Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012108.1 Kokia drynarioides strain JFW-HI SEQ_127107, 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: 265239
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1411 original size:115 final size:116
Alignment explanation
Indices: 1285--1608 Score: 354
Period size: 115 Copynumber: 2.8 Consensus size: 116
1275 AAAAATAATT
1285 TTTTTTTGTGTTGGCCATCAAATGGCTGACACTCCCTTTTCTCGAAAAAAATTACATTTTTGGGT
1 TTTTTTTGTGTTGGCCATCAAATGGCTGACACTCCCTTTTCTCGAAAAAAATTACATTTTTGGGT
* *
1350 GTTGGTTATTGCATGGTCGACA-CCCTTTT-TTGAGAAAAAAAATTT-CAAAA
66 GTTGGTCATTGCATGGTCGACACCCCTTTTCTCGAG--AAAAAATTTACAAAA
* * ** *
1400 TTTTTTGGTGTTGG-CATCAAATGGTTGACACTCATTTTTCTCGAAAAAAAATTGCATTTTTGGG
1 TTTTTTTGTGTTGGCCATCAAATGGCTGACACTCCCTTTTCTCG-AAAAAAATTACATTTTTGGG
* **
1464 TGTTGGTCATTGCATGGTTGACACCCCCTTTTCTCGAGAAAAAATTTACAATT
65 TGTTGGTCATTGCATGGTCGACA-CCCCTTTTCTCGAGAAAAAATTTACAAAA
* * * * * *
1517 TTTTTTTGTGTCGACTATGC-AATGGCCGACACCCCCTTTTCTCGAAAAAAAAAATTATATTTTT
1 TTTTTTTGTGTTGGCCAT-CAAATGGCTGACACTCCCTTTTCTCG---AAAAAAATTACATTTTT
* * * *
1581 GAGTGNTGGCCA-TGCATGGCCGACACCC
62 GGGTGTTGGTCATTGCATGGTCGACACCC
1609 AAAAATGTAA
Statistics
Matches: 174, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
114 26 0.15
115 53 0.30
116 9 0.05
117 21 0.12
118 28 0.16
119 12 0.07
120 25 0.14
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (116 bp):
TTTTTTTGTGTTGGCCATCAAATGGCTGACACTCCCTTTTCTCGAAAAAAATTACATTTTTGGGT
GTTGGTCATTGCATGGTCGACACCCCTTTTCTCGAGAAAAAATTTACAAAA
Found at i:1496 original size:57 final size:57
Alignment explanation
Indices: 1306--1519 Score: 211
Period size: 59 Copynumber: 3.7 Consensus size: 57
1296 TGGCCATCAA
* *
1306 ATGGCTGACACTCCCTTTTCTCG-AAAAAAATTACATTTTTGGGTGTTGGTTATTGC
1 ATGGTTGACACTCCCTTTTCTCGAAAAAAAATTACATTTTTGGGTGTTGGTCATTGC
* * * * * ***
1362 ATGGTCGACA--CCCTTTTTTGAGAAAAAAAATTTCAAAATTTTTTGGTGTTGG-CATCAA
1 ATGGTTGACACTCCCTTTTCT-CGAAAAAAAA-TT--ACATTTTTGGGTGTTGGTCATTGC
** *
1420 ATGGTTGACACTCATTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGTCATTGC
1 ATGGTTGACACTCCCTTTTCTCGAAAAAAAATTACATTTTTGGGTGTTGGTCATTGC
* *
1477 ATGGTTGACACCCCCTTTTCTCGAGAAAAAATTTACAATTTTT
1 ATGGTTGACACTCCCTTTTCTCGA-AAAAAAATTAC-ATTTTT
1520 TTTTGTGTCG
Statistics
Matches: 122, Mismatches: 26, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
54 8 0.07
55 1 0.01
56 29 0.24
57 26 0.21
58 22 0.18
59 30 0.25
60 6 0.05
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (57 bp):
ATGGTTGACACTCCCTTTTCTCGAAAAAAAATTACATTTTTGGGTGTTGGTCATTGC
Found at i:1751 original size:104 final size:107
Alignment explanation
Indices: 1593--1864 Score: 338
Period size: 104 Copynumber: 2.5 Consensus size: 107
1583 GTGNTGGCCA
* * **
1593 TGCATGGCCGACACCCAAAAATGTA-ATTTTTTTTCGAGAAAAGGGGGTGTCGGCCATTTGATGG
1 TGCATGGCCGACACCCAAAAA--TACATTTTTTTTCGAGAAAAAGGGGTGTCGGCCATTGGATAA
*
1657 CCAACACCAAAAAATTTTTAAAATTTTTTTCTCGAG-AAA-A-G-
64 CCAACA-CAAAAAAATTTTAAAATTTTTTTCTCGAGAAAAGAGGT
*
1698 TGCATGGTCGACACCCAAAAATACATTTTTTTTCGAGAAAAAGGGGTGTCGGCCATTGGATAACC
