Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold86
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: 1697160
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 169504 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:321104 original size:10 final size:10
Alignment explanation
Indices: 321089--321131 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
321079 AAACACATGA
321089 TATAATATTG
1 TATAATATTG
*
321099 TATAATATAG
1 TATAATATTG
*
321109 TATGATATTG
1 TATAATATTG
* *
321119 TATGATACTG
1 TATAATATTG
321129 TAT
1 TAT
321132 CATTTTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (10 bp):
TATAATATTG
Found at i:321246 original size:15 final size:15
Alignment explanation
Indices: 321228--321305 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 15
321218 AAGTAAAATG
321228 TTATATAATACAATA
1 TTATATAATACAATA
*
321243 TTATATTATAC-ATA
1 TTATATAATACAATA
321257 TTGTATCATATGATACAATA
1 -T-TAT-ATA--ATACAATA
* **
321277 ATATATTTTACAATA
1 TTATATAATACAATA
* *
321292 TCATACAATACAAT
1 TTATATAATACAAT
321306 TTCATGTGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
14 3 0.06
15 27 0.57
16 3 0.06
17 4 0.09
18 3 0.06
19 4 0.09
20 3 0.06
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (15 bp):
TTATATAATACAATA
Found at i:321282 original size:25 final size:25
Alignment explanation
Indices: 321254--321301 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
321244 TATATTATAC
*
321254 ATATTGTATC-ATATGATACAATAAT
1 ATATTGTA-CAATATCATACAATAAT
*
321279 ATATTTTACAATATCATACAATA
1 ATATTGTACAATATCATACAATA
321302 CAATTTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (25 bp):
ATATTGTACAATATCATACAATAAT
Found at i:321771 original size:20 final size:20
Alignment explanation
Indices: 321720--321772 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
321710 ATATGATATT
**
321720 ATACTGTATCATATGAAACA
1 ATACTGTATCATACCAAACA
* *
321740 ATATTGTTTCATACCAAACA
1 ATACTGTATCATACCAAACA
*
321760 ATACTATATCATA
1 ATACTGTATCATA
321773 GGAATCATGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (20 bp):
ATACTGTATCATACCAAACA
Found at i:322602 original size:177 final size:175
Alignment explanation
Indices: 322299--322869 Score: 738
Period size: 177 Copynumber: 3.2 Consensus size: 175
322289 CTTAATCATA
* * * *
322299 TCCAGCATCTGAAACCTATAGCTCAGACTCAGCATTCAAGCCTGTCAGGTGCTTCAGTATCATAA
1 TCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
* * *
322364 GATGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAATAACTTAGATATGATCATCAGAG
66 GACGCACCATCCAT-GAAGTCTGGTGAAATTAGGACAAGTAGTAACTTAGATAT-ATCATCAGAG
*** * *
322429 GGCACCTGTTTCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
129 GGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
* *
322476 TCCAGCATCCGAAACCTATGGCTCAGATTCAGTATTCAAGCCTGTCTGGTGCATCAGTATCATAA
1 TCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
322541 GACGCACCATCCATAGAAGTCTGGTGAAATTAGGACAAGTAGTAAC-TACGATATAATCATCAGA
66 GACGCACCATCCAT-GAAGTCTGGTGAAATTAGGACAAGTAGTAACTTA-GATAT-ATCATCAGA
322605 GGGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
128 GGGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
* * *
322653 TCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCATGTTTGGTGCATCAGTATCATAA
1 TCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
* * * ** * *
322718 GACACACCATCCATGCAAGTTTGGTG-AAGTACGGACCTGCAGTAACTTAGATAT-TGCTATCAA
66 GACGCACCATCCATG-AAGTCTGGTGAAATTA-GGACAAGTAGTAACTTAGATATAT-C-ATCAG
* * *
322781 AGGGCACCTGCAACAAAAACTTTAACCTGGTCCAACAACCTTAACCTCC
127 AGGGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
* * *
322830 TCCAGCATCTGAAA--TTTAGGACTCAGATTCAGCATCCAAG
1 TCCAGCATCCGAAACCTATA-G-CTCAGATTCAGCATTCAAG
322870 TCTTTCAAGT
Statistics
Matches: 351, Mismatches: 35, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
175 4 0.01
176 9 0.03
177 336 0.96
178 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (175 bp):
TCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
GACGCACCATCCATGAAGTCTGGTGAAATTAGGACAAGTAGTAACTTAGATATATCATCAGAGGG
CACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
Found at i:322946 original size:177 final size:174
Alignment explanation
Indices: 322299--322947 Score: 622
Period size: 177 Copynumber: 3.7 Consensus size: 174
322289 CTTAATCATA
* * * * * *
322299 TCCAGCATCTGAAACCTATA-GCTCAGACTCAGCATTCAAGCCTGTCAGGTGCTTCAGTATCATA
1 TCCAGCATCCGAAA--TATAGGCTCAGATTCAGCATCCAAG-CTTTCTGGTGCATCAGTATCA-A
* * * *
322363 AGATGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAATAACTTAGATA-TGATCATCAG
62 AGACGCACCATCCATGCAAGTCTGGTGAAGATAGGACAAGTAATAACTTAGATATTGCT-ATCAG
*** * *
322427 AGGGCACCTGTTTCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
126 AGGGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
* * *
322476 TCCAGCATCCGAAACCTAT-GGCTCAGATTCAGTATTCAAGCCTGTCTGGTGCATCAGTATCATA
1 TCCAGCATCCGAAA--TATAGGCTCAGATTCAGCATCCAAG-CTTTCTGGTGCATCAGTATCA-A
*
322540 AGACGCACCATCCATAG-AAGTCTGGTGAA-ATTAGGACAAGTAGTAAC-TACGATATAAT-C-A
62 AGACGCACCATCCAT-GCAAGTCTGGTGAAGA-TAGGACAAGTAATAACTTA-GATAT--TGCTA
322600 TCAGAGGGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
122 TCAGAGGGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
322653 TCCAGCATCCGAAACCTATA-GCTCAGATTCAGCA-CTCAAGCATGTT-TGGTGCATCAGTATCA
1 TCCAGCATCCGAAA--TATAGGCTCAGATTCAGCATC-CAAGC-T-TTCTGGTGCATCAGTATCA
* * ** * *
322715 TAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCTGCAGTAACTTAGATATTGCTATC
61 -AAGACGCACCATCCATGCAAGTCTGGTGAAGATA-GGACAAGTAATAACTTAGATATTGCTATC
* * * *
322779 AAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAACAACCTTAACCTCC
124 AGAGGGCACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
* * ** * * *
322830 TCCAGCATCTGAAATTTAGGACTCAGATTCAGCATCCAAGTCTTTCAAGTCCATAAGTAGGTC-C
1 TCCAGCATCCGAAATATAGG-CTCAGATTCAGCATCCAAG-CTTTCTGGTGCATCAGTA--TCAA
* * * *
322894 AGATGCATCATCCATGCAAGTTTGGTGAAGATAGGACAAGTAATAGCTTAGATA
62 AGACGCACCATCCATGCAAGTCTGGTGAAGATAGGACAAGTAATAACTTAGATA
322948 CAGGACCTGC
Statistics
Matches: 406, Mismatches: 41, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
175 4 0.01
176 10 0.02
177 381 0.94
178 8 0.02
179 2 0.00
180 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (174 bp):
TCCAGCATCCGAAATATAGGCTCAGATTCAGCATCCAAGCTTTCTGGTGCATCAGTATCAAAGAC
GCACCATCCATGCAAGTCTGGTGAAGATAGGACAAGTAATAACTTAGATATTGCTATCAGAGGGC
ACCTGCAACAAAAACTTTAACCTGCTCAAAAAACCTTAACCTCC
Found at i:327881 original size:13 final size:11
Alignment explanation
Indices: 327861--327913 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
327851 ATGCACATGG
327861 TTTTTTGTTTCT
1 TTTTTTGTTT-T
327873 TTGTTTTGTTTT
1 TT-TTTTGTTTT
327885 TTCTTTT-TTTT
1 TT-TTTTGTTTT
*
327896 TTTTTTGGTTT
1 TTTTTTGTTTT
*
327907 TATTTTG
1 TTTTTTG
327914 GGCTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.11
11 15 0.42
12 9 0.25
13 8 0.22
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:327899 original size:20 final size:20
Alignment explanation
Indices: 327860--327901 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
327850 TATGCACATG
*
327860 GTTTTTTGTTTCTTTGTTTT
1 GTTTTTTCTTTCTTTGTTTT
327880 GTTTTTTCTTT-TTT-TTTT
1 GTTTTTTCTTTCTTTGTTTT
327898 -TTTT
1 GTTTT
327902 GGTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 4 0.19
19 3 0.14
20 10 0.48
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.86
Consensus pattern (20 bp):
GTTTTTTCTTTCTTTGTTTT
Found at i:327901 original size:16 final size:16
Alignment explanation
Indices: 327861--327901 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
327851 ATGCACATGG
*
327861 TTTTTTGTTTCTTTGT
1 TTTTTTTTTTCTTTGT
*
327877 TTTGTTTTTTCTTT-T
1 TTTTTTTTTTCTTTGT
327892 TTTTTTTTTT
1 TTTTTTTTTT
327902 GGTTTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTCTTTGT
Found at i:332631 original size:2 final size:2
Alignment explanation
Indices: 332624--332707 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
332614 GTTTGTAAAC
332624 AG AG AG AG AG AG AG AG AG AG AG 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 AG AG AG
332666 AG AG AG AG AG AG AG AG AG AG AG AG -G 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 AG AG AG
332707 A
1 A
332708 TGCATAAATC
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 80 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:339028 original size:2 final size:2
Alignment explanation
Indices: 339021--339047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
339011 ACAATCTCAA
339021 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
339048 TACTATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:341984 original size:43 final size:43
Alignment explanation
Indices: 341932--342406 Score: 505
Period size: 43 Copynumber: 11.0 Consensus size: 43
341922 TTGACATACT
341932 TTAACCCACTGGTCTGGGGTGACATTGGAAACTGTCACCTACC
1 TTAACCCACTGGTCTGGGGTGACATTGGAAACTGTCACCTACC
* *
341975 TTGACCCACTGGTCTGGGGTGACGTTAGG-AACTGTCACCTACC
1 TTAACCCACTGGTCTGGGGTGACATT-GGAAACTGTCACCTACC
* *
342018 TTAACACACTGGTCTGGAGTGACATTGGAAACTGTCACCTACC
1 TTAACCCACTGGTCTGGGGTGACATTGGAAACTGTCACCTACC
* * *
342061 TTGACCTACTGGTCTGGGGTGACGTTAGG-AACTGTCACCTACC
1 TTAACCCACTGGTCTGGGGTGACATT-GGAAACTGTCACCTACC
* * *
342104 TTAACACACTGGTCTGGAGTGACATTGGGAACTGTCACCTACC
1 TTAACCCACTGGTCTGGGGTGACATTGGAAACTGTCACCTACC
* * *
342147 TTAACCCACTGGTCTGAGCTGACATTTGG-ACCTGTCACCTACC
1 TTAACCCACTGGTCTGGGGTGACA-TTGGAAACTGTCACCTACC
* *
342190 TTAACCCACTGGTCTGGAGTGACATTGGGAACTGTCACCTACC
1 TTAACCCACTGGTCTGGGGTGACATTGGAAACTGTCACCTACC
* * **
342233 TTAACCCACTGGTCTAGCGTTG-CATTGGAAACTGGGACCTACC
1 TTAACCCACTGGTCT-GGGGTGACATTGGAAACTGTCACCTACC
* * * * * **
342276 TTGACTCACTGATCTTGGGTTG-CATTGGGAACTGGGACCTACC
1 TTAACCCACTGGTC-TGGGGTGACATTGGAAACTGTCACCTACC
* * **
342319 TTAACCCACTGGTCTAGCGTTG-CATTGGAAACTGGGACCTACC
1 TTAACCCACTGGTCT-GGGGTGACATTGGAAACTGTCACCTACC
* * * * * **
342362 TTGACTCACTGATCTTGGGTTG-CATTGGGAACTGGGACCTACC
1 TTAACCCACTGGTC-TGGGGTGACATTGGAAACTGTCACCTACC
342405 TT
1 TT
342407 NNNNNNNNNN
Statistics
Matches: 376, Mismatches: 46, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
42 9 0.02
43 354 0.94
44 13 0.03
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (43 bp):
TTAACCCACTGGTCTGGGGTGACATTGGAAACTGTCACCTACC
Found at i:345567 original size:2 final size:2
Alignment explanation
Indices: 345560--345595 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
345550 GTACAATCTC
345560 AG AG AG AG AG AG AG AG 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
345596 TATTTCCTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:348420 original size:43 final size:42
Alignment explanation
Indices: 348355--348604 Score: 401
Period size: 43 Copynumber: 5.8 Consensus size: 42
348345 AGAAATACTA
*
348355 TTAACCCACTGGTCTGGGGTGACATTGGAAACTGTCACCTACC
1 TTAACCCACTGGTCT-GGGTGACATTGGGAACTGTCACCTACC
348398 TTAACCCACTGGTCTGGAGTGACATTGGGAACTGTCACCTACC
1 TTAACCCACTGGTCTGG-GTGACATTGGGAACTGTCACCTACC
*
348441 TTAACCCACTGGTTTGGGCTGACATTGGGAACTGTCACCTACC
1 TTAACCCACTGGTCTGGG-TGACATTGGGAACTGTCACCTACC
*
348484 TTAACCCACTGGTCTGGAGTGACTTTGGGAACTGTCACCTACC
1 TTAACCCACTGGTCTGG-GTGACATTGGGAACTGTCACCTACC
348527 TTAACCCACTGGTCTGGGCTGACATTGGGAACTGTCACCTACC
1 TTAACCCACTGGTCTGGG-TGACATTGGGAACTGTCACCTACC
* *
348570 TTAACCCACTGGTCTGGGGTGACGTTAGGAACTGT
