCTCTAATCAA
1 CACTTTGATGCTCTCTAATCAA
45420790 CACTT
1 CACTT
45420795 GGTTCTATCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (22 bp):
CACTTTGATGCTCTCTAATCAA
Found at i:45420805 original size:21 final size:22
Alignment explanation
Indices: 45420746--45420805 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
45420736 CTCTATTTAG
* *
45420746 CACTTTGATGCTATCTAATCAT
1 CACTTTGGTGCTATCTAATCAA
*
45420768 CACTTTGGTGCTCTCTAATCAA
1 CACTTTGGTGCTATCTAATCAA
*
45420790 CAC-TTGGTTCTATCTA
1 CACTTTGGTGCTATCTA
45420806 CTTATCACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 11 0.33
22 22 0.67
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (22 bp):
CACTTTGGTGCTATCTAATCAA
Found at i:45420837 original size:22 final size:22
Alignment explanation
Indices: 45420811--45420856 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
45420801 ATCTACTTAT
* *
45420811 CACTACAATGTTCTCTGTTTAG
1 CACTACAATGCTCTCTGTTCAG
45420833 CACTACAATGCTCTCTGTTCAG
1 CACTACAATGCTCTCTGTTCAG
45420855 CA
1 CA
45420857 ACACGGTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (22 bp):
CACTACAATGCTCTCTGTTCAG
Found at i:45424091 original size:20 final size:20
Alignment explanation
Indices: 45424068--45424107 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
45424058 ATCAAAAATT
45424068 TTAAAAATATATAAAA-TTAA
1 TTAAAAA-ATATAAAAGTTAA
*
45424088 TTAAAAAATTTAAAAGTTAA
1 TTAAAAAATATAAAAGTTAA
45424108 GTCCAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TTAAAAAATATAAAAGTTAA
Found at i:45424756 original size:20 final size:21
Alignment explanation
Indices: 45424712--45424764 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
45424702 TTTTTTGAAC
45424712 TTTT-TAAATTTTATTTAATAT
1 TTTTATAAATTTTATTT-ATAT
45424733 TTTTATAAATTTTAATTT-TA-
1 TTTTATAAATTTT-ATTTATAT
*
45424753 TTTTACAAATTT
1 TTTTATAAATTT
45424765 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 11 0.38
21 6 0.21
22 8 0.28
23 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATAAATTTTATTTATAT
Found at i:45426295 original size:15 final size:16
Alignment explanation
Indices: 45426265--45426313 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
45426255 TTCTTTTTGT
*
45426265 TTTTAAATATTTTTAAA
1 TTTT-AATATTATTAAA
*
45426282 TTTTAA-ATTATTAAT
1 TTTTAATATTATTAAA
*
45426297 TTTTAATATTTTTAAA
1 TTTTAATATTATTAAA
45426313 T
1 T
45426314 ATATATAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 13 0.48
16 10 0.37
17 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAATATTATTAAA
Found at i:45427266 original size:15 final size:16
Alignment explanation
Indices: 45427232--45427268 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
45427222 GTTAGTGAAC
45427232 AAAATAAATTAAATAT
1 AAAATAAATTAAATAT
*
45427248 -AAATAAA-TACATAT
1 AAAATAAATTAAATAT
45427262 AAAATAA
1 AAAATAA
45427269 GAATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATAAATTAAATAT
Found at i:45431013 original size:22 final size:22
Alignment explanation
Indices: 45430988--45431029 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
45430978 GAGTGTTGGT
45430988 TTAATCCTACAGAAAACACAGC
1 TTAATCCTACAGAAAACACAGC
45431010 TTAATCCTACAGAAAACACA
1 TTAATCCTACAGAAAACACA
45431030 TCCTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.26, G:0.07, T:0.19
Consensus pattern (22 bp):
TTAATCCTACAGAAAACACAGC
Found at i:45431407 original size:23 final size:23
Alignment explanation
Indices: 45431381--45431426 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
45431371 TTAATTTATC
45431381 AAATACAAA-AAAAATTAAAATTA
1 AAAT-CAAATAAAAATTAAAATTA
* *
45431404 AAATCAAATAAAACTTTAAATTA
1 AAATCAAATAAAAATTAAAATTA
45431427 GAAGGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (23 bp):
AAATCAAATAAAAATTAAAATTA
Found at i:45432118 original size:26 final size:26
Alignment explanation
Indices: 45432089--45432196 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
45432079 TGGTACAAAT
45432089 TGATAATGTG-TTAGGTAAATGTTCCA
1 TGATAATG-GATTAGGTAAATGTTCCA
* *
45432115 TGATAATGGATTAGGTAAATATTCAA
1 TGATAATGGATTAGGTAAATGTTCCA
*
45432141 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
45432167 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
45432193 TGAT
1 TGAT
45432197 GGACATTTCA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
25 1 0.01
26 74 0.99
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:45433680 original size:28 final size:26
Alignment explanation
Indices: 45433638--45433712 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
45433628 AAAAGCATCT
* * *
45433638 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
* *
45433666 AAATTACTGTTATACTCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
45433692 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
45433713 GGTTAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 22 0.55
