Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 67 of 163
Found at i:17406905 original size:84 final size:84
Alignment explanation
Indices: 17406765--17406935 Score: 342
Period size: 84 Copynumber: 2.0 Consensus size: 84
17406755 ACAACTTTAG
17406765 GTAGTAGGAATTTTTTTTATTTAGTCACTTAACTTTTTAAAATTAAATATTTTAATCACTCTAGC
1 GTAGTAGGAATTTTTTTTATTTAGTCACTTAACTTTTTAAAATTAAATATTTTAATCACTCTAGC
17406830 CGTTAACTTAGAAATACAA
66 CGTTAACTTAGAAATACAA
17406849 GTAGTAGGAATTTTTTTTATTTAGTCACTTAACTTTTTAAAATTAAATATTTTAATCACTCTAGC
1 GTAGTAGGAATTTTTTTTATTTAGTCACTTAACTTTTTAAAATTAAATATTTTAATCACTCTAGC
17406914 CGTTAACTTAGAAATACAA
66 CGTTAACTTAGAAATACAA
17406933 GTA
1 GTA
17406936 TTACGAGAAC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (84 bp):
GTAGTAGGAATTTTTTTTATTTAGTCACTTAACTTTTTAAAATTAAATATTTTAATCACTCTAGC
CGTTAACTTAGAAATACAA
Found at i:17414444 original size:18 final size:18
Alignment explanation
Indices: 17414418--17414452 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17414408 AATGTATTCT
*
17414418 AAATTATATAATATAAAA
1 AAATAATATAATATAAAA
17414436 AAATAATATAATATAAA
1 AAATAATATAATATAAA
17414453 GTATTATAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAATATAATATAAAA
Found at i:17415826 original size:26 final size:25
Alignment explanation
Indices: 17415760--17415827 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
17415750 CATTGCGCCC
* *
17415760 AGAGATGTCACTGCAAGAATCTGTCT
1 AGAG-TGTCACTGCATGAATATGTCT
*
17415786 AGAAGTATCGA-TGCATGAATATGTCT
1 AG-AGTGTC-ACTGCATGAATATGTCT
17415812 AGAGTTGTCACTGCAT
1 AGAG-TGTCACTGCAT
17415828 AAGAGGATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.09
26 28 0.82
27 3 0.09
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (25 bp):
AGAGTGTCACTGCATGAATATGTCT
Found at i:17423213 original size:17 final size:17
Alignment explanation
Indices: 17423170--17423214 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
17423160 ATTTCATTTT
**
17423170 TCATTGCATTTTTATTG
1 TCATTGCATTTACATTG
* *
17423187 TCACTACATTTACATTG
1 TCATTGCATTTACATTG
17423204 TCATTGCATTT
1 TCATTGCATTT
17423215 CCGTATATCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (17 bp):
TCATTGCATTTACATTG
Found at i:17435643 original size:29 final size:26
Alignment explanation
Indices: 17435576--17435773 Score: 94
Period size: 29 Copynumber: 6.9 Consensus size: 26
17435566 AAAAGGTTTG
*
17435576 GGGGTAAAATGGTAATTTTTAGTAAAATC
1 GGGGTAAAATGG-AA-TTTT-GGAAAATC
** * *
17435605 GAGATTAAAAATGGGATTTTGGAAAGTTC
1 G-GGGT-AAAATGGAATTTTGGAAA-ATC
*
17435634 AGGGGTAAAATGGTAATTTTGCTAAAATC
1 -GGGGTAAAATGG-AATTTTG-GAAAATC
* *
17435663 GGGGTCAAAATGGAATTTTGGAAGATTTG
1 GGGGT-AAAATGGAATTTTGGAA-A-ATC
*
17435692 GGGGT-AAATGGTAATTTTGGGTAAAATT
1 GGGGTAAAATGG-AATTTT-GG-AAAATC
* *
17435720 GGGGTTAAAAATGGAATTTAGGAAGATTC
1 GGGG-T-AAAATGGAATTTTGGAA-AATC
17435749 GGGGGT-AAATGGTAATTTTTGGAAA
1 -GGGGTAAAATGG-AA-TTTTGGAAA
17435774 GTTTAGGGGT
Statistics
Matches: 131, Mismatches: 19, Indels: 39
0.69 0.10 0.21
Matches are distributed among these distances:
27 14 0.11
28 40 0.31
29 46 0.35
30 18 0.14
31 13 0.10
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (26 bp):
GGGGTAAAATGGAATTTTGGAAAATC
Found at i:17435666 original size:28 final size:27
Alignment explanation
Indices: 17435576--17435738 Score: 82
Period size: 28 Copynumber: 5.7 Consensus size: 27
17435566 AAAAGGTTTG
17435576 GGGGT-AAAATGGTAATTTTTAGTAAAATC
1 GGGGTAAAAATGG-AA-TTTT-GTAAAATC
** * * *
17435605 GAGATTAAAAATGGGATTTTGGAAAGTTC
1 G-GGGTAAAAATGGAATTTTGTAAA-ATC
17435634 AGGGGT-AAAATGGTAATTTTGCTAAAATC
1 -GGGGTAAAAATGG-AATTTTG-TAAAATC
* * * *
17435663 GGGGTCAAAATGGAATTTTGGAAGATTTG
1 GGGGTAAAAATGGAATTTTGTAA-A-ATC
*
17435692 GGGGT--AAATGGTAATTTTGGGTAAAATT
1 GGGGTAAAAATGG-AATTTT--GTAAAATC
17435720 GGGGTTAAAAATGGAATTT
1 GGGG-TAAAAATGGAATTT
17435739 AGGAAGATTC
Statistics
Matches: 103, Mismatches: 16, Indels: 29
0.70 0.11 0.20
Matches are distributed among these distances:
27 8 0.08
28 35 0.34
29 32 0.31
30 15 0.15
31 13 0.13
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (27 bp):
GGGGTAAAAATGGAATTTTGTAAAATC
Found at i:17435746 original size:58 final size:59
Alignment explanation
Indices: 17435547--17435767 Score: 238
Period size: 58 Copynumber: 3.8 Consensus size: 59
17435537 GGAAATTTTA
* * * * **
17435547 GGGTTAAAAATGGGATTTTA-AAAGGTTTGGGGGTAAAATGGTAATTTTTAGTAAAATCG
1 GGGTTAAAAAT-GGAATTTAGGAAGATTCGGGGGTAAAATGGTAATTTTGGGTAAAATCG
* * * * * *
17435606 AGATTAAAAATGGGATTTTGGAA-AGTTCAGGGGTAAAATGGTAATTTT-GCTAAAATCG
1 GGGTTAAAAATGGAATTTAGGAAGA-TTCGGGGGTAAAATGGTAATTTTGGGTAAAATCG
* * * *
17435664 GGG-TCAAAATGGAATTTTGGAAGATTTGGGGGT-AAATGGTAATTTTGGGTAAAATTG
1 GGGTTAAAAATGGAATTTAGGAAGATTCGGGGGTAAAATGGTAATTTTGGGTAAAATCG
17435721 GGGTTAAAAATGGAATTTAGGAAGATTCGGGGGT-AAATGGTAATTTT
1 GGGTTAAAAATGGAATTTAGGAAGATTCGGGGGTAAAATGGTAATTTT
17435768 TGGAAAGTTT
Statistics
Matches: 135, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
56 13 0.10
57 35 0.26
58 55 0.41
59 32 0.24
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGTTAAAAATGGAATTTAGGAAGATTCGGGGGTAAAATGGTAATTTTGGGTAAAATCG
Found at i:17435769 original size:115 final size:116
Alignment explanation
Indices: 17435553--17435767 Score: 292
Period size: 115 Copynumber: 1.9 Consensus size: 116
17435543 TTTAGGGTTA
* * *
17435553 AAAATGGGATTTTAAAAGGTTTGGGGGTAAAATGGTAATTTTTAGTAAAATCGAGATTAAAAATG
1 AAAATGGAATTTTAAAAGATTTGGGGGTAAAATGGTAATTTTGAGTAAAATCGAGATTAAAAATG
* *
17435618 GGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTGCTAAAATCGGGGTC
66 GAATTTAGGAAAGTTCAGGGGTAAAATGGTAATTTTGCTAAAATCGGGGTC
** * * * *
17435669 AAAATGGAATTTTGGAAGATTTGGGGGT-AAATGGTAATTTTGGGTAAAATTGGGGTTAAAAATG
1 AAAATGGAATTTTAAAAGATTTGGGGGTAAAATGGTAATTTTGAGTAAAATCGAGATTAAAAATG
*
17435733 GAATTTAGG-AAGATTCGGGGGT-AAATGGTAATTTT
66 GAATTTAGGAAAG-TTCAGGGGTAAAATGGTAATTTT
17435768 TGGAAAGTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
114 16 0.19
115 46 0.53
116 24 0.28
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (116 bp):
AAAATGGAATTTTAAAAGATTTGGGGGTAAAATGGTAATTTTGAGTAAAATCGAGATTAAAAATG
GAATTTAGGAAAGTTCAGGGGTAAAATGGTAATTTTGCTAAAATCGGGGTC
Found at i:17435790 original size:30 final size:28
Alignment explanation
Indices: 17435620--17435806 Score: 118
Period size: 29 Copynumber: 6.5 Consensus size: 28
17435610 TAAAAATGGG
* *
17435620 ATTTTGGAAAGTTCAGGGGTAAAATGGTA
1 ATTTTGGAAAGTT-TGGGGTTAAATGGTA
* * * *
17435649 ATTTTGCTAAA-ATCGGGGTCAAAATGG-A
1 ATTTTG-GAAAGTTTGGGGT-TAAATGGTA
*
17435677 ATTTTGG-AAGATTTGGGGGTAAATGGTA
1 ATTTTGGAAAG-TTTGGGGTTAAATGGTA
*
17435705 ATTTTGGGTAAA-ATTGGGGTTAAAAATGG-A
1 ATTTT-GG-AAAGTTTGGGGTT--AAATGGTA
* * *
17435735 ATTTAGG-AAGATTCGGGGGTAAATGGTA
1 ATTTTGGAAAG-TTTGGGGTTAAATGGTA
17435763 ATTTTTGGAAAGTTTAGGGGTTAAATGGTA
1 A-TTTTGGAAAGTTT-GGGGTTAAATGGTA
17435793 ATTTTTGG-AAGTTT
1 A-TTTTGGAAAGTTT
17435807 TTAAGTCAAA
Statistics
Matches: 125, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
26 2 0.02
27 14 0.11
28 25 0.20
29 44 0.35
30 32 0.26
31 8 0.06
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (28 bp):
ATTTTGGAAAGTTTGGGGTTAAATGGTA
Found at i:17436151 original size:10 final size:10
Alignment explanation
Indices: 17436136--17436160 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17436126 CAAAAAGGAC
17436136 TAAATTAAAA
1 TAAATTAAAA
17436146 TAAATTAAAA
1 TAAATTAAAA
17436156 TAAAT
1 TAAAT
17436161 GGAAGGACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:17437206 original size:24 final size:23
Alignment explanation
Indices: 17437161--17437212 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
17437151 AGGAGTTGGG
*
17437161 TTGTATTTTTTCAAGAATAGGGT
1 TTGTATTTTTTCAAGAACAGGGT
17437184 TTGTATTGATTTTC-AGAACAGGGT
1 TTGTATT--TTTTCAAGAACAGGGT
17437208 TTGTA
1 TTGTA
17437213 ACCCCTTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
24 14 0.54
25 5 0.19
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (23 bp):
TTGTATTTTTTCAAGAACAGGGT
Found at i:17437616 original size:23 final size:24
Alignment explanation
Indices: 17437589--17437635 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
17437579 ACTTTTTAAT
* *
17437589 TTATATTTATTTTAAA-TTTAAAA
1 TTATATTAAGTTTAAATTTTAAAA
17437612 TTATATTAAGTTTAAATTTTAAAA
1 TTATATTAAGTTTAAATTTTAAAA
17437636 AAAACTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATATTAAGTTTAAATTTTAAAA
Found at i:17438158 original size:86 final size:87
Alignment explanation
Indices: 17438017--17438211 Score: 241
Period size: 86 Copynumber: 2.3 Consensus size: 87
17438007 ACCTGGTCTT
* *
17438017 CTTCTCTATGTCTCATC-GGAAGATGACCGCAATCATCTGTTTTACTTCGCCTCTCTGGATCTCC
1 CTTCTCTGTGTCTCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCGCCTCTCTGGATCTCC
* * *
17438081 TTAGGAAGACGAATTTGGTCCA
66 TCAGGAAGACAAATTCGGTCCA
* ** ** * *
17438103 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGGT-TGTTTTAATTTGCTTCTCTGGATCTCC
1 CTTCTCTGTGTCTCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCGCCTCTCTGGATCTCC
*
17438167 TCAGGAAGGCAAATTCGGTCCA
66 TCAGGAAGACAAATTCGGTCCA
* *
17438189 CTTCTCAGTGTCTCATCAAGAAG
1 CTTCTCTGTGTCTCATCAGGAAG
17438212 CTAACCATTT
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
86 77 0.84
87 15 0.16
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (87 bp):
CTTCTCTGTGTCTCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCGCCTCTCTGGATCTCC
TCAGGAAGACAAATTCGGTCCA
Found at i:17438611 original size:200 final size:199
Alignment explanation
Indices: 17438102--17438739 Score: 863
Period size: 200 Copynumber: 3.2 Consensus size: 199