1 TGCATGGCCGACACCCAAAAATACATTTTTTTTCGAGAAAAAGGGGTGTCGGCCATTGGATAACC
* *
1763 AACATAAAAAAATTTTAAATTTTTTTTCTCGAGAAAAGGGAGTGT
66 AACACAAAAAAATTTTAAAATTTTTTTCTCGAGAAAA--GAG-GT
* * * *
1808 TGCATGGCCAACACGCAAAAATGCAATTTTTTTTCGAGAAAAAGAGGTGTCGGCCAT
1 TGCATGGCCGACACCCAAAAATAC-ATTTTTTTTCGAGAAAAAGGGGTGTCGGCCAT
1865 GGTGTCGGCC
Statistics
Matches: 145, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
103 28 0.19
104 44 0.30
105 20 0.14
107 1 0.01
109 1 0.01
110 20 0.14
111 31 0.21
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (107 bp):
TGCATGGCCGACACCCAAAAATACATTTTTTTTCGAGAAAAAGGGGTGTCGGCCATTGGATAACC
AACACAAAAAAATTTTAAAATTTTTTTCTCGAGAAAAGAGGT
Found at i:2682 original size:17 final size:17
Alignment explanation
Indices: 2648--2682 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2638 AATGTATTAA
**
2648 TTATTATAAAATTTATT
1 TTATTATAAAATAAATT
2665 TTATTATAAAATAAATT
1 TTATTATAAAATAAATT
2682 T
1 T
2683 AGATTGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTATAAAATAAATT
Found at i:9015 original size:21 final size:21
Alignment explanation
Indices: 8991--9030 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8981 ATGAACTTTA
*
8991 ATTTTTTTAAATTTTGTATCT
1 ATTTTTTTAAATTTGGTATCT
9012 ATTTTTTTAAATTTGGTAT
1 ATTTTTTTAAATTTGGTAT
9031 TTGAATGAAT
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:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (21 bp):
ATTTTTTTAAATTTGGTATCT
Found at i:23090 original size:2 final size:2
Alignment explanation
Indices: 23083--23124 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
23073 TAATGATCTG
23083 AT AT AT AT 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 AT AT AT AT
23125 TTGTCGCTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24687 original size:36 final size:36
Alignment explanation
Indices: 24505--24688 Score: 215
Period size: 36 Copynumber: 5.1 Consensus size: 36
24495 TGATGACTAT
* * *
24505 TGTGAAAGTAAATATGGGGGTATGTTATTCATGTCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
* * *
24541 TGAGACTGTAAATATGTGGGTATGATATTCATGCCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
* * * *
24577 TCTGACAGTAAATGTATGGGTATGTTATTCATGCCG
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
*** * *
24613 TAAAATAGTAAATATGTGGATATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
* *
24649 TGTGACAGTAATTATGTGGGTATGTTATTCATGTCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
24685 TGTG
1 TGTG
24689 GTAGTGATTA
Statistics
Matches: 120, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 120 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.37
Consensus pattern (36 bp):
TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
Found at i:25152 original size:16 final size:16
Alignment explanation
Indices: 25082--25158 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
25072 ATATGACTGA
*
25082 ATGTGATTAATATGTG
1 ATGTGATTAATGTGTG
*
25098 ATGTGATAAATGT-TG
1 ATGTGATTAATGTGTG
* * * *
25113 AAGT-ATTCATTTGATTAA
1 ATGTGATTAATGTG--T-G
25131 ATGTGATTAATGTGTG
1 ATGTGATTAATGTGTG
*
25147 ATGTGATAAATG
1 ATGTGATTAATG
