Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 60 of 120
Found at i:17040481 original size:34 final size:34
Alignment explanation
Indices: 17040433--17040497 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
17040423 CAAATGGGCT
17040433 TGCGAATATTTTAGCCCAACACGAATTTATTGCC
1 TGCGAATATTTTAGCCCAACACGAATTTATTGCC
*
17040467 TGCGGATATTTTAGCCCAACACGAATTTATT
1 TGCGAATATTTTAGCCCAACACGAATTTATT
17040498 TTCCACAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (34 bp):
TGCGAATATTTTAGCCCAACACGAATTTATTGCC
Found at i:17042050 original size:14 final size:15
Alignment explanation
Indices: 17042020--17042054 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
17042010 ATTTAATACT
17042020 TTTAATAAATATTAA
1 TTTAATAAATATTAA
*
17042035 TTTAAT-AATTTTAA
1 TTTAATAAATATTAA
17042049 TTTAAT
1 TTTAAT
17042055 CCAAAGAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATAAATATTAA
Found at i:17043782 original size:10 final size:10
Alignment explanation
Indices: 17043767--17043823 Score: 75
Period size: 10 Copynumber: 5.9 Consensus size: 10
17043757 TATATTTTCT
17043767 TTATATATTA
1 TTATATATTA
17043777 -T-TATATTA
1 TTATATATTA
*
17043785 TTA-ACATTA
1 TTATATATTA
17043794 TTTATATATTA
1 -TTATATATTA
17043805 TTATATATTA
1 TTATATATTA
17043815 TTATATATT
1 TTATATATT
17043824 TAAATTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 7 0.17
9 7 0.17
10 22 0.54
11 5 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATATATTA
Found at i:17043823 original size:28 final size:27
Alignment explanation
Indices: 17043766--17043839 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
17043756 ATATATTTTC
17043766 TTTATATATTATTATATTATTAACATTA
1 TTTATATATTATTATA-TATTAACATTA
**
17043794 TTTATATATTATTATATATTATTATATA
1 TTTATATATTATTATATATTAACAT-TA
*
17043822 TTTAAAT-TTA-TATATATT
1 TTTATATATTATTATATATT
17043840 TAAATGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 8 0.19
27 10 0.24
28 24 0.57
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATATATTATTATATATTAACATTA
Found at i:17043837 original size:16 final size:16
Alignment explanation
Indices: 17043793--17043844 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
17043783 TATTAACATT
*
17043793 ATTTATATAT-TATTAT
1 ATTTATATATAT-TTAA
17043809 ATATTATTATATATTTAA
1 AT-TTA-TATATATTTAA
17043827 ATTTATATATATTTAA
1 ATTTATATATATTTAA
17043843 AT
1 AT
17043845 GATAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 15 0.47
17 6 0.19
18 10 0.31
19 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATATATATTTAA
Found at i:17044013 original size:21 final size:21
Alignment explanation
Indices: 17043973--17044011 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17043963 AAATCATGGA
17043973 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
17043994 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
17044012 TCATAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:17045949 original size:15 final size:15
Alignment explanation
Indices: 17045931--17045967 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
17045921 AAGAAGAAGG
17045931 ATTAAATCAATCTTA
1 ATTAAATCAATCTTA
**
17045946 ATTAAATTGATCTTA
1 ATTAAATCAATCTTA
17045961 ATTAAAT
1 ATTAAAT
17045968 TGTGGATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (15 bp):
ATTAAATCAATCTTA
Found at i:17045968 original size:15 final size:15
Alignment explanation
Indices: 17045940--17045969 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17045930 GATTAAATCA
17045940 ATCTTAATTAAATTG
1 ATCTTAATTAAATTG
17045955 ATCTTAATTAAATTG
1 ATCTTAATTAAATTG
17045970 TGGATTGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
ATCTTAATTAAATTG
Found at i:17046586 original size:21 final size:21
Alignment explanation
Indices: 17046560--17046602 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17046550 TAGTGTAAAA
17046560 AGAAAAAAAGTATGTGATGCT
1 AGAAAAAAAGTATGTGATGCT
17046581 AGAAAAAAAGTATGTGATGCT
1 AGAAAAAAAGTATGTGATGCT
17046602 A
1 A
17046603 AGATGGGCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (21 bp):
AGAAAAAAAGTATGTGATGCT
Found at i:17051043 original size:561 final size:559
Alignment explanation
Indices: 17049958--17051047 Score: 1645
Period size: 559 Copynumber: 1.9 Consensus size: 559
17049948 TATTTTTAAG
17049958 CTATAAAGTGGGTCATGCATGATTAAATTAAATAATAAAATATAAAGTTATATTTAATAATTCAT
1 CTATAAAGTGGGTCATGCATGATTAAATTAAATAATAAAATATAAAGTTATATTTAATAATTCAT
* * *
17050023 TTTTAATATTTCATTAATAAATTGAGTTTTAATTAATTAAATAAATTGATTAATTAAAGTGGTTA
66 TTTAAATATTTCATTAATAAATTGAGGTTTAATTAATTAAATAAATTGATTAATTAAAGTGCTTA
17050088 AATTATATTATTTGGTCCTCTAAACTATCTACTATTTTTGGACAGGGCTAAGAATTTTCTTCTAA
131 AATTATATTATTTGGTCCTCTAAACTATCTACTATTTTTGGACAGGGCTAAGAATTTTCTTCTAA
** * * *
17050153 TTGCAAAACCGTCCAACTTGGGGACCAATTCAACCCAATTTTTGGCTGCACATGGATGTCATAAA
196 TTGCAAAACCGTCCAAAGTGGGGACCAAGTCAAACCAATTTTTGACTGCACATGGATGTCATAAA
* * * * *
17050218 TCATTTTTTTGGTTTAATTATACAAAGTCCTTGAAGAGTTAAAGAAATCAGAGATTTTCCCGAAG
261 CCATATTTTTGGTTTAATTACACAAAGCCCTTGAAGAGTTAAAGAAATCAGAGATTTACCCGAAG
* * * *
17050283 ATTTACTGATGATCGATTTAGTGCTGAGTTGTTGTGACACTCAAATTAACCAAAAATCAAGGAAA
326 ATTTACTGATGACCGATTTAATCCTGAGTTGTTGTGACACTCAAATTAACCAAAAATCAAGAAAA
* * *
17050348 AATCAGCCACCTTTCCTCAATTCATGGCCGGCCACTCTTGGAGGAAGTTTCAAAGGATGGACACT
391 AATCAGCCACATTTCCTCAATTCATGGCCGACCACTCTTGGAGGAAGTGTCAAAGGATGGACACT
*
17050413 CCTATTTTTAGCAAACTAGCTCCCTTGCCTCACCTATAAATAAGAGCTCATTTCTCACTTTTTCA
456 CCTAATTTTAGCAAACTAGCTCCCTTGCCTCACCTATAAATAAGAGCTCATTTCTCACTTTTTCA
17050478 ATCATCCCTCATCTCATCATCTCTCACTCATTCATCATT
521 ATCATCCCTCATCTCATCATCTCTCACTCATTCATCATT
* **
17050517 CTATGAAGTGGGTCATGCATGATTAAATTAAATAATAAAATATAATTTTATATTTTAATAATTCA
1 CTATAAAGTGGGTCATGCATGATTAAATTAAATAATAAAATATAAAGTTATA-TTTAATAATTCA
*
17050582 TTTTAAATATTTCATTAATAAAATT-AGGTTTAATTAATTAAGTAAATTGATTAATTAAAGTGCT
65 TTTTAAATATTTCATTAAT-AAATTGAGGTTTAATTAATTAAATAAATTGATTAATTAAAGTGCT
** * * *
17050646 TAAATTA-ATTCATTTGGTCCTCTAAACTATCTGTTATTTTT-GATAGGTCTGAA-AGTTTTCTT
129 TAAATTATATT-ATTTGGTCCTCTAAACTATCTACTATTTTTGGACAGGGCT-AAGAATTTTCTT
*** *
17050708 CTAATTGCAAAACCGTCCAAAGTGGGGACCAAGTCAAACCAATTTTTGACTGCACATTTCTGATT
192 CTAATTGCAAAACCGTCCAAAGTGGGGACCAAGTCAAACCAATTTTTGACTGCACATGGATG-TC
* * * *
17050773 ATAAACCA-ATTTTTGGTTTAATTACATAAGGCCCTTGAAGAGTTAAAGAAATCATATATTTACC
256 ATAAACCATATTTTTGGTTTAATTACACAAAGCCCTTGAAGAGTTAAAGAAATCAGAGATTTACC
* * * *
17050837 TGAAGATTTGCTGGA-GACCGAGTCTTAATCCTGAGTTGTTGTGGCATTCAAATTGAA-CAAAAA
321 CGAAGATTTACT-GATGACCGA-T-TTAATCCTGAGTTGTTGTGACACTCAAATT-AACCAAAAA
* *
17050900 TCAAGAAAAAATTAGCCACATTTCCTCAATTCATGGCCGACCACTCTTGGAGGAGGTGTCAAAGG
382 TCAAGAAAAAATCAGCCACATTTCCTCAATTCATGGCCGACCACTCTTGGAGGAAGTGTCAAAGG
*
17050965 ATGGACACTCCTAATTTTAGCAAACTAGCTCCCTTGCCTCACCTATAAATAAGAGCTTATTTCTC
447 ATGGACACTCCTAATTTTAGCAAACTAGCTCCCTTGCCTCACCTATAAATAAGAGCTCATTTCTC
17051030 ACTTTTTCAATCATCCCT
512 ACTTTTTCAATCATCCCT
17051048 AATCCCTCAT
Statistics
Matches: 477, Mismatches: 45, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
559 184 0.39
560 114 0.24
561 177 0.37
562 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (559 bp):
CTATAAAGTGGGTCATGCATGATTAAATTAAATAATAAAATATAAAGTTATATTTAATAATTCAT
TTTAAATATTTCATTAATAAATTGAGGTTTAATTAATTAAATAAATTGATTAATTAAAGTGCTTA
AATTATATTATTTGGTCCTCTAAACTATCTACTATTTTTGGACAGGGCTAAGAATTTTCTTCTAA
TTGCAAAACCGTCCAAAGTGGGGACCAAGTCAAACCAATTTTTGACTGCACATGGATGTCATAAA
CCATATTTTTGGTTTAATTACACAAAGCCCTTGAAGAGTTAAAGAAATCAGAGATTTACCCGAAG
ATTTACTGATGACCGATTTAATCCTGAGTTGTTGTGACACTCAAATTAACCAAAAATCAAGAAAA
AATCAGCCACATTTCCTCAATTCATGGCCGACCACTCTTGGAGGAAGTGTCAAAGGATGGACACT
CCTAATTTTAGCAAACTAGCTCCCTTGCCTCACCTATAAATAAGAGCTCATTTCTCACTTTTTCA
ATCATCCCTCATCTCATCATCTCTCACTCATTCATCATT
Found at i:17051059 original size:14 final size:15
Alignment explanation
Indices: 17051040--17051086 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
17051030 ACTTTTTCAA
17051040 TCATCCCTAATCC-C
1 TCATCCCTAATCCTC
*
17051054 TCATCCCTCATCCTTC
1 TCATCCCTAATCC-TC
*
17051070 TCATCTCTAATCCTC
1 TCATCCCTAATCCTC
17051085 TC
1 TC
17051087 TCTCAACTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.43
15 4 0.14
16 12 0.43
ACGTcount: A:0.17, C:0.47, G:0.00, T:0.36
Consensus pattern (15 bp):
TCATCCCTAATCCTC
Found at i:17061460 original size:35 final size:35
Alignment explanation
Indices: 17061402--17061560 Score: 212
Period size: 35 Copynumber: 4.5 Consensus size: 35
17061392 TAATCCAAAT
17061402 GAAACACACCAGATGCTCATAAGAGCTAATCCATCC
1 GAAACACACCA-ATGCTCATAAGAGCTAATCCATCC
* * *
17061438 GGAACACATCAATGCTCATAAGAGCTAATCCATCT
1 GAAACACACCAATGCTCATAAGAGCTAATCCATCC
*
17061473 GAAACACACCAATGCTCATTAGAGCTAATCCATCC
1 GAAACACACCAATGCTCATAAGAGCTAATCCATCC
* * * *
17061508 GAAACACACCAATGCTTATAAAAG-TTATACATCC
1 GAAACACACCAATGCTCATAAGAGCTAATCCATCC
* *
17061542 GAAACAGATCAATGCTCAT
1 GAAACACACCAATGCTCAT
17061561 CAAAGCTTAA
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 24 0.22
35 75 0.69
36 9 0.08
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.21
Consensus pattern (35 bp):
GAAACACACCAATGCTCATAAGAGCTAATCCATCC
Found at i:17074709 original size:27 final size:27
Alignment explanation
Indices: 17074664--17074955 Score: 219
Period size: 27 Copynumber: 10.6 Consensus size: 27
17074654 CTATGTGTTA
* **
17074664 CACAAAGGCATCCCCTTTATAGATCAC
1 CACAAAGGCTTCCTTTTTATAGATCAC
**
17074691 CATGAAGGCTTCCTTTTTATAGATCAC
1 CACAAAGGCTTCCTTTTTATAGATCAC
* *
17074718 CACAAAGGCTTCCTTTTCAGAGATCAC
1 CACAAAGGCTTCCTTTTTATAGATCAC
* * * * *
17074745 CACAAATGTTTCCTATTCATAGATCGC
1 CACAAAGGCTTCCTTTTTATAGATCAC
* *
17074772 TACAAAGGCTTCCTTTTCATAGATAGCCACAC
1 CACAAAGGCTTCCTTTTTATAGAT-----CAC
* * *
17074804 CACAAAGGCTTTCTTTTTATATATCGC
1 CACAAAGGCTTCCTTTTTATAGATCAC
* * * *