27 1 0.03
28 17 0.43
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:45433905 original size:54 final size:53
Alignment explanation
Indices: 45433819--45433957 Score: 206
Period size: 54 Copynumber: 2.6 Consensus size: 53
45433809 GAAGCGTCCA
* * *
45433819 GGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGTCACATATATTTGTTCT
1 GGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
45433873 GGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
1 GGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
* *
45433927 GGTGGCTCTGCCACAATATCTGTATCTGGTG
1 GGTGGCTATGCCACATTATCTG-ATCTGGTG
45433958 ACTTCGTCAC
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 7 0.09
54 71 0.91
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (53 bp):
GGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
Found at i:45433953 original size:32 final size:27
Alignment explanation
Indices: 45433819--45433957 Score: 167
Period size: 27 Copynumber: 5.1 Consensus size: 27
45433809 GAAGCGTCCA
*
45433819 GGTGGCTATGCCACA-ATTATCTGATCT
1 GGTGGCTCTGCCACATA-TATCTGATCT
* * * *
45433846 AGTGGCTCTGTCACATATATTTGTTCT
1 GGTGGCTCTGCCACATATATCTGATCT
*
45433873 GGTGGCTATGCCACGAT-TATCTGATCT
1 GGTGGCTCTGCCAC-ATATATCTGATCT
*
45433900 GGTGGCTCTGCCACATATATCTGTTCT
1 GGTGGCTCTGCCACATATATCTGATCT
45433927 GGTGGCTCTGCCACA-ATATCTGTATCT
1 GGTGGCTCTGCCACATATATCTG-ATCT
45433954 GGTG
1 GGTG
45433958 ACTTCGTCAC
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
26 9 0.09
27 83 0.87
28 3 0.03
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (27 bp):
GGTGGCTCTGCCACATATATCTGATCT
Found at i:45433968 original size:27 final size:27
Alignment explanation
Indices: 45433819--45433975 Score: 162
Period size: 27 Copynumber: 5.8 Consensus size: 27
45433809 GAAGCGTCCA
*
45433819 GGTGGCTATGCCACAATTATCTG-ATCT
1 GGTGGCTCTGCCACAA-TATCTGTATCT
* * *
45433846 AGTGGCTCTGTCACATATATTTGT-TCT
1 GGTGGCTCTGCCACA-ATATCTGTATCT
* *
45433873 GGTGGCTATGCCACGATTATCTG-ATCT
1 GGTGGCTCTGCCAC-AATATCTGTATCT
45433900 GGTGGCTCTGCCACATATATCTGT-TCT
1 GGTGGCTCTGCCACA-ATATCTGTATCT
45433927 GGTGGCTCTGCCACAATATCTGTATCT
1 GGTGGCTCTGCCACAATATCTGTATCT
* *
45433954 GGTGACT-TCGTCACAATATCTG
1 GGTGGCTCT-GCCACAATATCTG
45433976 GCAGCCTCGC
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
26 10 0.09
27 97 0.89
28 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (27 bp):
GGTGGCTCTGCCACAATATCTGTATCT
Found at i:45440625 original size:29 final size:31
Alignment explanation
Indices: 45440575--45440636 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
45440565 AGTCTATATC
* *
45440575 TTTATTATTTTCAAAAGATTAAATTA-AATT
1 TTTATAATTTTCAAAAGATTAAAATATAATT
45440605 TTTATAATTTT-AAAAGATTAAAATATAATT
1 TTTATAATTTTCAAAAGATTAAAATATAATT
45440635 TT
1 TT
45440637 ACCTTTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (31 bp):
TTTATAATTTTCAAAAGATTAAAATATAATT
Found at i:45443468 original size:48 final size:48
Alignment explanation
Indices: 45443412--45443582 Score: 238
Period size: 48 Copynumber: 3.6 Consensus size: 48
45443402 CGTGTAACTA
* * *
45443412 TGTAAGACCATGTTTGGGACATGGAATCAGCATTGTTATGTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCATAGTTATGTGAGCCAG
*
45443460 TGTAAGACCATGTCTGGGACATGGCATC-GACATCA-TTATGTAAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAG-CAT-AGTTATGTGAGCCAG
* * *
45443508 TATAAAACCATGTCTGGGACATGGCATCAACATAGTTATGTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCATAGTTATGTGAGCCAG
*
45443556 TGTAAGACCATGTCTAGGACATGGCAT
1 TGTAAGACCATGTCTGGGACATGGCAT
45443583 TGGCATGAGG
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
47 2 0.02
48 106 0.98
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCAGCATAGTTATGTGAGCCAG
Found at i:45446109 original size:6 final size:6
Alignment explanation
Indices: 45446098--45446123 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45446088 ACACCGTAGG
45446098 GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GT
45446124 CATAGTCAGG
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:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:45446533 original size:12 final size:12
Alignment explanation
Indices: 45446516--45446553 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
45446506 TGGCCCGCCC
45446516 ATATTAATTTTT
1 ATATTAATTTTT
45446528 ATATT-ATTTTT
1 ATATTAATTTTT
*
45446539 ATA-TAATTTTA
1 ATATTAATTTTT
45446550 ATAT
1 ATAT
45446554 ATATAAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 1 0.04
11 17 0.74
12 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:45446704 original size:32 final size:31
Alignment explanation
Indices: 45446668--45446727 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
45446658 CAATTTAACA
*
45446668 AGCAAATGCCTCTAAAATAATAATAAAAAATT
1 AGCAAATACCTCTAAAATAATAA-AAAAAATT
*
45446700 AGCAAATACCTTTAAAATAATAAAAAAA
