Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold56
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: 1793205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 19648 characters in sequence are not A, C, G, or T
File 8 of 11
Found at i:1260560 original size:177 final size:178
Alignment explanation
Indices: 1259848--1261059 Score: 1308
Period size: 177 Copynumber: 6.8 Consensus size: 178
1259838 CAAGGAGAAA
* * *
1259848 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAAGACAAGGCGT
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* * * * * * *
1259913 CCTACTCCTTGAAGACTGAAAAATGCCACTAACTTATGTAGGCTTTAAAAGGAAAAGACGTCCTG
66 CCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTG
* *
1259978 CTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTTGGCTTTAAAAGGAAAAG
131 CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT---A--AAAAG
*
1260031 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* * * **
1260096 CC--CGTTTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTT-----G-AAAGGCAACCT
66 CCTAC-TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
* *
1260152 ACTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-GAAAG
130 GCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG
* * * ** * *
1260200 GCGTCCTACTCTTTGAGGGCTAGAAAATGCTACCAACTTGTGTGGGCTTT-----GAAAA-GCAT
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
*
1260259 CCTACTCTTTAAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCT
66 CCTACTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
*
1260317 ACTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAG
130 GCTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTGGGCTTT-----AAAAAG
* ** * *
1260371 GCGTCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCA
1 GCATCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * * *
1260435 TCCTACTCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTATAAAAAGAAAAGGCGTCCT
65 TCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
* *
1260500 GCTCTTTGAGGACT-AGAAGGTGCCATCAACTTGTGTGGGCTTT-AAAAG
130 GCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG
* * * * * *
1260548 GCGTCTTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTTGGTTTTAAAAGGAAAAGGTG
1 GCATCCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* *
1260612 TCCTACT-TCTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGTTTTAAAAGGAAAAGGCGTCC
65 TCCTACTCT-TTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* *
1260676 TACTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
129 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT---A--AAAAG
* *
1260731 GCATCCTACTCTTTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTT------AAAAGGCGT
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* * * **
1260790 CCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTTGTTTTTAAAAGGAAAAGGCGTCCTG
66 CCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTG
* * **
1260855 CTCCTTGAGGACTGAAAAGTGTCACCAACTTGTGTGATCTTTAAAAGGAAAAG
131 CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT---A--AAAAG
*
1260908 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGT
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* * * *
1260973 CCTACTCTTTGAGGACTAGAAAAATGCCACCAACTTGTATGGGCTTTAAAAGGAGAAGGCATCCT
66 CCTACTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
*
1261038 GCTCTTTGAAGACTGAAAAGTG
130 GCTCTTTGAGGACTGAAAAGTG
1261060 AAAGGAGAAA
Statistics
Matches: 892, Mismatches: 91, Indels: 91
0.83 0.08 0.08
Matches are distributed among these distances:
163 10 0.01
164 17 0.02
165 71 0.08
169 48 0.05
170 1 0.00
171 48 0.05
175 42 0.05
176 11 0.01
177 361 0.40
178 6 0.01
181 22 0.02
182 11 0.01
183 181 0.20
184 63 0.07
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (178 bp):
GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
CCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTG
CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG
Found at i:1260627 original size:238 final size:237
Alignment explanation
Indices: 1259851--1261025 Score: 1428
Period size: 238 Copynumber: 5.0 Consensus size: 237
1259841 GGAGAAAGCA
* * * *
1259851 TCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAAGACAAGGCGTCC
1 TCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * * * * *
1259915 TACTCCTTGAAGACTGAAAAATGCCACTAACTTATGTAGGCTTTAAAAGGAAAAGACGTCCTGCT
65 TACTTCTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACT
* * *
1259980 CCTTGAGGACTGAAAAGTGCCACCAACTTGTGTTGGCTTTAAAAGGAAAAGGCATCCTGCTCTTT
130 CCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGC-TTAAAAAGAAAAGGCATCCTACTCTTT
*
1260045 GAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
194 GAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT------AAAAGGCG
* * * * **
1260095 TCCCG-TTTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTT-----G-AAAGGCAACCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
*
1260152 AC-TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCTACT
66 ACTTC-TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACT
* * * *
1260210 CTTTGAGGGCTAGAAAA-TGCTACCAACTTGTGTGGGCTT----TGAAAA-GCATCCTACTCTTT
130 CCTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTAAAAAGAAAAGGCATCCTACTCTTT
* * *
1260269 AAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
194 GAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* *
1260313 TCCTACTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTCC
1 TCCTGCTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * *
1260377 TGC-TCTTTGAGGACTGAAAAATGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATCCTAC
65 TACTTC-TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTAC
* * *
1260441 TCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTATAAAAAGAAAAGGCGTCCTGCTCTT
129 TCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCT-TAAAAAGAAAAGGCATCCTACTCTT
*
1260506 TGAGGACTAGAAGGTGCCATCAACTTGTGTGGGCTTTAAAAGGCG
193 TGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* * * *
1260551 TCTTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTTGGTTTTAAAAGGAAAAGGTGTCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
* * *
1260616 ACTTCTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGTTTTAAAAGGAAAAGGCGTCCTACTC
66 ACTTCTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTC
*
1260681 CTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTG
131 CTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGC-TTAAAAAGAAAAGGCATCCTACTCTTTG
*
1260746 AGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAGGCG
195 AGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
* * **
1260789 TCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTTGTTTTTAAAAGGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
* * * * ** * *
1260854 GCTCCTTGAGGACTGAAAAGTGTCACCAACTTGTGTGATCTTTAAAAGGAAAAGGCATCCTGCTC
66 ACTTCTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTC
* * * *
1260919 TTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTT
131 CTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTAAAAAG-AAAAGGCATCCTACTCTTT
** *
1260983 GAGGACTAGAAAAATGCCACCAACTTGTATGGGCTTTAAAAGG
194 GAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1261026 AGAAGGCATC
Statistics
Matches: 814, Mismatches: 86, Indels: 67
0.84 0.09 0.07
Matches are distributed among these distances:
218 9 0.01
219 13 0.02
220 23 0.03
224 47 0.06
225 5 0.01
226 49 0.06
229 2 0.00
230 39 0.05
231 12 0.01
232 41 0.05
233 1 0.00
235 1 0.00
236 43 0.05
237 13 0.02
238 440 0.54
239 36 0.04
242 25 0.03
243 11 0.01
244 4 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (237 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
ACTTCTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTC
CTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTAAAAAGAAAAGGCATCCTACTCTTTGA
GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
Found at i:1264866 original size:421 final size:421
Alignment explanation
Indices: 1264082--1264891 Score: 1584
Period size: 421 Copynumber: 1.9 Consensus size: 421
1264072 ACAAAGCAGG
*
1264082 GGCTTCGCATAGGTATTTGAGGGGATCAAGTTTGATGATCAACCAAGTAGTATGGTACAACATGT
1 GGCTTCGCATAGGTATTTGAGGGGATCAAGTTTAATGATCAACCAAGTAGTATGGTACAACATGT
1264147 ATTATTTTGACCTCCGAGTCACCCAAGCTAGAGCATAACATAACTTTTCTACCACAGAATAGTTA
66 ATTATTTTGACCTCCGAGTCACCCAAGCTAGAGCATAACATAACTTTTCTACCACAGAATAGTTA
1264212 TCTTCATACTCTGTGAACTTCTTGCTCAGATAATAGATGGCTTGTTCTTTTCTTCCTAACTCATC
131 TCTTCATACTCTGTGAACTTCTTGCTCAGATAATAGATGGCTTGTTCTTTTCTTCCTAACTCATC
1264277 ATGTTGTCCTAGGACACAGCCCATAGAATTATCAAAAACTGAAAAGTACAAAACTAACGGTCTCC
196 ATGTTGTCCTAGGACACAGCCCATAGAATTATCAAAAACTGAAAAGTACAAAACTAACGGTCTCC
*
1264342 CAGGCACTGGTGGCACAAGTACTAGATGATTTGAAAGGTAATGCTTAACCTTATCGAAGGCTTCA
261 CAAGCACTGGTGGCACAAGTACTAGATGATTTGAAAGGTAATGCTTAACCTTATCGAAGGCTTCA
1264407 TGACACTCTTCATTCCATGCTCCAGGGCATTGTTTTCAAAGTAGTCGAAAGATCGGATCGCATTG
326 TGACACTCTTCATTCCATGCTCCAGGGCATTGTTTTCAAAGTAGTCGAAAGATCGGATCGCATTG
1264472 TTTTCATGACACTCTTCATTCTATGCTCCAA
391 TTTTCATGACACTCTTCATTCTATGCTCCAA
1264503 GGCTTCGCATAGGTATTTGAGGGGATCAAGTTTAATGATCAACCAAGTAGTATGGTACAACATGT
1 GGCTTCGCATAGGTATTTGAGGGGATCAAGTTTAATGATCAACCAAGTAGTATGGTACAACATGT
1264568 ATTATTTTGACCTCCGAGTCACCCAAGCTAGAGCATAACATAACTTTTCTACCACAGAATAGTTA
66 ATTATTTTGACCTCCGAGTCACCCAAGCTAGAGCATAACATAACTTTTCTACCACAGAATAGTTA
*
1264633 TCTTCATACTCTGTGAACTTCTTGCTCAGATAATAGATGGCTTGTTTTTTTCTTCCTAACTCATC
