Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009629.1 Hibiscus syriacus cultivar Beakdansim tig00117022_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: 453070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:4705 original size:15 final size:15
Alignment explanation
Indices: 4680--4713 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4670 AACGTCCTTT
4680 AAAATATTTTAAGA-
1 AAAATATTTTAAGAC
4694 AAAATCATTTTAAGAC
1 AAAAT-ATTTTAAGAC
4710 AAAA
1 AAAA
4714 ATTGGTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 9 0.50
16 4 0.22
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (15 bp):
AAAATATTTTAAGAC
Found at i:6875 original size:17 final size:17
Alignment explanation
Indices: 6853--6896 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
6843 AAAATGTAGT
*
6853 AATAATACTATTAATAA
1 AATAATAATATTAATAA
*
6870 AATAATAATATTAATAGT
1 AATAATAATATTAATA-A
6888 AATAATAAT
1 AATAATAAT
6897 TAAAACACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AATAATAATATTAATAA
Found at i:7234 original size:30 final size:30
Alignment explanation
Indices: 7198--7262 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
7188 TTTTGGCTCT
7198 AACGTCTTATTTTAGGATAAAATAGTCTCC
1 AACGTCTTATTTTAGGATAAAATAGTCTCC
*
7228 AACGTCTTATTTTAGGATAAAATAGTCTCT
1 AACGTCTTATTTTAGGATAAAATAGTCTCC
7258 AACGT
1 AACGT
7263 TTGATCTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (30 bp):
AACGTCTTATTTTAGGATAAAATAGTCTCC
Found at i:11940 original size:20 final size:18
Alignment explanation
Indices: 11908--11961 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
11898 AACTCTAAGA
11908 AAAATATAATAACTAAAT
1 AAAATATAATAACTAAAT
*
11926 AAAATATTAAGTAACTATAT
1 AAAATA-TAA-TAACTAAAT
*
11946 AGAAATAGAATAACTA
1 A-AAATATAATAACTA
11962 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 9 0.29
20 11 0.35
21 5 0.16
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (18 bp):
AAAATATAATAACTAAAT
Found at i:12253 original size:19 final size:19
Alignment explanation
Indices: 12229--12270 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
12219 ATATCCTGTC
* *
12229 AATAAAATATTATTTTAAA
1 AATAAAAGATTAATTTAAA
12248 AAT-AAAGATTAATTTAAA
1 AATAAAAGATTAATTTAAA
12266 AATAA
1 AATAA
12271 TTTTCATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAAAAGATTAATTTAAA
Found at i:15485 original size:24 final size:24
Alignment explanation
Indices: 15458--15562 Score: 138
Period size: 24 Copynumber: 4.4 Consensus size: 24
15448 TATATCAAAA
* * *
15458 ATCAAATCATAATTCACGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
* * *
15482 ATCATATCAAAATCCAGGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
*
15506 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
*
15530 ATCAGATCATAATCCATGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
15554 ATCAGATCA
1 ATCAGATCA
15563 GAAATCAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (24 bp):
ATCAGATCATAATCCAAGTCAAGT
Found at i:15582 original size:48 final size:48
Alignment explanation
Indices: 15476--15582 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
15466 ATAATTCACG
* * *
15476 TCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAG
1 TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
* * *
15524 TCAAGTATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAAA
1 TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAG-AATCCAAA
15572 TCGAA-AATCAG
1 TC-AAGAATCAG
15583 GTAAAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 47 0.90
49 5 0.10
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (48 bp):
TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
Found at i:17989 original size:22 final size:19
Alignment explanation
Indices: 17964--18011 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 19
17954 TAATGCCCGA
17964 TCAACGTCGGTCAAAGTTCCAG
1 TCAACGT-GGTCAAAG--CCAG
*
17986 TCAACTGTGGTCAACGCCAG
1 TCAAC-GTGGTCAAAGCCAG
18006 TCAACG
1 TCAACG
18012 ATCGACTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 9 0.38
22 12 0.50
23 2 0.08
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (19 bp):
TCAACGTGGTCAAAGCCAG
Found at i:33180 original size:2 final size:2
Alignment explanation
Indices: 33173--33211 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
33163 ATTAGACCGT
33173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33212 TTAACTCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35530 original size:12 final size:13
Alignment explanation
Indices: 35492--35538 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 13
35482 TAAAATTATA
35492 TAAATAATAATAT
1 TAAATAATAATAT
*
35505 TGATATAAATAATAT
1 T-AAAT-AATAATAT
35520 TAAATAA-AATAT
1 TAAATAATAATAT
35532 TATAATA
1 TA-AATA
35539 TTTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 7 0.24
13 7 0.24
14 6 0.21
15 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
TAAATAATAATAT
Found at i:39099 original size:14 final size:14
Alignment explanation
Indices: 39080--39107 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39070 AAAATTTCAC
39080 TTGTAACGTTTGCT
1 TTGTAACGTTTGCT
39094 TTGTAACGTTTGCT
1 TTGTAACGTTTGCT
39108 CCCATCGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
TTGTAACGTTTGCT
Found at i:40932 original size:15 final size:16
Alignment explanation
Indices: 40904--40935 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40894 AAAATCTTTC
40904 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
40920 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
40935 T
1 T
40936 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:41709 original size:16 final size:16
Alignment explanation
Indices: 41685--41718 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41675 TATCGCCGAC
*
41685 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
41701 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
41717 CG
1 CG
41719 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:43936 original size:114 final size:113
Alignment explanation
Indices: 43738--43950 Score: 277
Period size: 114 Copynumber: 1.9 Consensus size: 113
43728 TCAGTTTTGT
* * * * * *
43738 TAGCAGAAGTGATCAGAAACTGAAGTTTTCTTTACTTTGATTATAATTGAGGAGACAATATTTGT
1 TAGCAGAAGTGATCAGAAACTCAAGCTTTCTTTACGTAGATTATAATCGAGAAGACAATATTTGT
* *
43803 TATAAGAGTATAGTATTTGA-TTTTGGTCAAATTGTTGTTCTGGTCCA
66 TATAAAAGTATAGTATTTGATTTTTGGTAAAATTGTTGTTCTGGTCCA
*
43850 TAGCAGAAGTGATCAAGAAACTCAAGCTTTCTTATGCGTAGA-TATTAATCGAGAAGACAATATT
1 TAGCAGAAGTGATC-AGAAACTCAAGCTTTCTT-TACGTAGATTA-TAATCGAGAAGACAATATT
* * *
43914 TGTTGTAAAAGTATGGTTTTTGATTTTTGGTAAAATT
63 TGTTATAAAAGTATAGTATTTGATTTTTGGTAAAATT
43951 TGGTTTTGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
112 14 0.16
113 18 0.21
114 41 0.48
115 12 0.14
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (113 bp):
TAGCAGAAGTGATCAGAAACTCAAGCTTTCTTTACGTAGATTATAATCGAGAAGACAATATTTGT
TATAAAAGTATAGTATTTGATTTTTGGTAAAATTGTTGTTCTGGTCCA
Found at i:44836 original size:35 final size:35
Alignment explanation
Indices: 44787--44945 Score: 201
Period size: 35 Copynumber: 4.5 Consensus size: 35
44777 TAGTAAACCA
*
44787 TCCGTTCTAGTTGAATCGAAAGTGCGATGCCTCCT
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCT
* * * *
44822 TCGGTTCTACTTGAATCAAAAGTGCAATGCTTCCT
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCT
* *
44857 TCCGTTCTACTTGAATCAAAAGTGTGATGCCTCCT
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCT
* * * *
44892 TTCGTTCGACTTGAATCGAAAGTGTGATGCCTCAT
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCT
* *
44927 TCCATTCGACTTGAATCGA
1 TCCGTTCTACTTGAATCGA
44946 TGCAAACTTT
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 109 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (35 bp):
TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCT
Found at i:49389 original size:36 final size:36
Alignment explanation
Indices: 49337--49409 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
49327 TCTCAAGTCC
49337 ATATATTTTTAATATTTTTAATAACATTTTATTTAA
1 ATATATTTTTAATATTTTTAATAACATTTTATTTAA
* * *
49373 ATATTTTTTTACTATTTTTAATAATATTTTATTTAA
1 ATATATTTTTAATATTTTTAATAACATTTTATTTAA
49409 A
1 A
49410 AAAATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (36 bp):
ATATATTTTTAATATTTTTAATAACATTTTATTTAA
Found at i:63300 original size:56 final size:56
Alignment explanation
Indices: 63227--63357 Score: 199
Period size: 56 Copynumber: 2.3 Consensus size: 56
63217 AGCAGGGGCC
* * **
63227 CCGAAATCGAATATATCTTTCAGTTGTTGCCATTAATAAGCATAAAAATAGGGGTT
1 CCGAAATCGAATATATCTATCAGTTATTGCCATTAATAAGCATAAAAATAAAGGTT
