Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 58 of 203
Found at i:18683798 original size:16 final size:15
Alignment explanation
Indices: 18683774--18683807 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
18683764 AAATAAGGAG
*
18683774 AAAACAATAAAAAATA
1 AAAAAAATAAAAAA-A
18683790 AAAAAAATAAAAAAA
1 AAAAAAATAAAAAAA
18683805 AAA
1 AAA
18683808 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAAAATAAAAAAA
Found at i:18684383 original size:16 final size:17
Alignment explanation
Indices: 18684351--18684402 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
18684341 TATACATGTA
18684351 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
18684368 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
18684384 CT-ATAAAT-TA-AAAAT
1 -TAATAAATATATAAAAT
18684399 TAAT
1 TAAT
18684403 GATAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 11 0.37
17 10 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:18686028 original size:29 final size:28
Alignment explanation
Indices: 18685944--18686028 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
18685934 TAATAATTAT
*
18685944 TTTTTTTATAA-TTTATTAGATTTAT-TA
1 TTTTTTTATAATTTTATAAG-TTTATATA
* *
18685971 TATTTTTATAATATTTATAAGTTTTTATA
1 TTTTTTTATAAT-TTTATAAGTTTATATA
*
18686000 TTTTTTTATAATTTTAATAAGTTCATATA
1 TTTTTTTATAATTTT-ATAAGTTTATATA
18686029 AATTTTAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.21
28 7 0.15
29 31 0.65
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTTTTTATAATTTTATAAGTTTATATA
Found at i:18686108 original size:9 final size:9
Alignment explanation
Indices: 18685845--18686098 Score: 83
Period size: 9 Copynumber: 27.6 Consensus size: 9
18685835 TTTTTGATTT
18685845 TTTTTATAA
1 TTTTTATAA
18685854 TTTTTATAA
1 TTTTTATAA
* *
18685863 GTCTATATAA
1 -TTTTTATAA
*
18685873 -ATTT-TAA
1 TTTTTATAA
18685880 TTTTT-TAA
1 TTTTTATAA
18685888 TTTTTTTAATAA
1 --TTTTT-ATAA
* * *
18685900 TTCTAATAC
1 TTTTTATAA
18685909 TTTTT-TAA
1 TTTTTATAA
*
18685917 ATTTTA-AA
1 TTTTTATAA
18685925 TATTTTAAATAA
1 T-TTTT--ATAA
** **
18685937 TAATTATTT
1 TTTTTATAA
18685946 TTTTTATAA
1 TTTTTATAA
*
18685955 TTTATTA-GA
1 TTT-TTATAA
18685964 TTTATTAT-A
1 TTT-TTATAA
18685973 TTTTTATAA
1 TTTTTATAA
*
18685982 TATTTATAA
1 TTTTTATAA
*
18685991 GTTTTTATATT
1 -TTTTTATA-A
18686002 TTTTTATAA
1 TTTTTATAA
*
18686011 TTTTAATAA
1 TTTTTATAA
**
18686020 GTTCATATAAA
1 -TTTTTAT-AA
* **
18686031 TTTTAATGG
1 TTTTTATAA
*
18686040 TTTTAAT-A
1 TTTTTATAA
* *
18686048 TTTAATATTA
1 TTT-TTATAA
* *
18686058 TTTATATTA
1 TTTTTATAA
* *
18686067 TTTTTCTGA
1 TTTTTATAA
18686076 TTTTTATAA
1 TTTTTATAA
18686085 TTTTTATAA
1 TTTTTATAA
18686094 TTTTT
1 TTTTT
18686099 TCTGATTTTT
Statistics
Matches: 182, Mismatches: 43, Indels: 40
0.69 0.16 0.15
Matches are distributed among these distances:
7 3 0.02
8 23 0.13
9 100 0.55
10 45 0.25
11 5 0.03
12 6 0.03
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:18686116 original size:29 final size:29
Alignment explanation
Indices: 18686048--18686117 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
18686038 GGTTTTAATA
*
18686048 TTTAATATTATTTATATTATTTTTCTGATT
1 TTTAATATT-TTTATAATATTTTTCTGATT
18686078 TTT-ATAATTTTTATAAT-TTTTTCTGATT
1 TTTAAT-ATTTTTATAATATTTTTCTGATT
18686106 TTTAATCATTTT
1 TTTAAT-ATTTT
18686118 ATGAGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 14 0.39
29 16 0.44
30 6 0.17
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTAATATTTTTATAATATTTTTCTGATT
Found at i:18697897 original size:16 final size:16
Alignment explanation
Indices: 18697869--18697914 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
18697859 AGCAGTCCAT
18697869 ACATTTCACAATTTTAC
1 ACATTTCACAATTTT-C
18697886 ACATTT-ACAATTTTC
1 ACATTTCACAATTTTC
*
18697901 ATATTTCACAATTT
1 ACATTTCACAATTT
18697915 AACCCCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.46
Consensus pattern (16 bp):
ACATTTCACAATTTTC
Found at i:18700200 original size:10 final size:10
Alignment explanation
Indices: 18700185--18700251 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
18700175 TTAATAAAAT
18700185 TATTTTTATA
1 TATTTTTATA
*
18700195 TATTTTTAAATT
1 TATTTTT--ATA
*
18700207 TATTATTATA
1 TATTTTTATA
18700217 TATTATTTA-A
1 TATT-TTTATA
* * *
18700227 AATATTTATG
1 TATTTTTATA
18700237 TATTTTTATA
1 TATTTTTATA
18700247 TATTT
1 TATTT
18700252 CTTTGAAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
9 4 0.09
10 28 0.65
11 3 0.07
12 8 0.19
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (10 bp):
TATTTTTATA
Found at i:18700204 original size:22 final size:23
Alignment explanation
Indices: 18700179--18700233 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
18700169 TCAATATTAA
18700179 TAAAATTATTTTTATATATT-TT
1 TAAAATTATTTTTATATATTATT
* *
18700201 TAAATTTATTATTATATATTATT
1 TAAAATTATTTTTATATATTATT
18700224 TAAAA-TATTT
1 TAAAATTATTT
18700234 ATGTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAAAATTATTTTTATATATTATT
Found at i:18712112 original size:50 final size:50
Alignment explanation
Indices: 18712034--18712185 Score: 250
Period size: 50 Copynumber: 3.0 Consensus size: 50
18712024 CTGATCAGTA
* * *
18712034 ACAAGTGATAAGTGGTAGTTTAGTTACACTTATCTGATCAGTGATAAGTG
1 ACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTG
*
18712084 ACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCGGTGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTG
*
18712134 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACAAGTG
1 ACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGTG
18712185 A
1 A
18712186 TAAATGTGAT
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 65 0.68
51 30 0.32
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (50 bp):
ACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTG
Found at i:18714943 original size:31 final size:32
Alignment explanation
Indices: 18714884--18714951 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 32
18714874 TAATTTGATT
* *
18714884 ATTTTTAGTTTAATTATTTCTCATATTTTAAA
1 ATTTTTAGTTTAACTATTTCACATATTTTAAA
18714916 ATTTTTAGTTTAACTA-TTCACATATTTTAAA
1 ATTTTTAGTTTAACTATTTCACATATTTTAAA
18714947 ATTTT
1 ATTTT
18714952 AATCTTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.57
Consensus pattern (32 bp):
ATTTTTAGTTTAACTATTTCACATATTTTAAA
Found at i:18717070 original size:19 final size:19
Alignment explanation
Indices: 18717036--18717098 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
18717026 TTTTTAAATT
*
18717036 TTTTTATATAAAATTTAGAA
1 TTTTTATA-AATATTTAGAA
18717056 TTTTTATAAATATTTTA-AA
1 TTTTTATAAATA-TTTAGAA
* *
18717075 -TTTTAAAAATTATTTTGAA
1 TTTTTATAAA-TATTTAGAA
18717094 TTTTT
1 TTTTT
18717099 GAAAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 11 0.31
19 9 0.25
20 16 0.44
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTTATAAATATTTAGAA
Found at i:18717103 original size:20 final size:19
Alignment explanation
Indices: 18717048--18717118 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
18717038 TTTATATAAA
*
18717048 ATTTAGAATTTTTATAAA-T
1 ATTTTGAATTTTTA-AAATT
* *
18717067 ATTTTAAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
18717086 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
*
18717106 ATTTTGTATTTTT
1 ATTTTGAATTTTT
18717119 TGTTGAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 3 0.07
19 23 0.52
20 18 0.41
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:18717120 original size:21 final size:20
Alignment explanation
Indices: 18717048--18717118 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
18717038 TTTATATAAA
*
18717048 ATTTAGAATTTTT-ATAAA-T
1 ATTTTGAATTTTTGA-AAATT
* *
18717067 ATTTT-AAATTTTAAAAATT
1 ATTTTGAATTTTTGAAAATT
18717086 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
*
18717106 ATTTTGTATTTTT
1 ATTTTGAATTTTT
18717119 TGTTGAAAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 9 0.20
19 11 0.25
20 24 0.55
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:18717528 original size:70 final size:67
Alignment explanation
Indices: 18717412--18717539 Score: 175
Period size: 70 Copynumber: 1.9 Consensus size: 67
18717402 AATATAATAC
* * * **
18717412 TTTTGCCTTTTAACTTAATAAGTAAACATTTATTAAAATGACGTAGTTTTACCTTTTAACTTATT
1 TTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAGTTTTACCTTTTAACTTATT
18717477 AA
66 AA
*
18717479 TTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACAATGTAGTTTTACCTTTTA
1 TTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACAACGTAGTTTTACCTTTTA
18717540 TTCAAGCTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
67 13 0.25
68 3 0.06
69 3 0.06
70 33 0.63
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (67 bp):
TTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAGTTTTACCTTTTAACTTATT
AA
Found at i:18719329 original size:3 final size:3
Alignment explanation
Indices: 18719321--18719378 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
18719311 AATTATTTAT
* *
18719321 TTA TTA TTA -CA TTA -TA TCA TTA TGTA TTA TTA -TA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA
*
18719365 TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TT
18719379 TTAATTGTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
2 5 0.11
3 33 0.75
4 6 0.14
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:18719343 original size:23 final size:22
Alignment explanation
Indices: 18719317--18719366 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
18719307 ATTTAATTAT
18719317 TTATTTATTATTACATTATATCA
1 TTATTTATTATTACATTAT-TCA
* * *
18719340 TTATGTATTATTATATTATTTA
1 TTATTTATTATTACATTATTCA
18719362 TTATT
1 TTATT
18719367 ATTGTTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTTATTATTACATTATTCA
Found at i:18719354 original size:18 final size:18
Alignment explanation
Indices: 18719319--18719369 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
18719309 TTAATTATTT
18719319 ATTTATTATTACATTATATC
1 ATTTATTATT--ATTATATC
*
