Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_pilon, whole genome shotgun sequence
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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 50
Found at i:2151454 original size:145 final size:144
Alignment explanation
Indices: 2151207--2152309 Score: 994
Period size: 145 Copynumber: 7.6 Consensus size: 144
2151197 CAGTCTAATG
* * * *
2151207 AGGTTACAGTTCATAAGATTGAAGTGTTAGACATGTTTTCGATATAGGCAGGTAATTTAGGGGGA
1 AGGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTACTTTAGGGGGA
* * * * * * * * * *
2151272 AACAAAAGGAAAATATTTTGAGTAACTCTAGACTATTCATTCACTAATCATTGAGTAAACCTTAT
66 AATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTAA
*
2151337 CTGAAGAACCTAACG
131 CTG-AGAACCTAACA
* * * * * *
2151352 AGGTTGCAATTCATAATATTGAAGTGTTAGATGTGTTTTCGATATAGGCAGGCACTTTAGGGGGA
1 AGGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTACTTTAGGGGGA
* * * * * *
2151417 AACAAAAGGAAAATAGTTAGAGCAACACAAGAGTATTCACTTATTAATCATTTAATAATCCTTAA
66 AATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTAA
**
2151482 CTCGAG--CCTAATG
131 CT-GAGAACCTAACA
* * *
2151495 TGGTTACAGTTCATAACATTGAAGTGTTGGATATG-TTTCCATATAGGTAGGGTAGGTGCTTTAG
1 AGGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTA-GGTA----CTTTAG
* * * * *
2151559 GGGGAAGTGAAAGGAAAATACTAGTTAAAGCAGCGCAAGAGTATTCACTCACTAATCATTGAATG
61 GGGGAAATAAAAGG-AAA-A-TAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATA
** * **
2151624 AGTCTTAACTCGAGAATCTAATG
123 AACCTTAACT-GAGAACCTAACA
* * * ** * * * * *
2151647 AGGTTACAATTCATAAGATCGAAGCATTAGATGA-GTTTACGATCTAGGTTGGTGCTTTAGGGTG
1 AGGTTACAGTTCATAACATTGAAGTGTTAGAT-ATGTTTTCGATATAGGTAGGTACTTTAGGGGG
* ** * * * * * ** *
2151711 -AATAAAAGGAAAACAGCGAGAGCGATGCAAGGGTAGTCACTCACTAATC-CTGGTTAAACCTTG
65 AAATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTA
*
2151774 ACTTGAGTACCTAACAA
130 AC-TGAGAACCTAAC-A
* ** * * * *
2151791 AGGTTACAGTTCATAACATAT-ATGTGTTAGATATAATTTCAATATACGTTGGTA--TTA-TGGG
1 AGGTTACAGTTCATAACAT-TGAAGTGTTAGATATGTTTTCGATATAGGTAGGTACTTTAGGGGG
* * * *
2151852 AAATAAAAAGAAAATAGTTAGAGCAACTCAAGAG-ATTCACTCGCTAATCATTGAATAAA-CTAA
65 AAATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTA
**
2151915 GACTCGAGAATGTAACA
130 -ACT-GAGAACCTAACA
* * * * *
2151932 AGGTTACCGTTCATAACATTGAAGTGTTAGATAGGTTTTCGATATATGTAGGTAGTTTAGGGTGT
1 AGGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTACTTTAGGG-GG
* *** *
2151997 AAAAAAAAGGAAAATAGTTAGAGCAATTTAAGAGTATTCACTCACTAATCATTCAATAAACCTTA
65 AAATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTA
* *
2152062 ATGTGAGAATCTAACA
130 A-CTGAGAACCTAACA
** * * *
2152078 AGGTTACAGTTCATAACATCAAACTGTTAGGTATGTTTTCGATATGGGTAGGTA--TTAGGGGGA
1 AGGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTACTTTAGGGGGA
* * *
2152141 AATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATCCACTCACTAATAATTGAATAAATCTTAA
66 AATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTAA
2152206 CTTGAGAACCTAACA
131 C-TGAGAACCTAACA
* * * *
2152221 AGGTTACAGTTCATAACATT-AGAGTGTTTGATATGTTTTCGATAGAGGTAGTTCCTTTAGGGGG
1 AGGTTACAGTTCATAACATTGA-AGTGTTAGATATGTTTTCGATATAGGTAGGTACTTTAGGGGG
*
2152285 AAATAAAAGGAAAATAGTTTGAGCA
65 AAATAAAAGGAAAATAGTTAGAGCA
2152310 TCAGAATACT
Statistics
Matches: 767, Mismatches: 158, Indels: 66
0.77 0.16 0.07
Matches are distributed among these distances:
140 1 0.00
141 63 0.08
142 57 0.07
143 174 0.23
144 73 0.10
145 178 0.23
146 85 0.11
147 28 0.04
148 12 0.02
149 1 0.00
150 49 0.06
152 35 0.05
153 11 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (144 bp):
AGGTTACAGTTCATAACATTGAAGTGTTAGATATGTTTTCGATATAGGTAGGTACTTTAGGGGGA
AATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTAA
CTGAGAACCTAACA
Found at i:2152212 original size:143 final size:144
Alignment explanation
Indices: 2151207--2152309 Score: 922
Period size: 143 Copynumber: 7.6 Consensus size: 144
2151197 CAGTCTAATG
* * * * *
2151207 AGGTTACAGTTCATAAGATTGAAGTGTTAGACATGTTTTCGATATAGGCAGGTAATTTAGGGGGA
1 AGGTTACAGTTCATAACATTAAAGTGTTAGATATGTTTTCGATATAGGTAGGTCA-TTAGGGGGA
* * * * * * * * * *
2151272 AACAAAAGGAAAATATTTTGAGTAACTCTAGACTATTCATTCACTAATCATTGAGTAAACCTTAT
65 AATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTAA
*
2151337 C-TGAAGAACCTAACG
130 CTTG-AGAACCTAACA
* * * * * *
2151352 AGGTTGCAATTCATAATATTGAAGTGTTAGATGTGTTTTCGATATAGGCAGG-CACTTTAGGGGG
1 AGGTTACAGTTCATAACATTAAAGTGTTAGATATGTTTTCGATATAGGTAGGTCA--TTAGGGGG
* * * * * *
2151416 AAACAAAAGGAAAATAGTTAGAGCAACACAAGAGTATTCACTTATTAATCATTTAATAATCCTTA
64 AAATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTA
* **
2151481 ACTCGAG--CCTAATG
129 ACTTGAGAACCTAACA
* * * * * *
2151495 TGGTTACAGTTCATAACATTGAAGTGTTGGATATGTTTCCATATAGGTAGGGTAGGTGCTTTAGG
1 AGGTTACAGTTCATAACATTAAAGTGTTAGATATGTTTTC-GATA--TA-GGTAGGT-CATTAGG
* * * * *
2151560 GGGAAGTGAAAGGAAAATACTAGTTAAAGCAGCGCAAGAGTATTCACTCACTAATCATTGAATGA
61 GGGAAATAAAAGG-AAA-A-TAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAA
** * * **
2151625 GTCTTAACTCGAGAATCTAATG
123 ACCTTAACTTGAGAACCTAACA
* * ** ** * * * * *
2151647 AGGTTACAATTCATAAGATCGAAGCATTAGATGA-GTTTACGATCTAGGTTGGTGCTTTAGGGTG
1 AGGTTACAGTTCATAACATTAAAGTGTTAGAT-ATGTTTTCGATATAGGTAGGT-CATTAGGGGG
* ** * * * * * ** *
2151711 -AATAAAAGGAAAACAGCGAGAGCGATGCAAGGGTAGTCACTCACTAATC-CTGGTTAAACCTTG
64 AAATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTA
*
2151774 ACTTGAGTACCTAACAA
129 ACTTGAGAACCTAAC-A
* ** * * * *
2151791 AGGTTACAGTTCATAACA-TATATGTGTTAGATATAATTTCAATATACGTTGGT-ATTA-TGGGA
1 AGGTTACAGTTCATAACATTA-AAGTGTTAGATATGTTTTCGATATAGGTAGGTCATTAGGGGGA
* * * *
2151853 AATAAAAAGAAAATAGTTAGAGCAACTCAAGAG-ATTCACTCGCTAATCATTGAATAAA-CTAAG
65 AATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTA-
* **
2151916 ACTCGAGAATGTAACA
129 ACTTGAGAACCTAACA
* * * *
2151932 AGGTTACCGTTCATAACATTGAAGTGTTAGATAGGTTTTCGATATATGTAGGT-AGTTTAGGGTG
1 AGGTTACAGTTCATAACATTAAAGTGTTAGATATGTTTTCGATATAGGTAGGTCA--TTAGGG-G
* * *** *
2151996 TAAAAAAAAGGAAAATAGTTAGAGCAATTTAAGAGTATTCACTCACTAATCATTCAATAAACCTT
63 GAAATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTT
*
2152061 AA-TGTGAGAATCTAACA
128 AACT-TGAGAACCTAACA
* * * *
2152078 AGGTTACAGTTCATAACATCAAACTGTTAGGTATGTTTTCGATATGGGTAGGT-ATTAGGGGGAA
1 AGGTTACAGTTCATAACATTAAAGTGTTAGATATGTTTTCGATATAGGTAGGTCATTAGGGGGAA
* * *
2152142 ATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATCCACTCACTAATAATTGAATAAATCTTAAC
66 ATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTAAC
2152207 TTGAGAACCTAACA
131 TTGAGAACCTAACA
* * * * *
2152221 AGGTTACAGTTCATAACATTAGAGTGTTTGATATGTTTTCGATAGAGGTAGTTCCTTTAGGGGGA
1 AGGTTACAGTTCATAACATTAAAGTGTTAGATATGTTTTCGATATAGGTAGGT-CATTAGGGGGA
*
2152286 AATAAAAGGAAAATAGTTTGAGCA
65 AATAAAAGGAAAATAGTTAGAGCA
2152310 TCAGAATACT
Statistics
Matches: 765, Mismatches: 162, Indels: 62
0.77 0.16 0.06
Matches are distributed among these distances:
141 61 0.08
142 46 0.06
143 177 0.23
144 76 0.10
145 177 0.23
146 87 0.11
147 30 0.04
148 19 0.02
149 4 0.01
150 49 0.06
151 2 0.00
152 36 0.05
153 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (144 bp):
AGGTTACAGTTCATAACATTAAAGTGTTAGATATGTTTTCGATATAGGTAGGTCATTAGGGGGAA
ATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATTCACTCACTAATCATTGAATAAACCTTAAC
TTGAGAACCTAACA
Found at i:2152366 original size:288 final size:288
Alignment explanation
Indices: 2151341--2152385 Score: 660
Period size: 288 Copynumber: 3.6 Consensus size: 288
2151331 CCTTATCTGA
* * * * * * *
2151341 AGAACCTAACGAGGTTGCAATTCATAATATTGAAGTGTTAGAT-GTGTTTTCGATATAGGCAGGC
1 AGAACCTAACAAGGTTACAGTTCATAACATTGAAGTGTTAGATAG-GTTTTCGATAGAGGTAGGT
* * * * * **
2151405 ACTTTAGGG-GGAAACAAAAGGAAAATAGTTAGAGCAACACAAGAGTATTCACTTATTAATCATT
65 ACTTTAGGGTGGAAAAAAAAGGAAAATAGTTAGAGCAATAGAAGACTATTCACTCACCAATCATT
* * * * *** * *
2151469 TAATAATCCTTAACT-C--GAGCCTAATGTGGTTACAGTTCATAACAT--TGAAGTGTTGGATAT
130 CAATAAACCTTAA-TGCAACAACCTAACAAGGTTACAGTTCATAACATCAT-AACTGTTAGATAT
* * * * * * * *
2151529 -GTTTCCATATAGGTAGGGTAGGTGCTTTAGGGGGAAGTGAAAGGAAAATACTAGTTAAAGCAGC
193 AATTT-CA-ATA--TA-CGTAGGT--ATTA-GGGGAAATAAAAAG-AAA-A-TAGTTAGAGCAAC
* * ** *
2151593 GCAAGAGTATTCACTCACTAATCATTGAATGAGTCTTA-ACTCG
247 GCAAGAG-ATCCACTCACTAATAATTGAAT-AAACTAAGACTCG
* ** * * * ** * ** *
2151636 AGAATCTAATGAGGTTACAATTCATAAGATCGAAGCATTAGAT-GAGTTTACGATCTAGGTTGGT
1 AGAACCTAACAAGGTTACAGTTCATAACATTGAAGTGTTAGATAG-GTTTTCGATAGAGGTAGGT
* * * ** * ** * * *
2151700 GCTTTAGGGT-G-AATAAAAGGAAAACAGCGAGAGCGAT-GCAAGGGTAGTCACTCACTAATC-C
65 ACTTTAGGGTGGAAAAAAAAGGAAAATAGTTAGAGCAATAG-AAGACTATTCACTCACCAATCAT
*** * ** **
2151761 TGGTTAAACCTTGACTTG--AGTACCTAACAAAGGTTACAGTTCATAACAT-ATATGTGTTAGAT
129 TCAATAAACCTT-A-ATGCAACAACCTAAC-AAGGTTACAGTTCATAACATCATAACTGTTAGAT
* * *
2151823 ATAATTTCAATATACGTTGGTATTATGGGAAATAAAAAGAAAATAGTTAGAGCAACTCAAGAGAT
191 ATAATTTCAATATACGTAGGTATTAGGGGAAATAAAAAGAAAATAGTTAGAGCAACGCAAGAGAT
* * *
2151888 TCACTCGCTAATCATTGAATAAACTAAGACTCG
256 CCACTCACTAATAATTGAATAAACTAAGACTCG
** * * *
2151921 AGAATGTAACAAGGTTACCGTTCATAACATTGAAGTGTTAGATAGGTTTTCGATATATGTAGGTA
1 AGAACCTAACAAGGTTACAGTTCATAACATTGAAGTGTTAGATAGGTTTTCGATAGAGGTAGGTA
* * ** * *
2151986 GTTTAGGGTGTAAAAAAAAGGAAAATAGTTAGAGCAATTTAAGAGTATTCACTCACTAATCATTC
66 CTTTAGGGTGGAAAAAAAAGGAAAATAGTTAGAGCAATAGAAGACTATTCACTCACCAATCATTC
** * * * **
2152051 AATAAACCTTAATGTGAGAATCTAACAAGGTTACAGTTCATAACATCA-AACTGTTAGGTATGTT
131 AATAAACCTTAATGCAACAACCTAACAAGGTTACAGTTCATAACATCATAACTGTTAGATATAAT
* ** *
2152115 TTCGATATGGGTAGGTATTAGGGGGAAATAAAAGGAAAATAGTTAGAGCAACGCAAGAGTATCCA
196 TTCAATATACGTAGGTATTA-GGGGAAATAAAAAGAAAATAGTTAGAGCAACGCAAGAG-ATCCA
* *
2152180 CTCACTAATAATTGAATAAATCTTA-ACTTG
259 CTCACTAATAATTGAATAAA-CTAAGACTCG
* * *
2152210 AGAACCTAACAAGGTTACAGTTCATAACATT-AGAGTGTTTGATATGTTTTCGATAGAGGTAGTT
1 AGAACCTAACAAGGTTACAGTTCATAACATTGA-AGTGTTAGATAGGTTTTCGATAGAGGTAGGT
* * * * * * * * **
2152274 CCTTTAGGG-GGAAATAAAAGGAAAATAGTTTGAGC-ATCAGAATACTTTTCATTCGCCATTTGT
65 ACTTTAGGGTGGAAAAAAAAGGAAAATAGTTAGAGCAAT-AGAAGACTATTCACTCACCAATCAT
* * **
2152337 TGAATAAACCTTGACT-CAACAACCTAACAAGGTTGTAGTTCATAACATC
129 TCAATAAACCTT-AATGCAACAACCTAACAAGGTTACAGTTCATAACATC
2152386 CTGGTATTCA
Statistics
Matches: 593, Mismatches: 133, Indels: 55
0.76 0.17 0.07
Matches are distributed among these distances:
284 4 0.01
285 83 0.14
286 20 0.03
287 91 0.15
288 132 0.22
289 99 0.17
290 6 0.01
292 5 0.01
293 10 0.02
294 39 0.07
295 69 0.12
296 31 0.05
297 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (288 bp):
AGAACCTAACAAGGTTACAGTTCATAACATTGAAGTGTTAGATAGGTTTTCGATAGAGGTAGGTA
CTTTAGGGTGGAAAAAAAAGGAAAATAGTTAGAGCAATAGAAGACTATTCACTCACCAATCATTC
AATAAACCTTAATGCAACAACCTAACAAGGTTACAGTTCATAACATCATAACTGTTAGATATAAT
TTCAATATACGTAGGTATTAGGGGAAATAAAAAGAAAATAGTTAGAGCAACGCAAGAGATCCACT
