Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 35 of 290
Found at i:11851264 original size:94 final size:89
Alignment explanation
Indices: 11851068--11851287 Score: 212
Period size: 94 Copynumber: 2.4 Consensus size: 89
11851058 CGAGTCAGGT
* *
11851068 GCCGATGTCATGTCTCAGACATGGTCTTACACTAACACATCTCGTAGCCGATGCATGTCCCAGAC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAACACATCTCATAGCCGATGCATGTCCCAGAC
*
11851133 ATGTCTTACACTAGCTTACATCGCAAG
64 ATGTCTTACACTAGCTTAAATCG-AAG
* * * *
11851160 GCCAAAGCATGTCCCAGACATGTCTTACACTAGCACTTGTCTCA-ATGCCGATGCCATGTCCCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAACAC--ATCTCATA-GCCGATG-CATGTCCCAG
* *
11851224 ACATGGTCTTACACTGGCTCTTAAAAT-G-TG
62 ACAT-GTCTTACACTAG--CTT-AAATCGAAG
* * *
11851254 GCCGATGCATGTTCCAGACATGCCTTACGCTAAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAAC
11851288 TCACATTTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
90 14 0.13
91 14 0.13
92 16 0.15
93 14 0.13
94 40 0.38
96 4 0.04
97 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (89 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAACACATCTCATAGCCGATGCATGTCCCAGACAT
GTCTTACACTAGCTTAAATCGAAG
Found at i:11856464 original size:21 final size:21
Alignment explanation
Indices: 11856440--11856481 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11856430 TCCCCCACCT
*
11856440 CCCCCGATTCCTCAAGCTGTA
1 CCCCCGATGCCTCAAGCTGTA
*
11856461 CCCCCGATGCCTCAAGGTGTA
1 CCCCCGATGCCTCAAGCTGTA
11856482 GATCTGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
CCCCCGATGCCTCAAGCTGTA
Found at i:11876074 original size:46 final size:44
Alignment explanation
Indices: 11875974--11876081 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
11875964 TGTCTTTGAC
** * * *
11875974 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
* *
11876018 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCTTATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCC--ATATATAAT
11876064 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
11876082 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 30 0.55
46 25 0.45
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:11879259 original size:45 final size:45
Alignment explanation
Indices: 11879208--11879298 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
11879198 TCCCACTGGG
11879208 TTTTCCTAGTAAAGGTTTTTAACAAGACAACTTGTAATAGGAGAT
1 TTTTCCTAGTAAAGGTTTTTAACAAGACAACTTGTAATAGGAGAT
11879253 TTTTCCTAGTAAAGGTTTTTAACAAGACAACTTGTAATAGGAGAT
1 TTTTCCTAGTAAAGGTTTTTAACAAGACAACTTGTAATAGGAGAT
11879298 T
1 T
11879299 ATGTATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (45 bp):
TTTTCCTAGTAAAGGTTTTTAACAAGACAACTTGTAATAGGAGAT
Found at i:11879529 original size:22 final size:22
Alignment explanation
Indices: 11879504--11879546 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11879494 AACTTAATTC
**
11879504 ACATTTATTGATTGAATGTAAT
1 ACATTTATCAATTGAATGTAAT
11879526 ACATTTATCAATTGAATGTAA
1 ACATTTATCAATTGAATGTAA
11879547 AGGAGTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
ACATTTATCAATTGAATGTAAT
Found at i:11882288 original size:21 final size:22
Alignment explanation
Indices: 11882248--11882290 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11882238 AATTTTTGAA
11882248 AAACAACAAAAGTATCGATATT
1 AAACAACAAAAGTATCGATATT
* *
11882270 AAACAA-AAAGGTATTGATATT
1 AAACAACAAAAGTATCGATATT
11882291 TTGGTCTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (22 bp):
AAACAACAAAAGTATCGATATT
Found at i:11885086 original size:7 final size:7
Alignment explanation
Indices: 11885070--11885099 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
11885060 ATTACAAGGC
11885070 AAAAAT-
1 AAAAATA
11885076 AAAAATA
1 AAAAATA
11885083 AAAAATA
1 AAAAATA
11885090 AAAAATA
1 AAAAATA
11885097 AAA
1 AAA
11885100 TACCCGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:11885515 original size:18 final size:19
Alignment explanation
Indices: 11885478--11885525 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
11885468 TTCATTCTAG
11885478 AATTATAAAAAGCATAAAA
1 AATTATAAAAAGCATAAAA
* *
11885497 AATTATAAAATG-ATTAAA
1 AATTATAAAAAGCATAAAA
*
11885515 ATTTATAAAAA
1 AATTATAAAAA
11885526 TTATTAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
AATTATAAAAAGCATAAAA
Found at i:11885526 original size:19 final size:19
Alignment explanation
Indices: 11885480--11885545 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
11885470 CATTCTAGAA
* *
11885480 TTATAAAAA-GCATAAAAAA
1 TTATAAAAATG-ATTAAAAT
11885499 TTAT-AAAATGATTAAAAT
1 TTATAAAAATGATTAAAAT
* *
11885517 TTATAAAAATTATTAGAAGT
1 TTATAAAAATGATTA-AAAT
*
11885537 TAATAAAAA
1 TTATAAAAA
11885546 ATAAAAAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.36
19 14 0.36
20 11 0.28
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.32
Consensus pattern (19 bp):
TTATAAAAATGATTAAAAT
Found at i:11885595 original size:13 final size:13
Alignment explanation
Indices: 11885573--11885606 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11885563 AACCATAAAG
11885573 ATTTAGAAAAATT
1 ATTTAGAAAAATT
*
11885586 ATTTATAAAAATT
1 ATTTAGAAAAATT
11885599 A-TTAGAAA
1 ATTTAGAAA
11885607 TGAATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (13 bp):
ATTTAGAAAAATT
Found at i:11886199 original size:26 final size:25
Alignment explanation
Indices: 11886161--11886227 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
11886151 TGTTAATTAA
**
11886161 TTTCTAACCATTTTTATAAGTGGTTT
1 TTTCTAATTATTTTTAT-AGTGGTTT
*
11886187 TTTCTAATTATTTTT-TTGTGGTTT
1 TTTCTAATTATTTTTATAGTGGTTT
**
11886211 TTGATAAATTATTTTTA
1 TTTCT-AATTATTTTTA
11886228 CAAATTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.29
25 11 0.32
26 13 0.38
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.61
Consensus pattern (25 bp):
TTTCTAATTATTTTTATAGTGGTTT
Found at i:11888301 original size:69 final size:69
Alignment explanation
Indices: 11888190--11888320 Score: 192
Period size: 69 Copynumber: 1.9 Consensus size: 69
11888180 ATAGTACCTC
* * * *
11888190 CATTTCTTTGAGCCCCTCGCCGCTTTTCTGGAAACCCTGGAGGAGCTTTAACTTCACTCTCCCGT
1 CATTTCTTTCAGCCCCTCGCCGCTTATCTGGAAACCCCGGAGGAGCTTCAACTTCACTCTCCCGT
11888255 CCAT
66 CCAT
* *
11888259 CATTTCTTTCA-CTCCCTCGCCGCTTATCTGGAAACCCCGGAGGAGGTTCAACTTCAGTCTCC
1 CATTTCTTTCAGC-CCCTCGCCGCTTATCTGGAAACCCCGGAGGAGCTTCAACTTCACTCTCC
11888321 TGACCACTGG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 1 0.02
69 54 0.98
ACGTcount: A:0.17, C:0.35, G:0.18, T:0.31
Consensus pattern (69 bp):
CATTTCTTTCAGCCCCTCGCCGCTTATCTGGAAACCCCGGAGGAGCTTCAACTTCACTCTCCCGT
CCAT
Found at i:11890190 original size:19 final size:19
Alignment explanation
Indices: 11890144--11890191 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
11890134 TAAATATATT
* *
11890144 TTAAATTATAATTCAAATA
1 TTAAAATATATTTCAAATA
* *
11890163 -TAAACTATATTTTAAATA
1 TTAAAATATATTTCAAATA
11890181 TTAAAATATAT
1 TTAAAATATAT
11890192 GCAATAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAAATATATTTCAAATA
Found at i:11891783 original size:16 final size:16
Alignment explanation
Indices: 11891762--11891797 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11891752 AATCCCTAAC
* *
11891762 AATCTTCAAGTCCCTA
1 AATCTTCAAATACCTA
11891778 AATCTTCAAATACCTA
1 AATCTTCAAATACCTA
11891794 AATC
1 AATC
11891798 GATAGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.31
Consensus pattern (16 bp):
AATCTTCAAATACCTA
Found at i:11892896 original size:22 final size:22
Alignment explanation
Indices: 11892865--11892910 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
11892855 TTAAGCATAT
*
11892865 AATTTGGATAAATGTACTTTAC
1 AATTTCGATAAATGTACTTTAC
11892887 AATTTCGATAAATGTACTTTAC
1 AATTTCGATAAATGTACTTTAC
11892909 AA
1 AA
11892911 AAGCATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
AATTTCGATAAATGTACTTTAC
Found at i:11893707 original size:152 final size:152
Alignment explanation
Indices: 11893431--11893736 Score: 612
Period size: 152 Copynumber: 2.0 Consensus size: 152
11893421 TGGTTCTACT
11893431 AGACTACAAGAGCATTTTATATTAATATTAACATTGTATAAAATAACTCATATCAATAGTAAAAG
1 AGACTACAAGAGCATTTTATATTAATATTAACATTGTATAAAATAACTCATATCAATAGTAAAAG
11893496 GAAAAACTTACTACAAAAAATGGAAGATTTCCCTTAGATTTATCTAAGGTAGTTGACCTTTTAAT
66 GAAAAACTTACTACAAAAAATGGAAGATTTCCCTTAGATTTATCTAAGGTAGTTGACCTTTTAAT
11893561 GGAAGATTTCCTTTTTTGTTTA
131 GGAAGATTTCCTTTTTTGTTTA
11893583 AGACTACAAGAGCATTTTATATTAATATTAACATTGTATAAAATAACTCATATCAATAGTAAAAG
1 AGACTACAAGAGCATTTTATATTAATATTAACATTGTATAAAATAACTCATATCAATAGTAAAAG
11893648 GAAAAACTTACTACAAAAAATGGAAGATTTCCCTTAGATTTATCTAAGGTAGTTGACCTTTTAAT
66 GAAAAACTTACTACAAAAAATGGAAGATTTCCCTTAGATTTATCTAAGGTAGTTGACCTTTTAAT
11893713 GGAAGATTTCCTTTTTTGTTTA
131 GGAAGATTTCCTTTTTTGTTTA
11893735 AG
1 AG
11893737 TGGTTGGGCA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 154 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (152 bp):
AGACTACAAGAGCATTTTATATTAATATTAACATTGTATAAAATAACTCATATCAATAGTAAAAG
GAAAAACTTACTACAAAAAATGGAAGATTTCCCTTAGATTTATCTAAGGTAGTTGACCTTTTAAT
GGAAGATTTCCTTTTTTGTTTA
Found at i:11895832 original size:51 final size:51
Alignment explanation
Indices: 11895757--11895910 Score: 218
Period size: 51 Copynumber: 3.0 Consensus size: 51
11895747 TACGTGTAGC
* * * * *
11895757 AGCAACATTTTCTAGTCCATCTGATGTTGCAAAGTCACCAGCATATTCATT
1 AGCAACATTATCCACTCCAGCTGATGTTGCAAAATCACCAGCATATTCATT
* * *
11895808 AGCAACATTATCCACTCTAGCTGATGTTGCAAAATCACCAACATATTCATC
1 AGCAACATTATCCACTCCAGCTGATGTTGCAAAATCACCAGCATATTCATT
* *
11895859 AGCAACATTATCCACTCCATCTGATGTTGCAAAATCACTAGCATATTCATT
1 AGCAACATTATCCACTCCAGCTGATGTTGCAAAATCACCAGCATATTCATT
11895910 A
1 A
11895911 CCAGCAACTT
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 90 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (51 bp):
AGCAACATTATCCACTCCAGCTGATGTTGCAAAATCACCAGCATATTCATT
Found at i:11897192 original size:18 final size:16
Alignment explanation
Indices: 11897149--11897184 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11897139 GAATGCTATC
* *
11897149 GATTTAGGTATTTGAA
1 GATTTAGGGACTTGAA
11897165 GATTTAGGGACTTGAA
1 GATTTAGGGACTTGAA
11897181 GATT
1 GATT
11897185 GTTAGGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.39
Consensus pattern (16 bp):
GATTTAGGGACTTGAA
Found at i:11901095 original size:55 final size:55
Alignment explanation
Indices: 11900988--11901104 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 55
11900978 CCAAAAACAG
* **
11900988 CACGGGCGTGTGACACGCCCATGCCTTGATCCTGTGGCTGAACATGTCAAATTAA
1 CACGGGCGTGCGACACGCCCATGCCAAGATCCTGTGGCTGAACATGTCAAATTAA
* * * *
11901043 CACGGGCGTGCGACACGCCCGTGCCAAGCAATCGTG-GGC-GAACCTGTTAAATTAA
1 CACGGGCGTGCGACACGCCCATGCCAAG--ATCCTGTGGCTGAACATGTCAAATTAA
*
11901098 CAAGGGC
1 CACGGGC
11901105 ATAGGCCTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
55 44 0.85
56 3 0.06
57 5 0.10
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (55 bp):
CACGGGCGTGCGACACGCCCATGCCAAGATCCTGTGGCTGAACATGTCAAATTAA
Found at i:11907097 original size:40 final size:40
Alignment explanation
Indices: 11906999--11907261 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
11906989 TCCTCGTTCA
* * * * *
11906999 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
11907038 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
11907078 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