17438092 AATTTGGTCC
* *** *
17438102 ACTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGGTTGTTTTAATTTGCTTCTCTGGATCTCC
1 ACTTCTCTATATCTCATCAGGAAGATGACCGCCTCACTTG-TTTAATTCGCTTCTCTGGATCTCC
* * * *
17438167 TCAGGAAGG-CAAATTCGGTCCACTTCTCAGTGTCTCATCAAGAAGCTAACCA-TTTATTGCTTC
65 TCA-GAAGGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
** *
17438230 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTCGGGTTTGAAGATTTGCTCGCATTGAGCCTAGGT
129 GACCTGCTTCTCAGTGTCTCATCAGGAAGCT-GGGTACGAAGATTTGCTCGCTTTGAG-C---G-
* *
17438295 TTGATTTGGTCT
188 TTGAGTTGGTAT
* * * **
17438307 TCTTCTC-AGTGTCTCATCAGGAAGATGACCGCATCACTT-TTTAATTCGCTTCTCCAGATCTCC
1 ACTTCTCTA-TATCTCATCAGGAAGATGACCGCCTCACTTGTTTAATTCGCTTCTCTGGATCTCC
17438370 TCAAGAA-GACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
65 TC-AGAAGGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
*
17438434 GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGT
129 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGT
17438499 TGGTAT
194 TGGTAT
* *
17438505 ACTTCTCTATATCTCATCAGGAAGATGACCGCCTCATTTGTTTCAATTCGCTTCTTTGGATCTCC
1 ACTTCTCTATATCTCATCAGGAAGATGACCGCCTCACTTGTTT-AATTCGCTTCTCTGGATCTCC
* * *
17438570 TCAGAAGGACGAATTTGGTCCACTTCTCTGTATCCCATCAGGAAGCTAACCATTTTATTGTTTCG
65 TCAGAAGGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* * * *
17438635 ACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTACGAAGATTTGGTTGATTTGAGCGTTGAGTT
130 ACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTT
17438700 GGTAT
195 GGTAT
* *
17438705 ACTTCTCTGTATCTCATCAGAAAGATGACCGCCTC
1 ACTTCTCTATATCTCATCAGGAAGATGACCGCCTC
17438740 GCTGTCTTGT
Statistics
Matches: 388, Mismatches: 37, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
198 43 0.11
199 9 0.02
200 173 0.45
202 2 0.01
203 88 0.23
204 42 0.11
205 31 0.08
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (199 bp):
ACTTCTCTATATCTCATCAGGAAGATGACCGCCTCACTTGTTTAATTCGCTTCTCTGGATCTCCT
CAGAAGGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTG
GTAT
Found at i:17444644 original size:14 final size:14
Alignment explanation
Indices: 17444625--17444652 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17444615 TGGCTATTCC
17444625 TTCTTCAGGCTCGA
1 TTCTTCAGGCTCGA
17444639 TTCTTCAGGCTCGA
1 TTCTTCAGGCTCGA
17444653 ACATTACTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (14 bp):
TTCTTCAGGCTCGA
Found at i:17450932 original size:29 final size:30
Alignment explanation
Indices: 17450900--17450971 Score: 51
Period size: 29 Copynumber: 2.5 Consensus size: 30
17450890 TCAGGGGGCA
* * *
17450900 AAAAT-GTAATTTTGGGAAAATTTGAGGTT
1 AAAATGGTAATTTTGGGAAAATTCGGGGGT
* * **
17450929 AAAAATGG-GATTTT-AGAAGGTTCGGGGGT
1 -AAAATGGTAATTTTGGGAAAATTCGGGGGT
17450958 AAAATGGTAATTTT
1 AAAATGGTAATTTT
17450972 TAGTGAAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
28 7 0.22
29 14 0.44
30 10 0.31
31 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTGGGAAAATTCGGGGGT
Found at i:17451224 original size:58 final size:58
Alignment explanation
Indices: 17450900--17451263 Score: 275
Period size: 58 Copynumber: 6.2 Consensus size: 58
17450890 TCAGGGGGCA
* * * *
17450900 AAAAT-GTAATTTTGGG-AAAATTTGAGGTTAAAAATGGGATTTTA-GAAGGTTCGGGGGT
1 AAAATGGTAATTTTGGGCAAAA-TTGGGGTT-AAAAT-GGAATTTAGGAAGATTCGAGGGT
** ** * * **
17450958 AAAATGGTAATTTTTAGTGAAATTGAGGTTAAAAACATGG--TTTTGGAA-AGTTTAAGGGT
1 AAAATGGTAATTTTGGGCAAAATTGGGGTT--AAA-ATGGAATTTAGGAAGA-TTCGAGGGT
* * * * * *
17451017 AAAATAGTAATTTTGGTG--AAATCGGGGTCAAAAATAGAATTTTGGAAGATTCGGGGGT
1 AAAATGGTAATTTTGG-GCAAAATTGGGGT-TAAAATGGAATTTAGGAAGATTCGAGGGT
17451075 AAAATGGTAATTTTGGGCAAAATTGGGGTTAAAATGGAATTTAGGAAGATTCGAGGGT
1 AAAATGGTAATTTTGGGCAAAATTGGGGTTAAAATGGAATTTAGGAAGATTCGAGGGT
** *
17451133 AAAATGGTAATTTTGGGCAAAATCAGGGTTAAAATGGAATTTAGGAA-AGTTCGTGGGT
1 AAAATGGTAATTTTGGGCAAAATTGGGGTTAAAATGGAATTTAGGAAGA-TTCGAGGGT
* * * * *
17451191 AAAATGGTAATTTTTGG-AAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGTTTCG-GGGT
1 AAAATGGTAATTTTGGGCAAA-ATTGGGGTTAAAATGG-AA-TTTAGGAAGATTCGAGGGT
*
17451250 CAAAAT-ATAATTTT
1 -AAAATGGTAATTTT
17451264 TTCAAAGTTT
Statistics
Matches: 252, Mismatches: 35, Indels: 37
0.78 0.11 0.11
Matches are distributed among these distances:
56 3 0.01
57 8 0.03
58 151 0.60
59 62 0.25
60 26 0.10
61 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGGCAAAATTGGGGTTAAAATGGAATTTAGGAAGATTCGAGGGT
Found at i:17451255 original size:30 final size:30
Alignment explanation
Indices: 17450998--17451264 Score: 174
Period size: 30 Copynumber: 9.1 Consensus size: 30
17450988 AAAAACATGG
* ** *
17450998 TTTTGGAAAGTTTAAGGGTAAAATAGTAA-
1 TTTTGGAAAGATTCGGGGTAAAATGGTAAT
* *
17451027 TTTTGGTGAA-A-TCGGGGTCAAAAATAG-AA-
1 TTTTGG-AAAGATTCGGGGT--AAAATGGTAAT
17451056 TTTTGG-AAGATTCGGGGGTAAAATGGTAAT
1 TTTTGGAAAGATTC-GGGGTAAAATGGTAAT
*
17451086 TTTGGGCAAA-ATT-GGGGTTAAAATGG-AA-
1 TTTTGG-AAAGATTCGGGG-TAAAATGGTAAT
*
17451114 TTTAGG-AAGATTCGAGGGTAAAATGGTAAT
1 TTTTGGAAAGATTCG-GGGTAAAATGGTAAT
* *
17451144 TTTGGGCAAA-A-TCAGGGTTAAAATGG-AA-
1 TTTTGG-AAAGATTC-GGGGTAAAATGGTAAT
*
17451172 TTTAGGAAAG-TTCGTGGGTAAAATGGTAAT
1 TTTTGGAAAGATTCG-GGGTAAAATGGTAAT
* *
17451202 TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAAGATTCGGGGTAAAATGGTAAT
* *
17451232 TTTTGG-AAGTTTCGGGGTCAAAAT-ATAAT
1 TTTTGGAAAGATTCGGGGT-AAAATGGTAAT
17451261 TTTT
1 TTTT
17451265 TCAAAGTTTT
Statistics
Matches: 197, Mismatches: 15, Indels: 52
0.75 0.06 0.20
Matches are distributed among these distances:
26 2 0.01
27 9 0.05
28 43 0.22
29 52 0.26
30 79 0.40
31 8 0.04
32 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (30 bp):
TTTTGGAAAGATTCGGGGTAAAATGGTAAT
Found at i:17451265 original size:30 final size:29
Alignment explanation
Indices: 17451187--17451283 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 29
17451177 GAAAGTTCGT
*
17451187 GGGT-AAAATGGTAATTTTTGGAAAGTTTGG
1 GGGTCAAAATGATAATTTTTGG-AAGTTT-G
*
17451217 GGGT-AAAATGGTAATTTTTGGAAGTTTCG
1 GGGTCAAAATGATAATTTTTGGAAGTTT-G
** *
17451246 GGGTCAAAAT-ATAATTTTTTCAAAGTTTT
1 GGGTCAAAATGATAA-TTTTTGGAAGTTTG
17451275 GGGTCAAAA
1 GGGTCAAAA
17451284 ACGTAATTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.38
30 37 0.62
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (29 bp):
GGGTCAAAATGATAATTTTTGGAAGTTTG
Found at i:17452690 original size:24 final size:23
Alignment explanation
Indices: 17452645--17452696 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
17452635 AGGAGTTGGG
17452645 TTGTATTTTTTCAAGAACAGGGT
1 TTGTATTTTTTCAAGAACAGGGT
17452668 TTGTATTGATTTTCAA-AACAGGGT
1 TTGTATT--TTTTCAAGAACAGGGT
17452692 TTGTA
1 TTGTA
17452697 ACCCCTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.26
24 13 0.48
25 7 0.26
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (23 bp):
TTGTATTTTTTCAAGAACAGGGT
Found at i:17453100 original size:23 final size:24
Alignment explanation
Indices: 17453073--17453119 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
17453063 ACTTTTTAAT
* *
17453073 TTATATTTATTTTAAA-TTTAAAA
1 TTATATTAAGTTTAAATTTTAAAA
17453096 TTATATTAAGTTTAAATTTTAAAA
1 TTATATTAAGTTTAAATTTTAAAA
17453120 AAAACTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATATTAAGTTTAAATTTTAAAA
Found at i:17457748 original size:25 final size:25
Alignment explanation
Indices: 17457720--17457768 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
17457710 GGGTCAAAGT
*
17457720 AATTAAATTAACCCAATTAATTAAC
1 AATTAAATAAACCCAATTAATTAAC
* *
17457745 AATTTAATAAACCCAATTTATTAA
1 AATTAAATAAACCCAATTAATTAA
17457769 TGAAACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAAATAAACCCAATTAATTAAC
Found at i:17463433 original size:18 final size:18
Alignment explanation
Indices: 17463410--17463445 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17463400 GGTCTCGATT
*
17463410 TTTCAAGAGGTATCAATA
1 TTTCAAGAAGTATCAATA
*
17463428 TTTCAAGAATTATCAATA
1 TTTCAAGAAGTATCAATA
17463446 CTTGGCCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (18 bp):
TTTCAAGAAGTATCAATA
Found at i:17477492 original size:20 final size:19
Alignment explanation
Indices: 17477467--17477508 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17477457 AATTTTTAAA
* *
17477467 AAAAATATACTTAAAATTTT
1 AAAAATATA-TAAAAATTAT
17477487 AAAAATATATAAAAATTAT
1 AAAAATATATAAAAATTAT
17477506 AAA
1 AAA
17477509 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATATATAAAAATTAT
Found at i:17478403 original size:29 final size:31
Alignment explanation
Indices: 17478362--17478434 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
17478352 TTAATAGGTT
*
17478362 ATTTTTATAATTTTAAAAAATT-AAAT-TAA
1 ATTTTTATTATTTTAAAAAATTAAAATGTAA
* *
17478391 ATTTTTATTATTTTTAAAGATTAAAATGTAA
1 ATTTTTATTATTTTAAAAAATTAAAATGTAA
*
17478422 TTTTATTATTATT
1 ATTT-TTATTATT
17478435 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 19 0.51
30 4 0.11
31 6 0.16
32 8 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTTTATTATTTTAAAAAATTAAAATGTAA
Found at i:17478408 original size:30 final size:32
Alignment explanation
Indices: 17478362--17478443 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 32
17478352 TTAATAGGTT
*
17478362 ATTTTTA-TAATTTTAAAAAATT-AAAT-TAA
1 ATTTTTATTATTTTTAAAAAATTAAAATGTAA
*
17478391 ATTTTTATTATTTTT-AAAGATTAAAATGTAA
1 ATTTTTATTATTTTTAAAAAATTAAAATGTAA
*
17478422 TTTTATTATTATTAATTTAAAA
1 ATTT-TTATTATT--TTTAAAA
17478444 TTTTATAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
29 13 0.30
30 10 0.23
31 6 0.14
32 8 0.19
34 3 0.07
35 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
ATTTTTATTATTTTTAAAAAATTAAAATGTAA
