Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 88 of 89
Found at i:21043746 original size:6 final size:6
Alignment explanation
Indices: 21043737--21043977 Score: 109
Period size: 6 Copynumber: 42.8 Consensus size: 6
21043727 GACACACACA
21043737 CACGCG CACGCG CACGCG CA-GCG CACGCG CACGCG CACGCG CAC-CG
1 CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG
* * ** ** * *
21043783 --CGCG CACGCG CA--CA CACGCG CAC-CA CATACG CAAACA CA-GCA
1 CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG
* * * * * * *
21043825 CACACG CACACA CAGGCG CA--CA CACGCG CACACG CA--CA CACGCG
1 CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG
* * * * * * * *
21043869 CACACT CGCACA CACGCA CACGCA CACGCA CACGCG CA--CG CACGCG
1 CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG
* * * *
21043915 CACGCG CA--CG CACGCG CACGCG CACACG CACACG CACACG CACACG
1 CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG
* *
21043961 CACACG CACGCA CACGC
1 CACGCG CACGCG CACGC
21043978 ACGCACACAC
Statistics
Matches: 190, Mismatches: 29, Indels: 32
0.76 0.12 0.13
Matches are distributed among these distances:
3 1 0.01
4 19 0.10
5 14 0.07
6 156 0.82
ACGTcount: A:0.27, C:0.49, G:0.23, T:0.01
Consensus pattern (6 bp):
CACGCG
Found at i:21044057 original size:4 final size:4
Alignment explanation
Indices: 21044050--21045019 Score: 626
Period size: 4 Copynumber: 242.0 Consensus size: 4
21044040 CGCACACATG
* * * * * * * * *
21044050 CACA CACA CATA CAGA CATA CGCA CACG CACG CACG CACA CGCA CATA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * *
21044098 CAGA CATA CCCA CGCA CACA CACG CACA CACA CGCA CACA CACG CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * ** * * * * * * *
21044146 CTCA CGCA CACA TGCA CGCA CACA CGCA CGCA CGCA CGCA CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * *
21044194 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACGA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CAC-A CACA
* * * * * * * * * * *
21044243 CGCA CGCA CGCA CGCA CACA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
21044291 CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * *
21044339 CACG CACA CACG CACA CACG CACA CACG CACA CACG CACA CACG CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * *
21044387 CACG CACA CACG CACA CACG CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * *
21044435 CACA CACA CACA CACA GACA CACA CACA CACA CACA CACA CTCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
21044483 CGCA CGCA CTCA CGCA CTCA CGCA CACT CACG CACG CACG CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * *
21044531 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * *
21044579 CGCA CGCA CGCA CGCA CACA CACA CACG CACA CACG CACG CTCG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * *
21044627 CTCG CACA CGCA CACA CGCA CACA CACG CACA CGCA CACA CACG CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
21044675 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * *
21044723 CACA CACA CGCA CTCA CGCA CACG CACG CACG CACG CACG CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * *
21044771 CACG CACG CACG CACG CACG CACG CACG CACG CACA CACG CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * *
21044819 CACG CACA CACA CAGCA CACA CGCA CGCT CGCA CACA CACA CACG CACA
1 CACA CACA CACA CA-CA CACA CACA CACA CACA CACA CACA CACA CACA
* * * *
21044868 CACA CGCA CACA CGCA CACA CACG CACA CACG CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
21044916 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
21044964 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
21045012 CACA CACA
1 CACA CACA
21045020 TGCATGCATG
Statistics
Matches: 854, Mismatches: 110, Indels: 4
0.88 0.11 0.00
Matches are distributed among these distances:
4 848 0.99
5 6 0.01
ACGTcount: A:0.36, C:0.49, G:0.14, T:0.01
Consensus pattern (4 bp):
CACA
Found at i:21045637 original size:21 final size:21
Alignment explanation
Indices: 21045624--21045680 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
21045614 GGTAGCTTAT
21045624 GTAGCTAGCTAGGTAGTGTAG
1 GTAGCTAGCTAGGTAGTGTAG
21045645 GTAGCTAGCTAGGTAGTGTAG
1 GTAGCTAGCTAGGTAGTGTAG
21045666 GTAGCTAGCTAGGTA
1 GTAGCTAGCTAGGTA
21045681 CCTAATGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.11, G:0.37, T:0.28
Consensus pattern (21 bp):
GTAGCTAGCTAGGTAGTGTAG
Found at i:21048243 original size:29 final size:29
Alignment explanation
Indices: 21048210--21048276 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
21048200 TAAATATAAG
21048210 CATTCAAAGTT-AAACATTCAAACAAAAAA
1 CATTCAAA-TTCAAACATTCAAACAAAAAA
* *
21048239 CATTCAAATTCAAACATTCAATCTAAAAA
1 CATTCAAATTCAAACATTCAAACAAAAAA
*
21048268 CATTAAAAT
1 CATTCAAAT
21048277 GTTTAACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.55, C:0.18, G:0.01, T:0.25
Consensus pattern (29 bp):
CATTCAAATTCAAACATTCAAACAAAAAA
Found at i:21048270 original size:15 final size:15
Alignment explanation
Indices: 21048221--21048271 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
21048211 ATTCAAAGTT
* *
21048221 AAACATTCAAACAAA
1 AAACATTCAATCTAA
*
21048236 AAACATTCAAAT-T-C
1 AAACATTC-AATCTAA
21048250 AAACATTCAATCTAA
1 AAACATTCAATCTAA
21048265 AAACATT
1 AAACATT
21048272 AAAATGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 9 0.31
15 15 0.52
16 2 0.07
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.24
Consensus pattern (15 bp):
AAACATTCAATCTAA
Found at i:21050308 original size:21 final size:21
Alignment explanation
Indices: 21050243--21050319 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 21
21050233 ACCCTGTGGA
*
21050243 GGGTATCAATACCC-TCAAGG
1 GGGTATCGATACCCATCAAGG
*
21050263 GGGTATCGGTACCCACTCAAAGG
1 GGGTATCGATACCCA-TC-AAGG
21050286 GGGTA-CGATACCCATGCAAGG
1 GGGTATCGATACCCAT-CAAGG
21050307 GGGTATCGATACC
1 GGGTATCGATACC
21050320 TAGCCCATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
20 12 0.24
21 10 0.20
22 18 0.37
23 9 0.18
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (21 bp):
GGGTATCGATACCCATCAAGG
Found at i:21053968 original size:21 final size:21
Alignment explanation
Indices: 21053944--21053985 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21053934 ATAAGACTAT
21053944 TTTCATTTTTCA-ATTTTGAAA
1 TTTCATTTTT-ATATTTTGAAA
*
21053965 TTTCGTTTTTATATTTTGAAA
1 TTTCATTTTTATATTTTGAAA
21053986 ATAAACTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTCATTTTTATATTTTGAAA
Found at i:21057732 original size:49 final size:49
Alignment explanation
Indices: 21057655--21058008 Score: 269
Period size: 49 Copynumber: 7.3 Consensus size: 49
21057645 TCTACAATGT
* * * *
21057655 AAAATGGTGCA-TTTTGGAAGAAATGTGCCATTAATGCAATTTAAATAC
1 AAAACGGTGCATTTTTGGCAGAAATGTGCCACTAATGCAAGTTAAATAC
* * * **
21057703 ATAACAGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTTGATGA-
1 AAAACGGTGCATTTTTGGCAGAAATGTGCCACTAATGCAAGTTAAAT-AC
* * * * * *
21057752 AAAATGGTGGA-TTTTGGCTA-AAAGGTGCCATTAATGAAAGTTAAATGC
1 AAAACGGTGCATTTTTGGC-AGAAATGTGCCACTAATGCAAGTTAAATAC
** * * * * *
21057800 CTAACGGTGCATTCTTGGCAGAAAGGTGTCATTAATGCAAGTTAGATGA-
1 AAAACGGTGCATTTTTGGCAGAAATGTGCCACTAATGCAAGTTAAAT-AC
* * * *
21057849 AAAATGGTGCATTTTTGGTAGAAATGTGCCAGC-AATGGAAGTTAAATGC
1 AAAACGGTGCATTTTTGGCAGAAATGTGCCA-CTAATGCAAGTTAAATAC
** * * *
21057898 CCAACGGTGCATTTTT-GCAAGAAATATACCACTAATGCAAGTTAGATGA-
1 AAAACGGTGCATTTTTGGC-AGAAATGTGCCACTAATGCAAGTTAAAT-AC
* *
21057947 AAAATGGTGCATTTTTGGCAGAAATGTG-CACTAATGACAA-TTAAATGC
1 AAAACGGTGCATTTTTGGCAGAAATGTGCCACTAATG-CAAGTTAAATAC
*
21057995 ATAACGGTGCATTT
1 AAAACGGTGCATTT
21058009 CGACATAAAA
Statistics
Matches: 235, Mismatches: 56, Indels: 30
0.73 0.17 0.09
Matches are distributed among these distances:
48 72 0.31
49 160 0.68
50 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (49 bp):
AAAACGGTGCATTTTTGGCAGAAATGTGCCACTAATGCAAGTTAAATAC
Found at i:21057821 original size:97 final size:97
Alignment explanation
Indices: 21057655--21058027 Score: 432
Period size: 97 Copynumber: 3.8 Consensus size: 97
21057645 TCTACAATGT
* * * * *
21057655 AAAATGGTGCA-TTTTGGAAGAAATGTGCCATTAATGCAATTTAAATACATAACAGTGCATTTTT
1 AAAATGGTGCATTTTTGGTAGAAATGTGCCATTAATGAAAGTTAAATGCATAACGGTGCA-TTTT
*
21057719 GGCAGAAAGGTGCCACTAATGCAAGTTTGATGA
65 GGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * *
21057752 AAAATGGTGGA-TTTTGGCTA-AAAGGTGCCATTAATGAAAGTTAAATGCCTAACGGTGCATTCT
1 AAAATGGTGCATTTTTGG-TAGAAATGTGCCATTAATGAAAGTTAAATGCATAACGGTGCATT-T
* *
21057815 TGGCAGAAAGGTGTCATTAATGCAAGTTAGATGA
64 TGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
** * ** *
21057849 AAAATGGTGCATTTTTGGTAGAAATGTGCCAGCAATGGAAGTTAAATGCCCAACGGTGCATTTTT
1 AAAATGGTGCATTTTTGGTAGAAATGTGCCATTAATGAAAGTTAAATGCATAACGGTGCATTTTG
** *
21057914 GCAAGAAATATACCACTAATGCAAGTTAGATGA
66 GC-AGAAAGGTGCCACTAATGCAAGTTAGATGA
* * *
21057947 AAAATGGTGCATTTTTGGCAGAAATGTG-CACTAATGACAA-TTAAATGCATAACGGTGCATTTC
1 AAAATGGTGCATTTTTGGTAGAAATGTGCCATTAATGA-AAGTTAAATGCATAACGGTGCATTTT
* *
21058010 GACATAAAAGGTGCCACT
65 GGCA-GAAAGGTGCCACT
21058028 CATGGTTTAA
Statistics
Matches: 233, Mismatches: 36, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
96 3 0.01
97 133 0.57
98 97 0.42
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (97 bp):
AAAATGGTGCATTTTTGGTAGAAATGTGCCATTAATGAAAGTTAAATGCATAACGGTGCATTTTG
GCAGAAAGGTGCCACTAATGCAAGTTAGATGA
Found at i:21058005 original size:195 final size:194
Alignment explanation
Indices: 21057655--21058007 Score: 480
Period size: 195 Copynumber: 1.8 Consensus size: 194
21057645 TCTACAATGT
** * *
21057655 AAAATGGTGCATTTTGGAAGAAATGTGCCATTAATGCAATTTAAATACATAACAGTGCATTTTTG
1 AAAATGGTGCATTTTGGAAGAAATGTGCCAGCAATGCAAGTTAAATACACAACAGTGCATTTTTG
* * * * *
21057720 GCAGAAAGGTGCCACTAATGCAAGTTTGATGAAAAATGGTGGATTTTGGCTAAAAGGTGCCATTA
66 GCAGAAAGATACCACTAATGCAAGTTAGATGAAAAATGGTGCATTTTGGCTAAAAGGTGCCACTA
*
21057785 ATGAAAGTTAAATGCCTAACGGTGCATTCTTGGCAGAAAGGTGTCATTAATGCAAGTTAGATGA
