Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003885.1 Hibiscus syriacus cultivar Beakdansim tig00008386_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 757743
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 4
Found at i:372014 original size:20 final size:20
Alignment explanation
Indices: 371982--372033 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
371972 GTTGCGAAAA
* * *
371982 TCGCGTTGTGATTTTTCATT
1 TCGCGTTGCGATTTTCCAGT
*
372002 TCTCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
372022 TCGCGTTGCGAT
1 TCGCGTTGCGAT
372034 AGTTGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:372065 original size:116 final size:115
Alignment explanation
Indices: 371861--372091 Score: 322
Period size: 116 Copynumber: 2.0 Consensus size: 115
371851 TGCGATAGTT
**
371861 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTACGATTTTTCA
1 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATA-TCTACAGTTGTCGTTACGATAGTTCA
*
371926 AATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
65 AAATCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
* * * * * * *
371977 GAAAATCGCGTTGTGATTTTTCATTTCTCGTTGCGAT-TTTCCAGTTCG-CGTTGCGATAGTTGA
1 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATATCTACAGTT-GTCGTTACGATAGTTCA
372040 AAATCGTGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTG
65 AAATC--GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTG
372092 TGATAGTTAA
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
114 22 0.22
115 1 0.01
116 79 0.77
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (115 bp):
GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATATCTACAGTTGTCGTTACGATAGTTCAA
AATCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
Found at i:372192 original size:6 final size:6
Alignment explanation
Indices: 372181--372214 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
372171 GTATTACTAT
372181 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
372215 CGAGACGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:372744 original size:12 final size:11
Alignment explanation
Indices: 372712--372747 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
372702 GTCCGTCTCG
372712 GGTCGGGTCG-
1 GGTCGGGTCGT
372722 GGTCGGGTCGT
1 GGTCGGGTCGT
372733 GGTCGTGGTCGT
1 GGTCG-GGTCGT
372745 GGT
1 GGT
372748 AATGGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:372747 original size:6 final size:5
Alignment explanation
Indices: 372709--372743 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
372699 GCCGTCCGTC
372709 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
372744 TGGTAATGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:372753 original size:6 final size:6
Alignment explanation
Indices: 372744--372774 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
372734 GTCGTGGTCG
372744 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
372775 ACGTGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:372899 original size:22 final size:22
Alignment explanation
Indices: 372870--372962 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
372860 AATTTGGAAA
372870 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
372892 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
372914 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
372933 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
372954 ATCGCAACG
1 ATCGCAACG
372963 CAAAATGGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.23
20 3 0.05
21 13 0.23
22 27 0.48
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:372921 original size:19 final size:20
Alignment explanation
Indices: 372848--372962 Score: 72
Period size: 22 Copynumber: 5.6 Consensus size: 20
372838 CTTTTTTTTT
* *
372848 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
**
372867 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACG--AACTGTAG
* *
372889 ACTTTCGCAACAACAACTGTAG
1 ACTATCGCAAC--GAACTGTAG
* *
372911 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
** *
372930 AAAATCGCAACGACATTGTAG
1 ACTATCGCAACGA-ACTGTAG
372951 ACTATCGCAACG
1 ACTATCGCAACG
372963 CAAAATGGAA
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
19 24 0.34
20 3 0.04
21 15 0.21
22 29 0.41
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGAACTGTAG
Found at i:372938 original size:41 final size:41
Alignment explanation
Indices: 372893--372981 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
372883 CTGTAGACTT
**
372893 TCGCAACAACAACTGTAGACTATCGCAACG-AATTTGGAAAA
1 TCGCAACAAC-ACTGTAGACTATCGCAACGCAAAATGGAAAA
* *
372934 TCGCAACGACATTGTAGACTATCGCAACGCAAAATGGAAAA
1 TCGCAACAACACTGTAGACTATCGCAACGCAAAATGGAAAA
372975 TCGCAAC
1 TCGCAAC
372982 GCGAAATGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 18 0.42
41 25 0.58
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (41 bp):
TCGCAACAACACTGTAGACTATCGCAACGCAAAATGGAAAA
Found at i:372955 original size:40 final size:41
Alignment explanation
Indices: 372906--372982 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
372896 CAACAACAAC
**
372906 TGTAGACTATCGCAACG-AATTTGGAAAATCGCAACGACAT
1 TGTAGACTATCGCAACGCAAAATGGAAAATCGCAACGACAT
372946 TGTAGACTATCGCAACGCAAAATGGAAAATCGCAACG
1 TGTAGACTATCGCAACGCAAAATGGAAAATCGCAACG
372983 CGAAATGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 17 0.50
41 17 0.50
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
TGTAGACTATCGCAACGCAAAATGGAAAATCGCAACGACAT
Found at i:372979 original size:20 final size:20
Alignment explanation
Indices: 372954--373046 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
372944 ATTGTAGACT
*
372954 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
372974 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** **
372994 ATCGCAACGCGATTTTCAAA
1 ATCGCAACGCGAAATGGAAA
* *
373014 TATAGCAACGCGAAATGAAAA
1 -ATCGCAACGCGAAATGGAAA
373035 ATCGCAACGCGA
1 ATCGCAACGCGA
373047 TTTTCAACTA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:373022 original size:41 final size:41
Alignment explanation
Indices: 372977--373071 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
372967 ATGGAAAATC
*
372977 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAAATATA
1 GCAACGCGAAATGAAAAATCGCAACGCGATTTTCAAATATA
* *
373018 GCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATC
1 GCAACGCGAAATGAAAAATCGCAACGCGATTTTCAAATATA
373059 GCAACGCGAAATG
1 GCAACGCGAAATG
373072 CAACGCGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (41 bp):
GCAACGCGAAATGAAAAATCGCAACGCGATTTTCAAATATA
Found at i:373022 original size:61 final size:61
Alignment explanation
Indices: 372927--373046 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
372917 GCAACGAATT
* * *
372927 TGGAAAATCGCAACGACATTGTAGACTATCGCAACGCAAAATGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGACATTGTAGAATATAGCAACGCAAAATGAAAAATCGCAACGCGAAA
* *
372988 TGGAAAATCGCAACG-CGATTTTCA-AATATAGCAACGCGAAATGAAAAATCGCAACGCGA
1 TGGAAAATCGCAACGAC-ATTGT-AGAATATAGCAACGCAAAATGAAAAATCGCAACGCGA
373047 TTTTCAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 1 0.02
61 50 0.96
62 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (61 bp):
TGGAAAATCGCAACGACATTGTAGAATATAGCAACGCAAAATGAAAAATCGCAACGCGAAA
Found at i:373023 original size:21 final size:21
Alignment explanation
Indices: 372994--373067 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
372984 GAAATGGAAA
372994 ATCGCAACGCGATTTTCAAAT
1 ATCGCAACGCGATTTTCAAAT
* ** * *
373015 ATAGCAACGCGA-AATGAAAA
1 ATCGCAACGCGATTTTCAAAT
*
373035 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAAAT
373056 ATCGCAACGCGA
1 ATCGCAACGCGA
373068 AATGCAACGC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAAAT
Found at i:373290 original size:21 final size:21
Alignment explanation
Indices: 373264--373320 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
373254 ATCAATATAT
373264 AGGGTTATGATTTAGAGTTTA
1 AGGGTTATGATTTAGAGTTTA
373285 AGGGTTATGATTTAGAGTTTA
1 AGGGTTATGATTTAGAGTTTA
*
373306 AGGATTATGATTTAG
1 AGGGTTATGATTTAG
373321 GGATAGAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (21 bp):
AGGGTTATGATTTAGAGTTTA
Found at i:376413 original size:9 final size:9
Alignment explanation
Indices: 376401--376443 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
376391 AGGCTGCCTT
376401 CATTGCCAC
1 CATTGCCAC
376410 CATTGCCAC
1 CATTGCCAC
*
376419 CATTGCCTC
1 CATTGCCAC
*
376428 CAATGCCAC
1 CATTGCCAC
*
376437 CGTTGCC
1 CATTGCC
376444 CTTCTCCGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.19, C:0.44, G:0.14, T:0.23
Consensus pattern (9 bp):
CATTGCCAC
Found at i:384052 original size:88 final size:88
Alignment explanation
Indices: 383898--384070 Score: 328
Period size: 88 Copynumber: 2.0 Consensus size: 88
383888 TTAGAAACAT
*
383898 ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTTTGCCC
1 ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
383963 TACCACCTTAAAAGAAAATGGTA
66 TACCACCTTAAAAGAAAATGGTA
*
383986 ACCAGGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
1 ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
384051 TACCACCTTAAAAGAAAATG
66 TACCACCTTAAAAGAAAATG
384071 CAACTTGTGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (88 bp):
ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
TACCACCTTAAAAGAAAATGGTA
Found at i:386599 original size:19 final size:19
Alignment explanation
Indices: 386575--386635 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
386565 ATTTATATTA
* *
386575 TGATCTCTATTTTGATTTC
1 TGATCTCTGTTATGATTTC
386594 TGATCTCTGTTATGATTTC
1 TGATCTCTGTTATGATTTC
* * *
386613 TGATATCTGTTCTGATTTA
1 TGATCTCTGTTATGATTTC
386632 TGAT
1 TGAT
386636 ATCTCTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (19 bp):
TGATCTCTGTTATGATTTC
Found at i:386636 original size:19 final size:19
Alignment explanation
Indices: 386572--386639 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
386562 TTGATTTATA
* * *
386572 TTATGATCTCTATTTTGAT
1 TTATGATATCTGTTATGAT
* *
386591 TTCTGATCTCTGTTATGAT
1 TTATGATATCTGTTATGAT
* *
386610 TTCTGATATCTGTTCTGAT
1 TTATGATATCTGTTATGAT
386629 TTATGATATCT
1 TTATGATATCT
386640 CTGATTATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.54
Consensus pattern (19 bp):
TTATGATATCTGTTATGAT
Found at i:395607 original size:36 final size:36
Alignment explanation
Indices: 395560--395632 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
395550 AAGAGAACCA
*
395560 AAGCTAAAACATTGACGAGCCATCATTCGAACTTCT
1 AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
395596 AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
1 AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
395632 A
1 A
395633 CCGTAGACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (36 bp):
AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
Found at i:399217 original size:52 final size:52
Alignment explanation
Indices: 399139--399247 Score: 218
Period size: 52 Copynumber: 2.1 Consensus size: 52
399129 TAGATACATA
399139 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
1 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
399191 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
1 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
399243 TTACA
1 TTACA
399248 TAAAAATAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (52 bp):
TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
Found at i:400193 original size:2 final size:2
Alignment explanation
Indices: 400186--400217 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
400176 TTATCGACTA
400186 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
400218 GTGTTTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:401241 original size:14 final size:16
Alignment explanation
Indices: 401208--401253 Score: 69
Period size: 14 Copynumber: 2.9 Consensus size: 16
401198 TTATATAAAA
401208 TATATTTTTATTATAAT
1 TATATTTTTATTAT-AT
401225 TATATTTTTATT-T-T
1 TATATTTTTATTATAT
401239 TATATTTTTATTATA
1 TATATTTTTATTATA
401254 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 13 0.48
15 1 0.04
16 1 0.04
17 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTTTTATTATAT
Found at i:408075 original size:23 final size:23
Alignment explanation
Indices: 408026--408078 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
408016 ATTGCATCGA
* *
408026 AGTGCCACGTAGAATTATACCGG
1 AGTGCCACGTAGAATTACACAGG
* * *
408049 AGTGCCGCGTAGAATTGCACAGT
1 AGTGCCACGTAGAATTACACAGG
408072 AGTGCCA
1 AGTGCCA
408079 TATAATAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAATTACACAGG
Found at i:420283 original size:480 final size:481
Alignment explanation
Indices: 419144--420587 Score: 2872
Period size: 481 Copynumber: 3.0 Consensus size: 481
419134 ACTCACTTAA
419144 TTAACTTGGCTCTTTGCCCAAATTTCTGTTTTCCCCCTTAATTTTTTATTTTGCAGAGGTTCAGG
1 TTAACTTGGCTCTTTGCCCAAATTTCTGTTTTCCCCCTTAATTTTTTATTTTGCAGAGGTTCAGG
419209 CTTTGAATACATACACTGAGAGGAGAAAGAACAGCAGTGGGAAGTGAATTTTTTATGTTGTAAGA
66 CTTTGAATACATACACTGAGAGGAGAAAGAACAGCAGTGGGAAGTGAATTTTTTATGTTGTAAGA
419274 ATGATGAAAATTACCTCAACAATTCACAATTTCATAACAATTTTGTATTTGATTTTGTTTTAAAT
131 ATGATGAAAATTACCTCAACAATTCACAATTTCATAACAATTTTGTATTTGATTTTGTTTTAAAT
419339 TTGATTTGGCCGAGTAATGTAATGCAACAACGATTAATAGACTTCATCGTTTCTTGATCTTGAAC
196 TTGATTTGGCCGAGTAATGTAATGCAACAACGATTAATAGACTTCATCGTTTCTTGATCTTGAAC
419404 AAAAGATCCTACCGAATAATGCTTAATTCTTCCACAGTAATTGTCTTGCTTTAGAATCTTTAAGT
261 AAAAGATCCTACCGAATAATGCTTAATTCTTCCACAGTAATTGTCTTGCTTTAGAATCTTTAAGT
419469 TAGACATGCAGCATATCCTTCCTTCAACCTTCTTTTTTTTATATAAAAAACACTTCTTAATGTTG
326 TAGACATGCAGCATATCCTTCCTTCAACCTTCTTTTTTTTATATAAAAAACACTTCTTAATGTTG
419534 AGGCCTCCAGGTAAATCATACTCAGTTAGTTCTAGAGATGCTGCTGCAGAATATGTTAGAGAGAA
391 AGGCCTCCAGGTAAATCATACTCAGTTAGTTCTAGAGATGCTGCTGCAGAATATGTTAGAGAGAA
419599 TTGGAGAGGCCTCATATCAAATAAAG
456 TTGGAGAGGCCTCATATCAAATAAAG
*
419625 TTAACTTGGCTCTTTGCCCAAATTTCTGTTTTCCCCCTTAATTTTTTATTTTGCAGAGGTTCGGG
1 TTAACTTGGCTCTTTGCCCAAATTTCTGTTTTCCCCCTTAATTTTTTATTTTGCAGAGGTTCAGG
419690 CTTTGAATACATACACTGAGAGGAGAAAGAACAGCAGTGGGAAGTGAATTTTTTATGTTGTAAGA
66 CTTTGAATACATACACTGAGAGGAGAAAGAACAGCAGTGGGAAGTGAATTTTTTATGTTGTAAGA
419755 ATGATGAAAATTACCTCAACAATTCACAATTTCATAACAATTTTGTATTTGATTTTGTTTTAAAT
131 ATGATGAAAATTACCTCAACAATTCACAATTTCATAACAATTTTGTATTTGATTTTGTTTTAAAT
419820 TTGATTTGGCCGAGTAATGTAATGCAACAACGATTAATAGACTTCATCGTTTCTTGATCTTGAAC
196 TTGATTTGGCCGAGTAATGTAATGCAACAACGATTAATAGACTTCATCGTTTCTTGATCTTGAAC
419885 AAAAGATCCTACCGAATAATGCTTAATTCTTCCACAGTAATTGTCTTGCTTTAGAATCTTTAAGT
261 AAAAGATCCTACCGAATAATGCTTAATTCTTCCACAGTAATTGTCTTGCTTTAGAATCTTTAAGT
419950 TAGACATGCAGCATATCCTTCCTTCAACCTTC-TTTTTTTATATAAAAAACACTTCTTAATGTTG
326 TAGACATGCAGCATATCCTTCCTTCAACCTTCTTTTTTTTATATAAAAAACACTTCTTAATGTTG
420014 AGGCCTCCAGGTAAATCATACTCAGTTAGTTCTAGAGATGCTGCTGCAGAATATGTTAGAGAGAA
391 AGGCCTCCAGGTAAATCATACTCAGTTAGTTCTAGAGATGCTGCTGCAGAATATGTTAGAGAGAA
420079 TTGGAGAGGCCTCATATCAAATAAAG
456 TTGGAGAGGCCTCATATCAAATAAAG
420105 TTAACTTGGCTCTTTGCCCAAATTTCTGTTTTCCCCCTTAATTTTTTATTTTGCAGAGGTTCAGG
1 TTAACTTGGCTCTTTGCCCAAATTTCTGTTTTCCCCCTTAATTTTTTATTTTGCAGAGGTTCAGG
420170 CTTTGAATACATACACTGAGAGGAGAAAGAACAGCAGTGGGAAGTGAATTTTTTATGTTGTAAGA
66 CTTTGAATACATACACTGAGAGGAGAAAGAACAGCAGTGGGAAGTGAATTTTTTATGTTGTAAGA
420235 ATGATGAAAATTACCTCAACAATTCACAATTTCATAACAATTTTGTATTTGATTTTGTTTTAAAT
131 ATGATGAAAATTACCTCAACAATTCACAATTTCATAACAATTTTGTATTTGATTTTGTTTTAAAT
420300 TTGATTTGGCCGAGTAATGTAATGCAACAACGATTAATAGACTTCATCGTTTCTTGATCTTGAAC
196 TTGATTTGGCCGAGTAATGTAATGCAACAACGATTAATAGACTTCATCGTTTCTTGATCTTGAAC
420365 AAAAGATCCTACCGAATAATGCTTAATTCTTCCACAGTAATTGTCTTGCTTTAGAATCTTTAAGT
261 AAAAGATCCTACCGAATAATGCTTAATTCTTCCACAGTAATTGTCTTGCTTTAGAATCTTTAAGT
420430 TAGACATGCAGCATATCCTTCCTTCAACCTTCTTTTTTTTATATAAAAAACACTTCTTAATGTTG
326 TAGACATGCAGCATATCCTTCCTTCAACCTTCTTTTTTTTATATAAAAAACACTTCTTAATGTTG
420495 AGGCCTCCAGGTAAATCATACTCAGTTAGTTCTAGAGATGCTGCTGCAGAATATGTTAGAGAGAA
391 AGGCCTCCAGGTAAATCATACTCAGTTAGTTCTAGAGATGCTGCTGCAGAATATGTTAGAGAGAA
420560 TTGGAGAGGCCTCATATCAAATAAAG
456 TTGGAGAGGCCTCATATCAAATAAAG
420586 TT
1 TT
420588 GCTTCACCTC
Statistics
Matches: 960, Mismatches: 2, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
480 479 0.50
481 481 0.50
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (481 bp):
TTAACTTGGCTCTTTGCCCAAATTTCTGTTTTCCCCCTTAATTTTTTATTTTGCAGAGGTTCAGG
CTTTGAATACATACACTGAGAGGAGAAAGAACAGCAGTGGGAAGTGAATTTTTTATGTTGTAAGA
ATGATGAAAATTACCTCAACAATTCACAATTTCATAACAATTTTGTATTTGATTTTGTTTTAAAT
TTGATTTGGCCGAGTAATGTAATGCAACAACGATTAATAGACTTCATCGTTTCTTGATCTTGAAC
AAAAGATCCTACCGAATAATGCTTAATTCTTCCACAGTAATTGTCTTGCTTTAGAATCTTTAAGT
TAGACATGCAGCATATCCTTCCTTCAACCTTCTTTTTTTTATATAAAAAACACTTCTTAATGTTG
AGGCCTCCAGGTAAATCATACTCAGTTAGTTCTAGAGATGCTGCTGCAGAATATGTTAGAGAGAA
TTGGAGAGGCCTCATATCAAATAAAG
Found at i:421691 original size:15 final size:15
Alignment explanation
Indices: 421671--421705 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
421661 AGAAACATCT
421671 GCATCCATTCCAACC
1 GCATCCATTCCAACC
421686 GCATCCATTCCAACC
1 GCATCCATTCCAACC
421701 GCATC
1 GCATC
421706 AACTGCACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.46, G:0.09, T:0.20
Consensus pattern (15 bp):
GCATCCATTCCAACC
Found at i:422022 original size:28 final size:28
Alignment explanation
Indices: 421990--422049 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
421980 TAGTTTACCG
421990 TTTCTAAAAATCCTCCGATTTATATCCA
1 TTTCTAAAAATCCTCCGATTTATATCCA
* *
422018 TTTCTGAAAATCCTCCGATTTATATCTA
1 TTTCTAAAAATCCTCCGATTTATATCCA
422046 TTTC
1 TTTC
422050 ATTGCTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.43
Consensus pattern (28 bp):
TTTCTAAAAATCCTCCGATTTATATCCA
Found at i:422306 original size:17 final size:17
Alignment explanation
Indices: 422284--422320 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
422274 GATAAAAAGT
*
422284 TTGCATCTAGATTCTGC
1 TTGCATCTAGATCCTGC
*
422301 TTGCATCTATATCCTGC
1 TTGCATCTAGATCCTGC
422318 TTG
1 TTG
422321 TGATCCAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.43
Consensus pattern (17 bp):
TTGCATCTAGATCCTGC
Found at i:424466 original size:19 final size:19
Alignment explanation
Indices: 424428--424466 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
424418 TTTTATTTTT
424428 ATTTATTGTTTACTAAATTA
1 ATTTATTGTTTAC-AAATTA
424448 ATTTATTGTTATA-AAATTA
1 ATTTATTGTT-TACAAATTA
424467 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 10 0.56
21 2 0.11
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTTATTGTTTACAAATTA
Found at i:426149 original size:33 final size:33
Alignment explanation
Indices: 426112--426179 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
426102 AGAAAATTTT
*
426112 GATGGTACCGCCGACAAGGAGAAGAGAAGGCAA
1 GATGGTACCGCCGACAAGGAGAAAAGAAGGCAA
* *
426145 GATGGTACCGCCGGCAAGGAGAAAAGAATGCAA
1 GATGGTACCGCCGACAAGGAGAAAAGAAGGCAA
426178 GA
1 GA
426180 AAATATTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.35, T:0.07
Consensus pattern (33 bp):
GATGGTACCGCCGACAAGGAGAAAAGAAGGCAA
Found at i:433913 original size:36 final size:35
Alignment explanation
Indices: 433847--433916 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 35
433837 TAGCTTTTTT
433847 ATTATTTTAATAAAAATATAACATTATTTTTAAATA
1 ATTATTTTAATAAAAATATAACA-TATTTTTAAATA
433883 ATTATTTATAA-AAATAATATAACA-ACTTTTTAAA
1 ATTATTT-TAATAAA-AATATAACATA-TTTTTAAA
433917 GAAAATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
35 1 0.03
36 18 0.58
37 12 0.39
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (35 bp):
ATTATTTTAATAAAAATATAACATATTTTTAAATA
Found at i:435078 original size:56 final size:57
Alignment explanation
Indices: 435011--435124 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
435001 TTAATTTCAT
** *
435011 CCTTTGATTTCCCTGAA-CCAAACGATCCT-AAAAAGTGTAAAATTAAAAGAGTTTTA
1 CCTTTGATTTCCCACAATCC-AACGATCCTAAAAAAGTGTAAAACTAAAAGAGTTTTA
* * *
435067 CCTTTGATTTCCCACAATTCAACGATCTTAAAAAAGTGTAAAACTAAAATAGTTTTA
1 CCTTTGATTTCCCACAATCCAACGATCCTAAAAAAGTGTAAAACTAAAAGAGTTTTA
435124 C
1 C
435125 ACATTGTAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 23 0.46
57 27 0.54
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (57 bp):
CCTTTGATTTCCCACAATCCAACGATCCTAAAAAAGTGTAAAACTAAAAGAGTTTTA
Found at i:443176 original size:27 final size:27
Alignment explanation
Indices: 443141--443230 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 27
443131 TCAATTTAGT
443141 TATA-ATTTTAATAAATTAAAATAAAA
1 TATATATTTTAATAAATTAAAATAAAA
*
443167 TATATATTTT--TAAATGAAAATAAAAAA
1 TATATATTTTAATAAATTAAAAT--AAAA
*
443194 TAATATATTTTTAAATTAAGTTAATAATAAAA
1 T-ATATA-TTTT-AA-TAAATTAA-AATAAAA
443226 TATAT
1 TATAT
443231 TTAATAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
25 10 0.20
26 4 0.08
27 10 0.20
28 5 0.10
29 4 0.08
31 4 0.08
32 5 0.10
33 6 0.12
34 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
TATATATTTTAATAAATTAAAATAAAA
Found at i:443186 original size:25 final size:27
Alignment explanation
Indices: 443152--443209 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
443142 ATAATTTTAA
*
443152 TAAATTAAAAT-AAAAT-ATATATTTT
1 TAAATGAAAATAAAAATAATATATTTT
443177 TAAATGAAAATAAAAAATAATATATTTT
1 TAAATGAAAAT-AAAAATAATATATTTT
443205 TAAAT
1 TAAAT
443210 TAAGTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 10 0.34
27 5 0.17
28 14 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATGAAAATAAAAATAATATATTTT
Found at i:443199 original size:30 final size:27
Alignment explanation
Indices: 443141--443232 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 27
443131 TCAATTTAGT
* *
443141 TATAATTTT-AATAAATTAAAATAAAATA
1 TATATTTTTAAATAAAATAAAAT-AAA-A
443169 TATATTTTTAAATGAAAATAAAA-AATAA
1 TATATTTTTAAAT-AAAATAAAATAA-AA
**
443197 TATATTTTTAAATTAAGTTAATAATAAAA
1 TATATTTTTAAA-TAAAATAA-AATAAAA
443226 TATATTT
1 TATATTT
443233 AATAAGTTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 28 0.52
29 16 0.30
30 10 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
TATATTTTTAAATAAAATAAAATAAAA
Found at i:443233 original size:27 final size:26
Alignment explanation
Indices: 443192--443262 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
443182 GAAAATAAAA
*
443192 AATAATATATTTTTAAATTAAGTTAAT
1 AATAAAATA-TTTTAAATTAAGTTAAT
*
443219 AATAAAATATATTT-AA-TAAGTTGAT
1 AATAAAATAT-TTTAAATTAAGTTAAT
*
443244 -ATAAAATATTTTAAGTTAA
1 AATAAAATATTTTAAATTAA
443263 TATATATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.08
24 10 0.26
25 11 0.29
26 3 0.08
27 11 0.29
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.44
Consensus pattern (26 bp):
AATAAAATATTTTAAATTAAGTTAAT
Found at i:443252 original size:22 final size:20
Alignment explanation
Indices: 443209--443266 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 20
443199 TATTTTTAAA
443209 TTAAGTTAATAATAAAATATATT
1 TTAAGTTAAT-AT-AAA-ATATT
*
443232 TAATAAGTTGATATAAAATATT
1 T--TAAGTTAATATAAAATATT
443254 TTAAGTTAATATA
1 TTAAGTTAATATA
443267 TATACAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 11 0.35
22 6 0.19
23 4 0.13
24 2 0.06
25 8 0.26
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (20 bp):
TTAAGTTAATATAAAATATT
Found at i:443267 original size:22 final size:23
Alignment explanation
Indices: 443209--443268 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
443199 TATTTTTAAA
443209 TTAAGTTAATA-ATAAAATATAT
1 TTAAGTTAATATATAAAATATAT
443231 TTAA--TAAGTTGATATAAAATAT-T
1 TTAAGTTAA--T-ATATAAAATATAT
443254 TTAAGTTAATATATA
1 TTAAGTTAATATATA
443269 TACAATTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
20 3 0.09
22 10 0.31
23 7 0.22
24 9 0.28
25 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (23 bp):
TTAAGTTAATATATAAAATATAT
Found at i:443566 original size:39 final size:38
Alignment explanation
Indices: 443507--443624 Score: 113
Period size: 39 Copynumber: 3.1 Consensus size: 38
443497 AGGTTAAAAT
*
443507 AAATATTTTAA-AAA--ATAATTTAAAATGTTAATGTG
1 AAATATTTTAAGAAATTAGAATTTAAAATGTTAATGTG
*
443542 AAATATTTTAAGAAATTAAGAATTTAAAACGTT-ATGGTG
1 AAATATTTTAAGAAATT-AGAATTTAAAATGTTAAT-GTG
* *
443581 TCAA-ATTTTAAGAAATTAGAATTTTAGAATGTTAGA-GTG
1 -AAATATTTTAAGAAATTAGAA-TTTAAAATGTTA-ATGTG
443620 AAATA
1 AAATA
443625 ATTTGAGGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
35 11 0.16
36 3 0.04
38 8 0.12
39 42 0.63
40 2 0.03
41 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (38 bp):
AAATATTTTAAGAAATTAGAATTTAAAATGTTAATGTG
Found at i:446895 original size:14 final size:15
Alignment explanation
Indices: 446876--446906 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
446866 ATTTATTAAA
446876 TATTAACAAAAA-AT
1 TATTAACAAAAAGAT
446890 TATTAACAAAAAGAT
1 TATTAACAAAAAGAT
446905 TA
1 TA
446907 AGGATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (15 bp):
TATTAACAAAAAGAT
Found at i:448370 original size:21 final size:22
Alignment explanation
Indices: 448346--448395 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
448336 TTAACGATTC
448346 AATAAT-CAAAATG-TAAAAATT
1 AATAATAC-AAATGATAAAAATT
*
448367 AATAATACAAATGATTAAAATTT
1 AATAATACAAATGA-TAAAAATT
448390 AATAAT
1 AATAAT
448396 TTTTTACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
22 1 0.04
23 13 0.52
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (22 bp):
AATAATACAAATGATAAAAATT
Found at i:450021 original size:15 final size:15
Alignment explanation
Indices: 450001--450045 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
449991 TAATAATGTT
450001 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
450016 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
450031 AATTATTATAAAATA
1 ATTTATTTTAAAATA
450046 TGGATTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:450086 original size:33 final size:36
Alignment explanation
Indices: 450016--450100 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 36
450006 TTTTAAAATA
450016 ATTTATTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAAT-AATTATTATAAAATATGGATTG
* *
450053 ATTTATTTTAAAATAA-T-TTAT-TAGTATGGATTG
1 ATTTATTTTAAAATAATTATTATAAAATATGGATTG
450086 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
450101 TATATTGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 25 0.54
34 4 0.09
35 1 0.02
36 2 0.04
37 14 0.30
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.49
Consensus pattern (36 bp):
ATTTATTTTAAAATAATTATTATAAAATATGGATTG
Found at i:450178 original size:31 final size:31
Alignment explanation
Indices: 450143--450202 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
450133 TAGTTGTATG
*
450143 AATTATTTAAATTTCAGTATT-CTAAAACTAA
1 AATTATTTAAATCTCAGTATTAC-AAAACTAA
450174 AATTATTTAAATCTCAGTATTACAAAACT
1 AATTATTTAAATCTCAGTATTACAAAACT
450203 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTACAAAACTAA
Found at i:450811 original size:15 final size:15
Alignment explanation
Indices: 450793--450826 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
450783 ATTAATATTA
450793 ATTATAAATATAAAT
1 ATTATAAATATAAAT
*
450808 ATTATAATTATAAAT
1 ATTATAAATATAAAT
450823 -TTAT
1 ATTAT
450827 TTGCGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAAATATAAAT
Found at i:454831 original size:21 final size:20
Alignment explanation
Indices: 454745--454902 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
454735 AAATGACCAA
**
454745 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
454764 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
454784 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
454804 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
454825 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
454846 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
454866 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
