Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007063.1 Kokia drynarioides strain JFW-HI SEQ_121672, 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: 192682
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:10950 original size:21 final size:21
Alignment explanation
Indices: 10921--10980 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
10911 TTAGAAACAA
*
10921 TATAGACTTCTACCGATATAAG
1 TATA-ACTTCTACCGATAGAAG
10943 TATAACTTCTACCGATAGAAG
1 TATAACTTCTACCGATAGAAG
*
10964 TCAT-GCTTCTACCGATA
1 T-ATAACTTCTACCGATA
10981 CTAAAACCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 29 0.83
22 6 0.17
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (21 bp):
TATAACTTCTACCGATAGAAG
Found at i:13238 original size:42 final size:42
Alignment explanation
Indices: 13154--13388 Score: 208
Period size: 42 Copynumber: 5.5 Consensus size: 42
13144 TTATGCTTTA
* * * * **
13154 CCGAGTCATAAGTCTTCCTTTTTAAACATAATCTCACACTCATT
1 CCGAGACATGAGTCTTCC--TTTAATCATATTCTCATGCTCATT
* * * *
13198 CCGAGTCATGAGTCTTCCTTTAATCTTATTCTCATTCTCATC
1 CCGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATT
*
13240 CCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCA-T
1 CCGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATT
* ** *
13281 CCTGAGACATGAGTCTTCCTTAAAT-ATAACCTCATGCTCGTT
1 CC-GAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATT
* * * *
13323 TCGAG-CATCGAGTCTTCCATTCATAT-AAATTCTCATGCTCAAT
1 CCGAGACAT-GAGTCTTCC-TTTA-ATCATATTCTCATGCTCATT
13366 CCGAGACATGAGTCTTCCATTTA
1 CCGAGACATGAGTCTTCC-TTTA
13389 TACATCAAGT
Statistics
Matches: 161, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.02
41 25 0.16
42 82 0.51
43 31 0.19
44 20 0.12
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.37
Consensus pattern (42 bp):
CCGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATT
Found at i:17517 original size:788 final size:788
Alignment explanation
Indices: 15999--17568 Score: 2471
Period size: 788 Copynumber: 2.0 Consensus size: 788
15989 TGACAGAACC
* * *
15999 ATCATTCTCTAGTGACAAACGAGCATTCATGGCCCTCAATGCAAACAACGACTTTCAGCTTAAGG
1 ATCATTCTCTAGAGACAAACGAGCATTCATGGCCCTCAACGCAAACAACGACTTCCAGCTTAAGG
* *
16064 CATCAGTAATAACATTAGCCTTTCCCGGATGATAATCAATCATAAGGTTATAATCCTTCAGTAAC
66 CATCAGTAATAACATTAGCCTTTCCCGGATGATAATCAATCACAAGGTCATAATCCTTCAGTAAC
** * **
16129 TCTAACCATCACCGTTGTCTCAAATTCAATTCTTTTTGTGTCATCAATACTTCAAACTCCTATGA
131 TCTAACCATCACCACTGTATCAAATTCAATTCTTTTTGCATCATCAATACTTCAAACTCCTATGA
* *
16194 TTTGTAAAGATATGACATCTTTCACCATACAGATAATGTCGCCAAATCTTCAATGCAAAGACAAT
196 TCTGTAAAGATATGACATCTCTCACCATACAGATAATGTCGCCAAATCTTCAATGCAAAGACAAT
* * * * * * *
16259 GGCTGATAACTTAGAATCAGGAGTCGGATAATTCCCCTCATTTGGCTTCAATTGTCGAGAGACGT
261 GGCTGATAACTCAGAATAAGGAGTCGAATAATTCCCATCATGTGGCTTCAACTGTCAAGAGACGT
16324 AAAATATCACTTTCCCTACTTGCATCAATACATAACCCAACCCATTCAATAAGGCATCACTAAAA
326 AAAATATCACTTTCCCTACTTGCATCAATACATAACCCAACCCATTCAATAAGGCATCACTAAAA
16389 ACCACAAATTCCTTTCCAGTCTCAGGTTGTGTCAAGACTGCAGCCTCTGTTAGCATTTTCTTCAA
391 ACCACAAATTCCTTTCCAGTCTCAGGTTGTGTCAAGACTGCAGCCTCTGTTAGCATTTTCTTCAA
** *
16454 TCGATCAAAACTCTACTAACACTTTTCTGACCAAACAAACTGAACATTCTTCTGAAGTAACTTTC
456 TAAATCAAAACTCTACTAACACTTTTCTGACCAAACAAACTGAACATTCTTCTAAAGTAACTTTC
* * * *
16519 TCATTGGTAAGACTATAATGGGAAAATCTTTAACAAATCGTCAGTAATAGCCTGTTAATCCCAGA
521 TCATTGGCAAGACTATAATGGAAAAATCTTTAACAAATCATCAGTAATAGCCTGTTAATCCCAAA
* * * *
16584 AAACTGCGTTCTTTAAAAACATCCTTAGGGATTTTCTAATTAAGAATAGCAAAAACCTTACTCGG
586 AAAATGCGTACTTCAAAAACATCCTTAGGGATTTTCCAATTAAGAATAGCAAAAACCTTACTCGG
* * *
16649 ATCAACTCGTATTCCCTCCAAAGATACAACATGCCCTAGAAATCCAATCTCTCTAAGCCAGAATT
651 ATCAACCCGTATTCCCTCCAAAGAAACAACATGCCCTAGAAATCCAACCTCTCTAAGCCAGAATT
*
16714 CACACTTACTGAATTTCGTATACAACTGCTTTTCCTGTAGAATCTATAATACTTTTCTCAAATGC
716 CACACTTAATGAATTTCGTATACAACTGCTTTTCCTGTAGAATCTATAATACTTTTCTCAAATGC
16779 TGCGTATG
781 TGCGTATG
16787 ATCATTCTCTAGAGACAAACGAGCATTCATGGCCCTCAACGCAAACAACGACTTCCAGCTTAAGG
1 ATCATTCTCTAGAGACAAACGAGCATTCATGGCCCTCAACGCAAACAACGACTTCCAGCTTAAGG
16852 CATCAGTAATAACATTAGCCTTTCCCGGATGATAATCAATCACAAGGTCATAA-CCTTCAGTAAC
66 CATCAGTAATAACATTAGCCTTTCCCGGATGATAATCAATCACAAGGTCATAATCCTTCAGTAAC
* * *
16916 TCTAACTATCATCACTGTATCAAATTCAATTCTTTTTGCATCATCAAATACTTCAAACTCTTATG
131 TCTAACCATCACCACTGTATCAAATTCAATTCTTTTTGCATCATC-AATACTTCAAACTCCTATG
*
16981 ATCTGTAAAGATATGACATCTCTCACCATATAGATAATGTCGCCAAATCTTCAATGCAAAGACAA
195 ATCTGTAAAGATATGACATCTCTCACCATACAGATAATGTCGCCAAATCTTCAATGCAAAGACAA
* * * * *
17046 TGGCTGCTAACTCCA-AATAATGAGTTGAATAATTCCCATCATGTGGCTTCCACTGTCAAGAGGC
260 TGGCTGATAACT-CAGAATAAGGAGTCGAATAATTCCCATCATGTGGCTTCAACTGTCAAGAGAC
** **
17110 GTAAGCTATCACTTTCCCTACTTGCATCAATACATAACCCAACCCATTCAATAAGGCATCACTGT
324 GTAAAATATCACTTTCCCTACTTGCATCAATACATAACCCAACCCATTCAATAAGGCATCACTAA
* * **
17175 CAATCACAAATTCCTTTCTTGTCTCAGGTTGTGTCAAGACTAG-AGCCTCTGTTAGCATTTTCTT
389 AAACCACAAATTCCTTTCCAGTCTCAGGTTGTGTCAAGACT-GCAGCCTCTGTTAGCATTTTCTT
* *
17239 CAATAAATCAAAACTCTGCTAGCACTTTTCTGACCAAACAAACTGAACATTCTTCTAAAGTAACT
453 CAATAAATCAAAACTCTACTAACACTTTTCTGACCAAACAAACTGAACATTCTTCTAAAGTAACT
* * * *
17304 TTGTCATTGGCAAGGCTATAATGGAAAAATCTTTAACAAATCATCGGTAATAGCCTGTTAATCCT
518 TTCTCATTGGCAAGACTATAATGGAAAAATCTTTAACAAATCATCAGTAATAGCCTGTTAATCCC
* * * *
17369 AAAAAAATGTGTACTTCAGAAACATTCTTAGGGATTTTCCAATTAAGAATAGCAGAAACCTTACT
583 AAAAAAATGCGTACTTCAAAAACATCCTTAGGGATTTTCCAATTAAGAATAGCAAAAACCTTACT
* * * *
17434 CTGATCAACCCGTATTCCCTCCGAAGAAACAACATGCCTTAGAAATCCAACCTCTCTGAGCCAGA
648 CGGATCAACCCGTATTCCCTCCAAAGAAACAACATGCCCTAGAAATCCAACCTCTCTAAGCCAGA
* * * *
17499 ATTCACACTTAATGAATTTCGTATACAGCTGTTTTTCCTTTAGAATCTGTAATACTTTTCTCAAA
713 ATTCACACTTAATGAATTTCGTATACAACTGCTTTTCCTGTAGAATCTATAATACTTTTCTCAAA
17564 TGCTG
778 TGCTG
17569 TGCATAATCA
Statistics
Matches: 710, Mismatches: 69, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
787 49 0.07
788 659 0.93
789 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (788 bp):
ATCATTCTCTAGAGACAAACGAGCATTCATGGCCCTCAACGCAAACAACGACTTCCAGCTTAAGG
CATCAGTAATAACATTAGCCTTTCCCGGATGATAATCAATCACAAGGTCATAATCCTTCAGTAAC
TCTAACCATCACCACTGTATCAAATTCAATTCTTTTTGCATCATCAATACTTCAAACTCCTATGA
TCTGTAAAGATATGACATCTCTCACCATACAGATAATGTCGCCAAATCTTCAATGCAAAGACAAT
GGCTGATAACTCAGAATAAGGAGTCGAATAATTCCCATCATGTGGCTTCAACTGTCAAGAGACGT
AAAATATCACTTTCCCTACTTGCATCAATACATAACCCAACCCATTCAATAAGGCATCACTAAAA
ACCACAAATTCCTTTCCAGTCTCAGGTTGTGTCAAGACTGCAGCCTCTGTTAGCATTTTCTTCAA
TAAATCAAAACTCTACTAACACTTTTCTGACCAAACAAACTGAACATTCTTCTAAAGTAACTTTC
TCATTGGCAAGACTATAATGGAAAAATCTTTAACAAATCATCAGTAATAGCCTGTTAATCCCAAA
AAAATGCGTACTTCAAAAACATCCTTAGGGATTTTCCAATTAAGAATAGCAAAAACCTTACTCGG
ATCAACCCGTATTCCCTCCAAAGAAACAACATGCCCTAGAAATCCAACCTCTCTAAGCCAGAATT
CACACTTAATGAATTTCGTATACAACTGCTTTTCCTGTAGAATCTATAATACTTTTCTCAAATGC
TGCGTATG
Found at i:22334 original size:12 final size:12
Alignment explanation
Indices: 22317--22364 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
22307 TAGGTTCTTT
*
22317 TTCTTCTTTATC
1 TTCTTCTTTTTC
22329 TTCTTCCTTTCCTTC
1 TTCTT-CTTT--TTC
22344 TTCTTCTTTTTC
1 TTCTTCTTTTTC
*
22356 TTCATCTTT
1 TTCTTCTTT
22365 CTCCTTCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 16 0.52
13 4 0.13
14 4 0.13
15 7 0.23
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:24234 original size:14 final size:14
Alignment explanation
Indices: 24208--24240 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24198 AAACAACACC
24208 AAAAAGTGAAATAA
1 AAAAAGTGAAATAA
24222 ATAAAAG-GAAATAA
1 A-AAAAGTGAAATAA
24236 AAAAA
1 AAAAA
24241 TGCGTCGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (14 bp):
AAAAAGTGAAATAA
Found at i:33672 original size:29 final size:29
Alignment explanation
Indices: 33615--33672 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
33605 AGTACACAGG
**
33615 TAAGCTTTCTACCTTAGTAAGTTTGTAAC
1 TAAGCTTTCTACCTTAGTAAGTTCATAAC
**
33644 TAAGCTTTCTTGCTTAGTAAGTTCATAAC
1 TAAGCTTTCTACCTTAGTAAGTTCATAAC
33673 CAGTAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (29 bp):
TAAGCTTTCTACCTTAGTAAGTTCATAAC
Found at i:33841 original size:36 final size:37
