Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021101.1 Corchorus olitorius cultivar O-4 contig21134, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 246710
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:6246 original size:22 final size:22
Alignment explanation
Indices: 6215--6315 Score: 64
Period size: 22 Copynumber: 4.5 Consensus size: 22
6205 CAGATTATTG
6215 AAATTTCATAGTGTGGCTATCA
1 AAATTTCATAGTGTGGCTATCA
* * *
6237 AAGTTTCATAATGTACTGGTTA-CA
1 AAATTTCAT-A-GT-GTGGCTATCA
* **
6261 AAAATTCATAG-AAGG-TAATCA
1 AAATTTCATAGTGTGGCT-ATCA
* * *
6282 AAGTTTCATATTGTGTCTATCA
1 AAATTTCATAGTGTGGCTATCA
6304 AAATTTCATAGT
1 AAATTTCATAGT
6316 AAGATTGACA
Statistics
Matches: 57, Mismatches: 15, Indels: 14
0.66 0.17 0.16
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 10 0.18
22 24 0.42
23 3 0.05
24 11 0.19
25 5 0.09
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGTGTGGCTATCA
Found at i:6360 original size:22 final size:22
Alignment explanation
Indices: 6335--6404 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
6325 ACTAAATTCT
*
6335 ATAGGGAAGTTATCAACATTTC
1 ATAGGGAAGTTATCAAAATTTC
* *
6357 ATAGGGAGGTTATCAAAATTTT
1 ATAGGGAAGTTATCAAAATTTC
* * *
6379 ATA-GTATGATTATCCAAATTTC
1 ATAGGGAAG-TTATCAAAATTTC
6401 ATAG
1 ATAG
6405 TCTACCAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 3 0.08
22 36 0.92
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATAGGGAAGTTATCAAAATTTC
Found at i:6530 original size:22 final size:22
Alignment explanation
Indices: 6473--6579 Score: 94
Period size: 22 Copynumber: 4.9 Consensus size: 22
6463 TATCAAAATT
*
6473 AATTTCATA-TAGAGGTTATCACA
1 AATTTCATAGT-GTGGTTATCA-A
* *
6496 AATAT-ATACTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
6517 AATTTCAGAGTGTGGTGACCAA
1 AATTTCATAGTGTGGTTATCAA
*
6539 AATTTCATAG-GATGGTTATCAG
1 AATTTCATAGTG-TGGTTATCAA
*
6561 AATTTCATAGTGTAGTTAT
1 AATTTCATAGTGTGGTTAT
6580 TAAAGTTCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
21 6 0.09
22 56 0.82
23 6 0.09
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:6868 original size:22 final size:22
Alignment explanation
Indices: 6841--6900 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
6831 AATAATTAGG
*
6841 TTATCAAAATTTCATTGGG-AA
1 TTATCAAAATTTCATAGGGTAA
* *
6862 TTTATCAGAATTTTATAGGGTAA
1 -TTATCAAAATTTCATAGGGTAA
*
6885 TTATCAAAATTGCATA
1 TTATCAAAATTTCATA
6901 ATGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGTAA
Found at i:18279 original size:12 final size:13
Alignment explanation
Indices: 18255--18294 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
18245 ATATTTTCAA
18255 AAAAATAATTTTT
1 AAAAATAATTTTT
*
18268 AAAAATAATTTTG
1 AAAAATAATTTTT
*
18281 AAAATATTATTTTT
1 AAAA-ATAATTTTT
18295 TGTACTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAAAATAATTTTT
Found at i:21361 original size:81 final size:84
Alignment explanation
Indices: 21268--21474 Score: 260
Period size: 87 Copynumber: 2.5 Consensus size: 84
21258 CATCATAATC
* * * *
21268 ACCCACCGGCTCATGCGCCATCTCCAGTCGTCCATTCTGCA-C-C-GTCTCATGTTCCTTCTCAT
1 ACCCACCGGCTCATGCACCGTCTCCCGTCGTCCACTCTGCACCACGGTCTCATGTTCCTTCTCAT
*
21330 GCGCCAA-TCCATTCCGTCA
66 GCGCCAAGT-CATCCCGTCA
* *
21349 ACCCACCGGCTCATGCACCGTCTCCCGTCGTCAACTCTGCACCCATCGTGTCTCCTGTTCCTTCT
1 ACCCACCGGCTCATGCACCGTCTCCCGTCGTCCACTCTGCA-CCA-CG-GTCTCATGTTCCTTCT
*
21414 CATGCGCCAAGTCATCCCGTTA
63 CATGCGCCAAGTCATCCCGTCA
* *
21436 ACCCACCGTCTCCTGCACCGTCTCCCGTCGTCCACTCTG
1 ACCCACCGGCTCATGCACCGTCTCCCGTCGTCCACTCTG
21475 GCCCCACCAA
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
81 36 0.33
83 1 0.01
85 1 0.01
87 69 0.64
88 1 0.01
ACGTcount: A:0.14, C:0.44, G:0.15, T:0.26
Consensus pattern (84 bp):
ACCCACCGGCTCATGCACCGTCTCCCGTCGTCCACTCTGCACCACGGTCTCATGTTCCTTCTCAT
GCGCCAAGTCATCCCGTCA
Found at i:21493 original size:87 final size:87
Alignment explanation
Indices: 21317--21580 Score: 282
Period size: 87 Copynumber: 3.0 Consensus size: 87
21307 CACCGTCTCA
*
21317 TGTTCCTTCTCATGCGCCAA-TCCATTCCGTCAACCCACCGGCTCATGCACCGTCTCCCGTCGTC
1 TGTTCCTTCTCATGCGCCAAGT-CATTCCGTTAACCCACCGGCTCATGCACCGTCTCCCGTCGTC
* * ** *
21381 AACTCT-GCACCCATCGTGTCTCC
65 CACTCTGGC-CCCAACAAGTCCCC
* * *
21404 TGTTCCTTCTCATGCGCCAAGTCATCCCGTTAACCCACCGTCTCCTGCACCGTCTCCCGTCGTCC
1 TGTTCCTTCTCATGCGCCAAGTCATTCCGTTAACCCACCGGCTCATGCACCGTCTCCCGTCGTCC
*
21469 ACTCTGGCCCCACCAAGTCCCC
66 ACTCTGGCCCCAACAAGTCCCC
** ** * * * * * * *
21491 TGTAGCGGCTCCTGCACCAAGCCATTCTGCTAACCCACCGGCTCATGCCCCGTCTCCAGTCGTCC
1 TGTTCCTTCTCATGCGCCAAGTCATTCCGTTAACCCACCGGCTCATGCACCGTCTCCCGTCGTCC
*
21556 ACTCTGCCCCCAACAAG-CCTCC
66 ACTCTGGCCCCAACAAGTCC-CC
21578 TGT
1 TGT
21581 CGTGGCCAAT
Statistics
Matches: 149, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
86 2 0.01
87 144 0.97
88 3 0.02
ACGTcount: A:0.15, C:0.45, G:0.16, T:0.24
Consensus pattern (87 bp):
TGTTCCTTCTCATGCGCCAAGTCATTCCGTTAACCCACCGGCTCATGCACCGTCTCCCGTCGTCC
ACTCTGGCCCCAACAAGTCCCC
Found at i:22557 original size:13 final size:13
Alignment explanation
Indices: 22539--22564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22529 GACCTGTTTA
22539 CTTCCTAGTTCAT
1 CTTCCTAGTTCAT
22552 CTTCCTAGTTCAT
1 CTTCCTAGTTCAT
22565 ATCAACTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
CTTCCTAGTTCAT
Found at i:24392 original size:30 final size:30
Alignment explanation
Indices: 24356--24413 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
24346 TGATACCTTC
* * *
24356 TCCGCCACGGTTGCTACCTTTTCCACTACT
1 TCCGCCACAGTTGCCACCTCTTCCACTACT
*
24386 TCCGCCACAGTTTCCACCTCTTCCACTA
1 TCCGCCACAGTTGCCACCTCTTCCACTA
24414 TCATTTCTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.16, C:0.43, G:0.10, T:0.31
Consensus pattern (30 bp):
TCCGCCACAGTTGCCACCTCTTCCACTACT
Found at i:24858 original size:21 final size:21
Alignment explanation
Indices: 24834--24880 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
24824 AACATTAAGC
24834 ATAATGATTAAG-AAATGGAAA
1 ATAATGA-TAAGAAAATGGAAA
*
24855 ATAATTATAAGAAAATGGAAA
1 ATAATGATAAGAAAATGGAAA
*
24876 TTAAT
1 ATAAT
24881 CAGGAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (21 bp):
ATAATGATAAGAAAATGGAAA
Found at i:24867 original size:20 final size:21
Alignment explanation
Indices: 24842--24880 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24832 GCATAATGAT
24842 TAAG-AAATGGAAAATAATTA
1 TAAGAAAATGGAAAATAATTA
*
24862 TAAGAAAATGGAAATTAAT
1 TAAGAAAATGGAAAATAAT
24881 CAGGAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (21 bp):
TAAGAAAATGGAAAATAATTA
Found at i:29281 original size:5 final size:5
Alignment explanation
Indices: 29271--29298 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
29261 TATTGTTATT
29271 ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATA
29299 AACAACTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:41813 original size:12 final size:12
Alignment explanation
Indices: 41793--41822 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
41783 AACAACAGAA
41793 GCAACAAGATCAG
1 GCAA-AAGATCAG
41806 GCAAAAGATCAG
1 GCAAAAGATCAG
41818 GCAAA
1 GCAAA
41823 TGCTTGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (12 bp):
GCAAAAGATCAG
Found at i:58943 original size:42 final size:42
Alignment explanation
Indices: 58888--58978 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
58878 AGTGCATTAC
* *
58888 CTAA-ATTTTACTCCATCTCTAGAAAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAGAAAATTCATCAAAATAAAA
* *
58929 CTAATATTCTACTCCATCTTTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTCCATCTCTAGAAAATTCATCAAAATAAAA
*
58971 TTAATATT
1 CTAATATT
58979 AATTGTTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.09
42 40 0.91
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (42 bp):
CTAATATTCTACTCCATCTCTAGAAAATTCATCAAAATAAAA
Found at i:59358 original size:57 final size:58
Alignment explanation
Indices: 59297--59417 Score: 199
Period size: 61 Copynumber: 2.1 Consensus size: 58
59287 ACCTCAATAA
*
59297 AAAGGAAGTCGAATGATAAAT-AAAAAAAACCTTTTGTAAAATAAAAGAGGAATAAGG
1 AAAGGAAGTCGAATGATAAATAAAAAAAAAACTTTTGTAAAATAAAAGAGGAATAAGG
59354 AAAGGAAGTCGAATGATAAATAAGAAAAAAAAAACTTTTGTAAAATAAAAGAGGAATAAGG
1 AAAGGAAGTCGAATGATAAAT---AAAAAAAAAACTTTTGTAAAATAAAAGAGGAATAAGG
59415 AAA
1 AAA
59418 TATTAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
57 21 0.36
61 38 0.64
ACGTcount: A:0.59, C:0.04, G:0.19, T:0.18
Consensus pattern (58 bp):
AAAGGAAGTCGAATGATAAATAAAAAAAAAACTTTTGTAAAATAAAAGAGGAATAAGG
Found at i:59807 original size:22 final size:23
Alignment explanation
Indices: 59782--59827 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
59772 TAATATCCAC
59782 ACACAATTAAT-ATGTAAT-TAAA
1 ACACAATTAATCATG-AATATAAA
*
59804 ACACACTTAATCATGAATATAAA
1 ACACAATTAATCATGAATATAAA
59827 A
1 A
59828 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATGAATATAAA
Found at i:60316 original size:42 final size:44
Alignment explanation
Indices: 60266--60359 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
60256 AATGCATTAC
*
60266 CTAA-ATTCTACT-T-CATCTCTAGGTAATAT-ATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAAT-TCATCAAAATAAAG
60307 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
60352 CTAATATT
1 CTAATATT
60360 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 2 0.04
45 33 0.70
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:61952 original size:29 final size:27
Alignment explanation
Indices: 61919--61976 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 27
61909 GGTGGCACTA
*
61919 AATCTTACTGAGCTTAGGTTTTTAGATTG
1 AATCTT-CTGAGC-TAGGTTTTTAGACTG
61948 AA---TCTGAGCTAGGTTTTTAGACTG
1 AATCTTCTGAGCTAGGTTTTTAGACTG
61972 AATCT
1 AATCT
61977 GAGCCACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
24 16 0.64
25 6 0.24
26 1 0.04
29 2 0.08
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (27 bp):
AATCTTCTGAGCTAGGTTTTTAGACTG
Found at i:61963 original size:24 final size:25
Alignment explanation
Indices: 61926--61980 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
61916 CTAAATCTTA
*
61926 CTGAGCTTAGGTTTTTAGATTGAAT
1 CTGAGCTTAGGTTTTTAGACTGAAT
61951 CTGAGC-TAGGTTTTTAGACTGAAT
1 CTGAGCTTAGGTTTTTAGACTGAAT
61975 CTGAGC
1 CTGAGC
61981 CACTTATCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (25 bp):
CTGAGCTTAGGTTTTTAGACTGAAT
Found at i:62572 original size:5 final size:5
Alignment explanation
Indices: 62562--62595 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
62552 TTATATATAG
62562 TAAGA TAAGA TAAGA T-AG- TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
62596 GAGTATAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 1 0.04
4 4 0.15
5 22 0.81
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (5 bp):
TAAGA
Found at i:62581 original size:18 final size:18
Alignment explanation
Indices: 62558--62600 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 18
62548 ATTTTTATAT
62558 ATAGTAAGATAAGATAAG
1 ATAGTAAGATAAGATAAG
62576 ATAGTAAGATAAGATAAG
1 ATAGTAAGATAAGATAAG
62594 ATGAGTA
1 AT-AGTA
62601 TAACCATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
ATAGTAAGATAAGATAAG
Found at i:62585 original size:13 final size:13
Alignment explanation
Indices: 62567--62591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62557 TATAGTAAGA
62567 TAAGATAAGATAG
1 TAAGATAAGATAG
62580 TAAGATAAGATA
1 TAAGATAAGATA
62592 AGATGAGTAT
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:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (13 bp):
TAAGATAAGATAG
Found at i:65065 original size:46 final size:47
Alignment explanation
Indices: 64998--65091 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 47
64988 AATTCTCTCA
*
64998 ACCTTCAAAACTCAATCATTCAAAT-AAATAACATCGAAACTCATGG
1 ACCTTCAAAACTCAATCATTCAAATAAAACAACATCGAAACTCATGG
65044 ACCTTCAAAACTCAATCATTCAAATAAAACAACATCGAAACTCATGG
1 ACCTTCAAAACTCAATCATTCAAATAAAACAACATCGAAACTCATGG
65091 A
1 A
65092 GTGACAGTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 25 0.54
47 21 0.46
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.22
Consensus pattern (47 bp):
ACCTTCAAAACTCAATCATTCAAATAAAACAACATCGAAACTCATGG
Found at i:72635 original size:376 final size:376
Alignment explanation