25159 CTTAAATTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
14 5 0.11
15 5 0.11
16 22 0.50
17 2 0.05
18 3 0.07
19 7 0.16
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (16 bp):
ATGTGATTAATGTGTG
Found at i:25177 original size:49 final size:49
Alignment explanation
Indices: 25071--25177 Score: 135
Period size: 49 Copynumber: 2.2 Consensus size: 49
25061 TTTATTATAA
* * *
25071 AATATGACTGAATGTGATTAATATGTGATGTGATAAATGTTGAAGTATT
1 AATATGATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATT
* * * *
25120 CATTTGATTAAATGTGATTAATGTGTGATGTGATAAATGCTT-AAATTTT
1 AATATGATTAAATGTGATTAATATGTGATGTGATAAATG-TTGAAATATT
25169 AATATGATT
1 AATATGATT
25178 TATGCTTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
49 46 0.96
50 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.42
Consensus pattern (49 bp):
AATATGATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATT
Found at i:25193 original size:23 final size:23
Alignment explanation
Indices: 25147--25269 Score: 122
Period size: 23 Copynumber: 5.3 Consensus size: 23
25137 TTAATGTGTG
** **
25147 ATGTGATAAATGCTTAAATTTTA
1 ATGTGATTTATGCTTAAAAGTTA
*
25170 ATATGATTTATGCTTAAAAGTTA
1 ATGTGATTTATGCTTAAAAGTTA
* *
25193 ATGTGATTTATACTTAAAAATTA
1 ATGTGATTTATGCTTAAAAGTTA
*
25216 ATGTGATTTATGGTTAAAAGTTA
1 ATGTGATTTATGCTTAAAAGTTA
* * **
25239 A-GAAGACTTATGCTTAAGTGTTA
1 ATG-TGATTTATGCTTAAAAGTTA
25262 ATGTGATT
1 ATGTGATT
25270 AATGTGTAAA
Statistics
Matches: 80, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
22 1 0.01
23 78 0.98
24 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.42
Consensus pattern (23 bp):
ATGTGATTTATGCTTAAAAGTTA
Found at i:35957 original size:12 final size:12
Alignment explanation
Indices: 35936--35972 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
35926 ACAATTATCA
35936 TCAC-ACATTTC
1 TCACTACATTTC
35947 TCACTACATTTC
1 TCACTACATTTC
35959 TCACTACATTTC
1 TCACTACATTTC
35971 TC
1 TC
35973 TAATAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (12 bp):
TCACTACATTTC
Found at i:36034 original size:18 final size:18
Alignment explanation
Indices: 36011--36051 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36001 CATTTATTAA
36011 ATATTCATATATACATA-T
1 ATATTCATAT-TACATACT
*
36029 ATATTCATATTATATACT
1 ATATTCATATTACATACT
36047 ATATT
1 ATATT
36052 TCTATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTCATATTACATACT
Found at i:36057 original size:18 final size:18
Alignment explanation
Indices: 36018--36072 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
36008 TAAATATTCA
36018 TATATACATATATATTCATAT
1 TATATAC-TATAT-TTC-TAT
36039 TATATACTATATTTCTAT
1 TATATACTATATTTCTAT
*
36057 TATAAAC-A-ATTTCTAT
1 TATATACTATATTTCTAT
36073 ACCAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 8 0.24
17 1 0.03
18 9 0.27
19 3 0.09
20 5 0.15
21 7 0.21
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATACTATATTTCTAT
Found at i:54482 original size:19 final size:20
Alignment explanation
Indices: 54458--54497 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54448 CATTACAATG
*
