Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold733
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1111331
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.28
Warning! 184803 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:389031 original size:246 final size:245
Alignment explanation
Indices: 388591--389079 Score: 960
Period size: 246 Copynumber: 2.0 Consensus size: 245
388581 AGACGAAGTT
388591 GGGGGAGGGGGGGGGGCTTATGCTATACCTCCGGCGTTGGCGTCGGCATCCGGACCTGGTTAAAT
1 GGGGGAGGGGGGGGGGCTTATGCTATACCTCCGGCGTTGGCGTCGGCATCCGGACCTGGTTAAAT
388656 TTTTGTTGCAGGTCCTGTATCTAACTTATAACTTGACCTATCGTCACCAAACTTGCATGGATGGT
66 TTTTGTTGCAGGTCCTGTATCTAACTTATAACTTGACCTATCGTCACCAAACTTGCATGGATGGT
388721 GCATCTGGACCTACTTATGGAATTGAGAAACTTGCATGCTGAATCTTGCCCATGAATTTCAGATG
131 GCATCTGGACCTACTTATGGAATTGAGAAACTTGCATGCTGAATCTTGCCCATGAATTTCAGATG
388786 CTGGAGAAAGTTATGCTGTTTGGAGCTGGTTAAAGTTTTTGTTGCATGNGG
196 CTGGAGAAAGTTATGCTGTTTGGAGCTGGTTAAAGTTTTTGTTGCATG-GG
*
388837 GGGGGGGGGGGGGGGGCTTATGCTATACCTCCGGCGTTGGCGTCGGCATCCGGACCTGGTTAAAT
1 GGGGGAGGGGGGGGGGCTTATGCTATACCTCCGGCGTTGGCGTCGGCATCCGGACCTGGTTAAAT
388902 TTTTGTTGCAGGTCCTGTATCTAACTTATAACTTGACCTATCGTCACCAAACTTGCATGGATGGT
66 TTTTGTTGCAGGTCCTGTATCTAACTTATAACTTGACCTATCGTCACCAAACTTGCATGGATGGT
388967 GCATCTGGACCTACTTATGGAATTGAGAAACTTGCATGCTGAATCTTGCCCATGAATTTCAGATG
131 GCATCTGGACCTACTTATGGAATTGAGAAACTTGCATGCTGAATCTTGCCCATGAATTTCAGATG
389032 CTGGAGAAAGTTATGCTGTTTGGAGCTGGTTAAAGTTTTTGTTGCATG
196 CTGGAGAAAGTTATGCTGTTTGGAGCTGGTTAAAGTTTTTGTTGCATG
389080 TGCCCTTTGA
Statistics
Matches: 242, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 242 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.31
Consensus pattern (245 bp):
GGGGGAGGGGGGGGGGCTTATGCTATACCTCCGGCGTTGGCGTCGGCATCCGGACCTGGTTAAAT
TTTTGTTGCAGGTCCTGTATCTAACTTATAACTTGACCTATCGTCACCAAACTTGCATGGATGGT
GCATCTGGACCTACTTATGGAATTGAGAAACTTGCATGCTGAATCTTGCCCATGAATTTCAGATG
CTGGAGAAAGTTATGCTGTTTGGAGCTGGTTAAAGTTTTTGTTGCATGGG
Found at i:389347 original size:158 final size:157
Alignment explanation
Indices: 389059--389353 Score: 396
Period size: 158 Copynumber: 1.9 Consensus size: 157
389049 GTTTGGAGCT
** * *
389059 GGTTAAAGTTTTTGTTGCATGTGCCCTTTGATAGCCACTTCTAAGTTCCAAATGGTCCTAACTTC
1 GGTTAAAGTTTTTGGAGCAGGTGCCCTTTGATAGCCACTTCTAAGTT-CAAATGGTCCTAACTCC
* * *
389124 ACCAAACTTGCATGGATGATGCGTCTTATGATACTGTTGCACCTGACAGGATTGAATGCTGAATC
65 ACCAAACTTGCATAGATGATGCCTCTTATGATACTGATGCACCTGACAGGATTGAATGCTGAATC
389189 TAAGCCAAAGATTTCGGATGCTAGATGA
130 TAAGCCAAAGATTTCGGATGCTAGATGA
* * *
389217 GGTTAAGGTTTTTGGAGCAGGTGCCCTTTGATCGCCATTTCTAAGTT-AATACCT-GTCCTAACT
1 GGTTAAAGTTTTTGGAGCAGGTGCCCTTTGATAGCCACTTCTAAGTTCAA-A--TGGTCCTAACT
** * * *
389280 CCACTTAACTTGCATAGATGGTGCCTCTTATGATACTGATGCATCTGACAGGCTTGAATGCTGAA
63 CCACCAAACTTGCATAGATGATGCCTCTTATGATACTGATGCACCTGACAGGATTGAATGCTGAA
*
389345 TCTGAGCCA
128 TCTAAGCCA
389354 TAGGTGTCAG
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
156 2 0.02
157 1 0.01
158 114 0.97
159 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (157 bp):
GGTTAAAGTTTTTGGAGCAGGTGCCCTTTGATAGCCACTTCTAAGTTCAAATGGTCCTAACTCCA
CCAAACTTGCATAGATGATGCCTCTTATGATACTGATGCACCTGACAGGATTGAATGCTGAATCT
AAGCCAAAGATTTCGGATGCTAGATGA
Found at i:398201 original size:9 final size:8
Alignment explanation
Indices: 398179--398203 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
398169 TTGGGCGAAG
398179 AGTTTTTA
1 AGTTTTTA
398187 AGTTTTTA
1 AGTTTTTA
398195 AGTTTTTA
1 AGTTTTTA
398203 A
1 A
398204 ATCTTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
AGTTTTTA
Found at i:402184 original size:346 final size:342
Alignment explanation
Indices: 401482--402304 Score: 1032
Period size: 346 Copynumber: 2.4 Consensus size: 342
401472 AGTGATAATT
* * *
401482 TCCATGAGGCCCTCTACCAAAATTGTGAAATTCA-TAGCCCCTGGGTCAGGGGTACAGG--CTA-
1 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATTA-CCCCTGCGTCAGGGGTTCAGGCTCTAG
* * *
401543 -TAGAGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAGTCTTAGAAAATATTCTTTTC-T
65 CTAGAGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTT
* * *
401606 ACTCCGATATATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATGAGGCCCTCTACCAAA
130 ACTCCGAAATATATTTGTTAAAAACTAAATGCATGATTATGATGTACATGAGACCCTCTACCAAA
401671 ATTGTGAATTCATGACCTCTGGGTCAGCCCGGTCAGGGGTTCAGGCTCTAGGATGGGGCCAATAT
195 ATTGTGAATTCATGACCTCT--GT-----CGGTCAGGGGTTCAGGCTCTAGGATGGGGCCAATAT
**
401736 GGCAATATAGTAAAAATGTATTAAATCTTTGGAAATCTTCTCTACTCCCATATATATATTTGTTT
253 GGCAATATAGTAAAAATGTATTAAATCTTTAAAAATCTTCTCTACTCCCATATATATATTTGTTT
*
401801 AAAAATTAAATGCATGGTTATGATG
318 AAAAACTAAATGCATGGTTATGATG
* * * *
401826 TCCATCAAGCCCTCTACCACAATTGTAAAATTCATTACCCCTGCGTCAGGAGTTCAGGCTCTAGC
1 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATTACCCCTGCGTCAGGGGTTCAGGCTCTAGC
* * *
401891 TAGAGTGGGGCCAATATGGCCACATAG-TAAAACAGTATTAAATCTTAGGAAATCTTCTTCTCTT
66 TAGAGTGGGGCCAATATGGCCATATAGTTAAAA-TGTATTAAATCTTAGAAAATCTTCTTCTCTT
* *
401955 A-TCTC-AAATATATTTGTTTTAAAA-TTAATGCATGATTATGATATACATGTACATGAGACCCT
130 ACTC-CGAAATATATTTG-TTAAAAACTAAATGCATGATTATG------ATGTACATGAGACCCT
* * *
402017 CTACTAAAATTGTGAAATTCATGACCTCT-T-GGTCAGGGGTTCAGGTTCTAGGGTGGGGCCAAT
187 CTACCAAAATTGTG-AATTCATGACCTCTGTCGGTCAGGGGTTCAGGCTCTAGGATGGGGCCAAT
* * *
402080 ATGGCCATATAGTAAAAATGTATTAAATCTTTTAAAATAGTCTTCTCTTCTCCGATA-A-ATATT
251 ATGGCAATATAGTAAAAATGTATTAAATC-TTTAAAA-A-TCTTCTCTACTCCCATATATATATT
* *
402143 TG-TTAAAAACTAAATGCCTGGTTGTGATG
313 TGTTTAAAAACTAAATGCATGGTTATGATG
* *
402172 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGCGTCAGGGGTTCAGGCTCTTGC
1 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATTACCCCTGCGTCAGGGGTTCAGGCTCTAGC
* *
402237 TACG-GTGGGACCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTTTTCTCTT
66 TA-GAGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTT
402301 -CTCC
130 ACTCC
402305 AATACATGGG
Statistics
Matches: 417, Mismatches: 40, Indels: 43
0.83 0.08 0.09
Matches are distributed among these distances:
344 48 0.12
345 3 0.01
346 198 0.47
347 23 0.06
348 79 0.19
349 24 0.06
352 1 0.00
354 27 0.06
355 14 0.03
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (342 bp):
TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATTACCCCTGCGTCAGGGGTTCAGGCTCTAGC
TAGAGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTTA
CTCCGAAATATATTTGTTAAAAACTAAATGCATGATTATGATGTACATGAGACCCTCTACCAAAA
TTGTGAATTCATGACCTCTGTCGGTCAGGGGTTCAGGCTCTAGGATGGGGCCAATATGGCAATAT
AGTAAAAATGTATTAAATCTTTAAAAATCTTCTCTACTCCCATATATATATTTGTTTAAAAACTA
AATGCATGGTTATGATG
Found at i:402301 original size:172 final size:173
Alignment explanation
Indices: 401482--402304 Score: 875
Period size: 172 Copynumber: 4.8 Consensus size: 173
401472 AGTGATAATT
* * * *
401482 TCCATGAGGCCCTCTACCAAAATTGTGAAATTCAT-AGCCCCTGGGTCAGGGGTACAGGCTATAG
1 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGA-CCCCTGCGTCAGGGGTTCAGGCTCTAG
* * * *
401546 --A-GTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAGTCTTAGAAAATATTCTTTTCTAC
65 CTAGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTTC
401608 TCCGAT-ATATATTTG-TTAAAAACTAAATGCATGATTATGATG
130 TCCGATAATATATTTGTTTAAAAACTAAATGCATGATTATGATG
* *
401650 TCCATGAGGCCCTCTACCAAAATTGTG-AATTCATGACCTCTGGGTCAGCCCGGTCAGGGGTTCA
1 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACC-C-----CTG--C-GTCAGGGGTTCA
* * * * *
401714 GGCTCTAG---GATGGGGCCAATATGGCAATATAGTAAAAATGTATTAAATCTTTGGAAATCTTC
57 GGCTCTAGCTAGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTC
* *
401776 -TCTAC-TC-CC-ATATATATATTTGTTTAAAAATTAAATGCATGGTTATGATG
122 TTCT-CTTCTCCGATA-ATATATTTGTTTAAAAACTAAATGCATGATTATGATG
* * * * *
401826 TCCATCAAGCCCTCTACCACAATTGTAAAATTCATTACCCCTGCGTCAGGAGTTCAGGCTCTAGC
1 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGCGTCAGGGGTTCAGGCTCTAGC
* * *
401891 TAGAGTGGGGCCAATATGGCCACATAG-TAAAACAGTATTAAATCTTAGGAAATCTTCTTCTCTT
66 TAG-GTGGGGCCAATATGGCCATATAGTTAAAA-TGTATTAAATCTTAGAAAATCTTCTTCTCTT
* * * *
401955 ATCTC-A-AATATATTTGTTTTAAAA-TTAATGCATGATTATGATA
129 CTC-CGATAATATATTTGTTTAAAAACTAAATGCATGATTATGATG
* * *
401998 TACATGTACATGAGACCCTCTACTAAAATTGTGAAATTCATGACCTCTTG-GTCAGGGGTTCAGG
1 TCCATG---A--AG-CCCTCTACCAAAATTGTGAAATTCATGACC-CCTGCGTCAGGGGTTCAGG
* * ** **
402062 TTCTAG---GGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTTTAAAATAGTCTT
59 CTCTAGCTAGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTT
* * *
402124 CTCTTCTCCGATAA-ATATTTG-TTAAAAACTAAATGCCTGGTTGTGATG
124 CTCTTCTCCGATAATATATTTGTTTAAAAACTAAATGCATGATTATGATG
*
402172 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGCGTCAGGGGTTCAGGCTCTTGC
1 TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGCGTCAGGGGTTCAGGCTCTAGC
* *
402237 TACGGTGGGACCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTTTTCTCTTC
66 TA-GGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTTC
402302 TCC
130 TCC
402305 AATACATGGG
Statistics
Matches: 545, Mismatches: 69, Indels: 78
0.79 0.10 0.11
Matches are distributed among these distances:
167 12 0.02
168 95 0.17
169 3 0.01
171 8 0.01
172 121 0.22
173 31 0.06
174 80 0.15
175 22 0.04
176 114 0.21
177 12 0.02
178 44 0.08
179 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (173 bp):
TCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGCGTCAGGGGTTCAGGCTCTAGC
TAGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTTCT
CCGATAATATATTTGTTTAAAAACTAAATGCATGATTATGATG
Found at i:404221 original size:18 final size:19
Alignment explanation
Indices: 404175--404225 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
404165 GTCTGAATCA
*
404175 AATTCCTACAGGAAATACC
1 AATTCCTATAGGAAATACC
* *
404194 ATTCTCCTATAGGAAATA-T
1 AAT-TCCTATAGGAAATACC
404213 AATTCCTATAGGA
1 AATTCCTATAGGA
404226 CTTTTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.37
19 4 0.15
20 13 0.48
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (19 bp):
AATTCCTATAGGAAATACC
Found at i:407216 original size:44 final size:44
Alignment explanation
Indices: 407153--407240 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
407143 CCCCGTTTGC
407153 TGTCACATTGACAGCTTTTCTCTTGTTCTTCATATTGATCTATT
1 TGTCACATTGACAGCTTTTCTCTTGTTCTTCATATTGATCTATT
*
407197 TGTCACATTGACAGCTTTTCTCTTGTTCTTCATCTTGATCTATT
1 TGTCACATTGACAGCTTTTCTCTTGTTCTTCATATTGATCTATT
407241 CTCAGTAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (44 bp):
TGTCACATTGACAGCTTTTCTCTTGTTCTTCATATTGATCTATT
Found at i:410481 original size:58 final size:58
Alignment explanation
Indices: 410395--410741 Score: 586
Period size: 58 Copynumber: 6.0 Consensus size: 58
410385 TGAATGGCCT
* * *
410395 GAATAGTACAGATGTTCCATTGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCT
1 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCC
*
410453 GAATAGTACAGATGTTCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCC
1 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCC
* * *
410511 GAATAGTATAGATGTCCAAATGGTAGGTCCAAATGTAACAATGTATTAAACAGTGCCC
1 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCC
*
410569 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTATTAAACAGTGCCC
1 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCC
* *
410627 GAATAGTACAAATGTCCCAATGGTATGTCCAAATGTAACAATGTGTTAAACAGTGCCC
1 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCC
* *
410685 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTATACAATGCC
1 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCC
410742 TGGAACGTAC
Statistics
Matches: 274, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 274 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (58 bp):
GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCC
Found at i:410852 original size:58 final size:58
Alignment explanation
Indices: 410425--410852 Score: 215
Period size: 58 Copynumber: 7.4 Consensus size: 58
410415 TGGTAGGTCC
* * * * * **
410425 AAATGTAACAATGTGTTAAACAGTGCCT-GAATAGTACAGATGTTCCAATGGTAGGTCC
1 AAATGTAACAATGTGTTAAACAATGCCTGGAA-CGTACAGCTGTTCCAATGTTATGTGA
* * * * * * * **
410483 AAATGTAACAATGTGTTAAACAGTGCC-CGAATAGTATAGATG-TCCAAATGGTAGGTCC
1 AAATGTAACAATGTGTTAAACAATGCCTGGAA-CGTACAGCTGTTCC-AATGTTATGTGA
* * * * * * * * **
410541 AAATGTAACAATGTATTAAACAGTGCC-CGAATAGTACAGATGTCCCAATGGTAGGTCC
1 AAATGTAACAATGTGTTAAACAATGCCTGGAA-CGTACAGCTGTTCCAATGTTATGTGA
* * * * ** * * **
410599 AAATGTAACAATGTATTAAACAGTGCC-CGAATAGTACAAATGTCCCAATGGTATGTCC
1 AAATGTAACAATGTGTTAAACAATGCCTGGAA-CGTACAGCTGTTCCAATGTTATGTGA