Indices: 71612--72801 Score: 1986
Period size: 376 Copynumber: 3.1 Consensus size: 376
71602 TCAAGTAGGA
* *
71612 ATTACACGAACAGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCT
1 ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCT
*
71677 AACCAACCTTTATTCGATGCACCATTATACCTTCATGTATAATAGGAATGCCGCTGTTGTGCCTT
66 AACCAACCTTTATTCGATGCACCATTATACCTTCATGTATAATAGGAATGCCACTGTTGTGCCTT
* * * *
71742 CTAGAATTCAAAGAAAAAATGCCATGTAACAAAAGAGCTTGCATCGTTTGAAGAAAAGATAGAAC
131 TTAGCATTC-AA-AAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAA-AATAGATAGAAC
* * *
71807 AAAATCGAAACAAGGCATAGCTGCCATTTCATGGGCGTGCAGTGAATACTAAACAGTCAAAAATC
193 AAAATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAAC
71872 AACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGTACCAGAAGAAATGGAGTGGGCGAGGGA
258 AACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGTACCAGAAGAAATGGAGTGGGCGAGGGA
71937 GCATGAGCCTTCAAGATTGTTCATACTTCATTGCACAATAAGAGTTCCAGGTAG
323 GCATGAGCCTTCAAGATTGTTCATACTTCATTGCACAATAAGAGTTCCAGGTAG
71991 ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCATGCCACCACCACCACAAA
1 ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGG-A---ATG---CCACCACCACAAA
* *
72056 GAATTCTAACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCATTGTT
59 GAATTCTAACCAACCTTTATTCGATGCACCATTATACCTTCATGTATAATAGGAATGCCACTGTT
72121 GTGCCTTTTAGCATTCAAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATA
124 GTGCCTTTTAGCATTCAAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATA
*
72186 GAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGTGTGTGCAGTGAATACTAAACAGTCAAA
189 GAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAA
*
72251 AGACAACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGTACCAGAAGAAATGGAGTGGGCGA
254 AAACAACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGTACCAGAAGAAATGGAGTGGGCGA
*
72316 GGGAGCATGAGCCTTCAAGATTGTTCATACTTCATTGCACAATAAGATTTCCAGGTAG
319 GGGAGCATGAGCCTTCAAGATTGTTCATACTTCATTGCACAATAAGAGTTCCAGGTAG
72374 ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCT
1 ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCT
**
72439 AATTAACCTTTATTCGATGCACCATTATACCTTCATGTATAATAGGAATGCCACTGTTGTGCCTT
66 AACCAACCTTTATTCGATGCACCATTATACCTTCATGTATAATAGGAATGCCACTGTTGTGCCTT
* * * * *
72504 TTAGCATT-ATAAAAAGATGCCATGTACCAAAAGAACTTGTATCATTTGAAAATAGATATAACAA
131 TTAGCATTCA-AAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAA
72568 AATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAA
195 AATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAA
* * * * *
72633 CTTTGAGTATAAAGCTTAAATTGCTCATGGTGGTGAATCAGAAGAAATGGAGTGGACAAGGGAGC
260 CTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGTACCAGAAGAAATGGAGTGGGCGAGGGAGC
* * * * *
72698 ATGAGCCTTCAAGATTGTTCATATTTCGTTGCACTACAAGAGTTCCAGGTAT
325 ATGAGCCTTCAAGATTGTTCATACTTCATTGCACAATAAGAGTTCCAGGTAG
72750 ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCAC
1 ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCAC
72802 ATTGTGCCTT
Statistics
Matches: 766, Mismatches: 37, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
375 1 0.00
376 359 0.47
379 42 0.05
380 1 0.00
382 1 0.00
383 233 0.30
384 38 0.05
385 2 0.00
386 89 0.12
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (376 bp):
ATTACATGAACTGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCT
AACCAACCTTTATTCGATGCACCATTATACCTTCATGTATAATAGGAATGCCACTGTTGTGCCTT
TTAGCATTCAAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAAA
ATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAAC
TTTGAGTATAAAACTTAAATTGCTCATGGTGGTGTACCAGAAGAAATGGAGTGGGCGAGGGAGCA
TGAGCCTTCAAGATTGTTCATACTTCATTGCACAATAAGAGTTCCAGGTAG
Found at i:75885 original size:18 final size:18
Alignment explanation
Indices: 75864--75901 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
75854 TCGGATAAAG
75864 TCTCAATTTCCTGCATAA
1 TCTCAATTTCCTGCATAA
75882 TCTCAATTTCCTGCATAA
1 TCTCAATTTCCTGCATAA
75900 TC
1 TC
75902 CAGCAGCGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (18 bp):
TCTCAATTTCCTGCATAA
Found at i:80669 original size:41 final size:43
Alignment explanation
Indices: 80581--80670 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
80571 AATGGGCAAT
* *
80581 TTCTTTAATCCTCTAACTCTGCAAAATTTGAAAAATTGAACAG
1 TTCTTTAATCCTCTAACTCTGCAAAATTAGAAAAATTGAACAC
**
80624 TTCTTTAATCCTCTAACTCTGCACTA-TAGAAAATATT-AAC-C
1 TTCTTTAATCCTCTAACTCTGCAAAATTAGAAAA-ATTGAACAC
80665 TTCTTT
1 TTCTTT
80671 GTTTGCATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 6 0.14
42 9 0.21
43 27 0.64
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (43 bp):
TTCTTTAATCCTCTAACTCTGCAAAATTAGAAAAATTGAACAC
Found at i:83171 original size:19 final size:19
Alignment explanation
Indices: 83147--83184 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
83137 ATAATATCTA
83147 GTTAGATATTAAAATACTG
1 GTTAGATATTAAAATACTG
83166 GTTAGATATTAAAATACTG
1 GTTAGATATTAAAATACTG
83185 ATGATCAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (19 bp):
GTTAGATATTAAAATACTG
Found at i:86859 original size:16 final size:16
Alignment explanation
Indices: 86838--86899 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
86828 TCCGAACCTA
*
86838 AAAAAACTCAAAGCCG
1 AAAAAACTCAAACCCG
86854 AAAAAAC-CAGAACCCG
1 AAAAAACTCA-AACCCG
* *
86870 AAAAATCTGAAACCCG
1 AAAAAACTCAAACCCG
*
86886 ATAAAACTCAAACC
1 AAAAAACTCAAACC
86900 TGAACCTGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 2 0.05
16 35 0.92
17 1 0.03
ACGTcount: A:0.55, C:0.27, G:0.10, T:0.08
Consensus pattern (16 bp):
AAAAAACTCAAACCCG
Found at i:87149 original size:32 final size:32
Alignment explanation
Indices: 87106--87170 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
87096 AAAACCCAGT
*
87106 CCGAACCCGAATCAACTTGACCCAAATTTAAC
1 CCGAACCCGAATCAACCTGACCCAAATTTAAC
*
87138 CCGAACTCGAATCAACCTGACCCAAATTTAAC
1 CCGAACCCGAATCAACCTGACCCAAATTTAAC
87170 C
1 C
87171 TGACCTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.35, G:0.09, T:0.18
Consensus pattern (32 bp):
CCGAACCCGAATCAACCTGACCCAAATTTAAC
Found at i:87170 original size:16 final size:16
Alignment explanation
Indices: 87123--87175 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
87113 CGAATCAACT
87123 TGACCCAAATTTAACC
1 TGACCCAAATTTAACC
* * * *
87139 CGAACTCGAA-TCAACC
1 TG-ACCCAAATTTAACC
87155 TGACCCAAATTTAACC
1 TGACCCAAATTTAACC
87171 TGACC
1 TGACC
87176 TAAGTCAAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 5 0.19
16 17 0.63
17 5 0.19
ACGTcount: A:0.36, C:0.34, G:0.09, T:0.21
Consensus pattern (16 bp):
TGACCCAAATTTAACC
Found at i:94254 original size:36 final size:36
Alignment explanation
Indices: 94207--94276 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
94197 TTCAATAACC
* * *
94207 TTACATCTTTTGTGATTTTGGTTATCATATTTCTAA
1 TTACATCTTTTGTAATCTTGATTATCATATTTCTAA
*
94243 TTACATTTTTTGTAATCTTGATTATCATATTTCT
1 TTACATCTTTTGTAATCTTGATTATCATATTTCT
94277 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (36 bp):
TTACATCTTTTGTAATCTTGATTATCATATTTCTAA
Found at i:95098 original size:25 final size:25
Alignment explanation
Indices: 95064--95160 Score: 187
Period size: 25 Copynumber: 3.9 Consensus size: 25
95054 ACGTTTGCAC
95064 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTTGAATTAAAA
95089 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTTGAATTAAAA
95114 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTTGAATTAAAA
95139 AAATACCTAAGAATTT-AATTAA
1 AAATACCTAAGAATTTGAATTAA
95161 TGTAAGTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
24 6 0.08
25 66 0.92
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (25 bp):
AAATACCTAAGAATTTGAATTAAAA
Found at i:95205 original size:39 final size:40
Alignment explanation
Indices: 95151--95231 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
95141 ATACCTAAGA
*
95151 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
95190 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
95230 AT
1 AT
95232 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:96821 original size:16 final size:16
Alignment explanation
Indices: 96800--96831 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
96790 GAAAGGAATT
96800 CCGTTCATTATATTTG
1 CCGTTCATTATATTTG
96816 CCGTTCATTATATTTG
1 CCGTTCATTATATTTG
96832 AAAAGGGAGG
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:0.19, G:0.12, T:0.50
Consensus pattern (16 bp):
CCGTTCATTATATTTG
Found at i:97476 original size:9 final size:9
Alignment explanation
Indices: 97453--97486 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
97443 ACTCTAGCCC
97453 CTATATATA
1 CTATATATA
97462 -TATATATA
1 CTATATATA
97470 CTATATATA
1 CTATATATA
*
97479 CTAAATAT
1 CTATATAT
97487 TATTTGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (9 bp):
CTATATATA
Found at i:98914 original size:3 final size:3
Alignment explanation
Indices: 98906--98949 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
98896 ATTATAAGAA
* * *
98906 ATT ATT ATT ATT ATT ATT ATT ATT ATA ATG ATT ATT ATG ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
98950 GATTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:99290 original size:12 final size:12
Alignment explanation
Indices: 99260--99290 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
99250 CCTGGCAATC
*
99260 CGTGTTCCGTGT
1 CGTGTTTCGTGT
99272 CGTGTTTCGTGT
1 CGTGTTTCGTGT
99284 CGTGTTT
1 CGTGTTT
99291 ACATAGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.32, T:0.48
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:99792 original size:20 final size:21
Alignment explanation
Indices: 99755--99797 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
99745 AACCTGTTAA
*
99755 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
99776 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
99796 TT
1 TT
99798 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:99855 original size:42 final size:43
Alignment explanation
Indices: 99785--99867 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
99775 CTTAAACGTG
*
99785 TTAATCGTGTCTTGACACGATTAGGACACGAAACACGATAATT
1 TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATT
*
99828 TTAATCGTGTC-CGACACGATTCA-GACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATT-AGGACACGAAACACGATAA
99868 GTCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 25 0.68
43 12 0.32
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATT
Found at i:101058 original size:29 final size:29
Alignment explanation
Indices: 101007--101062 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
100997 TTGCGTCAAT
101007 GACATTTTACCCTCTAAACTTCAAATTAG
1 GACATTTTACCCTCTAAACTTCAAATTAG
*
101036 GACATTTTACCC-CTAAATTTTCAAATT
1 GACATTTTACCCTCTAAA-CTTCAAATT
101063 CAAGACAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
GACATTTTACCCTCTAAACTTCAAATTAG
Found at i:102420 original size:44 final size:44
Alignment explanation
Indices: 102357--102456 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
102347 CAAGCAGGTG
*
102357 AAAAACAGTATATATACTTAGAAGATTTCATACCAAGAAATTAC
1 AAAAATAGTATATATACTTAGAAGATTTCATACCAAGAAATTAC
102401 AAAAATAGTATATATACTTAGAAGATTTCATACCAAGAAATTAC
1 AAAAATAGTATATATACTTAGAAGATTTCATACCAAGAAATTAC
102445 AAAAATA-TATAT
1 AAAAATAGTATAT
102457 TGTATTGATA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 5 0.09
44 50 0.91
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (44 bp):
AAAAATAGTATATATACTTAGAAGATTTCATACCAAGAAATTAC
Found at i:111779 original size:22 final size:22
Alignment explanation
Indices: 111741--111956 Score: 152
Period size: 22 Copynumber: 9.8 Consensus size: 22
111731 AGATTTGAGA
*
111741 AGGTTATC-AAATCTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
* *
111762 TGGTTATCGAAATTTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
*
111784 ATCAGATTATCAAAATTT-ATA-AG
1 ---AGGTTATCAAAATTTCATAGAG
* * *
111807 AAGATTATCAAAATTTTATAGTG
1 -AGGTTATCAAAATTTCATAGAG
*** * * *
111830 TTATAATCAAAATTTCAAAGCG
1 AGGTTATCAAAATTTCATAGAG
*
111852 AGGTTATCAAAATTACATA-ATG
1 AGGTTATCAAAATTTCATAGA-G
* *
111874 TGATTATCAAAATTTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
* * * * *
111896 GGGTCAACAAGATTTTATAGAG
1 AGGTTATCAAAATTTCATAGAG
*
