Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 61 of 131
Found at i:19956282 original size:44 final size:44
Alignment explanation
Indices: 19956217--19956429 Score: 381
Period size: 44 Copynumber: 4.8 Consensus size: 44
19956207 ACTGGAATCA
*
19956217 CAAAACCTAGCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTG
1 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
19956261 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
1 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
*
19956305 CAAAACCTAGCTCCTTGACCAGCAGTGGAATAGGTTGAAGATTG
1 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
19956349 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
1 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
* * *
19956393 CAAAATCTAGCTCCTTAACCAGCAGTGGAATAGGTTG
1 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTG
19956430 GAAATCACAG
Statistics
Matches: 163, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 163 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (44 bp):
CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
Found at i:19956484 original size:132 final size:132
Alignment explanation
Indices: 19956217--19956484 Score: 326
Period size: 132 Copynumber: 2.0 Consensus size: 132
19956207 ACTGGAATCA
*
19956217 CAAAACCTAGCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAAACCTAGCTCCCTGACCA
1 CAAAACCTAGCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAAACCTAGCTCCCTAACCA
* * ** * * *
19956282 GCAGTGGAATAGGTTGAAGATTGCAAAACCTAGCTCCTTGACCAGCAGTGGAATAGGTTGAAGAT
66 GCAGTGGAATAGGTTGAAGATTGCAAAACCTAGCTCCCTAACCAGCAGCAGAATAGATGGAAGAC
*
19956347 TG
131 GG
* * *
19956349 CAAAACCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAAATCTAGCTCCTTAACCA
1 CAAAACCTAGCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAAACCTAGCTCCCTAACCA
* * * * * *
19956414 GCAGTGGAATAGGTTGGAA-A-T-CACAGATCTTGTCTCCCTAAGCAGTAGCAGAGTAGATGGAA
66 GCAGTGGAATAGGTT-GAAGATTGCA-AAACCTAG-CTCCCTAACCAGCAGCAGAATAGATGGAA
19956476 GACGG
128 GACGG
19956481 CAAA
1 CAAA
19956485 TCTTATCTTC
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 2 0.02
131 6 0.05
132 104 0.90
133 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (132 bp):
CAAAACCTAGCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAAACCTAGCTCCCTAACCA
GCAGTGGAATAGGTTGAAGATTGCAAAACCTAGCTCCCTAACCAGCAGCAGAATAGATGGAAGAC
GG
Found at i:19956571 original size:129 final size:129
Alignment explanation
Indices: 19956412--19956792 Score: 626
Period size: 129 Copynumber: 3.0 Consensus size: 129
19956402 GCTCCTTAAC
* * *
19956412 CAGCAGTGGAATAGGTT-GGAAATCACAGATCTTGTCTCCCTAAGCAGTAGCAGAGTAGAT-GGA
1 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCGAA
19956475 AGACGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGTTCTATATCCCTGGT
66 AG-CGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGTTCTATATCCCTGGT
*
19956540 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCGAA
1 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCGAA
19956605 AGCGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGTTCTATATCCCTGGT
66 AGCGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGTTCTATATCCCTGGT
* *
19956669 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCTTAAGCAGTAGCAGAGCAGATTGAA
1 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCGAA
* * * * *
19956734 AGCAGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTCAAGCAACAAG-TCT-TATCCCT
66 AGCGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGTTCTATATCCCT
19956793 CTGAAGTCAT
Statistics
Matches: 239, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
127 7 0.03
128 20 0.08
129 208 0.87
130 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (129 bp):
CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCGAA
AGCGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGTTCTATATCCCTGGT
Found at i:19956851 original size:44 final size:44
Alignment explanation
Indices: 19956803--19957106 Score: 147
Period size: 44 Copynumber: 7.0 Consensus size: 44
19956793 CTGAAGTCAT
* *
19956803 AGTGGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGAGGTTGC
1 AGTGGAGCAGACCGAAGAAGCAAATCTTATCTCCCTGAAGTTGC
* ** ** * *
19956847 AGTGGAGTAGATTGAAGTCG-ATAATCCTATCTCCCTGAAGTTGT
1 AGTGGAGCAGACCGAAGAAGCA-AATCTTATCTCCCTGAAGTTGC
* *** * * * *
19956891 AGTAGAGCAGATTAAAGTAA-TAGATCTTATCTCTCTGAAGTTAC
1 AGTGGAGCAGACCGAAG-AAGCAAATCTTATCTCCCTGAAGTTGC
* ** * * * ** * *
19956935 AGTAGAGTGGATC---GCATCAGGTCTTATCTCCTTGAGGTTGC
1 AGTGGAGCAGACCGAAGAAGCAAATCTTATCTCCCTGAAGTTGC
* * * * **
19956976 TGTGGAGCAGACTG-AGAAAACAAGTCTTATC-CCCTTGAAGTCAC
1 AGTGGAGCAGACCGAAG-AAGCAAATCTTATCTCCC-TGAAGTTGC
* *
19957020 AGTGGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGAGGTTGC
1 AGTGGAGCAGACCGAAGAAGCAAATCTTATCTCCCTGAAGTTGC
** ** *
19957064 AGTGGAGCAGATTGAAGTCG-ATAATCCTATCTCCCTGAAGTTG
1 AGTGGAGCAGACCGAAGAAGCA-AATCTTATCTCCCTGAAGTTG
19957107 TAATAGAGCA
Statistics
Matches: 192, Mismatches: 57, Indels: 22
0.71 0.21 0.08
Matches are distributed among these distances:
40 1 0.01
41 26 0.14
43 5 0.03
44 154 0.80
45 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
AGTGGAGCAGACCGAAGAAGCAAATCTTATCTCCCTGAAGTTGC
Found at i:19957032 original size:217 final size:223
Alignment explanation
Indices: 19956777--19957432 Score: 812
Period size: 217 Copynumber: 2.9 Consensus size: 223
19956767 AGATTCAAGC
*
19956777 AACAAGTCTTAT-CCCTCTGAAGTCATAGTGGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGA
1 AACAAGTCTTATCCCCT-TGAAGTCACAGTGGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGA
19956841 GGTTGCAGTGGAGTAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTAGAGCAGATTAA
65 GGTTGCAGTGGAGTAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTAGAGCAGATTAA
* * * *
19956906 AGTAATA-GATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGA
130 AATAA-AGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGA
* * * *
19956970 GGTTGCTGTGG-AG-C-AG-A-CTGA-GAA
194 GATTACAGTGGAAGACAAGAATCTAACGAA
19956994 AACAAGTCTTATCCCCTTGAAGTCACAGTGGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGAG
1 AACAAGTCTTATCCCCTTGAAGTCACAGTGGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGAG
* *
19957059 GTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAATAGAGCAGATTAAA
66 GTTGCAGTGGAGTAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAA
* *
19957124 ATAAAGGATCTTATCTCTCTGAAATTATAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGA
131 ATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGA
19957189 TTACAGTGGAATAGACCAAAGAATTTCTAATCGAA
196 TTACAGTGG-A-AGA-C-AAGAA--TCTAA-CGAA
* * * * * ** * *
19957224 AATGGTGAA-TCTTATCTCCC-TGAGGTTACAGTGGAGTAGATTGAAGCCAG-AAATCGTATCTC
1 AA----CAAGTCTTATC-CCCTTGAAGTCACAGTGGGGCAGACCGAAG-AAGCAAATCTTATCTC
* * * * * ** *
19957286 CCTAAGATTACAGTTGAGTAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTACAGTGGAGCAG
60 CCTGAGGTTGCAGTGGAGTAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTAGAGCAG
*
19957351 ATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCAGGTCTTATCTCC
125 ATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAGGTCTTATCTCC
*
19957416 CTGAGATTATAGTGGAA
190 CTGAGATTACAGTGGAA
19957433 TAGACCGAAG
Statistics
Matches: 382, Mismatches: 36, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
216 1 0.00
217 185 0.48
218 4 0.01
220 2 0.01
222 1 0.00
224 2 0.01
225 1 0.00
228 3 0.01
230 5 0.01
231 1 0.00
232 1 0.00
233 169 0.44
234 7 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (223 bp):
AACAAGTCTTATCCCCTTGAAGTCACAGTGGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGAG
GTTGCAGTGGAGTAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAA
ATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGA
TTACAGTGGAAGACAAGAATCTAACGAA
Found at i:19957299 original size:44 final size:43
Alignment explanation
Indices: 19957231--19957353 Score: 158
Period size: 44 Copynumber: 2.8 Consensus size: 43
19957221 GAAAATGGTG
* *
19957231 AATCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAGA-
1 AATCCTATCTCCCT-AAGTTACAGTGGAGTAGATTGAAGCC-GAT
* *
19957275 AATCGTATCTCCCTAAGATTACAGTTGAGTAGATTGAAGCCGAT
1 AATCCTATCTCCCTAAG-TTACAGTGGAGTAGATTGAAGCCGAT
*
19957319 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATT
1 AATCCTATCTCCCT-AAGTTACAGTGGAGTAGATT
19957354 AAAATAAAGG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
43 4 0.06
44 63 0.90
45 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
AATCCTATCTCCCTAAGTTACAGTGGAGTAGATTGAAGCCGAT
Found at i:19957385 original size:88 final size:88
Alignment explanation
Indices: 19957231--19957396 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
19957221 GAAAATGGTG
* * * **
19957231 AATCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAGAAATCGTATCTCCCTAAGATTA
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAAACAGAAATCGTATCTCCCTAAGATTA
*
19957296 CAGTTGAGTAGATTGAAGCCGAT
66 CAGTAGAGTAGATTGAAGCCGAT
* * *
19957319 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATA-AAGGATCTTATCTCTCTGAA-A
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAAACAGAA--ATCGTATCTCCCT-AAGA
19957381 TTACAGTAGAGTAGAT
63 TTACAGTAGAGTAGAT
19957397 AGCATCAGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
86 2 0.03
87 3 0.05
88 59 0.89
89 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (88 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAAACAGAAATCGTATCTCCCTAAGATTA
CAGTAGAGTAGATTGAAGCCGAT
Found at i:19957407 original size:233 final size:233
Alignment explanation
Indices: 19957041--19957521 Score: 766
Period size: 233 Copynumber: 2.1 Consensus size: 233
19957031 CCGAAGAAGC
* * * *
19957041 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
** * *
19957106 GTAATAGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTATAGTAGAGTAGATCGCATCA
66 ACAATAGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCA
19957171 GGTCTTATCTCCCTAAGATTACAGTGGAATAGACCAAAGAA-TTTCTAATCGAAAATGGTGAATC
131 GGTCTTATCTCCCTAAGATTACAGTGGAATAGACCAAAGAACTTT-TAATCGAAAATGGTGAATC