* * * * * * * **
410657 AAATGTAACAATGTGTTAAACAGTGCC-CGAATAGTACAGATGTCCCAATGGTAGGTCC
1 AAATGTAACAATGTGTTAAACAATGCCTGGAA-CGTACAGCTGTTCCAATGTTATGTGA
* * *
410715 AAATGTAACAATGTGTTATACAATGCCTGGAACGTACTGCTGTTCCATTGTTATGTGA
1 AAATGTAACAATGTGTTAAACAATGCCTGGAACGTACAGCTGTTCCAATGTTATGTGA
* ** * * * * *
410773 AAATGTAATAACATATGAAACAATGCTTGG-ACAGTACAGTTTTTCCAATGATTA-GTGA
1 AAATGTAACAATGTGTTAAACAATGCCTGGAAC-GTACAGCTGTTCCAATG-TTATGTGA
*
410831 GAATGTAACAATGTGTTAAACA
1 AAATGTAACAATGTGTTAAACA
410853 TTTGTATTGA
Statistics
Matches: 326, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
57 5 0.02
58 313 0.96
59 8 0.02
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (58 bp):
AAATGTAACAATGTGTTAAACAATGCCTGGAACGTACAGCTGTTCCAATGTTATGTGA
Found at i:410852 original size:174 final size:174
Alignment explanation
Indices: 410395--410798 Score: 486
Period size: 174 Copynumber: 2.3 Consensus size: 174
410385 TGAATGGCCT
* * * ** * * * * *
410395 GAATAGTACAGATGTTCCATTGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCTGAATAGT
1 GAATAGTACAGATGTCCCAATGGTAGGTCAAAATGTAACAACATATGAAACAATGCCCGAACAGT
* * * *
410460 ACAGATGTTCCAATGGTAGGTCCAAATGTAACAATGTGTTAAACAGTGCCCGAATAGTATAGATG
66 ACAAATGTCCCAATGGTATGTCCAAATGTAACAATGTGTTAAACAGTGCCCGAATAGTACAGATG
*
410525 TCCAAATGGTAGGTCCAAATGTAACAATGTATTAAACAGTGCCC
131 TCCAAATGGTAGGTCCAAATGTAACAATGTATTAAACAATGCCC
* ** * * *
410569 GAATAGTACAGATGTCCCAATGGTAGGTCCAAATGTAACAATGTATTAAACAGTGCCCGAATAGT
1 GAATAGTACAGATGTCCCAATGGTAGGTCAAAATGTAACAACATATGAAACAATGCCCGAACAGT
410634 ACAAATGTCCCAATGGTATGTCCAAATGTAACAATGTGTTAAACAGTGCCCGAATAGTACAGATG
66 ACAAATGTCCCAATGGTATGTCCAAATGTAACAATGTGTTAAACAGTGCCCGAATAGTACAGATG
* * * *
410699 TCCCAATGGTAGGTCCAAATGTAACAATGTGTTATACAATGCCTG
131 TCCAAATGGTAGGTCCAAATGTAACAATGTATTAAACAATGCC-C
* * * * * * * * *
410744 GAA-CGTACTGCTGTTCCATTGTTATGTGAAAATGTAATAACATATGAAACAATGC
1 GAATAGTACAGATGTCCCAATGGTAGGTCAAAATGTAACAACATATGAAACAATGC
410799 TTGGACAGTA
Statistics
Matches: 202, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
174 199 0.99
175 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (174 bp):
GAATAGTACAGATGTCCCAATGGTAGGTCAAAATGTAACAACATATGAAACAATGCCCGAACAGT
ACAAATGTCCCAATGGTATGTCCAAATGTAACAATGTGTTAAACAGTGCCCGAATAGTACAGATG
TCCAAATGGTAGGTCCAAATGTAACAATGTATTAAACAATGCCC
Found at i:411030 original size:58 final size:57
Alignment explanation
Indices: 410917--411099 Score: 173
Period size: 58 Copynumber: 3.3 Consensus size: 57
410907 GAAAGTAAAA
*
410917 TTGTTCCAATGGTAAATGAGAA-TC-A-ATGTG-TT-ACAAATGCATGG-TAGTACGG
1 TTGTTCCAATGGTAAATGAGAATTCAATATGTGTTTAAC-AATGCATGGATAGTACCG
* *
410969 TTGTTCCAATGGTAATTGAGAATTTCAATATGTGTTTAACAATGCATGGACAGTACCG
1 TTGTTCCAATGGTAAATGAGAA-TTCAATATGTGTTTAACAATGCATGGATAGTACCG
** * * * * *
411027 TTGTTTTAATGGTAAGTGAGAATGT-AACTATGTGTTAAACAATTCCTGGATAGTACCA
1 TTGTTCCAATGGTAAATGAGAAT-TCAA-TATGTGTTTAACAATGCATGGATAGTACCG
* *
411085 CTGTTCCACTGGTAA
1 TTGTTCCAATGGTAA
411100 GTAAGAATAT
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
52 21 0.20
54 2 0.02
55 1 0.01
56 5 0.05
57 14 0.13
58 64 0.60
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (57 bp):
TTGTTCCAATGGTAAATGAGAATTCAATATGTGTTTAACAATGCATGGATAGTACCG
Found at i:411100 original size:58 final size:57
Alignment explanation
Indices: 410918--411120 Score: 164
Period size: 58 Copynumber: 3.6 Consensus size: 57
410908 AAAGTAAAAT
* * * * ***
410918 TGTTCCAATGGTAAATGAG-A-ATCA-ATGTGTTACA-AATGCATGG-TAGTACGGT
1 TGTTCCAATGGTAAGTGAGAATATAATATGTGTTAAACAATGCATGGACAGTACCAC
* * * **
410970 TGTTCCAATGGTAATTGAGAATTTCAATATGTGTTTAACAATGCATGGACAGTACCGT
1 TGTTCCAATGGTAAGTGAGAATAT-AATATGTGTTAAACAATGCATGGACAGTACCAC
** * * * *
411028 TGTTTTAATGGTAAGTGAGAATGTAACTATGTGTTAAACAATTCCTGGATAGTACCAC
1 TGTTCCAATGGTAAGTGAGAATATAA-TATGTGTTAAACAATGCATGGACAGTACCAC
* * *
411086 TGTTCCACTGGTAAGTAAGAATATGATATGTGTTA
1 TGTTCCAATGGTAAGTGAGAATATAATATGTGTTA
411121 GACTTTAAGT
Statistics
Matches: 121, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
52 18 0.15
53 1 0.01
54 1 0.01
55 1 0.01
56 8 0.07
57 20 0.17
58 72 0.60
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (57 bp):
TGTTCCAATGGTAAGTGAGAATATAATATGTGTTAAACAATGCATGGACAGTACCAC
Found at i:411463 original size:2 final size:2
Alignment explanation
Indices: 411456--411501 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
411446 TGACTTGGAT
411456 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
411498 GA GA
1 GA GA
411502 ATTGAGTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:417979 original size:4 final size:4
Alignment explanation
Indices: 417970--418017 Score: 82
Period size: 4 Copynumber: 12.5 Consensus size: 4
417960 AGTTTAAACA
417970 ATCT ATCT ATCT ATCT ATCT ATC- -TCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
418016 AT
1 AT
418018 GTCTAAAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 40 0.95
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:417996 original size:22 final size:22
Alignment explanation
Indices: 417971--418015 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
417961 GTTTAAACAA
417971 TCTATCTATCTATCTATCTATC
1 TCTATCTATCTATCTATCTATC
417993 TCTATCTATCTATCTATCTATC
1 TCTATCTATCTATCTATCTATC
418015 T
1 T
418016 ATGTCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (22 bp):
TCTATCTATCTATCTATCTATC
Found at i:417998 original size:18 final size:18
Alignment explanation
Indices: 417975--418011 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
417965 AAACAATCTA
417975 TCTATCTATCTATCTATC
1 TCTATCTATCTATCTATC
417993 TCTATCTATCTATCTATC
1 TCTATCTATCTATCTATC
418011 T
1 T
418012 ATCTATGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (18 bp):
TCTATCTATCTATCTATC
Found at i:418022 original size:22 final size:22
Alignment explanation
Indices: 417973--418022 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
417963 TTAAACAATC
*
417973 TATCTATCTATCTATCTATCTC
1 TATCTATCTATCTATCTATCTA
417995 TATCTATCTATCTATCTATCTA
1 TATCTATCTATCTATCTATCTA
*
418017 TGTCTA
1 TATCTA
418023 AAACAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50
Consensus pattern (22 bp):
TATCTATCTATCTATCTATCTA
Found at i:424246 original size:16 final size:17
Alignment explanation
Indices: 424215--424270 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
424205 TAAGTCAGTG
*
424215 TCAG-TTGACCAACCAA
1 TCAGATTGACCAGCCAA
*
424231 TCAGATTG-TCAGCCAA
1 TCAGATTGACCAGCCAA
424247 TGTCAG-TTGACCAGCCAA
1 --TCAGATTGACCAGCCAA
424265 TCAGAT
1 TCAGAT
424271 AGTAAGTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 14 0.44
17 7 0.22
18 11 0.34
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (17 bp):
TCAGATTGACCAGCCAA
Found at i:424251 original size:34 final size:34
Alignment explanation
Indices: 424204--424475 Score: 237
Period size: 34 Copynumber: 7.9 Consensus size: 34
424194 CAAGTAGTTG
*
424204 GTAAGTCAGTGTCAGTTGACCAACCAATCAGATT
1 GTAAGTCAGTGTCAGTTGACCAACCAATCAGATA
* * * *
424238 GTCAGCCAATGTCAGTTGACCAGCCAATCAGATA
1 GTAAGTCAGTGTCAGTTGACCAACCAATCAGATA
**
424272 GTAAGTCAGTGTCAGTAAACCAACCAATCAGATA
1 GTAAGTCAGTGTCAGTTGACCAACCAATCAGATA
** *
424306 GTAAGTCAGTGTCAGTAAACCCACCAATCAGATA
1 GTAAGTCAGTGTCAGTTGACCAACCAATCAGATA
* ** *
424340 GTAAGTCAGTGTCAGTTGACCGACCGCTCAGATT
1 GTAAGTCAGTGTCAGTTGACCAACCAATCAGATA
* * * *
424374 GTCAG-CAAATGTCA-TTTAACATACCAATCAGA-A
1 GTAAGTC-AGTGTCAGTTGACCA-ACCAATCAGATA
* * *
424407 CATAAGTCATTGCCAGTTGACCAA-CAATCAGATGGTACA
1 -GTAAGTCAGTGTCAGTTGACCAACCAATCAGA---T--A
* *
424446 GTAAGTCAGTGTCAGTTGATCGACCAATCA
1 GTAAGTCAGTGTCAGTTGACCAACCAATCA
424476 ATTTGTCAGA
Statistics
Matches: 189, Mismatches: 37, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
33 13 0.07
34 145 0.77
35 6 0.03
38 18 0.10
39 7 0.04
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (34 bp):
GTAAGTCAGTGTCAGTTGACCAACCAATCAGATA
Found at i:424261 original size:18 final size:18
Alignment explanation
Indices: 424213--424265 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
424203 GGTAAGTCAG
*
424213 TGTCAGTTGACCAACCAA
1 TGTCAGTTGACCAGCCAA
*
424231 --TCAGATTG-TCAGCCAA
1 TGTCAG-TTGACCAGCCAA
424247 TGTCAGTTGACCAGCCAA
1 TGTCAGTTGACCAGCCAA
424265 T
1 T
424266 CAGATAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 10 0.36
17 6 0.21
18 12 0.43
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (18 bp):
TGTCAGTTGACCAGCCAA
Found at i:431445 original size:15 final size:14
Alignment explanation
Indices: 431425--431458 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
431415 TTAAGAAAAC
431425 AAAAACAACAACACA
1 AAAAACAACAACA-A
*
431440 AAAAACAATAACAA
1 AAAAACAACAACAA
431454 AAAAA
1 AAAAA
431459 TCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAAACAACAACAA
Found at i:432333 original size:30 final size:30
Alignment explanation
Indices: 432299--432406 Score: 189
Period size: 30 Copynumber: 3.6 Consensus size: 30
432289 CGACTACAGG
*
432299 TGCTCCAGTAACTAAGGCCCCAACAACGGT
1 TGCTCCAGTAACAAAGGCCCCAACAACGGT
432329 TGCTCCAGTAACAAAGGCCCCAACAACGGT
1 TGCTCCAGTAACAAAGGCCCCAACAACGGT
*
432359 TGCTCCGGTAACAAAGGCCCCAACAACGGT
1 TGCTCCAGTAACAAAGGCCCCAACAACGGT
*
432389 TGCTCCGGTAACAAAGGC
1 TGCTCCAGTAACAAAGGC
432407 TCCGGTAACA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (30 bp):
TGCTCCAGTAACAAAGGCCCCAACAACGGT
Found at i:432410 original size:15 final size:15
Alignment explanation
Indices: 432390--432421 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
432380 AACAACGGTT
432390 GCTCCGGTAACAAAG
1 GCTCCGGTAACAAAG
432405 GCTCCGGTAACAAAG
1 GCTCCGGTAACAAAG
432420 GC
1 GC
432422 CTCAACAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.12
Consensus pattern (15 bp):
GCTCCGGTAACAAAG
Found at i:432414 original size:45 final size:45
Alignment explanation
Indices: 432360--432454 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
432350 AACAACGGTT
** *
432360 GCTCCGGTAACAAAGGCCCCAACAACGGTTGCTCCGGTAACAAAG
1 GCTCCGGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAA
*
432405 GCTCCGGTAACAAAGGCCTCAACAACGGTTGCTCCAATAACAAAA
1 GCTCCGGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAA
432450 GCTCC
1 GCTCC
432455 AACAACGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.32, G:0.21, T:0.15
Consensus pattern (45 bp):
GCTCCGGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAA
Found at i:432439 original size:30 final size:30
Alignment explanation
Indices: 432405--432476 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
432395 GGTAACAAAG
* *
432405 GCTCCGGTAACAAAGGC-CTCAACAACGGTT
1 GCTCCAGTAACAAAAGCTC-CAACAACGGTT
*
432435 GCTCCAATAACAAAAGCTCCAACAACGGTT
1 GCTCCAGTAACAAAAGCTCCAACAACGGTT
*
432465 GCCCCAGTAACA
1 GCTCCAGTAACA
432477 TATACCCCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (30 bp):
GCTCCAGTAACAAAAGCTCCAACAACGGTT
Found at i:432457 original size:75 final size:75
Alignment explanation
Indices: 432330--432476 Score: 222
Period size: 75 Copynumber: 2.0 Consensus size: 75
432320 AACAACGGTT
** * *
432330 GCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCCGGTAACAAAGGCCCCAACAACGGTTGCTCC
1 GCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAAGCCCCAACAACGGTTGCCCC
*
432395 GGTAACAAAG
66 AGTAACAAAG
* * *
432405 GCTCCGGTAACAAAGGCCTCAACAACGGTTGCTCCAATAACAAAAGCTCCAACAACGGTTGCCCC
1 GCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAAGCCCCAACAACGGTTGCCCC
432470 AGTAACA
66 AGTAACA
432477 TATACCCCGG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.33, C:0.32, G:0.20, T:0.14
Consensus pattern (75 bp):
GCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAAGCCCCAACAACGGTTGCCCC
AGTAACAAAG
Found at i:432500 original size:105 final size:105
Alignment explanation
Indices: 432300--432505 Score: 277
Period size: 105 Copynumber: 2.0 Consensus size: 105
432290 GACTACAGGT
* * * *
432300 GCTCCAGTAACTAAGGCCCCAACAACGGTTGCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCC
1 GCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAAGCCCCAACAACGGTTGCCCC
* *
432365 GGTAACAAAGGCCCCAACAACGGTTGCTCCGGTAACAAAG
66 AGTAACAAAGACCCCAACAACGGTTGCTCCGGTAACAAAG
* * *
432405 GCTCCGGTAACAAAGGCCTCAACAACGGTTGCTCCAATAACAAAAGCTCCAACAACGGTTGCCCC
1 GCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAAGCCCCAACAACGGTTGCCCC
* * ** * *
432470 AGTAACATATACCCCGGCAACTGTTTCTCCGGTAAC
66 AGTAACAAAGACCCCAACAACGGTTGCTCCGGTAAC
432506 CAAGACCCCA
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 86 1.00