1 TTAACCCACTGGTCT-GGGTGACATTGGGAACTGT
348605 GACATCCATT
Statistics
Matches: 195, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
42 4 0.02
43 187 0.96
44 4 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (42 bp):
TTAACCCACTGGTCTGGGTGACATTGGGAACTGTCACCTACC
Found at i:358118 original size:2 final size:2
Alignment explanation
Indices: 358111--358148 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
358101 TTGAATCTTT
358111 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
358149 TCTGAAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:358288 original size:2 final size:2
Alignment explanation
Indices: 358281--358305 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
358271 CAACAGTTTT
358281 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 G
358306 CTAGAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:361984 original size:2 final size:2
Alignment explanation
Indices: 361977--362003 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
361967 TCTTTAAAAG
361977 TC 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 TC T
362004 TACACATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:370819 original size:1 final size:1
Alignment explanation
Indices: 370813--370837 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
370803 GTTTACATGT
370813 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
370838 GCAATATTTC
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:379340 original size:18 final size:18
Alignment explanation
Indices: 379317--379351 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
379307 GTGTGGGTGT
379317 GATGGACAGATGGTATGA
1 GATGGACAGATGGTATGA
379335 GATGGACAGATGGTATG
1 GATGGACAGATGGTATG
379352 TGAAAGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.40, T:0.23
Consensus pattern (18 bp):
GATGGACAGATGGTATGA
Found at i:383320 original size:2 final size:2
Alignment explanation
Indices: 383313--383346 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
383303 TTGGTCAGTA
383313 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
383347 TAATAAGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:387147 original size:16 final size:16
Alignment explanation
Indices: 387126--387157 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
387116 TTAAATGACA
387126 TTCAGGTCTTTAGTAT
1 TTCAGGTCTTTAGTAT
387142 TTCAGGTCTTTAGTAT
1 TTCAGGTCTTTAGTAT
387158 GTCCCGTATA
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:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (16 bp):
TTCAGGTCTTTAGTAT
Found at i:401656 original size:21 final size:21
Alignment explanation
Indices: 401624--401692 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
401614 TAGATATGTC
*
401624 TGAATTGAACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
* *
401645 TCAATTGTACCTATCTTTAAA
1 TGAATTGTACCTATCTTCAAA
*
401666 TGAATTTTACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
401687 TGAATT
1 TGAATT
401693 AGAGATAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
TGAATTGTACCTATCTTCAAA
Found at i:401723 original size:63 final size:63
Alignment explanation
Indices: 401645--401783 Score: 190
Period size: 63 Copynumber: 2.2 Consensus size: 63
401635 TATCTTCAAA
** *
401645 TCAATTGTACCTATCTTTAAATGAATTTTACCTATCTTCAAATGAATT-AGAGATAGGTATAAT
1 TCAATTGTACCTATCTTTAAATGAATTGAACCTATCTTCAAATGAATTGA-AGATAGGAATAAT
* * * *
401708 TCAATTGAACCTATCTTTAATTGAATTGAACCTATCTTTAATTGAATTGAAGATAGGAATAAT
1 TCAATTGTACCTATCTTTAAATGAATTGAACCTATCTTCAAATGAATTGAAGATAGGAATAAT
*
401771 TCATTTGTACCTA
1 TCAATTGTACCTA
401784 GGTATAATTC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 65 0.98
64 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (63 bp):
TCAATTGTACCTATCTTTAAATGAATTGAACCTATCTTCAAATGAATTGAAGATAGGAATAAT
Found at i:401728 original size:21 final size:21
Alignment explanation
Indices: 401710--401758 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
401700 GGTATAATTC
*
401710 AATTGAACCTATCTTTAATTG
1 AATTGAACCTATCTTTAAATG
*
401731 AATTGAACCTATCTTTAATTG
1 AATTGAACCTATCTTTAAATG
401752 AATTGAA
1 AATTGAA
401759 GATAGGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (21 bp):
AATTGAACCTATCTTTAAATG
Found at i:401750 original size:42 final size:42
Alignment explanation
Indices: 401624--401758 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 42
401614 TAGATATGTC
* * *
401624 TGAATTGAACCTATCTTCAAATCAATTGTACCTATCTTTAAA
1 TGAATTGAACCTATCTTCAAATGAATTGAACCTATCTTTAAT
** ** *
401666 TGAATTTTACCTATCTTCAAATGAATTAGAGA--TAGGTATAAT
1 TGAATTGAACCTATCTTCAAATGAATT-GA-ACCTATCTTTAAT
* * *
401708 TCAATTGAACCTATCTTTAATTGAATTGAACCTATCTTTAAT
1 TGAATTGAACCTATCTTCAAATGAATTGAACCTATCTTTAAT
401750 TGAATTGAA
1 TGAATTGAA
401759 GATAGGAATA
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
40 1 0.01
41 2 0.03
42 67 0.93
43 1 0.01
44 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (42 bp):
TGAATTGAACCTATCTTCAAATGAATTGAACCTATCTTTAAT
Found at i:401785 original size:21 final size:21
Alignment explanation
Indices: 401761--401817 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
401751 GAATTGAAGA
*
401761 TAGGAATAATTCATTTGTACC
1 TAGGTATAATTCATTTGTACC
401782 TAGGTATAATTCATTTGTACC
1 TAGGTATAATTCATTTGTACC
401803 TAGGTATAATT-ATTT
1 TAGGTATAATTCATTT
401818 AGAGATAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (21 bp):
TAGGTATAATTCATTTGTACC
Found at i:401804 original size:63 final size:63
Alignment explanation
Indices: 401669--401878 Score: 157
Period size: 63 Copynumber: 3.4 Consensus size: 63
401659 CTTTAAATGA
* * * *
401669 ATTT-TACCTATCTTCAAATGAATTAGAGATAGGTATAATTCAATTGAACCTATCTTTAATTG
1 ATTTGTACCTATCTTCAAATGAATTAGAGATAGGAATAATTCAATTGAACCTAGCTATAATTC
* * * * * * *
401731 AATTGAACCTATCTTTAATTGAATT-GAAGATAGGAATAATTCATTTGTACCTAGGTATAATTC
1 ATTTGTACCTATCTTCAAATGAATTAG-AGATAGGAATAATTCAATTGAACCTAGCTATAATTC
** * * * * *
401794 ATTTGTACCTA-GGT-ATAATTATTTAGAGATAGGTATAATT--ATTTACACCTATCT-TCAATT
1 ATTTGTACCTATCTTCA-AATGAATTAGAGATAGGAATAATTCAATTGA-ACCTAGCTAT-AATT
401854 C
63 C
*
401855 AATTGTACCTATCTTCAAAT-AATT
1 ATTTGTACCTATCTTCAAATGAATT
401879 GTACCTATCT
Statistics
Matches: 112, Mismatches: 28, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
60 3 0.03
61 25 0.22
62 27 0.24
63 57 0.51
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (63 bp):
ATTTGTACCTATCTTCAAATGAATTAGAGATAGGAATAATTCAATTGAACCTAGCTATAATTC
Found at i:401864 original size:21 final size:21
Alignment explanation
Indices: 401840--401913 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
401830 AATTATTTAC
401840 ACCTATCTTCAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
*
401861 ACCTATCTTCAAAT-AATTGT
1 ACCTATCTTCAATTCAATTGT
*
401881 ACCTATCTTTAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
401902 ACCTATCTTCAA
1 ACCTATCTTCAA
401914 ATGATTTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.38
21 30 0.62
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (21 bp):
ACCTATCTTCAATTCAATTGT
Found at i:401942 original size:20 final size:20
Alignment explanation
Indices: 401911--401963 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
401901 TACCTATCTT
401911 CAAATGATTTGAAGATAGGTA
1 CAAAT-ATTTGAAGATAGGTA
401932 C-AATCATTTGAAGATAGGTA
1 CAAAT-ATTTGAAGATAGGTA
401952 CAAATATTTGAA
1 CAAATATTTGAA
401964 TATATGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (20 bp):
CAAATATTTGAAGATAGGTA
Found at i:403668 original size:50 final size:49
Alignment explanation
Indices: 403551--403923 Score: 534
Period size: 50 Copynumber: 7.6 Consensus size: 49
403541 CCTCCTTAAA
* ** *
403551 TGCATATTGCCTGTAAAATGCTGAACAAAAGAGATGACTTTAAGGTTGT
1 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGCTTTAAGGTTGT
*
403600 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGCTTTTTAGG-TGTT
1 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGC-TTTAAGGTTG-T
* *
403650 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGACTTTTTAGGTTGT
1 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGC-TTTAAGGTTGT
*
403700 TGCACATTGCCTGTTTAATGCTGAGCAAAAGAGATGGCTTTAAGGTTGT
1 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGCTTTAAGGTTGT
** * *
403749 CACACATTGTCTGTTTAATGCTGAACAAAAGAGATGGCTTTTTAGGTTGT
1 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGC-TTTAAGGTTGT
* *
403799 TGCACATTGCCTGTTTAATGCTAAACAAAAGAGATGGCTGTAAGGTTGT
1 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGCTTTAAGGTTGT
* *
403848 TACACATTGCCTGTTTAATGCTAAACAAAAGAGATGGCTTTAA-GTTGT
1 TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGCTTTAAGGTTGT
* *
403896 TGTACATTGCCTGTTTAATGCTAAACAA
1 TGCACATTGCCTGTTTAATGCTGAACAA
403924 TTAAAGATTT
Statistics
Matches: 296, Mismatches: 24, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
48 31 0.10
49 130 0.44
50 133 0.45
51 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (49 bp):
TGCACATTGCCTGTTTAATGCTGAACAAAAGAGATGGCTTTAAGGTTGT
Found at i:403755 original size:99 final size:98
Alignment explanation
Indices: 403556--403923 Score: 542
Period size: 99 Copynumber: 3.7 Consensus size: 98
403546 TTAAATGCAT
** *
403556 ATTGCCTGTAAAATGCTGAACAAAAGAGATGACTTTAAGGTTGTTGCACATTGCCTGTTTAATGC
1 ATTGCCTGTTTAATGCTGAACAAAAGAGATGACTTTTAGGTTGTTGCACATTGCCTGTTTAATGC
* *
403621 TGAACAAAAGAGATGGCTTTTTAGG-TGTTTGCAC
66 TGAACAAAAGAGATGGC-TTTAAGGTTG-TTACAC
403655 ATTGCCTGTTTAATGCTGAACAAAAGAGATGACTTTTTAGGTTGTTGCACATTGCCTGTTTAATG
1 ATTGCCTGTTTAATGCTGAACAAAAGAGATGAC-TTTTAGGTTGTTGCACATTGCCTGTTTAATG
* *
403720 CTGAGCAAAAGAGATGGCTTTAAGGTTGTCACAC
65 CTGAACAAAAGAGATGGCTTTAAGGTTGTTACAC
* *
403754 ATTGTCTGTTTAATGCTGAACAAAAGAGATGGCTTTTTAGGTTGTTGCACATTGCCTGTTTAATG
1 ATTGCCTGTTTAATGCTGAACAAAAGAGATGAC-TTTTAGGTTGTTGCACATTGCCTGTTTAATG
* *
403819 CTAAACAAAAGAGATGGCTGTAAGGTTGTTACAC
65 CTGAACAAAAGAGATGGCTTTAAGGTTGTTACAC
* * * *
403853 ATTGCCTGTTTAATGCTAAACAAAAGAGATGGC-TTTAAGTTGTTGTACATTGCCTGTTTAATGC
1 ATTGCCTGTTTAATGCTGAACAAAAGAGATGACTTTTAGGTTGTTGCACATTGCCTGTTTAATGC
*
403917 TAAACAA
66 TGAACAA
403924 TTAAAGATTT
Statistics
Matches: 250, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
97 36 0.14
99 165 0.66
100 49 0.20
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (98 bp):
ATTGCCTGTTTAATGCTGAACAAAAGAGATGACTTTTAGGTTGTTGCACATTGCCTGTTTAATGC
TGAACAAAAGAGATGGCTTTAAGGTTGTTACAC
Found at i:417008 original size:4 final size:4
Alignment explanation
Indices: 417001--417108 Score: 189
Period size: 4 Copynumber: 26.8 Consensus size: 4
416991 TGGATGGATG
417001 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
* *
417049 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATC TATCA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT-A GATA
417098 GATA GATA GAT
1 GATA GATA GAT
417109 CAACTATTCA
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
4 97 0.98
5 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (4 bp):
GATA
Found at i:419120 original size:5 final size:5
Alignment explanation
Indices: 419110--419142 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
419100 AAAAAAGCAT
419110 AAACA AAACA AAACGA AAACA AAACA AAA-A AAA
1 AAACA AAACA AAAC-A AAACA AAACA AAACA AAA
419143 TTATTTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:419128 original size:11 final size:10
Alignment explanation