131 TCTTCATACTCTGTGAACTTCTTGCTCAGATAATAGATGGCTTGTTCTTTTCTTCCTAACTCATC
*
1264698 ATGTTGTCCTAGGACACAGCCCATAGAATTATCAAAAACTGAAAAGTACAAAACTAACTGTCTCC
196 ATGTTGTCCTAGGACACAGCCCATAGAATTATCAAAAACTGAAAAGTACAAAACTAACGGTCTCC
1264763 CAAGCACTGGTGGCACAAGTACTAGATGATTTGAAAGGTAATGCTTAACCTTATCGAAGGCTTCA
261 CAAGCACTGGTGGCACAAGTACTAGATGATTTGAAAGGTAATGCTTAACCTTATCGAAGGCTTCA
1264828 TGACACTCTTCATTCCATGCTCCAGGGCATTGTTTTCAAAGTAGTCGAAAGATCGGATCGCATT
326 TGACACTCTTCATTCCATGCTCCAGGGCATTGTTTTCAAAGTAGTCGAAAGATCGGATCGCATT
1264892 TGTTAGTTAA
Statistics
Matches: 385, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
421 385 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (421 bp):
GGCTTCGCATAGGTATTTGAGGGGATCAAGTTTAATGATCAACCAAGTAGTATGGTACAACATGT
ATTATTTTGACCTCCGAGTCACCCAAGCTAGAGCATAACATAACTTTTCTACCACAGAATAGTTA
TCTTCATACTCTGTGAACTTCTTGCTCAGATAATAGATGGCTTGTTCTTTTCTTCCTAACTCATC
ATGTTGTCCTAGGACACAGCCCATAGAATTATCAAAAACTGAAAAGTACAAAACTAACGGTCTCC
CAAGCACTGGTGGCACAAGTACTAGATGATTTGAAAGGTAATGCTTAACCTTATCGAAGGCTTCA
TGACACTCTTCATTCCATGCTCCAGGGCATTGTTTTCAAAGTAGTCGAAAGATCGGATCGCATTG
TTTTCATGACACTCTTCATTCTATGCTCCAA
Found at i:1275056 original size:79 final size:77
Alignment explanation
Indices: 1274923--1275232 Score: 243
Period size: 79 Copynumber: 3.9 Consensus size: 77
1274913 ACAACAGGAC
* * *
1274923 TGGAGTAT-CCTCGATTATGGAAAATCGGTATTCT-GAAAATAAAATCAAGG-TTGGAGTATCCC
1 TGGAGTATCCCT-GATTAT-GAAAATCGATATTTTAG-AAATAAAATC-GGGATTGGAGTATCCC
*
1274985 CTCGGAAATAATAGGGT
62 CTCGAAAATAA-AGGGT
* * * *
1275002 TAGAGTATCCCTGATTATAGAAAATCGGTGTTTT-GAAAATAAAATCGGGATTGGAGTATCCTCT
1 TGGAGTATCCCTGATTAT-GAAAATCGATATTTTAG-AAATAAAATCGGGATTGGAGTATCCCCT
* *
1275066 CAAAAATAACGGGAT
64 CGAAAATAAAGGG-T
* ** ** * * *
1275081 TGGAGTATCCCTGATTGTGAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTAGAGTAT-CTCTG
1 TGGAGTATCCCTGATTATG-AAAATCGATATTTTAGAAATAAAATCGGGATTGGAGTATCCCCT-
*
1275145 CGAAAATAACGGGGT
64 CGAAAATAA-AGGGT
* * * * * *
1275160 TGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGTCGGGATTGAAATATCCCCTC
1 TGGAGTATCCCTGATTATGA-AAATCGATATTTTAGAAATAAAATCGGGATTGGAGTATCCCCTC
*
1275225 GGAAATAA
65 GAAAATAA
1275233 CGGTGTGAAA
Statistics
Matches: 192, Mismatches: 30, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
78 11 0.06
79 171 0.89
80 10 0.05
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (77 bp):
TGGAGTATCCCTGATTATGAAAATCGATATTTTAGAAATAAAATCGGGATTGGAGTATCCCCTCG
AAAATAAAGGGT
Found at i:1275233 original size:79 final size:79
Alignment explanation
Indices: 1274977--1275235 Score: 265
Period size: 79 Copynumber: 3.3 Consensus size: 79
1274967 TCAAGGTTGG
* ** * * *
1274977 AGTATCCCCTCGGAAATAATAGGGTTAGAGTATCCCTGATTAT-AGAAAATCGGTGTTTT-GAAA
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAG-AAATCGATGTTTTAG-AA
* *
1275040 ATAAAATCGGGATTGG
64 ATAAAGTCGGGATTGA
* * * * *
1275056 AGTATCCTCTCAAAAATAACGGGATTGGAGTATCCCTGATTGTGAAAAATCGATGCTTTAGAAAT
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAGAAATCGATGTTTTAGAAAT
* *
1275121 AAAGCCGGGGTT-A
66 AAAGTCGGGATTGA
* * * *
1275134 GAGTAT-CTCTGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAA
1 -AGTATCCCCT-CGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAGAAATCGATGTTTTAGAA
1275198 ATAAAGTCGGGATTGA
64 ATAAAGTCGGGATTGA
* *
1275214 AATATCCCCTCGGAAATAACGG
1 AGTATCCCCTCGAAAATAACGG
1275236 TGTGAAAAAT
Statistics
Matches: 147, Mismatches: 27, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
78 4 0.03
79 137 0.93
80 6 0.04
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAGAAATCGATGTTTTAGAAAT
AAAGTCGGGATTGA
Found at i:1277780 original size:13 final size:13
Alignment explanation
Indices: 1277758--1277787 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1277748 GTAAACCTCG
*
1277758 AATGTTTCGATAC
1 AATGTATCGATAC
1277771 AATGTATCGATAC
1 AATGTATCGATAC
1277784 AATG
1 AATG
1277788 AATAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1277796 original size:20 final size:20
Alignment explanation
Indices: 1277769--1277824 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1277759 ATGTTTCGAT
1277769 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
1277789 ATAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1277809 ACAATGTATCGATACA
1 ACAATGTATCGATACA
1277825 TCTGGGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1279021 original size:46 final size:46
Alignment explanation
Indices: 1278896--1279109 Score: 229
Period size: 46 Copynumber: 4.7 Consensus size: 46
1278886 TCAAATTATT
* ** * * * *
1278896 TTAATTAAAAAATGTATAAAAAAGT-TTTTCTCAAATTAAATTAAA
1 TTAATTAAAAGATAAATAAAAAAATCTTATCTCTAATTATATTAAA
* * *
1278941 TTAATTAAAAG--AAATAAAGAAATCTTATCTCTAATTATTTTAAC
1 TTAATTAAAAGATAAATAAAAAAATCTTATCTCTAATTATATTAAA
* * * * *
1278985 TTAATTAAGAGACAAATTAATAAACCTTATCTCTAATT-TAATTAAA
1 TTAATTAAAAGATAAATAAAAAAATCTTATCTCTAATTAT-ATTAAA
* *
1279031 TTAATTAAAAGATAAATAAAGAAATCTTATCTCTAATTAAATTAAA
1 TTAATTAAAAGATAAATAAAAAAATCTTATCTCTAATTATATTAAA
*
1279077 TTAATTAAAAGATAAATGAAAAAATCTTATCTC
1 TTAATTAAAAGATAAATAAAAAAATCTTATCTC
1279110 GTAGGGATAA
Statistics
Matches: 140, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
43 8 0.06
44 25 0.18
45 11 0.08
46 96 0.69
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (46 bp):
TTAATTAAAAGATAAATAAAAAAATCTTATCTCTAATTATATTAAA
Found at i:1279062 original size:92 final size:90
Alignment explanation
Indices: 1278924--1279109 Score: 264
Period size: 92 Copynumber: 2.0 Consensus size: 90
1278914 AAAAAGTTTT
** *
1278924 TCTCAAATTAAATTAAATTAATTAAAAGAAATAAAGAAATCTTATCTCTAATTATTTTAACTTAA
1 TCTCAAATTAAATTAAATTAATTAAAAGAAATAAAGAAATCTTATCTCTAATTAAATTAAATTAA
* * *
1278989 TTAAGAGACAAATTAATAAACCTTA
66 TTAAAAGACAAATGAAAAAACCTTA
* *
1279014 TCTCTAATTTAATTAAATTAATTAAAAGATAAATAAAGAAATCTTATCTCTAATTAAATTAAATT
1 TCTCAAATTAAATTAAATTAATTAAAAG--AAATAAAGAAATCTTATCTCTAATTAAATTAAATT
* *
1279079 AATTAAAAGATAAATGAAAAAATCTTA
64 AATTAAAAGACAAATGAAAAAACCTTA
1279106 TCTC
1 TCTC
1279110 GTAGGGATAA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 26 0.31
92 58 0.69
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (90 bp):
TCTCAAATTAAATTAAATTAATTAAAAGAAATAAAGAAATCTTATCTCTAATTAAATTAAATTAA
TTAAAAGACAAATGAAAAAACCTTA
Found at i:1279182 original size:74 final size:74
Alignment explanation
Indices: 1279041--1279182 Score: 191
Period size: 74 Copynumber: 1.9 Consensus size: 74
1279031 TTAATTAAAA
* *
1279041 GATAAATAAAGAAATCTTATCTCTAATTAAATTAAATTAATTAAAAGATAAATGAAAAAATCTTA
1 GATAAATAAAGAAATCTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATGAAAAAAACTTA
1279106 TCTCGTAGG
66 TCTCGTAGG
* * *
1279115 GATAAATAAATG-AATTTTATCTTTAATTAAAATAAATTAATTAAGAGAT-AATGAGAAAGAAAC
1 GATAAATAAA-GAAATCTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATGA-AAA-AAAC
1279178 -TATCT
63 TTATCT
1279183 TTTTAAGAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
73 5 0.08
74 51 0.85
75 4 0.07
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (74 bp):
GATAAATAAAGAAATCTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATGAAAAAAACTTA
TCTCGTAGG
Found at i:1279347 original size:15 final size:15
Alignment explanation
Indices: 1279327--1279357 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1279317 AAACATTACA
1279327 CCAATTCTAAAAATT
1 CCAATTCTAAAAATT
1279342 CCAATTCTAAAAATT
1 CCAATTCTAAAAATT
1279357 C
1 C
1279358 TAAAGAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (15 bp):
CCAATTCTAAAAATT
Found at i:1280291 original size:16 final size:16
Alignment explanation
Indices: 1280205--1280330 Score: 52
Period size: 16 Copynumber: 7.8 Consensus size: 16
1280195 TTTTGTTGTT
1280205 TATT-TTTTAATAT-A
1 TATTATTTTAATATAA
*
1280219 T-TTATATTT-ATAT-T
1 TATTAT-TTTAATATAA
1280233 TATTACTTTTAATATAGA
1 TATTA-TTTTAATATA-A
* * **
1280251 AATAATTTTTAAT-TTT
1 TATTA-TTTTAATATAA
1280267 TATTA-TTTAATATAA
1 TATTATTTTAATATAA
1280282 TATTATTTTAATA-ACA
1 TATTATTTTAATATA-A
1280298 TATTTTATTATTTAATATAAA
1 TA--TTA-T-TTTAATAT-AA
*
1280319 TATAATTTTAAT
1 TATTATTTTAAT
1280331 TATTTTTAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
13 2 0.02
14 13 0.15
15 16 0.19
16 18 0.21
17 7 0.08
18 14 0.17
19 3 0.04
20 7 0.08
21 3 0.04
22 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (16 bp):
TATTATTTTAATATAA
Found at i:1280310 original size:36 final size:35
Alignment explanation
Indices: 1280264--1280372 Score: 127
Period size: 35 Copynumber: 3.1 Consensus size: 35
1280254 AATTTTTAAT
1280264 TTTTATTATTTAATATAATATTATTTTAATAACATA
1 TTTTATTATTTAATATAATATTATTTTAATAA-ATA
* *
1280300 TTTTATTATTTAATATAAATATAATTTTAAT-TAT-
1 TTTTATTATTTAATAT-AATATTATTTTAATAAATA
*
1280334 TTTTAATTATTTATTAT-ATA-TATTTTAATCAAATA
1 TTTT-ATTATTTAATATAATATTATTTTAAT-AAATA
1280369 TTTT
1 TTTT
1280373 TAATAATTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
32 8 0.13
33 3 0.05
34 6 0.10
35 17 0.27
36 16 0.25
37 13 0.21
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (35 bp):
TTTTATTATTTAATATAATATTATTTTAATAAATA
Found at i:1280321 original size:21 final size:21
Alignment explanation
Indices: 1280264--1280321 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 21
1280254 AATTTTTAAT
1280264 TTTTATTATTTAATAT-AATA
1 TTTTATTATTTAATATAAATA
*
1280284 --TTA-T-TTTAATA-ACATA
1 TTTTATTATTTAATATAAATA
1280300 TTTTATTATTTAATATAAATA
1 TTTTATTATTTAATATAAATA
1280321 T
1 T
1280322 AATTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