CACTAATAATTGAATAAACTAAGACTCG
Found at i:2158562 original size:20 final size:20
Alignment explanation
Indices: 2158522--2158563 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2158512 AATTTGATCC
* *
2158522 AAATCAACATTCTAACCTTA
1 AAATCAACATTCCAACATTA
*
2158542 AAATCAACATTCCAATATTA
1 AAATCAACATTCCAACATTA
2158562 AA
1 AA
2158564 TTCCAGCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATCAACATTCCAACATTA
Found at i:2158835 original size:10 final size:10
Alignment explanation
Indices: 2158809--2158845 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2158799 AACTTCTAAC
2158809 ATCAATTTCA
1 ATCAATTTCA
2158819 TATCAATTTCA
1 -ATCAATTTCA
2158830 ATCAATTTCA
1 ATCAATTTCA
2158840 A-CAATT
1 ATCAATT
2158846 CTCCATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.19
10 11 0.42
11 10 0.38
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATCAATTTCA
Found at i:2168623 original size:85 final size:85
Alignment explanation
Indices: 2168480--2168647 Score: 327
Period size: 85 Copynumber: 2.0 Consensus size: 85
2168470 TTTCACTAGA
*
2168480 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCTGAGTCTTGATAGATG
1 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
2168545 TCAAACTGGATGATACTGGC
66 TCAAACTGGATGATACTGGC
2168565 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
1 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
2168630 TCAAACTGGATGATACTG
66 TCAAACTGGATGATACTG
2168648 AATGGGTGCA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (85 bp):
TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
TCAAACTGGATGATACTGGC
Found at i:2170125 original size:114 final size:110
Alignment explanation
Indices: 2169979--2170180 Score: 278
Period size: 114 Copynumber: 1.8 Consensus size: 110
2169969 AATTTGCTCG
* * * * *
2169979 AGATTAGATTTCAACTTCGCGACGGAGGATATCCAACTCAAAGCCAATTCGATAAAACTAGATTG
1 AGATTAGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAA--C--TAAAACAAGATTG
2170044 GATTTCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
62 GATTTCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
* * **
2170093 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCAAGATTGGATT
1 AGATTAGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTAAAACAAGATTGGATT
*
2170158 TCAACTTCACGACGAAGGATATC
66 TCAACTTCACAACGAAGGATATC
2170181 CAATTCGAGG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
110 35 0.45
112 1 0.01
114 42 0.54
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (110 bp):
AGATTAGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTAAAACAAGATTGGATT
TCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
Found at i:2170181 original size:55 final size:55
Alignment explanation
Indices: 2169979--2170183 Score: 275
Period size: 55 Copynumber: 3.7 Consensus size: 55
2169969 AATTTGCTCG
* * * * * * ** *
2169979 AGATTAGATTTCAACTTCGCGACGGAGGATATCCAACTCAAAGCCAATTCGATAAAACT
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAA--C--TTACTCA
*
2170038 AGATTGGATTTCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
2170093 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
*
2170148 AGATTGGATTTCAACTTCACGACGAAGGATATCCAA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAA
2170184 TTCGAGGCTC
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
55 92 0.69
57 1 0.01
59 41 0.31
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (55 bp):
AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
Found at i:2170313 original size:120 final size:119
Alignment explanation
Indices: 2170151--2170618 Score: 639
Period size: 120 Copynumber: 3.9 Consensus size: 119
2170141 TTACTCAAGA
*
2170151 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * * *
2170216 CCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGCAGTAACATGCAATAC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACAT-CAATAC
* * *
2170271 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAATTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * ** *
2170336 CCTCAATTTCAACTTCACGACGAAGGATATCGTGCCCACCAACAACTTTTATCTTTAAA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAAC----ATCAAT-AC
* * *
2170395 TTGGATTTCAACTTTACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * **
2170460 CCACGATTTCAACTTCACGATGAAGGATCTCGTGCCCATAAGCAACATACAATAC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACAT-CAATAC
* *
2170515 TTGGATTTCAACTTCACGTCGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
2170580 CCACGATTTCAACTTCACGACGAAAGATATCATGCCCAC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCAC
2170619 TTATACAATG
Statistics
Matches: 302, Mismatches: 40, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
120 197 0.65
121 2 0.01
123 2 0.01
124 101 0.33
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (119 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATCAATAC
Found at i:2170526 original size:244 final size:244
Alignment explanation
Indices: 2170150--2170618 Score: 740
Period size: 244 Copynumber: 1.9 Consensus size: 244
2170140 CTTACTCAAG
* *
2170150 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
* * *
2170215 TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGCAGTAACATGCAATACTTGGATTTC
66 TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGAAGCAACATACAATACTTGGATTTC
* * * *
2170280 AACTTCACAACGAAGGATATCCAATTCAAGGCTCAATTTCACAACGAATGGGCCATCCTCAATTT
131 AACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACAATTT
* *
2170345 CAACTTCACGACGAAGGATATCGTGCCCACCAACAACTTTTATCTTTAA
196 CAACTTCACGACGAAAGATATCATGCCCACCAACAACTTTTATCTTTAA
* *
2170394 ATTGGATTTCAACTTTACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
* * * * * *
2170459 TCCACGATTTCAACTTCACGATGAAGGATCTCGTGCCCATAAGCAACATACAATACTTGGATTTC
66 TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGAAGCAACATACAATACTTGGATTTC
** *
2170524 AACTTCACGTCGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTT
131 AACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACAATTT
2170589 CAACTTCACGACGAAAGATATCATGCCCAC
196 CAACTTCACGACGAAAGATATCATGCCCAC
2170619 TTATACAATG
Statistics
Matches: 203, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
244 203 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (244 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGAAGCAACATACAATACTTGGATTTC
AACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACAATTT
CAACTTCACGACGAAAGATATCATGCCCACCAACAACTTTTATCTTTAA
Found at i:2172996 original size:36 final size:36
Alignment explanation
Indices: 2172955--2173042 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
2172945 AGGAACATTA
* * *
2172955 TCAAGTTAGATAAAATTTATTTTAAGGAAAACAATC
1 TCAAGTAAGATAAAATATATTTTAAGAAAAACAATC
* * *
2172991 TCAAGTGAGATAAAATATGTTTTAAGAAAAATAATC
1 TCAAGTAAGATAAAATATATTTTAAGAAAAACAATC
2173027 TCAAGTAAGATAAAAT
1 TCAAGTAAGATAAAAT
2173043 CATGAGTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (36 bp):
TCAAGTAAGATAAAATATATTTTAAGAAAAACAATC
Found at i:2174442 original size:48 final size:47
Alignment explanation
Indices: 2174332--2174473 Score: 158
Period size: 48 Copynumber: 2.9 Consensus size: 47
2174322 ATCATCATCA
* * *
2174332 CTTAGGAATTATCGCCTTTATTGAACACACAATCACCCCTTTTACCTCAAC
1 CTTAGGAATTATCACTTTTATTGAACTCAC---CA-CCCTTTTACCTCAAC
* * * *
2174383 CTTATGAATTATCACTTTTATTGGACTCACTACCCTTTGTACCTCGAC
1 CTTAGGAATTATCACTTTTATTGAACTCACCACCCTTT-TACCTCAAC
* *
2174431 CTTAGGTATTATTACTTTTATTGAACTCACCACCCTTTTACCT
1 CTTAGGAATTATCACTTTTATTGAACTCACCACCCTTTTACCT
2174474 TGTTTTTTTC
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
47 11 0.14
48 42 0.54
51 25 0.32
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.38
Consensus pattern (47 bp):
CTTAGGAATTATCACTTTTATTGAACTCACCACCCTTTTACCTCAAC
Found at i:2183513 original size:20 final size:20
Alignment explanation
Indices: 2183488--2183540 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
2183478 CTCGGAGGGA
2183488 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
2183508 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
2183528 ACCGATTCCCCCC
1 ACCGATTCCCCCC
2183541 TGTGTAACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.45, G:0.25, T:0.15
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:2187714 original size:17 final size:17
Alignment explanation
Indices: 2187692--2187725 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2187682 TTTTGGTGCA
*
2187692 GAGGGAATCGATACCCC
1 GAGGGAACCGATACCCC
*
2187709 GAGGGAACCGATTCCCC
1 GAGGGAACCGATACCCC
2187726 CTTTGAAGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.29, T:0.12
Consensus pattern (17 bp):
GAGGGAACCGATACCCC
Found at i:2198333 original size:14 final size:15
Alignment explanation
Indices: 2198314--2198344 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2198304 TAAATTAATC
2198314 AAAAAATAACAA-AA
1 AAAAAATAACAATAA
2198328 AAAAAATAACAATAA
1 AAAAAATAACAATAA
2198343 AA
1 AA
2198345 TTTTCTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACAATAA
Found at i:2199992 original size:25 final size:25
Alignment explanation
Indices: 2199958--2200079 Score: 178
Period size: 25 Copynumber: 4.9 Consensus size: 25
2199948 GAGTAGGGGA
2199958 TTAGGGTTTGAAACCCTAATCTATT
1 TTAGGGTTTGAAACCCTAATCTATT
*
2199983 TTAGGGTTTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTATT
*
2200008 TTAGGGTTTGAAACCCTAATC-AAT
1 TTAGGGTTTGAAACCCTAATCTATT
*
2200032 TTAGGGTTTAAAACCCTAATCTGA-T
1 TTAGGGTTTGAAACCCTAATCT-ATT
2200057 TTAGGGTTTGAAACCCTAATCTA
1 TTAGGGTTTGAAACCCTAATCTA
2200080 ACGGTTGCTG
Statistics
Matches: 88, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
24 25 0.28
25 59 0.67
26 4 0.05
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTATT
Found at i:2200060 original size:49 final size:50
Alignment explanation
Indices: 2199958--2200080 Score: 196
Period size: 49 Copynumber: 2.5 Consensus size: 50
2199948 GAGTAGGGGA
* * *
2199958 TTAGGGTTTGAAACCCTAATCTATTTTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAATCTAATTTAGGGTTTAAAACCCTAAATTGAT
2200008 TTAGGGTTTGAAACCCTAATC-AATTTAGGGTTTAAAACCCT-AATCTGAT
1 TTAGGGTTTGAAACCCTAATCTAATTTAGGGTTTAAAACCCTAAAT-TGAT
2200057 TTAGGGTTTGAAACCCTAATCTAA
1 TTAGGGTTTGAAACCCTAATCTAA
2200081 CGGTTGCTGG
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
48 3 0.04
49 42 0.62
50 23 0.34
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (50 bp):
TTAGGGTTTGAAACCCTAATCTAATTTAGGGTTTAAAACCCTAAATTGAT
Found at i:2200204 original size:3 final size:3
Alignment explanation
Indices: 2200196--2200243 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
2200186 GCAAAAATTG
**
2200196 TAA TAA TAA -AA T-A TAA TAA TAA TAA CGA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2200241 TAA