17074831 CACAAATGCTTTCTTTTCATTGAT-AGC
1 CACAAAGGCTTCCTTTTTATAGATCA-C
* * *
17074858 TACAAAGGCTTCCTTTTCATAGATCGC
1 CACAAAGGCTTCCTTTTTATAGATCAC
* * *
17074885 CACAAAGGCTTCATTTTCATTGAT-AGC
1 CACAAAGGCTTCCTTTTTATAGATCA-C
* **
17074912 CACAAAGGATTCCTTTCAATAGATCAC
1 CACAAAGGCTTCCTTTTTATAGATCAC
* *
17074939 CATAAAGGCTTTCTTTT
1 CACAAAGGCTTCCTTTT
17074956 ATGATGTATT
Statistics
Matches: 209, Mismatches: 47, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
27 186 0.89
28 1 0.00
32 22 0.11
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (27 bp):
CACAAAGGCTTCCTTTTTATAGATCAC
Found at i:17074746 original size:54 final size:54
Alignment explanation
Indices: 17074664--17074955 Score: 259
Period size: 54 Copynumber: 5.3 Consensus size: 54
17074654 CTATGTGTTA
* * ** * *
17074664 CACAAAGGCATCCCCTTT-ATAGATCACCATGAAGGCTTCCTTTTTATAGATCAC
1 CACAAAGGC-TTCCTTTTCATAGATCACCACAAAGGCTTCCTTTTCATAGATCGC
* * * *
17074718 CACAAAGGCTTCCTTTTCAGAGATCACCACAAATGTTTCCTATTCATAGATCGC
1 CACAAAGGCTTCCTTTTCATAGATCACCACAAAGGCTTCCTTTTCATAGATCGC
* * * *
17074772 TACAAAGGCTTCCTTTTCATAGATAGCCACACCACAAAGGCTTTCTTTTTATATATCGC
1 CACAAAGGCTTCCTTTTCATAGAT-----CACCACAAAGGCTTCCTTTTCATAGATCGC
* * * *
17074831 CACAAATGCTTTCTTTTCATTGAT-AGCTACAAAGGCTTCCTTTTCATAGATCGC
1 CACAAAGGCTTCCTTTTCATAGATCA-CCACAAAGGCTTCCTTTTCATAGATCGC
* * * *
17074885 CACAAAGGCTTCATTTTCATTGAT-AGCCACAAAGGATTCC-TTTCAATAGATCAC
1 CACAAAGGCTTCCTTTTCATAGATCA-CCACAAAGGCTTCCTTTTC-ATAGATCGC
* *
17074939 CATAAAGGCTTTCTTTT
1 CACAAAGGCTTCCTTTT
17074956 ATGATGTATT
Statistics
Matches: 195, Mismatches: 35, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
53 11 0.06
54 140 0.72
59 44 0.23
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (54 bp):
CACAAAGGCTTCCTTTTCATAGATCACCACAAAGGCTTCCTTTTCATAGATCGC
Found at i:17074814 original size:32 final size:32
Alignment explanation
Indices: 17074773--17074834 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
17074763 ATAGATCGCT
17074773 ACAAAGGCTTCCTTTTCATAGATAGCCACACC
1 ACAAAGGCTTCCTTTTCATAGATAGCCACACC
* * * *
17074805 ACAAAGGCTTTCTTTTTATATATCGCCACA
1 ACAAAGGCTTCCTTTTCATAGATAGCCACA
17074835 AATGCTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (32 bp):
ACAAAGGCTTCCTTTTCATAGATAGCCACACC
Found at i:17074850 original size:86 final size:86
Alignment explanation
Indices: 17074715--17074888 Score: 251
Period size: 86 Copynumber: 2.0 Consensus size: 86
17074705 TTTTATAGAT
*
17074715 CACCACAAAGGCTTCCTTTTCAGAGATCACCACAAATGTTTCCTATTCATAGATCGCTACAAAGG
1 CACCACAAAGGCTTCCTTTTCAGAGATCACCACAAATGTTTCCTATTCATAGATAGCTACAAAGG
17074780 CTTCCTTTTCATAGATAGCCA
66 CTTCCTTTTCATAGATAGCCA
* * * * * * *
17074801 CACCACAAAGGCTTTCTTTTTATATATCGCCACAAATGCTTT-CTTTTCATTGATAGCTACAAAG
1 CACCACAAAGGCTTCCTTTTCAGAGATCACCACAAATG-TTTCCTATTCATAGATAGCTACAAAG
*
17074865 GCTTCCTTTTCATAGATCGCCA
65 GCTTCCTTTTCATAGATAGCCA
17074887 CA
1 CA
17074889 AAGGCTTCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 75 0.96
87 3 0.04
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (86 bp):
CACCACAAAGGCTTCCTTTTCAGAGATCACCACAAATGTTTCCTATTCATAGATAGCTACAAAGG
CTTCCTTTTCATAGATAGCCA
Found at i:17074863 original size:113 final size:113
Alignment explanation
Indices: 17074695--17074955 Score: 300
Period size: 113 Copynumber: 2.4 Consensus size: 113
17074685 GATCACCATG
* *
17074695 AAGGCTTCCTTTTTATAGATCACCACAAAGGCTTCCTTTTCAGAGATCACCACAAATGTTTCCTA
1 AAGGCTTCCTTTTTATAGATCACCACAAAGGCTTCCTTTTCAGAGATCACCACAAAGGCTTCCTA
* *
17074760 TTCATAGATCGCTACAAAGGCTTCCTTTTCATAGATAGCCACACCACA
66 TTCATAGATCGCCACAAAGGCTTCATTTTCATAGATAGCCACACCACA
* * * * * ** *
17074808 AAGGCTTTCTTTTTATATATCGCCACAAATGCTTTCTTTTCATTGAT-AGCTACAAAGGCTTCCT
1 AAGGCTTCCTTTTTATAGATCACCACAAAGGCTTCCTTTTCAGAGATCA-CCACAAAGGCTTCCT
* *
17074872 TTTCATAGATCGCCACAAAGGCTTCATTTTCATTGATAG-----CCACA
65 ATTCATAGATCGCCACAAAGGCTTCATTTTCATAGATAGCCACACCACA
* ** * *
17074916 AAGGATTCCTTTCAATAGATCACCATAAAGGCTTTCTTTT
1 AAGGCTTCCTTTTTATAGATCACCACAAAGGCTTCCTTTT
17074956 ATGATGTATT
Statistics
Matches: 125, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
108 37 0.30
112 1 0.01
113 87 0.70
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (113 bp):
AAGGCTTCCTTTTTATAGATCACCACAAAGGCTTCCTTTTCAGAGATCACCACAAAGGCTTCCTA
TTCATAGATCGCCACAAAGGCTTCATTTTCATAGATAGCCACACCACA
Found at i:17081469 original size:7 final size:7
Alignment explanation
Indices: 17081457--17081483 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17081447 CCTATAAATA
17081457 AGAAAAG
1 AGAAAAG
17081464 AGAAAAG
1 AGAAAAG
17081471 AGAAAAG
1 AGAAAAG
17081478 AGAAAA
1 AGAAAA
17081484 AGAGCACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AGAAAAG
Found at i:17084083 original size:20 final size:20
Alignment explanation
Indices: 17084048--17084096 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
17084038 TATCATGTCT
*
17084048 TTGCTT-CTTCTTTACTTAC
1 TTGCTTGCTTGTTTACTTAC
17084067 TCT-CTTGCTTGTTTACTTAC
1 T-TGCTTGCTTGTTTACTTAC
17084087 TTGCTTGCTT
1 TTGCTTGCTT
17084097 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.08, C:0.24, G:0.10, T:0.57
Consensus pattern (20 bp):
TTGCTTGCTTGTTTACTTAC
Found at i:17084424 original size:50 final size:50
Alignment explanation
Indices: 17084361--17084484 Score: 140
Period size: 50 Copynumber: 2.5 Consensus size: 50
17084351 CGATGTCATA
* ** * * *
17084361 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCTATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
** * *
17084411 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCGTG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* *
17084461 TCCCAAACATGGTCTTACTTGGGA
1 TCCCAGACATGGTCTTACATGGGA
17084485 TCTCATTCTC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:17087643 original size:30 final size:30
Alignment explanation
Indices: 17087607--17087805 Score: 116
Period size: 30 Copynumber: 6.7 Consensus size: 30
17087597 TGGTTGACCC
* *
17087607 ATCCCTTTTCGTAATTCGATAACCGAAGTT
1 ATCCCTTTTCATAATTCGATAACCGAAGCT
* *
17087637 ATCCCTTTTCATAGTTCGATAGCCGAAGCT
1 ATCCCTTTTCATAATTCGATAACCGAAGCT
* * **** * *
17087667 ATCTCTTTTCATAATTTGATGGTTGTCA-CC
1 ATCCCTTTTCATAATTCGATAACCG-AAGCT
** ***
17087697 ATCCCTTTTCATTGTT-GATGGTCGAAGCT
1 ATCCCTTTTCATAATTCGATAACCGAAGCT
* * * *
17087726 ATCGCTTTTCATAGTTCGATAGCTGAAG-T
1 ATCCCTTTTCATAATTCGATAACCGAAGCT
* * * * * *
17087755 AATCCTTTTTCATATTTTGATAGCTGAAGCC
1 -ATCCCTTTTCATAATTCGATAACCGAAGCT
17087786 ATCCCTTTTCATAATTCGAT
1 ATCCCTTTTCATAATTCGAT
17087806 GGTAGTCACC
Statistics
Matches: 133, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
28 1 0.01
29 23 0.17
30 108 0.81
31 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATAACCGAAGCT
Found at i:17087718 original size:29 final size:29
Alignment explanation
Indices: 17087637--17087856 Score: 106
Period size: 30 Copynumber: 7.4 Consensus size: 29
17087627 AACCGAAGTT
* * ** *
17087637 ATCCCTTTTCATAGTTCGATAGCCGAAGCT
1 ATCCCTTTTCATTGTT-GATGGTTGAAGCC
* *
17087667 ATCTCTTTTCATAAT-TTGATGGTTGTCA-CC
1 ATCCCTTTTCAT--TGTTGATGGTTG-AAGCC
* *
17087697 ATCCCTTTTCATTGTTGATGGTCGAAGCT
1 ATCCCTTTTCATTGTTGATGGTTGAAGCC
* * * * **
17087726 ATCGCTTTTCATAGTTCGATAGCTGAAGTA
1 ATCCCTTTTCATTGTT-GATGGTTGAAGCC
* * * *
17087756 ATCCTTTTTCATATTTTGATAGCTGAAGCC
1 ATCCCTTTTCAT-TGTTGATGGTTGAAGCC
** * *
17087786 ATCCCTTTTCATAATTCGATGGTAGTCA-CC
1 ATCCCTTTTCATTGTT-GATGGTTG-AAGCC
* *
17087816 ATCCCTTTTCATTGTTGATGGTCGTCA-CC
1 ATCCCTTTTCATTGTTGATGGTTG-AAGCC
17087845 ATCCCTTTTCAT
1 ATCCCTTTTCAT
17087857 AATCGACAGC
Statistics
Matches: 147, Mismatches: 34, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
28 2 0.01
29 50 0.34
30 89 0.61
31 6 0.04
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (29 bp):
ATCCCTTTTCATTGTTGATGGTTGAAGCC
Found at i:17087739 original size:89 final size:89
Alignment explanation
Indices: 17087630--17087797 Score: 225
Period size: 89 Copynumber: 1.9 Consensus size: 89
17087620 ATTCGATAAC
* * *
17087630 CGAAGTTATCCCTTTTCATAGTTCGATAGCCGAAGCT-AT-CTCTTTTCATAATTTGATGGTTGT
1 CGAAGCTATCCCTTTTCATAGTTCGATAGCCGAAG-TAATCCT-TTTTCATAATTTGATAGCTG-
*
17087693 CA-CCATCCCTTTTCATTGTTGATGGT
63 AAGCCATCCCTTTTCATTGTTGATGGT
* * *
17087719 CGAAGCTATCGCTTTTCATAGTTCGATAGCTGAAGTAATCCTTTTTCATATTTTGATAGCTGAAG
1 CGAAGCTATCCCTTTTCATAGTTCGATAGCCGAAGTAATCCTTTTTCATAATTTGATAGCTGAAG
17087784 CCATCCCTTTTCAT
66 CCATCCCTTTTCAT
17087798 AATTCGATGG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
88 2 0.03
89 65 0.94
90 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.40
Consensus pattern (89 bp):
CGAAGCTATCCCTTTTCATAGTTCGATAGCCGAAGTAATCCTTTTTCATAATTTGATAGCTGAAG
CCATCCCTTTTCATTGTTGATGGT
Found at i:17087818 original size:30 final size:29
Alignment explanation
Indices: 17087784--17087859 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
17087774 ATAGCTGAAG
17087784 CCATCCCTTTTCATAATTCGATGGTAGTCA
1 CCATCCCTTTTCATAATT-GATGGTAGTCA
** *
17087814 CCATCCCTTTTCATTGTTGATGGTCGTCA
1 CCATCCCTTTTCATAATTGATGGTAGTCA
17087843 CCATCCCTTTTCATAAT
1 CCATCCCTTTTCATAAT
17087860 CGACAGCCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (29 bp):
CCATCCCTTTTCATAATTGATGGTAGTCA
Found at i:17087822 original size:119 final size:119
Alignment explanation
Indices: 17087611--17087893 Score: 365
Period size: 119 Copynumber: 2.4 Consensus size: 119
17087601 TGACCCATCC
* * * *
17087611 CTTTTCGTAATTCGATAACCGAAGTTATCCCTTTTCATAGTTCGATAGCCGAAGCTATCTCTTTT
1 CTTTTCATAATTCGATAACCGAAGTAATCCCTTTTCATAGTTCGATAGCCGAAGCCATCCCTTTT
* *
17087676 CATAATTTGATGGTTGTCACCATCCCTTTTCATTGTTGATGGTCGAAGCTATCG
66 CATAATTCGATGGTAGTCACCATCCCTTTTCATTGTTGATGGTCGAAGCTATCG
* * * * * * *
17087730 CTTTTCATAGTTCGATAGCTGAAGTAATCCTTTTTCATATTTTGATAGCTGAAGCCATCCCTTTT