Alignment explanation
Indices: 33801--33885 Score: 91
Period size: 42 Copynumber: 2.2 Consensus size: 37
33791 ATCTCACACC
* *
33801 CATTCT-GAGTCATGACTCTTCCTTTAATCTTATTCT
1 CATTCTCGAGACATGACTCTTCCTTTAATCATATTCT
*
33837 CATTCTTATCCCGAGACATGAGTCTTCCTTTAATCATATTCT
1 CATTC---T--CGAGACATGACTCTTCCTTTAATCATATTCT
33879 CATTCTC
1 CATTCTC
33886 ATCCTGAGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
36 5 0.12
37 1 0.03
39 2 0.05
42 32 0.80
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (37 bp):
CATTCTCGAGACATGACTCTTCCTTTAATCATATTCT
Found at i:33857 original size:42 final size:42
Alignment explanation
Indices: 33811--33922 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
33801 CATTCTGAGT
* * *
33811 CATGACTCTTCCTTTAATCTTATTCTCATTCTTATCCCGAGA
1 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
*
33853 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCTGAGA
1 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
* *
33895 CATGAGTCTTCCTTAAAT-ATATCCTCAT
1 CATGAGTCTTCCTTTAATCATATTCTCAT
33923 GCTTGTTTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
41 9 0.14
42 55 0.86
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (42 bp):
CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
Found at i:43023 original size:43 final size:43
Alignment explanation
Indices: 42952--43055 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
42942 TGCGGATTCT
* * *
42952 CCACAACTCATGTGAGCAGCATCATGTAGTTTAACATCCTGAC
1 CCACAACTCGTGTGAGCAGCATCATGTAGTCTAACATCCCGAC
* * *
42995 CCATAGCTCGTGTGAGCGGCATCATGTAGTCTAACATCCCGAC
1 CCACAACTCGTGTGAGCAGCATCATGTAGTCTAACATCCCGAC
*
43038 CCACAACTTGTGTGAGCA
1 CCACAACTCGTGTGAGCA
43056 TTATAGGATA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
CCACAACTCGTGTGAGCAGCATCATGTAGTCTAACATCCCGAC
Found at i:44542 original size:35 final size:36
Alignment explanation
Indices: 44455--44556 Score: 145
Period size: 35 Copynumber: 2.9 Consensus size: 36
44445 AACTACTTCG
* * *
44455 ATGGACTGCTTACGTCTCGGTTAGAGCGT-AAGGTT
1 ATGGATTGCTTACGTCTCGGTTAGAGCATAAAGCTT
*
44490 ATGGATTTGCTTACGTCTTGGTTAGAGCATAAAGCTT
1 ATGGA-TTGCTTACGTCTCGGTTAGAGCATAAAGCTT
44527 -TGGATTGCTTACGTCTCGGTTAGAGCATAA
1 ATGGATTGCTTACGTCTCGGTTAGAGCATAA
44557 TGCTATGTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 30 0.50
36 25 0.42
37 5 0.08
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (36 bp):
ATGGATTGCTTACGTCTCGGTTAGAGCATAAAGCTT
Found at i:44592 original size:56 final size:55
Alignment explanation
Indices: 44522--44667 Score: 177
Period size: 55 Copynumber: 2.6 Consensus size: 55
44512 TAGAGCATAA
* * * *
44522 AGCTTTGGATTGCTTACGTCTCGGTTAGAGCATAATGCTATGTATAGCTCGGGTTG
1 AGCTTTGGAATGCTTATGTCTCGGTTAGAGCATAAAGCTAT-TATAGCTCGGGTAG
* *
44578 AGCTTTGGAATGCTTATGTCTCGAG-TATAGCGTAAAGCTATTATAGCTCGGGTAG
1 AGCTTTGGAATGCTTATGTCTCG-GTTAGAGCATAAAGCTATTATAGCTCGGGTAG
* * * *
44633 AGCTTTGAAAGGCTCATGTCTCGATTAGAGCATAA
1 AGCTTTGGAATGCTTATGTCTCGGTTAGAGCATAA
44668 GGTTATTTCA
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
55 41 0.54
56 34 0.45
57 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (55 bp):
AGCTTTGGAATGCTTATGTCTCGGTTAGAGCATAAAGCTATTATAGCTCGGGTAG
Found at i:45310 original size:21 final size:21
Alignment explanation
Indices: 45270--45316 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
45260 ATAGTTCTAC
*
45270 CGATACAAGTGAGGCAACTAT
1 CGATACAAGTCAGGCAACTAT
* *
45291 CGATACAAGTCATGCTACTAT
1 CGATACAAGTCAGGCAACTAT
*
45312 TGATA
1 CGATA
45317 TTAAAAACTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (21 bp):
CGATACAAGTCAGGCAACTAT
Found at i:46031 original size:35 final size:35
Alignment explanation
Indices: 45982--46074 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 35
45972 TATTCGTTTA
45982 CTCCCTGTTAACCCAAAGGTCATTATGCTCATTTT
1 CTCCCTGTTAACCCAAAGGTCATTATGCTCATTTT
* * *
46017 CTCCCTATTGACCCAAAGTTCATTATGCTCATTTT
1 CTCCCTGTTAACCCAAAGGTCATTATGCTCATTTT
*
46052 CTCCTTGTTAACCCAAAGGTCAT
1 CTCCCTGTTAACCCAAAGGTCAT
46075 GCCTGTTCCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (35 bp):
CTCCCTGTTAACCCAAAGGTCATTATGCTCATTTT
Found at i:49937 original size:21 final size:21
Alignment explanation
Indices: 49885--49938 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
49875 CATGAGATAA
*
49885 TTCTACCGATACAAGTATCAC
1 TTCTATCGATACAAGTATCAC
* * *
49906 TTTTATTGATACAAGTCA-CGC
1 TTCTATCGATACAAGT-ATCAC
49927 TTCTATCGATAC
1 TTCTATCGATAC
49939 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (21 bp):
TTCTATCGATACAAGTATCAC
Found at i:59576 original size:8 final size:9
Alignment explanation
Indices: 59564--59588 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59554 TTGAAAAGAA
59564 AAAAAAATG
1 AAAAAAATG
59573 AAAAAAATG
1 AAAAAAATG
59582 AAAAAAA
1 AAAAAAA
59589 AAACAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAAATG
Found at i:69047 original size:21 final size:21
Alignment explanation
Indices: 69021--69072 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
69011 ACAGTGCAGA
*
69021 CTTCTACTGATACAAGTAGAG
1 CTTCTACCGATACAAGTAGAG
69042 CTTCTACCGATACAAGTAGAG
1 CTTCTACCGATACAAGTAGAG
69063 CTTCTACCGA
1 CTTCTACCGA
69073 AAAAACTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (21 bp):
CTTCTACCGATACAAGTAGAG
Found at i:75360 original size:17 final size:17
Alignment explanation
Indices: 75338--75372 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
75328 TCCAAAAACC
* *
75338 AGTAAAATAGAGAGAAA
1 AGTAAAACAAAGAGAAA
75355 AGTAAAACAAAGAGAAA
1 AGTAAAACAAAGAGAAA
75372 A
1 A
75373 TGAATGGGTG
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:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (17 bp):
AGTAAAACAAAGAGAAA
Found at i:77285 original size:25 final size:25
Alignment explanation
Indices: 77257--77309 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
77247 CCGACCCTCC
77257 TCAGATTCCACCCCAATGATTGGTG
1 TCAGATTCCACCCCAATGATTGGTG
77282 TCAGATTCCACCCCAATGATTGGTG
1 TCAGATTCCACCCCAATGATTGGTG
77307 TCA
1 TCA
77310 AGCCTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (25 bp):
TCAGATTCCACCCCAATGATTGGTG
Found at i:77642 original size:55 final size:56
Alignment explanation
Indices: 77520--77656 Score: 185
Period size: 56 Copynumber: 2.5 Consensus size: 56
77510 ATGACTAGAT
*
77520 AAAAAAATATTTTTTTATTTG-ATAAAGGAGGTGATGACCATGACTCCATAAGCACCC
1 AAAAAAATATTTTTTTATTTGAAAAAAGGAGGTGATGACCATGACT-C-TAAGCACCC
*
77577 -AAAAAATATTTTTTTATTTGAAAAAAGG-GGTGATGATCATGACT-T-AGCACACC
1 AAAAAAATATTTTTTTATTTGAAAAAAGGAGGTGATGACCATGACTCTAAGCAC-CC
77630 AAAAAAAATATTTTTTTATTTGAAAAA
1 -AAAAAAATATTTTTTTATTTGAAAAA
77657 GACTTGACCA
Statistics
Matches: 74, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
52 5 0.07
53 3 0.04
55 25 0.34
56 35 0.47
57 6 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (56 bp):
AAAAAAATATTTTTTTATTTGAAAAAAGGAGGTGATGACCATGACTCTAAGCACCC
Found at i:77703 original size:150 final size:149
Alignment explanation
Indices: 77529--77807 Score: 393
Period size: 150 Copynumber: 1.9 Consensus size: 149
77519 TAAAAAAATA
*
77529 TTTTTTTATTTGATAAAGGAGGTGATGACCATGACTCCATAAGCACCCAAAAAATATTTTTTTAT
1 TTTTTTTATTTGATAAAGGAGGTGATGACCATGACTCCATAAGCACCC-AAAAATATTTATTTAT
*
77594 TTGAAAAAAGG-GGTGATGATCATGA-CTTAGCACAC-CAAAAAAAATATTTTTTTATTTGAAAA
65 TTG-AAAAAGGTGGTGATGATCAT-ATCTTAGCAAACAC-AAAAAAATATTTTTTTATTTGAAAA
77656 AGACTTGACCATCACCCAAATTT
127 AGACTTGACCATCACCCAAATTT
* * *** * * *
77679 TTTTTTTATTTGATAAAGGGGGTGATGGCCATGACTTGGTCATCACTCAAAAATATTTATTTATT
1 TTTTTTTATTTGATAAAGGAGGTGATGACCATGACTCCATAAGCACCCAAAAATATTTATTTATT
*
77744 TGAAAAAGGTGGTGATGATTATATCTTAGCAAACATCAAAAAAATATTTTTTTATTTGAAAAAG
66 TGAAAAAGGTGGTGATGATCATATCTTAGCAAACA-CAAAAAAATATTTTTTTATTTGAAAAAG
77808 GAAGTGATGA
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
148 8 0.07
149 38 0.33
150 67 0.59
151 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (149 bp):
TTTTTTTATTTGATAAAGGAGGTGATGACCATGACTCCATAAGCACCCAAAAATATTTATTTATT
TGAAAAAGGTGGTGATGATCATATCTTAGCAAACACAAAAAAATATTTTTTTATTTGAAAAAGAC
TTGACCATCACCCAAATTT
Found at i:77752 original size:55 final size:52