1 TAA
2200244 CGGAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2200601 original size:92 final size:92
Alignment explanation
Indices: 2200479--2200736 Score: 426
Period size: 92 Copynumber: 2.8 Consensus size: 92
2200469 GGTCATCTTT
* *
2200479 AGGGATGATAACTCGGTTCCTACGTAATGAGGACGACTGGTTATCAGGTTGACACGGCTCTTACG
1 AGGG-TGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCTTACG
2200544 TGATGAAGAGATCTGGCCATCTAAAGGA
65 TGATGAAGAGATCTGGCCATCTAAAGGA
2200572 AGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCTTACGT
1 AGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCTTACGT
2200637 GATGAAGAGATCTGGCCATCTAAAGGA
66 GATGAAGAGATCTGGCCATCTAAAGGA
* * * *
2200664 AGGGTGATAACTCGGTTCCTACGTGATAAGGACGGCTGGTTATCCTAATGTTGACACGACTCCTA
1 AGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTAT-C--AGGTTGACACGGCTCTTA
2200729 CGTGATGA
63 CGTGATGA
2200737 GGAAGTCTGG
Statistics
Matches: 156, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
92 128 0.82
93 5 0.03
95 23 0.15
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (92 bp):
AGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCTTACGT
GATGAAGAGATCTGGCCATCTAAAGGA
Found at i:2213254 original size:15 final size:15
Alignment explanation
Indices: 2213236--2213267 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2213226 AAATTAATCA
2213236 AAAATAACAAAAAAT
1 AAAATAACAAAAAAT
*
2213251 AAAATAACAATAAAT
1 AAAATAACAAAAAAT
2213266 AA
1 AA
2213268 TTTCATAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAACAAAAAAT
Found at i:2214889 original size:25 final size:25
Alignment explanation
Indices: 2214855--2214915 Score: 106
Period size: 25 Copynumber: 2.4 Consensus size: 25
2214845 CTGAGTAGGG
2214855 TTAGGGTTTGAAACCCT-AATCTGTT
1 TTAGGGTTTGAAACCCTAAAT-TGTT
2214880 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
2214905 TTAGGGTTTGA
1 TTAGGGTTTGA
2214916 CTCGGTTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 32 0.91
26 3 0.09
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAATTGTT
Found at i:2215644 original size:31 final size:31
Alignment explanation
Indices: 2215609--2215669 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2215599 AAAGAGTTAT
2215609 GCTCAGTTCGATCCTGGCATGGGAATCTCTC
1 GCTCAGTTCGATCCTGGCATGGGAATCTCTC
2215640 GCTCAGTTCGATCCTGGCATGGGAATCTCT
1 GCTCAGTTCGATCCTGGCATGGGAATCTCT
2215670 ACTCCTTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.28, G:0.26, T:0.30
Consensus pattern (31 bp):
GCTCAGTTCGATCCTGGCATGGGAATCTCTC
Found at i:2223971 original size:21 final size:21
Alignment explanation
Indices: 2223945--2223986 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2223935 ACATATGGAA
2223945 AAGTTTCAAGAAACTCTACCC
1 AAGTTTCAAGAAACTCTACCC
2223966 AAGTTTCAAGAAACTCTACCC
1 AAGTTTCAAGAAACTCTACCC
2223987 GTTTGGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
AAGTTTCAAGAAACTCTACCC
Found at i:2225974 original size:15 final size:15
Alignment explanation
Indices: 2225942--2225970 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2225932 ATTAGTAATA
2225942 AAAAAATAACCTCAC
1 AAAAAATAACCTCAC
2225957 AAAAAA-AACCTCAC
1 AAAAAATAACCTCAC
2225971 CAAACACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACCTCAC
Found at i:2226297 original size:1 final size:1
Alignment explanation
Indices: 2226277--2226320 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
2226267 CTATTTAAAC
* * * *
2226277 TTTTTTCTTTCTTTTATTTTTTTTATTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2226321 GATTTGTACA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:2227444 original size:82 final size:83
Alignment explanation
Indices: 2227341--2227520 Score: 222
Period size: 82 Copynumber: 2.2 Consensus size: 83
2227331 GCTTTTTAAC
* * * *
2227341 AAACGCCACAATAGAGTGGTAAATTAGCGGCGTTTATACCACATACGCCACAATAGATTA-ACAT
1 AAACGCCGCAATAGAGTGGTAAATTAGCGACGTTTATACCACAAACACCACAATAGATTACACAT
*
2227405 ATAGTGGTATTTTAGTC-A
66 ATAGTGGCA-TTTAGTCTA
* ** *
2227423 AAACGCCGCAATAGA-TCGGTAAATTAGCGACGTTTATACCACAAATACCGTAATATATTACACA
1 AAACGCCGCAATAGAGT-GGTAAATTAGCGACGTTTATACCACAAACACCACAATAGATTACACA
*
2227487 TATAGTGGCATTTATTCTTA
65 TATAGTGGCATTTAGTC-TA
2227507 AAACGCCGCAATAG
1 AAACGCCGCAATAG
2227521 TGATAATTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
81 1 0.01
82 56 0.67
83 12 0.14
84 15 0.18
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (83 bp):
AAACGCCGCAATAGAGTGGTAAATTAGCGACGTTTATACCACAAACACCACAATAGATTACACAT
ATAGTGGCATTTAGTCTA
Found at i:2227583 original size:41 final size:41
Alignment explanation
Indices: 2227507--2227664 Score: 194
Period size: 41 Copynumber: 3.9 Consensus size: 41
2227497 TTTATTCTTA
* * *
2227507 AAACGCCGCAATAGTGATAATTAATAATGGCGTTTTTAGAC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
* * *
2227548 AAATGCCGCAATAGTGTTAATCAATAGTGGTGTTTTTAGAA
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
* * *
2227589 AAACGCCGTAATAGTTTTAATCAATAGTGGCATTTTTA-AC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
** *
2227629 AAACGCCATAATAGTG-TAATCAATAGTGGCATTTTT
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
2227665 TTGTATAAAC
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
39 20 0.19
40 15 0.15
41 68 0.66
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (41 bp):
AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
Found at i:2227675 original size:82 final size:83
Alignment explanation
Indices: 2227488--2227681 Score: 218
Period size: 82 Copynumber: 2.4 Consensus size: 83
2227478 TATTACACAT
* * * *
2227488 ATAGTGGCATTTATTCT-TAAAACGCCGCAATAGTGATAATTAATAATGGCGTTTTTAGACAAAT
1 ATAGTGGCATTT-TTTTGTAAAACGCCGCAATAGTGATAATCAATAATGGCATTTTTAGACAAAC
*
2227552 GCCGCAATAGTGTTAATCA
65 GCCACAATAGTGTTAATCA
* * * ** *
2227571 ATAGTGG--TGTTTTTAGAAAAACGCCGTAATAGTTTTAATCAATAGTGGCATTTTTA-ACAAAC
1 ATAGTGGCAT-TTTTTTGTAAAACGCCGCAATAGTGATAATCAATAATGGCATTTTTAGACAAAC
*
2227633 GCCATAATAGTG-TAATCA
65 GCCACAATAGTGTTAATCA
2227651 ATAGTGGCATTTTTTTGTATAAACGCCGCAA
1 ATAGTGGCATTTTTTTGTA-AAACGCCGCAA
2227682 AATGTTAAAT
Statistics
Matches: 91, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
80 13 0.14
81 25 0.27
82 46 0.51
83 7 0.08
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (83 bp):
ATAGTGGCATTTTTTTGTAAAACGCCGCAATAGTGATAATCAATAATGGCATTTTTAGACAAACG
CCACAATAGTGTTAATCA
Found at i:2229261 original size:13 final size:13
Alignment explanation
Indices: 2229243--2229268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2229233 TCCCGTCGTT
2229243 CTCTAATTCAAAA
1 CTCTAATTCAAAA
2229256 CTCTAATTCAAAA
1 CTCTAATTCAAAA
2229269 GAGTAGTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CTCTAATTCAAAA
Found at i:2237549 original size:21 final size:21
Alignment explanation
Indices: 2237525--2237593 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
2237515 CAGCCATAGC
*
2237525 AGCAGCGGAAGAAGAGAAAGA
1 AGCAGCGGAAGAACAGAAAGA
* * *
2237546 AGCAGCGGTAGCACAGAGAGA
1 AGCAGCGGAAGAACAGAAAGA
* *
2237567 AGCAGC-GACAGCACAGAGAGA
1 AGCAGCGGA-AGAACAGAAAGA
2237588 AGCAGC
1 AGCAGC
2237594 ATATCAACAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.43, C:0.19, G:0.36, T:0.01
Consensus pattern (21 bp):
AGCAGCGGAAGAACAGAAAGA
Found at i:2237606 original size:21 final size:21
Alignment explanation
Indices: 2237543--2237593 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2237533 AAGAAGAGAA
**
2237543 AGAAGCAGCGGTAGCACAGAG
1 AGAAGCAGCGACAGCACAGAG
2237564 AGAAGCAGCGACAGCACAGAG
1 AGAAGCAGCGACAGCACAGAG
2237585 AGAAGCAGC
1 AGAAGCAGC
2237594 ATATCAACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.35, T:0.02
Consensus pattern (21 bp):
AGAAGCAGCGACAGCACAGAG
Found at i:2238116 original size:42 final size:41
Alignment explanation
Indices: 2238008--2238172 Score: 161
Period size: 43 Copynumber: 3.9 Consensus size: 41
2237998 TTTTAGCAAC
* * ***
2238008 AACGCCGCAAAACATCAATGCCTACTGCGATATTTGTGAGAAA
1 AACGCCACAAAACATCAA-ACCTACTGCGGCGTTTGTG-GAAA
* * *
2238051 AATGCCACAAAACATCAAAACCTACTGCGCCGTTTGTGGGAA
1 AACGCCACAAAACATC-AAACCTACTGCGGCGTTTGTGGAAA
*
2238093 AACGCCACAAAACATCAACACCTACTGCGGCGTTT-TAGATAA
1 AACGCCACAAAACATCAA-ACCTACTGCGGCGTTTGTGGA-AA
* *
2238135 AATCGCCACTAAACATCATAACCTATTGCGGCGTTTGT
1 AA-CGCCACAAAACATCA-AACCTACTGCGGCGTTTGT
2238173 CTATAAAACA
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
41 4 0.04
42 37 0.36
43 58 0.56
44 4 0.04
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (41 bp):
AACGCCACAAAACATCAAACCTACTGCGGCGTTTGTGGAAA
Found at i:2238151 original size:85 final size:85
Alignment explanation
Indices: 2238008--2238172 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
2237998 TTTTAGCAAC
* ** *
2238008 AACGCCGCAAAACATCAATGCCTACTGCGATATTTGTGAGAAAAATGCCACAAAACATCAAAACC
1 AACGCCACAAAACATCAACACCTACTGCGACATTTGTGAGAAAAATGCCACAAAACATCAAAACC
2238073 TACTGCGCCGTTTGTGGGAA
66 TACTGCGCCGTTTGTGGGAA
* * * *
2238093 AACGCCACAAAACATCAACACCTACTGCGGCGTTT-T-AGATAAAATCGCCACTAAACATCATAA
1 AACGCCACAAAACATCAACACCTACTGCGACATTTGTGAGA-AAAAT-GCCACAAAACATCAAAA
* *
2238156 CCTATTGCGGCGTTTGT
64 CCTACTGCGCCGTTTGT
2238173 CTATAAAACA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 3 0.04
84 6 0.09
85 59 0.87
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (85 bp):
AACGCCACAAAACATCAACACCTACTGCGACATTTGTGAGAAAAATGCCACAAAACATCAAAACC
TACTGCGCCGTTTGTGGGAA
Found at i:2238190 original size:43 final size:43
Alignment explanation
Indices: 2238106--2238301 Score: 234
Period size: 43 Copynumber: 4.6 Consensus size: 43
2238096 GCCACAAAAC
* ** * * * *
2238106 ATCAACACCTACTGCGGCGTTT-TAGATAAAATCGCCACTAAAC
1 ATCAACACCTATTGCGGCGTTTGTCTA-AAAAACACCGCTAAAT
*
2238149 ATCATA-ACCTATTGCGGCGTTTGTCTATAAAACACCGCTAAAT
1 ATCA-ACACCTATTGCGGCGTTTGTCTAAAAAACACCGCTAAAT
* * *
2238192 ATCAATACCTATTGTGGCGTTTGTCTAAAAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTGTCTAAAAAACACCGCTAAAT
* *
2238235 ATCAACACCTATTGCAGTGTTTGTCTAAAAAACACCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTGTCTAAAAAACACCGCTAAAT
*
2238278 ATCAACACTTATTGCGGCGTTTGT
1 ATCAACACCTATTGCGGCGTTTGT
2238302 AAATATCAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 127 0.97
44 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (43 bp):
ATCAACACCTATTGCGGCGTTTGTCTAAAAAACACCGCTAAAT
Found at i:2238318 original size:28 final size:28
Alignment explanation
Indices: 2238273--2238329 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2238263 AAAACACCGC
* *
2238273 TAAATATCAACACTTATTGCGGCGTTTG
1 TAAATATCAAAACCTATTGCGGCGTTTG
2238301 TAAATATCAAAACCTATTGCGGCGTTTG
1 TAAATATCAAAACCTATTGCGGCGTTTG
2238329 T
1 T
2238330 CACACAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (28 bp):
TAAATATCAAAACCTATTGCGGCGTTTG
Found at i:2238346 original size:71 final size:71