*
63283 CCGAAATCGAATATATCTATCAGTTATTGCTATTAATAAGCATAAAAATAAAGGTT
1 CCGAAATCGAATATATCTATCAGTTATTGCCATTAATAAGCATAAAAATAAAGGTT
* *
63339 CTGAAATCGAATCTATCTA
1 CCGAAATCGAATATATCTA
63358 GAAAATAGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (56 bp):
CCGAAATCGAATATATCTATCAGTTATTGCCATTAATAAGCATAAAAATAAAGGTT
Found at i:71038 original size:23 final size:23
Alignment explanation
Indices: 70994--71038 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
70984 ATTATTATAT
*
70994 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
71017 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
71039 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:80107 original size:21 final size:21
Alignment explanation
Indices: 80082--80125 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
80072 TCGATAAAAA
80082 TTATTTAAAACATTATTATTT
1 TTATTTAAAACATTATTATTT
* *
80103 TTATTTAAAATATTATTGTTT
1 TTATTTAAAACATTATTATTT
80124 TT
1 TT
80126 TAATATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATTTAAAACATTATTATTT
Found at i:80176 original size:21 final size:21
Alignment explanation
Indices: 80151--80197 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
80141 AGTGTCTAAC
*
80151 AATAACAAAATCAGTATAAAT
1 AATAACAAAATCAGTAAAAAT
**
80172 AATAACAAAATTTGTAAAAAT
1 AATAACAAAATCAGTAAAAAT
80193 AATAA
1 AATAA
80198 TATTTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (21 bp):
AATAACAAAATCAGTAAAAAT
Found at i:90656 original size:84 final size:83
Alignment explanation
Indices: 90493--91489 Score: 937
Period size: 84 Copynumber: 12.1 Consensus size: 83
90483 TAAACAAACT
* * * * * ** * *
90493 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGTCCCCCGAGTTCGATTACAC
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
*
90555 TCAGCTTCGAAGGCACATC
66 TCAGC-TCAAAGGCACATC
* * * * *
90574 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCTACTACG
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACG
90639 CTCAGCTCAAAGGCACATC
65 CTCAGCTCAAAGGCACATC
** * * ** * *
90658 ATTTGTAGCATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* *
90720 TCAGCTTCGAGGGCACATC
66 TCAGC-TCAAAGGCACATC
* * *
90739 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACG
90804 CTCAGCTCAAAGGCACATC
65 CTCAGCTCAAAGGCACATC
* * * * ** * *
90823 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* * *
90885 TCAGCTTCGAGGGCATATC
66 TCAGC-TCAAAGGCACATC
* * *
90904 ATTCACAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACGC
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* *
90969 TCAGCTCCAAGGCATATC
66 TCAGCTCAAAGGCACATC
* * * * * * *
90987 ATTTGCATCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACG
* *
91052 CTTAGCTCAACGGCACATC
65 CTCAGCTCAAAGGCACATC
* * * ** * ** * *
91071 ATTTGCAGCATAGCTTAAGTCGAGAATAGCTATCTG---CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* * *
91133 TCAGCTTCGAGGGCATATC
66 TCAGC-TCAAAGGCACATC
* * *
91152 ATTCACAACATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* *
91217 TCAGCTCCAAGGCATATC
66 TCAGCTCAAAGGCACATC
* * * * * * *
91235 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAACACCTTTGAGTTCGACTACG
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACG
* *
91300 CTTAGCTCAACGGCACATC
65 CTCAGCTCAAAGGCACATC
* * * * * * * *
91319 ATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTG---CCAAAGACCCTCGAGTTCGATTACAC
1 ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
* * *
91381 TCAGCTTCGAGGGCATATC
66 TCAGC-TCAAAGGCACATC
* * * *
91400 ATTTACAGTATAACTCAAGGCTATG-AGGGTTATCTGTCACCAAAGACTTTCGAGTTCGACTACG
1 ATTTACAGCATAACTTAAGTCTA-GAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
91464 CTCAGCTCAAAGGCACATC
65 CTCAGCTCAAAGGCACATC
91483 ATTTACA
1 ATTTACA
91490 ATATAGCCCA
Statistics
Matches: 734, Mismatches: 158, Indels: 46
0.78 0.17 0.05
Matches are distributed among these distances:
80 97 0.13
81 187 0.25
82 1 0.00
83 101 0.14
84 300 0.41
85 48 0.07
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (83 bp):
ATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCAAAGGCACATC
Found at i:90771 original size:165 final size:164
Alignment explanation
Indices: 90493--91486 Score: 1181
Period size: 165 Copynumber: 6.0 Consensus size: 164
90483 TAAACAAACT
*
90493 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGTCCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * *
90558 GCTTCGAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACC
*
90623 TTCGAGTTCTACTACGCTCAGCTCAAAGGCACATC
130 TTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
* *
90658 ATTTGTAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
90723 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACC
90788 TTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
130 TTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
90823 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * *
90888 GCTTCGAGGGCATATCATTCACAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
* * *
90953 TCGAGTTTGACTACGCTCAGCTCCAAGGCATATC
131 TCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
* * * * * * *** * *
90987 ATTTGCATCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTACA
* * * * * * * * ** *
91052 CTTAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAATAGCTATCTG---CCAAAG
62 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAG
** * * * * *
91113 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
127 ACCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATC
** * * * * * ** * *
91152 ATTCACAACATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACAC
* * * * * * * * * * *
91217 TCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAC
63 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAG
* * *
91281 ACCTTTGAGTTCGACTACGCTTAGCTCAACGGCACATC
127 ACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
* *
91319 ATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * *
91384 GCTTCGAGGGCATATCATTTACAGTATAACTCAAGGCTATG-AGGGTTATCTGTCACCAAAGACT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA-GAAGGGTTATCTGTCACCAAAGACC
91448 TTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
130 TTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
91483 ATTT
1 ATTT
91487 ACAATATAGC
Statistics
Matches: 714, Mismatches: 102, Indels: 27
0.85 0.12 0.03
Matches are distributed among these distances:
164 232 0.32
165 357 0.50
166 1 0.00
167 78 0.11
168 46 0.06
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (164 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
TCGAGTTCGACTACGCTCAGCTCAAAGGCACATC
Found at i:91046 original size:248 final size:248
Alignment explanation
Indices: 90664--91486 Score: 1278
Period size: 248 Copynumber: 3.3 Consensus size: 248
90654 CATCATTTGT
* * * ** * *
90664 AGCATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-
* * * * * * * *
90726 TCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TAACCAAAAGACCTT
65 TCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA-CAAAAGACCTT
* *
90790 CGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
129 TGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTA
90855 TCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCAC
194 TCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCAC
*
90910 AGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACGCTCAGCT
1 AGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
* *
90975 CCAAGGCATATCATTTGCATCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTG
66 CCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTG
* * *
91040 AGTTCGACTACGCTTAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAATAGCTATC
131 AGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATC
91105 TGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCAC
196 TGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCAC
*
91158 AACATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
1 AGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
* *
91223 CCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAACACCTTTG
66 CCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTG
* *
91288 AGTTCGACTACGCTTAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATC
131 AGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATC
* *
91353 TGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTAC
196 TGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCAC
* * *
91406 AGTATAACTCAAGGCTATG-AGGGTTATCTGTCACCAAAGACTTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGTCTA-GAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