1 AGCAAATACCTCTAAAATAATAAAAAAA
45446728 TTTAACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (31 bp):
AGCAAATACCTCTAAAATAATAAAAAAAATT
Found at i:45447822 original size:21 final size:21
Alignment explanation
Indices: 45447792--45447835 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45447782 TTATATCATT
*
45447792 ATTATTATTATTATATT-TTAA
1 ATTATAATTATTAT-TTCTTAA
45447813 ATTATAATTATTATTTCTTAA
1 ATTATAATTATTATTTCTTAA
45447834 AT
1 AT
45447836 ATTAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATAATTATTATTTCTTAA
Found at i:45459933 original size:12 final size:12
Alignment explanation
Indices: 45459916--45459944 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
45459906 GAAAAGTTGC
45459916 AGAAAAACCTA-
1 AGAAAAACCTAG
45459927 AGAAAAACCTAG
1 AGAAAAACCTAG
45459939 AGAAAA
1 AGAAAA
45459945 CTAACGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.66, C:0.14, G:0.14, T:0.07
Consensus pattern (12 bp):
AGAAAAACCTAG
Found at i:45463293 original size:27 final size:27
Alignment explanation
Indices: 45463245--45463403 Score: 166
Period size: 27 Copynumber: 5.9 Consensus size: 27
45463235 GCGAGGCTAC
* *
45463245 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
45463272 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
45463298 CAGATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * *
45463325 CAGATAATTATGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
45463352 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
45463379 CAGATAATTGTGGCATAGGCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
45463404 GACGCTTCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.09
27 97 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:45463404 original size:54 final size:54
Alignment explanation
Indices: 45463263--45463406 Score: 227
Period size: 54 Copynumber: 2.7 Consensus size: 54
45463253 GTGACGAAGT
* *
45463263 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
* *
45463317 CACCAAATCAGATAATTATGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
45463371 CACCAGATCAGATAATTGTGGCATAGGCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
45463407 GCTTCCTCCA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.06
54 77 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:45471354 original size:38 final size:38
Alignment explanation
Indices: 45471311--45471384 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
45471301 TTCATCCTTT
45471311 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGGA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGGA
45471349 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGG
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGG
45471385 AAGGAGTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGGA
Found at i:45472670 original size:40 final size:40
Alignment explanation
Indices: 45472576--45472720 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
45472566 TACTCGAATG
*
45472576 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* * *
45472617 ACATCTGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
45472657 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
45472697 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
45472721 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.68
41 27 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:45473717 original size:21 final size:21
Alignment explanation
Indices: 45473693--45473735 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
45473683 ATAAATTAAC
45473693 CAGAGATAATTAGAAGTCATG
1 CAGAGATAATTAGAAGTCATG
45473714 CAGAGATAATTAGAAGTCATG
1 CAGAGATAATTAGAAGTCATG
45473735 C
1 C
45473736 CATATATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (21 bp):
CAGAGATAATTAGAAGTCATG
Found at i:45479951 original size:40 final size:40
Alignment explanation
Indices: 45479896--45480322 Score: 703
Period size: 40 Copynumber: 10.7 Consensus size: 40
45479886 GAGCATTGGA
45479896 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
45479936 ATATATCCGGGCTAAGA-CCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
45479975 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
45480015 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
45480055 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
45480095 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
45480135 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
45480175 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
45480215 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
45480255 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
45480295 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
45480323 AGGTGTTTGC
Statistics
Matches: 361, Mismatches: 25, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 38 0.11
