Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 80 of 85
Found at i:27839941 original size:25 final size:26
Alignment explanation
Indices: 27839892--27839948 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
27839882 CCGTTAAGAT
*
27839892 TTTTGACAATTTTACCCTCGGTAAAA
1 TTTTGACAATTTTACCCTCGATAAAA
*
27839918 TTTTGACCATTTTA-CCTCGATAAAA
1 TTTTGACAATTTTACCCTCGATAAAA
27839943 TTTTGA
1 TTTTGA
27839949 GAAAATTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Consensus pattern (26 bp):
TTTTGACAATTTTACCCTCGATAAAA
Found at i:27843797 original size:21 final size:21
Alignment explanation
Indices: 27843773--27843835 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
27843763 CACTTAATTT
27843773 TTAAAAGTTATGTAATAATCA
1 TTAAAAGTTATGTAATAATCA
* * *
27843794 TT-AACGCTTTTG-AAT--T-T
1 TTAAAAG-TTATGTAATAATCA
27843811 TTAAAAGTTATGTAATAATCA
1 TTAAAAGTTATGTAATAATCA
27843832 TTAA
1 TTAA
27843836 CGCTTTTGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
17 6 0.20
18 7 0.23
20 7 0.23
21 10 0.33
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (21 bp):
TTAAAAGTTATGTAATAATCA
Found at i:27843819 original size:38 final size:38
Alignment explanation
Indices: 27843768--27843844 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
27843758 TTTTTCACTT
27843768 AATTTTTAAAAGTTATGTAATAATCATTAACGCTTTTG
1 AATTTTTAAAAGTTATGTAATAATCATTAACGCTTTTG
27843806 AATTTTTAAAAGTTATGTAATAATCATTAACGCTTTTG
1 AATTTTTAAAAGTTATGTAATAATCATTAACGCTTTTG
27843844 A
1 A
27843845 GTTATTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (38 bp):
AATTTTTAAAAGTTATGTAATAATCATTAACGCTTTTG
Found at i:27854175 original size:15 final size:16
Alignment explanation
Indices: 27854152--27854181 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27854142 AAATAAAGGT
27854152 TAAATTGGTAAATAAG
1 TAAATTGGTAAATAAG
27854168 TAAA-TGGTAAATAA
1 TAAATTGGTAAATAA
27854182 AATTTATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (16 bp):
TAAATTGGTAAATAAG
Found at i:27855721 original size:18 final size:18
Alignment explanation
Indices: 27855700--27855746 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27855690 AAACATGCGT
**
27855700 ATATATATATGGAAATAA
1 ATATATATATAAAAATAA
*
27855718 ATATATACATAAAAATAA
1 ATATATATATAAAAATAA
*
27855736 ATATACATATA
1 ATATATATATA
27855747 TATATAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
ATATATATATAAAAATAA
Found at i:27856788 original size:44 final size:44
Alignment explanation
Indices: 27856740--27856857 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
27856730 TATTCTGTCT
* * *
27856740 GCTCCACTACAACTTCAGAGAGATAAGATT-T-GTGATTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGATTATAG-G-CTTAAATCC
* * *
27856784 GCTCCACTGCAACTTCAGGGAGATAGGATTATAGGCTTAAATCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTAAATCC
27856828 GCTCCACTGCAACTTCAGAGAGATAAGATT
1 GCTCCACTGCAACTTCAGAGAGATAAGATT
27856858 CGCCATTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 61 0.95
45 2 0.03
46 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTAAATCC
Found at i:27856801 original size:88 final size:89
Alignment explanation
Indices: 27856673--27856922 Score: 274
Period size: 88 Copynumber: 2.8 Consensus size: 89
27856663 GCCAATGGAA
* * * *
27856673 ATAAGATTTGCCATTTTGAGTCTGCCCCACTGCAACTTCAGGGGGATAAGACCTACTTATTCTGT
1 ATAAGATTCGCCATTTTGAATCCGCCCCACTGCAACTTCAGGGGGATAAGACCTACTTATTCAGT
27856738 CTGCTCCACTACAACTTCAGAGAG
66 CTGCTCCACTACAACTTCAGAGAG
* ** * * * * *
27856762 ATAAGATTTGTGATTTT-AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTA--TAGGCTTA
1 ATAAGATTCGCCATTTTGAATCCGCCCCACTGCAACTTCAGGGGGATAAGACCTACTTA---TTC
* *
27856823 AATCTGCTCCACTGCAACTTCAGAGAG
63 AGTCTGCTCCACTACAACTTCAGAGAG
** * * *
27856850 ATAAGATTCGCCATTTTGGGTCTGCCCCACTACAACTTCAGGGGGATAAGACCTGCTTATTCAGT
1 ATAAGATTCGCCATTTTGAATCCGCCCCACTGCAACTTCAGGGGGATAAGACCTACTTATTCAGT
27856915 CTGCTCCA
66 CTGCTCCA
27856923 TATACATAGA
Statistics
Matches: 128, Mismatches: 26, Indels: 14
0.76 0.15 0.08
Matches are distributed among these distances:
85 2 0.02
87 2 0.02
88 68 0.53
89 53 0.41
90 1 0.01
92 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (89 bp):
ATAAGATTCGCCATTTTGAATCCGCCCCACTGCAACTTCAGGGGGATAAGACCTACTTATTCAGT
CTGCTCCACTACAACTTCAGAGAG
Found at i:27857327 original size:18 final size:18
Alignment explanation
Indices: 27857306--27857352 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27857296 AAACATGCGT
**
27857306 ATATATATATGGAAATAA
1 ATATATATATAAAAATAA
*
27857324 ATATATACATAAAAATAA
1 ATATATATATAAAAATAA
*
27857342 ATATACATATA
1 ATATATATATA
27857353 TATATAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
ATATATATATAAAAATAA
Found at i:27858282 original size:18 final size:18
Alignment explanation
Indices: 27858261--27858307 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27858251 AAACATGCGT
**
27858261 ATATATATATGGAAATAA
1 ATATATATATAAAAATAA
*
27858279 ATATATACATAAAAATAA
1 ATATATATATAAAAATAA
*
27858297 ATATACATATA
1 ATATATATATA
27858308 TATATAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
ATATATATATAAAAATAA
Found at i:27859232 original size:955 final size:945
Alignment explanation
Indices: 27857119--27859017 Score: 3381
Period size: 955 Copynumber: 2.0 Consensus size: 945
27857109 ATATAGAAAA
* ** *
27857119 ATATTCGTTAGAAAAAAAATAAATATACATACATGTACATATAATTTTTAAAGAAAACATATATA
1 ATATTCGTTAGAAAAAAAATAAATAGACATACATG-ACATATAACCTCTAAAGAAAACATATATA
* * **
27857184 TATACATATATAATATAGAAAAATATTCGCTAGAAGAAAAATAAATATACATACATATATGTATA
65 TATACATATATAATATAG-AAAATATTCGCTAGAAGAAAAATAAATATAAATACATAAAAATATA
* *
27857249 TAAATAAATAGAAAAAATAAATTAAATAATAATTACATTATATTAAAAAACATGCGTATATATAT
129 TAAAAAAATAGAAAAAATAAATTAAATAATAATTACATTATATTAAAAAACATGCGTATAGATAT
27857314 ATGGAAATAAATATATACATAAAAATAAATATACATATATATATAGAAAGAAAAAAAAAGAAAAA
194 ATGGAAATAAATATATACATAAAAATAAATATACATATATATATAGAAAGAAAAAAAAAGAAAAA
27857379 AAATTACATATGAAAATAATAATTACATTATTAATTAAGGAGAAAAAAAGAAATAAAAATAAAAA
259 AAATTACATATGAAAATAATAATTACATTATTAATTAAGGAGAAAAAAAGAAATAAAAATAAAAA
27857444 AGGACTAAATTGAATTGTAAAATAAAAAACTGGGGCAAAGTCGCAAATAATTGAAGATCGGAGGA
324 AGGACTAAATTGAATTGTAAAATAAAAAACTGGGGCAAAGTCGCAAATAATTGAAGATCGGAGGA
*
27857509 CCTTATTGAACCCGCTAATAATTCAGAGGGGCTGGAAGGGCAATTTCTCCTTTTCCTCAAAACGG
389 CCTTATTGAACCCGCTAATAATTCAGAGGGGCTGGAAGGGCAATTTCCCCTTTTCCTCAAAACGG
*
27857574 CGTCGTTCAAGTAGGAATAAATTGAAATTGAAGAAAAATTAGAGGGTAAATTTAAAAAAAATTAA
454 CGTCGTTCAAGTAGGAATAAATTGAAATCGAAGAAAAATTAGAGGGTAAATTTAAAAAAAATTAA
27857639 AAAAACTTAATTGCAAAACTTCAAAAGGCGGAGGGGCTAAAAGCGCAATTTACCCCTCCGCTCAA
519 AAAAACTTAATTGCAAAACTTCAAAAGGCGGAGGGGCTAAAAGCGCAATTTACCCCTCCGCTCAA
* * *
27857704 AAACGCGTGGATCCTAGGTCGGGTCGGGTCGGAGTTGGGTCGACCCATGCCTAAAACGACGTCGT
584 AAACGCGCGAATCCTAGGTC--G-CGGGTC---G--GGGTCGACCCATGCCCAAAACGACGTCGT
27857769 TTTATTTGGCTATTTAAGCTAAAAACCTTTCAAAAATATTCATTTTTCATTTTCTTTTTAAAAAA
641 TTTATTTGGCTATTTAAGCTAAAAACCTTTCAAAAATATTCATTTTTCATTTTCTTTTTAAAAAA
27857834 AAACTAAATTCCCTAAAAAAAACTCTCCCCTTTTGCCCATCGTTCAGGCACCGTCCGGGTATCGG
706 AAACTAAATTCCCTAAAAAAAACTCTCCCCTTTTGCCCATCGTTCAGGCACCGTCCGGGTATCGG
27857899 TCAGTCATCGGCCACCGCGTCGGCCGTCGATCTGCAGCGTCGGCACCACCGTCTGCGGTGGCTGG
771 TCAGTCATCGGCCACCGCGTCGGCCGTCGATCTGCAGCGTCGGCACCACCGTCTGCGGTGGCTGG
27857964 AAAAGGAGAAAATCCCCTATTTGGCCTTTTAGACTCCCCTAAGCTCAAATCTGGGTTCAAATCCC
836 AAAAGGAGAAAATCCCCTATTTGGCCTTTTAGACTCCCCTAAGCTCAAATCTGGGTTCAAATCCC
27858029 TCGAAATATCAACAAAAATGCCCCAAAAGCCCGGGAAACCCTCGG
901 TCGAAATATCAACAAAAATGCCCCAAAAGCCCGGGAAACCCTCGG
* ** *
27858074 ATATTCGTTAGAAAAAAAATAAATATACATACATGTACATATAATTTTTAAAGAAAACATATATA
1 ATATTCGTTAGAAAAAAAATAAATAGACATACATG-ACATATAACCTCTAAAGAAAACATATATA
* * **
27858139 TATACATATATAATATAGAAAAATATTCGCTAGAAGAAAAATAAATATACATACATATATGTATA
65 TATACATATATAATATAG-AAAATATTCGCTAGAAGAAAAATAAATATAAATACATAAAAATATA
* *
27858204 TAAATAAATAGAAAAAATAAATTAAATAATAATTACATTATATTAAAAAACATGCGTATATATAT
129 TAAAAAAATAGAAAAAATAAATTAAATAATAATTACATTATATTAAAAAACATGCGTATAGATAT
27858269 ATGGAAATAAATATATACATAAAAATAAATATACATATATATATAGAAAGAAAAAAAAAGAAAAA
194 ATGGAAATAAATATATACATAAAAATAAATATACATATATATATAGAAAGAAAAAAAAAGAAAAA
27858334 AAATTACATATGAAAATAATAATTACATTATTAATTAAGGAGAAAAAAAGAAATAAAAATAAAAA
259 AAATTACATATGAAAATAATAATTACATTATTAATTAAGGAGAAAAAAAGAAATAAAAATAAAAA
27858399 AGGACTAAATTGAATTGTAAAATAAAAAACTGGGGCAAAGTCGCAAATAATTGAAGATCGGAGGA
324 AGGACTAAATTGAATTGTAAAATAAAAAACTGGGGCAAAGTCGCAAATAATTGAAGATCGGAGGA
27858464 CCTTATTGAACCCGCTAATAATTCAGAGGGGCTGGAAGGGCAATTTCCCCTTTTCCTCAAAACGG
389 CCTTATTGAACCCGCTAATAATTCAGAGGGGCTGGAAGGGCAATTTCCCCTTTTCCTCAAAACGG
* *
27858529 TGTCGTTCAAGTAGGAATAAATTGAAATCGAAGAAAAATTAGATGGTAAATTTAAAAAAAATTAA
454 CGTCGTTCAAGTAGGAATAAATTGAAATCGAAGAAAAATTAGAGGGTAAATTTAAAAAAAATTAA
* *
27858594 AAAAACTTAATTGCAAAACTTCAAAAGGCGGAGGGGCTAAAAGTGCAATTTACCCCTTCGCTCAA
519 AAAAACTTAATTGCAAAACTTCAAAAGGCGGAGGGGCTAAAAGCGCAATTTACCCCTCCGCTCAA
*
27858659 AAACGTGCGAATCCTAGG-C-CGGGTC-GGGTCGACCCATGCCCAAAACGACGTCGTTTTATTTG
584 AAACGCGCGAATCCTAGGTCGCGGGTCGGGGTCGACCCATGCCCAAAACGACGTCGTTTTATTTG
27858721 GCTATTTAAGCTAAAAACCTTTCAAAAATATTCATTTTTCATTTTCTTTTTAAAAAAAAACTAAA
649 GCTATTTAAGCTAAAAACCTTTCAAAAATATTCATTTTTCATTTTCTTTTTAAAAAAAAACTAAA
* *
27858786 TTCCCTCAAAAAAACTCTCCCCTTTTGCGCATCGTTCAGGCACCGTCCGGGTATCGGTCAGTCAT
714 TTCCCTAAAAAAAACTCTCCCCTTTTGCCCATCGTTCAGGCACCGTCCGGGTATCGGTCAGTCAT
27858851 CGGCCACCGCGTCGGCCGTCGATCTGCAGCGTCGGCACCACCGTCTGCGGTGGCTGGAAAAGGAG
779 CGGCCACCGCGTCGGCCGTCGATCTGCAGCGTCGGCACCACCGTCTGCGGTGGCTGGAAAAGGAG
27858916 AAAATCCCCTATTTGGCCTTTTAGACTCCCCTAAGCTCAAATCTGGGTTCAAATCCCTCGAAATA
844 AAAATCCCCTATTTGGCCTTTTAGACTCCCCTAAGCTCAAATCTGGGTTCAAATCCCTCGAAATA
27858981 TCAACAAAAATGCCCCAAAAGCCCGGGAAACCCTCGG
909 TCAACAAAAATGCCCCAAAAGCCCGGGAAACCCTCGG
27859018 CTTCCAGTCG
Statistics
Matches: 932, Mismatches: 12, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
944 331 0.36
950 6 0.01
954 1 0.00
955 594 0.64
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.26
Consensus pattern (945 bp):
ATATTCGTTAGAAAAAAAATAAATAGACATACATGACATATAACCTCTAAAGAAAACATATATAT
ATACATATATAATATAGAAAATATTCGCTAGAAGAAAAATAAATATAAATACATAAAAATATATA
AAAAAATAGAAAAAATAAATTAAATAATAATTACATTATATTAAAAAACATGCGTATAGATATAT
GGAAATAAATATATACATAAAAATAAATATACATATATATATAGAAAGAAAAAAAAAGAAAAAAA
ATTACATATGAAAATAATAATTACATTATTAATTAAGGAGAAAAAAAGAAATAAAAATAAAAAAG
GACTAAATTGAATTGTAAAATAAAAAACTGGGGCAAAGTCGCAAATAATTGAAGATCGGAGGACC
TTATTGAACCCGCTAATAATTCAGAGGGGCTGGAAGGGCAATTTCCCCTTTTCCTCAAAACGGCG
TCGTTCAAGTAGGAATAAATTGAAATCGAAGAAAAATTAGAGGGTAAATTTAAAAAAAATTAAAA
AAACTTAATTGCAAAACTTCAAAAGGCGGAGGGGCTAAAAGCGCAATTTACCCCTCCGCTCAAAA
ACGCGCGAATCCTAGGTCGCGGGTCGGGGTCGACCCATGCCCAAAACGACGTCGTTTTATTTGGC
TATTTAAGCTAAAAACCTTTCAAAAATATTCATTTTTCATTTTCTTTTTAAAAAAAAACTAAATT
CCCTAAAAAAAACTCTCCCCTTTTGCCCATCGTTCAGGCACCGTCCGGGTATCGGTCAGTCATCG
GCCACCGCGTCGGCCGTCGATCTGCAGCGTCGGCACCACCGTCTGCGGTGGCTGGAAAAGGAGAA
AATCCCCTATTTGGCCTTTTAGACTCCCCTAAGCTCAAATCTGGGTTCAAATCCCTCGAAATATC
AACAAAAATGCCCCAAAAGCCCGGGAAACCCTCGG
Found at i:27859486 original size:349 final size:350
Alignment explanation
Indices: 27859051--27859747 Score: 1353
Period size: 349 Copynumber: 2.0 Consensus size: 350
27859041 ACGACACCCT
27859051 CGGCCATCCACTGCGATCTGGGCACCTCTAAATGTTACTTCTTTCCTTTTTATTTGTTTTATTCG
1 CGGCCATCCACTGCGATCTGGGCACCTCTAAATGTTACTTCTTTCCTTTTTATTTGTTTTATTCG
27859116 TATGTAAAAGAAAAATAAAAGTAAATAAAAAAATATATAAAAAAACTTTAGATGTTAACCTTTGG
66 TATGTAAAAGAAAAATAAAAGTAAATAAAAAAATATATAAAAAAACTTTAGATGTTAACCTTTGG
27859181 ATTGATTGTATTGCTCTTAGTATTGAGTTTTCTCTTTTCGATTGTGGAAATAG-TTTTTTATTGA
131 ATTGATTGTATTGCTCTTAGTATTGAGTTTTCTCTTTTCGATTGTGGAAATAGTTTTTTTATTGA
*
27859245 TTTCCAATCCCCCTTTACAGTACATTAATGGCCTTCTTGTAGCCATAGTAATAATAAAAAAATAA
196 TTTCCAATCCCACTTTACAGTACATTAATGGCCTTCTTGTAGCCATAGTAATAATAAAAAAATAA
27859310 AGAAACAAATCATGCTTGATATCTCTTAATCTGCAAATCTTTTAATTTTGTTTCCCTTC-CTGTG
261 AGAAACAAATCATGCTTGATATCTCTTAATCTGCAAATCTTTTAATTTTGTTT-CCTTCTCTGTG
27859374 TCCATTCCTTACAGGTGAAGATTCGG