16 10 0.33
17 1 0.03
18 6 0.20
19 1 0.03
20 7 0.23
21 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTATTTAATATAAATA
Found at i:1280374 original size:70 final size:69
Alignment explanation
Indices: 1280231--1280372 Score: 177
Period size: 70 Copynumber: 2.0 Consensus size: 69
1280221 TATATTTATA
1280231 TTTATTACTTTTAATATAGAAATAATTTTTAATTTTTATTATTTAATATAATATTATTTTAATAA
1 TTTATTAC-TTTAATATAGAAATAATTTTTAATTTTTATTATTTAATATAATATTATTTTAATAA
1280296 CATAT
65 CATAT
* *
1280301 TTTATTA-TTTAATATA-AATATAATTTTAATTATTTTTAATTATTTATTAT-ATA-TATTTTAA
1 TTTATTACTTTAATATAGAA-ATAATTTT--TAATTTTT-ATTATTTAATATAATATTATTTTAA
1280362 TCAA-ATAT
62 T-AACATAT
1280370 TTT
1 TTT
1280373 TAATAATTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
67 2 0.03
68 17 0.26
69 16 0.25
70 19 0.29
71 11 0.17
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (69 bp):
TTTATTACTTTAATATAGAAATAATTTTTAATTTTTATTATTTAATATAATATTATTTTAATAAC
ATAT
Found at i:1280376 original size:36 final size:34
Alignment explanation
Indices: 1280262--1280383 Score: 108
Period size: 36 Copynumber: 3.5 Consensus size: 34
1280252 ATAATTTTTA
*
1280262 ATTTTTATTATTTAATATAATATTATTTTAATAACAT
1 ATTTTTATTATTTATTAT-ATA-TATTTTAATAA-AT
*
1280299 A-TTTTATTATTTAATATAAATATAATTTTAAT---T
1 ATTTTTATTATTT-AT-TATATAT-ATTTTAATAAAT
1280332 ATTTTTAATTATTTATTATATATATTTTAATCAAAT
1 ATTTTT-ATTATTTATTATATATATTTTAAT-AAAT
* *
1280368 ATTTTTAATAATTATT
1 ATTTTTATTATTTATT
1280384 TTTTTATTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
32 8 0.11
33 8 0.11
34 6 0.08
35 15 0.21
36 19 0.27
37 13 0.18
38 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (34 bp):
ATTTTTATTATTTATTATATATATTTTAATAAAT
Found at i:1283518 original size:21 final size:21
Alignment explanation
Indices: 1283494--1283538 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1283484 AGTTGTATCT
1283494 TTTTATCCAAAAAATGCATTA
1 TTTTATCCAAAAAATGCATTA
**
1283515 TTTTATCCAACTAATGCATTA
1 TTTTATCCAAAAAATGCATTA
1283536 TTT
1 TTT
1283539 CATCTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (21 bp):
TTTTATCCAAAAAATGCATTA
Found at i:1284192 original size:44 final size:44
Alignment explanation
Indices: 1284127--1284307 Score: 181
Period size: 44 Copynumber: 4.1 Consensus size: 44
1284117 TCAAATTTTC
* ** *
1284127 TCTCTAATCAAATTATTTTAATTAAAAGATGAAA-AAAAAGTTTT
1 TCTCTAATTAAATTAAATTAATTAAAAGAT-AAATAAAAAGTTTA
* *
1284171 TCTCAAATTAAATTAAATTAATT--AAGAAAAATAAAGAAGTCTTA
1 TCTCTAATTAAATTAAATTAATTAAAAGATAAATAAA-AAGT-TTA
** * **
1284215 TCTCTAATTATTTTAACTTAATTAAAAGATAAATTAATAAACATTA
1 TCTCTAATTAAATTAAATTAATTAAAAGATAAA-TAA-AAAGTTTA
*
1284261 TCTCTAATTTAATTAAATTAATTAAAAGATAAATAAAAA-TTTA
1 TCTCTAATTAAATTAAATTAATTAAAAGATAAATAAAAAGTTTA
1284304 TCTC
1 TCTC
1284308 GTAAAAATAA
Statistics
Matches: 112, Mismatches: 18, Indels: 15
0.77 0.12 0.10
Matches are distributed among these distances:
41 3 0.03
42 7 0.06
43 11 0.10
44 43 0.38
45 3 0.03
46 39 0.35
47 5 0.04
48 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (44 bp):
TCTCTAATTAAATTAAATTAATTAAAAGATAAATAAAAAGTTTA
Found at i:1285453 original size:21 final size:22
Alignment explanation
Indices: 1285383--1285453 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 22
1285373 ATAATATCCC
1285383 TTTTAAT-TTT-TT-TTTAA-A
1 TTTTAATATTTATTGTTTAATA
1285401 TTTTTAA-ATTTTATTGTTTAATA
1 -TTTTAATA-TTTATTGTTTAATA
*
1285424 TATTT-ATATTTA-TGTTTATTA
1 T-TTTAATATTTATTGTTTAATA
1285445 TTTTAATAT
1 TTTTAATAT
1285454 GAAAATAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
19 6 0.14
20 6 0.14
21 15 0.35
22 11 0.26
23 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTTAATATTTATTGTTTAATA
Found at i:1285507 original size:29 final size:30
Alignment explanation
Indices: 1285441--1285507 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1285431 ATTTATGTTT
*
1285441 ATTATTTTAATATGAAAATAATTTTTAATT
1 ATTATTTTAATATGAAAATAATTTTTAATA
* *
1285471 ATTA-TTTAATAT-AATATTA-TTTTAATA
1 ATTATTTTAATATGAAAATAATTTTTAATA
1285498 ATATATTTTA
1 AT-TATTTTA
1285508 TTATTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 9 0.28
28 7 0.22
29 12 0.38
30 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
ATTATTTTAATATGAAAATAATTTTTAATA
Found at i:1285509 original size:21 final size:24
Alignment explanation
Indices: 1285485--1285537 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
1285475 TTTAATATAA
*
1285485 TATTATTTTA-ATA-ATAT-ATTT
1 TATTATTTAATATAGATATAATTT
1285506 TATTATTTAATATAGATATAATTT
1 TATTATTTAATATAGATATAATTT
1285530 TAATTATT
1 T-ATTATT
1285538 CATTATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 9 0.33
22 3 0.11
23 4 0.15
24 5 0.19
25 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTATTTAATATAGATATAATTT
Found at i:1285544 original size:25 final size:23
Alignment explanation
Indices: 1285498--1285544 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1285488 TATTTTAATA
*
1285498 ATATATTTTATTATTTAATATAG
1 ATATATTTTATTATTCAATATAG
*
1285521 ATATAATTTTAATTATTCATTATA
1 ATAT-ATTTT-ATTATTCAATATA
1285545 CATTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATATTTTATTATTCAATATAG
Found at i:1291310 original size:20 final size:21
Alignment explanation
Indices: 1291282--1291334 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1291272 AAATACAAAT
* *
1291282 TATCGATACATTGCT-TGATG
1 TATCAATACATTGATATGATG
*
1291302 TATCAATACATTTATATGATG
1 TATCAATACATTGATATGATG
*
1291323 TATCAATGCATT
1 TATCAATACATT
1291335 ATCAGCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (21 bp):
TATCAATACATTGATATGATG
Found at i:1295200 original size:78 final size:78
Alignment explanation
Indices: 1295068--1295362 Score: 349
Period size: 80 Copynumber: 3.7 Consensus size: 78
1295058 TCAAGCTCGG
* * * * *
1295068 TTTTATTTCTAAAACACCGATTTTTTACTATTGGGGATGCTCCAACCTTATTATTTTCGAGAGGA
1 TTTTATTTCTAAAACACCAATTTTTTACCATCGGGGATACTCCAACCTTGTTATTTTCGAGAGGA
1295133 TACTCCAACCCGA
66 TACTCCAACCCGA
* * * * *
1295146 TTTTATTT-TCAAAACACCAATTTTTCACCATCGGGGATACTCTAATCTCGTTATTTTTGAGAGG
1 TTTTATTTCT-AAAACACCAATTTTTTACCATCGGGGATACTCCAACCTTGTTATTTTCGAGAGG
1295210 ATACTCCAACCTCGA
65 ATACTCCAACC-CGA
* * * ** *
1295225 TTTTATTTCTAAAACATCGATATTTTAATAATCGGGGATACTCCAACCTTGTTATTTTCGAGGGG
1 TTTTATTTCTAAAACACCAAT-TTTTTACCATCGGGGATACTCCAACCTTGTTATTTTCGAGAGG
*
1295290 ATATTCCAACCCTGA
65 ATACTCCAACCC-GA
* * * * *
1295305 TTTTATTTCTAAAACATCAATTTTTTACCATTGAGAATACTCCAACCCTGTTATTTTC
1 TTTTATTTCTAAAACACCAATTTTTTACCATCGGGGATACTCCAACCTTGTTATTTTC
1295363 AAGGGAATAC
Statistics
Matches: 183, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
77 1 0.01
78 63 0.34
79 51 0.28
80 68 0.37
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (78 bp):
TTTTATTTCTAAAACACCAATTTTTTACCATCGGGGATACTCCAACCTTGTTATTTTCGAGAGGA
TACTCCAACCCGA
Found at i:1296597 original size:60 final size:60
Alignment explanation
Indices: 1296525--1296641 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
1296515 CTGAGGGACA
* *
1296525 TTTATCTAATTTTCAAGCATTTTAGGGCCATTTCGAATATTTTCCATG-TTGTAAGGATTT
1 TTTATCTAATTTTCAAGCATTTTAGGACCATTTAGAATATTTTCCATGATT-TAAGGATTT
* * * * *
1296585 TTTATGTAATTTTCATGTATTTTAGGATCATTTAGAATATTTTTCATGATTTAAGGA
1 TTTATCTAATTTTCAAGCATTTTAGGACCATTTAGAATATTTTCCATGATTTAAGGA
1296642 CTATTATGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.49
Consensus pattern (60 bp):
TTTATCTAATTTTCAAGCATTTTAGGACCATTTAGAATATTTTCCATGATTTAAGGATTT
Found at i:1296682 original size:58 final size:59
Alignment explanation
Indices: 1296599--1296735 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 59
1296589 TGTAATTTTC
* * * *
1296599 ATGTATTTTAGGATCATTTAGAATATTTTTCATGAT-TTAAGGACTATTATGCAATTACT
1 ATGTATTTTAGGGTCATTTAAAATATATTCCATG-TCTTAAGGACTATTATGCAATTACT
* * **
1296658 -TGTATTTTAGGGTCATTTAAAATATATTCCATGTCTTAGGGACTATTATGTAATTTTT
1 ATGTATTTTAGGGTCATTTAAAATATATTCCATGTCTTAAGGACTATTATGCAATTACT
* *
1296716 ATGCATTTTAGAGTCATTTA
1 ATGTATTTTAGGGTCATTTA
1296736 GATTACTTCC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
57 1 0.02
58 48 0.73
59 17 0.26
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (59 bp):
ATGTATTTTAGGGTCATTTAAAATATATTCCATGTCTTAAGGACTATTATGCAATTACT
Found at i:1296746 original size:58 final size:56
Alignment explanation
Indices: 1296586--1296747 Score: 148
Period size: 58 Copynumber: 2.8 Consensus size: 56
1296576 TAAGGATTTT
* * *
1296586 TTATGTAATTTTCATGTATTTTAGGATCATTTAGAATATTTTTCATGATTTAAGGACTA
1 TTATGTAATTTTTATGTATTTTAGG-TCATTTAG-AT-TATTCCATGATTTAAGGACTA
* ** * *
1296645 TTATGCAATTACT-TGTATTTTAGGGTCATTTAAAATATATTCCATG-TCTTAGGGACTA
1 TTATGTAATTTTTATGTATTTTA-GGTCATTT-AGAT-TATTCCATGAT-TTAAGGACTA
*
1296703 TTATGTAATTTTTATGCATTTTAGAGTCATTTAGATTACTTCCAT
1 TTATGTAATTTTTATGTATTTTAG-GTCATTTAGATTA-TTCCAT
1296748 AATCTAAAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
57 3 0.04
58 54 0.64
59 27 0.32
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (56 bp):
TTATGTAATTTTTATGTATTTTAGGTCATTTAGATTATTCCATGATTTAAGGACTA
Found at i:1300063 original size:2 final size:2
Alignment explanation
Indices: 1300056--1300088 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1300046 ACTATGCCAT
1300056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1300089 GCAGATGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1301723 original size:16 final size:16
Alignment explanation
Indices: 1301694--1301741 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1301684 ATTTTATTAA