40 323 0.89
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:45482098 original size:39 final size:39
Alignment explanation
Indices: 45482014--45482124 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
45482004 AGATACTAAT
** *
45482014 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
45482054 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
45482094 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
45482125 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:45484953 original size:14 final size:14
Alignment explanation
Indices: 45484934--45484965 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
45484924 AGGTCATTTA
45484934 GCCCAACCAAACTG
1 GCCCAACCAAACTG
45484948 GCCCAACCAAACTG
1 GCCCAACCAAACTG
45484962 GCCC
1 GCCC
45484966 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:45490013 original size:14 final size:14
Alignment explanation
Indices: 45489994--45490025 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
45489984 AGGTCATTTA
45489994 GCCCAACCAAACTG
1 GCCCAACCAAACTG
*
45490008 GCCCAACCTAACTG
1 GCCCAACCAAACTG
45490022 GCCC
1 GCCC
45490026 GGTGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.47, G:0.16, T:0.09
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:45493046 original size:40 final size:40
Alignment explanation
Indices: 45492976--45493113 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
45492966 AAACCAAGTA
* * *
45492976 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
45493015 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
45493055 CCTTTGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
45493095 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
45493114 TTATCATCCG
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 14 0.16
40 76 0.84
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:45496626 original size:43 final size:42
Alignment explanation
Indices: 45496534--45496652 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 42
45496524 TTCATAACTA
* * * * *
45496534 TCCCAGACAAGGTCTTACACGAATCAAATA-CGATGCCGATG
1 TCCCAGACATGGTCTTACATGAATCACATATCGATGCCAACG
45496575 TCCCAGACATGGTCTTACATGTAATCACATATCGATGCCAACG
1 TCCCAGACATGGTCTTACATG-AATCACATATCGATGCCAACG
* *
45496618 TCCTAGACATGGTCTTACATGAGAACACATATCGA
1 TCCCAGACATGGTCTTACATGA-ATCACATATCGA
45496653 AAATCCTATG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 19 0.28
42 9 0.13
43 40 0.59
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACATGAATCACATATCGATGCCAACG
Found at i:45500019 original size:33 final size:33
Alignment explanation
Indices: 45499973--45500042 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
45499963 ATGTGGATTT
* *
45499973 TGGAGGATGCAAGTTAGATAGAAAAAGCACTTC
1 TGGAGGATCCAAGTTAGATAGAAAAAACACTTC
45500006 TGGAGGATCCAAGTTAGATAGAAAAAACACTTC
1 TGGAGGATCCAAGTTAGATAGAAAAAACACTTC
45500039 TGGA
1 TGGA
45500043 ACATGTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (33 bp):
TGGAGGATCCAAGTTAGATAGAAAAAACACTTC
Found at i:45504073 original size:41 final size:40
Alignment explanation
Indices: 45503946--45504090 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
45503936 CTCGCACAAG
* * * * *
45503946 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
45503986 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
45504026 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
45504067 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
45504091 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:45505325 original size:37 final size:37
Alignment explanation
Indices: 45505279--45505352 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
45505269 CAAGAACTCC
45505279 TTCCTCCTTCCTTAGAATTTT-GGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGG-CAAAAGAAATGAA
45505316 TTCCTCCTTCCTTAGAATTTTCGGCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCAAAAGAAATGAA
45505353 AAAGGATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (37 bp):
TTCCTCCTTCCTTAGAATTTTCGGCAAAAGAAATGAA
Found at i:45511994 original size:39 final size:40
Alignment explanation
Indices: 45511949--45512116 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
45511939 CGGGGTTTAG
* * *
45511949 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
45511988 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
45512028 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
45512068 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
45512109 CCGGATAT
1 CCGGATAT
45512117 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:45512099 original size:41 final size:40
Alignment explanation
Indices: 45511972--45512116 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
45511962 CTCGCACAAG
* * * * *
45511972 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
45512012 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