11907118 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
11907158 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
11907198 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
11907238 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
11907262 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:11915049 original size:40 final size:40
Alignment explanation
Indices: 11914951--11915213 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
11914941 TCCTCGTTCA
* * * * *
11914951 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
11914990 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
11915030 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
11915070 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
11915110 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
11915150 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
11915190 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
11915214 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:11917947 original size:42 final size:43
Alignment explanation
Indices: 11917888--11918080 Score: 166
Period size: 43 Copynumber: 4.5 Consensus size: 43
11917878 CCTGATTTCA
* **
11917888 TCACCGGCCA-TA-AGCCTGCTAGACCTTTAAGTCTGAAT-TCA-T
1 TCACCGG-CATTATAGCCTGCTAG-CCTTGAAG-CCCAATATCATT
* *
11917930 TCACCGGCATT-TCGCCTGCTAGGCTTGAAGCCCAATATCATT
1 TCACCGGCATTATAGCCTGCTAGCCTTGAAGCCCAATATCATT
* * * * *
11917972 TCACCGGCATTATAGCCTGCTAGGCC-CGAGGCCCGATATTATC
1 TCACCGGCATTATAGCCTGCTA-GCCTTGAAGCCCAATATCATT
* ** *
11918015 TCACCAGCATTATAGCCTGCTAGGCC-CAAAGCCCGATATCATT
1 TCACCGGCATTATAGCCTGCTA-GCCTTGAAGCCCAATATCATT
11918058 TCACCGGCATTATAGCCTGCTAG
1 TCACCGGCATTATAGCCTGCTAG
11918081 GCCCGAAGCC
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
40 4 0.03
41 11 0.09
42 30 0.24
43 80 0.63
44 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGCCTTGAAGCCCAATATCATT
Found at i:11918019 original size:43 final size:43
Alignment explanation
Indices: 11917929--11918099 Score: 245
Period size: 43 Copynumber: 4.0 Consensus size: 43
11917919 TCTGAATTCA
* ** *
11917929 TTCACCGGCATT-TCGCCTGCTAGGCTTGAAGCCCAATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATCAT
* *
11917971 TTCACCGGCATTATAGCCTGCTAGGCCCGAGGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATCAT
* * *
11918014 CTCACCAGCATTATAGCCTGCTAGGCCCAAAGCCCGATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATCAT
11918057 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGTATATCA
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCG-ATATCA
11918100 CATTTCGATA
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
42 12 0.11
43 95 0.84
44 6 0.05
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATCAT
Found at i:11925067 original size:18 final size:18
Alignment explanation
Indices: 11925044--11925084 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
11925034 AAGGATAAAT
11925044 TAATTAATGCTCCAATCA
1 TAATTAATGCTCCAATCA
11925062 TAATTAATGCTCCAATCA
1 TAATTAATGCTCCAATCA
11925080 TAATT
1 TAATT
11925085 GCACCTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (18 bp):
TAATTAATGCTCCAATCA
Found at i:11945040 original size:22 final size:22
Alignment explanation
Indices: 11945014--11945073 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
11945004 ACACATTGTC
* * *
11945014 GATAAACCACCACATATTTGCT
1 GATAAACCACCACATAATCGCA
**
11945036 GAT-AACGGCCACATAATCGCA
1 GATAAACCACCACATAATCGCA
*
11945057 GATAAACTACCACATAA
1 GATAAACCACCACATAA
11945074 CTTCCACCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.20
Consensus pattern (22 bp):
GATAAACCACCACATAATCGCA
Found at i:11947108 original size:40 final size:40
Alignment explanation
Indices: 11947010--11947352 Score: 451
Period size: 40 Copynumber: 8.6 Consensus size: 40
11947000 TCCTCGTTCA
* * * ** *
11947010 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
11947049 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
11947089 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
11947129 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
11947169 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
11947209 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
11947249 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
11947289 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
11947329 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
11947353 CAGCATTCAA
Statistics
Matches: 279, Mismatches: 20, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
39 37 0.13
40 234 0.84
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:11961044 original size:39 final size:40
Alignment explanation
Indices: 11960943--11961044 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
11960933 TATTCGAATG
*
11960943 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACT
*
11960983 ATATCCGGGCTAAAACCCGAAGGCATTTGTG-TGAGTTGA-T
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCT-AG-TGACT
11961023 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAATCCCGAAGG
11961045 TACTTGGGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
39 16 0.28
40 38 0.67
41 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACT
Found at i:11964456 original size:21 final size:22
Alignment explanation
Indices: 11964427--11964467 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
11964417 AAAAAAGGTG
11964427 AGATAGAATAT-TAAATTGAATA
1 AGATAGAAT-TGTAAATTGAATA
11964449 AGAT-GAATTGTAAATTGAA
1 AGATAGAATTGTAAATTGAA
11964468 ATAATTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 13 0.72
22 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (22 bp):
AGATAGAATTGTAAATTGAATA
Found at i:11970224 original size:93 final size:93
Alignment explanation
Indices: 11970112--11970282 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
11970102 GCCCATAAGT
* *
11970112 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
11970177 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
11970205 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
11970270 CGAGTTCGGATGC
66 CGAGTTCGGATGC
11970283 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:11970279 original size:46 final size:46
Alignment explanation
Indices: 11970104--11970279 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
11970094 TGTAACCCGC
* * *
11970104 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
11970150 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
11970200 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
11970243 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
11970280 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:11972715 original size:30 final size:30
Alignment explanation
Indices: 11972671--11972759 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
11972661 CAAAGATAAC
11972671 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
11972700 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
11972730 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
11972760 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:11972719 original size:15 final size:15
Alignment explanation
Indices: 11972671--11972750 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
11972661 CAAAGATAAC
*
11972671 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
11972685 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
11972700 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
11972715 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
11972730 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
11972745 AAGAAA
1 AAGAAA
11972751 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:11972759 original size:15 final size:15
Alignment explanation
Indices: 11972682--11972759 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
11972672 AGAAAACCGA
11972682 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
11972697 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
11972711 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
11972726 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
11972742 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
11972757 ATA
1 ATA
11972760 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:11977635 original size:47 final size:47
Alignment explanation
Indices: 11977529--11977635 Score: 142
Period size: 47 Copynumber: 2.3 Consensus size: 47
11977519 TGGAAGTATA
*
11977529 TGGTAGTATATCTGCAAATGTGGTGGCTTGTCCACAATTTGATTATG
1 TGGTAGTATATCTGCAAATGTGGTGGCTTGTCCACAATTTAATTATG
* * * * * *
11977576 TGGCACTATATCTTCACATGTGGTGGCTTGTCTACGATTTAATTATG
1 TGGTAGTATATCTGCAAATGTGGTGGCTTGTCCACAATTTAATTATG
*
11977623 TGGTAGTTTATCT
1 TGGTAGTATATCT
11977636 ACATTACTGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.41
Consensus pattern (47 bp):
TGGTAGTATATCTGCAAATGTGGTGGCTTGTCCACAATTTAATTATG
Found at i:11986237 original size:831 final size:831
Alignment explanation
Indices: 11984636--11986299 Score: 3328
Period size: 831 Copynumber: 2.0 Consensus size: 831
11984626 CCCGGTTGGC
11984636 TCGACACTTCGAGCTCCTCAGCACCGCGGCCCAAGAATCATCCCTTACCCTCATCAGCCAGATGT
1 TCGACACTTCGAGCTCCTCAGCACCGCGGCCCAAGAATCATCCCTTACCCTCATCAGCCAGATGT
11984701 CTCCACAAGGCATCTCAAGTATACTTAGCATGAGGATGATCGAGAGGCGCCGAGGAACCTACCCT
66 CTCCACAAGGCATCTCAAGTATACTTAGCATGAGGATGATCGAGAGGCGCCGAGGAACCTACCCT
11984766 CCCTAATATTGTCTAGCTCAATCTACCGAGGAGGAAGCCTACGAGGACATTCCTGATGATGTCCC
131 CCCTAATATTGTCTAGCTCAATCTACCGAGGAGGAAGCCTACGAGGACATTCCTGATGATGTCCC
11984831 TCCACAGCACGAGGACCCACCGACTCAACCACCACCACCCTCTCGTCCAGTTCATGCAGCGGCTT
196 TCCACAGCACGAGGACCCACCGACTCAACCACCACCACCCTCTCGTCCAGTTCATGCAGCGGCTT
11984896 CATATGCTGACATCTCTGAGTGCCTCACTCGATTTGAGCAACAGTGTTTTCAACGTTTTGACAAC
261 CATATGCTGACATCTCTGAGTGCCTCACTCGATTTGAGCAACAGTGTTTTCAACGTTTTGACAAC
11984961 ATTGATGCTACTCTACAGCAGATTTTTCAGCACCTCCACATCTCATCACCAGTCCCACCTAGCGA
326 ATTGATGCTACTCTACAGCAGATTTTTCAGCACCTCCACATCTCATCACCAGTCCCACCTAGCGA
11985026 ACCATCTAGCGATGAAGATGTTTAAAAACATTTATTTATTATTTTATGTTTTTCATTTTTATTAC
391 ACCATCTAGCGATGAAGATGTTTAAAAACATTTATTTATTATTTTATGTTTTTCATTTTTATTAC
11985091 AACTACTTTTATTTTTTATTTTTAGTTGATTTTAGAATTTTATTTTTAATTATCAATTTTGGTTA
456 AACTACTTTTATTTTTTATTTTTAGTTGATTTTAGAATTTTATTTTTAATTATCAATTTTGGTTA
11985156 TTTCTTTATGAGTAATTCTTCTTCCTAATATCCCCAAAAAAGTTCTTGATTTTATTACAGTTATA
521 TTTCTTTATGAGTAATTCTTCTTCCTAATATCCCCAAAAAAGTTCTTGATTTTATTACAGTTATA
11985221 TAGAGCTCCTCAGCTCATCATCGCATAGGAACTAAAAACTCCACTGGGAAAGGTTCTCCACGACT
586 TAGAGCTCCTCAGCTCATCATCGCATAGGAACTAAAAACTCCACTGGGAAAGGTTCTCCACGACT
11985286 GCCATGTCCTAATCAACCAAAACCATAGCTACCACTAGATATAATATTCTTTTCGTGCAGGACTT
651 GCCATGTCCTAATCAACCAAAACCATAGCTACCACTAGATATAATATTCTTTTCGTGCAGGACTT
11985351 ATGGACTAATGAACCTCTACGACCGCCAGAGTATCCTCCTCCACTCTCGAACCGATTACTCTCCA
716 ATGGACTAATGAACCTCTACGACCGCCAGAGTATCCTCCTCCACTCTCGAACCGATTACTCTCCA
11985416 AACCTCCAGTTCAAGGAATTCATCATACAGGAAGTTTCACTTCTCTCCATA
781 AACCTCCAGTTCAAGGAATTCATCATACAGGAAGTTTCACTTCTCTCCATA
11985467 TCGACACTTCGAGCTCCTCAGCACCGCGGCCCAAGAATCATCCCTTACCCTCATCAGCCAGATGT
1 TCGACACTTCGAGCTCCTCAGCACCGCGGCCCAAGAATCATCCCTTACCCTCATCAGCCAGATGT
11985532 CTCCACAAGGCATCTCAAGTATACTTAGCATGAGGATGATCGAGAGGCGCCGAGGAACCTACCCT
66 CTCCACAAGGCATCTCAAGTATACTTAGCATGAGGATGATCGAGAGGCGCCGAGGAACCTACCCT
11985597 CCCTAATATTGTCTAGCTCAATCTACCGAGGAGGAAGCCTACGAGGACATTCCTGATGATGTCCC
131 CCCTAATATTGTCTAGCTCAATCTACCGAGGAGGAAGCCTACGAGGACATTCCTGATGATGTCCC