Alignment explanation
Indices: 2238230--2238362 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 71
2238220 AAAACGCCGC
* * *
2238230 TAAATATCAACACCTATTGCAGTGTTTGTCTAAAAAACACCGCTAAATATCAACACTTATTGCGG
1 TAAATATCAAAACCTATTGCAGCGTTTGTCTAAAAAACACCGCTAAATATCAACACCTATTGCGG
2238295 CGTTTG
66 CGTTTG
* * *
2238301 TAAATATCAAAACCTATTGCGGCGTTTGTC-ACACAAACACCGCTAAATATCAATACCTATTG
1 TAAATATCAAAACCTATTGCAGCGTTTGTCTA-AAAAACACCGCTAAATATCAACACCTATTG
2238363 TGACATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 1 0.02
71 54 0.98
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (71 bp):
TAAATATCAAAACCTATTGCAGCGTTTGTCTAAAAAACACCGCTAAATATCAACACCTATTGCGG
CGTTTG
Found at i:2243738 original size:15 final size:15
Alignment explanation
Indices: 2243706--2243734 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2243696 AATTAGAAAT
2243706 AAAAAATAACCTCAC
1 AAAAAATAACCTCAC
2243721 AAAAAA-AACCTCAC
1 AAAAAATAACCTCAC
2243735 CAAACACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACCTCAC
Found at i:2244278 original size:22 final size:22
Alignment explanation
Indices: 2244253--2244298 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2244243 AATTGCATAA
2244253 ATATAAACATAAGAA-TGAAATG
1 ATATAAA-ATAAGAATTGAAATG
* *
2244275 ATATGAAATAATAATTGAAATG
1 ATATAAAATAAGAATTGAAATG
2244297 AT
1 AT
2244299 GGAATGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.57, C:0.02, G:0.13, T:0.28
Consensus pattern (22 bp):
ATATAAAATAAGAATTGAAATG
Found at i:2247754 original size:54 final size:54
Alignment explanation
Indices: 2247691--2248031 Score: 241
Period size: 54 Copynumber: 6.3 Consensus size: 54
2247681 ATACGTTCTT
* * ** *
2247691 TGGGGTGCACACGTAGTGTTGATATGGTAATTCA-AAATCTCATTATGAATTTCG
1 TGGGTTGCACACATAGTGCAGATATGGAAATTCATAAATCT-ATTATGAATTTCG
* *** *
2247745 TGGGTTGCACACTTAGTGCAGATATGGCCGTTCATAAA-CATATTATGAATTTTG
1 TGGGTTGCACACATAGTGCAGATATGGAAATTCATAAATC-TATTATGAATTTCG
* * * *
2247799 TAGGTTGCACACATAGTGCCA-ATACGGAAATTCATAAATTTATTATGAATTTCT
1 TGGGTTGCACACATAGTG-CAGATATGGAAATTCATAAATCTATTATGAATTTCG
** * * *
2247853 TAAGTTGCACACACAGTGCCA-ATACGGAAATTCATAAA-CTTATTATGAATTTCT
1 TGGGTTGCACACATAGTG-CAGATATGGAAATTCATAAATC-TATTATGAATTTCG
** * *
2247907 TAAGTTGCACACATAGTGCCA-ATATGGAAATTCATAAA-CTTGTTATGAATTTCT
1 TGGGTTGCACACATAGTG-CAGATATGGAAATTCATAAATC-TATTATGAATTTCG
** * * * * *
2247961 TAAGTTGCACACACAGTGCCA-ATACGAAAATTTATAAA-CTTATTATGAATTTCT
1 TGGGTTGCACACATAGTG-CAGATATGGAAATTCATAAATC-TATTATGAATTTCG
***
2248015 TAATTTGCACACATAGT
1 TGGGTTGCACACATAGT
2248032 TCCCATTAGG
Statistics
Matches: 252, Mismatches: 30, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
54 246 0.98
55 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (54 bp):
TGGGTTGCACACATAGTGCAGATATGGAAATTCATAAATCTATTATGAATTTCG
Found at i:2247871 original size:108 final size:107
Alignment explanation
Indices: 2247775--2248031 Score: 399
Period size: 108 Copynumber: 2.4 Consensus size: 107
2247765 GATATGGCCG
*
2247775 TTCATAAACATATTATGAATTT-TGTAGGTTGCACACATAGTGCCAATACGGAAATTCATAAATT
1 TTCATAAACATATTATGAATTTCT-TAAGTTGCACACATAGTGCCAATACGGAAATTCATAAATT
2247839 TATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
65 TATTATGAATTTCTTAAGTTGCACACACAGTG-CAATACGGAAA
* * *
2247883 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAGTGCCAATATGGAAATTCATAAACTT
1 TTCATAAACATATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAATTT
* *
2247948 GTTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
66 ATTATGAATTTCTTAAGTTGCACACACAGTG-CAATACGGAAA
* * *
2247991 TTTATAAACTTATTATGAATTTCTTAATTTGCACACATAGT
1 TTCATAAACATATTATGAATTTCTTAAGTTGCACACATAGT
2248032 TCCCATTAGG
Statistics
Matches: 140, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
108 139 0.99
109 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (107 bp):
TTCATAAACATATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAATTT
ATTATGAATTTCTTAAGTTGCACACACAGTGCAATACGGAAA
Found at i:2247970 original size:162 final size:162
Alignment explanation
Indices: 2247719--2248027 Score: 426
Period size: 162 Copynumber: 1.9 Consensus size: 162
2247709 TTGATATGGT
** * ***
2247719 AATTCAAAATCTCATTATGAATTTCGTGGGTTGCACACTTAGTGCAGATATGGCCGTTCATAAAC
1 AATTCAAAATCTCATTATGAATTTCGTAAGTTGCACACATAGTGCAGATATGGAAATTCATAAAC
* * * *
2247784 ATATTATGAATTTTGTAGGTTGCACACATAGTGCCAATACGGAAATTCATAAATTTATTATGAAT
66 ATATTATGAATTTTGTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAAT
2247849 TTCTTAAGTTGCACACACAGTGCCAATACGGA
131 TTCTTAAGTTGCACACACAGTGCCAATACGGA
* *
2247881 AATTCATAAA-CTTATTATGAATTTCTTAAGTTGCACACATAGTGCCA-ATATGGAAATTCATAA
1 AATTCA-AAATCTCATTATGAATTTCGTAAGTTGCACACATAGTG-CAGATATGGAAATTCATAA
* * *
2247944 ACTTGTTATGAATTTCT-TAAGTTGCACACACAGTGCCAATACGAAAATTTATAAACTTATTATG
64 ACATATTATGAATTT-TGTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATG
*
2248008 AATTTCTTAATTTGCACACA
128 AATTTCTTAAGTTGCACACA
2248028 TAGTTCCCAT
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
162 122 0.95
163 6 0.05
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (162 bp):
AATTCAAAATCTCATTATGAATTTCGTAAGTTGCACACATAGTGCAGATATGGAAATTCATAAAC
ATATTATGAATTTTGTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAAT
TTCTTAAGTTGCACACACAGTGCCAATACGGA
Found at i:2252960 original size:29 final size:29
Alignment explanation
Indices: 2252902--2253106 Score: 148
Period size: 29 Copynumber: 7.0 Consensus size: 29
2252892 AAGTTTTTGT
* * *
2252902 TTTTGGTTATTTTAGTCTTTTAAATGTCTA
1 TTTT-GTTATTTTAGTCCTTTAAGTTTCTA
*
2252932 TATTTGTTA-TTTAGTCCCTTAAGTTTCTA
1 T-TTTGTTATTTTAGTCCTTTAAGTTTCTA
*
2252961 TTTTTTTACTATTTTAGTCCTTTAAGTTT-T-
1 -TTTTGT--TATTTTAGTCCTTTAAGTTTCTA
* * * *
2252991 TTTTGCTATTTTAGTCCTTTAACTTTTTG
1 TTTTGTTATTTTAGTCCTTTAAGTTTCTA
* * * *
2253020 TTTTATCTAATTTAGTCCTTTAAGTTTTTG
1 TTTTGT-TATTTTAGTCCTTTAAGTTTCTA
* * *
2253050 TTTTGCTATTTTGGTCCTTTAACTTTCTA
1 TTTTGTTATTTTAGTCCTTTAAGTTTCTA
* * *
2253079 TTTT-TGCAATTTAGTCCTTTACGTTTCT
1 TTTTGT-TATTTTAGTCCTTTAAGTTTCT
2253107 GTGATTTTTA
Statistics
Matches: 140, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
27 19 0.14
28 1 0.01
29 67 0.48
30 31 0.22
31 6 0.04
32 16 0.11
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (29 bp):
TTTTGTTATTTTAGTCCTTTAAGTTTCTA
Found at i:2253036 original size:30 final size:29
Alignment explanation
Indices: 2252964--2253099 Score: 154
Period size: 29 Copynumber: 4.7 Consensus size: 29
2252954 GTTTCTATTT
* *
2252964 TTTTACTATTTTAGTCCTTTAA-GTTTT-
1 TTTTGCTATTTTAGTCCTTTAACTTTTTG
2252991 TTTTGCTATTTTAGTCCTTTAACTTTTTG
1 TTTTGCTATTTTAGTCCTTTAACTTTTTG
* * *
2253020 TTTTATCTAATTTAGTCCTTTAAGTTTTTG
1 TTTT-GCTATTTTAGTCCTTTAACTTTTTG
*
2253050 TTTTGCTATTTTGGTCCTTTAACTTTCTAT-
1 TTTTGCTATTTTAGTCCTTTAACTTT-T-TG
*
2253080 TTTTGC-AATTTAGTCCTTTA
1 TTTTGCTATTTTAGTCCTTTA
2253100 CGTTTCTGTG
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.23
28 4 0.04
29 34 0.37
30 33 0.35
31 1 0.01
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (29 bp):
TTTTGCTATTTTAGTCCTTTAACTTTTTG
Found at i:2253119 original size:59 final size:58
Alignment explanation
Indices: 2252945--2253130 Score: 191
Period size: 59 Copynumber: 3.2 Consensus size: 58
2252935 TTGTTATTTA
* * * * * *
2252945 GTCCCTTAAGTTTCTATTTTTTTACTATTTTAGTCCTTTAAGTTTTT-TTTGCTATTTTA
1 GTCCTTTAACTTTCTA-TTTTAT-CTAATTTAGTCCTTTAAGTTTTTGTTTTCTATTTTG
* *
2253004 GTCCTTTAACTTTTTGTTTTATCTAATTTAGTCCTTTAAGTTTTTGTTTTGCTATTTTG
1 GTCCTTTAACTTTCTATTTTATCTAATTTAGTCCTTTAAGTTTTTGTTTT-CTATTTTG
*
2253063 GTCCTTTAACTTTCTATTTT-TGC-AATTTAGTCCTTTACGTTTCTGTGATTTT-TATTTTG
1 GTCCTTTAACTTTCTATTTTAT-CTAATTTAGTCCTTTAAGTTT-T-TG-TTTTCTATTTTG
*
2253122 GTCCCTTAA
1 GTCCTTTAA
2253131 ATTTTTGAAT
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
57 22 0.20
58 27 0.25
59 54 0.50
60 2 0.02
61 4 0.04
ACGTcount: A:0.16, C:0.15, G:0.11, T:0.59
Consensus pattern (58 bp):
GTCCTTTAACTTTCTATTTTATCTAATTTAGTCCTTTAAGTTTTTGTTTTCTATTTTG
Found at i:2253914 original size:20 final size:19
Alignment explanation
Indices: 2253889--2253930 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2253879 CACAAACCAA
*
2253889 TTTTTTGTCTAAAAATGAT
1 TTTTTTTTCTAAAAATGAT
* *
2253908 TTTTTTTTCTTAAAATTAT
1 TTTTTTTTCTAAAAATGAT
2253927 TTTT
1 TTTT
2253931 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTTTTCTAAAAATGAT
Found at i:2260871 original size:21 final size:21
Alignment explanation
Indices: 2260839--2260894 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
2260829 AATCAAACCT
*
2260839 TGACTATT-ACGATGCTAACA
1 TGACAATTCACGATGCTAACA
* * * *
2260859 TGACAGTTCACGACGTTAATA
1 TGACAATTCACGATGCTAACA
*
2260880 TGACAATTCAAGATG
1 TGACAATTCACGATG
2260895 GCTGAGGATG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (21 bp):
TGACAATTCACGATGCTAACA
Found at i:2261136 original size:36 final size:36
Alignment explanation
Indices: 2261096--2261168 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2261086 AAACACTTAT
2261096 ACAAAACATTCCTATTAAATTAGTCGAGACATACAC
1 ACAAAACATTCCTATTAAATTAGTCGAGACATACAC
* *
2261132 ACAAAATATTCTTATTAAATTAGTCGAGACATACAC
1 ACAAAACATTCCTATTAAATTAGTCGAGACATACAC
2261168 A
1 A
2261169 TTTTGCATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.27
Consensus pattern (36 bp):
ACAAAACATTCCTATTAAATTAGTCGAGACATACAC
Found at i:2261627 original size:21 final size:21
Alignment explanation
Indices: 2261576--2261628 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2261566 ATTATGACTA
2261576 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2261597 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
*
2261618 TCGTAATGCGA
1 TCGCAATGCGA
2261629 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2261682 original size:41 final size:42
Alignment explanation
Indices: 2261637--2261730 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 42
2261627 GAATAAGTAA
* ** * *
2261637 ATCGCAACGCGAAT-TTGGAAAATCACAATGCGATACTGACT
1 ATCGCAACGCGAATAATACAAAATCACAACGCGATAATGACT
*
2261678 ATCGCAACGCG-ATAATACAAAATCGCAACGCGATAATGACT
1 ATCGCAACGCGAATAATACAAAATCACAACGCGATAATGACT
*
2261719 TTCGCAACGCGA
1 ATCGCAACGCGA
2261731 TACCGACTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 2 0.05
41 42 0.95
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (42 bp):
ATCGCAACGCGAATAATACAAAATCACAACGCGATAATGACT
Found at i:2261691 original size:20 final size:20
Alignment explanation
Indices: 2261666--2261772 Score: 99
Period size: 20 Copynumber: 5.3 Consensus size: 20
2261656 AAATCACAAT
*
2261666 GCGATACTGACTATCGCAAC
1 GCGATACTGACTTTCGCAAC
* **
2261686 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TTTCGCAAC
*
2261707 GCGATAATGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
* *
2261727 GCGATACCGACTTTCGCAAT
1 GCGATACTGACTTTCGCAAC