325 TCCATTCCTTACAGGTGAAGATTCGG
27859400 CGGCCATCCACTGCGATCTGGGCACCTCTAAATGTTACTTCTTTCCTTTTTATTTGTTTTATTCG
1 CGGCCATCCACTGCGATCTGGGCACCTCTAAATGTTACTTCTTTCCTTTTTATTTGTTTTATTCG
27859465 TATGTAAAAGAAAAATAAAAGTAAATAAAAAAATATATAAAAAAACTTTAGATGTTAACCTTTGG
66 TATGTAAAAGAAAAATAAAAGTAAATAAAAAAATATATAAAAAAACTTTAGATGTTAACCTTTGG
27859530 ATTGATTGTATTGCTCTTAGTATTGAGTTTTCTCTTTTCGATTGTGGAAATAGTTTTTTTATTGA
131 ATTGATTGTATTGCTCTTAGTATTGAGTTTTCTCTTTTCGATTGTGGAAATAGTTTTTTTATTGA
27859595 TTTCCAATCCCACTTTACAGTACATTAATGGCCTTCTTGTAGCCATAGTAATAATAAAAAAATAA
196 TTTCCAATCCCACTTTACAGTACATTAATGGCCTTCTTGTAGCCATAGTAATAATAAAAAAATAA
*
27859660 ATAAACAAATCATGCTTGATATCTCTTAATCTGCAAATCTTTTAATTTTGTTTCCTTCTCTGTGT
261 AGAAACAAATCATGCTTGATATCTCTTAATCTGCAAATCTTTTAATTTTGTTTCCTTCTCTGTGT
27859725 CCATTCCTTACAGGTGAAGATTC
326 CCATTCCTTACAGGTGAAGATTC
27859748 AGCTACGGCG
Statistics
Matches: 344, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
349 188 0.55
350 156 0.45
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (350 bp):
CGGCCATCCACTGCGATCTGGGCACCTCTAAATGTTACTTCTTTCCTTTTTATTTGTTTTATTCG
TATGTAAAAGAAAAATAAAAGTAAATAAAAAAATATATAAAAAAACTTTAGATGTTAACCTTTGG
ATTGATTGTATTGCTCTTAGTATTGAGTTTTCTCTTTTCGATTGTGGAAATAGTTTTTTTATTGA
TTTCCAATCCCACTTTACAGTACATTAATGGCCTTCTTGTAGCCATAGTAATAATAAAAAAATAA
AGAAACAAATCATGCTTGATATCTCTTAATCTGCAAATCTTTTAATTTTGTTTCCTTCTCTGTGT
CCATTCCTTACAGGTGAAGATTCGG
Found at i:27866530 original size:44 final size:44
Alignment explanation
Indices: 27866482--27866599 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
27866472 TATTCTGTCT
* * *
27866482 GCTCCACTACAACTTCAGAGAGATAAGATT-T-GTGATTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGATTATAG-G-CTTAAATCC
* * *
27866526 GCTCCACTGCAACTTCAGGGAGATAGGATTATAGGCTTAAATCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTAAATCC
*
27866570 GCTCCACTGCACCTTCAGAGAGATAAGATT
1 GCTCCACTGCAACTTCAGAGAGATAAGATT
27866600 CGCCATTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 60 0.95
45 2 0.03
46 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTAAATCC
Found at i:27866543 original size:88 final size:88
Alignment explanation
Indices: 27866427--27866798 Score: 265
Period size: 88 Copynumber: 4.3 Consensus size: 88
27866417 AAGATTTGCC
* * * * * *
27866427 ATTTTGAGTCTGCCCCACTGCAACTTCAGGGGGATAAGACCTACTTATTCTGTCTGCTCCACTAC
1 ATTTTGAATCCGCTCCACTGCAACTTCAGGGAGATAAGACCTAC-TATTCAGTCTGCTCCACTGC
*
27866492 AACTTCAGAGAGATAAGATTTGTG
65 AACTTCAGAGAGATAAGATTCGTG
* * * *
27866516 ATTTT-AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTA-TAGGCTTAAATCTGCTCCACT
1 ATTTTGAATCCGCTCCACTGCAACTTCAGGGAGATAAGACCTACTA---TTCAGTCTGCTCCACT
* **
27866578 GCACCTTCAGAGAGATAAGATTCGCC
63 GCAACTTCAGAGAGATAAGATTCGTG
** * * * * *
27866604 ATTTTGGGTCTGCCCCACTACAACTTCAGGGGGATAAGACCTGCTTATTCAGTCTGCTCC-CTGC
1 ATTTTGAATCCGCTCCACTGCAACTTCAGGGAGATAAGACCTAC-TATTCAGTCTGCTCCACTGC
*
27866668 AACTTC-----GATAAGACTCGCT-
65 AACTTCAGAGAGATAAGATTCG-TG
** * * * * * *
27866687 -TTCTTGGGTCTGCTCCATTGCAACTTCAGTGAGATAAGACC--CAATGTGA-TCTGCT-CTCTG
1 ATT-TTGAATCCGCTCCACTGCAACTTCAGGGAGATAAGACCTACTAT-TCAGTCTGCTCCACTG
27866747 CAACTTCAGAGAGATAAGA-TCTGTG
64 CAACTTCAGAGAGATAAGATTC-GTG
*
27866772 ATTTT-AATCCACTCCACTGCAACTTCA
1 ATTTTGAATCCGCTCCACTGCAACTTCA
27866799 AAGAGATGGA
Statistics
Matches: 224, Mismatches: 40, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
79 1 0.00
80 18 0.08
81 3 0.01
82 2 0.01
83 43 0.19
84 20 0.09
85 12 0.05
86 2 0.01
87 2 0.01
88 76 0.34
89 42 0.19
90 1 0.00
92 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (88 bp):
ATTTTGAATCCGCTCCACTGCAACTTCAGGGAGATAAGACCTACTATTCAGTCTGCTCCACTGCA
ACTTCAGAGAGATAAGATTCGTG
Found at i:27866827 original size:128 final size:132
Alignment explanation
Indices: 27866479--27866860 Score: 342
Period size: 128 Copynumber: 2.9 Consensus size: 132
27866469 ACTTATTCTG
* * *
27866479 TCTGCTCCACTACAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCAACTTCAG
1 TCTGCCCCACTACAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCAA
* * * * *
27866544 GGAGATAGGATTA-TAGGCTTAAATCTGCTCCACTGCACCTTCAGAGAGATAAGATTCGCCATTT
66 AGAGATAGGATTATTGGGCTT-AATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TCGCCAATG
*
27866608 TGGG
129 TGGA
* * * * * * *
27866612 TCTGCCCCACTACAACTTCAGGGGGATAAGACCTGCTTA-TTCAGTCTGCTCC-CTGCAACTTCG
1 TCTGCCCCACTACAACTTCAGAGAGATAAGATCTG-TGATTTTAATCCGCTCCACTGCAACTTC-
* * ** * * *
27866675 ATAAGA-CTCGCTTTCTTGGG-----TCTGCTCCATTGCAACTTCAGTGAGATAAGA-C-CCAAT
64 A-AAGAGATAGGATTATTGGGCTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCGCCAAT
27866732 GT-GA
128 GTGGA
* * * *
27866736 TCTG-CTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAA
1 TCTGCCCCACTACAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCAA
* *
27866800 AGAGAT-GGATTATTGGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTCGCCA
66 AGAGATAGGATTATTGGGC-TTAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TCGCCA
27866861 TCTTCAACCT
Statistics
Matches: 192, Mismatches: 41, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
122 14 0.07
123 35 0.18
124 15 0.08
125 5 0.03
126 1 0.01
128 56 0.29
130 1 0.01
131 3 0.02
132 10 0.05
133 45 0.23
134 7 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
TCTGCCCCACTACAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCAA
AGAGATAGGATTATTGGGCTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCGCCAATGTG
GA
Found at i:27866890 original size:44 final size:44
Alignment explanation
Indices: 27866841--27866938 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
27866831 ACTGTAACTT
* *
27866841 CAGGGAGATAAGA-TTCGCCATCTTCAACCTATTCCACTGCTGAC
1 CAGGGAGATAAGACTT-ACAATCTTCAACCTATTCCACTGCTGAC
* * *
27866885 TAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTC
1 CAGGGAGATAAGACTTACAATCTTCAACCTATTCCACTGCTGAC
27866929 CAGGGAGATA
1 CAGGGAGATA
27866939 GGGCTGGGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 45 0.96
45 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (44 bp):
CAGGGAGATAAGACTTACAATCTTCAACCTATTCCACTGCTGAC
Found at i:27867114 original size:44 final size:44
Alignment explanation
Indices: 27867061--27867204 Score: 137
Period size: 44 Copynumber: 3.3 Consensus size: 44
27867051 ATTGTCGGTG
27867061 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * ****
27867105 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
*
27867149 CAGGAAGGCAAGATCTGCAATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
*
27867193 CAGGGAGGCAAG
1 CAGGAAGGCAAG
27867205 GCTGGTGTCA
Statistics
Matches: 70, Mismatches: 28, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
43 18 0.26
44 35 0.50
45 17 0.24
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.23
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
Found at i:27867174 original size:176 final size:176
Alignment explanation
Indices: 27866940--27867521 Score: 680
Period size: 176 Copynumber: 3.3 Consensus size: 176
27866930 AGGGAGATAG
* * * * * * * ** *
27866940 GGCTGGGGTCATCGATCTGCTTTGCTGTCGGTGCAGGAAAGTAAAATCTATTATTTTTAACCTGT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * * * *
27867005 TTCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTACGATCTGCTTCATTGTCGGTGCAGGAAGGC
66 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTACGATCTGCTTCGTTGTCAGTACAGGAAGGC
* *
27867070 AAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAA
131 AAGATCTGCTATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAA
* *
27867116 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
27867181 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTC-ATTGATCTGCTTCGTTGTCAATACAGGAAGG
66 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTA-CGATCTGCTTCGTTGTCAGTACAGGAAGG
* * * ** * *
27867245 CAAGGTCTGTTATCTTCAGTCTGCTCCACTGCAACCTAGGAAGGCAA
130 CAAGATCTGCTATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAA
* ** * * **
27867292 GACTGGTGTCTTCGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * * ** * * * * * * *
27867357 TCCACTGTAATCTTGGGAGGCAAGACTGGTGTCTTCGATTTGCTTTGTTGTCTGTACAAGAAGGT
66 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTACGATCTGCTTCGTTGTCAGTACAGGAAGGC
* *
27867422 AAGATCTGCTATTTTCAACTTGCTCCACTGCAACCGAGGGAGGCAA
131 AAGATCTGCTATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAA
* * *
27867468 GGCTGGTGTCTTTGATCTGCTTCGCTGGCCGTACAGGAAGGCAAGATCTGCTAT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTAT
27867522 CTTCAATGAT
Statistics
Matches: 342, Mismatches: 62, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
175 1 0.00
176 341 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (176 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTACGATCTGCTTCGTTGTCAGTACAGGAAGGC
AAGATCTGCTATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAA
Found at i:27867246 original size:44 final size:43
Alignment explanation
Indices: 27867105--27867336 Score: 148
Period size: 44 Copynumber: 5.3 Consensus size: 43
27867095 CGCTGCAACC
* ** *
27867105 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTT-GATCTGCTTCGCTGTCAATA
* * * * * * **
27867149 CAGGAAGGCAAGATCTGCAAT-TTTTAACCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTG--GTGTCTTGATCTGCTTCGCTGTCAATA
* *
27867193 CAGGGAGGCAAGGCTGGTGTCATTGATCTGCTTCGTTGTCAATA
1 CAGGAAGGCAAGGCTGGTGTC-TTGATCTGCTTCGCTGTCAATA
* * * * * *
27867237 CAGGAAGGCAAGGTCTGTTATCTTCAGTCTGCTCCACTG-CAA-C
1 CAGGAAGGCAAGG-CTGGTGTCTTGA-TCTGCTTCGCTGTCAATA
* * *
27867280 CTAGGAAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTGTTAGTA
1 C-AGGAAGGCAAGGCTGGTGTCTT-GATCTGCTTCGCTGTCAATA
27867325 CAGGAAGGCAAG
1 CAGGAAGGCAAG
27867337 ATCTGCTATC
Statistics
Matches: 138, Mismatches: 38, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 34 0.25
44 68 0.49
45 30 0.22
46 3 0.02
47 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (43 bp):
CAGGAAGGCAAGGCTGGTGTCTTGATCTGCTTCGCTGTCAATA
Found at i:27867359 original size:264 final size:264
Alignment explanation
Indices: 27867009--27867526 Score: 685
Period size: 264 Copynumber: 2.0 Consensus size: 264
27866999 ACCTGTTTCG
* * * * *
27867009 CTGCAACCCAGGGAGGCAAGGCTAGTGTCTACGATCTGCTTCATTGTCGGTGCAGGAAGGCAAGA
1 CTGCAACCCAGGAAGGCAAGACTAGTGTCTACGATCTGCTTCACTGTCAGTACAGGAAGGCAAGA
* * * *
27867074 TCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTC
66 TCTGCTATCTTCAACCTGCTCCACTGCAACCCAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTC
* * * *
27867139 GCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAA
131 GCTGTCGGTACAAGAAGGCAAGATCTGCAATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAA
* * * *
27867204 GGCTGGTGTCATTGATCTGCTTCGTTGTCAATACAGGAAGGCAAGGTCTGTTATCTTCAGTCTGC
196 GGCTGGTGTCATTGATCTGCTTCGCTGGCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGC
27867269 TCCA
261 TCCA
* * * * *
27867273 CTGCAACCTAGGAAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGA
1 CTGCAACCCAGGAAGGCAAGACTAGTGTCTACGATCTGCTTCACTGTCAGTACAGGAAGGCAAGA
** * * ** * *
27867338 TCTGCTATCTTCAGTCTGCTCCACTGTAATCTTGGGAGGCAAGACTGGTGTCTTCGATTTGCTTT
66 TCTGCTATCTTCAACCTGCTCCACTGCAACCCAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTC
* * * * * *
27867403 GTTGTCTGTACAAGAAGGTAAGATCTGCTATTTTCAACTTGCTCCACTGCAACCGAGGGAGGCAA
131 GCTGTCGGTACAAGAAGGCAAGATCTGCAATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAA
* **
27867468 GGCTGGTGTCTTTGATCTGCTTCGCTGGCCGTACAGGAAGGCAAGATCTGCTATCTTCA
196 GGCTGGTGTCATTGATCTGCTTCGCTGGCAATACAGGAAGGCAAGATCTGCTATCTTCA
27867527 ATGATCTGTT
Statistics
Matches: 215, Mismatches: 39, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
264 215 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (264 bp):
CTGCAACCCAGGAAGGCAAGACTAGTGTCTACGATCTGCTTCACTGTCAGTACAGGAAGGCAAGA
TCTGCTATCTTCAACCTGCTCCACTGCAACCCAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTC
GCTGTCGGTACAAGAAGGCAAGATCTGCAATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAA
GGCTGGTGTCATTGATCTGCTTCGCTGGCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGC
TCCA