11985662 TCCACAGCACGAGGACCCACCGACTCAACCACCACCACCCTCTCGTCCAGTTCATGCAGCGGCTT
196 TCCACAGCACGAGGACCCACCGACTCAACCACCACCACCCTCTCGTCCAGTTCATGCAGCGGCTT
11985727 CATATGCTGACATCTCTGAGTGCCTCACTCGATTTGAGCAACAGTGTTTTCAACGTTTTGACAAC
261 CATATGCTGACATCTCTGAGTGCCTCACTCGATTTGAGCAACAGTGTTTTCAACGTTTTGACAAC
11985792 ATTGATGCTACTCTACAGCAGATTTTTCAGCACCTCCACATCTCATCACCAGTCCCACCTAGCGA
326 ATTGATGCTACTCTACAGCAGATTTTTCAGCACCTCCACATCTCATCACCAGTCCCACCTAGCGA
11985857 ACCATCTAGCGATGAAGATGTTTAAAAACATTTATTTATTATTTTATGTTTTTCATTTTTATTAC
391 ACCATCTAGCGATGAAGATGTTTAAAAACATTTATTTATTATTTTATGTTTTTCATTTTTATTAC
11985922 AACTACTTTTATTTTTTATTTTTAGTTGATTTTAGAATTTTATTTTTAATTATCAATTTTGGTTA
456 AACTACTTTTATTTTTTATTTTTAGTTGATTTTAGAATTTTATTTTTAATTATCAATTTTGGTTA
11985987 TTTCTTTATGAGTAATTCTTCTTCCTAATATCCCCAAAAAAGTTCTTGATTTTATTACAGTTATA
521 TTTCTTTATGAGTAATTCTTCTTCCTAATATCCCCAAAAAAGTTCTTGATTTTATTACAGTTATA
11986052 TAGAGCTCCTCAGCTCATCATCGCATAGGAACTAAAAACTCCACTGGGAAAGGTTCTCCACGACT
586 TAGAGCTCCTCAGCTCATCATCGCATAGGAACTAAAAACTCCACTGGGAAAGGTTCTCCACGACT
11986117 GCCATGTCCTAATCAACCAAAACCATAGCTACCACTAGATATAATATTCTTTTCGTGCAGGACTT
651 GCCATGTCCTAATCAACCAAAACCATAGCTACCACTAGATATAATATTCTTTTCGTGCAGGACTT
11986182 ATGGACTAATGAACCTCTACGACCGCCAGAGTATCCTCCTCCACTCTCGAACCGATTACTCTCCA
716 ATGGACTAATGAACCTCTACGACCGCCAGAGTATCCTCCTCCACTCTCGAACCGATTACTCTCCA
11986247 AACCTCCAGTTCAAGGAATTCATCATACAGGAAGTTTCACTTCTCTCCATA
781 AACCTCCAGTTCAAGGAATTCATCATACAGGAAGTTTCACTTCTCTCCATA
11986298 TC
1 TC
11986300 TTATTTTTAT
Statistics
Matches: 833, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
831 833 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (831 bp):
TCGACACTTCGAGCTCCTCAGCACCGCGGCCCAAGAATCATCCCTTACCCTCATCAGCCAGATGT
CTCCACAAGGCATCTCAAGTATACTTAGCATGAGGATGATCGAGAGGCGCCGAGGAACCTACCCT
CCCTAATATTGTCTAGCTCAATCTACCGAGGAGGAAGCCTACGAGGACATTCCTGATGATGTCCC
TCCACAGCACGAGGACCCACCGACTCAACCACCACCACCCTCTCGTCCAGTTCATGCAGCGGCTT
CATATGCTGACATCTCTGAGTGCCTCACTCGATTTGAGCAACAGTGTTTTCAACGTTTTGACAAC
ATTGATGCTACTCTACAGCAGATTTTTCAGCACCTCCACATCTCATCACCAGTCCCACCTAGCGA
ACCATCTAGCGATGAAGATGTTTAAAAACATTTATTTATTATTTTATGTTTTTCATTTTTATTAC
AACTACTTTTATTTTTTATTTTTAGTTGATTTTAGAATTTTATTTTTAATTATCAATTTTGGTTA
TTTCTTTATGAGTAATTCTTCTTCCTAATATCCCCAAAAAAGTTCTTGATTTTATTACAGTTATA
TAGAGCTCCTCAGCTCATCATCGCATAGGAACTAAAAACTCCACTGGGAAAGGTTCTCCACGACT
GCCATGTCCTAATCAACCAAAACCATAGCTACCACTAGATATAATATTCTTTTCGTGCAGGACTT
ATGGACTAATGAACCTCTACGACCGCCAGAGTATCCTCCTCCACTCTCGAACCGATTACTCTCCA
AACCTCCAGTTCAAGGAATTCATCATACAGGAAGTTTCACTTCTCTCCATA
Found at i:12004160 original size:17 final size:18
Alignment explanation
Indices: 12004140--12004177 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
12004130 TTTAATTTGT
12004140 TTTGTTTATTTTTC-TTA
1 TTTGTTTATTTTTCATTA
12004157 TTTGTTTATTTTTCATTA
1 TTTGTTTATTTTTCATTA
12004175 TTT
1 TTT
12004178 ATTTTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTGTTTATTTTTCATTA
Found at i:12004495 original size:13 final size:13
Alignment explanation
Indices: 12004466--12004494 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12004456 GCCAAGAAGG
12004466 TTTTGGAAATAAA
1 TTTTGGAAATAAA
12004479 TTTTGGAAAT-AA
1 TTTTGGAAATAAA
12004491 TTTT
1 TTTT
12004495 TTTACAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
TTTTGGAAATAAA
Found at i:12010201 original size:34 final size:33
Alignment explanation
Indices: 12010150--12010251 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 33
12010140 CAGTGTTGAA
* * *
12010150 CAGTCTGGGCCTAAGCCCATATCAGTCGCAATAT
1 CAGTGTGGGCCTTAGCCCATATCAGT-ACAATAT
*
12010184 CAGTGTGGGCCTTAGCCCA-ATACAGTAACAGTAT
1 CAGTGTGGGCCTTAGCCCATAT-CAGT-ACAATAT
* * *
12010218 CAATGTGGGCCTTAGCTCATTTCAGTACAATAT
1 CAGTGTGGGCCTTAGCCCATATCAGTACAATAT
12010251 C
1 C
12010252 CAAAATGCAT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 9 0.16
34 47 0.82
35 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (33 bp):
CAGTGTGGGCCTTAGCCCATATCAGTACAATAT
Found at i:12021564 original size:15 final size:15
Alignment explanation
Indices: 12021544--12021576 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12021534 TCAAATGACC
12021544 ATTGTTTGT-TATTTA
1 ATTG-TTGTCTATTTA
12021559 ATTGTTGTCTATTTA
1 ATTGTTGTCTATTTA
12021574 ATT
1 ATT
12021577 TAATTGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGTTGTCTATTTA
Found at i:12021725 original size:8 final size:8
Alignment explanation
Indices: 12021712--12021744 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
12021702 TGTTATACAA
12021712 TTCAACCT
1 TTCAACCT
12021720 TTCAACCT
1 TTCAACCT
12021728 TTCAACCT
1 TTCAACCT
12021736 TTCAACCT
1 TTCAACCT
12021744 T
1 T
12021745 AAGGCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.39
Consensus pattern (8 bp):
TTCAACCT
Found at i:12023784 original size:41 final size:40
Alignment explanation
Indices: 12023739--12023835 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 40
12023729 TAAGTCACTG
*
12023739 GCTAGGCACAAAGCCTGATA-CAAATGACCA-ACACGAAGCC
1 GCTAGGCACAAAGCCTGATATAAAAT-A-CAGACACGAAGCC
* * * *
12023779 TGCTAGGCATAGAGCTTGATATAAAATACAGGCACGAAGCC
1 -GCTAGGCACAAAGCCTGATATAAAATACAGACACGAAGCC
12023820 GCTAGGCACAAAGCCT
1 GCTAGGCACAAAGCCT
12023836 ACTAGGCATA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 15 0.33
41 27 0.59
42 4 0.09
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.14
Consensus pattern (40 bp):
GCTAGGCACAAAGCCTGATATAAAATACAGACACGAAGCC
Found at i:12023869 original size:56 final size:57
Alignment explanation
Indices: 12023774--12023884 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 57
12023764 GACCAACACG
* *
12023774 AAGCCTGCTAGGCATAGAGCTTGATATAAAATACAGGCACGAAGCC-GCTAGGCACA
1 AAGCCTACTAGGCATAGAGCCTGATATAAAATACAGGCACGAAGCCTGCTAGGCACA
12023830 AAGCCTACTAGGCATAGAGCCTGATAT-AAAT-CATCGGCACGAAGCCTGCTAGGCA
1 AAGCCTACTAGGCATAGAGCCTGATATAAAATACA--GGCACGAAGCCTGCTAGGCA
12023885 TATGGCCTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
54 2 0.04
55 4 0.08
56 36 0.72
57 8 0.16
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (57 bp):
AAGCCTACTAGGCATAGAGCCTGATATAAAATACAGGCACGAAGCCTGCTAGGCACA
Found at i:12035103 original size:33 final size:34
Alignment explanation
Indices: 12035042--12035106 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
12035032 TGCATTTTGT
12035042 ACTGATACTGTTACTGAATTGGGCTAAGGCCCAC
1 ACTGATACTGTTACTGAATTGGGCTAAGGCCCAC
12035076 ACTGATACTGTTACTGAA-TGGGCTAAGGCCC
1 ACTGATACTGTTACTGAATTGGGCTAAGGCCC
12035107 TAACTAAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (34 bp):
ACTGATACTGTTACTGAATTGGGCTAAGGCCCAC
Found at i:12038380 original size:6 final size:6
Alignment explanation
Indices: 12038368--12038410 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
12038358 GTCGAAGGTA
* * * *
12038368 AAGATG AATATG AAGATG AAGATG AAGGTG GAGATG AATATG A
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG A
12038411 GTACAAAGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.21
Consensus pattern (6 bp):
AAGATG
Found at i:12038385 original size:30 final size:30
Alignment explanation
Indices: 12038351--12038435 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 30
12038341 ACGAAGACGG
12038351 AGATGAAG-TCGAAGGTAAAGATGAATATGA
1 AGATGAAGAT-GAAGGTAAAGATGAATATGA
**
12038381 AGATGAAGATGAAGGTGGAGATGAATATG-
1 AGATGAAGATGAAGGTAAAGATGAATATGA
**
12038410 AGTACAAAGAT-AGAGGTAAAGATGAA
1 AG-ATGAAGATGA-AGGTAAAGATGAA
12038436 GACGATGGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
29 3 0.07
30 42 0.91
31 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.32, T:0.19
Consensus pattern (30 bp):
AGATGAAGATGAAGGTAAAGATGAATATGA
Found at i:12043755 original size:28 final size:28
Alignment explanation
Indices: 12043694--12043775 Score: 128
Period size: 28 Copynumber: 2.8 Consensus size: 28
12043684 TAACTTAAGC
*
12043694 ATAATTTAGGTACTAAATTAAAAAAATAAAT
1 ATAATTTAGGTAC--AATT-TAAAAATAAAT
12043725 ATAATTTAGGTACAATTTAAAAATAAAT
1 ATAATTTAGGTACAATTTAAAAATAAAT
12043753 ATAATTTAGGTACAATTTAAAAA
1 ATAATTTAGGTACAATTTAAAAA
12043776 AAAAACTCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
28 33 0.66
29 4 0.08
31 13 0.26
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (28 bp):
ATAATTTAGGTACAATTTAAAAATAAAT
Found at i:12045200 original size:14 final size:14
Alignment explanation
Indices: 12045181--12045208 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12045171 ATAGTGGTAT
12045181 AGTTGGAAGGCTTA
1 AGTTGGAAGGCTTA
12045195 AGTTGGAAGGCTTA
1 AGTTGGAAGGCTTA
12045209 GGCCTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.36, T:0.29
Consensus pattern (14 bp):
AGTTGGAAGGCTTA
Found at i:12050224 original size:20 final size:19
Alignment explanation
Indices: 12050180--12050226 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
12050170 TGAGTATTGT
* *
12050180 TTTTGATTATGTGATGGCT
1 TTTTGTTTATGTGATGGCA
12050199 TTTTGTTTATGTGATGGCCA
1 TTTTGTTTATGTGATGG-CA
12050219 TTTTGTTT
1 TTTTGTTT
12050227 GTATCTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.13, C:0.06, G:0.23, T:0.57
Consensus pattern (19 bp):
TTTTGTTTATGTGATGGCA
Found at i:12054149 original size:151 final size:151
Alignment explanation
Indices: 12053875--12054164 Score: 463
Period size: 151 Copynumber: 1.9 Consensus size: 151
12053865 TATGCCACAG
12053875 TACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACGTAGCTTAA
1 TACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACGTAGCTTAA
* *** * *
12053940 TGTTCGATGTCATTCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATTACTGCAGTCCTTTT
66 TGTTCAACAACATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTT
12054005 GTCTTGTGTAATATTTGCACT
131 GTCTTGTGTAATATTTGCACT
* * * ** *
12054026 TACATGAGAACACTAAAAAACTTTGTAGCTGGTGTTGGTATGGCTTTTCTTAAAATGTAGCTTAA
1 TACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACGTAGCTTAA
*
12054091 TGTTCAACAACATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCTTTTT
66 TGTTCAACAACATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTT
12054156 GTCTTGTGT
131 GTCTTGTGT
12054165 GATGTTTTCG
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 126 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (151 bp):
TACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACGTAGCTTAA
TGTTCAACAACATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTT
GTCTTGTGTAATATTTGCACT
Found at i:12067004 original size:21 final size:21
Alignment explanation
Indices: 12066975--12067015 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12066965 TGCTGGACAG
*
12066975 GAGCCGGAATGGGAGTGTTTA
1 GAGCCGGAATGAGAGTGTTTA
*
12066996 GAGCTGGAATGAGAGTGTTT
1 GAGCCGGAATGAGAGTGTTT
12067016 GGTTGCTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.27
Consensus pattern (21 bp):
GAGCCGGAATGAGAGTGTTTA
Found at i:12070246 original size:40 final size:40
Alignment explanation
Indices: 12070168--12070247 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
12070158 ATTAATTGAT
* *
12070168 AAGTCATTGCAGTAATGTCATACTAAATCTGATAAGTGTA
1 AAGTCATTGCAATAATGTCACACTAAATCTGATAAGTGTA
* * *
12070208 AAGTCATTGCAATAGTGTCACAC-AAAGTCTTATCAGTGTA
1 AAGTCATTGCAATAATGTCACACTAAA-TCTGATAAGTGTA
12070248 TACTAGTAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.09
40 31 0.91
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (40 bp):
AAGTCATTGCAATAATGTCACACTAAATCTGATAAGTGTA
Found at i:12071544 original size:20 final size:20