45512052 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
45512093 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
45512117 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:45513346 original size:38 final size:38
Alignment explanation
Indices: 45513304--45513379 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
45513294 CAAGAACTCC
* *
45513304 TTCCTCCTTCTTTAGAATTTTTGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
45513342 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
45513380 AAAGGATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:45514045 original size:21 final size:21
Alignment explanation
Indices: 45514021--45514074 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
45514011 CATTTTTTGA
* * *
45514021 AACTTCTTTTTCTTCAGCAAC
1 AACTTCCTTTTCTGCAACAAC
* *
45514042 AACTTCCTCTTCTGCAACATC
1 AACTTCCTTTTCTGCAACAAC
45514063 AACTTCCTTTTC
1 AACTTCCTTTTC
45514075 AACCATAGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.41
Consensus pattern (21 bp):
AACTTCCTTTTCTGCAACAAC
Found at i:45516508 original size:21 final size:21
Alignment explanation
Indices: 45516451--45516510 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
45516441 TGGTTTGTAG
*
45516451 ATGATAAGTAGTAGCCATTAT
1 ATGATAAGTAGTAGCCATTCT
45516472 ATGATTAA--A-T--CCATTCT
1 ATGA-TAAGTAGTAGCCATTCT
45516489 ATGATAAGTAGTAGCCATTCT
1 ATGATAAGTAGTAGCCATTCT
45516510 A
1 A
45516511 ATGCAGGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
16 3 0.09
17 10 0.31
18 1 0.03
19 2 0.06
20 1 0.03
21 12 0.38
22 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (21 bp):
ATGATAAGTAGTAGCCATTCT
Found at i:45518689 original size:27 final size:28
Alignment explanation
Indices: 45518638--45518694 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
45518628 ACCTAGACCT
45518638 CCTTATATGATAAAATGACTATTTT-CC
1 CCTTATATGATAAAATGACTATTTTGCC
* * * *
45518665 CCTTATATGGTAAGATGATTGTTTTGCC
1 CCTTATATGATAAAATGACTATTTTGCC
45518693 CC
1 CC
45518695 ATTGTGAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (28 bp):
CCTTATATGATAAAATGACTATTTTGCC
Found at i:45521095 original size:9 final size:9
Alignment explanation
Indices: 45521081--45521106 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45521071 ATGGATAGAT
45521081 GCTCAAAAG
1 GCTCAAAAG
45521090 GCTCAAAAG
1 GCTCAAAAG
45521099 GCTCAAAA
1 GCTCAAAA
45521107 ATCTTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (9 bp):
GCTCAAAAG
Found at i:45530690 original size:28 final size:28
Alignment explanation
Indices: 45530658--45530722 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
45530648 ATTTACTAGA
*
45530658 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
45530686 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
45530714 ATACCCCTA
1 ATACCCCTA
45530723 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:45530929 original size:29 final size:28
Alignment explanation
Indices: 45530828--45530918 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
45530818 AGGAAGCGTC
45530828 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
45530856 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
*
45530884 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
45530913 CTGGTG
1 CTGGTG
45530919 ACTCTGTCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:45531411 original size:18 final size:18
Alignment explanation
Indices: 45531372--45531412 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
45531362 TAATAAGGCC
* *
45531372 TTTTAATTATTTTTATGG
1 TTTTAATTACTTTTATGA
*
45531390 TTTTAATTACTTTTATTA
1 TTTTAATTACTTTTATGA
45531408 TTTTA
1 TTTTA
45531413 TTTTACTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTACTTTTATGA
Found at i:45538808 original size:2 final size:2
Alignment explanation
Indices: 45538803--45538846 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
45538793 AATATATATA
45538803 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
45538845 TG
1 TG
45538847 AATGAGATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:45539020 original size:15 final size:15
Alignment explanation
Indices: 45539002--45539058 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
45538992 TATCTGTTTT
45539002 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
45539017 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
45539032 ATTGAATTTATATTG
1 ATTGAATTTATATTG
45539047 ATTGAA-TTATAT
1 ATTGAATTTATAT
45539059 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:45539037 original size:30 final size:28
Alignment explanation
Indices: 45538998--45539056 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
45538988 TGAATATCTG
45538998 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
45539027 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
45539056 T
1 T