ACGTcount: A:0.31, C:0.33, G:0.20, T:0.17
Consensus pattern (105 bp):
GCTCCAGTAACAAAGGCCCCAACAACGGTTGCTCCAATAACAAAAGCCCCAACAACGGTTGCCCC
AGTAACAAAGACCCCAACAACGGTTGCTCCGGTAACAAAG
Found at i:432505 original size:30 final size:29
Alignment explanation
Indices: 432480--432536 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
432470 AGTAACATAT
* *
432480 ACCCCGGCAACTGTTTCTCCGGTAACCAAG
1 ACCCCAGCAACTATTTCTCCGGTAA-CAAG
* *
432510 ACCCCAGCCACTATTTTTCCGGTAACA
1 ACCCCAGCAACTATTTCTCCGGTAACA
432537 CCGATTCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.23
Consensus pattern (29 bp):
ACCCCAGCAACTATTTCTCCGGTAACAAG
Found at i:433092 original size:2 final size:2
Alignment explanation
Indices: 433085--433149 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
433075 AAGAACTTTT
* *
433085 GA GA GA GA GA GA GA GA GA GA AA G- GA AA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
433126 GA AA G- GA AA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
433150 TTAAAATATT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:433114 original size:23 final size:23
Alignment explanation
Indices: 433088--433149 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
433078 AACTTTTGAG
433088 AGAGAGAGAGAGAGAGAAAGGAA
1 AGAGAGAGAGAGAGAGAAAGGAA
433111 AGAGAGAGAGAGAGAGAAAGGAA
1 AGAGAGAGAGAGAGAGAAAGGAA
433134 AGAGAGAGAGAGAGAG
1 AGAGAGAGAGAGAGAG
433150 TTAAAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (23 bp):
AGAGAGAGAGAGAGAGAAAGGAA
Found at i:436989 original size:4 final size:4
Alignment explanation
Indices: 436963--437012 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
436953 ATCACATTTT
* * *
436963 GTCC GT-C GTCC GTCT GTCC GTCT GTCT GTCC GTCC GTCC GTCC GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
437010 GTC
1 GTC
437013 TGTAAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32
Consensus pattern (4 bp):
GTCC
Found at i:436989 original size:12 final size:12
Alignment explanation
Indices: 436969--437015 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
436959 TTTTGTCCGT
436969 CGTCCGTCTGTC
1 CGTCCGTCTGTC
*
436981 CGTCTGTCTGTC
1 CGTCCGTCTGTC
*
436993 CGTCCGTCCGTC
1 CGTCCGTCTGTC
437005 CGTCCGTCTGT
1 CGTCCGTCTGT
437016 AAACTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:446078 original size:18 final size:17
Alignment explanation
Indices: 446044--446077 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
446034 TGAATCAGAG
446044 CACAATTGTGATGAAAA
1 CACAATTGTGATGAAAA
446061 CACAACTTGT-ATGAAAA
1 CACAA-TTGTGATGAAAA
446078 ATTACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAATTGTGATGAAAA
Found at i:454845 original size:14 final size:14
Alignment explanation
Indices: 454828--454862 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
454818 TTGAATCTCG
*
454828 AATCTCGTATTTCA
1 AATCTCGCATTTCA
*
454842 AATCTCGCATTTCG
1 AATCTCGCATTTCA
454856 AATCTCG
1 AATCTCG
454863 ATATAGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (14 bp):
AATCTCGCATTTCA
Found at i:468210 original size:11 final size:11
Alignment explanation
Indices: 468194--468233 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
468184 TAAGCAAGTC
468194 CTTAAAGGTGG
1 CTTAAAGGTGG
*
468205 CTTAAAGGTGA
1 CTTAAAGGTGG
*
468216 CTTAAAGG-AG
1 CTTAAAGGTGG
468226 CTTAAAGG
1 CTTAAAGG
468234 CTATACAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:485092 original size:2 final size:2
Alignment explanation
Indices: 485085--485126 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
485075 GAATTTTAAT
485085 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
485127 GATCGACAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:486233 original size:70 final size:74
Alignment explanation
Indices: 486107--486243 Score: 228
Period size: 70 Copynumber: 1.9 Consensus size: 74
486097 CAAGACACCA
486107 AAGTCTAAAAAAAGACAAATTTATTCAAATGAAGAGAACATATTTAAACTTATCCAACATGATTA
1 AAGTCTAAAAAAAGACAAATTTATTC-AA-GAAGAGAACATATTTAAACTTATCCAACATGATTA
486172 TTGGATATTTT
64 TTGGATATTTT
486183 AAGTCT-AAAAAAGACAAATTTATTC-A-AAG-GAACATATTTAAACTTATCCAACATGATTATT
1 AAGTCTAAAAAAAGACAAATTTATTCAAGAAGAGAACATATTTAAACTTATCCAACATGATTATT
486244 TATTTTTATT
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
70 32 0.52
71 3 0.05
73 1 0.02
75 19 0.31
76 6 0.10
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (74 bp):
AAGTCTAAAAAAAGACAAATTTATTCAAGAAGAGAACATATTTAAACTTATCCAACATGATTATT
GGATATTTT
Found at i:486296 original size:5 final size:5
Alignment explanation
Indices: 486286--486314 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
486276 TTGCGTCGTT
486286 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
486315 TTGTTGGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:493081 original size:34 final size:34
Alignment explanation
Indices: 493038--493159 Score: 108
Period size: 34 Copynumber: 3.6 Consensus size: 34
493028 TGAGGAGCTG
493038 AATCAGATGGTAAGTCAATGTTAGTAAATCAACC
1 AATCAGATGGTAAGTCAATGTTAGTAAATCAACC
* * *
493072 AATCAGATGGTAGGTCAATG-TCGATAAGAT-AGCC
1 AATCAGATGGTAAGTCAATGTTAG-TAA-ATCAACC
* * * * *
493106 AATCAAATTGTGAGTCAATGTCAGTAAA-CTAACTT
1 AATCAGATGGTAAGTCAATGTTAGTAAATC-AAC-C
493141 AA-CAGATGGTAAGTCAATG
1 AATCAGATGGTAAGTCAATG
493160 CCAGCTAATG
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
33 3 0.04
34 60 0.88
35 5 0.07
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (34 bp):
AATCAGATGGTAAGTCAATGTTAGTAAATCAACC
Found at i:500199 original size:46 final size:46
Alignment explanation
Indices: 500149--500241 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
500139 TCAGTAGAGT
500149 ACAGAATGTACGAATCATTTATAACGAAACTCGAAAATAATATTTC
1 ACAGAATGTACGAATCATTTATAACGAAACTCGAAAATAATATTTC
500195 ACAGAATGTACGAATCATTTATAACGAAACTCGAAAATAATATTTC
1 ACAGAATGTACGAATCATTTATAACGAAACTCGAAAATAATATTTC
500241 A
1 A
500242 GACGATGCGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (46 bp):
ACAGAATGTACGAATCATTTATAACGAAACTCGAAAATAATATTTC
Found at i:500229 original size:21 final size:21
Alignment explanation
Indices: 500159--500229 Score: 54
Period size: 23 Copynumber: 3.2 Consensus size: 21
500149 ACAGAATGTA
500159 CGAATCATTTATAACGAAACT
1 CGAATCATTTATAACGAAACT
* * **
500180 CGAAAATAATATT-TCACAGAATGT
1 CG--AATCAT-TTATAAC-GAAACT
500204 ACGAATCATTTATAACGAAACT
1 -CGAATCATTTATAACGAAACT
500226 CGAA
1 CGAA
500230 AATAATATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
21 6 0.17
22 6 0.17
23 16 0.44
24 6 0.17
25 2 0.06
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (21 bp):
CGAATCATTTATAACGAAACT
Found at i:508942 original size:31 final size:31
Alignment explanation
Indices: 508907--508974 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
508897 ACAATAGTAA
508907 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
508938 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
508969 CATTCT
1 CATTCT
508975 TATGCATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.16, C:0.32, G:0.09, T:0.43
Consensus pattern (31 bp):
CATTCTCAGCAGTTATCTCTCTTTGCCCATT
Found at i:513007 original size:1 final size:1
Alignment explanation
Indices: 512997--513042 Score: 74
Period size: 1 Copynumber: 46.0 Consensus size: 1
512987 AGACAAAGTC
* *
512997 GGGGGTGGGGGGGGGNGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
513043 TAATATTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.96, T:0.02
Consensus pattern (1 bp):
G
Found at i:521488 original size:2 final size:2
Alignment explanation
Indices: 521481--521528 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
521471 ATTATTATTA
521481 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
521523 TC TC TC
1 TC TC TC
521529 GTGCACATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:522164 original size:2 final size:2
Alignment explanation
Indices: 522157--522211 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
522147 ATTCACGAAC
522157 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
522199 GA AA GA GA GA GA G
1 GA GA GA GA GA GA G
522212 TTTATCTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:524030 original size:35 final size:35
Alignment explanation
Indices: 523983--524102 Score: 204
Period size: 35 Copynumber: 3.4 Consensus size: 35
523973 GTTTACTGAT
*
523983 TGGTAAACTCACCTTATGTGTTGTCCGATCAAATG
1 TGGTAAACTCACCTTATGTGTTGTCCGATCCAATG
*
524018 TGGTAAATTCACCTTATGTGTTGTCCGATCCAATG
1 TGGTAAACTCACCTTATGTGTTGTCCGATCCAATG
*
524053 TGGTAAATTCACCTTATGTGTTGTCCGATCCAATG
1 TGGTAAACTCACCTTATGTGTTGTCCGATCCAATG
*
524088 TAGTAAACTCACCTT
1 TGGTAAACTCACCTT
524103 TATCTGTGAC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 81 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (35 bp):
TGGTAAACTCACCTTATGTGTTGTCCGATCCAATG
Found at i:526159 original size:1 final size:1
Alignment explanation
Indices: 526153--526177 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
526143 CTCCCTAGCT
526153 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
526178 TGGTCCCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:531249 original size:42 final size:42
Alignment explanation
Indices: 531190--531384 Score: 336
Period size: 42 Copynumber: 4.6 Consensus size: 42
531180 GTCCGTGCTC
* * *
531190 CAGTATAGCTTAACGGTAAATTTGTTTATCGCTATTGTAATA
1 CAGTATAGGTTATCGGTAAGTTTGTTTATCGCTATTGTAATA
*
531232 CAGTATAGGTTATCGGTAAGTTTGTTTATCGCTATTATAATA
1 CAGTATAGGTTATCGGTAAGTTTGTTTATCGCTATTGTAATA
*
531274 CAGTATAGGTTATCGGTAAATTTGTTTATCGCTATTGTAATA
1 CAGTATAGGTTATCGGTAAGTTTGTTTATCGCTATTGTAATA
531316 CAGTATAGGTTATCGGTAAGTTTGTTTATCGCTATTGTAATA
1 CAGTATAGGTTATCGGTAAGTTTGTTTATCGCTATTGTAATA
*
531358 CAGTATAGGTTATTGGTAAGTTTGTTT
1 CAGTATAGGTTATCGGTAAGTTTGTTT
531385 TCCGAAAACG
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 145 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (42 bp):
CAGTATAGGTTATCGGTAAGTTTGTTTATCGCTATTGTAATA
Found at i:532616 original size:54 final size:54
Alignment explanation
Indices: 532534--532636 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
532524 TTTAGTACAG
*
532534 GTTTCTTTTGTTTAAATGAATACAATTTCTATTTACTTACCATATTTGAGTCAT
1 GTTTCTTATGTTTAAATGAATACAATTTCTATTTACTTACCATATTTGAGTCAT
* **
532588 GTTTCTTATGTTTAATTGTTTACAATTTCTATTTACTTACCATATTTGA
1 GTTTCTTATGTTTAAATGAATACAATTTCTATTTACTTACCATATTTGA
532637 ATGTTAAGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (54 bp):
GTTTCTTATGTTTAAATGAATACAATTTCTATTTACTTACCATATTTGAGTCAT
Found at i:536671 original size:164 final size:164
Alignment explanation
Indices: 536129--536873 Score: 653
Period size: 171 Copynumber: 4.4 Consensus size: 164
536119 GATGACTGGT
* * * * * *
536129 TGCATGGTTATGGTGTCCATGAAGCCCTCTACCAAAACTGTGTAATTCATGGCCCCTGGGTCAGG
1 TGCATGATTATGATGTCCATAAAGCCCTC-ACCAAAATTGTGAAATTCATGACCCCTGGGTCAGG
* * *
536194 GGTTCAGGCTCTGAGG-TGGGGCCCATATGGCCAT-TGAGTTAAAATGTATTAAATCTTAGAAAA
65 GGTTCAGGCTCT-AGGATGGGGCCAATATGGCCATATAAGTTAAAATGTAATAAATCTTAGAAAA
536257 TCTTCTTCTCTACTCCTATATATATTTGTTAAAAACTAAA
129 TC-T-TT-TC-ACTCCTATATATATTTGTTAAAAACTAAA
* * * *
536297 TGCATGATTATGATGTCCATGAAGCCCTGAACCAAAATTGTGAAATTCATTACCCCTGTG-CGAG
1 TGCATGATTATGATGTCCATAAAGCCCT-CACCAAAATTGTGAAATTCATGACCCCTGGGTC-AG
* * * * * * *
536361 GGGTTCAGGCTCTAGGCTGGAGCAAATATGGCAATAT-ACTTTAAATGCAATAAATCTTTAAAGA
64 GGGTTCAGGCTCTAGGATGGGGCCAATATGGCCATATAAGTTAAAATGTAATAAATC-TT--AGA
** ** * *
536425 AAAAATTCTTCTTTCTCTCATATAAAGTTGTTAAAAAACTAAA
126 AAATCTT-TTCACTC-CT-ATATATATTTGTT-AAAAACTAAA
* * *
536468 TGCATTATTATGATGTCCATAAAGCCCTCAACAAAAATTGTGAAATTCATGGCCCCTGGGTCAGG
1 TGCATGATTATGATGTCCATAAAGCCCTC-ACCAAAATTGTGAAATTCATGACCCCTGGGTCAGG
* * * * * * *
536533 GATTCAGGCTCTTGGTTGGGGCCAATATGGCCATAT-TGTT-AAATGTATTGAATCTTAGAATAT
65 GGTTCAGGCTCTAGGATGGGGCCAATATGGCCATATAAGTTAAAATGTAATAAATCTTAGAAAAT
* *
536596 CTTTTCAACTCCTATGTATATTTGTTAAAAACTATA
130 CTTTTC-ACTCCTATATATATTTGTTAAAAACTAAA
* * * * *
536632 TGCATGATTATGATGTCAATAAAGCTCTCACCAAAAATTGTGAAATTCATGACTCCTGTGCCAGG
1 TGCATGATTATGATGTCCATAAAGCCCTCACC-AAAATTGTGAAATTCATGACCCCTGGGTCAGG
* * *
536697 GGTTCAGGCTCTAGGAAGGGGCCAATATGGTCATAT-AGTATAAAATGTAATAAATCTTAGAACA
65 GGTTCAGGCTCTAGGATGGGGCCAATATGGCCATATAAGT-TAAAATGTAATAAATCTTAGAAAA
* * * * ** * *
536761 TCTTCTTCTTTACTCCCACACATGTGGGTAAAAAACTTAA
129 TCTT-TTC---ACTCCTATATATATTTGTTAAAAACTAAA
* * * * * *
536801 TTCATGGTTATGATGTCCACT--ATCTCCTCTTCTAAAATTGTGAAATTCATGGCCCCTGGGTCA
1 TGCATGATTATGATGTCCA-TAAAGC-CCTC-ACCAAAATTGTGAAATTCATGACCCCTGGGTCA