*
91470 TCAAAGGCACATCATTT
65 TCCAAGGCACATCATTT
91487 ACAATATAGC
Statistics
Matches: 536, Mismatches: 36, Indels: 8
0.92 0.06 0.01
Matches are distributed among these distances:
246 27 0.05
248 480 0.90
249 29 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (248 bp):
AGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTG
AGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATC
TGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCAC
Found at i:105883 original size:26 final size:28
Alignment explanation
Indices: 105826--105884 Score: 68
Period size: 31 Copynumber: 2.1 Consensus size: 28
105816 CTGAGCTCGA
*
105826 CTCGACTCGACTCGAAAACTCTGAAATGGAG
1 CTCGACTCGACTCGAAAACTCTG--A-CGAG
105857 CTCGACTCGACTCGAAAACTC-G-CGAG
1 CTCGACTCGACTCGAAAACTCTGACGAG
105883 CT
1 CT
105885 TAAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
30 1 0.04
31 21 0.78
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.19
Consensus pattern (28 bp):
CTCGACTCGACTCGAAAACTCTGACGAG
Found at i:108398 original size:2 final size:2
Alignment explanation
Indices: 108327--108383 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
108317 TTCATGTATG
108327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
108369 TA -A TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
108384 TGGTATACGA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:109910 original size:33 final size:34
Alignment explanation
Indices: 109867--109933 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
109857 ATCTTATGTA
109867 TTTAGATTAATTGATAAATAT-TTTTAT-ATAAAAT
1 TTTAGATTAA-TGA-AAATATATTTTATAATAAAAT
109901 TTTA-ATTAATGAAAATATATTTTATAATAAAAT
1 TTTAGATTAATGAAAATATATTTTATAATAAAAT
109934 ATTATTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 6 0.19
32 9 0.29
33 12 0.39
34 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (34 bp):
TTTAGATTAATGAAAATATATTTTATAATAAAAT
Found at i:112009 original size:24 final size:25
Alignment explanation
Indices: 111982--112037 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
111972 CCCTAAATTA
*
111982 ATTTTACATCTTAGC-ATTAAAAAT
1 ATTTTACATCTTAACTATTAAAAAT
** *
112006 ATTTTTTTATCTTAACTATTAAATAT
1 A-TTTTACATCTTAACTATTAAAAAT
112032 ATTTTA
1 ATTTTA
112038 TTCTTTTTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 15 0.60
26 9 0.36
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTTACATCTTAACTATTAAAAAT
Found at i:112012 original size:26 final size:26
Alignment explanation
Indices: 111983--112036 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
111973 CCTAAATTAA
* *
111983 TTTTACATCTTAGC-ATTAAAAATAT
1 TTTTTCATCTTAACTATTAAAAATAT
* *
112008 TTTTTTATCTTAACTATTAAATATAT
1 TTTTTCATCTTAACTATTAAAAATAT
112034 TTT
1 TTT
112037 ATTCTTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTTTCATCTTAACTATTAAAAATAT
Found at i:112210 original size:34 final size:34
Alignment explanation
Indices: 112174--112240 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
112164 AATTTAAGAT
** *
112174 AAATATAATATATTTTTTGTAGTTAAGATAAAATA
1 AAATA-AATATATTTAATGTAGTTAAAATAAAATA
112209 AAATAAATATATTTAATGTAGTTAAAATAAAA
1 AAATAAATATATTTAATGTAGTTAAAATAAAA
112241 ATATATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATAAATATATTTAATGTAGTTAAAATAAAATA
Found at i:112701 original size:27 final size:26
Alignment explanation
Indices: 112671--112743 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
112661 CTTAACTTAT
112671 TAAATATATTTTATTCTTTTTGTAACC
1 TAAATATATTTTATTCTTTTT-TAACC
* **
112698 TAAA-AGTATATTTATTCTATTTTAATT
1 TAAATA-TAT-TTTATTCTTTTTTAACC
*
112725 TAAAATATATTTTAATCTT
1 T-AAATATATTTTATTCTT
112744 ATCCTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
26 1 0.03
27 18 0.49
28 17 0.46
29 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (26 bp):
TAAATATATTTTATTCTTTTTTAACC
Found at i:112714 original size:28 final size:26
Alignment explanation
Indices: 112672--112736 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
112662 TTAACTTATT
*
112672 AAATATATTTTATTCTTTTTGTAACCTA
1 AAATATA-TTTATTCTATTT-TAACCTA
**
112700 AAAGTATATTTATTCTATTTTAATTTA
1 AAA-TATATTTATTCTATTTTAACCTA
112727 AAATATATTT
1 AAATATATTT
112737 TAATCTTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.21
27 8 0.24
28 14 0.42
29 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (26 bp):
AAATATATTTATTCTATTTTAACCTA
Found at i:112931 original size:29 final size:29
Alignment explanation
Indices: 112885--112941 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
112875 ATGTAGTTAA
*
112885 ATAAAAATATATTCTTAAGTTAAGATAAG
1 ATAAAAATATATTCTTAAGTTAAAATAAG
*
112914 ATAAAAGATATGTT-TTAAGTTAAAATAA
1 ATAAAA-ATATATTCTTAAGTTAAAATAA
112942 TAATTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.35
Consensus pattern (29 bp):
ATAAAAATATATTCTTAAGTTAAAATAAG
Found at i:113693 original size:19 final size:21
Alignment explanation
Indices: 113669--113714 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
113659 GTTATTGGTA
113669 AATTTACATTT-A-TTTTAA-T
1 AATTTAC-TTTAATTTTTAACT
113688 AATTTACTTTAATTTTTAACT
1 AATTTACTTTAATTTTTAACT
113709 AATTTA
1 AATTTA
113715 TAATTTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.12
19 8 0.33
20 6 0.25
21 7 0.29
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTACTTTAATTTTTAACT
Found at i:116532 original size:2 final size:2
Alignment explanation
Indices: 116525--116573 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
116515 AATTTAAAAT
116525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116567 TA TA TA T
1 TA TA TA T
116574 TAAAATTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:121828 original size:37 final size:36
Alignment explanation
Indices: 121787--121860 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
121777 GTTGGAAAAT
*
121787 ATTTATAT-ATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTT-TTTAAAAAATTTAAAAT-ATAAA
*
121824 ATTTATATAATTTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAATTTTTTTAAAAAATTTAAAATATAAA
121860 A
1 A
121861 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 6 0.18
37 23 0.68
38 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATAATTTTTTTAAAAAATTTAAAATATAAA
Found at i:122880 original size:29 final size:29
Alignment explanation
Indices: 122840--122913 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
122830 TTTCATATGT
*
122840 TCATGTA-CTCATGTCCTTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
122868 TTATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
122897 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
122914 CTTCATATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 6 0.14
29 36 0.86
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:122946 original size:12 final size:12
Alignment explanation
Indices: 122929--122964 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
122919 TATCATGTTC
122929 TCATATCACATG
1 TCATATCACATG
*
122941 TCATATCACATA
1 TCATATCACATG
122953 TCATATCACATG
1 TCATATCACATG
122965 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:123449 original size:64 final size:63
Alignment explanation
Indices: 123272--123450 Score: 207
Period size: 64 Copynumber: 2.8 Consensus size: 63
123262 TAATGAAGGT
* * ** ** * * * **
123272 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTTTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTACTATTAATGGG
* *
123336 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTTGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTTT-ACTATTAATGGG
123400 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTT
123451 TTATTTTAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.03
64 94 0.97
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTACTATTAATGGG
Found at i:123469 original size:64 final size:63
Alignment explanation
Indices: 123335--123496 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 63
123325 TTATTTTTGG
* * * *
123335 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTTGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAAAGA
* *
123399 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATG-TTTCACTATTAAAGA
** *
123462 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
123497 ATTCAAACAA
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 4 0.05
64 78 0.91
65 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:125651 original size:32 final size:33
Alignment explanation
Indices: 125608--125676 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
125598 AAATGTTTCG