1 CTTTTCATAATTCGATAACCGAAGTAATCCCTTTTCATAGTTCGATAGCCGAAGCCATCCCTTTT
* * *
17087795 CATAATTCGATGGTAGTCACCATCCCTTTTCATTGTTGATGGTCGTCA-CCATCC
66 CATAATTCGATGGTAGTCACCATCCCTTTTCATTGTTGATGGTCG-AAGCTATCG
* *
17087849 CTTTTCATAA-TCGACAGCCGAAGCT-ATCCCTTTTCATAGTTCGAT
1 CTTTTCATAATTCGATAACCGAAG-TAATCCCTTTTCATAGTTCGAT
17087894 GATTGACATT
Statistics
Matches: 140, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
118 28 0.20
119 111 0.79
120 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (119 bp):
CTTTTCATAATTCGATAACCGAAGTAATCCCTTTTCATAGTTCGATAGCCGAAGCCATCCCTTTT
CATAATTCGATGGTAGTCACCATCCCTTTTCATTGTTGATGGTCGAAGCTATCG
Found at i:17097888 original size:23 final size:23
Alignment explanation
Indices: 17097846--17097889 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17097836 TTAATAAAAT
* *
17097846 ATTAATTAAATAACATTTATCTA
1 ATTAATTAAATAAAAATTATCTA
*
17097869 ATTAATTAATTAAAAATTATC
1 ATTAATTAAATAAAAATTATC
17097890 ACAAACATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAATTAAATAAAAATTATCTA
Found at i:17099897 original size:50 final size:50
Alignment explanation
Indices: 17099830--17100124 Score: 392
Period size: 50 Copynumber: 5.9 Consensus size: 50
17099820 TTTCATGTAC
* * * * ** *
17099830 TGCCAATGCCATATCCCAAATATGATCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
17099880 TGCCTATGCCATGTCCCAGACATGGTCTTAAAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
17099930 TGCCAACGACATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
17099980 TGCCAACGCCTTGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
17100030 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGGCCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
17100080 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCAT
17100125 AATTTCAATA
Statistics
Matches: 216, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 216 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:17099962 original size:100 final size:100
Alignment explanation
Indices: 17099781--17100124 Score: 397
Period size: 100 Copynumber: 3.5 Consensus size: 100
17099771 GAATATAACA
* * * * ** * * * * *
17099781 TGCCAAAGCTATGTCCCAGACATAGTCTTACACGGGATGTTTCATGTAC--TGCCAATGCCATAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTGCCAACGACATGT
* * * *
17099844 CCCAAATATGATCTTACATGGGAGTTCTCATATCGG
65 CCCAAACATGGTCTTACATGGGAGCTCTCATCTCGG
* * *
17099880 TGCCTATGCCATGTCCCAGACATGGTCTTAAAGGGGACCTCTCATCTCGGTGCCAACGACATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGACATGTC
* * *
17099945 CCAGACATGGTCTTACATGGGACCTCTCATCTCGA
66 CCAAACATGGTCTTACATGGGAGCTCTCATCTCGG
* * * * *
17099980 TGCCAACGCCTTGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGACATGTC
*
17100045 CCAAACATGGTCTTACATGGG-GCCTCTCATCTCAG
66 CCAAACATGGTCTTACATGGGAG-CTCTCATCTCGG
*
17100080 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
17100125 AATTTCAATA
Statistics
Matches: 206, Mismatches: 36, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
98 1 0.00
99 37 0.18
100 168 0.82
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (100 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGACATGTC
CCAAACATGGTCTTACATGGGAGCTCTCATCTCGG
Found at i:17100024 original size:150 final size:148
Alignment explanation
Indices: 17099791--17100212 Score: 447
Period size: 150 Copynumber: 2.8 Consensus size: 148
17099781 TGCCAAAGCT
* * ** * * * * *
17099791 ATGTCCCAGACATAGTCTTACACGGGATGTTTCATGT-ACTGCCAATGCCATATCCCAAATATGA
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-TGCCAATGCCATGTCCCAAACATGG
* * *
17099855 TCTTACATGGGAGTTCTCATATCGGTGCCTATGCCATGTCCCAGACATGGTCTTA-AAGGGGACC
65 TCTTACATGGGA-CTCTCATATCGGTGCCAATGCCATGTCCCAAACATGGTCTTACAAGGGG-CC
*
17099919 TCTCATCTCGGTGCCAACGAC
128 TCTCATCTCAGTGCCAACGAC
* *
17099940 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCTTGTCCCAAACATGG
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC-ATGCCAATGCCATGTCCCAAACATGG
* * * *
17100005 TCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGGCCT
65 TCTTACATGGGA-CTCTCATATCGGTGCCAATGCCATGTCCCAAACATGGTCTTACAAGGGGCCT
* *
17100070 CTCATCTCAGTGCCAATGCC
129 CTCATCTCAGTGCCAACGAC
* * *
17100090 ATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATTTCAATAAGGCCAATGCCATGTCCCAG
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-AT---GCCAATGCCATGTCCCAA
* * * *
17100155 ACATGGTCTTACACT-GG-CTCACATATCGATGTCGATGCCATGTCCCAAACATGGTCTT
59 ACATGGTCTTACA-TGGGACTCTCATATCGGTGCCAATGCCATGTCCCAAACATGGTCTT
17100213 CTATGAGATC
Statistics
Matches: 228, Mismatches: 35, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
149 31 0.14
150 120 0.53
151 6 0.03
153 6 0.03
154 34 0.15
156 30 0.13
157 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (148 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCATGCCAATGCCATGTCCCAAACATGGT
CTTACATGGGACTCTCATATCGGTGCCAATGCCATGTCCCAAACATGGTCTTACAAGGGGCCTCT
CATCTCAGTGCCAACGAC
Found at i:17104290 original size:14 final size:14
Alignment explanation
Indices: 17104271--17104301 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17104261 TGATTGTTTT
*
17104271 TAATCTAAATTTAC
1 TAATCTAAATTAAC
17104285 TAATCTAAATTAAC
1 TAATCTAAATTAAC
17104299 TAA
1 TAA
17104302 GAACGCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:17106159 original size:14 final size:14
Alignment explanation
Indices: 17106140--17106170 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17106130 TGATTGTTTT
*
17106140 TAATCTAAATTTAC
1 TAATCTAAATTAAC
17106154 TAATCTAAATTAAC
1 TAATCTAAATTAAC
17106168 TAA
1 TAA
17106171 GAATGCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:17108920 original size:5 final size:5
Alignment explanation
Indices: 17108912--17108941 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
17108902 TCATAATATA
*
17108912 ATTGT ATTGT TTTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
17108942 TTTCTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (5 bp):
ATTGT
Found at i:17112244 original size:2 final size:2
Alignment explanation
Indices: 17112237--17112275 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
17112227 AGTGTTGAAA
*
17112237 AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17112276 AACCAGATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17116747 original size:3 final size:3
Alignment explanation
Indices: 17116739--17116768 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17116729 TGAGTACCTA
17116739 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17116769 ATGGTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17119633 original size:18 final size:19
Alignment explanation
Indices: 17119612--17119654 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
17119602 TTTTACAATG
17119612 ATATTAATACAAAG-ATAT
1 ATATTAATACAAAGCATAT
* *
17119630 ATATT-CTAGAAAGCATAT
1 ATATTAATACAAAGCATAT
17119648 ATATTAA
1 ATATTAA
17119655 AGTAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (19 bp):
ATATTAATACAAAGCATAT
Found at i:17121154 original size:22 final size:22
Alignment explanation
Indices: 17121106--17121196 Score: 86
Period size: 22 Copynumber: 4.3 Consensus size: 22
17121096 TAAATACCAA
**
17121106 AAAATTATTTTAAAAAT-TTAAA
1 AAAATTATTTTAAAAATATT-TT
17121128 AAAATTATTTTAAAAATATTTT
1 AAAATTATTTTAAAAATATTTT
*
17121150 TAAATTA----AAAAA-ATTTT
1 AAAATTATTTTAAAAATATTTT
*
17121167 ACAAAGTATTTTAAAAATATTTT
1 A-AAATTATTTTAAAAATATTTT
17121190 AAAATTA
1 AAAATTA
17121197 AAAAAATTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
17 5 0.09
18 10 0.18
22 33 0.59
23 8 0.14
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (22 bp):
AAAATTATTTTAAAAATATTTT
Found at i:17121177 original size:40 final size:40
Alignment explanation
Indices: 17121117--17121222 Score: 167
Period size: 40 Copynumber: 2.6 Consensus size: 40
17121107 AAATTATTTT
* *
17121117 AAAAATTTAAAAAAATTATTTTAAAAATATTTTTAAATTAA
1 AAAAATTT-AAAAAAGTATTTTAAAAATATTTTAAAATTAA
* *
17121158 AAAAATTTTACAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
17121198 AAAAATTTAAAAAAGTATTTTAAAA
1 AAAAATTTAAAAAAGTATTTTAAAA
17121223 TTAAAAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 51 0.86
41 8 0.14
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (40 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:17121217 original size:29 final size:28
Alignment explanation
Indices: 17121174--17121241 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
17121164 TTTACAAAGT
*
17121174 ATTTTAAAAATATTTTAAAATTAAAAAA
1 ATTTAAAAAATATTTTAAAATTAAAAAA
17121202 ATTTAAAAAAGTATTTTAAAATTAAAAAA
1 ATTTAAAAAA-TATTTTAAAATTAAAAAA
*
17121231 A-TAAAAAAATA
1 ATTTAAAAAATA
17121242 AAATATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 2 0.05
28 16 0.43
29 19 0.51
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
ATTTAAAAAATATTTTAAAATTAAAAAA
Found at i:17125070 original size:3 final size:3
Alignment explanation
Indices: 17125062--17125101 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
17125052 GGAAGAGAGA
*
17125062 AAG AAG AAG AA- AAG AAG -AG AAG -AG AAG AAG GAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
17125102 GGGCGGGGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.19
3 26 0.81
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:17125321 original size:23 final size:22
Alignment explanation
Indices: 17125288--17125358 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 22
17125278 GTGTGTTGTC
*
17125288 TCATCAATTTTTTTTTTATTTTT
1 TCATCAGTTTTTTTTTT-TTTTT
* *
17125311 TCATCAGTTTTATTTATTGTTTT
1 TCATCAGTTTT-TTTTTTTTTTT
17125334 TCATCAGATTTTTTTTTCTTTTTT
1 TCATCAG-TTTTTTTTT-TTTTTT
17125358 T
1 T
17125359 TGTGTCAGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 25 0.62
24 15 0.38