536864 GGGGTTCAGG
63 GGGGTTCAGG
536874 ACATGGGAGT
Statistics
Matches: 466, Mismatches: 88, Indels: 45
0.78 0.15 0.08
Matches are distributed among these distances:
163 2 0.00
164 96 0.21
165 11 0.02
166 28 0.06
167 16 0.03
168 99 0.21
169 84 0.18
170 26 0.06
171 103 0.22
172 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (164 bp):
TGCATGATTATGATGTCCATAAAGCCCTCACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGG
GTTCAGGCTCTAGGATGGGGCCAATATGGCCATATAAGTTAAAATGTAATAAATCTTAGAAAATC
TTTTCACTCCTATATATATTTGTTAAAAACTAAA
Found at i:536700 original size:335 final size:336
Alignment explanation
Indices: 536129--536873 Score: 900
Period size: 335 Copynumber: 2.2 Consensus size: 336
536119 GATGACTGGT
* * * * *
536129 TGCATGGTTATGGTGTCCATGAAGCCCTCTACCAAAACTGTGTAATTCATGGCCCCTGGGTCAGG
1 TGCATGATTATGATGTCCAT-AAGCCCTCTACAAAAATTGTGAAATTCATGGCCCCTGGGTCAGG
*
536194 GGTTCAGGCTCTGAGGTGGGGCCCATATGGCCATTGAGTTAAAATGTATTAAATCTTAGAAAATC
65 GGTTCAGGCTCTGAGGTGGGGCCAATATGGCCATTGAGTTAAAATGTATTAAATCTTAGAAAATC
* * *
536259 TTCTTCTCTACTCCTATATATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATGAAGCCC
130 TTCTTCTCAACTCCTATATATATTTGTTAAAAACTAAATGCATGATTATGATGTCAATAAAGCCC
* * **
536324 TGAACCAAAATTGTGAAATTCATTACCCCTGTGCGAGGGGTTCAGGCTCTAGGCTGGAGCAAATA
195 TGAACCAAAATTGTGAAATTCATGACCCCTGTGCCAGGGGTTCAGGCTCTAGGAAGGAGCAAATA
* * *
536389 TGG-CAATATACT-TTAAATGCAATAAATCTTTAAAGAAAAAATTCTTCTTT-CTCTCATATAAA
260 TGGTC-ATATACTATAAAATGCAATAAATC-TT--AGAAAAAATTCTTCTTTACTCCCACA-AAA
* *
536451 GTTGTTAAAAAACTAAA
320 GTGGGTAAAAAACTAAA
* *
536468 TGCATTATTATGATGTCCATAAAGCCCTCAACAAAAATTGTGAAATTCATGGCCCCTGGGTCAGG
1 TGCATGATTATGATGTCCAT-AAGCCCTCTACAAAAATTGTGAAATTCATGGCCCCTGGGTCAGG
* * * * *
536533 GATTCAGGCTCTTG-GTTGGGGCCAATATGGCCATAT-TGTT-AAATGTATTGAATCTTAGAATA
65 GGTTCAGGCTC-TGAGGTGGGGCCAATATGGCCAT-TGAGTTAAAATGTATTAAATCTTAGAAAA
* *
536595 TC-T-TT-TCAACTCCTATGTATATTTGTTAAAAACTATATGCATGATTATGATGTCAATAAAGC
128 TCTTCTTCTCAACTCCTATATATATTTGTTAAAAACTAAATGCATGATTATGATGTCAATAAAGC
* * * * *
536657 TCT-CACCAAAAATTGTGAAATTCATGACTCCTGTGCCAGGGGTTCAGGCTCTAGGAAGGGGCCA
193 CCTGAACC-AAAATTGTGAAATTCATGACCCCTGTGCCAGGGGTTCAGGCTCTAGGAAGGAGCAA
* * * ** * *
536721 ATATGGTCATATAGTATAAAATGTAATAAATCTTAGAACATCTTCTTCTTTACTCCCACACATGT
257 ATATGGTCATATACTATAAAATGCAATAAATCTTAGAAAAAATTCTTCTTTACTCCCACAAAAGT
*
536786 GGGTAAAAAACTTAA
322 GGGTAAAAAACTAAA
* * * * *
536801 TTCATGGTTATGATGTCCACT-ATCTCCTCTTCTAAAATTGTGAAATTCATGGCCCCTGGGTCAG
1 TGCATGATTATGATGTCCA-TAAGC-CCTCTACAAAAATTGTGAAATTCATGGCCCCTGGGTCAG
536865 GGGTTCAGG
64 GGGTTCAGG
536874 ACATGGGAGT
Statistics
Matches: 349, Mismatches: 49, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
332 2 0.01
333 89 0.26
334 10 0.03
335 117 0.34
336 17 0.05
337 1 0.00
338 22 0.06
339 88 0.25
340 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (336 bp):
TGCATGATTATGATGTCCATAAGCCCTCTACAAAAATTGTGAAATTCATGGCCCCTGGGTCAGGG
GTTCAGGCTCTGAGGTGGGGCCAATATGGCCATTGAGTTAAAATGTATTAAATCTTAGAAAATCT
TCTTCTCAACTCCTATATATATTTGTTAAAAACTAAATGCATGATTATGATGTCAATAAAGCCCT
GAACCAAAATTGTGAAATTCATGACCCCTGTGCCAGGGGTTCAGGCTCTAGGAAGGAGCAAATAT
GGTCATATACTATAAAATGCAATAAATCTTAGAAAAAATTCTTCTTTACTCCCACAAAAGTGGGT
AAAAAACTAAA
Found at i:546098 original size:156 final size:153
Alignment explanation
Indices: 545814--546455 Score: 484
Period size: 156 Copynumber: 4.0 Consensus size: 153
545804 TAGAAAATTT
* *
545814 TCTTCTCTACTCCCATATATATTTGATAAAAACTAAATGCTTGATTATGATGTCCATTAAGCCCT
1 TCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATGC-TGATTATGATGTCCATGAAGCCCT
* * * * *
545879 ATACCTTAAA-TGTGAAATTCATGACCTC-CGGATCAGAGGTTCATGCTCTAGGGTTGGGCCAAT
65 CTA--TCAAATTGTGAAATTCATGACCTCTAGG-TCAGGGGTTCAGGCTCTAGGG-TGGGCCAAT
* *
545942 ATGGCCATATATTAAAAATGTATTCAAA
126 ATGGCCATATAGTAAAAATGTATTTAAA
* * *
545970 TCTTCTCTACTCCCATATATATTCGTTAAAATCTAAATGCCTTG-TTATGATGTCCATGAGGCCC
1 TCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATG-C-TGATTATGATGTCCATGAAGCCC
*
546034 TCTATTAAATTTGTGAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGGTGGGTCCAATA
64 TCTATCAAA-TTGTGAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGGTGGG-CCAATA
*
546099 TGGCCATATAGAAAAAATGTTTTTAAATCTTAGTAAA
127 TGGCCATATAGTAAAAATG----T--A--TT--TAAA
* * * *
546136 TCTTCTTCTCTACACCCATATATATTTGTTGAAAACTTAATGC-----ATGAT-T--ATGAGGCC
1 ---TCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATGCTGATTATGATGTCCATGAAGCC
* * * * * * *
546193 CTGTATCAAAATTATCAAATTCATGACC-CTTGGGTCAGGGGTTCAGGCTTTAGGTTGGGGCAAA
63 CTCTATC-AAATTGTGAAATTCATGACCTC-TAGGTCAGGGGTTCAGGCTCTAGGGT-GGGCCAA
*
546257 TATGGCCATATAGTGAAAATGTA-TTAAA
125 TATGGCCATATAGTAAAAATGTATTTAAA
* * * *
546285 TCTTAGAAAAAATTGTCTATACTCCCATATATATTTATTAAAAACTAAATGCCTGTTTATGATTT
1 TC-----------T-TCTCTACTCCCATATATATTTGTTAAAAACTAAATG-CTGATTATGATGT
* * ** * * *
546350 CCATGAAGCCCTCTACCAAACTTGTGAAATTCATGACCCCTAAATTAGGGATTCAGTCTCTAGGG
53 CCATGAAGCCCTCTATCAAA-TTGTGAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGG
*
546415 TTGGACCAATATGGCCATATAGTAAAAATGT-TTTAAA
117 -TGGGCCAATATGGCCATATAGTAAAAATGTATTTAAA
546452 TCTT
1 TCTT
546456 AAAAAAATCT
Statistics
Matches: 392, Mismatches: 48, Indels: 93
0.74 0.09 0.17
Matches are distributed among these distances:
146 2 0.01
149 4 0.01
151 1 0.00
154 6 0.02
155 5 0.01
156 119 0.30
157 7 0.02
158 31 0.08
159 2 0.01
160 74 0.19
161 6 0.02
162 2 0.01
163 5 0.01
164 7 0.02
165 1 0.00
166 6 0.02
167 77 0.20
168 3 0.01
169 34 0.09
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (153 bp):
TCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATGCTGATTATGATGTCCATGAAGCCCTC
TATCAAATTGTGAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGGTGGGCCAATATGGC
CATATAGTAAAAATGTATTTAAA
Found at i:546261 original size:160 final size:158
Alignment explanation
Indices: 546025--546463 Score: 414
Period size: 167 Copynumber: 2.7 Consensus size: 158
546015 TATGATGTCC
* * * *
546025 ATGAGGCCCTCTATTAAATTTGTGAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGGTG
1 ATGAGGCCCTCTATCAAAATTATCAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGGTG
* * * * ** * *
546090 GGTCCAATATGGCCATATAGAAAAAATGTTTTTAAATCTTAGTAAATCTTCTTCTCTACACCCAT
66 GGGCAAATATGGCCATATAGAAAAAATG-TATTAAATCTTAGAAAAAATT-GTCTATACACCCAT
* * *
546155 ATATATTTGTTGAAAACTTAATGCATGATT
129 ATATATTTATTAAAAACTAAATGCATGATT
* * * *
546185 ATGAGGCCCTGTATCAAAATTATCAAATTCATGACC-CTTGGGTCAGGGGTTCAGGCTTTAGGTT
1 ATGAGGCCCTCTATCAAAATTATCAAATTCATGACCTC-TAGGTCAGGGGTTCAGGCTCTAGGGT
** *
546249 GGGGCAAATATGGCCATATAGTGAAAATGTATTAAATCTTAGAAAAAATTGTCTATACTCCCATA
65 GGGGCAAATATGGCCATATAGAAAAAATGTATTAAATCTTAGAAAAAATTGTCTATACACCCATA
546314 TATATTTATTAAAAACTAAATGCCTGTTTATGATTT
130 TATATTTATTAAAAACTAAATG-C-----ATGA-TT
* * * * * * ** * * *
546350 CCATGAAGCCCTCTACCAAACTTGTGAAATTCATGACCCCTAAATTAGGGATTCAGTCTCTAGGG
1 --ATGAGGCCCTCTATCAAAATTATCAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGG
* * * * *
546415 TTGGACCAATATGGCCATATAGTAAAAATGTTTTAAATCTTA-AAAAAAT
64 TGGGGCAAATATGGCCATATAGAAAAAATGTATTAAATCTTAGAAAAAAT
546464 CTTCTTCTCT
Statistics
Matches: 227, Mismatches: 41, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
158 31 0.14
159 19 0.08
160 79 0.35
164 4 0.02
165 2 0.01
166 7 0.03
167 84 0.37
168 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (158 bp):
ATGAGGCCCTCTATCAAAATTATCAAATTCATGACCTCTAGGTCAGGGGTTCAGGCTCTAGGGTG
GGGCAAATATGGCCATATAGAAAAAATGTATTAAATCTTAGAAAAAATTGTCTATACACCCATAT
ATATTTATTAAAAACTAAATGCATGATT
Found at i:546377 original size:327 final size:316
Alignment explanation
Indices: 545689--546480 Score: 862
Period size: 327 Copynumber: 2.4 Consensus size: 316
545679 TGGTTGCATA
* * * * *
545689 GTTATGATGTCCATGAAGCCCGCTACCAAAATTGTGAAATTCATGGCCCCTGGGTCAGGAGTCCA
1 GTTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAGGTCAGGGGTTCA
* *
545754 GGCTCTAGGGTTGGGCCAATATGGCCATATA-ATAAAAATGTATTAAATCTTAGAAAATTTTCTT
66 GGCTCTAGGG-TGGGCCAATATGGCCATATAGA-AAAAATGTTTTAAATCTTAGAAAATCTTCTT
*
545818 CTCTACTCCCATATATATTTGATAAAAACTAAATGCTTGATTATGATGTCCATTAAGCCCTATAC
129 CTCTACTCCCATATATATTTGATAAAAACTAAATGCATGATTATGATG-------AGCCCTATAC
* * * * *
545883 CTTAAATGTGAAATTCATGACCTCCGGATCAGAGGTTCATGCTCTAGGGTTGGGCCAATATGGCC
187 CTAAAATATCAAATTCATGACCTCCGGATCAGAGGTTCAGGCTCTAGGGTTGGGCAAATATGGCC
* * * *
545948 ATATATTAAAAATGTATTCAAATCTTCTCTACTCCCATATATATTCGTTAAAATCTAAATGCCTT
252 ATATAGTAAAAATGTATTCAAATCTTCTATACTCCCATATATATTCATTAAAAACTAAATGCCTT
* ** * *
546013 GTTATGATGTCCATGAGGCCCTCTATTAAATTTGTGAAATTCATGACCTCTAGGTCAGGGGTTCA
1 GTTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAGGTCAGGGGTTCA
*
546078 GGCTCTAGGGTGGGTCCAATATGGCCATATAGAAAAAATGTTTTTAAATCTTAGTAAATCTTCTT
66 GGCTCTAGGGTGGG-CCAATATGGCCATATAGAAAAAATG-TTTTAAATCTTAGAAAATCTTCTT
* * * * * *
546143 CTCTACACCCATATATATTTGTTGAAAACTTAATGCATGATTATGA-G-GCCCTGTATC-AAAAT
129 CTCTACTCCCATATATATTTGATAAAAACTAAATGCATGATTATGATGAGCCCTATACCTAAAA-
* * * *
546205 TATCAAATTCATGACC-CTTGGGTCAGGGGTTCAGGCTTTA-GGTTGGGGCAAATATGGCCATAT
193 TATCAAATTCATGACCTC-CGGATCAGAGGTTCAGGCTCTAGGGTT-GGGCAAATATGGCCATAT
* *
546268 AGTGAAAATGTATT-AAATCTTAGAAAAAATTGTCTATACTCCCATATATATTTATTAAAAACTA
256 AGTAAAAATGTATTCAAATC-----------T-TCTATACTCCCATATATATTCATTAAAAACTA
546332 AATGCC-T
309 AATGCCTT
* * ** * *
546339 GTTTATGATTTCCATGAAGCCCTCTACCAAACTTGTGAAATTCATGACCCCTAAATTAGGGATTC
1 G-TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAGGTCAGGGGTTC
* * * *
546404 AGTCTCTAGGGTTGGACCAATATGGCCATATAGTAAAAATGTTTTAAATCTTAAAAAAATCTTCT
65 AGGCTCTAGGG-TGGGCCAATATGGCCATATAGAAAAAATGTTTTAAATCTT-AGAAAATCTTCT
546469 TCTCTACTCCCA
128 TCTCTACTCCCA
546481 CACATGTGGG
Statistics
Matches: 396, Mismatches: 51, Indels: 39
0.81 0.10 0.08
Matches are distributed among these distances:
315 13 0.03
316 68 0.17
323 4 0.01
324 89 0.22
325 63 0.16
326 14 0.04
327 142 0.36
328 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (316 bp):
GTTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAGGTCAGGGGTTCA
GGCTCTAGGGTGGGCCAATATGGCCATATAGAAAAAATGTTTTAAATCTTAGAAAATCTTCTTCT
CTACTCCCATATATATTTGATAAAAACTAAATGCATGATTATGATGAGCCCTATACCTAAAATAT
CAAATTCATGACCTCCGGATCAGAGGTTCAGGCTCTAGGGTTGGGCAAATATGGCCATATAGTAA
AAATGTATTCAAATCTTCTATACTCCCATATATATTCATTAAAAACTAAATGCCTT
Found at i:551058 original size:21 final size:21
Alignment explanation
Indices: 551029--551098 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
551019 CAAGCATAGT
* *
551029 ATAGTATTGAAATCTCATACC
1 ATAGCATTGGAATCTCATACC
* * * *
551050 CTAGCATTGGAATCTTAAATC
1 ATAGCATTGGAATCTCATACC
*
551071 ATAACATTGGAATCTCATACC
1 ATAGCATTGGAATCTCATACC
551092 ATAGCAT
1 ATAGCAT
551099 AGCAAACAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (21 bp):
ATAGCATTGGAATCTCATACC
Found at i:554488 original size:4 final size:4
Alignment explanation
Indices: 554479--554555 Score: 154
Period size: 4 Copynumber: 19.2 Consensus size: 4
554469 TAAATTGTTG
554479 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
554527 TAGA TAGA TAGA TAGA TAGA TAGA TAGA T
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA T
554556 GTGATTCTGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:555801 original size:29 final size:29
Alignment explanation
Indices: 555759--555818 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
555749 TTAAGGCAGT
555759 TAATGGAGTTATCTTCCCTTGCTTCTTCA
1 TAATGGAGTTATCTTCCCTTGCTTCTTCA
* *
555788 TAATGGAGTTATCTTCCTTTGCTTGTTCA
1 TAATGGAGTTATCTTCCCTTGCTTCTTCA
555817 TA
1 TA
555819 TTTAGTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (29 bp):
TAATGGAGTTATCTTCCCTTGCTTCTTCA
Found at i:567030 original size:4 final size:4
Alignment explanation
Indices: 567023--567114 Score: 168
Period size: 4 Copynumber: 23.0 Consensus size: 4
567013 CATATGGATG
567023 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
567071 GATA GATA GATA GATA GAT- GAATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA G-ATA GATA GATA GATA GATA GATA
567115 TGCGAATAAA
Statistics
Matches: 86, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
3 1 0.01
4 84 0.98
5 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:583656 original size:2 final size:2
Alignment explanation
Indices: 583649--583707 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
583639 TACCTCTATT
583649 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
583690 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