18719339 A-TTATGTATTATTATATT
1 ATTTAT-TATTATTATATC
18719357 ATTTATTATTATT
1 ATTTATTATTATT
18719370 GTTATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 15 0.54
19 8 0.29
20 5 0.18
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTATTATTATTATATC
Found at i:18719356 original size:8 final size:8
Alignment explanation
Indices: 18719312--18719368 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 8
18719302 TTACTATTTA
18719312 ATTAT-TT
1 ATTATATT
18719319 ATT-TATT
1 ATTATATT
*
18719326 ATTACATT
1 ATTATATT
18719334 A-TATCATT
1 ATTAT-ATT
*
18719342 A-TGTATT
1 ATTATATT
18719349 ATTATATT
1 ATTATATT
18719357 ATT-TATT
1 ATTATATT
18719364 ATTAT
1 ATTAT
18719369 TGTTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
6 1 0.02
7 21 0.51
8 19 0.46
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (8 bp):
ATTATATT
Found at i:18723564 original size:167 final size:167
Alignment explanation
Indices: 18723288--18723621 Score: 668
Period size: 167 Copynumber: 2.0 Consensus size: 167
18723278 TAATTAAAAT
18723288 TATTGCTCAGTTAACCTGGAAACCAACCAACCAACCCGACACCGATACGGCACTCAAGCAAAGAC
1 TATTGCTCAGTTAACCTGGAAACCAACCAACCAACCCGACACCGATACGGCACTCAAGCAAAGAC
18723353 AAAAGATATGGATCAAAGATTAGAAAAGCTCGAACAGTACCAGAAGGAGATGCAAGACCGGCTTC
66 AAAAGATATGGATCAAAGATTAGAAAAGCTCGAACAGTACCAGAAGGAGATGCAAGACCGGCTTC
18723418 AGCTACAAATGCAGGAGCGGTTAGACAAGATGAAGTG
131 AGCTACAAATGCAGGAGCGGTTAGACAAGATGAAGTG
18723455 TATTGCTCAGTTAACCTGGAAACCAACCAACCAACCCGACACCGATACGGCACTCAAGCAAAGAC
1 TATTGCTCAGTTAACCTGGAAACCAACCAACCAACCCGACACCGATACGGCACTCAAGCAAAGAC
18723520 AAAAGATATGGATCAAAGATTAGAAAAGCTCGAACAGTACCAGAAGGAGATGCAAGACCGGCTTC
66 AAAAGATATGGATCAAAGATTAGAAAAGCTCGAACAGTACCAGAAGGAGATGCAAGACCGGCTTC
18723585 AGCTACAAATGCAGGAGCGGTTAGACAAGATGAAGTG
131 AGCTACAAATGCAGGAGCGGTTAGACAAGATGAAGTG
18723622 AGAGATGTCT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (167 bp):
TATTGCTCAGTTAACCTGGAAACCAACCAACCAACCCGACACCGATACGGCACTCAAGCAAAGAC
AAAAGATATGGATCAAAGATTAGAAAAGCTCGAACAGTACCAGAAGGAGATGCAAGACCGGCTTC
AGCTACAAATGCAGGAGCGGTTAGACAAGATGAAGTG
Found at i:18731501 original size:44 final size:43
Alignment explanation
Indices: 18731446--18731688 Score: 141
Period size: 44 Copynumber: 5.5 Consensus size: 43
18731436 AGCAGGTTGA
*
18731446 AAGATAACAGATCTTGTCTTCATGTACTGGCTTGAAGTAGACC
1 AAGATAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGACC
* * *** * * * *
18731489 ATAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCG
1 A-AGATAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGA-CC
* * **
18731535 AAGA-AAGTAGATCTTGTCTTTATGTACTGGCGTGAAGTAGGTC
1 AAGATAA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGACC
* * * * * * *
18731578 ATAGATACCAGATCTTGCCTTCCCATACTAGTGGC--AAAGCAGATCG
1 A-AGATAACAGATCTTGTCTT--CAT-GTACTGGCGTGAAGTAGA-CC
* *
18731624 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
1 AAGATAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGA-CC
* * *
18731668 AAGATAGCAGGTCCTGTCTTC
1 AAGATAACAGATCTTGTCTTC
18731689 CTATATCGGT
Statistics
Matches: 142, Mismatches: 46, Indels: 23
0.67 0.22 0.11
Matches are distributed among these distances:
42 6 0.04
43 5 0.04
44 71 0.50
45 49 0.35
46 5 0.04
47 6 0.04
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
AAGATAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGACC
Found at i:18731549 original size:45 final size:45
Alignment explanation
Indices: 18731497--18731771 Score: 130
Period size: 44 Copynumber: 6.2 Consensus size: 45
18731487 CCATAGATAC
*
18731497 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAG
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAA
* * **** * * * * * *
18731542 TAGATCTTGTCTTTATGTACTGG-CGTGAAGTAGGTC-ATAGATAC
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGA-AGAAAA
* *
18731586 CAGATCTTGCCTTCCCATACTAGTGGCAAAGCAGATCGAAGAAAA
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAA
* *** * * * * * *
18731631 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAG
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAA
* * * * * * ** * *
18731675 CAGGTCCTGTCTTCCTATA-TCGGTAGCAAAGTGGATCGAA-TATA
1 CAGATCTTGCCTTCCCATACT-GGTGGCGAAGCAGATCGAAGAAAA
* ** *
18731719 CAGATTTTATCTTCCCATACTGGTGGCGAAGTAGATC-AAGGAAAA
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAA-GAAAA
18731764 CAGATCTT
1 CAGATCTT
18731772 ATCTCCCTAA
Statistics
Matches: 160, Mismatches: 62, Indels: 16
0.67 0.26 0.07
Matches are distributed among these distances:
43 4 0.03
44 87 0.54
45 68 0.43
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAA
Found at i:18731714 original size:89 final size:89
Alignment explanation
Indices: 18731446--18731673 Score: 366
Period size: 89 Copynumber: 2.6 Consensus size: 89
18731436 AGCAGGTTGA
* * *
18731446 AAGATAACAGATCTTGTCTTCATGTACTGGCTTGAAGTAGACCATAGATACCAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCATAGATACCAGATCTTGCCTTC
*
18731511 CCATACTGGTGGCGAAGCAGATCG
66 CCATACTGGTGGCAAAGCAGATCG
** * *
18731535 AAGAAAGTAGATCTTGTCTTTATGTACTGGCGTGAAGTAGGTCATAGATACCAGATCTTGCCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCATAGATACCAGATCTTGCCTTC
*
18731600 CCATACTAGTGGCAAAGCAGATCG
66 CCATACTGGTGGCAAAGCAGATCG
*
18731624 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCATAGATA
18731674 GCAGGTCCTG
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 125 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (89 bp):
AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCATAGATACCAGATCTTGCCTTC
CCATACTGGTGGCAAAGCAGATCG
Found at i:18733543 original size:15 final size:15
Alignment explanation
Indices: 18733525--18733554 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18733515 AAATTAAATC
18733525 ATTATGTATTATTAT
1 ATTATGTATTATTAT
*
18733540 ATTATTTATTATTAT
1 ATTATGTATTATTAT
18733555 TGTCATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTATGTATTATTAT
Found at i:18736756 original size:3 final size:3
Alignment explanation
Indices: 18736748--18736805 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
18736738 AATTATTTAT
* *
18736748 TTA TTA TTA -CA TTA -TA TCA TTA TGTA TTA TTA -TA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA
*
18736792 TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TT
18736806 TTAATTGTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
2 5 0.11
3 33 0.75
4 6 0.14
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:18736770 original size:23 final size:22
Alignment explanation
Indices: 18736744--18736793 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
18736734 ATTTAATTAT
18736744 TTATTTATTATTACATTATATCA
1 TTATTTATTATTACATTAT-TCA
* * *
18736767 TTATGTATTATTATATTATTTA
1 TTATTTATTATTACATTATTCA
18736789 TTATT
1 TTATT
18736794 ATTGTTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTTATTATTACATTATTCA
Found at i:18736781 original size:18 final size:18
Alignment explanation
Indices: 18736746--18736796 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
18736736 TTAATTATTT
18736746 ATTTATTATTACATTATATC
1 ATTTATTATT--ATTATATC
*
18736766 A-TTATGTATTATTATATT
1 ATTTAT-TATTATTATATC
18736784 ATTTATTATTATT
1 ATTTATTATTATT
18736797 GTTATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 15 0.54
19 8 0.29
20 5 0.18
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTATTATTATTATATC
Found at i:18736783 original size:8 final size:8
Alignment explanation
Indices: 18736739--18736795 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 8
18736729 TTACTATTTA
18736739 ATTAT-TT
1 ATTATATT
18736746 ATT-TATT
1 ATTATATT
*
18736753 ATTACATT
1 ATTATATT
18736761 A-TATCATT
1 ATTAT-ATT
*
18736769 A-TGTATT
1 ATTATATT
18736776 ATTATATT
1 ATTATATT
18736784 ATT-TATT
1 ATTATATT
18736791 ATTAT
1 ATTAT
18736796 TGTTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
6 1 0.02
7 21 0.51
8 19 0.46
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (8 bp):
ATTATATT
Found at i:18746739 original size:16 final size:16
Alignment explanation
Indices: 18746718--18746750 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18746708 ATTCTAATAT
18746718 CTTAAAAATGTACTCC
1 CTTAAAAATGTACTCC
18746734 CTTAAAAATGTACTCC
1 CTTAAAAATGTACTCC
18746750 C
1 C
18746751 ACTTAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.30
Consensus pattern (16 bp):
CTTAAAAATGTACTCC
Found at i:18753751 original size:109 final size:109
Alignment explanation
Indices: 18753466--18753879 Score: 566
Period size: 109 Copynumber: 3.8 Consensus size: 109
18753456 ACATTTGGCA
** * *
18753466 ATTTGGTTAAACGAGAAATCAAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* ** *
18753531 AACATTGCCTTATTTTTGAAAAGTTTAAAAAAAAAAGATATTTAGCT
66 AATATTGCCTTA-TTTTGAAAAGTTT--TTAAAAAGGATATTTAGCT
18753578 ATTTGGTCGAACGAGAAATCGAAA-CCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
*
18753642 AATATTGCCTTATTTTGAAAA-TTTTTGAAAAAGGATATTAAG-T
66 AATATTGCCTTATTTTGAAAAGTTTTT-AAAAAGGATATTTAGCT
* *
18753685 CATTTGGTGGAACGAGAAATCGAAACCCAGTACCTTAGTGCACGTTCCTCGAATTTCCAAACGCA
1 -ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCA
* *
18753750 AAATATTGCCTTTTTTTGAAAAGTTTTT-AAAAGAATATTTAGCT
65 AAATATTGCCTTATTTTGAAAAGTTTTTAAAAAGGATATTTAGCT
* * * * *
18753794 ATTTGGTCGAACGAGAAATCGAAACCCAGTACATTAGGGCATGTTTTCTCGAATTTCCAAAGGCT
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACG-TTCCTCGAATTTCCAAACGCA
* *
18753859 AAATATTGCCTCATTTAGAAA
65 AAATATTGCCTTATTTTGAAA
18753880 TTTTTTTGCT
Statistics
Matches: 272, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
107 1 0.00
108 87 0.32
109 99 0.36
110 14 0.05
111 50 0.18
112 21 0.08
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (109 bp):
ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AATATTGCCTTATTTTGAAAAGTTTTTAAAAAGGATATTTAGCT
Found at i:18754000 original size:4 final size:4
Alignment explanation
Indices: 18753993--18754052 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
18753983 CAATCATAGC
* * *