*
19957235 TTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAG
195 TTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
* * *
19957274 AAATCGTATCTCCCTAAGATTACAGTTGAGTAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
* *
19957339 ACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCA
66 ACAATAGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCA
* * *
19957404 GGTCTTATCTCCCTGAGATTATAGTGGAATAGACCGAAGAACTTTTAATCGAAAATGGTGAATCT
131 GGTCTTATCTCCCTAAGATTACAGTGGAATAGACCAAAGAACTTTTAATCGAAAATGGTGAATCT
* * *
19957469 TATCTTCTTGAGGTTACCGTGGAGCAGATTGAAGCCAG
196 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
19957507 AAATCTTATCTCCCT
1 AAATCTTATCTCCCT
19957522 GTGGTACAGT
Statistics
Matches: 226, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
233 223 0.99
234 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (233 bp):
AAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
ACAATAGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCA
GGTCTTATCTCCCTAAGATTACAGTGGAATAGACCAAAGAACTTTTAATCGAAAATGGTGAATCT
TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
Found at i:19958056 original size:13 final size:13
Alignment explanation
Indices: 19958038--19958071 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
19958028 ATTGTCTGCT
19958038 ACACCTCCAACTC
1 ACACCTCCAACTC
19958051 ACACCTCCAACTC
1 ACACCTCCAACTC
19958064 ACACCTCC
1 ACACCTCC
19958072 GTACAGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.56, G:0.00, T:0.15
Consensus pattern (13 bp):
ACACCTCCAACTC
Found at i:19959079 original size:22 final size:19
Alignment explanation
Indices: 19959033--19959070 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19959023 ATTAATTAAT
19959033 TTACTA-TTATTATTTTTA
1 TTACTATTTATTATTTTTA
* *
19959051 TTGCTATTTATTATTGTTA
1 TTACTATTTATTATTTTTA
19959070 T
1 T
19959071 CATTACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (19 bp):
TTACTATTTATTATTTTTA
Found at i:19959595 original size:19 final size:19
Alignment explanation
Indices: 19959571--19959607 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19959561 ATTTGTTTGG
19959571 TGCTTTGATTGACCTTTAT
1 TGCTTTGATTGACCTTTAT
*
19959590 TGCTTTGATTGATCTTTA
1 TGCTTTGATTGACCTTTA
19959608 ATTCATTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (19 bp):
TGCTTTGATTGACCTTTAT
Found at i:19968318 original size:35 final size:35
Alignment explanation
Indices: 19968279--19968373 Score: 154
Period size: 35 Copynumber: 2.7 Consensus size: 35
19968269 TCAGTTGCAC
* *
19968279 TAGCTCTTATGAGCATTGGTGTGTTTTGGTGGGAT
1 TAGCTCTTATGAGCATTGGTGTGTTTTAGAGGGAT
*
19968314 TAGCTTTTATGAGCATTGGTGTGTTTTAGAGGGAT
1 TAGCTCTTATGAGCATTGGTGTGTTTTAGAGGGAT
*
19968349 TAGCTCTTACGAGCATTGGTGTGTT
1 TAGCTCTTATGAGCATTGGTGTGTT
19968374 GTAACACTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.17, C:0.09, G:0.32, T:0.42
Consensus pattern (35 bp):
TAGCTCTTATGAGCATTGGTGTGTTTTAGAGGGAT
Found at i:19970251 original size:67 final size:68
Alignment explanation
Indices: 19970143--19970277 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 68
19970133 CTTAGTTTTA
19970143 ACAACGGATTTAAGTAAAAAGGTGATAAATTACATAGG-AAAAATCCTATATATTTTTCCGTTTA
1 ACAACGGATTTAAGTAAAAAGGTGATAAATTACATAGGAAAAAATCCTATATATTTTTCCGTTTA
19970207 CAT
66 CAT
*
19970210 ACAACGGATTTAAGTAAAAAGGTGATAAATTACATAGGAAAAAATCTTATATATTTTTCCGTTTA
1 ACAACGGATTTAAGTAAAAAGGTGATAAATTACATAGGAAAAAATCCTATATATTTTTCCGTTTA
19970275 CAT
66 CAT
19970278 GTGTTTGGAC
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 38 0.58
68 28 0.42
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (68 bp):
ACAACGGATTTAAGTAAAAAGGTGATAAATTACATAGGAAAAAATCCTATATATTTTTCCGTTTA
CAT
Found at i:19973571 original size:11 final size:11
Alignment explanation
Indices: 19973552--19973581 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19973542 TATTATAAAG
19973552 AAAAA-ATGAT
1 AAAAAGATGAT
19973562 AAAAAGATGAT
1 AAAAAGATGAT
19973573 AAAAAGATG
1 AAAAAGATG
19973582 GAAACCCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (11 bp):
AAAAAGATGAT
Found at i:19974601 original size:25 final size:25
Alignment explanation
Indices: 19974573--19974645 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 25
19974563 CTCGATATAT
*
19974573 GGCTCTTTGGAGCTTCCTGATTAAA
1 GGCTCTTTGGAGCTTCCCGATTAAA
* *
19974598 GGCTCTTTCATGAGCTTCCCGATTAAT
1 GGCTCTTT--GGAGCTTCCCGATTAAA
*
19974625 GGCTCTCTGGAGCTTCCCGAT
1 GGCTCTTTGGAGCTTCCCGAT
19974646 ATTGGCTCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 20 0.49
27 21 0.51
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.34
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCCGATTAAA
Found at i:19974735 original size:25 final size:25
Alignment explanation
Indices: 19974681--19974774 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
19974671 ATTAGCTCGT
*
19974681 ATGAGCTTCCCGTTA-ATGGCTC-T
1 ATGAGCTTCCCGTTACATGGCTCAA
*
19974704 CTAGAGCTTCCCGTTACATGGCTCAA
1 AT-GAGCTTCCCGTTACATGGCTCAA
* **
19974730 ATGAGCTTCTCGTTTTATGGCTCAA
1 ATGAGCTTCCCGTTACATGGCTCAA
*
19974755 AAGAGCTTCCCGTTTACATG
1 ATGAGCTTCCCG-TTACATG
19974775 TCTGCATAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
23 1 0.02
24 13 0.23
25 37 0.65
26 6 0.11
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAA
Found at i:19981546 original size:6 final size:6
Alignment explanation
Indices: 19981535--19981559 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19981525 ATCAATAATC
19981535 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
19981560 TTTCACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:19982770 original size:17 final size:18
Alignment explanation
Indices: 19982744--19982780 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19982734 ACACAAGGTC
19982744 CACCACCTTCT-GAATAT
1 CACCACCTTCTGGAATAT
*
19982761 CACCAGCTTCTGGAATAT
1 CACCACCTTCTGGAATAT
19982779 CA
1 CA
19982781 GATGTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (18 bp):
CACCACCTTCTGGAATAT
Found at i:19986784 original size:14 final size:14
Alignment explanation
Indices: 19986746--19986784 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19986736 TTAGACCTTG
19986746 AACCCTGGACCCTA
1 AACCCTGGACCCTA
* *
19986760 GACCATGGACCCTA
1 AACCCTGGACCCTA
*
19986774 AACCCTAGACC
1 AACCCTGGACC
19986785 TTGGACCTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.41, G:0.15, T:0.13
Consensus pattern (14 bp):
AACCCTGGACCCTA
Found at i:19986789 original size:21 final size:21
Alignment explanation
Indices: 19986737--19986800 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
19986727 TCTTTAACTT
* *
19986737 TAGACCTTGAACCCTGGACCC
1 TAGACCTTGGACCCTGAACCC
* *
19986758 TAGACCATGGACCCTAAACCC
1 TAGACCTTGGACCCTGAACCC
*
19986779 TAGACCTTGGACCTTGAACCC
1 TAGACCTTGGACCCTGAACCC
19986800 T
1 T
19986801 TAAGTCTAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (21 bp):
TAGACCTTGGACCCTGAACCC
Found at i:19988981 original size:36 final size:36
Alignment explanation
Indices: 19988941--19989016 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
19988931 TGACATTATG
19988941 GAATA-AATTAATGA-ATGATTAATAGATAATTGAAGT
1 GAATATAA-TAATGAGATGATTAATAGATAA-TGAAGT
* * *
19988977 GAATATGATATTGAGTTGATTAATAGATAATGAAGT
1 GAATATAATAATGAGATGATTAATAGATAATGAAGT
19989013 GAAT
1 GAAT
19989017 GTGATATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 20 0.57
37 15 0.43
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (36 bp):
GAATATAATAATGAGATGATTAATAGATAATGAAGT
Found at i:19988989 original size:17 final size:17
Alignment explanation
Indices: 19988969--19989026 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
19988959 TTAATAGATA
19988969 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
19988986 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
* *
19989005 AATGAAGTGAATGTGAT
1 ATTGAAGTGAATATGAT
19989022 ATTGA
1 ATTGA
19989027 GTTATGAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.06
17 15 0.47
18 3 0.09
19 10 0.31
20 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:19989022 original size:36 final size:37
Alignment explanation
Indices: 19988956--19989029 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
19988946 AATTAATGAA
19988956 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
19988993 TGATTAATAGATAA-TGAAGTGAATGTGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
19989029 T
1 T
19989030 ATGAAACGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 22 0.61
37 14 0.39
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.38
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:19989042 original size:20 final size:21
Alignment explanation
Indices: 19989017--19989062 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
19989007 TGAAGTGAAT
19989017 GTGATATTGAG-TTATGAAAC
1 GTGATATTGAGATTATGAAAC
*
19989037 GTGATATTGAGATTATGAAAT
1 GTGATATTGAGATTATGAAAC
19989058 GTGAT
1 GTGAT
19989063 TTTATGGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (21 bp):
GTGATATTGAGATTATGAAAC
Found at i:19989186 original size:40 final size:40
Alignment explanation
Indices: 19989142--19989269 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
19989132 GGTTCATCCA
19989142 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
1 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
* * * * * *
19989182 ACTAGCGTTGGGCGCA--A---ATATCGTTGGTTTATCCA
1 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
* * *
19989217 ACTAAATCTGGGCTCACTATTTATATCGTCAGTTTA-TCTG
1 ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTC-G
*
19989257 ACTAGCGCTGGGC
1 ACTAGAGCTGGGC
19989270 ACAAATATCG
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
35 26 0.41
37 1 0.02
38 1 0.02
39 1 0.02
40 35 0.55
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (40 bp):
ACTAGAGCTGGGCTCACTATTTATATCGTCGGTTTATTCG
Found at i:19989217 original size:75 final size:75
Alignment explanation
Indices: 19989089--19989303 Score: 317
Period size: 75 Copynumber: 2.9 Consensus size: 75
19989079 TGAGTAATTG
* * * *
