Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008357.1 Hibiscus syriacus cultivar Beakdansim tig00111096_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: 1459476
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:89 original size:13 final size:14
Alignment explanation
Indices: 56--95 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
46 ATTGTTTTTA
*
56 AAATAAAAAAATAG
1 AAATAAATAAATAG
*
70 AATTAAATAAA-AG
1 AAATAAATAAATAG
83 AAATAAATAAATA
1 AAATAAATAAATA
96 AATAATCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (14 bp):
AAATAAATAAATAG
Found at i:12050 original size:14 final size:14
Alignment explanation
Indices: 12027--12057 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12017 AATTTGGTTT
*
12027 ACTATGGGGGAAAC
1 ACTATAGGGGAAAC
12041 ACTATAGGGGAAAC
1 ACTATAGGGGAAAC
12055 ACT
1 ACT
12058 GACCCTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (14 bp):
ACTATAGGGGAAAC
Found at i:21696 original size:14 final size:14
Alignment explanation
Indices: 21673--21715 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
21663 CGTTCGTTTA
*
21673 TGTTTATTTATGTT
1 TGTTCATTTATGTT
*
21687 TGTTCGTTTATGTT
1 TGTTCATTTATGTT
21701 TGTTCATTTATGTT
1 TGTTCATTTATGTT
21715 T
1 T
21716 AGCTCAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.12, C:0.05, G:0.16, T:0.67
Consensus pattern (14 bp):
TGTTCATTTATGTT
Found at i:21714 original size:24 final size:24
Alignment explanation
Indices: 21654--21714 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
21644 TAATAAGTTC
*
21654 GTTCATTTACGTTCGTTTATGTTT
1 GTTCATTTATGTTCGTTTATGTTT
* *
21678 ATTTATGTT-TGTTCGTTTATGTTT
1 GTTCAT-TTATGTTCGTTTATGTTT
21702 GTTCATTTATGTT
1 GTTCATTTATGTT
21715 TAGCTCAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 2 0.07
24 26 0.87
25 2 0.07
ACGTcount: A:0.13, C:0.08, G:0.16, T:0.62
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTTATGTTT
Found at i:22862 original size:27 final size:26
Alignment explanation
Indices: 22832--22895 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
22822 ACCTGTGTAT
*
22832 CTGCCACGCGTCAGAATGGCGCGCCCC
1 CTGCC-CGCGTCAGAAAGGCGCGCCCC
*
22859 CTGCCCAGCGTCAGAAAGGCGCGTCCC
1 CTGCCC-GCGTCAGAAAGGCGCGCCCC
22886 CTGCCTCGCG
1 CTGCC-CGCG
22896 CTATATGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.94
28 1 0.03
ACGTcount: A:0.14, C:0.44, G:0.30, T:0.12
Consensus pattern (26 bp):
CTGCCCGCGTCAGAAAGGCGCGCCCC
Found at i:23085 original size:23 final size:22
Alignment explanation
Indices: 23046--23090 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
23036 TTATTATATT
*
23046 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
23069 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
23091 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:23097 original size:17 final size:18
Alignment explanation
Indices: 23060--23098 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
23050 ATATTTTGTA
23060 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
23078 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
23095 TTTA
1 TTTA
23099 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:25435 original size:35 final size:35
Alignment explanation
Indices: 25396--25475 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
25386 GTATTTCAGT
25396 TAATTTTGTT-T-ATTT-CCATTTAATATCAGTTATTG
1 TAATTTTGTTATCATTTACCATTTAATA-C--TTATTG
*
25431 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTATCATTTACCATTTAATACTTATTG
*
25466 TAAGTTTGTT
1 TAATTTTGTT
25476 GAATTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
35 23 0.59
36 1 0.03
37 5 0.13
38 10 0.26
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.55
Consensus pattern (35 bp):
TAATTTTGTTATCATTTACCATTTAATACTTATTG
Found at i:33855 original size:17 final size:16
Alignment explanation
Indices: 33833--33866 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
33823 TAAAAACAGT
33833 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
33850 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
33866 A
1 A
33867 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:44140 original size:17 final size:16
Alignment explanation
Indices: 44118--44151 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
44108 TAAAAACAAT
44118 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
44135 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
44151 A
1 A
44152 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:54020 original size:54 final size:54
Alignment explanation
Indices: 53938--54551 Score: 924
Period size: 54 Copynumber: 11.4 Consensus size: 54
53928 TACGGTAATT
* *
53938 TTGCACACATAGTACATGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
** * *
53992 TTGCACTTATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTCCGTGGG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* *
54046 TTGCACACATAGTGTCTGTACGGTTGTTCATCAACATATGATGAATTCTGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * *
54100 TTGCACATATAGTGCCTGTACGGTAGTTCATCAACATATGATGAATTCCATGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
**
54154 TTGCACACATAGTATCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * *
54208 TTGCACACATAGAGCCTGTACGGTTGTTCATCAAAATATGATGAATTACGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
*
54262 TTGCACACATAGTGCCTGTACGATTGTTCATCAACATATGATGAATTCCGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * *
54316 TTGCACACATAGTGCCTGTACGATTGTTCATCATCATATGATGAATTCTGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * **
54370 TTGCATACATAGTGCCTGTACTGTTGTTCATCAACATATGATGAATTATGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * * * **
54424 TTGAACACATAATGCATGTACGGTTGTTCATCAACATATGGTGAATTATGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* *
54478 TTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTTCGTG-G
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
54531 TTTGCACACATAGTGCCTGTA
1 -TTGCACACATAGTGCCTGTA
54552 GTACACCTAC
Statistics
Matches: 511, Mismatches: 48, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
53 1 0.00
54 510 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (54 bp):
TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
Found at i:54283 original size:26 final size:26
Alignment explanation
Indices: 54254--54337 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
54244 TATGATGAAT
54254 TACGTGAGTTGCACACATAGTGCCTG
1 TACGTGAGTTGCACACATAGTGCCTG
* **
54280 TACGAT-TGTT-CATCAACATATGATGAAT-
1 TACG-TGAGTTGCA-C-ACATA-G-TGCCTG
*
54308 TCCGTGAGTTGCACACATAGTGCCTG
1 TACGTGAGTTGCACACATAGTGCCTG
54334 TACG
1 TACG
54338 ATTGTTCATC
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 5 0.12
26 12 0.29
27 12 0.29
28 8 0.19
29 5 0.12
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (26 bp):
TACGTGAGTTGCACACATAGTGCCTG
Found at i:54514 original size:27 final size:27
Alignment explanation
Indices: 54430--54515 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
54420 TGAGTTGAAC
*
54430 ACATAATGCATGTACGGTTGTTCATCA
1 ACATAGTGCATGTACGGTTGTTCATCA
* * *
54457 ACATATGGTGAAT-TA-TGTGAGTTGCA-C-
1 ACATA--GTGCATGTACGGT-TGTT-CATCA
54484 ACATAGTGCATGTACGGTTGTTCATCA
1 ACATAGTGCATGTACGGTTGTTCATCA
54511 ACATA
1 ACATA
54516 TGATGAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 7 0.16
26 6 0.14
27 19 0.43
28 6 0.14
29 6 0.14
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (27 bp):
ACATAGTGCATGTACGGTTGTTCATCA
Found at i:56886 original size:74 final size:75
Alignment explanation
Indices: 56720--56976 Score: 363
Period size: 75 Copynumber: 3.4 Consensus size: 75
56710 CTTAACCGTT
* * * * * *
56720 TAAAATAAAATAGGCGCTACCTATTATGTTAAACTACCTATCGGTTTATTTGAAGGTTGCTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
*
56785 ATGTAAATGG
66 ATGTAAACGG
* * *
56795 TAAAATAAAATAGGCGCTATCTATTACGTTAAAATACCTA-CTGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
56859 ATGTAAACGG
66 ATGTAAACGG
* * *
56869 TAAAATAAAATACGCGCTACCTATTGCGTTAAACTACCTACCAATTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
*
56934 ATATAAACGG
66 ATGTAAACGG
* *
56944 TAAAATAAAATAAGCGCTACCTATTATGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA
56977 TAGGCGCTAC
Statistics
Matches: 163, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
74 65 0.40
75 98 0.60
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:56983 original size:23 final size:23
Alignment explanation
Indices: 56951--56996 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
56941 CGGTAAAATA
56951 AAATAAGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
*
56974 AAATAGGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
56997 GAACTAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTATGTT
Found at i:57642 original size:108 final size:108