Alignment explanation
Indices: 77680--77861 Score: 170
Period size: 55 Copynumber: 3.3 Consensus size: 52
77670 CCCAAATTTT
* * * *
77680 TTTTTTATTTGATAAAGGGGGTGATGGCCATGACTTGGTCATCACTC-AAAAATA
1 TTTTTTATTTGAAAAAGGAGGTGATGACTATGACTT-G-CA-CACTCAAAAAATA
* * *
77734 TTTATTTATTTGAAAAAGGTGGTGATGATTAT-ATCTTAGCAAACATCAAAAAAATA
1 TTT-TTTATTTGAAAAAGGAGGTGATGACTATGA-CTT-GCACAC-TC-AAAAAATA
*
77790 TTTTTTTATTTGAAAAAGGAAGTGATGACTATGACTTGACAAGCACTCAAAAAATA
1 -TTTTTTATTTGAAAAAGGAGGTGATGACTATGACTTG-C-A-CACTCAAAAAATA
77846 TTTTTTATTTGAAAAA
1 TTTTTTATTTGAAAAA
77862 TGGATGATGA
Statistics
Matches: 107, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
53 2 0.02
54 8 0.07
55 44 0.41
56 44 0.41
57 7 0.07
58 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (52 bp):
TTTTTTATTTGAAAAAGGAGGTGATGACTATGACTTGCACACTCAAAAAATA
Found at i:77801 original size:56 final size:56
Alignment explanation
Indices: 77679--77883 Score: 183
Period size: 56 Copynumber: 3.7 Consensus size: 56
77669 ACCCAAATTT
* ** * * * *
77679 TTTTTTTATTTGATAAAGGGGGTGATGGCCATGACTTGGTC-ATCACTC-AAAAATA
1 TTTTTTTATTTGAAAAAGGAAGTGATGACTATGACTT-GACAAACACTCAAAAAATA
* ** *
77734 TTTATTTATTTGAAAAAGGTGGTGATGATTAT-ATCTT-AGCAAACA-TCAAAAAAATA
1 TTTTTTTATTTGAAAAAGGAAGTGATGACTATGA-CTTGA-CAAACACTC-AAAAAATA
*
77790 TTTTTTTATTTGAAAAAGGAAGTGATGACTATGACTTGACAAGCACTCAAAAAATA
1 TTTTTTTATTTGAAAAAGGAAGTGATGACTATGACTTGACAAACACTCAAAAAATA
* *
77846 -TTTTTTATTTGAAAAATGG-A-TGATGACCATGGCTTGAC
1 TTTTTTTATTTGAAAAA-GGAAGTGATGACTATGACTTGAC
77884 CATCATCCAA
Statistics
Matches: 126, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
54 20 0.16
55 49 0.39
56 53 0.42
57 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (56 bp):
TTTTTTTATTTGAAAAAGGAAGTGATGACTATGACTTGACAAACACTCAAAAAATA
Found at i:78039 original size:137 final size:136
Alignment explanation
Indices: 77782--78044 Score: 319
Period size: 137 Copynumber: 1.9 Consensus size: 136
77772 GCAAACATCA
* * * *
77782 AAAAAATATTTTTTTATTTGAAAAAGGAAGTGATGACTATGACTTGACAAGCACTCAAAAAATAT
1 AAAAAATATTTTTTTATCTGAAAAAAGAAGTGATGACTATAACTTGACAAGCACCCAAAAAATAT
* * * * * *
77847 TTTTTATTTGAAAAATGGATGATGACCATGGCTTGACCATCATCCAAATTTTTTTTTTATCTGTC
66 TTTTTATCTGAAAAAAGGATGATGACCATGACTTGACAAACATCCAAA-TATTTTTTTATCTGTC
77912 ATCACCC
130 ATCACCC
* **
77919 AAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGTTATAACTTGACAAGCACCCAAAAAATAT
1 AAAAAATATTTTTTTATCTGAAAAAAGAAGTGATGACTATAACTTGACAAGCACCCAAAAAATA-
* * * * * *
77984 TTTTTTATCTGAAAAAAGAGGTGATGGCTATGACTTGGCAAACACTCAAAATTTTTTTTTA
65 TTTTTTATCTGAAAAAAG-GATGATGACCATGACTTGACAAACA-TCCAAATATTTTTTTA
78045 ATCTTAAAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
137 57 0.54
138 16 0.15
139 28 0.26
140 5 0.05
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (136 bp):
AAAAAATATTTTTTTATCTGAAAAAAGAAGTGATGACTATAACTTGACAAGCACCCAAAAAATAT
TTTTTATCTGAAAAAAGGATGATGACCATGACTTGACAAACATCCAAATATTTTTTTATCTGTCA
TCACCC
Found at i:78043 original size:56 final size:56
Alignment explanation
Indices: 77914--78034 Score: 197
Period size: 56 Copynumber: 2.2 Consensus size: 56
77904 TATCTGTCAT
* *
77914 CACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGTTATAACTTGACAAG
1 CACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGCTATAACTTGACAAA
* *
77970 CACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGCTATGACTTGGCAAA
1 CACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGCTATAACTTGACAAA
*
78026 CACTCAAAA
1 CACCCAAAA
78035 TTTTTTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (56 bp):
CACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGCTATAACTTGACAAA
Found at i:78096 original size:193 final size:193
Alignment explanation
Indices: 77717--78124 Score: 456
Period size: 193 Copynumber: 2.1 Consensus size: 193
77707 CCATGACTTG
* * * * * * *
77717 GTCATCACTC-AAAAATATTTATTTATTTGAAAAAGGTGGTGATGATTATATCTTAGCAAACATC
1 GTCATCACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGATTATAACTTAGCAAACACC
* * *
77781 AAAAAAATATTTTTTTATTTGAAAAAGGAAGTGATGACTATGACTTGACAAGCACTCAAAAAATA
66 AAAAAAATATTTTTTTATCTGAAAAAAGAAGTGATGACTATGACTTGACAAACACTCAAAAAATA
* * * *
77846 TTTTTTATTTGAAAAATGGATGATGACCATGGCTTGACCATCATCCAAATTTTTTTTTTATCT
131 TTTTTTATTTGAAAAAGGGATGATGACCATGGCTTGACAATCACCCAAATATTTTTTTTATCT
* *
77909 GTCATCACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGTTATAACTT-GACAAGCAC
1 GTCATCACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGATTATAACTTAG-CAAACAC
* * * * *
77973 CCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGGCTATGACTTGGCAAACACTC-AAAATT
65 CAAAAAAATATTTTTTTATCTGAAAAAAGAAGTGATGACTATGACTTGACAAACACTCAAAAAAT
* **
78037 TTTTTTTAATCTT-AAAAAGGGAATGATGGTCATGGCTTGGTA-AAT-ACCCAAA-ATTTTTTTT
130 ATTTTTT-AT-TTGAAAAAGGG-ATGATGACCATGGCTT-G-ACAATCACCCAAATATTTTTTTT
78098 ATCT
190 ATCT
* * *
78102 G--ATAAACAAAAAAATATTTTTTT
1 GTCATCACCCAAAAAATATTTTTTT
78125 GGGGTGTCGG
Statistics
Matches: 182, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
191 19 0.10
192 21 0.12
193 116 0.64
194 22 0.12
195 3 0.02
196 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (193 bp):
GTCATCACCCAAAAAATATTTTTTTATCTGAAAAAAGAGGTGATGATTATAACTTAGCAAACACC
AAAAAAATATTTTTTTATCTGAAAAAAGAAGTGATGACTATGACTTGACAAACACTCAAAAAATA
TTTTTTATTTGAAAAAGGGATGATGACCATGGCTTGACAATCACCCAAATATTTTTTTTATCT
Found at i:81525 original size:39 final size:39
Alignment explanation
Indices: 81480--81557 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
81470 CACGAAAATG
*
81480 TGTGATAGATATATTAATATTTATTAAAATTTATATAAA
1 TGTGATAGATATATTAATATTTATTAAAATTTACATAAA
* *
81519 TGTGATAGATATATTAATATTTATTTAAGTTTACATAAA
1 TGTGATAGATATATTAATATTTATTAAAATTTACATAAA
81558 AAAAATGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (39 bp):
TGTGATAGATATATTAATATTTATTAAAATTTACATAAA
Found at i:82624 original size:21 final size:21
Alignment explanation
Indices: 82600--82643 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
82590 AATCACATCC
* *
82600 AAACAATAAAAATATCAGCAA
1 AAACAATAAAAATAACAACAA
*
82621 AAACAATAGAAATAACAACAA
1 AAACAATAAAAATAACAACAA
82642 AA
1 AA
82644 GCAACACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.11
Consensus pattern (21 bp):
AAACAATAAAAATAACAACAA
Found at i:82649 original size:12 final size:12
Alignment explanation
Indices: 82634--82705 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 12
82624 CAATAGAAAT
* *
82634 AACAACAAAAGC
1 AACACCAAAAAC
82646 AACACCAAAAAC
1 AACACCAAAAAC
*
82658 AACACC-AAAAT
1 AACACCAAAAAC
*
82669 AATA--AAAAAC
1 AACACCAAAAAC
82679 ACACACCAAAAAC
1 A-ACACCAAAAAC
82692 AACA--AAAAAC
1 AACACCAAAAAC
82702 AACA
1 AACA
82706 ATATAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
10 15 0.30
11 9 0.18
12 19 0.38
13 7 0.14
ACGTcount: A:0.69, C:0.26, G:0.01, T:0.03
Consensus pattern (12 bp):
AACACCAAAAAC
Found at i:82698 original size:22 final size:21
Alignment explanation
Indices: 82646--82705 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
82636 CAACAAAAGC
*
82646 AACACCAAAAACAACACCAAA
1 AACAACAAAAACAACACCAAA
82667 ATA-ATA-AAAAACACACACCAAA
1 A-ACA-ACAAAAACA-ACACCAAA
82689 AACAACAAAAAACAACA
1 AACAAC-AAAAACAACA
82706 ATATAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
21 11 0.34
22 14 0.44
23 7 0.22
ACGTcount: A:0.70, C:0.27, G:0.00, T:0.03
Consensus pattern (21 bp):
AACAACAAAAACAACACCAAA
Found at i:82698 original size:23 final size:21
Alignment explanation
Indices: 82634--82705 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 21
82624 CAATAGAAAT
*
82634 AACAACAAAAGCAACACCAAAAAC
1 AACACCAAAA-CAACA--AAAAAC
* *
82658 AACACCAAAATAATAAAAAAC
1 AACACCAAAACAACAAAAAAC
82679 ACACACCAAAAACAACAAAAAAC
1 A-ACACC-AAAACAACAAAAAAC
82702 AACA
1 AACA
82706 ATATAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 7 0.17
22 8 0.20
23 17 0.41
24 9 0.22
ACGTcount: A:0.69, C:0.26, G:0.01, T:0.03
Consensus pattern (21 bp):
AACACCAAAACAACAAAAAAC
Found at i:82824 original size:13 final size:14
Alignment explanation
Indices: 82806--82834 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