111918 AGGTTATCAAAATTTCATAAAG
1 AGGTTATCAAAATTTCATAGAG
*
111940 AGGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCA
111957 AAATGTGATT
Statistics
Matches: 151, Mismatches: 36, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
21 22 0.15
22 110 0.73
23 4 0.03
24 3 0.02
25 12 0.08
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGAG
Found at i:111799 original size:25 final size:22
Alignment explanation
Indices: 111765--111827 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 22
111755 CATAGAGTGG
*
111765 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTT-ATAGAGA--AGA
111790 TTATCAAAATTTATA-AGAAGA
1 TTATCAAAATTTATAGAGAAGA
111811 TTATCAAAATTTTATAG
1 TTATCAAAA-TTTATAG
111828 TGTTATAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 12 0.34
22 6 0.17
23 3 0.09
24 3 0.09
25 11 0.31
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTATAGAGAAGA
Found at i:111973 original size:44 final size:44
Alignment explanation
Indices: 111788--111980 Score: 146
Period size: 44 Copynumber: 4.4 Consensus size: 44
111778 ATAGAGATCA
* * *
111788 GATTATCAAAATTT-AT-AAGAAGATTATCAAAATTTT-ATAGTGT
1 GATTATCAAAATTTCATAAAG-AGGTTATC-AAATTTTCAAAATGT
* * * * * *
111831 TATAATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
* * * * * *
111875 GATTATCAAAATTTCATAGAGGGGTCAACAAGATTTT-ATAGA-GA
1 GATTATCAAAATTTCATAAAGAGGTTATCAA-ATTTTCA-AAATGT
*
111919 GGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
*
111963 GATTACCAAAATTTCATA
1 GATTATCAAAATTTCATA
111981 GTGGTATTTC
Statistics
Matches: 113, Mismatches: 28, Indels: 17
0.72 0.18 0.11
Matches are distributed among these distances:
43 24 0.21
44 83 0.73
45 6 0.05
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
Found at i:112220 original size:22 final size:22
Alignment explanation
Indices: 112081--112641 Score: 282
Period size: 22 Copynumber: 25.7 Consensus size: 22
112071 TCAGGCAGGA
112081 TATCAAAATTTCATA-TGAAGGT
1 TATCAAAATTTCATAGTG-AGGT
* *
112103 TATTAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG-TGAGGT
* *
112125 TTTCAAAATTTCATA-CGAGGGT
1 TATCAAAATTTCATAGTGA-GGT
*
112147 TATCAAAATTTCATAGT-ATGT
1 TATCAAAATTTCATAGTGAGGT
* * *
112168 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGAGGT
** * *
112191 TAAAAAAATTTCATAATCAGGT
1 TATCAAAATTTCATAGTGAGGT
** *
112213 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTGAGGT
112235 TATCAAAA-TT--T-GT-A-GT
1 TATCAAAATTTCATAGTGAGGT
*
112251 TATCAAGATTTCATTAG-GAGGT
1 TATCAAAATTTCA-TAGTGAGGT
*
112273 TATCAAAATTTTATAGTGAGGTT
1 TATCAAAATTTCATAGTGAGG-T
*
112296 TATCAAAATTTTATAG-GAAGGTT
1 TATCAAAATTTCATAGTG-AGG-T
*
112319 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGTGAGGT
* * *
112341 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGAGGT
* * *
112363 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGAGGT
* *
112385 TA-CTAACAA-TTCATA-TAAATGT
1 TATC-AA-AATTTCATAGT-GAGGT
* * * ** *
112407 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAGTGAGGT
* *
112429 TATCAATATATCATA-TGTAGGT
1 TATCAAAATTTCATAGTG-AGGT
* * * *
112451 TATTAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-AGGT
* * * *
112474 TATCAAAATTCCATTGGGAAGT
1 TATCAAAATTTCATAGTGAGGT
112496 TATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATAGTGAGGT
* * **
112518 CT-TCAAAATTCCTTAGCAAGGT
1 -TATCAAAATTTCATAGTGAGGT
* *
112540 TAACAAAATTTCATAAG-AAGGT
1 TATCAAAATTTCAT-AGTGAGGT
** ***
112562 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATAGTGAGGT
* * * *
112583 TCTCGAAATTCCATAGT-ATCGT
1 TATCAAAATTTCATAGTGA-GGT
* *
112605 TATTAAAATTTCATAG-GAAGAT
1 TATCAAAATTTCATAGTG-AGGT
112627 TATCAAAATTTCATA
1 TATCAAAATTTCATA
112642 AGGAGGTCAT
Statistics
Matches: 407, Mismatches: 98, Indels: 68
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 1 0.00
20 3 0.01
21 27 0.07
22 294 0.72
23 67 0.16
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGAGGT
Found at i:112656 original size:22 final size:22
Alignment explanation
Indices: 112609--112656 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
112599 TATCGTTATT
* *
112609 AAAATTTCATAGGAAGATTATC
1 AAAATTTCATAGGAAGATCATA
*
112631 AAAATTTCATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGATCATA
112653 AAAA
1 AAAA
112657 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATCATA
Found at i:117577 original size:5 final size:5
Alignment explanation
Indices: 117569--117616 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
117559 CTATCATCAC
117569 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT A-C-T ATCTT A-C-T ATCTT
1 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT
117615 AT
1 AT
117617 TACTATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 4 0.10
4 4 0.10
5 31 0.79
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (5 bp):
ATCTT
Found at i:118335 original size:20 final size:20
Alignment explanation
Indices: 118291--118341 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
118281 TACTTCTGTT
**
118291 AAAAAAAAATCTATATCCAC
1 AAAAAAAAATCTATATAAAC
118311 AAAAAAAAATCTATGATAAAC
1 AAAAAAAAATCTAT-ATAAAC
118332 AAAACAAAAA
1 AAAA-AAAAA
118342 GTTTTCCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 14 0.52
21 8 0.30
22 5 0.19
ACGTcount: A:0.69, C:0.14, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAAAAATCTATATAAAC
Found at i:119325 original size:1 final size:1
Alignment explanation
Indices: 119319--119364 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
119309 TAGCTTTCGT
* * * *
119319 AAAAAAAAAAAAAAAAAAAAAACAAAAACAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
119365 TGATTTCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:119330 original size:6 final size:6
Alignment explanation
Indices: 119319--119364 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
119309 TAGCTTTCGT
* *
119319 AAAAA- AAAAAA AAAAAA AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
119365 TGATTTCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:120321 original size:44 final size:44
Alignment explanation
Indices: 120253--120377 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
120243 TGACAATCAA
* * * * * *
120253 ACCAAAATTACATAGAAAGATTATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
* ** *
120297 ACCAAAATTTCATATATCGGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
* *
120341 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAG
120378 GGAGGGAGGT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
Found at i:120382 original size:22 final size:22
Alignment explanation
Indices: 120253--120490 Score: 105
Period size: 22 Copynumber: 10.9 Consensus size: 22
120243 TGACAATCAA
* * *
120253 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * * *
120275 ATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATAGAGAGGTT
* **
120297 ACCAAAATTTCATATATCGGTT
1 ACCAAAATTTCATAGAGAGGTT
* * *
120319 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGAG-AGGTT
* *
120341 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
120363 ACCAAAATTTCATAGGGAGGGAGGTT
1 ACCAAAATTTCATA--GA--GAGGTT
* *
120389 ACCAAAA-TT--T---GTGCTT
1 ACCAAAATTTCATAGAGAGGTT
* *
120405 ATCAAAATTTCCTAGAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* * *
120427 AACAAAATTTTATAGGGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
*** * *
120449 ATGGAAATTTTATGGAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* *
120471 ATCGAAAA-TACATAGAGAGG
1 A-CCAAAATTTCATAGAGAGG
120491 ATATCACAGT
Statistics
Matches: 160, Mismatches: 43, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
19 1 0.01
21 1 0.01
22 125 0.78
23 5 0.03
24 1 0.01
25 2 0.01
26 13 0.08
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.31
Consensus pattern (22 bp):
ACCAAAATTTCATAGAGAGGTT
Found at i:120565 original size:23 final size:22
Alignment explanation
Indices: 120517--120566 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
120507 CTCATAGGGA
* * **
120517 GGTTATCGAAATTTCATGGTGT
1 GGTTATCAAAATTTCATAGTAC
120539 GGTTATCAAAATTTTCATAGTAC
1 GGTTATCAAAA-TTTCATAGTAC
120562 GGTTA
1 GGTTA
120567 CCAATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAC
Found at i:120633 original size:22 final size:22
Alignment explanation
Indices: 120586--120724 Score: 129
Period size: 22 Copynumber: 6.4 Consensus size: 22
120576 TTTAGTGTAA
* * *
120586 TTATTAAAATTTTATAG-GCAGA
1 TTATCAAAATTTCATAGTG-AGG
* *
120608 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
120630 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
120652 TTACCCAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
120674 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
*
120696 TTATCGAAATTTCATA-TGAGG
1 TTATCAAAATTTCATAGTGAGG
120717 TTATCAAA
1 TTATCAAA
120725 TTTGCAAAAT
Statistics
Matches: 94, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.12
22 82 0.87
23 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:120662 original size:44 final size:42
Alignment explanation
Indices: 120614--120741 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 42
120604 CAGATTATCA
120614 AAATTTCACACTGAGGTTATCGAAATTTCATAGTGTGGTTACCC
1 AAATTTCACA-TGAGGTTATC-AAATTTCATAGTGTGGTTACCC
* * * * *
120658 AAATTTCACAGTGTGGTTATCAAATTTTCATAGGGAGGTTATCG
1 AAATTTCACA-TGAGGTTATCAAA-TTTCATAGTGTGGTTACCC
* * *
120702 AAATTTCATATGAGGTTATCAAATTTGCAAAATGTGGTTA
1 AAATTTCACATGAGGTTATCAAATTT-CATAGTGTGGTTA
120742 TCTTTTTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 3 0.04
43 24 0.34
44 43 0.61
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (42 bp):
AAATTTCACATGAGGTTATCAAATTTCATAGTGTGGTTACCC
Found at i:120662 original size:66 final size:64
Alignment explanation
Indices: 120605--120727 Score: 156
Period size: 66 Copynumber: 1.9 Consensus size: 64
120595 TTTTATAGGC
* *
120605 AGATTATCAAAATTTCACACTGAGGTTATCGAAATTTCATAGTGTGGTTACCCAAATTTCACAGT
1 AGATTATCAAAATTTCACACGGAGGTTATCGAAATTTCATA-TGAGGTTA-CCAAATTTCACAGT
120670 G
64 G
* * * * * *
120671 TGGTTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATATGAGGTTATCAAATTT
1 AGATTATCAAAATTTCACACGGAGGTTATCGAAATTTCATATGAGGTTACCAAATTT
120728 GCAAAATGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 7 0.14
65 7 0.14
66 35 0.71
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (64 bp):
AGATTATCAAAATTTCACACGGAGGTTATCGAAATTTCATATGAGGTTACCAAATTTCACAGTG
Found at i:120742 original size:22 final size:21
Alignment explanation
Indices: 120608--120743 Score: 103
Period size: 22 Copynumber: 6.2 Consensus size: 21
120598 TATAGGCAGA
* * *
120608 TTATCAAAATTTCACACTGAGG
1 TTATC-AAATTTCAAAGTGTGG
*
120630 TTATCGAAATTTCATAGTGTGG
1 TTATC-AAATTTCAAAGTGTGG
* *
120652 TTACCCAAATTTCACAGTGTGG
1 TTA-TCAAATTTCAAAGTGTGG
* * *
120674 TTATCAAATTTTCATAGGGAGG
1 TTATCAAA-TTTCAAAGTGTGG
* *
120696 TTATCGAAATTTCATA-TGAGG
1 TTATC-AAATTTCAAAGTGTGG
*
120717 TTATCAAATTTGCAAAATGTGG
1 TTATCAAATTT-CAAAGTGTGG
120739 TTATC
1 TTATC
120744 TTTTTTTTTA
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.06
21 16 0.17
22 70 0.73
23 4 0.04
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (21 bp):
TTATCAAATTTCAAAGTGTGG
Found at i:122557 original size:44 final size:43
Alignment explanation
Indices: 122492--122615 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
122482 TGACAATCAA
* * * **
122492 ACCAAAATTACATAGGAAGGTTATTAAAATTTCATTGTGTTGTT
1 ACCAAAATTTCATAGG-AGGTTATCAAAATTTCATAGTGTAATT
* *
122536 ACCAAAATTTCATATGGAGGTTATCAAAACTTCGTAGTGTAATT
1 ACCAAAATTTCATA-GGAGGTTATCAAAATTTCATAGTGTAATT
* * *
122580 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATA
1 ACCAAAATTTCATA-GGAGGTTATCAAAATTTCATA
122616 AAAAAAAAGT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
44 64 0.97
45 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (43 bp):
ACCAAAATTTCATAGGAGGTTATCAAAATTTCATAGTGTAATT
Found at i:122672 original size:22 final size:22
Alignment explanation
Indices: 122494--122672 Score: 89
Period size: 22 Copynumber: 8.0 Consensus size: 22
122484 ACAATCAAAC
* *
122494 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* * *
122516 TAAAATTTCAT-TG-TGTTGTTAC
1 CAAAATTTCATATGAAG--GTTAT
*
122538 CAAAATTTCATATGGAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* *