54458 TTGTAA-AAATTTAGTAATT
1 TTGTAAGAAACTTAGTAATT
54477 TTGTAAGAAACTTAGTAATT
1 TTGTAAGAAACTTAGTAATT
54497 T
1 T
54498 ATAGAGTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (20 bp):
TTGTAAGAAACTTAGTAATT
Found at i:56218 original size:18 final size:18
Alignment explanation
Indices: 56195--56245 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
56185 CAGAAGGAAT
*
56195 AGCATATTGGCTCATTTA
1 AGCATACTGGCTCATTTA
* *
56213 AGCATACTAGCTCGA-TTG
1 AGCATACTGGCTC-ATTTA
56231 AGCATACTGGCTCAT
1 AGCATACTGGCTCAT
56246 AAGAGCATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (18 bp):
AGCATACTGGCTCATTTA
Found at i:88125 original size:14 final size:14
Alignment explanation
Indices: 88108--88156 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
88098 GCATTTAATT
88108 TTTATTTTTATTTA
1 TTTATTTTTATTTA
*
88122 TTTA-TTTTGTTTA
1 TTTATTTTTATTTA
*
88135 TTTACTTGTTA-TTA
1 TTTA-TTTTTATTTA
88149 TTTATTTT
1 TTTATTTT
88157 CATGTCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 15 0.52
14 11 0.38
15 3 0.10
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:98294 original size:37 final size:37
Alignment explanation
Indices: 98253--98363 Score: 118
Period size: 37 Copynumber: 3.0 Consensus size: 37
98243 TCACTGTGGG
98253 AATATTTTTGAAATGCACCCAAGACTGTCGCTGCATA
1 AATATTTTTGAAATGCACCCAAGACTGTCGCTGCATA
* * *
98290 AATATTCTTGAAATTGCATCC-AGAACTATCGCTGCATA
1 AATATTTTTGAAA-TGCACCCAAG-ACTGTCGCTGCATA
* * * *
98328 AGTATTCTTT-AATTGCACCCAAGAATGTCTCTGCAT
1 AATATT-TTTGAAATGCACCCAAGACTGTCGCTGCAT
98364 GAACATGTCC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
37 30 0.50
38 28 0.47
39 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (37 bp):
AATATTTTTGAAATGCACCCAAGACTGTCGCTGCATA
Found at i:98334 original size:38 final size:38
Alignment explanation
Indices: 98253--98351 Score: 123
Period size: 38 Copynumber: 2.7 Consensus size: 38
98243 TCACTGTGGG
* *
98253 AATATTTTTGAAA-TGCACCCAAGACTGTCGCTGCATA
1 AATATTCTTGAAATTGCACCCAAGACTATCGCTGCATA
*
98290 AATATTCTTGAAATTGCATCC-AGAACTATCGCTGCATA
1 AATATTCTTGAAATTGCACCCAAG-ACTATCGCTGCATA
* *
98328 AGTATTCTT-TAATTGCACCCAAGA
1 AATATTCTTGAAATTGCACCCAAGA
98352 ATGTCTCTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
37 24 0.45
38 29 0.55
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (38 bp):
AATATTCTTGAAATTGCACCCAAGACTATCGCTGCATA
Found at i:98382 original size:26 final size:26
Alignment explanation
Indices: 98353--98406 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
98343 CACCCAAGAA
*
98353 TGTCTCTGCATGAACATGTCCAAAAT
1 TGTCGCTGCATGAACATGTCCAAAAT
*
98379 TGTCGCTGCATGAACGTGTCCAAAAT
1 TGTCGCTGCATGAACATGTCCAAAAT
98405 TG
1 TG
98407 CACCCAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCCAAAAT
Found at i:99231 original size:16 final size:16
Alignment explanation
Indices: 99210--99240 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
99200 TTGTGGATCC
99210 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
99226 CATTTTATCTTTATT
1 CATTTTACCTTTATT
99241 TTCACACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:100043 original size:17 final size:17