Found at i:17478716 original size:17 final size:16
Alignment explanation
Indices: 17478681--17478736 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
17478671 TACTTTTTGC
*
17478681 ATTTTTAATATTT-ATT
1 ATTTTTAAT-TTTAAAT
17478697 ATTTTT-ATTTATAAAAT
1 ATTTTTAATTT-T-AAAT
17478714 ATTTTTTAATTTTAAAT
1 A-TTTTTAATTTTAAAT
17478731 ATTTTT
1 ATTTTT
17478737 TAAATTGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 11 0.32
17 8 0.24
18 6 0.18
19 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTAATTTTAAAT
Found at i:17478721 original size:18 final size:16
Alignment explanation
Indices: 17478698--17478738 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
17478688 ATATTTATTA
17478698 TTTTTATTTATAAAATAT
1 TTTTTATTT-T-AAATAT
17478716 TTTTTAATTTTAAATAT
1 TTTTT-ATTTTAAATAT
17478733 TTTTTA
1 TTTTTA
17478739 AATTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 11 0.50
18 6 0.27
19 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTATTTTAAATAT
Found at i:17480267 original size:14 final size:14
Alignment explanation
Indices: 17480250--17480290 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
17480240 ATAAAAAATG
17480250 TTTACAATATATAA
1 TTTACAATATATAA
* *
17480264 TTTATAATTTATAA
1 TTTACAATATATAA
17480278 TTTACAATATATA
1 TTTACAATATATA
17480291 TCATAAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTACAATATATAA
Found at i:17487255 original size:23 final size:20
Alignment explanation
Indices: 17487228--17487269 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
17487218 ATTAAATTAA
17487228 AATAAAATGATATTATTATTTGC
1 AATAAAAT--TATT-TTATTTGC
17487251 AATAAAATTATTTTATTTG
1 AATAAAATTATTTTATTTG
17487270 AGTTTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
23 8 0.42
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
AATAAAATTATTTTATTTGC
Found at i:17487534 original size:22 final size:23
Alignment explanation
Indices: 17487502--17487544 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
17487492 CTTATTATAA
17487502 AACAAAGAG-A-AATATAAAATG
1 AACAAAGAGAAGAATATAAAATG
17487523 AACAAGAGAGAAGAATATAAAA
1 AACAA-AGAGAAGAATATAAAA
17487545 ATAAAAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 1 0.05
24 9 0.47
ACGTcount: A:0.67, C:0.05, G:0.16, T:0.12
Consensus pattern (23 bp):
AACAAAGAGAAGAATATAAAATG
Found at i:17487846 original size:22 final size:22
Alignment explanation
Indices: 17487818--17487862 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
17487808 CCCCCCCGCG
17487818 GATATCCATCAATAAAAAATGT
1 GATATCCATCAATAAAAAATGT
*
17487840 GATATCCATCAATGAAAAATGT
1 GATATCCATCAATAAAAAATGT
17487862 G
1 G
17487863 CCTCGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (22 bp):
GATATCCATCAATAAAAAATGT
Found at i:17489560 original size:14 final size:14
Alignment explanation
Indices: 17489541--17489567 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17489531 TAGGCTTAGG
17489541 ATCAACATTATAAT
1 ATCAACATTATAAT
17489555 ATCAACATTATAA
1 ATCAACATTATAA
17489568 GCAAAATTTT
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:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCAACATTATAAT
Found at i:17490915 original size:19 final size:18
Alignment explanation
Indices: 17490870--17490916 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
17490860 CGAAAGGAAT
*
17490870 AGCATACTGGCTCGTTAG
1 AGCATACTGGCTCGTAAG
17490888 AGCATACTGGCTCGTAAG
1 AGCATACTGGCTCGTAAG
17490906 AGCAATACTGG
1 AGC-ATACTGG
17490917 ATCACAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (18 bp):
AGCATACTGGCTCGTAAG
Found at i:17495003 original size:5 final size:5
Alignment explanation
Indices: 17494984--17495068 Score: 59
Period size: 5 Copynumber: 17.0 Consensus size: 5
17494974 TTTCACACAG
* * **
17494984 ATCAT AT-ATT ATCAT ATCAT AAT-GT ATCAT AACAT AAGAT ATCAT ATCGA-
1 ATCAT ATCA-T ATCAT ATCAT -ATCAT ATCAT ATCAT ATCAT ATCAT ATC-AT
* * *
17495034 ATCAC AACAT AACAT ATCAT ATCAT ATCAT ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
17495069 GCCCTACCCC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.06
5 57 0.88
6 4 0.06
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (5 bp):
ATCAT
Found at i:17495062 original size:25 final size:26
Alignment explanation
Indices: 17494996--17495062 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
17494986 CATATATTAT
*
17494996 CATATCATAAT-G-TATCATAACATAA
1 CATATCAT-ATCGATATCACAACATAA
*
17495021 GATATCATATCGA-ATCACAACATAA
1 CATATCATATCGATATCACAACATAA
17495046 CATATCATATC-ATATCA
1 CATATCATATCGATATCA
17495063 TATCATGCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 3 0.08
25 33 0.92
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.30
Consensus pattern (26 bp):
CATATCATATCGATATCACAACATAA
Found at i:17511406 original size:16 final size:16
Alignment explanation
Indices: 17511385--17511426 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
17511375 TAGAAACTTA
17511385 GTTGTTATAGCGAAAT-
1 GTTGTTATAGCG-AATG
*
17511401 GTTGTTATAGCGGATG
1 GTTGTTATAGCGAATG
17511417 GTTGTTATAG
1 GTTGTTATAG
17511427 AAAGAGCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.24, C:0.05, G:0.31, T:0.40
Consensus pattern (16 bp):
GTTGTTATAGCGAATG
Found at i:17511781 original size:16 final size:16
Alignment explanation
Indices: 17511760--17511790 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17511750 AGAAATGAAC
17511760 CCTTAGTAGAAGGATA
1 CCTTAGTAGAAGGATA
17511776 CCTTAGTAGAAGGAT
1 CCTTAGTAGAAGGAT
17511791 TTTTCCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (16 bp):
CCTTAGTAGAAGGATA
Found at i:17515953 original size:27 final size:28
Alignment explanation
Indices: 17515923--17515975 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
17515913 ATAAGGTATA
17515923 TATGTCATTTTTTAAAAA-A-TTAGGGTT
1 TATGTCA-TTTTTAAAAATATTTAGGGTT
*
17515950 TATGTTATTTTTAAAAATATTTAGGG
1 TATGTCATTTTTAAAAATATTTAGGG
17515976 GAATAAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 7 0.30
28 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (28 bp):
TATGTCATTTTTAAAAATATTTAGGGTT
Found at i:17518095 original size:17 final size:17
Alignment explanation
Indices: 17518038--17518097 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
17518028 TTATATTTTA
*
17518038 AAAAATATTAATTACTAT
1 AAAAATATT-ATTATTAT
*
17518056 AAAAA-ATTATTAGTAT
1 AAAAATATTATTATTAT
*
17518072 GATAAAATATTATTTTTAT
1 -A-AAAATATTATTATTAT
17518091 AAAAATA
1 AAAAATA
17518098 AATAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 7 0.19
17 10 0.28
18 10 0.28
19 9 0.25
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (17 bp):
AAAAATATTATTATTAT
Found at i:17518443 original size:25 final size:25
Alignment explanation
Indices: 17518409--17518461 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
17518399 TCAAACACTT
17518409 TTTAAATAATTGAATATATTATTTG
1 TTTAAATAATTGAATATATTATTTG
17518434 TTTAAATAATTGAATATATTATTTG
1 TTTAAATAATTGAATATATTATTTG
17518459 TTT
1 TTT
17518462 CTACCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (25 bp):
TTTAAATAATTGAATATATTATTTG
Found at i:17519422 original size:19 final size:20
Alignment explanation
Indices: 17519400--17519446 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
17519390 TTTTTATACA
17519400 ATAATA-ATATTTTAATTTT
1 ATAATATATATTTTAATTTT
*
17519419 ATAATATATTTTTTAATTTT
1 ATAATATATATTTTAATTTT
17519439 -TAA-ATATA
1 ATAATATATA
17519447 ATTATATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATAATATATATTTTAATTTT
Found at i:17521179 original size:17 final size:16
Alignment explanation
Indices: 17521149--17521183 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17521139 TAAAAAATGT
*
17521149 TTAAAATAATTAAATA
1 TTAAAATAAATAAATA
17521165 TTAAAATAAAATAAATA
1 TTAAAAT-AAATAAATA
17521182 TT
1 TT
17521184 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATAAATAAATA
Found at i:17534993 original size:24 final size:24
Alignment explanation
Indices: 17534961--17535016 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
17534951 GCCAATAATG
17534961 GCCACATAGTTTTGCAGATAAACT
1 GCCACATAGTTTTGCAGATAAACT
17534985 GCCACATAGTTTTGCAGATAAACT
1 GCCACATAGTTTTGCAGATAAACT
17535009 GCCACATA
1 GCCACATA
17535017 TTTGCTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (24 bp):
GCCACATAGTTTTGCAGATAAACT
Found at i:17535160 original size:46 final size:46
Alignment explanation
Indices: 17535102--17535212 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 46
17535092 TTAGCGTTTT
* * * * *
17535102 TCATGCTTACATATCACTTGTCACGTATTT-CATATTTTAGCATGTC
1 TCATGCTCACATATCACATATAACG-ATTTCCACATTTTAGCATGTC
*
17535148 TCATGCTCACATATCACATATAACGATTTCCACATTTTAGCATGTG
1 TCATGCTCACATATCACATATAACGATTTCCACATTTTAGCATGTC
* *
17535194 TTATGTTCACATATCACAT
1 TCATGCTCACATATCACAT
17535213 TTCACTTAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (46 bp):
TCATGCTCACATATCACATATAACGATTTCCACATTTTAGCATGTC
Found at i:17535371 original size:20 final size:21
Alignment explanation
Indices: 17535346--17535411 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
17535336 GAAATCACAC
17535346 ATCATATG-TCACATAACA-TT
1 ATCATA-GATCACATAACACTT
*
17535366 ATCATAGATCGCATAACACTT
1 ATCATAGATCACATAACACTT
* *
17535387 ATAATAGATCACATAACACAT
1 ATCATAGATCACATAACACTT
17535408 ATCA
1 ATCA
17535412 CGATTTTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 15 0.38
21 23 0.59
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (21 bp):
ATCATAGATCACATAACACTT
Found at i:17536551 original size:12 final size:11
Alignment explanation