131 ATGAAAGTTAAATGCATAACGGTGCATTCTTGGCAGAAAGGTGTCATTAATGCAAGTTAGATGA
* * * * *
21057849 AAAATGGTGCATTTTTGGTAGAAATGTGCCAGCAATGGAAGTTAAATGCCCAACGGTGCATTTTT
1 AAAATGGTGCA-TTTTGGAAGAAATGTGCCAGCAATGCAAGTTAAATACACAACAGTGCATTTTT
* *
21057914 -GCAAGAAATATACCACTAATGCAAGTTAGATGAAAAATGGTGCATTTTTGGC-AGAAATGTG-C
65 GGC-AGAAAGATACCACTAATGCAAGTTAGATGAAAAATGGTGCA-TTTTGGCTA-AAAGGTGCC
21057976 ACTAATGACAA-TTAAATGCATAACGGTGCATT
127 ACTAATGA-AAGTTAAATGCATAACGGTGCATT
21058008 TCGACATAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
194 13 0.09
195 109 0.80
196 15 0.11
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (194 bp):
AAAATGGTGCATTTTGGAAGAAATGTGCCAGCAATGCAAGTTAAATACACAACAGTGCATTTTTG
GCAGAAAGATACCACTAATGCAAGTTAGATGAAAAATGGTGCATTTTGGCTAAAAGGTGCCACTA
ATGAAAGTTAAATGCATAACGGTGCATTCTTGGCAGAAAGGTGTCATTAATGCAAGTTAGATGA
Found at i:21065462 original size:15 final size:15
Alignment explanation
Indices: 21065444--21065496 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 15
21065434 TTTGAAATAA
21065444 TTAATTTTTTTTGTT
1 TTAATTTTTTTTGTT
21065459 TTAATTAGTGTTTTTGTT
1 TTAATT--T-TTTTTGTT
*
21065477 TTAATTTTTATTGTT
1 TTAATTTTTTTTGTT
21065492 TTAAT
1 TTAAT
21065497 GAAATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 18 0.53
16 1 0.03
17 1 0.03
18 14 0.41
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (15 bp):
TTAATTTTTTTTGTT
Found at i:21074487 original size:48 final size:49
Alignment explanation
Indices: 21074355--21074709 Score: 371
Period size: 49 Copynumber: 7.3 Consensus size: 49
21074345 TCTATAATGT
* * * * * *
21074355 AAAATGGTGTATTTTTGGCAGAAAGGTGCCATTAATGTAATTTAAATGCCT
1 AAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG--A
*
21074406 AAAA--GTGCATTTTTGGCAGAAAGGTGCCATTAATGCAAGTTAGATGA
1 AAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
** ** * * *
21074453 AAAATTATGCA-TTTTGGCAGAATTGTGCCATTAATGCAAGTTAAATGC
1 AAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
** * *
21074501 CTAACGGTGCATTCTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
1 AAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * *
21074550 AAAATGGTACA-TTTTGGCAGAAAGGTGTCACTAATGCAAGTTAAATGC
1 AAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
**
21074598 CTAATGGTGCATTTTTGGC-GAAAAGGTGCCACTAATGCAAGTTAGATGA
1 AAAATGGTGCATTTTTGGCAG-AAAGGTGCCACTAATGCAAGTTAGATGA
* * *
21074647 AAAATGATGCATTTTTGGCAGAAAGGTGCCACTAATGACAA-TTAAATGC
1 AAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATG-CAAGTTAGATGA
* *
21074696 ATAACGGTGCATTT
1 AAAATGGTGCATTT
21074710 CGACATAAAA
Statistics
Matches: 254, Mismatches: 43, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
47 4 0.02
48 81 0.32
49 161 0.63
50 4 0.02
51 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (49 bp):
AAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
Found at i:21074537 original size:97 final size:97
Alignment explanation
Indices: 21074367--21074709 Score: 501
Period size: 97 Copynumber: 3.5 Consensus size: 97
21074357 AATGGTGTAT
* * * **
21074367 TTTTGGCAGAAAGGTGCCATTAATGTAATTTAAATGCCTAAAAGTGCATTTTTGGCAGAAAGGTG
1 TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTG
* *
21074432 CCATTAATGCAAGTTAGATGAAAAATTATGCA
66 CCACTAATGCAAGTTAGATGAAAAATGATGCA
** * *
21074464 TTTTGGCAGAATTGTGCCATTAATGCAAGTTAAATGCCTAACGGTGCATTCTTGGCAGAAAGGTG
1 TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTG
* *
21074529 CCACTAATGCAAGTTAGATGAAAAATGGTACA
66 CCACTAATGCAAGTTAGATGAAAAATGATGCA
* *
21074561 TTTTGGCAGAAAGGTGTCACTAATGCAAGTTAAATGCCTAATGGTGCATTTTTGGC-GAAAAGGT
1 TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAG-AAAGGT
21074625 GCCACTAATGCAAGTTAGATGAAAAATGATGCA
65 GCCACTAATGCAAGTTAGATGAAAAATGATGCA
*
21074658 TTTTTGGCAGAAAGGTGCCACTAATGACAA-TTAAATGCATAACGGTGCATTT
1 -TTTTGGCAGAAAGGTGCCACTAATG-CAAGTTAAATGCCTAACGGTGCATTT
21074710 CGACATAAAA
Statistics
Matches: 221, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
96 1 0.00
97 173 0.78
98 44 0.20
99 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (97 bp):
TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTG
CCACTAATGCAAGTTAGATGAAAAATGATGCA
Found at i:21074709 original size:146 final size:145
Alignment explanation
Indices: 21074350--21074709 Score: 386
Period size: 146 Copynumber: 2.5 Consensus size: 145
21074340 ACTGCTCTAT
* * * * * *
21074350 AATGTAAAATGGTGTATTTTTGGCAGAAAGGTGCCATTAATGTA-ATTTAAATGCCTAAAAGTGC
1 AATGAAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATG-ACAATTAAATGCATAAAGGTGC
* * * **
21074414 ATTTTTGGCAGAAAGGTGCCATTAATGCAAGTTAGATGAAAAATTATGCATTTTGGCAGAATTGT
65 A-TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGAAAAATGATGCATTTTGGCAGAAAGGT
*
21074479 GCCATTAATGCAAGTTA
129 GCCACTAATGCAAGTTA
*** * * * * *
21074496 AATGCCTAACGGTGCATTCTTGGCAGAAAGGTGCCACTAATG-CAAGTTAGATG-AAAAATGGTA
1 AATGAAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGACAA-TTAAATGCATAAA-GGTG
* *** *
21074559 CATTTTGGCAGAAAGGTGTCACTAATGCAAGTTAAATGCCTAATGGTGCATTTTTGGC-GAAAAG
64 CATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGAAAAATGATGCA-TTTTGGCAG-AAAG
21074623 GTGCCACTAATGCAAGTTA
127 GTGCCACTAATGCAAGTTA
* * *
21074642 GATGAAAAATGATGCATTTTTGGCAGAAAGGTGCCACTAATGACAATTAAATGCATAACGGTGCA
1 AATGAAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGACAATTAAATGCATAAAGGTGCA
21074707 TTT
66 TTT
21074710 CGACATAAAA
Statistics
Matches: 172, Mismatches: 35, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
145 45 0.26
146 121 0.70
147 6 0.03
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (145 bp):
AATGAAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGACAATTAAATGCATAAAGGTGCA
TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGAAAAATGATGCATTTTGGCAGAAAGGTGC
CACTAATGCAAGTTA
Found at i:21075836 original size:17 final size:18
Alignment explanation
Indices: 21075796--21075838 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
21075786 ATGTTATAAA
*
21075796 TATTATAATAAATATTAT
1 TATTATTATAAATATTAT
*
21075814 TA-TATTATAATTA-TAT
1 TATTATTATAAATATTAT
21075830 TATTATTAT
1 TATTATTAT
21075839 TTTTAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTATAAATATTAT
Found at i:21077705 original size:18 final size:18
Alignment explanation
Indices: 21077679--21077717 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
21077669 TTAATTTTGT
*
21077679 TTTATTTATTTTACTAAC
1 TTTAATTATTTTACTAAC
21077697 TTTAATTATTTTACTAAC
1 TTTAATTATTTTACTAAC
21077715 TTT
1 TTT
21077718 GTTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATTATTTTACTAAC
Found at i:21077727 original size:22 final size:22
Alignment explanation
Indices: 21077674--21077727 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 22
21077664 TTGTTTTAAT
21077674 TTTGTTTTATTTATTTTACTAAC
1 TTTGTTTT-TTTATTTTACTAAC
**
21077697 ----TTTAATTATTTTACTAAC
1 TTTGTTTTTTTATTTTACTAAC
21077715 TTTGTTTTTTTAT
1 TTTGTTTTTTTAT
21077728 GTGTACAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 9
0.64 0.11 0.25
Matches are distributed among these distances:
18 13 0.57
19 3 0.13
22 7 0.30
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTGTTTTTTTATTTTACTAAC
Found at i:21080518 original size:18 final size:18
Alignment explanation
Indices: 21080495--21080556 Score: 124
Period size: 18 Copynumber: 3.4 Consensus size: 18
21080485 AAGCTTTGTA
21080495 ATAAAACTTTGTTTTAAT
1 ATAAAACTTTGTTTTAAT
21080513 ATAAAACTTTGTTTTAAT
1 ATAAAACTTTGTTTTAAT
21080531 ATAAAACTTTGTTTTAAT
1 ATAAAACTTTGTTTTAAT
21080549 ATAAAACT
1 ATAAAACT
21080557 GTTCTGAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (18 bp):
ATAAAACTTTGTTTTAAT
Found at i:21088526 original size:45 final size:45
Alignment explanation
Indices: 21088461--21088582 Score: 181
Period size: 45 Copynumber: 2.7 Consensus size: 45
21088451 ATCAACCTTG
* * *
21088461 AATCTGATCTTCACATAAGAGTAGTGAAACAGATTCTTTCAAGTC
1 AATCCGATCTCCACAGAAGAGTAGTGAAACAGATTCTTTCAAGTC
* *
21088506 AATTCGATCTCCACAGAAGAGTAATGAAACAGATTCTTTCAAGTC
1 AATCCGATCTCCACAGAAGAGTAGTGAAACAGATTCTTTCAAGTC
*
21088551 AATCCGATCTCCACGGAAGAGTAGTGGAAACA
1 AATCCGATCTCCACAGAAGAGTAGT-GAAACA
21088583 AGCAATGCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
45 62 0.91
46 6 0.09
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (45 bp):
AATCCGATCTCCACAGAAGAGTAGTGAAACAGATTCTTTCAAGTC
Found at i:21090061 original size:22 final size:22
Alignment explanation
Indices: 21090031--21090090 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
21090021 GATTGCCTAG
* *
21090031 GGGGAACAGATTCTCCCCCCAC
1 GGGGTACAGATTCCCCCCCCAC
*
21090053 GGGGTACAGATTCCCCCCCCAG
1 GGGGTACAGATTCCCCCCCCAC
21090075 GGGGTATC-GATTCCCC
1 GGGGTA-CAGATTCCCC
21090091 GGGAACAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.38, G:0.27, T:0.17
Consensus pattern (22 bp):
GGGGTACAGATTCCCCCCCCAC
Found at i:21093156 original size:20 final size:20
Alignment explanation
Indices: 21093103--21093160 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
21093093 CAGATTGCCT
21093103 AGGGGGTACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
* *
21093123 AAGGGGAACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
21093143 AGGGGGTATC-GATTCCCC
1 AGGGGGTA-CAGATTCCCC
21093161 GGGAACAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:21093391 original size:21 final size:21
Alignment explanation
Indices: 21093358--21093397 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
21093348 TTTTCGCAGA
*
21093358 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
21093380 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
21093398 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:21096202 original size:20 final size:20
Alignment explanation
Indices: 21096149--21096206 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
21096139 CAGATTGCCT
21096149 AGGGGGTACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
* *