19989089 ATATTGTCGGTTCATTAGACTAGCGCTGGGCAC-AATCATCGTTGGTTCATCCAACTAGAGCTGG
1 ATATCGTCGGTTTATTCGACTAGCGCTGGGCACAAAT-ATCGTTGGTTTATCCAACTAGAGCTGG
19989153 GCTCACTATTT
65 GCTCACTATTT
* * * *
19989164 ATATCGTCGGTTTATTCGACTAGCGTTGGGCGCAAATATCGTTGGTTTATCCAACTAAATCTGGG
1 ATATCGTCGGTTTATTCGACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGGG
19989229 CTCACTATTT
66 CTCACTATTT
*
19989239 ATATCGTCAGTTTA-TCTGACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGG
1 ATATCGTCGGTTTATTC-GACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGG
19989303 G
65 G
19989304 ATAACTGATT
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 2 0.02
75 120 0.96
76 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (75 bp):
ATATCGTCGGTTTATTCGACTAGCGCTGGGCACAAATATCGTTGGTTTATCCAACTAGAGCTGGG
CTCACTATTT
Found at i:19989229 original size:35 final size:35
Alignment explanation
Indices: 19989113--19989303 Score: 105
Period size: 35 Copynumber: 5.2 Consensus size: 35
19989103 TTAGACTAGC
* *
19989113 GCTGGGCAC-AATCATCGTTGGTTCATCCAACTAGA
1 GCTGGGCACAAAT-ATCGTTGGTTTATCCAACTAAA
* * * * **
19989148 GCTGGGCTCACTATTTATATCGTCGGTTTATTCGACTAGC
1 GCTGGG--CAC-A--AATATCGTTGGTTTATCCAACTAAA
* *
19989188 GTTGGGCGCAAATATCGTTGGTTTATCCAACTAAA
1 GCTGGGCACAAATATCGTTGGTTTATCCAACTAAA
* * ** ** **
19989223 TCTGGGCTCACTATTTATATCGTCAGTTTATCTGACTAGC
1 GCTGGG--CAC-A--AATATCGTTGGTTTATCCAACTAAA
*
19989263 GCTGGGCACAAATATCGTTGGTTTATCCAACTAGA
1 GCTGGGCACAAATATCGTTGGTTTATCCAACTAAA
19989298 GCTGGG
1 GCTGGG
19989304 ATAACTGATT
Statistics
Matches: 114, Mismatches: 31, Indels: 22
0.68 0.19 0.13
Matches are distributed among these distances:
35 54 0.47
37 7 0.06
38 6 0.05
40 45 0.39
41 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (35 bp):
GCTGGGCACAAATATCGTTGGTTTATCCAACTAAA
Found at i:19997143 original size:420 final size:421
Alignment explanation
Indices: 19996352--19997193 Score: 1668
Period size: 420 Copynumber: 2.0 Consensus size: 421
19996342 AACATCAGAA
*
19996352 TCATATAGTTCTTTAAGATATGCAAACCCAAGCAGTTTAGAATCTAAACTATCAAGTAAAGCATA
1 TCATATAGTTCCTTAAGATATGCAAACCCAAGCAGTTTAGAATCTAAACTATCAAGTAAAGCATA
19996417 CCTTCTTGATAATGCATTGACAACTATATTTTCCTTACCTTTCTTGTATTTGATGACATGGGGAA
66 CCTTCTTGATAATGCATTGACAACTATATTTTCCTTACCTTTCTTGTATTTGATGACATGGGGAA
19996482 AGGACTCAAGGTACTCGACCCACTTAGCATGCCTTTTATTTAGCTTGTGTTTTCCCTTAAGATGC
131 AGGACTCAAGGTACTCGACCCACTTAGCATGCCTTTTATTTAGCTTGTGTTTTCCCTTAAGATGC
19996547 TTCAATGCTTCATGGTTAGTGTGAATCACGAACTCCTTGGACCACAAATAGTGCTGCCAAGTTTC
196 TTCAATGCTTCATGGTTAGTGTGAATCACGAACTCCTTGGACCACAAATAGTGCTGCCAAGTTTC
19996612 TAGGGCTTGAATCAAAGCATACAACTCCTTGTCGTATGTTGGATAATTAAGGGCAACGTTGTTGA
261 TAGGGCTTGAATCAAAGCATACAACTCCTTGTCGTATGTTGGATAATTAAGGGCAACGTTGTTGA
19996677 GTTTCTTACTAAAGTAGGCAATAGGACATCCGACTTGTGTTAATACCGCTCTGATTCTTATCACT
326 GTTTCTTACTAAAGTAGGCAATAGGACATCCGACTTGTGTTAATACCGCTCTGATTCTTATCACT
19996742 GAGGCATCACACTCTAACTTGAAAGTGTTGT
391 GAGGCATCACACTCTAACTTGAAAGTGTTGT
19996773 TCATATAG-TCCTTAAGATATGCAAACCCAAGCAGTTTAGAATCTAAACTATCAAGTAAAGCATA
1 TCATATAGTTCCTTAAGATATGCAAACCCAAGCAGTTTAGAATCTAAACTATCAAGTAAAGCATA
19996837 CCTTCTTGATAATGCATTGACAACTATATTTTCCTTACCTTTCTTGTATTTGATGACATGGGGAA
66 CCTTCTTGATAATGCATTGACAACTATATTTTCCTTACCTTTCTTGTATTTGATGACATGGGGAA
19996902 AGGACTCAAGGTACTCGACCCACTTAGCATGCCTTTTATTTAGCTTGTGTTTTCCCTTAAGATGC
131 AGGACTCAAGGTACTCGACCCACTTAGCATGCCTTTTATTTAGCTTGTGTTTTCCCTTAAGATGC
19996967 TTCAATGCTTCATGGTTAGTGTGAATCACGAACTCCTTGGACCACAAATAGTGCTGCCAAGTTTC
196 TTCAATGCTTCATGGTTAGTGTGAATCACGAACTCCTTGGACCACAAATAGTGCTGCCAAGTTTC
19997032 TAGGGCTTGAATCAAAGCATACAACTCCTTGTCGTATGTTGGATAATTAAGGGCAACGTTGTTGA
261 TAGGGCTTGAATCAAAGCATACAACTCCTTGTCGTATGTTGGATAATTAAGGGCAACGTTGTTGA
19997097 GTTTCTTACTAAAGTAGGCAATAGGACATCCGACTTGTGTTAATACCGCTCTGATTCTTATCACT
326 GTTTCTTACTAAAGTAGGCAATAGGACATCCGACTTGTGTTAATACCGCTCTGATTCTTATCACT
19997162 GAGGCATCACACTCTAACTTGAAAGTGTTGT
391 GAGGCATCACACTCTAACTTGAAAGTGTTGT
19997193 T
1 T
19997194 AAAGTCAGGT
Statistics
Matches: 420, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
420 412 0.98
421 8 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (421 bp):
TCATATAGTTCCTTAAGATATGCAAACCCAAGCAGTTTAGAATCTAAACTATCAAGTAAAGCATA
CCTTCTTGATAATGCATTGACAACTATATTTTCCTTACCTTTCTTGTATTTGATGACATGGGGAA
AGGACTCAAGGTACTCGACCCACTTAGCATGCCTTTTATTTAGCTTGTGTTTTCCCTTAAGATGC
TTCAATGCTTCATGGTTAGTGTGAATCACGAACTCCTTGGACCACAAATAGTGCTGCCAAGTTTC
TAGGGCTTGAATCAAAGCATACAACTCCTTGTCGTATGTTGGATAATTAAGGGCAACGTTGTTGA
GTTTCTTACTAAAGTAGGCAATAGGACATCCGACTTGTGTTAATACCGCTCTGATTCTTATCACT
GAGGCATCACACTCTAACTTGAAAGTGTTGT
Found at i:20012410 original size:105 final size:105
Alignment explanation
Indices: 20012294--20012504 Score: 406
Period size: 105 Copynumber: 2.0 Consensus size: 105
20012284 AAATTTTAAT
20012294 TTTTTATTTTAATAAAGGGGGGTCAAA-TTTGGCCCAAGTACTAATCAGTTTTTTTAGTAAGATA
1 TTTTTATTTTAATAAAGGGGGGTCAAATTTTGGCCCAAGT-CTAATCAGTTTTTTTAGTAAGATA
20012358 CAATCTAAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAA
65 CAATCTAAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAA
20012399 TTTTTATTTTAATAAAGGGGGGTCAAATTTTGGCCCAAGTCTAATCAGTTTTTTTAGTAAGATAC
1 TTTTTATTTTAATAAAGGGGGGTCAAATTTTGGCCCAAGTCTAATCAGTTTTTTTAGTAAGATAC
20012464 AATCTAAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAA
66 AATCTAAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAA
20012504 T
1 T
20012505 ATCCATGCCT
Statistics
Matches: 105, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 93 0.89
106 12 0.11
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (105 bp):
TTTTTATTTTAATAAAGGGGGGTCAAATTTTGGCCCAAGTCTAATCAGTTTTTTTAGTAAGATAC
AATCTAAGTTTGAGGCCCAAGACAGCAAAAAGGAGGGAAA
Found at i:20019553 original size:21 final size:21
Alignment explanation
Indices: 20019528--20019571 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
20019518 ATCTTCGAGG
*
20019528 ATATGCAATCTTAGATATGAT
1 ATATGCAATCATAGATATGAT
20019549 ATATGCAATCATAGATATGAT
1 ATATGCAATCATAGATATGAT
20019570 AT
1 AT
20019572 GTAACCTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGCAATCATAGATATGAT
Found at i:20019582 original size:19 final size:19
Alignment explanation
Indices: 20019527--20019582 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
20019517 AATCTTCGAG
20019527 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
20019546 GATATATGCAATCATAGATAT
1 G--ATATGCAATCTTAGATAT
* *
20019567 GATATGTAACCTTAGA
1 GATATGCAATCTTAGA
20019583 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:20019589 original size:22 final size:23
Alignment explanation
Indices: 20019561--20019605 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
20019551 ATGCAATCAT
20019561 AGATATGA-TATGTAACCTTAGA
1 AGATATGATTATGTAACCTTAGA
* *
20019583 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAACCTTAGA
20019606 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGTAACCTTAGA
Found at i:20019615 original size:22 final size:23
Alignment explanation
Indices: 20019571--20019615 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20019561 AGATATGATA
*
20019571 TGTAACCTTAGAAGATATGATTT
1 TGTAACCTTAGAAGATATAATTT
* *
20019594 TGTAATCTTAG-AGATTTAATTT
1 TGTAACCTTAGAAGATATAATTT
20019616 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (23 bp):
TGTAACCTTAGAAGATATAATTT
Found at i:20025727 original size:26 final size:26
Alignment explanation
Indices: 20025696--20025747 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20025686 ATTATGCATA
*
20025696 AATTCATATATTCTTTTGTAAAGTCT
1 AATTCATATATTCCTTTGTAAAGTCT
20025722 AATTCATATATTCCTTTGTAAAGTCT
1 AATTCATATATTCCTTTGTAAAGTCT
20025748 TTGGTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (26 bp):
AATTCATATATTCCTTTGTAAAGTCT
Found at i:20028033 original size:44 final size:44
Alignment explanation
Indices: 20027985--20028128 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 44
20027975 AATAGCAGAT
* *
20027985 CTTGCCTTCCTGCACTGACAGTGAAGTAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACTGACAGCGAAGTAGATCGAAGACACCAGC
*** * * * * * * *
20028029 CTTGCCTCCCTGGGTTG-CAGCGGAGCAG-GCTGAAAATAGCAGAT
1 CTTGCCTCCCTGCACTGACAGCGAAGTAGATC-GAAGACACCAG-C
* * * *
20028073 CTTGCCTTCCTGCACCGACAACGAAGTAGATCGAAGTCACCAGC
1 CTTGCCTCCCTGCACTGACAGCGAAGTAGATCGAAGACACCAGC
20028117 CTTGCCTCCCTG
1 CTTGCCTCCCTG
20028129 GGTTGTAGTG
Statistics
Matches: 69, Mismatches: 27, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
42 1 0.01
43 16 0.23
44 36 0.52
45 15 0.22
46 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (44 bp):
CTTGCCTCCCTGCACTGACAGCGAAGTAGATCGAAGACACCAGC
Found at i:20028479 original size:88 final size:88
Alignment explanation
Indices: 20027892--20028469 Score: 798
Period size: 88 Copynumber: 6.6 Consensus size: 88
20027882 GTGAAGATAA
* * * * * * ** *
20027892 CAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACTAGTCTTGCCTCCATCTGTG
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
20027957 GCAGCAGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
20027980 CAGATCTTGCCTTCCTGCACTGACAGTGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
20028045 GCAGCGGAGCAGGCTGAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
20028068 CAGATCTTGCCTTCCTGCACCGACAACGAAGTAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
20028133 GTAGTGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
20028156 CAGATCTTGCCTTCCTTCACCGACAGCTAAGCATATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
20028221 GTAGCGGAGCAGGCTGAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * *
20028244 TAGATCTTGCCTTCCTGCACCGGA-AACGAAGCAAATCGAAGTCACCAGCCTTGCCTCCCTGGGT
1 CAGATCTTGCCTTCCTGCACC-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
* *
20028308 TGTAGTGGAGCAGGCTAAAAATAG
65 TGCAGCGGAGCAGGCTAAAAATAG
*
20028332 CAGATCTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
20028397 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * * * *
20028420 TAAATCTTGCCTTCCTGCACTGACAGCGAAGCAGATTGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
20028470 CTATCTCCCT
Statistics