Indices: 17536532--17536561 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
17536522 GTAAGGTGAG
17536532 AAAAAAGGAGT
1 AAAAAAGGAGT
17536543 AAAACAAGGAGT
1 AAAA-AAGGAGT
17536555 AAAAAAG
1 AAAAAAG
17536562 CGGATTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (11 bp):
AAAAAAGGAGT
Found at i:17536865 original size:19 final size:19
Alignment explanation
Indices: 17536841--17536878 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17536831 TTTAACTAAC
*
17536841 TTAATTAATTAATTAAAAA
1 TTAATTAACTAATTAAAAA
*
17536860 TTAATTAACTACTTAAAAA
1 TTAATTAACTAATTAAAAA
17536879 AATTAGGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAATTAACTAATTAAAAA
Found at i:17543003 original size:46 final size:46
Alignment explanation
Indices: 17542945--17543078 Score: 142
Period size: 46 Copynumber: 2.9 Consensus size: 46
17542935 TTGTCACTTA
*** * * *
17542945 CCACACTTTTAGCCTTTTTCATGCTCAGATATCACTTGTCACGATTT
1 CCACA-TTTTAGCCTGCATCATGCTCACATATCACATATCACGATTT
* *
17542992 TCACATTTTAGCCTGCATCATGCTCACATATCACATATCATGATTT
1 CCACATTTTAGCCTGCATCATGCTCACATATCACATATCACGATTT
* * * * *
17543038 CCACATTTTAGCATGTATTATACTCATATATCACATATCAC
1 CCACATTTTAGCCTGCATCATGCTCACATATCACATATCAC
17543079 ATAATCTCAT
Statistics
Matches: 72, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
46 68 0.94
47 4 0.06
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (46 bp):
CCACATTTTAGCCTGCATCATGCTCACATATCACATATCACGATTT
Found at i:17547150 original size:21 final size:21
Alignment explanation
Indices: 17547125--17547201 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
17547115 CTGAAGTTTG
*
17547125 TTGTATCGGTAGAAGTAATAA
1 TTGTATCGGTAGAAGTCATAA
* *
17547146 TTGTATCGGTAGCAGTCATAT
1 TTGTATCGGTAGAAGTCATAA
* *
17547167 TTGTATCGGTAGTAGTCATAC
1 TTGTATCGGTAGAAGTCATAA
17547188 TTGTATCGGTAGAA
1 TTGTATCGGTAGAA
17547202 CCTTCCCAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCATAA
Found at i:17550746 original size:28 final size:28
Alignment explanation
Indices: 17550706--17550786 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
17550696 CCCTTTACAT
17550706 ATGCGAACCCTAGGTAATATGTATAAAC
1 ATGCGAACCCTAGGTAATATGTATAAAC
* *
17550734 ATGCGAACCCTAGGTAATATTTACAAAC
1 ATGCGAACCCTAGGTAATATGTATAAAC
* *
17550762 ATGCGAACCCAAGCTAATATGTATA
1 ATGCGAACCCTAGGTAATATGTATA
17550787 TGTTGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (28 bp):
ATGCGAACCCTAGGTAATATGTATAAAC
Found at i:17551415 original size:25 final size:25
Alignment explanation
Indices: 17551359--17551415 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
17551349 CAAAATCAAA
*
17551359 TTTTA-TTTATTTTCTTTGATATTT
1 TTTTATTTTATTTTCATTGATATTT
* *
17551383 TTTGATTTTATTTTGATT-ATATTT
1 TTTTATTTTATTTTCATTGATATTT
17551407 CTTTTATTT
1 -TTTTATTT
17551416 AGTAAATGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.74
Consensus pattern (25 bp):
TTTTATTTTATTTTCATTGATATTT
Found at i:17551416 original size:24 final size:24
Alignment explanation
Indices: 17551359--17551416 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
17551349 CAAAATCAAA
*
17551359 TTTTATTTATTTTCTTTGATATTT
1 TTTTATTTATTTTCATTGATATTT
* *
17551383 TTTGATTTTATTTTGATT-ATATTT
1 TTTTA-TTTATTTTCATTGATATTT
17551407 CTTTTATTTA
1 -TTTTATTTA
17551417 GTAAATGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.72
Consensus pattern (24 bp):
TTTTATTTATTTTCATTGATATTT
Found at i:17552973 original size:61 final size:57
Alignment explanation
Indices: 17552867--17552997 Score: 165
Period size: 61 Copynumber: 2.2 Consensus size: 57
17552857 ATCACCTTAA
* *
17552867 TATTAAATTAATATAATATTATCAAGATAAATATTAGATTAAATTT-ATATTAAATC
1 TATTAAATTAATAGAATATTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
* *
17552923 TTATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTTAATTTAATTTTAAATC
1 -TATTAAATTAATAGAATA-TTA--T-CAAGATAAATATTAAATTAAATTTAATATTAAATC
*
17552985 TATTAAAATAATA
1 TATTAAATTAATA
17552998 TTATTTTTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
57 17 0.27
58 3 0.05
60 1 0.02
61 34 0.53
62 9 0.14
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (57 bp):
TATTAAATTAATAGAATATTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:17553005 original size:26 final size:26
Alignment explanation
Indices: 17552959--17553008 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
17552949 ACAAGATAAA
*
17552959 TATTAAATTTAATTTAATTTTAAATC
1 TATTAAATATAATTTAATTTTAAATC
*
17552985 TATTAAA-ATAATATTATTTTTAAA
1 TATTAAATATAAT-TTAATTTTAAA
17553009 ATATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTAAATATAATTTAATTTTAAATC
Found at i:17553228 original size:18 final size:20
Alignment explanation
Indices: 17553207--17553244 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
17553197 ATATTCTGCA
17553207 ACAACAAAAA-AAT-TTTCT
1 ACAACAAAAATAATATTTCT
17553225 ACAACAAAAATAATATTTCT
1 ACAACAAAAATAATATTTCT
17553245 GATAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (20 bp):
ACAACAAAAATAATATTTCT
Found at i:17553674 original size:31 final size:31
Alignment explanation
Indices: 17553603--17553676 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
17553593 TCCAATTTGG
* * *
17553603 TACCCAAACTTGACATATTTTTCCTAATTTGG
1 TACCTAAACTTGA-ATATTTTTCCTAAGTTGA
*
17553635 TACCTAAACTTG-ATATGTTTTCTTAAGTTGA
1 TACCTAAACTTGAATAT-TTTTCCTAAGTTGA
*
17553666 TACTTAAACTT
1 TACCTAAACTT
17553677 TTTGGGGGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 4 0.11
31 21 0.58
32 11 0.31
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (31 bp):
TACCTAAACTTGAATATTTTTCCTAAGTTGA
Found at i:17554221 original size:60 final size:58
Alignment explanation
Indices: 17554144--17554301 Score: 160
Period size: 59 Copynumber: 2.7 Consensus size: 58
17554134 AATTGAACCT
*
17554144 AAAAAAGCTTAGGTACCAAATTAGGAAAAA-TGACAAGTTCAGG-TATCAAATT-GGACCCCA
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGACAAG-TCAGGTTATCAAATTAGG----CA
* * * *
17554204 AAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGTCAAGTCTGGTTATCAAATTAGGCG
1 AAAAAAGTTTAGGTACCAAATTAG-GAAAAAGTGACAAGTCAGGTTATCAAATTAGGCA
* * * *
17554263 AAAAAATTTTAGGTACCAAATTAAGAAAATGTGTCAAGT
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGACAAGT
17554302 TCAAATACCA
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
58 13 0.15
59 23 0.27
60 23 0.27
61 9 0.11
62 15 0.18
63 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (58 bp):
AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGACAAGTCAGGTTATCAAATTAGGCA
Found at i:17554314 original size:58 final size:59
Alignment explanation
Indices: 17554204--17554315 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 59
17554194 TTGGACCCCA
*** *
17554204 AAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGTCAAGTCTGGTTATCAAATTAGGCG
1 AAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGTCAAGTCTAAATACCAAATTAGGCG
* * *
17554263 AAAAAATTTTAGGTACCAAATTA-AGAAAATGTGTCAAGT-TCAAATACCAAATT
1 AAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGTCAAGTCT-AAATACCAAATT
17554316 TTATATAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
57 1 0.02
58 22 0.49
59 22 0.49
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (59 bp):
AAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGTCAAGTCTAAATACCAAATTAGGCG
Found at i:17555398 original size:39 final size:38
Alignment explanation
Indices: 17555350--17555590 Score: 215
Period size: 39 Copynumber: 6.3 Consensus size: 38
17555340 TGACAGTCGC
* * *
17555350 GATCGTAAATCAGTAAACTGTTAGAAAATCGAAGGTCGT
1 GATCGTAAATCAATGAACTGTTAGAAAAT-GAAGGTTGT
* ** * *
17555389 GATCGTAAATTAACAAACCG-TA-AAAATG-AGAGTCGT
1 GATCGTAAATCAATGAACTGTTAGAAAATGAAG-GTTGT
* *
17555425 GATCGTAAATCAATGAATTGTTTGAAAATCGAAGGTTGT
1 GATCGTAAATCAATGAACTGTTAGAAAAT-GAAGGTTGT
* * * *
17555464 GATCGTAAATCATTGGAC-CTTA-AAAATGACA-GTTGC
1 GATCGTAAATCAATGAACTGTTAGAAAATGA-AGGTTGT
* *
17555500 GATCGTAAATCAACGAACAGTTAGAAAATTGAAGGTTGT
1 GATCGTAAATCAATGAACTGTTAGAAAA-TGAAGGTTGT
* *
17555539 GATCGTAAATCAATGAACTATTAGAAAATCGAAGGTTAT
1 GATCGTAAATCAATGAACTGTTAGAAAAT-GAAGGTTGT
*
17555578 GATTGTAAATCAA
1 GATCGTAAATCAA
17555591 CAAATCGTAA
Statistics
Matches: 164, Mismatches: 27, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
35 2 0.01
36 42 0.26
37 15 0.09
38 15 0.09
39 88 0.54
40 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (38 bp):
GATCGTAAATCAATGAACTGTTAGAAAATGAAGGTTGT
Found at i:17555429 original size:36 final size:36
Alignment explanation
Indices: 17555307--17555551 Score: 136
Period size: 39 Copynumber: 6.6 Consensus size: 36
17555297 CAATGAACTA
* * * * *
17555307 AAGTCATGATCGTAAATCAGC-GAGCTTTAAAAATG
1 AAGTCGTGATCGTAAATCAACAAACCGTTAAAAATG
* ** *
17555342 ACAGTCGCGATCGTAAATCAGTAAACTGTTAGAAAATCG
1 A-AGTCGTGATCGTAAATCAACAAACCGTTA-AAAAT-G
*
17555381 AAGGTCGTGATCGTAAATTAACAAACCG-TAAAAATG
1 AA-GTCGTGATCGTAAATCAACAAACCGTTAAAAATG
** ** *
17555417 AGAGTCGTGATCGTAAATCAATGAATTGTTTGAAAATCG
1 A-AGTCGTGATCGTAAATCAACAAACCG-TTAAAAAT-G
* ****
17555456 AAGGTTGTGATCGTAAATCATTGGACC-TTAAAAATG
1 AA-GTCGTGATCGTAAATCAACAAACCGTTAAAAATG
* * * *
17555492 ACAGTTGCGATCGTAAATCAACGAACAGTTAGAAAATTG
1 A-AGTCGTGATCGTAAATCAACAAACCGTTA-AAAA-TG
*
17555531 AAGGTTGTGATCGTAAATCAA
1 AA-GTCGTGATCGTAAATCAA
17555552 TGAACTATTA
Statistics
Matches: 165, Mismatches: 30, Indels: 26
0.75 0.14 0.12
Matches are distributed among these distances:
35 1 0.01
36 60 0.36
37 21 0.13
38 20 0.12
39 63 0.38
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
AAGTCGTGATCGTAAATCAACAAACCGTTAAAAATG
Found at i:17555436 original size:75 final size:75
Alignment explanation
Indices: 17555334--17555551 Score: 283