82796 ATTTTTTGTC
82806 TAAATCTAT-TTTT
1 TAAATCTATATTTT
82819 TAAATCTATATTTT
1 TAAATCTATATTTT
82833 TA
1 TA
82835 TCTAAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATCTATATTTT
Found at i:98397 original size:25 final size:25
Alignment explanation
Indices: 98363--98420 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
98353 AAACCAAATG
* *
98363 TATTAGGTTAGTGTAATGGCATGAA
1 TATTAGGTTAGTGGAATGACATGAA
*
98388 TATTAGGTTAGTGGAATGACATGAT
1 TATTAGGTTAGTGGAATGACATGAA
98413 TATTAGGT
1 TATTAGGT
98421 GAATATAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (25 bp):
TATTAGGTTAGTGGAATGACATGAA
Found at i:99597 original size:36 final size:36
Alignment explanation
Indices: 99550--99653 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
99540 GGTAACAGGC
*
99550 ATGACTTTTGGGTCAACAGGGAGAAAAATGAGCATA
1 ATGACTTTTGGGTCAACAGGGAGTAAAATGAGCATA
** *
99586 ATGACTTTTGGGTCAACAGGGAGTAAAACAAGCATC
1 ATGACTTTTGGGTCAACAGGGAGTAAAATGAGCATA
**
99622 ATGACCCTTGAGGTCAACAGGGAGTAAAATGA
1 ATGACTTTTG-GGTCAACAGGGAGTAAAATGA
99654 ATAACGATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 40 0.68
37 19 0.32
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (36 bp):
ATGACTTTTGGGTCAACAGGGAGTAAAATGAGCATA
Found at i:102207 original size:36 final size:36
Alignment explanation
Indices: 102151--102354 Score: 164
Period size: 36 Copynumber: 5.7 Consensus size: 36
102141 CAGTTCAAAA
* * *
102151 GAAG-GCATATGTCTCAGTTAGAGCGTATTGCT-AT
1 GAAGTGCATACGTCTCGGTTAGAGCGTAATGCTAAT
* * ** * *
102185 GATGTTGCATATGTCTCGGTTAGAGTATATTG-TTAT
1 GAAG-TGCATACGTCTCGGTTAGAGCGTAATGCTAAT
* * * * * *
102221 GATGTTTCATACATCTCAGTTAGAGTGTAATGCTAAG
1 GAAG-TGCATACGTCTCGGTTAGAGCGTAATGCTAAT
*
102258 GAAGTGCATACGTCTCGGTTAGA-CAGTAATGCTAAA
1 GAAGTGCATACGTCTCGGTTAGAGC-GTAATGCTAAT
* * *
102294 GAAGTGCATACATCTCGGTTAGAGCGTAATGCCAAG
1 GAAGTGCATACGTCTCGGTTAGAGCGTAATGCTAAT
* *
102330 GAAGTGCTTACATCTCGGTTAGAGC
1 GAAGTGCATACGTCTCGGTTAGAGC
102355 ATAAGGCCAT
Statistics
Matches: 142, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
34 3 0.02
35 1 0.01
36 132 0.93
37 6 0.04
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (36 bp):
GAAGTGCATACGTCTCGGTTAGAGCGTAATGCTAAT
Found at i:102279 original size:72 final size:70
Alignment explanation
Indices: 102148--102353 Score: 202
Period size: 72 Copynumber: 2.9 Consensus size: 70
102138 GAACAGTTCA
** * * * *
102148 AAAGAAG-GCATATGTCTCAGTTAGAGCGTATTGCT-ATGATGTTGCATATGTCTCGGTTAGAGT
1 AAAGAAGTGCATACATCTCAGTTAGAGCGTAATGCTAAGGAAG-TGCATACGTCTCGGTTAGAGT
102211 ATATTG-T
65 A-A-TGCT
* * * * *
102218 TATGATGTTTCATACATCTCAGTTAGAGTGTAATGCTAAGGAAGTGCATACGTCTCGGTTAGACA
1 AAAGAAG-TGCATACATCTCAGTTAGAGCGTAATGCTAAGGAAGTGCATACGTCTCGGTTAG--A
102283 GTAATGCT
63 GTAATGCT
* * * *
102291 AAAGAAGTGCATACATCTCGGTTAGAGCGTAATGCCAAGGAAGTGCTTACATCTCGGTTAGAG
1 AAAGAAGTGCATACATCTCAGTTAGAGCGTAATGCTAAGGAAGTGCATACGTCTCGGTTAGAG
102354 CATAAGGCCA
Statistics
Matches: 110, Mismatches: 20, Indels: 12
0.77 0.14 0.08
Matches are distributed among these distances:
70 6 0.05
72 90 0.82
73 10 0.09
74 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (70 bp):
AAAGAAGTGCATACATCTCAGTTAGAGCGTAATGCTAAGGAAGTGCATACGTCTCGGTTAGAGTA
ATGCT
Found at i:103428 original size:26 final size:26
Alignment explanation
Indices: 103399--103451 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
103389 AACATGGAAC
103399 ATAAGAAATTAACATCAAAATATAAA
1 ATAAGAAATTAACATCAAAATATAAA
* *
103425 ATAAGAAATTAACATTAGAATATAAA
1 ATAAGAAATTAACATCAAAATATAAA
103451 A
1 A
103452 CAAATAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.25
Consensus pattern (26 bp):
ATAAGAAATTAACATCAAAATATAAA
Found at i:103840 original size:51 final size:50
Alignment explanation
Indices: 103759--103913 Score: 238
Period size: 51 Copynumber: 3.1 Consensus size: 50
103749 AAATACAAAA
*
103759 AAAATATATATACAAGTATAATTCAATGATAAAAGAATAAGCGGTACTATG
1 AAAAT-TATATACAAGTATAATTCATTGATAAAAGAATAAGCGGTACTATG
*
103810 AAAATTATATACAAAGTATAATTCATTGATAAAAGAATAAGCAGTACTATG
1 AAAATTATATAC-AAGTATAATTCATTGATAAAAGAATAAGCGGTACTATG
* * * *
103861 AAAATTATATATAATTATAATTCATTGATAAAAGAATAAGCGTTAGTATG
1 AAAATTATATACAAGTATAATTCATTGATAAAAGAATAAGCGGTACTATG
103911 AAA
1 AAA
103914 TAAACCTGTG
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
50 44 0.46
51 52 0.54
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.30
Consensus pattern (50 bp):
AAAATTATATACAAGTATAATTCATTGATAAAAGAATAAGCGGTACTATG
Found at i:107666 original size:21 final size:19
Alignment explanation
Indices: 107625--107668 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
107615 CTTTTATTCG
*
107625 TTTTTTTTAAAATTAAACC
1 TTTTTTTAAAAATTAAACC
*
107644 TTTTGTTTAAAAATTTAATCC
1 TTTT-TTTAAAAA-TTAAACC
107665 TTTT
1 TTTT
107669 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTTTTAAAAATTAAACC
Found at i:116165 original size:21 final size:21
Alignment explanation
Indices: 116141--116182 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
116131 TGCCCTTTTT
116141 TATGTTTTCTTAAAACTTAAA
1 TATGTTTTCTTAAAACTTAAA
116162 TATGTTTTCTTAAAACTTAAA
1 TATGTTTTCTTAAAACTTAAA
116183 CCCTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (21 bp):
TATGTTTTCTTAAAACTTAAA
Found at i:116263 original size:22 final size:22
Alignment explanation
Indices: 116171--116264 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 22
116161 ATATGTTTTC
116171 TTAAAACTTAAACCCTTTTATTT
1 TTAAAA-TTAAACCCTTTTATTT
* *
116194 TT-TAATT-AATCCTTTTATTCGTTTT
1 TTAAAATTAAACCCTTTTA-----TTT
*
116219 TTTAAATTAAACCCTTTTA-TT
1 TTAAAATTAAACCCTTTTATTT
* *
116240 TTAAAATTTAATCCTTTTATTT
1 TTAAAATTAAACCCTTTTATTT
116262 TTA
1 TTA
116265 TTTCTTTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
20 9 0.16
21 20 0.36
22 7 0.12
23 2 0.04
25 5 0.09
26 4 0.07
27 9 0.16
ACGTcount: A:0.30, C:0.13, G:0.01, T:0.56
Consensus pattern (22 bp):
TTAAAATTAAACCCTTTTATTT
Found at i:116733 original size:17 final size:18
Alignment explanation
Indices: 116711--116774 Score: 87
Period size: 17 Copynumber: 3.6 Consensus size: 18
116701 TTTAAACTGG
116711 TTTAAATTTATC-TTAAA
1 TTTAAATTTATCTTTAAA
116728 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTATC--TTTAAA
*
116748 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATCTTTAAA
116765 TTTAAATTTA
1 TTTAAATTTA
116775 ATCAAATTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
17 27 0.64
19 1 0.02
20 14 0.33
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATCTTTAAA
Found at i:117581 original size:22 final size:22
Alignment explanation
Indices: 117549--117598 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
117539 TAATAATAGG
* *
117549 ATAATATTAATGACATTAATTA
1 ATAATAGTAATGACAATAATTA
* *
117571 ATAATAGTAATTATAATAATTA
1 ATAATAGTAATGACAATAATTA
117593 ATAATA
1 ATAATA
117599 ACAATAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAATAGTAATGACAATAATTA
Found at i:117608 original size:22 final size:22
Alignment explanation
Indices: 117565--117608 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
117555 TTAATGACAT
** *
117565 TAATTAATAATAGTAATTATAA
1 TAATTAATAATAACAATAATAA
117587 TAATTAATAATAACAATAATAA
1 TAATTAATAATAACAATAATAA
117609 CTTTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATTAATAATAACAATAATAA
Found at i:118820 original size:29 final size:29
Alignment explanation
Indices: 118755--118955 Score: 165
Period size: 29 Copynumber: 6.8 Consensus size: 29
118745 AAAGGTCCCT
* *
118755 AAACTATCCAAAAATTCCATTTTTGACCTC
1 AAACT-TCCAAAAATTACATTTTTAACCTC
* *
118785 AACACTTCCAAAAATTATATTTTTAACCTT
1 AA-ACTTCCAAAAATTACATTTTTAACCTC
* * *
118815 GAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTACATTTTTAA-CCTC
* *
118845 AAACTTCCAAAAAATACATTTTTACCCTC
1 AAACTTCCAAAAATTACATTTTTAACCTC
* * * * *
118874 GAACCTCCAAAAATTCCATTTTTTACCCC
1 AAACTTCCAAAAATTACATTTTTAACCTC
*
118903 AAAACTTTCAAAAATTACCA-TTTT-ACCTCC
1 -AAACTTCCAAAAATTA-CATTTTTAACCT-C
* *
118933 GAA-TGTCCAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTACATTTTT
118956 GATCTCGATT
Statistics
Matches: 136, Mismatches: 28, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