* * * *
125608 GTTTTAGTGTTT-AATATGATTCAAATATGTTA
1 GTTTTAATGTTTCAATAAGACTCAAATACGTTA
*
125640 GTTTTAATGTTTCAATAAGACTCAAATACGTTG
1 GTTTTAATGTTTCAATAAGACTCAAATACGTTA
125673 GTTT
1 GTTT
125677 ATTTTTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.46
Consensus pattern (33 bp):
GTTTTAATGTTTCAATAAGACTCAAATACGTTA
Found at i:125765 original size:21 final size:21
Alignment explanation
Indices: 125728--125787 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
125718 GCTGCAAAAA
125728 TAATAA-AATAA-AAATATAT
1 TAATAATAATAATAAATATAT
125747 TAATAATAATAATAAATATA-
1 TAATAATAATAATAAATATAT
125767 TATATAAT-ATAATAAA-ATAT
1 TA-ATAATAATAATAAATATAT
125787 T
1 T
125788 TTTATAGATC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.24
20 16 0.43
21 12 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAATAAATATAT
Found at i:125767 original size:23 final size:24
Alignment explanation
Indices: 125726--125781 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
125716 GGGCTGCAAA
125726 AATAATAA-AATAAAAATATAT-T
1 AATAATAATAATAAAAATATATAT
*
125748 AATAATAATAATAAATATATATAT
1 AATAATAATAATAAAAATATATAT
125772 AAT-ATAATAA
1 AATAATAATAA
125782 AATATTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 8 0.26
23 19 0.61
24 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AATAATAATAATAAAAATATATAT
Found at i:125793 original size:21 final size:21
Alignment explanation
Indices: 125727--125793 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
125717 GGCTGCAAAA
* *
125727 ATAATAAAATAAAAATATATTA
1 ATAATATAAT-AAAATATATTT
*
125749 ATAATAATAAT-AAATATATAT
1 ATAAT-ATAATAAAATATATTT
*
125770 ATAATATAATAAAATATTTTT
1 ATAATATAATAAAATATATTT
125791 ATA
1 ATA
125794 GATCCGGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.13
21 24 0.63
22 5 0.13
23 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATATAATAAAATATATTT
Found at i:130592 original size:11 final size:11
Alignment explanation
Indices: 130576--130602 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
130566 ATAATATTGA
130576 AACTCGACTCG
1 AACTCGACTCG
130587 AACTCGACTCG
1 AACTCGACTCG
130598 AACTC
1 AACTC
130603 AAAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.37, G:0.15, T:0.19
Consensus pattern (11 bp):
AACTCGACTCG
Found at i:130656 original size:11 final size:11
Alignment explanation
Indices: 130639--130682 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
130629 GCTCAATTTT
130639 AAGCTCGAATC
1 AAGCTCGAATC
* *
130650 CAGCTCGATTC
1 AAGCTCGAATC
130661 AAGCTCGAACTC
1 AAGCTCGAA-TC
*
130673 AAACTCGAAT
1 AAGCTCGAAT
130683 TTGAACCTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (11 bp):
AAGCTCGAATC
Found at i:130955 original size:36 final size:37
Alignment explanation
Indices: 130879--130957 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
130869 AAAGTTTACA
*
130879 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
1 AAATATGACAACACATCCAAATTTATAAAAAGATGAC
* *
130916 AAATATGACAACATATCCAAATTTAT-ACAAGATGAC
1 AAATATGACAACACATCCAAATTTATAAAAAGATGAC
130952 AAATAT
1 AAATAT
130958 CTTGATAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 15 0.38
37 24 0.62
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (37 bp):
AAATATGACAACACATCCAAATTTATAAAAAGATGAC
Found at i:133972 original size:7 final size:7
Alignment explanation
Indices: 133960--133985 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
133950 ATGCATAACT
133960 TAAACCC
1 TAAACCC
133967 TAAACCC
1 TAAACCC
133974 TAAACCC
1 TAAACCC
133981 TAAAC
1 TAAAC
133986 TCTATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:134942 original size:20 final size:20
Alignment explanation
Indices: 134899--134942 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
134889 TAGTTGTATT
**
134899 ATAAAATTTTTAATATATTT
1 ATAAAATTTTTAATATATCA
134919 ATAAAATTTTATAAT-TATCA
1 ATAAAATTTT-TAATATATCA
134939 ATAA
1 ATAA
134943 TGTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAAATTTTTAATATATCA
Found at i:146790 original size:19 final size:19
Alignment explanation
Indices: 146766--146804 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
146756 AGAATGGGTA
146766 TGTTTTGGTTCCACTTTAC
1 TGTTTTGGTTCCACTTTAC
146785 TGTTTTGGTTCCACTTTAC
1 TGTTTTGGTTCCACTTTAC
146804 T
1 T
146805 CCCACTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.15, T:0.54
Consensus pattern (19 bp):
TGTTTTGGTTCCACTTTAC
Found at i:150501 original size:3 final size:3
Alignment explanation
Indices: 150487--150556 Score: 97
Period size: 3 Copynumber: 23.0 Consensus size: 3
150477 TAAAATGTAT
* *
150487 TAA TAA -AA TAA TAA TAA TAC TAA TATA TAA TAA TAA TAC TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A
150533 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
150557 AATTAAATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 52 0.87
4 6 0.10
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:150518 original size:19 final size:19
Alignment explanation
Indices: 150494--150556 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
150484 TATTAATAAA
150494 ATAATAATAATACTAATAT
1 ATAATAATAATACTAATAT
150513 ATAATAATAATACTAATAT
1 ATAATAATAATACTAATAT
*
150532 ATAATAATAATAATAATA-
1 ATAATAATAATACTAATAT
150550 ATAATAA
1 ATAATAA
150557 AATTAAATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 7 0.16
19 36 0.84
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAATAATAATACTAATAT
Found at i:150954 original size:41 final size:40
Alignment explanation
Indices: 150897--150975 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
150887 TGGTTATCTA
150897 GGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTCGG
1 GGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTCGG
* *
150937 GGGGATGACAC-GACTCATATGTGATGAAGAGTTCTGGTC
1 GGGG-TGACACAG-CTCATACGTGATGAAGAGATCTGGTC
150976 ATCTTTAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 5 0.14
41 30 0.86
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.23
Consensus pattern (40 bp):
GGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTCGG
Found at i:151150 original size:133 final size:133
Alignment explanation
Indices: 150753--151251 Score: 635
Period size: 135 Copynumber: 3.7 Consensus size: 133
150743 GAAGAGTTCG
* * * * * * *
150753 GGTTGTCTAAGGGTGACACAATTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACTG-CTC
1 GGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACAC-GACTC
* *
150817 ATACGTGATGAAGAGTTCTTGGCCATCTTTAGTAAGCGTGATAACTCGGTTCCTACGCGATGAGG
65 ATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGG
150882 ACGGCT
129 AC-GCT
*
150888 GGTTATCTAGGGGTGACAC-AGCTCATACGTGATGAAGAGATCTGGTCGGGGGGATGACACGACT
1 GGTTATCTAGGGGTGACACGA-CTCCTACGTGATGAAGAGATCTGGTC-GGGGGATGACACGACT
* * *
150952 CATATGTGATGAAGAGTTCTGGTCATCTTTAGGAATGGTGATAACTCGGTTCCTACGCGATGAGG
64 CATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGG
151017 ACAGCT
129 AC-GCT
* * * * *
151023 GGTTATCTATGGTTGACACGACTCCTACGCGATGAGGAGATCTAGTC-GGGGATGACACGACTCA
1 GGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGACTCA
* * * * *
151087 TACGTGATGAAGAGTTATGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTATGTGATGAGGAC
66 TACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGAC
151152 GTCT
131 G-CT
* * * * * *
151156 GGTTATCTAGGGGTGACACGGCTCCTACGTGATTAAGAGACCTGGTCAGGAGATGACACGGCTCA
1 GGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGACTCA
* *
151221 TACATGATGAAGAGTTCTGGTCATCTTTAGG
66 TACGTGATGAAGAGTTCTGGCCATCTTTAGG
151252 GATAATGATT
Statistics
Matches: 318, Mismatches: 40, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
132 1 0.00
133 115 0.36
134 44 0.14
135 126 0.40
136 32 0.10
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (133 bp):
GGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGACTCA
TACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGAC
GCT
Found at i:151521 original size:27 final size:26
Alignment explanation
Indices: 151464--151522 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
151454 AGAGACACAA
*
151464 TCTCAAAGATTTTTCAAAAGGAACAG
1 TCTCAAAGATTTTTCAAAAGAAACAG
* ** *
151490 ACTCAAAGATTTTTCTCAAGAAAACTG
1 TCTCAAAGATTTTTCAAAAG-AAACAG
151517 TCTCAA
1 TCTCAA
151523 GAGAGACAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (26 bp):
TCTCAAAGATTTTTCAAAAGAAACAG
Found at i:151844 original size:66 final size:65
Alignment explanation
Indices: 151768--151948 Score: 213
Period size: 64 Copynumber: 2.8 Consensus size: 65
151758 AAATTTTCTT
** * * *
151768 AAAAGAGACAAACCTTTGTTTTCATAA-AAACAGACTTAAAGTTTTTTCTTCAAAAGGAACTGTC