Period size: 75 Copynumber: 2.9 Consensus size: 75
17555324 CAGCGAGCTT
* * *
17555334 TAAAAATGACAGTCGCGATCGTAAATCAGTAAACTGTTAGAAAATCGAAGGTCGTGATCGTAAAT
1 TAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTTAGAAAATCGAAGGTTGTGATCGTAAAT
*
17555399 TAACAAACCG
66 CAACAAACCG
* * * *
17555409 TAAAAATGAGAGTCGTGATCGTAAATCAATGAATTGTTTGAAAATCGAAGGTTGTGATCGTAAAT
1 TAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTTAGAAAATCGAAGGTTGTGATCGTAAAT
**** *
17555474 CATTGGACCT
66 CAACAAACCG
* * * *
17555484 TAAAAATGACAGTTGCGATCGTAAATCAACGAACAGTTAGAAAATTGAAGGTTGTGATCGTAAAT
1 TAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTTAGAAAATCGAAGGTTGTGATCGTAAAT
17555549 CAA
66 CAA
17555552 TGAACTATTA
Statistics
Matches: 121, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 121 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (75 bp):
TAAAAATGACAGTCGCGATCGTAAATCAATGAACTGTTAGAAAATCGAAGGTTGTGATCGTAAAT
CAACAAACCG
Found at i:17555750 original size:93 final size:93
Alignment explanation
Indices: 17555637--17555880 Score: 247
Period size: 93 Copynumber: 2.6 Consensus size: 93
17555627 TAAGAAAGTC
* * * * * *
17555637 AAAGGTTGTGGTCATAAATCAGCAAATCGTAAGAAAGCCAAAGGTCGTGATCGTAAATCAATGGA
1 AAAGGTTGTGATCGTAAATCAGCAAACCATAAGAAAGCCGAAGGTCGTGATCGTAAATCAACGGA
*
17555702 -CTACAAGATTCGTAAAACCTCATAAATA
66 CCT-CAAGATTCATAAAACCTCATAAATA
* ** * * * * * * *
17555730 AAAGATTGTGATCGTAAATCAATAGACCATAGGAGAGCTGAAGATCGTGATTGCAAATCAACGGA
1 AAAGGTTGTGATCGTAAATCAGCAAACCATAAGAAAGCCGAAGGTCGTGATCGTAAATCAACGGA
* * * *
17555795 CCTCGAGATTCATAAAATCTCGTATATA
66 CCTCAAGATTCATAAAACCTCATAAATA
* * * *
17555823 AAAGGTTGTGATTGTAAATCAGGAAGCCATAAGAAAGCCGAAGGTTGTGATCGTAAAT
1 AAAGGTTGTGATCGTAAATCAGCAAACCATAAGAAAGCCGAAGGTCGTGATCGTAAAT
17555881 AACAGACTGT
Statistics
Matches: 116, Mismatches: 34, Indels: 2
0.76 0.22 0.01
Matches are distributed among these distances:
93 114 0.98
94 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (93 bp):
AAAGGTTGTGATCGTAAATCAGCAAACCATAAGAAAGCCGAAGGTCGTGATCGTAAATCAACGGA
CCTCAAGATTCATAAAACCTCATAAATA
Found at i:17555948 original size:39 final size:37
Alignment explanation
Indices: 17555850--17555962 Score: 100
Period size: 39 Copynumber: 2.9 Consensus size: 37
17555840 ATCAGGAAGC
* * *
17555850 CATAAGAAAGCCGAAGGTTGTGATCGTAAATAACAGA
1 CATAAGAAAGCCGAAAGTCGTGATCGTAAATAACAAA
* ** * *
17555887 CTGTAAGAAAGTTGAAAATCGTGATCGTAAATCAGCATAA
1 C-ATAAGAAAGCCGAAAGTCGTGATCGTAAAT-AACA-AA
* *
17555927 CATAAGAAAGGCGAAAGTCGTGATCATAAATGAACA
1 CATAAGAAAGCCGAAAGTCGTGATCGTAAAT-AACA
17555963 GATCGTGAGA
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
37 1 0.02
38 24 0.41
39 31 0.53
40 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.20
Consensus pattern (37 bp):
CATAAGAAAGCCGAAAGTCGTGATCGTAAATAACAAA
Found at i:17561974 original size:40 final size:39
Alignment explanation
Indices: 17561930--17562076 Score: 143
Period size: 40 Copynumber: 3.7 Consensus size: 39
17561920 ATATTGTAGT
* *
17561930 TGAACTAGCAGTGAAACTGTAAACACTACGACATTACAAC
1 TGAACTAGTAGTGACACTGTAAACACTACGA-ATTACAAC
* * ** *
17561970 TGAACTGGTAATGACACTGTAAACACTTTGATAATACAAC
1 TGAACTAGTAGTGACACTGTAAACACTACGA-ATTACAAC
* * * *
17562010 TGAACTGGAAGTGACATTGCAAACACTAC-AATGCTACAAC
1 TGAACTAGTAGTGACACTGTAAACACTACGAAT--TACAAC
*
17562050 TGAACTAGTAGTGACATTGTAAACACT
1 TGAACTAGTAGTGACACTGTAAACACT
17562077 GCTAGATTAC
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 85 0.98
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (39 bp):
TGAACTAGTAGTGACACTGTAAACACTACGAATTACAAC
Found at i:17564440 original size:25 final size:23
Alignment explanation
Indices: 17564412--17564457 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
17564402 GTTAGATCAA
17564412 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAA-TCT-AAAAAATAATTAG
*
17564437 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
17564458 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:17569403 original size:39 final size:39
Alignment explanation
Indices: 17569310--17569517 Score: 121
Period size: 40 Copynumber: 5.2 Consensus size: 39
17569300 GAATAGTTAC
* * * *
17569310 TGAACTGATAGTGACACTGTGAACACTGCAATATTATAGT
1 TGAACTG-TAGTGACACTGTAAACACTGCAACATTACAAT
* * *
17569350 TGAATTGGCAGTGACACTGTAAACA-TGCGACATTACAAT
1 TGAACT-GTAGTGACACTGTAAACACTGCAACATTACAAT
* * * * ** *
17569389 TGAACTAGTAGTGACACTATAAACACTACGATAACACAAC
1 TGAACT-GTAGTGACACTGTAAACACTGCAACATTACAAT
* * * * *
17569429 TGAACCGATAGTGACACTATAAACACTGCAATACTACAAC
1 TGAACTG-TAGTGACACTGTAAACACTGCAACATTACAAT
* * * * * * *
17569469 TGAACTAGCAATGATACTATAAACACTGCTAGATTACCAT
1 TGAACT-GTAGTGACACTGTAAACACTGCAACATTACAAT
*
17569509 CGAACTGTA
1 TGAACTGTA
17569518 ATATAATTGT
Statistics
Matches: 132, Mismatches: 32, Indels: 9
0.76 0.18 0.05
Matches are distributed among these distances:
39 34 0.26
40 96 0.73
41 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (39 bp):
TGAACTGTAGTGACACTGTAAACACTGCAACATTACAAT
Found at i:17573158 original size:23 final size:22
Alignment explanation
Indices: 17573109--17573157 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
17573099 TAAAATTTTT
* *
17573109 AAAAATTTTCCAAATCTAAATG
1 AAAAATTTTCCAAACCTAAATA
*
17573131 AAAAATTTTTCAAACCTAAATA
1 AAAAATTTTCCAAACCTAAATA
17573153 AAAAA
1 AAAAA
17573158 AATTTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATTTTCCAAACCTAAATA
Found at i:17573163 original size:22 final size:22
Alignment explanation
Indices: 17573109--17573164 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17573099 TAAAATTTTT
* *
17573109 AAAAATTTTCCAAATCTAAATGA
1 AAAAATTTT-CAAACCTAAATAA
*
17573132 AAAATTTTTCAAACCTAAATAA
1 AAAAATTTTCAAACCTAAATAA
*
17573154 AAAAAATTTCA
1 AAAAATTTTCA
17573165 TTTTAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAATTTTCAAACCTAAATAA
Found at i:17584433 original size:82 final size:82
Alignment explanation
Indices: 17584294--17584533 Score: 331
Period size: 82 Copynumber: 2.9 Consensus size: 82
17584284 AACAAATTCC
* * * *
17584294 GTCAATTCATGGCACCC-GATGCCTAGCGAATAAATCGCAATAAGTGAGCCCAACTCTAGTTGGA
1 GTCAATTCCTGGCACCCAG-TGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGA
17584358 TTAACCAACGATAGTTTT
65 TTAACCAACGATAGTTTT
** * * *
17584376 GTCAATTCCTGGCACTTAGTGCTTAGCGGATAAACCGCAATAAGTGAGCTCAGCTCTAGTTTGAT
1 GTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGAT
*
17584441 TAACTAACTG-TAGTTTT
66 TAACCAAC-GATAGTTTT
* *
17584458 GTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACTGTAATAAGTGAGCCCAGCTCTAGTTGGAT
1 GTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGAT
*
17584523 TAGCCAACGAT
66 TAACCAACGAT
17584534 TTTGCGCCCA
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
81 1 0.01
82 133 0.98
83 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (82 bp):
GTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGAT
TAACCAACGATAGTTTT
Found at i:17585304 original size:2 final size:2
Alignment explanation
Indices: 17585297--17585343 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
17585287 TTCTGAAAAT
17585297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17585339 TA TA T
1 TA TA T
17585344 CCTCATTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17588576 original size:24 final size:24
Alignment explanation
Indices: 17588481--17588583 Score: 161
Period size: 24 Copynumber: 4.3 Consensus size: 24
17588471 ACTCTGTCTA
*
17588481 GGCTCGTAAGAGCTAATCATTCTA
1 GGCTCGTAAGAGCTAATCATTCTG
*
17588505 GGCTCGTAAGAGCTAATCATTTTG
1 GGCTCGTAAGAGCTAATCATTCTG
*
17588529 GGCTCATAAGAGCTAATCATTCTG
1 GGCTCGTAAGAGCTAATCATTCTG
*
17588553 GGCTCGTAAGAGTTAATCATTCTG
1 GGCTCGTAAGAGCTAATCATTCTG
*
17588577 GGTTCGT
1 GGCTCGT
17588584 GTTGGCTAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAATCATTCTG
Found at i:17591592 original size:17 final size:18
Alignment explanation
Indices: 17591556--17591602 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
17591546 ATATATTTCT
*
17591556 TTTCTTTTCTCTTTTATTC
1 TTTCTTTT-TGTTTTATTC
17591575 -TTCTTTCTTGTTTT-TTC
1 TTTCTTT-TTGTTTTATTC
17591592 TTTCTTTTTGT
1 TTTCTTTTTGT
17591603 GAATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.28
18 17 0.68
19 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTCTTTTTGTTTTATTC
Found at i:17598350 original size:37 final size:37
Alignment explanation
Indices: 17598308--17598414 Score: 133
Period size: 37 Copynumber: 2.9 Consensus size: 37
17598298 AATGTCGCTA
17598308 CATGAGCACTTCTAGATTGCACCCAAAACTGTCGCCG
1 CATGAGCACTTCTAGATTGCACCCAAAACTGTCGCCG
* * *
17598345 CATGAGCACTTCCAAATTGCACCCAAAACTGTCGCCT
1 CATGAGCACTTCTAGATTGCACCCAAAACTGTCGCCG
* ** * * *
17598382 CAGGAATATTTCTAGAATGCACCCAATACTGTC
1 CATGAGCACTTCTAGATTGCACCCAAAACTGTC
17598415 ACTGCATAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (37 bp):
CATGAGCACTTCTAGATTGCACCCAAAACTGTCGCCG
Found at i:17598538 original size:26 final size:26
Alignment explanation
Indices: 17598486--17598538 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
17598476 TACCCAGGAA
* *
17598486 TGTCGCTGTATGAACATGTACAGAAT
1 TGTCGCTGCATGAACATGTACAAAAT
* *
17598512 TGTCGCTGCATGAACGTGTCCAAAAT
1 TGTCGCTGCATGAACATGTACAAAAT
17598538 T
1 T
17598539 ACGCCTAGAA
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:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTACAAAAT
Found at i:17601773 original size:17 final size:17
Alignment explanation
Indices: 17601761--17601818 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
17601751 TAATTGTCCT
17601761 TGCATTTTCATTGTCAC
1 TGCATTTTCATTGTCAC
**
17601778 TGCATTTTTGTTGTCAC