583708 ATTGAATACA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:584770 original size:28 final size:28
Alignment explanation
Indices: 584730--584897 Score: 311
Period size: 28 Copynumber: 6.0 Consensus size: 28
584720 TTCTCGGCCT
*
584730 TTATCCCCACTTATCAACGACGAGTAAG
1 TTATCCCCTCTTATCAACGACGAGTAAG
584758 TTATCCCCTCTTATCAACGACGAGTAAG
1 TTATCCCCTCTTATCAACGACGAGTAAG
584786 -TATCCCCCTCTTATCAACGACGAGTAAG
1 TTAT-CCCCTCTTATCAACGACGAGTAAG
584814 TTATCCCCTCTTATCAACGACGAGTAAG
1 TTATCCCCTCTTATCAACGACGAGTAAG
584842 TTATCCCCTCTTATCAACGACGAGTAAG
1 TTATCCCCTCTTATCAACGACGAGTAAG
584870 TTATCCCCTCTTATCAACGACGAGTAAG
1 TTATCCCCTCTTATCAACGACGAGTAAG
584898 CGGTGTAGTT
Statistics
Matches: 137, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
27 3 0.02
28 131 0.96
29 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
TTATCCCCTCTTATCAACGACGAGTAAG
Found at i:585068 original size:20 final size:20
Alignment explanation
Indices: 585040--585081 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
585030 AAGTGTATTG
585040 AATTCCCAACGATGATTTAT
1 AATTCCCAACGATGATTTAT
*
585060 AATTTCCAACGATGATTTAT
1 AATTCCCAACGATGATTTAT
585080 AA
1 AA
585082 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (20 bp):
AATTCCCAACGATGATTTAT
Found at i:589700 original size:165 final size:160
Alignment explanation
Indices: 589297--589714 Score: 484
Period size: 165 Copynumber: 2.5 Consensus size: 160
589287 TGCCGATTTT
*
589297 GTAGGGTGGGGCCACAATGGGGGATCGAAGTTAAACAAAGGA-ATATAGAGTAAATCTTTAAAAA
1 GTAGGGT-GGGCCACAATGGGGGGTCGAAGTT-AACAAAGGATATATAGAGTAAATCTTTAAAAA
* * *
589361 TCTTCTTCTCAGAAACTAATCAGCCGGCAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATG
64 --TTCTTCTCAGAAACTAATCAGCAGGCAAAGCCGAAACTTGTGTGAAAGCATCCTCAGGTAATG
* * *
589426 TAGATTCAAATTTGTGAAAATCATAACTCTGTGG
127 TAGATTCAAAGTTGTGAAAATCATAACCCAGTGG
* * * * * * * *
589460 GTAGGTTTGGGCCACAATGGGAGGTCGATGTTTTACATATGAATAAACAGAGTAAATCTTTAAAA
1 GTAGG-GTGGGCCACAATGGGGGGTCGAAG-TTAACA-AAGGATATATAGAGTAAATCTTTAAAA
*
589525 ATCTTCTTCTCAGAAACTAATCAGTCAGG-AAAGCCGAAACTTGTGTGAAAGCATCCTCAGGTAG
63 A--TTCTTCTCAGAAACTAATCAG-CAGGCAAAGCCGAAACTTGTGTGAAAGCATCCTCAGGTAA
*
589589 TGTAGATTCAAAGTTGTGAAAATCATGATCCCCAG-GG
125 TGTAGATTCAAAGTTGTGAAAATCAT-A-ACCCAGTGG
* *
589626 GTAGGGTGGTGCCACAATGGGGGGGGTCAAAGCTTAACAAAGGGATATATAGGGTAAATCTTTAA
1 GTAGGGTGG-GCCACAAT--GGGGGGTCGAAG-TTAACAAA-GGATATATAGAGTAAATCTTTAA
589691 AAA-TCTTCTCAGAAACTAATCAGC
61 AAATTCTTCTCAGAAACTAATCAGC
589715 CAGATAATTC
Statistics
Matches: 216, Mismatches: 28, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
163 27 0.12
164 7 0.03
165 123 0.57
166 19 0.09
167 4 0.02
168 36 0.17
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (160 bp):
GTAGGGTGGGCCACAATGGGGGGTCGAAGTTAACAAAGGATATATAGAGTAAATCTTTAAAAATT
CTTCTCAGAAACTAATCAGCAGGCAAAGCCGAAACTTGTGTGAAAGCATCCTCAGGTAATGTAGA
TTCAAAGTTGTGAAAATCATAACCCAGTGG
Found at i:616175 original size:21 final size:23
Alignment explanation
Indices: 616139--616180 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
616129 ATTTTTACGG
616139 GGGGAAAGATGGCACTATATATT
1 GGGGAAAGATGGCACTATATATT
616162 GGGGAAA-A-GGCACTATATA
1 GGGGAAAGATGGCACTATATA
616181 ACACCAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (23 bp):
GGGGAAAGATGGCACTATATATT
Found at i:624560 original size:12 final size:12
Alignment explanation
Indices: 624530--624572 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
624520 ATTTTGTCCA
624530 TCTGTCCGTCGG
1 TCTGTCCGTCGG
*
624542 TCCGTCCGGTC-G
1 TCTGTCC-GTCGG
*
624554 TCTGTCCGTCTG
1 TCTGTCCGTCGG
624566 TCTGTCC
1 TCTGTCC
624573 ATCTGTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.00, C:0.37, G:0.28, T:0.35
Consensus pattern (12 bp):
TCTGTCCGTCGG
Found at i:624733 original size:1 final size:1
Alignment explanation
Indices: 624727--624760 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
624717 TCAAAACTGT
* *
624727 AAAAAAAAAAAAAAAAAGAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
624761 GGGGGGGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:624748 original size:17 final size:17
Alignment explanation
Indices: 624728--624761 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
624718 CAAAACTGTA
624728 AAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAG
*
624745 AAAAAAGAAAAAAAAAG
1 AAAAAAAAAAAAAAAAG
624762 GGGGGGGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAG
Found at i:638559 original size:32 final size:32
Alignment explanation
Indices: 638515--638578 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
638505 ATATTCAATC
* *
638515 CAACTCCTTACAAAATATGAAAATGTACTGTT
1 CAACTCCATACAAAATATGAAAAAGTACTGTT
* *
638547 CAACTCCATACAAACTATGAAAAAGTTCTGTT
1 CAACTCCATACAAAATATGAAAAAGTACTGTT
638579 TTATCTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (32 bp):
CAACTCCATACAAAATATGAAAAAGTACTGTT
Found at i:639840 original size:16 final size:16
Alignment explanation
Indices: 639819--639850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
639809 CCCGGGAAAA
*
639819 AAATTCCTTTTGAGGG
1 AAATTCCCTTTGAGGG
639835 AAATTCCCTTTGAGGG
1 AAATTCCCTTTGAGGG
639851 GTTTTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (16 bp):
AAATTCCCTTTGAGGG
Found at i:640639 original size:166 final size:165
Alignment explanation
Indices: 640353--640805 Score: 642
Period size: 166 Copynumber: 2.7 Consensus size: 165
640343 GAATCATCTG
* * *
640353 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTTAATTTC-
1 GCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTCG
* *
640417 AACCCCCATTGCGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTA
66 ACCCCCCATTGTGGCCCCACCCTA-CCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTA
* *
640482 CCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTA
130 CCAGAGGATGCTTCCACACAAGTGTCAGCTTTCCTA
* * * * *
640518 -AT-CTTATGGTTCATGAGAAGAAGATTTTTAAAGATTTACTCTGTATATTCCTATGTAAAAGTT
1 GCTGATTA-GGTTC-TGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTT
* *
640581 CGACCCCCCATTGTGGCCCCACCCTATCCCCGGGGGTCATGATTTTCGCAACTTTGAATCTACAT
64 CGACCCCCCATTGTGGCCCCACCCTA-CCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAC
* *
640646 TACCAGAGGATGCTTTCACACAAGTGTCAGCTTTCCTG
128 TACCAGAGGATGCTTCCACACAAGTGTCAGCTTTCCTA
* * *
640684 GCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTAACTCTTTATATTCCTATGTTAAACTTCG
1 GCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTCG
* * *
640749 ACCCCCCATTGTGTCCCCACCCTACCCTCAGGGGTAATGATTTTCACAACTTTGAAT
66 ACCCCCCATTGTGGCCCCACCCTACCC-CGGGGGTCATGATTTTCACAACTTTGAAT
640806 NCATCAAATT
Statistics
Matches: 255, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
163 3 0.01
164 5 0.02
165 50 0.20
166 189 0.74
167 5 0.02
168 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (165 bp):
GCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTCG
ACCCCCCATTGTGGCCCCACCCTACCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTAC
CAGAGGATGCTTCCACACAAGTGTCAGCTTTCCTA
Found at i:641523 original size:105 final size:105
Alignment explanation
Indices: 641404--641692 Score: 537
Period size: 105 Copynumber: 2.8 Consensus size: 105
641394 ATATTCGATC
641404 TTTTCCATTTGTATTGTATAATTTTCTATTTGTATTGTATATTTTTTTCATTTGCATTATATAAT
1 TTTTCCATTTGTATTGTATAATTTTCTATTTGTATTGTATATTTTTTTCATTTGCATTATATAAT
641469 TTTCATTTGTATTCTACAATTTTCCATTTGTATTCTGTAA
66 TTTCATTTGTATTCTACAATTTTCCATTTGTATTCTGTAA
641509 TTTTCCATTTGTATTGTATAATTTTCTATTTGTATTGTATATTTTTTTCATTTGCATTATATAAT
1 TTTTCCATTTGTATTGTATAATTTTCTATTTGTATTGTATATTTTTTTCATTTGCATTATATAAT
641574 TTTCATTTGTATTCTACAATTTTCCATTTGTATTCTGTAA
66 TTTCATTTGTATTCTACAATTTTCCATTTGTATTCTGTAA
* *
641614 TTTTCCATTTGTATTGTATAATTTTCTATTTGTATTGTATA-TTTTTT-ATTTGTATTGTATAAT
1 TTTTCCATTTGTATTGTATAATTTTCTATTTGTATTGTATATTTTTTTCATTTGCATTATATAAT
641677 TTTCTATTTGTATTCT
66 TTTC-ATTTGTATTCT
641693 TTAATTATAC
Statistics
Matches: 181, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
103 18 0.10
104 17 0.09
105 146 0.81
ACGTcount: A:0.22, C:0.09, G:0.08, T:0.61
Consensus pattern (105 bp):
TTTTCCATTTGTATTGTATAATTTTCTATTTGTATTGTATATTTTTTTCATTTGCATTATATAAT
TTTCATTTGTATTCTACAATTTTCCATTTGTATTCTGTAA
Found at i:641698 original size:21 final size:21
Alignment explanation
Indices: 641404--641690 Score: 337
Period size: 21 Copynumber: 13.7 Consensus size: 21
641394 ATATTCGATC
*
641404 TTTTCCATTTGTATTGTATAA
1 TTTTCTATTTGTATTGTATAA
*
641425 TTTTCTATTTGTATTGTATAT
1 TTTTCTATTTGTATTGTATAA
* * *
641446 TTTTTTCATTTGCATTATATAA
1 TTTTCT-ATTTGTATTGTATAA
* *
641468 TTTTC-ATTTGTATTCTACAA
1 TTTTCTATTTGTATTGTATAA
* * *
641488 TTTTCCATTTGTATTCTGTAA
1 TTTTCTATTTGTATTGTATAA
*
641509 TTTTCCATTTGTATTGTATAA
1 TTTTCTATTTGTATTGTATAA
*
641530 TTTTCTATTTGTATTGTATAT
1 TTTTCTATTTGTATTGTATAA
* * *
641551 TTTTTTCATTTGCATTATATAA
1 TTTTCT-ATTTGTATTGTATAA
* *
641573 TTTTC-ATTTGTATTCTACAA
1 TTTTCTATTTGTATTGTATAA
* * *
641593 TTTTCCATTTGTATTCTGTAA
1 TTTTCTATTTGTATTGTATAA
*
641614 TTTTCCATTTGTATTGTATAA
1 TTTTCTATTTGTATTGTATAA
641635 TTTTCTATTTGTATTGTAT-A
1 TTTTCTATTTGTATTGTATAA
*
641655 TTTTTTATTTGTATTGTATAA
1 TTTTCTATTTGTATTGTATAA
641676 TTTTCTATTTGTATT
1 TTTTCTATTTGTATT
641691 CTTTAATTAT
Statistics
Matches: 230, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
20 53 0.23
21 145 0.63
22 32 0.14
ACGTcount: A:0.22, C:0.09, G:0.08, T:0.61
Consensus pattern (21 bp):
TTTTCTATTTGTATTGTATAA
Found at i:641739 original size:20 final size:20
Alignment explanation
Indices: 641695--641735 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
641685 TGTATTCTTT
641695 AATTATACAATACAAATTGA
1 AATTATACAATACAAATTGA
* *
641715 TATTATAGAATACAAA-TGA
1 AATTATACAATACAAATTGA
641734 AA
1 AA
641736 ATTAATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (20 bp):
AATTATACAATACAAATTGA
Found at i:645077 original size:1 final size:1
Alignment explanation
Indices: 645044--645070 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
645034 CTTGTCAAGC
645044 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
645071 GGAAAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:655236 original size:17 final size:17
Alignment explanation
Indices: 655211--655243 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
655201 TTCAATATGT
655211 TATGATATCTTATGTTA
1 TATGATATCTTATGTTA
*
655228 TATGTTATCTTATGTT
1 TATGATATCTTATGTT
655244 TCAATATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (17 bp):
TATGATATCTTATGTTA
Found at i:656418 original size:16 final size:16
Alignment explanation
Indices: 656397--656428 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
656387 AGGAATCACC
656397 CCATCCATCTGTCTGT
1 CCATCCATCTGTCTGT
656413 CCATCCATCTGTCTGT
1 CCATCCATCTGTCTGT
656429 TCGAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (16 bp):
CCATCCATCTGTCTGT
Found at i:656703 original size:146 final size:146
Alignment explanation
Indices: 656432--656832 Score: 570
Period size: 146 Copynumber: 2.7 Consensus size: 146
656422 TGTCTGTTCG
* *
656432 AAATTTGTGTCCGGTCCATATCTTTCTTATGAAGAAACATTGGAAATTCTTACTTCACACAAAGA
1 AAATTTGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA
* * * * *
656497 TTGCTTATGACCTAAGGGCGTGTCATGACCTTGACCCAAGGTAATTCGGGCATGGCCAAGGTCAC
66 TTGCTTATGACCTAAGGGTGTGTCATGACTTTGACCCAAGGTCATTCGGACAAGGCCAAGGTCAC
656562 TGGCAGAAAAAGTGCA
131 TGGCAGAAAAAGTGCA
*
656578 AAATTTGTGTCCGGTCCATATCTTTCTTATGGAGAAACAGTGGAAGTTCTTACTTCACACAAAGA
1 AAATTTGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA
* * * *
656643 TTGCTTCTGACCTAAAGGTGTGTTATGACTTTGACCCAAGGTCATTCGGACAAGGTCAAGGTCAC
66 TTGCTTATGACCTAAGGGTGTGTCATGACTTTGACCCAAGGTCATTCGGACAAGGCCAAGGTCAC
656708 TGGCAGAAAAAGTGCA
131 TGGCAGAAAAAGTGCA
* * * ** * * **
656724 AAATTTTTGTCCGGTCCATATCTTTCTTATAGACAAGTATTGGAAGTTTTTAATTCACATTAAGA
1 AAATTTGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA
* * *
656789 TTGCTTATAATCC-GAGGGTGTGTCATGACTTTGACCCAAAGTCA
66 TTGCTTATGA-CCTAAGGGTGTGTCATGACTTTGACCCAAGGTCA
656833 ATTGAGAGAT
Statistics
Matches: 226, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
146 224 0.99
147 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (146 bp):
AAATTTGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA
TTGCTTATGACCTAAGGGTGTGTCATGACTTTGACCCAAGGTCATTCGGACAAGGCCAAGGTCAC
TGGCAGAAAAAGTGCA
Found at i:660023 original size:16 final size:16
Alignment explanation
Indices: 660004--660040 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
659994 GTCTCATGAA
660004 GGTGATGCCTCATTTT