21096169 AAGGGGAACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
21096189 AGGGGGTATC-GATTCCCC
1 AGGGGGTA-CAGATTCCCC
21096207 GGGAACAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:21096438 original size:21 final size:21
Alignment explanation
Indices: 21096405--21096444 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
21096395 TTTTCGCAGA
*
21096405 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
21096427 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
21096445 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:21099253 original size:20 final size:20
Alignment explanation
Indices: 21099198--21099245 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
21099188 CAGATTGCCT
21099198 AGGGGGTACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
* *
21099218 AAGGGGAACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
21099238 AGGGGGTA
1 AGGGGGTA
21099246 TCGATTCCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.33, T:0.12
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:21099487 original size:21 final size:21
Alignment explanation
Indices: 21099454--21099493 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
21099444 TTTTTGCAGA
*
21099454 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
21099476 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
21099494 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:21099747 original size:34 final size:32
Alignment explanation
Indices: 21099708--21099777 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
21099698 TATTGTAAAG
* *
21099708 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
21099742 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
21099774 GGGA
1 GGGA
21099778 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:21102299 original size:20 final size:20
Alignment explanation
Indices: 21102246--21102302 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
21102236 CAGATTGCCT
*
21102246 AGGGGGTACAGATTCCTCCC
1 AGGGGGTACAGATTCCCCCC
* *
21102266 AAGGGGAACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
21102286 AGGGGGTATC-GATTCCC
1 AGGGGGTA-CAGATTCCC
21102303 TGGGAATAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.18
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:21103821 original size:17 final size:17
Alignment explanation
Indices: 21103801--21103842 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
21103791 AATAGCTTAC
21103801 TAAATGAACTAAATTC-A
1 TAAATGAACT-AATTCTA
*
21103818 TAAATGAACTAATTCTG
1 TAAATGAACTAATTCTA
21103835 TAAATGAA
1 TAAATGAA
21103843 ATAGAAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (17 bp):
TAAATGAACTAATTCTA
Found at i:21110308 original size:21 final size:20
Alignment explanation
Indices: 21110281--21110342 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 20
21110271 TTTTTCCAGC
*
21110281 AAAAGGATTGATCCCTTAGGA
1 AAAAGGATTGATCCCTTA-AA
* * *
21110302 GAAAGGATAGATCCTTTTTAAA
1 AAAAGGATTGATCC--CTTAAA
21110324 AAAAGGATTGATCCCTTAA
1 AAAAGGATTGATCCCTTAA
21110343 CTAGAAGGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
22 13 0.41
23 3 0.09
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (20 bp):
AAAAGGATTGATCCCTTAAA
Found at i:21110437 original size:21 final size:21
Alignment explanation
Indices: 21110413--21110471 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
21110403 TTGATCCCTA
21110413 TAAAAAAGGATCTAT-CACTTT
1 TAAAAAAGGATCTATCCA-TTT
*
21110434 TAAAAAATGATCTATCCATTT
1 TAAAAAAGGATCTATCCATTT
*
21110455 TAAAAAAGGATCGATCC
1 TAAAAAAGGATCTATCC
21110472 CTTCGCTGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (21 bp):
TAAAAAAGGATCTATCCATTT
Found at i:21110761 original size:38 final size:38
Alignment explanation
Indices: 21110710--21110786 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
21110700 AAACTCAATT
21110710 TGACAATTTGAACTTGAATTCCTCATCTGTTAAAATGA
1 TGACAATTTGAACTTGAATTCCTCATCTGTTAAAATGA
21110748 TGACAATTTGAACTTGAATTCCTCATCTGTTAAAATGA
1 TGACAATTTGAACTTGAATTCCTCATCTGTTAAAATGA
21110786 T
1 T
21110787 CGTTATACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (38 bp):
TGACAATTTGAACTTGAATTCCTCATCTGTTAAAATGA
Found at i:21111189 original size:24 final size:26
Alignment explanation
Indices: 21111123--21111179 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
21111113 AACATATCAC
* *
21111123 ATACTTAAACCAGTGAAATTTAACAT
1 ATACTTACACCACTGAAATTTAACAT
*
21111149 GTACTTACACCACTGAAA-TTAACAT
1 ATACTTACACCACTGAAATTTAACAT
21111174 AT-CTTA
1 ATACTTA
21111180 TACCGATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.15
25 8 0.30
26 15 0.56
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (26 bp):
ATACTTACACCACTGAAATTTAACAT
Found at i:21111207 original size:49 final size:49
Alignment explanation
Indices: 21111150--21111246 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
21111140 ATTTAACATG
*
21111150 TACTTACACCACTGAAATTAACAT-ATCTTATACCGA-TGAAGCTATCACA
1 TACTTACACCACTGAAATTAAC-TCATATTATACC-ATTGAAGCTATCACA
* *
21111199 TACTTACACCATTGAAATTAACTCATATTATACCATTGAAGTTATCAC
1 TACTTACACCACTGAAATTAACTCATATTATACCATTGAAGCTATCAC
21111247 TACACCAGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 2 0.05
49 41 0.95
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (49 bp):
TACTTACACCACTGAAATTAACTCATATTATACCATTGAAGCTATCACA
Found at i:21111214 original size:25 final size:24
Alignment explanation
Indices: 21111186--21111246 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
21111176 CTTATACCGA
*
21111186 TGAAGCTATCACATACTTACACCAT
1 TGAAGTTATCACATA-TTACACCAT
* * * *
21111211 TGAAATTAACTCATATTATACCAT
1 TGAAGTTATCACATATTACACCAT
21111235 TGAAGTTATCAC
1 TGAAGTTATCAC
21111247 TACACCAGTG
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (24 bp):
TGAAGTTATCACATATTACACCAT
Found at i:21111354 original size:23 final size:23
Alignment explanation
Indices: 21111324--21111371 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
21111314 CTTATCAAAC
21111324 TTATCTTGATATTCACTTTTCCA
1 TTATCTTGATATTCACTTTTCCA
21111347 TTATCTTGATATTCACTTTTCCA
1 TTATCTTGATATTCACTTTTCCA
21111370 TT
1 TT
21111372 CAATGCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (23 bp):
TTATCTTGATATTCACTTTTCCA
Found at i:21118862 original size:75 final size:75
Alignment explanation
Indices: 21118670--21118907 Score: 304
Period size: 75 Copynumber: 3.2 Consensus size: 75
21118660 TCCATAAAAC
* * * **
21118670 TTATCACATACTTACACCAGTGAAATTTAGCATGTAATTACACCACTGAAATTG-ACACATTTTA
1 TTATCACATACTTACA-CAGTGAAATTTAACATGTAATTACACCACTAAAAATGAACACATACTA
*
21118734 TTCCAATGAAG
65 TACCAATGAAG
** *
21118745 TTATTGCATACTTACA-AGTGAAATTTAACATGTATTTACACCACT-AAAATGAACACATACTAT
1 TTATCACATACTTACACAGTGAAATTTAACATGTAATTACACCACTAAAAATGAACACATACTAT
*
21118808 ACAAATGAAG
66 ACCAATGAAG
* * * *
21118818 TTATCACATATTTACACTAGTGAAATTTAACATATACTTACACCACTAAAAAT-AAAACATACTA
1 TTATCACATACTTACAC-AGTGAAATTTAACATGTAATTACACCACTAAAAATGAACACATACTA
21118882 TACCAATGAAG
65 TACCAATGAAG
21118893 TTATCACATACTTAC
1 TTATCACATACTTAC
21118908 TGTAATATCC
Statistics
Matches: 142, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
72 5 0.04
73 57 0.40
75 75 0.53
76 5 0.04
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (75 bp):
TTATCACATACTTACACAGTGAAATTTAACATGTAATTACACCACTAAAAATGAACACATACTAT
ACCAATGAAG
Found at i:21120949 original size:19 final size:19
Alignment explanation
Indices: 21120913--21120989 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
21120903 ATTTCAGGCA
** *
21120913 AAGAGTATATATACTTTCT
1 AAGAGTATGGATACTTTCC
*
21120932 AAGAGTATGGATAATTTCCCC
1 AAGAGTATGGATACTTT--CC
** *
21120953 AAGAGTATCAATATTTTCC
1 AAGAGTATGGATACTTTCC
21120972 AAGAGTATGGATACTTTC
1 AAGAGTATGGATACTTTC
21120990 AGTAATAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 31 0.67
21 15 0.33
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (19 bp):
AAGAGTATGGATACTTTCC
Found at i:21120960 original size:40 final size:40
Alignment explanation
Indices: 21120913--21120989 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
21120903 ATTTCAGGCA
*
21120913 AAGAGTAT-ATATACTTTCTAAGAGTATGGATAATTTCCCC
1 AAGAGTATCA-ATACTTTCCAAGAGTATGGATAATTTCCCC
* *
21120953 AAGAGTATCAATATTTTCCAAGAGTATGGATACTTTC
1 AAGAGTATCAATACTTTCCAAGAGTATGGATAATTTC
21120990 AGTAATAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (40 bp):
AAGAGTATCAATACTTTCCAAGAGTATGGATAATTTCCCC
Found at i:21127471 original size:2 final size:2
Alignment explanation
Indices: 21127464--21127488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21127454 TCAATCTACA
21127464 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21127489 CAATCACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21127654 original size:13 final size:13
Alignment explanation
Indices: 21127633--21127697 Score: 69
Period size: 13 Copynumber: 5.0 Consensus size: 13
21127623 AATGACGCTC
*
21127633 AATGCGCGTCATA
1 AATGAGCGTCATA
21127646 AATGAGCGTCATA
1 AATGAGCGTCATA
* *
21127659 AATGTGTGTCATA
1 AATGAGCGTCATA
*
21127672 AATGCA-TGTCATA
1 AATG-AGCGTCATA
*
21127685 AATGCGCGTCATA
1 AATGAGCGTCATA
21127698 GATTTATGAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:21127669 original size:26 final size:26
Alignment explanation
Indices: 21127633--21127697 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
21127623 AATGACGCTC
21127633 AATGCGCGTCATAAATG-AGCGTCATA
1 AATGCGCGTCATAAATGCA-CGTCATA
* * *
21127659 AATGTGTGTCATAAATGCATGTCATA
1 AATGCGCGTCATAAATGCACGTCATA
21127685 AATGCGCGTCATA
1 AATGCGCGTCATA
21127698 GATTTATGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (26 bp):
AATGCGCGTCATAAATGCACGTCATA
Found at i:21128068 original size:26 final size:26
Alignment explanation
Indices: 21128028--21128090 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
21128018 ATAAATGACA
21128028 CTTA-GTGTA-TATGGTGGACACGAC
1 CTTATGTGTATTATGGTGGACACGAC
*