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.70
Consensus pattern (22 bp):
TCATCAGTTTTTTTTTTTTTTT
Found at i:17125463 original size:16 final size:18
Alignment explanation
Indices: 17125444--17125476 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
17125434 AAACATAGTC
17125444 ATTTTAT-TT-TTTTAAA
1 ATTTTATATTATTTTAAA
17125460 ATTTTATATTATTTTAA
1 ATTTTATATTATTTTAA
17125477 TAAAAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTATATTATTTTAAA
Found at i:17130350 original size:25 final size:25
Alignment explanation
Indices: 17130300--17130369 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
17130290 TGGACCCATT
* **
17130300 TTCATAGCTCGTGTGAG-ACTTTTGA
1 TTCACAGCTCGTGTGAGCA-TCCTGA
*
17130325 TTTACAGCTCGTGTGAGCATCCTGA
1 TTCACAGCTCGTGTGAGCATCCTGA
*
17130350 TTCACAACTCGTGTGAGCAT
1 TTCACAGCTCGTGTGAGCAT
17130370 ACATGTACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATCCTGA
Found at i:17132060 original size:101 final size:102
Alignment explanation
Indices: 17131940--17132133 Score: 302
Period size: 102 Copynumber: 1.9 Consensus size: 102
17131930 AAAGTAATGG
* *
17131940 TCACGTGTGTAGTACTATATGTAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACC-GAATGATAATGGTCACATGTGTAGT
* *
17132003 ACTATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
65 ACTATGTGCAAGCTACTATGCGAACCGAATAGTTTCGA
* *
17132041 TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTATCGAATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACCGAATGATAATGGTCACATGTGTAGTA
*
17132106 CTATGTGCAAGCTACTATGTGAACCGAA
66 CTATGTGCAAGCTACTATGCGAACCGAA
17132134 CATCATTGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
100 6 0.07
101 38 0.45
102 40 0.48
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACCGAATGATAATGGTCACATGTGTAGTA
CTATGTGCAAGCTACTATGCGAACCGAATAGTTTCGA
Found at i:17132064 original size:51 final size:49
Alignment explanation
Indices: 17131936--17132133 Score: 209
Period size: 51 Copynumber: 3.9 Consensus size: 49
17131926 AGTGAAAGTA
* *
17131936 ATGGTCACGTGTGTAGTACTATATGTAGGCTACTACGTGTACCGGAATG-
1 ATGGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACC-GAATGT
* * * *
17131985 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGT
1 AT-GGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACCGAAT-GT
* * * *
17132036 TTCGATCACGTGTGTAGTACTATATGCAGGCTACTACGTGTATCGAATGGT
1 AT-GGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACCGAAT-GT
* * * *
17132087 AATGGTCACATGTGTAGTACTATGTGCAAGCTACTATGTGAACCGAA
1 -ATGGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACCGAA
17132134 CATCATTGAT
Statistics
Matches: 121, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
49 6 0.05
50 36 0.30
51 78 0.64
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
ATGGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACCGAATGT
Found at i:17132184 original size:45 final size:45
Alignment explanation
Indices: 17132128--17132222 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
17132118 TACTATGTGA
* *
17132128 ACCGAACATCATTGATTAGTAAAGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
* * *
17132173 ACCGGACATCATTGATTAATAAGGTGGTTGTTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
17132218 ACCGA
1 ACCGA
17132223 GTATCTGTTA
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:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
Found at i:17132367 original size:8 final size:8
Alignment explanation
Indices: 17132354--17132378 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17132344 ATTGTGATTG
17132354 AAAGTGAA
1 AAAGTGAA
17132362 AAAGTGAA
1 AAAGTGAA
17132370 AAAGTGAA
1 AAAGTGAA
17132378 A
1 A
17132379 TTATGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (8 bp):
AAAGTGAA
Found at i:17134790 original size:15 final size:16
Alignment explanation
Indices: 17134770--17134799 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17134760 TGGTGCCTTG
17134770 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
17134785 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
17134800 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:17139401 original size:8 final size:8
Alignment explanation
Indices: 17139388--17139417 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
17139378 AAGATGATAC
17139388 TTTTATTT
1 TTTTATTT
*
17139396 TTTTATGT
1 TTTTATTT
17139404 TTTTATTT
1 TTTTATTT
17139412 TTTTAT
1 TTTTAT
17139418 ATTTGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:17141789 original size:36 final size:36
Alignment explanation
Indices: 17141742--17141888 Score: 186
Period size: 36 Copynumber: 4.1 Consensus size: 36
17141732 AAAAAAAGAA
* *
17141742 TTTGTATACATAATAGGGTTCACATATATATAAGGG
1 TTTGTATACATAATAGGGTTCACATACATGTAAGGG
** *
17141778 TTTGTATACATAATAGGGTTTGCATACATGTAAGGA
1 TTTGTATACATAATAGGGTTCACATACATGTAAGGG
* *
17141814 TTTGTATACATAATAGGGTTTACATACATGTAAGTG
1 TTTGTATACATAATAGGGTTCACATACATGTAAGGG
* * * *
17141850 TTCGCATACATAATAAGGTTCACATACATGACAAGGG
1 TTTGTATACATAATAGGGTTCACATACATG-TAAGGG
17141887 TT
1 TT
17141889 CGTAGAAACA
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
36 90 0.94
37 6 0.06
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (36 bp):
TTTGTATACATAATAGGGTTCACATACATGTAAGGG
Found at i:17141878 original size:18 final size:18
Alignment explanation
Indices: 17141742--17141869 Score: 91
Period size: 18 Copynumber: 7.1 Consensus size: 18
17141732 AAAAAAAGAA
* *
17141742 TTTGTATACATAATAGGG
1 TTTGCATACATAATAAGG
** *
17141760 TTCACATATAT-ATAAGGG
1 TTTGCATACATAATAA-GG
* *
17141778 TTTGTATACATAATAGGG
1 TTTGCATACATAATAAGG
*
17141796 TTTGCATACAT-GTAAGG
1 TTTGCATACATAATAAGG
* *
17141813 ATTTGTATACATAATAGGG
1 -TTTGCATACATAATAAGG
* *
17141832 TTTACATACAT-GTAAGTG
1 TTTGCATACATAATAAG-G
*
17141850 TTCGCATACATAATAAGG
1 TTTGCATACATAATAAGG
17141868 TT
1 TT
17141870 CACATACATG
Statistics
Matches: 81, Mismatches: 23, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
17 10 0.12
18 60 0.74
19 11 0.14
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (18 bp):
TTTGCATACATAATAAGG
Found at i:17141885 original size:18 final size:18
Alignment explanation
Indices: 17141819--17141885 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
17141809 AAGGATTTGT
* * *
17141819 ATACATAATAGGGTTTAC
1 ATACATGATAAGGTTCAC
*
17141837 ATACATG-TAAGTGTTCGC
1 ATACATGATAAG-GTTCAC
*
17141855 ATACATAATAAGGTTCAC
1 ATACATGATAAGGTTCAC
*
17141873 ATACATGACAAGG
1 ATACATGATAAGG
17141886 GTTCGTAGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 32 0.82
19 4 0.10
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (18 bp):
ATACATGATAAGGTTCAC
Found at i:17142365 original size:27 final size:27
Alignment explanation
Indices: 17142335--17142386 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
17142325 CTCAACTCTT
* * *
17142335 CAAAACATATTTGTGAGCTTGGCTCGC
1 CAAAACATATATGTAAGCTTAGCTCGC
17142362 CAAAACATATATGTAAGCTTAGCTC
1 CAAAACATATATGTAAGCTTAGCTC
17142387 ACCAGAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (27 bp):
CAAAACATATATGTAAGCTTAGCTCGC
Found at i:17153197 original size:18 final size:18
Alignment explanation
Indices: 17153176--17153212 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17153166 AAGAGTGAAA
*
17153176 AATAAGGGATAACATAGT
1 AATAAGGGACAACATAGT
17153194 AATAAGGGACAACATAGT
1 AATAAGGGACAACATAGT
17153212 A
1 A
17153213 TCATGAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (18 bp):
AATAAGGGACAACATAGT
Found at i:17157934 original size:11 final size:11
Alignment explanation
Indices: 17157884--17157936 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
17157874 ATAAAAGTTC
17157884 TAAAATA-AAT
1 TAAAATAGAAT
17157894 TAAATATATGAAT
1 TAAA-ATA-GAAT
*
17157907 TCAAAATAGACT
1 T-AAAATAGAAT
*
17157919 CAAAATAGAAT
1 TAAAATAGAAT
17157930 TAAAATA
1 TAAAATA
17157937 ACCATTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (11 bp):
TAAAATAGAAT
Found at i:17158024 original size:3 final size:3
Alignment explanation
Indices: 17158016--17158063 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
17158006 AAAGATAAAC
17158016 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17158064 CATATACTCG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17159698 original size:100 final size:99
Alignment explanation
Indices: 17159573--17159938 Score: 473
Period size: 100 Copynumber: 3.7 Consensus size: 99
17159563 TAACTCGCAA
** * * * * * **
17159573 CTTTAAT-CTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCC
1 CTTTAATCCT-TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGT-GCTTTAATCTGCTCC
* * * *
17159637 ACTACACCGCCTGGGAAGTAAGATTCGCTGTTGTAG
64 ACTGCATCGCCAGGGAGGTAAGATTCGCTGTTGTAG
17159673 CTTTAATCCTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGACTTTAATCTGCTCCA
1 CTTTAATCCTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTG-CTTTAATCTGCTCCA
* * * * *
17159738 CTGCATCGTCAGGGAGGTAATATTCACTGCTGTGG
65 CTGCATCGCCAGGGAGGTAAGATTCGCTGTTGTAG
*
17159773 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCCTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGT-GCTTTAATCTGCTCCA
*
17159838 CTGCATCGCCAGGGCGGTAAGATTCGCTGTTGTAG
65 CTGCATCGCCAGGGAGGTAAGATTCGCTGTTGTAG
* * *
17159873 CTTTAATCTTTTTAACTGCAGTGTTGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCCTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGT-GCTTTAATCTGCTCCA
17159938 C
65 C
17159939 GATGTGGCTT
Statistics
Matches: 236, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
99 1 0.00
100 232 0.98
101 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (99 bp):
CTTTAATCCTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGCTTTAATCTGCTCCAC
TGCATCGCCAGGGAGGTAAGATTCGCTGTTGTAG
Found at i:17159703 original size:50 final size:50