18753993 AAAT AAAT AAAT AAAT AAACT AAAGT AAAT AAA- AAA- GAAC ACAT AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAA-T AAAT AAAT AAAT AAAT AAAT AAAT
*
18754041 AAAT ACAT AAAT
1 AAAT AAAT AAAT
18754053 GAACATAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 5 0.11
4 33 0.72
5 8 0.17
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:18754021 original size:22 final size:22
Alignment explanation
Indices: 18753993--18754070 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
18753983 CAATCATAGC
18753993 AAATAAATAAATAAATAAAC-T
1 AAATAAATAAATAAATAAACAT
*
18754014 AAAGTAAATAAA-AAAGAACACAT
1 AAA-TAAATAAATAAATAA-ACAT
* *
18754037 AAATAAATACATAAATGAACAT
1 AAATAAATAAATAAATAAACAT
*
18754059 AAAAACAATAAA
1 AAATA-AATAAA
18754071 GAAAAATAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 8 0.17
22 25 0.54
23 13 0.28
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.18
Consensus pattern (22 bp):
AAATAAATAAATAAATAAACAT
Found at i:18754377 original size:3 final size:3
Alignment explanation
Indices: 18754369--18754446 Score: 52
Period size: 3 Copynumber: 25.7 Consensus size: 3
18754359 TAGATGAAGA
* * * *
18754369 AAT AAT AAT AAT AACT AAT AAT AAC AAC AAT AAT AAT AAA AGAT GAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * *
18754416 AAT -AT ATT AAA AAT AAT GAAG AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
18754447 AAATGCTAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
2 4 0.07
3 49 0.83
4 6 0.10
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:18755123 original size:18 final size:18
Alignment explanation
Indices: 18755077--18755123 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
18755067 GTTTCGAAAG
*
18755077 AAAGAAAAATAAAGAGAA
1 AAAGAAAAATAAAAAGAA
* *
18755095 AAATAAGAATAAAAAGAA
1 AAAGAAAAATAAAAAGAA
18755113 AAAGAAAAATA
1 AAAGAAAAATA
18755124 TAACTTATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAGAAAAATAAAAAGAA
Found at i:18756022 original size:88 final size:86
Alignment explanation
Indices: 18755951--18756284 Score: 447
Period size: 88 Copynumber: 3.8 Consensus size: 86
18755941 TCTTTGATCT
* * *
18755951 GCTCCACTACAACCGAGGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGTTGTCAATGAAGGAAG
1 GCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGAAGGAAG
18756016 GCAAGATCTTTTGTCTTCAACCA
66 GCAAGATC--TTGTCTTCAACCA
* * *
18756039 GCTCCACCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTTGCTGTCAATGCAGGAAG
1 GCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGAAGGAAG
*
18756104 GCAAGATATGTTGTCTTCAACCA
66 GCAAG--ATCTTGTCTTCAACCA
* *
18756127 GCTCCA-TCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTTGCTGTCAATGCAGGAA
1 GCTCCACT-ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGAAGGAA
*
18756191 GGCAAGATCTGTTGTCTTGAACCA
65 GGCAAGATC--TTGTCTTCAACCA
* * * * *
18756215 GCTCCGCTACAATCGAGAGAGGCAAGGTTTGTATCTTCGACCTGCTTCGCTGTCAAT-ACAGGAA
1 GCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGA-AGGAA
18756279 GGCAAG
65 GGCAAG
18756285 CTCTATAACT
Statistics
Matches: 222, Mismatches: 17, Indels: 14
0.88 0.07 0.06
Matches are distributed among these distances:
86 2 0.01
88 217 0.98
89 1 0.00
90 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (86 bp):
GCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGAAGGAAG
GCAAGATCTTGTCTTCAACCA
Found at i:18756106 original size:44 final size:44
Alignment explanation
Indices: 18756058--18756284 Score: 130
Period size: 44 Copynumber: 5.2 Consensus size: 44
18756048 CAACCGAGAG
* *
18756058 AGGCAAGGTTTGTGTCTTCGATCTACTTTGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGAACTACTTTGCTGTCAATACAGGA
* * * ** *
18756102 AGGCAAGATATGTTGTCTTC-AACCAGC--T-CCATCACA-ACCGAGA
1 AGGCAAGGTTTG-TGTCTTCGAACTA-CTTTGCTGTCA-ATACAG-GA
* *
18756145 GAGGCAAGGTTTGTGTCTTCGATCTACTTTGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGAACTACTTTGCTGTCAATACAGGA
* * * ** *
18756190 AGGCAAGATCTGTTGTCTT-GAACCAGCTCCGCT-ACAAT-C-GAGA
1 AGGCAAGGTTTG-TGTCTTCGAACTA-CTTTGCTGTCAATACAG-GA
* * * *
18756233 GAGGCAAGGTTTGTATCTTCGACCTGCTTCGCTGTCAATACAGGA
1 -AGGCAAGGTTTGTGTCTTCGAACTACTTTGCTGTCAATACAGGA
18756278 AGGCAAG
1 AGGCAAG
18756285 CTCTATAACT
Statistics
Matches: 134, Mismatches: 31, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
42 7 0.05
43 26 0.19
44 68 0.51
45 26 0.19
46 7 0.05
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGAACTACTTTGCTGTCAATACAGGA
Found at i:18756254 original size:176 final size:176
Alignment explanation
Indices: 18755951--18756284 Score: 517
Period size: 176 Copynumber: 1.9 Consensus size: 176
18755941 TCTTTGATCT
* * *
18755951 GCTCCACTACAACCGAGGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGTTGTCAATGAAGGAAG
1 GCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGAAGGAAG
* * *
18756016 GCAAGATCTTTTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATC
66 GCAAGATCTGTTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTATCTTCGACC
* *
18756081 TACTTTGCTGTCAATGCAGGAAGGCAAGATATGTTGTCTTCAACCA
131 TACTTCGCTGTCAATACAGGAAGGCAAGATATGTTGTCTTCAACCA
* *
18756127 GCTCCA-TCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTTGCTGTCAATGCAGGAA
1 GCTCCACT-ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGAAGGAA
* * * *
18756191 GGCAAGATCTGTTGTCTTGAACCAGCTCCGCTACAATCGAGAGAGGCAAGGTTTGTATCTTCGAC
65 GGCAAGATCTGTTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTATCTTCGAC
*
18756256 CTGCTTCGCTGTCAATACAGGAAGGCAAG
130 CTACTTCGCTGTCAATACAGGAAGGCAAG
18756285 CTCTATAACT
Statistics
Matches: 142, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
175 1 0.01
176 141 0.99
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (176 bp):
GCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTGTCAATGAAGGAAG
GCAAGATCTGTTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTATCTTCGACC
TACTTCGCTGTCAATACAGGAAGGCAAGATATGTTGTCTTCAACCA
Found at i:18758380 original size:7 final size:7
Alignment explanation
Indices: 18758363--18758417 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
18758353 TGACCTCTCC
18758363 TTTTTCAT
1 TTTTTC-T
18758371 TTTCTT-T
1 TTT-TTCT
18758378 TTTTTCT
1 TTTTTCT
18758385 TTTTTCTT
1 TTTTTC-T
18758393 TTTTTCT
1 TTTTTCT
18758400 TTTTTCT
1 TTTTTCT
*
18758407 TCTTTCT
1 TTTTTCT
18758414 TTTT
1 TTTT
18758418 CTCCTATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 2 0.05
7 28 0.67
8 10 0.24
9 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:18758383 original size:15 final size:16
Alignment explanation
Indices: 18758363--18758407 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
18758353 TGACCTCTCC
18758363 TTTTTC-ATTTTCTTT
1 TTTTTCTATTTTCTTT
*
18758378 TTTTTCTTTTTTC-TT
1 TTTTTCTATTTTCTTT
*
18758393 TTTTTCTTTTTTCTT
1 TTTTTCTATTTTCTT
18758408 CTTTCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 21 0.78
16 6 0.22
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTATTTTCTTT
Found at i:18758390 original size:22 final size:22
Alignment explanation
Indices: 18758363--18758416 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
18758353 TGACCTCTCC
18758363 TTTTTCATTTTCTT-TTTTTTCT
1 TTTTTC-TTTTCTTCTTTTTTCT
*
18758385 TTTTTCTTTTTTTCTTTTTTCT
1 TTTTTCTTTTCTTCTTTTTTCT
*
18758407 TCTTTCTTTT
1 TTTTTCTTTT
18758417 TCTCCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTCTTTTCTTCTTTTTTCT
Found at i:18758417 original size:15 final size:15
Alignment explanation
Indices: 18758370--18758417 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
18758360 TCCTTTTTCA
18758370 TTTTCTTTTTTTTCTT
1 TTTTC-TTTTTTTCTT
18758386 TTTTCTTTTTTTCTT
1 TTTTCTTTTTTTCTT
*
18758401 TTTTC-TTCTTTCTT
1 TTTTCTTTTTTTCTT
18758415 TTT
1 TTT
18758418 CTCCTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 11 0.35
15 15 0.48
16 5 0.16
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTCTTTTTTTCTT
Found at i:18759178 original size:17 final size:18
Alignment explanation
Indices: 18759146--18759182 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
18759136 TCTGCACAGT
18759146 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
18759164 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
18759181 AT
1 AT
18759183 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:18762573 original size:108 final size:109
Alignment explanation
Indices: 18762325--18762719 Score: 634
Period size: 108 Copynumber: 3.6 Consensus size: 109
18762315 TGGTTAAACG
* * *
18762325 AGAAATCAAAACCCAGCACCTTAGGGTACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTAT
1 AGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTAT
18762390 TTTTGAAAAGTTTTTCTTAAAAG-ATATTTAGCTATTTGGTCGAACA
66 TTTTGAAAAG--TTT-TTAAAAGAATATTTAGCTATTTGGTCGAACA
18762436 AGAAATCGAAA-CCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTAT
1 AGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTAT
18762500 TTTTGAAAAGTTTTTAAAAGAATATTTAGCTATTTGGTCGAACA
66 TTTTGAAAAGTTTTTAAAAGAATATTTAGCTATTTGGTCGAACA
18762544 AGAAATCGAAA-CCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTAT
1 AGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTAT
*
18762608 TTTTGAAAAGTTTTTAAAAGAATATTTAGCTATTTGGTCGAACG
66 TTTTGAAAAGTTTTTAAAAGAATATTTAGCTATTTGGTCGAACA
* * * * * * *
18762652 AGAAATCGAAACCCAGTACATTAGGGCATGTTTTCTCGAATTTCCAAAGGCTAAATATTGCCTCA
1 AGAAATCGAAACCCAGTACCTTAGGGCACG-TTCCTCGAATTTCCAAACGCAAAACATTGCCTTA
18762717 TTT
65 TTT
18762720 AGAAATTTTT
Statistics
Matches: 270, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
107 7 0.03
108 144 0.53
109 16 0.06
110 93 0.34
111 10 0.04
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (109 bp):
AGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTAT
TTTTGAAAAGTTTTTAAAAGAATATTTAGCTATTTGGTCGAACA
Found at i:18762863 original size:22 final size:22
Alignment explanation
Indices: 18762838--18762902 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
18762828 CAATCATAGC
18762838 AAATAAATAAATAAAC-TAAAGT
1 AAATAAATAAATAAACATAAA-T
*
18762860 AAATAAA-AAAGAACACATAAAT