Alignment explanation
Indices: 57511--57994 Score: 418
Period size: 108 Copynumber: 4.4 Consensus size: 108
57501 TGTTAATATT
* ** * * * *
57511 TATTTATAACAAAATAAAAAATTAACCTATTTTGTTGTTGTGGGATTTCGAAGG-CCCAATCAGC
1 TATTGATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGTCCC-ATCAGC
57575 TTAAACTTTGGTAACATTTTAGGCGCTACATAATATGTTGATAA
65 TTAAACTTTGGTAACATTTTAGGCGCTACATAATATGTTGATAA
* * * **
57619 TATTAATAACAAAATAAGTAATTAACTTATTTCGTTATCGTCATATTTCTAAGGTCCCATCAGCT
1 TATTGATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGTCCCATCAGCT
* * * * *
57684 TAAACTTTGATAATATTTTGGGCGTTACCTAATATGTTGATAA
66 TAAACTTTGGTAACATTTTAGGCGCTACATAATATGTTGATAA
* * * * *
57727 TATTGATAATAAATTAAGTAATCAACCTATTTTGTTATCGTCGAATTTCTAAGGTCTCATCAGCT
1 TATTGATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGTCCCATCAGC-
*** * ** * ** *
57792 TTAAAAAGACGTTACCTACTACATTAAATAAACGCTACTTGTTATGTT-ATTA
65 TT---AA-AC-TTTGGTA--ACATT--TTAGGCGCTACATAATATGTTGATAA
* * **** * * * ** *
57844 TGGTTTATAA-TGTTTCCAGTAATTAGCCTATTTTGTTATCGTCGGATTTCTAAGGACCTGTCAA
1 T-ATTGATAACAAAAT-AAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGTCCCATCAG
57908 CTTAAACTTTGGTAACATTTTAGGCGCTACATAATATGTTGATAA
64 CTTAAACTTTGGTAACATTTTAGGCGCTACATAATATGTTGATAA
57953 TATTGATAAC-AAATCAAGTAATTAACCTATTTTGTTATCGTC
1 TATTGATAACAAAAT-AAGTAATTAACCTATTTTGTTATCGTC
57995 ATATTTTTAA
Statistics
Matches: 292, Mismatches: 69, Indels: 30
0.75 0.18 0.08
Matches are distributed among these distances:
108 191 0.65
109 9 0.03
110 5 0.02
112 6 0.02
113 4 0.01
114 6 0.02
116 4 0.01
117 8 0.03
118 59 0.20
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (108 bp):
TATTGATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGTCCCATCAGCT
TAAACTTTGGTAACATTTTAGGCGCTACATAATATGTTGATAA
Found at i:57945 original size:226 final size:226
Alignment explanation
Indices: 57635--58097 Score: 626
Period size: 226 Copynumber: 2.0 Consensus size: 226
57625 TAACAAAATA
* * * * *
57635 AGTAATTAACTTATTTCGTTATCGTCATATTTCTAAGGTCCCATCAGCTTAAACTTTGATAATAT
1 AGTAATTAACCTATTTCGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
* * * * *
57700 TTTGGGCGTTACCTAATATGTTGATAATATTGATAATAAATTAAGTAATCAACCTATTTTGTTAT
66 TTTAGGCGCTACATAATATGTTGATAATATTGATAACAAATCAAGTAATCAACCTATTTTGTTAT
* *
57765 CGTCGA-ATTTCTAAGG-TCTCATCAGCTTTAAAAAGACGTTACCTACTACATTAAATAAACGCT
131 CGTC-ATATTTCTAAGGCTC-CATCAACTTTAAAAAGACGATACCTACTACATTAAATAAACGCT
*
57828 ACT-TGTTATGTTATTATGGTTTATAATGTTTCC
194 A-TATGTTATGTTATTATGGTTGATAATGTTTCC
* * * ** *
57861 AGTAATTAGCCTATTTTGTTATCGTCGGATTTCTAAGGACCTGTCAACTTAAACTTTGGTAACAT
1 AGTAATTAACCTATTTCGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
*
57926 TTTAGGCGCTACATAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGCTACATAATATGTTGATAATATTGATAACAAATCAAGTAATCAACCTATTTTGTTAT
* * * * * * *
57991 CGTCATATTTTTAAGGCTCCATCAACTTTAAAATGGCGATACCTATTACGTTACATAAGCGCTAT
131 CGTCATATTTCTAAGGCTCCATCAACTTTAAAAAGACGATACCTACTACATTAAATAAACGCTAT
*
58056 ATGTTATGTTATTATGGTTGATAATGTTTCT
196 ATGTTATGTTATTATGGTTGATAATGTTTCC
58087 AGTAATTAACC
1 AGTAATTAACC
58098 GGTTATGTTA
Statistics
Matches: 205, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
225 2 0.01
226 201 0.98
227 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (226 bp):
AGTAATTAACCTATTTCGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
TTTAGGCGCTACATAATATGTTGATAATATTGATAACAAATCAAGTAATCAACCTATTTTGTTAT
CGTCATATTTCTAAGGCTCCATCAACTTTAAAAAGACGATACCTACTACATTAAATAAACGCTAT
ATGTTATGTTATTATGGTTGATAATGTTTCC
Found at i:63839 original size:4 final size:4
Alignment explanation
Indices: 63820--63884 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
63810 CCGTTATATT
* * * * *
63820 TTTA TTTC TTTC TTTA TTTA TTTA TTTA TTT- TTTG TTTG TTTGT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA
63868 TTTA TTTTA TTTTA TTT
1 TTTA -TTTA -TTTA TTT
63885 CAATTAAGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
3 3 0.06
4 39 0.72
5 12 0.22
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:75977 original size:11 final size:10
Alignment explanation
Indices: 75960--76067 Score: 74
Period size: 10 Copynumber: 10.1 Consensus size: 10
75950 GAAAAAAACC
75960 AAAAAAAAAG
1 AAAAAAAAAG
75970 AAAGAAAAAATAG
1 -AA-AAAAAA-AG
75983 AAAAAAAACAG
1 AAAAAAAA-AG
75994 -AAAAAAAAG
1 AAAAAAAAAG
76003 AAAACGAAAAAG
1 AAAA--AAAAAG
* *
76015 AAAGAAAATG
1 AAAAAAAAAG
* * *
76025 GAGAAGAAAG
1 AAAAAAAAAG
* *
76035 AAAAATATAG
1 AAAAAAAAAG
76045 AAAAAGAAAAG
1 AAAAA-AAAAG
76056 AAAAGAAAAAG
1 AAAA-AAAAAG
76067 A
1 A
76068 GGAAAAAATG
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
9 2 0.03
10 31 0.41
11 23 0.30
12 18 0.24
13 2 0.03
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.04
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:76011 original size:6 final size:6
Alignment explanation
Indices: 75960--76067 Score: 50
Period size: 6 Copynumber: 18.0 Consensus size: 6
75950 GAAAAAAACC
* * *
75960 AAAA-A AAAAGA AAGAA-A AAATAGA AAAAAA ACAGAAAA AAAAGA AAACGA
1 AAAAGA AAAAGA AA-AAGA AAA-AGA AAAAGA A-A-AAGA AAAAGA AAAAGA
* * *
76010 AAAAG- -AAAGA AAATGG AGAAGA AAGAA-A AATATAGA AAAAG- AAAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AA-AAGA AA-A-AGA AAAAGA AAAAGA
76056 AAAAGA AAAAGA
1 AAAAGA AAAAGA
76068 GGAAAAAATG
Statistics
Matches: 80, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
4 4 0.05
5 15 0.19
6 41 0.51
7 12 0.15
8 8 0.10
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:76017 original size:32 final size:31
Alignment explanation
Indices: 75948--76022 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
75938 AAATATAAAT
*
75948 AAGAAAAAAACCAAAAAAAAAGAAAGAAAAA
1 AAGAAAAAAAACAAAAAAAAAGAAAGAAAAA
*
75979 ATAGAAAAAAAACAGAAAAAAAAGAAA-ACGAAA
1 A-AGAAAAAAAACA-AAAAAAAAGAAAGA-AAAA
*
76012 AAGAAAGAAAA
1 AAGAAAAAAAA
76023 TGGAGAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 1 0.03
32 21 0.55
33 16 0.42
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.01
Consensus pattern (31 bp):
AAGAAAAAAAACAAAAAAAAAGAAAGAAAAA
Found at i:76037 original size:26 final size:26
Alignment explanation
Indices: 75970--76067 Score: 87
Period size: 26 Copynumber: 3.8 Consensus size: 26
75960 AAAAAAAAAG
* *
75970 AAAGAAAA-AATAGAAAAA-AAACAGA
1 AAAGAAAAGAAAAGAAAAAGAAAGA-A
75995 AAA-AAAAGAAAACGAAAAAGAAAGAA
1 AAAGAAAAGAAAA-GAAAAAGAAAGAA
* * * *
76021 AATGGAGAAG-AAAGAAAAATATAGAA
1 AA-AGAAAAGAAAAGAAAAAGAAAGAA
76047 AAAGAAAAGAAAAGAAAAAGA
1 AAAGAAAAGAAAAGAAAAAGA
76068 GGAAAAAATG
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
24 4 0.07
25 11 0.19
26 32 0.55
27 7 0.12
28 4 0.07
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAGAAAAGAAAAGAAAAAGAAAGAA
Found at i:76064 original size:10 final size:10
Alignment explanation
Indices: 75960--76064 Score: 60
Period size: 9 Copynumber: 10.4 Consensus size: 10
75950 GAAAAAAACC
*
75960 AAAAAAAAAG
1 AAAAGAAAAG
75970 -AAAGAAAA-
1 AAAAGAAAAG
* *
75978 AATAGAAAAA
1 AAAAGAAAAG
75988 AAACAGAAAA-
1 AAA-AGAAAAG
75998 AAAAGAAAACG
1 AAAAGAAAA-G
76009 AAAA-AGAAAG
1 AAAAGA-AAAG
*
76019 AAAATGGAGAAG
1 AAAA--GAAAAG
76031 -AAAGAAAA-
1 AAAAGAAAAG
*
76039 ATATAGAAAAAG
1 A-AAAG-AAAAG
76051 AAAAGAAAAG
1 AAAAGAAAAG
76061 AAAA
1 AAAA
76065 AGAGGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 26
0.69 0.06 0.24
Matches are distributed among these distances:
9 24 0.32
10 23 0.31
11 23 0.31
12 4 0.05
13 1 0.01
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:76075 original size:16 final size:16
Alignment explanation
Indices: 75960--76067 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 16
75950 GAAAAAAACC
*
75960 AAAAA-AAAAGAAAGAA
1 AAAAAGAAAAGAAA-AG
*
75976 AAAATAGAAAA-AAAAC
1 AAAA-AGAAAAGAAAAG
75992 AGAAAA-AAAAGAAAACG
1 A-AAAAGAAAAGAAAA-G
76009 AAAAAG-AAAGAAAATGGAG
1 AAAAAGAAAAG-AAA---AG
*
76028 AAGAAAGAAAA-ATATAG
1 AA-AAAGAAAAGA-AAAG
76045 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
76061 AAAAAGA
1 AAAAAGA
76068 GGAAAAAATG
Statistics
Matches: 74, Mismatches: 4, Indels: 28
0.70 0.04 0.26
Matches are distributed among these distances:
15 4 0.05
16 37 0.50
17 16 0.22
18 4 0.05
19 4 0.05
20 6 0.08
21 3 0.04
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:81177 original size:17 final size:16
Alignment explanation
Indices: 81146--81179 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
81136 CACGTGAGGA
81146 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
81162 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
81179 T
1 T
81180 CTGTTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:81613 original size:45 final size:45
Alignment explanation
Indices: 81519--81861 Score: 523
Period size: 45 Copynumber: 7.6 Consensus size: 45
81509 GTAAGCATGC
* * *