1 TGCATTTTCATTGTCAC
* * *
17601795 TACATCTAT-ATTGTCAT
1 TGCAT-TTTCATTGTCAC
17601812 TGCATTT
1 TGCATTT
17601819 CCATATATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
16 1 0.03
17 29 0.91
18 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (17 bp):
TGCATTTTCATTGTCAC
Found at i:17602900 original size:37 final size:37
Alignment explanation
Indices: 17602853--17602928 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
17602843 AATGTCGCTA
* * *
17602853 CATGAGCACTTCTAGATTGCGCCCAAAACTGTCGCCG
1 CATGACCACTTCCAGATTGCACCCAAAACTGTCGCCG
* *
17602890 CATGACCACTTCCAGATTGCACCCAAAGCTGTTGCCG
1 CATGACCACTTCCAGATTGCACCCAAAACTGTCGCCG
17602927 CA
1 CA
17602929 GGAATATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (37 bp):
CATGACCACTTCCAGATTGCACCCAAAACTGTCGCCG
Found at i:17603036 original size:36 final size:37
Alignment explanation
Indices: 17602931--17603040 Score: 127
Period size: 38 Copynumber: 3.0 Consensus size: 37
17602921 TTGCCGCAGG
* *
17602931 AATATTTTCGAAA-TGCACCCAAGATTGTCACTGCATA
1 AATATTTTC-AAATTGCACCCAAGAATGTCGCTGCATA
* *
17602968 AATATTCTTCAAATTGCATCCAA-AACTATCGCTGCATA
1 AATATT-TTCAAATTGCACCCAAGAA-TGTCGCTGCATA
*
17603006 AGTATTTTC-AATTGCACCCAAGAATGTCGCTGCAT
1 AATATTTTCAAATTGCACCCAAGAATGTCGCTGCAT
17603041 GAACATGTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
36 21 0.34
37 15 0.24
38 26 0.42
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.31
Consensus pattern (37 bp):
AATATTTTCAAATTGCACCCAAGAATGTCGCTGCATA
Found at i:17603082 original size:26 final size:26
Alignment explanation
Indices: 17603032--17603082 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
17603022 CCCAAGAATG
* *
17603032 TCGCTGCATGAACATGTATATAATTT
1 TCGCTGCATGAACATGTACAGAATTT
* *
17603058 TCGCTGCATGAACGTGTCCAGAATT
1 TCGCTGCATGAACATGTACAGAATT
17603083 GCGCCTAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (26 bp):
TCGCTGCATGAACATGTACAGAATTT
Found at i:17612343 original size:12 final size:12
Alignment explanation
Indices: 17612328--17612352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17612318 GCTCTCTAGC
17612328 TTTCCCTTCCAT
1 TTTCCCTTCCAT
17612340 TTTCCCTTCCAT
1 TTTCCCTTCCAT
17612352 T
1 T
17612353 CCTTTTCCGA
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:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTCCCTTCCAT
Found at i:17615186 original size:5 final size:5
Alignment explanation
Indices: 17615176--17615210 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
17615166 TTGCAACAAG
* *
17615176 ATTTT ATTTT ACTTT ATTTT ATTTT AATTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
17615211 TAGTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:17615196 original size:15 final size:15
Alignment explanation
Indices: 17615176--17615210 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
17615166 TTGCAACAAG
*
17615176 ATTTTATTTTACTTT
1 ATTTTATTTTAATTT
17615191 ATTTTATTTTAATTT
1 ATTTTATTTTAATTT
17615206 ATTTT
1 ATTTT
17615211 TAGTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTATTTTAATTT
Found at i:17625677 original size:17 final size:18
Alignment explanation
Indices: 17625655--17625697 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
17625645 ATAGTTTGCA
17625655 TGCATTTTTA-TTGTCAT
1 TGCATTTTTATTTGTCAT
17625672 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA-TTTGTCAT
17625691 TGCATTT
1 TGCATTT
17625698 CTTTTGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (18 bp):
TGCATTTTTATTTGTCAT
Found at i:17625702 original size:17 final size:16
Alignment explanation
Indices: 17625655--17625704 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 16
17625645 ATAGTTTGCA
17625655 TGCATTTTTATTGTCAT
1 TGCATTTTT-TTGTCAT
17625672 TGCATTTTTATTTTGTCAT
1 TGCA--TTT-TTTTGTCAT
17625691 TGCATTTCTTTTGT
1 TGCATTT-TTTTGT
17625705 TAGTTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 13 0.45
19 14 0.48
20 2 0.07
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TGCATTTTTTTGTCAT
Found at i:17626304 original size:6 final size:6
Alignment explanation
Indices: 17626283--17626339 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
17626273 AGTCACTTGA
17626283 AAAAAG AAAATGAG AAAAAG --AAAG AAAAAG -AAAAG AGAAAAG -AAAAG
1 AAAAAG AAAA--AG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG
*
17626330 AAGAAG AAAA
1 AAAAAG AAAA
17626340 TGTTTGCTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
4 4 0.10
5 10 0.24
6 17 0.40
7 5 0.12
8 6 0.14
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:17626308 original size:18 final size:18
Alignment explanation
Indices: 17626284--17626328 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
17626274 GTCACTTGAA
17626284 AAAAGAAAATGAGAAAA-AG
1 AAAAGAAAA--AGAAAAGAG
17626303 -AAAGAAAAAGAAAAGAG
1 AAAAGAAAAAGAAAAGAG
17626320 AAAAGAAAA
1 AAAAGAAAA
17626329 GAAGAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
18 16 0.67
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGAG
Found at i:17626310 original size:23 final size:24
Alignment explanation
Indices: 17626283--17626341 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
17626273 AGTCACTTGA
17626283 AAAAAGAAAATGAGAAAA-AGAAAG
1 AAAAAGAAAATGAGAAAAGA-AAAG
17626307 AAAAAGAAAA-GAGAAAAGAAAAG
1 AAAAAGAAAATGAGAAAAGAAAAG
*
17626330 AAGAAGAAAATG
1 AAAAAGAAAATG
17626342 TTTGCTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (24 bp):
AAAAAGAAAATGAGAAAAGAAAAG
Found at i:17626317 original size:11 final size:11
Alignment explanation
Indices: 17626295--17626339 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
17626285 AAAGAAAATG
17626295 AGAAAAAG-AA
1 AGAAAAAGAAA
17626305 AGAAAAAGAAA
1 AGAAAAAGAAA
17626316 AGAGAAAAGAAA
1 AGA-AAAAGAAA
*
17626328 AGAAGAAGAAA
1 AGAAAAAGAAA
17626339 A
1 A
17626340 TGTTTGCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 8 0.25
11 13 0.41
12 11 0.34
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:17651459 original size:18 final size:19
Alignment explanation
Indices: 17651409--17651459 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 19
17651399 ATGAATTTTC
**
17651409 TCTTTTTTCTCTACTCAAT
1 TCTTTTTTCTCTTTTCAAT
*
17651428 TCTTTTTTAT-TTTTC-AT
1 TCTTTTTTCTCTTTTCAAT
*
17651445 TGTTTTTTCTCTTTT
1 TCTTTTTTCTCTTTT
17651460 TGGCCATACT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 10 0.38
18 7 0.27
19 9 0.35
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.71
Consensus pattern (19 bp):
TCTTTTTTCTCTTTTCAAT
Found at i:17664269 original size:9 final size:9
Alignment explanation
Indices: 17664255--17664281 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17664245 TTAGTAAAGG
17664255 TTTAAAATT
1 TTTAAAATT
17664264 TTTAAAATT
1 TTTAAAATT
17664273 TTTAAAATT
1 TTTAAAATT
17664282 CAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAAAATT
Found at i:17667171 original size:14 final size:14
Alignment explanation
Indices: 17667111--17667173 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
17667101 AGTCATAAAC
17667111 TAAAATTAAAAATAGA
1 TAAAA-TAAAAATA-A
17667127 -AAAATAAATAATAA
1 TAAAATAAA-AATAA
* *
17667141 -ACAATGAAGAA-AA
1 TAAAAT-AAAAATAA
17667154 TAAAATAAAAATAA
1 TAAAATAAAAATAA
17667168 TAAAAT
1 TAAAAT
17667174 CTATATCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 6 0.15
14 23 0.59
15 10 0.26
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.21
Consensus pattern (14 bp):
TAAAATAAAAATAA
Found at i:17677400 original size:51 final size:50
Alignment explanation
Indices: 17677345--17677606 Score: 353
Period size: 51 Copynumber: 5.1 Consensus size: 50
17677335 CAAACTATCA
*
17677345 CGTGAGAAAATGAATCTTGTATGGATTAAAGGTCCGATGACTAAGTGTCAT
1 CGTGAGTAAATGAATCTT-TATGGATTAAAGGTCCGATGACTAAGTGTCAT
* *
17677396 CGTGAGTGAATGAATCCTTTATGGATTAATGGTCCGATGACTAAGTGTCAT
1 CGTGAGTAAATGAAT-CTTTATGGATTAAAGGTCCGATGACTAAGTGTCAT
* * *
17677447 CGTGAATAAATGAATCCTATATGGATTAAAGGTTCGATGACTAAGTGTCAT
1 CGTGAGTAAATGAAT-CTTTATGGATTAAAGGTCCGATGACTAAGTGTCAT
** * * *
17677498 AATGAGTGAATGAATCCTTTATGGATTAATGGTTCGATGACTAAGTGTCAT
1 CGTGAGTAAATGAAT-CTTTATGGATTAAAGGTCCGATGACTAAGTGTCAT
* * *
17677549 CGTGAGTAAATGAATCATGTATGGATTAAAGGTCCGATGACTAAATGTTAT
1 CGTGAGTAAATGAATC-TTTATGGATTAAAGGTCCGATGACTAAGTGTCAT
17677600 CGTGAGT
1 CGTGAGT
17677607 TTACAGATTC
Statistics
Matches: 187, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
50 1 0.01
51 183 0.98
52 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (50 bp):
CGTGAGTAAATGAATCTTTATGGATTAAAGGTCCGATGACTAAGTGTCAT
Found at i:17677606 original size:102 final size:102
Alignment explanation
Indices: 17677325--17677606 Score: 431
Period size: 102 Copynumber: 2.8 Consensus size: 102
17677315 TAGATGAAAG
* * * * *
17677325 GGTTCGATGACAAACTATCA-CGTGAGAAAATGAATCTTGTATGGATTAAAGGTCCGATGACTAA
1 GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCATGTATGGATTAAAGGTCCGATGACTAA
17677389 GTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
66 GTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
* * * * *
17677426 GGTCCGATGACTAAGTGTCATCGTGAATAAATGAATCCTATATGGATTAAAGGTTCGATGACTAA
1 GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCATGTATGGATTAAAGGTCCGATGACTAA
**
17677491 GTGTCATAATGAGTGAATGAATCCTTTATGGATTAAT
66 GTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
17677528 GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCATGTATGGATTAAAGGTCCGATGACTAA
1 GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCATGTATGGATTAAAGGTCCGATGACTAA
* *
17677593 ATGTTATCGTGAGT
66 GTGTCATCGTGAGT
17677607 TTACAGATTC
Statistics