Indices: 419110--419142 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
419100 AAAAAAGCAT
419110 AAACAAAACA
1 AAACAAAACA
419120 AAACGAAAACA
1 AAAC-AAAACA
419131 AAACAAAA-A
1 AAACAAAACA
419140 AAA
1 AAA
419143 TTATTTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 8 0.36
11 10 0.45
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (10 bp):
AAACAAAACA
Found at i:444359 original size:334 final size:328
Alignment explanation
Indices: 443838--444443 Score: 847
Period size: 334 Copynumber: 1.8 Consensus size: 328
443828 AGTAAAGAGG
* * ** * *
443838 AAGATTTTTTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCTTAGAGCCTGAA
1 AAGATTTTCTAAGAATTAATACATTTGCACAATATGGCCATATTGGCCCCACCCTAGAGCCTGAA
* * * * *
443903 CCCTGCCACTGGGGTCATGAATTTCACAATTTCGGTAGAGGGCTTCATTGACATCATAATCATGC
66 CCCTGACACAGGGGCCATGAATTTCACAATTTCGGTAGAGGGCTTCATGGACATAATAATCATGC
*** * *
443968 ATTTAGTTTTTAACAAATATAGATAAGAGTTGAAAAGAAGATTTTATAAGATTTAATATATTTTT
131 ATTTAGTTTTTAACAAATATAGATAAGAGAAAAAAAGAAGATTTTATAAGATTTAATACATGTTT
* * *
444033 ACTATATGGCCATATTTG-CCCCACCCTAGAGCCAGAACCCCTGACCCAGGGGCCATGAATTTCA
196 ACTATATAGCCATA-TCGACCCCACCCTAGAGCCAGAACCCCTGACCAAGGGGCCATGAATTTCA
*
444097 CAATTTAG-TAGAAGCCTCATGAAATATTTGAATTTAGTTTTTAACAAATATACATGGGAGTAGA
260 CAATCTAGATAGAAGCCTCATGAAATATTTGAATTTAGTTTTTAACAAATATACATGGGAGTAGA
444161 GAAA
325 GAAA
*
444165 AAGATTTTCTAAGAATTAATACATTTGCACAATATGGCCATATTTGCCCCACCCTAGAGCCTGAA
1 AAGATTTTCTAAGAATTAATACATTTGCACAATATGGCCATATTGGCCCCACCCTAGAGCCTGAA
** * ** *
444230 CCCCTGATGCAGGGGCCATGAATTTCACAATTTTGGTATCGGGCTTCATGGACATAATTATCATG
66 -CCCTGACACAGGGGCCATGAATTTCACAATTTCGGTAGAGGGCTTCATGGACATAATAATCATG
* *
444295 CATTTAGTTTTTAACAAATATATACATGTATAGGAGAAAAAAAGAAGATTTTCTAAGATTTAATA
130 CATTTAGTTTTTAAC-AA-ATAT--A-G-ATAAGAGAAAAAAAGAAGATTTTATAAGATTTAATA
* *
444360 CATGTTTACTATATAGCCATATCGACTCCACCCTAGAGCCAGAACCCCTGACCAAGGGGTCATGA
189 CATGTTTACTATATAGCCATATCGACCCCACCCTAGAGCCAGAACCCCTGACCAAGGGGCCATGA
444425 ATTTCACAATCTAGATAGA
254 ATTTCACAATCTAGATAGA
444444 GGGCTTCGTG
Statistics
Matches: 239, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
327 58 0.24
328 68 0.28
329 2 0.01
330 4 0.02
332 1 0.00
333 3 0.01
334 99 0.41
335 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (328 bp):
AAGATTTTCTAAGAATTAATACATTTGCACAATATGGCCATATTGGCCCCACCCTAGAGCCTGAA
CCCTGACACAGGGGCCATGAATTTCACAATTTCGGTAGAGGGCTTCATGGACATAATAATCATGC
ATTTAGTTTTTAACAAATATAGATAAGAGAAAAAAAGAAGATTTTATAAGATTTAATACATGTTT
ACTATATAGCCATATCGACCCCACCCTAGAGCCAGAACCCCTGACCAAGGGGCCATGAATTTCAC
AATCTAGATAGAAGCCTCATGAAATATTTGAATTTAGTTTTTAACAAATATACATGGGAGTAGAG
AAA
Found at i:444426 original size:174 final size:171
Alignment explanation
Indices: 443733--444463 Score: 745
Period size: 160 Copynumber: 4.4 Consensus size: 171
443723 NNNATGTCCT
* *
443733 GAACCCCTGACCAAGGGGCCATGAATTTCATAATTTTGGTAGAGGGCTTCATGGACATCATAATC
1 GAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATAATAATC
* ** * * * * * *
443798 ACGAATTTAGTTTTTTGC----ACACATGTTTA-GAGTAAAGAGGAAGATTTTTTAAGATTTAAT
66 ATGAATTTAGTTTTTAACAAATATACATG-ATAGGAGAAAAAAAGAAGATTTTCTAAGATTTAAT
* * *
443858 ACATTTTTACTATATGGCCATATTGGCCCCACCTTAGAGCCT
130 ACATTTTTACTATATGGCCATATTTGCCCCACCCTAGAGCCA
* * * * *
443900 GAA-CCCTG-CCACTGGGGTCATGAATTTCACAATTTCGGTAGAGGGCTTCATTGACATCATAAT
1 GAACCCCTGACCA-AGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATAATAAT
* * *** *
443963 CATGCATTTAGTTTTTAACAAATAT--A-GATAAGAGTTGAAAAGAAGATTTTATAAGATTTAAT
65 CATGAATTTAGTTTTTAACAAATATACATGATAGGAGAAAAAAAGAAGATTTTCTAAGATTTAAT
*
444025 ATATTTTTACTATATGGCCATATTTGCCCCACCCTAGAGCCA
130 ACATTTTTACTATATGGCCATATTTGCCCCACCCTAGAGCCA
* * * *
444067 GAACCCCTGACCCAGGGGCCATGAATTTCACAA-TTTAGTAGA-AGCCTCAT-G--A-AAT-AT-
1 GAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATAATAATC
* * * *
444124 TTGAATTTAGTTTTTAACAAATATACATG---GGAGTAGAGAAA-AAGATTTTCTAAGAATTAAT
66 ATGAATTTAGTTTTTAACAAATATACATGATAGGAG-AAAAAAAGAAGATTTTCTAAGATTTAAT
** * *
444185 ACATTTGCACAATATGGCCATATTTGCCCCACCCTAGAGCCT
130 ACATTTTTACTATATGGCCATATTTGCCCCACCCTAGAGCCA
* ** *
444227 GAACCCCTGATGC-AGGGGCCATGAATTTCACAATTTTGGTATCGGGCTTCATGGACATAATTAT
1 GAACCCCTGA-CCAAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATAATAAT
*
444291 CATGCATTTAGTTTTTAACAAATATATACATGTATAGGAGAAAAAAAGAAGATTTTCTAAGATTT
65 CATGAATTTAGTTTTTAAC-AA-ATATACATG-ATAGGAGAAAAAAAGAAGATTTTCTAAGATTT
* * * *
444356 AATACATGTTTACTATATAGCCATA-TCGACTCCACCCTAGAGCCA
127 AATACATTTTTACTATATGGCCATATTTG-CCCCACCCTAGAGCCA
* * * * * *
444401 GAACCCCTGACCAAGGGGTCATGAATTTCACAATCTAGATAGAGGGCTTCGTGGACATCATAA
1 GAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATAATAA
444464 CAATGCAACC
Statistics
Matches: 463, Mismatches: 71, Indels: 53
0.79 0.12 0.09
Matches are distributed among these distances:
160 110 0.24
161 12 0.03
162 9 0.02
163 3 0.01
165 5 0.01
166 77 0.17
167 80 0.17
168 40 0.09
169 4 0.01
170 10 0.02
173 8 0.02
174 105 0.23
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (171 bp):
GAACCCCTGACCAAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATAATAATC
ATGAATTTAGTTTTTAACAAATATACATGATAGGAGAAAAAAAGAAGATTTTCTAAGATTTAATA
CATTTTTACTATATGGCCATATTTGCCCCACCCTAGAGCCA
Found at i:444480 original size:174 final size:174
Alignment explanation
Indices: 443837--444480 Score: 466
Period size: 174 Copynumber: 3.8 Consensus size: 174
443827 GAGTAAAGAG
* * ** * * * * *
443837 GAAGATTTTTTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCTTAGAGCCTGA
1 GAAGATTTTCTAAGAATTAATACATTTGCACAATATAGCCATATTCGCCCCACCCTAGAGCCAGA
* * * * * *
443902 A-CCCTG--CCACTGGGGTCATGAATTTCACAATTTCGGTAGAGGGCTTCATTGACATCA-TAAT
66 ACCCCTGATCCA--GGGGCCATGAATTTCACAATCTAGATAGAGGGCTTCATGGACATAATTAA-
*** * ***
443963 CATGCATTTAGTTTTTAAC-AA-ATAT--A-G-ATAAGAGTTGAAAA
128 CATGCAACCAGTTTTTAACAAATATATACATGTATAGGAGAAAAAAA
* * * ** * * *
444004 GAAGATTTTATAAGATTTAATATATTTTTACTATATGGCCATATTTGCCCCACCCTAGAGCCAGA
1 GAAGATTTTCTAAGAATTAATACATTTGCACAATATAGCCATATTCGCCCCACCCTAGAGCCAGA
* * * * *
444069 ACCCCTGACCCAGGGGCCATGAATTTCACAATTTAG-TAGA-AGCCTCAT-GAAAT-ATT----T
66 ACCCCTGATCCAGGGGCCATGAATTTCACAATCTAGATAGAGGGCTTCATGGACATAATTAACAT
** * *
444126 G-AATTTAGTTTTTAAC-AA-ATATACATG----GGAGTAGAGAAA
131 GCAA-CCAGTTTTTAACAAATATATACATGTATAGGAG-AAAAAAA
* * *
444165 -AAGATTTTCTAAGAATTAATACATTTGCACAATATGGCCATATTTGCCCCACCCTAGAGCCTGA
1 GAAGATTTTCTAAGAATTAATACATTTGCACAATATAGCCATATTCGCCCCACCCTAGAGCCAGA
* * * * ** *
444229 ACCCCTGATGCAGGGGCCATGAATTTCACAATTTTGGTATCGGGCTTCATGGACATAATTATCAT
66 ACCCCTGATCCAGGGGCCATGAATTTCACAATCTAGATAGAGGGCTTCATGGACATAATTAACAT
***
444294 GCATTTAGTTTTTAACAAATATATACATGTATAGGAGAAAAAAA
131 GCAACCAGTTTTTAACAAATATATACATGTATAGGAGAAAAAAA
* * * *
444338 GAAGATTTTCTAAGATTTAATACATGTT-TACTATATAGCCATA-TCGACTCCACCCTAGAGCCA
1 GAAGATTTTCTAAGAATTAATACAT-TTGCACAATATAGCCATATTCG-CCCCACCCTAGAGCCA
* * *
444401 GAACCCCTGA-CCAAGGGGTCATGAATTTCACAATCTAGATAGAGGGCTTCGTGGACATCA-TAA
64 GAACCCCTGATCC-AGGGGCCATGAATTTCACAATCTAGATAGAGGGCTTCATGGACATAATTAA
444464 CAATGCAACCAGTTTTT
128 C-ATGCAACCAGTTTTT
444481 TTCCTCCGAG
Statistics
Matches: 394, Mismatches: 54, Indels: 51
0.79 0.11 0.10
Matches are distributed among these distances:
159 1 0.00
160 113 0.29
161 5 0.01
162 7 0.02
163 5 0.01
164 4 0.01
165 5 0.01
166 6 0.02
167 65 0.16
168 41 0.10
169 3 0.01
170 12 0.03
173 11 0.03
174 114 0.29
175 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (174 bp):
GAAGATTTTCTAAGAATTAATACATTTGCACAATATAGCCATATTCGCCCCACCCTAGAGCCAGA
ACCCCTGATCCAGGGGCCATGAATTTCACAATCTAGATAGAGGGCTTCATGGACATAATTAACAT
GCAACCAGTTTTTAACAAATATATACATGTATAGGAGAAAAAAA
Found at i:452014 original size:72 final size:72
Alignment explanation
Indices: 451931--452143 Score: 305
Period size: 72 Copynumber: 3.0 Consensus size: 72
451921 ATAATAATAA
*
451931 TAATAACAATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGG
1 TAATAATAATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGG
451996 AAGACCC
66 AAGACCC
* * * *
452003 TAATAATAATAATAGAATTGAAAAAGAAACCGA-AGAATAATAGAAGGGTCTTCCGCTGAAGACG
1 TAATAATAATAAGAAAAGTGAAAAAGAAA-CAATAGAATAATAGAAGGGTCTTCCGCTGAAGACG
452067 GAAGACCC
65 GAAGACCC
*
452075 ------TAATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGTAGGGTCTTCCGCTGAAGACGG
1 TAATAATAATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGG
*
452134 GAGACCC
66 AAGACCC
452141 TAA
1 TAA
452144 CGAAACGTAG
Statistics
Matches: 125, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
65 2 0.02
66 57 0.46
72 64 0.51
73 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.17
Consensus pattern (72 bp):
TAATAATAATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGG
AAGACCC
Found at i:452117 original size:66 final size:66
Alignment explanation
Indices: 451938--452143 Score: 306
Period size: 66 Copynumber: 3.0 Consensus size: 66
451928 TAATAATAAC
451938 AATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGGAAGACCC
1 AATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGGAAGACCC
452003 T
66 T
* *
452004 AATAATAATAATAGAATTGAAAAAGAAACCGA-AGAATAATAGAAGGGTCTTCCGCTGAAGACGG
1 AATAA-GA-AA-AG---TGAAAAAGAAA-CAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGG
452068 AAGACCCT
59 AAGACCCT
* *
452076 AATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGTAGGGTCTTCCGCTGAAGACGGGAGACCC
1 AATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGGAAGACCC
452141 T
66 T
452142 AA
1 AA
452144 CGAAACGTAG
Statistics
Matches: 126, Mismatches: 6, Indels: 16
0.85 0.04 0.11
Matches are distributed among these distances:
65 2 0.02
66 56 0.44
67 1 0.01
68 2 0.02
69 4 0.03
70 2 0.02
71 1 0.01
72 56 0.44
73 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.17
Consensus pattern (66 bp):
AATAAGAAAAGTGAAAAAGAAACAATAGAATAATAGAAGGGTCTTCCGCTGAAGACGGAAGACCC
T
Found at i:452812 original size:10 final size:10
Alignment explanation
Indices: 452797--452822 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
452787 ATTTGATCAC
452797 ATAATACAAT
1 ATAATACAAT
452807 ATAATACAAT
1 ATAATACAAT
452817 ATAATA
1 ATAATA
452823 TTGTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAATACAAT
Found at i:453196 original size:98 final size:97
Alignment explanation
Indices: 453056--453276 Score: 268
Period size: 98 Copynumber: 2.3 Consensus size: 97
453046 ATGCATATTG
* * * * *
453056 TATCATATGATACA-ATAATAT-ATATTACAATATCATAAAATACAATTTCATGTTATATGATAA
1 TATCGTATGATACATATTATATAATATTAAAATATCATAAAATACAATTTCATGTGATATAATAA
*
453119 TATATCATAAAAACCAATATCATA-TCATACAA
66 TATATCACAAAAACCAATATCATAGT-ATACAA
* *
453151 TATCGTATGATACGATATTATATAATATTAAAATATCATATAATACAATTTCATGTGATATAATT
1 TATCGTATGATAC-ATATTATATAATATTAAAATATCATAAAATACAATTTCATGTGATATAATA
* * * *
453216 CTATATTACGAAAACCAATATCATAGTTTACAA
65 ATATATCACAAAAACCAATATCATAGTATACAA
* *
453249 TATTGTATGATACAATATTATAGAATAT
1 TATCGTATGATAC-ATATTATATAATAT
453277 ACAATATTGT
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
95 12 0.11
96 1 0.01
97 6 0.06
98 87 0.81
99 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (97 bp):
TATCGTATGATACATATTATATAATATTAAAATATCATAAAATACAATTTCATGTGATATAATAA
TATATCACAAAAACCAATATCATAGTATACAA
Found at i:453359 original size:16 final size:18
Alignment explanation
Indices: 453338--453381 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
453328 TTGTATCATG
453338 TCATAAAATAATA-AAT-