Found at i:27867378 original size:44 final size:44
Alignment explanation
Indices: 27867238--27867381 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 44
27867228 TTGTCAATAC
* * * *
27867238 AGGAAGGCAAGGTCTGTTATCTTCAGTCTGCTCCACTGCAACCT
1 AGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTAATCT
* * * * *
27867282 AGGAAGGCAAGA-CTGGTGTCTTC-GATCTGCTTCGCTGTTAGTAC-
1 AGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTCCACTG-TAAT-CT
27867326 AGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTAATCT
1 AGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTAATCT
* *
27867370 TGGGAGGCAAGA
1 AGGAAGGCAAGA
27867382 CTGGTGTCTT
Statistics
Matches: 79, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
42 1 0.01
43 20 0.25
44 37 0.47
45 20 0.25
46 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (44 bp):
AGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTAATCT
Found at i:27867527 original size:88 final size:88
Alignment explanation
Indices: 27867009--27867527 Score: 603
Period size: 88 Copynumber: 5.9 Consensus size: 88
27866999 ACCTGTTTCG
* * ** * *
27867009 CTGCAACCCAGGGAGGCAAGGCTAGTGTCTACGATCTGCTTCATTGTCGGTGCAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
* * * *
27867074 TCTGCTATTTTTAACCTGCTCCG
66 TCTGCTATCTTCAACTTGCTCCA
* *
27867097 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
* * * * *
27867162 TCTGCAATTTTTAACCTGCTCCG
66 TCTGCTATCTTCAACTTGCTCCA
* *
27867185 CTGCAACCCAGGGAGGCAAGGCTGGTGTCATT-GATCTGCTTCGTTGTCAATACAGGAAGGCAAG
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTC-TTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAG
* * *
27867249 GTCTGTTATCTTC-AGTCTGCTCCA
65 ATCTGCTATCTTCAACT-TGCTCCA
* * * *
27867273 CTGCAACCTAGGAAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
*
27867338 TCTGCTATCTTC-AGTCTGCTCCA
66 TCTGCTATCTTCAACT-TGCTCCA
* * ** * * * * * * *
27867361 CTGTAATCTTGGGAGGCAAGACTGGTGTCTTCGATTTGCTTTGTTGTCTGTACAAGAAGGTAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
*
27867426 TCTGCTATTTTCAACTTGCTCCA
66 TCTGCTATCTTCAACTTGCTCCA
* * * *
27867449 CTGCAACCGAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGGCCGTACAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
27867514 TCTGCTATCTTCAA
66 TCTGCTATCTTCAA
27867528 TGATCTGTTC
Statistics
Matches: 375, Mismatches: 52, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
87 3 0.01
88 368 0.98
89 4 0.01
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
TCTGCTATCTTCAACTTGCTCCA
Found at i:27868900 original size:14 final size:15
Alignment explanation
Indices: 27868877--27868909 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
27868867 ATCGATGCTT
27868877 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
27868891 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
27868906 TTCC
1 TTCC
27868910 CAACTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:27876218 original size:24 final size:24
Alignment explanation
Indices: 27876180--27876233 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
27876170 ATCCAAGCAA
* * *
27876180 GCTTTGTGCCGGTGTATTTATTGG
1 GCTTTGGGCCAGTGTATTTATCGG
*
27876204 GCTTTGGGCCAGTGTGTTTATCGG
1 GCTTTGGGCCAGTGTATTTATCGG
27876228 GCTTTG
1 GCTTTG
27876234 TGCCTAGCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.07, C:0.15, G:0.35, T:0.43
Consensus pattern (24 bp):
GCTTTGGGCCAGTGTATTTATCGG
Found at i:27876658 original size:13 final size:13
Alignment explanation
Indices: 27876640--27876685 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
27876630 GAACTTTGTT
27876640 ATTTAATTTTATA
1 ATTTAATTTTATA
27876653 ATTTAATTTT-T-
1 ATTTAATTTTATA
27876664 ATTTAATTTTATA
1 ATTTAATTTTATA
*
27876677 ATTTTATTT
1 ATTTAATTT
27876686 GTTATGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 10 0.33
12 2 0.07
13 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTAATTTTATA
Found at i:27876670 original size:24 final size:25
Alignment explanation
Indices: 27876634--27876699 Score: 107
Period size: 24 Copynumber: 2.6 Consensus size: 25
27876624 GGATAGGAAC
27876634 TTTGTTATTTAATTTTATAATTTAA
1 TTTGTTATTTAATTTTATAATTTAA
*
27876659 TTT-TTATTTAATTTTATAATTTTA
1 TTTGTTATTTAATTTTATAATTTAA
27876683 TTTGTTATGTTAATTTT
1 TTTGTTAT-TTAATTTT
27876700 TGTAAGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
24 23 0.61
25 7 0.18
26 8 0.21
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (25 bp):
TTTGTTATTTAATTTTATAATTTAA
Found at i:27876698 original size:13 final size:11
Alignment explanation
Indices: 27876638--27876700 Score: 63
Period size: 13 Copynumber: 5.2 Consensus size: 11
27876628 AGGAACTTTG
27876638 TTATTTAATTT
1 TTATTTAATTT
27876649 TATAATTTAATTT
1 T-T-ATTTAATTT
27876662 TTATTTAATTT
1 TTATTTAATTT
*
27876673 TATAATTTTATTT
1 T-T-ATTTAATTT
27876686 GTTATGTTAATTT
1 -TTAT-TTAATTT
27876699 TT
1 TT
27876701 GTAAGATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
11 11 0.25
12 7 0.16
13 25 0.57
14 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TTATTTAATTT
Found at i:27886000 original size:48 final size:48
Alignment explanation
Indices: 27885925--27886070 Score: 177
Period size: 48 Copynumber: 3.1 Consensus size: 48
27885915 TACTATGCGT
* * * *
27885925 ACCGATAATCTGTTATGACACACGGGTGGGACGGTCTGTGTGCAAGCC
1 ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
* * *
27885973 ACCGATATTCTGTTGTGACACAAGGGTGGCACGGACTATGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * *
27886021 ACCAAGAATCTGTTATTACACGA-GGTGGTACGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
27886068 ACC
1 ACC
27886071 AAGAAATTTG
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 25 0.30
48 58 0.70
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (48 bp):
ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
Found at i:27895270 original size:21 final size:22
Alignment explanation
Indices: 27895229--27895271 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27895219 TCAAGCTCTT
27895229 CAATGCAATGTTCTGAAAATAC
1 CAATGCAATGTTCTGAAAATAC
27895251 CAATGCAATGTTCT-AAAATAC
1 CAATGCAATGTTCTGAAAATAC
27895272 AACTAAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (22 bp):
CAATGCAATGTTCTGAAAATAC
Found at i:27920618 original size:18 final size:17
Alignment explanation
Indices: 27920595--27920630 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27920585 ATAACCAACG
*
27920595 AATAAAAATAACTAAAAA
1 AATAAAAA-AAATAAAAA
27920613 AATAAAAAAAATAAAAA
1 AATAAAAAAAATAAAAA
27920630 A
1 A
27920631 TGAATCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AATAAAAAAAATAAAAA
Found at i:27924131 original size:16 final size:16
Alignment explanation
Indices: 27924112--27924148 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
27924102 TATTTTATTA
*
27924112 TTTTATTATTCCGAAT
1 TTTTATTATTCCAAAT
*
27924128 TTTTATTATTCTAAAT
1 TTTTATTATTCCAAAT
27924144 TTTTA
1 TTTTA
27924149 ATAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTATTATTCCAAAT
Found at i:27926816 original size:18 final size:19
Alignment explanation
Indices: 27926773--27926810 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27926763 TAACATATAG
27926773 TTAAT-AATTTTAAAATTT
1 TTAATAAATTTTAAAATTT
*
27926791 TTAATAAATTTTTAAATTT
1 TTAATAAATTTTAAAATTT
27926810 T
1 T
27926811 ACTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATAAATTTTAAAATTT
Found at i:27934347 original size:32 final size:32
Alignment explanation
Indices: 27934306--27934370 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
27934296 CAACCCATAA
*
27934306 TACCTAGATCCTATCTAAAAATGCGTTACAAG
1 TACCTAGATCCTATCTAAAAAAGCGTTACAAG
27934338 TACCTAGATCCTATCTAAAAAAGCGTTACAAG
1 TACCTAGATCCTATCTAAAAAAGCGTTACAAG
27934370 T
1 T
27934371 TTATCAATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (32 bp):
TACCTAGATCCTATCTAAAAAAGCGTTACAAG
Found at i:27934804 original size:49 final size:49
Alignment explanation
Indices: 27934732--27934830 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
27934722 CCTATAATTC
27934732 AATACAAATAAAAAATAACCCAACACTAAGCCATATATTGAATCCAACT
1 AATACAAATAAAAAATAACCCAACACTAAGCCATATATTGAATCCAACT
*
27934781 AATACAAATAAATAATAACCCAACACTAAGCCATATATTGAATCCAACT
1 AATACAAATAAAAAATAACCCAACACTAAGCCATATATTGAATCCAACT
27934830 A
1 A
27934831 GTAATAACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.53, C:0.22, G:0.04, T:0.21
Consensus pattern (49 bp):
AATACAAATAAAAAATAACCCAACACTAAGCCATATATTGAATCCAACT
Found at i:27934828 original size:24 final size:24
Alignment explanation
Indices: 27934751--27934828 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
27934741 AAAAAATAAC
27934751 CCAACACTAAGCCATATATTGAAT
1 CCAACACTAAGCCATATATTGAAT
* *** * * *
27934775 CCAACTAATACAAATAAATAAT-AAC
1 CCAAC-ACTA-AGCCATATATTGAAT
27934800 CCAACACTAAGCCATATATTGAAT
1 CCAACACTAAGCCATATATTGAAT
27934824 CCAAC
1 CCAAC
27934829 TAGTAATAAC
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
23 6 0.16
24 15 0.41
25 10 0.27
26 6 0.16
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.22
Consensus pattern (24 bp):
CCAACACTAAGCCATATATTGAAT
Found at i:27934843 original size:49 final size:49
Alignment explanation
Indices: 27934732--27934845 Score: 176
Period size: 49 Copynumber: 2.3 Consensus size: 49
27934722 CCTATAATTC
* *
27934732 AATACAAATAAAAAATAACCCAACACTAAGCCATATATTGAATCCAACT
1 AATACAAACAAATAATAACCCAACACTAAGCCATATATTGAATCCAACT
*
27934781 AATACAAATAAATAATAACCCAACACTAAGCCATATATTGAATCCAACT
1 AATACAAACAAATAATAACCCAACACTAAGCCATATATTGAATCCAACT
*
27934830 AGTA-ATAACAAATAAT
1 AATACA-AACAAATAAT
27934846 GAGGGAATTC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 1 0.02
49 60 0.98
ACGTcount: A:0.54, C:0.20, G:0.04, T:0.22
Consensus pattern (49 bp):
AATACAAACAAATAATAACCCAACACTAAGCCATATATTGAATCCAACT
Found at i:27941514 original size:54 final size:54
Alignment explanation
Indices: 27941426--27941540 Score: 176
Period size: 54 Copynumber: 2.1 Consensus size: 54
27941416 TTCAATCTGC
* *
27941426 TCCACTGCAACTTCAGAAAGATAAGATCTGTCATAATTTGTTACTTTAATCAGT
1 TCCACTGCAACTTCAGAAAGATAAGATCTATCATAATTTGTTACATTAATCAGT
* * * *
27941480 TCCATTGCAACTTTAGGAAGATAAGATCTATCATAATTTGTTGCATTAATCAGT
1 TCCACTGCAACTTCAGAAAGATAAGATCTATCATAATTTGTTACATTAATCAGT
27941534 TCCACTG
1 TCCACTG
27941541 TAATGCCAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (54 bp):
TCCACTGCAACTTCAGAAAGATAAGATCTATCATAATTTGTTACATTAATCAGT
Found at i:27941637 original size:197 final size:197
Alignment explanation
Indices: 27941300--27941672 Score: 570
Period size: 197 Copynumber: 1.9 Consensus size: 197
27941290 CGACTTCAGA
* * * *
27941300 AAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAATGCTAGGGAAATAAGATT
1 AAGATAAGATCCACCATAATTTGTAGCATTAATCAGTTCCACTGCAATGCCAGGGAAATAAGATT
* * **
27941365 CTCTGTCTTCAGTCTACTCTGCTACAACATTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCA
66 CACTGTCTTCAGTCTACTCCGCTACAACATTAGGGAGATAACACTGGTGGCTTCAATCTGCTCCA
* *
27941430 CTGCAACTTCAGAAAGATAAGATCTGTCATAATTTGTTA-CTTTAATCAGTTCCATTGCAACTTT
131 CTGAAACTTCAGAAAGATAAGATCTGTAATAATTTG-TAGCTTTAATCAGTTCCATTGCAACTTT
27941494 AGG
195 AGG
* * * *
27941497 AAGATAAGATCTATCATAATTTGTTGCATTAATCAGTTCCACTGTAATGCCAGGGAAATAAGATT
1 AAGATAAGATCCACCATAATTTGTAGCATTAATCAGTTCCACTGCAATGCCAGGGAAATAAGATT
* *
27941562 CACTGTCTTCAGTCTGCTCCGCTGCAAC-TTCAGGGAGATAACACTGGTGGCTTCAATCTGCTCC
66 CACTGTCTTCAGTCTACTCCGCTACAACATT-AGGGAGATAACACTGGTGGCTTCAATCTGCTCC
27941626 ACTGAAACTTCAGAAAGATAAGATCTGTAATAATTTGTAGCTTTAAT
130 ACTGAAACTTCAGAAAGATAAGATCTGTAATAATTTGTAGCTTTAAT
27941673 ATGTTCTGCT
Statistics
Matches: 158, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
196 4 0.03
197 154 0.97
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (197 bp):
AAGATAAGATCCACCATAATTTGTAGCATTAATCAGTTCCACTGCAATGCCAGGGAAATAAGATT
CACTGTCTTCAGTCTACTCCGCTACAACATTAGGGAGATAACACTGGTGGCTTCAATCTGCTCCA
CTGAAACTTCAGAAAGATAAGATCTGTAATAATTTGTAGCTTTAATCAGTTCCATTGCAACTTTA
GG
Found at i:27941755 original size:143 final size:143
Alignment explanation