1 AAATAAATAAATAA-ACATAAAT
* *
18762882 AAATACATAAATGAACATAAA
1 AAATAAATAAATAAACATAAA
18762903 AAACAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 5 0.14
22 23 0.64
23 8 0.22
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.18
Consensus pattern (22 bp):
AAATAAATAAATAAACATAAAT
Found at i:18763223 original size:3 final size:3
Alignment explanation
Indices: 18763215--18763298 Score: 64
Period size: 3 Copynumber: 27.7 Consensus size: 3
18763205 TAGATGAAGA
* * *
18763215 AAT AAT AAT AAT AAT AAT AACT AAT AAT AAC AAA AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
18763261 AGAT GAT AAT -AT ATT AAA AAT AAT GAAG AA- AAT AAT AA
1 A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
18763299 AAATGGTAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
2 4 0.06
3 54 0.84
4 6 0.09
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:18763243 original size:22 final size:22
Alignment explanation
Indices: 18763215--18763256 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18763205 TAGATGAAGA
* *
18763215 AATAATAATAATAATAATAACT
1 AATAATAACAAAAATAATAACT
18763237 AATAATAACAAAAATAATAA
1 AATAATAACAAAAATAATAA
18763257 TAAAAGATGA
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:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAATAACAAAAATAATAACT
Found at i:18763271 original size:31 final size:30
Alignment explanation
Indices: 18763218--18763284 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
18763208 ATGAAGAAAT
*
18763218 AATAATAATAATAATAACTAATAATAACAAA
1 AATAATAATAAAAATAACTAAT-ATAACAAA
* **
18763249 AATAATAATAAAAGATGA-TAATATATTAAA
1 AATAATAATAAAA-ATAACTAATATAACAAA
18763279 AATAAT
1 AATAAT
18763285 GAAGAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 12 0.39
31 16 0.52
32 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (30 bp):
AATAATAATAAAAATAACTAATATAACAAA
Found at i:18763993 original size:18 final size:18
Alignment explanation
Indices: 18763947--18763993 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
18763937 GTTTCGAAAG
*
18763947 AAAGAAAAATAAAGAGAA
1 AAAGAAAAATAAAAAGAA
* *
18763965 AAATAAGAATAAAAAGAA
1 AAAGAAAAATAAAAAGAA
18763983 AAAGAAAAATA
1 AAAGAAAAATA
18763994 TAACTTATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAGAAAAATAAAAAGAA
Found at i:18765692 original size:12 final size:13
Alignment explanation
Indices: 18765675--18765706 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
18765665 AGGGACACAT
18765675 GCCCGTGTCC-TA
1 GCCCGTGTCCGTA
18765687 GCCCGTGTCCGTA
1 GCCCGTGTCCGTA
18765700 -CCCGTGT
1 GCCCGTGT
18765707 AACTCACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.89
13 2 0.11
ACGTcount: A:0.06, C:0.41, G:0.28, T:0.25
Consensus pattern (13 bp):
GCCCGTGTCCGTA
Found at i:18766992 original size:7 final size:7
Alignment explanation
Indices: 18766980--18767010 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
18766970 AAATCACTAC
18766980 TATCTCA
1 TATCTCA
18766987 TATCTCA
1 TATCTCA
18766994 TATCTCA
1 TATCTCA
18767001 TATCTCA
1 TATCTCA
18767008 TAT
1 TAT
18767011 ACATGCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (7 bp):
TATCTCA
Found at i:18771950 original size:17 final size:18
Alignment explanation
Indices: 18771915--18771950 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
18771905 TAAAATGGCT
18771915 TATTTTATATTAATTTAAG
1 TATTTTATATT-ATTTAAG
18771934 TATTTTATATT-TTTAAG
1 TATTTTATATTATTTAAG
18771951 CTATGAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TATTTTATATTATTTAAG
Found at i:18776117 original size:14 final size:17
Alignment explanation
Indices: 18776098--18776135 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
18776088 ATTTATTTCT
18776098 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
18776112 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
18776129 TAATATA
1 TAATATA
18776136 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:18776143 original size:12 final size:11
Alignment explanation
Indices: 18776115--18776158 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
18776105 ATATTTATAA
18776115 TATAATTAATT
1 TATAATTAATT
*
18776126 TAATAATATACTT
1 T-ATAAT-TAATT
18776139 TATAATTAATT
1 TATAATTAATT
18776150 TATATATTA
1 TATA-ATTA
18776159 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:18776162 original size:20 final size:23
Alignment explanation
Indices: 18776110--18776172 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
18776100 ATATAATATT
18776110 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
18776132 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
18776157 TATATAAATAAATAAT
1 TATATATATAATTAAT
18776173 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:18776174 original size:20 final size:20
Alignment explanation
Indices: 18776127--18776175 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
18776117 TAATTAATTT
*
18776127 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
18776147 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
18776167 AATAATATA
1 AATAATATA
18776176 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:18781711 original size:20 final size:20
Alignment explanation
Indices: 18781686--18781723 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18781676 GTTTTTCTAG
18781686 TTTAAATTATTT-TGTTAAAT
1 TTTAAATT-TTTATGTTAAAT
18781706 TTTAAATTTTTATGTTAA
1 TTTAAATTTTTATGTTAA
18781724 TAAAGGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTTATGTTAAAT
Found at i:18785196 original size:17 final size:18
Alignment explanation
Indices: 18785162--18785197 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
18785152 AAAATGGCTT
18785162 ATTTTATATTAATTTAAGC
1 ATTTTATATT-ATTTAAGC
18785181 ATTTTATATT-TTTAAGC
1 ATTTTATATTATTTAAGC
18785198 TATAAAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTTATATTATTTAAGC
Found at i:18785757 original size:15 final size:16
Alignment explanation
Indices: 18785721--18785760 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
18785711 ACTTTTTCAA
*
18785721 TCATCCCTCATCCCTC
1 TCATCTCTCATCCCTC
*
18785737 TCATCTCTCAT-CCTT
1 TCATCTCTCATCCCTC
18785752 TCATCTCTC
1 TCATCTCTC
18785761 TCATCCTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.12, C:0.47, G:0.00, T:0.40
Consensus pattern (16 bp):
TCATCTCTCATCCCTC
Found at i:18785761 original size:24 final size:23
Alignment explanation
Indices: 18785728--18785772 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
18785718 CAATCATCCC
18785728 TCATCCCTCTCATCTCTCATCCTT
1 TCATCCCTCTCATC-CTCATCCTT
*
18785752 TCATCTCTCTCATCCTCATCC
1 TCATCCCTCTCATCCTCATCC
18785773 CTCAGCTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (23 bp):
TCATCCCTCTCATCCTCATCCTT
Found at i:18785770 original size:15 final size:16
Alignment explanation
Indices: 18785720--18785771 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
18785710 CACTTTTTCA
*
18785720 ATCATCCCTCATCCCTC
1 ATCATCTCTCAT-CCTC
18785737 -TCATCTCTCATCCTTTC
1 ATCATCTCTCATCC--TC
18785754 ATC-TCTCTCATCCTC
1 ATCATCTCTCATCCTC
18785769 ATC
1 ATC
18785772 CCTCAGCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 7 0.23
16 10 0.32
17 12 0.39
18 2 0.06
ACGTcount: A:0.15, C:0.46, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATCTCTCATCCTC
Found at i:18789952 original size:3 final size:3
Alignment explanation
Indices: 18789940--18789986 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
18789930 AATTCTTCCC
18789940 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
18789987 CAAACATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:18792997 original size:22 final size:22
Alignment explanation
Indices: 18792972--18793016 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
18792962 TTGTATTCAA
18792972 TCCATTTAATCTTATGCATAAT
1 TCCATTTAATCTTATGCATAAT
18792994 TCCATTTAATCTTATGCATAAT
1 TCCATTTAATCTTATGCATAAT
18793016 T
1 T
18793017 TGTGATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (22 bp):
TCCATTTAATCTTATGCATAAT
Found at i:18794008 original size:21 final size:20
Alignment explanation
Indices: 18793982--18794054 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 20
18793972 ATTTCTTAAT
*
18793982 AATATATATTTTATAGATATA
1 AATATATTTTTTATA-ATATA
18794003 AATATATTTTAATTACATATATATA
1 AATATATTTT--TT--ATA-ATATA
*
18794028 AATATATTTATTTACAATATA
1 AATATATTT-TTTATAATATA
18794049 AATATA
1 AATATA
18794055 AAATTATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 20 0.45
22 2 0.05
23 2 0.05
24 2 0.05
25 17 0.39
26 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (20 bp):
AATATATTTTTTATAATATA
Found at i:18794031 original size:25 final size:23
Alignment explanation
Indices: 18793998--18794048 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
18793988 TATTTTATAG
18793998 ATATAAATATATTTTAATTACATAT
1 ATATAAATATA-TTTAATTACA-AT
*
18794023 ATATAAATATATTTATTTACAAT
1 ATATAAATATATTTAATTACAAT
18794046 ATA
1 ATA
18794049 AATATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 9 0.36
25 11 0.44
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAAATATATTTAATTACAAT
Found at i:18796109 original size:37 final size:37
Alignment explanation
Indices: 18796024--18796099 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
18796014 CGAAGAGTAT
18796024 AAGGACTTATGACATATTTTAACCTTAATATATTTAG
1 AAGGACTTATGACATATTTTAACCTTAATATATTTAG
18796061 AAGGACTTATGACATATTTTAACCTTAATATATTTAG
1 AAGGACTTATGACATATTTTAACCTTAATATATTTAG
18796098 AA
1 AA
18796100 ATGTTTATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (37 bp):
AAGGACTTATGACATATTTTAACCTTAATATATTTAG
Found at i:18804390 original size:28 final size:28
Alignment explanation
Indices: 18804348--18804402 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
18804338 AGCATAAAAG
18804348 GAAGGGTAGTAAAACTTAAGTCTTTATA
1 GAAGGGTAGTAAAACTTAAGTCTTTATA
*
18804376 GAAGGGTAGTGAAACTTAAGTCTTTAT
1 GAAGGGTAGTAAAACTTAAGTCTTTAT
18804403 TCATACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (28 bp):