1 TCATAAAATAATATAATA
*
453354 TCATAAAACAATATAATA
1 TCATAAAATAATATAATA
*
453372 TTATAAAATA
1 TCATAAAATA
453382 TTGTATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.52
17 3 0.13
18 8 0.35
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (18 bp):
TCATAAAATAATATAATA
Found at i:453532 original size:20 final size:20
Alignment explanation
Indices: 453509--453561 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
453499 ATATGATATC
453509 ATATTGTATCATATCAAACA
1 ATATTGTATCATATCAAACA
* *
453529 ATATTGTTTCATATCATACA
1 ATATTGTATCATATCAAACA
* *
453549 ATACTATATCATA
1 ATATTGTATCATA
453562 GGAATCATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (20 bp):
ATATTGTATCATATCAAACA
Found at i:454526 original size:19 final size:19
Alignment explanation
Indices: 454499--454535 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
454489 GAGGGCACCT
*
454499 GCTCAAAAAACTTTAACCA
1 GCTCAAAAAACCTTAACCA
*
454518 GCTCTAAAAACCTTAACC
1 GCTCAAAAAACCTTAACC
454536 TCCTCCACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCAAAAAACCTTAACCA
Found at i:454548 original size:177 final size:177
Alignment explanation
Indices: 454180--454616 Score: 531
Period size: 177 Copynumber: 2.4 Consensus size: 177
454170 CTTAACTTTA
* * * * *
454180 TCCAGCATCCGAAACCTATGGCTCAGACTCAGCATACTGATGCACTGTCAGGTGCATCAGTATCA
1 TCCACCATCCGAAACCTATGGCTCCGATTCAGCAT--TCAAGC-CTGTCAGGTGCATCAGTATCA
* * * * * * *
454245 TAAGAC-CCCATCCATGGAAGTCTGGTGAAGGAAGGACAAGTAATAACTAAGATATCATCATCAG
63 TAAGACGACCATCCACGCAAGTCTGATGAAGGAAGAACAAGGAATAACTAAGATATAATCATCAG
* *
454309 AGGGCACCTGTTTCAAAAACTTTATTTAACCAGCTCTTAAAACCTTAACCTCC
128 AGGGCACCTGTCTCAAAAAC--T-TTTAACCAGCTCTAAAAACCTTAACCTCC
454362 TCCACCATCCGAAACCTATGGCTCCGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAA
1 TCCACCATCCGAAACCTATGGCTCCGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAA
* ** * * * *
454427 GACGAACCATCCACGCAAGTTTGATGAAGTTAGAACCAGGAGTAGCTAAGATATAATCATTAGAG
66 GACG-ACCATCCACGCAAGTCTGATGAAGGAAGAACAAGGAATAACTAAGATATAATCATCAGAG
454492 GGCACCTG-CTCAAAAAAC-TTTAACCAGCTCTAAAAACCTTAACCTCC
130 GGCACCTGTCTC-AAAAACTTTTAACCAGCTCTAAAAACCTTAACCTCC
* * * *
454539 TCCACCATCCAAAACATATGGC-CCAAATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATA
1 TCCACCATCCGAAACCTATGGCTCC-GATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATA
454603 AGACGCACCATCCA
65 AGACG-ACCATCCA
454617 TACAAGTTAA
Statistics
Matches: 225, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
176 2 0.01
177 98 0.44
179 27 0.12
180 6 0.03
181 60 0.27
182 32 0.14
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (177 bp):
TCCACCATCCGAAACCTATGGCTCCGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAA
GACGACCATCCACGCAAGTCTGATGAAGGAAGAACAAGGAATAACTAAGATATAATCATCAGAGG
GCACCTGTCTCAAAAACTTTTAACCAGCTCTAAAAACCTTAACCTCC
Found at i:454787 original size:155 final size:156
Alignment explanation
Indices: 454474--454779 Score: 497
Period size: 155 Copynumber: 2.0 Consensus size: 156
454464 AGGAGTAGCT
* *
454474 AAGATATAATCATTAGAGGGCACCTGCTCAAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
1 AAGATATAATCATCAGAGGGCACCTGCACAAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
454539 TCCACCATCCAAAACATATGGCCCAAATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAA
66 TCCACCATCCAAAACATATGGCCCAAATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAA
454604 GACGCACCATCCATACAAGTTAAGTG
131 GACGCACCATCCATACAAGTTAAGTG
* *
454630 AAGATATAATCATCAGAGGGCACCTGCAC-CAAAACTTTAACCAGCTCTAAAAACCTTAACCTCT
1 AAGATATAATCATCAGAGGGCACCTGCACAAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
* ** * * * *
454694 TCCAGCATCCGCAACTTATTGCTCAGATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAA
66 TCCACCATCCAAAACATATGGCCCAAATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAA
*
454759 GACGCATCATCCATACAAGTT
131 GACGCACCATCCATACAAGTT
454780 TGGTGAAGTT
Statistics
Matches: 138, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
155 111 0.80
156 27 0.20
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (156 bp):
AAGATATAATCATCAGAGGGCACCTGCACAAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
TCCACCATCCAAAACATATGGCCCAAATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAA
GACGCACCATCCATACAAGTTAAGTG
Found at i:454851 original size:19 final size:19
Alignment explanation
Indices: 454827--454868 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
454817 ATCAATAGGC
*
454827 ACCTGCAACAAAAACTTTA
1 ACCTGCAACAAAAACCTTA
**
454846 ACCTGCTCCAAAAACCTTA
1 ACCTGCAACAAAAACCTTA
454865 ACCT
1 ACCT
454869 CTCCCAGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.21
Consensus pattern (19 bp):
ACCTGCAACAAAAACCTTA
Found at i:454872 original size:18 final size:19
Alignment explanation
Indices: 454835--454872 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
454825 GCACCTGCAA
*
454835 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTGCTC
454854 CAAAAACCTTAACCT-CTC
1 CAAAAACCTTAACCTGCTC
454872 C
1 C
454873 CAGCCTCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.24
Consensus pattern (19 bp):
CAAAAACCTTAACCTGCTC
Found at i:454947 original size:332 final size:331
Alignment explanation
Indices: 454333--454956 Score: 844
Period size: 332 Copynumber: 1.9 Consensus size: 331
454323 AAAAACTTTA
* *
454333 TTTAACCAGCTCTTAAAACCTTAACCTCCTCCACCATCCGAAACCTATGGCTCCGATTCAGCATT
1 TTTAACCAGCTCTAAAAACCTTAACCTCCTCCACCATCCGAAACCTATGGCTCAGATTCAGCATT
*
454398 CAAGCCTGTCAGGTGCATCAGTATCATAAGACGAACCATCCACGCAAGTTTGATGAAGTTAGAAC
66 CAAGCCTGTCAGGTGCATCAGTATCATAAGACGAACCATCCACACAAGTTTGATGAAGTTAGAAC
* * * * *
454463 CAGGAGTAGCTAAGATATAATCATTAGAGGGCACCTGCTCAAAAAACTTTAACCAGCTCTAAAAA
131 CAGGAGTAACTAAGATAT-ATCATCAGAAGGCACCTGCACAAAAAACTTTAACCAGCTCCAAAAA
* * *
454528 CCTTAACCTCCTCCACCATCCAAAACATATGGCCCAAATTCAGCATTCAAGCTTGTCAGGTGCAT
195 CCTTAACCTCCTCCACCATCCAAAACATATAGCCCAAATTCAGCACTCAAGCCTGTCAGGTGCAT
*
454593 CAGTATCATAAGACGCACCATCCATACAAGTTAAGTGAAGATATAATCATCAGAGGGCACCTGCA
260 CAGTATCATAAGACACACCATCCATACAAGTTAAGTGAAGATATAATCATCAGAGGGCACCTGCA
454658 CCAAAAC
325 CCAAAAC
* * * * *
454665 TTTAACCAGCTCTAAAAACCTTAACCTCTTCCAGCATCCGCAACTTATTGCTCAGATTCAGCATT
1 TTTAACCAGCTCTAAAAACCTTAACCTCCTCCACCATCCGAAACCTATGGCTCAGATTCAGCATT
* * * * * *
454730 CAAGCTTGTCAGGTGCATCAGTATCATAAGACGCATCATCCATACAAGTTTGGTGAAGTTAGGAC
66 CAAGCCTGTCAGGTGCATCAGTATCATAAGACGAACCATCCACACAAGTTTGATGAAGTTAGAAC
* * *
454795 CAGTAGTAACTTAGATAT-TGCTATCA-ATAGGCACCTGCA-ACAAAAACTTTAACCTGCTCCAA
131 CAGGAGTAACTAAGATATAT-C-ATCAGA-AGGCACCTGCACA-AAAAACTTTAACCAGCTCCAA
* * * * *
454857 AAACCTTAACCT-CTCCCAGCC-TCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGG
192 AAACCTTAACCTCCT-CCA-CCATCCAAAACATATAGCCCAAATTCAGCACTCAAGCCTGTCAGG
* * *
454920 TTCATCAGTATCATAAGACATACCATCCATGCAAGTT
255 TGCATCAGTATCATAAGACACACCATCCATACAAGTT
454957 GGTGAAGTAA
Statistics
Matches: 252, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
330 1 0.00
331 5 0.02
332 244 0.97
333 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (331 bp):
TTTAACCAGCTCTAAAAACCTTAACCTCCTCCACCATCCGAAACCTATGGCTCAGATTCAGCATT
CAAGCCTGTCAGGTGCATCAGTATCATAAGACGAACCATCCACACAAGTTTGATGAAGTTAGAAC
CAGGAGTAACTAAGATATATCATCAGAAGGCACCTGCACAAAAAACTTTAACCAGCTCCAAAAAC
CTTAACCTCCTCCACCATCCAAAACATATAGCCCAAATTCAGCACTCAAGCCTGTCAGGTGCATC
AGTATCATAAGACACACCATCCATACAAGTTAAGTGAAGATATAATCATCAGAGGGCACCTGCAC
CAAAAC
Found at i:455006 original size:176 final size:176
Alignment explanation
Indices: 454641--455055 Score: 550
Period size: 177 Copynumber: 2.4 Consensus size: 176
454631 AGATATAATC
* * * * * *
454641 ATCAGAGGGCACCTGCACCAAAACTTTAACCAGCTCTAAAAACCTTAACCTCTTCCAGCATCCGC
1 ATCAAAGGGCACCTGCACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCCGA
* * * * * *
454706 AACTTATTGCTCAGATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCATCATCC
66 AACCTATAGCTCAGATTCAGCACTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCC
* * *
454771 ATACAAGTTTGGTGAAGTTAGGACCAGTAGTAACTTAGATATTGCT
131 ATACAAGTTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCA
*
454817 ATCAATA-GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCCTCC
1 ATCAA-AGGGCACCTGC-ACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCC
* * *
454881 GAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTTCATCAGTATCATAAGACATACCAT
64 GAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCAT
*
454946 CCATGCAAG-TTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCA
129 CCATACAAGTTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCA
* * *
454993 ATCAAAGGGCACCTGC-CATACAAACTTTAACCTGGTCCAACAACCTTAATCTC-CTCCAGCATC
1 ATCAAAGGGCACCTGCACA-A-AAACTTTAACCTGCTCCAAAAACCTTAACCTCTC-CCAGCATC
455056 AGGAATTTAG
Statistics
Matches: 209, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
174 2 0.01
175 3 0.01
176 98 0.47
177 106 0.51
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (176 bp):
ATCAAAGGGCACCTGCACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCCGA
AACCTATAGCTCAGATTCAGCACTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCC
ATACAAGTTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCA
Found at i:455076 original size:176 final size:176
Alignment explanation
Indices: 454648--455080 Score: 507
Period size: 176 Copynumber: 2.5 Consensus size: 176
454638 ATCATCAGAG
* * * * * *
454648 GGCACCTGC-ACCAAAACTTTAACCAGCTCTAAAAACCTTAACCTCTTCCAGCATCCGCAACTTA
1 GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCAGAAAC-TA
* * * * * *
454712 TTGCTCAGATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCATCATCCATACAA
65 TAGCCCAGATTCAGCACTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATACAA
* * *
454777 GTTTGGTGAAGTTAGGACCAGTAGTAACTTAGATATTGCTATCAATA
130 GTTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAATA
* *
454824 GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCCTCCGAAACCTA
1 GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCAGAAA-CTA
* * * * *
454889 TAGCTCAGATTCAGCACTCAAGCCTGTCTGGTTCATCAGTATCATAAGACATACCATCCATGCAA
65 TAGCCCAGATTCAGCACTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATACAA
454954 G-TTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAA-A
130 GTTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAATA
* * * * * * *
454999 GGGCACCTGCCATACAAACTTTAACCTGGTCCAACAACCTTAATCTC-CTCCAGCATCAGGAA-T
1 -GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTC-CCAGCATCAGAAACT
*
455062 TTAGGACCCAGATTCAGCA
64 ATA-G-CCCAGATTCAGCA
455081 TCCAAGTCTT
Statistics
Matches: 222, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
174 3 0.01
175 3 0.01
176 111 0.50
177 104 0.47
178 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (176 bp):
GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCAGAAACTAT
AGCCCAGATTCAGCACTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATACAAG
TTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAATA
Found at i:455125 original size:176 final size:173
Alignment explanation
Indices: 454648--455140 Score: 467
Period size: 176 Copynumber: 2.8 Consensus size: 173
454638 ATCATCAGAG
* * * * * *
454648 GGCACCTGC-ACCAAAACTTTAACCAGCTCTAAAAACCTTAACCTCTTCCAGCATCCGCAACTTA
1 GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCAGAAAC-TA
* * * * * * * * *
454712 TTGCTCAGATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCATCATCCATACAA
65 TAGCCCAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATC---AGAAGCATCATCCATGCAA
* * *
454777 GTTTGGTGAAGTTAGGACCAGTAGTAACTTAGATATTGCTATCAATA
127 GTTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAATA
* *
454824 GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCCTCCGAAACCTA
1 GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCAGAAA-CTA
* ** * * *
454889 TAGCTCAGATTCAGCACTCAAGCCTGTCTGGTTCATCAGTATCATAAGACATACCATCCATGCAA
65 TAGCCCAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCAGAAG-CAT--CATCCATGCAA
454954 G-TTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAA-A
127 GTTTGGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAATA
* * * * * * *
454999 GGGCACCTGCCATACAAACTTTAACCTGGTCCAACAACCTTAATCTC-CTCCAGCATCAGGAA-T
1 -GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTC-CCAGCATCAGAAACT
* * * *
455062 TTAGGACCCAGATTCAGCA-TCCAAGTCTTTCAAGTCCATAAGTAGGTCCAGATGCATCATCCAT
64 ATA-G-CCCAGATTCAGCACT-CAAGCCTGTCAAGTCCATAAGTA--T-CAGAAGCATCATCCAT
455126 GCAAGTTTGGTGAAG
123 GCAAGTTTGGTGAAG
455141 ACAGGACAAG
Statistics
Matches: 267, Mismatches: 36, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
174 6 0.02
175 7 0.03
176 140 0.52
177 105 0.39
178 5 0.02
179 4 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (173 bp):
GGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCTCCCAGCATCAGAAACTAT
AGCCCAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCAGAAGCATCATCCATGCAAGTTT
GGTGAAGTAAGGACCAGCAGTAACTTAGATATTGCAATCAATA
Found at i:458310 original size:21 final size:21
Alignment explanation
Indices: 458286--458335 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
458276 GATATACTAT
458286 GAGATTTGTATGGTATGCTAC
1 GAGATTTGTATGGTATGCTAC
*
458307 GAGATTTGTATGGTATGCTAT
1 GAGATTTGTATGGTATGCTAC
458328 GAGATTTG
1 GAGATTTG
458336 AACAAAAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.06, G:0.30, T:0.40
Consensus pattern (21 bp):
GAGATTTGTATGGTATGCTAC
Found at i:458496 original size:15 final size:15
Alignment explanation
Indices: 458476--458509 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
458466 ATTAATGTTG
458476 TATGCTATGCTATGA
1 TATGCTATGCTATGA
*
458491 TATGCTATGGTATGA
1 TATGCTATGCTATGA
458506 TATG
1 TATG
458510 ACGAATGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (15 bp):
TATGCTATGCTATGA
Found at i:458559 original size:21 final size:21
Alignment explanation
Indices: 458534--458588 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
458524 ATGAAAGTGT
458534 ATGCTATGGTATGAGATTTCA
1 ATGCTATGGTATGAGATTTCA
458555 ATGCTATGGTATGAGATTTCA
1 ATGCTATGGTATGAGATTTCA
*
458576 ATGCTATGCTATG
1 ATGCTATGGTATG
458589 CTATGGTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (21 bp):
ATGCTATGGTATGAGATTTCA
Found at i:461348 original size:179 final size:179
Alignment explanation
Indices: 461039--461650 Score: 783
Period size: 179 Copynumber: 3.4 Consensus size: 179
461029 GTGAAATGGA
* * * * *
461039 GTACCCCATATGCAATATTTTGCTAAAAAAGACTTAGTTCAAAAGCTGGTATTTTTTTCATAAAA
1 GTACCCTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAAT
* * * * *
461104 AATCAGAAATAAAAATCCTAG-AAGTATGCACACCTCCGATACATGTACAATTAATCTGCAAAAG
66 TATCAGAAATCAAAATCCTAGCAA-TATGCACACCTCTGATATATGTATAATTAATCTGCAAAAG
* * ** *
461168 AACAACTTTTTATCTAT-AAAACTGTAGGAATAATTATACGTACAATGAGG
130 AACAAATTTCTATCT-TGAAAACTGTAGGAGGAATTATCCGTACAATGAGG
* * * * * * *
461218 TTACCTTATATGCAATATTTTGCTAAAAATTGATTAACTTCAAACGCTGGTA-TTTTTTCACAAA
1 GTACCCTATATGCAATATTTTGCCAAAAA-TGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* * * *
461282 TCATCAGTAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTATAATTGATCTGGAAAAG
65 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTATAATTAATCTGCAAAAG
* * *
461347 AA-AAATTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCATACAATGAGG
130 AACAAATTT-CTATCTTGAAAACTGTAGGAGGAATTATCCGTACAATGAGG
461397 GTACCCTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCATAAAT
1 GTACCCTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAAT
* *
461461 TATC-GAAAATCAAAATCCTAGCAATATGCATACCTCTGATATA--T-TAATTAATCTGCAAAAA
66 TATCAG-AAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTATAATTAATCTGCAAAAG
* *
461522 AACAAATTCCTATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGG
130 AACAAATTTCTATCTTGAAAACTGTAGGAGGAATTATCCGTACAATGAGG
* *
461572 GTACCCTATATGCAATATTTTGCCAAAAAATGACGAAGTTCAAAAGCTGGTATTTTTTTCATTAA
1 GTACCCTATATGCAATATTTTGCC-AAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
*
461637 TTATCAGTAATCAA
65 TTATCAGAAATCAA
461651 TTTTAACTTA
Statistics
Matches: 378, Mismatches: 46, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
175 78 0.21
176 32 0.08
177 23 0.06
178 76 0.20
179 150 0.40
180 19 0.05
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (179 bp):
GTACCCTATATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAAT
TATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTATAATTAATCTGCAAAAGA
ACAAATTTCTATCTTGAAAACTGTAGGAGGAATTATCCGTACAATGAGG
Found at i:464442 original size:19 final size:19
Alignment explanation
Indices: 464405--464443 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
464395 CACCTACTTT
* *
464405 AAAAACTTTAACCAGCTCC
1 AAAAACCTTAACCACCTCC
*
464424 AAAAACCTTAACCTCCTCC
1 AAAAACCTTAACCACCTCC
464443 A
1 A
464444 GCATCCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.36, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAAACCTTAACCACCTCC
Found at i:467085 original size:146 final size:144
Alignment explanation
Indices: 466774--467172 Score: 505
Period size: 146 Copynumber: 2.7 Consensus size: 144
466764 CTTCCTCTAT
* * ** * * *
466774 TGACCTTGGGTCAAGGTCATGATACACCCTCAGGTTGTAAGCAATC-TTGATGTGAATTCAGAAC
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGGAATCTTTG-TGTGAAGTAAGAAC
* * * * * *
466838 TTCCAAGGTTTCTT-TATATGAAAGATGTGGACCGGACACGAATTTTGCACTTTTTTGTCAGTGA
65 TTCCAATGTTT-TTCCATA-AAAAGATGTGGACCGGACACAAATTTTGAACTTTTTTGCCAGTGA
*
466902 CCTTGACCTTGTCCAAA
128 CCTTGACCTTGCCCAAA
* * *
466919 TGACCTTAGGTCAAGGTCATGACACACCCTTAGGTCATAAGGAATCTTTGTTTGAAGTAAAAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGGAATCTTTGTGTGAAGTAAGAACT
* * *
466984 TCCAATGTTTTTCCATTAAAAACATATGGACCGGACTCAAATTTTGAACTTTTTTTGCCAGTGAC
66 TCCAATGTTTTTCCA-TAAAAAGATGTGGACCGGACACAAATTTTGAAC-TTTTTTGCCAGTGAC
*
467049 CTTGCCCTTGCCCAAA
129 CTTGACCTTGCCCAAA
* *
467065 TGACCTTGGGTCAAGGTCATGACACATCCTTAGGTCAAAAGGAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGGAATCTTTGTGTGAAGTAAGAACT
* *
467130 TCCAATGTTTCTCCATAAGAAAGATGTGGACCGGACACGAATT
66 TCCAATGTTTTTCCATAA-AAAGATGTGGACCGGACACAAATT
467173 GAACAGACAG
Statistics
Matches: 218, Mismatches: 31, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
144 2 0.01
145 89 0.41
146 127 0.58
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (144 bp):
TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGGAATCTTTGTGTGAAGTAAGAACT
TCCAATGTTTTTCCATAAAAAGATGTGGACCGGACACAAATTTTGAACTTTTTTGCCAGTGACCT
TGACCTTGCCCAAA
Found at i:467191 original size:8 final size:8
Alignment explanation
Indices: 467178--467213 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
467168 GAATTGAACA
467178 GACAGACG
1 GACAGACG
467186 GACAGACG
1 GACAGACG
*
467194 GACGGACG
1 GACAGACG
*
467202 GACGGACG
1 GACAGACG
467210 GACA
1 GACA
467214 AGGTGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.42, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:467192 original size:12 final size:12
Alignment explanation
Indices: 467175--467213 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
467165 CACGAATTGA
*
467175 ACAGACAGACGG
1 ACAGACGGACGG
467187 ACAGACGGACGG
1 ACAGACGGACGG
*
467199 ACGGACGGACGG
1 ACAGACGGACGG
467211 ACA
1 ACA
467214 AGGTGATTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:467197 original size:4 final size:4
Alignment explanation
Indices: 467182--467212 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
467172 TGAACAGACA
*
467182 GACG GACA GACG GACG GACG GACG GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GAC
467213 AAGGTGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.26, G:0.45, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:475910 original size:2 final size:2
Alignment explanation
Indices: 475903--475971 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
475893 ATATTTATTG
* *
475903 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CG
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
475945 CT CT CT CT TT CT CT TT TT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
475972 GAAAAATATA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.45, G:0.01, T:0.54
Consensus pattern (2 bp):
CT
Found at i:476447 original size:142 final size:142
Alignment explanation
Indices: 476189--476474 Score: 428
Period size: 142 Copynumber: 2.0 Consensus size: 142
476179 CAGGATGTTC
* * **
476189 CACGTGATAAAGGTCATAAACTGTGCGTAATTTTGATGTAAACTAAGAACATTTGAGTGCGTTTT
1 CACGTGATAAAGGGCATAAACTGTGCATAATTTCAATGTAAACTAAGAACATTTGAGTGCGTTTT
* * ** *
476254 TATATATGTCATGTATCTGAAGAGAGCCGTTGGATTTCCAGGGAAAATACATTTACGTGTACTTT
66 TATATATGTCAGGTATCTGAAAAGAGCCGCGGGATTTCCAGGGAAAATACATCTACGTGTACTTT
476319 ATATTTAGCTTT
131 ATATTTAGCTTT
* * *
476331 CACGTGATATAGGGCATGAACTGTGCATAATTTCAATGTAATCTAAGAACATTTGAGTGCGTTTT
1 CACGTGATAAAGGGCATAAACTGTGCATAATTTCAATGTAAACTAAGAACATTTGAGTGCGTTTT
* * *
476396 TATATATGTCAGGTATCTTAAAAGAGCCGCGGGATTTCCAGGGAAATTACATCTACGTGTATTTT
66 TATATATGTCAGGTATCTGAAAAGAGCCGCGGGATTTCCAGGGAAAATACATCTACGTGTACTTT
*
476461 ATATTTAGTTTT
131 ATATTTAGCTTT
476473 CA
1 CA
476475 TCTTATTACA
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
142 128 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (142 bp):
CACGTGATAAAGGGCATAAACTGTGCATAATTTCAATGTAAACTAAGAACATTTGAGTGCGTTTT
TATATATGTCAGGTATCTGAAAAGAGCCGCGGGATTTCCAGGGAAAATACATCTACGTGTACTTT
ATATTTAGCTTT
Found at i:480548 original size:4 final size:4
Alignment explanation
Indices: 480539--480660 Score: 228
Period size: 4 Copynumber: 30.8 Consensus size: 4
480529 GCGTATGTTT
*
480539 TCTA TCTA TCTA TCCA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
480587 TCTA TC-A TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
480634 TCTA TCTA TCTA TCTA TCTA TCTA TCT
1 TCTA TCTA TCTA TCTA TCTA TCTA TCT
480661 NNNNNNNNNN
Statistics
Matches: 115, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
3 3 0.03
4 112 0.97
ACGTcount: A:0.25, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
TCTA
Found at i:481898 original size:14 final size:14
Alignment explanation
Indices: 481879--481911 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
481869 GGTAAAGTTA
481879 GCTACTAGTAACTG
1 GCTACTAGTAACTG
481893 GCTACTAGTAACTG
1 GCTACTAGTAACTG
481907 GCTAC
1 GCTAC
481912 GAGAAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (14 bp):
GCTACTAGTAACTG
Found at i:481945 original size:37 final size:37
Alignment explanation
Indices: 481893--481985 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
481883 CTAGTAACTG
481893 GCTACTAGTAACTGGCTACGAGAAGT-AAGAAAAGCTA
1 GCTACTAGTAACTGGCTACGAG-AGTAAAGAAAAGCTA
* * * * *
481930 GCTACTAGTAGCTGGCTACGAGATTAAATAAAAGTTG
1 GCTACTAGTAACTGGCTACGAGAGTAAAGAAAAGCTA
481967 GCTACTAGTAACTGGCTAC
1 GCTACTAGTAACTGGCTAC