Indices: 27941480--27942006 Score: 670
Period size: 143 Copynumber: 3.7 Consensus size: 143
27941470 TTTAATCAGT
* * * * * * * **
27941480 TCCATTGCAACTTTAGGAAGATAAGATCTA-TCATAATTTGTTGCATTAATCAGTTCCACTGTAA
1 TCCACTGCAACTTCAGAAAGATAAGAT-TAGCCATAATTTGTAGCTTTAATCTGTTCCACTACAA
* * * **
27941544 TGCCAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAACACTGG
65 CGCTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTGCAACTTCAAGGAGATAAGGCTGG
27941609 TGGCTTCAATCTGC
130 TGGCTTCAATCTGC
* ** * **
27941623 TCCACTGAAACTTCAGAAAGATAAGATCT-GTAATAATTTGTAGCTTTAATATGTTCTGCTACAA
1 TCCACTGCAACTTCAGAAAGATAAGAT-TAGCCATAATTTGTAGCTTTAATCTGTTCCACTACAA
* *
27941687 CGCTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTTCGC-GACAACTTCAAGGAGATAAGGCTA
65 CGCTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTG-CAACTTCAAGGAGATAAGGCTG
27941751 GTGGCTTCAATCTGC
129 GTGGCTTCAATCTGC
*
27941766 TCCATTGCAACTTCA-AGAAGATAAGATTAGCCATAATTTGTAGCTTTAATCTGTTCCACTACAA
1 TCCACTGCAACTTCAGA-AAGATAAGATTAGCCATAATTTGTAGCTTTAATCTGTTCCACTACAA
* * *
27941830 CGGC-AGGGAAATAAGATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTC-AGGTAGATAAGGTT
65 C-GCTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTGCAACTTCAAGG-AGATAAGGCT
27941893 GGTGGCTTCAATCTGC
128 GGTGGCTTCAATCTGC
* ** *
27941909 TCCACTGCAACTTCAGAAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCCACTGTAAT
1 TCCACTGCAACTTCAGAAAGATAAGATTAGCCATAATTTGTAGCTTTAATCTGTTCCACTACAAC
* *
27941974 GCTAGGGAAATAAGATTCGCCGTCTTCAGTCTG
66 GCTAGGGAAATAAGATTCACTGTCTTCAGTCTG
27942007 TTTCGCTAGA
Statistics
Matches: 336, Mismatches: 39, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
142 8 0.02
143 324 0.96
144 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (143 bp):
TCCACTGCAACTTCAGAAAGATAAGATTAGCCATAATTTGTAGCTTTAATCTGTTCCACTACAAC
GCTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGT
GGCTTCAATCTGC
Found at i:27941824 original size:286 final size:286
Alignment explanation
Indices: 27941480--27942012 Score: 782
Period size: 286 Copynumber: 1.9 Consensus size: 286
27941470 TTTAATCAGT
* * * * ** *
27941480 TCCATTGCAACTTTAGGAAGATAAGATCTATCATAATTTGTTGCATTAATCAGTTCCACTGTAAT
1 TCCATTGCAACTTCAAGAAGATAAGATCTACCATAATTTGTAGCATTAATCAGTTCCACTACAAC
*
27941545 GCCAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAACACTGGT
66 GCCAGGGAAATAAGATTCACTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAACACTGGT
*
27941610 GGCTTCAATCTGCTCCACTGAAACTTCAGAAAGATAAGA-TCTGTAATAATTTGTAGCTTTAATA
131 GGCTTCAATCTGCTCCACTGAAACTTCAGAAAGATAAGATTC-GCAATAATTTGTAGCTTTAATA
** *
27941674 TGTTCTGCTACAACGCTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTTCGCGACAACTTCAAG
195 TGTTCCACTACAACGCTAGGGAAATAAGATTCACCGTCTTCAGTCTGCTTCGCGACAACTTCAAG
27941739 GAGATAAGGCTAGTGGCTTCAATCTGC
260 GAGATAAGGCTAGTGGCTTCAATCTGC
* *
27941766 TCCATTGCAACTTCAAGAAGATAAGAT-TAGCCATAATTTGTAGCTTTAATCTGTTCCACTACAA
1 TCCATTGCAACTTCAAGAAGATAAGATCTA-CCATAATTTGTAGCATTAATCAGTTCCACTACAA
* * * ***
27941830 CGGCAGGGAAATAAGATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTCAGGTAGATAAGGTTGG
65 CGCCAGGGAAATAAGATTCACTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAACACTGG
* * *
27941895 TGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTCGCCATAATTTGTAGCTTTAATC
130 TGGCTTCAATCTGCTCCACTGAAACTTCAGAAAGATAAGATTCGCAATAATTTGTAGCTTTAATA
** * * *
27941960 TGTTCCACTGTAATGCTAGGGAAATAAGATTCGCCGTCTTCAGTCTGTTTCGC
195 TGTTCCACTACAACGCTAGGGAAATAAGATTCACCGTCTTCAGTCTGCTTCGC
27942013 TAGAGATAAG
Statistics
Matches: 217, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
285 2 0.01
286 213 0.98
287 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (286 bp):
TCCATTGCAACTTCAAGAAGATAAGATCTACCATAATTTGTAGCATTAATCAGTTCCACTACAAC
GCCAGGGAAATAAGATTCACTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAACACTGGT
GGCTTCAATCTGCTCCACTGAAACTTCAGAAAGATAAGATTCGCAATAATTTGTAGCTTTAATAT
GTTCCACTACAACGCTAGGGAAATAAGATTCACCGTCTTCAGTCTGCTTCGCGACAACTTCAAGG
AGATAAGGCTAGTGGCTTCAATCTGC
Found at i:27949971 original size:14 final size:14
Alignment explanation
Indices: 27949952--27949999 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
27949942 GAGTTATAAC
27949952 TATTTAAATAATAT
1 TATTTAAATAATAT
*
27949966 TATTTAAATAGTAT
1 TATTTAAATAATAT
*
27949980 AATATTAAATGAATAAT
1 TAT-TTAAAT-AAT-AT
27949997 TAT
1 TAT
27950000 GTTTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 15 0.56
15 6 0.22
16 2 0.07
17 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (14 bp):
TATTTAAATAATAT
Found at i:27958906 original size:27 final size:27
Alignment explanation
Indices: 27958888--27959176 Score: 328
Period size: 27 Copynumber: 10.7 Consensus size: 27
27958878 AATGCCCCCA
* *
27958888 TAGGGTAAAATAACCGAAATACCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * * * *
27958915 TAAGGCATAAT-ACCGAAATACCCCTA
1 TAGGGTAAAATGACCGTAATACCCCTG
* *
27958941 TAAGGTAAAATGATCGTAATACCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
27958968 TAGGGTAAAATGATCGTAATGCCCTTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
27958995 TAGGATAAAGTAACCGTAATACCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* *
27959022 TAGGGTAAAATGTCCGTAATGCCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
*
27959049 TAGGGTAAAATGACCGTAATGCCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
*
27959076 TAGGATAAAATGACCGTAATACCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* *
27959103 TAGGGTAAAATGATCGTAATGCCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* ** * *
27959130 TACGGTAAAATGATGGTAATACCCTTA
1 TAGGGTAAAATGACCGTAATACCCCTG
*
27959157 TAGGGTAAAATGACAGTAAT
1 TAGGGTAAAATGACCGTAAT
27959177 GCCCTGGTGG
Statistics
Matches: 224, Mismatches: 37, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 23 0.10
27 201 0.90
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
TAGGGTAAAATGACCGTAATACCCCTG
Found at i:27959292 original size:24 final size:23
Alignment explanation
Indices: 27959217--27959298 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
27959207 CTCGAGGTCA
* *
27959217 AATGATT-ATTTTGTCTGTGGTTA
1 AATGATTGATTTT-TCTGTGTTTG
* *
27959240 AATGACTGATTTGTCTGTGTTTGG
1 AATGATTGATTTTTCTGTGTTT-G
*
27959264 TATGATTGATTTTTCTGTGATTTG
1 AATGATTGATTTTTCTGTG-TTTG
27959288 AATGATTGATT
1 AATGATTGATT
27959299 ATGAGGATGG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
23 14 0.29
24 31 0.65
25 3 0.06
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (23 bp):
AATGATTGATTTTTCTGTGTTTG
Found at i:27959422 original size:27 final size:27
Alignment explanation
Indices: 27959370--27959434 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
27959360 AGTACTGTAT
* *
27959370 TGGTGGCTCTG-CACAATCACTGTTAC
1 TGGTGGCTTTGCCACAATCACTATTAC
27959396 TGGTGGCTTTGCCACATAT-ACTATTAC
1 TGGTGGCTTTGCCACA-ATCACTATTAC
**
27959423 TGGCAGCTTTGC
1 TGGTGGCTTTGC
27959435 TGCGATACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.30
27 21 0.64
28 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
TGGTGGCTTTGCCACAATCACTATTAC
Found at i:27959451 original size:26 final size:26
Alignment explanation
Indices: 27959413--27959463 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
27959403 TTTGCCACAT
27959413 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* * *
27959439 ATACTGTTGCTGGCAGTTTTGCTGC
1 ATACTATTACTGGCAGCTTTGCTGC
27959464 AATGCCACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:27959511 original size:32 final size:32
Alignment explanation
Indices: 27959470--27959705 Score: 198
Period size: 32 Copynumber: 7.4 Consensus size: 32
27959460 CTGCAATGCC
*
27959470 ACTGATGGCTTTGTGTCGATCATAGTACCGTT
1 ACTGATGGCTTTGTGCCGATCATAGTACCGTT
* *
27959502 ACTGATGGCTTTGTGCCAATCATAGTACCATT
1 ACTGATGGCTTTGTGCCGATCATAGTACCGTT
* * *
27959534 ACTGATGGCTTTGTGCTGATCATATTATCGTT
1 ACTGATGGCTTTGTGCCGATCATAGTACCGTT
* * * *
27959566 A-TCGATGGCTGTGTACCGATCAT-TTCACTGTT
1 ACT-GATGGCTTTGTGCCGATCATAGT-ACCGTT
* *
27959598 ACTGATGGCTGTGTGCC-AGTCATA-TCACTC-CT
1 ACTGATGGCTTTGTGCCGA-TCATAGT-AC-CGTT
* *
27959630 ACTGATGGCTTTATGCCGATCAT-GTTACTGTT
1 ACTGATGGCTTTGTGCCGATCATAG-TACCGTT
* * * *
27959662 GCTGATGGCTGTGTGCCGATCATA-TCACTGCT
1 ACTGATGGCTTTGTGCCGATCATAGT-ACCGTT
27959694 ACTGATGGCTTT
1 ACTGATGGCTTT
27959706 TTGCTAATCA
Statistics
Matches: 166, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
31 5 0.03
32 158 0.95
33 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (32 bp):
ACTGATGGCTTTGTGCCGATCATAGTACCGTT
Found at i:27959600 original size:64 final size:64
Alignment explanation
Indices: 27959470--27959734 Score: 211
Period size: 64 Copynumber: 4.2 Consensus size: 64
27959460 CTGCAATGCC
* * * * * **
27959470 ACTGATGGCTTTGTG-TCGATCATAGTACCGTTACTGATGGCTTTGTGCCAATCATAGTACCATT
1 ACTGATGGCTGTGTGCT-GATCATATTATCGTTACTGATGGCTTTGTGCCGATCATATTACTGTT
* * *
27959534 ACTGATGGCTTTGTGCTGATCATATTATCGTTA-TCGATGGCTGTGTACCGATCAT-TTCACTGT
1 ACTGATGGCTGTGTGCTGATCATATTATCGTTACT-GATGGCTTTGTGCCGATCATATT-ACTGT
27959597 T
64 T
* * * * *
27959598 ACTGATGGCTGTGTGC-CAGTCATATCACTC-CTACTGATGGCTTTATGCCGATCATGTTACTGT
1 ACTGATGGCTGTGTGCTGA-TCATATTA-TCGTTACTGATGGCTTTGTGCCGATCATATTACTGT
27959661 T
64 T
* * * * * ** *
27959662 GCTGATGGCTGTGTGCCGATCATATCA-CTGCTACTGATGGCTTTTTGCTAATCACATTACTG-T
1 ACTGATGGCTGTGTGCTGATCATATTATC-GTTACTGATGGCTTTGTGCCGATCATATTACTGTT
*
27959725 ACTTATGGCT
1 ACTGATGGCT
27959735 TGTAGCCATT
Statistics
Matches: 167, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 12 0.07
64 147 0.88
65 7 0.04
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (64 bp):
ACTGATGGCTGTGTGCTGATCATATTATCGTTACTGATGGCTTTGTGCCGATCATATTACTGTT
Found at i:27959637 original size:96 final size:96
Alignment explanation
Indices: 27959471--27959703 Score: 260
Period size: 96 Copynumber: 2.4 Consensus size: 96
27959461 TGCAATGCCA
* ** * * *
27959471 CTGATGGCTTTGTGTCGATCATAGT-ACCGTTACTGATGGCTTTGTGCCAATCATAGTACCATTA
1 CTGATGGCTGTGTACCGATCATA-TCACTGTTACTGATGGCTGTGTGCCAATCATAGTACCACTA
* *
27959535 CTGATGGCTTTGTGCTGATCATATTA-TCGTT-
65 CTGATGGCTTTATGCCGATCATATTACT-GTTG
* * *
27959566 ATCGATGGCTGTGTACCGATCATTTCACTGTTACTGATGGCTGTGTGCCAGTCATA-TCACTC-C
1 CT-GATGGCTGTGTACCGATCATATCACTGTTACTGATGGCTGTGTGCCAATCATAGT-AC-CAC
*
27959629 TACTGATGGCTTTATGCCGATCATGTTACTGTTG
63 TACTGATGGCTTTATGCCGATCATATTACTGTTG
* *
27959663 CTGATGGCTGTGTGCCGATCATATCACTGCTACTGATGGCT
1 CTGATGGCTGTGTACCGATCATATCACTGTTACTGATGGCT
27959704 TTTTGCTAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
95 3 0.03
96 110 0.95
97 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (96 bp):
CTGATGGCTGTGTACCGATCATATCACTGTTACTGATGGCTGTGTGCCAATCATAGTACCACTAC
TGATGGCTTTATGCCGATCATATTACTGTTG
Found at i:27959752 original size:22 final size:21
Alignment explanation
Indices: 27959727--27959791 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
27959717 ATTACTGTAC
27959727 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* *
27959749 TTATAGCTTATAGCTA-TCTTGT
1 TTATGGCTT-TAGCCATTC-TGT
*
27959771 TTACGGCTCTTAGCCATTCTG
1 TTATGGCT-TTAGCCATTCTG
27959792 ACTATTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.06
22 29 0.85
23 3 0.09
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:27959814 original size:26 final size:26
Alignment explanation
Indices: 27959785--27959837 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
27959775 GGCTCTTAGC
* * *
27959785 CATTCTGACTATTGGCAGCTCTGCTG
1 CATTATGACTACTGGCAGCTATGCTG
*
27959811 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGGCAGCTATGCTG
27959837 C
1 C
27959838 GATATTGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (26 bp):
CATTATGACTACTGGCAGCTATGCTG
Found at i:27962654 original size:13 final size:13
Alignment explanation
Indices: 27962636--27962662 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27962626 TATTAATAGT
27962636 TCAATATTCAAAA
1 TCAATATTCAAAA
27962649 TCAATATTCAAAA
1 TCAATATTCAAAA
27962662 T
1 T
27962663 TTCTAGAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (13 bp):