Matches: 440, Mismatches: 48, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 2 0.00
88 436 0.99
89 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGCTAAAAATAG
Found at i:20028535 original size:44 final size:44
Alignment explanation
Indices: 20028469--20028844 Score: 419
Period size: 44 Copynumber: 8.7 Consensus size: 44
20028459 TGACCCCAGC
* *
20028469 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
20028513 CCTATCTCCTTGGACAGGAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * *
20028557 CCTATCTCCCTGGTCAACAGTGGAAGAGGTTAAAGATTGAGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
20028601 TCTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
20028639 CTTATCTCCCTGGACAGCAGTGGAATAGATTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
20028683 CCTATCTCCCTGGTA-AGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGG-ACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * * *
20028727 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGA-AT
* * * * * *
20028771 CCTATCTCCCTAGTCAGCAGTGGAATAGGATGAAGATCGTGAAC
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
20028815 CCTATCTCCCT-GAGCAGCAGTGGAGTAGGT
1 CCTATCTCCCTGGA-CAGCAGTGGAATAGGT
20028845 GGAAAATAGC
Statistics
Matches: 283, Mismatches: 38, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
38 32 0.11
39 2 0.01
40 1 0.00
42 1 0.00
43 4 0.01
44 241 0.85
45 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:20028674 original size:170 final size:170
Alignment explanation
Indices: 20028471--20028798 Score: 471
Period size: 170 Copynumber: 1.9 Consensus size: 170
20028461 ACCCCAGCCC
* * * *
20028471 TATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCTTGG-ACAGGAGTG
1 TATCTCCCTAGACAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGGTA-AGCAGTG
* * *
20028535 GAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAACAGTGGAAGAGGTTAAAGATTG-AGA
65 GAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAACAGTGGAAGAGATTAAAGATTGTAG-
* *
20028599 ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAATCT
129 ATCCTATCTCCCTAGGCAGCAGTGGAATAGATTAAAGAATCT
*
20028641 TATCTCCCTGGACAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGGTAAGCAGTGG
1 TATCTCCCTAGACAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGGTAAGCAGTGG
* * * * * *
20028706 AATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAGGT
66 AATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAACAGTGGAAGAGATTAAAGATTGTAGAT
*
20028771 CCTATCTCCCTAGTCAGCAGTGGAATAG
131 CCTATCTCCCTAGGCAGCAGTGGAATAG
20028799 GATGAAGATC
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
170 136 0.98
171 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (170 bp):
TATCTCCCTAGACAGCAGTGGAATAGATTAAAGATTGTGAATCCTATCTCCCTGGTAAGCAGTGG
AATAGGTTAAAGATTGAGAATCCTATCTCCCTGGGCAACAGTGGAAGAGATTAAAGATTGTAGAT
CCTATCTCCCTAGGCAGCAGTGGAATAGATTAAAGAATCT
Found at i:20028677 original size:126 final size:129
Alignment explanation
Indices: 20028470--20028826 Score: 463
Period size: 126 Copynumber: 2.7 Consensus size: 129
20028460 GACCCCAGCC
* * * * * *
20028470 CTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCTTGGACAGGAGTG
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA---TGAATCCTATCTCCCTGGACAGCAGTG
*
20028535 GAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAA-CAGTGGAAGAGGTTAAAGATTGAGA
63 GAATAGATTAAAGATTGTGAATCCTATCTCCCTGGT-AAGCAGTGGAAGAGGTTAAAGATTGAGA
20028599 ATT
127 ATT
*
20028602 CTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A-GAATCTTATCTCCCTGGACAGCAGTGGAA
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATGAATCCTATCTCCCTGGACAGCAGTGGAA
* *
20028664 TAGATTAAAGATTGTGAATCCTATCTCCCTGGTAAGCAGTGGAATAGGTTGAAGATTGAGAATT
66 TAGATTAAAGATTGTGAATCCTATCTCCCTGGTAAGCAGTGGAAGAGGTTAAAGATTGAGAATT
* * *
20028728 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAGGTCCTATCTCCCTAGTCAGCAGTG
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA-TG-A-ATCCTATCTCCCTGGACAGCAGTG
* * *
20028793 GAATAGGA-TGAAGATCGTGAACCCTATCTCCCTG
63 GAATA-GATTAAAGATTGTGAATCCTATCTCCCTG
20028827 AGCAGCAGTG
Statistics
Matches: 201, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
125 2 0.01
126 114 0.57
127 2 0.01
128 1 0.00
130 2 0.01
131 3 0.01
132 75 0.37
133 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (129 bp):
CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATGAATCCTATCTCCCTGGACAGCAGTGGAA
TAGATTAAAGATTGTGAATCCTATCTCCCTGGTAAGCAGTGGAAGAGGTTAAAGATTGAGAATT
Found at i:20029632 original size:17 final size:18
Alignment explanation
Indices: 20029618--20029701 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 18
20029608 ATAATCTTTG
20029618 AGGATATGCAATCTTAGA
1 AGGATATGCAATCTTAGA
*
20029636 TATGATATGCAATCTTAGA
1 -AGGATATGCAATCTTAGA
*
20029655 TATGATATATGCAATCTTAGA
1 -A-G-GATATGCAATCTTAGA
* * *
20029676 TATGATATGTAACCTTAGA
1 -AGGATATGCAATCTTAGA
20029695 A-GATATG
1 AGGATATG
20029702 ATTTTGTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
17 6 0.11
18 1 0.02
19 32 0.57
21 17 0.30
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.35
Consensus pattern (18 bp):
AGGATATGCAATCTTAGA
Found at i:20029644 original size:19 final size:19
Alignment explanation
Indices: 20029620--20029694 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
20029610 AATCTTTGAG
20029620 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
20029639 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
20029658 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
* *
20029679 GATATGTAACCTTAGA
1 GATATGCAATCTTAGA
20029695 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 33 0.63
21 19 0.37
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:20029666 original size:21 final size:21
Alignment explanation
Indices: 20029621--20029683 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
20029611 ATCTTTGAGG
20029621 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
20029640 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
20029661 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
20029682 AT
1 AT
20029684 GTAACCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.45
21 23 0.55
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:20029701 original size:22 final size:23
Alignment explanation
Indices: 20029673--20029717 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
20029663 ATGCAATCTT
20029673 AGATATGA-TATGTAACCTTAGA
1 AGATATGATTATGTAACCTTAGA
* *
20029695 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAACCTTAGA
20029718 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGTAACCTTAGA
Found at i:20029727 original size:22 final size:23
Alignment explanation
Indices: 20029683--20029727 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20029673 AGATATGATA
*
20029683 TGTAACCTTAGAAGATATGATTT
1 TGTAACCTTAGAAGATATAATTT
* *
20029706 TGTAATCTTAG-AGATTTAATTT
1 TGTAACCTTAGAAGATATAATTT
20029728 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (23 bp):
TGTAACCTTAGAAGATATAATTT
Found at i:20029960 original size:3 final size:3
Alignment explanation
Indices: 20029952--20029991 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
20029942 ATTAATTTTG
*
20029952 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
20029992 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20029960 original size:15 final size:15
Alignment explanation
Indices: 20029936--20029990 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
20029926 GTTTTTAGTC
20029936 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
20029950 TGTTATTATTATTTT
1 TATTATTATTAATTT
20029965 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
20029979 ATATTATTATTA
1 -TATTATTATTA
20029991 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:20029967 original size:12 final size:12
Alignment explanation
Indices: 20029938--20029989 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
20029928 TTTTAGTCTA
20029938 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
20029950 TGTTATTATTAT
1 TTTTATTATTAT
20029962 TTTTATTATTAT
1 TTTTATTATTAT
20029974 ATTATATATTATTAT
1 -TT-T-TATTATTAT
20029989 T
1 T
20029990 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:20033414 original size:2 final size:2
Alignment explanation
Indices: 20033407--20033433 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20033397 CAATAATAGA
20033407 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 A
20033434 ATTTTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20039433 original size:46 final size:44
Alignment explanation
Indices: 20039366--20039455 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 44
20039356 AACAGATACA
*
20039366 CGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAATGATATC
1 CGGTGGATTCAGCACACAGCAACCA-CC-TTATAATCAATGATATC
* *
20039412 CGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAATGATATC
1 CGGT-GGATTCAGCACACAGCAACCACCTTATAATCAATGATATC
20039456 GGTTCACATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 15 0.38
45 2 0.05
46 20 0.50
47 3 0.08
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (44 bp):
CGGTGGATTCAGCACACAGCAACCACCTTATAATCAATGATATC
Found at i:20045219 original size:16 final size:16
Alignment explanation
Indices: 20045198--20045229 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20045188 GTTCTGTTGC
*
20045198 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
20045214 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
20045230 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:20045517 original size:51 final size:51
Alignment explanation
Indices: 20045462--20045640 Score: 181
Period size: 51 Copynumber: 3.5 Consensus size: 51
20045452 CACATAGTAG
* *
20045462 CATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGCCTGCA
1 CATAGTACTACACACGTGACCATCACTATCAGATACACGTAGTAGCCTGCA
* * *
20045513 CATAGTACTACACACGTGATCGA--AGCTATCCAGTATGCA--TAGTAGCCTGTA
1 CATAGTACTACACACGTGA-CCATCA-CTAT-CAG-ATACACGTAGTAGCCTGCA
* * * * *
20045564 CATAGTACTACACATGCGACCTATCA-T-TCCGATAAACGTAGTAGCCTACA