GAAGGGTAGTAAAACTTAAGTCTTTATA
Found at i:18808821 original size:21 final size:22
Alignment explanation
Indices: 18808797--18808841 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
18808787 TTGAATTTTA
18808797 AAATTT-TAAAAATAAAAAATT
1 AAATTTCTAAAAATAAAAAATT
* *
18808818 AAATTTCTAAAAATAGAAATTT
1 AAATTTCTAAAAATAAAAAATT
18808840 AA
1 AA
18808842 GGATTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATTTCTAAAAATAAAAAATT
Found at i:18810757 original size:21 final size:21
Alignment explanation
Indices: 18810720--18810759 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18810710 GTCTATGATG
*
18810720 CTTGTTAAAAAACAAATCTCC
1 CTTGTGAAAAAACAAATCTCC
18810741 CTTGTGAAAGAAA-AAATCT
1 CTTGTGAAA-AAACAAATCT
18810760 TGTGTGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (21 bp):
CTTGTGAAAAAACAAATCTCC
Found at i:18820699 original size:23 final size:21
Alignment explanation
Indices: 18820672--18820717 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 21
18820662 ATGTTAAGTA
18820672 AATATATTATATTATTATATAAT
1 AATATATTATATTA--ATATAAT
18820695 AATATATTATATTAATATAAT
1 AATATATTATATTAATATAAT
18820716 AA
1 AA
18820718 AACAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATATTATATTAATATAAT
Found at i:18820773 original size:20 final size:19
Alignment explanation
Indices: 18820729--18820773 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
18820719 ACAAATAAAT
* *
18820729 AAAAAGAAAAAGGAAATAG
1 AAAAAGAAAAAAGAAACAG
18820748 AAAAAGAAAGAAAGAAACAG
1 AAAAAGAAA-AAAGAAACAG
*
18820768 AGAAAG
1 AAAAAG
18820774 CCAAATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAACAG
Found at i:18827678 original size:38 final size:38
Alignment explanation
Indices: 18827619--18827724 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
18827609 CATTTTTAAG
*
18827619 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
18827656 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
18827694 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
18827725 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:18828116 original size:19 final size:17
Alignment explanation
Indices: 18828092--18828208 Score: 59
Period size: 16 Copynumber: 6.9 Consensus size: 17
18828082 TAATATTAGA
18828092 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
18828111 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
*
18828131 AAAATATATACAATGA-T
1 AAAATATATATAAT-ATT
* * *
18828148 AATATATATAAAAGA-T
1 AAAATATATATAATATT
* *
18828164 -ATATGTATAT-ATAATT
1 AAAATATATATAAT-ATT
*
18828180 -ATATA-ATATAATATT
1 AAAATATATATAATATT
18828195 AAAATATA-ATAATA
1 AAAATATATATAATA
18828209 CGACATAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 19 0.24
17 17 0.21
18 2 0.03
19 8 0.10
20 9 0.11
21 2 0.03
22 6 0.08
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:18828422 original size:3 final size:3
Alignment explanation
Indices: 18828407--18828450 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
18828397 AAGCATAAAC
*
18828407 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18828451 TTGGAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:18828580 original size:3 final size:3
Alignment explanation
Indices: 18828549--18828616 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
18828539 ATACACGTAC
* * * *
18828549 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
18828596 ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
18828617 CAAGGATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:18829097 original size:11 final size:12
Alignment explanation
Indices: 18829081--18829116 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
18829071 GAAAAAAAAA
18829081 GAAGAGAG-AGG
1 GAAGAGAGAAGG
18829092 GAAGAGAGAAGG
1 GAAGAGAGAAGG
18829104 G-AGAGAGAAGG
1 GAAGAGAGAAGG
18829115 GA
1 GA
18829117 GGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:18829277 original size:27 final size:27
Alignment explanation
Indices: 18829227--18829278 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
18829217 ATATTTTTTT
* *
18829227 TTATTTTTTTATGTTTATATTATATTG
1 TTATTTTTATATGTTTATAGTATATTG
* *
18829254 TTATTTTTATATTTTTTTAGTATAT
1 TTATTTTTATATGTTTATAGTATAT
18829279 ATATATGGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (27 bp):
TTATTTTTATATGTTTATAGTATATTG
Found at i:18836110 original size:16 final size:16
Alignment explanation
Indices: 18836089--18836119 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18836079 TGTACTAGTC
*
18836089 TCTTGTCTTGTCAATG
1 TCTTGTCTTGACAATG
18836105 TCTTGTCTTGACAAT
1 TCTTGTCTTGACAAT
18836120 ACTCAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (16 bp):
TCTTGTCTTGACAATG
Found at i:18840684 original size:41 final size:40
Alignment explanation
Indices: 18840495--18840747 Score: 416
Period size: 40 Copynumber: 6.2 Consensus size: 40
18840485 ACATAACTCT
* *
18840495 AGTGTTTGCTATCAGATATGCATATTGACATTGGTGAGACG
1 AGTGTTTGC-AACAGATATGCATATTGACATTGGTGAGATG
18840536 AGTGTTTGCAACAGATATGCATATTGACATTGGTGAGATG
1 AGTGTTTGCAACAGATATGCATATTGACATTGGTGAGATG
*
18840576 AGTGTTTGCAACAGATATGCATATTGACACTGGTGAGATG
1 AGTGTTTGCAACAGATATGCATATTGACATTGGTGAGATG
*
18840616 AGTGTTTGTAACAGATATGCATATTGACATTGGTGAGATG
1 AGTGTTTGCAACAGATATGCATATTGACATTGGTGAGATG
* *
18840656 AGTATTTGCAATCAGATGTGCATATTGACATTGGTGAGATG
1 AGTGTTTGCAA-CAGATATGCATATTGACATTGGTGAGATG
*
18840697 AGTGTTTGCAATCAGATATGCATATTGACATTGGTGAGACG
1 AGTGTTTGCAA-CAGATATGCATATTGACATTGGTGAGATG
18840738 AGTGTTTGCA
1 AGTGTTTGCA
18840748 TATATTTACT
Statistics
Matches: 200, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 115 0.57
41 85 0.43
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (40 bp):
AGTGTTTGCAACAGATATGCATATTGACATTGGTGAGATG
Found at i:18840695 original size:23 final size:23
Alignment explanation
Indices: 18840628--18840696 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
18840618 TGTTTGTAAC
*
18840628 AGATATGCATATTGACATTGGTG
1 AGATGTGCATATTGACATTGGTG
* * * *
18840651 AGATGAGTAT-TTG-CA---ATC
1 AGATGTGCATATTGACATTGGTG
18840669 AGATGTGCATATTGACATTGGTG
1 AGATGTGCATATTGACATTGGTG
18840692 AGATG
1 AGATG
18840697 AGTGTTTGCA
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
18 9 0.28
19 3 0.09
20 2 0.06
21 2 0.06
22 3 0.09
23 13 0.41
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (23 bp):
AGATGTGCATATTGACATTGGTG
Found at i:18846699 original size:289 final size:288
Alignment explanation
Indices: 18846152--18846739 Score: 849
Period size: 289 Copynumber: 2.0 Consensus size: 288
18846142 AGAATAGATA
* * * * *
18846152 TCTAAACAAAAGAAATGTTGTTCAAGGAGGTATATATTTAGATTTAACTAATATTCTTATAGCAG
1 TCTAAACAAAACAAATGTTGCTCAAGGAGGAATATATTTAGATTTAACTAATACTCCTAT---A-
* *
18846217 AGCAGACTATGAAAAAATCATACATGATTGGGCACAATCTATGATTATATTTGTTAACAATAATA
62 AGCAGACTATGAAAAAATCATACATGATTGGGCACAATCTATGACTATATTTGTTAACAATAAGA
*
18846282 TGTGGTCAAAAGAAAAACTTTTAAACTATGTTAGAACATTTTAAGGAGATGTTTTATAATTCCTA
127 TGTGGTCAAAAG-AAAACTTTTAAACTATGTTAGAACATTTCAAGGAGATGTTTTATAATTCCTA
* *
18846347 AGAAGATGGAAAGAATCAAAAAAAAGAAAAGAATAAAAAGGGCAGTTAATCAATCAAATTGGAAC
191 AGAAGATGGAAAGAATCAAAAAAAAGAAAAGAACAAAAAGGGCAGTCAATCAATCAAATTGGAAC
*
18846412 TCTCAAAGATTTATTAAAAGGGTTAACTTTTAT
256 TCCCAAAGATTTATTAAAAGGGTTAACTTTTAT
* *
18846445 TCTAAACAAAACAAATGTTGCTCAAGGAGGAATATATTTAGATTTAATTTATACTCCTAT-AGCA
1 TCTAAACAAAACAAATGTTGCTCAAGGAGGAATATATTTAGATTTAACTAATACTCCTATAAGCA
* *
18846509 GACTATGAAAAAATCATAGATGATTGGGCACAATTTATGACTATATTTGTTAACAATAAGATGTG
66 GACTATGAAAAAATCATACATGATTGGGCACAATCTATGACTATATTTGTTAACAATAAGATGTG
* *
18846574 GTCAAAAG-AAATTTTTAAACTACTTTGTTGGAACATTTCAAGGAGATGTTTTATAATTCCTAAG
131 GTCAAAAGAAAACTTTTAAACTA---TGTTAGAACATTTCAAGGAGATGTTTTATAATTCCTAAG
* * * * * *
18846638 AAGAT-GAGAAGAATCAGAATAAGGAAAAGAACAGAAAGGGTAGTCAATCAATCAGATTGGAACT
193 AAGATGGA-AAGAATCAAAAAAAAGAAAAGAACAAAAAGGGCAGTCAATCAATCAAATTGGAACT
* *
18846702 CCCAAAGGTTTATTAAAATGGTTAACTTTTAT
257 CCCAAAGATTTATTAAAAGGGTTAACTTTTAT
18846734 TCTAAA
1 TCTAAA
18846740 AACAGGATCT
Statistics
Matches: 266, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
286 13 0.05
288 75 0.28
289 125 0.47
293 53 0.20
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (288 bp):
TCTAAACAAAACAAATGTTGCTCAAGGAGGAATATATTTAGATTTAACTAATACTCCTATAAGCA
GACTATGAAAAAATCATACATGATTGGGCACAATCTATGACTATATTTGTTAACAATAAGATGTG
GTCAAAAGAAAACTTTTAAACTATGTTAGAACATTTCAAGGAGATGTTTTATAATTCCTAAGAAG
ATGGAAAGAATCAAAAAAAAGAAAAGAACAAAAAGGGCAGTCAATCAATCAAATTGGAACTCCCA
AAGATTTATTAAAAGGGTTAACTTTTAT
Found at i:18868752 original size:21 final size:21
Alignment explanation
Indices: 18868728--18868767 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18868718 AAACTTTTAA
18868728 TCGAT-CCCAATCAAATTAACT
1 TCGATACCCAATC-AATTAACT
*
18868749 TCGATAGCCAATCAATTAA
1 TCGATACCCAATCAATTAA
18868768 TCAAACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (21 bp):
TCGATACCCAATCAATTAACT
Found at i:18870885 original size:23 final size:23
Alignment explanation
Indices: 18870822--18870893 Score: 101
Period size: 24 Copynumber: 3.1 Consensus size: 23
18870812 TTTTAATTCA
18870822 TTAAAGTTAGCCCATTTATTTATT
1 TTAAAGTTAGCCCATTTATTT-TT
* *
18870846 TTAAATTTAGTCC-TTTATTTTT
1 TTAAAGTTAGCCCATTTATTTTT
18870868 TTAAAGTTAGCCCATTTATATTTT
1 TTAAAGTTAGCCCATTTAT-TTTT
18870892 TT
1 TT
18870894 TCTATTACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.31
23 12 0.29
24 17 0.40
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (23 bp):
TTAAAGTTAGCCCATTTATTTTT
Found at i:18871062 original size:21 final size:22
Alignment explanation
Indices: 18871037--18871103 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
18871027 ATTTTATGTA
18871037 ATTATATTATTATCATAC-ATT
1 ATTATATTATTATCATACTATT
*
18871058 TTTATATTATT-TC--ACTATT
1 ATTATATTATTATCATACTATT
*
18871077 ATTATCATTATTATCATA-TAGT
1 ATTAT-ATTATTATCATACTATT
18871099 ATTAT
1 ATTAT
18871104 TAATTGAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
20 8 0.21
21 12 0.32