TCAATATTCAAAA
Found at i:27965066 original size:13 final size:13
Alignment explanation
Indices: 27965048--27965073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27965038 ACCTTAAAAC
27965048 CTTCTTCCAATGT
1 CTTCTTCCAATGT
27965061 CTTCTTCCAATGT
1 CTTCTTCCAATGT
27965074 GAAACCTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
CTTCTTCCAATGT
Found at i:27969226 original size:11 final size:11
Alignment explanation
Indices: 27969212--27969242 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
27969202 AAAAACACTG
27969212 TTTTCACACCA
1 TTTTCACACCA
27969223 TTTTCACACCA
1 TTTTCACACCA
27969234 TTTTCACAC
1 TTTTCACAC
27969243 TACCTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (11 bp):
TTTTCACACCA
Found at i:27973537 original size:41 final size:41
Alignment explanation
Indices: 27973490--27973574 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
27973480 TTCATCGAAA
*
27973490 ATTACTTAGTACAAATCGTTTATCACACTCCAAACATTCAT
1 ATTACTTAGTACAAATCGTTTATCACACGCCAAACATTCAT
*
27973531 ATTACTTATTACAAATCGTTTATCACACGCCAAACATTCAT
1 ATTACTTAGTACAAATCGTTTATCACACGCCAAACATTCAT
27973572 ATT
1 ATT
27973575 CTTCCATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (41 bp):
ATTACTTAGTACAAATCGTTTATCACACGCCAAACATTCAT
Found at i:27988844 original size:51 final size:49
Alignment explanation
Indices: 27988764--27988909 Score: 164
Period size: 42 Copynumber: 3.1 Consensus size: 49
27988754 TCACTGTGAT
*
27988764 TTGCCTGTCCTATTTACATCTCATCGGAGGCTACACCATGAGTGTTCTTA
1 TTGCCTGT-CTATTTACATCTCATAGGAGGCTACACCATGAGTGTTCTTA
*
27988814 TATGCCTGTCTGATTTACATCTAATAGGAGGCTACACCATGA----TC---
1 T-TGCCTGTCT-ATTTACATCTCATAGGAGGCTACACCATGAGTGTTCTTA
* *
27988858 -TGCCTGTCCAATTTACATCTCATTGGAGGCTACACCATGAGTGTTCTTA
1 TTGCCTGT-CTATTTACATCTCATAGGAGGCTACACCATGAGTGTTCTTA
27988907 TTG
1 TTG
27988910 TCACCCTAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 22
0.75 0.05 0.21
Matches are distributed among these distances:
42 35 0.44
43 1 0.01
46 2 0.03
47 2 0.03
50 5 0.06
51 35 0.44
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (49 bp):
TTGCCTGTCTATTTACATCTCATAGGAGGCTACACCATGAGTGTTCTTA
Found at i:27998158 original size:127 final size:126
Alignment explanation
Indices: 27997904--27998145 Score: 403
Period size: 127 Copynumber: 1.9 Consensus size: 126
27997894 CCTAATTCAT
* *
27997904 TCACTTTTGCGATTTATTCATTTCTTAAATTAATATGTCATAATATAATTCCCAATGTTGCCATA
1 TCACTTTTACGATTTAATCATTTCTTAAATTAATATGTCATAATATAATTCCCAATGTTGCCATA
* **
27997969 ACTCAAAATTTCCCTTTTTGTCACTTTATTTCTTATTTTACTCTTGGGCAACAAAACTTTTC
66 ACTCAAAATTTCCCTTTTTGTCACTTTATTTCTTATTTTACTATAAGGCAAC-AAACTTTTC
*
27998031 TCACTTTTATGATTTAATCATTTCTTAAATTAATATGTCATAATATAATTCCCAATGTTGCCATA
1 TCACTTTTACGATTTAATCATTTCTTAAATTAATATGTCATAATATAATTCCCAATGTTGCCATA
27998096 ACTCAAAATTTCCCTTTTTGTCACTTTATTTCCTTATTTTACTATCAAGG
66 ACTCAAAATTTCCCTTTTTGTCACTTTATTT-CTTATTTTACTAT-AAGG
27998146 ATATCTACTT
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
127 93 0.87
128 12 0.11
129 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (126 bp):
TCACTTTTACGATTTAATCATTTCTTAAATTAATATGTCATAATATAATTCCCAATGTTGCCATA
ACTCAAAATTTCCCTTTTTGTCACTTTATTTCTTATTTTACTATAAGGCAACAAACTTTTC
Found at i:27998445 original size:27 final size:27
Alignment explanation
Indices: 27998415--27998716 Score: 345
Period size: 27 Copynumber: 11.2 Consensus size: 27
27998405 GGATATAACA
27998415 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * ** **
27998442 GTCATTTTACCTTGTGGCAGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
27998469 GTCATTGTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
27998496 GTCATTCTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
** *
27998523 GTCATTTTATGCTATGGGGGT-TTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
27998549 GTAATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
27998576 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
** * *
27998603 GTCATTTTACATTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
27998630 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
27998657 ATCATTCTACCCTATGGGGTTTATTTTG
1 GTCATTTTACCCTATGGGG-GTATTTCG
* * *
27998685 GACATTCTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
27998712 GTCAT
1 GTCAT
27998717 AATAGTGTAA
Statistics
Matches: 228, Mismatches: 45, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
26 22 0.10
27 182 0.80
28 24 0.11
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:27998599 original size:134 final size:135
Alignment explanation
Indices: 27998413--27998716 Score: 371
Period size: 134 Copynumber: 2.3 Consensus size: 135
27998403 AGGGATATAA
* *
27998413 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTGTGGCAGTATTTTAGTCATTGTA
1 CAGTAATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTGTGGCAGTATTTCAGTCATTGTA
* * * * **
27998478 CCCTATGGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTCGGTCATTTTATGCTATGGGGG
66 CACTATAGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTCGATCATTCTACCCTATGGGGG
27998543 TT-TT
131 TTATT
* * *
27998547 CAGTAATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCTATG-GG-GGTATTTCGGTCATTT
1 CAGTAATTTTACCCTATGGGGGTATTTCGGTCATTTTA-CCT-TGTGGCAGTATTTCAGTCATTG
* * * *
27998610 TACATTATAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTGATCATTCTACCCTATGGG
64 TACACTATAGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTCGATCATTCTACCCTATGGG
*
27998675 GTTTATT
129 GGTTATT
** * * *
27998682 TTGGACATTCTACCCTATGGGGGTATTTCAGTCAT
1 CAGTA-ATTTTACCCTATGGGGGTATTTCGGTCAT
27998717 AATAGTGTAA
Statistics
Matches: 145, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
134 107 0.74
135 9 0.06
136 29 0.20
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (135 bp):
CAGTAATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTGTGGCAGTATTTCAGTCATTGTA
CACTATAGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTCGATCATTCTACCCTATGGGGG
TTATT
Found at i:28008945 original size:24 final size:25
Alignment explanation
Indices: 28008913--28008960 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
28008903 AAGGAAATGA
* *
28008913 AGAACAATGAAAGGGAA-TGAAGAG
1 AGAAAAATGAAAGAGAAGTGAAGAG
*
28008937 AGAAAAATGAGAGAGAAGTGAAGA
1 AGAAAAATGAAAGAGAAGTGAAGA
28008961 AATGAATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.33, T:0.08
Consensus pattern (25 bp):
AGAAAAATGAAAGAGAAGTGAAGAG
Found at i:28009399 original size:19 final size:19
Alignment explanation
Indices: 28009375--28009413 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28009365 TATATTATGA
28009375 ATTAATACACATAGTTTGG
1 ATTAATACACATAGTTTGG
28009394 ATTAATACACATAGTTTGG
1 ATTAATACACATAGTTTGG
28009413 A
1 A
28009414 CTGTCTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (19 bp):
ATTAATACACATAGTTTGG
Found at i:28022341 original size:15 final size:15
Alignment explanation
Indices: 28022321--28022359 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
28022311 ACACATGGTC
28022321 GTGTCACCTGGCCAT
1 GTGTCACCTGGCCAT
28022336 GTGTCACACCTGGCCAT
1 GTGT--CACCTGGCCAT
28022353 GTGTCAC
1 GTGTCAC
28022360 ACATGGTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
17 15 0.68
ACGTcount: A:0.15, C:0.33, G:0.26, T:0.26
Consensus pattern (15 bp):
GTGTCACCTGGCCAT
Found at i:28022347 original size:17 final size:17
Alignment explanation
Indices: 28022325--28022361 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
28022315 ATGGTCGTGT
28022325 CACCTGGCCATGTGTCA
1 CACCTGGCCATGTGTCA
28022342 CACCTGGCCATGTGTCA
1 CACCTGGCCATGTGTCA
28022359 CAC
1 CAC
28022362 ATGGTAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.22
Consensus pattern (17 bp):
CACCTGGCCATGTGTCA
Found at i:28026350 original size:48 final size:48
Alignment explanation
Indices: 28026279--28026393 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
28026269 ACACCAGCTT
* * *
28026279 GTGGACAAGCCACCACAGAGATACCGATGAACGGTCACATAGCACATC
1 GTGGATAAACCACCACATAGATACCGATGAACGGTCACATAGCACATC
* * *
28026327 GTGGATAAACCACCACATAGATACCGATGAGCTGTCACATAGCATATC
1 GTGGATAAACCACCACATAGATACCGATGAACGGTCACATAGCACATC
*
28026375 GTGCATAAACCACCACATA
1 GTGGATAAACCACCACATA
28026394 ATTGTCGGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.17
Consensus pattern (48 bp):
GTGGATAAACCACCACATAGATACCGATGAACGGTCACATAGCACATC
Found at i:28039555 original size:17 final size:17
Alignment explanation
Indices: 28039533--28039566 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28039523 CACTAACATG
*
28039533 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
28039550 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
28039567 TATATTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:28040040 original size:21 final size:21
Alignment explanation
Indices: 28040016--28040065 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
28040006 CATTTTCAAT
* *
28040016 AACTTCTTCTTCTTCAGCAAC
1 AACTTCCTCTTCTGCAGCAAC
**
28040037 AACTTCCTCTTCTGCAGCAGT
1 AACTTCCTCTTCTGCAGCAAC
28040058 AACTTCCT
1 AACTTCCT
28040066 TCTCAACAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.34, G:0.08, T:0.36
Consensus pattern (21 bp):
AACTTCCTCTTCTGCAGCAAC
Found at i:28047999 original size:19 final size:19
Alignment explanation
Indices: 28047975--28048011 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28047965 ATTCAAACCC
*
28047975 CAAGATTAAACAATAAAAG
1 CAAGATTAAAAAATAAAAG
28047994 CAAGATTAAAAAATAAAA
1 CAAGATTAAAAAATAAAA
28048012 CATTTCACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (19 bp):
CAAGATTAAAAAATAAAAG
Found at i:28056274 original size:17 final size:17
Alignment explanation
Indices: 28056252--28056284 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28056242 GTACATGAGT
*
28056252 AAAATATTGTGTTTTTC
1 AAAATATTATGTTTTTC
28056269 AAAATATTATGTTTTT
1 AAAATATTATGTTTTT
28056285 TCTGCTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (17 bp):
AAAATATTATGTTTTTC
Found at i:28056932 original size:18 final size:19
Alignment explanation
Indices: 28056905--28056951 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
28056895 CCAAGTACGT
* *
28056905 AAACCCTTACTTTTATATG
1 AAACCTTTACCTTTATATG
*
28056924 -AACCTTTACCTTTGTATG
1 AAACCTTTACCTTTATATG
28056942 CAAACCTTTA
1 -AAACCTTTA
28056952 TATATATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 15 0.65
20 8 0.35
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (19 bp):
AAACCTTTACCTTTATATG
Found at i:28056976 original size:17 final size:17
Alignment explanation
Indices: 28056936--28056987 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
28056926 CCTTTACCTT
*
28056936 TGTATGCAAACCTTTATA
1 TGTATGCAAACC-CTATA
* *
28056954 TATATGTAAACCCTATA
1 TGTATGCAAACCCTATA
*
28056971 TGTATGCGAACCCTATA
1 TGTATGCAAACCCTATA
28056988 CGCATGCAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (17 bp):
TGTATGCAAACCCTATA
Found at i:28057470 original size:23 final size:22
Alignment explanation
Indices: 28057444--28057543 Score: 101
Period size: 23 Copynumber: 4.4 Consensus size: 22
28057434 AACGTATGCT
*
28057444 ACAAAGGCTATACAGAATACGCC
1 ACAAAGGCT-TATAGAATACGCC
* **
28057467 ACAAAGGCTTCATAGATTAAACC
1 ACAAAGGCTT-ATAGAATACGCC
*
28057490 ACAAAGGCTTTATAGAATACGCT
1 ACAAAGGC-TTATAGAATACGCC
* *
28057513 ATACAGGCTTCATAGAATACGCC
1 ACAAAGGCTT-ATAGAATACGCC
28057536 ACAAAGGC
1 ACAAAGGC
28057544 ATTACAGAGA
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
22 3 0.05
23 56 0.92
24 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (22 bp):
ACAAAGGCTTATAGAATACGCC
Found at i:28057494 original size:46 final size:46
Alignment explanation
Indices: 28057444--28057551 Score: 128
Period size: 46 Copynumber: 2.3 Consensus size: 46
28057434 AACGTATGCT
*
28057444 ACAAAGGCTATACAGAATACGCCACAAAGGCTTCATAGATTAAACC
1 ACAAAGGCTATACAGAATACGCCACAAAGGCTTCATAGAATAAACC
* * * * * **
28057490 ACAAAGGCTTTATAGAATACGCTATACAGGCTTCATAGAATACGCC
1 ACAAAGGCTATACAGAATACGCCACAAAGGCTTCATAGAATAAACC
28057536 ACAAAGGC-ATTACAGA