1 CATAGTACTACACACGTGACC-ATCACTATCAGATACACGTAGTAGCCTGCA
20045614 CATAGTACTACACACGTGACCATCACT
1 CATAGTACTACACACGTGACCATCACT
20045641 TTCACTTTCA
Statistics
Matches: 103, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
48 3 0.03
49 6 0.06
50 33 0.32
51 52 0.50
52 4 0.04
53 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
CATAGTACTACACACGTGACCATCACTATCAGATACACGTAGTAGCCTGCA
Found at i:20047229 original size:17 final size:17
Alignment explanation
Indices: 20047203--20047235 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20047193 TTTAAAAAGG
20047203 TTTTTTATAT-AGTGAT
1 TTTTTTATATGAGTGAT
20047219 TTTTGTTATATGAGTGA
1 TTTT-TTATATGAGTGA
20047236 GTTATTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (17 bp):
TTTTTTATATGAGTGAT
Found at i:20048382 original size:20 final size:19
Alignment explanation
Indices: 20048335--20048383 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
20048325 TTTATTGAAA
*
20048335 ATGAATCAATATATATGTT
1 ATGAAACAATATATATGTT
*
20048354 AT-AATACAATTTATCATGTT
1 ATGAA-ACAATATAT-ATGTT
20048374 ATGAAACAAT
1 ATGAAACAAT
20048384 GTAAATCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 12 0.48
21 2 0.08
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (19 bp):
ATGAAACAATATATATGTT
Found at i:20053714 original size:42 final size:42
Alignment explanation
Indices: 20053538--20053740 Score: 195
Period size: 42 Copynumber: 4.8 Consensus size: 42
20053528 AACTCACACA
* * * *
20053538 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCATATATCG
*
20053580 ATGCCAATAG--CCAG-CTATGGTCTTACAAGAATC-TCATATCG
1 ATGCCAAT-GTCCCAGAC-ATGGTCTTACACGAATCAT-ATATCG
* * *
20053621 ATGCCAATGTCGCAGACATGGTCTCACACGAATC-TCATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCAT-ATATCG
*
20053663 ATGCTAATGTCCCAGACATGGTCTTACACGAATCATATAAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATAT-ATCG
* *
20053705 ATCCCAATGTCCCAGACATGGTGTTACACGTAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCA
20053741 CATCTCAGTA
Statistics
Matches: 136, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.01
41 17 0.12
42 106 0.78
43 11 0.08
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATATCG
Found at i:20079087 original size:17 final size:18
Alignment explanation
Indices: 20079055--20079090 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20079045 TACTTCAATC
*
20079055 TCTTTTTCAATTTTCTTT
1 TCTTTTTCAATATTCTTT
20079073 TCTTTTTCAA-ATTCTTT
1 TCTTTTTCAATATTCTTT
20079090 T
1 T
20079091 TCACTCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTTTTTCAATATTCTTT
Found at i:20079177 original size:22 final size:24
Alignment explanation
Indices: 20079126--20079178 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
20079116 TTTCACTCTC
*
20079126 TTTCGCTT-TTTCAATTTCTTGTT
1 TTTCGTTTCTTTCAATTTCTTGTT
20079149 TTT--TTTCTTTC-ATTTCTT-TT
1 TTTCGTTTCTTTCAATTTCTTGTT
20079169 TTTCGTTTCT
1 TTTCGTTTCT
20079179 CGATTTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 9 0.35
23 3 0.12
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.72
Consensus pattern (24 bp):
TTTCGTTTCTTTCAATTTCTTGTT
Found at i:20084239 original size:29 final size:29
Alignment explanation
Indices: 20084197--20084258 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
20084187 CAACATCCTC
* *
20084197 GGTGATTTGAAGTCCACCCGACCTACCAA
1 GGTGATTTCAAGTCCACCCGACCCACCAA
* *
20084226 GGTGATTTCAAGTCCCCCCGACCCACCAC
1 GGTGATTTCAAGTCCACCCGACCCACCAA
20084255 GGTG
1 GGTG
20084259 CTTAACGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (29 bp):
GGTGATTTCAAGTCCACCCGACCCACCAA
Found at i:20084532 original size:23 final size:23
Alignment explanation
Indices: 20084506--20084556 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
20084496 CTATAAAAGT
20084506 AGACATAATTGTGCTATAGAAAC
1 AGACATAATTGTGCTATAGAAAC
20084529 AGACATAATTGTGCTATAGAAAC
1 AGACATAATTGTGCTATAGAAAC
20084552 AGACA
1 AGACA
20084557 AAACCATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (23 bp):
AGACATAATTGTGCTATAGAAAC
Found at i:20088939 original size:11 final size:12
Alignment explanation
Indices: 20088919--20088958 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
20088909 TAAATGGTTC
20088919 ATTTATATATTT
1 ATTTATATATTT
*
20088931 -TTTAAATATTT
1 ATTTATATATTT
20088942 ATTTATATATTAT
1 ATTTATATATT-T
20088955 ATTT
1 ATTT
20088959 TTAGCTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATATATTT
Found at i:20094611 original size:96 final size:97
Alignment explanation
Indices: 20094436--20094628 Score: 379
Period size: 96 Copynumber: 2.0 Consensus size: 97
20094426 AGAGCATTAC
20094436 CGAACAATCAGAACAACATTTAACATCAAAACATCTCAATAAAATAATTTTACATTAATTAAATA
1 CGAACAATCAGAACAACATTTAACATCAAAACATCTCAATAAAATAATTTTACATTAATTAAATA
20094501 AATCTTATTAAAAACTTATCAAACATATGCAT
66 AATCTTATTAAAAACTTATCAAACATATGCAT
20094533 CGAACAATCA-AACAACATTTAACATCAAAACATCTCAATAAAATAATTTTACATTAATTAAATA
1 CGAACAATCAGAACAACATTTAACATCAAAACATCTCAATAAAATAATTTTACATTAATTAAATA
20094597 AATCTTATTAAAAACTTATCAAACATATGCAT
66 AATCTTATTAAAAACTTATCAAACATATGCAT
20094629 TTAGGCCAAA
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 86 0.90
97 10 0.10
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.30
Consensus pattern (97 bp):
CGAACAATCAGAACAACATTTAACATCAAAACATCTCAATAAAATAATTTTACATTAATTAAATA
AATCTTATTAAAAACTTATCAAACATATGCAT
Found at i:20122234 original size:19 final size:19
Alignment explanation
Indices: 20122207--20122248 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20122197 AAAATTAATT
*
20122207 TTAATCAAATTAAATT-AAA
1 TTAACCAAATT-AATTAAAA
20122226 TTAACCAAATTAATTAAAA
1 TTAACCAAATTAATTAAAA
20122245 TTAA
1 TTAA
20122249 TATGATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAACCAAATTAATTAAAA
Found at i:20122879 original size:25 final size:25
Alignment explanation
Indices: 20122837--20122884 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
20122827 TTGTAGAGAG
20122837 AAAATTCTCTAAAGATATTATTTCAA
1 AAAATTCTCTAAAGATATT-TTTCAA
* *
20122863 AAAATT-TCTAGATATATTTTTC
1 AAAATTCTCTAAAGATATTTTTC
20122885 TTATTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 10 0.50
26 6 0.30
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (25 bp):
AAAATTCTCTAAAGATATTTTTCAA
Found at i:20128786 original size:49 final size:49
Alignment explanation
Indices: 20128714--20128811 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
20128704 TGAGTAACAT
20128714 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
1 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
20128763 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
1 GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
20128812 ATCTTTCTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.18
Consensus pattern (49 bp):
GAACCAAACACAACAAAGAAACAATGTAATTACTTTCAATAGGAAAGTA
Found at i:20130393 original size:75 final size:75
Alignment explanation
Indices: 20130270--20130419 Score: 246
Period size: 75 Copynumber: 2.0 Consensus size: 75
20130260 TCTATGCCTC
20130270 TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
1 TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
*
20130335 TGGCATATTA
66 TGACATATTA
* * * * *
20130345 TATCTTCTTAGAGTCATAAGCTTCGATGTTTAAGACAAAGCATCTCTCCAATTGGACTTGATAGA
1 TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
20130410 TGACATATTA
66 TGACATATTA
20130420 GTCTTTCAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (75 bp):
TATCTTCTCAGAGTCATAAGCTTCAATATTCAAGACAAAGCATCTCTCCAATTGGACTTGATAAA
TGACATATTA
Found at i:20134502 original size:25 final size:24
Alignment explanation
Indices: 20134474--20134529 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
20134464 GCGAGCCATT
20134474 TATCGAGAAGCTCAAGAGAGTCAAA
1 TATCG-GAAGCTCAAGAGAGTCAAA
**
20134499 TATCGGAAAGCTCGTGAGAGTCAAA
1 TATCGG-AAGCTCAAGAGAGTCAAA
20134524 TATCGG
1 TATCGG
20134530 GATGCTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (24 bp):
TATCGGAAGCTCAAGAGAGTCAAA
Found at i:20135715 original size:21 final size:22
Alignment explanation
Indices: 20135674--20135716 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
20135664 TAAATAAATG
20135674 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
20135697 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
20135717 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:20135862 original size:26 final size:27
Alignment explanation
Indices: 20135811--20135867 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
20135801 ACAAAATAGC
* *
20135811 AAAATGAAAATAGGGGAGAAAGGAAAG
1 AAAAAGAAAATAGGGAAGAAAGGAAAG
20135838 AAAAAGAAAA-AGGGAAGGAAA-GAAAG
1 AAAAAGAAAATAGGGAA-GAAAGGAAAG
20135864 AAAA
1 AAAA
20135868 TTTGCGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.04
Consensus pattern (27 bp):
AAAAAGAAAATAGGGAAGAAAGGAAAG
Found at i:20136795 original size:21 final size:19
Alignment explanation
Indices: 20136749--20136804 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
20136739 AATCTTCAAG
*
20136749 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
20136768 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
20136787 GATATATGCAATCTTAGA
1 G--ATATGCAATCTTAGA
20136805 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 18 0.56
21 14 0.44
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:20136808 original size:24 final size:23
Alignment explanation
Indices: 20136762--20136827 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
20136752 ATGTAATCTT
*
20136762 AGATATGA-TATGCAGTCTT---
1 AGATATGATTATGCAATCTTAGA
20136781 AGATATGATATATGCAATCTTAGA
1 AGATATGAT-TATGCAATCTTAGA
* *
20136805 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
20136828 GATTTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 8 0.21
21 10 0.26
23 12 0.31
24 9 0.23
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:20136826 original size:23 final size:24
Alignment explanation
Indices: 20136781--20136827 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
20136771 ATGCAGTCTT