21128052 CTTATGTGTATTATGGTGGGCACGAC
1 CTTATGTGTATTATGGTGGACACGAC
21128078 CTTATGTGTATTA
1 CTTATGTGTATTA
21128091 GCACTTCGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 4 0.11
25 5 0.14
26 27 0.75
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (26 bp):
CTTATGTGTATTATGGTGGACACGAC
Found at i:21129497 original size:18 final size:18
Alignment explanation
Indices: 21129475--21129522 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
21129465 AAAGATGGTC
21129475 ATGAGATCATTAATGATT
1 ATGAGATCATTAATGATT
*
21129493 CTGAGATCATTAATGATT
1 ATGAGATCATTAATGATT
*
21129511 ATAAGATCATTA
1 ATGAGATCATTA
21129523 CAAGTACGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (18 bp):
ATGAGATCATTAATGATT
Found at i:21130148 original size:20 final size:20
Alignment explanation
Indices: 21130114--21130153 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
21130104 TATTTTTTAA
*
21130114 TAAAAAATATTAA-TTAAAT
1 TAAAAAATATCAATTTAAAT
21130133 TAAAAAATAATCAATTTAAAT
1 TAAAAAAT-ATCAATTTAAAT
21130154 CATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAAATATCAATTTAAAT
Found at i:21131368 original size:17 final size:17
Alignment explanation
Indices: 21131338--21131372 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21131328 TAGTGAGTTA
21131338 TATAAATATATTTTTAT
1 TATAAATATATTTTTAT
* *
21131355 TATAACTATGTTTTTAT
1 TATAAATATATTTTTAT
21131372 T
1 T
21131373 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (17 bp):
TATAAATATATTTTTAT
Found at i:21133141 original size:13 final size:13
Alignment explanation
Indices: 21133125--21133150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21133115 TTTCAGATAA
21133125 ACACATTAAGATC
1 ACACATTAAGATC
21133138 ACACATTAAGATC
1 ACACATTAAGATC
21133151 CAAAGGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
ACACATTAAGATC
Found at i:21134755 original size:110 final size:110
Alignment explanation
Indices: 21134562--21134773 Score: 397
Period size: 110 Copynumber: 1.9 Consensus size: 110
21134552 GCAAGCCCAA
*
21134562 GTCAATTAGAAAATTAAAGAATATGGCTTTTATCAAAACTAAAAGAATAATATATACTCGATTAG
1 GTCAATTAGAAAATTAAAGAATAAGGCTTTTATCAAAACTAAAAGAATAATATATACTCGATTAG
*
21134627 ATCCAGATCACTGCTTGTAGACTTCGAGTTATATGAAGAATGTAC
66 AGCCAGATCACTGCTTGTAGACTTCGAGTTATATGAAGAATGTAC
*
21134672 GTCAATTAGAAAATTAAAGAATAAGGCTTTTATCAAAACTAAAAGAATAATATATACTTGATTAG
1 GTCAATTAGAAAATTAAAGAATAAGGCTTTTATCAAAACTAAAAGAATAATATATACTCGATTAG
21134737 AGCCAGATCACTGCTTGTAGACTTCGAGTTATATGAA
66 AGCCAGATCACTGCTTGTAGACTTCGAGTTATATGAA
21134774 CAATTTATGA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 99 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (110 bp):
GTCAATTAGAAAATTAAAGAATAAGGCTTTTATCAAAACTAAAAGAATAATATATACTCGATTAG
AGCCAGATCACTGCTTGTAGACTTCGAGTTATATGAAGAATGTAC
Found at i:21147046 original size:5 final size:5
Alignment explanation
Indices: 21147036--21147088 Score: 63
Period size: 5 Copynumber: 10.4 Consensus size: 5
21147026 CTGATTTATT
* *
21147036 TAAAA TAAAA TAAAA TAAAA TAAACA TAGAAA TACAA -AAAA TAAAA TAGAA
1 TAAAA TAAAA TAAAA TAAAA TAAA-A TA-AAA TAAAA TAAAA TAAAA TAAAA
21147087 TA
1 TA
21147089 GATGAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.07
5 31 0.74
6 6 0.14
7 2 0.05
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:21147166 original size:14 final size:13
Alignment explanation
Indices: 21147147--21147191 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
21147137 TGCACCAATT
21147147 TAAATAAAAATAA
1 TAAATAAAAATAA
*
21147160 GTAAATAAAATAAAA
1 -TAAATAAAA-ATAA
*
21147175 TAAGTAAAAATAA
1 TAAATAAAAATAA
21147188 TAAA
1 TAAA
21147192 AAATGACCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.23
14 17 0.65
15 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (13 bp):
TAAATAAAAATAA
Found at i:21147174 original size:18 final size:17
Alignment explanation
Indices: 21147148--21147192 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
21147138 GCACCAATTT
21147148 AAATAAAAATAAGTAAATA
1 AAAT-AAAATAAGTAAA-A
21147167 AAATAAAATAAGTAAAA
1 AAATAAAATAAGTAAAA
21147184 ATAATAAAA
1 A-AATAAAA
21147193 AATGACCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.08
18 19 0.76
19 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAAAATAAGTAAAA
Found at i:21149498 original size:200 final size:196
Alignment explanation
Indices: 21149131--21149757 Score: 609
Period size: 200 Copynumber: 3.1 Consensus size: 196
21149121 TACCCTTGAA
** * * * * *
21149131 CTGAGTGAAATTGAACTCGGAAGCTTTTGCTCGATAAATAGTTATTATCGCCTTAAGCTATGTTA
1 CTGAGTGAAATCAAACTCGAAAGCTTTTGCTTGAAAAATAGTTCTTATCGCCTTAAGCTATGTCA
* * * * *
21149196 AATTTTCACAGGGAAGTGGTTTCTTGTTGCCAAATAAAAATCAACCTTGGTCTTCTTCTT-GCTT
66 AATTTT-ACTGGGAAGTGGTTCCTTGTTGCCAAAT--TAATCAACCTTAGTCTTCTTATTGGCTT
* * * * * *
21149260 AAAGATCTCACTTTAAAATTTTACCTGAAGGCAGTTTCTTGCTGCTACCATGTAGTTGTTGTGCC
128 AAAGACCTCA-TTT-AAATTTTACCAGAAGGTAGTTTCTTGCTGCTACCATGTGGTTGATGCGCC
21149325 CTCGAG
191 CTCGAG
* * *
21149331 CTGAGTGAAATCAAACTCGAAAGCTTTTACTTGAAAAAAAGTTCTTCTCGCCTTAAGCTATGTCA
1 CTGAGTGAAATCAAACTCGAAAGCTTTTGCTTGAAAAATAGTTCTTATCGCCTTAAGCTATGTCA
21149396 AATTTTGACTGGGAA-TGGTTCCTTGTTGCCAAATCGTAATCAACCTTAGTCTTCTTATTGGCTT
66 AATTTT-ACTGGGAAGTGGTTCCTTGTTGCCAAAT--TAATCAACCTTAGTCTTCTTATTGGCTT
* * * ** * * ** **
21149460 AAAGACCTCAGTTTCAATTTTGATCGGAAGGTAGTTTCTCACTACTACCATATGGTCAATGCGTT
128 AAAGACCTCA-TTTAAATTTT-ACCAGAAGGTAGTTTCTTGCTGCTACCATGTGGTTGATGCGCC
21149525 CTCGAG
191 CTCGAG
* * * * * *
21149531 ATGAGTGGAATCAAACTCGAAAGC-TTTGGTTGACAAATAGCTCTTATCGCCTTAAGCTATGTAG
1 CTGAGTGAAATCAAACTCGAAAGCTTTTGCTTGAAAAATAGTTCTTATCGCCTTAAGCTATGT-C
* * * * * *
21149595 AAATTTTATTAGAAAGTGGTTCTTTGTTGCCAAATTACAGTCAACC-TAGGTTTTTTTATTGGCT
65 AAATTTTACTGGGAAGTGGTTCCTTGTTGCCAAATTA-A-TCAACCTTA-GTCTTCTTATTGGCT
* *
21149659 TAGAA-ACCTCATATTAAATTTTTACCATAAGGTAG-TTCATTGCTGCTACCATGCGGTTGATGC
127 TA-AAGACCTCAT-TTAAA-TTTTACCAGAAGGTAGTTTC-TTGCTGCTACCATGTGGTTGATGC
*
21149722 ACCCTCGAG
188 GCCCTCGAG
* *
21149731 CTGAATGGAATCAAACTCGAAAGCTTT
1 CTGAGTGAAATCAAACTCGAAAGCTTT
21149758 GGTTAACAGC
Statistics
Matches: 349, Mismatches: 66, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
198 2 0.01
199 88 0.25
200 251 0.72
201 8 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (196 bp):
CTGAGTGAAATCAAACTCGAAAGCTTTTGCTTGAAAAATAGTTCTTATCGCCTTAAGCTATGTCA
AATTTTACTGGGAAGTGGTTCCTTGTTGCCAAATTAATCAACCTTAGTCTTCTTATTGGCTTAAA
GACCTCATTTAAATTTTACCAGAAGGTAGTTTCTTGCTGCTACCATGTGGTTGATGCGCCCTCGA
G
Found at i:21151472 original size:17 final size:17
Alignment explanation
Indices: 21151450--21151482 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21151440 ATATTGCCAA
21151450 TATGGTAATTCACAAAT
1 TATGGTAATTCACAAAT
21151467 TATGGTAATTCACAAA
1 TATGGTAATTCACAAA
21151483 CAAATTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
TATGGTAATTCACAAAT
Found at i:21151489 original size:71 final size:71
Alignment explanation
Indices: 21151396--21151536 Score: 219
Period size: 71 Copynumber: 2.0 Consensus size: 71
21151386 ATAGTGCCAA
* * * * * *
21151396 TATGGTAATTCACAAACTAATTATGAATTACTTAGGTTGCACACATATTGCCAATATGGTAATTC
1 TATGGTAATTCACAAACAAATTATGAATTACTTAAGTAGCACACATAGTGCCAATACGATAATTC
21151461 ACAAAT
66 ACAAAT
*
21151467 TATGGTAATTCACAAACAAATTATGAATTACTTAAGTAGCATACATAGTGCCAATACGATAATTC
1 TATGGTAATTCACAAACAAATTATGAATTACTTAAGTAGCACACATAGTGCCAATACGATAATTC
21151532 ACAAA
66 ACAAA
21151537 CAAATTATGA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (71 bp):
TATGGTAATTCACAAACAAATTATGAATTACTTAAGTAGCACACATAGTGCCAATACGATAATTC
ACAAAT
Found at i:21151554 original size:54 final size:54
Alignment explanation
Indices: 21151470--21151645 Score: 273
Period size: 54 Copynumber: 3.3 Consensus size: 54
21151460 CACAAATTAT
* *
21151470 GGTAATTCACAAACAAATTATGAATTACTTAAGTAGCATACATAGTGCCAATAC
1 GGTAATTCACAAACAAATTATGAATTACTTAAGTTGCACACATAGTGCCAATAC
* *
21151524 GATAATTCACAAACAAATTATGAATTACTTAAGTTGCACACATAGTTCCAATAC
1 GGTAATTCACAAACAAATTATGAATTACTTAAGTTGCACACATAGTGCCAATAC
* * * *
21151578 GGTAATTCACAAACTAATTATGAATAAGTTAGGTTGCACACATAGTGCCAATAC
1 GGTAATTCACAAACAAATTATGAATTACTTAAGTTGCACACATAGTGCCAATAC
21151632 GGTAATTCA-AAACA
1 GGTAATTCACAAACA
21151646 TATGCATTAA
Statistics
Matches: 111, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 4 0.04
54 107 0.96
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (54 bp):
GGTAATTCACAAACAAATTATGAATTACTTAAGTTGCACACATAGTGCCAATAC
Found at i:21152240 original size:16 final size:16
Alignment explanation
Indices: 21152219--21152277 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
21152209 CATTATATAG
21152219 TTTTGAAAATTATGGT
1 TTTTGAAAATTATGGT
*
21152235 TTTTGAAAATATAT-AT
1 TTTTGAAAAT-TATGGT
21152251 AGTTTTGAAAA-TATGGT
1 --TTTTGAAAATTATGGT
*
21152268 TTTTTAAAAT
1 TTTTGAAAAT
21152278 AAAATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 8 0.23
16 14 0.40
17 4 0.11
18 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTTGAAAATTATGGT
Found at i:21152271 original size:33 final size:34
Alignment explanation
Indices: 21152212--21152278 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
21152202 AGTAGTACAT
21152212 TATATAGTTTTGAAAATTATGGTTTTTGAAAATA
1 TATATAGTTTTGAAAATTATGGTTTTTGAAAATA
*
21152246 TATATAGTTTTGAAAA-TATGGTTTTTTAAAATA
1 TATATAGTTTTGAAAATTATGGTTTTTGAAAATA
21152279 AAATAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (34 bp):
TATATAGTTTTGAAAATTATGGTTTTTGAAAATA
Found at i:21152300 original size:45 final size:45
Alignment explanation
Indices: 21152246--21152359 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
21152236 TTTGAAAATA
* *
21152246 TATATAGTTTTGAAAATATGGTTTTTTAAAATAAAATAAATATAT
1 TATATAGTTTTGAAAATATAGTTTTTGAAAATAAAATAAATATAT
* * *
21152291 TATATAGTTTTAAAAATATAGTTTTTGAAAGTAATATAAATATAT
1 TATATAGTTTTGAAAATATAGTTTTTGAAAATAAAATAAATATAT
*
21152336 TATATA-TTTTGGAAATCA-AGTTTT
1 TATATAGTTTTGAAAAT-ATAGTTTT
21152360 AAAACATAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