*
1301694 TAAAAATTATTATATTT
1 TAAAAAATA-TATATTT
*
1301711 TAAAAAATATATATGT
1 TAAAAAATATATATTT
1301727 TAAAAAA-ATA-ATTT
1 TAAAAAATATATATTT
1301741 T
1 T
1301742 TTATGTAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 3 0.11
16 13 0.46
17 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAAAAATATATATTT
Found at i:1301734 original size:17 final size:17
Alignment explanation
Indices: 1301690--1301736 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
1301680 AACAATTTTA
1301690 TTAATAAAAATTATTATAT
1 TTAA-AAAAA-TATTATAT
*
1301709 TTTAAAAAATA-TATAT
1 TTAAAAAAATATTATAT
1301725 GTTAAAAAAATA
1 -TTAAAAAAATA
1301737 ATTTTTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 12 0.48
18 5 0.20
19 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAAAAAATATTATAT
Found at i:1305961 original size:19 final size:20
Alignment explanation
Indices: 1305917--1305963 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1305907 TGGCAACTCC
*
1305917 ATTTTTTTTAATTTTACTTT
1 ATTTTTTTTAATTTTACTGT
* *
1305937 AATTTTTTTATTTTTA-TGT
1 ATTTTTTTTAATTTTACTGT
1305956 ATTTTTTT
1 ATTTTTTT
1305964 AAAATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTAATTTTACTGT
Found at i:1307906 original size:25 final size:23
Alignment explanation
Indices: 1307878--1307924 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1307868 TAGATTTCGA
*
1307878 CATGTTTATTAATTCATGTCATATT
1 CATG-TTATT-ATTCATGACATATT
*
1307903 CATGTTATTTTTCATGACATAT
1 CATGTTATTATTCATGACATAT
1307925 CATATTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 5 0.25
25 4 0.20
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
CATGTTATTATTCATGACATATT
Found at i:1308341 original size:24 final size:24
Alignment explanation
Indices: 1308314--1308366 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1308304 ATACATTACC
1308314 GTTCACATATCACTATTCATAACT
1 GTTCACATATCACTATTCATAACT
** *
1308338 GTTCATGTATCACTATTCATCACT
1 GTTCACATATCACTATTCATAACT
1308362 GTTCA
1 GTTCA
1308367 TCACTGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.40
Consensus pattern (24 bp):
GTTCACATATCACTATTCATAACT
Found at i:1308359 original size:10 final size:10
Alignment explanation
Indices: 1308346--1308377 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1308336 CTGTTCATGT
*
1308346 ATCACTATTC
1 ATCACTGTTC
1308356 ATCACTGTTC
1 ATCACTGTTC
1308366 ATCACTGTTC
1 ATCACTGTTC
1308376 AT
1 AT
1308378 GTATCGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (10 bp):
ATCACTGTTC
Found at i:1308367 original size:24 final size:24
Alignment explanation
Indices: 1308321--1308367 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1308311 ACCGTTCACA
1308321 TATCACTATTCATAACTGTTCATG
1 TATCACTATTCATAACTGTTCATG
*
1308345 TATCACTATTCATCACTGTTCAT
1 TATCACTATTCATAACTGTTCAT
1308368 CACTGTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (24 bp):
TATCACTATTCATAACTGTTCATG
Found at i:1310538 original size:21 final size:21
Alignment explanation
Indices: 1310487--1310530 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1310477 TAATTTTCTT
* *
1310487 GAAAAGAAATTAAATGAATTA
1 GAAAAGAAAATAAATAAATTA
1310508 GAAAAGAAAATAAATAAATTA
1 GAAAAGAAAATAAATAAATTA
1310529 GA
1 GA
1310531 GGAGAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (21 bp):
GAAAAGAAAATAAATAAATTA
Found at i:1310543 original size:21 final size:21
Alignment explanation
Indices: 1310487--1310543 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1310477 TAATTTTCTT
** *
1310487 GAAAAGAAATTAAATGAATTA
1 GAAAAGAAAAGAAATAAATTA
*
1310508 GAAAAGAAAATAAATAAATTA
1 GAAAAGAAAAGAAATAAATTA
**
1310529 GAGGAGAAAAGAAAT
1 GAAAAGAAAAGAAAT
1310544 GAGTTGCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (21 bp):
GAAAAGAAAAGAAATAAATTA
Found at i:1312924 original size:20 final size:20
Alignment explanation
Indices: 1312899--1312940 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1312889 TGTTCATAAA
*
1312899 TTTGGTTTTATCAATTTAGC
1 TTTGGTTTTATCAACTTAGC
1312919 TTTGGTTTTATCAACTTAGC
1 TTTGGTTTTATCAACTTAGC
1312939 TT
1 TT
1312941 AAAACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTGGTTTTATCAACTTAGC
Found at i:1313123 original size:18 final size:18
Alignment explanation
Indices: 1313100--1313136 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1313090 ATGAGAGTTC
1313100 ATAAAAAGGGAGAGAATA
1 ATAAAAAGGGAGAGAATA
*
1313118 ATAAAAATGGAGAGAATA
1 ATAAAAAGGGAGAGAATA
1313136 A
1 A
1313137 ATTTGGCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (18 bp):
ATAAAAAGGGAGAGAATA
Found at i:1313943 original size:21 final size:20
Alignment explanation
Indices: 1313917--1313955 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1313907 AGGTCAAAAC
1313917 CCTAGAAAGTATCGATACACA
1 CCTAG-AAGTATCGATACACA
*
1313938 CCTAGATGTATCGATACA
1 CCTAGAAGTATCGATACA
1313956 TATTGCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTAGAAGTATCGATACACA
Found at i:1314124 original size:10 final size:10
Alignment explanation
Indices: 1314111--1314135 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1314101 TGTATCATTA
1314111 TTCATCACTG
1 TTCATCACTG
1314121 TTCATCACTG
1 TTCATCACTG
1314131 TTCAT
1 TTCAT
1314136 GTATCGATAC
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:0.20, C:0.28, G:0.08, T:0.44
Consensus pattern (10 bp):
TTCATCACTG
Found at i:1314263 original size:20 final size:21
Alignment explanation
Indices: 1314217--1314263 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1314207 AATTTCAAAT
*
1314217 GCATGTATCGATACATTATGA
1 GCATGTATCGATACATTAGGA
1314238 --ATTGTATCGATACA-TAGGA
1 GCA-TGTATCGATACATTAGGA
1314257 GCATGTA
1 GCATGTA
1314264 AGTGCGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (21 bp):
GCATGTATCGATACATTAGGA
Found at i:1315165 original size:24 final size:22
Alignment explanation
Indices: 1315113--1315165 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
1315103 TAAATTTTAA
*
1315113 AATATATATTTATTCATATTGT
1 AATATATATTTATTCATATTAT
*
1315135 -ATGATATGATTATATTTATATTAT
1 AAT-ATAT-ATT-TATTCATATTAT
1315159 AATATAT
1 AATATAT
1315166 TAAAATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.08
22 4 0.16
23 3 0.12
24 14 0.56
25 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
AATATATATTTATTCATATTAT
Found at i:1318361 original size:20 final size:19
Alignment explanation
Indices: 1318336--1318408 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1318326 CTGTTAGTTT
**
1318336 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
1318356 CATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
*
1318375 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
1318396 -ATGTATCGATACA
1 CATGTATCGATACA
1318409 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1318380 original size:19 final size:20
Alignment explanation
Indices: 1318336--1318389 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1318326 CTGTTAGTTT
**
1318336 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
1318356 CATGTATCAATACAA-TGAA
1 CATGTATCGATACAATTGAA
1318375 CATGTATCGATACAA
1 CATGTATCGATACAA
1318390 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1320756 original size:22 final size:21
Alignment explanation
Indices: 1320721--1320770 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1320711 GTTGTTGATG
*
1320721 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1320741 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1320762 AATTTGAAG
1 ATTTTGAAG
1320771 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1320767 original size:21 final size:22
Alignment explanation
Indices: 1320728--1320770 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1320718 ATGATTTTGA
* *
1320728 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1320750 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1320771 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1321918 original size:13 final size:13
Alignment explanation
Indices: 1321900--1321926 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1321890 ACATTATGCT
1321900 TTGTATCGATACA
1 TTGTATCGATACA
1321913 TTGTATCGATACA
1 TTGTATCGATACA
1321926 T
1 T
1321927 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1322036 original size:33 final size:33
Alignment explanation
Indices: 1321976--1322042 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1321966 CTTCCACTGT
*
1321976 TTGTATCGATACATGGTACAATATATCGATACA
1 TTGTATCGATACATGATACAATATATCGATACA
* *
1322009 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGAT-ACAATATATCGATACA
1322042 T
1 T
1322043 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATATATCGATACA
Found at i:1324953 original size:13 final size:13
Alignment explanation
Indices: 1324935--1324959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1324925 AGATTGCCTA
1324935 GTATCGATACATT
1 GTATCGATACATT
1324948 GTATCGATACAT
1 GTATCGATACAT
1324960 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1324972 original size:20 final size:21
Alignment explanation
Indices: 1324947--1324999 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1324937 ATCGATACAT
**
1324947 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1324967 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1324988 TGTATCGATACA
1 TGTATCGATACA
1325000 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1325078 original size:13 final size:13
Alignment explanation