1 GGTGATGCCTCATTTT
660020 GGTGATGCCTCATTTT
1 GGTGATGCCTCATTTT
660036 GGTGA
1 GGTGA
660041 GCTTTGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.41
Consensus pattern (16 bp):
GGTGATGCCTCATTTT
Found at i:661855 original size:2 final size:2
Alignment explanation
Indices: 661848--661883 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
661838 GTGAAATGTT
*
661848 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
661884 TAATGACATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:667208 original size:2 final size:2
Alignment explanation
Indices: 667201--667239 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
667191 CTTGCAGATG
667201 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
667240 GAGGTGCAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:679029 original size:19 final size:19
Alignment explanation
Indices: 679007--679049 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
678997 ACACGGATGG
* *
679007 TGGATTGCAACAGGTATCT
1 TGGATTGCAACAGGCACCT
*
679026 TGGATTGTAACAGGCACCT
1 TGGATTGCAACAGGCACCT
679045 TGGAT
1 TGGAT
679050 GAAATAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (19 bp):
TGGATTGCAACAGGCACCT
Found at i:684268 original size:316 final size:321
Alignment explanation
Indices: 683683--684325 Score: 1095
Period size: 316 Copynumber: 2.0 Consensus size: 321
683673 CATGTAATGA
683683 GAAAGCAAAACTCATAAGTTTTTTTAGGCAATTGAATATGAGAATCAGGTCATGAAAATGTTAAT
1 GAAAGCAAAACTCATAAGTTTTTTTAGGCAATTGAATATGAGAATCAGGTCATGAAAA--TTAAT
* *
683748 ACGGTACATCACATTTAAAATAATTAGTGAAAATTTCTTCAAGAATGTGCGAGGGAACCAATCAG
64 A--GTACAT--CATTTAAAATAATTAATGAAAATTTCTTCAAGAAAGTGCGAGGGAACCAATCAG
**
683813 GATAGGGTATGAGTTGTACATGAGATGGAGAAAAACTTGATGAGTTGGCACATGGTCAGTAAGTG
125 GATAGGGTATGAGTTGTACATGAGATGGAGAAAAACTCAATGAGTTGGCACATGGTCAGTAAGTG
683878 GATGTGAGTATGGGTATCTTACAATGACATCATCAGTCATGCAGCACAAAGGTGACAGCCAAAGT
190 GATGTGAGTATGGGTATCTTACAATGACATCATCAGTCATGCAGCACAAAGGTGACAGCCAAAGT
683943 CTGTACTCAAAACTCTTACAATCAGCTTCTACCTCTGTTGAACACTCGCAGAGCTCTCAGTCACA
255 CTGTACTCAAAACTCTTACAATCAGCTTCTACCTCTGTTGAACACTCGCAGAGCTCTCAGTCACA
684008 TT
320 TT
*
684010 NGAAAGCAAAACTCATCAGTTTTTTTAGGCAATTGAATATGAGAATCAGGTCATGAAAA-T-AT-
1 -GAAAGCAAAACTCATAAGTTTTTTTAGGCAATTGAATATGAGAATCAGGTCATGAAAATTAATA
*
684072 G-A-AGT-A-TTAACATAATTAATG-AAATTGTCTTCAAGAAAGTGCGAGGGAACCAATCAGGAT
65 GTACA-TCATTTAAAATAATTAATGAAAATT-TCTTCAAGAAAGTGCGAGGGAACCAATCAGGAT
684132 AGGGTATGAGTTGTACATGAGATGGAGAAAAACTCAATGAGTTGGCACATGGTCAGTAAGTGGAT
128 AGGGTATGAGTTGTACATGAGATGGAGAAAAACTCAATGAGTTGGCACATGGTCAGTAAGTGGAT
684197 GTGAGTATGGGTATCTTACAATGACATCATCAGTCATGCAGCACAAAGGTGACAGCCAAAGTCTG
193 GTGAGTATGGGTATCTTACAATGACATCATCAGTCATGCAGCACAAAGGTGACAGCCAAAGTCTG
684262 TACTCAAAACTCTTACAATCAGCTTCTACCTCTGTTGAACACTCGCAGAGCTCTCAGTCACATT
258 TACTCAAAACTCTTACAATCAGCTTCTACCTCTGTTGAACACTCGCAGAGCTCTCAGTCACATT
684326 TTTTTTTCAA
Statistics
Matches: 307, Mismatches: 6, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
315 5 0.02
316 237 0.77
317 1 0.00
319 1 0.00
320 2 0.01
321 1 0.00
324 2 0.01
325 1 0.00
328 57 0.19
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (321 bp):
GAAAGCAAAACTCATAAGTTTTTTTAGGCAATTGAATATGAGAATCAGGTCATGAAAATTAATAG
TACATCATTTAAAATAATTAATGAAAATTTCTTCAAGAAAGTGCGAGGGAACCAATCAGGATAGG
GTATGAGTTGTACATGAGATGGAGAAAAACTCAATGAGTTGGCACATGGTCAGTAAGTGGATGTG
AGTATGGGTATCTTACAATGACATCATCAGTCATGCAGCACAAAGGTGACAGCCAAAGTCTGTAC
TCAAAACTCTTACAATCAGCTTCTACCTCTGTTGAACACTCGCAGAGCTCTCAGTCACATT
Found at i:687989 original size:16 final size:16
Alignment explanation
Indices: 687965--687999 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
687955 CCTATTGTGG
687965 TTTGCTTGTTTGTTTT
1 TTTGCTTGTTTGTTTT
*
687981 TTTGTTTGTTTGTTTT
1 TTTGCTTGTTTGTTTT
687997 TTT
1 TTT
688000 ACATCAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (16 bp):
TTTGCTTGTTTGTTTT
Found at i:688802 original size:20 final size:20
Alignment explanation
Indices: 688777--688814 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
688767 CGTGTATTAT
688777 TTCTTTGAATGTTGAATCTA
1 TTCTTTGAATGTTGAATCTA
688797 TTCTTTGAATGTTGAATC
1 TTCTTTGAATGTTGAATC
688815 CATTAGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (20 bp):
TTCTTTGAATGTTGAATCTA
Found at i:688997 original size:47 final size:47
Alignment explanation
Indices: 688944--690016 Score: 1637
Period size: 47 Copynumber: 23.0 Consensus size: 47
688934 GATTATCAGA
* * *
688944 CATTGGGGAATGTAATAATTTATTGTAACGACCAATCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* * *
688991 CATTGGGGAATGTAATAATTTATCGTAATGACCAAGCCCTTTGA-TT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* *
689037 -ATTGGGGTATGCAATAATTTATTGTAATGACCAAGTTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* ** *
689083 CATTGGGGTATGCAATAATTTATTGTAACAACCAATCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* * * * *
689130 CACTGGGGAATGTAATAATTTTATTGTAACGACCAATCCCTTTGATTT
1 CATTGGGGTATGTAATAA-TTTATTGTAATGACCAAGCTCTTTGATTT
* * *
689178 CATTGGGGAATGTAATAATTTATCGTAATGACCAAGCCCTTTGA-TT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* *
689224 -ATTGGGGTATGTAATAATTTATTGTAACGACCAATCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* *
689270 CATT-GGGAATGTAATAATTTATCGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689316 CATTGGGGTATGTAATAATTTATTGTAATTACCAAGCTCTTTGA-TT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689362 -ATTGGGGTATGTAATAATTCATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
689408 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* * *
689455 CATTGGGATTTGTAAAAATTTATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* * * * * *
689502 CATTGGGATTTGTAAAAATCTATTGTAATAACCAAGCTCATTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689549 CATTAGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGA-TT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* *
689595 -ATTGGGGTATGTAATGATTCATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* * *
689641 CATTGGGATATGTAAAAATCTATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
689688 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689735 CATTGGGGTATGTAATAATTTATTGTAATAACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689782 CATTGGGGTATTTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689829 CATTGGGGTATGTAATAATTTATTGTAATAACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
689876 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGA-TT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689922 -ATTGGGGTATGTAATAATTCATTGTAATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* *
689968 CATTGGGGTATGTAATAATCTATTGTTATGACCAAGCTCTTTGATTT
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
690015 CA
1 CA
690017 GGCTCTGGAC
Statistics
Matches: 943, Mismatches: 71, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
45 199 0.21
46 62 0.07
47 638 0.68
48 44 0.05
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (47 bp):
CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
Found at i:689335 original size:186 final size:187
Alignment explanation
Indices: 688944--690016 Score: 1617
Period size: 186 Copynumber: 5.8 Consensus size: 187
688934 GATTATCAGA
* * * *
688944 CATTGGGGAATGTAATAATTTATTGTAACGACCAATCTCTTTGATTTCATTGGGGAATGTAATAA
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* * *
689009 TTTATCGTAATGACCAAGCCCTTTGA-TT-ATTGGGGTATGCAATAATTTATTGTAATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
* * * ** *
689072 TTCTTTGATTTCATTGGGGTATGCAATAATTTATTGTAACAACCAATCTCTTTGATTT
131 CTCTTTGATTTCATT-GGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* * * * * *
689130 CACTGGGGAATGTAATAATTTTATTGTAACGACCAATCCCTTTGATTTCATTGGGGAATGTAATA
1 CATTGGGGTATGTAATAA-TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATA
* * *
689195 ATTTATCGTAATGACCAAGCCCTTTGA-TT-ATTGGGGTATGTAATAATTTATTGTAACGACCAA
65 ATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAA
* *
689258 TCTCTTTGATTTCATTGGGAATGTAATAATTTATCGTAATGACCAAGCTCTTTGATTT
130 GCTCTTTGATTTCATTGGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
*
689316 CATTGGGGTATGTAATAATTTATTGTAATTACCAAGCTCTTTGA-TT-ATTGGGGTATGTAATAA
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
*
689379 TTCATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
* *
689444 CTCTTTGATTTCATTGGGATTTGTAAAAATTTATTGTAATGACCAAGCTCTTTGATTT
131 CTCTTTGATTTCATTGGGA-ATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
* * * * * * *
689502 CATTGGGATTTGTAAAAATCTATTGTAATAACCAAGCTCATTGATTTCATTAGGGTATGTAATAA
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* *
689567 TTTATTGTAATGACCAAGCTCTTTGA-TT-ATTGGGGTATGTAATGATTCATTGTAATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
* *
689630 CTCTTTGATTTCATTGGGATATGTAAAAATCTATTGTAATGACCAAGCTCTTTGATTT
131 CTCTTTGATTTCATTGGGA-ATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
689688 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* *
689753 TTTATTGTAATAACCAAGCTCTTTGATTTCATTGGGGTATTTAATAATTTATTGTAATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
* *
689818 CTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATAACCAAGCTCTTTGATTT
131 CTCTTTGATTTCATT-GGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
689876 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGA-TT-ATTGGGGTATGTAATAA
1 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* * *
689939 TTCATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATCTATTGTTATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
690004 CTCTTTGATTTCA
131 CTCTTTGATTTCA
690017 GGCTCTGGAC
Statistics
Matches: 819, Mismatches: 59, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
183 39 0.05
184 4 0.00
185 74 0.09
186 404 0.49
187 128 0.16
188 167 0.20
189 3 0.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (187 bp):
CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
CTCTTTGATTTCATTGGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTT
Found at i:689358 original size:233 final size:233
Alignment explanation
Indices: 688944--690016 Score: 1622
Period size: 233 Copynumber: 4.6 Consensus size: 233
688934 GATTATCAGA
* * *
688944 CATTGGGGAATGTAATAATTTATTGTAACGACCAATCTCTTTGATTTCATTGGGGAATGTAATAA
1 CATTGGGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* * *
689009 TTTATCGTAATGACCAAGCCCTTTGA-TT-ATTGGGGTATGCAATAATTTATTGTAATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
* * ** * *
689072 TTCTTTGATTTCATTGGGGTATGCAATAATTTATTGTAACAACCAATCTCTTTGATTTCACTGGG
131 CTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGA-TT-ATTGGG
* * * * *
689137 GAATGTAATAATTTTATTGTAACGACCAATCCCTTTGATTT
194 GTATGTAATAA-TTCATTGTAATGACCAAGCTCTTTGATTT
* *
689178 CATTGGGGAATGTAATAATTTATCGTAATGACCAAGCCCTTTGA-TT-ATTGGGGTATGTAATAA
1 CATTGGGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* * * *
689241 TTTATTGTAACGACCAATCTCTTTGATTTCATT-GGGAATGTAATAATTTATCGTAATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
*
689305 CTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATTACCAAGCTCTTTGATTATTGGGGT
131 CTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTATTGGGGT
689370 ATGTAATAATTCATTGTAATGACCAAGCTCTTTGATTT
196 ATGTAATAATTCATTGTAATGACCAAGCTCTTTGATTT
* * * *
689408 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGATTTGTAAAAA
1 CATTGGGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* * * * *
689473 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGATTTGTAAAAATCTATTGTAATAACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
* *
689538 CTCATTGATTTCATTAGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTATTGGGGT
131 CTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTATTGGGGT
*
689603 ATGTAATGATTCATTGTAATGACCAAGCTCTTTGATTT
196 ATGTAATAATTCATTGTAATGACCAAGCTCTTTGATTT
* *
689641 CATT-GGGATATGTAAAAATCTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATA
1 CATTGGGGA-ATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATA
*
689705 ATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATAACCAA
65 ATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAA
*
689770 GCTCTTTGATTTCATTGGGGTATTTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGG
130 GCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGA-TT-ATTGG
* *
689835 GGTATGTAATAATTTATTGTAATAACCAAGCTCTTTGATTT
193 GGTATGTAATAATTCATTGTAATGACCAAGCTCTTTGATTT
*
689876 CATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGA-TT-ATTGGGGTATGTAATAA