44 14 0.23
45 47 0.77
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.46
Consensus pattern (45 bp):
TATATAGTTTTGAAAATATAGTTTTTGAAAATAAAATAAATATAT
Found at i:21160543 original size:27 final size:25
Alignment explanation
Indices: 21160487--21160548 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 25
21160477 GGTTTCTTTA
* *
21160487 AAATAAAACAAAATACAATAAATGTAG
1 AAAT-AAA-AAAATAAAATAAATATAG
21160514 AAATAAAAAAATAAAATAAAATATATG
1 AAATAAAAAAATAAAAT-AAATATA-G
21160541 AAATAAAA
1 AAATAAAA
21160549 TGATCTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 9 0.29
26 9 0.29
27 13 0.42
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (25 bp):
AAATAAAAAAATAAAATAAATATAG
Found at i:21160619 original size:13 final size:14
Alignment explanation
Indices: 21160595--21160625 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
21160585 TACACCAATT
21160595 TAAATAAAAATAAG
1 TAAATAAAAATAAG
21160609 TAAAT-AAAATAAG
1 TAAATAAAAATAAG
21160622 TAAA
1 TAAA
21160626 AACAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (14 bp):
TAAATAAAAATAAG
Found at i:21161677 original size:3 final size:3
Alignment explanation
Indices: 21161658--21161731 Score: 51
Period size: 3 Copynumber: 23.0 Consensus size: 3
21161648 TAATACTTAC
* *
21161658 AAT AATT AAT AATT AAT AAT AAT AAT AAC ACA- AAA AAT AAT AAT AATT
1 AAT AA-T AAT AA-T AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA-T
* *
21161706 CAT AAT AAGT AGT AAT AAT AAGT AAT
1 AAT AAT AA-T AAT AAT AAT AA-T AAT
21161732 TAAAAATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
2 1 0.02
3 43 0.74
4 14 0.24
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21164203 original size:13 final size:12
Alignment explanation
Indices: 21164176--21164200 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21164166 CAATGTTGGG
21164176 ATAAAAATGAGA
1 ATAAAAATGAGA
21164188 ATAAAAATGAGA
1 ATAAAAATGAGA
21164200 A
1 A
21164201 ATAGTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
ATAAAAATGAGA
Found at i:21169458 original size:44 final size:44
Alignment explanation
Indices: 21169405--21169508 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 44
21169395 ATGTTCGAAT
21169405 TCCAACTTATTTCTCT-CACTATGTTGGAGCTATTACCA-ACATTA
1 TCCAACTTATTTC-CTACACTATGTTGGAGCTATTACCAGA-ATTA
* *
21169449 TCCAACTTATTTCCTAAGACTATGTTGGAGCTATTACTAGAATTA
1 TCCAACTTATTTCCT-ACACTATGTTGGAGCTATTACCAGAATTA
*
21169494 CCCAACTTATTTCCT
1 TCCAACTTATTTCCT
21169509 GAGTCTCACA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
43 2 0.04
44 13 0.24
45 38 0.70
46 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (44 bp):
TCCAACTTATTTCCTACACTATGTTGGAGCTATTACCAGAATTA
Found at i:21182596 original size:20 final size:20
Alignment explanation
Indices: 21182573--21182613 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21182563 GTCACAAATT
* *
21182573 TTTATTTTATAATTATTAAA
1 TTTATTATATAATTATAAAA
*
21182593 TTTATTATATTATTATAAAA
1 TTTATTATATAATTATAAAA
21182613 T
1 T
21182614 GATCATTGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTATATAATTATAAAA
Found at i:21194713 original size:21 final size:20
Alignment explanation
Indices: 21194687--21194736 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21194677 AATTTTGTCA
21194687 CGAAGGACCTA-TGAAATATCC
1 CGAAGGACC-ACTG-AATATCC
* *
21194708 CGAAGGATCACTGTATATCC
1 CGAAGGACCACTGAATATCC
21194728 CGAAGGACC
1 CGAAGGACC
21194737 GCGTAGACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (20 bp):
CGAAGGACCACTGAATATCC
Found at i:21197793 original size:26 final size:26
Alignment explanation
Indices: 21197764--21197818 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
21197754 TAATCCTATT
21197764 TCTGATCTGAATTATGGAAAGGAGAA
1 TCTGATCTGAATTATGGAAAGGAGAA
*
21197790 TCTGATCTGAATTGTGGAAAGGAGAA
1 TCTGATCTGAATTATGGAAAGGAGAA
21197816 TCT
1 TCT
21197819 TTTATCTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (26 bp):
TCTGATCTGAATTATGGAAAGGAGAA
Found at i:21197947 original size:5 final size:5
Alignment explanation
Indices: 21197937--21197967 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
21197927 CATGCATGAA
21197937 CATAT CATAT CATAT CATAT CATAT C-TAT CA
1 CATAT CATAT CATAT CATAT CATAT CATAT CA
21197968 CACAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:21198342 original size:21 final size:20
Alignment explanation
Indices: 21198316--21198365 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21198306 AATTTTGTCT
21198316 CGAAGGACC-TATGAAATATCC
1 CGAAGGACCAT-TG-AATATCC
* *
21198337 CGAAGGATCATTGTATATCC
1 CGAAGGACCATTGAATATCC
21198357 CGAAGGACC
1 CGAAGGACC
21198366 GCGTAGACGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 14 0.56
21 10 0.40
22 1 0.04
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
CGAAGGACCATTGAATATCC
Found at i:21205455 original size:23 final size:23
Alignment explanation
Indices: 21205413--21205474 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
21205403 TTGGTGCAGA
* *
21205413 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
21205435 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
21205458 GGGAACTGATTCCCCCT
1 GGGAACCGATTCCCCCT
21205475 GTAAGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:21205493 original size:21 final size:22
Alignment explanation
Indices: 21205413--21205495 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
21205403 TTGGTGCAGA
21205413 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
21205435 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
*
21205458 GGGAA-CTGATTCCCCC-TGTAA-
1 GGGAATC-GATACCCCCTTG-AAG
*
21205479 GGGAATCTATACCCCCT
1 GGGAATCGATACCCCCT
21205496 AGAGGTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
21 14 0.27
22 18 0.35
23 20 0.38
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:21207103 original size:18 final size:18
Alignment explanation
Indices: 21207068--21207106 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21207058 GGAGCAGCAC
* *
21207068 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACATCCA
*
21207086 GAGGAACAACCTCATCCA
1 GAGGAACAACCACATCCA
21207104 GAG
1 GAG
21207107 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.23, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACATCCA
Found at i:21211081 original size:22 final size:22
Alignment explanation
Indices: 21211053--21211095 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21211043 CGCTAAGTCT
21211053 ATGACTTAGTGAGGCATTAAAA
1 ATGACTTAGTGAGGCATTAAAA
21211075 ATGACTTAGTGAGGCATTAAA
1 ATGACTTAGTGAGGCATTAAA
21211096 CACATTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (22 bp):
ATGACTTAGTGAGGCATTAAAA
Found at i:21212151 original size:24 final size:23
Alignment explanation
Indices: 21212087--21212151 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 23
21212077 TTTCAATTTC
21212087 CCCTTAA-AGTGCATCGATGCAT
1 CCCTTAACAGTGCATCGATGCAT
* *
21212109 -TC-T-ACAGTGTATCGATGCAT
1 CCCTTAACAGTGCATCGATGCAT
21212129 CCCTTAACATGTGCATCGATGCA
1 CCCTTAACA-GTGCATCGATGCA
21212152 CTAATTGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 2 0.06
22 1 0.03
23 3 0.09
24 12 0.35
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (23 bp):
CCCTTAACAGTGCATCGATGCAT
Found at i:21212166 original size:42 final size:41
Alignment explanation
Indices: 21212087--21212167 Score: 94
Period size: 42 Copynumber: 1.9 Consensus size: 41
21212077 TTTCAATTTC
*
21212087 CCCTTAAAGTGCATCGATGCATTCTACAGTGTATCGATGCAT
1 CCCTTAAAGTGCATCGATGCA-TCTACAGTGCATCGATGCAT
*
21212129 CCCTTAACATGTGCATCGATGCA-CTA-ATTGCATTCGATG
1 CCCTTAA-A-GTGCATCGATGCATCTACAGTGCA-TCGATG
21212168 TTTCCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
41 4 0.12
42 16 0.47
43 1 0.03
44 13 0.38
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (41 bp):
CCCTTAAAGTGCATCGATGCATCTACAGTGCATCGATGCAT
Found at i:21214789 original size:45 final size:46
Alignment explanation
Indices: 21214738--21214841 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 46
21214728 AAGTCTCTTA
*
21214738 GAAATAAGTTGGATAATGCTGGCAATAGCTCCAACATA-TTTTTAG
1 GAAATAAGTTGGATAATGCTGGCAATAACTCCAACATAGTTTTTAG
* * * *
21214783 GAAATAAATTGGGTAATGCTGGTAATAACTCCAATATAGTTTTTAG
1 GAAATAAGTTGGATAATGCTGGCAATAACTCCAACATAGTTTTTAG
21214829 GAAATAAGTTGGA
1 GAAATAAGTTGGA
21214842 ATGTTCTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 33 0.65
46 18 0.35
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (46 bp):
GAAATAAGTTGGATAATGCTGGCAATAACTCCAACATAGTTTTTAG
Found at i:21216671 original size:20 final size:20
Alignment explanation
Indices: 21216634--21216670 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
21216624 TTTCACGAGG
21216634 GATCGATCCTTTTGAAAAGA
1 GATCGATCCTTTTGAAAAGA
*
21216654 GATCGATTC-TTTGAAAA
1 GATCGATCCTTTTGAAAA
21216671 ACAGAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GATCGATCCTTTTGAAAAGA
Found at i:21220584 original size:267 final size:265
Alignment explanation
Indices: 21220032--21220594 Score: 805
Period size: 267 Copynumber: 2.1 Consensus size: 265
21220022 TATTATTTCG
* *
21220032 GGTCGGGTTGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTAGGGT
1 GGTCGGGTAGGGTTTCTAATTCATATATTCGGGTCAGGTCGGGTGAAACTTTATTTTGGTAGGGT
* * *
21220097 CGGGTCGATTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCAGGTTTAGGGTGAAAAATACTC
66 CGGGTCGAGTTTTTAAGTGTGATATCCGGGTCGAGTCGAGTTCAGGTTTAGGGTGAAAAATACTC
* * *
21220162 GACCCCAAAATATATATAATTTTACCTTATATGTTTAGGAATAATTATAATAATACCCCTCTATA
131 GACCCCAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTATAATAATACCCCTCTATA
* *
21220227 TATAATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGT
196 TATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAAAAAAAATAATTTTTTTATTATTTCGGGT
21220292 CAGGTC
261 CA-GTC
* * * *
21220298 GGGTCGGGTAGGATTTCTAATTCATATATTCGGGTTAGGTCGGGTGAAACTTTATTTTGTTCGGG