* *
2261747 GCGATTCTGACTTTCACAAC
1 GCGATACTGACTTTCGCAAC
*
2261767 GAGATA
1 GCGATA
2261773 ATACATAATC
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.72
21 16 0.23
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (20 bp):
GCGATACTGACTTTCGCAAC
Found at i:2261793 original size:41 final size:41
Alignment explanation
Indices: 2261657--2261792 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
2261647 GAATTTGGAA
* * *
2261657 AATCACAATGCGATACTGACTATCGCAACGCGATAATACAA
1 AATCGCAATGCGATACTGACTTTCGCAACGCGATAATACAT
* * **
2261698 AATCGCAACGCGATAATGACTTTCGCAACGCGATACCGAC-T
1 AATCGCAATGCGATACTGACTTTCGCAACGCGATA-ATACAT
* * * *
2261739 -TTCGCAATGCGATTCTGACTTTCACAACGAGATAATACAT
1 AATCGCAATGCGATACTGACTTTCGCAACGCGATAATACAT
2261779 AATCGCAATGCGAT
1 AATCGCAATGCGAT
2261793 TTTAAAGCGC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 29 0.38
41 43 0.57
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
AATCGCAATGCGATACTGACTTTCGCAACGCGATAATACAT
Found at i:2262313 original size:20 final size:20
Alignment explanation
Indices: 2262290--2262328 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2262280 TCAAATTCGC
2262290 GTTGCGATTGTCATTTTCAT
1 GTTGCGATTGTCATTTTCAT
*
2262310 GTTGCGATTTTCATTTTCA
1 GTTGCGATTGTCATTTTCA
2262329 GAAACTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTGTCATTTTCAT
Found at i:2264247 original size:20 final size:20
Alignment explanation
Indices: 2264222--2264274 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2264212 TAGTTTACTT
2264222 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
2264242 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
2264262 TCGCAACGCGAAA
1 TCGCAACGCGAAA
2264275 TGAAATTCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.26, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:2264284 original size:19 final size:19
Alignment explanation
Indices: 2264221--2264343 Score: 80
Period size: 19 Copynumber: 6.6 Consensus size: 19
2264211 ATAGTTTACT
*
2264221 TTCGCAACGCGAAAATG-AC
1 TTCGCAACGCG-AAATGAAA
**
2264240 TATCGCAACGCGGAAATG-GC
1 T-TCGCAACGC-GAAATGAAA
2264260 TATCGCAACGCGAAATGAAA
1 T-TCGCAACGCGAAATGAAA
*
2264280 TTCGCAATGCGAAATGAAA
1 TTCGCAACGCGAAATGAAA
* *
2264299 ATCGCAA--CGACA--AAA
1 TTCGCAACGCGAAATGAAA
*
2264314 -TCGCAGCGCGAAATGAAA
1 TTCGCAACGCGAAATGAAA
* *
2264332 ATCGCAATGCGA
1 TTCGCAACGCGA
2264344 TTTGTGTTTC
Statistics
Matches: 86, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.06
15 3 0.03
16 4 0.05
17 4 0.05
18 3 0.03
19 39 0.45
20 27 0.31
21 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (19 bp):
TTCGCAACGCGAAATGAAA
Found at i:2264374 original size:14 final size:14
Alignment explanation
Indices: 2264350--2264414 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
2264340 GCGATTTGTG
*
2264350 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
*
2264364 TTTGTCGTTGCGAT
1 TTTCTCGTTGCGAT
2264378 TTTCATTTCGCATTGCGAT
1 TTTC---TCG--TTGCGAT
2264397 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
2264411 TTTC
1 TTTC
2264415 ATTTCGCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 26 0.60
16 3 0.07
17 3 0.07
19 11 0.26
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.49
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:2264387 original size:33 final size:33
Alignment explanation
Indices: 2264350--2264433 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
2264340 GCGATTTGTG
* *
2264350 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
2264383 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
2264416 TTTCGCATTGCGATTTTC
1 TTTCGCATTGCGATTTTC
2264434 ATTTCGCGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
Found at i:2264395 original size:19 final size:19
Alignment explanation
Indices: 2264371--2264467 Score: 114
Period size: 19 Copynumber: 5.3 Consensus size: 19
2264361 GATTTTGTCG
2264371 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2264390 TTGCGATTTTC---TCG--
1 TTGCGATTTTCATTTCGCA
2264404 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2264423 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
** *
2264442 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
2264462 TTGCGA
1 TTGCGA
2264468 AAGTAAGTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.16
16 3 0.04
17 3 0.04
19 39 0.57
20 13 0.19
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2264478 original size:20 final size:20
Alignment explanation
Indices: 2264435--2264493 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
2264425 GCGATTTTCA
* * *
2264435 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAAAGTAAG
2264455 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
2264475 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
2264494 ACTATTCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:2264920 original size:21 final size:21
Alignment explanation
Indices: 2264896--2264962 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2264886 TCATTCCTCG
2264896 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2264917 AGAGGCCACTATCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2264938 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2264959 AGAG
1 AGAG
2264963 CCCGATTCAT
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2264920 original size:42 final size:42
Alignment explanation
Indices: 2264844--2264962 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
2264834 GACTCACCTG
* * * * * * *
2264844 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
2264886 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
2264928 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2264963 CCCGATTCAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 59 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:2266355 original size:14 final size:14
Alignment explanation
Indices: 2266313--2266349 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2266303 GATTGTTTAA
*
2266313 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
2266327 ATGATTTGTAAAAT
1 TTGATTTGTAAAAT
2266341 TTGATTTGT
1 TTGATTTGT
2266350 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:2266472 original size:19 final size:19
Alignment explanation
Indices: 2266456--2266550 Score: 87
Period size: 19 Copynumber: 5.3 Consensus size: 19
2266446 AAAAATGACT
2266456 ATCGCAATC-CGAAATGAAA
1 ATCGCAA-CGCGAAATGAAA
2266475 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2266494 ATCGCAA--CG--A-GATA
1 ATCGCAACGCGAAATGAAA
***
2266508 ATCGCGTTGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2266527 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
2266546 ATCGC
1 ATCGC
2266551 GTTGCGATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
14 8 0.13
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 46 0.74
20 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2266557 original size:19 final size:19
Alignment explanation
Indices: 2266507--2266557 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2266497 GCAACGAGAT
2266507 AATCGCGTTGCGAAATGAA
1 AATCGCGTTGCGAAATGAA
***
2266526 AATCGCAACGCGAAACT-AA
1 AATCGCGTTGCGAAA-TGAA
2266545 AATCGCGTTGCGA
1 AATCGCGTTGCGA
2266558 TTTTCATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (19 bp):
AATCGCGTTGCGAAATGAA
Found at i:2266995 original size:21 final size:21
Alignment explanation
Indices: 2266944--2266996 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2266934 TCCATGGCTA
2266944 TCGCAATGCGATTTTCAAAAT
1 TCGCAATGCGATTTTCAAAAT
** **
2266965 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCAAAAT
2266986 TCGCAATGCGA
1 TCGCAATGCGA
2266997 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTTCAAAAT
Found at i:2267029 original size:21 final size:20
Alignment explanation
Indices: 2266986--2267078 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 20
2266976 TTTTCCCAAT
*
2266986 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
2267006 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
* * **
2267027 TCGCAATACG-ATACTGACTA
1 TCGCAATGCGAATA-AGAAAA
*
2267047 TCGCAATGCG-ATAATACAAAA
1 TCGCAATGCGAAT-A-AGAAAA
2267068 TCGCAATGCGA
1 TCGCAATGCGA
2267079 TACTGACTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.02
20 27 0.49
21 27 0.49
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:2267050 original size:41 final size:41
Alignment explanation
Indices: 2267023--2267100 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
2267013 GCGAATTTGG
2267023 AAAATCGCAATACGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAATACGATACTGACTATCGCAATGCGATAATAC
* * * *
2267064 AAAATCGCAATGCGATACTGACTTTTGCAACGCGATA
1 AAAATCGCAATACGATACTGACTATCGCAATGCGATA
2267101 TTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAATACGATACTGACTATCGCAATGCGATAATAC
Found at i:2267051 original size:20 final size:20
Alignment explanation
Indices: 2267026--2267133 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
2267016 AATTTGGAAA
*
2267026 ATCGCAATACGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
2267046 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
2267067 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
2267087 TTTGCAACGCGATATTGACT
1 ATCGCAATGCGATACTGACT
* * *
2267107 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
2267127 ATCGCAA
1 ATCGCAA
2267134 CGAGATAATA
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.03
20 53 0.74
21 15 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2267262 original size:12 final size:12
Alignment explanation
Indices: 2267243--2267276 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2267233 CTCTCCGGCG
2267243 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2267255 ATATCCGTTCCT
1 ACATCCGTTCCT
2267267 ACATCC-TTCC
1 ACATCCGTTCC
2267277 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2267857 original size:24 final size:24
Alignment explanation
Indices: 2267837--2267883 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2267827 AAATTTGGTC
2267837 TTGGTCAATACCCGGACTTTGATA
1 TTGGTCAATACCCGGACTTTGATA
* *
2267861 TTGGTCAATACTCGGATTTTGAT
1 TTGGTCAATACCCGGACTTTGAT
2267884 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACCCGGACTTTGATA
Found at i:2268075 original size:12 final size:12
Alignment explanation
Indices: 2268058--2268082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2268048 ATATAATCCT
2268058 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2268070 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2268082 G
1 G
2268083 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2270387 original size:20 final size:20
Alignment explanation
Indices: 2270362--2270417 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2270352 CAACGGGGAA