Alignment explanation
Indices: 17159573--17159932 Score: 251
Period size: 50 Copynumber: 7.2 Consensus size: 50
17159563 TAACTCGCAA
** * * *
17159573 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTAG
* * ** * ** * * * * *
17159623 CTTCAATCTATTCCACTACACCGCCTGGGAAGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTAG
*
17159673 CTTTAATCCT-TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGT-G
1 CTTTAAT-CTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTAG
* ** * * * * * *
17159722 ACTTTAATCTGCTCCACTGC-ATCGTCAGGGAGGTAATATTCACTGCTGTGG
1 -CTTTAATCTGTTTAACTGCAAT-GTCGGGGAAGCAAGATTCACTGATGTAG
* * *
17159773 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGG
1 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTAG
* ** * * ** * * *
17159823 CTTTAATCTGCTCCACTGC-ATCGCCAGGGCGGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTAACTGCAAT-GTCGGGGAAGCAAGATTCACTGATGTAG
* * * * *
17159873 CTTTAATCTTTTTAACTGCAGTGTTGGGGAAGCAAGATTCACCGATGTGG
1 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTAG
17159923 CTTTAATCTG
1 CTTTAATCTG
17159933 CTCCACGATG
Statistics
Matches: 229, Mismatches: 73, Indels: 16
0.72 0.23 0.05
Matches are distributed among these distances:
49 7 0.03
50 216 0.94
51 6 0.03
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (50 bp):
CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTAG
Found at i:17159916 original size:200 final size:200
Alignment explanation
Indices: 17159573--17159938 Score: 552
Period size: 200 Copynumber: 1.8 Consensus size: 200
17159563 TAACTCGCAA
** * * * *
17159573 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTAGCTTCAATCTACTCCA
*
17159638 CTACACCGCCTGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCCTTTTAACTGCAATGTCGGGGA
66 CTACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCCTTTTAACTGCAATGTCGGGGA
17159703 AGCAAGATTCACCGATGTGACTTTAATCTGCTCCACTGCATCGTCAGGGAGGTAATATTCACTGC
131 AGCAAGATTCACCGATGTGACTTTAATCTGCTCCACTGCATCGTCAGGGAGGTAATATTCACTGC
17159768 TGTGG
196 TGTGG
* * * * *
17159773 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTAGCTTCAATCTACTCCA
* * ** * * *
17159838 CTGCATCGCCAGGGCGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAGTGTTGGGGA
66 CTACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCCTTTTAACTGCAATGTCGGGGA
*
17159903 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCAC
131 AGCAAGATTCACCGATGTGACTTTAATCTGCTCCAC
17159939 GATGTGGCTT
Statistics
Matches: 146, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
200 146 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (200 bp):
CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTAGCTTCAATCTACTCCA
CTACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCCTTTTAACTGCAATGTCGGGGA
AGCAAGATTCACCGATGTGACTTTAATCTGCTCCACTGCATCGTCAGGGAGGTAATATTCACTGC
TGTGG
Found at i:17159945 original size:23 final size:23
Alignment explanation
Indices: 17159915--17159961 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
17159905 CAAGATTCAC
17159915 CGATGTGGCTTTAATCTGCTCCA
1 CGATGTGGCTTTAATCTGCTCCA
* *
17159938 CGATGTGGCTTTAATTTTCTCCA
1 CGATGTGGCTTTAATCTGCTCCA
17159961 C
1 C
17159962 TGCATCGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (23 bp):
CGATGTGGCTTTAATCTGCTCCA
Found at i:17160109 original size:44 final size:44
Alignment explanation
Indices: 17160081--17160172 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
17160071 CCTTTATTTT
*
17160081 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* ** * *
17160125 AATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
17160169 AATC
1 AATC
17160173 TGTGGCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:17162470 original size:16 final size:15
Alignment explanation
Indices: 17162434--17162467 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17162424 TTTTCTCTCA
17162434 TTTTT-ATTTTGATT
1 TTTTTGATTTTGATT
*
17162448 TTTTTGATTTTTATT
1 TTTTTGATTTTGATT
17162463 TTTTT
1 TTTTT
17162468 TGAAAGGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTGATTTTGATT
Found at i:17167401 original size:3 final size:3
Alignment explanation
Indices: 17167393--17167427 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17167383 NNNNNNNNNN
17167393 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17167428 CATATACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17172342 original size:23 final size:22
Alignment explanation
Indices: 17172299--17172342 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
17172289 TTCTAAGTCG
17172299 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
17172322 ATATTCACTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
17172343 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:0.27, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:17172535 original size:51 final size:49
Alignment explanation
Indices: 17172479--17172626 Score: 188
Period size: 50 Copynumber: 3.0 Consensus size: 49
17172469 TGACCATTAC
* *
17172479 CATCCGGTACACGTAGTAGCCTGCACGTAGTACTACACACGTGATCGAAA
1 CATCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCAAA
* * * * * * *
17172529 CTATCCGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACCCAT
1 C-ATCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA
17172579 CATTCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CA-TCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
17172627 TAACTTTCAC
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
49 1 0.01
50 43 0.53
51 37 0.46
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (49 bp):
CATCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA
Found at i:17172647 original size:101 final size:99
Alignment explanation
Indices: 17172438--17172631 Score: 250
Period size: 101 Copynumber: 1.9 Consensus size: 99
17172428 TGTTCAGTTC
* ** *
17172438 ACATAGTAGCCTATACATAATACTATGCATGTGACCATTACCATCCGGTACACGTAGTAGCCTGC
1 ACATAGTAGCCTACACATAATACTACACATGCGACCATTA-CATCCGGTACACGTAGTAGCCTGC
* *
17172503 ACGTAGTACTACACACGTGATCGAAACTATCCGGT
65 ACATAGTACTACACACGTGATCCAAACTATCCGGT
*
17172538 ACGCATAGTAGCCTACACATAGTACTACACATGCGACCCA-T-CATTCCGGTACACGTAGTAGCC
1 A--CATAGTAGCCTACACATAATACTACACATGCGA-CCATTACA-TCCGGTACACGTAGTAGCC
17172601 TGCACATAGTACTACACACGTGA-CCATAACT
62 TGCACATAGTACTACACACGTGATCCA-AACT
17172632 TTCACTTTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
100 5 0.06
101 45 0.55
102 29 0.35
103 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (99 bp):
ACATAGTAGCCTACACATAATACTACACATGCGACCATTACATCCGGTACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCCAAACTATCCGGT
Found at i:17178983 original size:20 final size:21
Alignment explanation
Indices: 17178958--17179001 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
17178948 ACTTATTCGA
*
17178958 TTATTTGA-TTTCTTGTT-TTT
1 TTATTT-ATTTTCTTATTATTT
17178978 TTATTTATTTTCTTATTATTT
1 TTATTTATTTTCTTATTATTT
17178999 TTA
1 TTA
17179002 GTATACCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 14 0.67
21 6 0.29
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (21 bp):
TTATTTATTTTCTTATTATTT
Found at i:17186685 original size:16 final size:15
Alignment explanation
Indices: 17186660--17186693 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17186650 GAAGATGATA
*
17186660 ATAATTAATATACATT
1 ATAATAAATATA-ATT
17186676 ATAATAAATATAATT
1 ATAATAAATATAATT
17186691 ATA
1 ATA
17186694 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:17192002 original size:16 final size:16
Alignment explanation
Indices: 17191983--17192039 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
17191973 TTGGTGGCAA
17191983 TGAGTTCAACCAGGCT
1 TGAGTTCAACCAGGCT
* * *
17191999 TGAGCTCTATC---CT
1 TGAGTTCAACCAGGCT
17192012 TGAGTTCAACCAGGCT
1 TGAGTTCAACCAGGCT
*
17192028 TGTGTTCAACCA
1 TGAGTTCAACCA
17192040 TAGTGCATCT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
13 10 0.32
16 21 0.68
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (16 bp):
TGAGTTCAACCAGGCT
Found at i:17194917 original size:17 final size:17
Alignment explanation
Indices: 17194891--17194923 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17194881 TTTAGGAACA
17194891 AAATAAAAATAAAATAC
1 AAATAAAAATAAAATAC
*
17194908 AAATACAAATAAAATA
1 AAATAAAAATAAAATA
17194924 AAGATAACAA
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:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAAATAAAATAC
Found at i:17208429 original size:17 final size:17
Alignment explanation
Indices: 17208407--17208443 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
17208397 ATTGAGATAA
*
17208407 AAATAAATAACCAAAAT
1 AAATAAATAACAAAAAT
*
17208424 AAATAAATAAGAAAAAT
1 AAATAAATAACAAAAAT
17208441 AAA
1 AAA
17208444 CTAATGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAAATAACAAAAAT
Found at i:17208478 original size:21 final size:21
Alignment explanation
Indices: 17208438--17208478 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17208428 AAATAAGAAA
* **
17208438 AATAAACTAATGAATTAGATC
1 AATAAACTAATCAAGAAGATC
17208459 AATAAACTAATCAAGAAGAT
1 AATAAACTAATCAAGAAGAT
17208479 TAACTCACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (21 bp):
AATAAACTAATCAAGAAGATC
Found at i:17216119 original size:104 final size:103
Alignment explanation
Indices: 17215817--17216112 Score: 531
Period size: 103 Copynumber: 2.9 Consensus size: 103
17215807 TAGCCGTTAT
** *
17215817 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
17215882 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
17215920 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
17215985 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAA-CCCCCTTTTCATTTCAAAGATA