Indices: 1325060--1325098 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1325050 ACACACAATA
1325060 TGTATCGATACAT
1 TGTATCGATACAT
1325073 TGTATCGATACAT
1 TGTATCGATACAT
1325086 TGTATCGATACAT
1 TGTATCGATACAT
1325099 CCTAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1331282 original size:13 final size:13
Alignment explanation
Indices: 1331249--1331289 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
1331239 CAGCATTCTC
*
1331249 TGTATCGATACATTG
1 TGTATCGATACA--A
1331264 TGTATCGATACAA
1 TGTATCGATACAA
1331277 TGTATCGATACAA
1 TGTATCGATACAA
1331290 AGGGTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
15 12 0.48
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1331455 original size:20 final size:20
Alignment explanation
Indices: 1331420--1331460 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1331410 CAAATTTCTT
1331420 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1331442 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1331461 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1331762 original size:20 final size:21
Alignment explanation
Indices: 1331722--1331773 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1331712 CCTCTAGGCA
*
1331722 GCACCCACCAGGTCACGACC-G
1 GCACCC-CCAGGTCACAACCGG
*
1331743 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCACAACCGG
1331764 GCAGCCCCCA
1 GCA-CCCCCA
1331774 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 10 0.37
22 6 0.22
ACGTcount: A:0.21, C:0.50, G:0.25, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCACAACCGG
Found at i:1333186 original size:21 final size:22
Alignment explanation
Indices: 1333148--1333192 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1333138 CGAAATTGTT
1333148 AAATTATTTTATTAAAGGGGAG
1 AAATTATTTTATTAAAGGGGAG
*
1333170 AAATT-TTTTGATTAAGGGGGAG
1 AAATTATTTT-ATTAAAGGGGAG
1333192 A
1 A
1333193 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.36
Consensus pattern (22 bp):
AAATTATTTTATTAAAGGGGAG
Found at i:1333766 original size:13 final size:13
Alignment explanation
Indices: 1333748--1333772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1333738 AGATTGCACA
1333748 GTATCGATACATT
1 GTATCGATACATT
1333761 GTATCGATACAT
1 GTATCGATACAT
1333773 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1333785 original size:20 final size:21
Alignment explanation
Indices: 1333760--1333812 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1333750 ATCGATACAT
**
1333760 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1333780 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1333801 TGTATCGATACA
1 TGTATCGATACA
1333813 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1335661 original size:107 final size:107
Alignment explanation
Indices: 1335475--1335684 Score: 402
Period size: 107 Copynumber: 2.0 Consensus size: 107
1335465 TATACTTGGA
*
1335475 TTTTATTTTTAAGCACTAAAGGTGAAGCTTTATAAAAATTCATCACCTTTTGTAAAATTGTTCAA
1 TTTTATTTTTAAGCACTAAAGATGAAGCTTTATAAAAATTCATCACCTTTTGTAAAATTGTTCAA
*
1335540 AATGAAAAAGGTTACTCCTTATCTAGCATAAGAAGTGATGGG
66 AATGAAAAAGGTTACTCCTTATCTAGCATAAAAAGTGATGGG
1335582 TTTTATTTTTAAGCACTAAAGATGAAGCTTTATAAAAATTCATCACCTTTTGTAAAATTGTTCAA
1 TTTTATTTTTAAGCACTAAAGATGAAGCTTTATAAAAATTCATCACCTTTTGTAAAATTGTTCAA
1335647 AATGAAAAAGGTTACTCCTTATCTAGCATAAAAAGTGA
66 AATGAAAAAGGTTACTCCTTATCTAGCATAAAAAGTGA
1335685 CCATGGAAGA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (107 bp):
TTTTATTTTTAAGCACTAAAGATGAAGCTTTATAAAAATTCATCACCTTTTGTAAAATTGTTCAA
AATGAAAAAGGTTACTCCTTATCTAGCATAAAAAGTGATGGG
Found at i:1347169 original size:33 final size:33
Alignment explanation
Indices: 1347127--1347191 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1347117 TTTGAAGCAA
*
1347127 TGTATTGATACAAT-TCATCATGTATCAATACAT
1 TGTATTGATACAATGT-ACCATGTATCAATACAT
*
1347160 TGTATTGATACAATGTACCATGTATCGATACA
1 TGTATTGATACAATGTACCATGTATCAATACA
1347192 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (33 bp):
TGTATTGATACAATGTACCATGTATCAATACAT
Found at i:1349963 original size:3 final size:3
Alignment explanation
Indices: 1349955--1349985 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1349945 CGAGTCAACT
*
1349955 TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1349986 TGATGGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:1350837 original size:42 final size:42
Alignment explanation
Indices: 1350778--1350903 Score: 252
Period size: 42 Copynumber: 3.0 Consensus size: 42
1350768 GCTATAGAAG
1350778 ATTGTTTCTCTCAGGTGTTAATCCGATGAAGGAAATTAGGCT
1 ATTGTTTCTCTCAGGTGTTAATCCGATGAAGGAAATTAGGCT
1350820 ATTGTTTCTCTCAGGTGTTAATCCGATGAAGGAAATTAGGCT
1 ATTGTTTCTCTCAGGTGTTAATCCGATGAAGGAAATTAGGCT
1350862 ATTGTTTCTCTCAGGTGTTAATCCGATGAAGGAAATTAGGCT
1 ATTGTTTCTCTCAGGTGTTAATCCGATGAAGGAAATTAGGCT
1350904 CTGATACCAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (42 bp):
ATTGTTTCTCTCAGGTGTTAATCCGATGAAGGAAATTAGGCT
Found at i:1351759 original size:13 final size:13
Alignment explanation
Indices: 1351748--1351793 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
1351738 AACATGTATT
*
1351748 GATACAATGTATC
1 GATACAATGAATC
1351761 GATACAATGAATC
1 GATACAATGAATC
*
1351774 GATACAATGAATA
1 GATACAATGAATC
1351787 GATACAA
1 GATACAA
1351794 AGCAATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (13 bp):
GATACAATGAATC
Found at i:1356235 original size:32 final size:32
Alignment explanation
Indices: 1356191--1356253 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1356181 GACTCTATAG
1356191 AGATAGAATTGATAGA-ATTAAGACTTATCTAA
1 AGATAGAATTGATAGAGATTAA-ACTTATCTAA
*
1356223 AGATA-AAGTTGATAGAGTTTAAACTTATCTA
1 AGATAGAA-TTGATAGAGATTAAACTTATCTA
1356254 GGATTTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 2 0.07
32 22 0.79
33 4 0.14
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.33
Consensus pattern (32 bp):
AGATAGAATTGATAGAGATTAAACTTATCTAA
Found at i:1361355 original size:32 final size:32
Alignment explanation
Indices: 1361307--1361369 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1361297 TAAAACTCTA
* * *
1361307 TAGAGATATAGCTGATAGTGTTTAGACTTATC
1 TAGAGATAGAGCTGATAGAGTTTAAACTTATC
*
1361339 TAGAGATAGAGTTGATAGAGTTTAAACTTAT
1 TAGAGATAGAGCTGATAGAGTTTAAACTTAT
1361370 AAGTCAAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (32 bp):
TAGAGATAGAGCTGATAGAGTTTAAACTTATC
Found at i:1361881 original size:21 final size:22
Alignment explanation
Indices: 1361855--1361896 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1361845 TGCCACCACC
1361855 ATAGTT-AAAGGAG-TTTTGGAG
1 ATAGTTGAAA-GAGCTTTTGGAG
1361876 ATAGTTGAAAGAGCTTTTGGA
1 ATAGTTGAAAGAGCTTTTGGA
1361897 TACTAGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (22 bp):
ATAGTTGAAAGAGCTTTTGGAG
Found at i:1364752 original size:32 final size:32
Alignment explanation
Indices: 1364716--1364778 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1364706 TAAAACTCTA
* *
1364716 TAGAGATATAGCTGATAGTGTTTAAACTTATC
1 TAGAGATAGAGCTGATAGAGTTTAAACTTATC
*
1364748 TAGAGATAGAGTTGATAGAGTTTAAACTTAT
1 TAGAGATAGAGCTGATAGAGTTTAAACTTAT
1364779 TTGGGTTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (32 bp):
TAGAGATAGAGCTGATAGAGTTTAAACTTATC
Found at i:1367321 original size:19 final size:19
Alignment explanation
Indices: 1367293--1367329 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1367283 CCAAGCATGG
1367293 TGCAACAGCAAGGATGGCA
1 TGCAACAGCAAGGATGGCA
*
1367312 TGCAATAGCAAGGATGGC
1 TGCAACAGCAAGGATGGC
1367330 GATCCTTAAT
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:0.35, C:0.19, G:0.32, T:0.14
Consensus pattern (19 bp):
TGCAACAGCAAGGATGGCA
Found at i:1367643 original size:46 final size:46
Alignment explanation
Indices: 1367561--1367734 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
1367551 CTAAATTTAA
1367561 ATTAAATTAATT-AAA-A-AAATAAAGAAATCTTATCTCTAATTAT
1 ATTAAATTAATTAAAAGATAAATAAAGAAATCTTATCTCTAATTAT
* * * * * *
1367604 TTTAACTTAATTAAGAGACAAATTAATAAA-CTTTATCTCTAATT-T
1 ATTAAATTAATTAAAAGATAAATAAAGAAATC-TTATCTCTAATTAT
* *
1367649 AATTAAATTAATCAAAAGATAAATAAAGAAATCTTATCTCTAATTAA
1 -ATTAAATTAATTAAAAGATAAATAAAGAAATCTTATCTCTAATTAT
1367696 ATTAAATTAATTAAAAGATAAATGAAA-AAATCTTATCTC
1 ATTAAATTAATTAAAAGATAAAT-AAAGAAATCTTATCTC
1367735 GTAAGGATAA
Statistics
Matches: 109, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
43 10 0.09
44 2 0.02
45 3 0.03
46 90 0.83
47 4 0.04
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (46 bp):
ATTAAATTAATTAAAAGATAAATAAAGAAATCTTATCTCTAATTAT
Found at i:1367732 original size:92 final size:90
Alignment explanation
Indices: 1367505--1367734 Score: 247
Period size: 92 Copynumber: 2.5 Consensus size: 90
1367495 ACAAATTTTC
* ** * *
1367505 TCTCTAATCAAATTATTTTAACTAAAAGATGAATAAAAAAGT-TT-T-TCTAAATTTAAATTAAA
1 TCTCTAATTAAATTAAATTAATTAAAAGATAAATAAAAAA-TCTTATCTCTAAATTTAAATTAAA
*
1367567 TTAATTAAAAAAATAAAGAAATCTTA
65 TTAATAAAAAAAATAAAGAAATCTTA
** * * * *
1367593 TCTCTAATTATTTTAACTTAATTAAGAGACAAATTAATAAA-CTTTATCTCT-AATTT-AATTAA
1 TCTCTAATTAAATTAAATTAATTAAAAGATAAA-TAAAAAATC-TTATCTCTAAATTTAAATTAA
1367655 ATTAATCAAAAGATAAATAAAGAAATCTTA
64 ATTAAT-AAAA-A-AAATAAAGAAATCTTA
1367685 TCTCTAATTAAATTAAATTAATTAAAAGATAAATGAAAAAATCTTATCTC
1 TCTCTAATTAAATTAAATTAATTAAAAGATAAAT-AAAAAATCTTATCTC
1367735 GTAAGGATAA
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
88 24 0.21
89 20 0.17
90 9 0.08
91 5 0.04
92 56 0.49
93 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (90 bp):