2270362 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
2270382 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
2270402 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
2270418 CGCAATGCGA
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:0.41, C:0.23, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2270483 original size:19 final size:19
Alignment explanation
Indices: 2270436--2270519 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
2270426 GAAATGAAAA
2270436 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2270452 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2270469 TTGCATTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2270488 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
2270507 TCGCATTGCGATT
1 TCGCATTGCGATT
2270520 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
14 11 0.19
16 3 0.05
17 2 0.04
19 41 0.72
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2272481 original size:12 final size:12
Alignment explanation
Indices: 2272466--2272490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2272456 ATTCCAGAAG
2272466 TAAGCACTTATA
1 TAAGCACTTATA
2272478 TAAGCACTTATA
1 TAAGCACTTATA
2272490 T
1 T
2272491 GTTTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAGCACTTATA
Found at i:2272577 original size:19 final size:20
Alignment explanation
Indices: 2272523--2272589 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2272513 TAGTTTACTT
* *
2272523 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2272543 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2272563 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2272582 TCGCAACG
1 TCGCAACG
2272590 ATAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2272597 original size:14 final size:14
Alignment explanation
Indices: 2272578--2272636 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2272568 ATGCGAAATG
2272578 AAAATCGCAACGAT
1 AAAATCGCAACGAT
2272592 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
*
2272610 GAAAATCGCAACGAC
1 -AAAATCGCAACGAT
2272625 AAAATCGCAACG
1 AAAATCGCAACG
2272637 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 22 0.56
15 1 0.03
16 2 0.05
17 2 0.05
18 2 0.05
19 10 0.26
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:2272604 original size:33 final size:33
Alignment explanation
Indices: 2272562--2272653 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
2272552 GGAAATGGCT
*
2272562 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2272595 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2272628 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2272654 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2272616 original size:19 final size:19
Alignment explanation
Indices: 2272562--2272658 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
2272552 GGAAATGGCT
2272562 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2272581 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
2272595 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2272614 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
2272628 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2272647 ATCGCAATGCGA
1 ATCGCAATGCGA
2272659 TTTTGTGTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.31
15 3 0.05
16 4 0.06
17 4 0.06
18 3 0.05
19 31 0.48
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2272730 original size:20 final size:20
Alignment explanation
Indices: 2272705--2272751 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2272695 TTCATTTCGT
2272705 GTTGCGATAGCCATTTCCGC
1 GTTGCGATAGCCATTTCCGC
* *
2272725 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGCCATTTCCGC
2272745 GTTGCGA
1 GTTGCGA
2272752 AAGTAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGCCATTTCCGC
Found at i:2272762 original size:20 final size:20
Alignment explanation
Indices: 2272722--2272777 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2272712 TAGCCATTTC
* * *
2272722 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
2272742 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
2272762 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
2272778 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:2275233 original size:20 final size:20
Alignment explanation
Indices: 2275203--2275275 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
2275193 GATTATGTAT
*
2275203 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2275223 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
2275243 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
2275263 TATCGCGTTGCGA
1 TATCGCGTTGCGA
2275276 TTTTGTATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2275399 original size:21 final size:22
Alignment explanation
Indices: 2275347--2275399 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2275337 ATTTACTTAT
2275347 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2275368 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2275389 TCGCATTGCGA
1 TCGCATTGCGA
2275400 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2276312 original size:21 final size:21
Alignment explanation
Indices: 2276288--2276327 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2276278 TTTTCAAAGG
2276288 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
**
2276309 CATGCATTGATGCATCAAT
1 CATGCACCGATGCATCAAT
2276328 GAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:2284482 original size:21 final size:21
Alignment explanation
Indices: 2284458--2284497 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2284448 TTTTCAAAGG
2284458 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
2284479 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
2284498 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:2284547 original size:19 final size:19
Alignment explanation
Indices: 2284523--2284561 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2284513 TCGAATGCAT
*
2284523 TCCATGCACCGATGCACTC
1 TCCATGCACCAATGCACTC
*
2284542 TCCATGCATCAATGCACTC
1 TCCATGCACCAATGCACTC
2284561 T
1 T
2284562 GATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCATGCACCAATGCACTC
Found at i:2284585 original size:64 final size:66
Alignment explanation
Indices: 2284458--2284603 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 66
2284448 TTTTCAAAGG
* *
2284458 CATGCACCGATGCA-TCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCA
1 CATGCACCGATGCACTC-ATACCATGCATCAATGCATC-ATGAATAAATTAAAACATCGAATGCA
2284522 TTC
64 TTC
* *
2284525 CATGCACCGATGCACTC-T-CCATGCATCAATGCACTC-TGATTTAATTAAAACATCGAATGCAT
1 CATGCACCGATGCACTCATACCATGCATCAATGCA-TCATGAATAAATTAAAACATCGAATGCAT
*
2284587 TT
65 TC
* *
2284589 GATGCATCGATGCAC
1 CATGCACCGATGCAC
2284604 CAGGCTATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
64 37 0.53
65 14 0.20
66 3 0.04
67 14 0.20
68 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (66 bp):
CATGCACCGATGCACTCATACCATGCATCAATGCATCATGAATAAATTAAAACATCGAATGCATT
C
Found at i:2284602 original size:45 final size:44
Alignment explanation
Indices: 2284534--2284651 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 44
2284524 CCATGCACCG
*
2284534 ATGCACTCTCCATGCATCAATGCACTCTG-ATTTAATTAAAACATCGA
1 ATGCACT-T-CATGCATCGATGCACTCTGCATTT--TTAAAACATCGA
* * * *
2284581 ATGCATTTGATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGA
1 ATGCACTTCATGCATCGATGCACTC-TGC-ATTTTTAAAACATCGA
*
2284626 ATGCACTTCATGTATCGATGCACTCT
1 ATGCACTTCATGCATCGATGCACTCT
2284652 TAGTGCACCG
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
44 1 0.02
45 45 0.78
46 2 0.03
47 10 0.17
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (44 bp):
ATGCACTTCATGCATCGATGCACTCTGCATTTTTAAAACATCGA
Found at i:2286467 original size:26 final size:27
Alignment explanation
Indices: 2286435--2286496 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
2286425 AAATATTTAC
*
2286435 TAGTCATTTGA-CCTATAAGGGT-ATT
1 TAGTCATTTGAGCCAATAAGGGTGATT
* *
2286460 TCGGTCATTTTAGCCAATAAGGGTGATT
1 T-AGTCATTTGAGCCAATAAGGGTGATT
2286488 TAGTCATTT
1 TAGTCATTT
2286497 TTGGTTCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 1 0.03
26 8 0.27
27 17 0.57
28 4 0.13
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (27 bp):
TAGTCATTTGAGCCAATAAGGGTGATT
Found at i:2292283 original size:28 final size:27
Alignment explanation
Indices: 2292251--2292320 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
2292241 TATTATTTAA
2292251 ATATTTACTAATCATTTGA-CCTATAAGG
1 ATATTT-C-AATCATTTGAGCCTATAAGG
* *
2292279 ATATTTCATTCATTTTAGCCTATAAGG
1 ATATTTCAATCATTTGAGCCTATAAGG
* *
2292306 GTAATTCAATCATTT
1 ATATTTCAATCATTT
2292321 TTATTTCCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 8 0.22
27 22 0.61
28 6 0.17
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (27 bp):
ATATTTCAATCATTTGAGCCTATAAGG
Found at i:2305724 original size:16 final size:16
Alignment explanation
Indices: 2305703--2305736 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2305693 CGGCGAGATA
2305703 GACGATTGGAGTGATG
1 GACGATTGGAGTGATG
2305719 GACGATTGGAGTGATG
1 GACGATTGGAGTGATG
2305735 GA
1 GA
2305737 GAGAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.44, T:0.24
Consensus pattern (16 bp):
GACGATTGGAGTGATG
Found at i:2306735 original size:19 final size:20
Alignment explanation
Indices: 2306702--2306750 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2306692 AAATGATTTT
* * *
2306702 ATTTTGAAAGCCAAAGTT-G
1 ATTTTGAAAACCAAAATTAA
*
2306721 ATTTTGAAAATCAAAATTAA
1 ATTTTGAAAACCAAAATTAA
2306741 ATTTTGAAAA
1 ATTTTGAAAA
2306751 ATTATTTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
ATTTTGAAAACCAAAATTAA
Found at i:2310383 original size:3 final size:3
Alignment explanation
Indices: 2310375--2310405 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2310365 CGTCCCAACT
2310375 TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
2310406 CGACTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2312763 original size:131 final size:131
Alignment explanation
Indices: 2312563--2313058 Score: 632
Period size: 131 Copynumber: 3.8 Consensus size: 131
2312553 TTGATATTGA
* * * * * * *
2312563 GAATAGTAATATCTTTTCATTTCAATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGTTCAT
1 GAATAGTGATATCTCTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
* * * * *
2312628 TTATTCTTGATTGGAAATAATTTGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCGATATTGATTTTTAAGAC
2312693 G
131 G
* * * * ** * *
2312694 GAATAGTGTTATCTCTTCATTTCGATTAGAGAAATAAATGATTGTTTTAAGGTATGCTATGTAAT
1 GAATAGTGATATCTCTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
* * *
2312759 TTATTCTCAATTGGAAATCATTAGATATTATCGTTTTCACTTGAATTGATATTGATTTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCGATATTGATTTTTAAGAC
2312824 G
131 G
* * * * *
2312825 GTATAATGATATCTCTTCATTTTGATTAGAGCAATAAATGACTGCTTTAAGGTATAAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
* * * *
2312890 TTATTCTCGATTTGAAATCATTAGATATTATTGTTTTCACTTGAATCGATATTGAATTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCGATATTGATTTTTAAGAC
2312955 G
131 G
* * **
2312956 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACAACTTTAAGGTATGAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
* ** *
2313021 TTATTCTCTATCAGAAATAATTAGATATTATCATTTTC
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
2313059 TCTATTAGAA
Statistics
Matches: 312, Mismatches: 53, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
131 312 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (131 bp):
GAATAGTGATATCTCTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCGATATTGATTTTTAAGAC
G
Found at i:2320604 original size:29 final size:30
Alignment explanation
Indices: 2320541--2320604 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 30
2320531 ACAACCCACT
* * *
2320541 ATTTTCCAAATTTGCCAAATTGGTCCTCAA
1 ATTTTCAAAAATTACCAAATTGGTCCTCAA
*
2320571 CTTTTCAAAAATTACCAAA-TGGTACCT-AA
1 ATTTTCAAAAATTACCAAATTGGT-CCTCAA
2320600 ATTTT
1 ATTTT
2320605 TCTAAGGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (30 bp):
ATTTTCAAAAATTACCAAATTGGTCCTCAA
Found at i:2332598 original size:14 final size:14
Alignment explanation
Indices: 2332581--2332728 Score: 58
Period size: 14 Copynumber: 10.9 Consensus size: 14
2332571 GTACTTTGCC
*
2332581 TGAAGAAAGAAAAA
1 TGAAAAAAGAAAAA
2332595 TGAAAAAAGAAAAA
1 TGAAAAAAGAAAAA
* *
2332609 AGAAAATAA-AGAAA
1 TGAAAA-AAGAAAAA
* *
2332623 -G-AAAATGGAAAA
1 TGAAAAAAGAAAAA
* *
2332635 TGGAAAATG-AAAA
1 TGAAAAAAGAAAAA
*
2332648 TG-AAAATGAAAAA
1 TGAAAAAAGAAAAA
* ** *
2332661 T-TAAATTGAAAAT
1 TGAAAAAAGAAAAA
** *
2332674 TGAAAATTG-AAAT
1 TGAAAAAAGAAAAA
*
2332687 TGAAAAATGAAAAA
1 TGAAAAAAGAAAAA
*
2332701 TGAAAAAAAAGAAAA
1 TGAAAAAAGA-AAAA
* *
2332716 TAAAAAAATAAAA
1 TGAAAAAAGAAAA
2332729 GGGGTTCAAG
Statistics
Matches: 110, Mismatches: 15, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
11 1 0.01
12 12 0.11
13 35 0.32
14 48 0.44
15 14 0.13
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
TGAAAAAAGAAAAA
Found at i:2332601 original size:7 final size:7
Alignment explanation
Indices: 2332589--2332707 Score: 90
Period size: 7 Copynumber: 17.9 Consensus size: 7
2332579 CCTGAAGAAA
2332589 GAAAAAT
1 GAAAAAT
*
2332596 GAAAAAA
1 GAAAAAT
*
2332603 GAAAAAA
1 GAAAAAT
2332610 G-AAAAT
1 GAAAAAT
*
2332616 -AAAGAAA
1 GAAA-AAT
2332623 G-AAAAT
1 GAAAAAT
*
2332629 GGAAAAT
1 GAAAAAT
*
2332636 GGAAAAT
1 GAAAAAT
2332643 G-AAAAT
1 GAAAAAT
2332649 G-AAAAT
1 GAAAAAT
2332655 GAAAAAT
1 GAAAAAT
* *
2332662 -TAAATT
1 GAAAAAT
*
2332668 GAAAATT
1 GAAAAAT
*
2332675 GAAAATT
1 GAAAAAT
*
2332682 G-AAATT
1 GAAAAAT
2332688 GAAAAAT
1 GAAAAAT
2332695 GAAAAAT
1 GAAAAAT
2332702 GAAAAA
1 GAAAAA
2332708 AAAGAAAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
6 31 0.32
7 66 0.68
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
GAAAAAT
Found at i:2332623 original size:20 final size:21
Alignment explanation
Indices: 2332586--2332660 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 21
2332576 TTGCCTGAAG
2332586 AAAGAAAAATGAAAAAAGAAA
1 AAAGAAAAATGAAAAAAGAAA
2332607 AAAG-AAAAT-AAAGAAAG-AA
1 AAAGAAAAATGAAA-AAAGAAA
* * * *
2332626 AATGGAAAATGGAAAATG-AA
1 AAAGAAAAATGAAAAAAGAAA
*
2332646 AATG-AAAATGAAAAA
1 AAAGAAAAATGAAAAA
2332661 TTAAATTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 18 0.38
20 23 0.49
21 6 0.13
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.09
Consensus pattern (21 bp):
AAAGAAAAATGAAAAAAGAAA
Found at i:2334080 original size:134 final size:134
Alignment explanation
Indices: 2333790--2334229 Score: 532
Period size: 134 Copynumber: 3.3 Consensus size: 134
2333780 ACTAATCGAA
* * * * * ** *
2333790 CTCGATTCAATCTTCTCT-AAAAATAGCGGAATGAATCAA-TTTTCCCGATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
* * * *
2333853 AGAAGAAGCAGAACATATCCCTCTCTTTCAAGACTTGATCTTCCCTGAGTAACAGTGGAACAAGT
66 AGAAGAAGCAGAACAAATCCCTTTTTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGT
*
2333918 CTGC
131 CTAC
* *
2333922 CTCGATTCAACCTTTCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
* * *
2333987 AGAAGAAGCGGAACAAATCCCTTTTTTTCTAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGT
66 AGAAGAAGCAGAACAAATCCCTTTTTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGT
2334052 CTAC
131 CTAC
* *
2334056 CTCGACTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTT-TCAGATCAT-ATTTTGCCT
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCT-AGATC-TGATTTTCCCT
* * * * **
2334119 CAAGAAGCAA-CAAAACACAT-CATTCTTTTTCCAGATTTGATCTTCCCTGAGTAGTAGTGGAAC
64 CAAGAAG-AAGCAGAACAAATCCCTT-TTTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAAC
*
2334182 AAGTCTTC
127 AAGTCTAC
* * *
2334190 CTAGATTCAGTCTTCCCTGAATAACAGTGGAATGAATCAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA
2334230 TGTTTCTCGA
Statistics
Matches: 267, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
132 15 0.06
133 22 0.08
134 227 0.85
135 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
AGAAGAAGCAGAACAAATCCCTTTTTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGT
CTAC
Found at i:2334411 original size:3 final size:3
Alignment explanation
Indices: 2334403--2334524 Score: 190
Period size: 3 Copynumber: 40.0 Consensus size: 3
2334393 ATCTTGACTC
2334403 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2334451 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT GAGT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
2334497 TAT TAT TAT TAAT TAT TAC TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT
2334525 AAATAAAATA
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
3 106 0.95
4 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2335529 original size:20 final size:20
Alignment explanation
Indices: 2335494--2335531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2335484 AATTTTTTTT
**
2335494 TTAAAAAAAATTGTTTAAAA
1 TTAAAAAAAAAGGTTTAAAA
2335514 TTAAAAAAAAAGGTTTAA
1 TTAAAAAAAAAGGTTTAA
2335532 GTTGTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (20 bp):
TTAAAAAAAAAGGTTTAAAA
Found at i:2337301 original size:131 final size:131
Alignment explanation
Indices: 2337102--2337594 Score: 632
Period size: 131 Copynumber: 3.8 Consensus size: 131
2337092 CGATATTGAG
* * ** * * *
2337102 AATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGACTGCATTAAGGCATGAGAGATCATT
1 AATAGTGATATCTCTTCATTTCAATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATT
* * * *
2337167 TATTCTCGATTGGAAATAATTCGATATTATTGTTTTCTCTCGAATCAATATTGATTTTTAAGATG
66 TATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGATTTTTAAGATG
2337232 A
131 A
* * * *
2337233 AATAGTGATATCTCTTCATTTCAATTAGTGCAATAAATTATTGCTTTAAGGTATGAGATG-TCAT
1 AATAGTGATATCTCTTCATTTCAATTGGAGCAATAAATGACTGCTTTAAGGTATGAGA-GATCAT
* * *
2337297 TTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGATTTTTAAGAT
65 TTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGATTTTTAAGAT
*
2337362 GG
130 GA
* * * * *
2337364 AATAATGATATATCTTCATTTCGATTGGAGCAATAAATGATTCCTTTAAGGTATGAGAGATCATT
1 AATAGTGATATCTCTTCATTTCAATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATT
* * * * *
2337429 TATTCTTGACTAG-AA-CATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACG
66 TATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGATTTTTAAGATG
2337492 A
131 A
* * *
2337493 TATAGTGATATCTTTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGATCATT
1 AATAGTGATATCTCTTCATTTCAATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATT
* * * *
2337558 TATTCGCGATCAAAAATAATTAGATATTATCATTTTC
66 TATTCTCGATTAGAAATAATTAGATATTATCGTTTTC
2337595 TCTCTTAGAA
Statistics
Matches: 312, Mismatches: 46, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
129 110 0.35
130 5 0.02
131 196 0.63
132 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (131 bp):
AATAGTGATATCTCTTCATTTCAATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATT
TATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGATTTTTAAGATG
A
Found at i:2337530 original size:260 final size:262
Alignment explanation
Indices: 2337116--2337594 Score: 676
Period size: 260 Copynumber: 1.8 Consensus size: 262
2337106 GTAATATCTT
* * * * *
2337116 TTCATTTCGGTTGGAGTAATAAATGACTGCATTAAGGCATGAGAGATCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGCAATAAATGACTCCATTAAGGCATGAGAGATCATTTATTCTCGACTAGA
* * * * *
2337181 AATAATTCGATATTATTGTTTTCTCTCGAATCAATATTGATTTTTAAGATGAAATAGTGATATCT
66 AATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCT
* * * * **
2337246 CTTCATTTCAATTAGTGCAATAAATTATTGCTTTAAGGTATGAGATG-TCATTTATTCTCGATTG
131 CTTCATTTCAATTAGAGCAATAAATGACTGCTTTAAGGTATGAGA-GATCATTTATTCGCGATCA
* * *
2337310 GAAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGATTTTTAAGATGGAATAATGATAT
195 AAAATAATTAGATATTATCATTTTCACTCGAATCGATATTGATTTTTAAGATGGAATAATGATAT
2337375 ATC
260 ATC
* * * *
2337378 TTCATTTCGATTGGAGCAATAAATGATTCCTTTAAGGTATGAGAGATCATTTATTCTTGACTAG-
1 TTCATTTCGATTGGAGCAATAAATGACTCCATTAAGGCATGAGAGATCATTTATTCTCGACTAGA
* *
2337442 AA-CATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACGATATAGTGATATCT
66 AATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCT
* * *
2337506 TTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCGCGATCAA
131 CTTCATTTCAATTAGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCGCGATCAA
2337571 AAATAATTAGATATTATCATTTTC
196 AAATAATTAGATATTATCATTTTC
2337595 TCTCTTAGAA
Statistics
Matches: 188, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
259 1 0.01
260 130 0.69
261 2 0.01
262 55 0.29
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (262 bp):
TTCATTTCGATTGGAGCAATAAATGACTCCATTAAGGCATGAGAGATCATTTATTCTCGACTAGA
AATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCT
CTTCATTTCAATTAGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCGCGATCAA
AAATAATTAGATATTATCATTTTCACTCGAATCGATATTGATTTTTAAGATGGAATAATGATATA
TC
Found at i:2339111 original size:16 final size:16
Alignment explanation
Indices: 2339075--2339129 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2339065 ATAGACTAAG
* *
2339075 TAAAAATTAAAACGAA
1 TAAAAAATAAAACAAA
* *
2339091 CAAAAAATAGAACAAA
1 TAAAAAATAAAACAAA
*
2339107 TAAAAAATAAAATAAAA
1 TAAAAAATAAAA-CAAA
2339124 TAAAAA
1 TAAAAA
2339130 CAAGATAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 22 0.71
17 9 0.29
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (16 bp):
TAAAAAATAAAACAAA
Found at i:2339157 original size:27 final size:27