17216024 T-GTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
17216088 GAATCAGCACATAGCAACCCCCTTT
65 GAATCAGCACATAGCAACCCCCTTT
17216113 CACATTTATT
Statistics
Matches: 187, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
103 114 0.61
104 73 0.39
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:17216177 original size:29 final size:30
Alignment explanation
Indices: 17216144--17216200 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
17216134 CCACCCAACT
17216144 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * * *
17216173 TTTTGCATAATTAGACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
17216201 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:17218893 original size:23 final size:23
Alignment explanation
Indices: 17218837--17218894 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
17218827 ACATGCAATT
17218837 AAAAATTAAAA-ACTAAAAACGA
1 AAAAATTAAAATACTAAAAACGA
* *
17218859 AAGAAAATAAAATACT-ATAACGA
1 AA-AAATTAAAATACTAAAAACGA
17218882 AAAAATTGAAAAT
1 AAAAATT-AAAAT
17218895 TTTCCTGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 6 0.20
23 21 0.70
24 3 0.10
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAAATTAAAATACTAAAAACGA
Found at i:17236385 original size:6 final size:6
Alignment explanation
Indices: 17236374--17236401 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17236364 GACTTGAATG
17236374 AATATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATA
17236402 AACAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:17236798 original size:12 final size:12
Alignment explanation
Indices: 17236769--17236805 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
17236759 AATTGAGATA
17236769 AAAATAAATAATG
1 AAAATAAATAA-G
17236782 AAAATAAATAAG
1 AAAATAAATAAG
17236794 AAAATAAA-AAG
1 AAAATAAATAAG
17236805 A
1 A
17236806 CGATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.17
12 9 0.38
13 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATAAATAAG
Found at i:17242040 original size:21 final size:21
Alignment explanation
Indices: 17242016--17242055 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17242006 GTGATGTCGC
17242016 GACACAGGAGCTCCATGTCTT
1 GACACAGGAGCTCCATGTCTT
* * *
17242037 GACACTGGAGTTCGATGTC
1 GACACAGGAGCTCCATGTC
17242056 GTGATGCACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
GACACAGGAGCTCCATGTCTT
Found at i:17247515 original size:22 final size:22
Alignment explanation
Indices: 17247452--17247517 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
17247442 TATTGTTCAA
* *
17247452 ACATGAGAGCTTAGTACGTGAA
1 ACATGAGAGCTTAGTACGTTAG
17247474 ACATGAGAGCTTAGTACGTTAG
1 ACATGAGAGCTTAGTACGTTAG
*
17247496 CCATGAGAGCTTAGTACGTTAG
1 ACATGAGAGCTTAGTACGTTAG
17247518 GCATTACCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (22 bp):
ACATGAGAGCTTAGTACGTTAG
Found at i:17248519 original size:20 final size:20
Alignment explanation
Indices: 17248465--17248511 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17248455 GCTTGTACGG
17248465 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
* * * *
17248485 ATCTGCAGTTTGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
17248505 GTTTGCA
1 GTTTGCA
17248512 TTACGGTGAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (20 bp):
GTTTGCACTTCGGTGCCTCT
Found at i:17252671 original size:12 final size:11
Alignment explanation
Indices: 17252658--17252711 Score: 76
Period size: 12 Copynumber: 4.9 Consensus size: 11
17252648 TGAATTAATA
17252658 TTTTCTTTTTT
1 TTTTCTTTTTT
17252669 ATTTTCTTTTTT
1 -TTTTCTTTTTT
17252681 TCTTTCTTTTTT
1 T-TTTCTTTTTT
17252693 TTTT-TTTTTT
1 TTTTCTTTTTT
17252703 TTTT-TTTTT
1 TTTTCTTTTT
17252712 GAGAAAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 15 0.37
11 4 0.10
12 22 0.54
ACGTcount: A:0.02, C:0.07, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:17252679 original size:1 final size:1
Alignment explanation
Indices: 17252658--17252711 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
17252648 TGAATTAATA
* * * * *
17252658 TTTTCTTTTTTATTTTCTTTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17252712 GAGAAAAGTA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.07, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:17258212 original size:22 final size:22
Alignment explanation
Indices: 17258184--17258226 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17258174 GTTATGGCTA
17258184 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
17258206 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
17258227 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:17259943 original size:13 final size:13
Alignment explanation
Indices: 17259927--17259957 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
17259917 TTTTTCTTCC
17259927 TTTTTTTCT-AAT
1 TTTTTTTCTCAAT
17259939 TTTTTTTCTCAAT
1 TTTTTTTCTCAAT
17259952 TTTTTT
1 TTTTTT
17259958 CCACAATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTCTCAAT
Found at i:17272744 original size:12 final size:12
Alignment explanation
Indices: 17272719--17272757 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17272709 ACTCGCTTCT
* *
17272719 TTACTTACTCAC
1 TTACTTGCTTAC
*
17272731 TTACTTGTTTAC
1 TTACTTGCTTAC
17272743 TTACTTGCTTAC
1 TTACTTGCTTAC
17272755 TTA
1 TTA
17272758 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:17273084 original size:50 final size:50
Alignment explanation
Indices: 17272957--17273192 Score: 174
Period size: 50 Copynumber: 4.6 Consensus size: 50
17272947 TGATAATACA
* * ** * * *
17272957 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTTC-TGT-AC
1 TGCCAATGCCATGTCCCAGACATAGTCTTACATGGGA-CCTCTCATATCAG
* * **
17273006 TGCCAATGCCA-GATCCCAGATATAGTCTTGCATGGGAGTTCTCATATCAG
1 TGCCAATGCCATG-TCCCAGACATAGTCTTACATGGGACCTCTCATATCAG
* * ** * * *
17273056 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATATCAG
* *
17273106 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 TGCCAATGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCAT-A--TC-A-G
*
17273161 ATGTCAATGCCATGTCCCAGACA-ACGTCTTAC
1 -TGCCAATGCCATGTCCCAGACATA-GTCTTAC
17273193 GTGTGATCTC
Statistics
Matches: 148, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
48 6 0.04
49 33 0.22
50 78 0.53
51 1 0.01
53 2 0.01
55 1 0.01
56 27 0.18
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATATCAG
Found at i:17280644 original size:50 final size:50
Alignment explanation
Indices: 17280529--17280760 Score: 218
Period size: 50 Copynumber: 4.5 Consensus size: 50
17280519 TACCAAAGCT
* ** * * *
17280529 ATGTCCCAGACATAGTCTTACATGGGATGTTTTC-TATAC--TGCAAATGAC
1 ATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATAT-CGGTGCCAATGCC
* * ** * *
17280578 ATATCCCAGATATGGTCTTACATGGGAGTTCTCGTATCGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCC
** *
17280628 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCC
* *
17280678 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATTCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAATGCC
17280734 ATGTCCCAGACATGGTCTTACATGGGA
1 ATGTCCCAGACATGGTCTTACATGGGA
17280761 TCTCATTCCC
Statistics
Matches: 153, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
48 6 0.04
49 27 0.18
50 81 0.53
53 2 0.01
56 37 0.24
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCC
Found at i:17286746 original size:17 final size:17
Alignment explanation
Indices: 17286724--17286756 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17286714 TGTTAGTGCA
*
17286724 TATTGTCGTTGCATTTC
1 TATTGTCATTGCATTTC
17286741 TATTGTCATTGCATTT
1 TATTGTCATTGCATTT
17286757 TGATTTTAGT
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:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (17 bp):
TATTGTCATTGCATTTC
Found at i:17289438 original size:18 final size:19
Alignment explanation
Indices: 17289400--17289444 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
17289390 ATCTTAAAGG
*
17289400 AGGAGAAATGAGAAGAGAAA
1 AGGA-AAATGAGAAGAAAAA
*
17289420 A-GAAAATGAGAATAAAAA
1 AGGAAAATGAGAAGAAAAA
17289438 AGGAAAA
1 AGGAAAA
17289445 GTTGCAGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 14 0.64
19 7 0.32
20 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (19 bp):
AGGAAAATGAGAAGAAAAA
Found at i:17297479 original size:87 final size:86
Alignment explanation
Indices: 17297322--17297485 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 86
17297312 TGCATGCATA
* * *
17297322 AGGTTGAGTTCTTACTCTTAATTCATTCATAGCCCAGGGTTTGGGTGGTCCTATTGAGACAAACT
1 AGGTTGAGTTATTACTCTTAATTCATTCATAGCCCAGAGTTTGGGTGGTCCTAGTGAGACAAACT
17297387 TGATGAATTCACTGACATATG
66 TGATGAATTCACTGACATATG
* * * **
17297408 AGGTTGAGTTTATTACTCTTAA-TGAGTTCATATCCCATAGTTTGGGTGGTCCTAGTGAGACGGA
1 AGGTTGAG-TTATTACTCTTAATTCA-TTCATAGCCCAGAGTTTGGGTGGTCCTAGTGAGACAAA
17297472 CTTGATGAATTCAC
64 CTTGATGAATTCAC
17297486 CAAATTTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 10 0.15
87 58 0.85
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (86 bp):
AGGTTGAGTTATTACTCTTAATTCATTCATAGCCCAGAGTTTGGGTGGTCCTAGTGAGACAAACT
TGATGAATTCACTGACATATG
Found at i:17297890 original size:19 final size:19
Alignment explanation
Indices: 17297866--17297909 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17297856 AGGGATCAAA
* *
17297866 TTGAGACAAATCAT-AAATT
1 TTGAGA-AAAACATGAAAAT
17297885 TTGAGAAAAACATGAAAAT
1 TTGAGAAAAACATGAAAAT
17297904 TTGAGA
1 TTGAGA
17297910 TGTAGGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (19 bp):
TTGAGAAAAACATGAAAAT
Found at i:17299222 original size:40 final size:40
Alignment explanation
Indices: 17299097--17299225 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
17299087 GACATTAAAA
* * *
17299097 TGCATTTAGAGGGTATCAAAGTACAAACAAGGGCACATATG