28 3 0.02
29 64 0.47
30 64 0.47
31 5 0.04
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTAACCTC
Found at i:118833 original size:59 final size:59
Alignment explanation
Indices: 118756--118957 Score: 234
Period size: 59 Copynumber: 3.4 Consensus size: 59
118746 AAGGTCCCTA
* * *
118756 AACTATCCAAAAATTCCATTTTTGACCTCAACACTTCCAAAAATTATATTTTTAACCTTG
1 AACTATCCAAAAATTCCATTTTTGACC-CAAAACTTCCAAAAATTACATTTTTAACCTCG
* * *
118816 AACT-TCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAAATACATTTTTACCCTCG
1 AACTATCCAAAAATTCCATTTTTGACCC-AAAACTTCCAAAAATTACATTTTTAACCTCG
* * *
118875 AAC-CTCCAAAAATTCCATTTTTTACCCCAAAACTTTCAAAAATTACCA-TTTT-ACCTCCG
1 AACTATCCAAAAATTCCATTTTTGA-CCCAAAACTTCCAAAAATTA-CATTTTTAACCT-CG
*
118934 AA-TGTCCAAAAATTCCATTTTTGA
1 AACTATCCAAAAATTCCATTTTTGA
118958 TCTCGATTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
58 4 0.03
59 111 0.90
60 9 0.07
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
AACTATCCAAAAATTCCATTTTTGACCCAAAACTTCCAAAAATTACATTTTTAACCTCG
Found at i:118975 original size:59 final size:59
Alignment explanation
Indices: 118864--119072 Score: 217
Period size: 59 Copynumber: 3.5 Consensus size: 59
118854 AAAAATACAT
* ** * *
118864 TTTTACCCTCGAACCTCCAAAAATTCCATTTTTTA-CCCCAAAACTTT-C-AAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCC---ATTTTCCTAAAAATTACCA
* * *
118923 TTTTACCTCCGAATGTCCAAAAATTCCATTTTTGATCTCGATTTTCCTAAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCCATTTTCCTAAAAATTACCA
* ** * * *
118982 TTTTACCCCCGAATGTCCAAAAATTCTATTTTTGATCCCCATTTTTTTAAAAGTTATCG
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCCATTTTCCTAAAAATTACCA
* * *
119041 TTTTACCCCCGAGTGTCTAAAAAATCCATTTT
1 TTTTACCCCCGAATGTCCAAAAATTCCATTTT
119073 CTAACATCGA
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
57 4 0.03
58 1 0.01
59 119 0.94
60 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (59 bp):
TTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCCATTTTCCTAAAAATTACCA
Found at i:118975 original size:118 final size:118
Alignment explanation
Indices: 118761--119022 Score: 282
Period size: 118 Copynumber: 2.2 Consensus size: 118
118751 CCCTAAACTA
* * * *
118761 TCCAAAAATTCCATTTTTGACCTCAACACTTCCAAAAATTATATTTTTAACCTTGAACTTCCAAA
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTAACCTCGAACTTCCAAA
*
118826 AATTCCATTTTTAACCCTAAAACTTCCAAAAAATA-CATTTTTACCCTCGAACC
66 AATTCCATTTTTAACCCTAAAACTTCCAAAAAATACCA-TTTTACCCCCGAACC
* *
118879 TCCAAAAATTCCATTTTTTACCCCAAAACTTTCAAAAATTACCA-TTTT-ACCTCCGAA-TGTCC
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTA-CATTTTTAACCT-CGAACT-TCC
* * ** ** * **
118941 AAAAATTCCATTTTTGA-TCTCGATTTTCCTAAAAATTACCATTTTACCCCCGAATG
63 AAAAATTCCATTTTTAACCCTAAAACTTCC-AAAAAATACCATTTTACCCCCGAACC
*
118997 TCCAAAAATTCTATTTTTGATCCCCA
1 TCCAAAAATTCCATTTTTGA-CCCCA
119023 TTTTTTTAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
117 12 0.10
118 100 0.83
119 8 0.07
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (118 bp):
TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTAACCTCGAACTTCCAAA
AATTCCATTTTTAACCCTAAAACTTCCAAAAAATACCATTTTACCCCCGAACC
Found at i:119006 original size:29 final size:30
Alignment explanation
Indices: 118820--119150 Score: 122
Period size: 29 Copynumber: 11.3 Consensus size: 30
118810 ACCTTGAACT
***
118820 TCCAAAAATT-CCATTTTTAACCCTAAAACT-
1 TCCAAAAATTACCATTTTT-ACCCCCGAA-TG
* * **
118850 TCCAAAAAATA-CATTTTTACCCTCGAACC
1 TCCAAAAATTACCATTTTTACCCCCGAATG
**
118879 TCCAAAAATT-CCATTTTTTACCCCAAAACT-
1 TCCAAAAATTACCA-TTTTTACCCCCGAA-TG
* *
118909 TTCAAAAATTACCA-TTTTACCTCCGAATG
1 TCCAAAAATTACCATTTTTACCCCCGAATG
* * * *
118938 TCCAAAAATT-CCATTTTTGA-TCTCGATTT
1 TCCAAAAATTACCATTTTT-ACCCCCGAATG
118967 TCCTAAAAATTACCA-TTTTACCCCCGAATG
1 TCC-AAAAATTACCATTTTTACCCCCGAATG
* * * *
118997 TCCAAAAATT-CTATTTTTGATCCCC-ATTTT
1 TCCAAAAATTACCATTTTT-ACCCCCGA-ATG
** * * * *
119027 TTTAAAAGTTATC-GTTTTACCCCCGAGTG
1 TCCAAAAATTACCATTTTTACCCCCGAATG
* * * **
119056 TCTAAAAAAT-CCATTTTCTAACATCGAACT-
1 TCCAAAAATTACCATTTT-TACCCCCGAA-TG
* * * *
119086 TCCCAAAATTACTA-TTTTACCCTCGAGA-A
1 TCCAAAAATTACCATTTTTACCCCCGA-ATG
*
119115 TCC-AAAATTACCA-TTTTACCCCCGAATA
1 TCCAAAAATTACCATTTTTACCCCCGAATG
119143 TCCAAAAA
1 TCCAAAAA
119151 GTCTCAATTT
Statistics
Matches: 223, Mismatches: 53, Indels: 51
0.68 0.16 0.16
Matches are distributed among these distances:
27 1 0.00
28 31 0.14
29 91 0.41
30 91 0.41
31 9 0.04
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTTACCCCCGAATG
Found at i:119123 original size:28 final size:28
Alignment explanation
Indices: 119088--119149 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
119078 ATCGAACTTC
* *
119088 CCAAAATTACTATTTTACCCTCGAGA-AT
1 CCAAAATTACCATTTTACCCCCGA-ATAT
119116 CCAAAATTACCATTTTACCCCCGAATAT
1 CCAAAATTACCATTTTACCCCCGAATAT
119144 CCAAAA
1 CCAAAA
119150 AGTCTCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.39, C:0.29, G:0.05, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAATAT
Found at i:121365 original size:33 final size:33
Alignment explanation
Indices: 121323--121390 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
121313 CAGTAGAATT
121323 ATAGAGTAGGAGAGAGGTTGGCTACTGACTTGC
1 ATAGAGTAGGAGAGAGGTTGGCTACTGACTTGC
121356 ATAGAGTAGGAGAGAGGTTGGCTACTGACTTGC
1 ATAGAGTAGGAGAGAGGTTGGCTACTGACTTGC
121389 AT
1 AT
121391 TGTATCGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.12, G:0.35, T:0.25
Consensus pattern (33 bp):
ATAGAGTAGGAGAGAGGTTGGCTACTGACTTGC
Found at i:121556 original size:21 final size:21
Alignment explanation
Indices: 121506--121561 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
121496 CTAGTGATTT
*
121506 TAGTATCGGTAGAAGCATACC
1 TAGTATCAGTAGAAGCATACC
* * *
121527 TTGTTTCAGTAGAAGTA-ACTC
1 TAGTATCAGTAGAAGCATAC-C
121548 TAGTATCAGTAGAA
1 TAGTATCAGTAGAA
121562 CCATCTCAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (21 bp):
TAGTATCAGTAGAAGCATACC
Found at i:125482 original size:28 final size:28
Alignment explanation
Indices: 125451--125530 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
125441 TTAGGCAAAT
*
125451 CCTTGTGGTAATTTTCGTAAAGAACAAC
1 CCTTGTGGCAATTTTCGTAAAGAACAAC
* *
125479 CCTTATGGCAATTTTTGTAAAGAACAAC
1 CCTTGTGGCAATTTTCGTAAAGAACAAC
* *
125507 CATTGTGGCGATTTTCGTAAAGAA
1 CCTTGTGGCAATTTTCGTAAAGAA
125531 AGCCTTTGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (28 bp):
CCTTGTGGCAATTTTCGTAAAGAACAAC
Found at i:126357 original size:17 final size:18
Alignment explanation
Indices: 126337--126371 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
126327 CCTAGTAAAT
126337 TTAGG-TTTAGTTATTTC
1 TTAGGTTTTAGTTATTTC
126354 TTAGGTTTTAGTTATTTC
1 TTAGGTTTTAGTTATTTC
126372 ATTTTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (18 bp):
TTAGGTTTTAGTTATTTC
Found at i:126961 original size:3 final size:3
Alignment explanation
Indices: 126953--126978 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
126943 TTTTAGCATA
126953 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
126979 AAAATCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:130235 original size:20 final size:20
Alignment explanation
Indices: 130194--130235 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
130184 CATCTTTAGG
*
130194 TTTTTTAAAATTATCATTAAT
1 TTTTTTAAAAATATCA-TAAT
130215 TTTTTTAAAAAATATCA-AAT
1 TTTTTT-AAAAATATCATAAT
130235 T
1 T
130236 GATCTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 9 0.47
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTTAAAAATATCATAAT
Found at i:133584 original size:26 final size:26
Alignment explanation
Indices: 133546--133598 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
133536 AGAGATAAGC
* *
133546 GGTTAGAACATACTGAGTGCAAGTAT
1 GGTTAGAAAATACGGAGTGCAAGTAT
*
133572 GGTTAGAAAATACGGAGTGCATGTAT
1 GGTTAGAAAATACGGAGTGCAAGTAT
133598 G
1 G
133599 CGTTTTTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.26
Consensus pattern (26 bp):
GGTTAGAAAATACGGAGTGCAAGTAT
Found at i:148036 original size:39 final size:39
Alignment explanation