45539057 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:45539469 original size:23 final size:23
Alignment explanation
Indices: 45539433--45539517 Score: 88
Period size: 21 Copynumber: 3.9 Consensus size: 23
45539423 TTTATCGATC
* *
45539433 AGGCACTTTATGTGTCGTATTTT
1 AGGCACCTCATGTGTCGTATTTT
* *
45539456 AGGCACCTCGTGTGTCGTA--TC
1 AGGCACCTCATGTGTCGTATTTT
45539477 AGGCACCTCATGTGTC--ATTTT
1 AGGCACCTCATGTGTCGTATTTT
* *
45539498 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
45539518 ACTGATCAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
21 31 0.62
23 18 0.36
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.39
Consensus pattern (23 bp):
AGGCACCTCATGTGTCGTATTTT
Found at i:45539512 original size:42 final size:43
Alignment explanation
Indices: 45539430--45539517 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 43
45539420 GGCTTTATCG
* * *
45539430 ATCAGGCACTTTATGTGTCGTATTTTAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCG-ATTTTAGGCACCTCATGTGTCGT
* *
45539474 ATCAGGCACCTCATGTGTC-ATTTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGATTTTAGGCACCTCATGTGTCGT
45539516 AT
1 AT
45539518 ACTGATCAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 22 0.56
44 17 0.44
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (43 bp):
ATCAGGCACCTCATGTGTCGATTTTAGGCACCTCATGTGTCGT
Found at i:45539700 original size:18 final size:19
Alignment explanation
Indices: 45539679--45539719 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
45539669 AATGAAATGA
45539679 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
45539697 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
45539716 GAAA
1 GAAA
45539720 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:45541927 original size:43 final size:43
Alignment explanation
Indices: 45541819--45541961 Score: 143
Period size: 43 Copynumber: 3.3 Consensus size: 43
45541809 GCCAATGTCT
* *
45541819 CAGACGTGGTCTTACATGT-AATCAAATATCGATGCCACCATCC
1 CAGACGTGGTCTTACATGTAAATCAAGTAT-GATGCCAACATCC
* * *
45541862 CAGATAG-GGCCTTACATG-AAATCAAGTATGATGCTAACATCC
1 CAGA-CGTGGTCTTACATGTAAATCAAGTATGATGCCAACATCC
* *
45541904 CAGACGTGGTCTTACACGTAAATCATAAGT-CGATGCCAA-AGTCC
1 CAGACGTGGTCTTACATGTAAATC--AAGTATGATGCCAACA-TCC
45541948 CAGACGTGGTCTTA
1 CAGACGTGGTCTTA
45541962 GATGATAACA
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 24 0.29
43 29 0.35
44 25 0.30
45 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (43 bp):
CAGACGTGGTCTTACATGTAAATCAAGTATGATGCCAACATCC
Found at i:45548615 original size:30 final size:30
Alignment explanation
Indices: 45548581--45548640 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
45548571 TGAGAAATAA
45548581 CCTTTCATGTATGAAGCTAATGATATGAGG
1 CCTTTCATGTATGAAGCTAATGATATGAGG
45548611 CCTTTCATGTATGAAGCTAATGATATGAGG
1 CCTTTCATGTATGAAGCTAATGATATGAGG
45548641 TTTACATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (30 bp):
CCTTTCATGTATGAAGCTAATGATATGAGG
Found at i:45561537 original size:104 final size:104
Alignment explanation
Indices: 45561415--45561638 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
45561405 AATGGATATC
45561415 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
45561480 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
45561519 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
45561584 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
45561623 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
45561639 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:45562000 original size:29 final size:29
Alignment explanation
Indices: 45561967--45562030 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
45561957 TAATCCACCA
45561967 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
45561996 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
45562026 CCCAA
1 CCCAA
45562031 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:45562004 original size:30 final size:30
Alignment explanation
Indices: 45561974--45562030 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
45561964 CCACCCAACT
45561974 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
45562003 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
45562031 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:45569013 original size:70 final size:72
Alignment explanation
Indices: 45568899--45569049 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
45568889 GGGGAATCAT
* *
45568899 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
45568963 GATATCG
66 GATATCG
***
45568970 CACTTAGCAA-CCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
45569034 GATATCG
66 GATATCG
45569041 CACTTAGCA
1 CACTTAGCA
45569050 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 34 0.46
71 40 0.54
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Done.