122560 CAAAACTTCGTAGTGTAA--TTAT
1 CAAAATTTCATA-TG-AAGGTTAT
* *
122582 CAAAATTTCATA-CAGAGGTTAC
1 CAAAATTTCATATGA-AGGTTAT
** *
122604 CAAAATTTCATAAAAAAAAAGTTAT
1 CAAAATTTCAT---ATGAAGGTTAT
* * * *
122629 CAAAATCTCTTATGGAGATTAT
1 CAAAATTTCATATGAAGGTTAT
*
122651 CAAAATTTCATACGAAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
122673 TGAAATTTTA
Statistics
Matches: 114, Mismatches: 30, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 1 0.01
22 88 0.77
23 4 0.04
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATATGAAGGTTAT
Found at i:122763 original size:42 final size:42
Alignment explanation
Indices: 122716--122813 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
122706 AGAACGTTAA
122716 CAAAATTTCATAGGGAGGGAGGTTATCAAAATTTGTTCTTAT
1 CAAAATTTCATAGGGAGGGAGGTTATCAAAATTTGTTCTTAT
*
122758 CAAAATTTCATAGGGAGGGAGGTTATCAAAATTTGTTTTTAT
1 CAAAATTTCATAGGGAGGGAGGTTATCAAAATTTGTTCTTAT
*
122800 CAAAATTTCCTAGG
1 CAAAATTTCATAGG
122814 ATGGTTAACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (42 bp):
CAAAATTTCATAGGGAGGGAGGTTATCAAAATTTGTTCTTAT
Found at i:122841 original size:22 final size:22
Alignment explanation
Indices: 122796--123147 Score: 86
Period size: 22 Copynumber: 15.6 Consensus size: 22
122786 AAATTTGTTT
*
122796 TTATCAAAATTTCCTA-GGATGG
1 TTATCAAAATTTCATAGGGA-GG
*
122818 TTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
*
122840 TTATGAAAATATT-AT-GGAGAGG
1 TTATCAAAAT-TTCATAGG-GAGG
* ** *
122862 TTATCAAAATTGCATATAGAGA
1 TTATCAAAATTTCATAGGGAGG
* * *
122884 ATATCACAATTTCATTCTTATAGGGAAG
1 TTATCA-AA----ATT-TCATAGGGAGG
* * *
122912 TTATCGAAATTCCAT-GGTGTGG
1 TTATCAAAATTTCATAGG-GAGG
* * * *
122934 TTGTCAAAATTTTCATAGTGCGA
1 TTATCAAAA-TTTCATAGGGAGG
* * ** * *
122957 TTA-C-CAATTTTATAATGTGA
1 TTATCAAAATTTCATAGGGAGG
*
122977 TTATCAAAATTTCATAGACAATGAGG
1 TTATCAAAATTTCATAG----GGAGG
* * * *
123003 TTATCAAAACTTCATTGTGTGG
1 TTATCAAAATTTCATAGGGAGG
* * * *
123025 TTATCAGAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGGGAGG
* ** *
123047 TTATCAAAATTTCACATTGTGG
1 TTATCAAAATTTCATAGGGAGG
* **
123069 TTATCAAATTTTCATATTGAGG
1 TTATCAAAATTTCATAGGGAGG
* * ***
123091 TTATCGAAATTTCACAATAAGG
1 TTATCAAAATTTCATAGGGAGG
* * * *
123113 TTATCAAATTTTCGTAGTGTGG
1 TTATCAAAATTTCATAGGGAGG
*
123135 TTATCAATATTTC
1 TTATCAAAATTTC
123148 TACGTTGGAG
Statistics
Matches: 246, Mismatches: 64, Indels: 40
0.70 0.18 0.11
Matches are distributed among these distances:
20 13 0.05
21 8 0.03
22 173 0.70
23 19 0.08
24 1 0.00
26 18 0.07
27 5 0.02
28 9 0.04
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:123068 original size:44 final size:44
Alignment explanation
Indices: 123001--123147 Score: 163
Period size: 44 Copynumber: 3.3 Consensus size: 44
122991 TAGACAATGA
* * *
123001 GGTTATCAAAACTTCA-TTGTGTGGTTATCAGAA-TTTCACAGTGT
1 GGTTATCAAAATTTCACAT-TGTGGTTATCA-AATTTTCATAGTGT
* *
123045 GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCATATTGA
1 GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCATAGTGT
* * ** *
123089 GGTTATCGAAATTTCACAATAAGGTTATCAAATTTTCGTAGTGT
1 GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCATAGTGT
*
123133 GGTTATCAATATTTC
1 GGTTATCAAAATTTC
123148 TACGTTGGAG
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.02
44 84 0.97
45 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (44 bp):
GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCATAGTGT
Found at i:123093 original size:66 final size:66
Alignment explanation
Indices: 123001--123146 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 66
122991 TAGACAATGA
** * * ** *
123001 GGTTATCAAAACTTCATTGTGTGGTTATC-AGAATTTCACAGTGTGGTTATCAAAATTTCACATT
1 GGTTATCAAATTTTCATTGTGAGGTTATCGA-AATTTCACAATAAGGTTATCAAAATTTCACAGT
123065 GT
65 GT
* **
123067 GGTTATCAAATTTTCATAT-TGAGGTTATCGAAATTTCACAATAAGGTTATCAAATTTTCGTAGT
1 GGTTATCAAATTTTCAT-TGTGAGGTTATCGAAATTTCACAATAAGGTTATCAAAATTTCACAGT
123131 GT
65 GT
123133 GGTTATCAATATTT
1 GGTTATCAA-ATTT
123147 CTACGTTGGA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
66 61 0.91
67 6 0.09
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (66 bp):
GGTTATCAAATTTTCATTGTGAGGTTATCGAAATTTCACAATAAGGTTATCAAAATTTCACAGTG
T
Found at i:125028 original size:130 final size:130
Alignment explanation
Indices: 124794--125046 Score: 452
Period size: 130 Copynumber: 1.9 Consensus size: 130
124784 GGACAAATGT
* *
124794 CAACAGGAGAAAAGCCAAATGTTGAGCATACAACAATTTGAGGATACCTTTAATAGTAAGGTATA
1 CAACAGGAGAAAAGCCAAATGTTGAGCATACAACAATTTGAGGATAACTTTAATAATAAGGTATA
*
124859 GATTAACAAAAAAATTATATTACACAAGATGTAACTTAAAATCAGTTTTCATCAAACTGAGCATA
66 GATTAACAAAAAAATTATATTACACAAAATGTAACTTAAAATCAGTTTTCATCAAACTGAGCATA
* *
124924 CAACAGGAGAAATGCCAAATGTTGAGCATACAACAGTTTGAGGATAACTTTAATAATAAGGTATA
1 CAACAGGAGAAAAGCCAAATGTTGAGCATACAACAATTTGAGGATAACTTTAATAATAAGGTATA
*
124989 GATTAACAAAAAAATTATATTACACAAAATGTAATTTAAAATCAGTTTTCATCAAACT
66 GATTAACAAAAAAATTATATTACACAAAATGTAACTTAAAATCAGTTTTCATCAAACT
125047 TCAATCCCAC
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 117 1.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (130 bp):
CAACAGGAGAAAAGCCAAATGTTGAGCATACAACAATTTGAGGATAACTTTAATAATAAGGTATA
GATTAACAAAAAAATTATATTACACAAAATGTAACTTAAAATCAGTTTTCATCAAACTGAGCATA
Found at i:129398 original size:20 final size:20
Alignment explanation
Indices: 129373--129410 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
129363 GTACACTTGG
129373 AGTACGGATTAACGAATTGC
1 AGTACGGATTAACGAATTGC
129393 AGTACGGATTAACGAATT
1 AGTACGGATTAACGAATT
129411 TGCTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (20 bp):
AGTACGGATTAACGAATTGC
Found at i:130541 original size:28 final size:28
Alignment explanation
Indices: 130488--130541 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
130478 GCCTAGGTTC
*
130488 TTTGCTCCACGAAAAACACCACAAAACA
1 TTTGCTCCACGAAAAACACCAAAAAACA
* *
130516 TTTGCTTCAC-AAGAACACCTAAAAAA
1 TTTGCTCCACGAAAAACACC-AAAAAA
130542 AGAAGGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.19
Consensus pattern (28 bp):
TTTGCTCCACGAAAAACACCAAAAAACA
Found at i:134300 original size:64 final size:64
Alignment explanation
Indices: 134135--134395 Score: 346
Period size: 65 Copynumber: 4.1 Consensus size: 64
134125 TGTTCCACTG
* * * **
134135 GGGAAACTGCAGGGGGGCCAACCACTGGGGTCTTACGGCACACGACCTGATTTGACGTTCCGAT
1 GGGAGACTGCAGGGGGGCCAACCACTGGGGTCTTACGGCACACGACCTGATTTAACGTCCCTCT
* * *
134199 GGCGAGACTGCAGGGGGGCTAACCACTGGGGTCTTACGGCGCACCACCTGATTTAACGTCCCTCT
1 GG-GAGACTGCAGGGGGGCCAACCACTGGGGTCTTACGGCACACGACCTGATTTAACGTCCCTCT
* *
134264 GGGAGACTGCAGGTGGGCCAACCACTGGGGTCTTACGGCACACGACCTGATTTAACGTCCCTTT
1 GGGAGACTGCAGGGGGGCCAACCACTGGGGTCTTACGGCACACGACCTGATTTAACGTCCCTCT
* ** * *
134328 GGGGAGACTGCAGGTGGGCTTA-CACT-AGGTCTTACGGCGCACGACCTGATTTAACGTCCCTCT
1 -GGGAGACTGCAGGGGGGCCAACCACTGGGGTCTTACGGCACACGACCTGATTTAACGTCCCTC-
134391 T
64 T
134392 GGGA
1 GGGA
134396 AGCAAGGCAG
Statistics
Matches: 176, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
63 37 0.21
64 64 0.36
65 75 0.43
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.21
Consensus pattern (64 bp):
GGGAGACTGCAGGGGGGCCAACCACTGGGGTCTTACGGCACACGACCTGATTTAACGTCCCTCT
Found at i:134509 original size:23 final size:25
Alignment explanation
Indices: 134401--134536 Score: 159
Period size: 25 Copynumber: 5.5 Consensus size: 25
134391 TGGGAAGCAA
* * * *
134401 GGCAGTCCTTCTTAGGGGAGTTTGT
1 GGCATTCCCTCTTTGGGGAGCTTGT
* *
134426 GGCATTCCCTCTTTAGGGAGCTTGA
1 GGCATTCCCTCTTTGGGGAGCTTGT
*
134451 GGCATTCTCTCTTTGGGGAGCTTGT
1 GGCATTCCCTCTTTGGGGAGCTTGT
134476 GGCATTCCCTCTTTGGGGAG-TT-T
1 GGCATTCCCTCTTTGGGGAGCTTGT
* *
134499 GGCATTACCTCTTTGGGGAGCTTGA
1 GGCATTCCCTCTTTGGGGAGCTTGT
**
134524 GGCGGTCCCTCTT
1 GGCATTCCCTCTT
134537 AAGGAGCTTG
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
23 20 0.21
24 4 0.04
25 70 0.74
ACGTcount: A:0.11, C:0.22, G:0.32, T:0.35
Consensus pattern (25 bp):
GGCATTCCCTCTTTGGGGAGCTTGT
Found at i:134522 original size:48 final size:50
Alignment explanation
Indices: 134410--134547 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 50
134400 AGGCAGTCCT
* *
134410 TCTTAGGGGAGTTTGTGGCATTCCCTCTTTAGGGAGCTTGAGGCATTCTC
1 TCTTTGGGGAGCTTGTGGCATTCCCTCTTTAGGGAGCTTGAGGCATTCTC
* *
134460 TCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAG-TT-TGGCATTAC-C
1 TCTTTGGGGAGCTTGTGGCATTCCCTCTTTAGGGAGCTTGAGGCATT-CTC
* ** *
134508 TCTTTGGGGAGCTTGAGGCGGTCCCTC-TTAAGGAGCTTGA
1 TCTTTGGGGAGCTTGTGGCATTCCCTCTTTAGGGAGCTTGA
134548 TGGGAGCGCA
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
47 6 0.08
48 33 0.44
49 3 0.04
50 33 0.44
ACGTcount: A:0.13, C:0.20, G:0.32, T:0.35
Consensus pattern (50 bp):
TCTTTGGGGAGCTTGTGGCATTCCCTCTTTAGGGAGCTTGAGGCATTCTC
Found at i:134846 original size:50 final size:49
Alignment explanation
Indices: 134792--134959 Score: 119
Period size: 50 Copynumber: 3.4 Consensus size: 49
134782 TCTTACGACT
*
134792 GAGAAAGATGGCGCTCCGCCTGATTTCCGTCCAGTGGGGGAATTATTGCA
1 GAGAAAGATGGCG-TCCGCCTGATTTCCGCCCAGTGGGGGAATTATTGCA
* * * * ** ** *
134842 GAGAATGA-GGCGTCCGCCCG-TCTTACGGCCC-GTCATGGGGTCTTACGGCC
1 GAGAAAGATGGCGTCCGCCTGAT-TT-CCGCCCAGT--GGGGGAATTATTGCA
* * * *
134892 GAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGTA
1 GAGAAAGATGGCG-TCCGCCTGATTTCCGCCCAGTGGGGGAATTATTGCA
*
134942 GAGAATGAT-GCGTCCGCC
1 GAGAAAGATGGCGTCCGCC
134960 GGTCTTACGG
Statistics
Matches: 85, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
47 1 0.01
48 16 0.19
49 11 0.13
50 39 0.46
51 8 0.09
52 9 0.11
53 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (49 bp):
GAGAAAGATGGCGTCCGCCTGATTTCCGCCCAGTGGGGGAATTATTGCA
Found at i:134934 original size:100 final size:100
Alignment explanation
Indices: 134743--135247 Score: 762
Period size: 100 Copynumber: 5.1 Consensus size: 100
134733 TTACTATCTG
* * * * *
134743 GAATGACGGTGTCTGCCGGTCTTACGACCCGTCATGGGGTCTTACGACTGAGAAAGATGGCGCTC
1 GAATGA-GGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTC
* * **
134808 CGCCTGATTTCCGTCCAGTGGGGGAATTATTGCAGA
65 GGCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGA
*
134844 GAATGAGGCGTCCGCCCGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
1 GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
*
134909 GCCTGATTGCCCCCCAGTGGGGGAATTATTGTAGA
66 GCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGA
* *
134944 GAATGATGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAAAAAGATGGCGCTCG
1 GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
* * *
135009 GCCTAATTGCCCCACAGTGGAGGAATTATTGCAGA
66 GCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGA
* * * *
135044 GAATGATGTGTCCGCTGGTCTTACGG-CCGTCATGGGGTCTTACGGCCGAGAAAGATGGCACTCG
1 GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
*
135108 GCCTGATTG-CCCCCAGTGGTGGAATTATTGCAGA
66 GCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGA
* *
135142 GAATGAGGCGTCCGCCAGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
1 GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
* *
135207 GCCTGATTGCCCCACAGTGGGAGAATTATTGCAGA
66 GCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGA
135242 GAATGA
1 GAATGA
135248 TCCAAGAGAA
Statistics
Matches: 368, Mismatches: 34, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
98 45 0.12
99 89 0.24
100 228 0.62
101 6 0.02
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (100 bp):
GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
GCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGA
Found at i:135183 original size:198 final size:199
Alignment explanation
Indices: 134743--135248 Score: 775
Period size: 198 Copynumber: 2.5 Consensus size: 199
134733 TTACTATCTG
* * * *
134743 GAATGACGGTGTCTGCCGGTCTTACGACCCGTCATGGGGTCTTACGACTGAGAAAGATGGCGCTC
1 GAATGA-GGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTC
* * * *
134808 CGCCTGATTTCCGTC-CAGTGGGGGAATTATTGCAGAGAATGAGGCGTCCGCCCGTCTTACGGCC
65 GGCCTGATTGCC-CCACAGT-GGGGAATTATTGCAGAGAATGATGCGTCCGCCCGTCTTACGGCC
*
134872 CGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTA
128 CGTCATGGGGTCTTACGGCCGAGAAAGATGGCACTCGGCCTGATTGCCCCCCAGTGGGGGAATTA
*
134937 TTGTAGA
193 TTGCAGA
* * *