1 ACAAAGGCTA-TACAGA
28057552 GAATTACTGT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (46 bp):
ACAAAGGCTATACAGAATACGCCACAAAGGCTTCATAGAATAAACC
Found at i:28067991 original size:50 final size:50
Alignment explanation
Indices: 28067923--28068043 Score: 152
Period size: 50 Copynumber: 2.4 Consensus size: 50
28067913 CCAAATATTT
* ** * *
28067923 TCTTACATGGGAGTTCTCATATCGGTGCCCATGCAATGTCCCAGACATGG
1 TCTTACAGGGGACCTCTCATATCGGTGCCAACGCAATGTCCCAGACATGG
* * *
28067973 TCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGG
1 TCTTACAGGGGACCTCTCATATCGGTGCCAACGCAATGTCCCAGACATGG
* *
28068023 TTTTACATGGGACCTCTCATA
1 TCTTACAGGGGACCTCTCATA
28068044 ACCTCAATAA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TCTTACAGGGGACCTCTCATATCGGTGCCAACGCAATGTCCCAGACATGG
Found at i:28072470 original size:19 final size:18
Alignment explanation
Indices: 28072429--28072471 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
28072419 AATTTTTGTC
* *
28072429 ATAAAATAATTAATTTTT
1 ATAAAATAATTAAATTAT
28072447 ATAAAATAATTAAATTAT
1 ATAAAATAATTAAATTAT
28072465 ATTAAAA
1 A-TAAAA
28072472 ATTTGAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAAATAATTAAATTAT
Found at i:28081483 original size:94 final size:94
Alignment explanation
Indices: 28081264--28081486 Score: 261
Period size: 94 Copynumber: 2.4 Consensus size: 94
28081254 GTCGTTCCAG
* * * * * *
28081264 TATGGTAGATTCAATCTAACCCACTGAAACTTCAGGGGTTGAGAATTAGTAGCTTCAATCTACTC
1 TATGGTAGATTTAATCCAACCCACTGAAACTTGAAGGGTTAAGAATTAGTAACTTCAATCTACTC
* * * * *
28081329 GACTGTAACTTCCGGGAGGTAAGATTCGC
66 CACTGCAACTTCAGGGAGATAAGATTCAC
* * * *
28081358 TATCGTAGATTTAATCCGACCCACT-ATAACTTGAAGGGTATAAG-ATTTGTAACTTCAATCTGC
1 TATGGTAGATTTAATCCAACCCACTGA-AACTTGAAGGGT-TAAGAATTAGTAACTTCAATCTAC
28081421 TCCACTGCAACTTCAGGGAGATAAGATTCAC
64 TCCACTGCAACTTCAGGGAGATAAGATTCAC
* *
28081452 TATGGTAGATTTAATCCAACCCATTGCAACTTGAA
1 TATGGTAGATTTAATCCAACCCACTGAAACTTGAA
28081487 AGCTCTAAGA
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
93 1 0.01
94 103 0.96
95 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (94 bp):
TATGGTAGATTTAATCCAACCCACTGAAACTTGAAGGGTTAAGAATTAGTAACTTCAATCTACTC
CACTGCAACTTCAGGGAGATAAGATTCAC
Found at i:28081944 original size:14 final size:14
Alignment explanation
Indices: 28081925--28081951 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28081915 GTGCTCCAGT
28081925 TGAACTGAACCGAG
1 TGAACTGAACCGAG
28081939 TGAACTGAACCGA
1 TGAACTGAACCGA
28081952 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:28096697 original size:17 final size:18
Alignment explanation
Indices: 28096677--28096719 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
28096667 TTCCTAAAGC
*
28096677 ATAAAAAAATATAAAT-A
1 ATAAAAAAATAAAAATAA
*
28096694 ATAAATAAATAAAAATAA
1 ATAAAAAAATAAAAATAA
28096712 ATAAAAAA
1 ATAAAAAA
28096720 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAAAATAA
Found at i:28096701 original size:21 final size:21
Alignment explanation
Indices: 28096677--28096733 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
28096667 TTCCTAAAGC
*
28096677 ATAAAAAAATATAAATAATAA
1 ATAAAAAAATATAAATAAAAA
28096698 ATAAATAAAA-ATAAATAAAAA
1 ATAAA-AAAATATAAATAAAAA
*
28096719 AGAAAAAAAATATAA
1 A-TAAAAAAATATAA
28096734 TTTGGGGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (21 bp):
ATAAAAAAATATAAATAAAAA
Found at i:28096709 original size:10 final size:10
Alignment explanation
Indices: 28096677--28096718 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
28096667 TTCCTAAAGC
28096677 ATAAA-AAAA
1 ATAAATAAAA
28096686 TATAAATAATAA
1 -ATAAATAA-AA
28096698 ATAAATAAAA
1 ATAAATAAAA
28096708 ATAAATAAAA
1 ATAAATAAAA
28096718 A
1 A
28096719 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 18 0.60
11 10 0.33
12 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:28096710 original size:14 final size:15
Alignment explanation
Indices: 28096687--28096716 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28096677 ATAAAAAAAT
28096687 ATAAATAATAAATAA
1 ATAAATAATAAATAA
28096702 ATAAA-AATAAATAA
1 ATAAATAATAAATAA
28096716 A
1 A
28096717 AAAGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAATAATAAATAA
Found at i:28097360 original size:10 final size:10
Alignment explanation
Indices: 28097342--28097388 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
28097332 ATTTTAGGAT
28097342 TTTAT-TTTA
1 TTTATCTTTA
28097351 TTTATCTTTA
1 TTTATCTTTA
28097361 TTTATCTTTA
1 TTTATCTTTA
* * *
28097371 ATTA-ATGTA
1 TTTATCTTTA
28097380 TTTATCTTT
1 TTTATCTTT
28097389 TTGAGAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 11 0.37
10 19 0.63
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:28104966 original size:144 final size:143
Alignment explanation
Indices: 28104744--28105008 Score: 333
Period size: 144 Copynumber: 1.8 Consensus size: 143
28104734 TCTGATCCAC
* * ** *
28104744 TGTAACTTCAGGGATATAGGAGTTGTAGCTTATCTTGCTCCACTGTAATTTCAAGGAGATAAGAT
1 TGTAACTTCAGGGATATAGGAATTATAGCTTATCTTGCTCCACTACAACTTCAAGGAGATAAGAT
* *
28104809 GCTCTATAGTAAATTCA-ATCCAACCCACTGCAATTTCAGGGGT-GTAGGATTTGTAGTTGTAGC
66 GCTCTATAGTAAATT-AGATCCAACCCACTGCAACTTCAGGGGTAATA-GATTTGTAGTTGTAGC
28104872 TTTATTTTAACCCAT
129 TTTATTTTAACCCAT
*
28104887 TGTAACTTCAGGGTTATAGGAATTATAGCTTCATCTTGCTCCACTACAACTTC-AGAGAGATAAG
1 TGTAACTTCAGGGATATAGGAATTATAGCTT-ATCTTGCTCCACTACAACTTCAAG-GAGATAAG
* ** *
28104951 ATTCAT-TAT-GTTAAATTAGATCTGACCCACTGCGACTTCAGGGGTAATAGATTTGTAG
64 ATGC-TCTATAG-TAAATTAGATCCAACCCACTGCAACTTCAGGGGTAATAGATTTGTAG
28105009 CTTCATCTTG
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
143 32 0.31
144 69 0.66
145 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (143 bp):
TGTAACTTCAGGGATATAGGAATTATAGCTTATCTTGCTCCACTACAACTTCAAGGAGATAAGAT
GCTCTATAGTAAATTAGATCCAACCCACTGCAACTTCAGGGGTAATAGATTTGTAGTTGTAGCTT
TATTTTAACCCAT
Found at i:28105017 original size:94 final size:93
Alignment explanation
Indices: 28104880--28105271 Score: 434
Period size: 94 Copynumber: 4.2 Consensus size: 93
28104870 GCTTTATTTT
* * * * * * *
28104880 AACCCATTGTAACTTCAGGGTTATAGGAATTATAGCTTC-ATCTTGCTCCACTACAACTTCAGAG
1 AACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGG
* * *
28104944 AGATAAGATTCATTATGTTAAATTAGATCT
66 AGATAAGATTCACTATG-TAGATTA-ATCC
* *
28104974 GACCCACTGCGACTTCAGGGGTAATA-GATTTGTAGCTTC-ATCTTGCTCCACTGCAACTTCAGG
1 AACCCACTGCAACTTCAGGGGT-ATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGG
** *
28105037 GAGATAAGATTTGCTATGGTAGATCCAATCC
65 GAGATAAGATTCACTAT-GTAGAT-TAATCC
**
28105068 AACCCACTAAAACTTCAGGGGTATAGGATTTGTAGCTTCAAT-TTGCTCCACTGCAACTTCAGGG
1 AACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGG
*
28105132 AGGTAAGATTCACTATAGTAGATTAAATCC
66 AGATAAGATTCACTAT-GTAGATT-AATCC
* * *
28105162 AACCCACTGCAACTTGAAGGGTATAGGATTTGTAGCTTCAATC-TGCTCCCCTGCAACTTCAGGG
1 AACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGG
** *
28105226 AGATAAGATTTGCTATGGTAGATTTAATTC
66 AGATAAGATTCACTAT-GTAGA-TTAATCC
* *
28105256 GACCCATTGCAACTTC
1 AACCCACTGCAACTTC
28105272 TAGGCTCTAA
Statistics
Matches: 253, Mismatches: 37, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
93 3 0.01
94 241 0.95
95 9 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (93 bp):
AACCCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGG
AGATAAGATTCACTATGTAGATTAATCC
Found at i:28105047 original size:44 final size:44
Alignment explanation
Indices: 28104977--28105237 Score: 147
Period size: 44 Copynumber: 5.6 Consensus size: 44
28104967 TAGATCTGAC
* *
28104977 CCACTGCGACTTCAGGGG-TAATAGATTTGTAGCTTC-ATCTTGCT
1 CCACTGCAACTTCAGGGGAT-A-AGATTTGTAGCTTCAATCCTGCT
* **
28105021 CCACTGCAACTTCAGGGAGATAAGATTTGCTATGGTAGATCCAATCCAAC-
1 CCACTGCAACTTCAGGG-GATAAGATTTG-TA-GCT---T-CAATCCTGCT
** * *
28105071 CCACTAAAACTTCAGGGGTATAGGATTTGTAGCTTCAAT-TTGCT
1 CCACTGCAACTTCAGGGG-ATAAGATTTGTAGCTTCAATCCTGCT
* * * **
28105115 CCACTGCAACTTCAGGGAGGTAAGATTCACTATAGTAGATTAAATCCAAC-
1 CCACTGCAACTTCAGGG-GATAAGA-T---T-T-GTAGCTTCAATCCTGCT
* * *
28105165 CCACTGCAACTTGAAGGGTATAGGATTTGTAGCTTCAAT-CTGCT
1 CCACTGCAACTT-CAGGGGATAAGATTTGTAGCTTCAATCCTGCT
*
28105209 CCCCTGCAACTTCAGGGAGATAAGATTTG
1 CCACTGCAACTTCAGGG-GATAAGATTTG
28105238 CTATGGTAGA
Statistics
Matches: 162, Mismatches: 33, Indels: 44
0.68 0.14 0.18
Matches are distributed among these distances:
43 7 0.04
44 75 0.46
45 8 0.05
46 4 0.02
48 3 0.02
49 6 0.04
50 50 0.31
51 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGGATAAGATTTGTAGCTTCAATCCTGCT
Found at i:28105169 original size:188 final size:188
Alignment explanation
Indices: 28104890--28105248 Score: 519
Period size: 188 Copynumber: 1.9 Consensus size: 188
28104880 AACCCATTGT
*
28104890 AACTTCAGGGTTATAGGAATTATAGCTTCATCTTGCTCCACTACAACTTCAGAGAGATAAGATTC
1 AACTTCAGGGGTATAGGAATTATAGCTTCATCTTGCTCCACTACAACTTCAGAGAGATAAGATTC
* * ** * *
28104955 ATTATGTTAAATTAGATCTGACCCACTGCGACTTCAGGGGTAATA-GATTTGTAGCTTC-ATCTT
66 ACTATGTTAAATTAAATCCAACCCACTGCAACTTCAAGGGT-ATAGGATTTGTAGCTTCAATC-T
28105018 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGTAGATCCAATCCAACCCACTAA
129 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGTAGATCCAATCCAACCCACTAA
* * * * *
28105078 AACTTCAGGGGTATAGGATTTGTAGCTTCAAT-TTGCTCCACTGCAACTTCAGGGAGGTAAGATT
1 AACTTCAGGGGTATAGGAATTATAGCTTC-ATCTTGCTCCACTACAACTTCAGAGAGATAAGATT
* *
28105142 CACTATAG-TAGATTAAATCCAACCCACTGCAACTTGAAGGGTATAGGATTTGTAGCTTCAATCT
65 CACTAT-GTTAAATTAAATCCAACCCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCAATCT
*
28105206 GCTCCCCTGCAACTTCAGGGAGATAAGATTTGCTATGGTAGAT
129 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGTAGAT
28105249 TTAATTCGAC
Statistics
Matches: 152, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
187 3 0.02
188 143 0.94
189 6 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (188 bp):
AACTTCAGGGGTATAGGAATTATAGCTTCATCTTGCTCCACTACAACTTCAGAGAGATAAGATTC
ACTATGTTAAATTAAATCCAACCCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCAATCTGC
TCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGTAGATCCAATCCAACCCACTAA
Found at i:28107346 original size:464 final size:466
Alignment explanation
Indices: 28106478--28107407 Score: 1846
Period size: 464 Copynumber: 2.0 Consensus size: 466
28106468 ATTACAATTG
28106478 TTAGGTAACTAATGAATTAATTATTTAAATGGATTGAAATTGTAATTAATGGACACAGTACATAA
1 TTAGGTAACTAATGAATTAATTATTTAAATGGATTGAAATTGTAATTAATGGACACAGTACATAA
28106543 TCAGTACATGTTTAATCATCTAAGGTAGCTAAGGGTTAGATTAGCAATGGTATCTGACGATACAT
66 TCAGTACATGTTTAATCATCTAAGGTAGCTAAGGGTTAGATTAGCAATGGTATCTGACGATACAT
28106608 TTGCCTTACATAACTTGCAAGATTATTGTGATTAAATTGTTTCAAGGTAAGGATACTTTGTTACC
131 TTGCCTTACATAACTTGCAAGATTATTGTGATTAAATTGTTTCAAGGTAAGGATACTTTGTTACC
28106673 TCACATAGCCTTTTATGTGCTTATTAAGTCGAGGTAATTGTTTGAATTGACATAGGTATGTGTAC
196 TCACATAGCCTTTTATGTGCTTATTAAGTCGAGGTAATTGTTTGAATTGACATAGGTATGTGTAC
28106738 AAGAGATTATTTCGATTTAATAAGTACTTATGTGCAATAACATATTTGCCTATTAAGATTTGTTT
261 AAGAGATTATTTCGATTTAATAAGTACTTATGTGCAATAACATATTTGCCTATTAAGATTTGTTT
28106803 AATCGGTTGAATTGACATATGAATATAGTCAAGAGATAAATGGATTTTGGTAAGTGAGTATGTTC
326 AATCGGTTGAATTGACATATGAATATAGTCAAGAGATAAATGGATTTTGGTAAGTGAGTATGTTC
28106868 ATTAGTTAGTAAATTACCGAGTTGCCGTGAATTTATTCGTAACAATATAAACATGAGTTTAAT-A
391 ATTAGTTAGTAAATTACCGAGTTGCCGTGAATTTATTCGTAACAATATAAACATGAGTTTAATAA
28106932 -TCTAAGTTAA
456 TTCTAAGTTAA
28106942 TTAGGTAACTAATGAATTAATTATTTAAATGGATTGAAATTGTAATTAATGGACACAGTACATAA
1 TTAGGTAACTAATGAATTAATTATTTAAATGGATTGAAATTGTAATTAATGGACACAGTACATAA
28107007 TCAGTACATGTTTAATCATCTAAGGTAGCTAAGGGTTAGATTAGCAATGGTATCTGACGATACAT
66 TCAGTACATGTTTAATCATCTAAGGTAGCTAAGGGTTAGATTAGCAATGGTATCTGACGATACAT
28107072 TTGCCTTACATAACTTGCAAGATTATTGTGATTAAATTGTTTCAAGGTAAGGATACTTTGTTACC
131 TTGCCTTACATAACTTGCAAGATTATTGTGATTAAATTGTTTCAAGGTAAGGATACTTTGTTACC
28107137 TCACATAGCCTTTTATGTGCTTATTAAGTCGAGGTAATTGTTTGAATTGACATAGGTATGTGTAC
196 TCACATAGCCTTTTATGTGCTTATTAAGTCGAGGTAATTGTTTGAATTGACATAGGTATGTGTAC
28107202 AAGAGATTATTTCGATTTAATAAGTACTTATGTGCAATAACATATTTGCCTATTAAGATTTGTTT