Alignment explanation
Indices: 100023--100055 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
100013 TAATAAAATT
100023 TTTTAAATTAAAATTTA
1 TTTTAAATTAAAATTTA
*
100040 TTTTAATTTAAAATTT
1 TTTTAAATTAAAATTT
100056 CCAATTACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAATTAAAATTTA
Found at i:101477 original size:30 final size:29
Alignment explanation
Indices: 101417--101486 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
101407 CCCCCTATAT
*
101417 TTTTGAAAATTTAGATTTGGCCTCCAAAC
1 TTTTAAAAATTTAGATTTGGCCTCCAAAC
*
101446 TTTCTAAAAATTT-GAATTTGGCC-CTCGAAC
1 TTT-TAAAAATTTAG-ATTTGGCCTC-CAAAC
*
101476 TTTTCAAAATT
1 TTTTAAAAATT
101487 CCATTTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (29 bp):
TTTTAAAAATTTAGATTTGGCCTCCAAAC
Found at i:104822 original size:41 final size:41
Alignment explanation
Indices: 104733--104920 Score: 200
Period size: 41 Copynumber: 4.5 Consensus size: 41
104723 TTATGCTGTA
* * *
104733 TCGAGTCATAAGTCTTCCTT-TTACCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATT--CATAATCTCATTCTCATC
104775 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
* * *
104816 TTGAGACATGATTCTTCCCTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
* * * * * *
104857 TCGAGACATGATTCTTCCATTTTTTACAATTTCTCATGCTCAAC
1 TCGAGACATGAGTCTTCC-TTATTCATAA--TCTCATTCTCATC
104901 -CAGAGACATGAGTCTTCCTT
1 TC-GAGACATGAGTCTTCCTT
104921 TTTATACATC
Statistics
Matches: 127, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
41 72 0.57
42 24 0.19
43 5 0.04
44 26 0.20
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.40
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
Found at i:107794 original size:5 final size:5
Alignment explanation
Indices: 107770--107812 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
107760 CTTAAAACCC
*
107770 AAGAA AAGGAAA AAGAAA AAGAA AAGCA AAGAA AAGAA AAGAA
1 AAGAA AA-G-AA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA
107813 GGAAAAGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 22 0.65
6 8 0.24
7 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:107806 original size:15 final size:14
Alignment explanation
Indices: 107781--107819 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
107771 AGAAAAGGAA
107781 AAAGAAAAAGAAAAG
1 AAAG-AAAAGAAAAG
107796 CAAAGAAAAGAAAAG
1 -AAAGAAAAGAAAAG
*
107811 AAGGAAAAG
1 AAAGAAAAG
107820 TCAAGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 10 0.45
16 4 0.18
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:108684 original size:23 final size:23
Alignment explanation
Indices: 108658--108715 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
108648 AGAGAGAAAA
*
108658 GAAAAGAAAAGAAAAGAAAAAGG
1 GAAAAGAAAAAAAAAGAAAAAGG
108681 GAAAAGAAAAAAAAAGAAAAAGG
1 GAAAAGAAAAAAAAAGAAAAAGG
108704 GAAAAGAAAAAA
1 GAAAAGAAAAAA
108716 GAAAAAGGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
GAAAAGAAAAAAAAAGAAAAAGG
Found at i:108684 original size:28 final size:26
Alignment explanation
Indices: 108634--108722 Score: 94