81519 AAATAAGCTTATGAGCTTAT-GACAT-AATGGCAATTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGA-ATAAATGGTAAGTATATTAGTA
* *
81563 AAATAAGCTTACGAGCTAATGGAATAAATGCTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
*
81608 AAATAAGATTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
81653 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
81698 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATT-GATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAG-TA
* *
81743 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
* *
81788 AAATAAGCTTGCGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
* *
81833 AAATAAGCTTACAAACTTATAGG-ATAAAT
1 AAATAAGCTTACGAGCTTAT-GGAATAAAT
81862 TATAAGAAAT
Statistics
Matches: 279, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
44 21 0.08
45 255 0.91
46 3 0.01
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
Found at i:83156 original size:22 final size:22
Alignment explanation
Indices: 83131--83174 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
83121 TTAAACCACT
83131 ATAAACAAGTTTGTCCGTACTG
1 ATAAACAAGTTTGTCCGTACTG
83153 ATAAACAAGTTTGTCCGTACTG
1 ATAAACAAGTTTGTCCGTACTG
83175 TAATGGAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (22 bp):
ATAAACAAGTTTGTCCGTACTG
Found at i:85636 original size:37 final size:36
Alignment explanation
Indices: 85586--85703 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 36
85576 CCCATTATCA
* * * *
85586 TTTTTCAACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTTAAAGAAACATTTACCAAACTTTG-AAAACCAT
85623 TTTTTAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTTAAAGAAACATTTACCAAACTTTGAAAACCAT
*
85658 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATT
1 TTTTTAAAGAAACATTTACCAAACTTTGAAAACCA-T
85695 TTTTTAAAG
1 TTTTTAAAG
85704 TTGGTTACCA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 34 0.47
36 6 0.08
37 33 0.45
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
TTTTTAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:85659 original size:21 final size:21
Alignment explanation
Indices: 85635--85695 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
85625 TTTAAAGAAA
85635 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
85656 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
85670 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
85691 CATTT
1 CATTT
85696 TTTTAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:92957 original size:60 final size:62
Alignment explanation
Indices: 92904--93021 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 62
92894 AAAGTTTGGG
* *
92904 GAAAAATTTAGAATGA-ACGTTATAGTTTAGGGATGAAATT-GAA-ATGTTCAAAAGTTTACA
1 GAAAAATTTAGAATGATA-GTCATAATTTAGGGATGAAATTAGAATATGTTCAAAAGTTTACA
**
92964 GACGAATTTAGAATGATAGTCATAATTTAGGGATGAAATTAGAATAT-TT-AAAAGTTTA
1 GAAAAATTTAGAATGATAGTCATAATTTAGGGATGAAATTAGAATATGTTCAAAAGTTTA
93022 AGATTAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
60 43 0.84
61 6 0.12
62 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.33
Consensus pattern (62 bp):
GAAAAATTTAGAATGATAGTCATAATTTAGGGATGAAATTAGAATATGTTCAAAAGTTTACA
Found at i:108700 original size:29 final size:30
Alignment explanation
Indices: 108667--108737 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
108657 ATTCTCTTAA
*
108667 TTAGTGACCAAAACATAAATTT-TGAAAGT
1 TTAGTGACCAAAACATAAATTTAAGAAAGT
* * ** *
108696 TTAGTGGCTAAATTATAAATTTAAGAAATT
1 TTAGTGACCAAAACATAAATTTAAGAAAGT
*
108726 TTAGGGACCAAA
1 TTAGTGACCAAA
108738 GTGGTAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.32
Consensus pattern (30 bp):
TTAGTGACCAAAACATAAATTTAAGAAAGT
Found at i:111906 original size:22 final size:20
Alignment explanation
Indices: 111855--111908 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
111845 GAATTAAACT
*
111855 AGTATCGATACTCTAGTATG
1 AGTATCGATACTATAGTATG
*
111875 AGTATTGATACTATGATGT-TG
1 AGTATCGATACTAT-A-GTATG
111896 AGGTATCGATACT
1 A-GTATCGATACT
111909 TGACTGAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTATAGTATG
Found at i:113356 original size:21 final size:21
Alignment explanation
Indices: 113331--113398 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
113321 CGTCAATACT
*
113331 AAAATTAAATAAACAGAATAA
1 AAAATTAAATAAACAAAATAA
* *
113352 AAAATAAAATAAATAAAATAA
1 AAAATTAAATAAACAAAATAA
*
113373 AATATTATAAATAAA-ATAAATAA
1 AA-AAT-TAAATAAACA-AAATAA
113396 AAA
1 AAA
113399 TAAAAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 20 0.51
22 4 0.10
23 15 0.38
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (21 bp):
AAAATTAAATAAACAAAATAA
Found at i:113362 original size:5 final size:5
Alignment explanation
Indices: 113330--113403 Score: 57
Period size: 5 Copynumber: 15.0 Consensus size: 5
113320 ACGTCAATAC
* * **
113330 TAAAA TTAAA TAAACA GAATAA -AAAA TAAAA T-AAA TAAAA TAAAA TATTA
1 TAAAA TAAAA TAAA-A TAA-AA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
113380 T-AAA TAAAA T-AAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA T-AAAA TAAAA
113404 ATATTTAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
4 12 0.22
5 34 0.62
6 8 0.15
7 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:113365 original size:9 final size:9
Alignment explanation
Indices: 113353--113402 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
113343 ACAGAATAAA
113353 AAATAAAAT
1 AAATAAAAT
113362 AAATAAAAT
1 AAATAAAAT
**
113371 AAAATATTAT
1 -AAATAAAAT
113381 AAATAAAAT
1 AAATAAAAT
113390 AAATAAAAAT
1 AAAT-AAAAT
113400 AAA
1 AAA
113403 AATATTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 20 0.57
10 15 0.43
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:113376 original size:19 final size:19
Alignment explanation
Indices: 113352--113402 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
113342 AACAGAATAA
113352 AAAATAAAATAAATAAAAT
1 AAAATAAAATAAATAAAAT
**
113371 AAAATATTATAAATAAAAT
1 AAAATAAAATAAATAAAAT
113390 -AAATAAAAATAAA
1 AAAAT-AAAATAAA
113403 AATATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATAAAATAAATAAAAT
Found at i:113426 original size:28 final size:29
Alignment explanation
Indices: 113353--113425 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 29
113343 ACAGAATAAA
113353 AAATAAAATAAAT-AAAATAAAATATTAT
1 AAATAAAATAAATAAAAATAAAATATTAT
113381 AAATAAAATAAATAAAAATAAAAATATT-T
1 AAATAAAATAAATAAAAAT-AAAATATTAT
*
113410 -AAT-AAATACATAAAAA
1 AAATAAAATAAATAAAAA
113426 AATGTTCGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 12 0.29
28 16 0.38
29 6 0.14
30 8 0.19
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (29 bp):
AAATAAAATAAATAAAAATAAAATATTAT
Found at i:115221 original size:3 final size:3
Alignment explanation
Indices: 115213--115335 Score: 138
Period size: 3 Copynumber: 39.0 Consensus size: 3
115203 GTTTATTTAT
* * *
115213 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATTA CTA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* *
115259 ATA ATA ATA ATA ATTA GTA ATA ATA ATTA ATA ATT ATA ATA ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
*
115306 AGTA ATA TTA ATTA ATA ATA ATA ATTA ATA
1 A-TA ATA ATA A-TA ATA ATA ATA A-TA ATA
115336 TGTACAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
3 87 0.84
4 16 0.16
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:115262 original size:13 final size:11
Alignment explanation
Indices: 115209--115327 Score: 69
Period size: 10 Copynumber: 11.1 Consensus size: 11
115199 TTTAGTTTAT
115209 TTATATAATAA
1 TTATATAATAA
115220 -TAGTAATAATAA
1 TTA-T-ATAATAA
115232 -TA-ATAATAA
1 TTATATAATAA
115241 -TA-ATAATAA
1 TTATATAATAA
115250 TTACTATTAATAA
1 TTA-TA-TAATAA
115263 -TA-ATAATAA
1 TTATATAATAA
*
115272 TTA-GTAATAA
1 TTATATAATAA
*
115282 TAAT-TAATAA
1 TTATATAATAA
115292 TTATAATAATAA
1 TTAT-ATAATAA
* *
115304 TAAGTAATATTAA
1 TTA-T-ATAATAA
115317 TTA-ATAATAA
1 TTATATAATAA
115327 T
1 T
115328 AATTAATATG
Statistics
Matches: 90, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
9 22 0.24
10 31 0.34
11 1 0.01
12 20 0.22
13 16 0.18
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (11 bp):
TTATATAATAA
Found at i:115347 original size:26 final size:23
Alignment explanation
Indices: 115213--115336 Score: 91
Period size: 22 Copynumber: 5.6 Consensus size: 23
115203 GTTTATTTAT
* *
115213 ATAATAA-TAGTAATAA-TAATA
1 ATAATAAGTAATATTAATTAATA
* *
115234 ATAATAA-TAATAATAATTACTA
1 ATAATAAGTAATATTAATTAATA
* * *
115256 TTAATAA-TAATAATAATTAGTA
1 ATAATAAGTAATATTAATTAATA
* *
115278 ATAATAATTAATAATTATAATAATA
1 ATAATAAGTAAT-ATTA-ATTAATA
115303 AT-A-A-GTAATATTAATTAATA
1 ATAATAAGTAATATTAATTAATA
*
115323 ATAATAATTAATAT
1 ATAATAAGTAATAT
115337 GTACAATTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
20 8 0.09
21 20 0.24
22 35 0.41
23 11 0.13
24 4 0.05