454887 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
454903 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:454918 original size:40 final size:40
Alignment explanation
Indices: 454869--455023 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
454859 CGATTTTCCA
* ** *
454869 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
454909 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
454949 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
454989 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
455024 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:454931 original size:20 final size:20
Alignment explanation
Indices: 454869--455022 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
454859 CGATTTTCCA
* ** *
454869 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
454889 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
454909 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
454929 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
454949 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
454969 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
454989 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
455010 AAATCGCAACGCG
1 AAATCGCAACGCG
455023 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:455444 original size:33 final size:33
Alignment explanation
Indices: 455405--455475 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
455395 TTCACTTAGA
*
455405 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
455438 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
455471 TTTCA
1 TTTCA
455476 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:455626 original size:19 final size:19
Alignment explanation
Indices: 455602--455722 Score: 109
Period size: 19 Copynumber: 6.8 Consensus size: 19
455592 ACTGTCGCAA
455602 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
455621 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
455635 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
455654 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
455668 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*** *
455687 TTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
455707 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
455723 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
14 20 0.25
16 6 0.08
17 6 0.08
19 33 0.41
20 15 0.19
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:455638 original size:14 final size:14
Alignment explanation
Indices: 455619--455675 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
455609 TTTCATTTCG
455619 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
455633 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
455652 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
455666 CGTTGCGATT
1 CGTTGCGATT
455676 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:455713 original size:39 final size:33
Alignment explanation
Indices: 455602--455722 Score: 188
Period size: 33 Copynumber: 3.5 Consensus size: 33
455592 ACTGTCGCAA
455602 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
455635 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
455668 TTGCGATTTTCATTTCGCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCG
455707 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
455723 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
33 54 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 25 0.30
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:457579 original size:93 final size:93
Alignment explanation
Indices: 457420--457888 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
457410 TAGATTGCTT
*
457420 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
457485 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
457513 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
457578 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
457606 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
457671 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
457699 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
457764 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
457792 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
457857 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
457884 AGTAA
1 AGTAA
457889 TGCAATCCAT
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 369 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:457976 original size:19 final size:19
Alignment explanation
Indices: 457936--458064 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
457926 TAGTTTACTT
* *
457936 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
457956 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
457975 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
457994 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
458008 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
458027 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
458041 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
458060 TCGCA
1 TCGCA
458065 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:458015 original size:33 final size:32
Alignment explanation
Indices: 457972--458064 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
457962 CGCGAAACCA
**
457972 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
458004 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
458037 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
458065 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:458062 original size:52 final size:52
Alignment explanation
Indices: 457936--458064 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
457926 TAGTTTACTT
**
457936 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
457988 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
458041 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
458065 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:458082 original size:19 final size:19
Alignment explanation
Indices: 458060--458178 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
458050 GAAACCAAAA
*
458060 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
458079 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
458095 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
458112 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
458128 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
458145 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
458164 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
458179 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:458101 original size:14 final size:14
Alignment explanation
Indices: 458082--458138 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
458072 TTTCATTTCG
458082 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
458096 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
458113 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
458129 CGTTGCGATT
1 CGTTGCGATT
458139 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:458107 original size:33 final size:33
Alignment explanation
Indices: 458065--458157 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
458055 CAAAATCGCA
*
458065 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
458098 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
458131 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
458158 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:460139 original size:14 final size:14
Alignment explanation
Indices: 460120--460155 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
460110 ATTGTTTAAT
460120 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
460134 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
460148 TGATTTGT
1 TGATTTGT
460156 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:460286 original size:19 final size:19
Alignment explanation
Indices: 460262--460359 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
460252 AAAATTGACT
460262 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
460281 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
460300 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
460314 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
460333 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
460353 ATCGCAA
1 ATCGCAA
460360 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:460391 original size:53 final size:53
Alignment explanation
Indices: 460262--460378 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
460252 AAAATTGACT
460262 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
460314 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
460367 ATCGCAATGCGA
1 ATCGCAATGCGA
460379 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:460396 original size:19 final size:19
Alignment explanation
Indices: 460368--460556 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
460358 AACGGGAGAA
* *
460368 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
460387 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
460403 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