20136781 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
20136805 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
20136828 GATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:20137056 original size:23 final size:23
Alignment explanation
Indices: 20137012--20137056 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
20137002 TCTTATTTTG
* *
20137012 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
20137035 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
20137057 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:20139234 original size:50 final size:50
Alignment explanation
Indices: 20139122--20139368 Score: 201
Period size: 50 Copynumber: 4.8 Consensus size: 50
20139112 ATTTGGGTAA
* *
20139122 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* * *
20139178 AGAGGTCTCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
20139228 AGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * ** *
20139278 AGAACTCCCATGTATGACCATATCTGGGATACGGCATTGGCA-TTATA-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
20139326 AAAACATCCCATGTAAGACCATGTCTAGGACATGGCCTTGGCA
1 -AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
20139369 TGTTATTGTC
Statistics
Matches: 158, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.23
50 79 0.50
52 1 0.01
53 2 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:20148487 original size:35 final size:36
Alignment explanation
Indices: 20148421--20148496 Score: 136
Period size: 35 Copynumber: 2.1 Consensus size: 36
20148411 TTTATTACCA
*
20148421 GTTTAAGGTTTAGTTAGTATTTTTATCAAAAAAAAG
1 GTTTAAGGTTTAGTCAGTATTTTTATCAAAAAAAAG
20148457 GTTTAAGGTTTAGTCAGTA-TTTTATCAAAAAAAAG
1 GTTTAAGGTTTAGTCAGTATTTTTATCAAAAAAAAG
20148492 GTTTA
1 GTTTA
20148497 GGCAGTAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 21 0.54
36 18 0.46
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (36 bp):
GTTTAAGGTTTAGTCAGTATTTTTATCAAAAAAAAG
Found at i:20148524 original size:14 final size:14
Alignment explanation
Indices: 20148505--20148548 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
20148495 TAGGCAGTAG
*
20148505 AAGAAGAAAAGAAA
1 AAGAAGAAGAGAAA
* *
20148519 AAGAAGAGGAGAAG
1 AAGAAGAAGAGAAA
20148533 AAGAAGAAGAGAAA
1 AAGAAGAAGAGAAA
20148547 AA
1 AA
20148549 AATGGAAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAGAAA
Found at i:20149285 original size:26 final size:26
Alignment explanation
Indices: 20149249--20149300 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
20149239 CAAATTGCAG
20149249 ATGAAAAATACCAATTGGTTTCTAAC
1 ATGAAAAATACCAATTGGTTTCTAAC
20149275 ATGAAAAATACCAATTGGTTTCTAAC
1 ATGAAAAATACCAATTGGTTTCTAAC
20149301 CCTTAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
ATGAAAAATACCAATTGGTTTCTAAC
Found at i:20149652 original size:3 final size:3
Alignment explanation
Indices: 20149639--20149674 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
20149629 TTTTACAGTC
*
20149639 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
20149675 GTTATTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:20150794 original size:19 final size:20
Alignment explanation
Indices: 20150772--20150813 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
20150762 TTTATATCAA
*
20150772 TTTTAATATTTTTA-TATTT
1 TTTTAACATTTTTATTATTT
*
20150791 TTTTACCATTTTTATTATTT
1 TTTTAACATTTTTATTATTT
20150811 TTT
1 TTT
20150814 AAGAATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTAACATTTTTATTATTT
Found at i:20150892 original size:19 final size:19
Alignment explanation
Indices: 20150870--20150929 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
20150860 TTTCATTATT
*
20150870 TTTTTATAATTTATTAGAA
1 TTTTTATAATTTTTTAGAA
* **
20150889 TTTTTATATTTTTTTACCA
1 TTTTTATAATTTTTTAGAA
*
20150908 TTTTTATTATTTTTTAAGAA
1 TTTTTATAATTTTTT-AGAA
20150928 TT
1 TT
20150930 CTAATACGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 28 0.88
20 4 0.12
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTATAATTTTTTAGAA
Found at i:20151018 original size:10 final size:9
Alignment explanation
Indices: 20150991--20151116 Score: 77
Period size: 9 Copynumber: 14.1 Consensus size: 9
20150981 AGATTTTTCT
20150991 ATTTTTATA
1 ATTTTTATA
*
20151000 ATATTTATA
1 ATTTTTATA
20151009 AGTTTTTATA
1 A-TTTTTATA
20151019 TATTTTTATA
1 -ATTTTTATA
*
20151029 ATTTTAATA
1 ATTTTTATA
*
20151038 AGTTTATATCA
1 A-TTTTTAT-A
*
20151049 ATTTTAAT-
1 ATTTTTATA
20151057 A-TTTT-TA
1 ATTTTTATA
*
20151064 ATATTTA-A
1 ATTTTTATA
20151072 TATTTTTAT-
1 -ATTTTTATA
* *
20151081 ATTTGTTCTT
1 ATTT-TTATA
20151091 ATTTTTAT-
1 ATTTTTATA
*
20151099 ATTTTTATG
1 ATTTTTATA
20151108 A-TTTTATA
1 ATTTTTATA
20151116 A
1 A
20151117 AAAAAATTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 24 0.26
9 31 0.34
10 29 0.32
11 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:20151026 original size:20 final size:18
Alignment explanation
Indices: 20150991--20151038 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
20150981 AGATTTTTCT
20150991 ATTTTTATAATATTTATA
1 ATTTTTATAATATTTATA
*
20151009 AGTTTTTATATATTTTTATA
1 A-TTTTTATA-ATATTTATA
*
20151029 ATTTTAATAA
1 ATTTTTATAA
20151039 GTTTATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTTTATAATATTTATA
Found at i:20151038 original size:29 final size:30
Alignment explanation
Indices: 20150990--20151066 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
20150980 TAGATTTTTC
*
20150990 TATTTTTATAATATTT-ATAAGTTTTTAT-A
1 TATTTTTATAAT-TTTAATAAGTTTATATCA
20151019 TATTTTTATAATTTTAATAAGTTTATATCA
1 TATTTTTATAATTTTAATAAGTTTATATCA
* *
20151049 -ATTTTAATATTTTTAATA
1 TATTTTTATAATTTTAATA
20151067 TTTAATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 3 0.07
29 39 0.91
30 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (30 bp):
TATTTTTATAATTTTAATAAGTTTATATCA
Found at i:20151111 original size:9 final size:8
Alignment explanation
Indices: 20150967--20151112 Score: 69
Period size: 8 Copynumber: 16.4 Consensus size: 8
20150957 AAGTTTTAAG
20150967 TTTTATGAT
1 TTTTAT-AT
*
20150976 TTATTAGAT
1 TT-TTATAT
*
20150985 TTTTCTAT
1 TTTTATAT
20150993 TTTTATAAT
1 TTTTAT-AT
*
20151002 ATTTATAAGTT
1 TTTTAT-A--T
20151013 TTTATATAT
1 TTT-TATAT
20151022 TTTTATAAT
1 TTTTAT-AT
*
20151031 TTTAATAAGT
1 TTTTAT-A-T
*
20151041 TTATATCAAT
1 TTTTAT--AT
*
20151051 TTTAATAT
1 TTTTATAT
20151059 TTTTA-AT
1 TTTTATAT
*
20151066 ATTTAATAT
1 -TTTTATAT
20151075 TTTTATAT
1 TTTTATAT
*
20151083 TTGTTCTTAT
1 TT-TT-ATAT
20151093 TTTTATAT
1 TTTTATAT
20151101 TTTTATGAT
1 TTTTAT-AT
20151110 TTT
1 TTT
20151113 ATAAAAAAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
7 2 0.02
8 40 0.37
9 39 0.36
10 18 0.17
11 6 0.06
12 3 0.03
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (8 bp):
TTTTATAT
Found at i:20152714 original size:27 final size:27
Alignment explanation
Indices: 20152676--20152766 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
20152666 GGCCATGACA
*
20152676 TACTTTGAATGGATCGCCTTTGTGGCG
1 TACTCTGAATGGATCGCCTTTGTGGCG
* **
20152703 TACTCTGAATGGTTCGCCTTAATGGCG
1 TACTCTGAATGGATCGCCTTTGTGGCG
* * * * *
20152730 TACTTTGTAT-GATTGCCTGTGTGGTG
1 TACTCTGAATGGATCGCCTTTGTGGCG
*
20152756 TATTCTGAATG
1 TACTCTGAATG
20152767 AAGGCTTTAT
Statistics
Matches: 48, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
26 17 0.35
27 31 0.65
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.40
Consensus pattern (27 bp):
TACTCTGAATGGATCGCCTTTGTGGCG
Found at i:20158249 original size:14 final size:14
Alignment explanation
Indices: 20158230--20158256 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20158220 ATGGAAAAAA
20158230 AATTTAGGTACCAG
1 AATTTAGGTACCAG
20158244 AATTTAGGTACCA
1 AATTTAGGTACCA
20158257 ATCTGGGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
AATTTAGGTACCAG
Found at i:20162463 original size:25 final size:25
Alignment explanation
Indices: 20162433--20162482 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20162423 AAGTAATCCA
20162433 CCCACTGAGAATTGCAAAGATCAAG
1 CCCACTGAGAATTGCAAAGATCAAG
20162458 CCCACTGAGAATTGCAAAGATCAAG
1 CCCACTGAGAATTGCAAAGATCAAG
20162483 TATTGGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (25 bp):
CCCACTGAGAATTGCAAAGATCAAG
Found at i:20163377 original size:16 final size:16
Alignment explanation
Indices: 20163358--20163389 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20163348 TCATGAGTAG
20163358 GGGTGTTCATTCGGTT
1 GGGTGTTCATTCGGTT
20163374 GGGTGTTCATTCGGTT
1 GGGTGTTCATTCGGTT
20163390 AACCGACCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.38, T:0.44
Consensus pattern (16 bp):
GGGTGTTCATTCGGTT
Found at i:20163572 original size:9 final size:9
Alignment explanation
Indices: 20163558--20163606 Score: 89
Period size: 9 Copynumber: 5.4 Consensus size: 9
20163548 TTTGGTTAAA
20163558 AATTAACCG
1 AATTAACCG
20163567 AATTAACCG
1 AATTAACCG
20163576 AATTAACCG
1 AATTAACCG
*
20163585 AATTACCCG
1 AATTAACCG
20163594 AATTAACCG
1 AATTAACCG
20163603 AATT
1 AATT
20163607 GAATCCACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:20163658 original size:12 final size:13
Alignment explanation
Indices: 20163626--20163673 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
20163616 ACATAATAAA
* *
20163626 TTATTTTTGGACT
1 TTATTTTTAGATT
*
20163639 TTAGTTTTAG-TT
1 TTATTTTTAGATT
20163651 TTATTTTTAGAATT
1 TTATTTTTAG-ATT
20163665 TTATTTTTA
1 TTATTTTTA
20163674 TTTATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 10 0.34
13 8 0.28
14 11 0.38
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (13 bp):
TTATTTTTAGATT
Found at i:20164599 original size:27 final size:27
Alignment explanation
Indices: 20164569--20164633 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
20164559 GCCTATCAAT
20164569 GCGCCAATGAAGGTGCCTCACAGAGAG
1 GCGCCAATGAAGGTGCCTCACAGAGAG
*
20164596 GCGCCAATGAAGGTGCCTCATAGAGAG
1 GCGCCAATGAAGGTGCCTCACAGAGAG
20164623 GCGCCAATGAA
1 GCGCCAATGAA
20164634 TATTGTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.32, T:0.12
Consensus pattern (27 bp):
GCGCCAATGAAGGTGCCTCACAGAGAG