1 -GGTCGGGTAGGGTTTCTAATTCATATATTCGGGTCAGGTCGGGTGAAACTTTATTTTGGTAGGG
* * *
21220363 TCGGGTC-AGGTTTTTAAGTGTGATATCCGGGTTGAGTCGGGTTCGGGTTTAGGGTGAAAAA-AC
65 TCGGGTCGA-GTTTTTAAGTGTGATATCCGGGTCGAGTCGAGTTCAGGTTTAGGGTGAAAAATAC
21220426 -CGACCTGACTCGAAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTATAATAATACC
129 TCGACC---C-C--AAAAAATATATAATTTTACCTTATATATTTAAGAATAATTATAATAATACC
21220490 CCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAAAAAATAATAATTTTTTTATT
188 CCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAAAAAA-AATAATTTTTTTATT
* *
21220555 ATTTTGTGTC-GT-
252 ATTTCGGGTCAGTC
* *
21220567 GTTC-GGTCGGGTTTCTAATTCATATATT
1 GGTCGGGTAGGGTTTCTAATTCATATATT
21220595 GAATAAAAAT
Statistics
Matches: 266, Mismatches: 22, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
265 5 0.02
266 3 0.01
267 133 0.50
268 4 0.02
269 1 0.00
270 2 0.01
271 95 0.36
272 23 0.09
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (265 bp):
GGTCGGGTAGGGTTTCTAATTCATATATTCGGGTCAGGTCGGGTGAAACTTTATTTTGGTAGGGT
CGGGTCGAGTTTTTAAGTGTGATATCCGGGTCGAGTCGAGTTCAGGTTTAGGGTGAAAAATACTC
GACCCCAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTATAATAATACCCCTCTATA
TATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAAAAAAAATAATTTTTTTATTATTTCGGGT
CAGTC
Found at i:21221006 original size:17 final size:18
Alignment explanation
Indices: 21220984--21221030 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
21220974 TATGGAATTG
*
21220984 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
21221001 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
21221019 GATTCTAATTCC
1 GATTCCAATTCC
21221031 CTCAGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:21221883 original size:20 final size:20
Alignment explanation
Indices: 21221860--21221908 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
21221850 CATGCAGCTT
*
21221860 CAACTGCCTCGATGCATTAG
1 CAACTACCTCGATGCATTAG
*
21221880 CAACTATCTCGATGCATTAG
1 CAACTACCTCGATGCATTAG
21221900 CAACTACCT
1 CAACTACCT
21221909 TTCCATCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (20 bp):
CAACTACCTCGATGCATTAG
Found at i:21227720 original size:32 final size:32
Alignment explanation
Indices: 21227679--21227743 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
21227669 AGAAAACCAA
21227679 GGAAAAGATCCTTACCTTGCTGGAAATAGATT
1 GGAAAAGATCCTTACCTTGCTGGAAATAGATT
21227711 GGAAAAGATCCTTACCTTGCTGGAAATAGATT
1 GGAAAAGATCCTTACCTTGCTGGAAATAGATT
21227743 G
1 G
21227744 AAATTGGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (32 bp):
GGAAAAGATCCTTACCTTGCTGGAAATAGATT
Found at i:21234165 original size:28 final size:28
Alignment explanation
Indices: 21234081--21234180 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
21234071 CTTTTTCTTT
* * *
21234081 TAAGTATCTAAAGTATTTTTTGGTCAAAA
1 TAAGTACCTAAAAT-TTTTTTCGTCAAAA
* *
21234110 CAAGTACCCAAAGTTATTTTTTTCGTCAAAA
1 TAAGTACCTAAA---ATTTTTTTCGTCAAAA
* * * *
21234141 TAGGTACTTAAAATTTTTTTTGTCAAGA
1 TAAGTACCTAAAATTTTTTTCGTCAAAA
21234169 TAAGTACCTAAA
1 TAAGTACCTAAA
21234181 GTATTAGTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
28 24 0.44
29 9 0.16
31 21 0.38
32 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (28 bp):
TAAGTACCTAAAATTTTTTTCGTCAAAA
Found at i:21234312 original size:28 final size:28
Alignment explanation
Indices: 21234272--21234367 Score: 115
Period size: 28 Copynumber: 3.3 Consensus size: 28
21234262 GTTTGAAGAG
*
21234272 TTTAGGTACCTATTTTGA-CATAAAATAT
1 TTTAGGTACCTATTTTGACCA-AAAATAC
21234300 TTTAGGTACCTATTTTGACCAAAAAGATAAC
1 TTTAGGTACCTATTTTGACC-AAAA-AT-AC
*
21234331 TTTGGGTA-CTAATTTTGACCAAAAATAC
1 TTTAGGTACCT-ATTTTGACCAAAAATAC
21234359 TTTAGGTAC
1 TTTAGGTAC
21234368 TTAAAAGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
28 27 0.46
29 6 0.10
30 9 0.15
31 17 0.29
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (28 bp):
TTTAGGTACCTATTTTGACCAAAAATAC
Found at i:21256451 original size:24 final size:25
Alignment explanation
Indices: 21256404--21256466 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 25
21256394 ATTGAATCTC
21256404 AAAACATTTATTTACCTAAGGGGAA
1 AAAACATTTATTTACCTAAGGGGAA
21256429 AAAACATTTATTTACCTAA-GGGAA
1 AAAACATTTATTTACCTAAGGGGAA
21256453 ATAAAC-TTCTATTT
1 A-AAACATT-TATTT
21256467 TTCCCAATCG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 8 0.22
25 28 0.78
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (25 bp):
AAAACATTTATTTACCTAAGGGGAA
Found at i:21263310 original size:21 final size:21
Alignment explanation
Indices: 21263277--21263323 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
21263267 AAGGTGCTAG
*
21263277 GTTGGTAAAAAACAGAAGGTT
1 GTTGGGAAAAAACAGAAGGTT
*
21263298 GTTGGGAAGAAACAGAAGGTT
1 GTTGGGAAAAAACAGAAGGTT
21263319 GTTGG
1 GTTGG
21263324 ATTGGTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.23
Consensus pattern (21 bp):
GTTGGGAAAAAACAGAAGGTT
Found at i:21265342 original size:21 final size:21
Alignment explanation
Indices: 21265316--21265362 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21265306 TAGATAACTT
21265316 AACTTGCCTCTACCTTTTAGA
1 AACTTGCCTCTACCTTTTAGA
*
21265337 AACTTGCCTCTACCTTTTAGG
1 AACTTGCCTCTACCTTTTAGA
21265358 AACTT
1 AACTT
21265363 ACGAACAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (21 bp):
AACTTGCCTCTACCTTTTAGA
Found at i:21271888 original size:26 final size:26
Alignment explanation
Indices: 21271835--21271888 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
21271825 TATATGTAAT
* * *
21271835 TAAAAATATTAAATATTTAATTATAC
1 TAAAAAAATTAAATATCTAATTACAC
* *
21271861 TAAAAAAATTAAATATCTATTTGCAC
1 TAAAAAAATTAAATATCTAATTACAC
21271887 TA
1 TA
21271889 GGAAATCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAAAAAATTAAATATCTAATTACAC
Found at i:21290764 original size:18 final size:18
Alignment explanation
Indices: 21290737--21290782 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
21290727 TTAGACACAC
*
21290737 TTAAACATATCTAGAAAT
1 TTAAAAATATCTAGAAAT
21290755 TTAAAAATATCTAGAAAT
1 TTAAAAATATCTAGAAAT
21290773 TTAAAAATAT
1 TTAAAAATAT
21290783 TTTTCAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (18 bp):
TTAAAAATATCTAGAAAT
Found at i:21292749 original size:38 final size:39
Alignment explanation
Indices: 21292702--21292781 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 39
21292692 CAACATAGTT
**
21292702 AATCGAACTTGTTACGACTCTCGAATGCAGGTATGTT-A
1 AATCGAACTTGTTACGACTCGAGAATGCAGGTATGTTCA
*
21292740 AATCGAACTTGTTATGACTCGAGAATGCAGGTATGTTCA
1 AATCGAACTTGTTACGACTCGAGAATGCAGGTATGTTCA
21292779 AAT
1 AAT
21292782 TTTTTTTCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 34 0.89
39 4 0.11
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (39 bp):
AATCGAACTTGTTACGACTCGAGAATGCAGGTATGTTCA
Found at i:21293454 original size:2 final size:2
Alignment explanation
Indices: 21293447--21293476 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21293437 AAGAAGATAA
21293447 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
21293477 GCATGACCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21294961 original size:28 final size:27
Alignment explanation
Indices: 21294930--21294989 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 27
21294920 TACTAACATT
21294930 CTAACTTTTTTTATTTTTATTGTT-TATA
1 CTAAC-TTTTTTATTTTTATTGTTCT-TA
21294958 CTAAC--TTTTATTTTTATTGTTCTTA
1 CTAACTTTTTTATTTTTATTGTTCTTA
21294983 CTAACTT
1 CTAACTT
21294990 ACTAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 23 0.79
26 1 0.03
28 5 0.17
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.63
Consensus pattern (27 bp):
CTAACTTTTTTATTTTTATTGTTCTTA
Found at i:21294971 original size:25 final size:25
Alignment explanation
Indices: 21294938--21294989 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
21294928 TTCTAACTTT
21294938 TTTTATTTTTATTGTT-TATACTAAC
1 TTTTATTTTTATTGTTCT-TACTAAC
21294963 TTTTATTTTTATTGTTCTTACTAAC
1 TTTTATTTTTATTGTTCTTACTAAC
21294988 TT
1 TT
21294990 ACTAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.21, C:0.10, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTTATTTTTATTGTTCTTACTAAC
Found at i:21297219 original size:10 final size:9
Alignment explanation
Indices: 21297197--21297254 Score: 53
Period size: 9 Copynumber: 5.9 Consensus size: 9
21297187 ATCAATGCAA
21297197 TTATTTTTT
1 TTATTTTTT
21297206 TTATTTTGTT
1 TTATTTT-TT
21297216 TTATTTCATTTT
1 TTA-TT--TTTT
*
21297228 TTATTTATT
1 TTATTTTTT
*
21297237 TTGTTTATTT
1 TTATTT-TTT
21297247 TTATTTTT
1 TTATTTTT
21297255 ACTTAGTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 17 0.43
10 12 0.30
11 4 0.10
12 5 0.12
13 2 0.05
ACGTcount: A:0.14, C:0.02, G:0.03, T:0.81
Consensus pattern (9 bp):
TTATTTTTT
Found at i:21297255 original size:21 final size:22
Alignment explanation
Indices: 21297203--21297255 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
21297193 GCAATTATTT
*
21297203 TTTTTA-TTTTGTTTTATTTCA
1 TTTTTATTTTTATTTTATTTCA
* *
21297224 TTTTT-TATTTATTTTGTTT-A
1 TTTTTATTTTTATTTTATTTCA
21297244 TTTTTATTTTTA
1 TTTTTATTTTTA
21297256 CTTAGTCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTTATTTTATTTCA
Found at i:21297278 original size:24 final size:25
Alignment explanation
Indices: 21297241--21297296 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
21297231 TTTATTTTGT
*
21297241 TTATTTTTATTTTTACTTA-GTCTA
1 TTATTTTTACTTTTACTTATGTCTA
* ** *
21297265 TTATTTTTCCTTTTTGTTATGTTTA
1 TTATTTTTACTTTTACTTATGTCTA
21297290 TTATTTT
1 TTATTTT
21297297 CATATTTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.71
Consensus pattern (25 bp):
TTATTTTTACTTTTACTTATGTCTA
Found at i:21297278 original size:25 final size:24
Alignment explanation
Indices: 21297241--21297296 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
21297231 TTTATTTTGT
21297241 TTATTTTTATTTTTACTTA-GTCTA
1 TTATTTTTATTTTT-CTTATGTCTA
* * *
21297265 TTATTTTTCCTTTTTGTTATGTTTA
1 TTATTTTT-ATTTTTCTTATGTCTA