Period size: 23 Copynumber: 3.4 Consensus size: 26
108624 CATTTTACCT
* * *
108634 AAAAAAAACAGAAGAGAGAGAAAAGAA
1 AAAAAAAAAAGAA-AAAGGGAAAAGAA
108661 AAGAAAAGAAAAGAAAAAGGGAAAAG--
1 AA-AAAA-AAAAGAAAAAGGGAAAAGAA
108687 -AAAAAAAAAGAAAAAGGGAAAAGAA
1 AAAAAAAAAAGAAAAAGGGAAAAGAA
*
108712 AAAAGAAAAAG
1 AAAAAAAAAAG
108723 GAGAGGTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
23 18 0.34
24 4 0.08
25 1 0.02
26 9 0.17
27 2 0.04
28 13 0.25
29 6 0.11
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAGAAAAAGGGAAAAGAA
Found at i:108686 original size:13 final size:13
Alignment explanation
Indices: 108668--108714 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
108658 GAAAAGAAAA
108668 GAAAAGAAAAAGG
1 GAAAAGAAAAAGG
108681 GAAAAGAAAAA--
1 GAAAAGAAAAAGG
108692 -AAAAGAAAAAGG
1 GAAAAGAAAAAGG
108704 GAAAAGAAAAA
1 GAAAAGAAAAA
108715 AGAAAAAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.32
13 21 0.68
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAGG
Found at i:108720 original size:5 final size:5
Alignment explanation
Indices: 108652--108700 Score: 62
Period size: 5 Copynumber: 9.2 Consensus size: 5
108642 CAGAAGAGAG
*
108652 AGAAA AGAAA AGAAA AGAAA AGAAAA AGGGAAA AGAAA AAAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AG-AAA A--GAAA AGAAA AGAAA AGAAA
108700 A
1 A
108701 AGGGAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 30 0.77
6 4 0.10
7 4 0.10
8 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:109667 original size:49 final size:49
Alignment explanation
Indices: 109538--109802 Score: 168
Period size: 49 Copynumber: 5.5 Consensus size: 49
109528 CTCTAAAGAC
* * * * * *
109538 GTGAAGGAAAAGATTGAGGCCGTAACGACGAATCTCGTACCCTAG-GAAT
1 GTGAAGGGAAATATTGAGGCCGCAAAGGCGAATCTTGTACCCTAGAG-AT
**
109587 GTGAAGGGAAATATTGAGGCCATAACA-GCGAATCTTGTACCCTAGAGAT
1 GTGAAGGGAAATATTGAGGCCGCAA-AGGCGAATCTTGTACCCTAGAGAT
* * * * *
109636 GTGAAGGGAAATATTGAGGCTGCAAAGGCGAACCTTATA-CTTAGAAAT
1 GTGAAGGGAAATATTGAGGCCGCAAAGGCGAATCTTGTACCCTAGAGAT
** * ** * * * *
109684 AAGAAAGCCAA-ATTGAAGCCGCAACGGCGAATCTTGAACCCTAAAGAT
1 GTGAAGGGAAATATTGAGGCCGCAAAGGCGAATCTTGTACCCTAGAGAT
** * * * * *
109732 GTGAAGGGAAAGGTCGAGGCCTCAACA-ACGAACCTTATACCCTAGAGAT
1 GTGAAGGGAAATATTGAGGCCGCAA-AGGCGAATCTTGTACCCTAGAGAT
* *
109781 GT---CGGAAAGATTGAGGCCGCAA
1 GTGAAGGGAAATATTGAGGCCGCAA
109803 TAGTTAATCT
Statistics
Matches: 164, Mismatches: 46, Indels: 15
0.73 0.20 0.07
Matches are distributed among these distances:
46 16 0.10
47 21 0.13
48 26 0.16
49 100 0.61
50 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (49 bp):
GTGAAGGGAAATATTGAGGCCGCAAAGGCGAATCTTGTACCCTAGAGAT
Found at i:110199 original size:75 final size:75
Alignment explanation
Indices: 110070--110249 Score: 225
Period size: 75 Copynumber: 2.4 Consensus size: 75
110060 ATGAAGCGGT
* * * * *
110070 CATCTTCCTGATGAGCTACAGAGAAGTGGACTAAATCAACGAAGCAAAGGTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAAAGAAGTGGACCAAATCAACAAAGCAAAGCTCAATGTGAGTGAAA
*
110135 CTTTAAACCC
66 CTTCAAACCC
* * * * * *