1 TGCATTCAG-GGGTACCGAAGTACAAACAAGGGCACATATG
* * *
17299138 TGCAGTCAGGGGTACCGAAGTATAAACAAGGGCACGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAAGGGCACATATG
*
17299178 TGCATTCAGGGGTACCGAAGTACAAAC-GGGGACACATATG
1 TGCATTCAGGGGTACCGAAGTACAAACAAGGG-CACATATG
17299218 TGCATTCA
1 TGCATTCA
17299226 TATATAACCT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 3 0.04
40 67 0.87
41 7 0.09
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (40 bp):
TGCATTCAGGGGTACCGAAGTACAAACAAGGGCACATATG
Found at i:17313375 original size:44 final size:44
Alignment explanation
Indices: 17313311--17313409 Score: 180
Period size: 44 Copynumber: 2.2 Consensus size: 44
17313301 CTAGGCATAC
* *
17313311 GGATACCCTTTCGGGGTCTCTACTGGCATAAGTTATACACGACA
1 GGATACCCTTCCGGGCTCTCTACTGGCATAAGTTATACACGACA
17313355 GGATACCCTTCCGGGCTCTCTACTGGCATAAGTTATACACGACA
1 GGATACCCTTCCGGGCTCTCTACTGGCATAAGTTATACACGACA
17313399 GGATACCCTTC
1 GGATACCCTTC
17313410 TAGTCTCACA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (44 bp):
GGATACCCTTCCGGGCTCTCTACTGGCATAAGTTATACACGACA
Found at i:17320011 original size:56 final size:57
Alignment explanation
Indices: 17319939--17320083 Score: 181
Period size: 56 Copynumber: 2.6 Consensus size: 57
17319929 AAAATCTGCC
* *
17319939 TAAAAAAAGGAGAAGATAATCTTGGGATGTT-AGTTTTTATCTTAG-AAAAAATAATT
1 TAAAAAAAGGAGAAGATAATCTTGGGATGTTGA-TTTTTATCCTAGAAAAAAAGAATT
* ** *
17319995 TAAAAAAAGGAGAAGATATTCTCAGGTTGTTGATTTTTATCCTAGAAAAAAAGAATT
1 TAAAAAAAGGAGAAGATAATCTTGGGATGTTGATTTTTATCCTAGAAAAAAAGAATT
*
17320052 T-AGAAAAGGAGAAGATAATCTT-GGATTGTTGA
1 TAAAAAAAGGAGAAGATAATCTTGGGA-TGTTGA
17320084 AAAAAGAATT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
55 2 0.03
56 62 0.82
57 12 0.16
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (57 bp):
TAAAAAAAGGAGAAGATAATCTTGGGATGTTGATTTTTATCCTAGAAAAAAAGAATT
Found at i:17320122 original size:41 final size:42
Alignment explanation
Indices: 17320041--17320123 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
17320031 TTATCCTAGA
* *
17320041 AAAAAAGAATTTAGAAAAGGAGAAGATAATCTTGGATTGTTG
1 AAAAAAGAATTTAGAAAAGGAGAAGATAAACATGGATTGTTG
* *
17320083 AAAAAAGAATTTA-AAAAGGAGAATATAAACATGGGTTGTTG
1 AAAAAAGAATTTAGAAAAGGAGAAGATAAACATGGATTGTTG
17320124 GATTTACCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 24 0.65
42 13 0.35
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.25
Consensus pattern (42 bp):
AAAAAAGAATTTAGAAAAGGAGAAGATAAACATGGATTGTTG
Found at i:17325795 original size:54 final size:57
Alignment explanation
Indices: 17325656--17325796 Score: 216
Period size: 57 Copynumber: 2.5 Consensus size: 57
17325646 TCTGCTTAAA
* * * * *
17325656 AAAAAGAGGAGAATATAATCCTGGGATGTTGGTTTTTATCCTAGAAAAGAAAATTTT
1 AAAAAGAGGAGAAGATAATCTTGGGTTGTTAGTTTTTATCCTAGAAAAGAAAATATT
17325713 AAAAAGAGGAGAAGATAATCTTGGGTTGTTAGTTTTTATCCTAGAAAA-AAAA-ATT
1 AAAAAGAGGAGAAGATAATCTTGGGTTGTTAGTTTTTATCCTAGAAAAGAAAATATT
17325768 AAAAA-AGGAGAAGATAATCTTGGGTTGTT
1 AAAAAGAGGAGAAGATAATCTTGGGTTGTT
17325797 GAAAAAATAA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 24 0.30
55 7 0.09
56 4 0.05
57 44 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (57 bp):
AAAAAGAGGAGAAGATAATCTTGGGTTGTTAGTTTTTATCCTAGAAAAGAAAATATT
Found at i:17325835 original size:43 final size:41
Alignment explanation
Indices: 17325756--17325836 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 41
17325746 TTTTATCCTA
* *
17325756 GAAAAAAAAATTAAAAAAGGAGAAGATAATCTTGGGTTGTT
1 GAAAAAAAAATTAAAAAAGGAGAAGATAAACATGGGTTGTT
*
17325797 GAAAAAATAATTTAAAAAGAGGAGAAGATAAACATGGGTT
1 GAAAAAA-AAATTAAAAA-AGGAGAAGATAAACATGGGTT
17325837 CATGGATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 7 0.20
42 9 0.26
43 19 0.54
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.22
Consensus pattern (41 bp):
GAAAAAAAAATTAAAAAAGGAGAAGATAAACATGGGTTGTT
Found at i:17331805 original size:7 final size:7
Alignment explanation
Indices: 17331787--17331820 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
17331777 CTGTTAATTC
17331787 TTTTTAT
1 TTTTTAT
*
17331794 TTTTTTT
1 TTTTTAT
17331801 ATTTTTAT
1 -TTTTTAT
17331809 TTTTTAT
1 TTTTTAT
17331816 TTTTT
1 TTTTT
17331821 TAAAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:17331807 original size:15 final size:15
Alignment explanation
Indices: 17331787--17331822 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
17331777 CTGTTAATTC
17331787 TTTTTATTTTTT-TT
1 TTTTTATTTTTTATT
17331801 ATTTTTATTTTTTATT
1 -TTTTTATTTTTTATT
17331817 TTTTTA
1 TTTTTA
17331823 AAAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTATTTTTTATT
Found at i:17331813 original size:13 final size:13
Alignment explanation
Indices: 17331795--17331819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17331785 TCTTTTTATT
17331795 TTTTTTATTTTTA
1 TTTTTTATTTTTA
17331808 TTTTTTATTTTT
1 TTTTTTATTTTT
17331820 TTAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:17332061 original size:18 final size:18
Alignment explanation
Indices: 17332038--17332072 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17332028 TTTAAATTCA
*
17332038 TTATTATGGTTATTGTGT
1 TTATTATGATTATTGTGT
17332056 TTATTATGATTATTGTG
1 TTATTATGATTATTGTG
17332073 ATGTTGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (18 bp):
TTATTATGATTATTGTGT
Found at i:17332472 original size:106 final size:106
Alignment explanation
Indices: 17332312--17332520 Score: 364
Period size: 106 Copynumber: 2.0 Consensus size: 106
17332302 ATGCAAAATC
*
17332312 TCAAAATAAGGCAATATTTCGCGTTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
1 TCAAAATAAGGCAATATTTCGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
* *
17332377 AATTTCTCGTTCGACCGAATAGCCAAATATCCTTTTAACTT
66 AATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAACTT
*
17332418 TCAAAATAAGGCAATATTTTGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
1 TCAAAATAAGGCAATATTTCGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
* *
17332483 GATTTCTCGTTCGACTAAATAGCCAAATATCCTCTTAA
66 AATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAA
17332521 AACTTCAAAG
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 97 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (106 bp):
TCAAAATAAGGCAATATTTCGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
AATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAACTT
Found at i:17337099 original size:12 final size:12
Alignment explanation
Indices: 17337082--17337106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17337072 TAAGGCAGGA
17337082 GCCCAACACAAG
1 GCCCAACACAAG
17337094 GCCCAACACAAG
1 GCCCAACACAAG
17337106 G
1 G
17337107 ACTAACACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (12 bp):
GCCCAACACAAG
Found at i:17344035 original size:84 final size:84
Alignment explanation
Indices: 17343894--17344598 Score: 1193
Period size: 84 Copynumber: 8.4 Consensus size: 84
17343884 CGAAAGAAAC
* *
17343894 CAAGTCTTATCCCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
17343959 GTAGTGGAGCAGATCACAT
66 GTAGTGGAGCAGATCACAT
*
17343978 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGAAAAAAGAAACCAGATCTTATCTCCCTAAGCA
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
17344043 GTAGTGGAGCAGATCACAT
66 GTAGTGGAGCAGATCACAT
*
17344062 CAAGTCTTATCTCCCTAAGCAGTAGCGAAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
17344127 GTAGTGGAGCAGATCACAT
66 GTAGTGGAGCAGATCACAT
* *
17344146 CAAGTCTTATCTCCCTAAGCAGTAGCAGAGCAGAAAAAAGAAACCAGATCTTATCTCCCTAAGCA
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
17344211 GTAGTGGAGCAGATCACAT
66 GTAGTGGAGCAGATCACAT
* *
17344230 CAAGTCTTATCTCCCTAAACAGTAGCGGAGTAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
*
17344295 GTAGTGGGGCAGATCACAT
66 GTAGTGGAGCAGATCACAT
* *
17344314 CAAGTCTTATCCCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
17344379 GTAGTGGAGCAGATCACAT
66 GTAGTGGAGCAGATCACAT
*
17344398 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGACCTTATCTCCCTAAGCA
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
17344463 GTAGTGGAGCAGATCACAT
66 GTAGTGGAGCAGATCACAT
* * *
17344482 AAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAG---ATAG-AACCATAGATCTTATCTCCCTAAG
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACC--AGATCTTATCTCCCTAAG
* *
17344543 CAGTAGTGGAGCAAATCGCAT
64 CAGTAGTGGAGCAGATCACAT
* *
17344564 CAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGAC
1 CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGAC
17344599 GAAACCAACC
Statistics
Matches: 588, Mismatches: 29, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
80 4 0.01
81 3 0.01
82 67 0.11
84 514 0.87
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (84 bp):
CAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCA
GTAGTGGAGCAGATCACAT
Found at i:17346159 original size:8 final size:8
Alignment explanation
Indices: 17346146--17346187 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
17346136 CTGTTAATTC
17346146 TTTTTATT
1 TTTTTATT
17346154 TTTTTATT
1 TTTTTATT
*
17346162 TTTTT-TA
1 TTTTTATT
17346169 TTTTTATT
1 TTTTTATT
17346177 TTTTTATT
1 TTTTTATT
17346185 TTT
1 TTT
17346188 AAAAGAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 6 0.19
8 25 0.81
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:17346172 original size:14 final size:13
Alignment explanation
Indices: 17346146--17346187 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
17346136 CTGTTAATTC
*
17346146 TTTTTATTTT-TT
1 TTTTTTTTTTATT
*
17346158 TATTTTTTTTATT
1 TTTTTTTTTTATT
17346171 TTTATTTTTTTATT
1 TTT-TTTTTTTATT
17346185 TTT
1 TTT
17346188 AAAAGAGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 8 0.32
13 4 0.16
14 13 0.52