460420 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
460439 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
460455 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
460472 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
460491 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
460510 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
460528 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
460544 TCGCATTGCGATT
1 TCGCATTGCGATT
460557 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 14 0.10
18 1 0.01
19 76 0.52
20 16 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:460431 original size:52 final size:52
Alignment explanation
Indices: 460368--460570 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
460358 AACGGGAGAA
* *
460368 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
460420 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
460472 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
460528 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
460571 GTAATTTCCG
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 2 0.01
50 2 0.01
51 3 0.02
52 80 0.57
53 24 0.17
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:460578 original size:33 final size:33
Alignment explanation
Indices: 460425--460570 Score: 195
Period size: 33 Copynumber: 4.2 Consensus size: 33
460415 TCATTTCGCA
460425 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
460458 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
460494 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
460530 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
460563 TTGCGATT
1 TTGCGATT
460571 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
32 1 0.01
33 47 0.47
34 14 0.14
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:462993 original size:24 final size:24
Alignment explanation
Indices: 462959--463005 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
462949 CTGAAACATC
462959 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
462983 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
463006 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:463716 original size:20 final size:20
Alignment explanation
Indices: 463688--463997 Score: 352
Period size: 20 Copynumber: 15.5 Consensus size: 20
463678 AAATTTCAGT
* *
463688 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
463708 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
463728 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
463748 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
463768 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
463788 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
463808 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
463828 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
463848 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
463868 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
463888 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
463908 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
463928 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
463948 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
463968 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
463988 GTTGCGATTT
1 GTTGCGATTT
463998 TGGAAAATCG
Statistics
Matches: 256, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
20 255 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:464014 original size:21 final size:21
Alignment explanation
Indices: 463984--464066 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
463974 ATTTTCATAT
*
463984 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
464005 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
464026 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
464047 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
464067 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:464057 original size:42 final size:43
Alignment explanation
Indices: 463964--464062 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
463954 ATTTATGTGT
* *
463964 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
464005 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
464047 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
464063 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:464349 original size:24 final size:23
Alignment explanation
Indices: 464322--464374 Score: 54
Period size: 25 Copynumber: 2.2 Consensus size: 23
464312 AGATATAATC
*
464322 AAATACCAATAA-AAAAGTTTATTT
1 AAATACAAATAATAAAA-TTTA-TT
*
464346 AAATTTCAAATAATAAAATTTATT
1 AAA-TACAAATAATAAAATTTATT
464370 AAATA
1 AAATA
464375 TTTAATCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
23 1 0.04
24 8 0.33
25 11 0.46
26 4 0.17
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATACAAATAATAAAATTTATT
Found at i:472400 original size:23 final size:23
Alignment explanation
Indices: 472373--472447 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
472363 ATTATTATAT
472373 GGCACTACGATGTAATTCTACGC
1 GGCACTACGATGTAATTCTACGC
* *
472396 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGATGTAATTCTACGC
472419 GGCACTACGATGTAATTCTACGC
1 GGCACTACGATGTAATTCTACGC
472442 GGCACT
1 GGCACT
472448 TCGGTGCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGATGTAATTCTACGC
Found at i:473027 original size:11 final size:11
Alignment explanation
Indices: 473011--473041 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
473001 GACTCGTATC
473011 CGGGTTGGGTA
1 CGGGTTGGGTA
473022 CGGGTTGGGTA
1 CGGGTTGGGTA
473033 CGGGTTGGG
1 CGGGTTGGG
473042 GGTGTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.10, G:0.58, T:0.26
Consensus pattern (11 bp):
CGGGTTGGGTA
Found at i:486033 original size:15 final size:15
Alignment explanation
Indices: 486013--486042 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
486003 AGATATTGGG
486013 TATTATAATACCCAA
1 TATTATAATACCCAA
486028 TATTATAATACCCAA
1 TATTATAATACCCAA
486043 GGGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
TATTATAATACCCAA
Found at i:498350 original size:60 final size:60
Alignment explanation
Indices: 498237--498351 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
498227 CGACTAGGGC
* * *
498237 ATTATTTTGTTGAATCTACTGACTATTAAAAGTTACAAAATGATCTCTTAACTATAGAGT
1 ATTATTTTGTCGAATCTACTGACTATTAAAAGTTACAAAATGATCACTCAACTATAGAGT
* * * *
498297 ATTATTTTGTCGAGTCT-CTCGATTATTAAAA-TTAATAAAATGGTCACTCAACTAT
1 ATTATTTTGTCGAATCTACT-GACTATTAAAAGTT-ACAAAATGATCACTCAACTAT
498352 TCATATGTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (60 bp):
ATTATTTTGTCGAATCTACTGACTATTAAAAGTTACAAAATGATCACTCAACTATAGAGT
Found at i:500600 original size:2 final size:2
Alignment explanation
Indices: 500593--500623 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
500583 ATAAAAATAA
500593 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
500624 TATCTCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:500742 original size:19 final size:19
Alignment explanation
Indices: 500718--500758 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
500708 TTCACGTTTA
500718 TTGAACATCAAGGCATCGC
1 TTGAACATCAAGGCATCGC
500737 TTGAACATCAAGGCATCGC
1 TTGAACATCAAGGCATCGC
500756 TTG
1 TTG
500759 GAGAAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (19 bp):
TTGAACATCAAGGCATCGC
Found at i:512855 original size:8 final size:8
Alignment explanation
Indices: 512842--512869 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
512832 AGATTCTCCC
512842 ATATGTAT
1 ATATGTAT
512850 ATATGTAT
1 ATATGTAT
512858 ATATGTAT
1 ATATGTAT
512866 ATAT
1 ATAT
512870 ATCTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:516399 original size:9 final size:9
Alignment explanation
Indices: 516385--516425 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
516375 AGTGAAAATG
516385 AAAAAATAA
1 AAAAAATAA
516394 AAAAAATAA
1 AAAAAATAA
*
516403 AAAAAATAT
1 AAAAAATAA
516412 AAAAAATGAA
1 AAAAAAT-AA
516422 AAAA
1 AAAA
516426 TGGAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 24 0.83
10 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:516431 original size:9 final size:9
Alignment explanation
Indices: 516379--516439 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 9
516369 AAAATGAGTG
516379 AAAAT-GAA
1 AAAATAGAA
*
516387 AAAATAAAA
1 AAAATAGAA
*
516396 AAAATAAAA
1 AAAATAGAA
*
516405 AAAATATAA
1 AAAATAGAA
516414 AAAAT-GAA
1 AAAATAGAA
*
516422 AAAATGGAA
1 AAAATAGAA
*
516431 AAAAAAGAA
1 AAAATAGAA
516440 GGGTTCAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
8 12 0.26
9 34 0.74
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.11
Consensus pattern (9 bp):
AAAATAGAA
Found at i:517426 original size:55 final size:55
Alignment explanation
Indices: 517358--517785 Score: 587
Period size: 55 Copynumber: 7.9 Consensus size: 55
517348 GGTTTCCCAA
* *
517358 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
517413 CGATCGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
** * *
517468 CGATCATTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
517523 CGATTGGTGAAGATTGCTCGAGTCTTACACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
517578 CGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