Alignment explanation
Indices: 12071519--12071558 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12071509 ATTCCTAGGG
12071519 AAGATAAGATAGAATTATTT
1 AAGATAAGATAGAATTATTT
* *
12071539 AAGATAAGTTAGCATTATTT
1 AAGATAAGATAGAATTATTT
12071559 TTATTTTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (20 bp):
AAGATAAGATAGAATTATTT
Found at i:12071938 original size:18 final size:20
Alignment explanation
Indices: 12071903--12071939 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
12071893 CTAGCATAGA
*
12071903 TCTCTCTCTCTCTCTCATTT
1 TCTCTCTCTCTCTATCATTT
12071923 TCTCTC-CTCT-TATCATT
1 TCTCTCTCTCTCTATCATT
12071940 CCAATTTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.38
19 4 0.25
20 6 0.38
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (20 bp):
TCTCTCTCTCTCTATCATTT
Found at i:12075942 original size:20 final size:20
Alignment explanation
Indices: 12075914--12075952 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12075904 AAAATTTTAG
12075914 TTTTGTTAAATAGTAAATGA
1 TTTTGTTAAATAGTAAATGA
*
12075934 TTTTTTTAAATAGTAAATG
1 TTTTGTTAAATAGTAAATG
12075953 TCAGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTTGTTAAATAGTAAATGA
Found at i:12075960 original size:20 final size:20
Alignment explanation
Indices: 12075919--12075961 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12075909 TTTAGTTTTG
**
12075919 TTAAATAGTAAATGATTTTT
1 TTAAATAGTAAATGATAGTT
12075939 TTAAATAGTAAATG-TCAGTT
1 TTAAATAGTAAATGAT-AGTT
12075959 TTA
1 TTA
12075962 TTTCAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (20 bp):
TTAAATAGTAAATGATAGTT
Found at i:12077287 original size:13 final size:14
Alignment explanation
Indices: 12077271--12077303 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12077261 CCTCCAAAAT
12077271 TTTACTCCCC-CCA
1 TTTACTCCCCGCCA
*
12077284 TTTACTCCCCGCTA
1 TTTACTCCCCGCCA
12077298 TTTACT
1 TTTACT
12077304 TCCCTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.15, C:0.42, G:0.03, T:0.39
Consensus pattern (14 bp):
TTTACTCCCCGCCA
Found at i:12088694 original size:20 final size:20
Alignment explanation
Indices: 12088654--12088699 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
12088644 AAACATATAA
* **
12088654 ATTTTGAATTTTTTATGAAT
1 ATTTTGAATTTTTAAAAAAT
12088674 ATTTTGAATTTTTAAAAAAT
1 ATTTTGAATTTTTAAAAAAT
12088694 ATTTTG
1 ATTTTG
12088700 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAAAT
Found at i:12097989 original size:43 final size:43
Alignment explanation
Indices: 12097928--12098087 Score: 302
Period size: 43 Copynumber: 3.7 Consensus size: 43
12097918 CACATTAGGT
*
12097928 GATGTCAATGAAAGTAGATCTAGTAACTCAAGCTATTTGCTCG
1 GATGTCAATGAAACTAGATCTAGTAACTCAAGCTATTTGCTCG
12097971 GATGTCAATGAAACTAGATCTAGTAACTCAAGCTATTTGCTCG
1 GATGTCAATGAAACTAGATCTAGTAACTCAAGCTATTTGCTCG
12098014 GATGTCAATGAAACTAGATCTAGTAACTCAAGCTATTTGCTCG
1 GATGTCAATGAAACTAGATCTAGTAACTCAAGCTATTTGCTCG
*
12098057 GATGTCAATGGAACTAGATCTAGTAACTCAA
1 GATGTCAATGAAACTAGATCTAGTAACTCAA
12098088 ATACTAAAGA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 115 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (43 bp):
GATGTCAATGAAACTAGATCTAGTAACTCAAGCTATTTGCTCG
Found at i:12100131 original size:25 final size:26
Alignment explanation
Indices: 12100076--12100136 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
12100066 TGTTAACTAT
* *
12100076 TTAAACTATAAAAATTATATTATTTTA
1 TTAAA-TATAAAAAATATATTATTATA
12100103 -TAAATATAAAAAATATA-TATTATA
1 TTAAATATAAAAAATATATTATTATA
12100127 TTAAAT-TAAA
1 TTAAATATAAA
12100137 GTAGATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 10 0.32
25 17 0.55
26 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAAATATAAAAAATATATTATTATA
Found at i:12105073 original size:40 final size:40
Alignment explanation
Indices: 12104975--12105237 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
12104965 TCCTCGTTCA
* * * * *
12104975 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
12105014 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
12105054 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
12105094 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
12105134 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
12105174 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
12105214 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
12105238 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:12113026 original size:40 final size:40
Alignment explanation
Indices: 12112928--12113190 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
12112918 TCCTCGTTCA
* * * * *
12112928 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
12112967 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
12113007 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
12113047 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
12113087 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
12113127 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
12113167 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
12113191 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:12134218 original size:15 final size:15
Alignment explanation
Indices: 12134198--12134237 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
12134188 TTGCGAATGG
*
12134198 CCATAGCAATAACAT
1 CCATAGCAAAAACAT
12134213 CCATAGCAAAAACAT
1 CCATAGCAAAAACAT
12134228 CCATAGCAAA
1 CCATAGCAAA
12134238 TAATTGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.28, G:0.07, T:0.15
Consensus pattern (15 bp):
CCATAGCAAAAACAT
Found at i:12141955 original size:22 final size:21
Alignment explanation
Indices: 12141930--12141977 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
12141920 CCTATTATTC
**
12141930 ATTTAGAATTGTCTTATTGTTT
1 ATTTA-AATTGTCTTATCATTT
*
12141952 ATTTTAAATTGTTTTATCATTT
1 A-TTTAAATTGTCTTATCATTT
12141974 ATTT
1 ATTT
12141978 CATTTCTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.14
22 15 0.68
23 4 0.18
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.62
Consensus pattern (21 bp):
ATTTAAATTGTCTTATCATTT
Found at i:12143764 original size:17 final size:18
Alignment explanation
Indices: 12143742--12143811 Score: 74
Period size: 17 Copynumber: 3.9 Consensus size: 18
12143732 ATCTGCTCCC
12143742 CCCCCAAA-TTTTACTTT
1 CCCCCAAACTTTTACTTT
*
12143759 CCCCCAAACTTTTGC--T
1 CCCCCAAACTTTTACTTT
* *
12143775 CCCCAAAACTTTTTATTTT
1 CCCCCAAAC-TTTTACTTT
12143794 CCCCCTAAACTTTTACTT
1 CCCCC-AAACTTTTACTT
12143812 CTCACCCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 9 0.21
17 12 0.29
18 5 0.12
19 12 0.29
20 4 0.10
ACGTcount: A:0.23, C:0.36, G:0.01, T:0.40
Consensus pattern (18 bp):
CCCCCAAACTTTTACTTT
Found at i:12144248 original size:45 final size:45
Alignment explanation
Indices: 12144184--12144278 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
12144174 GTATATAAAA
*
12144184 GATTAATAAATAAATTATGA-GGTGATGAAAGTTAATAAAAAATCT
1 GATTAATAAATAAATTATGACGG-GATAAAAGTTAATAAAAAATCT
* *
12144229 GATTAATAAATAAATTATGACGGGATAAAAGTTAATAACAAATTT
1 GATTAATAAATAAATTATGACGGGATAAAAGTTAATAAAAAATCT
12144274 GATTA
1 GATTA
12144279 CGGTGGGTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 44 0.96
46 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.32
Consensus pattern (45 bp):
GATTAATAAATAAATTATGACGGGATAAAAGTTAATAAAAAATCT
Found at i:12144573 original size:31 final size:31
Alignment explanation
Indices: 12144538--12144601 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
12144528 AAATAGATAA
12144538 ATGTGGAAAAAAGAGTAATTTTTGAGCAAGC
1 ATGTGGAAAAAAGAGTAATTTTTGAGCAAGC
* * *
12144569 ATGTGGCAAATAGAGTAATTTTTTAGCAAGC
1 ATGTGGAAAAAAGAGTAATTTTTGAGCAAGC
12144600 AT
1 AT
12144602 AATCAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (31 bp):
ATGTGGAAAAAAGAGTAATTTTTGAGCAAGC
Found at i:12148667 original size:91 final size:90
Alignment explanation
Indices: 12148595--12149173 Score: 800
Period size: 91 Copynumber: 6.4 Consensus size: 90
12148585 GCGTGAGCCA
* * *** * *
12148595 AGGCTCAACTCACCTCTCGCAATATAAGTCG-A-TTTTTTTGAAAGGCAAAAATTGAAAAAC-AG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTA-
* * *
12148657 AAATTGAAAATACCTCGGCATGTGACCTG
65 AAATTGAAATTACCTC--AACGTG-CCTG
** * ** * *** *
12148686 AGGCTCAACTCGTCTCTCGCAATACGAGTTG-ATTTTTTTT---TTATTTTTTTTGACAA-C-AG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTA-
* *
12148745 AAATTGAAATTACCTCAGCATGTCCTG
65 AAATTGAAATTACCTCAACGTG-CCTG
12148772 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
12148837 AATTGAAATTACCTCAACGTGCCTTG
66 AATTGAAATTACCTCAACGTGCC-TG
12148863 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
12148928 AATTGAAATTACCTCAACGTGCCTTG
66 AATTGAAATTACCTCAACGTGCC-TG
12148954 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
12149019 AATTGAAATTACCTCAACGTGCCTTG
66 AATTGAAATTACCTCAACGTGCC-TG
12149045 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
12149110 AATTGAAATTACCTCAACGTGCCTTG
66 AATTGAAATTACCTCAACGTGCC-TG
12149136 AGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTT
12149174 GAAAGACAAA
Statistics
Matches: 447, Mismatches: 33, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
86 34 0.08
87 9 0.02
88 18 0.04
89 6 0.01
90 18 0.04
91 354 0.79
92 8 0.02
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (90 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
AATTGAAATTACCTCAACGTGCCTG
Found at i:12148973 original size:182 final size:172
Alignment explanation
Indices: 12148595--12149671 Score: 1020
Period size: 182 Copynumber: 6.3 Consensus size: 172
12148585 GCGTGAGCCA
* * *** * *
12148595 AGGCTCAACTCACCTCTCGCAATATAAGTCGATTTTTTTGAAAGGCAAAAATTGAAAAACAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAAGCA-AAA
* * * ** *
12148660 TTGAAAATACCTCGGCATGTGACC-TGAGGCTCAACTCGTCTCTCGCAATACGAGTTGATTTTTT
65 TTGAAATTACCTC--AACGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*** * *** * *
12148724 TTTTATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTCC-TG
127 TGAAATATAAATTGA-AA-AGAAATTGAAATTACCTCAACGTG-CCTTG
12148772 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTTTTGAAAAATATAAATTGAAAAGC-AA
12148837 AATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTT
63 AATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTT
12148902 TTGAAAAATATAAATTGAAAAGCTAAAATTGAAATTACCTCAACGTGCCTTG
126 TTG--AAATATAAATTGAAAAG---AAATTGAAATTACCTCAACGTGCCTTG
12148954 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTTTTGAAAAATATAAATTGAAAAGC-AA
12149019 AATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTT
63 AATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTT
12149084 TTGAAAAATATAAATTGAAAAGCTAAAATTGAAATTACCTCAACGTGCCTTG
126 TTG--AAATATAAATTGAAAAG---AAATTGAAATTACCTCAACGTGCCTTG
*
12149136 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG--------AAA--G-ACA--AAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAAGCAAAAT
* * * * **
12149187 TGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTG--
66 TGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
* * * *
12149250 ------A--CAACAGAAATTGAAATTACCTCAGCGTGTCTTG
131 ATATAAATTGAAAAGAAATTGAAATTACCTCAACGTGCCTTG
*
12149284 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATTAATTGAAAAGCAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTGAAAAATATAAATTGAAAAGCA-AA
*