110145 CATCTTCCTGACGATATACAAAAAAGTGGACCAAGTCAACAAAGTAGAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAAAGAAGTGGACCAAATCAACAAAGCAAAGCTCAATGTGAGTGAAA
*
110210 CTTCGAACCC
66 CTTCAAACCC
* *
110220 CATCTTCTTGATGAGATATAAAGAAGTGGA
1 CATCTTCCTGATGAGATACAAAGAAGTGGA
110250 TTAAAACAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 87 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (75 bp):
CATCTTCCTGATGAGATACAAAGAAGTGGACCAAATCAACAAAGCAAAGCTCAATGTGAGTGAAA
CTTCAAACCC
Found at i:110368 original size:123 final size:122
Alignment explanation
Indices: 110145--110986 Score: 550
Period size: 123 Copynumber: 6.7 Consensus size: 122
110135 CTTTAAACCC
* * * * ** ** * *
110145 CATCTTCCTGACGATATACAAAAAAGTGGACCAAGTCAACAAAGTAGAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAGAACTCAATGTGAGTGAAA
* * * * *
110210 CTTCGAACCCCATCTTCTTGATGAGATATAAAGAAGTGGATTAAAACAATAAACCAGT
66 CTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATAAAGC-GT
* * *
110268 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAG-TGAAACTCAATGTGAGCGAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAG-AACTCAATGTGAGTGAA
* *
110332 ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT-GAGTCAAAACAATAAAGTGGT
65 ACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGA-TCAAAACAATAAAG-CGT
* * *
110391 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCAATGAAGCAGAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAGAACTCAATGTGAGTGAAA
*
110456 CTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGAT
66 CTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATAAAGCG-T
* * * *
110514 CATCTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAAG-ATGTCATCTTC-TTGATGAG
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCA-G--AAC-TCAATG-TGAG
* ** * * * ** * *
110577 ATATAGAGAAC-T-AGA--CCA-AAT-C-AATGAAACGA-AGCTCAA-TGTGAGT-GAAAC-TTC
61 ---T-GA-AACTTCAAACCCCATCTTCCTGATGAGA-TATAG-AGAAGTG-GA-TCAAAACAAT-
*
110631 AAA-CCT
116 AAAGCGT
* * * * * ** * *
110637 AATCTTCCTGATGAGATATAGAGAAATGGATCAAAATAATGAAGTGGTCATCTTCCTGATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAG--AAC-T-C-AAT--G-T
* * * * *
110702 ACAAAGAAGTGGACACTTTAAACCCCATTTTCTTGATGAGATATAGAGAAGTGGATCAAAATAAT
58 -----G-AGT-GAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAAT
* *
110767 GAAGTGGT
116 AAAG-CGT
* * * *
110775 CATCTTCCTGATGAGATACAAAGAAGTGGACCAAATCAACGAAGC-GAAGCTCAATGTGAGTAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAGAA-CTCAATGTGAGTGAA
* * * * * *
110839 ACTTTAAACCCCATCTTCTTGATGAGATACAGAGAAGT-GAGTCAAAATAATGAAGTGGT
65 ACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGA-TCAAAACAATAAAG-CGT
* * * * * * * *
110898 CATCTTTCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGGAGCTCAATGCGAGCGAAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAGAACTCAATGTGAGTGAAA
110963 CTTCAAACCCCATCTTCCTGATGA
66 CTTCAAACCCCATCTTCCTGATGA
110987 AGTGGTCATC
Statistics
Matches: 572, Mismatches: 98, Indels: 98
0.74 0.13 0.13
Matches are distributed among these distances:
122 7 0.01
123 422 0.74
124 20 0.03
125 17 0.03
126 9 0.02
127 3 0.01
128 3 0.01