517631 CGATTGTTGAAGATTGCTCGAGTCTTATACCCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
517686 CGATTGATGAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * * *
517739 CGATTATTAAAGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 CGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
517786 AGCGAACCCG
Statistics
Matches: 335, Mismatches: 33, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
53 91 0.27
54 8 0.02
55 236 0.70
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:517647 original size:108 final size:110
Alignment explanation
Indices: 517365--517785 Score: 613
Period size: 108 Copynumber: 3.9 Consensus size: 110
517355 CAACGATCGT
** * *
517365 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATCGTTGAAGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGC
* *
517430 TCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGACGCGA-TCA
66 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* *
517474 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGGTGAAGATTG
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTG
*
517539 CTCGAGTCTTACACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
65 CTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
*
517585 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGC
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGC
*
517648 TCGAGTCTTATACCCTCTGAAGAAATAGGGGGCAGACGCGATTGA
66 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* * * *
517693 TGAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTAAAGATTG-
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGC
* *
517755 TCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
66 T-CGAGTCT-TATACTCTCTGAAGAAATAGGG
517786 AGCGAACCCG
Statistics
Matches: 286, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
107 2 0.01
108 174 0.61
109 2 0.01
110 106 0.37
111 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (110 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGC
TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
Found at i:517770 original size:163 final size:164
Alignment explanation
Indices: 517365--517785 Score: 582
Period size: 163 Copynumber: 2.6 Consensus size: 164
517355 CAACGATCGT
* * **
517365 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATCGTTGAAGATTGT
1 TGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTG-
* * *
517430 TCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGACGCGATCATTGAAAATTGTTCGAGTCTTA
65 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCATTGAAAATTGCTCGAGTCTTA
* *
517495 TACTCTCTGAAGAAATAGGGGGCAGACACGATTGG
130 TACCCTCTGAAGAAATAGGGGGCAGACACGATTGA
*
517530 TGAAGATTGCTCGAGTCTTACACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA-TGAAGATTG
1 TGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-ATTGAAGATTG
* ** *
517594 T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGCTCGAGTCTTA
65 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCATTGAAAATTGCTCGAGTCTTA
*
517658 TACCCTCTGAAGAAATAGGGGGCAGACGCGATTGA
130 TACCCTCTGAAGAAATAGGGGGCAGACACGATTGA
* * * *
517693 TGAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTAAAGATTGT
1 TGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTGT
* *
517756 CCGAGT-TCTATACTCTCTAAAGAAAGAGGG
66 -CGAGTCT-TATACTCTCTGAAGAAATAGGG
517786 AGCGAACCCG
Statistics
Matches: 228, Mismatches: 23, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
160 1 0.00
161 44 0.19
162 4 0.02
163 120 0.53
164 1 0.00
165 58 0.25
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (164 bp):
TGAAGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTGT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCATTGAAAATTGCTCGAGTCTTAT
ACCCTCTGAAGAAATAGGGGGCAGACACGATTGA
Found at i:522092 original size:25 final size:23
Alignment explanation
Indices: 522065--522109 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
522055 AGATGATCGT
*
522065 TATT-TTAAAAAAATATTTTTAA
1 TATTATTAAAAAAATATATTTAA
*
522087 TATTATTAAAAACATATATTTAA
1 TATTATTAAAAAAATATATTTAA
522110 CATATAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATTAAAAAAATATATTTAA
Found at i:522284 original size:15 final size:16
Alignment explanation
Indices: 522253--522285 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
522243 ATATATGAAC
522253 TAAATTAGATGATCAA
1 TAAATTAGATGATCAA
522269 TAAATTAGAT-ATCAA
1 TAAATTAGATGATCAA
522284 TA
1 TA
522286 TCATTTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (16 bp):
TAAATTAGATGATCAA
Found at i:526182 original size:3 final size:3
Alignment explanation
Indices: 526170--526249 Score: 85
Period size: 3 Copynumber: 27.0 Consensus size: 3
526160 CCATTTGTTT
* *
526170 TTA TTA -TA TTA TTA TTA TT- TTA TTTA TCA CTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* *
526213 TTA TTA TTA TTT TTA TTA TTA TTAA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
526250 CAAACAGATC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
2 6 0.09
3 52 0.81
4 6 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:526236 original size:32 final size:32
Alignment explanation
Indices: 526170--526249 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 32
526160 CCATTTGTTT
526170 TTATTATATTATTATTATTTTATTTATCACTA
1 TTATTATATTATTATTATTTTATTTATCACTA
* * *
526202 TTATTATTTTATTATTATTATT-TTTATTATTA
1 TTATTATATTATTATTATT-TTATTTATCACTA
526234 TTAATTAATATTATTA
1 TT-ATT-ATATTATTA
526250 CAAACAGATC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 28 0.68
33 5 0.12
34 8 0.20
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (32 bp):
TTATTATATTATTATTATTTTATTTATCACTA
Found at i:531137 original size:31 final size:31
Alignment explanation
Indices: 531099--531193 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
531089 GAACCTCGGC
* *
531099 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
531130 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
531161 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
531192 AA
1 AA
531194 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:531351 original size:21 final size:21
Alignment explanation
Indices: 531327--531366 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
531317 CATATATCTC
531327 ATATCATAT-CACATGTATTAT
1 ATAT-ATATACACATGTATTAT
*
531348 ATATATATATACATGTATT
1 ATATATATACACATGTATT
531367 CATGTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (21 bp):
ATATATATACACATGTATTAT
Found at i:531961 original size:64 final size:65
Alignment explanation
Indices: 531850--531994 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 65
531840 TCTTTCAATG
* * * * *
531850 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTTATTTTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATACATAAAAGGCATTCGATGTTCTTTATTTT-
531914 A
65 A
* * *
531915 AAGG-ATGCATCGATGCATTA-TCTATGCATCGATACATCAAAGGCATTCGATGTTCTTTCTTTT
1 AAGGAATGCATCGATGCACTACT-TATGCATCGATACATAAAAGGCATTCGATGTTCTTTATTTT
531978 A
65 A
531979 AAGGAATGCATCGATG
1 AAGGAATGCATCGATG
531995 TACTTATGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 47 0.67
65 22 0.31
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATACATAAAAGGCATTCGATGTTCTTTATTTTA
Found at i:545365 original size:15 final size:15
Alignment explanation
Indices: 545347--545376 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
545337 GATATTAGTA
545347 TTAAGTTATTAAAAT
1 TTAAGTTATTAAAAT
545362 TTAAGTTATTAAAAT
1 TTAAGTTATTAAAAT
545377 AAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
TTAAGTTATTAAAAT
Found at i:558236 original size:120 final size:121
Alignment explanation
Indices: 558016--558254 Score: 369
Period size: 120 Copynumber: 2.0 Consensus size: 121
558006 AAATAATGAT
**
558016 GTGGCATTATGATACGCCGTCACTTATGTATTTGTGATTTGTGTAATGTTATCACTTATATACAC
1 GTGGCATTATGATACGCCGTCACTTATGTACATGTGATTTGTGTAATGTTATCACTTATATACAC
558081 ATGTCATCACATATGTATATATGATATGAATCACGTCATCACTTATGTACACGTAC
66 ATGTCATCACATATGTATATATGATATGAATCACGTCATCACTTATGTACACGTAC
*
558137 GTGGCA-TATGATACGACAC-T-ACTTATGTACATGTGATTTGTGTTATGTTATCACTTATATA-
1 GTGGCATTATGATACG-C-CGTCACTTATGTACATGTGATTTGTGTAATGTTATCACTTATATAC
* * *
558198 ATCATGTCATCACGTATGTATATGTGATATGAGTCACGTCATCACTTATGTACACGT
64 A-CATGTCATCACATATGTATATATGATATGAATCACGTCATCACTTATGTACACGT
558255 GAAATGTGTT
Statistics
Matches: 109, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
119 1 0.01
120 99 0.91
121 8 0.07
122 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (121 bp):
GTGGCATTATGATACGCCGTCACTTATGTACATGTGATTTGTGTAATGTTATCACTTATATACAC
ATGTCATCACATATGTATATATGATATGAATCACGTCATCACTTATGTACACGTAC
Found at i:560318 original size:20 final size:20
Alignment explanation
Indices: 560293--560333 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
560283 TCGTTCGTTA
560293 CTTGAAATTCAGACTCCAAC
1 CTTGAAATTCAGACTCCAAC
560313 CTTGAAATTCAGACTCCAAC
1 CTTGAAATTCAGACTCCAAC
560333 C
1 C
560334 ACGTCATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (20 bp):
CTTGAAATTCAGACTCCAAC
Found at i:570515 original size:21 final size:21
Alignment explanation
Indices: 570489--570528 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
570479 TAAAGCATCC
*
570489 AATAATAATATTTTCGGTAGA
1 AATAATAATATTTTAGGTAGA
*