1 AAAAGAGACAAAATTTTGTTTTCA-AAGAAACATACTCAAAGTTTTTT-TTCAAAAGAAACTGTC
151832 TA
64 TA
* * * * *
151834 AAAAGAGACAAAATTTTGTTTCCAAAGAAACATACTCAAAG-ATTCTTTCAAAAGAAACTTTCTC
1 AAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTCAAAGTTTTTTTTCAAAAGAAACTGTCTA
* * *
151898 AAAAGAGAAAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTTTTTCA
1 AAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTCAAAGTTTTTTTTCA
151949 TTTTGTTTTA
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
64 53 0.54
65 12 0.12
66 33 0.34
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.30
Consensus pattern (65 bp):
AAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTCAAAGTTTTTTTTCAAAAGAAACTGTCTA
Found at i:152068 original size:30 final size:31
Alignment explanation
Indices: 152014--152072 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
152004 GAGACAAAGT
152014 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
*
152045 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
152073 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:152150 original size:36 final size:37
Alignment explanation
Indices: 152109--152213 Score: 140
Period size: 36 Copynumber: 2.8 Consensus size: 37
152099 CATAATTTGG
* *
152109 AAAATTGTCTCAAGTGAGACAACATTTGTTTTT-AGA
1 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTGAGA
* * *
152145 GAAATTGTCTCAAACGAGACAAAAATTGTTTTTGAGA
1 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTGAGA
*
152182 AAAATTATCTCAAGCGAGACAAAAATTTGTTT
1 AAAATTGTCTCAAGCGAGAC-AAAATTTGTTT
152214 CAAGAAAAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 28 0.48
37 20 0.34
38 10 0.17
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (37 bp):
AAAATTGTCTCAAGCGAGACAAAATTTGTTTTTGAGA
Found at i:152200 original size:37 final size:36
Alignment explanation
Indices: 152109--152222 Score: 138
Period size: 37 Copynumber: 3.1 Consensus size: 36
152099 CATAATTTGG
* * *
152109 AAAATTGTCTCAAGTGAGACAACATTTGTTTTTAGA
1 AAAATTGTCTCAAGCGAGACAAAAATTGTTTTTAGA
* *
152145 GAAATTGTCTCAAACGAGACAAAAATTGTTTTTGAGA
1 AAAATTGTCTCAAGCGAGACAAAAATTGTTTTT-AGA
* **
152182 AAAATTATCTCAAGCGAGACAAAAATTTGTTTCAAGA
1 AAAATTGTCTCAAGCGAGACAAAAA-TTGTTTTTAGA
152219 AAAA
1 AAAA
152223 CACCCTCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
36 28 0.42
37 32 0.48
38 6 0.09
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (36 bp):
AAAATTGTCTCAAGCGAGACAAAAATTGTTTTTAGA
Found at i:156323 original size:17 final size:17
Alignment explanation
Indices: 156285--156323 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
156275 GAATAATAAA
*
156285 TAAAATAAGAAAAAATG
1 TAAAATAACAAAAAATG
* *
156302 GAAAATAACAAAACATG
1 TAAAATAACAAAAAATG
156319 TAAAA
1 TAAAA
156324 AATAATAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (17 bp):
TAAAATAACAAAAAATG
Found at i:156417 original size:17 final size:17
Alignment explanation
Indices: 156397--156443 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
156387 TATTAATGGA
156397 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
* *
156414 GTAAAAGAAATTAAAATG
1 GTAAAA-AAATAAAAAAG
156432 G-AATAAAAATAA
1 GTAA-AAAAATAA
156444 TGTGTACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:156523 original size:26 final size:26
Alignment explanation
Indices: 156469--156523 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
156459 TAGTATTTAC
*
156469 TAATACAAATAAAAATAATAAATATA
1 TAATACAAATAAAAATAATAAATAAA
*
156495 TAATACTAAGTAAAACA-AATAAA-AAA
1 TAATAC-AAATAAAA-ATAATAAATAAA
156521 TAA
1 TAA
156524 AGATATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 11 0.44
27 13 0.52
28 1 0.04
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (26 bp):
TAATACAAATAAAAATAATAAATAAA
Found at i:156570 original size:4 final size:4
Alignment explanation
Indices: 156561--156603 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
156551 TAATTGAAAA
* *
156561 AAAT AAAT AAAT AAA- AAAT ATAAT ATAT ATAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAA
156604 AACAAAATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.80
5 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:156632 original size:39 final size:39
Alignment explanation
Indices: 156589--156671 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
156579 TATAATATAT
156589 ATATAAATAAATAA-AAACAAAATAGAATATTAAGAAAAA
1 ATATAAATAAA-AACAAACAAAATAGAATATTAAGAAAAA
* ** * *
156628 ATATATATAAAAACGTATAAAATATAATATTAAGAAAAA
1 ATATAAATAAAAACAAACAAAATAGAATATTAAGAAAAA
156667 ATATA
1 ATATA
156672 TACATAGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 2 0.05
39 36 0.95
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (39 bp):
ATATAAATAAAAACAAACAAAATAGAATATTAAGAAAAA
Found at i:156742 original size:17 final size:15
Alignment explanation
Indices: 156720--156766 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
156710 ATACATATAT
156720 ATATATAATGATATAAA
1 ATATATAAT-A-ATAAA
156737 ATATAT-ATAATAAA
1 ATATATAATAATAAA
156751 ATAATATAAT-ATAAA
1 AT-ATATAATAATAAA
156766 A
1 A
156767 AAAATGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.25
15 11 0.39
16 4 0.14
17 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
ATATATAATAATAAA
Found at i:156759 original size:13 final size:13
Alignment explanation
Indices: 156732--156815 Score: 57
Period size: 13 Copynumber: 6.3 Consensus size: 13
156722 ATATAATGAT
156732 ATAAAATATATATA
1 ATAAAATA-ATATA
156746 ATAAAATAATATA
1 ATAAAATAATATA
* *
156759 ATATAAAAAAAATGA
1 ATA-AAATAATAT-A
* *
156774 ATATAGTAA-ATAA
1 ATAAAATAATAT-A
156787 ATAAAA-AATATA
1 ATAAAATAATATA
*
156799 ATGAAA-AATATA
1 ATAAAATAATATA
156811 TATAA
1 -ATAA
156816 GGGACGAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
12 14 0.25
13 20 0.36
14 18 0.32
15 4 0.07
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (13 bp):
ATAAAATAATATA
Found at i:156764 original size:10 final size:9
Alignment explanation
Indices: 156703--156764 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 9
156693 TTAATACATC
156703 TATACATATA
1 TATA-ATATA
*
156713 CATATATATA
1 TATA-ATATA
156723 TATAATGATA
1 TATAAT-ATA
*
156733 TAAAATATA
1 TATAATATA
156742 TATAATA-A
1 TATAATATA
*
156750 AATAATATAA
1 TATAATAT-A
156760 TATAA
1 TATAA
156765 AAAAAATGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 7 0.17
9 11 0.26
10 24 0.57
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (9 bp):
TATAATATA
Found at i:158324 original size:110 final size:110
Alignment explanation
Indices: 158180--158386 Score: 290
Period size: 110 Copynumber: 1.9 Consensus size: 110
158170 AATCGGGAAA
* * * *
158180 TTGTTTGTTGACAGCCAGTCACCCCTTCGCTGTGAAATTGAGCTTTTGTTATCTTGAGTTCAATA
1 TTGTTTGTTGACAACCAGTCACCCCTTCGCTGTGAAACTGAGCTTGTGTTATCTTGAGTCCAATA
* *
158245 -TCATTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
66 TTC-CTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
* ** * * *
158290 TTGTTTGTTGACAATCAGTTGCCCCTTCGTTGTGAAGCTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAACCAGTCACCCCTTCGCTGTGAAACTGAGCTTGTGTTATCTTGAGTCCAATA
158355 TTCCTCGCTGTGAAGTTGAAATTGACTCTGAA
66 TTCCTCGCTGTGAAGTTGAAATTGACTCTGAA
158387 ACTGGGAAGC
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
110 82 0.98
111 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (110 bp):
TTGTTTGTTGACAACCAGTCACCCCTTCGCTGTGAAACTGAGCTTGTGTTATCTTGAGTCCAATA
TTCCTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAG
Found at i:159222 original size:67 final size:68
Alignment explanation
Indices: 159077--159239 Score: 190
Period size: 68 Copynumber: 2.4 Consensus size: 68
159067 GGAAACGATC
* * * * *
159077 TCAAAGATATCTGTTGTTTCATGAAAAACGGTCTCAAGGGAAATAAAATTTTGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAA
159142 TAAAT
64 TAAAT
** *
159147 TTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTT-AGGAGAAAT
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGG-GAAAT
159210 AAAT
65 AAAT
*
159214 TCAAAGA-TTT-TGTTTCAAGGGAAACT
1 TCAAAGATTTTGTGTTTCAAGAGAAACT
159240 TGGAAACTGT
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
65 15 0.19
66 6 0.07
67 22 0.27
68 29 0.36
69 3 0.04
70 6 0.07
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (68 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATA
AAT
Found at i:159507 original size:106 final size:106
Alignment explanation
Indices: 159375--159591 Score: 281
Period size: 106 Copynumber: 2.0 Consensus size: 106
159365 TGTATTGTTC
*
159375 CGAGTCCAATATCCTCCACCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCACCGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACA
* * *
159440 GCCAGTCGCCCCTTCATTGTGAAGTTGAGCGTGTGCTCTCT
66 ACCAGCCGCCCCTTCATTGTGAAGTTGAACGTGTGCTCTCT
* * * * * **
159481 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCACCGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACA
* * * * * *
159546 ACCAGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGCCCCTTCATTGTGAAGTTGAACGTGTGCTCTCT
159587 CGAGT
1 CGAGT
159592 GGCACGATAT
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.32
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCACCGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCATTGTGAAGTTGAACGTGTGCTCTCT
Found at i:161229 original size:69 final size:69
Alignment explanation
Indices: 161152--161289 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
161142 TCTCTATCTC
*
161152 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGAAAATGATTGTGCTTGATCAATC
161217 TCAT
66 TCAT
* *
161221 TTGATGCTCTATGATCTTTGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGAAAATGATTGTGCTTGATCAATC
161286 TCAT
66 TCAT
161290 AGTTTGAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:161391 original size:13 final size:14
Alignment explanation
Indices: 161361--161410 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 14
161351 TTTTTCTTCA
161361 ATTTTC-CTTTGTT
1 ATTTTCTCTTTGTT
*
161374 TTTTTCTCTTT-TT
1 ATTTTCTCTTTGTT
*
161387 ATTTTCTCTTTGCT
1 ATTTTCTCTTTGTT
161401 -TTTTCTCTTT
1 ATTTTCTCTTT
161411 TTGTTCTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTTTCTCTTTGTT
Found at i:161403 original size:26 final size:26
Alignment explanation
Indices: 161361--161412 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
161351 TTTTTCTTCA
*
161361 ATTTTCCTTTGTTTTTTTCTCTTTTT
1 ATTTTCCTTTGTCTTTTTCTCTTTTT
161387 ATTTTCTCTTTG-CTTTTTCTCTTTTT
1 ATTTTC-CTTTGTCTTTTTCTCTTTTT
161413 GTTCTGATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTGTCTTTTTCTCTTTTT
Found at i:164487 original size:17 final size:17
Alignment explanation
Indices: 164449--164487 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
164439 GAATAATAAA
*
164449 TAAAATAAGAAAAAATG
1 TAAAATAACAAAAAATG
* *
164466 GAAAATAACAAAACATG
1 TAAAATAACAAAAAATG
164483 TAAAA
1 TAAAA
164488 AATAATAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (17 bp):
TAAAATAACAAAAAATG
Found at i:164582 original size:18 final size:18
Alignment explanation
Indices: 164561--164608 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
164551 TATTAATGAA
164561 GTAAAAAAAATAAAAAAG
1 GTAAAAAAAATAAAAAAG
* * *
164579 GTAAAAGAAATTAAAATG
1 GTAAAAAAAATAAAAAAG
*
164597 G-AATAAAAATAA
1 GTAAAAAAAATAA
164609 TGTATACATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (18 bp):
GTAAAAAAAATAAAAAAG
Found at i:164840 original size:18 final size:18
Alignment explanation
Indices: 164697--164841 Score: 72
Period size: 18 Copynumber: 8.2 Consensus size: 18
164687 AAAGATATAC
164697 ATAATATTAAGAAAAAA-
1 ATAATATTAAGAAAAAAT
* *
164714 A-AGTAAT-AGAAAAAA-
1 ATAATATTAAGAAAAAAT
* * *
164729 ATAAAATAAAGTAAAAAT
1 ATAATATTAAGAAAAAAT
* *
164747 ATAATATATATA-TATAAAT
1 ATAATAT-TA-AGAAAAAAT
*
164766 A-AATA--AAAACAAAAAT
1 ATAATATTAAGA-AAAAAT
*
164782 AGAATATTAAGAAAAAAT
1 ATAATATTAAGAAAAAAT
* *
164800 ATATATATAAACGTATAAAAT
1 ATA-ATATTAA-G-AAAAAAT
*
164821 ATAATTTTAAGAAAAAAT
1 ATAATATTAAGAAAAAAT
164839 ATA
1 ATA
164842 TATACATAGT
Statistics
Matches: 96, Mismatches: 19, Indels: 25
0.69 0.14 0.18
Matches are distributed among these distances:
14 1 0.01
15 10 0.10
16 12 0.12
17 12 0.12
18 27 0.28
19 18 0.19
20 7 0.07
21 9 0.09
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (18 bp):
ATAATATTAAGAAAAAAT
Found at i:164932 original size:25 final size:25
Alignment explanation
Indices: 164886--164934 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
164876 ATACATATAC
* *
164886 ATATATATATATATAATGATATAAG
1 ATATATATATATAAAATAATATAAG
164911 ATATATATA-ATAAAAATAATATAA
1 ATATATATATAT-AAAATAATATAA
164935 TATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
ATATATATATATAAAATAATATAAG
Found at i:164996 original size:40 final size:37
Alignment explanation
Indices: 164911--164997 Score: 86
Period size: 40 Copynumber: 2.3 Consensus size: 37
164901 ATGATATAAG
*
164911 ATATATATAATAAAAATAATATAATATAAATAAAAAA
1 ATATATATAATAAAAATAATAAAATATAAATAAAAAA
* * * *
164948 AGGAATATAGTAA-ATAAATAAATAAAATATAATTAAAAAT
1 A--TATATA-TAATAAAAAT-AATAAAATATAAATAAAAAA
164988 ATATATATAA
1 ATATATATAA
164998 GGGACGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
37 4 0.10
38 5 0.12
39 10 0.25
40 21 0.52
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (37 bp):
ATATATATAATAAAAATAATAAAATATAAATAAAAAA
Found at i:165932 original size:32 final size:32
Alignment explanation
Indices: 165879--165940 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
165869 GCAAAAAATG
* *
165879 ACACAAACAAAATAAACGAAATAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
* *
165911 ACACAAATAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
165941 ATATGTAGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
Found at i:169153 original size:18 final size:18
Alignment explanation
Indices: 169126--169163 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
169116 TCGGGTTAGC
169126 TTGTACTGGGCCTCAGGA
1 TTGTACTGGGCCTCAGGA
* *
169144 TTGTAGTGGGCTTCAGGA
1 TTGTACTGGGCCTCAGGA
169162 TT
1 TT
169164 AGCCTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (18 bp):
TTGTACTGGGCCTCAGGA
Found at i:169201 original size:3 final size:3
Alignment explanation
Indices: 169185--169243 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
169175 CAAAATGTAT
*
169185 TAA TAA -AA -AA TAA TAA TAC TAA TATA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
169229 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
169244 AATTTAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:173516 original size:51 final size:51
Alignment explanation
Indices: 173448--173549 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
173438 TTTAATGTTA
173448 CTAACAATATTACAAAAATAAAAATGAAATTACTACGAGTTGGTTTAAGTG
1 CTAACAATATTACAAAAATAAAAATGAAATTACTACGAGTTGGTTTAAGTG
* *
173499 CTAACAATATTATAAAAATAAAAATGAAATTATTACGAGTTGGTTTAAGTG
1 CTAACAATATTACAAAAATAAAAATGAAATTACTACGAGTTGGTTTAAGTG
173550 GTAAGTAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (51 bp):
CTAACAATATTACAAAAATAAAAATGAAATTACTACGAGTTGGTTTAAGTG
Found at i:173710 original size:2 final size:2
Alignment explanation
Indices: 173703--173736 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
173693 AAGAGCAACA
173703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173737 CAAATTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:183969 original size:31 final size:27
Alignment explanation
Indices: 183934--183991 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 27
183924 TAAGTTAGAT
183934 GGCCATATTGAAATAATAATAATAATACAAG
1 GGCCATATT-AAA-AA-AATAA-AATACAAG
183965 GGCCATATTAAAAAAATAAAATACAAG
1 GGCCATATTAAAAAAATAAAATACAAG
183992 ATCTTCACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 2 0.07
30 3 0.11
31 9 0.33
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (27 bp):
GGCCATATTAAAAAAATAAAATACAAG
Found at i:184056 original size:36 final size:37
Alignment explanation
Indices: 184015--184084 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
184005 CTTTTTTACT
184015 TTATATTTACTCTCAAGA-TTTCAATTTTGTCCTACC
1 TTATATTTACTCTCAAGATTTTCAATTTTGTCCTACC
*
184051 TTATATTTAGTCTCAAGATTTTCAATTTTGTCCT
1 TTATATTTACTCTCAAGATTTTCAATTTTGTCCT
184085 CTGGTACTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (37 bp):
TTATATTTACTCTCAAGATTTTCAATTTTGTCCTACC
Found at i:189847 original size:26 final size:26
Alignment explanation
Indices: 189811--189861 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
189801 ATCATCTGGG
* *
189811 AGAGAGATCGTTTTCACAATTAAGTA
1 AGAGAAATCGTCTTCACAATTAAGTA
189837 AGAGAAATCGTCTTCACAATTAAGT
1 AGAGAAATCGTCTTCACAATTAAGT
189862 CAGCCGCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (26 bp):
AGAGAAATCGTCTTCACAATTAAGTA
Found at i:190712 original size:29 final size:29
Alignment explanation
Indices: 190670--190728 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
190660 ATTTTCACCT
190670 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
190699 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
190728 A
1 A
190729 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:195385 original size:29 final size:29
Alignment explanation
Indices: 195343--195401 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