1 CATTGGGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
* * *
689939 TTCATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATCTATTGTTATGACCAAG
66 TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
690004 CTCTTTGATTTCA
131 CTCTTTGATTTCA
690017 GGCTCTGGAC
Statistics
Matches: 765, Mismatches: 65, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
230 66 0.09
231 17 0.02
232 88 0.12
233 464 0.61
234 47 0.06
235 80 0.10
236 3 0.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (233 bp):
CATTGGGGAATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAA
TTTATTGTAATGACCAAGCTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAG
CTCTTTGATTTCATTGGGGTATGTAATAATTTATTGTAATGACCAAGCTCTTTGATTATTGGGGT
ATGTAATAATTCATTGTAATGACCAAGCTCTTTGATTT
Found at i:692115 original size:24 final size:24
Alignment explanation
Indices: 692074--692134 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
692064 GTGAAACCTA
*** *
692074 CACTAAGGATAATTCTGTATTCGC
1 CACTAAGGATAGCCCTGTATTCAC
*
692098 CACTAAGGATAGCCCTGTATTCAT
1 CACTAAGGATAGCCCTGTATTCAC
*
692122 CAATAAGGATAGC
1 CACTAAGGATAGC
692135 TATGTATCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (24 bp):
CACTAAGGATAGCCCTGTATTCAC
Found at i:692193 original size:24 final size:24
Alignment explanation
Indices: 692101--692383 Score: 125
Period size: 24 Copynumber: 11.8 Consensus size: 24
692091 TATTCGCCAC
* * *
692101 TAAGGATAGCCCTGTATTCATCAA
1 TAAGGATAGCCATGTATCCTTCAA
* * *
692125 TAAGGATAGCTATGTATCCTCCAT
1 TAAGGATAGCCATGTATCCTTCAA
* * *
692149 TATGGATAACCCTGTATCCTTCAA
1 TAAGGATAGCCATGTATCCTTCAA
* *
692173 TAAGGACAGCCATGTATCCTTCAC
1 TAAGGATAGCCATGTATCCTTCAA
* * * *
692197 T-TGAGACACCTCA-GTATCCCTT-TA
1 TAAG-GATAGC-CATGTAT-CCTTCAA
* **
692221 TAGGGATAGCCATACAT-CTTCAA
1 TAAGGATAGCCATGTATCCTTCAA
**
692244 CTAAGGATAGCCATACAT-CTTCAA
1 -TAAGGATAGCCATGTATCCTTCAA
* **
692268 CAAAGGATAGCCATACAT-CTTCAA
1 -TAAGGATAGCCATGTATCCTTCAA
**
692292 CTAAGGATAGCCATACAT-CTTCAA
1 -TAAGGATAGCCATGTATCCTTCAA
* **
692316 CAAAGGATAGCCATACAT-CTTCAA
1 -TAAGGATAGCCATGTATCCTTCAA
* * *
692340 CTAAGGATACCCCTATATCCTTCACA
1 -TAAGGATAGCCATGTATCCTTCA-A
* *
692366 -AAGGATACCCCTGTATCC
1 TAAGGATAGCCATGTATCC
692384 ACCTCTAAGG
Statistics
Matches: 214, Mismatches: 36, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
22 3 0.01
23 4 0.02
24 194 0.91
25 12 0.06
26 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (24 bp):
TAAGGATAGCCATGTATCCTTCAA
Found at i:692276 original size:48 final size:48
Alignment explanation
Indices: 692224--692372 Score: 255
Period size: 48 Copynumber: 3.1 Consensus size: 48
692214 CCCTTTATAG
692224 GGATAGCCATACATCTTCAACTAAGGATAGCCATACATCTTCAACAAA
1 GGATAGCCATACATCTTCAACTAAGGATAGCCATACATCTTCAACAAA
692272 GGATAGCCATACATCTTCAACTAAGGATAGCCATACATCTTCAACAAA
1 GGATAGCCATACATCTTCAACTAAGGATAGCCATACATCTTCAACAAA
* * *
692320 GGATAGCCATACATCTTCAACTAAGGATACCCCTATATCCTTC-ACAAA
1 GGATAGCCATACATCTTCAACTAAGGATAGCCATACAT-CTTCAACAAA
692368 GGATA
1 GGATA
692373 CCCCTGTATC
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
48 93 0.96
49 4 0.04
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (48 bp):
GGATAGCCATACATCTTCAACTAAGGATAGCCATACATCTTCAACAAA
Found at i:692370 original size:72 final size:72
Alignment explanation
Indices: 692224--692372 Score: 228
Period size: 72 Copynumber: 2.1 Consensus size: 72
692214 CCCTTTATAG
* *
692224 GGATAGCCATACATCTTCAACTAAGGATAGCCATACATCTTCAACAAAGGATAGCCATACATCTT
1 GGATAGCCATACATCTTCAACAAAGGATAGCCATACATCTTCAACAAAGGATACCCATACATCTT
*
692289 CAACTAA
66 CAACAAA
* * *
692296 GGATAGCCATACATCTTCAACAAAGGATAGCCATACATCTTCAACTAAGGATACCCCTATATCCT
1 GGATAGCCATACATCTTCAACAAAGGATAGCCATACATCTTCAACAAAGGATACCCATACAT-CT
692361 TC-ACAAA
65 TCAACAAA
692368 GGATA
1 GGATA
692373 CCCCTGTATC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
72 66 0.94
73 4 0.06
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (72 bp):
GGATAGCCATACATCTTCAACAAAGGATAGCCATACATCTTCAACAAAGGATACCCATACATCTT
CAACAAA
Found at i:692393 original size:24 final size:24
Alignment explanation
Indices: 692339--692396 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
692329 TACATCTTCA
**
692339 ACTAAGGATACCCCTATATCCTTC
1 ACTAAGGATACCCCTATATCCACC
* *
692363 ACAAAGGATACCCCTGTATCCACC
1 ACTAAGGATACCCCTATATCCACC
*
692387 TCTAAGGATA
1 ACTAAGGATA
692397 GCCTTTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.12, T:0.24
Consensus pattern (24 bp):
ACTAAGGATACCCCTATATCCACC
Found at i:692394 original size:72 final size:72
Alignment explanation
Indices: 692224--692399 Score: 183
Period size: 72 Copynumber: 2.4 Consensus size: 72
692214 CCCTTTATAG
* ** *
692224 GGATAGCCATACATCTTCAACTAAGGATAGCCATACATCTTCAACAAAGGATAGCCATACATCTT
1 GGATACCCATACATCCACAACTAAGGATAGCCATACATCTTCAACAAAGGATACCCATACATCTT
*
692289 CAACTAA
66 CAACAAA
* ** * * * *
692296 GGATAGCCATACATCTTCAACAAAGGATAGCCATACATCTTCAACTAAGGATACCCCTATATCCT
1 GGATACCCATACATCCACAACTAAGGATAGCCATACATCTTCAACAAAGGATACCCATACAT-CT
692361 TC-ACAAA
65 TCAACAAA
* ** **
692368 GGATACCCCTGTATCCACCTCTAAGGATAGCC
1 GGATACCCATACATCCACAACTAAGGATAGCC
692400 TTTTATTACT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 84 0.95
73 4 0.05
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (72 bp):
GGATACCCATACATCCACAACTAAGGATAGCCATACATCTTCAACAAAGGATACCCATACATCTT
CAACAAA
Found at i:699682 original size:25 final size:25
Alignment explanation
Indices: 699642--699758 Score: 114
Period size: 25 Copynumber: 4.7 Consensus size: 25
699632 AATAATATTT
* *
699642 TTGG-TTTTTATGTACAGCATTTCT
1 TTGGTTTTTTATATACAGCATTTCA
699666 TTGGTTTTTTATATACAGCATTTCA
1 TTGGTTTTTTATATACAGCATTTCA
* *
699691 TT-GTTTTTCATACACAGCATTTCA
1 TTGGTTTTTTATATACAGCATTTCA
* * * *
699715 TAGATTTTTTAAATACAGCATATT-G
1 TTGGTTTTTTATATACAGCAT-TTCA
*
699740 TTGCTTTTTATATATACAG
1 TTGGTTTTT-TATATACAG
699759 AAATTACTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
24 25 0.33
25 41 0.54
26 10 0.13
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.50
Consensus pattern (25 bp):
TTGGTTTTTTATATACAGCATTTCA
Found at i:702430 original size:39 final size:39
Alignment explanation
Indices: 702376--702681 Score: 414
Period size: 39 Copynumber: 7.8 Consensus size: 39
702366 AGCTAAATAA
* * *
702376 TGTTTTCTGTTTTATAACACAGAGAAATCATATGTTTAC
1 TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
* * *
702415 TGTTTACTGTGTTATAACACAGAGAAACCAGATGTTTAC
1 TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
* * *
702454 TGTTTACAGTTTTATAACACACTGATATCAGATGTTTAC
1 TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
* *
702493 TGTTTACAGTTTTATAACACACTGAAATCAGATGTTTAC
1 TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
* * * *
702532 TGTTTACAGTTTTATAAAACAGAGAAACCAGATGTTTAC
1 TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
* *
702571 TGTTTATTGTTTTATAACACACTGAAATCAGATGTTTAC
1 TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
* *
702610 TGTTTATTGTTTTATAACACACTGAAATCAGATGTTTAC
1 TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
* * *
702649 TGTTTACTCTTTTATAACACAGAGAAACCAGAT
1 TGTTTACTGTTTTATAACACACAGAAATCAGAT
702682 CCCTGGCCCC
Statistics
Matches: 241, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 241 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (39 bp):
TGTTTACTGTTTTATAACACACAGAAATCAGATGTTTAC
Found at i:702569 original size:117 final size:117
Alignment explanation
Indices: 702384--702681 Score: 488
Period size: 117 Copynumber: 2.5 Consensus size: 117
702374 AATGTTTTCT
** * *
702384 GTTTTATAACACAGAGAAATCATATGTTTACTGTTTACTGTGTTATAACACAGAGAAACCAGATG
1 GTTTTATAACACACTGAAATCAGATGTTTACTGTTTACTGTTTTATAACACAGAGAAACCAGATG
*
702449 TTTACTGTTTACAGTTTTATAACACACTGATATCAGATGTTTACTGTTTACA
66 TTTACTGTTTACAGTTTTATAACACACTGAAATCAGATGTTTACTGTTTACA
* *
702501 GTTTTATAACACACTGAAATCAGATGTTTACTGTTTACAGTTTTATAAAACAGAGAAACCAGATG
1 GTTTTATAACACACTGAAATCAGATGTTTACTGTTTACTGTTTTATAACACAGAGAAACCAGATG
** **
702566 TTTACTGTTTATTGTTTTATAACACACTGAAATCAGATGTTTACTGTTTATT
66 TTTACTGTTTACAGTTTTATAACACACTGAAATCAGATGTTTACTGTTTACA
*
702618 GTTTTATAACACACTGAAATCAGATGTTTACTGTTTACTCTTTTATAACACAGAGAAACCAGAT
1 GTTTTATAACACACTGAAATCAGATGTTTACTGTTTACTGTTTTATAACACAGAGAAACCAGAT
702682 CCCTGGCCCC
Statistics
Matches: 167, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 167 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (117 bp):
GTTTTATAACACACTGAAATCAGATGTTTACTGTTTACTGTTTTATAACACAGAGAAACCAGATG
TTTACTGTTTACAGTTTTATAACACACTGAAATCAGATGTTTACTGTTTACA
Found at i:711272 original size:21 final size:21
Alignment explanation
Indices: 711233--711273 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
711223 GAAATGAAGA
*
711233 CGTAACTTTCGCGAGTAAACC
1 CGTAACTTGCGCGAGTAAACC
* *
711254 CGTAACTTGCTCGATTAAAC
1 CGTAACTTGCGCGAGTAAAC
711274 GCAAAACTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
CGTAACTTGCGCGAGTAAACC
Found at i:712557 original size:2 final size:2
Alignment explanation
Indices: 712550--712589 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
712540 ACATGCCGCA
712550 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
712590 AGTATACTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:715180 original size:14 final size:14
Alignment explanation
Indices: 715161--715190 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
715151 CGGCTGGGAT
715161 AGTGTTATTATTGC
1 AGTGTTATTATTGC
715175 AGTGTTATTATTGC
1 AGTGTTATTATTGC
715189 AG
1 AG
715191 ATCTTTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (14 bp):
AGTGTTATTATTGC
Found at i:718149 original size:2 final size:2
Alignment explanation
Indices: 718142--718174 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
718132 TGTCGCATCC
718142 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
718175 AGTAAACTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:718694 original size:12 final size:12
Alignment explanation
Indices: 718677--718706 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
718667 GTAGGGGATG
718677 TGTTTTTTTTTT
1 TGTTTTTTTTTT
718689 TGTTTTTTTTTT
1 TGTTTTTTTTTT
718701 T-TTTTT
1 TGTTTTT
718707 GGGGGGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TGTTTTTTTTTT
Found at i:722116 original size:25 final size:25
Alignment explanation
Indices: 722088--722198 Score: 161
Period size: 25 Copynumber: 4.4 Consensus size: 25
722078 GAGAATTCCG
*
722088 TCCCAGGGTTCTACAGAGAA-TAGTA
1 TCCCAGGGTTCAACAGAGAACT-GTA
*
722113 TCCCAGGGTTCAACAGAAAACTGTA
1 TCCCAGGGTTCAACAGAGAACTGTA
722138 TCCCAGGGTTCAACAGAGAACTGTA
1 TCCCAGGGTTCAACAGAGAACTGTA
* * *
722163 TCCCAGGGTTCCACTGAGAACTATA
1 TCCCAGGGTTCAACAGAGAACTGTA
722188 TCCCAGGGTTC
1 TCCCAGGGTTC
722199 CTGAGAGCAG
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
25 78 0.99
26 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (25 bp):
TCCCAGGGTTCAACAGAGAACTGTA
Found at i:723669 original size:167 final size:169
Alignment explanation
Indices: 723479--723863 Score: 551
Period size: 169 Copynumber: 2.3 Consensus size: 169
723469 AAAAACTGGT
* *
723479 TGCATAATTATGATGTCCATGAGGCCCTCTACCAAAATTGTGAAATTCATG-GCCCTGGGTCAGG
1 TGCATGATTATGATGTACATGAGGCCCTCTACCAAAATTGTGAAATTCATGAGCCCTGGGTCAGG
* * * * *
723543 GGTTCTGG-C-TCTTGGGTTGGGCTAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAA
66 GGTTCAGGACAT-TAGGGTGGGGCCAATATGACCATATAGTAAAAATGTATTAAATCTTAGAAAA
* *
723606 TCTTCTACTCTACTCCCATATATATTTGTTAAAAACTAAA
130 TCTCCTACTCTACTCCCATATATATTTATTAAAAACTAAA
* * * * *
723646 TGCATGATTATGAGGTACATGAGGCCCTCTACCAAAATTGTAAAATTCATGATCCCTGTGTCGGG
1 TGCATGATTATGATGTACATGAGGCCCTCTACCAAAATTGTGAAATTCATGAGCCCTGGGTCAGG
*
723711 GGTTCAGGACATTAGGGTGGGGCCAATATGACCATATAGTAAAAATGTATTCAATCTTAGAAAAT
66 GGTTCAGGACATTAGGGTGGGGCCAATATGACCATATAGTAAAAATGTATTAAATCTTAGAAAAT
*
723776 CTCCTTCTCTACTCCCATATATATTTATTAAAAACTAAA
131 CTCCTACTCTACTCCCATATATATTTATTAAAAACTAAA
* * * * *
723815 TGCCTGGTTATAATGTTCATGAAGCCCTCTACCAAAATTGTGAAATTCA
1 TGCATGATTATGATGTACATGAGGCCCTCTACCAAAATTGTGAAATTCA
723864 ATTCAATGGT
Statistics
Matches: 192, Mismatches: 23, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
167 47 0.24
168 17 0.09
169 127 0.66
170 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (169 bp):
TGCATGATTATGATGTACATGAGGCCCTCTACCAAAATTGTGAAATTCATGAGCCCTGGGTCAGG
GGTTCAGGACATTAGGGTGGGGCCAATATGACCATATAGTAAAAATGTATTAAATCTTAGAAAAT
CTCCTACTCTACTCCCATATATATTTATTAAAAACTAAA