12149349 ATTGAAATTACCTCAACGTGCATTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG
64 ATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * *
12149412 ------ACA---AACAGAAATTGAAATTACCTCAGCGTGTCC-TG
129 AAATATAAATTGAAAAGAAATTGAAATTACCTCAACGTG-CCTTG
** * * *
12149447 AGGCTCAACTCATTTCTCGTAATATGAGTTGA--TTTTTG-AAAA-ATAGATTGAAACA-AAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAA-AGCAAAA
** ** ***
12149507 TTGACAA-TACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
65 TTGA-AATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * * *
12149571 AAACATAAATTGAACAGAAATTGAAACTACCTCAACGTGTCTTG
129 AAATATAAATTGAAAAGAAATTGAAATTACCTCAACGTGCCTTG
** * * *
12149615 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTT-AAAGACAAAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAA
12149672 TACCTCAGCA
Statistics
Matches: 786, Mismatches: 65, Indels: 105
0.82 0.07 0.11
Matches are distributed among these distances:
148 56 0.07
149 1 0.00
150 7 0.01
151 4 0.01
153 1 0.00
157 51 0.06
158 14 0.02
159 8 0.01
160 7 0.01
161 2 0.00
162 7 0.01
163 66 0.08
164 55 0.07
165 55 0.07
167 1 0.00
168 60 0.08
169 1 0.00
170 9 0.01
171 12 0.02
176 2 0.00
177 63 0.08
178 2 0.00
179 54 0.07
180 3 0.00
181 10 0.01
182 235 0.30
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (172 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAAGCAAAAT
TGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
ATATAAATTGAAAAGAAATTGAAATTACCTCAACGTGCCTTG
Found at i:12149089 original size:273 final size:250
Alignment explanation
Indices: 12148595--12149727 Score: 1151
Period size: 273 Copynumber: 4.5 Consensus size: 250
12148585 GCGTGAGCCA
* *
12148595 AGGCTCAACTCACCTCTCGCAATATAAGTCGATTTTTTTGAAAGGCAAAAATTGAAAAACAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-G--AAAA--G-----CA-AAA
* * * *
12148660 TTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCGTCTCTCGCAATACGAGTTGATTTTTTT
55 TTGAAAATACCTC--AACGTGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTTTT
* *** ** * *
12148725 TTTATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTCC-TGAGGCTCAACTCACCTCT
116 TTGAAAATAATTGAAAACA-AAATTGAAATTACCTCAGCGTG-CCTTGAGGCTCAACTCACCTCT
12148789 CGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAAAATTGAAATTACCTCAA
179 CGCAATATGAGTTGAA-TTTTTTTGAAAAATATAAATTGAAAAGC-AAAATTGAAATTACCTCAA
12148854 CGTGCCTTG
242 CGTGCCTTG
12148863 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTTTTG--------AAA--GAAAAGC-AA
* *
12148928 AATTGAAATTACCTCAACGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTT
53 AATTGAAAATACCTCAACGTGACC-TGAGGCTCAACTCATCTCTCGCAATATGAGTTG-A-TTTT
*
12148992 TTTGAAAAATATAAATTGAAAAGCTAAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCA
115 TTTG--AAA-AT-AATTGAAAA-C-AAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCA
12149057 CCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATTGAAAAGCTAAAATTGAAATTAC
174 CCTCTCGCAATATGAGTTGAA-TTTTTTTGAAAAATATAAATTGAAAAGC-AAAATTGAAATTAC
12149122 CTCAACGTGCCTTG
237 CTCAACGTGCCTTG
*
12149136 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAG-ACA--AAAATTGAAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGAAAAGCAAAATTGAAAATACC
* * * * * * *
12149197 TCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAA-CA--G--
66 TCAACGTGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTGAAAATAATTGAA
*
12149257 ----AAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAT
131 AACAAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAT
* *
12149318 TTTTTTGAAAAATATTAATTGAAAAGCAGAAATTGAAATTACCTCAACGTGCATTG
196 TTTTTTGAAAAATATAAATTGAAAAGCA-AAATTGAAATTACCTCAACGTGCCTTG
* * *
12149374 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGACA-AACAG--AAATTGAAATTACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGAAAAGCAAAATTGAAAATACC
* * * *
12149434 TCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGA--TTTTTGAAAAATAGATTG
66 TCAACGTGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTG-AAAATA-ATTG
* * **
12149497 AAACAAAAAATTGACAA-TACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
129 AAA-ACAAAATTGA-AATTACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * *
12149561 G-A--TTTTTGAAAAACATAAATTGAACAG--AAATTGAAACTACCTCAACGTGTCTTG
192 GAATTTTTTTGAAAAATATAAATTGAAAAGCAAAATTGAAATTACCTCAACGTGCCTTG
** *
12149615 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTT-AAAG-ACA--AAAATTGAAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGAAAAGCAAAATTGAAAATACC
* * * * *
12149676 TCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTT
66 TCAACGTGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTT
12149728 TTANNNNNNN
Statistics
Matches: 766, Mismatches: 55, Indels: 112
0.82 0.06 0.12
Matches are distributed among these distances:
235 6 0.01
236 3 0.00
237 67 0.09
238 86 0.11
239 58 0.08
240 1 0.00
241 54 0.07
242 60 0.08
243 5 0.01
244 27 0.04
246 1 0.00
247 52 0.07
248 2 0.00
249 1 0.00
251 1 0.00
252 2 0.00
254 8 0.01
255 1 0.00
256 51 0.07
257 1 0.00
259 2 0.00
260 1 0.00
262 3 0.00
267 2 0.00
268 71 0.09
269 2 0.00
270 32 0.04
271 2 0.00
272 9 0.01
273 145 0.19
274 1 0.00
275 1 0.00
277 4 0.01
278 3 0.00
279 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (250 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGAAAAGCAAAATTGAAAATACC
TCAACGTGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTGAAAATAATTGAA
AACAAAATTGAAATTACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAT
TTTTTTGAAAAATATAAATTGAAAAGCAAAATTGAAATTACCTCAACGTGCCTTG
Found at i:12149190 original size:74 final size:74
Alignment explanation
Indices: 12149098--12149328 Score: 347
Period size: 74 Copynumber: 3.1 Consensus size: 74
12149088 AAAATATAAA
* * *
12149098 TTGAAAAGCTAAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAA-CAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
12149163 GTTGA-TTTT
65 GTTGATTTTT
* * **
12149172 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAA-ACAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
12149237 GTTGATTTTT
65 GTTGATTTTT
* *
12149247 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
12149312 TTGAATTTTT
66 TTG-ATTTTT
12149322 TTGAAAA
1 TTGAAAA
12149329 ATATTAATTG
Statistics
Matches: 140, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
74 118 0.84
75 22 0.16
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (74 bp):
TTGAAAACAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTT
Found at i:12149429 original size:73 final size:73
Alignment explanation
Indices: 12149336--12149488 Score: 229
Period size: 73 Copynumber: 2.1 Consensus size: 73
12149326 AAAATATTAA
*
12149336 TTGAAAAGCAGAAATTGAAATTACCTCAACGTG-CATTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAGCAGAAATTGAAATTACCTCAACGTGTC-CTGAGGCTCAACTCACCTCTCGCAATATG
12149400 AGTTGATTT
65 AGTTGATTT
* ** *
12149409 TTGACAAA-CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATG
1 TTGA-AAAGCAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
12149473 AGTTGATTT
65 AGTTGATTT
12149482 TTGAAAA
1 TTGAAAA
12149489 ATAGATTGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
72 3 0.04
73 66 0.90
74 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (73 bp):
TTGAAAAGCAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:12149477 original size:163 final size:157
Alignment explanation
Indices: 12149172--12149725 Score: 582
Period size: 158 Copynumber: 3.5 Consensus size: 157
12149162 AGTTGATTTT
* * **
12149172 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAACA-AAAAATTG-AAATACCTCAGCGTG-CTTGAGGCTCAACTCACCTCTCGCAATATGA
**
12149237 GTTGATTTTTTTGAC-AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCT
63 GTTGA--TTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCT
12149301 CGCAATATGAGTTGAATTTTTTTGAAAAATATTAA
126 CGCAATATGAGTTG-ATTTTTTTGAAAAATA--AA
* *
12149336 TTGAAA-AGCAGAAATTGAAATTACCTCAACGTGCATTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAACA--AAAAATTGAAA-TACCTCAGCGTGC-TTGAGGCTCAACTCACCTCTCGCAATATG
*
12149400 AGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTC
62 AGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTC
* *
12149465 GTAATATGAGTTGA--TTTTTGAAAAATAGA
127 GCAATATGAGTTGATTTTTTTGAAAAATAAA
* **
12149494 TTGAAACAAAAAATTGACAATACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAACAAAAAATTGA-AATACCTCAGCGTG-CTTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
12149559 TTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAAC
64 TTGATTTTTG----AC----A---AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAAC
12149624 TCATTTCTCGCAATATGAGTTGA-TTTTTT------TAAA
118 TCATTTCTCGCAATATGAGTTGATTTTTTTGAAAAATAAA
* **
12149657 --G--AC-AAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTGAAACAAAAAATTG-AAATACCTCAGCGTG-CTTGAGGCTCAACTCACCTCTCGCAATATGAG
12149717 TTGATTTTT
64 TTGATTTTT
12149726 TTTTANNNNN
Statistics
Matches: 343, Mismatches: 27, Indels: 46
0.82 0.06 0.11
Matches are distributed among these distances:
157 57 0.17
158 67 0.20
159 4 0.01
160 13 0.04
161 3 0.01
162 9 0.03
163 67 0.20
164 57 0.17
165 1 0.00
168 60 0.17
169 5 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (157 bp):
TTGAAACAAAAAATTGAAATACCTCAGCGTGCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAA
TATGAGTTGATTTTTTTGAAAAATAAA
Found at i:12149561 original size:84 final size:84
Alignment explanation
Indices: 12149415--12149725 Score: 360
Period size: 84 Copynumber: 3.8 Consensus size: 84
12149405 ATTTTTGACA
* * *
12149415 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGAT
1 AACAAAAATTGAAACTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
*
12149480 TTTTG-AAAA-ATAGATTG
66 TTTTGAAAAACATAAATTG
* * * **
12149497 AAACAAAAAATTGACAA-TACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 -AAC-AAAAATTGA-AACTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
12149561 GATTTTTGAAAAACATAAATTG
63 GATTTTTGAAAAACATAAATTG
* * *
12149583 AACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
1 AACAAAAATTGAAACTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
*
12149648 TTTT-------TTAAA--G
66 TTTTGAAAAACATAAATTG
* * *
12149658 -ACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
1 AACAAAAATTGAAACTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
12149722 TTTT
66 TTTT
12149726 TTTTANNNNN
Statistics
Matches: 202, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
74 64 0.32
75 1 0.00
77 4 0.02
83 5 0.02
84 112 0.55
85 9 0.04
86 7 0.03
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (84 bp):
AACAAAAATTGAAACTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
TTTTGAAAAACATAAATTG
Found at i:12149564 original size:157 final size:157
Alignment explanation
Indices: 12149172--12149725 Score: 596
Period size: 168 Copynumber: 3.5 Consensus size: 157
12149162 AGTTGATTTT
* * **
12149172 TTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAA-ACAAAAATTG-AAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
**
12149237 GTTGATTTTTTTGAC-AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCT
64 GTTGA--TTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCT
12149301 CGCAATATGAGTTGAATTTTTTTGAAAAATATTAA
127 CGCAATATGAGTTG-A--TTTTTGAAAAATA-TAA
* * *
12149336 TTGAAAAGCAGAAATTGAAATTACCTCAACGTGCATTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAA-CAAAAATTGAAA-TACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