22 8 0.21
23 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.55
Consensus pattern (22 bp):
ATTATATTATTATCATACTATT
Found at i:18877120 original size:86 final size:84
Alignment explanation
Indices: 18876961--18877238 Score: 430
Period size: 84 Copynumber: 3.3 Consensus size: 84
18876951 TTTCAATCTT
* *
18876961 GTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCAC
1 GTTTTTAGAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCAC
18877026 AGCTGTAATATTTAGTGGC
66 AGCTGTAATATTTAGTGGC
* * ** *
18877045 GTTTTTAGGAAAACGCCACAAACAATGCTTGTTCCAGACCACGCAAAATGGTGTCGTTTCTGTTC
1 GTTTTTAGAAAAACGCCACAAAAAATGC-AATTCCAGACCACG-AAAACGGTGTCGTTTCTGTTC
18877110 ACAGCTGTAATATTTAGTGGC
64 ACAGCTGTAATATTTAGTGGC
** *
18877131 GTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTTGTTTCTGTTCAC
1 GTTTTTAGAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCAC
18877196 AGCTGTAATATTTAGTGGC
66 AGCTGTAATATTTAGTGGC
*
18877215 GTTTTTACCAAAAACGCCACAAAA
1 GTTTTTA-GAAAAACGCCACAAAA
18877239 CGGTGTTAAT
Statistics
Matches: 177, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
84 73 0.41
85 39 0.22
86 65 0.37
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (84 bp):
GTTTTTAGAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTGTTCAC
AGCTGTAATATTTAGTGGC
Found at i:18877262 original size:84 final size:82
Alignment explanation
Indices: 18877003--18877272 Score: 253
Period size: 86 Copynumber: 3.2 Consensus size: 82
18876993 CCAGACCACG
**
18877003 AAAACGGTGTCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTA-GGAAAACGCCACAAA
1 AAAACGGTGTCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTACCAAAAACGCCACAAA
** *
18877067 CA-ATGCTTGTTCCAGACCACGC
66 -AGATG-TTAAT--ATA--ACGC
* *
18877089 AAAATGGTGTCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTT-CTAAAAACGCCACAAA
1 AAAACGGTGTCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTACCAAAAACGCCACAAA
* * *
18877153 AAATG-CAAT-TCCAGACCAC
66 AGATGTTAATAT--A-A-CGC
*
18877172 GAAAACGGTGTTGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTACCAAAAACGCCACAA
1 -AAAACGGTGTCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTACCAAAAACGCCACAA
*
18877237 AACGGTGTTAATATAATCGC
65 AA-GATGTTAATATAA-CGC
* **
18877257 TAAACGACGTCGTTTC
1 AAAACGGTGTCGTTTC
18877273 CGGAACAGAT
Statistics
Matches: 153, Mismatches: 21, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
82 1 0.01
83 3 0.02
84 59 0.39
85 20 0.13
86 66 0.43
87 3 0.02
88 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (82 bp):
AAAACGGTGTCGTTTCTGTTCACAGCTGTAATATTTAGTGGCGTTTTTACCAAAAACGCCACAAA
AGATGTTAATATAACGC
Found at i:18878465 original size:11 final size:11
Alignment explanation
Indices: 18878445--18878473 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18878435 GAATATCTCA
18878445 AACT-ATGGGT
1 AACTAATGGGT
18878455 AACTAATGGGT
1 AACTAATGGGT
18878466 AACTAATG
1 AACTAATG
18878474 TATTATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:18878681 original size:13 final size:13
Alignment explanation
Indices: 18878663--18878764 Score: 73
Period size: 13 Copynumber: 7.5 Consensus size: 13
18878653 TAGACAAGAG
*
18878663 ATACTAATGCATA
1 ATACTAGTGCATA
18878676 ATACTAGTGCATA
1 ATACTAGTGCATA
18878689 ATACTAGTGCAATA
1 ATACTAGTGC-ATA
* *
18878703 CTACTACTGCACATA
1 ATACTAGTG--CATA
* *
18878718 TTACTA--ACAATCA
1 ATACTAGTGC-AT-A
*
18878731 CCTTACTAGTGCATA
1 --ATACTAGTGCATA
18878746 ATACTAGTGCATA
1 ATACTAGTGCATA
18878759 ATACTA
1 ATACTA
18878765 ATTCTTTCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
11 1 0.01
12 2 0.03
13 41 0.56
14 10 0.14
15 15 0.21
16 3 0.04
17 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (13 bp):
ATACTAGTGCATA
Found at i:18880285 original size:21 final size:21
Alignment explanation
Indices: 18880259--18880304 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
18880249 CTACAACTTA
18880259 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCGGAAGCGAGGG
* * *
18880280 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCGGAAGCGAGGG
18880301 AAGC
1 AAGC
18880305 GGAAGCTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.48, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGAAGCGAGGG
Found at i:18880312 original size:21 final size:21
Alignment explanation
Indices: 18880272--18880328 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
18880262 CAGAGGCGGA
**
18880272 AGCGAGGGAAGCAGCGGCTGC
1 AGCGAGGGAAGCAGAAGCTGC
*
18880293 AGCGAGGGAAGCGGAAGCTGC
1 AGCGAGGGAAGCAGAAGCTGC
* *
18880314 AACGAGAGAAGCAGA
1 AGCGAGGGAAGCAGA
18880329 GCAGAGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.44, T:0.04
Consensus pattern (21 bp):
AGCGAGGGAAGCAGAAGCTGC
Found at i:18880755 original size:42 final size:42
Alignment explanation
Indices: 18880646--18880901 Score: 237
Period size: 42 Copynumber: 6.1 Consensus size: 42
18880636 TAGTGGCGTT
* *
18880646 TTTGTATAAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCG
1 TTTGTATAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* *
18880688 TTTGTAAAAAAAATGCCACTAAAGAACATGTTCTTTAGCGGCG
1 TTTGT-ATAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* * * * * *
18880731 CTTGTAGAAAAACGCCGCTAAAGAACACGTTCTTTAGAGGTG
1 TTTGTATAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* * * *
18880773 CTTAGGA-AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCG
1 -TTTGTATAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* * * * * *
18880815 TTTTTCCT-TAAGCGCCGCTAAAGAACATGTTCTTTAGTGGCG
1 TTTGT-ATAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* * ** * *
18880857 TTTTTTTCTAAGCGCCACTAAAGAACATGGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
18880899 TTT
1 TTT
18880902 TTGTTTGTAA
Statistics
Matches: 179, Mismatches: 30, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
41 3 0.02
42 136 0.76
43 40 0.22
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
TTTGTATAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
Found at i:18881772 original size:38 final size:39
Alignment explanation
Indices: 18881684--18881782 Score: 137
Period size: 38 Copynumber: 2.6 Consensus size: 39
18881674 CTTGTAAGTA
* * *
18881684 AAAAGTTGCGATCGTAAATCAACGGACCGTGAGAAAGCC
1 AAAAGTTGTGATCGTAAATCAGCAGACCGTGAGAAAGCC
* *
18881723 AAAGGTCGTGATCGTAAATCAGCAGACCGT-AGAAAGCC
1 AAAAGTTGTGATCGTAAATCAGCAGACCGTGAGAAAGCC
*
18881761 AAAAGTTGTGATCATAAATCAG
1 AAAAGTTGTGATCGTAAATCAG
18881783 TGGACCACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 27 0.52
39 25 0.48
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (39 bp):
AAAAGTTGTGATCGTAAATCAGCAGACCGTGAGAAAGCC
Found at i:18881948 original size:93 final size:92
Alignment explanation
Indices: 18881834--18882063 Score: 262
Period size: 93 Copynumber: 2.5 Consensus size: 92
18881824 GATCATACCG
* *
18881834 CGAGATTCATAAAATCTCGTAAGTAAAAGGTAATGATCATAAATCAACGGACCGTAAGAAAGTCA
1 CGAGATTCATAAAATC-CGTAAGTAAAAGGTAATGATCATAAATCAACGGACCGTAAAAAAGCCA
*
18881899 AATGTCATAATCGTAAATCAACGGACCA
65 AAGGTCATAATCGTAAATCAACGGACCA
* * * * * **
18881927 CGAGATTCATAAAATACCGTAAGTAAAAGATTATGATCGTAAATTAGCGGATTGTAAAAAAGCCA
1 CGAGATTCATAAAAT-CCGTAAGTAAAAGGTAATGATCATAAATCAACGGACCGTAAAAAAGCCA
** * * **
18881992 AAGGTTGTTATCGTAAATCAGCGGACTG
65 AAGGTCATAATCGTAAATCAACGGACCA
* **
18882020 CGAGATTCATAAAATCCTGTGAGTAAAAGGTCGTGATCATAAAT
1 CGAGATTCATAAAATCC-GTAAGTAAAAGGTAATGATCATAAAT
18882064 GTTACACTCC
Statistics
Matches: 114, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
92 2 0.02
93 111 0.97
94 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (92 bp):
CGAGATTCATAAAATCCGTAAGTAAAAGGTAATGATCATAAATCAACGGACCGTAAAAAAGCCAA
AGGTCATAATCGTAAATCAACGGACCA
Found at i:18890682 original size:13 final size:14
Alignment explanation
Indices: 18890666--18890694 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18890656 GTGTTGTGTG
18890666 ATGA-TTTTGTTAA
1 ATGAGTTTTGTTAA
18890679 ATGAGTTTTGTTAA
1 ATGAGTTTTGTTAA
18890693 AT
1 AT
18890695 ATTGATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (14 bp):
ATGAGTTTTGTTAA
Found at i:18892707 original size:46 final size:46
Alignment explanation
Indices: 18892606--18892931 Score: 383
Period size: 46 Copynumber: 7.6 Consensus size: 46
18892596 TATGTATGAT
*
18892606 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
18892649 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
18892695 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
18892741 CACTTATCACTTTGTCACTTGATAAGATAA--GTA--T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
18892777 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
18892823 CACTTATCACTTTGTCTCTTGAACAGATAA--GT-G-T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
18892859 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
18892905 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
18892932 AGTACTCAAA
Statistics
Matches: 245, Mismatches: 15, Indels: 43
0.81 0.05 0.14
Matches are distributed among these distances:
36 55 0.22
38 5 0.02
39 1 0.00
40 4 0.02
41 4 0.02
42 4 0.02
43 11 0.04
44 10 0.04
45 20 0.08
46 131 0.53
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:18892782 original size:36 final size:36
Alignment explanation
Indices: 18892741--18892895 Score: 141
Period size: 36 Copynumber: 4.0 Consensus size: 36
18892731 CTAAGGCTAA
18892741 CACTTATCACTTTGTCACTTGATAAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATAAGATAAGTATAG
* *
18892777 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATAAGATAA--GTA--T--AG
* *
18892819 CTACCACTTATCACTTTGTCTCTTGA-ACAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATA-AGATAAGTATAG
* * *
18892859 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATAAGATAAGTATAG
18892895 C
1 C
18892896 TAAAGCTACC
Statistics
Matches: 98, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
36 61 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 26 0.27
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATAAGATAAGTATAG
Found at i:18892832 original size:82 final size:83
Alignment explanation
Indices: 18892695--18892931 Score: 399
Period size: 82 Copynumber: 2.9 Consensus size: 83
18892685 CTAAGGCTAC
* * * *
18892695 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
18892760 TGATA-AGATAAGTATAG
66 TGATACAGATAAGTATAG
18892777 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
18892842 TGA-ACAGATAAGTGTAG
66 TGATACAGATAAGTATAG
*
18892859 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
18892924 TGAT-CAGA
66 TGATACAGA
18892932 AGTACTCAAA
Statistics
Matches: 147, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
81 1 0.01
82 146 0.99
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (83 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATACAGATAAGTATAG
Found at i:18892909 original size:128 final size:126
Alignment explanation
Indices: 18892606--18892931 Score: 374
Period size: 128 Copynumber: 2.6 Consensus size: 126
18892596 TATGTATGAT
* * * *
18892606 CACTTATCACTTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTG
1 CACTTATCACTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTTG
* *
18892670 ATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAG
66 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTGAACAGATAAGTGTAG
* ** * * * * * *
18892731 CTAAGGC-TAACACTTATCACTTTG-TCACTTGA-T-AAGATAAGTATAGCACTTATCACTTTTT
1 C--A--CTTATCACTTATCAC-TTGATCAGATAAGTGTAGCTAAG-CTACCACTTATCACTTTAT
* *
18892792 CACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGAACAGATAAGTGT
60 CACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTGAACAGATAAGTGT
18892857 AG
125 AG
* *
18892859 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCAC-TTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTATCACT
18892924 TGATCAGA
64 TGATCAGA
18892932 AGTACTCAAA
Statistics
Matches: 161, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
124 1 0.01
125 9 0.06
126 12 0.07
127 7 0.04
128 120 0.75
129 10 0.06
130 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (126 bp):
CACTTATCACTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTTG
ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTGAACAGATAAGTGTAG
Found at i:18898709 original size:36 final size:36
Alignment explanation
Indices: 18898662--18898802 Score: 140
Period size: 36 Copynumber: 3.6 Consensus size: 36
18898652 AAAATAGTTA
18898662 TCACTTGATCAGATAAGTATAGCACTTATCACTTTT
1 TCACTTGATCAGATAAGTATAGCACTTATCACTTTT
*
18898698 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTG
1 TCACTTGATCAGATAA--GTA--T--AG----CACTTATCACTTTT
* *
18898744 TCTA-TTGATCAGATAAGTGTAACACTTATCACTTTT
1 TC-ACTTGATCAGATAAGTATAGCACTTATCACTTTT
*
18898780 TCACTTGATCAGATAAGTGTAGC
1 TCACTTGATCAGATAAGTATAGC
18898803 TAAAGCTACC
Statistics
Matches: 88, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
35 1 0.01
36 49 0.56
38 3 0.03
40 2 0.02
42 3 0.03
44 2 0.02
46 27 0.31
47 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (36 bp):
TCACTTGATCAGATAAGTATAGCACTTATCACTTTT
Found at i:18898752 original size:46 final size:46
Alignment explanation
Indices: 18898684--18898838 Score: 197
Period size: 46 Copynumber: 3.6 Consensus size: 46
18898674 ATAAGTATAG
18898684 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
18898730 CACTTATCACTTTGTCTA-TTGATCAGATAA--GT-G-T--A---A-
1 CACTTATCACTTTTTC-ACTTGATCAGATAAGTGTAGCTAAAGCTAC
18898766 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
18898812 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
18898839 AGTACTCAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
35 1 0.01
36 27 0.29
37 1 0.01
38 2 0.02
39 1 0.01
40 2 0.02
42 2 0.02
43 1 0.01
44 2 0.02
45 1 0.01
46 52 0.56
47 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:18898803 original size:82 final size:82
Alignment explanation
Indices: 18898666--18898838 Score: 310
Period size: 82 Copynumber: 2.1 Consensus size: 82
18898656 TAGTTATCAC
*
18898666 TTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
1 TTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
*
18898731 ACTTATCACTTTGTCTA
66 ACTTATCACTTTATCTA
*
18898748 TTGATCAGATAAGTGTAACACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
1 TTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
*
18898813 ACTTATCACTTTATCTC
66 ACTTATCACTTTATCTA
18898830 TTGATCAGA
1 TTGATCAGA
18898839 AGTACTCAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 87 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (82 bp):
TTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
ACTTATCACTTTATCTA
Found at i:18907133 original size:48 final size:48
Alignment explanation
Indices: 18907054--18907145 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
18907044 TTATGCAATG
* *
18907054 CTAAACTTGGTTTTCCACTATCTACATTCTTATCACTATTTATCATTA
1 CTAAACTTGGTCTTCCACTATCTACACTCTTATCACTATTTATCATTA
* * *
18907102 CTAAACTTGGTCTTCCACTGTGTACACTCTTATCATTATTTATC
1 CTAAACTTGGTCTTCCACTATCTACACTCTTATCACTATTTATC
18907146 CCTTCTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.45
Consensus pattern (48 bp):
CTAAACTTGGTCTTCCACTATCTACACTCTTATCACTATTTATCATTA
Found at i:18909572 original size:5 final size:5
Alignment explanation
Indices: 18909562--18909600 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
18909552 CGCTCTTTCC
18909562 TTCTT TTC-T TTC-T TTCTT TTCTT TTCTT TTC-T TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
18909601 TTAATTTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:18909574 original size:9 final size:9
Alignment explanation
Indices: 18909566--18909600 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
18909556 CTTTCCTTCT
18909566 TTTC-TTTC
1 TTTCTTTTC
18909574 TTTCTTTTC
1 TTTCTTTTC
18909583 TTTTCTTTTC
1 -TTTCTTTTC
18909593 TTTCTTTT
1 TTTCTTTT
18909601 TTAATTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 4 0.16
9 12 0.48
10 9 0.36
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:18915677 original size:10 final size:10
Alignment explanation
Indices: 18915661--18915696 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
18915651 AACTATTTAA
18915661 ATATTTTATT
1 ATATTTTATT
*
18915671 TTATTTTATT
1 ATATTTTATT
18915681 ATATTTTATT
1 ATATTTTATT
18915691 AT-TTTT
1 ATATTTT
18915697 CAATGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
ATATTTTATT
Found at i:18933833 original size:19 final size:21
Alignment explanation
Indices: 18933791--18933843 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 21
18933781 ATTTCTTTTT
18933791 TGCATT-CATTTCATGCATCA
1 TGCATTACATTTCATGCATCA
18933811 -GCATTACATTTCAT-CAT-A
1 TGCATTACATTTCATGCATCA
*
18933829 TGCATTAAATTTCAT
1 TGCATTACATTTCAT
18933844 AAAAAGACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 21 0.70
20 8 0.27
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.42
Consensus pattern (21 bp):
TGCATTACATTTCATGCATCA
Found at i:18947532 original size:44 final size:44
Alignment explanation
Indices: 18947410--18947910 Score: 414
Period size: 44 Copynumber: 11.0 Consensus size: 44
18947400 GTCTCCATAG
* * *
18947410 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
18947454 CCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
1 -CA-----AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
* * *
18947504 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
* * * * * *
18947548 CAGATCTTATCTCCCTAAAATTGTAGTGGAGTAGATTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
* * *
18947592 -ATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
1 CA--AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
* * * * * *
18947637 GCAAATCTTATCTTCTTGGAGTTGCAATGGAGCAGATTGAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
* *
18947682 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
* * * * * * * * * * *
18947726 CGAGTCTTATTTCCTTAAAATTGCAGTGG-GACAAACTAAGGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-TAGATTAAAGCTA
* * * * * *
18947770 CAAATTTTATCTCTCTGAAGTTGCAGTAGACCAGATTAAAACTAAAACCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGT-G----GAGT-AGA-TTAAAGCTA
* *
18947821 CAAATCTTATCTCCATGAAGTTGCAGTGGAGTAGATTACAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
** *
18947865 CAAATCTTATCTCCCTGAAGTTATAGCGGAGTAGATTGAAA-CTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT-AAAGCTA
18947909 CA
1 CA
18947911 CTTCCCATAC
Statistics
Matches: 371, Mismatches: 66, Indels: 39
0.78 0.14 0.08
Matches are distributed among these distances:
43 2 0.01
44 210 0.57
45 81 0.22
46 3 0.01
47 1 0.00
49 3 0.01
50 43 0.12
51 28 0.08
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTA
Found at i:18947716 original size:178 final size:179
Alignment explanation
Indices: 18947412--18947909 Score: 495
Period size: 183 Copynumber: 2.7 Consensus size: 179
18947402 CTCCATAGCA
* * * *
18947412 AATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGTTACCATGGCGAATCTTATCTCCCTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG----CATAGCAAATCTTATCTCCCTG
* * **
18947477 AAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTA
62 AAGTTGCAATGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAATTACAGTGGAGCAGATTA
*
18947542 AAGCTAC-AGATCTTATCTCCCTAAAATTGTAGTGGAGTAGATTGAAGATAATG
127 AAGCTACGAG-TCTTATCTCCCTAAAATTGCAGTGGAGTAGATTGAAGATAATG
* * *
18947595 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-ATAGCAAATCTTATCTTCTTGGAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCAAATCTTATCTCCCTGAAGT
* *
18947659 TGCAATGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGC
66 TGCAATGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAATTACAGTGGAGCAGATTAAAGC
* * * * * *** **
18947724 TACGAGTCTTATTTCCTTAAAATTGCAGTGG-GACAAACT-AAGGCCACA
131 TACGAGTCTTATCTCCCTAAAATTGCAGTGGAG-TAGATTGAAGATAATG
* * * * * * *
18947772 AATTTTATCTCTCTGAAGTTGCAGTAGACCAGATTAAAACTAAAACCTA-CAAATCTTATCTCCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC----A--TAGCAAATCTTATCTCCC
* * * * * * *