Indices: 147814--148353 Score: 275
Period size: 39 Copynumber: 13.8 Consensus size: 39
147804 AATGGCGTAT
* *
147814 CTTCAATCTACCCTC-TGA-TAGGGTAAGAGATTGGCTGG
1 CTTCAATCTGCCC-CATGATTAGGGTAAGAGATTGGATGG
* * * * ** *
147852 TCTTTAATTTGTCCCATGGTCGGGGTAAGAGATT-GACGTGT
1 -CTTCAATCTGCCCCATGATTAGGGTAAGAGATTGGA--TGG
* * * *
147893 CTTCAATCTACCCTC-TAATTAGGGTAAAAAATTGGAT-G
1 CTTCAATCTGCCC-CATGATTAGGGTAAGAGATTGGATGG
* * * *
147931 TTTCAAT-TGCTCCATGA-TCGGAGTAAAAGATTGGATGATG
1 CTTCAATCTGCCCCATGATTAGG-GTAAGAGATTGGATG--G
* * * ** *
147971 GTTGTAATCTGCCCCATAATCGGGGTAAGAGATTGGGTGG
1 CTT-CAATCTGCCCCATGATTAGGGTAAGAGATTGGATGG
* *
148011 CTTCAATTTGCCCCATGATTAGGGTAAGAGATTGGATGAT
1 CTTCAATCTGCCCCATGATTAGGGTAAGAGATTGGATG-G
* **
148051 TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
1 CTTCAATCTGCCCCATGATTAGGGTAAGAGATTGGATGG
* * * *
148090 TTTCAATCTGCCTCC-TGATTGGGGTAATAGATTGGAGTGT
1 CTTCAATCTGCC-CCATGATTAGGGTAAGAGATTGGA-TGG
*** * *
148130 CTTCAATCTGCCTTTTAATTAAGGTAA-AGATTGGAT-G
1 CTTCAATCTGCCCCATGATTAGGGTAAGAGATTGGATGG
* * ** *
148167 CTTTCAATTTGCCCCATGA-TCGGAGTAAGAGATTGTCTGT
1 C-TTCAATCTGCCCCATGATTAGG-GTAAGAGATTGGATGG
* * **
148207 CTTCAATTTGCCCTC-TAATTAGGGTCAA-AGATTAAAT-G
1 CTTCAATCTGCCC-CATGATTAGGGT-AAGAGATTGGATGG
* * ** ** **
148245 TTTCAATTTGCCCCATGATCGGGGTAAGAGATTGCCTAT
1 CTTCAATCTGCCCCATGATTAGGGTAAGAGATTGGATGG
*
148284 CTTCAATCTGCCCTC-TTATTAGGGTAAGAGATTTGGAT-G
1 CTTCAATCTGCCC-CATGATTAGGGTAAGAGA-TTGGATGG
* * **
148323 CTTCGATCTGCCCTATGATCGGGGTAAGAGA
1 CTTCAATCTGCCCCATGATTAGGGTAAGAGA
148354 CCTGTAAAAT
Statistics
Matches: 376, Mismatches: 94, Indels: 62
0.71 0.18 0.12
Matches are distributed among these distances:
36 4 0.01
37 24 0.06
38 49 0.13
39 159 0.42
40 109 0.29
41 8 0.02
42 21 0.06
43 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
CTTCAATCTGCCCCATGATTAGGGTAAGAGATTGGATGG
Found at i:148249 original size:77 final size:77
Alignment explanation
Indices: 147813--148353 Score: 470
Period size: 79 Copynumber: 6.9 Consensus size: 77
147803 GAATGGCGTA
* * * * * *
147813 TCTTCAATCTACCCTCTGA-TAGGGTAAGAGATTGGCTGGTCTTTAATTTGTCCCATGGTCGGGG
1 TCTTCAATCTGCCCTCTAATTAGGGTAAGAGATTGGAT-GT-TTCAATTTGCCCCATGATCGGGG
147877 TAAGAGATTGACGTG
64 TAAGAGATTGAC-TG
* * * * *
147892 TCTTCAATCTACCCTCTAATTAGGGTAAAAAATTGGATGTTTCAA-TTGCTCCATGATCGGAGTA
1 TCTTCAATCTGCCCTCTAATTAGGGTAAGAGATTGGATGTTTCAATTTGCCCCATGATCGGGGTA
*
147956 AAAGATTGGA-TG
66 AGAGATT-GACTG
* * ** * * **
147968 ATGGTTGTAATCTGCCC-CATAATCGGGGTAAGAGATTGGGTGGCTTCAATTTGCCCCATGATTA
1 -T-CTT-CAATCTGCCCTC-TAATTAGGGTAAGAGATTGGAT-GTTTCAATTTGCCCCATGATCG
148032 GGGTAAGAGATTGGA-TG
61 GGGTAAGAGATT-GACTG
* * ** * *
148049 ATTTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGGTTTCAATCTGCCTCC-TGATTGG
1 -TCTTCAATCTGCCCTC-TAATTAGGGTAAGAGATTGGAT-GTTTCAATTTGCC-CCATGATCGG
* *
148112 GGTAATAGATTGGAGTG
62 GGTAAGAGATT-GACTG
* * * *
148129 TCTTCAATCTGCCTTTTAATTAAGGTAA-AGATTGGATGCTTTCAATTTGCCCCATGATCGGAGT
1 TCTTCAATCTGCCCTCTAATTAGGGTAAGAGATTGGATG-TTTCAATTTGCCCCATGATCGGGGT
*
148193 AAGAGATTGTCTG
65 AAGAGATTGACTG
* **
148206 TCTTCAATTTGCCCTCTAATTAGGGTCAA-AGATTAAATGTTTCAATTTGCCCCATGATCGGGGT
1 TCTTCAATCTGCCCTCTAATTAGGGT-AAGAGATTGGATGTTTCAATTTGCCCCATGATCGGGGT
* *
148270 AAGAGATTGCCTA
65 AAGAGATTGACTG
* * * * *
148283 TCTTCAATCTGCCCTCTTATTAGGGTAAGAGATTTGGATGCTTCGATCTGCCCTATGATCGGGGT
1 TCTTCAATCTGCCCTCTAATTAGGGTAAGAGA-TTGGATGTTTCAATTTGCCCCATGATCGGGGT
148348 AAGAGA
65 AAGAGA
148354 CCTGTAAAAT
Statistics
Matches: 384, Mismatches: 62, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
76 4 0.01
77 112 0.29
78 86 0.22
79 127 0.33
80 27 0.07
81 28 0.07
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (77 bp):
TCTTCAATCTGCCCTCTAATTAGGGTAAGAGATTGGATGTTTCAATTTGCCCCATGATCGGGGTA
AGAGATTGACTG
Found at i:158433 original size:24 final size:25
Alignment explanation
Indices: 158406--158452 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
158396 AACAATTTGT
*
158406 ATTAA-ATTAAAAAGAGAAAAAAAA
1 ATTAAGATTAAAAACAGAAAAAAAA
* *
158430 ATTAAGGTTAAAAACATAAAAAA
1 ATTAAGATTAAAAACAGAAAAAA
158453 GGAGAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (25 bp):
ATTAAGATTAAAAACAGAAAAAAAA
Found at i:159364 original size:23 final size:22
Alignment explanation
Indices: 159328--159372 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
159318 TTTCTAAATG
*
159328 ATAATAAAATAATATATGTATA
1 ATAAAAAAATAATATATGTATA
*
159350 ATAAAAAATATAATATATTTATA
1 ATAAAAAA-ATAATATATGTATA
159373 TATCAAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAAAAAAATAATATATGTATA
Found at i:160222 original size:17 final size:18
Alignment explanation
Indices: 160191--160229 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
160181 CATAATTTTA
160191 AAAGTAAAAACTAAAAAT
1 AAAGTAAAAACTAAAAAT
*
160209 AAAGT-AAAATTAAAAAT
1 AAAGTAAAAACTAAAAAT
160226 AAAG
1 AAAG
160230 AGAGTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (18 bp):
AAAGTAAAAACTAAAAAT
Found at i:160731 original size:21 final size:23
Alignment explanation
Indices: 160692--160738 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
160682 TTTAATTAAA
**
160692 TAAATTTAATTAATTG-AAATTT
1 TAAATTTAATTAAAAGAAAATTT
160714 TAAA-TTAATTAAAAGAAAATTT
1 TAAATTTAATTAAAAGAAAATTT
160736 TAA
1 TAA
160739 TCTGGTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAATTTAATTAAAAGAAAATTT
Found at i:163042 original size:209 final size:208
Alignment explanation
Indices: 162498--163163 Score: 920
Period size: 209 Copynumber: 3.2 Consensus size: 208
162488 TGAACTGGTT
* * * * *
162498 ATCTTCCTGATGAGATA-TAGAGAAGTATACCAACTCGACGAAATCAGGCTCAAAGTAAGCAAAT
1 ATCTTCCTGATGAGATACT-GAGAAGTAGACCAAATCAACGAAACCAAGCTCAAAGTAAGCAAAT
** * *
162562 CTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTC
65 CTTCGAACC-CAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAGCGATTACCTTC
* * * * * *
162627 CTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGATTAAA
129 CTGATGAGATACAGAGAAGTGAACCAGATCCGCCTTCCTGATGAGATACAAAGAAGCGGATTAAA
162692 ACAAGTGATGCGGTC
194 ACAAGTGATGCGGTC
* * *
162707 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT---C---A--ATGCTCAAAGTGAGCAAATC
1 ATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAACGAAACCAAGCTCAAAGTAAGCAAATC
* *
162764 TTCGAACCCTTGTTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAGCGATTACCTTCC
66 TTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAGCGATTACCTTCC
* * * *
162829 TGATGAGATACAGAGAAGTGAACCAGATCCGCCTTCCTGATGAGACACAAAGAAGTGGGTCAAAA
130 TGATGAGATACAGAGAAGTGAACCAGATCCGCCTTCCTGATGAGATACAAAGAAGCGGATTAAAA
*
162894 CAAGTGATGCGATC
195 CAAGTGATGCGGTC
* * *
162908 ATC-TCTCTGATGAGATACCGAGAAGTAGACCAAATCAATGAAACCAAGCTTAAAGTAAGCAAAT
1 ATCTTC-CTGATGAGATACTGAGAAGTAGACCAAATCAACGAAACCAAGCTCAAAGTAAGCAAAT
*
162972 CTTCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGATTACCTTC
65 CTTCGAAC-CCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAGCGATTACCTTC
* *
163037 CTGATGAGATACAGAGAAGTGAACCAGATCCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAA
129 CTGATGAGATACAGAGAAGTGAACCAGATCCGCCTTCCTGATGAGATACAAAGAAGCGGATTAAA
163102 ACAAGTGATGCGGTC
194 ACAAGTGATGCGGTC
* *
163117 ATCTTCCTGATGAGATACTGAGAAGTAGACTAAATCAACGACACCAA
1 ATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAACGAAACCAA
163164 ACCATTGAAG
Statistics
Matches: 402, Mismatches: 42, Indels: 26
0.86 0.09 0.06
Matches are distributed among these distances:
200 3 0.01
201 173 0.43
203 1 0.00
206 1 0.00
207 1 0.00
209 218 0.54
210 5 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (208 bp):
ATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAACGAAACCAAGCTCAAAGTAAGCAAATC
TTCGAACCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAGCGATTACCTTCCT
GATGAGATACAGAGAAGTGAACCAGATCCGCCTTCCTGATGAGATACAAAGAAGCGGATTAAAAC
AAGTGATGCGGTC
Found at i:163480 original size:17 final size:17
Alignment explanation
Indices: 163457--163567 Score: 116
Period size: 17 Copynumber: 6.4 Consensus size: 17
163447 CTAAACCCAT
163457 TTTAAATTTATTTT-AA
1 TTTAAATTTATTTTAAA
163473 TATTAAATTTATTTTAAA