Found at i:20167974 original size:132 final size:132
Alignment explanation
Indices: 20167777--20168055 Score: 470
Period size: 132 Copynumber: 2.1 Consensus size: 132
20167767 GCAACTTCAA
* * *
20167777 GGAGATAGGAA-TACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCT
1 GGAGATA-GAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGGAAAAACCACCATCT
*
20167841 TCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCC
65 TCGATCTACTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCC
20167906 CAG
130 CAG
* * *
20167909 GGAGATAGAATTACTGGCTTTAATGCACTCCACTGTAACCTCCGGGAGGGAAAAACCCCCATCTT
1 GGAGATAGAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGGAAAAACCACCATCTT
*
20167974 CGATCTGCTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCCC
66 CGATCTACTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCCC
20168039 AG
131 AG
20168041 GGAGATAGAATTACT
1 GGAGATAGAATTACT
20168056 TTCTTCGATC
Statistics
Matches: 138, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
131 3 0.02
132 135 0.98
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (132 bp):
GGAGATAGAATTACTGGCTTCAATGCACTCCACTGTAACCTCAGGGAGGGAAAAACCACCATCTT
CGATCTACTCCACTACTGCCTAAGGAGATAAGATCTGTAAACTTCAATCTATTCCACTGCTGCCC
AG
Found at i:20168109 original size:44 final size:44
Alignment explanation
Indices: 20168054--20168453 Score: 372
Period size: 44 Copynumber: 9.0 Consensus size: 44
20168044 GATAGAATTA
* *
20168054 CTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* * ***
20168098 CTTTATTCGATCTACTTCGACACCAGTATGGGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTG
* * *
20168143 GTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* ***
20168187 CTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTG
* * *
20168232 GTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* * *** *
20168276 CTTTCTTCGATCTGCTTCACCACCAGTATGGGAAGACAATATCTG
1 CTTTCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTG
* * ** * *
20168321 GTATCTTTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTG
1 CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* * * * *** *
20168365 CTTTCTTTGACCTGCTTTGC-CACCAGTATGGGAAGGCAAGATCTG
1 CTTTCTTCGATCTAC-TT-CACGCCAGTACATGAAGACAAGATCTG
* * *
20168410 GTATC-TCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTG
1 CTTTCTTC-GATCTACTTCACGCCAGTACATGAAGACAAGATCTG
20168454 TTATCTTTGA
Statistics
Matches: 277, Mismatches: 72, Indels: 14
0.76 0.20 0.04
Matches are distributed among these distances:
43 1 0.00
44 142 0.51
45 133 0.48
46 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
Found at i:20168463 original size:89 final size:89
Alignment explanation
Indices: 20168057--20168453 Score: 607
Period size: 89 Copynumber: 4.5 Consensus size: 89
20168047 AGAATTACTT
* * * *
20168057 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTGCTTTATTCGATCTACTTCGA-CAC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC-ACCAC
20168121 CAGTATGGGAAGACAAGATCTGGTA
65 CAGTATGGGAAGACAAGATCTGGTA
* *
20168146 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
20168211 AGTATGGGAAGACAAGATCTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
*
20168235 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
*
20168300 AGTATGGGAAGACAATATCTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
* * * * * * **
20168324 TCTTTAATCTACTTCAAGCCAGTACATAAAGACAAGATCTGCTTTCTTTGACCTGCTTTGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
*
20168389 AGTATGGGAAGGCAAGATCTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
* *
20168413 TCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTG
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
20168454 TTATCTTTGA
Statistics
Matches: 287, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
88 1 0.00
89 286 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (89 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
AGTATGGGAAGACAAGATCTGGTA
Found at i:20168470 original size:22 final size:22
Alignment explanation
Indices: 20168439--20168481 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20168429 CTCCAGTACA
*
20168439 TGAAGACAAGATCTGTTATCTT
1 TGAAGACAAGATCTGGTATCTT
*
20168461 TGAAGGCAAGATCTGGTATCT
1 TGAAGACAAGATCTGGTATCT
20168482 CTGATCTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (22 bp):
TGAAGACAAGATCTGGTATCTT
Found at i:20168502 original size:66 final size:66
Alignment explanation
Indices: 20168396--20168639 Score: 479
Period size: 66 Copynumber: 3.7 Consensus size: 66
20168386 ACCAGTATGG
20168396 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTGTTATCTT
1 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTGTTATCTT
20168461 T
66 T
*
20168462 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTT
1 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTGTTATCTT
20168527 T
66 T
20168528 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTGTTATCTT
1 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTGTTATCTT
20168593 T
66 T
20168594 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGA
1 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGA
20168640 GATAAGGCTT
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 176 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (66 bp):
GAAGGCAAGATCTGGTATCTCTGATCTACTTCACTCCAGTACATGAAGACAAGATCTGTTATCTT
T
Found at i:20168536 original size:22 final size:22
Alignment explanation
Indices: 20168505--20168613 Score: 69
Period size: 22 Copynumber: 5.0 Consensus size: 22
20168495 CGCCAGTACA
*
20168505 TGAAGACAAGATCTGTTATCTT
1 TGAAGACAAGATCTGGTATCTT
* *
20168527 TGAAGGCAAGATCTGGTATCTC
1 TGAAGACAAGATCTGGTATCTT
** *** ** *
20168549 TGATCTACTTCACTCCAGTA-C-A
1 TGA-AGACAAGA-TCTGGTATCTT
*
20168571 TGAAGACAAGATCTGTTATCTT
1 TGAAGACAAGATCTGGTATCTT
*
20168593 TGAAGGCAAGATCTGGTATCT
1 TGAAGACAAGATCTGGTATCT
20168614 CTGATCTACT
Statistics
Matches: 60, Mismatches: 23, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
20 4 0.07
21 4 0.07
22 44 0.73
23 3 0.05
24 5 0.08
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (22 bp):
TGAAGACAAGATCTGGTATCTT
Found at i:20169341 original size:22 final size:22
Alignment explanation
Indices: 20169313--20169355 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20169303 CTTTCTGCCG
*
20169313 ATTTAGGTACCACAAGACTACT
1 ATTTAGGTACAACAAGACTACT
20169335 ATTTAGGTACAACAAGACTAC
1 ATTTAGGTACAACAAGACTAC
20169356 CACATGCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (22 bp):
ATTTAGGTACAACAAGACTACT
Found at i:20176562 original size:20 final size:20
Alignment explanation
Indices: 20176537--20176576 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20176527 TAAAGGTCTA
*
20176537 TAATGCATATAATGTGATGC
1 TAATGCATATAATGCGATGC
*
20176557 TAATGCATATGATGCGATGC
1 TAATGCATATAATGCGATGC
20176577 ATGAGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
TAATGCATATAATGCGATGC
Found at i:20182691 original size:31 final size:29
Alignment explanation
Indices: 20182622--20182691 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
20182612 ACCTCAGATT
* *
20182622 ACATTTTAGTCACTTATATTTGAAATGTT
1 ACATTTTAGTCACTTACATTTGAAATGTA
* * *
20182651 ATATTTTAGTCACTTACATTATCGTATTGTA
1 ACATTTTAGTCACTTACATT-T-GAAATGTA
20182682 ACATTTTAGT
1 ACATTTTAGT
20182692 TACTGAGCCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 18 0.55
30 1 0.03
31 14 0.42
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (29 bp):
ACATTTTAGTCACTTACATTTGAAATGTA
Found at i:20183033 original size:203 final size:203
Alignment explanation
Indices: 20182684--20183094 Score: 795
Period size: 203 Copynumber: 2.0 Consensus size: 203
20182674 GTATTGTAAC
*
20182684 ATTTTAGTTACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
1 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
20182749 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
66 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
20182814 AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTCTTATTTTCCATTATCTTTTGTTT
131 AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTCTTATTTTCCATTATCTTTTGTTT
20182879 CTCCCTCT
196 CTCCCTCT
20182887 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
1 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
*
20182952 TTATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
66 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
*
20183017 AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTCTTATTTTCCATTCTCTTTTGTTT
131 AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTCTTATTTTCCATTATCTTTTGTTT
20183082 CTCCCTCT
196 CTCCCTCT
20183090 ATTTT
1 ATTTT
20183095 CCTCCCTTTT
Statistics
Matches: 205, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
203 205 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (203 bp):
ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTCTTATTTTCCATTATCTTTTGTTT
CTCCCTCT
Found at i:20187996 original size:17 final size:17
Alignment explanation
Indices: 20187970--20188009 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
20187960 GAATGGAGGT
*
20187970 AAATTAAGATCATTTTG
1 AAATTCAGATCATTTTG
20187987 AAATTCAGATCATTTTG
1 AAATTCAGATCATTTTG
20188004 AAATTC
1 AAATTC
20188010 TACTTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (17 bp):
AAATTCAGATCATTTTG
Found at i:20189598 original size:20 final size:20
Alignment explanation
Indices: 20189561--20189599 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20189551 AATGACTTGG
*
20189561 AAAATTTTAATTTCGAGACC
1 AAAATTTTAAATTCGAGACC
20189581 AAAATTTTTAAATT-GAGAC
1 AAAA-TTTTAAATTCGAGAC
20189600 GTTTCGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAATTTTAAATTCGAGACC
Found at i:20195448 original size:27 final size:27
Alignment explanation
Indices: 20195380--20195451 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
20195370 GGAAATCATA
* *
20195380 TAGAGTACGCCACCAAGGCATTCCATT
1 TAGAGTTCGCCACAAAGGCATTCCATT
* * ** * *
20195407 CAGAATTTTCTACAAAGGCATTCCTTT
1 TAGAGTTCGCCACAAAGGCATTCCATT
20195434 TAGAGTTCGCCACAAAGG
1 TAGAGTTCGCCACAAAGG