25 7 0.08
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (23 bp):
ATAATAAGTAATATTAATTAATA
Found at i:117049 original size:11 final size:11
Alignment explanation
Indices: 117035--117059 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
117025 TTTTATTCTA
117035 TTTTTTTCTTT
1 TTTTTTTCTTT
117046 TTTTTTTCTTT
1 TTTTTTTCTTT
117057 TTT
1 TTT
117060 AGGTTTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:121825 original size:21 final size:21
Alignment explanation
Indices: 121799--121842 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
121789 CCAGGGCGTA
121799 GTGTAACATCCTCCATGCCAG
1 GTGTAACATCCTCCATGCCAG
121820 GTGTAACATCCTCCATGCCAG
1 GTGTAACATCCTCCATGCCAG
121841 GT
1 GT
121843 TAGTGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (21 bp):
GTGTAACATCCTCCATGCCAG
Found at i:127993 original size:11 final size:11
Alignment explanation
Indices: 127963--128001 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
127953 TACTAAAATT
127963 AAATAAAATAGA
1 AAATAAAATA-A
127975 ATAA-AAAATAA
1 A-AATAAAATAA
127986 AAATAAAATAA
1 AAATAAAATAA
127997 AAATA
1 AAATA
128002 TTACTATCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 14 0.56
12 7 0.28
13 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:128001 original size:17 final size:18
Alignment explanation
Indices: 127963--127999 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
127953 TACTAAAATT
*
127963 AAAT-AAAATAGAATAAA
1 AAATAAAAATAAAATAAA
127980 AAATAAAAATAAAATAAA
1 AAATAAAAATAAAATAAA
127998 AA
1 AA
128000 TATTACTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (18 bp):
AAATAAAAATAAAATAAA
Found at i:129999 original size:90 final size:89
Alignment explanation
Indices: 129828--129991 Score: 283
Period size: 90 Copynumber: 1.8 Consensus size: 89
129818 TCCCGAATAT
* * * *
129828 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
129893 GGTAACTTGAATATAAAAGGATTA
66 GGTAACTTGAATATAAAAGGATTA
129917 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
129982 GGGTAACTTG
65 GGGTAACTTG
129992 GCTATAAAGG
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
89 7 0.10
90 63 0.90
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
GGTAACTTGAATATAAAAGGATTA
Found at i:131341 original size:13 final size:13
Alignment explanation
Indices: 131273--131357 Score: 52
Period size: 13 Copynumber: 6.5 Consensus size: 13
131263 ATAGTAGTAG
131273 TAATAATATAATAA
1 TAATAATAT-ATAA
*
131287 TTAATAATA-ACAA
1 -TAATAATATATAA
* * *
131300 TTATATTA-ATGA
1 TAATAATATATAA
*
131312 TAATAATACT-TAG
1 TAATAATA-TATAA
131325 TAATAATATATAA
1 TAATAATATATAA
131338 TAATAA-ATATTAA
1 TAATAATATA-TAA
*
131351 TAGTAAT
1 TAATAAT
131358 GTTGATTAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
12 18 0.33
13 28 0.52
15 8 0.15
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:131373 original size:3 final size:3
Alignment explanation
Indices: 131273--131357 Score: 55
Period size: 3 Copynumber: 27.3 Consensus size: 3
131263 ATAGTAGTAG
* * * *
131273 TAA TAA T-A TAA TAA TTAA TAA TAA CAA TTA TAT TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
131318 TACT TAG TAA TAA TATA TAA TAA TAAA TAT TAA TAG TAA T
1 TA-A TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA T
131358 GTTGATTAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
2 2 0.03
3 49 0.79
4 11 0.18
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:135489 original size:21 final size:21
Alignment explanation
Indices: 135463--135502 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
135453 ACGATGGTCG
*
135463 CAATAGCGTCCGCGACAGCCA
1 CAATAGCATCCGCGACAGCCA
*
135484 CAATAGCATTCGCGACAGC
1 CAATAGCATCCGCGACAGC
135503 TGCAATCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (21 bp):
CAATAGCATCCGCGACAGCCA
Found at i:135508 original size:21 final size:21
Alignment explanation
Indices: 135461--135508 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
135451 TCACGATGGT
*
135461 CGCAATAGCGTCCGCGACAGC
1 CGCAATAGCATCCGCGACAGC
* *
135482 CACAATAGCATTCGCGACAGC
1 CGCAATAGCATCCGCGACAGC
*
135503 TGCAAT
1 CGCAAT
135509 CACGATAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (21 bp):
CGCAATAGCATCCGCGACAGC
Found at i:139020 original size:35 final size:37
Alignment explanation
Indices: 138956--139024 Score: 124
Period size: 35 Copynumber: 1.9 Consensus size: 37
138946 TTTAAGAACT
138956 TAACCAAGCAGAAAAAATTCTTTTTCAGCCCTCAAAC
1 TAACCAAGCAGAAAAAATTCTTTTTCAGCCCTCAAAC
138993 TAACCAAGCAG-AAAAA-TCTTTTTCAGCCCTCA
1 TAACCAAGCAGAAAAAATTCTTTTTCAGCCCTCA
139025 GCTAATGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 16 0.50
36 5 0.16
37 11 0.34
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.25
Consensus pattern (37 bp):
TAACCAAGCAGAAAAAATTCTTTTTCAGCCCTCAAAC
Found at i:143608 original size:34 final size:37
Alignment explanation
Indices: 143529--143624 Score: 146
Period size: 34 Copynumber: 2.7 Consensus size: 37
143519 TTGGGTTGGA
*
143529 TTTTTTAAGTGTGATATTCGGGT-TGAGTCGGGTGGG
1 TTTTTTAAGTGTGATATTCGGGTCGGAGTCGGGTGGG
*
143565 TTTTTTAAGTGTGATATTCGGGTCGGA-TC-GG-GGT
1 TTTTTTAAGTGTGATATTCGGGTCGGAGTCGGGTGGG
143599 TTTTTTAAGTGTGATATTCGGGTCGG
1 TTTTTTAAGTGTGATATTCGGGTCGG
143625 GTCATGTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
34 28 0.49
35 2 0.04
36 25 0.44
37 2 0.04
ACGTcount: A:0.15, C:0.07, G:0.35, T:0.43
Consensus pattern (37 bp):
TTTTTTAAGTGTGATATTCGGGTCGGAGTCGGGTGGG
Found at i:144188 original size:17 final size:18
Alignment explanation
Indices: 144166--144212 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
144156 TATGGAATTG
144166 GATTCCAATTCC-TAACA
1 GATTCCAATTCCTTAACA
*
144183 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTAACA
144201 GATTCCAATTCC
1 GATTCCAATTCC
144213 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTAACA
Found at i:152172 original size:45 final size:45
Alignment explanation
Indices: 152110--152199 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
152100 TATTACTCTC
* *
152110 ACTATGTTGGAGTTATTACCAGAATTACCCAACTTATTTCCTAAG
1 ACTATGTTGAAGATATTACCAGAATTACCCAACTTATTTCCTAAG
* *
152155 ACTATGTTGAAGATATTACTAGCATTACCCAACTTATTTCCTAAG
1 ACTATGTTGAAGATATTACCAGAATTACCCAACTTATTTCCTAAG
152200 TCTCTCATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (45 bp):
ACTATGTTGAAGATATTACCAGAATTACCCAACTTATTTCCTAAG
Found at i:156473 original size:21 final size:21
Alignment explanation
Indices: 156431--156473 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
156421 GATTCTCTGC
**
156431 AAGATTTTATAGCTTCGGCAA
1 AAGATTTTATAGCTTCAACAA
*
156452 AAGATTTTATGGCTTCAACAA
1 AAGATTTTATAGCTTCAACAA
156473 A
1 A
156474 GGCCTTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
AAGATTTTATAGCTTCAACAA
Found at i:172960 original size:32 final size:32
Alignment explanation
Indices: 172923--172992 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
172913 TTCCCTGCTC
172923 ATAACAGAAATCTCAGCTTCAAATTCCTCCTA
1 ATAACAGAAATCTCAGCTTCAAATTCCTCCTA
*
172955 ATAACAGAAATCTCAGCTTCAAATTCCTCGTA
1 ATAACAGAAATCTCAGCTTCAAATTCCTCCTA
172987 ATAACA
1 ATAACA
172993 TCGTATGTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.27
Consensus pattern (32 bp):
ATAACAGAAATCTCAGCTTCAAATTCCTCCTA
Found at i:200261 original size:17 final size:17
Alignment explanation
Indices: 200218--200263 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
200208 TCATTTTAAT
*
200218 TTTTATTACATGTAATTA
1 TTTTATTACA-ATAATTA
200236 -TTTAGTTACAATAATTA
1 TTTTA-TTACAATAATTA
200253 TTTTATTACAA
1 TTTTATTACAA
200264 AGTACCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTTATTACAATAATTA
Found at i:205536 original size:22 final size:22
Alignment explanation
Indices: 205511--205561 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
205501 CTACGGCGAC
205511 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
**
205533 ATCCGTCCCCATCTCCGGTGAA
1 ATCCGTCCCCATCTCCGACGAA
205555 ATCCGTC
1 ATCCGTC
205562 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:207950 original size:20 final size:20
Alignment explanation
Indices: 207927--207995 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
207917 GAAACTTAAA
207927 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
207947 ATCGCAATGC-AGAAATGACT
1 ATCGCAACGCGA-AAATGACT
**
207967 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
207987 ATCGCAACG
1 ATCGCAACG
207996 GGATAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:208028 original size:53 final size:53
Alignment explanation
Indices: 207947--208089 Score: 180
Period size: 53 Copynumber: 2.7 Consensus size: 53
207937 GAAAATGACT
** * ** *
207947 ATCGCAATGCAGAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGC-GAAATGAAAATCGCAACGCGAATTTAAAAATCGCAACGGGAAA
* * *