570510 AATAATAATGTTTTAGGTA
1 AATAATAATATTTTAGGTA
570529 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (21 bp):
AATAATAATATTTTAGGTAGA
Found at i:579480 original size:25 final size:25
Alignment explanation
Indices: 579424--579493 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 25
579414 AAAATGAAAA
*
579424 TAAAATATTTTTAAATTAATTTAATAG
1 TAAAATA-TTTT-AATTAAGTTAATAG
579451 TAAAATATATTTAA-TAAGTTAATA-
1 TAAAATAT-TTTAATTAAGTTAATAG
579475 TAAAAATATTTTAAGTTAA
1 T-AAAATATTTTAA-TTAA
579494 TATATGGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 6 0.16
25 16 0.42
26 6 0.16
27 10 0.26
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
TAAAATATTTTAATTAAGTTAATAG
Found at i:579498 original size:23 final size:23
Alignment explanation
Indices: 579444--579497 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 23
579434 TTAAATTAAT
579444 TTAATAGTAAAATATATTTAATAAG
1 TTAATA-TAAAATATATTT-ATAAG
579469 TTAATATAAAA-ATATTT-TAAG
1 TTAATATAAAATATATTTATAAG
579490 TTAATATA
1 TTAATATA
579498 TGGATATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 12 0.41
23 6 0.21
24 5 0.17
25 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
TTAATATAAAATATATTTATAAG
Found at i:580399 original size:31 final size:31
Alignment explanation
Indices: 580355--580430 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
580345 TTAACTCGGG
*
580355 GTGACCA-CATCTTAATTATATAAAAACGAAA
1 GTGACCATC-TCTTAATTAAATAAAAACGAAA
* *
580386 GTGACCATCTCTTAATTAAATAAAAATGTAA
1 GTGACCATCTCTTAATTAAATAAAAACGAAA
* *
580417 GTGATCATATCTTA
1 GTGACCATCTCTTA
580431 TGTATTTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (31 bp):
GTGACCATCTCTTAATTAAATAAAAACGAAA
Found at i:582041 original size:16 final size:16
Alignment explanation
Indices: 582022--582052 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
582012 AATACTAAAT
*
582022 TATTAATTTGCTAATC
1 TATTAATTTCCTAATC
582038 TATTAATTTCCTAAT
1 TATTAATTTCCTAAT
582053 AAATATCAAG
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:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (16 bp):
TATTAATTTCCTAATC
Found at i:591180 original size:20 final size:20
Alignment explanation
Indices: 591155--591247 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
591145 TTTTCCCAAT
591155 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
591175 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
591195 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
591216 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
591237 TCGCAATGCGA
1 TCGCAATGCGA
591248 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:591197 original size:41 final size:41
Alignment explanation
Indices: 591152--591247 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
591142 CGATTTTCCC
591152 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
591193 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
591234 AAATCGCAATGCGA
1 AATTCGCAATGCGA
591248 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:591201 original size:21 final size:20
Alignment explanation
Indices: 591155--591247 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
591145 TTTTCCCAAT
*
591155 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
591175 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
591195 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
591216 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
591237 TCGCAATGCGA
1 TCGCAATGCGA
591248 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:591260 original size:41 final size:41
Alignment explanation
Indices: 591174--591308 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
591164 GAATAAGTAA
* * *
591174 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
591215 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
591256 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
591297 TTCGCAACGCGA
1 ATCGCAACGCGA
591309 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:591261 original size:20 final size:20
Alignment explanation
Indices: 591236--591329 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
591226 AATTGGGAAA
*
591236 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
591256 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
591277 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
591297 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
591317 TTCGCAACGCGAT
1 ATCGCAACGCGAT
591330 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:591911 original size:19 final size:19
Alignment explanation
Indices: 591887--591931 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
591877 GCAACGAGAT
*
591887 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
591906 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
591925 AATCGCA
1 AATCGCA
591932 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:592016 original size:20 final size:19
Alignment explanation
Indices: 591927--592148 Score: 207
Period size: 19 Copynumber: 12.1 Consensus size: 19
591917 GAAACCAAAA
*
591927 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
591946 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
591965 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
591984 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
592003 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
592023 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
592043 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
592059 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
592076 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
592090 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
592109 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
592129 ATCTCGTT--GATTTTCATT
1 -TCGCGTTGCGATTTTCATT
592147 TC
1 TC
592149 AACCAAAGAC
Statistics
Matches: 175, Mismatches: 15, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
14 20 0.11
15 1 0.01
16 3 0.02
17 5 0.03
18 10 0.06
19 77 0.44
20 58 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:592075 original size:33 final size:33
Alignment explanation
Indices: 592038--592125 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
592028 GTTGCGATTT
* *
592038 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
592071 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
592104 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
592126 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:594226 original size:21 final size:21
Alignment explanation
Indices: 594202--594268 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
594192 TCATTCCTCG
594202 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
594223 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
594244 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
594265 AGAG
1 AGAG
594269 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:594226 original size:42 final size:42
Alignment explanation
Indices: 594146--594268 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
594136 GCCCGACTCG
* * * * ** *
594146 CCTATCATCCCTCAAGAGTCCACTCCTATTGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
594188 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
594230 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
594269 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:595644 original size:14 final size:14
Alignment explanation
Indices: 595625--595660 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
595615 ATTGTTTAAT
595625 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
595639 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
595653 TGATTTGT
1 TGATTTGT
595661 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:595841 original size:19 final size:19
Alignment explanation
Indices: 595819--595902 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
595809 CGAAATTAAA
*
595819 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
595838 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
595857 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
595873 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
595890 TTCGCATTGCGAT
1 TTCGCATTGCGAT
595903 AGTAATTTCC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 37 0.65
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:595911 original size:52 final size:53
Alignment explanation
Indices: 595823--595922 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 53
595813 ATTAAATTCG
** *
595823 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATAGTAATTTCCGCATTGCGATTCTCT
*
595875 CGTTGCGATTTTCATTTCGCATTGCGATAGTAATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGATAGTAATTTCCGCATTGCGAT
595923 GGACATTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 33 0.77
53 10 0.23
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (53 bp):
CGTTGCGATTTTCATTTCGCATTGCGATAGTAATTTCCGCATTGCGATTCTCT
Found at i:599680 original size:14 final size:14
Alignment explanation
Indices: 599661--599697 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
599651 CATCAATTAA
599661 ACAAATCAACATTT
1 ACAAATCAACATTT
*
599675 ACAAATCAACTTTT
1 ACAAATCAACATTT
599689 ACAAATCAA
1 ACAAATCAA