Matches: 160, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 16 0.10
102 144 0.90
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (102 bp):
GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCATGTATGGATTAAAGGTCCGATGACTAA
GTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
Found at i:17684163 original size:51 final size:51
Alignment explanation
Indices: 17684079--17684412 Score: 481
Period size: 51 Copynumber: 6.5 Consensus size: 51
17684069 TAGACGAAAG
* * * *
17684079 GGTCCGATGACAAACTGTCATCATGAATAAATGAAT-CTTGTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTT-TATGGATTAAA
* *
17684130 GGTCCGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* * *
17684181 GGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* * *
17684232 GGTCCGATGACTAAGTGTTATCGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* *
17684283 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTGTGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* *
17684334 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTATATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* * *
17684385 AGTCCAATGACTAAATGTCATCGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
17684413 TTATAGATTC
Statistics
Matches: 254, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
51 251 0.99
52 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
Found at i:17690892 original size:18 final size:16
Alignment explanation
Indices: 17690857--17690898 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
17690847 GGTAATTGCA
*
17690857 TGCATTTTATTTTCAT
1 TGCATTTTATTGTCAT
17690873 TGCATTGTTACTTGTCAT
1 TGCATT-TTA-TTGTCAT
17690891 TGCATTTT
1 TGCATTTT
17690899 TCATATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 5 0.22
18 12 0.52
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (16 bp):
TGCATTTTATTGTCAT
Found at i:17697309 original size:29 final size:28
Alignment explanation
Indices: 17697258--17697338 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
17697248 AAATACATAA
*
17697258 AAATTTTATT-AAATTATGGAAAACTCATT
1 AAATTTTATTAAAATTAT--AAAAATCATT
17697287 AAATTTTATTAAAATTTATAAAAATCATT
1 AAATTTTATTAAAA-TTATAAAAATCATT
* * *
17697316 AGAAATTAATTAAAACTATAAAA
1 A-AATTTTATTAAAATTATAAAA
17697339 TTTATAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 27 0.60
30 14 0.31
31 4 0.09
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (28 bp):
AAATTTTATTAAAATTATAAAAATCATT
Found at i:17697374 original size:36 final size:37
Alignment explanation
Indices: 17697296--17697374 Score: 90
Period size: 36 Copynumber: 2.1 Consensus size: 37
17697286 TAAATTTTAT
* *
17697296 TAAAATTTATAAAAATCATTAGAAATTAATTAAAACTA
1 TAAAATTTATAAAAAGCA-TAGAAATTAATTAAAACCA
* *
17697334 TAAAATTTAT-AAAAGCA-AGTAATTTATTAAAAACCA
1 TAAAATTTATAAAAAGCATAGAAATTAATT-AAAACCA
17697370 TAAAA
1 TAAAA
17697375 AATTAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 9 0.25
36 11 0.31
37 6 0.17
38 10 0.28
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (37 bp):
TAAAATTTATAAAAAGCATAGAAATTAATTAAAACCA
Found at i:17699511 original size:16 final size:16
Alignment explanation
Indices: 17699451--17699514 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
17699441 GAATGAATAA
17699451 GGAGGTGGCGAGCTAG
1 GGAGGTGGCGAGCTAG
* *
17699467 TGGA-GTGGTGAG-TAA
1 -GGAGGTGGCGAGCTAG
*
17699482 GCAGGAT-GCTGAGCTAG
1 GGAGG-TGGC-GAGCTAG
17699499 GGAGGTGGCGAGCTAG
1 GGAGGTGGCGAGCTAG
17699515 CGAAGGTTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
14 2 0.06
15 4 0.11
16 19 0.53
17 11 0.31
ACGTcount: A:0.22, C:0.11, G:0.50, T:0.17
Consensus pattern (16 bp):
GGAGGTGGCGAGCTAG
Found at i:17700388 original size:54 final size:54
Alignment explanation
Indices: 17700329--17701046 Score: 601
Period size: 54 Copynumber: 13.3 Consensus size: 54
17700319 GTAAGACTCA
* * **
17700329 AAAAATCATGTAAGTATAAGGTTGTGATCTTAAATTGGCGAGCCACAAGATTTG
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
* * * * **
17700383 GAAAATCTTGTAAGTATAAGGTTACGATTTTAAATCAGCAAGCCACAAGATACG
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
* * * **
17700437 AAAAATCTTGTAAATATAAGG-CGACGATCTTAAATCAACGAGCTGCAAGATTTG
1 AAAAATCTTGTAAGTATAAGGTTG-CGATCTTAAATCAGCGAGCCACAAGATTTG
* ** * * * *
17700491 AAAAATCTTGTAAGTAAAAGGTTGTAACCTTAAATCGGCGAGCTACAAGATTCG
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
* *
17700545 AAAAATCTTGTAAGTATAAGGCTACGATCTTAAAT-AGGCGAGCCACAAGATTT-
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCA-GCGAGCCACAAGATTTG
* * * * * * *
17700598 AGAAAATCTTGTAAAATATAAAGCTGTGATCTTAAATC-GACAAACCACAAGATTCG
1 A-AAAATCTTGT-AAGTATAAGGTTGCGATCTTAAATCAG-CGAGCCACAAGATTTG
* * ** * *
17700654 AAAAATCTTATAAGTATAAGGTTGTGATCTTAAATCAATGAACCGCAAGATTTG
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
* * * * * *
17700708 AAAAATCTTATAAGTATAAGGCTGCGATCTTAAATCAGTGAACCGCAAGAGTTG
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
* ** * * *
17700762 AAAAATCTTGTAAGTATAAGGTTGTGATCTTAAATTGGTGAGCCAAAAGA-TTA
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
* *
17700815 AGAAAATCTTGTAAATATAAGGTTGCGATCTTAAATCAGCGAGCCACAATATTT-
1 A-AAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
* ** * *
17700869 AGAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGC-AAACAGTAAG-TTTCA
1 A-AAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCA-CAAGATTT-G
* * * * ** * *
17700924 AAAAATCTTGTATGTATAAAGTTGCAATCTTAAA-CCGATAAACCATAAGATTTG
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAG-CGAGCCACAAGATTTG
** * * * * * * *
17700978 GGAAGTCTTGTAAATATAAGATTGCAATCTTAAATC-GACGAGTCATAATATTTG
1 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAG-CGAGCCACAAGATTTG
*
17701032 GAAAATCTTGTAAGT
1 AAAAATCTTGTAAGT
17701047 TGCGAATTGA
Statistics
Matches: 542, Mismatches: 104, Indels: 36
0.79 0.15 0.05
Matches are distributed among these distances:
53 12 0.02
54 476 0.88
55 53 0.10
56 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (54 bp):
AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCAGCGAGCCACAAGATTTG
Found at i:17704164 original size:26 final size:25
Alignment explanation
Indices: 17704135--17704191 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
17704125 TTAAATTAGA
*
17704135 TAAAATCATTAAAATTTTATTAGAGG
1 TAAAATCATAAAAATTTTATT-GAGG
** *
17704161 TAAAATTGTAAAAATTTTATTGGGG
1 TAAAATCATAAAAATTTTATTGAGG
17704186 TAAAAT
1 TAAAAT
17704192 TGAGATGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.39
Consensus pattern (25 bp):
TAAAATCATAAAAATTTTATTGAGG
Found at i:17704187 original size:25 final size:26
Alignment explanation
Indices: 17704145--17704193 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
17704135 TAAAATCATT
17704145 AAAATTTTATTAGAGGTAAAATTGTA
1 AAAATTTTATTAGAGGTAAAATTGTA
*
17704171 AAAATTTTATT-GGGGTAAAATTG
1 AAAATTTTATTAGAGGTAAAATTG
17704194 AGATGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (26 bp):
AAAATTTTATTAGAGGTAAAATTGTA
Found at i:17705231 original size:3 final size:3
Alignment explanation
Indices: 17705225--17705256 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17705215 ACTATTATTA
17705225 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
17705257 AGGGTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:17705818 original size:16 final size:17
Alignment explanation
Indices: 17705780--17705817 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
17705770 TGGTTTATGA
17705780 TTTTTTGGATTTAGGGG
1 TTTTTTGGATTTAGGGG
*
17705797 TATTTTGG-TTTA-GGG
1 TTTTTTGGATTTAGGGG
17705812 TTTTTT
1 TTTTTT
17705818 TAATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 8 0.42
16 4 0.21
17 7 0.37
ACGTcount: A:0.11, C:0.00, G:0.29, T:0.61
Consensus pattern (17 bp):
TTTTTTGGATTTAGGGG
Found at i:17706380 original size:90 final size:88
Alignment explanation
Indices: 17706194--17706390 Score: 225
Period size: 90 Copynumber: 2.2 Consensus size: 88
17706184 TATTGTTTTA
* * * * **
17706194 GATTTATTTGTATTAAATTATTTGGTTATTATACATGACAACTTGATTTCTTTGTATTTTATCAT
1 GATTTGTTTGTATTAAATTATTTGGTTATTATACATGACAAATGGATTTATTTGTATTAAATCAT
** * *
17706259 CTTTCATGTGTATGACAGAAATG
66 CTAGCATGTGCATGAAAGAAATG
* * *
17706282 GATATGTTTGTATTAAATTATTTGGTTTTTGTACATGACAGAAATGGATTTATTTGTATTAAAGT
1 GATTTGTTTGTATTAAATTATTTGGTTATTATACATGAC--AAATGGATTTATTTGTATTAAA-T
* *
17706347 -GTGTAGCATGTGCATGAAAGAAATG
63 CATCTAGCATGTGCATGAAAGAAATG
17706372 GATTTGTTTGTATTAAATT
1 GATTTGTTTGTATTAAATT
17706391 TTTTTTTGTA
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
88 35 0.39
90 54 0.60
91 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (88 bp):
GATTTGTTTGTATTAAATTATTTGGTTATTATACATGACAAATGGATTTATTTGTATTAAATCAT
CTAGCATGTGCATGAAAGAAATG
Found at i:17706810 original size:20 final size:19
Alignment explanation
Indices: 17706786--17706866 Score: 63
Period size: 20 Copynumber: 4.1 Consensus size: 19
17706776 TCAATCGAGA
17706786 TAAACAACAAAGAATCGAT
1 TAAACAACAAAGAATCGAT
* * *
17706805 TCAAACAATAATGAATTGAT
1 T-AAACAACAAAGAATCGAT
* * *
17706825 TAAAGAAGTAAAGAATTGATT
1 TAAACAA-CAAAGAATCGA-T
*
17706846 TAAAACAACAAACAATCGAT
1 T-AAACAACAAAGAATCGAT
17706866 T
1 T
17706867 GGAATAAGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.12
20 28 0.57
21 10 0.20
22 5 0.10
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (19 bp):
TAAACAACAAAGAATCGAT
Found at i:17707132 original size:42 final size:40
Alignment explanation
Indices: 17707029--17707189 Score: 164
Period size: 42 Copynumber: 3.9 Consensus size: 40
17707019 GTTGGAGTTT
* * *
17707029 GAATCGAGTTAAAAAA-CAAATAATCGA-TTCAAACAATAA
1 GAATCGA-TTAAAAAAGCAAAGAATCAATTTAAAACAATAA