12149401 GTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCG
64 GTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCG
* *
12149466 TAATATGAGTTGATTTTTGAAAAATA-GA
129 CAATATGAGTTGATTTTTGAAAAATATAA
* **
12149494 TTG-AAACAAAAAATTGACAATACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAC-AAAAATTGA-AATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
* *
12149558 GTTGATTTTTGAAAAACATAAATTGAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAA
64 GTTGATTTTTG----AC----A---AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAA
12149623 CTCATTTCTCGCAATATGAGTTGATTTTT------T-T-A
118 CTCATTTCTCGCAATATGAGTTGATTTTTGAAAAATATAA
* * * **
12149655 ---AAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTGAAAACAAAAATTG-AAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAG
12149717 TTGATTTTT
65 TTGATTTTT
12149726 TTTTANNNNN
Statistics
Matches: 341, Mismatches: 30, Indels: 44
0.82 0.07 0.11
Matches are distributed among these distances:
156 1 0.00
157 61 0.18
158 63 0.18
159 4 0.01
160 13 0.04
161 3 0.01
162 10 0.03
163 63 0.18
164 57 0.17
165 1 0.00
168 65 0.19
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (157 bp):
TTGAAAACAAAAATTGAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCA
ATATGAGTTGATTTTTGAAAAATATAA
Found at i:12149709 original size:74 final size:74
Alignment explanation
Indices: 12149588--12149727 Score: 253
Period size: 74 Copynumber: 1.9 Consensus size: 74
12149578 AATTGAACAG
* *
12149588 AAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
12149653 TAAAGACAA
66 TAAAGACAA
*
12149662 AAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
12149727 T
66 T
12149728 TTANNNNNNN
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (74 bp):
AAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
TAAAGACAA
Found at i:12172609 original size:42 final size:43
Alignment explanation
Indices: 12172562--12172642 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 43
12172552 TGTGGGTTAG
12172562 TATTTGGTACACTGGTAGTGTA-TTTTTTTATTCTACAATTAA
1 TATTTGGTACACTGGTAGTGTATTTTTTTTATTCTACAATTAA
*
12172604 TATTTGGTACACTGGTAGTGTATTTTTTTTATTTTACAA
1 TATTTGGTACACTGGTAGTGTATTTTTTTTATTCTACAA
12172643 GCAGCCTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 22 0.59
43 15 0.41
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.52
Consensus pattern (43 bp):
TATTTGGTACACTGGTAGTGTATTTTTTTTATTCTACAATTAA
Found at i:12179535 original size:8 final size:8
Alignment explanation
Indices: 12179522--12179592 Score: 63
Period size: 8 Copynumber: 8.2 Consensus size: 8
12179512 TTATTAAAAT
12179522 AATTATAA
1 AATTATAA
12179530 AATTATAA
1 AATTATAA
*
12179538 AAATATAA
1 AATTATAA
12179546 AATTTATTAA
1 AA-TTA-TAA
12179556 ACATTA-AA
1 A-ATTATAA
*
12179564 AATAATAA
1 AATTATAA
12179572 AATTCATATA
1 AATT-ATA-A
12179582 AACTTATAA
1 AA-TTATAA
12179591 AA
1 AA
12179593 ATTTTAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
7 3 0.06
8 25 0.48
9 8 0.15
10 13 0.25
11 3 0.06
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (8 bp):
AATTATAA
Found at i:12179563 original size:25 final size:28
Alignment explanation
Indices: 12179525--12179594 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 28
12179515 TTAAAATAAT
*
12179525 TATAAA-ATTATAAAAAT-ATAAAATTTA
1 TATAAACA-TATAAAAATAATAAAATTCA
12179552 T-TAAACAT-TAAAAATAATAAAATTCA
1 TATAAACATATAAAAATAATAAAATTCA
*
12179578 TATAAACTTATAAAAAT
1 TATAAACATATAAAAAT
12179595 TTTAAAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 7 0.19
26 15 0.41
27 8 0.22
28 7 0.19
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (28 bp):
TATAAACATATAAAAATAATAAAATTCA
Found at i:12179639 original size:50 final size:51
Alignment explanation
Indices: 12179558--12179653 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
12179548 TTTATTAAAC
12179558 ATTAAAAATAATAAAATTCATATAAACTTATAAAAATTTTA-AAAACATAT
1 ATTAAAAATAATAAAATTCATATAAACTTATAAAAATTTTATAAAACATAT
* *
12179608 ATTAAAAATCTAATAAATTTTA-ATAAA-TTATAAAAATTTTATAAAA
1 ATTAAAAA--TAATAAAATTCATATAAACTTATAAAAATTTTATAAAA
12179654 TTAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
50 22 0.54
51 9 0.22
52 10 0.24
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (51 bp):
ATTAAAAATAATAAAATTCATATAAACTTATAAAAATTTTATAAAACATAT
Found at i:12179660 original size:18 final size:17
Alignment explanation
Indices: 12179609--12179661 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 17
12179599 AAAACATATA
*
12179609 TTAAAAATCTAATAAATT
1 TTAAAAAT-TAAAAAATT
12179627 TTAATAAATTATAAAAATT
1 TTAA-AAATTA-AAAAATT
12179646 TTATAAAATTAAAAAA
1 TTA-AAAATTAAAAAA
12179662 AACACATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 11 0.35
19 19 0.61
20 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATTAAAAAATT
Found at i:12179741 original size:29 final size:31
Alignment explanation
Indices: 12179672--12179744 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
12179662 AACACATTTC
* * *
12179672 AAAT-ATTCAAAATTTTATAAAAATGTATAA
1 AAATCATTAAAAATTATATAAAAATATATAA
* *
12179702 AAATTATTAAAAATTATATAAACATATA-AA
1 AAATCATTAAAAATTATATAAAAATATATAA
*
12179732 AAATCATAAAAAA
1 AAATCATTAAAAA
12179745 ATAAACTAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (31 bp):
AAATCATTAAAAATTATATAAAAATATATAA
Found at i:12179744 original size:10 final size:10
Alignment explanation
Indices: 12179504--12179744 Score: 55
Period size: 10 Copynumber: 24.8 Consensus size: 10
12179494 ATATTTTCTC
12179504 ATAAAAAATT
1 ATAAAAAATT
12179514 ATTAAAATAATT
1 A-TAAAA-AATT
12179526 AT--AAAATT
1 ATAAAAAATT
12179534 AT-AAAAA-T
1 ATAAAAAATT
*
12179542 AT-AAAATTT
1 ATAAAAAATT
* *
12179551 ATTAAACA-T
1 ATAAAAAATT
12179560 -T-AAAAA-T
1 ATAAAAAATT
*
12179567 A-ATAAAATT
1 ATAAAAAATT
* *
12179576 CATATAAACTT
1 -ATAAAAAATT
12179587 AT-AAAAATT
1 ATAAAAAATT
*
12179596 TTAAAAACATAT
1 ATAAAAA-AT-T
*
12179608 ATTAAAAA-T
1 ATAAAAAATT
* *
12179617 CTAATAAATT
1 ATAAAAAATT
* *
12179627 TTAATAAATT
1 ATAAAAAATT
12179637 AT-AAAAATT
1 ATAAAAAATT
* *
12179646 TTATAAAATT
1 ATAAAAAATT
* **
12179656 AAAAAAAACAC
1 ATAAAAAA-TT
***
12179667 ATTTCAAA-T
1 ATAAAAAATT
**
12179676 ATTCAAAATT
1 ATAAAAAATT
*
12179686 TTATAAAAATGT
1 ATA-AAAAAT-T
12179698 AT-AAAAATT
1 ATAAAAAATT
*
12179707 ATTAAAAATT
1 ATAAAAAATT
*
12179717 ATATAAACA-T
1 ATA-AAAAATT
*
12179727 ATAAAAAATC
1 ATAAAAAATT
12179737 ATAAAAAA
1 ATAAAAAA
12179745 ATAAACTAGA
Statistics
Matches: 170, Mismatches: 39, Indels: 44
0.67 0.15 0.17
Matches are distributed among these distances:
7 5 0.03
8 18 0.11
9 43 0.25
10 62 0.36
11 29 0.17
12 13 0.08
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:12180313 original size:20 final size:19
Alignment explanation
Indices: 12180280--12180325 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
12180270 TTATATGATT
*
12180280 TTTTTTATAATTTTTATAA
1 TTTTTTATAATTTTCATAA
*
12180299 TTTTTTATGACTTTTCATAA
1 TTTTTTAT-AATTTTCATAA
*
12180319 GTTTTTA
1 TTTTTTA
12180326 AGAATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTTTATAATTTTCATAA
Found at i:12180529 original size:20 final size:20
Alignment explanation
Indices: 12180491--12180527 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
12180481 AAAAAAAATT
12180491 AATTTCTTTCCTATTTTTAC
1 AATTTCTTTCCTATTTTTAC
*
12180511 AATTT-TTTTCTATTTTT
1 AATTTCTTTCCTATTTTT
12180528 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (20 bp):
AATTTCTTTCCTATTTTTAC
Found at i:12184610 original size:11 final size:11
Alignment explanation
Indices: 12184591--12184634 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
12184581 AGTTTAGATA
*
12184591 TTATTTTATTT
1 TTATCTTATTT
*
12184602 TTATCTTA-TC
1 TTATCTTATTT
12184612 TTATCTTATTT
1 TTATCTTATTT
*
12184623 TTATTTTATTT
1 TTATCTTATTT
12184634 T
1 T
12184635 GAAATTAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATCTTATTT
Found at i:12184615 original size:21 final size:21
Alignment explanation
Indices: 12184591--12184631 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12184581 AGTTTAGATA
*
12184591 TTATTTTATTTTTATCTTATC
1 TTATCTTATTTTTATCTTATC
*
12184612 TTATCTTATTTTTATTTTAT
1 TTATCTTATTTTTATCTTAT
12184632 TTTGAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATCTTATTTTTATCTTATC
Found at i:12190049 original size:47 final size:46
Alignment explanation
Indices: 12189981--12190331 Score: 243
Period size: 47 Copynumber: 7.5 Consensus size: 46
12189971 TTGTACGCCG
* * *
12189981 GTGTAAGACATGTCTGAGACATGCTTCTGCCACATTATGAGAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCA
* * * * *
12190027 GTGTAAGACCATGTCTGGGACATGGAATCGG-CATCCA-GACGAGGGCTA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA--CATTATGAGAGCCA
* * * *
12190075 GTGTAAGACATGTCTAGGG-TATACATCAGCCATATTATGAGAGCCA
1 GTGTAAGACATGTCT-GGGACATGCATCGGCCACATTATGAGAGCCA
** *
12190121 GTGTAAGACCATGTCTGGGACATGGCATCGG-CACAGAGATGAGTGCCA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACA-TTATGAGAGCCA
* * * *
12190169 GAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GA-GATAGCTA
1 GTGTAAGACATGTCTGGGACATGCATCGG-C-C-ACATTATGAGAGCCA
* ** * * * * *
12190216 GTGTAAGACGTGTCTGGGACACACATCGGCTAGGAGT-T--GTGCTA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCA-CATTATGAGAGCCA
*
12190260 GTGTAAGACATGTCTGGGACATGCATCGGCACGCATATATGAGAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGC-CACAT-TATGAGAGCCA
*
12190308 GTGTAAGACCATGTCTAGGACATG
1 GTGTAAGA-CATGTCTGGGACATG
12190332 GCGTCGGCAA
Statistics
Matches: 234, Mismatches: 47, Indels: 45
0.72 0.14 0.14
Matches are distributed among these distances:
44 33 0.14
45 3 0.01
46 39 0.17
47 82 0.35
48 57 0.24
49 17 0.07
50 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (46 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCA
Found at i:12190175 original size:94 final size:94
Alignment explanation
Indices: 12190009--12190183 Score: 271
Period size: 94 Copynumber: 1.9 Consensus size: 94
12189999 ACATGCTTCT
*
12190009 GCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGAATCGGCATCCAGACGAGGGCT
1 GCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGAATCGGCATCCAGACGAGGGCC
*
12190074 AGTGTAAGACATGTCTAGGGTATACATCA
66 AGAGTAAGACATGTCTAGGGTATACATCA
* * * * *
12190103 GCCATATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CAGAGATGAGTGC
1 GCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGAATCGGCATC-CAGACGAGGGC
12190167 CAGAGTAAGACATGTCT
65 CAGAGTAAGACATGTCT
12190184 GGGACATGCA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 1 0.01
94 72 0.99
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (94 bp):
GCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGAATCGGCATCCAGACGAGGGCC
AGAGTAAGACATGTCTAGGGTATACATCA
Found at i:12190339 original size:141 final size:141
Alignment explanation
Indices: 12189981--12190340 Score: 380
Period size: 141 Copynumber: 2.6 Consensus size: 141
12189971 TTGTACGCCG
* * *
12189981 GTGTAAGACATGTCTGAGACATGCTTCTGC-CACAT-TATGAGAGCCAGTGTAAGACCATGTCTG
1 GTGTAAGACATGTCTGGGACATGCATCGGCAC-CATATATGAGAGCCAGTGTAAGACCATGTCTG
* * * *
12190044 GGACATGGAATCGGCATCCAGACGAGGGCTAGTGTAAGACATGTCTAGGGTATACATCAGCCATA
65 GGACATGGCATCGGCATCCAGACGAGAGCTAGTGTAAGACATGTCTAGGGCACACATCAGCCATA
**
12190109 TTATGAGAGCCA
130 GGATGAGAGCCA
* * * *
12190121 GTGTAAGACCATGTCTGGGACATGGCATCGGCA-CAGAGATGAGTGCCAGAGTAAGA-CATGTCT
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCACCATATATGAGAGCCAGTGTAAGACCATGTCT