599698 TTAAACAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:600267 original size:14 final size:14
Alignment explanation
Indices: 600248--600284 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
600238 CATCAATTAA
600248 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
600262 ACAAATCATCTTTT
1 ACAAATCAACATTT
600276 ACAAATCAA
1 ACAAATCAA
600285 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:600834 original size:14 final size:14
Alignment explanation
Indices: 600815--600851 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
600805 CATCAATTAA
600815 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
600829 ACAAATCATCTTTT
1 ACAAATCAACATTT
600843 ACAAATCAA
1 ACAAATCAA
600852 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:601078 original size:567 final size:570
Alignment explanation
Indices: 599304--601097 Score: 3280
Period size: 567 Copynumber: 3.1 Consensus size: 570
599294 TTTAACAATT
*
599304 ATTATTGAATTCTAGGTACTTAACCAAATATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
599369 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
599434 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
599499 AATGCGAAAATGGTTATCGCAACGAGAAAATCACAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
599564 TCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATTAC
261 TCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATTAC
*
599629 ATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCAACTTTTACAAA
326 ATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTTACAAA
599694 TCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAATCA
391 TCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAATCA
599759 ACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAAACCAA
456 ACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAAACCAA
599824 ACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
521 ACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
599874 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
599939 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
* *
600004 GAGTTTGAATATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGA
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
600069 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGA-----
600134 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
256 T--TT----T---C---T--CGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
600199 TC-ACAAATCAACTATTACATTTCAACAC-AATTATGTACACATCAATTAAACAAATCAACATTT
307 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
600262 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAT-ATAATTCTTATTTCTTCATCA
372 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
600326 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
437 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
600391 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
502 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
*
600456 TCAA
567 GCAA
600460 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
600525 CTTGCATTATGTGTA-TTTATGTGTGCACTTTTAACATTTTCAGTTA-GCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
600588 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
600653 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCAAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
600718 TCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATTAC
261 TCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATTAC
600783 ATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTTACAAA
326 ATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTTACAAA
600848 TCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAATCA
391 TCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAATCA
*
600912 ACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGTAGAAACCAA
456 ACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAAACCAA
600977 ACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
521 ACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
601027 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAG--TATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
601090 CTGGCATT
66 CTTGCATT
601098 TGACTTACCA
Statistics
Matches: 1190, Mismatches: 12, Indels: 49
0.95 0.01 0.04
Matches are distributed among these distances:
565 69 0.06
566 35 0.03
567 270 0.23
570 252 0.21
573 1 0.00
575 1 0.00
577 4 0.00
579 1 0.00
581 1 0.00
584 140 0.12
585 31 0.03
586 234 0.20
587 78 0.07
588 26 0.02
589 47 0.04
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (570 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
TCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATTAC
ATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTTACAAA
TCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAATCA
ACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAAACCAA
ACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
Found at i:602737 original size:19 final size:18
Alignment explanation
Indices: 602711--602862 Score: 130
Period size: 14 Copynumber: 8.9 Consensus size: 18
602701 ACGAAACTTA
602711 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
602729 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** *
602750 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
602768 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
602783 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
602801 AAATCGCAA--CGAAA--
1 AAATCGCAACGCGAAATG
602815 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
602833 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
602847 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
602863 CACAAATCGC
Statistics
Matches: 111, Mismatches: 9, Indels: 30
0.74 0.06 0.20
Matches are distributed among these distances:
14 27 0.24
16 22 0.20
17 4 0.04
18 20 0.18
19 22 0.20
20 15 0.14
21 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:602737 original size:39 final size:34
Alignment explanation
Indices: 602710--602862 Score: 147
Period size: 32 Copynumber: 4.5 Consensus size: 34
602700 CACGAAACTT
* *
602710 AAAATCGCAACGCGAAATGACTATCGCAACGCGGAA
1 AAAATCGCAACGCGAAATGA-AATCGCAACAC-GAA
** * *
602746 ATGGCTATCGCAATGCGAAATGAAAATCGC-A-ACGAC
1 A---AAATCGCAACGCGAAATG-AAATCGCAACACGAA
602782 AAAATCGCAACGCGAAATGAAATCGC-A-ACGAA
1 AAAATCGCAACGCGAAATGAAATCGCAACACGAA
*
602814 AAAATCGCAACGCGAAATGAAATCGC-A-ACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACACGAA
602846 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
602863 CACAAATCGC
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
32 60 0.59
33 15 0.15
36 4 0.04
37 1 0.01
38 1 0.01
39 20 0.20
40 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (34 bp):
AAAATCGCAACGCGAAATGAAATCGCAACACGAA
Found at i:602748 original size:20 final size:19
Alignment explanation
Indices: 602713--602843 Score: 90
Period size: 19 Copynumber: 7.5 Consensus size: 19
602703 GAAACTTAAA
602713 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
602732 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
602752 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
602771 ATCGCAA--CGACAA--A--
1 ATCGCAACGCGA-AATGACT
*
602785 ATCGCAACGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
*
602803 ATCGCAA--CGAAA--A-A
1 ATCGCAACGCGAAATGACT
*
602817 ATCGCAACGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
602835 ATCGCAACG
1 ATCGCAACG
602844 ACAAAATCGC
Statistics
Matches: 96, Mismatches: 5, Indels: 23
0.77 0.04 0.19
Matches are distributed among these distances:
14 16 0.17
15 2 0.02
16 14 0.15
17 4 0.04
18 20 0.21
19 23 0.24
20 17 0.18
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:602810 original size:32 final size:32
Alignment explanation
Indices: 602752--602862 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
602742 GGAAATGGCT
*
602752 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
602785 ATCGCAACGCGAAATGAAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
602817 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
602849 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
602863 CACAAATCGC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 60 0.80
33 15 0.20
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:602910 original size:14 final size:14
Alignment explanation
Indices: 602891--602948 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
602881 TTTCATTTCG
602891 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
602905 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
602921 CGCGTTGCAATTTTGT
1 --CGTTGCGATTTTGT
*
602937 CGTTGTGATTTT
1 CGTTGCGATTTT
602949 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 21 0.60
16 4 0.11
18 10 0.29
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:602921 original size:32 final size:33
Alignment explanation
Indices: 602874--602964 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
602864 ACAAATCGCA
602874 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
602907 TTGCGA-TTTCATTTCGCGTTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
602939 TTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
602965 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Done.