Alignment explanation
Indices: 2339101--2339185 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 27
2339091 CAAAAAATAG
2339101 AACAAATAAAAAATAAAATAAAATAAA
1 AACAAATAAAAAATAAAATAAAATAAA
* *
2339128 AACAAGATAAAACATAAATATAAAAGAAA
1 AACAA-ATAAAAAATAAA-ATAAAATAAA
* *
2339157 CAA-AAATATAAAAGAAACA-AAAATAAA
1 -AACAAATAAAAAATAAA-ATAAAATAAA
2339184 AA
1 AA
2339186 ACGTAAAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
27 12 0.25
28 21 0.44
29 11 0.23
30 2 0.04
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.13
Consensus pattern (27 bp):
AACAAATAAAAAATAAAATAAAATAAA
Found at i:2339186 original size:17 final size:17
Alignment explanation
Indices: 2339137--2339185 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
2339127 AAACAAGATA
*
2339137 AAACATAAATATAAAAG
1 AAACAAAAATATAAAAG
2339154 AAACAAAAATATAAAAG
1 AAACAAAAATATAAAAG
2339171 AAACAAAAATA-AAAA
1 AAACAAAAATATAAAA
2339186 ACGTAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 4 0.13
17 27 0.87
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (17 bp):
AAACAAAAATATAAAAG
Found at i:2341150 original size:13 final size:14
Alignment explanation
Indices: 2341132--2341162 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2341122 GGTCAAATAA
2341132 GGTCAACGGTC-AC
1 GGTCAACGGTCAAC
2341145 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
2341159 GGTC
1 GGTC
2341163 GGGTCGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:2341173 original size:24 final size:23
Alignment explanation
Indices: 2341145--2341204 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 23
2341135 CAACGGTCAC
2341145 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC-ACGGTCGGGTCG
*
2341169 GGTCAACGGTC-GGGTCGGGTCG
1 GGTCAACGGTCACGGTCGGGTCG
2341191 GGTCAGACCGGTCA
1 GGTCA-A-CGGTCA
2341205 GACTGGTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 15 0.47
23 1 0.03
24 16 0.50
ACGTcount: A:0.15, C:0.25, G:0.43, T:0.17
Consensus pattern (23 bp):
GGTCAACGGTCACGGTCGGGTCG
Found at i:2341174 original size:17 final size:17
Alignment explanation
Indices: 2341152--2341189 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2341142 CACGGTCAAC
2341152 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2341169 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2341186 GGTC
1 GGTC
2341190 GGGTCAGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2341179 original size:7 final size:7
Alignment explanation
Indices: 2341132--2341162 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2341122 GGTCAAATAA
2341132 GGTCAAC
1 GGTCAAC
2341139 GGTC-AC
1 GGTCAAC
2341145 GGTCAAC
1 GGTCAAC
2341152 GGTCAAC
1 GGTCAAC
2341159 GGTC
1 GGTC
2341163 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:2348405 original size:24 final size:23
Alignment explanation
Indices: 2348377--2348436 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 23
2348367 CAACGTTCAC
2348377 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTCAA-GGTCGGGTCG
2348401 GGTCAACGGTC-AGGTCGGGTCG
1 GGTCAACGGTCAAGGTCGGGTCG
2348423 GGTCATACCGGTCA
1 GGTCA-A-CGGTCA
2348437 GACCGGTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
22 15 0.45
23 2 0.06
24 16 0.48
ACGTcount: A:0.17, C:0.25, G:0.40, T:0.18
Consensus pattern (23 bp):
GGTCAACGGTCAAGGTCGGGTCG
Found at i:2348406 original size:17 final size:17
Alignment explanation
Indices: 2348384--2348421 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2348374 CACGGTCAAC
*
2348384 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCAGGTCG
2348401 GGTCAACGGTCAGGTCG
1 GGTCAACGGTCAGGTCG
2348418 GGTC
1 GGTC
2348422 GGGTCATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCAGGTCG
Found at i:2353916 original size:78 final size:79
Alignment explanation
Indices: 2353769--2353917 Score: 171
Period size: 78 Copynumber: 1.9 Consensus size: 79
2353759 AACCCACCAT
* * **
2353769 ATTTTTCTTTTCTCTATTTCTTTTGTTCTTTCTCTTCTTTTTTCAATTTAGGGCGCCCTTTTGAG
1 ATTTTTCTTTTCTCTATTTCTTTTCTTCTTTCTCTTCTTTTTTCAATTTAGGACGCCCTTCGGAG
2353834 TTTTCACACTAATC
66 TTTTCACACTAATC
* * **
2353848 ATTTTTCTCTTTCT-TA-TTCTTTTCTTTTTTTTCTT-TTTTTTCCGTCTTAGGACGCCCTCTCG
1 ATTTTTCT-TTTCTCTATTTCTTTTCTTCTTTCTCTTCTTTTTTCAAT-TTAGGACGCCCT-TCG
2353910 GA-TTTTCA
63 GAGTTTTCA
2353918 TCCTAAGCGA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
77 8 0.14
78 33 0.56
79 13 0.22
80 5 0.08
ACGTcount: A:0.11, C:0.22, G:0.09, T:0.58
Consensus pattern (79 bp):
ATTTTTCTTTTCTCTATTTCTTTTCTTCTTTCTCTTCTTTTTTCAATTTAGGACGCCCTTCGGAG
TTTTCACACTAATC
Found at i:2355656 original size:78 final size:79
Alignment explanation
Indices: 2355509--2355657 Score: 171
Period size: 78 Copynumber: 1.9 Consensus size: 79
2355499 AACCCACCAT
* * **
2355509 ATTTTTCTTTTCTCTATTTCTTTTGTTCTTTCTCTTCTTTTTTCAATTTAGGGCGCCCTTTTGAG
1 ATTTTTCTTTTCTCTATTTCTTTTCTTCTTTCTCTTCTTTTTTCAATTTAGGACGCCCTTCGGAG
2355574 TTTTCACACTAATC
66 TTTTCACACTAATC
* * **
2355588 ATTTTTCTCTTTCT-TA-TTCTTTTCTTTTTTTTCTT-TTTTTTCCGTCTTAGGACGCCCTCTCG
1 ATTTTTCT-TTTCTCTATTTCTTTTCTTCTTTCTCTTCTTTTTTCAAT-TTAGGACGCCCT-TCG
2355650 GA-TTTTCA
63 GAGTTTTCA
2355658 TCCTAAGCGA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
77 8 0.14
78 33 0.56
79 13 0.22
80 5 0.08
ACGTcount: A:0.11, C:0.22, G:0.09, T:0.58
Consensus pattern (79 bp):
ATTTTTCTTTTCTCTATTTCTTTTCTTCTTTCTCTTCTTTTTTCAATTTAGGACGCCCTTCGGAG
TTTTCACACTAATC
Found at i:2365928 original size:27 final size:25
Alignment explanation
Indices: 2365898--2365983 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 25
2365888 AAAAATGAAC
2365898 AAAATAAATTAAACAAATAAAAAAATA
1 AAAATAAATTAAA-AAA-AAAAAAATA
* *
2365925 AAAATAAAATAAAATAAAAACAAGATA
1 AAAATAAATTAAAA-AAAAA-AAAATA
* *
2365952 AAACATAAATATAAAAGAAACAAAATA
1 AAA-ATAAAT-TAAAAAAAAAAAAATA
2365979 AAAAT
1 AAAAT
2365984 CATAAAAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 6 0.12
27 30 0.61
28 8 0.16
29 5 0.10
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAATAAATTAAAAAAAAAAAAATA
Found at i:2365938 original size:16 final size:15
Alignment explanation
Indices: 2365898--2365954 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
2365888 AAAAATGAAC
*
2365898 AAAATAAATTAAACAA
1 AAAATAAAATAAA-AA
2365914 ATAAA-AAAATAAAAA
1 A-AAATAAAATAAAAA
2365929 TAAAATAAAATAAAAA
1 -AAAATAAAATAAAAA
*
2365945 CAAGATAAAA
1 -AAAATAAAA
2365955 CATAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 5 0.14
16 27 0.77
17 3 0.09
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAATAAAATAAAAA
Found at i:2365946 original size:34 final size:34
Alignment explanation
Indices: 2365882--2365967 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
2365872 TATACTAAGT
*
2365882 AAAAATAAAAATGAACAAAATAAATTAAACAA-ATAA
1 AAAAATAAAAAT-AA-AAAATAAATAAAACAAGAT-A
*
2365918 AAAAATAAAAATAAAATA-AAATAAAAACAAGATA
1 AAAAATAAAAATAAAAAATAAAT-AAAACAAGATA
* *
2365952 AAACATAAATATAAAA
1 AAAAATAAAAATAAAA
2365968 GAAACAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
33 4 0.09
34 24 0.55
35 4 0.09
36 12 0.27
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (34 bp):
AAAAATAAAAATAAAAAATAAATAAAACAAGATA
Found at i:2368206 original size:41 final size:40
Alignment explanation
Indices: 2368123--2368209 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 40
2368113 ATCAAATTTT
* *
2368123 AATTAAATAAAAAATAATAAAATTAAATATTATATTTTTCA
1 AATTAAATAAAAAATAATAAAATTAAATA-TATAGTTATCA
*
2368164 AATTTAATAAAAAATATATAAAACTTAAATGA-A-AGTTATCA
1 AATTAAATAAAAAATA-ATAAAA-TTAAAT-ATATAGTTATCA
2368205 AATTA
1 AATTA
2368210 TCTAGTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
41 25 0.64
42 7 0.18
43 6 0.15
44 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (40 bp):
AATTAAATAAAAAATAATAAAATTAAATATATAGTTATCA
Found at i:2373114 original size:147 final size:147
Alignment explanation
Indices: 2372902--2373202 Score: 557
Period size: 147 Copynumber: 2.0 Consensus size: 147
2372892 CCTCATTCTA
* * *
2372902 CAAGTTTCATAGATCAAAAGGGAAGGTAAGATCATTGTTCTTCACTTCTTTATACTTCAATTGCG
1 CAAGTTCCATAAATCAAAAGGGAAGGTAAGATCATTGTTCTTCACATCTTTATACTTCAATTGCG
* *
2372967 TCCTAATTCCTTCCTATAATATACTTTGTGTTACAGGATTCTTGGGTTCCTTGTTTGGCTAGAGA
66 TCCTAATTCCTTCCTATAATATACTTTGTGTTACAAGATTCTTGGATTCCTTGTTTGGCTAGAGA
2373032 AAGAGTGTAAAATCAAC
131 AAGAGTGTAAAATCAAC
2373049 CAAGTTCCATAAATCAAAAGGGAAGGTAAGATCATTGTTCTTCACATCTTTATACTTCAATTGCG
1 CAAGTTCCATAAATCAAAAGGGAAGGTAAGATCATTGTTCTTCACATCTTTATACTTCAATTGCG
2373114 TCCTAATTCCTTCCTATAATATACTTTGTGTTACAAGATTCTTGGATTCCTTGTTTGGCTAGAGA
66 TCCTAATTCCTTCCTATAATATACTTTGTGTTACAAGATTCTTGGATTCCTTGTTTGGCTAGAGA
2373179 AAGAGTGTAAAATCAAC
131 AAGAGTGTAAAATCAAC
2373196 CAAGTTC
1 CAAGTTC
2373203 AGAAAGGAAA
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 149 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (147 bp):
CAAGTTCCATAAATCAAAAGGGAAGGTAAGATCATTGTTCTTCACATCTTTATACTTCAATTGCG
TCCTAATTCCTTCCTATAATATACTTTGTGTTACAAGATTCTTGGATTCCTTGTTTGGCTAGAGA
AAGAGTGTAAAATCAAC
Found at i:2375227 original size:64 final size:65
Alignment explanation
Indices: 2375152--2375284 Score: 189
Period size: 65 Copynumber: 2.1 Consensus size: 65
2375142 AAACTAATTA
* *
2375152 CATTCGATGTTTC-AAAGAGTCAGGAGTGCATCGATGCATGG-TCTGTGCATCGTTACACAAAAT
1 CATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCT-TGTGCATCGGTACACAAAAT
2375215 G
65 G
* * * *
2375216 CATTCGATGTTTCAAAATATTCAAGAGTTCATTGATGCATGGCTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
2375281 CATT
1 CATT
2375285 TGAAATAGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 13 0.21
65 47 0.77
66 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
CATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
Found at i:2383862 original size:65 final size:65
Alignment explanation
Indices: 2383788--2383922 Score: 236
Period size: 65 Copynumber: 2.1 Consensus size: 65
2383778 ACACTACTTA
2383788 CATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGG-TCTGTGCATCGGTACACAAAAT
1 CATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCT-TGTGCATCGGTACACAAAAT
2383852 G
65 G
* *
2383853 CATTTGATGTTTTAAAATATTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
2383918 CATTC
1 CATTC
2383923 AAAATGGGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
65 65 0.98
66 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (65 bp):
CATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
Found at i:2384056 original size:19 final size:20
Alignment explanation
Indices: 2384021--2384058 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2384011 TTGTAAATTT
2384021 GTTTCAAAAAAATATTTTAA
1 GTTTCAAAAAAATATTTTAA
2384041 GTTT-AAAACAAA-ATTTTA
1 GTTTCAAAA-AAATATTTTA
2384059 CACTTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
GTTTCAAAAAAATATTTTAA
Done.