134944 GAATGATGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAAAAAGATGGCGCTCG
1 GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
* * **
135009 GCCTAATTGCCCCACAGTGGAGGAATTATTGCAGAGAATGATGTGTCCGCTGGTCTTACGG-CCG
66 GCCTGATTGCCCCACAGTGG-GGAATTATTGCAGAGAATGATGCGTCCGCCCGTCTTACGGCCCG
*
135073 TCATGGGGTCTTACGGCCGAGAAAGATGGCACTCGGCCTGATTG-CCCCCAGTGGTGGAATTATT
130 TCATGGGGTCTTACGGCCGAGAAAGATGGCACTCGGCCTGATTGCCCCCCAGTGGGGGAATTATT
135137 GCAGA
195 GCAGA
*
135142 GAATGAGGCGTCCGCCAGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
1 GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
135207 GCCTGATTGCCCCACAGTGGGAGAATTATTGCAGAGAATGAT
66 GCCTGATTGCCCCACAGTGGG-GAATTATTGCAGAGAATGAT
135249 CCAAGAGAAG
Statistics
Matches: 279, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
197 1 0.00
198 123 0.44
199 49 0.18
200 100 0.36
201 6 0.02
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (199 bp):
GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
GCCTGATTGCCCCACAGTGGGGAATTATTGCAGAGAATGATGCGTCCGCCCGTCTTACGGCCCGT
CATGGGGTCTTACGGCCGAGAAAGATGGCACTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTG
CAGA
Found at i:138048 original size:21 final size:22
Alignment explanation
Indices: 138024--138069 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
138014 GAATTTCGAG
* *
138024 AACCTTTTTAT-AAATTTTTTT
1 AACCTTCTTATGAAATTTTGTT
138045 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
138067 AAC
1 AAC
138070 ATTCCTAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.52
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:138316 original size:22 final size:22
Alignment explanation
Indices: 138035--138653 Score: 222
Period size: 22 Copynumber: 28.5 Consensus size: 22
138025 ACCTTTTTAT
** * *
138035 AAATTTTTTTAACCTTCTTATG
1 AAATTTTGATAACCTCCCTATG
* * * *
138057 AAATTTTGTTAACATTCCTAAG
1 AAATTTTGATAACCTCCCTATG
* *
138079 GAATTTTGA-AGACCTCACTATG
1 AAATTTTGATA-ACCTCCCTATG
* **
138101 AAATTTTGATAACTTCCGAATG
1 AAATTTTGATAACCTCCCTATG
*
138123 AAATTTTGATAACCAACAACACTATG
1 AAATTTTGATAACC-TC--C-CTATG
* * **
138149 AGATGTTGATAACCTCTATATG
1 AAATTTTGATAACCTCCCTATG
* * * * **
138171 ATATATTGATAATCACGTTATG
1 AAATTTTGATAACCTCCCTATG
* * * *
138193 AAAATTTAAAAACCTCCATATG
1 AAATTTTGATAACCTCCCTATG
* * * *
138215 -AATTGTT-AGTAATCACACTCTG
1 AAATT-TTGA-TAACCTCCCTATG
* * * *
138237 AAATTTTGATAATCACACTATA
1 AAATTTTGATAACCTCCCTATG
* * *
138259 AAATTGTGATAACCT-CGTATA
1 AAATTTTGATAACCTCCCTATG
*
138280 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCCCTATG
*
138303 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCCTATG
* *
138325 AAATCTTGATAA-----CTA-C
1 AAATTTTGATAACCTCCCTATG
*
138341 AAATTTTGATAACCTCTCTATG
1 AAATTTTGATAACCTCCCTATG
** **
138363 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
138385 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* * *
138407 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCCCTATG
* ** *
138429 AAATTTTGA-AAACTAAACTATA
1 AAATTTTGATAACCT-CCCTATG
* *
138451 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATG
*
138473 AAATTTTGATATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
* * *
138493 AAATTTTGATCA-CTCCATAGTA
1 AAATTTTGATAACCTCCCTA-TG
* * * *
138515 AAAGTTTAATAAGCTTCC--T-
1 AAATTTTGATAACCTCCCTATG
* **
138534 -AATTTAG-TAACCAT-AGTATG
1 AAATTTTGATAACC-TCCCTATG
**
138554 AAATTTTGATAACCTCCCCGTG
1 AAATTTTGATAACCTCCCTATG
* * *
138576 AAATATT-AGTAACCTTCTTATG
1 AAATTTTGA-TAACCTCCCTATG
* * *
138598 AAATTTTGTTAACCACACTATG
1 AAATTTTGATAACCTCCCTATG
**
138620 AAATTCTT-ATAACCTTGCTATG
1 AAATT-TTGATAACCTCCCTATG
*
138642 ACATTTTGATAA
1 AAATTTTGATAA
138654 TCTCTTTGAT
Statistics
Matches: 435, Mismatches: 125, Indels: 74
0.69 0.20 0.12
Matches are distributed among these distances:
16 11 0.03
17 6 0.01
18 5 0.01
19 5 0.01
20 15 0.03
21 31 0.07
22 312 0.72
23 33 0.08
25 2 0.00
26 15 0.03
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:138701 original size:22 final size:22
Alignment explanation
Indices: 138676--138914 Score: 135
Period size: 22 Copynumber: 10.8 Consensus size: 22
138666 CCTTTCTATA
*
138676 AAATTGTGATAACCACATTATG
1 AAATTTTGATAACCACATTATG
** ** *
138698 AAATTTCAATAACC-TTTCTAAG
1 AAATTTTGATAACCACAT-TATG
* **
138720 AAATTTTAATAACCTGATTCTATG
1 AAATTTTGATAACCACA-T-TATG
* *
138744 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACATTATG
* *
138766 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACATTATG
* * **
138788 AAATTTTGGTAACCTTC-CCATG
1 AAATTTTGATAACC-ACATTATG
**
138810 AAATTTTGATAACTTTCA-TATG
1 AAATTTTGATAAC-CACATTATG
* **
138832 AAATTTTGGTAACCACACGATG
1 AAATTTTGATAACCACATTATG
* * * *
138854 GAATTTTGATAACCTCCTCATG
1 AAATTTTGATAACCACATTATG
* *
138876 AAATTATAATAACCATC-TTATG
1 AAATTTTGATAACCA-CATTATG
*
138898 AAATTTTTATAACCACA
1 AAATTTTGATAACCACA
138915 CAGAGACAAG
Statistics
Matches: 171, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
21 4 0.02
22 147 0.86
23 2 0.01
24 18 0.11
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACATTATG
Found at i:138726 original size:78 final size:78
Alignment explanation
Indices: 138585--138731 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 78
138575 GAAATATTAG
* * * * * * *
138585 TAACCTTCTTATGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTTGCTATGACATTTTG
1 TAACCTTCTTATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTTGCTAAGAAATTTTA
138650 ATAATCTCTTTGA
66 ATAATCTCTTTGA
* *
138663 TAACCTT-TCTATAAAATTGTGATAACCACATTATGAAATT-TCAATAACCTTTCTAAGAAATTT
1 TAACCTTCT-TATAAAATTGTGATAACCACACTATGAAATTCT-AATAACCTTGCTAAGAAATTT
138726 TAATAA
64 TAATAA
138732 CCTGATTCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
77 2 0.03
78 56 0.97
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (78 bp):
TAACCTTCTTATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTTGCTAAGAAATTTTA
ATAATCTCTTTGA
Found at i:138800 original size:44 final size:43
Alignment explanation
Indices: 138671--138915 Score: 170
Period size: 44 Copynumber: 5.5 Consensus size: 43
138661 GATAACCTTT
* * * *** **
138671 CTATAAAATTGTGATAACCACATTATGAAATTTCAATAACCTTT
1 CTATGAAATTTTGATAACCACACTATGAAATTTTGGTAACC-AC
* * **
138715 CTAAGAAATTTTAATAACCTGATTCTATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAACC--ACACTATGAAATTTTGGTAACCAC
* *
138760 ACTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCTTC
1 -CTATGAAATTTTGATAACCACACTATGAAATTTTGGTAACC-AC
* **
138805 CCATGAAATTTTGATAACTTTCA-TATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAAC-CACACTATGAAATTTTGGTAACCAC
* * * * **
138848 ACGATGGAATTTTGATAACCTC-CTCATGAAATTATAATAACCATC
1 -CTATGAAATTTTGATAACCACACT-ATGAAATTTTGGTAACCA-C
* *
138893 TTATGAAATTTTTATAACCACAC
1 CTATGAAATTTTGATAACCACAC
138916 AGAGACAAGA
Statistics
Matches: 157, Mismatches: 34, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
43 4 0.03
44 116 0.74
45 5 0.03
46 32 0.20
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCACACTATGAAATTTTGGTAACCAC
Found at i:138839 original size:66 final size:66
Alignment explanation
Indices: 138753--138915 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 66
138743 GAAATTTTGG
* * *
138753 TAACCA-CACTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCTTCC-CATGAAATTT
1 TAACCATCA-TATGAAATTTTGGTAACCACACGATGAAATTTTGATAACC-TCCTCATGAAATTA
*
138816 TGA
64 TAA
** *
138819 TAACTTTCATATGAAATTTTGGTAACCACACGATGGAATTTTGATAACCTCCTCATGAAATTATA
1 TAACCATCATATGAAATTTTGGTAACCACACGATGAAATTTTGATAACCTCCTCATGAAATTATA
138884 A
66 A
* **
138885 TAACCATCTTATGAAATTTTTATAACCACAC
1 TAACCATCATATGAAATTTTGGTAACCACAC
138916 AGAGACAAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 3 0.04
66 78 0.94
67 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (66 bp):
TAACCATCATATGAAATTTTGGTAACCACACGATGAAATTTTGATAACCTCCTCATGAAATTATA
A
Found at i:140945 original size:6 final size:6
Alignment explanation
Indices: 140934--140978 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
140924 AAATACTATT
140934 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TAT
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TAT
140979 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:153071 original size:77 final size:77
Alignment explanation
Indices: 152967--153111 Score: 290
Period size: 77 Copynumber: 1.9 Consensus size: 77
152957 CATACATTTA
152967 AGCCAATGTTTTTGTGTTCTTGCCAAGCCATTTCAAACCGAAAGGGTCGAGGGAAGGGGAAGGGG
1 AGCCAATGTTTTTGTGTTCTTGCCAAGCCATTTCAAACCGAAAGGGTCGAGGGAAGGGGAAGGGG
153032 GGGGGGGGGGGC
66 GGGGGGGGGGGC
153044 AGCCAATGTTTTTGTGTTCTTGCCAAGCCATTTCAAACCGAAAGGGTCGAGGGAAGGGGAAGGGG
1 AGCCAATGTTTTTGTGTTCTTGCCAAGCCATTTCAAACCGAAAGGGTCGAGGGAAGGGGAAGGGG
153109 GGG
66 GGG
153112 AATGGTCATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.21
Consensus pattern (77 bp):
AGCCAATGTTTTTGTGTTCTTGCCAAGCCATTTCAAACCGAAAGGGTCGAGGGAAGGGGAAGGGG
GGGGGGGGGGGC
Found at i:155376 original size:325 final size:320
Alignment explanation
Indices: 153967--156282 Score: 2120
Period size: 325 Copynumber: 7.1 Consensus size: 320
153957 CATATTTTTT
* * * * * * *
153967 AATTAATTTTTAATTAAATCGAAACAAGATTTAAATACT-GTAAAAGCAAATCATTAAATCCAAT
1 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * * * * **** * *
154031 ATGTCTAAGATTTGATTAAAT-AATATAGATATTTCAAGGAGTATTGGCACCAAATATCATGCAA
66 GTGGCTGAGATTAGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAA
** ** * *
154095 AACTGAGCCG-GGGTCCGAAACGCGTTTTTATCCAAAAACCA-TGATGGTTAGTACACGATTTTG
131 AACTGAATCGAGGCCCCGAAACGCGTTTTTAGCCAAAAA-CAGTGATGGTTAGTACACGATTTCG
* * * *
154158 GCTAAAATTTTGAAAAAACTGACTCGAAAA-GTTTTCCTCAA-TTTTTGCCTATAATACTCATAA
195 GC--------T--AAAAACTGACCCGAAAATTTTTTCCTCAATTTTTTGCC-ACAATACTCAGAA
* * * * *
154221 AAACTATATAATTTAAGGCCAAAAATATTGAAGGGGTTTTCACGCTT-TCAATATCGTTTATCCA
249 AAAATATATAATTCAACGCCAAAAA-ATTGAAGGGTTTTTCACGCTTCT-AATATCGTTT-TTCA
154285 -TTTTTTCCG
311 TTTTTTTCCG
* * * * * *
154294 AATTTATTTCAAATTAAATCGAAACAAGATTCAGATGTTCGTAAGAACAGATCCTAAAATCTAAT
1 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * *
154359 ATCGCTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTTTTTATGCCAAAAACCATGCAA
66 GTGGCTGAGATTAGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAA
* * * * *
154424 AACTGAGTCAAGGCCCCGACACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGA
131 AACTGAATCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTCGG
* *** * *
154489 CTAAAAACTGATCCGAAAAAAAAAATTT-CTGAATTTTTTGCCACAATACTAAGAAAAAATATAT
196 CTAAAAACTGACCCG---AAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATAT
* * * *
154553 AATTCAACGCCAAAAAGAGTGACA-GGCTTTTCGCGCTTCTAATATCGTTTTTTCATTTTTTTCA
258 AATTCAACGCCAAAAA-ATTGA-AGGGTTTTTCACGCTTCTAATATCG-TTTTTCATTTTTTTCC
154617 G
320 G
* * * *
154618 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCGAT
1 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * ** *
154683 GTGGCTGAGATTTGCTTCGATGAAT-TGAAATATTTCAAGGAGTCTTTGCGCCAAAAAACATGCA
66 GTGGCTGAGATTAGGTTAGATGAATAT-AGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCA
** ** * * * *
154747 AAGTTGAGCCTG-GGCTCCGGAACACGTTTTTAGCCAAAAATCA-TGATGGTTTGTACACGATTT
130 AAACTGAATC-GAGGCCCCGAAACGCGTTTTTAGCCAAAAA-CAGTGATGGTTAGTACACGATTT
* * * *
154810 CGGCTAAAATTTTGCAATAACTGGCCCGAAGAGTTTTTCCTCAATTTTTTGCCGCAATACTCAGA
193 CGGCT---A------AA-AACTGACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGA
* * * * *
154875 AAAAATTTATAATTCAACGCCAATAAAACTAAAGGGTTTATCACGCTTCTAATATCGTTTTCCCA
248 AAAAATATATAATTCAACGCCAA-AAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTT-TCA
*
154940 -TTTTTTCAG
311 TTTTTTTCCG
* * *
154949 AATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCCCGTAAAAATAAATCCTTAAATCCAAT
1 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * *
155014 GTGGTTGAGATTTA-GTTAGATGAATATAGATATTTCAAGGAGACTTTATGCCAAAAACCATGGA
66 GTGGCTGAGA-TTAGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCA
* * * *
155078 AAATTGAATCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGCTAATACCCGATTTCG
130 AAACTGAATCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTCG
* * * * * *
155143 GCTAAAAACTGACCCGAACAATTTTTTTTCTAAACTTTTTGCCGCAATACTAATAAAAAATATAT
195 GCTAAAAACTGACCCGAA-AA-TTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATAT
*
155208 AATTCAATGCCAAAAAATTGAAGGGTTTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCC
258 AATTCAACGCCAAAAAATTGAAGGG-TTTTTCACGCTTCTAATATCGTTTTTCA--TTTTTTTCC
155273 G
320 G
* * * *
155274 AATTTATTTCTAATTAAAACGAAATAAGATTCAGATGCTCGCAAAAACAAATCCTTAAATCAAAT
1 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * * *
155339 GTGGCAGAGATTAGGTTAGATGAACATAGACATTTCAAGGAGTCTTTCTGCCAAAAATCTTGCAA
66 GTGGCTGAGATTAGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAA
* * * * **
155404 AACT-AAGTCGAGGCCCCAAAACGCTTTTTTAGCCCAAAAACCGTGATGATTAGTACATAATTTC
131 AACTGAA-TCGAGGCCCCGAAACGCGTTTTTAG-CCAAAAACAGTGATGGTTAGTACACGATTTC
* * * * * * * *
155468 TGCAAAAAACTAACACGAAAAATTTTTCTTCTGAATTTTTTTCCATAATACTCAGAAAAAATATA
194 GGCTAAAAACTGACCCG-AAAATTTTT-TCCTCAATTTTTTGCCACAATACTCAGAAAAAATATA
* * * * **
155533 TAATTTAACGCCAAAAAGCTTGGCA-GGCTTTTCTTGCTTCTAATATCGTTTTTCCATTTTTTTC
257 TAATTCAACGCCAAAAA-ATT-GAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CATTTTTTTC
155597 CG
319 CG
* * * * * *
155599 AATTAATTTTTAACTT-AATCGAACCAAGATTCAGATGTTCGTAAAAACAAATCATTATATCCAA
1 AATTTATTTCTAA-TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * * *
155663 TGTGGCCGATATTTA-GTTCGATGAATATAAATATTTCAAGGAGTCTTTGTGCCAAAAATCATGC
65 TGTGGCTGAGA-TTAGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGC
* * * * * * * *
155727 AAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTACTACACGATTTC
129 AAAACTGAATCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTC
* * *
155792 GGCTAAAATTTTGCAAAAAATGGCCCGAAAAGTTTTTTCCTCAATTTTTTGCCACAATAATCAGA
194 GGC--------T--AAAAACTGACCCGAAAA-TTTTTTCCTCAATTTTTTGCCACAATACTCAGA
* *
155857 AAAATATGAGTATAATTCAATGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTC
248 AAAA-AT-A-TATAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-
* *
155922 CATCTTTTT-AG
309 CATTTTTTTCCG
* **
155933 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATCCTCGTAAAAACATTTCCTTAAATCCAAT
1 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * *
155998 GTGGCTGAGATTTGGTTACATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGTAG
66 GTGGCTGAGATTAGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAA
* * * * * * * *
156063 AACT-AAGTTGAGGCCCCTAAACGCATATTTAACCAAAAACAGTGATGATTAGTAAATGATTTCG
131 AACTGAA-TCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTCG
* * ** * * *
156127 GGTAAAAACTGACACGAAAAAATTTTCCTCAATTTTTTGCCATAATACTCAGCAAAAATATATGA
195 GCTAAAAACTGACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAA
* * *
156192 TTCAACGCAAAAAAGAATCGAAGGG-TTTTCACGCTTCTAATATCGTTTTTCCTTTTATTTTCCG
260 TTCAACGC-CAAAA-AATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CATTT-TTTTCCG
* *
156256 AATTAATTTCTAATTAAATCAAAACAA
1 AATTTATTTCTAATTAAATCGAAACAA
156283 CACGATTTCG
Statistics
Matches: 1629, Mismatches: 287, Indels: 150
0.79 0.14 0.07
Matches are distributed among these distances:
320 22 0.01
321 44 0.03
322 31 0.02
323 197 0.12
324 233 0.14
325 288 0.18
326 114 0.07
327 41 0.03
328 37 0.02
329 45 0.03
330 49 0.03
331 182 0.11
332 73 0.04
333 41 0.03
334 179 0.11
335 36 0.02
336 17 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (320 bp):
AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTAGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAA
AACTGAATCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACACGATTTCGG
CTAAAAACTGACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
TCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCCG
Found at i:157178 original size:332 final size:330
Alignment explanation
Indices: 156281--157546 Score: 1140
Period size: 332 Copynumber: 3.8 Consensus size: 330
156271 AAATCAAAAC
* * *
156281 AACACGATTTCGGCTAAAGTTTTACAAAAATTGACCCGAAAGATA-ATTCCTCAATTTTTA-ACT
1 AACACGATTTCGGCTAAA-TTTTACAAAAATTGACCC-AAA-ATATTTTTCTCAATTTTTAGACG
* * * * * * *
156344 AAAATACTCATAAAAAATATATAATTCGACATCAAAAGGTTTGAATGGTTTTTAACGCTTCTAAT
63 AAAATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAAT
* * * * * *
156409 ATTGCTTTT-C-TTATTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
128 ATCGTTTTTCCTTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGT
* * * *
156472 AAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGCTTAGATGAATATAG--ATATTTCAAG
193 -AAAAACAAATCTTTAAATCCAATGTGGCTAAGATTTGGTTAGATG-ATATAGATATATTTCAAG
* * * * * * **
156535 GATTCTTAGCACCAAAAATCATGCAAAACTTAGTGGGGCCCCGAAACGCGTTTTTAGTCGAAAAC
256 GAGTCTTGGCGCAAAAAATCATGCAAAACTGACTGGGGCCCCGAAACGCGTTTTTAGTAAAAAAC
156600 CGTGAGAGTT
321 CGTGAGAGTT
* * * * * * *
156610 AGAAAACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAGAGATTTTTCCTCAATTTCTAG-C
1 --AACACGATTTCGGCT-AAATTTTACAAAAATTGACCCAAAATATTTTT-CTCAATTTTTAGAC
* * * * *
156674 GAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAAGCCTTTTTCACACTTCTA
62 GAAAATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGC-TTTTCACGCTTCTA
* * *
156739 ATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTAAATACT
126 ATATCGTTTTTCCT-TTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCT
* * * * * *
156804 TGTAAAATCAAAT-TGTAAATTACAATGTGGCTAAGATTTGGTTAGATTATTATAGATATATTTT
190 CGTAAAAACAAATCTTTAAA-TCCAATGTGGCTAAGATTTGGTTAGATGA-TATAGATATATTTC
* *
156868 GAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGACTCTGGGCCCC-AGAACGCGTTTTTAGGTA
253 AAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGACT-GGGGCCCCGA-AACGCGTTTTTA-GTA
156932 AAAAACCGTGATG-G-T
315 AAAAACCGTGA-GAGTT
*
156947 -ACACGATTTCGGCTGAAATTTTACAAAAATTGACCCAAAATATTTTTCTCAATTTTTAGAC-AC
1 AACACGATTTCGGCT-AAATTTTACAAAAATTGACCCAAAATATTTTTCTCAATTTTTAGACGAA
* * * *
157010 AATACTCATAAAAAATATATCATTCAAACACCAAAAAGATTGAAGGGCTTCTCTCGCTTCTAATA
65 AATACTCATAAAAAATATATAATTC-AACACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATA
* * *
157075 TCGTTTTTCCTTTTTTTTTTCAAATTAATTTCTAATAAAATCGAAACATGATTCAAATGCTCGTA
129 TCGTTTTTCCTTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTA
*
157140 AAAACAAATCTTTAAATCCAATGTGGCTAAGATTTGGTTAGATGA-ATATATATATTTCAAGGAG
194 AAAACAAATCTTTAAATCCAATGTGGCTAAGATTTGGTTAGATGATATAGATATATTTCAAGGAG
* * * * *** *
157204 TTTTGCCAG-AAAAAATCATGCAACACTGAACTGGGGCCCCGAAACGCGTTTTAAACCAAAAATC
259 TCTTGGC-GCAAAAAATCATGCAAAACTG-ACTGGGGCCCCGAAACGCGTTTTTAGTAAAAAACC
*
157268 GTGATTTCGACTAAT
322 GTGA----GAGT--T
* * * * *
157283 GTACACAATTTCAGCTAATATTTTGA-AAAAATTGA-CCAGAAATATTTTTTCTCAAATTTT-GT
1 -AACACGATTTCGGCTAA-ATTTT-ACAAAAATTGACCCA-AAATA-TTTTTCTCAATTTTTAGA
* * * * * * *
157345 CTAAGATACTCATAATATATATATATATAATTCAACTCCGAAAAGATTG-GAGGACATTTCATGC
61 CGAAAATACTCATAA-A-A-A-ATATATAATTCAACACCAAAAAGATTGAAAGG-CTTTTCACGC
* * * ** * * * *
157409 TTTTAATATCGTTTTT-C-ATATTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGGTTCAGA
121 TTCTAATATCGTTTTTCCTTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAA
* * * * * *
157472 TGCTCGTAACATCAAATCCTTAAATGCAATGTGGCTGAA-ATTTGATTAGATGA-ATA-TTGATA
186 TGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCT-AAGATTTGGTTAGATGATATAGAT-ATA
*
157534 TTTGAAGGAGTCT
249 TTTCAAGGAGTCT
157547 ATGTGACACT
Statistics
Matches: 764, Mismatches: 128, Indels: 77
0.79 0.13 0.08
Matches are distributed among these distances:
329 12 0.02
330 60 0.08
331 85 0.11
332 107 0.14
333 72 0.09
334 96 0.13
335 45 0.06
336 38 0.05
337 25 0.03
338 46 0.06
339 28 0.04
340 98 0.13
341 6 0.01
342 36 0.05
343 10 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (330 bp):
AACACGATTTCGGCTAAATTTTACAAAAATTGACCCAAAATATTTTTCTCAATTTTTAGACGAAA
ATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATC
GTTTTTCCTTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAA
AACAAATCTTTAAATCCAATGTGGCTAAGATTTGGTTAGATGATATAGATATATTTCAAGGAGTC
TTGGCGCAAAAAATCATGCAAAACTGACTGGGGCCCCGAAACGCGTTTTTAGTAAAAAACCGTGA
GAGTT
Found at i:167286 original size:329 final size:325
Alignment explanation
Indices: 166695--167755 Score: 896
Period size: 329 Copynumber: 3.3 Consensus size: 325
166685 AAATACTAAT
* * ** * * *
166695 AAAAATATATAATTCGACATCAAAAAGATTGAAGAG-CTTTTAACGCTTCTAATATTGTTTTTCC
1 AAAAATATACAATTCAACGCCAAAAAAATTGAA-AGCCTTTTCACGCTTCTAATATCGTTTTTCC
* * *
166759 TATTTTTTTTCCGATTTAATTTCTAATTAAACCAAAACAAGATTCAGATGCTCGT-AAAACAAAT
65 TA-TTTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAACAAAT
* **
166823 CCTTAAATCCAATGTGTCTAAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACC
129 CCTTAAATACAATGTGGATAAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACC
* * **
166888 AAAATTCATACAAAACTGATCCGGGCCTCGGAACGCGTTTTTAATCGAAAACCGTGATAGTTAGT
194 AAAATTCATACAAAACTGATCAGGGCCTCAGAACGCGTTTTTAATAAAAAACCGTGATAG-T-GT
166953 ACACGATTTCGGC-TT-TACAAAAATTGA-ACCGAAAGATTTTCCTCAATTTCTAGAGAAAATAC
257 ACACGATTTCGGCATTCTACAAAAATTGACA-CGAAAGATTTT-CTCAATTTCTAGAGAAAATAC
167015 TCAT-A
320 TCATAA
* * * * * *
167020 AAAAATATACGATTCAATGCAAATAAAAAAATTTAAAGCCTTTTTCACTCTTCTTATATCGTTTT
1 AAAAATATACAATTCAACGC---CAAAAAAATTGAAAGCC-TTTTCACGCTTCTAATATCGTTTT
* * * *
167085 TCCTATTTTATTTCCAAATTAATTGCTGATTAAATC-AAACAAGATTTAGATACTCGTAAAAACA
62 TCCTATTTT-TTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAACA
* *
167149 AATCCTTAAATACAATGTGGATGAGATTTGGTTAGATGAATATTATATATATTTCAAGGAGTCTT
126 AATCCTTAAATACAATGTGGATAAGATTTGGTTAGATGAATA--A-AGATATTTCAAGGAGTCTT
* ** *
167214 GGCGCCGAAAA-TCATGTAAAACTGACTCAGGGCC-CAGAACGCGTTTTTAGCTAAAAAACCGTG
188 GGCACC-AAAATTCATACAAAACTGA-TCAGGGCCTCAGAACGCGTTTTTA-ATAAAAAACCGTG
* *
167277 AT-G-GTACACGATTTCGGCTAAAATTCTACAAAAATTGACACGAAATATTTTCTCAATTTTTAG
250 ATAGTGTACACGATTTCGGC----ATTCTACAAAAATTGACACGAAAGATTTTCTCAATTTCTAG
** * *
167340 CTACAATACTTATAA
311 AGAAAATACTCATAA
* * * *
167355 AAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGC-TCTAATATCGTTTTTGCT
1 AAAAATATACAATTCAACGCCAAAAAAATTGAAAGCCTTTTCACGCTTCTAATATCGTTTTTCCT
* * * *
167419 A-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATATTTGTAAAAAC-AA---
66 ATTTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAACAAATCC
** * * **
167479 -T---GGC--T-TGG---A-A-TTGGTTAGATGAATATAGATATTTCAAGTAGTCTCAGCACCAA
131 TTAAATACAATGTGGATAAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCAA
* * * * * * * *
167532 AAATCATGCAAAACTGAACCGGGCCAT-GGAACGCGTTTTTTAGTCAAAAACTGTGAT-GAT-TA
196 AATTCATACAAAACTGATCAGGGCC-TCAGAACGCG-TTTTTAATAAAAAACCGTGATAG-TGTA
* * * * * *** *
167594 CACGATTTCGGCTAAAATTTTGCAAAAATTGGCCCGAAAGATATTTTCTCAATTTTTACCCATAA
258 CACGATTTCGGC----ATTCTACAAAAATTGACACGAAAG--ATTTTCTCAATTTCTAGAGAAAA
167659 TACTCATAA
317 TACTCATAA
* * * * * * * *
167668 AAAAATATATAATTCACCGCCAAAAAGATTGAAGGGCTTTTCATGCTTTTAATATCG-TTTTCAT
1 AAAAATATACAATTCAACGCCAAAAAAATTGAAAGCCTTTTCACGCTTCTAATATCGTTTTTCCT
167732 ATTTTTTAT--GAATTAATTTCTAAT
66 ATTTTTT-TCCGAATTAATTTCTAAT
167756 ATAGATGAAT
Statistics
Matches: 617, Mismatches: 86, Indels: 78
0.79 0.11 0.10
Matches are distributed among these distances:
309 10 0.02
310 53 0.09
311 43 0.07
313 107 0.17
314 15 0.02
315 2 0.00
318 3 0.00
319 1 0.00
321 1 0.00
324 1 0.00
325 14 0.02
327 2 0.00
328 59 0.10
329 131 0.21
330 17 0.03
331 9 0.01
332 63 0.10
333 23 0.04
334 22 0.04
335 40 0.06
336 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (325 bp):
AAAAATATACAATTCAACGCCAAAAAAATTGAAAGCCTTTTCACGCTTCTAATATCGTTTTTCCT
ATTTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAACAAATCC
TTAAATACAATGTGGATAAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCAA
AATTCATACAAAACTGATCAGGGCCTCAGAACGCGTTTTTAATAAAAAACCGTGATAGTGTACAC
GATTTCGGCATTCTACAAAAATTGACACGAAAGATTTTCTCAATTTCTAGAGAAAATACTCATAA
Found at i:167747 original size:313 final size:313
Alignment explanation
Indices: 167176--167755 Score: 800
Period size: 313 Copynumber: 1.9 Consensus size: 313
167166 TGGATGAGAT
* ** * * *
167176 TTGGTTAGATGAATATTATATATATTTCAAGGAGTCTTGGCGCCGAAAATCATGTAAAACTGACT
1 TTGGTTAGATGAATATTATAGATATTTCAAGGAGTCTCAGCACCAAAAATCATGCAAAACTGACT
167241 CAGGGCCCAGAACGCGTTTTTAGCTAAAAAACCGTGATGGTACACGATTTCGGCTAAAATTCTAC
66 CAGGGCCCAGAACGCGTTTTTAGCTAAAAAACCGTGATGGTACACGATTTCGGCTAAAATTCTAC
* * *
167306 AAAAATTGACACGAAATATTTTCTCAATTTTTAGCTACAATACTTATAAAAAAATATATAATTCA
131 AAAAATTGACACGAAATATTTTCTCAATTTTTACCCACAATACTCATAAAAAAATATATAATTCA
*
167371 ACGCCAAAAAGATTGAAAGGCTTTTCACGCTCTAATATCGTTTTTGCTATTTTTTCCGAATTAAT