* *
17707068 TGAATAGATTAAAGAAGCAAAGAATCAATTTAAAACAATAA
1 -GAATCGATTAAAAAAGCAAAGAATCAATTTAAAACAATAA
* *
17707109 GATATCGATTGAAATAAGCAAAGAATCAATTTAAAACAACAAA
1 GA-ATCGATT-AAAAAAGCAAAGAATCAATTTAAAACAA-TAA
* * *
17707152 CAATCTATTCAAAAAAGCAAAGAATCAACTTAAAACAA
1 GAATCGATT-AAAAAAGCAAAGAATCAATTTAAAACAA
17707190 AAAAGCAAAC
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
39 7 0.07
40 17 0.17
41 17 0.17
42 59 0.57
43 3 0.03
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.20
Consensus pattern (40 bp):
GAATCGATTAAAAAAGCAAAGAATCAATTTAAAACAATAA
Found at i:17707194 original size:21 final size:20
Alignment explanation
Indices: 17707037--17707194 Score: 83
Period size: 21 Copynumber: 7.7 Consensus size: 20
17707027 TTGAATCGAG
* *
17707037 TTAAAA-AACAAATAATCGA
1 TTAAAACAACAAAGAATCAA
* * *
17707056 TTCAAACAATAATGAAT-AGA
1 TTAAAACAACAAAGAATCA-A
*
17707076 TTAAAGA-AGCAAAGAATCAA
1 TTAAA-ACAACAAAGAATCAA
* *
17707096 TTTAAAACAA-TAAGATATCGA
1 -TTAAAACAACAAAGA-ATCAA
* *
17707117 TTGAAATAAGCAAAGAATCAA
1 TTAAAACAA-CAAAGAATCAA
* *
17707138 TTTAAAACAACAAACAATCTA
1 -TTAAAACAACAAAGAATCAA
17707159 TTCAAAA-AAGCAAAGAATCAA
1 TT-AAAACAA-CAAAGAATCAA
*
17707180 CTTAAAACAAAAAAG
1 -TTAAAACAACAAAG
17707195 CAAACCTAAC
Statistics
Matches: 102, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
19 5 0.05
20 36 0.35
21 46 0.45
22 15 0.15
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.20
Consensus pattern (20 bp):
TTAAAACAACAAAGAATCAA
Found at i:17707420 original size:21 final size:21
Alignment explanation
Indices: 17707396--17707456 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
17707386 GAAAAAAAAT
17707396 GATTTAAAACAACAAACAATC
1 GATTTAAAACAACAAACAATC
* * *
17707417 GATTGAAATA-AGCAAAGAATC
1 GATTTAAA-ACAACAAACAATC
* *
17707438 CATTTAAAACAATAAACAA
1 GATTTAAAACAACAAACAA
17707457 AACAACTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.20
Consensus pattern (21 bp):
GATTTAAAACAACAAACAATC
Found at i:17707420 original size:41 final size:42
Alignment explanation
Indices: 17707361--17707457 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
17707351 GAATTAAGTT
* *
17707361 AAACAAAAAAGAAACGATT-AAAGAAGAAAAAAAAT-GATTTA
1 AAACAAAAAACAAACGATTGAAAGAAG-AAAAAAATCCATTTA
* * * * *
17707402 AAACAACAAACAATCGATTGAAATAAGCAAAGAATCCATTTA
1 AAACAAAAAACAAACGATTGAAAGAAGAAAAAAATCCATTTA
*
17707444 AAACAATAAACAAA
1 AAACAAAAAACAAA
17707458 ACAACTTATA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 22 0.49
42 23 0.51
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.15
Consensus pattern (42 bp):
AAACAAAAAACAAACGATTGAAAGAAGAAAAAAATCCATTTA
Found at i:17707635 original size:20 final size:20
Alignment explanation
Indices: 17707610--17707732 Score: 81
Period size: 20 Copynumber: 6.0 Consensus size: 20
17707600 GTTGGAATCT
17707610 GAATCGAGTT-AAACAACAAA
1 GAATCGA-TTAAAACAACAAA
* * * *
17707630 GAATCGATTCAAATAATAAT
1 GAATCGATTAAAACAACAAA
*
17707650 GAATCGATTAAAGA-AGCAAA
1 GAATCGATTAAA-ACAACAAA
**
17707670 GAATTTATTTAAAACAAC-AA
1 GAATCGA-TTAAAACAACAAA
* *
17707690 GCAATCGATTGAAACTAGCAAA
1 G-AATCGATTAAAAC-AACAAA
*
17707712 GAATTGATTTAAAACAACAAA
1 GAATCGA-TTAAAACAACAAA
17707733 CAATTGATTC
Statistics
Matches: 78, Mismatches: 17, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
19 2 0.03
20 43 0.55
21 24 0.31
22 9 0.12
ACGTcount: A:0.53, C:0.12, G:0.13, T:0.22
Consensus pattern (20 bp):
GAATCGATTAAAACAACAAA
Found at i:17707713 original size:42 final size:41
Alignment explanation
Indices: 17707611--17707777 Score: 140
Period size: 42 Copynumber: 4.0 Consensus size: 41
17707601 TTGGAATCTG
* * * * **
17707611 AATCGAGTTAAACAA-CAAAGAATCGA-TTCAAATAATAATG
1 AATCGA-TTAAACAAGCAAAGAATTGATTTAAAACAACAAAC
* * *
17707651 AATCGATTAAAGAAGCAAAGAATTTATTTAAAACAACAAGC
1 AATCGATTAAACAAGCAAAGAATTGATTTAAAACAACAAAC
*
17707692 AATCGATTGAAACTAGCAAAGAATTGATTTAAAACAACAAAC
1 AATCGATT-AAACAAGCAAAGAATTGATTTAAAACAACAAAC
* * * * * * *
17707734 AATTGATTCAAAGAAGTACATAATCGATTTAAAACAACGAAC
1 AATCGATT-AAACAAGCAAAGAATTGATTTAAAACAACAAAC
17707776 AA
1 AA
17707778 ACCTAACTTA
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
39 7 0.07
40 15 0.15
41 17 0.17
42 64 0.62
ACGTcount: A:0.53, C:0.13, G:0.12, T:0.22
Consensus pattern (41 bp):
AATCGATTAAACAAGCAAAGAATTGATTTAAAACAACAAAC
Found at i:17707732 original size:21 final size:21
Alignment explanation
Indices: 17707666--17707741 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
17707656 ATTAAAGAAG
*
17707666 CAAAGAATTTATTTAAAACAA
1 CAAAGAATTGATTTAAAACAA
* * *
17707687 C-AAGCAATCGA-TTGAAACTAG
1 CAAAG-AATTGATTTAAAAC-AA
17707708 CAAAGAATTGATTTAAAACAA
1 CAAAGAATTGATTTAAAACAA
*
17707729 CAAACAATTGATT
1 CAAAGAATTGATT
17707742 CAAAGAAGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
20 9 0.21
21 25 0.58
22 9 0.21
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (21 bp):
CAAAGAATTGATTTAAAACAA
Found at i:17708042 original size:42 final size:42
Alignment explanation
Indices: 17707949--17708142 Score: 196
Period size: 42 Copynumber: 4.7 Consensus size: 42
17707939 AGTTAAACAA
* * ** * *
17707949 CAAAGAATCAA-TTCAAACAATAATGAATAGATT-AAAAAAG
1 CAAAGAATCAATTTAAAACAACAAACAATCGATTCAAAGAAG
* **
17707989 CAAAGAATCAATTTAAAACAACAAGA-AATCGATTGAAATTAG
1 CAAAGAATCAATTTAAAACAACAA-ACAATCGATTCAAAGAAG
* * * *
17708031 CAACGATTCAATTTAAAATAACAAATAATCGATTCAAAGAAG
1 CAAAGAATCAATTTAAAACAACAAACAATCGATTCAAAGAAG
* ** * *
17708073 CAAAGATTTGATTTAAAATAACAAACAATCAATTCAAAGAAG
1 CAAAGAATCAATTTAAAACAACAAACAATCGATTCAAAGAAG
17708115 CAAAGAATCAATTTAAAACAACAAACAA
1 CAAAGAATCAATTTAAAACAACAAACAA
17708143 ACCTAGCTCA
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 11 0.09
41 18 0.14
42 100 0.78
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (42 bp):
CAAAGAATCAATTTAAAACAACAAACAATCGATTCAAAGAAG
Found at i:17708139 original size:21 final size:21
Alignment explanation
Indices: 17707943--17708139 Score: 102
Period size: 21 Copynumber: 9.5 Consensus size: 21
17707933 GAATAGAGTT
*
17707943 AAACAACAAAGAATCAA-TTC
1 AAACAACAAAGAATCAATTTA
* *
17707963 AAACAATAATGAAT-AGA-TTA
1 AAACAACAAAGAATCA-ATTTA
17707983 AAA-AAGCAAAGAATCAATTTA
1 AAACAA-CAAAGAATCAATTTA
* *
17708004 AAACAAC-AAGAAATCGATTGA
1 AAACAACAAAG-AATCAATTTA
** * * *
17708025 AATTAGCAACGATTCAATTTA
1 AAACAACAAAGAATCAATTTA
* * * *
17708046 AAATAACAAATAATCGATTCA
1 AAACAACAAAGAATCAATTTA
* * **
17708067 AAGA-AGCAAAGATTTGATTTA
1 AA-ACAACAAAGAATCAATTTA
* * *
17708088 AAATAACAAACAATCAATTCA
1 AAACAACAAAGAATCAATTTA
*
17708109 AAGA-AGCAAAGAATCAATTTA
1 AA-ACAACAAAGAATCAATTTA
17708130 AAACAACAAA
1 AAACAACAAA
17708140 CAAACCTAGC
Statistics
Matches: 130, Mismatches: 36, Indels: 21
0.70 0.19 0.11
Matches are distributed among these distances:
19 3 0.02
20 30 0.23
21 91 0.70
22 6 0.05
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (21 bp):
AAACAACAAAGAATCAATTTA
Found at i:17708542 original size:47 final size:47
Alignment explanation
Indices: 17708479--17708577 Score: 141
Period size: 47 Copynumber: 2.1 Consensus size: 47
17708469 TTAATAACCC
17708479 CAATACCAGTAGTCACATAAGTTGGT-TTTCCATTTCAAA-AACAACAA
1 CAATACCAGTAGTCACATAAGTTGGTCTTT-CATTT-AAACAACAACAA
*
17708526 CAATACCAGGTA-TCACATAAGTTGGTCTTTCATTTAAACAACAAGAA
1 CAATACCA-GTAGTCACATAAGTTGGTCTTTCATTTAAACAACAACAA
17708573 CAATA
1 CAATA
17708578 TTACAAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
46 3 0.06
47 39 0.81
48 6 0.12
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (47 bp):
CAATACCAGTAGTCACATAAGTTGGTCTTTCATTTAAACAACAACAA
Found at i:17708870 original size:3 final size:3
Alignment explanation
Indices: 17708852--17708892 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
17708842 GCATCTCCAT
17708852 TTC TTC -TC TTAC -TC TTC TTC -TC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
17708893 CCTCCTCCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.15
3 28 0.82
4 1 0.03
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:17708871 original size:14 final size:14
Alignment explanation
Indices: 17708852--17708915 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
17708842 GCATCTCCAT
17708852 TTCTTCTCTTAC-TC
1 TTCTTCTCTT-CTTC
17708866 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
*
17708880 TTCTTCTTCTTCTCC
1 TTCTTC-TCTTCTTC
* * * *
17708895 TCCTCCTCCTCCTC
1 TTCTTCTCTTCTTC
17708909 TTCTTCT
1 TTCTTCT
17708916 TCTATTGCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 1 0.03
14 28 0.70
15 11 0.28
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:17710570 original size:20 final size:20
Alignment explanation
Indices: 17710534--17710571 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17710524 GAGATTCAAA
*
17710534 TTTTTATATTATTTTAATAG
1 TTTTTATATTATATTAATAG
17710554 TTTTCTATATTA-ATTAAT
1 TTTT-TATATTATATTAAT
17710572 TTTTTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTTATATTATATTAATAG
Found at i:17710613 original size:16 final size:15
Alignment explanation
Indices: 17710594--17710624 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
17710584 TTTTAAAACG
17710594 TTATTTTTTTTCTCAA
1 TTATTTTTTTT-TCAA
17710610 TTATTTTTTTTTCAA
1 TTATTTTTTTTTCAA
17710625 AAACAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTTTTTTTCAA
Found at i:17713013 original size:13 final size:13
Alignment explanation
Indices: 17712995--17713019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17712985 TTAAAACTAA
17712995 AATTAACTAAATT
1 AATTAACTAAATT
17713008 AATTAACTAAAT
1 AATTAACTAAAT
17713020 AACACGATAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Done.