195333 ATTTTCACCT
195343 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
195372 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
195401 A
1 A
195402 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:199186 original size:31 final size:31
Alignment explanation
Indices: 199141--199201 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
199131 AATTAAAATA
* *
199141 TAATTTTAGAAAAATAATTGAATGATTAAAG
1 TAATATTAGAAAAATAATTAAATGATTAAAG
*
199172 TAATATTATAAAAATAATTAAATGATTAAA
1 TAATATTAGAAAAATAATTAAATGATTAAA
199202 TATATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (31 bp):
TAATATTAGAAAAATAATTAAATGATTAAAG
Found at i:199485 original size:19 final size:18
Alignment explanation
Indices: 199453--199503 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
199443 CCAATTATAT
**
199453 TTTTTATTTT-ATTACTA
1 TTTTTATTTTAATTAAAA
199470 TTTTTATTTTAAATTAAAA
1 TTTTTATTTT-AATTAAAA
199489 TTTTTATTTTTAATT
1 TTTTTA-TTTTAATT
199504 TCAAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
19 15 0.52
20 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTATTTTAATTAAAA
Found at i:199499 original size:20 final size:20
Alignment explanation
Indices: 199469--199511 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
199459 TTTTATTACT
199469 ATTTTTATTTTAAATT-AAA
1 ATTTTTATTTTAAATTCAAA
*
199488 ATTTTTATTTTTAATTTCAAA
1 ATTTTTA-TTTTAAATTCAAA
199509 ATT
1 ATT
199512 ATTTTACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTATTTTAAATTCAAA
Found at i:201936 original size:14 final size:14
Alignment explanation
Indices: 201914--201964 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
201904 TCGGTAATAT
*
201914 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
201928 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
201942 GTT-A---ATGTGC
1 GTTCATTTATGTTC
201952 GTTCATTTATGTT
1 GTTCATTTATGTT
201965 TAGCTCAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
13 1 0.03
14 20 0.67
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:201943 original size:24 final size:24
Alignment explanation
Indices: 201911--201964 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
201901 CGTTCGGTAA
* *
201911 TATGTTCGTTTATGTTCGTTCATT
1 TATGTTCGTTAATGTGCGTTCATT
201935 TATGTTCGTTAATGTGCGTTCATT
1 TATGTTCGTTAATGTGCGTTCATT
201959 TATGTT
1 TATGTT
201965 TAGCTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.11, G:0.19, T:0.56
Consensus pattern (24 bp):
TATGTTCGTTAATGTGCGTTCATT
Found at i:202167 original size:20 final size:20
Alignment explanation
Indices: 202130--202167 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
202120 AAAATATATT
*
202130 TTCATTTATATTTGTTTACA
1 TTCATTTATATTTATTTACA
*
202150 TTCATTTATGTTTATTTA
1 TTCATTTATATTTATTTA
202168 TTGTGTTTGT
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:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (20 bp):
TTCATTTATATTTATTTACA
Found at i:202247 original size:47 final size:47
Alignment explanation
Indices: 202164--202276 Score: 118
Period size: 47 Copynumber: 2.4 Consensus size: 47
202154 TTTATGTTTA
* * ** **
202164 TTTATTGTGTTTGTTTACGTTCGTTCATTTGTGTTCGTTTACGCTCG
1 TTTATTGTGTTCGTTTATGTTCGTTCACATCCGTTCGTTTACGCTCG
* * *
202211 TTTATTGTGTTCGTTTATGTTCGTTTACATCCGTTCGTTTATGTTCG
1 TTTATTGTGTTCGTTTATGTTCGTTCACATCCGTTCGTTTACGCTCG
* *
202258 TTCATTTGTGTTCGCTTAT
1 TTTA-TTGTGTTCGTTTAT
202277 CATTTAAATG
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
47 41 0.76
48 13 0.24
ACGTcount: A:0.10, C:0.15, G:0.19, T:0.56
Consensus pattern (47 bp):
TTTATTGTGTTCGTTTATGTTCGTTCACATCCGTTCGTTTACGCTCG
Found at i:202276 original size:24 final size:24
Alignment explanation
Indices: 202168--202276 Score: 112
Period size: 24 Copynumber: 4.6 Consensus size: 24
202158 TGTTTATTTA
* *
202168 TTGTGTTTGTTTACGTTCGTTCAT
1 TTGTGTTCGTTTATGTTCGTTCAT
* * *
202192 TTGTGTTCGTTTACGCTCGTTTA-
1 TTGTGTTCGTTTATGTTCGTTCAT
* *
202215 TTGTGTTCGTTTATGTTCGTTTAC
1 TTGTGTTCGTTTATGTTCGTTCAT
* **
202239 ATCCGTTCGTTTATGTTCGTTCAT
1 TTGTGTTCGTTTATGTTCGTTCAT
*
202263 TTGTGTTCGCTTAT
1 TTGTGTTCGTTTAT
202277 CATTTAAATG
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
23 21 0.30
24 49 0.70
ACGTcount: A:0.09, C:0.16, G:0.20, T:0.55
Consensus pattern (24 bp):
TTGTGTTCGTTTATGTTCGTTCAT
Found at i:211428 original size:23 final size:23
Alignment explanation
Indices: 211398--211451 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
211388 GCCAAACTTA
*
211398 GAAATGGTATGCTATTTTTACTC
1 GAAATGGTATGCTAATTTTACTC
211421 GAAATGGTATGCTAATTTTACTC
1 GAAATGGTATGCTAATTTTACTC
*
211444 GACATGGT
1 GAAATGGT
211452 CAATAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (23 bp):
GAAATGGTATGCTAATTTTACTC
Found at i:212844 original size:33 final size:32
Alignment explanation
Indices: 212802--212906 Score: 115
Period size: 33 Copynumber: 3.3 Consensus size: 32
212792 AGGAGAGCCA
*
212802 GATTAGTGTTACTTTCTTCGTAATCGTGTGCCG
1 GATTCGTGTTACTTTCTTCGTAATCGTGTG-CG
* *
212835 GATTCGTGTTACTTTCTTTGTAATCGTGT-CA
1 GATTCGTGTTACTTTCTTCGTAATCGTGTGCG
* * *
212866 GATTCGTTTTACTTT-TCCATAATCGTGTGTCG
1 GATTCGTGTTACTTTCTTCGTAATCGTGTG-CG
*
212898 GGTTCGTGT
1 GATTCGTGT
212907 GAACTTTTTC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 10 0.17
31 15 0.25
32 8 0.13
33 27 0.45
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (32 bp):
GATTCGTGTTACTTTCTTCGTAATCGTGTGCG
Found at i:221032 original size:20 final size:20
Alignment explanation
Indices: 221007--221053 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
220997 CCGGTTCACA
* *
221007 CTGGTTTTACAGGTTTTCAG
1 CTGGTTCTACAGGTTTCCAG
*
221027 CTGGTTCTACCGGTTTCCAG
1 CTGGTTCTACAGGTTTCCAG
*
221047 CCGGTTC
1 CTGGTTC
221054 CATGTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.38
Consensus pattern (20 bp):
CTGGTTCTACAGGTTTCCAG
Found at i:227068 original size:50 final size:50
Alignment explanation
Indices: 227010--227122 Score: 163
Period size: 50 Copynumber: 2.3 Consensus size: 50
227000 TTAGCAGGAA
* * * * *
227010 AGCGCGCCCCGTGCACTGCGCTATATGCTGATTTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTGCACTGCGATATACGCTGATCTGGCGCCACGTGGGTAT
* *
227060 AGCGCGCCCCCTGCCCTGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACTGCGATATACGCTGATCTGGCGCCACGTGGGTAT
227110 AGCGCGCCCCCTG
1 AGCGCGCCCCCTG
227123 ATCCGCGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.13, C:0.34, G:0.32, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACTGCGATATACGCTGATCTGGCGCCACGTGGGTAT
Found at i:227135 original size:50 final size:49
Alignment explanation
Indices: 227010--227136 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 49
227000 TTAGCAGGAA
* * * * *
227010 AGCGCGCCCCGTGCACTGCGCTATATGCTGATTTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTG-ACCGCGCTATACGCTGATCTGGCGCCACGTGGGTAT
* * *
227060 AGCGCGCCCCCTGCCCTGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGACC-GCGCTATACGCTGATCTGGCGCCACGTGGGTAT
227110 AGCGCGCCCCCTGATCCGCGCTATACG
1 AGCGCGCCCCCTGA-CCGCGCTATACG
227137 TCACGTAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 62 0.95
51 2 0.03
ACGTcount: A:0.14, C:0.34, G:0.31, T:0.21
Consensus pattern (49 bp):
AGCGCGCCCCCTGACCGCGCTATACGCTGATCTGGCGCCACGTGGGTAT
Found at i:228606 original size:8 final size:8
Alignment explanation
Indices: 228593--228619 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
228583 TTAAATTAAA
228593 TTAAAATG
1 TTAAAATG
228601 TTAAAATG
1 TTAAAATG
228609 TTAAAATG
1 TTAAAATG
228617 TTA
1 TTA
228620 TCGTATCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (8 bp):
TTAAAATG
Found at i:229195 original size:50 final size:50
Alignment explanation
Indices: 229128--229232 Score: 156
Period size: 50 Copynumber: 2.1 Consensus size: 50
229118 CGGATCAGGG
* * *
229128 GCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGGCAGGGGGC
1 GCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCGGGGCAGGGGGC
* * *
229178 GCGCTGTACCCACGTGGCGCCAAATCAGCATATAGCGCGGTGCAGGGGGC
1 GCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCGGGGCAGGGGGC
229228 GCGCT
1 GCGCT
229233 TTCCTGCTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.18, C:0.31, G:0.36, T:0.14
Consensus pattern (50 bp):
GCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCGGGGCAGGGGGC
Found at i:232215 original size:13 final size:13
Alignment explanation
Indices: 232197--232221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
232187 TCTTGTTACT
232197 TTTTGTTTTTTTG
1 TTTTGTTTTTTTG
232210 TTTTGTTTTTTT
1 TTTTGTTTTTTT
232222 ACTGTTTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTGTTTTTTTG
Found at i:238271 original size:24 final size:24
Alignment explanation
Indices: 238244--238306 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
238234 TTTGAATATT
*
238244 AAAAAATAAAAATAAATATATTAA
1 AAAAAATAAAAATAAATATAATAA
* *
238268 AAAAAATTAAACATATATATAATAA
1 AAAAAA-TAAAAATAAATATAATAA
* *
238293 AAATATTAAAAATA
1 AAAAAATAAAAATA
238307 TTAACCAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAAAATAAAAATAAATATAATAA
Found at i:239778 original size:7 final size:7
Alignment explanation
Indices: 239760--239811 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
239750 GAGTGTGTGA
239760 GAAGAA-
1 GAAGAAT
239766 GAAGAAT
1 GAAGAAT
239773 GAAGAAT
1 GAAGAAT
*
239780 GAAGAAA
1 GAAGAAT
239787 GAATGAAT
1 GAA-GAAT
* *
239795 GAAAAAG
1 GAAGAAT
239802 GAAGAA-
1 GAAGAAT
239808 GAAG
1 GAAG
239812 CTACTACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 10 0.26
7 23 0.59
8 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (7 bp):
GAAGAAT
Found at i:239806 original size:18 final size:18
Alignment explanation
Indices: 239766--239811 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
239756 GTGAGAAGAA
*
239766 GAAGAATGAAGAATGAAG
1 GAAGAATGAAGAATAAAG
*
239784 AAAGAATGAATGAA-AAAG
1 GAAGAATGAA-GAATAAAG
239802 GAAGAA-GAAG
1 GAAGAATGAAG
239812 CTACTACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 17 0.71
19 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (18 bp):
GAAGAATGAAGAATAAAG
Found at i:241270 original size:22 final size:23
Alignment explanation
Indices: 241236--241278 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
241226 ATATAATAAA
241236 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
241259 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
241279 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:250373 original size:59 final size:59
Alignment explanation
Indices: 250306--250429 Score: 248
Period size: 59 Copynumber: 2.1 Consensus size: 59
250296 TTGAACATCA
250306 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
1 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
250365 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
1 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
250424 GCCAAA
1 GCCAAA
250430 GTAAAATATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (59 bp):
GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
Found at i:251918 original size:25 final size:25
Alignment explanation
Indices: 251887--251946 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
251877 ATTTAGGGGA
251887 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
251912 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
251937 TTAGGGTTTG
1 TTAGGGTTTG
251947 TTGGGCTCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:252012 original size:3 final size:3
Alignment explanation
Indices: 252004--252043 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
251994 ATTAATAAAC
252004 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
252044 CGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:252029 original size:22 final size:22
Alignment explanation
Indices: 251996--252039 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
251986 AATATGTAAT
251996 TAATAAACATAATAATAATAAA
1 TAATAAACATAATAATAATAAA
252018 TAATAATA-ATAATAATAATAAA
1 TAATAA-ACATAATAATAATAAA
252040 ATAACGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAACATAATAATAATAAA
Found at i:252299 original size:40 final size:40
Alignment explanation
Indices: 252201--252314 Score: 93
Period size: 43 Copynumber: 2.8 Consensus size: 40
252191 TGTTGGGGAC
* * * ***
252201 GACACTGCTCATACGTGATGAAGAGTTCTTGTCGTCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA---T
* * * * *
252244 GACATGGTTCCTACGTGATGAGGACATCTGGTCGGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
*
252284 GACACGGCTCATACGTGATGAAGAGTTCTGG
1 GACACGGCTCATACGTGATGAAGAGATCTGG
252315 CCATCTAAAG
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
40 26 0.48
43 28 0.52
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (40 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
Found at i:252428 original size:40 final size:40
Alignment explanation
Indices: 252372--252483 Score: 197
Period size: 40 Copynumber: 2.8 Consensus size: 40
252362 TATCTATGGT
* * *
252372 TGACATGGCTCCTACGTGATGAGGAGATCTGGTCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
252412 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
252452 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
252484 CCATCTAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
Found at i:253093 original size:15 final size:15
Alignment explanation
Indices: 253069--253112 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
253059 AAGATGATCT
*
253069 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
253084 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
253099 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
253113 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:253533 original size:32 final size:32
Alignment explanation
Indices: 253478--253538 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
253468 AGAGACAACA
* *
253478 TTTGCTTTTAAAGAAATAGACTCAAAGATGAT
1 TTTGCTTTTAAAGAAACAAACTCAAAGATGAT
253510 TTTG-TTTTAAGAGAAACAAACTCAAAGAT
1 TTTGCTTTTAA-AGAAACAAACTCAAAGAT
253539 TTTCAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (32 bp):
TTTGCTTTTAAAGAAACAAACTCAAAGATGAT
Found at i:253656 original size:66 final size:67
Alignment explanation
Indices: 253568--253765 Score: 229
Period size: 67 Copynumber: 3.0 Consensus size: 67
253558 AAAGATTTAC
* ** * * * * *
253568 TTCAAGAGAAACGGTCTCAAGAGATACAAAATTCAATTT-AAGAGAAACAGATTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
253632 GT
66 GT
* ***
253634 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
253699 GT
66 GT
*** *
253701 TTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAA-AATTCAATTTCAAAAGAAACAAACTCAAAGATTTT
253765 T
65 T
253766 TTCACAAAAT
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
66 32 0.28
67 84 0.72
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (67 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
GT
Found at i:253669 original size:37 final size:36
Alignment explanation
Indices: 253628--253749 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
253618 ATTCAAAGAT
*
253628 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAA
* * * *
253665 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG---AT
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
253695 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAA-AA
*
253732 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
253750 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 21 0.31
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 37 0.54
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
Found at i:253703 original size:67 final size:67
Alignment explanation
Indices: 253610--253804 Score: 265
Period size: 67 Copynumber: 3.0 Consensus size: 67
253600 TCAATTTAAG
* *
253610 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
253675 AA
66 AA
*
253677 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAA-AATTTTGTTTC
*
253741 CAA
65 AAA
* * * * *
253744 AGAAACAAACTCAAAGA-TTTT-TTTC-ACA-AAATTGTCTCAAGAGATACAAAACTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
253805 GACTCAAAGA
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
63 24 0.21
64 4 0.03
65 4 0.03
66 6 0.05
67 77 0.67
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
AA
Found at i:253832 original size:52 final size:53
Alignment explanation
Indices: 253752--253856 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 53
253742 AAAGAAACAA
*
253752 ACTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGATACAAAACTTTGTTTCAG
1 ACTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
*
253806 ACTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
253857 AAATAAATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 40 0.82
54 9 0.18
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:253897 original size:24 final size:25
Alignment explanation
Indices: 253852--253898 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
253842 CAAAACTTTG
*
253852 TTTCAAAATAAATAGACTCAAAGTT
1 TTTCAAAAGAAATAGACTCAAAGTT
*
253877 TTTCAAAAGAAA-CGACTCAAAG
1 TTTCAAAAGAAATAGACTCAAAG
253899 ATATTTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (25 bp):
TTTCAAAAGAAATAGACTCAAAGTT
Done.