481986 TAGTAACTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
36 2 0.04
37 47 0.96
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (37 bp):
GCTACTAGTAACTGGCTACGAGAGTAAAGAAAAGCTA
Found at i:481984 original size:14 final size:14
Alignment explanation
Indices: 481965--481999 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
481955 AAATAAAAGT
481965 TGGCTACTAGTAAC
1 TGGCTACTAGTAAC
481979 TGGCTACTAGTAAC
1 TGGCTACTAGTAAC
481993 TGGCTAC
1 TGGCTAC
482000 GAGAAGTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (14 bp):
TGGCTACTAGTAAC
Found at i:481985 original size:51 final size:51
Alignment explanation
Indices: 481930--482036 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 51
481920 AGAAAAGCTA
* * * * *
481930 GCTACTAGTAGCTGGCTACGAG-ATTAAATAAAAGTTGGCTACTAGTAACTG
1 GCTACTAGTAACTGGCTACGAGAAGT-AAGAAAAGCTAGCTACTAGTAACTG
481981 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTG
1 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTG
482032 GCTAC
1 GCTAC
482037 GAGATGAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
51 48 0.96
52 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (51 bp):
GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTG
Found at i:482021 original size:88 final size:88
Alignment explanation
Indices: 481872--482041 Score: 322
Period size: 88 Copynumber: 1.9 Consensus size: 88
481862 TCAGATAGGT
481872 AAAGTTAGCTACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTA
1 AAAGTTAGCTACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTA
*
481937 GTAGCTGGCTACGAGATTAAATA
66 GTAACTGGCTACGAGATTAAATA
*
481960 AAAGTTGGCTACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTA
1 AAAGTTAGCTACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTA
482025 GTAACTGGCTACGAGAT
66 GTAACTGGCTACGAGAT
482042 GAAAGAAACT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (88 bp):
AAAGTTAGCTACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTA
GTAACTGGCTACGAGATTAAATA
Found at i:505630 original size:190 final size:189
Alignment explanation
Indices: 505307--505685 Score: 749
Period size: 190 Copynumber: 2.0 Consensus size: 189
505297 CTCTTGGAGT
505307 GGATTTTGAGTACAAACGTGAATTGATAATGGGCGATATAATGCAAATAGCTCTTATTTCTTCGT
1 GGATTTTGAGTACAAACGTGAATTGATAATGGGCGATATAATGCAAATAGCTCTTATTTCTTCGT
505372 CATTGAAACATACTGGTCCTTTGTCTCTATCCTACGATATCATGCATTGCCAGTCTGGCAGGCAT
66 CATTGAAACATACTGGTCCTTTGTCTCTATCCTACGATATCATGCATTGCCAGTCTGGCAGGCAT
505437 GCCAGTCTATCATTGACAACGTGTTGAATCAAAGTACTGAGATGAGTTGATAATCAGGA
131 GCCAGTCTATCATTGACAACGTGTTGAATCAAAGTACTGAGATGAGTTGATAATCAGGA
505496 NGGATTTTGAGTACAAACGTGAATTGATAATGGGCGATATAATGCAAATAGCTCTTATTTCTTCG
1 -GGATTTTGAGTACAAACGTGAATTGATAATGGGCGATATAATGCAAATAGCTCTTATTTCTTCG
505561 TCATTGAAACATACTGGTCCTTTGTCTCTATCCTACGATATCATGCATTGCCAGTCTGGCAGGCA
65 TCATTGAAACATACTGGTCCTTTGTCTCTATCCTACGATATCATGCATTGCCAGTCTGGCAGGCA
505626 TGCCAGTCTATCATTGACAACGTGTTGAATCAAAGTACTGAGATGAGTTGATAATCAGGA
130 TGCCAGTCTATCATTGACAACGTGTTGAATCAAAGTACTGAGATGAGTTGATAATCAGGA
505686 ATCAGATATT
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 189 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (189 bp):
GGATTTTGAGTACAAACGTGAATTGATAATGGGCGATATAATGCAAATAGCTCTTATTTCTTCGT
CATTGAAACATACTGGTCCTTTGTCTCTATCCTACGATATCATGCATTGCCAGTCTGGCAGGCAT
GCCAGTCTATCATTGACAACGTGTTGAATCAAAGTACTGAGATGAGTTGATAATCAGGA
Found at i:506779 original size:17 final size:16
Alignment explanation
Indices: 506757--506791 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
506747 AAGAGGATCA
506757 TAATAGTTACACATTAG
1 TAATAGTTACACA-TAG
*
506774 TAATAGTTTCACATAG
1 TAATAGTTACACATAG
506790 TA
1 TA
506792 CCCTAGGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (16 bp):
TAATAGTTACACATAG
Found at i:509804 original size:4 final size:4
Alignment explanation
Indices: 509795--509842 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
509785 AGTTGCGTCT
* * * * *
509795 ACAG ACAG ACGG ACAG ACGG ACAG ACGG ACGG ACAG ACAG ACGG ACAG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
509843 GGTGAAACCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:509811 original size:8 final size:8
Alignment explanation
Indices: 509798--509842 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
509788 TGCGTCTACA
509798 GACAGACG
1 GACAGACG
509806 GACAGACG
1 GACAGACG
509814 GACAGACG
1 GACAGACG
* *
509822 GACGGACA
1 GACAGACG
509830 GACAGACG
1 GACAGACG
509838 GACAG
1 GACAG
509843 GGTGAAACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.38, C:0.24, G:0.38, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:509812 original size:12 final size:12
Alignment explanation
Indices: 509795--509842 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
509785 AGTTGCGTCT
* *
509795 ACAGACAGACGG
1 ACAGACGGACAG
509807 ACAGACGGACAG
1 ACAGACGGACAG
*
509819 ACGGACGGACAG
1 ACAGACGGACAG
509831 ACAGACGGACAG
1 ACAGACGGACAG
509843 GGTGAAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:512564 original size:14 final size:14
Alignment explanation
Indices: 512545--512574 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
512535 CTTAATTAGT
512545 CATGGACTCATTGA
1 CATGGACTCATTGA
512559 CATGGACTCATTGA
1 CATGGACTCATTGA
512573 CA
1 CA
512575 ATTAAAAAAA
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:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (14 bp):
CATGGACTCATTGA
Found at i:513899 original size:13 final size:13
Alignment explanation
Indices: 513881--513905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
513871 CCCCCCCCCT
513881 AAACAAAAAACAA
1 AAACAAAAAACAA
513894 AAACAAAAAACA
1 AAACAAAAAACA
513906 TAGGTAATCA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAAAAAACAA
Found at i:514008 original size:18 final size:16
Alignment explanation
Indices: 513987--514043 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 16
513977 TCCATTATGA
*
513987 AAAATCGTAATATTACTT
1 AAAAT-GTAATATTAC-G
514005 AAAATGATAATATTACG
1 AAAATG-TAATATTACG
514022 AAAAGTTGTAATATTAC-
1 AAAA--TGTAATATTACG
514039 AAAAT
1 AAAAT
514044 AAAATAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
17 9 0.26
18 23 0.66
19 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAATGTAATATTACG
Found at i:519732 original size:4 final size:4
Alignment explanation
Indices: 519723--519770 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
519713 AGTTGCGTCT
* * * * *
519723 ACAG ACAG ACGG ACAG ACGG ACAG ACGG ACGG ACAG ACAG ACGG ACAG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
519771 GGTGAAACCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:519739 original size:8 final size:8
Alignment explanation
Indices: 519726--519770 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
519716 TGCGTCTACA
519726 GACAGACG
1 GACAGACG
519734 GACAGACG
1 GACAGACG
519742 GACAGACG
1 GACAGACG
* *
519750 GACGGACA
1 GACAGACG
519758 GACAGACG
1 GACAGACG
519766 GACAG
1 GACAG
519771 GGTGAAACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.38, C:0.24, G:0.38, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:519740 original size:12 final size:12
Alignment explanation
Indices: 519723--519770 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
519713 AGTTGCGTCT
* *
519723 ACAGACAGACGG
1 ACAGACGGACAG
519735 ACAGACGGACAG
1 ACAGACGGACAG
*
519747 ACGGACGGACAG
1 ACAGACGGACAG
519759 ACAGACGGACAG
1 ACAGACGGACAG
519771 GGTGAAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:529462 original size:19 final size:20
Alignment explanation
Indices: 529440--529479 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
529430 TTTTCCATAT
*
529440 ATAATTTAGTTTTT-TTTTA
1 ATAATATAGTTTTTCTTTTA
*
529459 ATAATATATTTTTTCTTTTA
1 ATAATATAGTTTTTCTTTTA
529479 A
1 A
529480 CGGATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (20 bp):
ATAATATAGTTTTTCTTTTA
Found at i:529833 original size:2 final size:2
Alignment explanation
Indices: 529828--529863 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
529818 TTTGTGTGTT
*
529828 AG AG AG AG AG AG AG AG AG AA 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
529864 TTTTATATGA
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:541571 original size:2 final size:2
Alignment explanation
Indices: 541566--541595 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
541556 ACTCTCTCGA
541566 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
541596 AACACATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:543046 original size:22 final size:22
Alignment explanation
Indices: 543020--543062 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
543010 GAGTTGCAAA
* *
543020 GGCGAAAGTGCGAGAGTGCGAC
1 GGCGAAAGAGCGAAAGTGCGAC
*
543042 GGCGAAGGAGCGAAAGTGCGA
1 GGCGAAAGAGCGAAAGTGCGA
543063 AGATGCGACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.47, T:0.07
Consensus pattern (22 bp):
GGCGAAAGAGCGAAAGTGCGAC
Found at i:543055 original size:30 final size:30
Alignment explanation
Indices: 543021--543078 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
543011 AGTTGCAAAG
543021 GCGAAAGTGCG-AGAGTGCGACGGCGAAGGA
1 GCGAAAGTGCGAAGA-TGCGACGGCGAAGGA
543051 GCGAAAGTGCGAAGATGCGACGGCGAAG
1 GCGAAAGTGCGAAGATGCGACGGCGAAG
543079 CGCGAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.31, C:0.17, G:0.45, T:0.07
Consensus pattern (30 bp):
GCGAAAGTGCGAAGATGCGACGGCGAAGGA
Found at i:543069 original size:8 final size:7
Alignment explanation
Indices: 543025--543113 Score: 51
Period size: 8 Copynumber: 12.4 Consensus size: 7
543015 GCAAAGGCGA
543025 AAGTGCG
1 AAGTGCG
543032 AGAGTGCG
1 A-AGTGCG
*
543040 ACG-GCG
1 AAGTGCG
*
543046 AAGGAGCG
1 AA-GTGCG
543054 AAAGTGCG
1 -AAGTGCG
543062 AAGATGCG
1 AAG-TGCG
*
543070 ACG-GCG
1 AAGTGCG
*
543076 AAGCGCG
1 AAGTGCG
543083 AAGATGCG
1 AAG-TGCG
*
543091 ATG-GCG
1 AAGTGCG
543097 AAAGTGCG
1 -AAGTGCG
543105 AAG-GCG
1 AAGTGCG
543111 AAG
1 AAG
543114 GAGCGATACT
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
6 18 0.28
7 17 0.26
8 28 0.43
9 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.44, T:0.08
Consensus pattern (7 bp):
AAGTGCG
Found at i:543084 original size:21 final size:22
Alignment explanation
Indices: 543051--543107 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
543041 CGGCGAAGGA
*
543051 GCGAAAGTGCGAAGATGCGACG
1 GCGAAAGCGCGAAGATGCGACG
*
543073 GCG-AAGCGCGAAGATGCGATG
1 GCGAAAGCGCGAAGATGCGACG
*
543094 GCGAAAGTGCGAAG
1 GCGAAAGCGCGAAG
543108 GCGAAGGAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.32, C:0.18, G:0.42, T:0.09
Consensus pattern (22 bp):
GCGAAAGCGCGAAGATGCGACG
Found at i:543097 original size:14 final size:15
Alignment explanation
Indices: 543073--543113 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
543063 AGATGCGACG
543073 GCGAAGCGCGAAGA-T
1 GCGAAG-GCGAAGAGT
*
543088 GCGATGGCGAA-AGT
1 GCGAAGGCGAAGAGT
543102 GCGAAGGCGAAG
1 GCGAAGGCGAAG
543114 GAGCGATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.05
14 16 0.73
15 5 0.23
ACGTcount: A:0.32, C:0.17, G:0.44, T:0.07
Consensus pattern (15 bp):
GCGAAGGCGAAGAGT
Found at i:543809 original size:22 final size:23
Alignment explanation
Indices: 543781--543833 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
543771 TTATAAAAAG
543781 GCGAAGGCGGA-AGCGCGAAGAT
1 GCGAAGGCGGAGAGCGCGAAGAT