* * * *
12190184 GGGACAT-GCATCGGCCTCGACAGA-GATAGCTAGTGTAAGACGTGTCT-GGGACACACATC-GG
64 GGGACATGGCATCGGCATC--CAGACGAGAGCTAGTGTAAGACATGTCTAGGG-CACACATCAGC
* * *
12190245 C-TAGGA-GTTGTGCTA
126 CATAGGATG-AGAGCCA
*
12190260 GTGTAAGACATGTCTGGGACATGCATCGGCACGCATATATGAGAGCCAGTGTAAGACCATGTCTA
1 GTGTAAGACATGTCTGGGACATGCATCGGCAC-CATATATGAGAGCCAGTGTAAGACCATGTCTG
*
12190325 GGACATGGCGTCGGCA
65 GGACATGGCATCGGCA
12190341 ATATATCCCA
Statistics
Matches: 181, Mismatches: 27, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
137 9 0.05
138 15 0.08
139 34 0.19
140 35 0.19
141 62 0.34
142 26 0.14
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (141 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCACCATATATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGGCATCCAGACGAGAGCTAGTGTAAGACATGTCTAGGGCACACATCAGCCATAG
GATGAGAGCCA
Found at i:12194165 original size:22 final size:21
Alignment explanation
Indices: 12194123--12194166 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
12194113 TTAATCATCA
*
12194123 TTTCAATAAATTAATAAAAAT
1 TTTCAATAAATTAAAAAAAAT
12194144 TTTCAAATAAA-TAAAAATAAAT
1 TTTC-AATAAATTAAAAA-AAAT
12194166 T
1 T
12194167 AAAATTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTCAATAAATTAAAAAAAAT
Found at i:12194194 original size:16 final size:16
Alignment explanation
Indices: 12194167--12194202 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
12194157 AAAATAAATT
12194167 AAAATTACATT-ATAA
1 AAAATTACATTAATAA
12194182 AAAATTGACATTAATAA
1 AAAATT-ACATTAATAA
12194199 AAAA
1 AAAA
12194203 ATCACAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAATTACATTAATAA
Found at i:12194370 original size:103 final size:103
Alignment explanation
Indices: 12194180--12194701 Score: 453
Period size: 95 Copynumber: 5.2 Consensus size: 103
12194170 ATTACATTAT
* * *
12194180 AAAAAATTGACATTAATAAAAAAATCACAAAATACTAAACTAAACACTAACAATTTATATAATCT
1 AAAAAATT-ACATTACTAAAAAAATCACAAAACACTAACCTAAACACTAACAATTTATA-AA-CT
12194245 AATCATAAATTACTAACAAAATAACTATAAATTATTTTTAA
63 AATCATAAATTACTAACAAAATAACTATAAATTATTTTTAA
* *
12194286 AAAAAATTACATTACTAAAAAAATCACAAAACCCTAACCTAAACAATAACAATTTATAAACTAAT
1 AAAAAATTACATTACTAAAAAAATCACAAAACACTAACCTAAACACTAACAATTTATAAACTAAT
* *
12194351 CATAAATTACTAACAAAATAACTAT-GA-CATTTTTAA
66 CATAAATTACTAACAAAATAACTATAAATTATTTTTAA
* * * * * *
12194387 AAAAAA-AATCATTA-TTAATAATTCAC-AAA-A-T-A-CTTAACACTAACAATTTATAATCTAA
1 AAAAAATTA-CATTACTAAAAAAATCACAAAACACTAACCTAAACACTAACAATTTATAAACTAA
* **
12194445 TCATAAATTACTAACAAAATAACTGTAAAATTATTTTTTTT
65 TCATAAATTACTAACAAAATAACTAT-AAATTA-TTTTTAA
* * * * * *
12194486 AAAAATTTACATTACT-AAAAAATCACAAATCACAAATCACAAAACACTAATAATTTATAACCTA
1 AAAAAATTACATTACTAAAAAAATCACAAAACACTAA-C-CTAAACACTAACAATTTATAAACTA
* *
12194550 ATCATAAATTACCAACAAAATAA-T-T-AA-CA-----AA
64 ATCATAAATTACTAACAAAATAACTATAAATTATTTTTAA
* ** * * * *
12194581 ATAATTTTACATTAATAAAAAAATCACAACATACTAAACTAAACA-TAACAATTTAT-AACATAA
1 AAAAAATTACATTACTAAAAAAATCACAAAACACTAACCTAAACACTAACAATTTATAAAC-TAA
* * * * * *
12194644 TCCT-AATTACTAACAAAATAATTTTAAAATAATTATAA
65 TCATAAATTACTAACAAAATAACTATAAATTATTTTTAA
12194682 AAAAAA-TACATT-CATAAAAA
1 AAAAAATTACATTAC-TAAAAA
12194702 TTATTAAACC
Statistics
Matches: 338, Mismatches: 52, Indels: 58
0.75 0.12 0.13
Matches are distributed among these distances:
92 18 0.05
93 17 0.05
94 7 0.02
95 63 0.19
96 18 0.05
97 2 0.01
98 1 0.00
99 26 0.08
100 26 0.08
101 26 0.08
102 3 0.01
103 31 0.09
104 3 0.01
105 46 0.14
106 51 0.15
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.30
Consensus pattern (103 bp):
AAAAAATTACATTACTAAAAAAATCACAAAACACTAACCTAAACACTAACAATTTATAAACTAAT
CATAAATTACTAACAAAATAACTATAAATTATTTTTAA
Found at i:12194452 original size:95 final size:101
Alignment explanation
Indices: 12194180--12194572 Score: 397
Period size: 106 Copynumber: 3.8 Consensus size: 101
12194170 ATTACATTAT
* * *
12194180 AAAAAATTGACATTAATAAAAAAATCACAAAATACTAAACTAAACACTAACAATTTATATAATCT
1 AAAAAAAT-ACATTACTAAAAAAATCAC-AAA-ACTAACCTAAACACTAACAA-TT-TATAATCT
*
12194245 AATCATAAATTACTAACAAAATAACTATAAATTATTTTTAA
61 AATCATAAATTACTAACAAAATAACTATAAATTATTTTAAA
* * *
12194286 AAAAAATTACATTACTAAAAAAATCACAAAACCCTAACCTAAACAATAACAATTTATAAACTAAT
1 AAAAAAATACATTACTAAAAAAATCACAAAA--CTAACCTAAACACTAACAATTTATAATCTAAT
*
12194351 CATAAATTACTAACAAAATAACTATGACA-T-TTTTAAA
64 CATAAATTACTAACAAAATAACTAT-AAATTATTTTAAA
* * * *
12194388 AAAAAAAT-CATTA-TTAATAATTCACAAAA-T-A-CTTAACACTAACAATTTATAATCTAATCA
1 AAAAAAATACATTACTAAAAAAATCACAAAACTAACCTAAACACTAACAATTTATAATCTAATCA
* ***
12194448 TAAATTACTAACAAAATAACTGTAAAATTATTTTTTTT
66 TAAATTACTAACAAAATAACTAT-AAATTA-TTTTAAA
** * * * *
12194486 AAAAATTTACATTACT-AAAAAATCACAAATCACAAATCACAAAACACTAATAATTTATAACCTA
1 AAAAAAATACATTACTAAAAAAATCACAAA--ACTAA-C-CTAAACACTAACAATTTATAATCTA
*
12194550 ATCATAAATTACCAACAAAATAA
62 ATCATAAATTACTAACAAAATAA
12194573 TTAACAAAAT
Statistics
Matches: 243, Mismatches: 29, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
95 50 0.21
96 2 0.01
97 1 0.00
98 10 0.04
99 16 0.07
100 14 0.06
101 6 0.02
102 13 0.05
103 38 0.16
104 7 0.03
105 35 0.14
106 51 0.21
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.30
Consensus pattern (101 bp):
AAAAAAATACATTACTAAAAAAATCACAAAACTAACCTAAACACTAACAATTTATAATCTAATCA
TAAATTACTAACAAAATAACTATAAATTATTTTAAA
Found at i:12194657 original size:198 final size:199
Alignment explanation
Indices: 12194189--12194701 Score: 536
Period size: 198 Copynumber: 2.6 Consensus size: 199
12194179 TAAAAAATTG
12194189 ACATTAATAAAAAAATCACAAAATACTAAACTAAACACTAACAATTTATATA-ATCTAATCATAA
1 ACATTAATAAAAAAATCACAAAATACTAAACTAAACA-TAACAATTTATA-ACA--TAATCATAA
12194253 ATTACTAACAAAATAACTAT-AAATTATTTTTAAAAAAAATTACATTACTAAAAAAATCACAAAA
62 ATTACTAACAAAATAACTATAAAATTATTTTTAAAAAAAATTACATTACTAAAAAAATCACAAAA
* * * * *
12194317 CCCTAACCTAAACAATAACAATTTATAAACTAATCATAAATTACTAACAAAATAACTATGACATT
127 CACAAACCAAAACAATAACAATTTATAAACTAATCATAAATTACCAACAAAATAACTATAACA--
12194382 TTTAAAAAAAAA
190 --TAAAAAAAAA
* * * *
12194394 ATCATT-ATTAATAATTCACAAAATACTTAAC---AC-TAACAATTTATAATC-TAATCATAAAT
1 A-CATTAATAAAAAAATCACAAAATACTAAACTAAACATAACAATTTATAA-CATAATCATAAAT
* ** * *
12194453 TACTAACAAAATAACTGTAAAATTATTTTTTTTAAAAATTTACATTACT-AAAAAATCACAAATC
64 TACTAACAAAATAACTATAAAATTA-TTTTTAAAAAAAATTACATTACTAAAAAAATCACAAAAC
* * *
12194517 ACAAATCACAAAACACTAATAATTTATAACCTAATCATAAATTACCAACAAAATAA-T-TAACA-
128 ACAAA-C-CAAAACAATAACAATTTATAAACTAATCATAAATTACCAACAAAATAACTATAACAT
****
12194579 AAATAATTTT
191 AAA-AAAAAA
* *
12194589 ACATTAATAAAAAAATCACAACATACTAAACTAAACATAACAATTTATAACATAATCCT-AATTA
1 ACATTAATAAAAAAATCACAAAATACTAAACTAAACATAACAATTTATAACATAATCATAAATTA
* * * *
12194653 CTAACAAAATAATTTTAAAA-TAATTATAAAAAAAA-TACATT-CATAAAAA
66 CTAACAAAATAACTATAAAATTATTTTTAAAAAAAATTACATTAC-TAAAAA
12194702 TTATTAAACC
Statistics
Matches: 258, Mismatches: 34, Indels: 41
0.77 0.10 0.12
Matches are distributed among these distances:
194 8 0.03
195 30 0.12
196 12 0.05
197 2 0.01
198 54 0.21
199 47 0.18
200 34 0.13
201 43 0.17
202 2 0.01
205 22 0.09
206 4 0.02
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (199 bp):
ACATTAATAAAAAAATCACAAAATACTAAACTAAACATAACAATTTATAACATAATCATAAATTA
CTAACAAAATAACTATAAAATTATTTTTAAAAAAAATTACATTACTAAAAAAATCACAAAACACA
AACCAAAACAATAACAATTTATAAACTAATCATAAATTACCAACAAAATAACTATAACATAAAAA
AAAA
Found at i:12194689 original size:15 final size:17
Alignment explanation
Indices: 12194669--12194701 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12194659 AAATAATTTT
12194669 AAAATA-ATT-ATAAAA
1 AAAATACATTCATAAAA
12194684 AAAATACATTCATAAAA
1 AAAATACATTCATAAAA
12194701 A
1 A
12194702 TTATTAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATACATTCATAAAA
Found at i:12195259 original size:30 final size:31
Alignment explanation
Indices: 12195223--12195286 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
12195213 ACTTATTTTA
12195223 TTGTTAATTTTTTT-ATTATTTTAAAGGCAT
1 TTGTTAATTTTTTTAATTATTTTAAAGGCAT
*
12195253 TTGTTAATTTTTTTAATTATTTTAGAGGCAT
1 TTGTTAATTTTTTTAATTATTTTAAAGGCAT
12195284 TTG
1 TTG
12195287 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTTTAATTATTTTAAAGGCAT
Found at i:12195404 original size:18 final size:18
Alignment explanation
Indices: 12195369--12195408 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
12195359 GAAATATTTA
*
12195369 TTTTGATGTTTTTAATAT
1 TTTTGATGTTTATAATAT
12195387 TTTTGATGTATTATATATAT
1 TTTTGATGT-TTATA-ATAT
12195407 TT
1 TT
12195409 AAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTGATGTTTATAATAT
Found at i:12209031 original size:29 final size:30
Alignment explanation
Indices: 12208972--12209032 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
12208962 CTTAAATAAA
* * *
12208972 AACTTTTGAATAGTTTAATGACCATTTTAT
1 AACTTTTGAATAGTTGAATGACCAATATAT
* *
12209002 AACTTTTTAA-AGTTGATTGACCAATATAT
1 AACTTTTGAATAGTTGAATGACCAATATAT
12209031 AA
1 AA
12209033 ATTTACTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (30 bp):
AACTTTTGAATAGTTGAATGACCAATATAT
Found at i:12214868 original size:33 final size:33
Alignment explanation
Indices: 12214824--12214926 Score: 116
Period size: 33 Copynumber: 3.1 Consensus size: 33
12214814 CAACCCACTA
*
12214824 CCACCTCAGTACTCCAGTCATCCCAACTCGTAT
1 CCACCTCAGTACTCCACTCATCCCAACTCGTAT
* * * *
12214857 CCACCTTAGTACTCCACTCCTCTCGACTCGTAT
1 CCACCTCAGTACTCCACTCATCCCAACTCGTAT
* * * * *
12214890 CCACCGCCGTACTCCACTCTTCCCATCCCGTAT
1 CCACCTCAGTACTCCACTCATCCCAACTCGTAT
12214923 CCAC
1 CCAC
12214927 TGCCTTACTC
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.19, C:0.47, G:0.09, T:0.25
Consensus pattern (33 bp):
CCACCTCAGTACTCCACTCATCCCAACTCGTAT
Found at i:12215289 original size:74 final size:76
Alignment explanation
Indices: 12215133--12215293 Score: 254
Period size: 74 Copynumber: 2.1 Consensus size: 76
12215123 TAATTTAAAT
* * *
12215133 AACTTTATATTTATGTAATGACTTTTTTTCCATTTTAGTTATTAATTTTAGGGGTTTTTTTTCAA
1 AACTTTGTATTTATGTAATGACTTTTTTTCCATTTCAGTTATTAATTTTAGGGGTTTTTTTACAA
* *
12215198 TTTAAATAGTC
66 TTTAAATAATA
12215209 AACTTTGTATTTATGTAATGACTTTTTTT-CATTTCAGTTATTAATTTTAGGGG-TTTTTTACAA
1 AACTTTGTATTTATGTAATGACTTTTTTTCCATTTCAGTTATTAATTTTAGGGGTTTTTTTACAA
*
12215272 TTTAAGTAATA
66 TTTAAATAATA
12215283 AACTTTGTATT
1 AACTTTGTATT
12215294 ATTTACGTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 28 0.35
75 23 0.29
76 28 0.35
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.54
Consensus pattern (76 bp):
AACTTTGTATTTATGTAATGACTTTTTTTCCATTTCAGTTATTAATTTTAGGGGTTTTTTTACAA
TTTAAATAATA
Found at i:12217227 original size:38 final size:38
Alignment explanation
Indices: 12217173--12217247 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
12217163 ATATTGGAAG
12217173 TTCGTTTGGGTAGGAAGGTGTCGAAGAAATCATCACAT
1 TTCGTTTGGGTAGGAAGGTGTCGAAGAAATCATCACAT
* *
12217211 TTCGTTTGGGTTGGAAGGTGTCGAAGACATCATCACA
1 TTCGTTTGGGTAGGAAGGTGTCGAAGAAATCATCACA
12217248 CTATCATCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (38 bp):
TTCGTTTGGGTAGGAAGGTGTCGAAGAAATCATCACAT
Found at i:12221539 original size:40 final size:40
Alignment explanation
Indices: 12221493--12221716 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
12221483 CTTGCGCAAG
* * * * *
12221493 GCCTTCGGGTCTTAGCCCGAATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
*
12221533 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