TCTCTAATTAAATTAAATTAATTAAAAGATAAATAAAAAATCTTATCTCTAAATTTAAATTAAAT
TAATAAAAAAAATAAAGAAATCTTA
Found at i:1367807 original size:74 final size:74
Alignment explanation
Indices: 1367666--1367807 Score: 184
Period size: 74 Copynumber: 1.9 Consensus size: 74
1367656 TTAATCAAAA
* *
1367666 GATAAATAAAGAAATCTTATCTCTAATTAAATTAAATTAATTAAAAGATAAATGAAAAAATCTTA
1 GATAAATAAAGAAATCTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATGAAAAAAACTTA
1367731 TCTCGTAAG
66 TCTCGTAAG
* *
1367740 GATAAATAAATG-AAT-TTGATCTTTAATTAAAATAAATTAATTAAGAGAT-AATGAGAAAGAAA
1 GATAAATAAA-GAAATCTT-ATCTCTAATTAAAATAAATTAATTAAAAGATAAATGA-AAA-AAA
1367802 C-TATCT
62 CTTATCT
1367808 TTTAAGAACT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
73 7 0.12
74 49 0.82
75 4 0.07
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.32
Consensus pattern (74 bp):
GATAAATAAAGAAATCTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATGAAAAAAACTTA
TCTCGTAAG
Found at i:1368955 original size:21 final size:21
Alignment explanation
Indices: 1368898--1368955 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 21
1368888 AATTTTTAAT
1368898 TTTTATTATTTAATAT-AATA
1 TTTTATTATTTAATATAAATA
* *
1368918 --TTA-T-TTTGATA-ACATA
1 TTTTATTATTTAATATAAATA
1368934 TTTTATTATTTAATATAAATA
1 TTTTATTATTTAATATAAATA
1368955 T
1 T
1368956 AATTTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 11
0.65 0.09 0.26
Matches are distributed among these distances:
16 9 0.32
17 1 0.04
18 6 0.21
19 1 0.04
20 6 0.21
21 5 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTATTATTTAATATAAATA
Found at i:1371973 original size:5 final size:5
Alignment explanation
Indices: 1371963--1371993 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1371953 TAAAAAATAA
1371963 TTAAT TTAAT TTAAT TTAAT TTAAT TATAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT T-TAAT
1371994 AATATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:1371983 original size:15 final size:16
Alignment explanation
Indices: 1371959--1371993 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1371949 TTAATAAAAA
1371959 ATAA-TTAATTTAATT
1 ATAATTTAATTTAATT
1371974 -TAATTTAATTTAATT
1 ATAATTTAATTTAATT
1371989 ATAAT
1 ATAAT
1371994 AATATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.17
15 11 0.61
16 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATAATTTAATTTAATT
Found at i:1373582 original size:39 final size:39
Alignment explanation
Indices: 1373443--1373677 Score: 176
Period size: 39 Copynumber: 6.1 Consensus size: 39
1373433 TAAGTACCTA
** * **
1373443 TAAAAACCTAATTTTGACTAAAAAACA-CTAAATAGAAT
1 TAAAAACCTAATTTTGACTAAAAATTATCAAAATAGCCT
* * *
1373481 T-AAAACCTAATTTTAACTTAAAATTATCAAAATAACCT
1 TAAAAACCTAATTTTGACTAAAAATTATCAAAATAGCCT
* * * *
1373519 TAAAGACCTAGTTTTGGGC-CAAAATTATCAAAATAGCCT
1 TAAAAACCTAATTTT-GACTAAAAATTATCAAAATAGCCT
*
1373558 TAAAAACCTAATTTTTACTAAAAATTAT-AAAATAGCCT
1 TAAAAACCTAATTTTGACTAAAAATTATCAAAATAGCCT
* * * **
1373596 TAAAAGGCTTGATTTTGAC-AAAAATTATTGAAATAGCC-
1 TAAAA-ACCTAATTTTGACTAAAAATTATCAAAATAGCCT
** * * * * * *
1373634 TAAAGGCTTGATTTTGAATCAAAGTTACCAAAATAGCCT
1 TAAAAACCTAATTTTGACTAAAAATTATCAAAATAGCCT
1373673 TAAAA
1 TAAAA
1373678 GCTCAATTTT
Statistics
Matches: 157, Mismatches: 32, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
37 33 0.21
38 52 0.33
39 71 0.45
40 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (39 bp):
TAAAAACCTAATTTTGACTAAAAATTATCAAAATAGCCT
Found at i:1373620 original size:77 final size:78
Alignment explanation
Indices: 1373482--1373634 Score: 186
Period size: 77 Copynumber: 2.0 Consensus size: 78
1373472 AAATAGAATT
* * *
1373482 AAAACCTAATTTTAACTTAAAATTATCAAAATAACCTTAAAGACCTAGTTTTGGGCCAAAATTAT
1 AAAACCTAATTTTAACTAAAAATTATCAAAATAACCTTAAAGACCTAGTTTTGGACAAAAATTAT
1373547 CAAAATAGCCTTA
66 CAAAATAGCCTTA
* * * *
1373560 AAAACCTAATTTTTACTAAAAATTAT-AAAATAGCCTTAAA-AGGCTTGATTTT-GACAAAAATT
1 AAAACCTAATTTTAACTAAAAATTATCAAAATAACCTTAAAGA-CCTAG-TTTTGGACAAAAATT
**
1373622 ATTGAAATAGCCT
64 ATCAAAATAGCCT
1373635 AAAGGCTTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.02
77 35 0.55
78 28 0.44
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (78 bp):
AAAACCTAATTTTAACTAAAAATTATCAAAATAACCTTAAAGACCTAGTTTTGGACAAAAATTAT
CAAAATAGCCTTA
Found at i:1373648 original size:37 final size:39
Alignment explanation
Indices: 1373539--1373678 Score: 144
Period size: 38 Copynumber: 3.6 Consensus size: 39
1373529 GTTTTGGGCC
* * * *
1373539 AAAATTATCAAAATAGCCTTAAAA-ACCTAATTTTTACTA
1 AAAATTAT-AAAATAGCCTTAAAAGGCTTGATTTTGACTA
1373578 AAAATTATAAAATAGCCTTAAAAGGCTTGATTTTGAC-A
1 AAAATTATAAAATAGCCTTAAAAGGCTTGATTTTGACTA
* * *
1373616 AAAATTATTGAAATAGCC-T-AAAGGCTTGATTTTGAATC
1 AAAATTA-TAAAATAGCCTTAAAAGGCTTGATTTTGACTA
* *
1373654 AAAGTTACCAAAATAGCCTTAAAAG
1 AAAATTA-TAAAATAGCCTTAAAAG
1373679 CTCAATTTTA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
37 16 0.19
38 38 0.45
39 27 0.32
40 4 0.05
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.31
Consensus pattern (39 bp):
AAAATTATAAAATAGCCTTAAAAGGCTTGATTTTGACTA
Found at i:1373701 original size:39 final size:39
Alignment explanation
Indices: 1373539--1373701 Score: 111
Period size: 38 Copynumber: 4.2 Consensus size: 39
1373529 GTTTTGGGCC
* * * *
1373539 AAAATTATCAAAATAGCCTTAAAAAC-CTAATTTTTACTA
1 AAAATTACCAAAATAGCCTTAAAAGCTC-AATTTTAACCA
* ** *
1373578 AAAATTA-TAAAATAGCCTTAAAAGGCTTGATTTTGA-CA
1 AAAATTACCAAAATAGCCTTAAAA-GCTCAATTTTAACCA
*** * ** *
1373616 AAAATTATTGAAATAGCC-TAAAGGCTTGATTTTGAATC-
1 AAAATTACCAAAATAGCCTTAAAAGCTCAATTTT-AACCA
*
1373654 AAAGTTACCAAAATAGCCTTAAAAGCTCAATTTTAACCA
1 AAAATTACCAAAATAGCCTTAAAAGCTCAATTTTAACCA
*
1373693 AAATTTACC
1 AAAATTACC
1373702 TTAAAAGCCT
Statistics
Matches: 99, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
37 10 0.10
38 45 0.45
39 44 0.44
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (39 bp):
AAAATTACCAAAATAGCCTTAAAAGCTCAATTTTAACCA
Found at i:1373746 original size:39 final size:38
Alignment explanation
Indices: 1373703--1373783 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
1373693 AAATTTACCT
1373703 TAAAAGCCTAGTTTCGACAAAAAATTTAC-AAAATAGCCC
1 TAAAAGCCTAGTTTCGAC-AAAAA-TTACTAAAATAGCCC
* * * * *
1373742 TAAAAGCTTGGTTTTGACTAAAATTACTAAAATAGCTC
1 TAAAAGCCTAGTTTCGACAAAAATTACTAAAATAGCCC
1373780 TAAA
1 TAAA
1373784 TATTCGATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 4 0.11
38 17 0.47
39 15 0.42
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (38 bp):
TAAAAGCCTAGTTTCGACAAAAATTACTAAAATAGCCC
Found at i:1374878 original size:13 final size:13
Alignment explanation
Indices: 1374860--1374884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1374850 CATAAAGTGT
1374860 TGTATCGATACAA
1 TGTATCGATACAA
1374873 TGTATCGATACA
1 TGTATCGATACA
1374885 TATTTTTTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1374966 original size:13 final size:13
Alignment explanation
Indices: 1374948--1374975 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1374938 ATTACTCAAA
1374948 TGTATCGATACAT
1 TGTATCGATACAT
1374961 TGTATCGATACAT
1 TGTATCGATACAT
1374974 TG
1 TG
1374976 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1375109 original size:52 final size:52
Alignment explanation
Indices: 1374981--1375101 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
1374971 CATTGATCTT
*
1374981 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
* *
1375033 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
*
1375085 TGTATCAATACATGCAG
1 TGTATCGATACATGCAG
1375102 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
Found at i:1378238 original size:23 final size:24
Alignment explanation
Indices: 1378202--1378248 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1378192 AACATAAAAA
1378202 ATTTTCAAACATTTT-AATTTTTT
1 ATTTTCAAACATTTTGAATTTTTT
* *
1378225 ATTTTTAAATATTTTGAATTTTTT
1 ATTTTCAAACATTTTGAATTTTTT
1378249 TCTTAAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (24 bp):
ATTTTCAAACATTTTGAATTTTTT
Found at i:1379715 original size:59 final size:58
Alignment explanation
Indices: 1379636--1379919 Score: 249
Period size: 59 Copynumber: 4.8 Consensus size: 58
1379626 TCACGCATAT
* * *
1379636 TAAGGA-TTATTATGCAATTTTCATGCATTTTGGGACCATTTAGAACATTTTTCGTGTC
1 TAAGGACTT-TTATCCAATTTTCATGCATTTTAGGACCATTTAGAACATTTTTCGTGTA
* * * * *
1379694 TTAGGTA-TTATTATCCAATTTTCATACATTTTAAGG-TCACTTAGAACATTTTTCGTAATA
1 TAAGG-ACTT-TTATCCAATTTTCATGCATTTT-AGGACCATTTAGAACATTTTTCGT-GTA
* * * *
1379754 TAAGGACTTTTATGCAATTTTCATGCATTTTA-AAGCCATTTAGAATATTTTTCATGATA
1 TAAGGACTTTTATCCAATTTTCATGCATTTTAGGA-CCATTTAGAACATTTTTCGTG-TA
* * * *
1379813 TAAGGACTTTTA-CGAATTTTCATGCATTATAGGATCATTTAGAACATTTTCTATGTTGTA
1 TAAGGACTTTTATCCAATTTTCATGCATTTTAGGACCATTTAGAACATTTT-T-CG-TGTA
** * *
1379873 TAA--ACTTTTATGTAATTTTCATGCATTTTAGGATCATATAGAACATT
1 TAAGGACTTTTATCCAATTTTCATGCATTTTAGGACCATTTAGAACATT
1379920 GTTCATGATT
Statistics
Matches: 185, Mismatches: 29, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
58 42 0.23
59 127 0.69
60 14 0.08
61 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (58 bp):
TAAGGACTTTTATCCAATTTTCATGCATTTTAGGACCATTTAGAACATTTTTCGTGTA
Found at i:1379915 original size:117 final size:118
Alignment explanation
Indices: 1379645--1379928 Score: 312
Period size: 117 Copynumber: 2.4 Consensus size: 118
1379635 TTAAGGATTA
* * * *
1379645 TTATGCAATTTTCATGCATTTTGGGACCATTTAGAACATTTTTCGTG-TCTTAGGTATTATTATC