1 T-TTAAATTTATTTTAAA
****
163491 TTTAAATTTGAAAACAAA
1 TTTAAATTT-ATTTTAAA
* *
163509 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
163526 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
163544 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
163561 TTTAAAT
1 TTTAAAT
163568 AAATGAAAGT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
16 1 0.01
17 46 0.59
18 31 0.40
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:163494 original size:6 final size:6
Alignment explanation
Indices: 163457--163567 Score: 83
Period size: 6 Copynumber: 19.2 Consensus size: 6
163447 CTAAACCCAT
* *
163457 TTTAAA TTT--A TTTTAA TATTAAA TTT-AT TTTAAA TTTAAA TTTGAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
** * *
163504 -ACAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTATA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
163550 ATT--A TTCTAAA TTTAAA T
1 TTTAAA TT-TAAA TTTAAA T
163568 AAATGAAAGT
Statistics
Matches: 82, Mismatches: 13, Indels: 20
0.71 0.11 0.17
Matches are distributed among these distances:
4 6 0.07
5 13 0.16
6 52 0.63
7 11 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:163518 original size:35 final size:35
Alignment explanation
Indices: 163475--163567 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 35
163465 TATTTTAATA
163475 TTAAATTTATTTTAAATTTAAATTTGA-AAACAAAT
1 TTAAATTTATTTTAAATTTAAATTT-ATAAACAAAT
* * ***
163510 TTAAATTTAATTTAAGTTTAAATTTATATTTAAAT
1 TTAAATTTATTTTAAATTTAAATTTATAAACAAAT
* *
163545 TTAAAATTATTCTAAATTTAAAT
1 TTAAATTTATTTTAAATTTAAAT
163568 AAATGAAAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
34 1 0.02
35 47 0.98
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (35 bp):
TTAAATTTATTTTAAATTTAAATTTATAAACAAAT
Found at i:164305 original size:3 final size:3
Alignment explanation
Indices: 164297--164323 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
164287 TTAATAGCAC
164297 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
164324 AGGAAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:165455 original size:30 final size:28
Alignment explanation
Indices: 165418--166031 Score: 190
Period size: 29 Copynumber: 20.9 Consensus size: 28
165408 GAAGACCCCC
*
165418 AAACTCTTCCAAACATTACATTTTAACCT
1 AAACTCTT-CAAAAATTACATTTTAACCT
* *
165447 ATAACTCTTTAAAAATCACATTTTAACCCCT
1 A-AACTCTTCAAAAATTACATTTTAA--CCT
* *
165478 AAACTTTTCAAAAATTACATTTTGACCT
1 AAACTCTTCAAAAATTACATTTTAACCT
* * * * *
165506 CGAATTCTTCAAAAATCACATTTTTGCACCC
1 -AAACTCTTCAAAAATTACA-TTTT-AACCT
* * *
165537 AAACT-TCACAAAAATCACATTTTTATCCTT
1 AAACTCT-TCAAAAATTACA-TTTTAACC-T
* * * *
165567 GAACT-TCCAAAAATTACATTTTTGACCCC
1 AAACTCTTCAAAAATTACA-TTTT-AACCT
** *
165596 AAAC-CTTCAAAAAAGCACATTTTTATCCT
1 AAACTCTTC-AAAAATTACA-TTTTAACCT
* * *
165625 CGAACT-TTCAAAAATTCCATTTTAACCCC
1 -AAACTCTTCAAAAATTACATTTTAA-CCT
* *
165654 AAAATCTTCAAAAATCACCATTTTACACCT
1 AAACTCTTCAAAAATTA-CATTTTA-ACCT
* *
165684 AAACT-TTCAAAAATTCCATTTTTGACCCT
1 AAACTCTTCAAAAATTACA-TTTT-AACCT
* * *
165713 AAAATCTTTAAAAATTACCATTTTACCCCT
1 AAACTCTTCAAAAATTA-CATTTTA-ACCT
* * *
165743 AAACT-TCCAAAAA-TACCATTTTTTACCCC
1 AAACTCTTCAAAAATTA-CA--TTTTAACCT
* * * *
165772 AAATTTTTCAAAAATCACCATTTTACCCT
1 AAACTCTTCAAAAATTA-CATTTTAACCT
* *
165801 TAAC-CTTCCAAAAA-TACCATTTTTGACCT
1 AAACTCTT-CAAAAATTA-CA-TTTTAACCT
* *
165830 CAAACT-TTCCAAAAATTACCATTTTACCCC
1 -AAACTCTT-CAAAAATTA-CATTTTAACCT
*
165860 CAAC-CTTCCAAAAA-TACCATTTTAACCTT
1 AAACTCTT-CAAAAATTA-CATTTTAACC-T
* *
165889 AAACT-TTCCAAAAATTATCATTTTACCCCC
1 AAACTCTT-CAAAAATTA-CATTTTA-ACCT
165919 AAAC-C-TCTAAAAA-TACCATTTTTAACCT
1 AAACTCTTC-AAAAATTA-CA-TTTTAACCT
* *
165947 CAAA-TTTTCCAAAAATTACCATTTTACCCTT
1 -AAACTCTT-CAAAAATTA-CATTTTAACC-T
*
165978 GAA-T-TTCCAAAAATT-CTATTTTTAACCT
1 AAACTCTT-CAAAAATTAC-A-TTTTAACCT
*
166006 CGAACT-TTCCAAAAATTACCATTTTA
1 -AAACTCTT-CAAAAATTA-CATTTTA
166032 CCCTCGAATT
Statistics
Matches: 454, Mismatches: 80, Indels: 101
0.71 0.13 0.16
Matches are distributed among these distances:
27 1 0.00
28 45 0.10
29 190 0.42
30 188 0.41
31 29 0.06
32 1 0.00
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (28 bp):
AAACTCTTCAAAAATTACATTTTAACCT
Found at i:165520 original size:59 final size:59
Alignment explanation
Indices: 165414--166049 Score: 381
Period size: 59 Copynumber: 10.8 Consensus size: 59
165404 CCTAGAAGAC
* * ** *
165414 CCCCAAACTCTTCCAAACATTA-CATTTTAACCTATAACTCTT-TAAAAATCACA-TTTTAA
1 CCCCAAACT-TTTCAAAAATTACCATTTT-ACCTCGAA-TCTTCCAAAAATCACATTTTTAA
*
165473 CCCCTAAACTTTTCAAAAATTA-CATTTTGACCTCGAATTCTT-CAAAAATCACATTTTT-G
1 CCCC-AAACTTTTCAAAAATTACCATTTT-ACCTCGAA-TCTTCCAAAAATCACATTTTTAA
** * * * *
165532 CACCCAAACTTCACAAAAATCA-CATTTTTATCCTTGAA-CTTCCAAAAATTACATTTTTGA
1 C-CCCAAACTTTTCAAAAATTACCA-TTTTA-CCTCGAATCTTCCAAAAATCACATTTTTAA
* *
165592 CCCCAAAC-CTTCAAAAA--AGCACATTTTTATCCTCGAA-CTTTCAAAAATTC-CA-TTTTAA
1 CCCCAAACTTTTCAAAAATTA-C-CA-TTTTA-CCTCGAATCTTCCAAAAA-TCACATTTTTAA
* * * * * * *
165650 CCCCAAAATCTTCAAAAATCACCATTTTACAC-CTAAACTTTCAAAAATTC-CATTTTTGA
1 CCCCAAACTTTTCAAAAATTACCATTTTAC-CTCGAATCTTCCAAAAA-TCACATTTTTAA
* * * * * *
165709 CCCTAAAATCTTT-AAAAATTACCATTTTACCCCTAAACTTCCAAAAAT-ACCATTTTTTA
1 CCCCAAACT-TTTCAAAAATTACCATTTTACCTCGAATCTTCCAAAAATCA-CATTTTTAA
* * * * *
165768 CCCCAAATTTTTCAAAAATCACCATTTTACC-CTTAACCTTCCAAAAAT-ACCATTTTTGA
1 CCCCAAACTTTTCAAAAATTACCATTTTACCTC-GAATCTTCCAAAAATCA-CATTTTTAA
* * * * *
165827 CCTCAAACTTTCCAAAAATTACCATTTTACCCCCAACCTTCCAAAAAT-ACCA-TTTTAA
1 CCCCAAACTTTTCAAAAATTACCATTTTACCTCGAATCTTCCAAAAATCA-CATTTTTAA
** * * * * * * *
165885 CCTTAAACTTTCCAAAAATTATCATTTTACCCCCAAACCTCTAAAAAT-ACCATTTTTAA
1 CCCCAAACTTTTCAAAAATTACCATTTTACCTCGAATCTTCCAAAAATCA-CATTTTTAA
* * *
165944 CCTCAAA-TTTTCCAAAAATTACCATTTTACCCTTGAAT-TTCCAAAAATTC-TATTTTTAA
1 CCCCAAACTTTT-CAAAAATTACCATTTTA-CCTCGAATCTTCCAAAAA-TCACATTTTTAA
* * *
166003 CCTCGAACTTTCCAAAAATTACCATTTTACCCTCGAAT-TTCCAAAAA
1 CCCCAAACTTTTCAAAAATTACCATTTTA-CCTCGAATCTTCCAAAAA
166050 ATTCCATTTT
Statistics
Matches: 489, Mismatches: 58, Indels: 60
0.81 0.10 0.10
Matches are distributed among these distances:
56 1 0.00
57 4 0.01
58 103 0.21
59 344 0.70
60 36 0.07
61 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (59 bp):
CCCCAAACTTTTCAAAAATTACCATTTTACCTCGAATCTTCCAAAAATCACATTTTTAA
Found at i:165750 original size:176 final size:172
Alignment explanation
Indices: 165568--166097 Score: 570
Period size: 176 Copynumber: 3.0 Consensus size: 172
165558 TTTATCCTTG
* ** * *
165568 AACTTCCAAAAATTA-CATTTTTGACCCCAAACCTTCAAAAAAGCA-CATTTTTATCCTCGAACT
1 AACTTCCAAAAA-TACCATTTTTAACCCCAAATTTTC-AAAAATCACCA-TTTTACCCT-GAACT
* * *
165631 TTCAAAAATTCCA-TTTTAACCCCAAAATCTT-CAAAAATCACCATTTTACACCTAAACTTTCAA
62 TTCAAAAATTCCATTTTTAACCTCAAACT-TTCCAAAAATTACCATTTTAC-CCTAAACTTTCAA
*
165694 AAATTCCATTTTTGACCCTAAAATCTTTAAAAATTACCATTTTACCCCTA
125 AAATTCCA-TTTTGACCCT-AAATCTTTAAAAATTACCATTTTACCCCCA
* * *
165744 AACTTCCAAAAATACCATTTTTTACCCCAAATTTTTCAAAAATCACCATTTTACCCTTAACCTTC
1 AACTTCCAAAAATACCATTTTTAACCCCAAA-TTTTCAAAAATCACCATTTTACCCTGAA-CTTT
* * * * *
165809 CAAAAATACCATTTTTGACCTCAAACTTTCCAAAAATTACCATTTTACCCCCAACCTTCCAAAAA
64 CAAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTA-CCCTAAACTTTCAAAAA
* * * *
165874 TACCATTTTAACCTTAAA-CTTTCCAAAAATTATCATTTTACCCCCA
128 TTCCATTTTGACCCTAAATCTTT--AAAAATTACCATTTTACCCCCA
* * * *
165920 AACCTCTAAAAATACCATTTTTAACCTCAAATTTTCCAAAAATTACCATTTTACCCTTGAA-TTT
1 AACTTCCAAAAATACCATTTTTAACCCCAAATTTT-CAAAAATCACCATTTTACCC-TGAACTTT
* * *
165984 CCAAAAATTCTATTTTTAACCTCGAACTTTCCAAAAATTACCATTTTACCCTCGAA-TTTCCAAA
64 -CAAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTACCCT-AAACTTT-C-AA
* *
166048 AAATTCCATTTTGACCCTAAATCTTTGAAAATTACCATTTTGCCCCCA
125 AAATTCCATTTTGACCCTAAATCTTTAAAAATTACCATTTTACCCCCA
166096 AA
1 AA
166098 GTGTCTAAAA
Statistics
Matches: 297, Mismatches: 41, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
174 4 0.01
175 18 0.06
176 197 0.66
177 73 0.25
178 5 0.02
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (172 bp):
AACTTCCAAAAATACCATTTTTAACCCCAAATTTTCAAAAATCACCATTTTACCCTGAACTTTCA
AAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTACCCTAAACTTTCAAAAATTC
CATTTTGACCCTAAATCTTTAAAAATTACCATTTTACCCCCA
Found at i:165755 original size:29 final size:29
Alignment explanation
Indices: 165423--166093 Score: 313
Period size: 30 Copynumber: 22.9 Consensus size: 29
165413 CCCCCAAACT
* *
165423 CTTCCAAACATTA-CATTTTA-ACCTATAA
1 CTTCCAAAAATTACCATTTTACCCCTA-AA
** *
165451 CTCTTTAAAAATCA-CATTTTAACCCCTAAA
1 CT-TCCAAAAATTACCATTTT-ACCCCTAAA
* * * *
165481 CTTTTCAAAAATTA-CATTTTGACCTCGAATT
1 C-TTCCAAAAATTACCATTTT-ACCCCTAA-A
* *
165512 CTT-CAAAAATCA-CATTTTTGCACCC-AAA
1 CTTCCAAAAATTACCA-TTTTAC-CCCTAAA
* * * *
165540 CTTCACAAAAATCA-CATTTTTATCCTTGAA
1 CTTC-CAAAAATTACCA-TTTTACCCCTAAA
165570 CTTCCAAAAATTA-CATTTTTGACCCC-AAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCTAAA
* ** * *
165599 CCTTCAAAAAAGCA-CATTTTTA-TCCTCGAA
1 -CTTCCAAAAATTACCA-TTTTACCCCT-AAA
* *
165629 CTTTCAAAAATT-CCATTTTAACCCCAAAA
1 CTTCCAAAAATTACCATTTT-ACCCCTAAA
* *
165658 TCTT-CAAAAATCACCATTTTACACCTAAA
1 -CTTCCAAAAATTACCATTTTACCCCTAAA
*
165687 CTTTCAAAAATT-CCATTTTTGA-CCCTAAAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCT-AAA
*
165717 TCTT-TAAAAATTACCATTTTACCCCTAAA
1 -CTTCCAAAAATTACCATTTTACCCCTAAA
165746 CTTCCAAAAA-TACCATTTTTTACCCC-AAA
1 CTTCCAAAAATTACCA--TTTTACCCCTAAA
* * * * *
165775 TTTTTCAAAAATCACCATTTTACCCTTAAC
1 -CTTCCAAAAATTACCATTTTACCCCTAAA
*
165805 CTTCCAAAAA-TACCATTTTTGACCTC-AAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCTAAA
* *
165834 CTTTCCAAAAATTACCATTTTACCCCCAAC
1 C-TTCCAAAAATTACCATTTTACCCCTAAA
* *
165864 CTTCCAAAAA-TACCATTTTAACCTTAAA
1 CTTCCAAAAATTACCATTTTACCCCTAAA
* *
165892 CTTTCCAAAAATTATCATTTTACCCCCAAA
1 C-TTCCAAAAATTACCATTTTACCCCTAAA
* * *
165922 CCTCTAAAAA-TACCATTTTTA-ACCTCAAA
1 CTTCCAAAAATTACCA-TTTTACCCCT-AAA
* * *
165951 TTTTCCAAAAATTACCATTTTACCCTTGAA
1 -CTTCCAAAAATTACCATTTTACCCCTAAA
* * * *
165981 TTTCCAAAAATT-CTATTTTTA-ACCTCGAA
1 CTTCCAAAAATTACCA-TTTTACCCCT-AAA
*
166010 CTTTCCAAAAATTACCATTTTA-CCCTCGAA
1 C-TTCCAAAAATTACCATTTTACCCCT-AAA
*
166040 TTTCCAAAAAATT-CCATTTTGA-CCCTAAA
1 CTTCC-AAAAATTACCATTTT-ACCCCTAAA
** *
166069 TCTT-TGAAAATTACCATTTTGCCCC
1 -CTTCCAAAAATTACCATTTTACCCC
166094 CAAAGTGTCT
Statistics
Matches: 504, Mismatches: 86, Indels: 105
0.73 0.12 0.15
Matches are distributed among these distances:
28 60 0.12
29 202 0.40
30 212 0.42
31 30 0.06
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCTAAA
Found at i:167558 original size:16 final size:16
Alignment explanation
Indices: 167513--167559 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
167503 AAATTAATAG
*
167513 TTATTTAAATAGTTTC
1 TTATTTAAATATTTTC
*
167529 TTATGTAAAGTATTTTC
1 TTATTTAAA-TATTTTC
167546 -TATTTAAATTATTT
1 TTATTTAAA-TATTT
167560 ACGCAATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (16 bp):
TTATTTAAATATTTTC
Found at i:179083 original size:21 final size:21
Alignment explanation
Indices: 179059--179101 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
179049 ACTTTTTCTA
179059 AAGTTAAAA-GTCAAAATCATT
1 AAGTTAAAAGGT-AAAATCATT
179080 AAGTTAAAAGGTAAAATCATT
1 AAGTTAAAAGGTAAAATCATT
179101 A
1 A
179102 TATTGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAATCATT
Found at i:180348 original size:19 final size:21
Alignment explanation
Indices: 180309--180348 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
180299 AAATCATGGA
*
180309 TAAATTCAAGCGATTCTTTTT
1 TAAATTCAAGCGATACTTTTT
180330 TAAATTCAAGC-A-ACTTTTT
1 TAAATTCAAGCGATACTTTTT
180349 CATAGGCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAATTCAAGCGATACTTTTT
Found at i:180497 original size:20 final size:20
Alignment explanation
Indices: 180469--180516 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
180459 TAATCCACAT
180469 ATAAT-TTTT-TTAAAGAAAA
1 ATAATATTTTATT-AAGAAAA
* *
180488 TTAATATTTTATTTAGAAAA
1 ATAATATTTTATTAAGAAAA
180508 ATAATATTT
1 ATAATATTT
180517 AATGAATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 18 0.75
21 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
ATAATATTTTATTAAGAAAA
Found at i:180639 original size:20 final size:19
Alignment explanation
Indices: 180613--180653 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
180603 TTTAAACTTT
180613 ATTTAAT-AT-TTTTATAA
1 ATTTAATAATGTTTTATAA
*
180630 TTTTAATAATGTTTTATAA
1 ATTTAATAATGTTTTATAA
180649 ATTTA
1 ATTTA
180654 TAAAAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 6 0.30
18 2 0.10
19 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTAATAATGTTTTATAA
Found at i:187746 original size:24 final size:24
Alignment explanation
Indices: 187683--187747 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
187673 CATCTATATA
*
187683 TGAATCTGAAATTGTATTTGTATC
1 TGAATCTGAAATTGTATTTGAATC
** * *
187707 TGTGTCTGCAACTGTATTTGAATC
1 TGAATCTGAAATTGTATTTGAATC
* *
187731 TGAATTTGGAATTGTAT
1 TGAATCTGAAATTGTAT
187748 CTATATTTAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (24 bp):
TGAATCTGAAATTGTATTTGAATC
Found at i:187783 original size:48 final size:48
Alignment explanation
Indices: 187674--187784 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
187664 TTGAATATGC
* * * *
187674 ATCTATATATGAATCTGAAATTGTATTTGTATCTGTGTCTGCAACTGT
1 ATCTATATATGAATTTGAAATTGTATCTATATCTATGTCTGCAACTGT
* * * *
187722 ATTTGA-ATCTGAATTTGGAATTGTATCTATATTTATGTCTGCAACTGT
1 ATCT-ATATATGAATTTGAAATTGTATCTATATCTATGTCTGCAACTGT
*
187770 ATCTATATTTGAATT
1 ATCTATATATGAATT
187785 GCATATGTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
47 1 0.02
48 49 0.96
49 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (48 bp):
ATCTATATATGAATTTGAAATTGTATCTATATCTATGTCTGCAACTGT
Found at i:189709 original size:32 final size:32
Alignment explanation
Indices: 189650--189714 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
189640 TACCTCTTTA
* *
189650 AATATATATATATATTAAATTGTATTCTTTTT
1 AATATATATATATATTAAATTGAATTCTATTT
*
189682 AATATATATATATATATATATT-AATTCTATTT
1 AATATATATATATAT-TAAATTGAATTCTATTT
189714 A
1 A
189715 CTTTAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (32 bp):
AATATATATATATATTAAATTGAATTCTATTT
Found at i:189844 original size:18 final size:18
Alignment explanation
Indices: 189821--189868 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
189811 TGTGGGCAAA
*
189821 ATAATTTGTACAATTTAT
1 ATAATTTGTACAATCTAT
*
189839 ATAATTTGTATAATCTAT
1 ATAATTTGTACAATCTAT
*
189857 ATACTTT-TACAA
1 ATAATTTGTACAA
189869 CTTTTTTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (18 bp):
ATAATTTGTACAATCTAT
Found at i:191622 original size:17 final size:17
Alignment explanation
Indices: 191600--191666 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
191590 TAAACCTTTT
191600 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
191617 TTAAATTTATTTTAA-A
1 TTAAATTTATTTTAAGA
** *
191633 TTTAAATTTAAATTAAGT
1 -TTAAATTTATTTTAAGA
191651 TTAAATTTACTTTTAA
1 TTAAATTTA-TTTTAA
191667 ATTTAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
16 1 0.02
17 37 0.88
18 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:191648 original size:5 final size:6
Alignment explanation
Indices: 191599--191673 Score: 68
Period size: 6 Copynumber: 13.0 Consensus size: 6
191589 CTAAACCTTT
* *
191599 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
191645 -TTAAG TTTAAA TTTACT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
191674 ATTCATAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
5 13 0.24
6 41 0.76
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:191691 original size:35 final size:33
Alignment explanation
Indices: 191618--191692 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 33
191608 ATTTTAAGAT
* *
191618 TAAATTTATTTTAAATTTAAATTTAAATTAAGTT
1 TAAATTTATTTTAAATTTAAATTCAAA-TAAGTC
191652 TAAATTTACTTTTAAATTTAAAATTCATAA-AAGTC
1 TAAATTTA-TTTTAAATTT-AAATTCA-AATAAGTC
191687 TAAATT
1 TAAATT
191693 ACAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
34 8 0.22
35 20 0.56
36 6 0.17
37 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (33 bp):
TAAATTTATTTTAAATTTAAATTCAAATAAGTC
Done.