196 ACGCCAAAAAGATTGAAAGGCTTTTCACGCTCTAATATCGTTTTTGCTATTTTTTACGAATTAAT
167436 TTCTAATTAAATCGAAACATGATTCAGATATTTGTAAAAACAATGGCTTGGAA
261 TTCTAATTAAATCGAAACATGATTCAGATATTTGTAAAAACAATGGCTTGGAA
*
167489 TTGGTTAGATG-A-A-TATAGATATTTCAAGTAGTCTCAGCACCAAAAATCATGCAAAACTGAAC
1 TTGGTTAGATGAATATTATAGATATTTCAAGGAGTCTCAGCACCAAAAATCATGCAAAACTG-AC
* * *
167551 -C-GGG-CCATGGAACGCGTTTTTTAG-TCAAAAACTGTGATGATTACACGATTTCGGCTAAAAT
65 TCAGGGCCCA--GAACGCG-TTTTTAGCTAAAAAACCGTGATG-GTACACGATTTCGGCTAAAAT
* * * * *
167612 TTTGCAAAAATTGGCCCGAAAGATATTTTCTCAATTTTTACCCATAATACTCATAAAAAAATATA
126 TCTACAAAAATTGACACG-AA-ATATTTTCTCAATTTTTACCCACAATACTCATAAAAAAATATA
* * * *
167677 TAATTCACCGCCAAAAAGATTGAAGGGCTTTTCATGCTTTTAATATCG-TTTT-CATATTTTTTA
189 TAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGC-TCTAATATCGTTTTTGC-TATTTTTTA
*
167740 TGAATTAATTTCTAAT
252 CGAATTAATTTCTAAT
167756 ATAGATGAAT
Statistics
Matches: 234, Mismatches: 24, Indels: 18
0.85 0.09 0.07
Matches are distributed among these distances:
308 3 0.01
309 3 0.01
310 60 0.26
311 44 0.19
312 4 0.02
313 111 0.47
314 9 0.04
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (313 bp):
TTGGTTAGATGAATATTATAGATATTTCAAGGAGTCTCAGCACCAAAAATCATGCAAAACTGACT
CAGGGCCCAGAACGCGTTTTTAGCTAAAAAACCGTGATGGTACACGATTTCGGCTAAAATTCTAC
AAAAATTGACACGAAATATTTTCTCAATTTTTACCCACAATACTCATAAAAAAATATATAATTCA
ACGCCAAAAAGATTGAAAGGCTTTTCACGCTCTAATATCGTTTTTGCTATTTTTTACGAATTAAT
TTCTAATTAAATCGAAACATGATTCAGATATTTGTAAAAACAATGGCTTGGAA
Found at i:171765 original size:2 final size:2
Alignment explanation
Indices: 171758--171783 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
171748 TCCTTAACTA
171758 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
171784 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:173393 original size:25 final size:25
Alignment explanation
Indices: 173346--173398 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
173336 AGACACTTTC
173346 TATGGGCTTCATAGTTAACTTAATGTA
1 TATGGGCTT-ATAGTTAACTTAAT-TA
* *
173373 TATGGGCTT-TAGTTTAGTTAATTA
1 TATGGGCTTATAGTTAACTTAATTA
173397 TA
1 TA
173399 AAATATTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 11 0.46
27 9 0.38
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (25 bp):
TATGGGCTTATAGTTAACTTAATTA
Found at i:175040 original size:29 final size:30
Alignment explanation
Indices: 174987--175052 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
174977 CTTTTCCTCT
174987 TCTTTCTTCTCTCCCCTTTCACTCTCGTTC
1 TCTTTCTTCTCTCCCCTTTCACTCTCGTTC
* * *
175017 TCTTTCTTCT-TCTCCTTTCCCTCTCTTTC
1 TCTTTCTTCTCTCCCCTTTCACTCTCGTTC
*
175046 TTTTTCT
1 TCTTTCT
175053 GTAGGAGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.02, C:0.39, G:0.02, T:0.58
Consensus pattern (30 bp):
TCTTTCTTCTCTCCCCTTTCACTCTCGTTC
Found at i:175953 original size:15 final size:16
Alignment explanation
Indices: 175935--175964 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
175925 ATAAATAATA
175935 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
175950 ATATTATAATCTAAA
1 ATATTATAATCTAAA
175965 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:176211 original size:7 final size:7
Alignment explanation
Indices: 176199--176240 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
176189 TTCGTGATTT
176199 TATATAG
1 TATATAG
176206 TATATAG
1 TATATAG
176213 --TATAG
1 TATATAG
176218 TATATAG
1 TATATAG
176225 TATATAG
1 TATATAG
176232 TATAATAG
1 TAT-ATAG
176240 T
1 T
176241 GTAGTAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.16
7 22 0.69
8 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
TATATAG
Found at i:176223 original size:19 final size:19
Alignment explanation
Indices: 176199--176235 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
176189 TTCGTGATTT
176199 TATATAGTATATAGTATAG
1 TATATAGTATATAGTATAG
176218 TATATAGTATATAGTATA
1 TATATAGTATATAGTATA
176236 ATAGTGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
TATATAGTATATAGTATAG
Found at i:176235 original size:12 final size:12
Alignment explanation
Indices: 176201--176228 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
176191 CGTGATTTTA
176201 TATAGTATATAG
1 TATAGTATATAG
176213 TATAGTATATAG
1 TATAGTATATAG
176225 TATA
1 TATA
176229 TAGTATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (12 bp):
TATAGTATATAG
Found at i:182465 original size:21 final size:21
Alignment explanation
Indices: 182441--182507 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
182431 AATTCTCTGT
182441 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
182462 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
182483 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
182504 AAAT
1 AAAT
182508 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:182487 original size:42 final size:42
Alignment explanation
Indices: 182428--182508 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
182418 GCTAAGTCTT
182428 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
182470 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
182509 CTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:184530 original size:2 final size:2
Alignment explanation
Indices: 184523--184560 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
184513 TCTTATTGGA
184523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184561 TTGATGTTAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190235 original size:15 final size:15
Alignment explanation
Indices: 190215--190253 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
190205 TTTTGTTCTT
190215 TCGTTTTCAATTGCA
1 TCGTTTTCAATTGCA
190230 TCGTTTTCAATTGCA
1 TCGTTTTCAATTGCA
190245 TCGTTTTCA
1 TCGTTTTCA
190254 TAATCATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.49
Consensus pattern (15 bp):
TCGTTTTCAATTGCA
Found at i:196473 original size:6 final size:6
Alignment explanation
Indices: 196456--196485 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
196446 TGGCTTTTTC
*
196456 AATAAA ACTAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
196486 TTATTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:197983 original size:16 final size:16
Alignment explanation
Indices: 197962--198002 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
197952 GAAACTTTCC
197962 CTTTCAATCAAACCCT
1 CTTTCAATCAAACCCT
197978 CTTTCAATCAAACCCT
1 CTTTCAATCAAACCCT
197994 CTTTCAATC
1 CTTTCAATC
198003 CTCCTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (16 bp):
CTTTCAATCAAACCCT
Found at i:206283 original size:88 final size:88
Alignment explanation
Indices: 206134--206310 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
206124 CCCTTCTTTT
206134 TCCAAATATATTTCTAAATTGTCATTATTAAATAATATTTTAATTATTCCACTATTAAAATAATG
1 TCCAAATATATTTCTAAATTGTCATTATTAAATAATATTTTAATTATTCCACTATTAAAATAATG
206199 GAAATTTAGACTATCCTCATTAA
66 GAAATTTAGACTATCCTCATTAA
206222 TCCAAATATATTTCTAAATTGTCATTATTAAATAATATTTTAATTATTCCACTATTAAAATAATG
1 TCCAAATATATTTCTAAATTGTCATTATTAAATAATATTTTAATTATTCCACTATTAAAATAATG
206287 GAAATTTAGACTATCCTCATTAA
66 GAAATTTAGACTATCCTCATTAA
206310 T
1 T
206311 TAGGATCCAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (88 bp):
TCCAAATATATTTCTAAATTGTCATTATTAAATAATATTTTAATTATTCCACTATTAAAATAATG
GAAATTTAGACTATCCTCATTAA
Found at i:207444 original size:22 final size:22
Alignment explanation
Indices: 207419--207515 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
207409 ATATTATTAT
207419 AATTTCATAAGGAGGTTATCAA
1 AATTTCATAAGGAGGTTATCAA
* * *
207441 AATTCCAT-AGTGTGGTTACCAA
1 AATTTCATAAG-GAGGTTATCAA
* * *
207463 AATTTCATATGAAAGTTATCAA
1 AATTTCATAAGGAGGTTATCAA
* *
207485 AATTTCAT-GGGAAGGTCATCAA
1 AATTTCATAAGG-AGGTTATCAA
207507 AATTTCATA
1 AATTTCATA
207516 GTGGTTGCCA
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
21 3 0.05
22 54 0.93
23 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAAGGAGGTTATCAA
Found at i:207545 original size:66 final size:64
Alignment explanation
Indices: 207431--207583 Score: 171
Period size: 66 Copynumber: 2.3 Consensus size: 64
207421 TTTCATAAGG
* * * *
207431 AGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATGGG
1 AGGTTATCAAAATTTCATA--GTGGTTACCAAAATTTCATAGGAAAGTTATCAAAATTTCATAGA
207496 A
64 A
* * * * *
207497 AGGTCATCAAAATTTCATAGTGGTTGCCAAACTTTCATAGGATCAAGTTATTAAAATTTCTTAGA
1 AGGTTATCAAAATTTCATAGTGGTTACCAAAATTTCATAGGA--AAGTTATCAAAATTTCATAGA
207562 A
64 A
**
207563 AGGTTATTGAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
207584 CTGGTTATCA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
64 20 0.27
66 53 0.73
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (64 bp):
AGGTTATCAAAATTTCATAGTGGTTACCAAAATTTCATAGGAAAGTTATCAAAATTTCATAGAA
Found at i:207658 original size:22 final size:21
Alignment explanation
Indices: 207622--207783 Score: 103
Period size: 22 Copynumber: 7.4 Consensus size: 21
207612 ATCAAAGAGA
* *
207622 TTATCAAAATGTCATAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
*
207644 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
*
207666 TTAACAAAATTTCATAAG-GAGG
1 TT-ATAAAATTTCAT-AGTGAGG
* * *
207688 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
*
207710 TTATCAAAATTTCATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
** ** *
207732 TTATCAAAATTTTTTAGTTTGA
1 TTAT-AAAATTTCATAGTGAGG
*
207754 TTATCAAAATTTCATA-TGAAAG
1 TTAT-AAAATTTCATAGTG-AGG
207776 TTATAAAA
1 TTATAAAA
207784 GTCTCATTTT
Statistics
Matches: 111, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
21 10 0.09
22 96 0.86
23 5 0.05
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:207675 original size:44 final size:42
Alignment explanation
Indices: 207626--207743 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 42
207616 AAGAGATTAT
* * *
207626 CAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAG-GAGGTTATAA-AATTTCATAGGGAGGTTAA
* * *
207670 CAAAATTTCATAAGGAGGTTACTAATATTTCATGGGGAGGTTAT
1 CAAAATTTCAT-AGGAGGTTA-TAAAATTTCATAGGGAGGTTAA
*
207714 CAAAATTTCATAGTGTGGTTATCAAAATTT
1 CAAAATTTCATAG-GAGGTTAT-AAAATTT
207744 TTTAGTTTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
43 3 0.05
44 54 0.87
45 5 0.08
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (42 bp):
CAAAATTTCATAGGAGGTTATAAAATTTCATAGGGAGGTTAA
Found at i:207766 original size:66 final size:66
Alignment explanation
Indices: 207618--207769 Score: 166
Period size: 66 Copynumber: 2.3 Consensus size: 66
207608 GGTTATCAAA
*
207618 GAGATTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAA
1 GAGATTATCAAAATTTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAA
207683 G
66 G
* * * * * *
207684 GAGGTTA-CTAATATTTCATGGGGAGGTTATCAA-AATTTCATAGTGTGGTTATCAAAATTT-TT
1 GAGATTATC-AAAATTTCATAGCGAGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCAT
*
207746 TAG
64 AAG
**
207749 TTTGATTATCAAAATTTCATA
1 -GAGATTATCAAAATTTCATA
207770 TGAAAGTTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
65 4 0.06
66 62 0.90
67 3 0.04
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (66 bp):
GAGATTATCAAAATTTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAA
G
Found at i:208031 original size:44 final size:43
Alignment explanation
Indices: 207888--208039 Score: 130
Period size: 44 Copynumber: 3.4 Consensus size: 43
207878 TTTATAGGAA
* * * *
207888 GATTATCAAAATTTCAT-AGTGTTGTTATCAAAGTTACATAATGT
1 GATTATCAAAATTTCATAAG-G-AGTTATCAAATTTTCAAAATGT
* * * * *
207932 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAAAAGT
1 GATTATCAAAATTTCATA-AGGAGTTATC-AAATTTT-CA-AAATGT
207979 --TTATCAAAATTTCATAAGGAAGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAGG-AGTTATCAAATTTTCAAAATGT
*
208021 GATTACCAAAATTTCATAA
1 GATTATCAAAATTTCATAA
208040 TGGTATTTCT
Statistics
Matches: 86, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
42 5 0.06
43 1 0.01
44 47 0.55
45 26 0.30
46 3 0.03
47 4 0.05
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (43 bp):
GATTATCAAAATTTCATAAGGAGTTATCAAATTTTCAAAATGT
Found at i:208041 original size:22 final size:22
Alignment explanation
Indices: 207888--208041 Score: 100
Period size: 22 Copynumber: 7.0 Consensus size: 22
207878 TTTATAGGAA
*
207888 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAATG-T