1 TTATGCAATTTTCATGCATTTTAGGACCATTTAGAACATTTTTCATGATATAAGGTATTATTATC
*
1379709 CAATTTTCATACATTTTAAGGTCACTTAGAACATTTTTCGTAATATAAGGACTT
66 CAATTTTCATACATTATAAGGTCACTTAGAACATTTTTCGTAATATAA-GACTT
* *
1379763 TTATGCAATTTTCATGCATTTTA-AAGCCATTTAGAATATTTTTCATGATATAAGG-ACTT-TTA
1 TTATGCAATTTTCATGCATTTTAGGA-CCATTTAGAACATTTTTCATGATATAAGGTA-TTATTA
* * * * **
1379825 -CGAATTTTCATGCATTAT-AGGATCATTTAGAACATTTTCTATGTTGTATAA-ACTT
64 TCCAATTTTCATACATTATAAGG-TCACTTAGAACATTTT-T-CGTAATATAAGACTT
* * * *
1379880 TTATGTAATTTTCATGCATTTTAGGATCATATAGAACATTGTTCATGAT
1 TTATGCAATTTTCATGCATTTTAGGACCATTTAGAACATTTTTCATGAT
1379929 TTAGTGATTA
Statistics
Matches: 140, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
116 3 0.02
117 76 0.54
118 47 0.34
119 14 0.10
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (118 bp):
TTATGCAATTTTCATGCATTTTAGGACCATTTAGAACATTTTTCATGATATAAGGTATTATTATC
CAATTTTCATACATTATAAGGTCACTTAGAACATTTTTCGTAATATAAGACTT
Found at i:1379983 original size:58 final size:59
Alignment explanation
Indices: 1379886--1380029 Score: 139
Period size: 58 Copynumber: 2.5 Consensus size: 59
1379876 ACTTTTATGT
* * * * ** * *
1379886 AATTTTCATGCATTTTAGGATCATATAGAACATTGTTCATGAT-TTAGTGATTATTTTGC
1 AATTTACATGCATTTTAGGGTCATTTAAAACATACTTCATG-TCTTAGGGACTATTTTGC
* *
1379945 AA-TTACATGCATTTTAGGGTCATTTAAAATATACTTCATGTCTTAGGGACTATTTTGT
1 AATTTACATGCATTTTAGGGTCATTTAAAACATACTTCATGTCTTAGGGACTATTTTGC
** * *
1380003 AATTTTTATACATTTTAGGGCCATTTA
1 AATTTACATGCATTTTAGGGTCATTTA
1380030 GATTTCAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
57 1 0.01
58 46 0.67
59 22 0.32
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (59 bp):
AATTTACATGCATTTTAGGGTCATTTAAAACATACTTCATGTCTTAGGGACTATTTTGC
Found at i:1381438 original size:2 final size:2
Alignment explanation
Indices: 1381431--1381459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1381421 AAGAACCAAA
1381431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1381460 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1381464 original size:2 final size:2
Alignment explanation
Indices: 1381459--1381489 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1381449 ATATATATAT
1381459 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1381490 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1382218 original size:74 final size:74
Alignment explanation
Indices: 1382097--1382248 Score: 304
Period size: 74 Copynumber: 2.1 Consensus size: 74
1382087 AATTACTATT
1382097 ATTAAATAAATAAAATCGATGGAGATGAGATAAATCATGGTGAAAACCAAGCGAATGTTTAATAT
1 ATTAAATAAATAAAATCGATGGAGATGAGATAAATCATGGTGAAAACCAAGCGAATGTTTAATAT
1382162 AACATTATA
66 AACATTATA
1382171 ATTAAATAAATAAAATCGATGGAGATGAGATAAATCATGGTGAAAACCAAGCGAATGTTTAATAT
1 ATTAAATAAATAAAATCGATGGAGATGAGATAAATCATGGTGAAAACCAAGCGAATGTTTAATAT
1382236 AACATTATA
66 AACATTATA
1382245 ATTA
1 ATTA
1382249 TAGAGAAATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.28
Consensus pattern (74 bp):
ATTAAATAAATAAAATCGATGGAGATGAGATAAATCATGGTGAAAACCAAGCGAATGTTTAATAT
AACATTATA
Found at i:1384968 original size:68 final size:70
Alignment explanation
Indices: 1384845--1384982 Score: 199
Period size: 68 Copynumber: 2.0 Consensus size: 70
1384835 TATAACAATT
* * * * *
1384845 CTTTTTTATGATTTTTTTTTAAAAAAATTGTATAACTTAATGCATTCATATATATATATATATAT
1 CTTTTTCATGATTTTTTTTT-AAAAAATTGTACAACTTAATACATACATACATATATATATATAT
1384910 ATATAA
65 ATATAA
*
1384916 CTTTTTCATGA-TTTTTTTT-AAAAATTGTACAACTTAATACATACATCCATATATATATATATA
1 CTTTTTCATGATTTTTTTTTAAAAAATTGTACAACTTAATACATACATACATATATATATATATA
1384979 TATA
66 TATA
1384983 TATATATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
68 43 0.70
70 8 0.13
71 10 0.16
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (70 bp):
CTTTTTCATGATTTTTTTTTAAAAAATTGTACAACTTAATACATACATACATATATATATATATA
TATAA
Found at i:1384971 original size:2 final size:2
Alignment explanation
Indices: 1384964--1384992 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1384954 ACATACATCC
1384964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1384993 GCCTTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1387140 original size:17 final size:18
Alignment explanation
Indices: 1387109--1387146 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1387099 TAATTATTTT
1387109 TTTATATTATATTAA-AA
1 TTTATATTATATTAATAA
* *
1387126 TTTATATTGTGTTAATAA
1 TTTATATTATATTAATAA
1387144 TTT
1 TTT
1387147 TTTTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTATATTATATTAATAA
Found at i:1387483 original size:18 final size:16
Alignment explanation
Indices: 1387413--1387507 Score: 64
Period size: 16 Copynumber: 5.8 Consensus size: 16
1387403 TATGTCATAA
* *
1387413 ATTTTAATACATTAAT
1 ATTTTAATATATTTAT
* * * * *
1387429 AATTCAATTTATATAA
1 ATTTTAATATATTTAT
1387445 ATTTTAATATATTTAT
1 ATTTTAATATATTTAT
* *
1387461 CTTTTTATATCATATTAT
1 ATTTTAATAT-AT-TTAT
*
1387479 ATTTTATTATATTTAT
1 ATTTTAATATATTTAT
* *
1387495 ATTATAATCTATT
1 ATTTTAATATATT
1387508 AAGATATAAA
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
16 42 0.74
17 4 0.07
18 11 0.19
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAATATATTTAT
Found at i:1387491 original size:10 final size:11
Alignment explanation
Indices: 1387472--1387500 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1387462 TTTTTATATC
1387472 ATATTATATTT
1 ATATTATATTT
1387483 -TATTATATTT
1 ATATTATATTT
1387493 ATATTATA
1 ATATTATA
1387501 ATCTATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATTATATTT
Found at i:1387761 original size:33 final size:31
Alignment explanation
Indices: 1387724--1387788 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
1387714 GTAATACAAT
1387724 ACAAATAGATAAACATGTCAAAATTTATACTAA
1 ACAAAT-GATAAACATGTCAAAATTTATA-TAA
* * **
1387757 ACAAATTATTAATGTGTCAAAATTTATATAA
1 ACAAATGATAAACATGTCAAAATTTATATAA
1387788 A
1 A
1387789 TATATAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.14
32 18 0.64
33 6 0.21
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.32
Consensus pattern (31 bp):
ACAAATGATAAACATGTCAAAATTTATATAA
Found at i:1387839 original size:21 final size:22
Alignment explanation
Indices: 1387815--1387857 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1387805 TATAATTATA
1387815 ATATAAAAAAATAATAT-GAAT
1 ATATAAAAAAATAATATAGAAT
** *
1387836 ATATTGACAAATAATATAGAAT
1 ATATAAAAAAATAATATAGAAT
1387858 TAAGAGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (22 bp):
ATATAAAAAAATAATATAGAAT
Found at i:1388156 original size:52 final size:53
Alignment explanation
Indices: 1388098--1388202 Score: 151
Period size: 52 Copynumber: 2.0 Consensus size: 53
1388088 AAGACAAATT
* *
1388098 TGTAAAATCTACATATA-AATAATTATTAACGCATC-AAATTTATATAAATATA
1 TGTAAAATCTACATATAGAA-AATTAATAACGCATCAAAATATATATAAATATA
* *
1388150 TGTAAAATCTACATATAGAAAATTAATAACGTATCAAAATATATATACATATA
1 TGTAAAATCTACATATAGAAAATTAATAACGCATCAAAATATATATAAATATA
1388203 ATAAATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
52 30 0.64
53 17 0.36
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (53 bp):
TGTAAAATCTACATATAGAAAATTAATAACGCATCAAAATATATATAAATATA
Found at i:1388199 original size:36 final size:36
Alignment explanation
Indices: 1388159--1388232 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
1388149 ATGTAAAATC
*
1388159 TACATATAGA-AAATTAATAACGTA-TCAAAATATATA
1 TACATATA-ATAAATTAATAAAG-AGTCAAAATATATA
* *
1388195 TACATATAATAAATTATTAAAGAGTCAAAATTTATA
1 TACATATAATAAATTAATAAAGAGTCAAAATATATA
1388231 TA
1 TA
1388233 GCTAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (36 bp):
TACATATAATAAATTAATAAAGAGTCAAAATATATA
Found at i:1388714 original size:2 final size:2
Alignment explanation
Indices: 1388709--1388748 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1388699 CAAAAAATAC
* *
1388709 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1388749 TCACTGTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1389792 original size:20 final size:21
Alignment explanation
Indices: 1389767--1389811 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1389757 AATAATTATT
1389767 TAAAA-TATATATTTAATAAA
1 TAAAATTATATATTTAATAAA
* * *
1389787 TAAAATTTTATTTTTATTAAA
1 TAAAATTATATATTTAATAAA
1389808 TAAA
1 TAAA
1389812 TAATTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTATATATTTAATAAA
Found at i:1390726 original size:15 final size:15
Alignment explanation
Indices: 1390706--1390735 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1390696 GCATGGATAT
*
1390706 GATAAGAAGAAAAAG
1 GATAAGAAAAAAAAG
1390721 GATAAGAAAAAAAAG
1 GATAAGAAAAAAAAG
1390736 CAGACAGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (15 bp):
GATAAGAAAAAAAAG
Found at i:1391102 original size:4 final size:4
Alignment explanation
Indices: 1391095--1391138 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
1391085 TCCTACATAA
*
1391095 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATTT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1391139 TTCAAGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
ATCT
Found at i:1392371 original size:31 final size:31
Alignment explanation
Indices: 1392336--1392411 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1392326 GTTTACTAGT
* *
1392336 AAAATTCAATTAAAAATTAAAGTTAAATAAC
1 AAAATTCAATAAAAAATCAAAGTTAAATAAC
* * *
1392367 AAAA-TCAAATAAAAAATCGAAGTTTAATTAC
1 AAAATTC-AATAAAAAATCAAAGTTAAATAAC
*
1392398 AAAATTCAACAAAA
1 AAAATTCAATAAAA