20195452 TTATTCTTAC
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (27 bp):
TAGAGTTCGCCACAAAGGCATTCCATT
Found at i:20200737 original size:14 final size:14
Alignment explanation
Indices: 20200718--20200756 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
20200708 ATAACGGTGA
20200718 TAATAATAATAAAT
1 TAATAATAATAAAT
*
20200732 TAATAATAATAGAT
1 TAATAATAATAAAT
20200746 TAATAATAATA
1 TAATAATAATA
20200757 TTACTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:20200739 original size:17 final size:17
Alignment explanation
Indices: 20200717--20200756 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20200707 AATAACGGTG
20200717 ATAATAATA-ATAAATTA
1 ATAATAATAGATAAA-TA
*
20200734 ATAATAATAGATTAATA
1 ATAATAATAGATAAATA
20200751 ATAATA
1 ATAATA
20200757 TTACTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAATAATAGATAAATA
Found at i:20201377 original size:23 final size:20
Alignment explanation
Indices: 20201334--20201383 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 20
20201324 TTTCCTAAAC
20201334 AAAGAAACTGAAAAAAAGAA
1 AAAGAAACTGAAAAAAAGAA
*
20201354 AAAGAACAGTGAAGAAAAACGAA
1 AAAGAA-ACTGAA-AAAAA-GAA
20201377 AAAGAAA
1 AAAGAAA
20201384 AAAACGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 5 0.19
22 6 0.23
23 9 0.35
ACGTcount: A:0.72, C:0.06, G:0.18, T:0.04
Consensus pattern (20 bp):
AAAGAAACTGAAAAAAAGAA
Found at i:20201836 original size:17 final size:15
Alignment explanation
Indices: 20201805--20201839 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
20201795 AAAACTGAAC
20201805 ATTTTATTATTATTT
1 ATTTTATTATTATTT
20201820 ATTTTA-TA-TATTT
1 ATTTTATTATTATTT
20201833 ATTTTAT
1 ATTTTAT
20201840 ATCTGGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.58
14 2 0.11
15 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTATTATTATTT
Found at i:20213605 original size:36 final size:36
Alignment explanation
Indices: 20213552--20213623 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
20213542 GAATTCTTTC
20213552 TTCTTGATTTTTCAGCTCCTGTCCAGCAGCCAAACA
1 TTCTTGATTTTTCAGCTCCTGTCCAGCAGCCAAACA
20213588 TTCTTGA-TTTTCTAGCTCCTGTCCAGCAGCCAAACA
1 TTCTTGATTTTTC-AGCTCCTGTCCAGCAGCCAAACA
20213624 CTCAGTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 5 0.14
36 30 0.86
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (36 bp):
TTCTTGATTTTTCAGCTCCTGTCCAGCAGCCAAACA
Found at i:20215642 original size:10 final size:10
Alignment explanation
Indices: 20215627--20215655 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
20215617 GAATTAGTCT
20215627 GTTTCCTAAA
1 GTTTCCTAAA
20215637 GTTTCCTAAA
1 GTTTCCTAAA
20215647 GTTTCCTAA
1 GTTTCCTAA
20215656 GTTAGGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (10 bp):
GTTTCCTAAA
Found at i:20223757 original size:11 final size:13
Alignment explanation
Indices: 20223741--20223773 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20223731 ATTTCACGGA
20223741 AAAATTTCG-T-G
1 AAAATTTCGTTCG
20223752 AAAATTTCGTTCG
1 AAAATTTCGTTCG
20223765 AAAATTTCG
1 AAAATTTCG
20223774 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (13 bp):
AAAATTTCGTTCG
Found at i:20224474 original size:28 final size:30
Alignment explanation
Indices: 20224438--20224493 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
20224428 TCCGAGATTT
*
20224438 GGGGAAAAAT-GTAAATTTGC-AAAGTTTA
1 GGGGAAAAATCATAAATTTGCTAAAGTTTA
* *
20224466 GGGGCAAAATCATAATTTTGCTAAAGTT
1 GGGGAAAAATCATAAATTTGCTAAAGTT
20224494 CGAGTCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
29 8 0.35
30 6 0.26
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (30 bp):
GGGGAAAAATCATAAATTTGCTAAAGTTTA
Found at i:20225217 original size:50 final size:50
Alignment explanation
Indices: 20225049--20225284 Score: 339
Period size: 50 Copynumber: 4.7 Consensus size: 50
20225039 NNNNNNNNNN
* * ***
20225049 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * *
20225100 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
*
20225151 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
*
20225201 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGCT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
20225251 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
20225285 TATCGAATGA
Statistics
Matches: 167, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
49 3 0.02
50 87 0.52
51 73 0.44
52 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:20227077 original size:22 final size:22
Alignment explanation
Indices: 20227050--20227091 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20227040 TTAACTATAC
20227050 TTTTTAGCACATATTCCTTTGT
1 TTTTTAGCACATATTCCTTTGT
* *
20227072 TTTTTAGCACGTTTTCCTTT
1 TTTTTAGCACATATTCCTTT
20227092 CTCTTTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.10, T:0.57
Consensus pattern (22 bp):
TTTTTAGCACATATTCCTTTGT
Found at i:20232241 original size:7 final size:6
Alignment explanation
Indices: 20232225--20232272 Score: 69
Period size: 6 Copynumber: 7.7 Consensus size: 6
20232215 TCACATATTT
*
20232225 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AATAAAG AGCAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG A-AAAAG AAAA
20232273 GTTTAATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:20239951 original size:51 final size:50
Alignment explanation
Indices: 20239824--20240011 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 50
20239814 TATCATTCGA
* * * * **
20239824 TACACGTATTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
* * *
20239874 TTCACGTAGTAGCCTACACATAGTACTAGACACGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA-CCTTCCGG
* * * * *
20239925 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATC-TCTCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-AACCTTC-CGG
*
20239976 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTG
20240012 GTTATAGGCA
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
50 39 0.34
51 76 0.66
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
Found at i:20243512 original size:35 final size:35
Alignment explanation
Indices: 20243466--20243537 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
20243456 CCCGGAAAAC
20243466 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
1 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
*
20243501 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCTAA
1 TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
20243536 TT
1 TT
20243538 AATAATTGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.38
Consensus pattern (35 bp):
TTCTAACCTCGGGTACATTCTTTGGCTGCTCCCAA
Found at i:20247396 original size:50 final size:51
Alignment explanation
Indices: 20247334--20247517 Score: 194
Period size: 51 Copynumber: 3.6 Consensus size: 51
20247324 TATTATTCGA
** * ** *
20247334 TACACGTAGTAGCCTTAACATAGTACTACACACT-TGATCAAAATTTTCGGT
1 TACACGTAGTAGCCTGCACATAGTACTACACA-TGTGACCAAAACCTTCCGT
*
20247385 T-CATGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCGT
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCGT
* ** * *
20247435 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCT-TCCGT
* * *
20247486 TACAAGTAATAGCCTGCACTTAGTACTACACA
1 TACACGTAGTAGCCTGCACATAGTACTACACA
20247518 CGTGTTTATA
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 41 0.36
51 70 0.62
52 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCGT
Found at i:20254234 original size:33 final size:37
Alignment explanation
Indices: 20254165--20254258 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 37
20254155 GGGCACAGAA
*
20254165 AGTGCATACTGGCACATAAAGTGCATATTGACACACAT
1 AGTGCATACTGGCACATATAGTG-ATATTGACACACAT
*
20254203 TGTGCATACTGGCACATATAGTG-TA-T-A-ACACAT
1 AGTGCATACTGGCACATATAGTGATATTGACACACAT
* *
20254236 AGTGCATATTGGCACACATAGTG
1 AGTGCATACTGGCACATATAGTG
20254259 CATCATCGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 26 0.51
34 1 0.02
35 1 0.02
36 2 0.04
38 21 0.41
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (37 bp):
AGTGCATACTGGCACATATAGTGATATTGACACACAT
Found at i:20254254 original size:19 final size:19
Alignment explanation
Indices: 20254060--20254261 Score: 101
Period size: 19 Copynumber: 10.9 Consensus size: 19
20254050 AAGTCAATAT
20254060 TGGCACACATAGTGCATAC
1 TGGCACACATAGTGCATAC
** * ** *
20254079 TAACACA-AAATGTTAATAT
1 TGGCACACATA-GTGCATAC
***
20254098 TGGCACACATAACACATAC
1 TGGCACACATAGTGCATAC
* * * * *
20254117 TAGAACATAAAGTGCATGC
1 TGGCACACATAGTGCATAC
* * *
20254136 TAGCACAAATAGTTCATAC
1 TGGCACACATAGTGCATAC
* * *
20254155 GGGCACAGAAAGTGCATAC
1 TGGCACACATAGTGCATAC
* * *
20254174 TGGCACATAAAGTGCATAT
1 TGGCACACATAGTGCATAC
* *
20254193 TGACACACATTGTGCATAC
1 TGGCACACATAGTGCATAC
*
20254212 TGGCACATATAGTG--TA-
1 TGGCACACATAGTGCATAC
* *
20254228 T--AACACATAGTGCATAT
1 TGGCACACATAGTGCATAC
20254245 TGGCACACATAGTGCAT
1 TGGCACACATAGTGCAT
20254262 CATCGGATAA
Statistics
Matches: 130, Mismatches: 46, Indels: 14
0.68 0.24 0.07
Matches are distributed among these distances:
14 9 0.07
16 3 0.02
17 3 0.02
18 2 0.02
19 111 0.85
20 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (19 bp):
TGGCACACATAGTGCATAC
Found at i:20262425 original size:11 final size:11
Alignment explanation
Indices: 20262409--20262433 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20262399 GTTTAGATGA
20262409 AATTAACTATT
1 AATTAACTATT
20262420 AATTAACTATT
1 AATTAACTATT
20262431 AAT
1 AAT
20262434 ACCTCCTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTAACTATT
Found at i:20274339 original size:37 final size:37
Alignment explanation
Indices: 20274298--20274371 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
20274288 CACAATTAAC
20274298 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
1 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
20274335 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
1 CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
20274372 TAACTCCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (37 bp):
CTCAAAATTTTATACTAATTTCACTCTAGGCCTAATT
Done.