208001 ATCGCAATGCGAAATAAAAATCGCAACGCGAA-ATAAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAATTTAAAAATCGCAACGGGAAA
208053 ATCGCAATGCGAAAATGAAAATCGCAACGCGAATTTA
1 ATCGCAATGCG-AAATGAAAATCGCAACGCGAATTTA
208090 GTTTCACGTT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 25 0.33
53 39 0.51
54 12 0.16
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAATTTAAAAATCGCAACGGGAAA
Found at i:208071 original size:20 final size:19
Alignment explanation
Indices: 208000--208085 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
207990 GCAACGGGAT
*
208000 AATCGCAATGCGAAATAAA
1 AATCGCAACGCGAAATAAA
208019 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
208038 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATAAA
* *
208052 AATCGCAATGCGAAAATGAA
1 AATCGCAACGCG-AAATAAA
208072 AATCGCAACGCGAA
1 AATCGCAACGCGAA
208086 TTTAGTTTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
14 11 0.19
16 2 0.03
17 2 0.03
19 28 0.48
20 15 0.26
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:208079 original size:34 final size:33
Alignment explanation
Indices: 208017--208081 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
208007 ATGCGAAATA
208017 AAAATCGCAACGCGAAATAAAAATCGCAACGTG
1 AAAATCGCAACGCGAAATAAAAATCGCAACGTG
* *
208050 AAAATCGCAATGCGAAAATGAAAATCGCAACG
1 AAAATCGCAACGCG-AAATAAAAATCGCAACG
208082 CGAATTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATAAAAATCGCAACGTG
Found at i:208113 original size:19 final size:20
Alignment explanation
Indices: 208086--208124 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
208076 GCAACGCGAA
*
208086 TTTAGTTTCACGTTGCGATT
1 TTTAGTTTCACATTGCGATT
*
208106 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCACATTGCGATT
208125 ATCTTGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCACATTGCGATT
Found at i:208758 original size:21 final size:21
Alignment explanation
Indices: 208664--208770 Score: 65
Period size: 21 Copynumber: 5.1 Consensus size: 21
208654 CCCGACTCAC
*
208664 CTGTCATCGTTCAAGAGGCTT
1 CTGTCATCGTTCAAGAGGCCT
* *
208685 CT-CCTATCTTTCAAGAGGTCC-
1 CTGTC-ATCGTTCAAGAGG-CCT
* ** * *
208706 CTATCATCCCTCAAGAGTCCC
1 CTGTCATCGTTCAAGAGGCCT
** *
208727 CTCCCACCGTTCAAGAGGCCT
1 CTGTCATCGTTCAAGAGGCCT
* *
208748 CTGTCATCGTTGAAGAGGTCT
1 CTGTCATCGTTCAAGAGGCCT
208769 CT
1 CT
208771 CCCACCATTC
Statistics
Matches: 63, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.05
21 58 0.92
22 2 0.03
ACGTcount: A:0.20, C:0.33, G:0.19, T:0.29
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCT
Found at i:208784 original size:21 final size:21
Alignment explanation
Indices: 208716--208785 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
208706 CTATCATCCC
* *
208716 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGGCCTCTCCCACCGT
** *
208737 TCAAGAGGCCTCTGTCATCGT
1 TCAAGAGGCCTCTCCCACCGT
* * *
208758 TGAAGAGGTCTCTCCCACCAT
1 TCAAGAGGCCTCTCCCACCGT
208779 TCAAGAG
1 TCAAGAG
208786 CCCGATTCAC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGAGGCCTCTCCCACCGT
Found at i:210174 original size:14 final size:14
Alignment explanation
Indices: 210155--210191 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
210145 GCTTGTTTAA
210155 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
210169 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
210183 TTGATTTGT
1 TTGATTTGT
210192 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:210336 original size:20 final size:20
Alignment explanation
Indices: 210311--210388 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
210301 AGGTACACTT
*
210311 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
210331 TCGCAATGCGAAAATCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
210351 TTGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
210371 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
210389 TTCGCGTTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:210400 original size:19 final size:20
Alignment explanation
Indices: 210378--210420 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
210368 AAATCGCAAC
*
210378 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
210397 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
210417 GCGA
1 GCGA
210421 TTTTCTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:210454 original size:20 final size:20
Alignment explanation
Indices: 210429--210543 Score: 124
Period size: 20 Copynumber: 5.8 Consensus size: 20
210419 GATTTTCTTA
*
210429 TTGCGATAGTCAAATTCCCG
1 TTGCGATAGTCAAATTCACG
* *
210449 TTGCGATAATTAAATTCACG
1 TTGCGATAGTCAAATTCACG
* *
210469 TT-CTGATATTCAAATTCGCG
1 TTGC-GATAGTCAAATTCACG
** *
210489 TTGCGATAGTCAAATTTGCA
1 TTGCGATAGTCAAATTCACG
*
210509 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCAAATTCACG
*
210529 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
210544 GAATGTGTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 79 0.98
21 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCACG
Found at i:210524 original size:60 final size:60
Alignment explanation
Indices: 210429--210543 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
210419 GATTTTCTTA
* * *
210429 TTGCGATAGTCAAATTCCCGTTGCGATAATTAAATTCACGTT-CTGATATTCAAATTCGCG
1 TTGCGATAGTCAAATTCCCATTGCGATAATCAAATTCACATTGC-GATATTCAAATTCGCG
** *
210489 TTGCGATAGTCAAATTTGCATTGCGATAGTCAAATTCACATTGCGATATTCAAAT
1 TTGCGATAGTCAAATTCCCATTGCGATAATCAAATTCACATTGCGATATTCAAAT
210544 GAATGTGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (60 bp):
TTGCGATAGTCAAATTCCCATTGCGATAATCAAATTCACATTGCGATATTCAAATTCGCG
Found at i:210735 original size:18 final size:18
Alignment explanation
Indices: 210714--210748 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
210704 AAGCCGGTTG
*
210714 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
210732 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
210749 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:212804 original size:14 final size:14
Alignment explanation
Indices: 212785--212821 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
212775 TCCCGTGGCA
212785 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
212799 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
212813 TTCTTCTTC
1 TT-TTCTTC
212822 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:213742 original size:17 final size:17
Alignment explanation
Indices: 213720--213774 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
213710 CGGATGGGGA
213720 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
213737 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
*
213754 AGGATGTTGTTGGATAT
1 AGGATGTCGTTGGATAT
213771 AGGA
1 AGGA
213775 ACGGATGTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.25, C:0.04, G:0.36, T:0.35
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:214005 original size:20 final size:20
Alignment explanation
Indices: 213924--214012 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
213914 GAAATTCAAT
*
213924 GTTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
213944 GTTACGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * * **
213964 ATTGTGATTTTGT-ATTATCGC
1 GTTGCGA--TAGTCAGAATCGC
*
213985 GTTGCGATAATCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
214005 GTTGCGAT
1 GTTGCGAT
214013 TTACATATTC
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
19 2 0.04
20 36 0.69
21 11 0.21
22 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:214045 original size:61 final size:61
Alignment explanation
Indices: 213924--214045 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
213914 GAAATTCAAT
* * * * **
213924 GTTGCGATAGTCATAATCGCGTTACGATAGTCAGAATCGCATTGTGATTTTGTATTATCGC
1 GTTGCGATAATCAGAATCGCGTTACGATAGTCAGAATCGCATTCTGATTTTCTAAAATCGC
* * * *
213985 GTTGCGATAATCAGAATCGCGTTGCGAT-TTACATATTCGCATTCTGATTTTCTAAAATCGC
1 GTTGCGATAATCAGAATCGCGTTACGATAGT-CAGAATCGCATTCTGATTTTCTAAAATCGC
214046 AACGCGAATT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 1 0.02
61 49 0.98
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (61 bp):
GTTGCGATAATCAGAATCGCGTTACGATAGTCAGAATCGCATTCTGATTTTCTAAAATCGC
Found at i:214143 original size:19 final size:19
Alignment explanation
Indices: 214119--214155 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
214109 TGTAATACTG
*
214119 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
214138 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
214156 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:215030 original size:15 final size:15
Alignment explanation
Indices: 215010--215038 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
215000 GCTAGACGGG
215010 CGGATGCGGGGCGGA
1 CGGATGCGGGGCGGA
215025 CGGATGCGGGGCGG
1 CGGATGCGGGGCGG
215039 GTAATGACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.21, G:0.62, T:0.07