1392412 TAAAAAACAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 2 0.05
31 33 0.89
32 2 0.05
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.25
Consensus pattern (31 bp):
AAAATTCAATAAAAAATCAAAGTTAAATAAC
Found at i:1394457 original size:2 final size:2
Alignment explanation
Indices: 1394450--1394484 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1394440 GACGGTATTT
1394450 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1394485 TTGGCAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1398124 original size:20 final size:21
Alignment explanation
Indices: 1398081--1398140 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
1398071 GTTGGGCTCA
* *
1398081 ATGTATTGATACATTTTA-CT
1 ATGTATTGATACAATTCATCT
1398101 ATGTATTGATACAATTCATC-
1 ATGTATTGATACAATTCATCT
** *
1398121 ATGTATCAATACAATGCATC
1 ATGTATTGATACAATTCATC
1398141 GATGCTAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGTATTGATACAATTCATCT
Found at i:1398222 original size:19 final size:20
Alignment explanation
Indices: 1398198--1398244 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1398188 TTAAGTGTGT
1398198 ATCGATACTAAG-AACATGA
1 ATCGATACTAAGCAACATGA
* *
1398217 ATCGATACTAAGCAATATGT
1 ATCGATACTAAGCAACATGA
1398237 ATCGATAC
1 ATCGATAC
1398245 ATTTGGGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGATACTAAGCAACATGA
Found at i:1398242 original size:20 final size:19
Alignment explanation
Indices: 1398195--1398244 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1398185 CAATTAAGTG
1398195 TGTATCGATACTAAGAACA
1 TGTATCGATACTAAGAACA
* *
1398214 TGAATCGATACTAAGCAATA
1 TGTATCGATACTAAG-AACA
1398234 TGTATCGATAC
1 TGTATCGATAC
1398245 ATTTGGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (19 bp):
TGTATCGATACTAAGAACA
Found at i:1398805 original size:21 final size:21
Alignment explanation
Indices: 1398781--1398851 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1398771 ATACTCCTCC
1398781 TTAATAAAATTTTTCTCCCCT
1 TTAATAAAATTTTTCTCCCCT
*
1398802 TTAATGAAATATTTAATACT-CCCT
1 TTAAT-AAA-ATTT--TTCTCCCCT
* * *
1398826 CTTGATAGAATTTTTCTCCCCC
1 -TTAATAAAATTTTTCTCCCCT
1398848 TTAA
1 TTAA
1398852 CAAATTATCC
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 11 0.29
22 6 0.16
23 8 0.21
24 6 0.16
25 7 0.18
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (21 bp):
TTAATAAAATTTTTCTCCCCT
Found at i:1400389 original size:13 final size:13
Alignment explanation
Indices: 1400371--1400419 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
1400361 ATAGTGCCTA
*
1400371 TGTATCGATATAG
1 TGTATCGATACAG
* *
1400384 TGTATCGACACAA
1 TGTATCGATACAG
*
1400397 TATATCGATACAG
1 TGTATCGATACAG
1400410 TGTATCGATA
1 TGTATCGATA
1400420 GTAAGAACAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1406307 original size:20 final size:22
Alignment explanation
Indices: 1406284--1406326 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1406274 CAAAGCAATA
1406284 TGTATCGATAC-TTCT-GGGTT
1 TGTATCGATACTTTCTAGGGTT
*
1406304 TGTATTGATACTTTCTAGGGTT
1 TGTATCGATACTTTCTAGGGTT
1406326 T
1 T
1406327 TGACCTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (22 bp):
TGTATCGATACTTTCTAGGGTT
Found at i:1407070 original size:18 final size:18
Alignment explanation
Indices: 1407047--1407082 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1407037 ATAATCTCAC
*
1407047 CTTTTTATAAAGCAAGTT
1 CTTTTTATAAAACAAGTT
1407065 CTTTTTATAAAACAAGTT
1 CTTTTTATAAAACAAGTT
1407083 TATTTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (18 bp):
CTTTTTATAAAACAAGTT
Found at i:1408812 original size:31 final size:31
Alignment explanation
Indices: 1408777--1408843 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1408767 TAAAACCGTT
1408777 TTTGATGAAAAAT-G-AAAAGAAATGATGTAAA
1 TTTGATG-AAAATCGAAAAAGAAATGATG-AAA
* *
1408808 TTTGATGAAATTCGAAAAAGAATTGATGAAA
1 TTTGATGAAAATCGAAAAAGAAATGATGAAA
1408839 TTTGA
1 TTTGA
1408844 GATTGAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.12
31 16 0.50
32 12 0.38
ACGTcount: A:0.49, C:0.01, G:0.19, T:0.30
Consensus pattern (31 bp):
TTTGATGAAAATCGAAAAAGAAATGATGAAA
Found at i:1408950 original size:13 final size:13
Alignment explanation
Indices: 1408932--1408968 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1408922 ATAGTTCCCT
*
1408932 TGTATCGATACAG
1 TGTATCGATACAA
1408945 TGTATCGATACAA
1 TGTATCGATACAA
1408958 TGTATCGATAC
1 TGTATCGATAC
1408969 TATAAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1415255 original size:13 final size:13
Alignment explanation
Indices: 1415237--1415261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1415227 ACCAAGATCA
1415237 TGTATCGATACAT
1 TGTATCGATACAT
1415250 TGTATCGATACA
1 TGTATCGATACA
1415262 AAGCAATATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1415295 original size:20 final size:22
Alignment explanation
Indices: 1415272--1415312 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1415262 AAGCAATATG
1415272 TATCGATAC-TTCT-GGGTTTC
1 TATCGATACTTTCTAGGGTTTC
1415292 TATCGATACTTTCTAGGGTTT
1 TATCGATACTTTCTAGGGTTT
1415313 TGACCTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (22 bp):
TATCGATACTTTCTAGGGTTTC
Found at i:1417423 original size:68 final size:67
Alignment explanation
Indices: 1417303--1417494 Score: 204
Period size: 68 Copynumber: 2.8 Consensus size: 67
1417293 TTTGATCATC
* * * * * * * *
1417303 ATCTCAACATATTACCAAATGACAAGAAGTCACCTATACTAGTAAACAACCTCAAAAGACTAATT
1 ATCTCAACATATAAGCAAATGAC-ATAAGTCACCTATGCTAATAAGCGACCTCAAAAGACTAATC
1417368 GAT
65 GAT
* * * * * * *
1417371 ATCTTAGCATATAAGTAAATGACACTAAGTCACCTATGTTAATAAGCGACCTCAAAGGTCTGATC
1 ATCTCAACATATAAGCAAATGACA-TAAGTCACCTATGCTAATAAGCGACCTCAAAAGACTAATC
1417436 GAT
65 GAT
* *
1417439 ATCTCAACATATAAGCAAGTGATATCAAGTCACCTATGCTAATAAGCGACCTCAAA
1 ATCTCAACATATAAGCAAATGACAT-AAGTCACCTATGCTAATAAGCGACCTCAAA
1417495 TATTTGATCA
Statistics
Matches: 101, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
67 2 0.02
68 99 0.98
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.25
Consensus pattern (67 bp):
ATCTCAACATATAAGCAAATGACATAAGTCACCTATGCTAATAAGCGACCTCAAAAGACTAATCG
AT
Found at i:1417503 original size:68 final size:68
Alignment explanation
Indices: 1417295--1417547 Score: 202
Period size: 68 Copynumber: 3.7 Consensus size: 68
1417285 GTTAAAAGTT
* * * * ** * * * *
1417295 TGATCATCATCTCAACATATTACCAAATGACAAGAAGTCACCTATACTAGTAAACAACCTCAAAA
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTC-AAA
1417360 GA-C
65 GATC
* ** * * * * * * *
1417363 TAATTGATATCTTAGCATATAAGTAAATGACACTAAGTCACCTATGTTAATAAGCGACCTCAAAG
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTCAAAG
*
1417428 GTC
66 ATC
* * * * *
1417431 TGATCGATATCTCAACATATAAGCAAGTGATATCAAGTCACCTATGCTAATAAGCGACCTCAAAT
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTCAAAG
*
1417496 ATT
66 ATC
* * * * *
1417499 TGATCAACATCTTAGCATATAAGTAAGTGACACCAAGTTACTTATGCTA
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTA
1417548 GTGAAAAAGC
Statistics
Matches: 144, Mismatches: 40, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
67 4 0.03
68 140 0.97
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (68 bp):
TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTCAAAG
ATC
Found at i:1418070 original size:39 final size:39
Alignment explanation
Indices: 1417958--1418077 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 39
1417948 TAAGTACCTA
* * * * *
1417958 TAAAAACTCAGTTTTGACTAAAAATCACCAAAATAGCTC
1 TAAAAACTAAGTTTTAACTCAAAATTACCAAAATAGCTT
*
1417997 T-AAAACTCAGTTTTAACTCAAAATTACCAAAATAGCTT
1 TAAAAACTAAGTTTTAACTCAAAATTACCAAAATAGCTT
* * * *
1418035 TAAAAATCTAATTTTTACCT-AAAATTATCAAAATAGCCT
1 TAAAAA-CTAAGTTTTAACTCAAAATTACCAAAATAGCTT
1418074 TAAA
1 TAAA
1418078 GGCTCGATTT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 34 0.49
39 26 0.37
40 10 0.14
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (39 bp):
TAAAAACTAAGTTTTAACTCAAAATTACCAAAATAGCTT
Found at i:1418126 original size:38 final size:39
Alignment explanation
Indices: 1418055--1418251 Score: 113
Period size: 39 Copynumber: 5.1 Consensus size: 39
1418045 ATTTTTACCT
*
1418055 AAAATTATCAAAATAGCCTTAAAGGCTCGATTTTGACAA
1 AAAATTATCAAAATAGCCTAAAAGGCTCGATTTTGACAA
* *
1418094 AAAATTATTAAAATAGCC-AAAAGGC-CTGATTTTGA-ATC
1 AAAATTATCAAAATAGCCTAAAAGGCTC-GATTTTGACA-A
* * * * ***
1418132 AAAGTTACCAAAATAGCCTCAAAA-GCCCAATTCAAACCAA
1 AAAATTATCAAAATAGCCT-AAAAGGCTCGATTTTGA-CAA
* * * *
1418172 AAAATT-CCAAAATAACCTGAAAGGC-CTAGTTTTGAACAA
1 AAAATTATCAAAATAGCCTAAAAGGCTCGA-TTTTG-ACAA
* * * *
1418211 AAATTTA-CAAAATAGCCCTAAAA-GCTTGGTTTTGACTA
1 AAAATTATCAAAATAG-CCTAAAAGGCTCGATTTTGACAA
1418249 AAA
1 AAA
1418252 TTTGATTTTG
Statistics
Matches: 120, Mismatches: 25, Indels: 27
0.70 0.15 0.16
Matches are distributed among these distances:
37 2 0.02
38 40 0.33
39 60 0.50
40 17 0.14
41 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.25
Consensus pattern (39 bp):
AAAATTATCAAAATAGCCTAAAAGGCTCGATTTTGACAA
Found at i:1419783 original size:8 final size:8
Alignment explanation
Indices: 1419772--1419809 Score: 53
Period size: 7 Copynumber: 4.9 Consensus size: 8
1419762 ACTAGAAAAG
1419772 AAAAAG-A
1 AAAAAGAA
1419779 AAAAAG-A
1 AAAAAGAA
1419786 AAAAAGAA
1 AAAAAGAA
1419794 AAAAAGAA
1 AAAAAGAA
1419802 AAAGAAGA
1 AAA-AAGA
1419810 GAGGGTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 13 0.45
8 12 0.41
9 4 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Done.