Found at i:727503 original size:26 final size:26
Alignment explanation
Indices: 727467--727534 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
727457 TTATTTTTTA
*
727467 CAATCCTATCCTATTGAATCATGTAT
1 CAATCCTATCCTATCGAATCATGTAT
727493 CAATCCTATCCTATCGAATCATGTAT
1 CAATCCTATCCTATCGAATCATGTAT
*
727519 CAATCCTATCGTATCG
1 CAATCCTATCCTATCG
727535 TGCGTGTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (26 bp):
CAATCCTATCCTATCGAATCATGTAT
Found at i:728673 original size:21 final size:21
Alignment explanation
Indices: 728599--728676 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
728589 AACATCGTTT
* ** *
728599 ATCCTTTCCTATCGTGTATCA
1 ATCCTATCCTATCGTGCGTGA
* *
728620 ATCCTATCCTATCATGCGTGT
1 ATCCTATCCTATCGTGCGTGA
** * *
728641 ATATTGTTCTATCGTGCGTGA
1 ATCCTATCCTATCGTGCGTGA
728662 ATCCTATCCTATCGT
1 ATCCTATCCTATCGT
728677 TTATCTTGTA
Statistics
Matches: 41, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.41
Consensus pattern (21 bp):
ATCCTATCCTATCGTGCGTGA
Found at i:739032 original size:12 final size:12
Alignment explanation
Indices: 739011--739039 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
739001 TTATATTACA
739011 ATAT-ACACAAG
1 ATATAACACAAG
739022 ATATAACACAAG
1 ATATAACACAAG
739034 ATATAA
1 ATATAA
739040 GATATCAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (12 bp):
ATATAACACAAG
Found at i:740985 original size:2 final size:2
Alignment explanation
Indices: 740978--741044 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
740968 TATGTATGCA
740978 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
741020 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
741045 GAAGTTGACG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:741084 original size:22 final size:23
Alignment explanation
Indices: 741042--741085 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
741032 TCTCTCTCTC
*
741042 TCTGAAGTTGACGGTAACATAAT
1 TCTGAAGTTGACGATAACATAAT
741065 TCTGAAGTTGAC-ATAACATAA
1 TCTGAAGTTGACGATAACATAA
741086 ATCTAGTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (23 bp):
TCTGAAGTTGACGATAACATAAT
Found at i:753418 original size:37 final size:37
Alignment explanation
Indices: 753376--753457 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
753366 ACAGTTTCGA
* * *
753376 AGGAGACTTCATCAAAACGTTTTAACACAAATGCTAT
1 AGGAGACTTCATCAAAACGCTATAACACAAATACTAT
*
753413 AGGAGACTTTATCAAAACGCTATAACACAAATACTAT
1 AGGAGACTTCATCAAAACGCTATAACACAAATACTAT
*
753450 AGAAGACT
1 AGGAGACT
753458 GAATTACGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (37 bp):
AGGAGACTTCATCAAAACGCTATAACACAAATACTAT
Found at i:754681 original size:14 final size:13
Alignment explanation
Indices: 754654--754678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
754644 TTTTATAAAA
754654 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
754667 AAAAAAAAAGAA
1 AAAAAAAAAGAA
754679 AGATTCAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:755789 original size:488 final size:488
Alignment explanation
Indices: 754868--755796 Score: 1795
Period size: 488 Copynumber: 1.9 Consensus size: 488
754858 TTTTTCGATC
*
754868 TTATTTAAAAATAACAAACAAATCTCTTAAAAGTAGTTTTTGTTTTCTCTTTCCGAGCTAATACA
1 TTATCTAAAAATAACAAACAAATCTCTTAAAAGTAGTTTTTGTTTTCTCTTTCCGAGCTAATACA
754933 ATTCTGGCCTCCGTTAAAGGTCTTATTTTTATTTACCGGGATAATTTTTTTATTCGAATTTTATC
66 ATTCTGGCCTCCGTTAAAGGTCTTATTTTTATTTACCGGGATAATTTTTTTATTCGAATTTTATC
754998 TAGTACTAGTATATGAAATAGTTTTCCTCTTTTAATTTACTTTTTCATAAATAACTGATAAAAAT
131 TAGTACTAGTATATGAAATAGTTTTCCTCTTTTAATTTACTTTTTCATAAATAACTGATAAAAAT
* *
755063 CGCTGTTCATTGTGAATGAAAGAAAAAAAGTACATGTTTGCAATACTTCGTTTCAAAACACTCTA
196 CGCTGCTCATTGTGAATGAAAGAAAAAAAGTACATGTTTGCAATACTTCGTTACAAAACACTCTA
*
755128 ACGAGAACTGCATGTTCACTACAGCTGGTTAGAGTTGATTTATTTTGAAATTCAGCTCAGCTTAA
261 ACGAGAACTGCATGTTCACCACAGCTGGTTAGAGTTGATTTATTTTGAAATTCAGCTCAGCTTAA
755193 AATCCCTGTGTTTTAAAATTAGTATGTTGTTTTAAGGAATGTGACAACAATATGATAATCGCTTT
326 AATCCCTGTGTTTTAAAATTAGTATGTTGTTTTAAGGAATGTGACAACAATATGATAATCGCTTT
* *
755258 TCCTTTATTTTGGCACCTCGGCTTAGATAATGTTATTACGTTTTGAGAAAGGATGTAATTGAAAT
391 TCCTTTATTTTGGCACCTCAGCTTAGATAATGTCATTACGTTTTGAGAAAGGATGTAATTGAAAT
755323 TTTTGTCTATTTATCAGCACAGTAAAACACGGT
456 TTTTGTCTATTTATCAGCACAGTAAAACACGGT
755356 TTATCTAAAAATAACAAACAAATCTCTTAAAAGTAGTTTTTGTTTTCTCTTTCCGAGCTAATACA
1 TTATCTAAAAATAACAAACAAATCTCTTAAAAGTAGTTTTTGTTTTCTCTTTCCGAGCTAATACA
755421 ATTCTGGCCTCCGTTAAAGGTCTTATTTTTATTTACCGGGATAATTTTTTTATTCGAATTTTATC
66 ATTCTGGCCTCCGTTAAAGGTCTTATTTTTATTTACCGGGATAATTTTTTTATTCGAATTTTATC
755486 TAGTACTAGTATATGAAATAGTTTTCCTCTTTTAATTTACTTTTTCATAAATAACTGATAAAAAT
131 TAGTACTAGTATATGAAATAGTTTTCCTCTTTTAATTTACTTTTTCATAAATAACTGATAAAAAT
755551 CGCTGCTCATTGTGAATGAAAGAAAAAAAGTACATGTTTGCAATACTTCGTTACAAAACACTCTA
196 CGCTGCTCATTGTGAATGAAAGAAAAAAAGTACATGTTTGCAATACTTCGTTACAAAACACTCTA
755616 ACGAGAACTGCATGTTCACCACAGCTGGTTAGAGTTGATTTATTTTGAAATTCAGCTCAGCTTAA
261 ACGAGAACTGCATGTTCACCACAGCTGGTTAGAGTTGATTTATTTTGAAATTCAGCTCAGCTTAA
*
755681 AATCCCTGTGTTTTAAAATTTGTATGTTGTTTTAAGGAATGTGACAACAATATGATAATCGCTTT
326 AATCCCTGTGTTTTAAAATTAGTATGTTGTTTTAAGGAATGTGACAACAATATGATAATCGCTTT
755746 TCCTTTATTTTGGCACCTCAGCTTAGATAATGTCATTACGTTTTGAGAAAG
391 TCCTTTATTTTGGCACCTCAGCTTAGATAATGTCATTACGTTTTGAGAAAG
755797 CATTGGCGGA
Statistics
Matches: 434, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
488 434 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (488 bp):
TTATCTAAAAATAACAAACAAATCTCTTAAAAGTAGTTTTTGTTTTCTCTTTCCGAGCTAATACA
ATTCTGGCCTCCGTTAAAGGTCTTATTTTTATTTACCGGGATAATTTTTTTATTCGAATTTTATC
TAGTACTAGTATATGAAATAGTTTTCCTCTTTTAATTTACTTTTTCATAAATAACTGATAAAAAT
CGCTGCTCATTGTGAATGAAAGAAAAAAAGTACATGTTTGCAATACTTCGTTACAAAACACTCTA
ACGAGAACTGCATGTTCACCACAGCTGGTTAGAGTTGATTTATTTTGAAATTCAGCTCAGCTTAA
AATCCCTGTGTTTTAAAATTAGTATGTTGTTTTAAGGAATGTGACAACAATATGATAATCGCTTT
TCCTTTATTTTGGCACCTCAGCTTAGATAATGTCATTACGTTTTGAGAAAGGATGTAATTGAAAT
TTTTGTCTATTTATCAGCACAGTAAAACACGGT
Found at i:757595 original size:2 final size:2
Alignment explanation
Indices: 757588--757624 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
757578 TGGTCACCCA
*
757588 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
757625 GCTATGTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:762187 original size:27 final size:27
Alignment explanation
Indices: 762157--762211 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
762147 TTAACAAAGT
762157 TTACAGATATTGCCTAAACTCTTATTC
1 TTACAGATATTGCCTAAACTCTTATTC
762184 TTACAGATATTGCCTAAACTCTTATTC
1 TTACAGATATTGCCTAAACTCTTATTC
762211 T
1 T
762212 GTTGTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (27 bp):
TTACAGATATTGCCTAAACTCTTATTC
Found at i:764234 original size:27 final size:27
Alignment explanation
Indices: 764204--764258 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
764194 TTAACAAAGT
764204 TTACAGATATTGCCTAAACTCTTATTC
1 TTACAGATATTGCCTAAACTCTTATTC
764231 TTACAGATATTGCCTAAACTCTTATTC
1 TTACAGATATTGCCTAAACTCTTATTC
764258 T
1 T
764259 GTTGTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (27 bp):
TTACAGATATTGCCTAAACTCTTATTC
Found at i:768020 original size:21 final size:21
Alignment explanation
Indices: 767996--768055 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
767986 AAAAATGTTA
* *
767996 TTAATACTAGATAAATAGACG
1 TTAATACGAGATAAAAAGACG
* * *
768017 TTAAAACGAGCTAAAAAGTCG
1 TTAATACGAGATAAAAAGACG
*
768038 TTATTACGAGATAAAAAG
1 TTAATACGAGATAAAAAG
768056 GTTTATCAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (21 bp):
TTAATACGAGATAAAAAGACG
Found at i:768182 original size:4 final size:4
Alignment explanation
Indices: 768168--768242 Score: 55
Period size: 4 Copynumber: 18.8 Consensus size: 4
768158 CACGTGAGTC
* * * * * *
768168 TCTG GCTG TCTG TCTG TCAG TCTG TTTG TCCG TATG TC-G ATCTC TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG -TCTG TCTG
*
768216 TCTG TCTG TC-G ATCTG TCCG TCTG TCT
1 TCTG TCTG TCTG -TCTG TCTG TCTG TCT
768243 CTTTCTTCAT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
3 2 0.04
4 50 0.94
5 1 0.02
ACGTcount: A:0.05, C:0.27, G:0.24, T:0.44
Consensus pattern (4 bp):
TCTG
Found at i:768226 original size:20 final size:20
Alignment explanation
Indices: 768168--768242 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
768158 CACGTGAGTC
*
768168 TCTGGCTGTCTGTCTGTC-A
1 TCTGTCTGTCTGTCTGTCGA
* * *
768187 GTCTGTTTGTCCGTATGTCGA
1 -TCTGTCTGTCTGTCTGTCGA
*
768208 TCTCTCTGTCTGTCTGTCGA
1 TCTGTCTGTCTGTCTGTCGA
*
768228 TCTGTCCGTCTGTCT
1 TCTGTCTGTCTGTCT
768243 CTTTCTTCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.05, C:0.27, G:0.24, T:0.44
Consensus pattern (20 bp):
TCTGTCTGTCTGTCTGTCGA
Found at i:771492 original size:24 final size:24
Alignment explanation
Indices: 771460--771514 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
771450 ACTTTATTTC
771460 AGTAAACGTGCATAGACCGTTTGA
1 AGTAAACGTGCATAGACCGTTTGA
771484 AGTAAACGTGCATAGACCGTTTGA
1 AGTAAACGTGCATAGACCGTTTGA
771508 AGTAAAC
1 AGTAAAC
771515 ATTTGCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (24 bp):
AGTAAACGTGCATAGACCGTTTGA
Found at i:773225 original size:165 final size:164
Alignment explanation
Indices: 772887--773469 Score: 732
Period size: 164 Copynumber: 3.5 Consensus size: 164
772877 AAAGAATCAT
* *
772887 CTGGCTGATGAGTTTCT--G-AGAAGATTTTTAAAGATTTACCCTATATATTCCTTTGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCT-TATATTCCTTTGTTAAACT
* * * * * *
772949 TTGACCCCCCATTGTGACCCCACCCTACCCCTGGGGATCATGATTTTCACAACTTT-CA-C-A-A
65 TCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGG-TCATGATTTTCACAAATTTGAATCTACA
* *
773010 CTACCTGGGGATGCTTTCACACAAGTTTCAGTTTTC
129 CTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
* * * * *
773046 CTGACTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTGTTTATTCCTATGTAAAACA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCT-TATATTCCTTTGTTAAACT
* * * * *
773111 TCGATCTCCCATTGTGGCCCTAACCTACCCCCAGGGTTATGATTTTCACAAATTTGAATCTACAC
65 TCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAAATTTGAATCTACAC
*
773176 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
130 TACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
* * *
773211 CTGGCTAATTAGTTTCTGGGAAGAAGATTTTTAAAGATTTACTC-TAAATTCCTTTGTTAAACTT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTTATATTCCTTTGTTAAACTT
* * *
773275 CGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCAGGATTTTCAAAAATTTGAATCTACAT
66 CGATCCCCCATTGTGGCCCCACCCTACCCCC-GGGGTCATGATTTTCACAAATTTGAATCTACAC
* * *
773340 TACCTGATGATGCTTTCACTCAAGTTTTAGCTTTC
130 TACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
* *
773375 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATAATTATTCATTTGTTA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC--T-T-A-TATTCCTTTGTTA
*
773440 AACTTCGACCCCCCATTGTGGCCCCACCCT
61 AACTTCGATCCCCCATTGTGGCCCCACCCT
773470 CAGGTGAGCT
Statistics
Matches: 362, Mismatches: 48, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
159 15 0.04
161 18 0.05
162 67 0.19
163 44 0.12
164 101 0.28
165 75 0.21
168 1 0.00
169 1 0.00
170 40 0.11
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (164 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTTATATTCCTTTGTTAAACTT
CGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAAATTTGAATCTACACT
ACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
Found at i:774863 original size:4 final size:4
Alignment explanation
Indices: 774854--774895 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
774844 AAAGTTTACA
* * *
774854 GACG GACG GACG GACA GACA GACG GACA GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
774896 AAAATGTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.33, C:0.26, G:0.40, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:781965 original size:16 final size:16
Alignment explanation
Indices: 781864--781964 Score: 175
Period size: 16 Copynumber: 6.3 Consensus size: 16
781854 TTTTCTCCAA
781864 GAACGAAAGTACCCAG
1 GAACGAAAGTACCCAG
* *
781880 GAACGCAAGTACCCAA
1 GAACGAAAGTACCCAG
781896 GAACGAAAGTACCCAG
1 GAACGAAAGTACCCAG
781912 GAACGAAAGTACCCAG
1 GAACGAAAGTACCCAG
781928 GAACGAAAGTACCCAG
1 GAACGAAAGTACCCAG
*
781944 GAACGTAAGTACCCAG
1 GAACGAAAGTACCCAG
781960 GAACG
1 GAACG
781965 TTTTCTCCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 80 1.00
ACGTcount: A:0.43, C:0.26, G:0.25, T:0.07
Consensus pattern (16 bp):
GAACGAAAGTACCCAG
Done.