Consensus pattern (15 bp):
CGGATGCGGGGCGGA
Found at i:216215 original size:10 final size:9
Alignment explanation
Indices: 216191--216225 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
216181 ATTATTATGA
216191 ATATTTTTT
1 ATATTTTTT
*
216200 AAATTTTTT
1 ATATTTTTT
216209 AGTATTTTTT
1 A-TATTTTTT
216219 ATATTTT
1 ATATTTT
216226 AATTCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (9 bp):
ATATTTTTT
Found at i:218356 original size:36 final size:36
Alignment explanation
Indices: 218265--218357 Score: 107
Period size: 37 Copynumber: 2.6 Consensus size: 36
218255 AAAAATAAAT
*
218265 ACATTAAGAAAATTAAATAAAAATATTACAAACTAA
1 ACATTAAGAAAATTAAATAAAAACATTACAAACTAA
* * * * *
218301 ATAATAAAAAAAATTAAATAGAAACATTA-AATATTAA
1 A-CATTAAGAAAATTAAATAAAAACATTACAA-ACTAA
218338 ACATTAAGAAAATTAAATAA
1 ACATTAAGAAAATTAAATAA
218358 TAAAAACATT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
36 18 0.40
37 27 0.60
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (36 bp):
ACATTAAGAAAATTAAATAAAAACATTACAAACTAA
Found at i:218860 original size:21 final size:20
Alignment explanation
Indices: 218836--218890 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
218826 GCTGCAGTGG
*
218836 CATCTGAACTAGTTGTGGTGC
1 CATCTGAAC-AGTTATGGTGC
218857 CATCTGAAACAGTTATGGTGC
1 CATCTG-AACAGTTATGGTGC
218878 CATCTGAATCAGT
1 CATCTGAA-CAGT
218891 GGTGTACCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (20 bp):
CATCTGAACAGTTATGGTGC
Found at i:219513 original size:22 final size:24
Alignment explanation
Indices: 219473--219521 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
219463 AACTAAAACA
*
219473 AATATATATAATTCTTATAAAAAT
1 AATATATATAATTCATATAAAAAT
*
219497 AATAT-TATAATT-ATATAACAAT
1 AATATATATAATTCATATAAAAAT
219519 AAT
1 AAT
219522 TAAAGGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 7 0.30
24 5 0.22
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AATATATATAATTCATATAAAAAT
Found at i:220477 original size:18 final size:18
Alignment explanation
Indices: 220430--220484 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
220420 TTCCCCTAAT
* *
220430 TAAATAAATAATATAAAAAT
1 TAAA-AAATAA-ATAAATAC
* *
220450 TAAAATATAAATTAATAC
1 TAAAAAATAAATAAATAC
220468 TAAAAAATAAATAAATA
1 TAAAAAATAAATAAATA
220485 AAACATTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 20 0.69
19 5 0.17
20 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAATAAATAAATAC
Found at i:220480 original size:24 final size:23
Alignment explanation
Indices: 220433--220478 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
220423 CCCTAATTAA
*
220433 ATAAATAATATAAAAATTAAAAT
1 ATAAATAATATAAAAAATAAAAT
220456 ATAAATTAATACTAAAAAATAAA
1 ATAAA-TAATA-TAAAAAATAAA
220479 TAAATAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 5 0.25
25 10 0.50
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
ATAAATAATATAAAAAATAAAAT
Found at i:220643 original size:26 final size:26
Alignment explanation
Indices: 220614--220671 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
220604 GTAAAACAAA
220614 AATAATACAATAAAAT-ATAATAAAAT
1 AATAA-ACAATAAAATGATAATAAAAT
* * * *
220640 AATAAACTATTAAATGATTATAATAT
1 AATAAACAATAAAATGATAATAAAAT
220666 AATAAA
1 AATAAA
220672 AAAATTCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (26 bp):
AATAAACAATAAAATGATAATAAAAT
Found at i:223317 original size:15 final size:15
Alignment explanation
Indices: 223299--223327 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
223289 CATAATCATT
223299 AAAACAATAAATTTG
1 AAAACAATAAATTTG
223314 AAAACAATAAATTT
1 AAAACAATAAATTT
223328 AGTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAACAATAAATTTG
Found at i:223468 original size:2 final size:2
Alignment explanation
Indices: 223463--223499 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
223453 TATCATTAAT
223463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
223500 ATTGATTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:227412 original size:20 final size:20
Alignment explanation
Indices: 227376--227413 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
227366 ATCCTATTCC
**
227376 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
227396 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
227414 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:230191 original size:22 final size:22
Alignment explanation
Indices: 230153--230210 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
230143 AGAACCCGTG
230153 GGGGGTATCGATT-CCCTCCAA
1 GGGGGTATCGATTCCCCTCCAA
* * **
230174 GGGGGAATCGGTTCCCCTTTAA
1 GGGGGTATCGATTCCCCTCCAA
230196 GGGGGTATCGATTCC
1 GGGGGTATCGATTCC
230211 TCTTGCACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTCCAA
Found at i:234073 original size:22 final size:21
Alignment explanation
Indices: 234031--234070 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
234021 AAGACTATTT
*
234031 TCATTTTTTTATTTTGAAATA
1 TCATTTTTGTATTTTGAAATA
234052 TCATTTTTGTATTTTGAAA
1 TCATTTTTGTATTTTGAAA
234071 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (21 bp):
TCATTTTTGTATTTTGAAATA
Found at i:237519 original size:20 final size:20
Alignment explanation
Indices: 237494--237552 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
237484 ATTTGAGGTG
*
237494 TGTAGTATCGATACTCTAGT
1 TGTAGTATCGATACCCTAGT
237514 TGTAGTATCGATACCCTAGT
1 TGTAGTATCGATACCCTAGT
237534 TGTAGTATCGATACCCTAG
1 TGTAGTATCGATACCCTAG
237553 GGTCAAGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (20 bp):
TGTAGTATCGATACCCTAGT
Found at i:237563 original size:21 final size:20
Alignment explanation
Indices: 237495--237569 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
237485 TTTGAGGTGT
* *
237495 GTAGTATCGATACTCTAGTT
1 GTAGTATCGATACCCTAGTG
*
237515 GTAGTATCGATACCCTAGTT
1 GTAGTATCGATACCCTAGTG
237535 GTAGTATCGATACCCTAG-G
1 GTAGTATCGATACCCTAGTG
237554 GTCAAGTATCGATACC
1 GT--AGTATCGATACC
237570 ATATGAGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
19 2 0.04
20 37 0.73
21 12 0.24
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (20 bp):
GTAGTATCGATACCCTAGTG
Found at i:242922 original size:6 final size:6
Alignment explanation
Indices: 242911--242939 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
242901 TTGCAATAAA
242911 GAATAG GAATAG GAATAG GAATAG GAATA
1 GAATAG GAATAG GAATAG GAATAG GAATA
242940 CTAGCAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
GAATAG
Found at i:244999 original size:18 final size:17
Alignment explanation
Indices: 244976--245012 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
244966 AGACCTCACC
244976 ATTTAATTCCTTTTAATA
1 ATTTAATTCCTTTT-ATA
*
244994 ATTTAATTTCTTTTATA
1 ATTTAATTCCTTTTATA
245011 AT
1 AT
245013 AAATTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAATTCCTTTTATA
Found at i:247137 original size:22 final size:22
Alignment explanation
Indices: 247109--247162 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
247099 TTTGTCATTG
*
247109 GTATCGATACATGTATCAAAAC
1 GTATCGATACATGTATCAAAAA
*
247131 GTATCGATACATGTGTCAAAAA
1 GTATCGATACATGTATCAAAAA
*
247153 GTAGCGATAC
1 GTATCGATAC
247163 TTTATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (22 bp):
GTATCGATACATGTATCAAAAA
Found at i:248841 original size:24 final size:24
Alignment explanation
Indices: 248822--248877 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
248812 CGAAATTTAT
248822 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
248846 ATTTAAGTTCAAACT-ACAATT-AA
1 ATTGAAATTCAAACTCA-AATTGAA
248869 ATATGAAAT
1 AT-TGAAAT
248878 GAACATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:249563 original size:131 final size:130
Alignment explanation
Indices: 249289--249649 Score: 375
Period size: 131 Copynumber: 2.7 Consensus size: 130
249279 AATAATTTTA
* * * * ** *
249289 CGAGTGAAAGCGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTTTCGTGCAATAAAAC
1 CGAGTGAAAACGATAATATCTAATTATTTCCAATC-AAAATAAATGACCTCTCATACCTTAAAGC
* * * * * ** *
249354 AATCATTTATTACCCCTAATTGAAATAAAGAGATATTACTATTTCTTCTTAAAATTCAATATCGA
65 AATCATTTATTACTCC-AATCGAAATAAAGAGATATCACTATTCCATCTTAAAAAACAATATCAA
249419 TT
129 TT
* * * *
249421 CAAGTGAAAACGATGATATCTAATGATTTACAATCAATAATAAATGACCTCTCATACCTTAAAGC
1 CGAGTGAAAACGATAATATCTAATTATTTCCAATCAA-AATAAATGACCTCTCATACCTTAAAGC
* * * *
249486 GATCATTTATTGCTCCAATCGAAATAAAGAGATATCACTATTCCATCTTAAAAAACGATATTAAT
65 AATCATTTATTACTCCAATCGAAATAAAGAGATATCACTATTCCATCTTAAAAAACAATATCAAT
249551 T
130 T
* * * * * *
249552 CGAGAGAAAACG-TCAATATCAAATTTTTTCCAATCGAGAATAAATAACCTCTCATTCCTTAAAG
1 CGAGTGAAAACGAT-AATATCTAATTATTTCCAATC-AAAATAAATGACCTCTCATACCTTAAAG
* *
249616 CAATCATTTATTACTCCGACCGAAATGAAA-AGAT
64 CAATCATTTATTACTCCAATCGAAAT-AAAGAGAT
249650 TTTACTTTTC