*
12221573 GCCTTCGGGT-TTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
* * * *
12221612 GCCTTCGGGTCTTAGCCCAGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-GCTAGCACAAAT
* * * * *
12221652 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-GCTAGCACAAAT
*
12221693 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
12221717 CATTCGAATA
Statistics
Matches: 156, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 39 0.25
40 87 0.56
41 30 0.19
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:12221587 original size:79 final size:80
Alignment explanation
Indices: 12221457--12221716 Score: 285
Period size: 79 Copynumber: 3.3 Consensus size: 80
12221447 CTCAAGTAAT
* * * * * * * * *
12221457 CTTCGGGATTTAG-CCGGATATAACTACTTGCGC-AAGGCCTTCGGGTCTTAGCCCGAATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
12221520 CACTAGCATAAATGC
66 CACTAGCACAAATGC
* *
12221535 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGT-TTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
*
12221598 TCGCTAGCACAAATGC
65 TCACTAGCACAAATGC
* * * * * * *
12221614 CTTCGGGTCTTAGCCCAGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
12221679 CACCTAGCACAAAAGC
66 CA-CTAGCACAAATGC
12221695 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
12221717 CATTCGAATA
Statistics
Matches: 151, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
78 13 0.09
79 79 0.52
80 27 0.18
81 32 0.21
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:12233901 original size:24 final size:24
Alignment explanation
Indices: 12233869--12233914 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
12233859 AAATGTTAAA
12233869 ATTTTCTATTAAGAATTGTACTGT
1 ATTTTCTATTAAGAATTGTACTGT
12233893 ATTTTCTATTAAGAATTGTACT
1 ATTTTCTATTAAGAATTGTACT
12233915 ATGGTAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (24 bp):
ATTTTCTATTAAGAATTGTACTGT
Found at i:12242412 original size:42 final size:43
Alignment explanation
Indices: 12242319--12242427 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
12242309 GACTTATGAT
* *
12242319 TTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTTGAA
1 TTACATGTAAGACCCTGTCTGGGACAGTGGCATCGTATTTGAA
* * *
12242362 CT-CGTGTAAGACCCTGTCTGGGACAGTGGCATTG-ATATTG-A
1 TTACATGTAAGACCCTGTCTGGGACAGTGGCATCGTAT-TTGAA
12242403 TTACATGTAAGACCAC-GTCTGGGAC
1 TTACATGTAAGACC-CTGTCTGGGAC
12242428 GTTGACATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
41 4 0.07
42 50 0.89
43 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
TTACATGTAAGACCCTGTCTGGGACAGTGGCATCGTATTTGAA
Found at i:12258105 original size:16 final size:16
Alignment explanation
Indices: 12258084--12258116 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12258074 CTATAATTCC
12258084 CCAAAAATCCCGAAAT
1 CCAAAAATCCCGAAAT
*
12258100 CCAAAAGTCCCGAAAT
1 CCAAAAATCCCGAAAT
12258116 C
1 C
12258117 TTGAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.33, G:0.09, T:0.12
Consensus pattern (16 bp):
CCAAAAATCCCGAAAT
Found at i:12259329 original size:16 final size:16
Alignment explanation
Indices: 12259304--12259346 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
12259294 ATGAATCGGC
*
12259304 AAAAGTCGAAATG-TCG
1 AAAAGCCGAAATGCT-G
12259320 AAAAGCCGAAATGCTG
1 AAAAGCCGAAATGCTG
12259336 AAAAGCCGAAA
1 AAAAGCCGAAA
12259347 GTTTGGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (16 bp):
AAAAGCCGAAATGCTG
Found at i:12259636 original size:29 final size:29
Alignment explanation
Indices: 12259569--12259636 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
12259559 TGAATGTGAC
* *
12259569 TGGGCCTAACGGGCCATATAAGTGTGATT
1 TGGGCCTAATGGGCCATATAAGTGTAATT
12259598 TGGGCCTAATGGGCCATATACAG-GTAATT
1 TGGGCCTAATGGGCCATATA-AGTGTAATT
12259627 TGGGCCTAAT
1 TGGGCCTAAT
12259637 AGTCCCTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAGTGTAATT
Found at i:12263585 original size:21 final size:21
Alignment explanation
Indices: 12263561--12263605 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
12263551 AAGCATGGGG
12263561 AAAGAGGCAAAGCTTTTGAGT
1 AAAGAGGCAAAGCTTTTGAGT
*
12263582 AAAGAGTCAAAGCTTTTGAGT
1 AAAGAGGCAAAGCTTTTGAGT
12263603 AAA
1 AAA
12263606 TGAGAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (21 bp):
AAAGAGGCAAAGCTTTTGAGT
Found at i:12265124 original size:34 final size:34
Alignment explanation
Indices: 12265086--12265159 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
12265076 TTCAGTGCTC
** * *
12265086 TTTGGTTGTGTGGGATGGATACACTTATGTGCAA
1 TTTGGTTGTGAAGGATGAATACACTTATGTACAA
*
12265120 TTTGGTTGTGAAGGATGAATGCACTTATGTACAA
1 TTTGGTTGTGAAGGATGAATACACTTATGTACAA
12265154 TTTGGT
1 TTTGGT
12265160 GTATTTAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.08, G:0.30, T:0.39
Consensus pattern (34 bp):
TTTGGTTGTGAAGGATGAATACACTTATGTACAA
Found at i:12268118 original size:16 final size:18
Alignment explanation
Indices: 12268094--12268130 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12268084 TTTTTAAATA
*
12268094 TTAATGAGT-TTAGGTTT
1 TTAATGAGTATTAAGTTT
12268111 TTAA-GAGTATTAAGTTT
1 TTAATGAGTATTAAGTTT
12268128 TTA
1 TTA
12268131 TGGGTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (18 bp):
TTAATGAGTATTAAGTTT
Found at i:12271528 original size:21 final size:21
Alignment explanation
Indices: 12271494--12271533 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12271484 CTATTTGGCT
*
12271494 AAAGAAAATAAAAGATTGTCA
1 AAAGAAAACAAAAGATTGTCA
* *
12271515 AAAGAAAACCAAAGGTTGT
1 AAAGAAAACAAAAGATTGT
12271534 GAGATTGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.17
Consensus pattern (21 bp):
AAAGAAAACAAAAGATTGTCA
Found at i:12272535 original size:69 final size:68
Alignment explanation
Indices: 12272442--12272627 Score: 246
Period size: 69 Copynumber: 2.7 Consensus size: 68
12272432 TAGTTGTGAT
* * *
12272442 CGTAGGTCATCGAGTAGTTTTAGGAGTTGCGATCTTCAATCAGCTAACCTTTATAATATCAATTA
1 CGTAGGTCATCAAGTA-TTTTAGGAGTTGCGATCTTAAATCAGCTAACCTTTATAATATCAACTA
12272507 TGAA
65 TGAA
* * * *
12272511 CGTAGGTCATCAAGTTATTCTAGGAGTTGCGATCTTAAATCAACTAATCTTTATAATATCAACTG
1 CGTAGGTCATCAAG-TATTTTAGGAGTTGCGATCTTAAATCAGCTAACCTTTATAATATCAACTA
12272576 TGAA
65 TGAA
* * * *
12272580 CGTAGGTCATCGAACTATTTTAGGAGTTACAATATTAAATCAGCTAAC
1 CGTAGGTCATC-AAGTATTTTAGGAGTTGCGATCTTAAATCAGCTAAC
12272628 TCGAAGAAAC
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
69 97 0.96
70 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (68 bp):
CGTAGGTCATCAAGTATTTTAGGAGTTGCGATCTTAAATCAGCTAACCTTTATAATATCAACTAT
GAA
Found at i:12272726 original size:106 final size:107
Alignment explanation
Indices: 12272539--12272784 Score: 316
Period size: 106 Copynumber: 2.3 Consensus size: 107
12272529 TCTAGGAGTT
* *
12272539 GCGATCTTAAATCAACTAA-TCTTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTTAG
1 GCGATCTTAAATCAGCTAACT-TTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTTAA
* * *
12272603 GAGTTACAATATTAAATCAGCTAACTC-GAAGAAACTTAGGTA
65 GAGTTACAATATTAAATCAACTAACTCAAAAAAAACTTAGGTA
* * ** * *
12272645 GTGATCTTAAATCGGCTAACTTTTATAATATCAGTTGTGAACGTAGGTCATCGATCTGTTTTAAG
1 GCGATCTTAAATCAGCTAACTTTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTTAAG
*** * *
12272710 AGTTGTGATATTAAATCAACTATCTCAAAAAAAACTTAGGTT
66 AGTTACAATATTAAATCAACTAACTCAAAAAAAACTTAGGTA
*
12272752 GCGATCTTAAATTAGCTAACTTTTATAATATCA
1 GCGATCTTAAATCAGCTAACTTTTATAATATCA
12272785 TTACTTCTAT
Statistics
Matches: 119, Mismatches: 19, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
106 76 0.64
107 43 0.36
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (107 bp):
GCGATCTTAAATCAGCTAACTTTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTTAAG
AGTTACAATATTAAATCAACTAACTCAAAAAAAACTTAGGTA
Found at i:12276590 original size:93 final size:93
Alignment explanation
Indices: 12276431--12276602 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
12276421 CGCCCATAAG
* * * * *
12276431 CGAACTCGGACTCAACTCGATGAGCTCGGGCGTTCGCATCCATTAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
12276496 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
12276524 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
12276589 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
12276603 TCAACCATCC
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:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:12276592 original size:46 final size:46
Alignment explanation
Indices: 12276424--12276599 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
12276414 TGTAACCCGC
* * * * *
12276424 CCATAAGCGAACTCGGACTCAACTCGATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
12276470 CCATTAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
12276520 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
12276563 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
12276600 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:12276618 original size:46 final size:44
Alignment explanation
Indices: 12276470--12276618 Score: 144
Period size: 46 Copynumber: 3.2 Consensus size: 44
12276460 GCGTTCGCAT
12276470 CCAT-TAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA
1 CCATCTAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---A
* * *
12276517 -CATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATCT-AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAA
*
12276563 CCAT-AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAA
1 CCATCTAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAA
12276607 CCATCCTAGTGA
1 CCAT-CTAGTGA
12276619 CATGTCACTT
Statistics
Matches: 84, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 36 0.43
47 32 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (44 bp):
CCATCTAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAA
Found at i:12281592 original size:31 final size:31
Alignment explanation
Indices: 12281554--12281616 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
12281544 TCTACCACAC
12281554 TGCTGGCACCCAGGTTTAACAAATCTCGAGT
1 TGCTGGCACCCAGGTTTAACAAATCTCGAGT
* *
12281585 TGCTGGCACTCGGGTTTAACAAATCTCGAGT
1 TGCTGGCACCCAGGTTTAACAAATCTCGAGT
12281616 T
1 T
12281617 CCTTACACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (31 bp):
TGCTGGCACCCAGGTTTAACAAATCTCGAGT
Found at i:12296615 original size:41 final size:41
Alignment explanation
Indices: 12296559--12296638 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
12296549 TTTAGCAGCG
12296559 TTTTTGTCAAAACGCCGCTAAAAACT-GAGCAATAGCGGCAT
1 TTTTTGTCAAAACGCCGCTAAAAA-TAGAGCAATAGCGGCAT
* *
12296600 TTTTTGTTAAAACGCCGCTAAAAATAGAGCATTAGCGGC
1 TTTTTGTCAAAACGCCGCTAAAAATAGAGCAATAGCGGC
12296639 GCTTTTGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (41 bp):
TTTTTGTCAAAACGCCGCTAAAAATAGAGCAATAGCGGCAT
Found at i:12296670 original size:41 final size:41
Alignment explanation
Indices: 12296625--12296743 Score: 157
Period size: 41 Copynumber: 2.9 Consensus size: 41
12296615 CGCTAAAAAT
**
12296625 AGAGCATTAGCGGCGCTTTTGGTGAAACGGTACTAAAGACC
1 AGAGCATTAGCGGCGCTTTTGGTGAAACGCCACTAAAGACC
* * *
12296666 AGAGCATTAGCGGCGCTTTTGGTGAAATGCCGCTAAATACC
1 AGAGCATTAGCGGCGCTTTTGGTGAAACGCCACTAAAGACC
* * * *
12296707 AGAGCATTAGTGACGCTTTTGGTAAAACGCCGCTAAA
1 AGAGCATTAGCGGCGCTTTTGGTGAAACGCCACTAAA
12296744 ATCCTAAACC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (41 bp):
AGAGCATTAGCGGCGCTTTTGGTGAAACGCCACTAAAGACC
Done.