* *
207911 G-TTATCAAAGTTACATAATGT
1 GATTATCAAAATTTCATAATGT
*
207932 GATTATCAAAATTTCATAGA-GG
1 GATTATCAAAATTTCATA-ATGT
* * * * ***
207954 GGTCAACAAAATTTTATAGAAAA
1 GATTATCAAAATTTCATA-ATGT
*
207977 GTTTATCAAAATTTCATAA-G-
1 GATTATCAAAATTTCATAATGT
* *
207997 GAAGTTATCAAATTTTCAAAATGT
1 G-A-TTATCAAAATTTCATAATGT
*
208021 GATTACCAAAATTTCATAATG
1 GATTATCAAAATTTCATAATG
208042 GTATTTCTGG
Statistics
Matches: 101, Mismatches: 23, Indels: 15
0.73 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 79 0.78
23 18 0.18
24 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:208173 original size:64 final size:65
Alignment explanation
Indices: 208091--208242 Score: 202
Period size: 64 Copynumber: 2.4 Consensus size: 65
208081 ACCAAATTAG
*
208091 GAAGGTTATTA-AACTTTTATTA-TGGAGTAATCAAAATTTCAAGGAGGATATCAAAAT-TTCAT
1 GAAGGTTATCAGAA-TTTTA-TAGTGGAGTAATCAAAATTTCAAGGAGGATATCAAAATATTCAT
208153 AT
64 AT
** ** *
208155 GAAGGTTATCAGAATTTTATAGTTTAGTTTTCGAAATTTCAAGGAGGATATCAAAATATTCATAT
1 GAAGGTTATCAGAATTTTATAGTGGAGTAATCAAAATTTCAAGGAGGATATCAAAATATTCATAT
*
208220 GAAGGTTATCAGAATTTCATAGT
1 GAAGGTTATCAGAATTTTATAGT
208243 TTAGTTTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
63 2 0.03
64 45 0.58
65 31 0.40
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (65 bp):
GAAGGTTATCAGAATTTTATAGTGGAGTAATCAAAATTTCAAGGAGGATATCAAAATATTCATAT
Found at i:208242 original size:65 final size:64
Alignment explanation
Indices: 208121--208284 Score: 247
Period size: 65 Copynumber: 2.5 Consensus size: 64
208111 TATGGAGTAA
*
208121 TCAAAATTTCAAGGAGGATATCAAAATTTCATATGAAGGTTATCAGAATTTTATAGTTTAGTTT
1 TCAAAATTTCAAGGAGGATATCAAAATTTCATATGAAGGTTATCAGAATTTCATAGTTTAGTTT
*
208185 TCGAAATTTCAAGGAGGATATCAAAATATTCATATGAAGGTTATCAGAATTTCATAGTTTAGTTT
1 TCAAAATTTCAAGGAGGATATCAAAAT-TTCATATGAAGGTTATCAGAATTTCATAGTTTAGTTT
* * * *
208250 TCAAAACTTCATAAGAGGGTTAGCAAAATTTCATA
1 TCAAAATTTCA-AGGA-GGATATCAAAATTTCATA
208285 GTATGTAGAT
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 26 0.29
65 45 0.50
66 9 0.10
67 10 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (64 bp):
TCAAAATTTCAAGGAGGATATCAAAATTTCATATGAAGGTTATCAGAATTTCATAGTTTAGTTT
Found at i:208320 original size:22 final size:22
Alignment explanation
Indices: 208120--208368 Score: 90
Period size: 22 Copynumber: 11.5 Consensus size: 22
208110 TTATGGAGTA
208120 ATCAAAATTTCA-A-GGAGGA-T
1 ATCAAAATTTCATAGGGA-GATT
* * *
208140 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGATT
* * **
208162 ATCAGAATTTTATAGTTTAG-TT
1 ATCAAAATTTCATAG-GGAGATT
* *
208184 TTCGAAATTTCA-A-GGAGGA-T
1 ATCAAAATTTCATAGGGA-GATT
* * *
208204 ATCAAAATATTCATATGAAGGTT
1 ATCAAAAT-TTCATAGGGAGATT
* **
208227 ATCAGAATTTCATAGTTTAG-TT
1 ATCAAAATTTCATAG-GGAGATT
* *
208249 TTCAAAACTTCATAAGAGG-G-TT
1 ATCAAAATTTCAT-AG-GGAGATT
* * *
208271 AGCAAAATTTCATA-GTATG-TAG
1 ATCAAAATTTCATAGGGA-GAT-T
208293 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGATT
* ** *
208315 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATT
** *
208337 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGATT
208359 ATCAAAATTT
1 ATCAAAATTT
208369 GTAGTAATCA
Statistics
Matches: 166, Mismatches: 46, Indels: 32
0.68 0.19 0.13
Matches are distributed among these distances:
19 2 0.01
20 20 0.12
21 10 0.06
22 115 0.69
23 19 0.11
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGATT
Found at i:208341 original size:44 final size:44
Alignment explanation
Indices: 208120--208779 Score: 231
Period size: 44 Copynumber: 15.2 Consensus size: 44
208110 TTATGGAGTA
208120 ATCAAAATTTCA-A-GGAGGA-TATCAAAATTTCAT-ATGAAGGTT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAATG-AGGTT
* * ** * * * *
208162 ATCAGAATTTTATAGTTTAG-TTTTCGAAATTTC--AAGGAGGAT
1 ATCAAAATTTCATAG-GGAGATTATCAAAATTTCATAATGAGGTT
* * * * * *
208204 ATCAAAATATTCATATGAAGGTTATCAGAATTTCATAGTTTA-GTT
1 ATCAAAAT-TTCATAGGGAGATTATCAAAATTTCATA-ATGAGGTT
* * * * * *
208249 TTCAAAACTTCATAAGAGG-G-TTAGCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATAATGAGGT-T
*
208293 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
** * * *
208337 ATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT-A-GTA
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * *
208375 ATCAAGATTTCATAAGGAGATTATCAAAATTTTAT-ATGGAGGTTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT-GAGG-TT
* * * **
208420 ATCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAATGAGGTT
* * * * * *
208465 ATCACAATTTCATAGTGTGATTATCAAAATTTCAGAATGTGATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * * *
208509 A-CTAACAA-TTCATATGGAGGTT-TTAAAATTTTCATAACGTGGTT
1 ATC-AA-AATTTCATAGGGAGATTATCAAAA-TTTCATAATGAGGTT
** * ** * ** * * *
208553 ATCAGTATATCATATAGAGGTTATCAACGTCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATG-AGGTT
* * * *
208598 ATCAAATTTTCATTGGGA-AGTTATCAAAATTTCATAGTGAGATCT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGGT-T
* * *
208643 -TCAAAA-TTCTTTAGGGAGGTTAACAAAATTTCATAA-GAAGGTT
1 ATCAAAATTTC-ATAGGGAGATTATCAAAATTTCATAATG-AGGTT
** *** * * * * * *
208686 AAAAAAATTT-ATAAAAAGGTTCTCGAAATTCCATAGT-ATCGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGA-GGTT
* *** * *
208729 ATTAAAATTTCATAAAAAGGTTATCAAAATTTCATAATGAGGTC
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
208773 ATCAAAA
1 ATCAAAA
208780 ATAGTATAAT
Statistics
Matches: 448, Mismatches: 126, Indels: 86
0.68 0.19 0.13
Matches are distributed among these distances:
38 26 0.06
39 3 0.01
40 1 0.00
41 3 0.01
42 27 0.06
43 67 0.15
44 213 0.48
45 87 0.19
46 21 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
Found at i:208406 original size:22 final size:22
Alignment explanation
Indices: 208375--208779 Score: 158
Period size: 22 Copynumber: 18.3 Consensus size: 22
208365 ATTTGTAGTA
* * *
208375 ATCAAGATTTCATAAGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* *
208397 ATCAAAATTTTATATGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
208420 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
208443 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
208465 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* ** * *
208487 ATCAAAATTTCAGAATGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
208509 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* ** *
208531 -TTAAAATTTTCATAACGTGGTT
1 ATCAAAA-TTTCATAGGGAGGTT
** * **
208553 ATCAGTATATCATATAGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** * **
208575 ATCAACGTCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
208598 ATCAAATTTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
208620 ATCAAAATTTCATAGTGAGATCT
1 ATCAAAATTTCATAGGGAGGT-T
*
208643 -TCAAAA-TTCTTTAGGGAGGTT
1 ATCAAAATTTC-ATAGGGAGGTT
* * *
208664 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** ***
208686 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
208707 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATAGGGA-GGTT
* ***
208729 ATTAAAATTTCATAAAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
208751 ATCAAAATTTCATAATGAGGTC
1 ATCAAAATTTCATAGGGAGGTT
208773 ATCAAAA
1 ATCAAAA
208780 ATAGTATAAT
Statistics
Matches: 288, Mismatches: 80, Indels: 30
0.72 0.20 0.08
Matches are distributed among these distances:
20 2 0.01
21 23 0.08
22 198 0.69
23 65 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:208417 original size:82 final size:84
Alignment explanation
Indices: 208293--208452 Score: 218
Period size: 82 Copynumber: 1.9 Consensus size: 84
208283 TAGTATGTAG
* *
208293 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG-TTATCAAAAAATCATAGGGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAATGAGGTTTATCAAAAAATCATAGGAAGG
208357 -TTATCAAAATTTGTAGTA
66 TTTATCAAAATTTGTAGTA
* * * ** *
208375 ATCAAGATTTCATAAGGAGATTATCAAAATTTTAT-ATGGAGGTTTATCAAAATTTTATAGGAAG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAT-GAGGTTTATCAAAAAATCATAGGAAG
208439 GTTTATCAAAATTT
65 GTTTATCAAAATTT
208453 CATAGCGAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 2 0.03
82 35 0.52
83 18 0.27
84 12 0.18
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (84 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAATGAGGTTTATCAAAAAATCATAGGAAGG
TTTATCAAAATTTGTAGTA
Found at i:208425 original size:23 final size:22
Alignment explanation
Indices: 208395--208496 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 22
208385 CATAAGGAGA
208395 TTATCAAAATTTTATATGGAGGT
1 TTATCAAAATTTTATA-GGAGGT
208418 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGG-AGGT
*
208441 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAG-GAGGT
* * * *
208463 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAG-GAGGT
208485 TTATCAAAATTT
1 TTATCAAAATTT
208497 CAGAATGTGA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
21 1 0.01
22 30 0.42
23 39 0.55
24 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAGGT
Found at i:209186 original size:24 final size:24
Alignment explanation
Indices: 209154--209201 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
209144 CAGTGGGTGC
209154 ACAAATCTGGAATTTATAATTTGT
1 ACAAATCTGGAATTTATAATTTGT
*
209178 ACAAATCTGGAATTTATTATTTGT
1 ACAAATCTGGAATTTATAATTTGT
209202 TTATTTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.44
Consensus pattern (24 bp):
ACAAATCTGGAATTTATAATTTGT
Found at i:212059 original size:19 final size:20
Alignment explanation
Indices: 212014--212065 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
212004 TCTAATGATC
212014 TCATCTGTACAGTATCTAATA
1 TCATCTGTACAG-ATCTAATA
* * *
212035 TAATCTGTACA-ATGTAATT
1 TCATCTGTACAGATCTAATA
212054 TCATCTGTACAG
1 TCATCTGTACAG
212066 TTGCTAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.62
21 10 0.38
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (20 bp):
TCATCTGTACAGATCTAATA
Found at i:215704 original size:12 final size:12
Alignment explanation
Indices: 215681--215714 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
215671 CAAAAGCCCG
215681 TTTAAT-ATTAT
1 TTTAATAATTAT
215692 TTTAATAATTAT
1 TTTAATAATTAT
*
215704 TTTAAGAATTA
1 TTTAATAATTA
215715 AATTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TTTAATAATTAT
Found at i:225611 original size:15 final size:16
Alignment explanation
Indices: 225583--225612 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
225573 CTTAATTGCA
225583 AAAGAAAGGGAAAAAG
1 AAAGAAAGGGAAAAAG
225599 AAAGAAA-GGAAAAA
1 AAAGAAAGGGAAAAA
225613 AAACTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAAGAAAGGGAAAAAG
Found at i:225613 original size:16 final size:16
Alignment explanation
Indices: 225583--225613 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
225573 CTTAATTGCA
*
225583 AAAGAAAGGGAAAAAG
1 AAAGAAAGGAAAAAAG
225599 AAAGAAAGGAAAAAA
1 AAAGAAAGGAAAAAA
225614 AACTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGAAAGGAAAAAAG
Found at i:232462 original size:19 final size:20
Alignment explanation
Indices: 232438--232475 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
232428 TGTGCCATTC
232438 ACTCATTAAC-ATCTAATCT
1 ACTCATTAACAATCTAATCT
*
232457 ACTCATTAGCAATCTAATC
1 ACTCATTAACAATCTAATC
232476 AGGTGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (20 bp):
ACTCATTAACAATCTAATCT
Found at i:239653 original size:13 final size:13
Alignment explanation
Indices: 239635--239670 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
239625 AAACAACTGA
239635 AAAACACTTCAGG
1 AAAACACTTCAGG
*
239648 AAAACATTTCAGG
1 AAAACACTTCAGG
*
239661 AAAGCACTTC
1 AAAACACTTC
239671 TGGATTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (13 bp):
AAAACACTTCAGG
Found at i:243979 original size:41 final size:41
Alignment explanation
Indices: 243922--244001 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
243912 TTCCAAGTTC
243922 CAATATTGATTTTAGG-TAAATTGTTAGGAATCGAAATCTTT
1 CAATATTGATTTTAGGATAAATTGTTAGGAATC-AAATCTTT
243963 CAATATT-ATTATTAGGTAATAAATTGTTAGGAATCAAAT
1 CAATATTGATT-TTAGG--ATAAATTGTTAGGAATCAAAT
244002 ATTACTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
40 3 0.09
41 12 0.34
43 4 0.11
44 16 0.46
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (41 bp):
CAATATTGATTTTAGGATAAATTGTTAGGAATCAAATCTTT
Done.