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:17346188 original size:14 final size:15
Alignment explanation
Indices: 17346154--17346188 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
17346144 TCTTTTTATT
17346154 TTTTTATTTTTTTTA
1 TTTTTATTTTTTTTA
17346169 TTTTTA-TTTTTTTA
1 TTTTTATTTTTTTTA
17346183 TTTTTA
1 TTTTTA
17346189 AAAGAGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:17346424 original size:18 final size:18
Alignment explanation
Indices: 17346401--17346435 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17346391 TTTAAATTCA
*
17346401 TTATTATGGTTATTGTGT
1 TTATTATGATTATTGTGT
17346419 TTATTATGATTATTGTG
1 TTATTATGATTATTGTG
17346436 ATGTTGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (18 bp):
TTATTATGATTATTGTGT
Found at i:17346835 original size:106 final size:106
Alignment explanation
Indices: 17346675--17346883 Score: 373
Period size: 106 Copynumber: 2.0 Consensus size: 106
17346665 ATGCAAAATC
*
17346675 TCAAAATAAGGCAATATTTCGCGTTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
1 TCAAAATAAGGCAATATTTCGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
* *
17346740 GATTTCTCGTTCGACCGAATAGCCAAATATCCTTTTAACTT
66 GATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAACTT
*
17346781 TCAAAATAAGGCAATATTTTGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
1 TCAAAATAAGGCAATATTTCGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
*
17346846 GATTTCTCGTTCGACTAAATAGCCAAATATCCTCTTAA
66 GATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAA
17346884 AACTTCAAAG
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (106 bp):
TCAAAATAAGGCAATATTTCGCATTTGGAAGATTCGGGAAATTGTGCCCTAACGTGCTGGGTTTC
GATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAACTT
Found at i:17351001 original size:2 final size:2
Alignment explanation
Indices: 17350994--17351027 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17350984 TTGGGCACCA
17350994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17351028 TTCATCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17352914 original size:98 final size:98
Alignment explanation
Indices: 17352799--17353001 Score: 325
Period size: 98 Copynumber: 2.1 Consensus size: 98
17352789 ATATAAAAAT
* *
17352799 TTTAAAAGAGCATCCACTCATCCAAGATTTAAGAAACCACACCAAATACGTTAGGGCACGATCCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCAAATACGTTAGGGCACAATCCC
17352864 TTTAGAATCCCAAACTCGGAATATTTCCTTTAA
66 TTTAGAATCCCAAACTCGGAATATTTCCTTTAA
* * * *
17352897 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCAAATACGTTAGGGCACAATCCC
* * *
17352962 TTTAGAATCTCAAACTCGGAATATTTCTTTTAC
66 TTTAGAATCCCAAACTCGGAATATTTCCTTTAA
17352995 TTTAAAA
1 TTTAAAA
17353002 AATCTTCATT
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCAAATACGTTAGGGCACAATCCC
TTTAGAATCCCAAACTCGGAATATTTCCTTTAA
Found at i:17355105 original size:132 final size:132
Alignment explanation
Indices: 17354901--17355285 Score: 621
Period size: 132 Copynumber: 2.9 Consensus size: 132
17354891 ATTGGATACG
* * * * *
17354901 ACCTGCTCCACTACTGCTTAGGGAAACAAGGCTTGGTGGC-TAAATCTGCTTCCCACTATCTTGG
1 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
* * *
17354965 AAAGATAAGATTTGATGTCTTCGATTTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATCTT
66 AAAGATAAGATTTGACGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
17355030 CA
131 CA
*
17355032 ACCTTCTCCACTGCTGCTCAGAGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
1 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
* *
17355097 AAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
66 AAAGATAAGATTTGACGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
17355162 CA
131 CA
17355164 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
1 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
* * *
17355229 AAAGATAAGA-TTCACCGTCTTCGATCCGCTCCACTACTGCTCAGGGAGATAAGATCT
66 AAAGATAAGATTTGA-CGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
17355286 GGTGTTTCAC
Statistics
Matches: 235, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
131 35 0.15
132 200 0.85
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
ACCTTCTCCACTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
AAAGATAAGATTTGACGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
CA
Found at i:17355147 original size:44 final size:44
Alignment explanation
Indices: 17355099--17355283 Score: 126
Period size: 44 Copynumber: 4.2 Consensus size: 44
17355089 TATCTTGGAA
* * *
17355099 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTCAGGG
** * * *
17355143 AGATAAGA-TCTACAATCTTCAACCTTCTCCACTGCTGCTCAGGG
1 AGATAAGATTC-ACCGTCTTCAATCTGCTCCACTACTGCTCAGGG
* * **** * * * *
17355187 AGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTA-T-CT-TGGAA
1 AGATAAGATTCACCGTCTTCAATCTGC-T-CCACTACTGCTCAGG-G
* *
17355231 AGATAAGATTCACCGTCTTCGATCCGCTCCACTACTGCTCAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTCAGGG
17355275 AGATAAGAT
1 AGATAAGAT
17355284 CTGGTGTTTC
Statistics
Matches: 99, Mismatches: 34, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
42 6 0.06
43 6 0.06
44 77 0.78
45 5 0.05
46 5 0.05
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (44 bp):
AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTCAGGG
Found at i:17366294 original size:98 final size:98
Alignment explanation
Indices: 17366172--17366374 Score: 318
Period size: 98 Copynumber: 2.1 Consensus size: 98
17366162 ATATAAAAAT
* * *
17366172 TTTAAAATAGCATCCATTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCC
1 TTTAAAAGAACATCCATTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
17366237 TTTAGAATCCCAAACTCGGAATATTTCCTTTAA
66 TTTAGAATCCCAAACTCGGAATATTTCCTTTAA
* *
17366270 TTTAAAAGAACATCCACTT-ATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
1 TTTAAAAGAACATCCA-TTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCC
* * *
17366334 CTTTAGAATCTCAAACTTGGAATATTTCCTTTAC
65 CTTTAGAATCCCAAACTCGGAATATTTCCTTTAA
17366368 TTTAAAA
1 TTTAAAA
17366375 AATCTTCATT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
98 94 0.98
99 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (98 bp):
TTTAAAAGAACATCCATTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
TTTAGAATCCCAAACTCGGAATATTTCCTTTAA
Found at i:17366777 original size:13 final size:13
Alignment explanation
Indices: 17366759--17366786 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17366749 TTATGTTTTT
17366759 TAGTAGAAATATA
1 TAGTAGAAATATA
17366772 TAGTAGAAATATA
1 TAGTAGAAATATA
17366785 TA
1 TA
17366787 CATAAAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (13 bp):
TAGTAGAAATATA
Found at i:17379133 original size:24 final size:24
Alignment explanation
Indices: 17379101--17379155 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
17379091 TATATGATGC
17379101 TATTGTGAATTGTAAAAGAAAACA
1 TATTGTGAATTGTAAAAGAAAACA
*
17379125 TATTGTGAATTGTAGAAGAAAACA
1 TATTGTGAATTGTAAAAGAAAACA
17379149 TATTGTG
1 TATTGTG
17379156 TTAAAATGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.33
Consensus pattern (24 bp):
TATTGTGAATTGTAAAAGAAAACA
Found at i:17396257 original size:23 final size:23
Alignment explanation
Indices: 17396192--17396259 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
17396182 CCACACTTAT
* * *
17396192 ATGTAGCCGAAGCTACTACAGAT
1 ATGTAGCCGAAGCTACCACTGAA
*
17396215 ATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
17396238 ATGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
17396260 TCAATAACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:17396513 original size:18 final size:17
Alignment explanation
Indices: 17396478--17396516 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
17396468 ATTTTCCTTC
17396478 CACATTCAATATTAATT
1 CACATTCAATATTAATT
17396495 CACATATCAGATA-TAATT
1 CACAT-TCA-ATATTAATT
17396513 CACA
1 CACA
17396517 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 12 0.60
19 3 0.15
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (17 bp):
CACATTCAATATTAATT
Found at i:17402962 original size:17 final size:17
Alignment explanation
Indices: 17402922--17402963 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
17402912 TCATTCATGT
* *
17402922 AAACATATATAACACCC
1 AAACATGTATAACACCA
17402939 AAACATGTATAACACCA
1 AAACATGTATAACACCA
17402956 AAACATGT
1 AAACATGT
17402964 TCTTTACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (17 bp):
AAACATGTATAACACCA
Found at i:17403494 original size:23 final size:22
Alignment explanation
Indices: 17403468--17403543 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 22
17403458 ATAAGTGCCA
17403468 CACTGATATGTAGCTGAAGCTAC
1 CACTGATATGTAGC-GAAGCTAC
*
17403491 CACTGATATGTAGCCATAGCTAC
1 CACTGATATGTAGCGA-AGCTAC
* * *
17403514 CATTGAAATGTAACCGAAGCTAC
1 CACTGATATGT-AGCGAAGCTAC
17403537 CACTGAT
1 CACTGAT
17403544 CAAGAACACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.02
23 40 0.91
24 3 0.07
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (22 bp):
CACTGATATGTAGCGAAGCTAC
Found at i:17404678 original size:60 final size:60
Alignment explanation
Indices: 17404581--17404702 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
17404571 ATTTACTTAG
* *
17404581 GTACCCCTGAATGCACATATGTGCCCTTGTTTGTACTTCGATATCCCTGAATGCACATAC
1 GTACCCCTAAATGCACATATGTGCCCTTGTTTGTACTTCGATACCCCTGAATGCACATAC
* * * * *
17404641 GTACCCCTAAATGCTCATATGTGTCCTTGATTT-TACTTTGGTACCCCTGAATGTACATAC
1 GTACCCCTAAATGCACATATGTGCCCTTG-TTTGTACTTCGATACCCCTGAATGCACATAC
17404701 GT
1 GT
17404703 GCCTTAGTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 51 0.94
61 3 0.06
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.34
Consensus pattern (60 bp):
GTACCCCTAAATGCACATATGTGCCCTTGTTTGTACTTCGATACCCCTGAATGCACATAC
Done.