261 AAGAGATTATTTCGATTTAATAAGTACTTATGTGCAATAACATATTTGCCTATTAAGATTTGTTT
28107267 AATCGGTTGAATTGACATATGAATATAGTCAAGAGATAAATGGATTTTGGTAAGTGAGTATGTTC
326 AATCGGTTGAATTGACATATGAATATAGTCAAGAGATAAATGGATTTTGGTAAGTGAGTATGTTC
28107332 ATTAGTTAGTAAATTACCGAGTTGCCGTGAATTTATTCGTAACAATATAAACATGAGTTTAATAA
391 ATTAGTTAGTAAATTACCGAGTTGCCGTGAATTTATTCGTAACAATATAAACATGAGTTTAATAA
28107397 TTCTAAGTTAA
456 TTCTAAGTTAA
28107408 GAAATGTAAT
Statistics
Matches: 464, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
464 453 0.98
465 1 0.00
466 10 0.02
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (466 bp):
TTAGGTAACTAATGAATTAATTATTTAAATGGATTGAAATTGTAATTAATGGACACAGTACATAA
TCAGTACATGTTTAATCATCTAAGGTAGCTAAGGGTTAGATTAGCAATGGTATCTGACGATACAT
TTGCCTTACATAACTTGCAAGATTATTGTGATTAAATTGTTTCAAGGTAAGGATACTTTGTTACC
TCACATAGCCTTTTATGTGCTTATTAAGTCGAGGTAATTGTTTGAATTGACATAGGTATGTGTAC
AAGAGATTATTTCGATTTAATAAGTACTTATGTGCAATAACATATTTGCCTATTAAGATTTGTTT
AATCGGTTGAATTGACATATGAATATAGTCAAGAGATAAATGGATTTTGGTAAGTGAGTATGTTC
ATTAGTTAGTAAATTACCGAGTTGCCGTGAATTTATTCGTAACAATATAAACATGAGTTTAATAA
TTCTAAGTTAA
Found at i:28115885 original size:22 final size:22
Alignment explanation
Indices: 28115855--28115899 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28115845 TGTTTCATTT
*
28115855 TTTTTGTTGTGTTTGCATTGCA
1 TTTTGGTTGTGTTTGCATTGCA
* *
28115877 TTTTGGTTGTTTTTGCGTTGCA
1 TTTTGGTTGTGTTTGCATTGCA
28115899 T
1 T
28115900 CCAATCACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.09, G:0.24, T:0.60
Consensus pattern (22 bp):
TTTTGGTTGTGTTTGCATTGCA
Found at i:28131583 original size:31 final size:31
Alignment explanation
Indices: 28131486--28131585 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 31
28131476 TGTTTTAATG
*
28131486 AATTTAATATTTATCTAGATAATATTTTATT
1 AATTTAATATTTATCTTGATAATATTTTATT
* * * * **
28131517 AATTTTATATTAAT-ATGA-GATATTAAATTT
1 AATTTAATATTTATCTTGATAATATTTTA-TT
*
28131547 AATTTAACATTTATCTTGATAATATTTTATT
1 AATTTAATATTTATCTTGATAATATTTTATT
28131578 AATTTAAT
1 AATTTAAT
28131586 GTTAATATGA
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
29 6 0.12
30 15 0.29
31 24 0.47
32 6 0.12
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (31 bp):
AATTTAATATTTATCTTGATAATATTTTATT
Found at i:28135308 original size:25 final size:25
Alignment explanation
Indices: 28135270--28135328 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
28135260 CATTTATTTA
* *
28135270 AGTGTTATAGTGATGAAAGTGTTAC
1 AGTGATATAATGATGAAAGTGTTAC
28135295 AGTGATATAATGATGAAAGTGTTAC
1 AGTGATATAATGATGAAAGTGTTAC
*
28135320 AATGATATA
1 AGTGATATA
28135329 TGTGCTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (25 bp):
AGTGATATAATGATGAAAGTGTTAC
Found at i:28136250 original size:17 final size:17
Alignment explanation
Indices: 28136213--28136252 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
28136203 TGAATTTTAT
*
28136213 TTTATATATTTTTAGATA
1 TTTA-ATATTTTTAGAAA
*
28136231 TTTAATATTTTTATAAA
1 TTTAATATTTTTAGAAA
28136248 TTTAA
1 TTTAA
28136253 AGTTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTAATATTTTTAGAAA
Found at i:28136294 original size:22 final size:21
Alignment explanation
Indices: 28136255--28136299 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
28136245 AAATTTAAAG
*
28136255 TTATATTTATCAAATAATTTAT
1 TTATATTTAACAAATAA-TTAT
**
28136277 TTATATTTAACACTTAATTAT
1 TTATATTTAACAAATAATTAT
28136298 TT
1 TT
28136300 TTTAAATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATATTTAACAAATAATTAT
Found at i:28141161 original size:23 final size:22
Alignment explanation
Indices: 28141118--28141161 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
28141108 TTCTAAGTCG
28141118 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
28141141 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
28141162 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:28141269 original size:45 final size:45
Alignment explanation
Indices: 28141205--28141299 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
28141195 TAACAGATAC
* * * * *
28141205 TCGGTGGATTCAGCACATAGTAACCACCTTATTAATCAATGATGT
1 TCGGTGGAATCAACACATAGCAACCACCTTACTAATAAATGATGT
*
28141250 TCGGTGGAATCAACACATAGCAACTACCTTACTAATAAATGATGT
1 TCGGTGGAATCAACACATAGCAACCACCTTACTAATAAATGATGT
28141295 TCGGT
1 TCGGT
28141300 TCACATAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (45 bp):
TCGGTGGAATCAACACATAGCAACCACCTTACTAATAAATGATGT
Found at i:28141363 original size:51 final size:52
Alignment explanation
Indices: 28141296--28141440 Score: 190
Period size: 50 Copynumber: 2.8 Consensus size: 52
28141286 AAATGATGTT
* * *
28141296 CGGTTCACATAGTAGCCTGCACATAGTACTATACATGTGACCATTACCA-TC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTC
* * *
28141347 TGAG-ACACGTAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTC
1 CG-GTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTC
*
28141397 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
28141441 CACTTTCACT
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
49 5 0.06
50 39 0.49
51 35 0.44
52 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (52 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTC
Found at i:28147142 original size:127 final size:127
Alignment explanation
Indices: 28146916--28147172 Score: 401
Period size: 127 Copynumber: 2.0 Consensus size: 127
28146906 AGAAGTAAAC
* * *
28146916 TAGAGCAGGTGATGATGTGATTTCCAGAGCTTGAATTGTTTGGAAAGTAGCTCGATTGGGTTGGA
1 TAGAGCAGGTGATGATGTGAGTTCCAGAACTTGAATAGTTTGGAAAGTAGCTCGATTGGGTTGGA
**
28146981 TCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTATGAGCTAAAGAACCT
66 TCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTAACAGCTAAAGAACCT
* *
28147043 TAGAGCAGGTGATGATGTGAGTTCTC-GAATTTGAATAGTTTGGGAAA-TAGCTCGATTGGGTTT
1 TAGAGCAGGTGATGATGTGAGTTC-CAGAACTTGAATAGTTT-GGAAAGTAGCTCGATTGGGTTG
* *
28147106 GATCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTGTAGTAGTAACAGCTAAAGAACCT
64 GATCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTAACAGCTAAAGAACCT
28147170 TAG
1 TAG
28147173 CTATATTAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
127 113 0.95
128 6 0.05
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (127 bp):
TAGAGCAGGTGATGATGTGAGTTCCAGAACTTGAATAGTTTGGAAAGTAGCTCGATTGGGTTGGA
TCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTAACAGCTAAAGAACCT
Found at i:28155694 original size:50 final size:50
Alignment explanation
Indices: 28155635--28155735 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
28155625 ATTTCTTGGG
28155635 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
1 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
28155685 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
1 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
28155735 T
1 T
28155736 CTAGCATCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (50 bp):
TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
Found at i:28157919 original size:27 final size:30
Alignment explanation
Indices: 28157883--28157964 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 30
28157873 AAATGTGAAG
28157883 GGGGTTGCTAAGTGCTGATTCCC-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCCACTCATA
*
28157910 GGGGTTGCTAAGTGCTGATTCCCTGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCC--ACTCATA
28157942 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
28157965 ACCGTATCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 23 0.48
30 1 0.02
31 2 0.04
32 2 0.04
33 20 0.42
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.32
Consensus pattern (30 bp):
GGGGTTGCTAAGTGCTGATTCCCACTCATA
Found at i:28157974 original size:102 final size:102
Alignment explanation
Indices: 28157798--28158008 Score: 388
Period size: 102 Copynumber: 2.1 Consensus size: 102
28157788 NNNNNNNNNN
*
28157798 ATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCC
1 ATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCC
*
28157863 ACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTG
66 ACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTG
*
28157900 ATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGACTCATTGGTGGTTGCTAAGTGCTGATTCC
1 ATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCC
28157965 ACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTG
66 ACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTG
28158002 A-TCCCCC
1 ATTCCCCC
28158009 GACTCATTGG
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
101 6 0.06
102 100 0.94
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (102 bp):
ATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCC
ACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTG
Found at i:28162830 original size:18 final size:19
Alignment explanation
Indices: 28162807--28162843 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28162797 ATTATCACAT
*
28162807 ATGTAACACATAAT-TATG
1 ATGTAAAACATAATCTATG
28162825 ATGTAAAACATAATCTATG
1 ATGTAAAACATAATCTATG
28162844 GAATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
ATGTAAAACATAATCTATG
Found at i:28163811 original size:25 final size:25
Alignment explanation
Indices: 28163783--28163832 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28163773 TTTATAGGAA
*
28163783 CCTTTAAGCAAATTACCTTTTTTTT
1 CCTTTAAGCAAATTAACTTTTTTTT
* * *
28163808 CCTTTTATCAAATTAATTTTTTTTT
1 CCTTTAAGCAAATTAACTTTTTTTT
28163833 TAAAAAAGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.02, T:0.58
Consensus pattern (25 bp):
CCTTTAAGCAAATTAACTTTTTTTT
Found at i:28171051 original size:49 final size:49
Alignment explanation
Indices: 28170984--28171180 Score: 205
Period size: 49 Copynumber: 4.0 Consensus size: 49
28170974 CCATATAGGC
* *
28170984 TTCCCAAATGACTCGCCACAAAGGCTTTACAGATGATCCACCACAAAGG
1 TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
* * * * *** *
28171033 TTCCTAGATGTCTTGCCACAAAGGTTTTACAAATGATTTGCCACAAAGC
1 TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
** * * *
28171082 TTCCCAGATGACTCATCACAAAGGCTTTACAGACGATCCACCAAAAAGG
1 TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
* * * **
28171131 CTTCCCAAATGACTCGCCATAAAGGCTTTACAAATTATCTGCCACAAAGG
1 -TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
28171181 CTTTACAGAT
Statistics
Matches: 114, Mismatches: 33, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
49 75 0.66
50 39 0.34
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (49 bp):
TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
Found at i:28171103 original size:98 final size:99
Alignment explanation
Indices: 28170982--28171179 Score: 272
Period size: 98 Copynumber: 2.0 Consensus size: 99
28170972 CACCATATAG
* * * * * *
28170982 GCTTCCCAAATGACTCGCCACAAAGGCTTTACAGATGATCCACCACAAAGG-TTCCTAGATGTCT
1 GCTTCCCAAATGACTCACCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
* * *
28171046 TGCCACAAAGGTTTTACAAATGATTTGCCACAAA
66 CGCCACAAAGGCTTTACAAATGATCTGCCACAAA
* *
28171080 GCTTCCCAGATGACTCATCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
1 GCTTCCCAAATGACTCACCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
* *
28171145 CGCCATAAAGGCTTTACAAATTATCTGCCACAAA
66 CGCCACAAAGGCTTTACAAATGATCTGCCACAAA
28171179 G
1 G
28171180 GCTTTACAGA
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
98 46 0.53
99 40 0.47
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.23
Consensus pattern (99 bp):
GCTTCCCAAATGACTCACCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
CGCCACAAAGGCTTTACAAATGATCTGCCACAAA
Found at i:28171199 original size:50 final size:49
Alignment explanation
Indices: 28171145--28171334 Score: 170
Period size: 50 Copynumber: 3.8 Consensus size: 49
28171135 CCAAATGACT
* *
28171145 CGCCATAAAGGCTTTACAAATTATCTGCCACAAAGGCTTTACAGATTATC
1 CGCCATAAAGGCTTT-CAGATTATCTGCCACAAAGGCTTTACAGATGATC
* * *
28171195 CGCCATAAAGGCTTCTGAGA-TATCTTCTCACAAAGGCTTTACAGATGATT
1 CGCCATAAAGGCTT-TCAGATTATCTGC-CACAAAGGCTTTACAGATGATC
* * ** * *