21297290 TTATTTT
1 TTATTTT
21297297 CATATTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.71
Consensus pattern (24 bp):
TTATTTTTATTTTTCTTATGTCTA
Found at i:21300009 original size:95 final size:93
Alignment explanation
Indices: 21299841--21300084 Score: 321
Period size: 95 Copynumber: 2.7 Consensus size: 93
21299831 TATAATATTA
* *
21299841 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTATAGCAATTGGTTAAACGCCCTGGCTTTATGG
1 TATACTATACAATAAAGC-TGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
* *
21299905 ATAATATTCAGCTAGCCTGATAAAGGTGAT
65 ATAAGATTCAGCTAACCTGATAAAGGTG-T
*
21299935 TATACTATACAATAAAGCTGAGACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 TATACTATACAATAAAGCTGAG-TTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
21300000 ATAAGATTCAGCTAACCTGATAAAGGTGT
65 ATAAGATTCAGCTAACCTGATAAAGGTGT
* *
21300029 T-TAC-AT---AT-----TGAGTTGTCCCTTTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
1 TATACTATACAATAAAGCTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGA
21300084 T
66 T
21300085 TCAGCTAGCT
Statistics
Matches: 140, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
83 41 0.29
84 4 0.03
89 2 0.01
92 2 0.01
93 3 0.02
94 10 0.07
95 78 0.56
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (93 bp):
TATACTATACAATAAAGCTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTGT
Found at i:21301511 original size:36 final size:35
Alignment explanation
Indices: 21301433--21301900 Score: 378
Period size: 36 Copynumber: 13.7 Consensus size: 35
21301423 AAATATTGTC
*
21301433 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA-
1 TTTGTCTCTCTTGAGACAGTTTC-CTTGAAACAAAT
*
21301468 TTT-TCTCTCTTGAGGCAGTTTCCATTGAAACAAAT
1 TTTGTCTCTCTTGAGACAGTTTCC-TTGAAACAAAT
*
21301503 TTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAT
1 TTTGTCTCTCTTGAGACAGTTT-CCTTGAAACAAAT
* *
21301539 TTTATCTCTCTTTAGACAGTTTCCCTTGAAACAAA-
1 TTTGTCTCTCTTGAGACAGTTT-CCTTGAAACAAAT
* *
21301574 ---G--TCT-TTGA-ATATGTTTTCCTTAAAACAAAT
1 TTTGTCTCTCTTGAGACA-G-TTTCCTTGAAACAAAT
* ** * * *
21301604 TTTGTCTCCCTTGAGGTAGTTTCTTTTGGAACTAAGT
1 TTTGTCTCTCTTGAGACAGTTTC-CTTGAAAC-AAAT
* ** *
21301641 TTTGTCTCTCTTGAAACAAATT--TTG--TC----
1 TTTGTCTCTCTTGAGACAGTTTCCTTGAAACAAAT
21301668 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
1 TTTGTCTCTCTTGAGACAGTTTC-CTTGAAACAAAT
21301704 TTTGTCTCTCTTGAGACAGTTTTCCTTGAAACAAA-
1 TTTGTCTCTCTTGAGACAG-TTTCCTTGAAACAAAT
* * *
21301739 ---ATCT-T-TT-A-ATATGTTTTCCTTGAAATAAAT
1 TTTGTCTCTCTTGAGACA-G-TTTCCTTGAAACAAAT
* * * *
21301769 TTTGTCTCCCTTGAGACAGCTTT-TTTTAAACTAAGT
1 TTTGTCTCTCTTGAGACAG-TTTCCTTGAAAC-AAAT
21301805 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
1 TTTGTCTCTCTTGAGACAGTTTC-CTTGAAACAAAT
21301841 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGT
1 TTTGTCTCTCTTGAGACAGTTT-CCTTGAAACAAA-T
21301878 TTTGTCTCTCTTGAGACAGTTTC
1 TTTGTCTCTCTTGAGACAGTTTC
21301901 TATTGTAACA
Statistics
Matches: 350, Mismatches: 43, Indels: 79
0.74 0.09 0.17
Matches are distributed among these distances:
27 19 0.05
28 4 0.01
29 32 0.09
30 11 0.03
31 1 0.00
32 5 0.01
33 5 0.01
34 30 0.09
35 22 0.06
36 162 0.46
37 59 0.17
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTGTCTCTCTTGAGACAGTTTCCTTGAAACAAAT
Found at i:21301516 original size:70 final size:72
Alignment explanation
Indices: 21301433--21301738 Score: 229
Period size: 65 Copynumber: 4.5 Consensus size: 72
21301423 AAATATTGTC
* *
21301433 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA-TTT-TCTCTCTTGAGGCAGTTTCCATTGA
1 TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCATTGA
21301496 AACAAAT
66 AACAAAT
* * * *
21301503 TTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAATTTTATCTCTCTTTAGACAGTTTCCCTTGA
1 TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCATTGA
21301568 AACAAA-
66 AACAAAT
* * * * * * ** **
21301574 ---G--TCT-TTGA-ATATGTTTTCCTTAAAACAAATTTTGTCTCCCTTGAGGTAGTTTCTTTTG
1 TTTGTCTCTCTTGAGACA-ATTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCATTG
* *
21301632 GAACTAAGT
65 AAAC-AAAT
* * * *
21301641 TTTGTCTCTCTTGAAACAAATT---TTG--TC----TTTGTCTCTCTTGAGACAGTTTCTC-TTG
1 TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTC-CATTG
21301696 AAACAAAT
65 AAACAAAT
* *
21301704 TTTGTCTCTCTTGAGACAGTTTTCCTTGAAACAAA
1 TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
21301739 ATCTTTTAAT
Statistics
Matches: 182, Mismatches: 33, Indels: 41
0.71 0.13 0.16
Matches are distributed among these distances:
63 22 0.12
64 28 0.15
65 44 0.24
66 8 0.04
68 3 0.02
70 35 0.19
71 3 0.02
72 31 0.17
73 6 0.03
74 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (72 bp):
TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCATTGA
AACAAAT
Found at i:21301694 original size:25 final size:26
Alignment explanation
Indices: 21301641--21301694 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
21301631 GGAACTAAGT
* *
21301641 TTTGTCTCTCTTGAAACAAATTTTGTC
1 TTTGTCTCTCTTGAAAC-AAGTTTCTC
*
21301668 TTTGTCTCTCTTGAGAC-AGTTTCTC
1 TTTGTCTCTCTTGAAACAAGTTTCTC
21301693 TT
1 TT
21301695 GAAACAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
27 16 0.67
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (26 bp):
TTTGTCTCTCTTGAAACAAGTTTCTC
Found at i:21301758 original size:165 final size:169
Alignment explanation
Indices: 21301503--21301968 Score: 597
Period size: 165 Copynumber: 2.7 Consensus size: 169
21301493 TGAAACAAAT
* * * *
21301503 TTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAATTTTATCTCTCTTTAGACAGTTTCCCTTGA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTGA
* * ** *
21301568 AACAAAGTCTTTGAATATGTTTTCCTTAAAACAAATTTTGTCTCCCTTGAGGTAGTTTCTTTTGG
66 AACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTT-A
*
21301633 AACTAAGTTTTGTCTCTCTTGAAACA-AAT-T-TTG-TC-
130 AACTAAGTTTTGTCTCTCTTGAAACAGAATCTCTTGAACA
*
21301668 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTGA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTGA
* *
21301733 AACAAAATCTTTTAATATGTTTTCCTTGAAATAAATTTTGTCTCCCTTGAGACAGCTTT-TTTTA
66 AACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAG-TTTCTTTTA
* **
21301797 AACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
130 AACTAAGTTTTGTCTCTCTTGAAACAGAATCTCTTG-AAC--A
*
21301840 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG-TTTCTAT
1 -TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTTC-CT
* * *
21301904 TGTAACACCAATCTTTGAATATG-TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTC
63 TGAAACA-AAATCTTTGAATATGTTTTC-CTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTC
21301968 T
125 T
21301969 CTTGAAACAT
Statistics
Matches: 262, Mismatches: 23, Indels: 21
0.86 0.08 0.07
Matches are distributed among these distances:
164 25 0.10
165 114 0.44
166 4 0.02
167 3 0.01
169 1 0.00
173 38 0.15
174 31 0.12
175 23 0.09
176 23 0.09
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (169 bp):
TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTGA
AACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAA
ACTAAGTTTTGTCTCTCTTGAAACAGAATCTCTTGAACA
Found at i:21302009 original size:35 final size:35
Alignment explanation
Indices: 21301963--21302052 Score: 135
Period size: 35 Copynumber: 2.6 Consensus size: 35
21301953 CCTTGAGACA
* * *
21301963 GTTTCTCTTGAAACATAAAAAAAACTTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
* *
21301998 GTTTCTCTTGAAGCACAAATAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
21302033 GTTTCTCTTGAAACACAAAA
1 GTTTCTCTTGAAACACAAAA
21302053 GACCTTCGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:21302424 original size:3 final size:3
Alignment explanation
Indices: 21302395--21302443 Score: 57
Period size: 3 Copynumber: 16.0 Consensus size: 3
21302385 ATACAAAAAC
21302395 ATT A-T ATT A-T ATT ATTT ATTT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT
21302441 ATT
1 ATT
21302444 TATTTTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 28 0.65
4 11 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:21303174 original size:12 final size:12
Alignment explanation
Indices: 21303157--21303206 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
21303147 AATGAAATTA
21303157 TTATTTT-TTATT
1 TTATTTTATT-TT
*
21303169 TTATTTCATTTT
1 TTATTTTATTTT
21303181 TTA-TTTATTTGT
1 TTATTTTATTT-T
21303193 TTATTTTTATTTT
1 TTA-TTTTATTTT
21303206 T
1 T
21303207 ACTTAGCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 6 0.19
12 15 0.47
13 4 0.12
14 7 0.22
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:21303187 original size:16 final size:17
Alignment explanation
Indices: 21303159--21303190 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21303149 TGAAATTATT
21303159 ATTTTTTATTTTATTTC
1 ATTTTTTATTTTATTTC
21303176 ATTTTTTA-TTTATTT
1 ATTTTTTATTTTATTT
21303191 GTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTTTATTTTATTTC
Found at i:21308490 original size:66 final size:68
Alignment explanation
Indices: 21308392--21308640 Score: 270
Period size: 66 Copynumber: 3.8 Consensus size: 68
21308382 TACTCAAAAT
*
21308392 AAAGTTTTTATCTCTTTTGAGAC-ATTGTCTTTTGAA-ACACAAATCTTTGAGTAT-TTATCATT
1 AAAGTTTTTATCTCTCTTGAGACAATT-TCTTTTGAAGA-A-AAATCTTTGAGTATGTT-TCATT
*
21308454 T-AAAAC
62 TGGAAAC
* *
21308460 -AAGTTTTT-TCTCTCTTGGGACAATTTCTTTTGAAGAAAAATCTTTGAGTCTGTTT-ATTTGGA
1 AAAGTTTTTATCTCTCTTGAGACAATTTCTTTTGAAGAAAAATCTTTGAGTATGTTTCATTTGGA
21308522 AAC
66 AAC
* * *
21308525 AAAATTTTATATCT-TC-TGAAACAGTTTCTTTTGAAGAAAAATCTTTGAGTATGTTTC-TTTGG
1 AAAGTTTT-TATCTCTCTTGAGACAATTTCTTTTGAAGAAAAATCTTTGAGTATGTTTCATTTGG
21308587 AAAC
65 AAAC
* * *
21308591 AAAG-TTTTGTCTCTCTTGAGACAGTATCTTTTGAA-AGAAAATCTTTGAGT
1 AAAGTTTTTATCTCTCTTGAGACAATTTCTTTTGAAGA-AAAATCTTTGAGT
21308641 CTATTTCTCT
Statistics
Matches: 157, Mismatches: 13, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
64 8 0.05
65 24 0.15
66 107 0.68
67 15 0.10
68 3 0.02