* *
543803 GCGAAGGC-GAGAGTGCGAAGTT
1 GCGAAGGCGGAGAGCGCGAAGAT
*
543825 GCGATGGCG
1 GCGAAGGCG
543834 AAGGAGCGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.26, C:0.17, G:0.47, T:0.09
Consensus pattern (23 bp):
GCGAAGGCGGAGAGCGCGAAGAT
Found at i:543842 original size:22 final size:22
Alignment explanation
Indices: 543781--543842 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
543771 TTATAAAAAG
*
543781 GCGAAGGCG-GAAGCGCGAAGAT
1 GCGAAGGCGAG-AGAGCGAAGAT
* *
543803 GCGAAGGCGAGAGTGCGAAGTT
1 GCGAAGGCGAGAGAGCGAAGAT
*
543825 GCGATGGCGA-AGGAGCGA
1 GCGAAGGCGAGA-GAGCGA
543843 TAGTAGTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.47, T:0.08
Consensus pattern (22 bp):
GCGAAGGCGAGAGAGCGAAGAT
Found at i:545160 original size:14 final size:14
Alignment explanation
Indices: 545143--545190 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
545133 CATCTTCGCG
*
545143 CTTCGCCGTCGCAT
1 CTTCGCCGTCGCAC
*
545157 CTTCGCACTTTCGCAC
1 CTTCGC-C-GTCGCAC
*
545173 CTTTGCCGTCGCAC
1 CTTCGCCGTCGCAC
545187 CTTC
1 CTTC
545191 ACACTTTTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 15 0.56
15 2 0.07
16 10 0.37
ACGTcount: A:0.08, C:0.44, G:0.17, T:0.31
Consensus pattern (14 bp):
CTTCGCCGTCGCAC
Found at i:545217 original size:22 final size:22
Alignment explanation
Indices: 545157--545217 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
545147 GCCGTCGCAT
*
545157 CTTCGC-ACTTTCGCACCTTTGC
1 CTTCGCAAC-TTCGCACTTTTGC
* * *
545179 CGTCGCACCTTCACACTTTTGC
1 CTTCGCAACTTCGCACTTTTGC
545201 CTTCGCAACTTCGCACT
1 CTTCGCAACTTCGCACT
545218 CTCGCACCTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.13, C:0.41, G:0.13, T:0.33
Consensus pattern (22 bp):
CTTCGCAACTTCGCACTTTTGC
Found at i:546900 original size:34 final size:34
Alignment explanation
Indices: 546857--546924 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
546847 GAATCTTTAG
* *
546857 AAAAAAATAAGGAACTCTGTTCATATGCATAGAA
1 AAAAAAATAAAGAACTCTGTTAATATGCATAGAA
546891 AAAAAAATAAAGAACTCTGTTAATATGCATAGAA
1 AAAAAAATAAAGAACTCTGTTAATATGCATAGAA
546925 GTATCATTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.24
Consensus pattern (34 bp):
AAAAAAATAAAGAACTCTGTTAATATGCATAGAA
Found at i:549942 original size:21 final size:22
Alignment explanation
Indices: 549918--549974 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
549908 AGTAAAACGT
549918 ATGCAACGAATGCGAGAGTT-G
1 ATGCAACGAATGCGAGAGTTCG
*
549939 ATGCAACGTAA-GCGAGGGTTCG
1 ATGCAACG-AATGCGAGAGTTCG
*
549961 -TGCAACGTATGCGA
1 ATGCAACGAATGCGA
549975 AAGCTCGTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 27 0.87
22 3 0.10
ACGTcount: A:0.30, C:0.18, G:0.33, T:0.19
Consensus pattern (22 bp):
ATGCAACGAATGCGAGAGTTCG
Found at i:550246 original size:17 final size:17
Alignment explanation
Indices: 550224--550258 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
550214 ACCGTAATGT
550224 CTCGTGTATAATACGCA
1 CTCGTGTATAATACGCA
550241 CTCGTGTATAATACGCA
1 CTCGTGTATAATACGCA
550258 C
1 C
550259 CCCCAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (17 bp):
CTCGTGTATAATACGCA
Found at i:552548 original size:11 final size:11
Alignment explanation
Indices: 552514--552557 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
552504 TCCTTCGGGA
552514 TCTCACTGCG-
1 TCTCACTGCGC
552524 TCTCTA-TCGCGC
1 TCTC-ACT-GCGC
552536 TCTCACTGCGC
1 TCTCACTGCGC
552547 TCTCACTGCGC
1 TCTCACTGCGC
552558 ATCCACAGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.17
11 20 0.67
12 5 0.17
ACGTcount: A:0.09, C:0.43, G:0.18, T:0.30
Consensus pattern (11 bp):
TCTCACTGCGC
Found at i:558146 original size:1 final size:1
Alignment explanation
Indices: 558114--558139 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
558104 ATGAAGAATC
558114 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
558140 CAGGGGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:569808 original size:13 final size:13
Alignment explanation
Indices: 569790--569814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
569780 TTCTACGGGC
569790 TTAGTGGCTGCTG
1 TTAGTGGCTGCTG
569803 TTAGTGGCTGCT
1 TTAGTGGCTGCT
569815 AGCTTCAGCC
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:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (13 bp):
TTAGTGGCTGCTG
Found at i:577886 original size:141 final size:140
Alignment explanation
Indices: 577632--577912 Score: 553
Period size: 141 Copynumber: 2.0 Consensus size: 140
577622 AAATGAAGCT
577632 AAATCACAATTATCTTGTCAAATTATTAAATAAACTACGAGGCTTACAAACCTGTTATCTGCCGC
1 AAATCACAATTATCTTGTCAAATTATTAAATAAACTACGAGGCTTACAAACCTGTTATCTGCCGC
577697 TTGTCCTCCGATCCCTCAATTTCTACTATAAACTTAATGAAAACAGTTCATTGTACTCTTACATA
66 TTGTCCTCCGATCCCTCAATTTCTACTATAAACTTAATGAAAACAGTTCATTGTACTCTTACATA
577762 CCTGTTTACC
131 CCTGTTTACC
577772 NAAATCACAATTATCTTGTCAAATTATTAAATAAACTACGAGGCTTACAAACCTGTTATCTGCCG
1 -AAATCACAATTATCTTGTCAAATTATTAAATAAACTACGAGGCTTACAAACCTGTTATCTGCCG
577837 CTTGTCCTCCGATCCCTCAATTTCTACTATAAACTTAATGAAAACAGTTCATTGTACTCTTACAT
65 CTTGTCCTCCGATCCCTCAATTTCTACTATAAACTTAATGAAAACAGTTCATTGTACTCTTACAT
577902 ACCTGTTTACC
130 ACCTGTTTACC
577913 TCATAAGGAA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.34
Consensus pattern (140 bp):
AAATCACAATTATCTTGTCAAATTATTAAATAAACTACGAGGCTTACAAACCTGTTATCTGCCGC
TTGTCCTCCGATCCCTCAATTTCTACTATAAACTTAATGAAAACAGTTCATTGTACTCTTACATA
CCTGTTTACC
Found at i:579904 original size:42 final size:42
Alignment explanation
Indices: 579857--579940 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
579847 GCTCACTATA
579857 ATTAGGGCTTTTCGAATTTCGGTAC-AAAAGACCTATTGTTTT
1 ATTAGGGCTTTTCGAATTTCGGT-CGAAAAGACCTATTGTTTT
*
579899 ATTAGGGCTTTTCGACTTTCGGTCGAAAAGACCTATTGTTTT
1 ATTAGGGCTTTTCGAATTTCGGTCGAAAAGACCTATTGTTTT
579941 CGTCTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (42 bp):
ATTAGGGCTTTTCGAATTTCGGTCGAAAAGACCTATTGTTTT
Found at i:583968 original size:146 final size:146
Alignment explanation
Indices: 583317--583969 Score: 840
Period size: 146 Copynumber: 4.5 Consensus size: 146
583307 TAAAACTGTT
* * * *
583317 GGTCATAAGCAATATTTGTGTGAAGTTAGAACATT-CAATGCTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGATTCTCCATAAAAAAGAT-ATGGA
* ** * *
583380 CCGGACACGAATTTTGCACTATTTTCC--CCAACGACCTTGACCTTGCCCAAATGACCTTGGATC
64 CTGGACACGAATTTTGCA-T-TTTTCCTGCCAGTGACCTTGACCTTACCCAAATGACCTTGGGTC
*
583443 AAGGTCATGACATACCCTTA
127 AAGGTCATGACACACCCTTA
* * * * *
583463 GGTCATAAGCAATCTTTGTGTGAATTAAGAACTTCCAATGTTTCTCCATAACAACGATATGGACA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGATTCTCCATAAAAAAGATATGGACT
** *
583528 GGACATAAATTTTGCACTTTT-CTGCCAGTGACCTTGACCTTGA-CCAAATGACCTTGGGTCAAG
66 GGACACGAATTTTGCATTTTTCCTGCCAGTGACCTTGACCTT-ACCCAAATGACCTTGGGTCAAG
* *
583591 GTCAT-A-ACACACTGA
130 GTCATGACACACCCTTA
* * * *
583606 AGTCATTAGCAATCTTTGTGTGAA-TAAAGAACTTCCAATAACTCTCCAT-AAAAAGATATGGAC
1 GGTCATAAGCAATCTTTGTGTGAAGT-AAGAACTTCCAATGATTCTCCATAAAAAAGATATGGAC
* * *
583669 TGGACACAAATTTTGTATTTTTCCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
65 TGGACACGAATTTTGCATTTTTCCTGCCAGTGACCTTGACCTTACCCAAATGACCTTGGGTCAAG
583734 GTCATGACACACCCTTA
130 GTCATGACACACCCTTA
* ** * * *
583751 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATAATTCTCCATACGAAATATATAGAAT
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGATTCTCCATAAAAAAGATATGGACT
* * *
583816 GGACACGAATTTTGTATTTTTCCTGCCAGTGACCTTGGCCTTACCCGAATGACCTTGGGTCAAGG
66 GGACACGAATTTTGCATTTTTCCTGCCAGTGACCTTGACCTTACCCAAATGACCTTGGGTCAAGG
583881 TCATGACACACCCTTA
131 TCATGACACACCCTTA
* *
583897 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAAGGTTTCTCCATAAAAAAGATATGGACT
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGATTCTCCATAAAAAAGATATGGACT
583962 GGACACGA
66 GGACACGA
583970 TTGCACAGAC
Statistics
Matches: 444, Mismatches: 51, Indels: 24
0.86 0.10 0.05
Matches are distributed among these distances:
142 31 0.07
143 94 0.21
144 6 0.01
145 94 0.21
146 219 0.49
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (146 bp):
GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGATTCTCCATAAAAAAGATATGGACT
GGACACGAATTTTGCATTTTTCCTGCCAGTGACCTTGACCTTACCCAAATGACCTTGGGTCAAGG
TCATGACACACCCTTA
Found at i:584004 original size:12 final size:12
Alignment explanation
Indices: 583974--584007 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
583964 ACACGATTGC
*
583974 ACAGACAGACGG
1 ACAGACGGACGG
583986 ACAGACGGACGG
1 ACAGACGGACGG
583998 ACAGACGGAC
1 ACAGACGGAC
584008 AAGGTGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.26, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:584383 original size:2 final size:2
Alignment explanation
Indices: 584378--584428 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
584368 TAGAAACACA
584378 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
584420 CT CT CT CT C
1 CT CT CT CT C
584429 AACCATTCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:588342 original size:11 final size:11
Alignment explanation
Indices: 588326--588355 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
588316 CTTTGTATAC
588326 AAACTAATAAA
1 AAACTAATAAA
*
588337 AAACTAATAAT
1 AAACTAATAAA
588348 AAACTAAT
1 AAACTAAT
588356 TTTCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (11 bp):
AAACTAATAAA
Found at i:595353 original size:2 final size:2
Alignment explanation
Indices: 595346--595412 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
595336 GAAATATTTT
*
595346 GA GA GA GA AA 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
595388 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 G
595413 TGTGTGTGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:596865 original size:2 final size:2
Alignment explanation
Indices: 596858--596904 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
596848 AAATGAAATA
*
596858 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT 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
596900 TC TC T
1 TC TC T
596905 GGGTAATCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:600327 original size:37 final size:37
Alignment explanation
Indices: 600277--600470 Score: 325
Period size: 37 Copynumber: 5.2 Consensus size: 37
600267 TATTTATTAG
* * *
600277 ATGTTTTTACACCTACATGTATAGATATATGTAAATA
1 ATGTTTTTACACCTACATGTATATACATATTTAAATA
600314 ATGTTTTTACACCTACATGTATATACATATTTAAATA
1 ATGTTTTTACACCTACATGTATATACATATTTAAATA
*
600351 ATGTTTTTACTCCTACATGTATATACATATTTAAATA
1 ATGTTTTTACACCTACATGTATATACATATTTAAATA
* *
600388 TTGTTTTTACACCTACGTGTATATACATATTTAAATA
1 ATGTTTTTACACCTACATGTATATACATATTTAAATA
*
600425 ATGTTTTTACACCTACATGTATATACATATGTAAATA
1 ATGTTTTTACACCTACATGTATATACATATTTAAATA
600462 ATGTTTTTA
1 ATGTTTTTA
600471 TCCTTTTGTT
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 147 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (37 bp):
ATGTTTTTACACCTACATGTATATACATATTTAAATA
Found at i:601303 original size:112 final size:111
Alignment explanation
Indices: 601111--601325 Score: 279
Period size: 112 Copynumber: 1.9 Consensus size: 111
601101 TAAACAAAGC
* * * **
601111 TTTTGTTTACATTTTGAATGTTGAAGTTAAATTCCAGTTTTAGACCTGAAATGATTGTTTTAAAC
1 TTTTGTTTACATTTTGAATGTTGAAGTAAAATACCAGTTTTAGACCTAAAATGA-TGTGCTAAAC
*
601176 GGTAGAAACTGTTTATTTAAGATTAAAATGAAAAAGAACAACAAAAA
65 GGTAGAAACTCTTTATTTAAGATTAAAATGAAAAAGAACAACAAAAA