18947836 TGAAGTTGCAGTGGAGTAGATTACAGCTACAAATCTTATCTCCCTGAAGTTATAGCGGAGTAGAT
60 TGAAGTTGCAATGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAATTACAGTGGAGCAGAT
18947901 TGAAA-CTAC
125 T-AAAGCTAC
18947910 ACTTCCCATA
Statistics
Matches: 265, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
177 38 0.14
178 107 0.40
179 2 0.01
182 1 0.00
183 112 0.42
184 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (179 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCAAATCTTATCTCCCTGAAGT
TGCAATGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAATTACAGTGGAGCAGATTAAAGC
TACGAGTCTTATCTCCCTAAAATTGCAGTGGAGTAGATTGAAGATAATG
Found at i:18949493 original size:52 final size:52
Alignment explanation
Indices: 18949437--18949653 Score: 220
Period size: 52 Copynumber: 4.2 Consensus size: 52
18949427 ATTCAGTCCC
18949437 TTATTTATTTAATTTCAGCCTTTCATGAATTTTTTTATTATTTACTTATTTA
1 TTATTTATTTAATTTCAGCCTTTCATGAATTTTTTTATTATTTACTTATTTA
* *
18949489 TTATTGCA---ACTTT-AGCCTTTCATGAA-TTTTTTATTATTTACTTATTTA
1 TTATT-TATTTAATTTCAGCCTTTCATGAATTTTTTTATTATTTACTTATTTA
* * *
18949537 TT-TATTATTGTAATTTTAGCCTTTCATGAATTTTTTTATT-TTTAATTACTTA
1 TTAT-TTATT-TAATTTCAGCCTTTCATGAATTTTTTTATTATTTACTTATTTA
* * *
18949589 TT-TATTATTACAATTTCAACCTTTCATGAATTTTTTTA--CTTTACTATTATTTA
1 TTAT-TTATT-TAATTTCAGCCTTTCATGAATTTTTTTATTATTTAC--TTATTTA
18949642 CTTATTTATTTA
1 -TTATTTATTTA
18949654 TTGTTGCCTT
Statistics
Matches: 139, Mismatches: 13, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
47 2 0.01
48 25 0.18
49 13 0.09
50 4 0.03
51 8 0.06
52 62 0.45
53 17 0.12
54 7 0.05
55 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (52 bp):
TTATTTATTTAATTTCAGCCTTTCATGAATTTTTTTATTATTTACTTATTTA
Found at i:18949528 original size:26 final size:25
Alignment explanation
Indices: 18949499--18949580 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
18949489 TTATTGCAAC
18949499 TTTAGCCTTTCATGAATTTTTTATT
1 TTTAGCCTTTCATGAATTTTTTATT
* * ** * *
18949524 ATTTA-CTTATTTATTTATTATTGTAAT
1 -TTTAGCCT-TTCATGAATT-TTTTATT
18949551 TTTAGCCTTTCATGAATTTTTTTATT
1 TTTAGCCTTTCATGAA-TTTTTTATT
18949577 TTTA
1 TTTA
18949581 ATTACTTATT
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
25 2 0.05
26 29 0.73
27 9 0.22
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.62
Consensus pattern (25 bp):
TTTAGCCTTTCATGAATTTTTTATT
Found at i:18949561 original size:101 final size:99
Alignment explanation
Indices: 18949441--18949649 Score: 282
Period size: 101 Copynumber: 2.1 Consensus size: 99
18949431 AGTCCCTTAT
* * *
18949441 TTATTTAATTTCAGCCTTTCATGAATTTTTTTA-TTATTTACTTATTTATTATTGCAACTTT-AG
1 TTATTTAATTTCAGCCTTTCATGAATTTTTTTATTTAATTACTTATTTATTATTACAA-TTTCAA
18949504 CCTTTCATGAATTTTTTATTA-TTTACTTATTTATTTA-
65 CCTTTCATGAA-TTTTT-TTACTTTAC-TA-TTATTTAC
*
18949541 TTATTGTAATTTTAGCCTTTCATGAATTTTTTTATTTTTAATTACTTATTTATTATTACAATTTC
1 TTATT-TAATTTCAGCCTTTCATGAATTTTTTTA--TTTAATTACTTATTTATTATTACAATTTC
18949606 AACCTTTCATGAATTTTTTTACTTTACTATTATTTAC
63 AACCTTTCATGAATTTTTTTACTTTACTATTATTTAC
18949643 TTATTTA
1 TTATTTA
18949650 TTTATTGTTG
Statistics
Matches: 98, Mismatches: 4, Indels: 13
0.85 0.03 0.11
Matches are distributed among these distances:
100 5 0.05
101 36 0.37
102 10 0.10
103 13 0.13
104 34 0.35
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (99 bp):
TTATTTAATTTCAGCCTTTCATGAATTTTTTTATTTAATTACTTATTTATTATTACAATTTCAAC
CTTTCATGAATTTTTTTACTTTACTATTATTTAC
Found at i:18949663 original size:104 final size:100
Alignment explanation
Indices: 18949436--18949663 Score: 277
Period size: 104 Copynumber: 2.2 Consensus size: 100
18949426 GATTCAGTCC
* * *
18949436 CTTATTTATTTAATTTCAGCCTTTCATGAATTTTTTTATTATTTACTTATTTATTATTGCAACTT
1 CTTATTTATTTAATTT-TGCCTTTCATGAATTTTTTTATTAATTACTTATTTATTATTACAACTT
*
18949501 TAGCCTTTCATGAATTTTTTATTATTTACTTATTTA
65 TAACCTTTCATGAATTTTTTATTATTTACTTATTTA
*
18949537 TTTA-TTATTGTAATTTTAGCCTTTCATGAATTTTTTTATTTTTAATTACTTATTTATTATTACA
1 CTTATTTATT-TAATTTT-GCCTTTCATGAATTTTTTTA---TTAATTACTTATTTATTATTACA
18949601 A-TTTCAACCTTTCATGAA-TTTTT-TTACTTTACTATTATTTA
61 ACTTT-AACCTTTCATGAATTTTTTATTA-TTTAC--TTATTTA
18949642 CTTATTTATTT-ATTGTTGCCTT
1 CTTATTTATTTAATT-TTGCCTT
18949664 ACCGTTTATT
Statistics
Matches: 110, Mismatches: 6, Indels: 19
0.81 0.04 0.14
Matches are distributed among these distances:
100 5 0.05
101 29 0.26
102 3 0.03
103 13 0.12
104 42 0.38
105 13 0.12
106 5 0.05
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (100 bp):
CTTATTTATTTAATTTTGCCTTTCATGAATTTTTTTATTAATTACTTATTTATTATTACAACTTT
AACCTTTCATGAATTTTTTATTATTTACTTATTTA
Found at i:18951557 original size:7 final size:7
Alignment explanation
Indices: 18951545--18951569 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18951535 AAACCACTAA
18951545 TTCTGGG
1 TTCTGGG
18951552 TTCTGGG
1 TTCTGGG
18951559 TTCTGGG
1 TTCTGGG
18951566 TTCT
1 TTCT
18951570 AATAAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (7 bp):
TTCTGGG
Found at i:18960986 original size:120 final size:120
Alignment explanation
Indices: 18960843--18961082 Score: 444
Period size: 120 Copynumber: 2.0 Consensus size: 120
18960833 TACAATCATT
*
18960843 AGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATCATAAT
1 AGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAAT
* *
18960908 TATTTTAAATTATATTTTATAGTATAATATATTATGATTTTAGTAAATTCATATA
66 TATTTTAAATTATATTTTATAATATAATATATTATAATTTTAGTAAATTCATATA
18960963 AGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAAT
1 AGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAAT
*
18961028 TATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATATA
66 TATTTTAAATTATATTTTATAATATAATATATTATAATTTTAGTAAATTCATATA
18961083 TTCTATTAAA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (120 bp):
AGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAAT
TATTTTAAATTATATTTTATAATATAATATATTATAATTTTAGTAAATTCATATA
Found at i:18961035 original size:26 final size:25
Alignment explanation
Indices: 18960997--18961055 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
18960987 ATTAAATTAT
*
18960997 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
18961023 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
18961049 ATATTAT
1 ATATTAT
18961056 ATATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:18961054 original size:15 final size:15
Alignment explanation
Indices: 18961010--18961065 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
18961000 TTTTTGTTAA
*
18961010 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
18961025 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
18961036 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
18961051 ATTATATATTATAAT
1 ATTATATTTTATAAT
18961066 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:18961307 original size:21 final size:21
Alignment explanation
Indices: 18961282--18961334 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
18961272 CGTTGTTTCT
*
18961282 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
18961303 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
18961324 AATCTCACCGC
1 AATCTCACCGC
18961335 CACCGTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:18962432 original size:11 final size:11
Alignment explanation
Indices: 18962411--18962471 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
18962401 ACTAATCCTA
18962411 TCTCAAATTTCC
1 TCTC-AATTTCC
* *
18962423 TCCCAATTTCT
1 TCTCAATTTCC
*
18962434 TCTAAATTTCC
1 TCTCAATTTCC
*
18962445 TCTCAATTTGC
1 TCTCAATTTCC
*
18962456 TCTCAAATTCC
1 TCTCAATTTCC
18962467 T-TCAA
1 TCTCAA
18962472 AATTTCTCTC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
10 4 0.10
11 33 0.82
12 3 0.08
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.43
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:18962466 original size:22 final size:22
Alignment explanation
Indices: 18962411--18962485 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 22
18962401 ACTAATCCTA
*
18962411 TCTCAAATTTCCTCCCAATTTC
1 TCTCAAATTTCCTCTCAATTTC
18962433 T-TCTAAATTTCCTCTCAATTTGC
1 TCTC-AAATTTCCTCTCAATTT-C
18962456 TCTCAAA-TTCCT-TCAAAATTTC
1 TCTCAAATTTCCTCTC--AATTTC
18962478 TCTCAAAT
1 TCTCAAAT
18962486 CCATATTTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
21 4 0.09
22 30 0.65
23 10 0.22
24 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.01, T:0.43
Consensus pattern (22 bp):
TCTCAAATTTCCTCTCAATTTC
Found at i:18962485 original size:11 final size:11
Alignment explanation
Indices: 18962411--18962485 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
18962401 ACTAATCCTA
18962411 TCTCAAATTTC
1 TCTCAAATTTC
*
18962422 -CTCCCAATTTC
1 TCT-CAAATTTC
18962433 T-TCTAAATTTCC
1 TCTC-AAATTT-C
18962445 TCTC-AATTTGC
1 TCTCAAATTT-C
*
18962456 TCTCAAATTCC
1 TCTCAAATTTC
18962467 T-TCAAAATTTC
1 TCTC-AAATTTC
18962478 TCTCAAAT
1 TCTCAAAT
18962486 CCATATTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
10 5 0.10
11 36 0.71
12 8 0.16
13 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.01, T:0.43
Consensus pattern (11 bp):
TCTCAAATTTC
Found at i:18962504 original size:51 final size:51
Alignment explanation
Indices: 18962447--18962544 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
18962437 AAATTTCCTC
18962447 TCAATTTGCTCTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCTCAAATTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
* * * * *
18962498 TCAATTTGCTCTCAAGTTCCTCTTAAATTTTTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTT
18962545 TTAAATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:18962566 original size:10 final size:10
Alignment explanation
Indices: 18962542--18962588 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
18962532 TAAATCCCTA
*
18962542 TTTTTAAATA
1 TTTTTAAATT
*
18962552 ATTTTAAATT
1 TTTTTAAATT
*
18962562 TTTTT-TATT
1 TTTTTAAATT
*
18962571 TTTTTAAACT
1 TTTTTAAATT
18962581 TTTTTAAA
1 TTTTTAAA
18962589 CCGTAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTTAAATT
Done.