Statistics
Matches: 188, Mismatches: 37, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
130 1 0.01
131 119 0.63
132 68 0.36
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (130 bp):
CGAGTGAAAACGATAATATCTAATTATTTCCAATCAAAATAAATGACCTCTCATACCTTAAAGCA
ATCATTTATTACTCCAATCGAAATAAAGAGATATCACTATTCCATCTTAAAAAACAATATCAATT
Found at i:252298 original size:21 final size:21
Alignment explanation
Indices: 252272--252316 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
252262 GATTTCTGGG
* *
252272 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
252293 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
252314 CAA
1 CAA
252317 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:253836 original size:31 final size:31
Alignment explanation
Indices: 253715--253842 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
253705 AGAGTCGAGG
*
253715 GTTTACCTATGTTCTACGGAATATATGGACAA
1 GTTTACCTATGTTCTACGGAACATATGGAC-A
* *
253747 TTTTACCTATG-TCTTTC-GAGACATATGGACA
1 GTTTACCTATGTTC-TACGGA-ACATATGGACA
* *
253778 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * *
253809 GTTTACCTAGGTTCTTCGGGACCTATGGATA
1 GTTTACCTATGTTCTACGGAACATATGGACA
253840 GTT
1 GTT
253843 ACCGAGGATC
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
31 53 0.68
32 25 0.32
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:253868 original size:30 final size:30
Alignment explanation
Indices: 253834--253900 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
253824 TCGGGACCTA
253834 TGGATAGTTACCGAGGATCTTTATGACATC
1 TGGATAGTTACCGAGGATCTTTATGACATC
*
253864 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACATC
253894 TGGATAG
1 TGGATAG
253901 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACATC
Found at i:258797 original size:31 final size:31
Alignment explanation
Indices: 258676--258803 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
258666 AGAGTCGAGG
*
258676 GTTTACCTTTGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
258707 GTTTTACCTATG-TCTTTC-GAGATATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
258739 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * *
258770 GTTTACCTAGGTTCTTCGGGACCTATGGATA
1 GTTTACCTATGTTCTACGGAACATATGGACA
258801 GTT
1 GTT
258804 ACCGAGGATC
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
31 52 0.67
32 26 0.33
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:258823 original size:30 final size:30
Alignment explanation
Indices: 258789--258861 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
258779 GGTTCTTCGG
*
258789 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
258819 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
258849 GACCTCTGGATAG
1 GACCTCTGGATAG
258862 GTCCTTTGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:259626 original size:9 final size:9
Alignment explanation
Indices: 259609--259639 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
259599 ATTAATTAAT
*
259609 TAATAATAA
1 TAATTATAA
259618 TAATTATAA
1 TAATTATAA
259627 TAATTATAA
1 TAATTATAA
259636 TAAT
1 TAAT
259640 AAAATGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATTATAA
Found at i:278829 original size:30 final size:30
Alignment explanation
Indices: 278793--278855 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
278783 ACAGTAGACA
*
278793 TTGCATATCGACCTCCAGTGGCAACTGGTT
1 TTGCATATCGACCTCCAATGGCAACTGGTT
*
278823 TTGCATATTGACCTCCAATGGCAACTGGTT
1 TTGCATATCGACCTCCAATGGCAACTGGTT
278853 TTG
1 TTG
278856 TATCTGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (30 bp):
TTGCATATCGACCTCCAATGGCAACTGGTT
Found at i:281401 original size:144 final size:144
Alignment explanation
Indices: 281141--281427 Score: 558
Period size: 144 Copynumber: 2.0 Consensus size: 144
281131 TTCTTACGAG
281141 ACTTAGGTTGGTTTTGCTATGGCGAGAAGTTATTTTACGCTAAGAATGATTAGTGTGTCTATGCT
1 ACTTAGGTTGGTTTTGCTATGGCGAGAAGTTATTTTACGCTAAGAATGATTAGTGTGTCTATGCT
281206 TAGGCTGTCTAACAGGATTACTAGATTATTCAAGAACGGTTGCTACGACAATACTACACGACATG
66 TAGGCTGTCTAACAGGATTACTAGATTATTCAAGAACGGTTGCTACGACAATACTACACGACATG
281271 AGCTACAACCTTTC
131 AGCTACAACCTTTC
281285 ACTTAGGTTGGTTTTGCTATGGCGAGAAGTTATTTTACGCTAAGAATGATTTAGTGTG-CTATGC
1 ACTTAGGTTGGTTTTGCTATGGCGAGAAGTTATTTTACGCTAAGAATGA-TTAGTGTGTCTATGC
281349 TTAGGCTGTCTAACAGGATTACTAGATTATTCAAGAACGGTTGCTACGACAATACTACACGACAT
65 TTAGGCTGTCTAACAGGATTACTAGATTATTCAAGAACGGTTGCTACGACAATACTACACGACAT
281414 GAGCTACAACCTTT
130 GAGCTACAACCTTT
281428 GGTTTGTCAA
Statistics
Matches: 142, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
144 134 0.94
145 8 0.06
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (144 bp):
ACTTAGGTTGGTTTTGCTATGGCGAGAAGTTATTTTACGCTAAGAATGATTAGTGTGTCTATGCT
TAGGCTGTCTAACAGGATTACTAGATTATTCAAGAACGGTTGCTACGACAATACTACACGACATG
AGCTACAACCTTTC
Found at i:286788 original size:24 final size:26
Alignment explanation
Indices: 286756--286805 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 26
286746 TGCCACGACT
286756 TCAACCCATTTGG-AAACAT-GTCTA
1 TCAACCCATTTGGAAAACATAGTCTA
286780 TCAACCCATTTGGAAAACATAGTCTA
1 TCAACCCATTTGGAAAACATAGTCTA
286806 CTACCAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.54
25 6 0.25
26 5 0.21
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (26 bp):
TCAACCCATTTGGAAAACATAGTCTA
Found at i:292961 original size:71 final size:71
Alignment explanation
Indices: 292879--293012 Score: 252
Period size: 71 Copynumber: 1.9 Consensus size: 71
292869 TAACAATCTA
292879 AACTTTGAAACTAAAACTCAACCAAAAAAAGTCAA-CACAATATAATTAAACATTAGTGAAAAAG
1 AACTTTGAAACTAAAACTCAACC-AAAAAAGTCAACCACAATATAATTAAACATTAGTGAAAAAG
292943 GAAAACT
65 GAAAACT
292950 AACTTTGAAACTAAAACTCAACCAAAAAAGTCAACCACAATATAATTAAACATTAGTGAAAAA
1 AACTTTGAAACTAAAACTCAACCAAAAAAGTCAACCACAATATAATTAAACATTAGTGAAAAA
293013 AAGGAAAGCC
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
70 11 0.18
71 51 0.82
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.20
Consensus pattern (71 bp):
AACTTTGAAACTAAAACTCAACCAAAAAAGTCAACCACAATATAATTAAACATTAGTGAAAAAGG
AAAACT
Found at i:294276 original size:44 final size:44
Alignment explanation
Indices: 294240--294379 Score: 168
Period size: 44 Copynumber: 3.3 Consensus size: 44
294230 AAAATAAATC
*
294240 TAAATAA-TAAT-TATTAATTTATTAATACATAATAAAAATGA-
1 TAAATAACTAATCTATTAATTTATTAATAAATAATAAAAATGAT
*
294281 TAAATTAACTAATCTATTAATTTCTTAATAAATAATAAAAATGA-
1 TAAA-TAACTAATCTATTAATTTATTAATAAATAATAAAAATGAT
* *
294325 TATATTAACTAATCTATTAATTTTTTAATAAATAAT-AAAAT-AT
1 TA-AATAACTAATCTATTAATTTATTAATAAATAATAAAAATGAT
294368 TATAATAA-TAAT
1 TA-AATAACTAAT
294380 ATTTTTAATA
Statistics
Matches: 89, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
41 4 0.04
42 8 0.09
43 16 0.18
44 60 0.67
45 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (44 bp):
TAAATAACTAATCTATTAATTTATTAATAAATAATAAAAATGAT
Found at i:302327 original size:50 final size:50
Alignment explanation
Indices: 302235--302381 Score: 206
Period size: 50 Copynumber: 2.9 Consensus size: 50
302225 AGATAGGCGC
* * *
302235 AGTCTTGAAAGGTTGGTTAGATAATAATGTCTT-AATGACTTCACCTTGACT
1 AGTCTT-AAAGATTGGTTAGGTAATAATTTCTTCAATG-CTTCACCTTGACT
* *
302286 ATTCTTAAAGATTGGTTAGGTAATAATTTCTTCAATGCTTCACCTTGCCT
1 AGTCTTAAAGATTGGTTAGGTAATAATTTCTTCAATGCTTCACCTTGACT
* *
302336 AGTCTTAAAGATTCGTTAGGTAATAATTTCTTCAATACTTCACCTT
1 AGTCTTAAAGATTGGTTAGGTAATAATTTCTTCAATGCTTCACCTT
302382 TTGAGTCCCC
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
50 78 0.90
51 9 0.10
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (50 bp):
AGTCTTAAAGATTGGTTAGGTAATAATTTCTTCAATGCTTCACCTTGACT
Found at i:307513 original size:19 final size:19
Alignment explanation
Indices: 307491--307537 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
307481 AAAATCGCCA
307491 TGCGATCTCTAATTCGCAT
1 TGCGATCTCTAATTCGCAT
307510 TGCGATCTCTAATTCGCAT
1 TGCGATCTCTAATTCGCAT
*
307529 TGTGATCTC
1 TGCGATCTC
307538 CACTATCGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (19 bp):
TGCGATCTCTAATTCGCAT
Found at i:307600 original size:20 final size:20
Alignment explanation
Indices: 307575--307903 Score: 178
Period size: 20 Copynumber: 16.4 Consensus size: 20
307565 TTGAAAATTA
*
307575 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCAATTCG
*
307595 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCAATTCG
* ** *
307615 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCAATTCG
*
307636 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCAATTCG
* ** *
307656 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCAATTCG
*
307677 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCAATTCG
* ** *
307697 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCAATTCG
*
307718 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCAATTCG