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (68 bp):
AAAGTTTTTATCTCTCTTGAGACAATTTCTTTTGAAGAAAAATCTTTGAGTATGTTTCATTTGGA
AAC
Found at i:21308608 original size:132 final size:132
Alignment explanation
Indices: 21308397--21308642 Score: 324
Period size: 132 Copynumber: 1.9 Consensus size: 132
21308387 AAAATAAAGT
* * *
21308397 TTTTATCTCTTTTGAGACATTGTCTTTTGAAACACAAATCTTTGAGTATTTATCATTTAAAACAA
1 TTTTATATCTTCTGAAACATTGTCTTTTGAAACACAAATCTTTGAGTATTTATCATTTAAAACAA
* * *
21308462 GTTTTTTCTCTCTTGGGACAATTTCTTTTG-AAGAAAAATCTTTGAGTCTGTTTATTTGGAAACA
66 GTTTTGTCTCTCTTGAGACAATATCTTTTGAAAG-AAAATCTTTGAGTCTGTTTATTTGGAAACA
21308526 AAA
130 AAA
*
21308529 TTTTATATCTTCTGAAACAGTT-TCTTTTGAAGA-A-AAATCTTTGAGTATGTT-TC-TTTGGAA
1 TTTTATATCTTCTGAAACA-TTGTCTTTTGAA-ACACAAATCTTTGAGTAT-TTATCATTT-AAA
*
21308589 ACAAAGTTTTGTCTCTCTTGAGACAGTATCTTTTGAAAGAAAATCTTTGAGTCT
62 AC-AAGTTTTGTCTCTCTTGAGACAATATCTTTTGAAAGAAAATCTTTGAGTCT
21308643 ATTTCTCTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
130 3 0.03
131 20 0.20
132 71 0.71
133 6 0.06
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (132 bp):
TTTTATATCTTCTGAAACATTGTCTTTTGAAACACAAATCTTTGAGTATTTATCATTTAAAACAA
GTTTTGTCTCTCTTGAGACAATATCTTTTGAAAGAAAATCTTTGAGTCTGTTTATTTGGAAACAA
AA
Found at i:21308668 original size:30 final size:29
Alignment explanation
Indices: 21308621--21308721 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 29
21308611 ACAGTATCTT
*
21308621 TTGAAAGAAAATCTTTGAGTCTATTTCTC
1 TTGAAACAAAATCTTTGAGTCTATTTCTC
*
21308650 TTTAAACAAAAGTCTTTGAGTCTATTTCTC
1 TTGAAACAAAA-TCTTTGAGTCTATTTCTC
*
21308680 TTGAAACAAACATCTTTGAGATC-ATTTCCC
1 TTGAAACAAA-ATCTTTGAG-TCTATTTCTC
21308710 TTGAAACAAAAT
1 TTGAAACAAAAT
21308722 TTTTTCTTCC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
29 11 0.17
30 51 0.78
31 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (29 bp):
TTGAAACAAAATCTTTGAGTCTATTTCTC
Found at i:21309031 original size:83 final size:83
Alignment explanation
Indices: 21308936--21309095 Score: 257
Period size: 83 Copynumber: 1.9 Consensus size: 83
21308926 TTGCCTATCG
*
21308936 TCCTCATGACGTAGAAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTCA
1 TCCTCATCACGTAGAAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTCA
21309001 CCCCTAGATAACGATCCA
66 CCCCTAGATAACGATCCA
* * * * * *
21309019 TCCTCATCACGTAGGAACCGTGTCATCTCCCGACCAGACCTCTTCATCATGTAGGATCCGTGTCA
1 TCCTCATCACGTAGAAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTCA
21309084 CCCCTAGATAAC
66 CCCCTAGATAAC
21309096 TAATAGTCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.23
Consensus pattern (83 bp):
TCCTCATCACGTAGAAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTCA
CCCCTAGATAACGATCCA
Found at i:21309073 original size:40 final size:40
Alignment explanation
Indices: 21308936--21309083 Score: 129
Period size: 40 Copynumber: 3.6 Consensus size: 40
21308926 TTGCCTATCG
* * * * *
21308936 TCCTCATGACGTAGAAACCGTGTCATCTCCCAACCAAACC
1 TCCTCATCATGTAGGAACCGTGTCATCTCCCGACCAGACC
* * **
21308976 TCCTCATCATGTAGGAGCCGCGTCA-C-CCCTAGATAACGATCC
1 TCCTCATCATGTAGGAACCGTGTCATCTCCC--GACCA-GA-CC
*
21309018 ATCCTCATCACGTAGGAACCGTGTCATCTCCCGACCAGACC
1 -TCCTCATCATGTAGGAACCGTGTCATCTCCCGACCAGACC
* *
21309059 TCTTCATCATGTAGGATCCGTGTCA
1 TCCTCATCATGTAGGAACCGTGTCA
21309084 CCCCTAGATA
Statistics
Matches: 84, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
38 3 0.04
39 1 0.01
40 44 0.52
41 3 0.04
42 4 0.05
43 25 0.30
44 1 0.01
45 3 0.04
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (40 bp):
TCCTCATCATGTAGGAACCGTGTCATCTCCCGACCAGACC
Found at i:21309106 original size:83 final size:83
Alignment explanation
Indices: 21308935--21309118 Score: 246
Period size: 83 Copynumber: 2.2 Consensus size: 83
21308925 ATTGCCTATC
* *
21308935 GTCCTCATGACGTAGAAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTC
1 GTCCTCATCACGTAGGAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTC
*
21309000 ACCCCTAGATAACGATCCA
66 ACCCCTAGATAACAAT-CA
* * * * *
21309019 -TCCTCATCACGTAGGAACCGTGTCATCTCCCGACCAGACCTCTTCATCATGTAGGATCCGTGTC
1 GTCCTCATCACGTAGGAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTC
21309083 ACCCCTAGATAACTAAT-A
66 ACCCCTAGATAAC-AATCA
* *
21309101 GTCCTCATCGCATAGGAA
1 GTCCTCATCACGTAGGAA
21309119 TGTGTTATCA
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
82 1 0.01
83 85 0.97
84 2 0.02
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.23
Consensus pattern (83 bp):
GTCCTCATCACGTAGGAACCGTGTCATCTCCCAACCAAACCTCCTCATCATGTAGGAGCCGCGTC
ACCCCTAGATAACAATCA
Found at i:21312168 original size:32 final size:32
Alignment explanation
Indices: 21312132--21312211 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 32
21312122 ATTTATTAAT
21312132 ATTCTAATTTTTATTTTATTGCTT-ATACTAAC
1 ATTCTAATTTTTATTTTATTG-TTCATACTAAC
21312164 ATTCTAAAATTTTTTATTTTATTGTTCATACTAAC
1 ATTCT--AA-TTTTTATTTTATTGTTCATACTAAC
*
21312199 -TT-TTATTTTTATT
1 ATTCTAATTTTTATT
21312212 GTTCTTACTA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
30 8 0.19
31 1 0.02
32 5 0.12
33 1 0.02
34 6 0.14
35 22 0.51
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (32 bp):
ATTCTAATTTTTATTTTATTGTTCATACTAAC
Found at i:21312202 original size:24 final size:25
Alignment explanation
Indices: 21312175--21312225 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
21312165 TTCTAAAATT
21312175 TTTTA-TTTTATTGTTCATACTAAC
1 TTTTATTTTTATTGTTCATACTAAC
*
21312199 TTTTATTTTTATTGTTCTTACTAAC
1 TTTTATTTTTATTGTTCATACTAAC
21312224 TT
1 TT
21312226 ACTAACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.22, C:0.12, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTATTTTTATTGTTCATACTAAC
Found at i:21312221 original size:60 final size:57
Alignment explanation
Indices: 21312135--21312245 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 57
21312125 TATTAATATT
*
21312135 CTAATTTTTATTTTATTGCTTATACTAACATT-CTAAAATTTTTTATTTTATTGTTCATA
1 CTAACTTTTATTTTATTGCTTATACTAAC-TTACTAAAA--TTTTATTTTATTGTTCATA
* *
21312194 CTAACTTTTATTTTTATTG-TTCTTACTAACTTACTAACATTTTATTTTATTG
1 CTAACTTTTA-TTTTATTGCTT-ATACTAACTTACTAAAATTTTATTTTATTG
21312246 CACAACTAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
58 13 0.28
59 13 0.28
60 20 0.43
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.58
Consensus pattern (57 bp):
CTAACTTTTATTTTATTGCTTATACTAACTTACTAAAATTTTATTTTATTGTTCATA
Found at i:21313889 original size:15 final size:17
Alignment explanation
Indices: 21313869--21313900 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21313859 CATAATATAA
21313869 TAAATT-CAAG-TAGAT
1 TAAATTACAAGATAGAT
21313884 TAAATTACAAGATAGAT
1 TAAATTACAAGATAGAT
21313901 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATTACAAGATAGAT
Found at i:21315407 original size:32 final size:31
Alignment explanation
Indices: 21315358--21315464 Score: 110
Period size: 31 Copynumber: 3.4 Consensus size: 31
21315348 TAAGTGTAAA
*
21315358 AATTCAAT-AAGTTTAATGATCAATTTGTAAT
1 AATTCAATAAAGTTTAATGAT-AATTTATAAT
*
21315389 AGTTCAATAAAGTTTAATGATAATTTATAAT
1 AATTCAATAAAGTTTAATGATAATTTATAAT
* * *
21315420 AATTTAATATAA-TTTAATGAAAATTATATAAC
1 AATTCAATA-AAGTTTAATGATAATT-TATAAT
**
21315452 AATTTGATAAAGT
1 AATTCAATAAAGT
21315465 AAATGATTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
31 37 0.57
32 28 0.43
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (31 bp):
AATTCAATAAAGTTTAATGATAATTTATAAT
Found at i:21315791 original size:14 final size:14
Alignment explanation
Indices: 21315772--21315827 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
21315762 CGTTCGTGAA
*
21315772 CGTTCGATTATGTT
1 CGTTCGTTTATGTT
*
21315786 CGTTCGGTTATG-T
1 CGTTCGTTTATGTT
21315799 --TT-GTTTATGTT
1 CGTTCGTTTATGTT
*
21315810 CGTTTGTTTATGTT
1 CGTTCGTTTATGTT
21315824 CGTT
1 CGTT
21315828 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.08
13 3 0.08
14 24 0.67
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:21315806 original size:24 final size:24
Alignment explanation
Indices: 21315779--21315848 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
21315769 GAACGTTCGA
*
21315779 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGTTTATGTTTGT
* *
21315803 TTATGTTCGTTTGTTTATGTTCGT
1 TTATGTTCGTTCGTTTATGTTTGT
* *
21315827 TTATGTTCATTCATTTATGTTT
1 TTATGTTCGTTCGTTTATGTTT
21315849 AATTCAATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (24 bp):
TTATGTTCGTTCGTTTATGTTTGT
Found at i:21315828 original size:14 final size:14
Alignment explanation
Indices: 21315797--21315828 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
21315787 GTTCGGTTAT
21315797 GTTTGTTTATGTTC
1 GTTTGTTTATGTTC
21315811 GTTTGTTTATGTTC
1 GTTTGTTTATGTTC
21315825 GTTT
1 GTTT
21315829 ATGTTCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (14 bp):
GTTTGTTTATGTTC
Found at i:21316588 original size:10 final size:10
Alignment explanation
Indices: 21316573--21316647 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
21316563 GGGTCTCCAA
21316573 CGTTTATGTT
1 CGTTTATGTT
21316583 CGTTTATGTT
1 CGTTTATGTT
21316593 CG----TGTT
1 CGTTTATGTT
*
21316599 CATTTATGTT
1 CGTTTATGTT
*
21316609 CGTGTT-CGTTT
1 CGT-TTATG-TT
*
21316620 ATGTTTATGTT
1 -CGTTTATGTT
21316631 CGTTTATGTT
1 CGTTTATGTT
21316641 CGTTTAT
1 CGTTTAT
21316648 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 5 0.10
10 35 0.69
11 8 0.16
12 3 0.06
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:21316604 original size:16 final size:16
Alignment explanation
Indices: 21316579--21316643 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
21316569 CCAACGTTTA
21316579 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
21316595 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
**
21316611 TGTTCGTTTATGTTTA
1 TGTTCGTTTATGTTCG
21316627 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
21316643 T
1 T
21316644 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Done.