28171245 CACCACAAAGGCATCGCAGATGA-CTCGTCACAAAGGCTTTACAGATGATC
1 CGCCATAAAGGC-TTTCAGATTATCT-GCCACAAAGGCTTTACAGATGATC
* * *
28171295 CGCCATAAAGGCTTCCTAGA-TGTCATACCACAAAGGCTTT
1 CGCCATAAAGGCTTTC-AGATTATC-TGCCACAAAGGCTTT
28171335 TCAAATCAAT
Statistics
Matches: 110, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
49 8 0.07
50 98 0.89
51 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (49 bp):
CGCCATAAAGGCTTTCAGATTATCTGCCACAAAGGCTTTACAGATGATC
Found at i:28171316 original size:25 final size:25
Alignment explanation
Indices: 28170997--28171308 Score: 201
Period size: 25 Copynumber: 12.6 Consensus size: 25
28170987 CCAAATGACT
28170997 CGCCACAAAGGCTTTACAGATGATC
1 CGCCACAAAGGCTTTACAGATGATC
* *
28171022 CACCACAAAGG--TTCCTAGATG-TC
1 CGCCACAAAGGCTTTAC-AGATGATC
* * * *
28171045 TTGCCACAAAGGTTTTACAAATGATT
1 -CGCCACAAAGGCTTTACAGATGATC
* **
28171071 TGCCACAAA-GCTTCCCAGATGA-C
1 CGCCACAAAGGCTTTACAGATGATC
** *
28171094 TCATCACAAAGGCTTTACAGACGATC
1 -CGCCACAAAGGCTTTACAGATGATC
* * ** *
28171120 CACCAAAAAGGCTTCCCAAATGA-C
1 CGCCACAAAGGCTTTACAGATGATC
* * *
28171144 TCGCCATAAAGGCTTTACAAATTATC
1 -CGCCACAAAGGCTTTACAGATGATC
* *
28171170 TGCCACAAAGGCTTTACAGATTATC
1 CGCCACAAAGGCTTTACAGATGATC
* *
28171195 CGCCATAAAGGCTTCT-GAGAT-ATC
1 CGCCACAAAGGCTT-TACAGATGATC
** *
28171219 TTCTCACAAAGGCTTTACAGATGATT
1 CGC-CACAAAGGCTTTACAGATGATC
* * **
28171245 CACCACAAAGGCATCGCAGATGA-C
1 CGCCACAAAGGCTTTACAGATGATC
*
28171269 TCGTCACAAAGGCTTTACAGATGATC
1 -CGCCACAAAGGCTTTACAGATGATC
*
28171295 CGCCATAAAGGCTT
1 CGCCACAAAGGCTT
28171309 CCTAGATGTC
Statistics
Matches: 218, Mismatches: 53, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
23 5 0.02
24 35 0.16
25 167 0.77
26 11 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (25 bp):
CGCCACAAAGGCTTTACAGATGATC
Found at i:28171351 original size:100 final size:100
Alignment explanation
Indices: 28171173--28171356 Score: 257
Period size: 100 Copynumber: 1.8 Consensus size: 100
28171163 AATTATCTGC
* *
28171173 CACAAAGGCTTTACAGATTATCCGCCATAAAGGCTTCTGAGATATCTTCTCACAAAGGCTTTACA
1 CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTTCTGAGATATCTACTCACAAAGGCTTTACA
* *
28171238 GATGATTCACCACAAAGGCATCGCAGATGACTCGT
66 AATAATTCACCACAAAGGCATCGCAGATGACTCGT
* *
28171273 CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTTCCT-AGATGTCATAC-CACAAAGGCTTTT
1 CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTT-CTGAGATATC-TACTCACAAAGGCTTTA
*
28171336 CAAATCAATT-GCCACAAAGGC
64 CAAAT-AATTCACCACAAAGGC
28171357 TTGGTTTGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 67 0.91
101 7 0.09
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (100 bp):
CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTTCTGAGATATCTACTCACAAAGGCTTTACA
AATAATTCACCACAAAGGCATCGCAGATGACTCGT
Found at i:28172649 original size:41 final size:41
Alignment explanation
Indices: 28172599--28172684 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
28172589 AAATCCTTAG
*
28172599 ATACTGCTCATGGGAAGATACTTTAACACTAATATACACCA
1 ATACCGCTCATGGGAAGATACTTTAACACTAATATACACCA
*
28172640 ATACCGCTCATGGGAAGATACTTTAACGCTAATATACACCA
1 ATACCGCTCATGGGAAGATACTTTAACACTAATATACACCA
28172681 ATAC
1 ATAC
28172685 TTTAATGCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (41 bp):
ATACCGCTCATGGGAAGATACTTTAACACTAATATACACCA
Found at i:28177840 original size:12 final size:13
Alignment explanation
Indices: 28177815--28177840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28177805 TAAACAACAT
28177815 ACAAATTAAAAAA
1 ACAAATTAAAAAA
28177828 ACAAATTAAAAAA
1 ACAAATTAAAAAA
28177841 GTAACAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
ACAAATTAAAAAA
Found at i:28182407 original size:33 final size:36
Alignment explanation
Indices: 28182360--28182538 Score: 163
Period size: 42 Copynumber: 4.8 Consensus size: 36
28182350 GTTATCCGTT
*
28182360 ATCGGTGGATTCAGCACTTAGCAACCACCA-A-TGA
1 ATCGGTGGAATCAGCACTTAGCAACCACCACATTGA
* *
28182394 ATCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTTAA
1 ATCGGTGGAATCAGCACTTAGCAACCAC---CACA-TTGA
28182433 GATACGGTGGAATCAGCACTTAGCAACCACCA-A-TGA
1 -AT-CGGTGGAATCAGCACTTAGCAACCACCACATTGA
* *
28182469 TTCGG-GGAATCAGCACTTAGCAACCCCCTTTACATTTAGA
1 ATCGGTGGAATCAGCACTTAGCAACCACC---ACA-TT-GA
28182509 ATACGGTGGAATCAGCACTTAGCAACCACC
1 AT-CGGTGGAATCAGCACTTAGCAACCACC
28182539 TTTATAGTCA
Statistics
Matches: 118, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
33 42 0.36
34 8 0.07
35 1 0.01
36 5 0.04
37 2 0.02
38 1 0.01
39 5 0.04
40 5 0.04
41 6 0.05
42 43 0.36
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (36 bp):
ATCGGTGGAATCAGCACTTAGCAACCACCACATTGA
Found at i:28182458 original size:42 final size:41
Alignment explanation
Indices: 28182399--28182541 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 41
28182389 AATGAATCGG
28182399 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTT-AGATACGGT
* *
28182441 GGAATCAGCACTTAGCAACCAC---CA-A--T-GATTCGG-
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAGATACGGT
28182474 GGAATCAGCACTTAGCAACCCCCTTT-ACATTTAGAATACGGT
1 GGAATCAGCACTTAGCAA-CCCCTTTCACATTTAG-ATACGGT
28182516 GGAATCAGCACTTAGCAACCACCTTT
1 GGAATCAGCACTTAGCAACC-CCTTT
28182542 ATAGTCAATG
Statistics
Matches: 86, Mismatches: 4, Indels: 22
0.77 0.04 0.20
Matches are distributed among these distances:
33 18 0.21
34 9 0.10
36 2 0.02
37 1 0.01
38 1 0.01
39 3 0.03
40 1 0.01
41 7 0.08
42 44 0.51
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTTAGATACGGT
Found at i:28182485 original size:75 final size:75
Alignment explanation
Indices: 28182362--28182538 Score: 304
Period size: 75 Copynumber: 2.4 Consensus size: 75
28182352 TATCCGTTAT
*
28182362 CGGTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTT-A
28182426 CATTTA-AGATA
65 CATTTAGA-ATA
*
28182437 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTTAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
28182502 ATTTAGAATA
66 ATTTAGAATA
28182512 CGGTGGAATCAGCACTTAGCAACCACC
1 CGGTGGAATCAGCACTTAGCAACCACC
28182539 TTTATAGTCA
Statistics
Matches: 98, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
75 90 0.92
76 8 0.08
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
ATTTAGAATA
Found at i:28182642 original size:51 final size:51
Alignment explanation
Indices: 28182566--28182744 Score: 200
Period size: 51 Copynumber: 3.5 Consensus size: 51
28182556 CCGGTTCACA
* *
28182566 TAGTAGCCTGCACGTAGTACTACACATGTGACCATTTCCATC-CGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTT-CTTCTCGATACACG
* *** *
28182617 TAGTAGCCTGCACATAGTACTACACATGTGATCAAAGCTTCTCGATACACA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTCTTCTCGATACACG
* * * * *
28182668 TAGTAGCCTTCACTTAGTACTACACATTTGACCATTAT-TTCTCGGTACATG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATT-TCTTCTCGATACACG
* *
28182719 TAGTAGCCTTCACACAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
28182745 CGTGTTCATC
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 3 0.03
51 104 0.97
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTTCTTCTCGATACACG
Found at i:28187915 original size:13 final size:13
Alignment explanation
Indices: 28187899--28187934 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28187889 ATTTTGTACT
*
28187899 ACCATTTGATATA
1 ACCATTTCATATA
*
28187912 ACCATTACATATA
1 ACCATTTCATATA
28187925 ACCATTTCAT
1 ACCATTTCAT
28187935 TTTATGCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (13 bp):
ACCATTTCATATA
Found at i:28213351 original size:16 final size:16
Alignment explanation
Indices: 28213330--28213365 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28213320 CAGCAATGAT
28213330 AGCTTAATTTTATTTA
1 AGCTTAATTTTATTTA
28213346 AGCTTAATTTTATTTA
1 AGCTTAATTTTATTTA
28213362 AGCT
1 AGCT
28213366 AGGATGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
AGCTTAATTTTATTTA
Found at i:28215366 original size:13 final size:13
Alignment explanation
Indices: 28215350--28215375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28215340 AGTATTATGT
28215350 TTTATTTATTTAA
1 TTTATTTATTTAA
28215363 TTTATTTATTTAA
1 TTTATTTATTTAA
28215376 ATTTCAGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTTATTTAA
Found at i:28218796 original size:12 final size:12
Alignment explanation
Indices: 28218779--28218806 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28218769 TAATCATGAT
28218779 TAAGTAAACAAG
1 TAAGTAAACAAG
28218791 TAAGTAAACAAG
1 TAAGTAAACAAG
28218803 TAAG
1 TAAG
28218807 AGAGTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:28223663 original size:41 final size:41
Alignment explanation
Indices: 28223612--28223705 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
28223602 ATCATTCTGA
28223612 CATTGTCTTACAAAATCTATTATATCTCATGATTTACAATAC
1 CATTG-CTTACAAAATCTATTATATCTCATGATTTACAATAC
*
28223654 CATTGCTTACAAAATCTATTATATCTCATGGTTTACAATAC
1 CATTGCTTACAAAATCTATTATATCTCATGATTTACAATAC
28223695 CATTGCTTACA
1 CATTGCTTACA
28223706 CCGTTTCTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 46 0.90
42 5 0.10
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (41 bp):
CATTGCTTACAAAATCTATTATATCTCATGATTTACAATAC
Found at i:28228630 original size:36 final size:37
Alignment explanation
Indices: 28228582--28228658 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
28228572 CATGTCTAGG
28228582 ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
1 ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
28228619 ACAT-GCATTGGCATTATTGAGGTTATGAGAGGTCCC
1 ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
28228655 ACAT
1 ACAT
28228659 AAGACCATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 36 0.90
37 4 0.10
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (37 bp):
ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
Found at i:28235187 original size:17 final size:17
Alignment explanation
Indices: 28235165--28235202 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
28235155 AAGCTTCCGC
28235165 AAACGAATAATGTTTTG
1 AAACGAATAATGTTTTG
28235182 AAACGAATAATGTTTTG
1 AAACGAATAATGTTTTG
28235199 AAAC
1 AAAC
28235203 TATCACTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (17 bp):
AAACGAATAATGTTTTG
Found at i:28238697 original size:22 final size:22
Alignment explanation
Indices: 28238672--28238720 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
28238662 AAGGTCGCCT
28238672 TAACTACTTTAGCTTTCTGAAC
1 TAACTACTTTAGCTTTCTGAAC
28238694 TAACTACTTTAGCTTTCTGAAC
1 TAACTACTTTAGCTTTCTGAAC
28238716 TAACT
1 TAACT
28238721 CATCGAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (22 bp):
TAACTACTTTAGCTTTCTGAAC
Found at i:28244904 original size:19 final size:20
Alignment explanation
Indices: 28244862--28244905 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
28244852 TATGTTTCAC
28244862 TTTAATTTCTATTTTTAATG
1 TTTAATTTCTATTTTTAATG
28244882 -TTAATTT-TATTTGTT-ATG
1 TTTAATTTCTATTT-TTAATG
28244900 TTTAAT
1 TTTAAT
28244906 AAGGGGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTAATTTCTATTTTTAATG
Found at i:28245374 original size:17 final size:17
Alignment explanation
Indices: 28245354--28245413 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
28245344 CGCCTATCGT
28245354 TGCCACAAACCCGTCGC
1 TGCCACAAACCCGTCGC
** * ** *
28245371 TGCCGTAAGCCTATTGC
1 TGCCACAAACCCGTCGC
28245388 TGCCACAAACCCGTCGC
1 TGCCACAAACCCGTCGC
*
28245405 TGCCGCAAA
1 TGCCACAAA
28245414 ATCCCTTACT
Statistics
Matches: 30, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (17 bp):
TGCCACAAACCCGTCGC
Found at i:28245384 original size:34 final size:34
Alignment explanation
Indices: 28245345--28245409 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
28245335 GTTGCTGCAC
*
28245345 GCCTATCGTTGCCACAAACCCGTCGCTGCCGTAA
1 GCCTATCGCTGCCACAAACCCGTCGCTGCCGTAA
*
28245379 GCCTATTGCTGCCACAAACCCGTCGCTGCCG
1 GCCTATCGCTGCCACAAACCCGTCGCTGCCG
28245410 CAAAATCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (34 bp):
GCCTATCGCTGCCACAAACCCGTCGCTGCCGTAA
Done.