* * *
307738 CGTTGCGATAGTCTACAGTT-G
1 CGTTGCGAT--TTTCCAATTCG
307759 TCGTTGCGATTTTCCAAATT--
1 -CGTTGCGATTTTCC-AATTCG
** * *
307779 CGTTGCGATAGTCTACA-GCTG
1 CGTTGCGATTTTCCA-ATTC-G
307800 TCGTTGCGATTTTCCAAATT--
1 -CGTTGCGATTTTCC-AATTCG
*
307820 CGTTGCGA------AAGTCG
1 CGTTGCGATTTTCCAATTCG
* *
307834 CGTTGCGATTTTCTAGTTCG
1 CGTTGCGATTTTCCAATTCG
* ** *
307854 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCAATTCG
*
307875 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCAATTCG
307895 CGTTGCGAT
1 CGTTGCGAT
307904 AGTCTACAGT
Statistics
Matches: 229, Mismatches: 57, Indels: 46
0.69 0.17 0.14
Matches are distributed among these distances:
12 3 0.01
14 8 0.03
18 1 0.00
19 20 0.09
20 104 0.45
21 64 0.28
22 28 0.12
23 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTTCCAATTCG
Found at i:307619 original size:61 final size:61
Alignment explanation
Indices: 307550--307903 Score: 259
Period size: 61 Copynumber: 5.9 Consensus size: 61
307540 CTATCGCAAA
* * *
307550 TTCGCGTTGCGATAATTGAAAATTACGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAG
* * * ** *
307611 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAATTCGCGTTGCGAT-TTTCCAG
* *** * * ** *
307673 ATCGCGTTGCGAT--TTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTGAAAATT-GCGTTGCGAT-TTTCCAATTCGCGTTGCGATTTTCCAG
* * * *
307734 TTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACA
1 TTCGCGTTGCGATAGT-TGAAAATTG-CGTTGCGATTTTCC-AATTCGCGTTGCGAT--TTTCCA
307796 G
61 G
* * ** * *
307797 CT-GTCGTTGCGAT-TTTCCAAATT-CGTTGCGA------AAGTCGCGTTGCGATTTTCTAG
1 TTCG-CGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAG
* *
307850 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGAT
1 TTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAATTCGCGTTGCGAT
307904 AGTCTACAGT
Statistics
Matches: 224, Mismatches: 46, Indels: 46
0.71 0.15 0.15
Matches are distributed among these distances:
53 17 0.08
54 7 0.03
55 17 0.08
60 12 0.05
61 99 0.44
62 38 0.17
63 33 0.15
64 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (61 bp):
TTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAG
Found at i:307637 original size:41 final size:41
Alignment explanation
Indices: 307592--307906 Score: 379
Period size: 41 Copynumber: 7.9 Consensus size: 41
307582 ATTTTCCATT
307592 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
*
307633 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
307674 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
* *
307715 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCT-ACAG
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT-TGAAAA
* * *
307756 TTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCT--ACA
1 TCG-CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGT-TGAAAA
* * *
307796 GCTGTCGTTGCGATTTTCCAAATT--CGTTGC-------GAAAG
1 TC-G-CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTTGAAAA
*
307831 TCGCGTTGCGATTTTCTAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
307872 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
307907 CTACAGTTGT
Statistics
Matches: 241, Mismatches: 18, Indels: 30
0.83 0.06 0.10
Matches are distributed among these distances:
32 3 0.01
33 13 0.05
34 7 0.03
35 2 0.01
41 198 0.82
42 15 0.06
43 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
Found at i:307638 original size:21 final size:21
Alignment explanation
Indices: 307612--307726 Score: 126
Period size: 21 Copynumber: 5.6 Consensus size: 21
307602 ATTTTCCAGT
307612 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
307633 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
307653 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
307674 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTGAAAA
307694 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
307715 TCGCGTTGCGAT
1 TCGCGTTGCGAT
307727 TTTCCAGTTC
Statistics
Matches: 72, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
20 30 0.42
21 42 0.58
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:307644 original size:82 final size:82
Alignment explanation
Indices: 307551--307885 Score: 252
Period size: 82 Copynumber: 4.2 Consensus size: 82
307541 TATCGCAAAT
* * **
307551 TCGCGTTGCGATAATTGAAAATT-ACGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTCCAGTTC
1 TCGCGTTGCGAT--TTGAAAATTCACGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCAGTTC
307614 GCGTTGCGATAGTTGAAAA
64 GCGTTGCGATAGTTGAAAA
*** * * *
307633 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTCGC
1 TCGCGTTGCGATTTGAAAATTCACGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCAGTTCGC
307698 GTTGCGATAGTTGAAAA
66 GTTGCGATAGTTGAAAA
*** * * * * * *
307715 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAG-TCTACAGTTGTCGTTGCGATTTTCCAAATT
1 TCGCGTTGCGATTTGAAAATTCACGTTGCGATAGTTC-AAAATCG-CGTTGCGATTTTCC-AGTT
*
307779 --CGTTGCGATAGTCT--ACA
63 CGCGTTGCGATAGT-TGAAAA
* ** * *
307796 GCTGTCGTTGCGATTTTCCAAATT--CGTTGC----G---AAAGTCGCGTTGCGATTTTCTAGTT
1 TC-G-CGTTGCGA-TTTGAAAATTCACGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCAGTT
307852 CGCGTTGCGATAGTTGAAAA
63 CGCGTTGCGATAGTTGAAAA
307872 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
307886 TCCAGTTCGC
Statistics
Matches: 213, Mismatches: 27, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
73 6 0.03
74 22 0.10
75 18 0.08
76 3 0.01
78 1 0.00
80 5 0.02
81 13 0.06
82 112 0.53
83 23 0.11
84 10 0.05
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (82 bp):
TCGCGTTGCGATTTGAAAATTCACGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCAGTTCGC
GTTGCGATAGTTGAAAA
Found at i:307763 original size:22 final size:22
Alignment explanation
Indices: 307738--307809 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
307728 TTCCAGTTCG
*
307738 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
* * *
307760 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGATGT
*
307779 CGTTGCGATAGTCTACAGCTGT
1 CGTTGCGATAGTCTACAGATGT
307801 CGTTGCGAT
1 CGTTGCGAT
307810 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGATGT
Found at i:307783 original size:19 final size:19
Alignment explanation
Indices: 307759--307827 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
307749 TCTACAGTTG
307759 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
307778 TCGTTGCGATAGTCTACAGCT
1 TCGTTGCGAT--TTTCCAAAT
307799 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
307819 TCGTTGCGA
1 TCGTTGCGA
307828 AAGTCGCGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:308077 original size:5 final size:5
Alignment explanation
Indices: 308043--308121 Score: 95
Period size: 5 Copynumber: 14.6 Consensus size: 5
308033 AGTATTACCA
308043 CGACC ACGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC ACGACC
1 CGACC -CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC -CGACC
*
308093 CGACC CGACC CCACC ACGACC CGACC CGA
1 CGACC CGACC CGACC -CGACC CGACC CGA
308122 GACGAGACGA
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
5 37 0.54
6 32 0.46
ACGTcount: A:0.27, C:0.56, G:0.18, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:308087 original size:21 final size:21
Alignment explanation
Indices: 308039--308121 Score: 130
Period size: 21 Copynumber: 3.8 Consensus size: 21
308029 GATAAGTATT
308039 ACCACGACCACGACCACGACCACG
1 ACCACGACC-CGACC-CGACC-CG
308063 ACCACGACCCGACCCGACCCG
1 ACCACGACCCGACCCGACCCG
*
308084 ACCACGACCCGACCCGACCCC
1 ACCACGACCCGACCCGACCCG
308105 ACCACGACCCGACCCGA
1 ACCACGACCCGACCCGA
308122 GACGAGACGA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
21 39 0.67
22 5 0.09
23 5 0.09
24 9 0.16
ACGTcount: A:0.28, C:0.55, G:0.17, T:0.00
Consensus pattern (21 bp):
ACCACGACCCGACCCGACCCG
Found at i:312072 original size:3 final size:3
Alignment explanation
Indices: 312064--312136 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
312054 TTTTTATCTA
312064 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
312111 TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
312137 AATATATATT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:312148 original size:11 final size:11
Alignment explanation
Indices: 312132--312163 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
312122 TTATTATTAT
312132 TATTAAATATA
1 TATTAAATATA
312143 TATTAAATATA
1 TATTAAATATA
312154 TATATAAATA
1 TAT-TAAATA
312164 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:312651 original size:14 final size:14
Alignment explanation
Indices: 312632--312658 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
312622 AGAGAGACGG
312632 AGAGAAAAAAAAAC
1 AGAGAAAAAAAAAC
312646 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
312659 AGATATACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAAAAAC
Done.