* *
601223 TTTTGTTTACATTTTGAATGTTGAAGTAAAAATACCATTTTTATACCCTAAAATGA-GTGCTAAA
1 TTTTGTTTACATTTTGAATGTTGAAGT-AAAATACCAGTTTTAGA-CCTAAAATGATGTGCTAAA
* *** *
601287 CGTTAGAAACTCTTTATTTATTCTTAAAATGAATAAGAA
64 CGGTAGAAACTCTTTATTTAAGATTAAAATGAAAAAGAA
601326 GATAGACAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
112 66 0.75
113 13 0.15
114 9 0.10
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (111 bp):
TTTTGTTTACATTTTGAATGTTGAAGTAAAATACCAGTTTTAGACCTAAAATGATGTGCTAAACG
GTAGAAACTCTTTATTTAAGATTAAAATGAAAAAGAACAACAAAAA
Found at i:609158 original size:42 final size:42
Alignment explanation
Indices: 609111--609283 Score: 346
Period size: 42 Copynumber: 4.1 Consensus size: 42
609101 ACACAAAAGT
609111 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
1 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
609153 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
1 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
609195 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
1 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
609237 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
1 TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
609279 TGTGG
1 TGTGG
609284 TCCTCTTCCT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 131 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (42 bp):
TGTGGCGTCCAGCAACCAATAGCTACATGTACATCCCTTACC
Found at i:614800 original size:2 final size:2
Alignment explanation
Indices: 614793--614830 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
614783 AGAGAAAAAT
614793 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
614831 ATAAAGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:616714 original size:69 final size:69
Alignment explanation
Indices: 616603--616735 Score: 232
Period size: 69 Copynumber: 1.9 Consensus size: 69
616593 CGATAACATA
* *
616603 CCGTCAGAAGACATTGTACGGAATGGCGTGCTACCCGATATCATTGGTA-ATGGTGAACTACGCG
1 CCGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTAGA-GGAGAACTACGCG
616667 GTATT
65 GTATT
616672 CCGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTAGAGGAGAACTACGCG
1 CCGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTAGAGGAGAACTACGCG
616736 AAATAACGTC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 60 0.98
70 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (69 bp):
CCGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTAGAGGAGAACTACGCGG
TATT
Found at i:616765 original size:69 final size:69
Alignment explanation
Indices: 616604--616752 Score: 228
Period size: 69 Copynumber: 2.2 Consensus size: 69
616594 GATAACATAC
* * **
616604 CGTCAGAAGACATTGTACGGAATGGCGTGCTACCCGATATCATTGGTAATGGTGAACTACGCGGT
1 CGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTAATGGAGAACTACGCGAA
**
616669 ATTC
66 ATAA
616673 CGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTAGA-GGAGAACTACGCGA
1 CGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTA-ATGGAGAACTACGCGA
616737 AATAA
65 AATAA
616742 CGTCAGAAGAC
1 CGTCAGAAGAC
616753 CTTGGAGGGA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
69 72 0.99
70 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (69 bp):
CGTCAGAAGACATTGTACGGAATGGAGTGCTACCCGATATCATTGGTAATGGAGAACTACGCGAA
ATAA
Found at i:661839 original size:21 final size:21
Alignment explanation
Indices: 661809--661848 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
661799 CAAAACAACA
*
661809 TCCTTGTTTTCCACATCATTC
1 TCCTTATTTTCCACATCATTC
**
661830 TCCTTATTTTTGACATCAT
1 TCCTTATTTTCCACATCAT
661849 CCTCTTCTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.05, T:0.50
Consensus pattern (21 bp):
TCCTTATTTTCCACATCATTC
Found at i:667518 original size:21 final size:21
Alignment explanation
Indices: 667494--667552 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
667484 GCACGATTCT
*
667494 GATACACGAACTATCACGCAC
1 GATACACGAACGATCACGCAC
667515 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
*
667536 GATACACGGACGATCAC
1 GATACACGAACGATCAC
667553 TAACTTACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.32, G:0.19, T:0.12
Consensus pattern (21 bp):
GATACACGAACGATCACGCAC
Found at i:667527 original size:11 final size:11
Alignment explanation
Indices: 667494--667549 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
667484 GCACGATTCT
667494 GATACACGAAC
1 GATACACGAAC
* *
667505 TAT-CACGCAC
1 GATACACGAAC
667515 GATACACGAAC
1 GATACACGAAC
*
667526 GAT-CACGCAC
1 GATACACGAAC
*
667536 GATACACGGAC
1 GATACACGAAC
667547 GAT
1 GAT
667550 CACTAACTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
10 17 0.46
11 20 0.54
ACGTcount: A:0.38, C:0.30, G:0.20, T:0.12
Consensus pattern (11 bp):
GATACACGAAC
Found at i:672003 original size:37 final size:38
Alignment explanation
Indices: 671953--672027 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 38
671943 CGGTTCAACA
671953 TGATATTACGCAGTTTATGTCTTATTT-AACAATGACC
1 TGATATTACGCAGTTTATGTCTTATTTAAACAATGACC
*
671990 TGATATTATGCAGTTTATGTCTTATTTAAACAATGACC
1 TGATATTACGCAGTTTATGTCTTATTTAAACAATGACC
672028 GTAAATCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 26 0.72
38 10 0.28
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (38 bp):
TGATATTACGCAGTTTATGTCTTATTTAAACAATGACC
Found at i:678182 original size:163 final size:160
Alignment explanation
Indices: 677932--678319 Score: 429
Period size: 163 Copynumber: 2.4 Consensus size: 160
677922 AGTAGCTACG
* * * * * *
677932 TCATCTCTTGGGATATAATTGGGGCTGTCCTATATATGTGCAATAAGGTTTTAAAAGTTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATT
* * *
677997 AAATCCAGGGAGTCAAATAGTAGCAGAAAATTGATGTTTATCAATGAAAAAAACCCATAGATCCA
66 AAATCCAGGAAGTCAAATAGTAGCAGAAAATTGACGCTTATCAAT-AAAAAAA--CATAGATCCA
* *
678062 AGAGCTCCTCTAATGATTTAATGGATAGACACA
128 AGAACTCCTCTAATGATTAAATGGATAGACACA
* * * *
678095 TCATATCTTGGAATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAATTTTTAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATT
** * * ** * *
678160 TCATCCAGGAAGT-AATATAGTAGCAGAAAATTGACGCTTATTACTTCAAAAACATAGATCCTAT
66 AAATCCAGGAAGTCAA-ATAGTAGCAGAAAATTGACGCTTATCAATAAAAAAACATAGATCCAAG
* *
678224 AACTCCTTTTATGATTAAATGGATAGACACA
130 AACTCCTCTAATGATTAAATGGATAGACACA
** * * * * *
678255 TCATATCTTGGGATATGATAGAAACTGTTCCATAGATATGCATTACGGTTTTTAAAA-ATTAAAT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGG-TTTTAAAAGTTTAAAT
678319 T
65 T
678320 TAACCCTAAG
Statistics
Matches: 189, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
160 84 0.44
161 8 0.04
162 7 0.04
163 90 0.48
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (160 bp):
TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATT
AAATCCAGGAAGTCAAATAGTAGCAGAAAATTGACGCTTATCAATAAAAAAACATAGATCCAAGA
ACTCCTCTAATGATTAAATGGATAGACACA
Found at i:678284 original size:160 final size:162
Alignment explanation
Indices: 677956--678319 Score: 421
Period size: 160 Copynumber: 2.3 Consensus size: 162
677946 ATAATTGGGG
* * *
677956 CTGTCCTATATATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGGAGTCAAATAGTAGC
1 CTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGAAGTCAAATAGTAGC
* * * *
678021 AGAAAATTGATGTTTATCAATGAAAAAAACCCATAGATCCAAGAGCTCCTCTAATGATTTAATGG
66 AGAAAATTGACGCTTATCAATGAAAAAAA-CCATAGATCCAAGAACTCCTCTAATGATTAAATGG
**
678086 ATAGACACATCATATCTTGGAATATGATAGGGA
130 ATAGACACATCATATCTTGGAATATGATAGAAA
* * * **
678119 CTGTTCTATAGATGTGCAGTAAGGTTTTAAAATTTTTAATTTCATCCAGGAAGT-AATATAGTAG
1 CTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGAAGTCAA-ATAGTAG
* * ** * * * *
678183 CAGAAAATTGACGCTTATTACT-TCAAAAA-CATAGATCCTATAACTCCTTTTATGATTAAATGG
65 CAGAAAATTGACGCTTATCAATGAAAAAAACCATAGATCCAAGAACTCCTCTAATGATTAAATGG
*
678246 ATAGACACATCATATCTTGGGATATGATAGAAA
130 ATAGACACATCATATCTTGGAATATGATAGAAA
* * * * *
678279 CTGTTCCATAGATATGCATTACGGTTTTTAAAA-ATTAAATT
1 CTGTTCTATAGATGTGCAATAAGG-TTTTAAAAGTTTAAATT
678320 TAACCCTAAG
Statistics
Matches: 170, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
160 84 0.49
161 8 0.05
162 7 0.04
163 71 0.42
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (162 bp):
CTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGAAGTCAAATAGTAGC
AGAAAATTGACGCTTATCAATGAAAAAAACCATAGATCCAAGAACTCCTCTAATGATTAAATGGA
TAGACACATCATATCTTGGAATATGATAGAAA
Found at i:680492 original size:163 final size:160
Alignment explanation
Indices: 680242--680629 Score: 429
Period size: 163 Copynumber: 2.4 Consensus size: 160
680232 AGTAGCTACG
* * * * * *
680242 TCATCTCTTGGGATATAATTGGGGCTGTCCTATATATGTGCAATAAGGTTTTAAAAGTTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATT
* * *
680307 AAATCCAGGGAGTCAAATAGTAGCAGAAAATTGATGTTTATCAATGAAAAAAACCCATAGATCCA
66 AAATCCAGGAAGTCAAATAGTAGCAGAAAATTGACGCTTATCAAT-AAAAAAA--CATAGATCCA
* *
680372 AGAGCTCCTCTAATGATTTAATGGATAGACACA
128 AGAACTCCTCTAATGATTAAATGGATAGACACA
* * * *
680405 TCATATCTTGGAATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAATTTTTAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATT
** * * ** * *
680470 TCATCCAGGAAGT-AATATAGTAGCAGAAAATTGACGCTTATTACTTCAAAAACATAGATCCTAT
66 AAATCCAGGAAGTCAA-ATAGTAGCAGAAAATTGACGCTTATCAATAAAAAAACATAGATCCAAG
* *
680534 AACTCCTTTTATGATTAAATGGATAGACACA
130 AACTCCTCTAATGATTAAATGGATAGACACA
** * * * * *
680565 TCATATCTTGGGATATGATAGAAACTGTTCCATAGATATGCATTACGGTTTTTAAAA-ATTAAAT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGG-TTTTAAAAGTTTAAAT
680629 T
65 T
680630 TAACCCTAAG
Statistics
Matches: 189, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
160 84 0.44
161 8 0.04
162 7 0.04
163 90 0.48
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (160 bp):
TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATT
AAATCCAGGAAGTCAAATAGTAGCAGAAAATTGACGCTTATCAATAAAAAAACATAGATCCAAGA
ACTCCTCTAATGATTAAATGGATAGACACA
Found at i:680594 original size:160 final size:162
Alignment explanation
Indices: 680266--680629 Score: 421
Period size: 160 Copynumber: 2.3 Consensus size: 162
680256 ATAATTGGGG
* * *
680266 CTGTCCTATATATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGGAGTCAAATAGTAGC
1 CTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGAAGTCAAATAGTAGC
* * * *
680331 AGAAAATTGATGTTTATCAATGAAAAAAACCCATAGATCCAAGAGCTCCTCTAATGATTTAATGG
66 AGAAAATTGACGCTTATCAATGAAAAAAA-CCATAGATCCAAGAACTCCTCTAATGATTAAATGG
**
680396 ATAGACACATCATATCTTGGAATATGATAGGGA
130 ATAGACACATCATATCTTGGAATATGATAGAAA
* * * **
680429 CTGTTCTATAGATGTGCAGTAAGGTTTTAAAATTTTTAATTTCATCCAGGAAGT-AATATAGTAG
1 CTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGAAGTCAA-ATAGTAG
* * ** * * * *
680493 CAGAAAATTGACGCTTATTACT-TCAAAAA-CATAGATCCTATAACTCCTTTTATGATTAAATGG
65 CAGAAAATTGACGCTTATCAATGAAAAAAACCATAGATCCAAGAACTCCTCTAATGATTAAATGG
*
680556 ATAGACACATCATATCTTGGGATATGATAGAAA
130 ATAGACACATCATATCTTGGAATATGATAGAAA
* * * * *
680589 CTGTTCCATAGATATGCATTACGGTTTTTAAAA-ATTAAATT
1 CTGTTCTATAGATGTGCAATAAGG-TTTTAAAAGTTTAAATT
680630 TAACCCTAAG
Statistics
Matches: 170, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
160 84 0.49
161 8 0.05
162 7 0.04
163 71 0.42
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (162 bp):
CTGTTCTATAGATGTGCAATAAGGTTTTAAAAGTTTAAATTAAATCCAGGAAGTCAAATAGTAGC
AGAAAATTGACGCTTATCAATGAAAAAAACCATAGATCCAAGAACTCCTCTAATGATTAAATGGA
TAGACACATCATATCTTGGAATATGATAGAAA
Done.