129 3 0.01
130 6 0.01
131 8 0.01
132 2 0.00
133 3 0.01
134 6 0.01
135 4 0.01
136 11 0.02
137 11 0.02
138 37 0.06
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (122 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCAGAACTCAATGTGAGTGAAA
CTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATAAAGCGT
Found at i:110534 original size:171 final size:171
Alignment explanation
Indices: 110343--110714 Score: 579
Period size: 171 Copynumber: 2.2 Consensus size: 171
110333 CTTCAAACCC
110343 CATCTTCCTGATGAGATACAGAGAAGT-GAGTCAAAACAATAAAG-TGGTCATCTTCTTGATGAG
1 CATCTTCCTGATGAGATACAGAGAAGTGGA-TCAAAACAATAAAGAT-GTCATCTTCTTGATGAG
* * * *
110406 ATACAGAGAAGTGGACCAAATCAATGAAGC-AGAGCTCAATGTGAGTGAAACTTCAAACCCCATC
64 ATACAGAGAACTAGACCAAATCAATGAAACGA-AGCTCAATGTGAGTGAAACTTCAAACCCAATC
*
110470 TTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGAT
128 TTCCTGATGAGATATAGAGAAATGGATCAAAACAATGAAGCGAT
* *
110514 CATCTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAAGATGTCATCTTCTTGATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGATGTCATCTTCTTGATGAGAT
* *
110579 ATAGAGAACTAGACCAAATCAATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCTAATCTTC
66 ACAGAGAACTAGACCAAATCAATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCAATCTTC
* * *
110644 CTGATGAGATATAGAGAAATGGATCAAAATAATGAAGTGGT
131 CTGATGAGATATAGAGAAATGGATCAAAACAATGAAGCGAT
*
110685 CATCTTCCTGATGAGATACAAAGAAGTGGA
1 CATCTTCCTGATGAGATACAGAGAAGTGGA
110715 CACTTTAAAC
Statistics
Matches: 184, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
171 180 0.98
172 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (171 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGATGTCATCTTCTTGATGAGAT
ACAGAGAACTAGACCAAATCAATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCAATCTTC
CTGATGAGATATAGAGAAATGGATCAAAACAATGAAGCGAT
Found at i:110537 original size:48 final size:48
Alignment explanation
Indices: 110466--110604 Score: 190
Period size: 48 Copynumber: 2.9 Consensus size: 48
110456 CTTCAAACCC
110466 CATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAG-CGAT
1 CATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGACG-T
* * *
110514 CATCTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAAGATGT
1 CATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGACGT
* * * * *
110562 CATCTTCTTGATGAGATATAGAGAACTAGACCAAATCAATGAA
1 CATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAA
110605 ACGAAGCTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
48 79 0.99
49 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (48 bp):
CATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGACGT
Found at i:110789 original size:213 final size:215
Alignment explanation
Indices: 110524--111149 Score: 692
Period size: 213 Copynumber: 2.9 Consensus size: 215
110514 CATCTTCCTA
* * * * *
110524 ATGAGATACAGAGAAGTGGATCAAAACAATGAAGAT-GTCATCTTCTTGATGAGATATAGAGAAC
1 ATGAGATATAGAGAAGTGGATCAAAATAATGAAG-TGGTCATCTTCCTGATGAGATACAGAGAAG
* * *
110588 TAGACCAAATCAATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCTAATCTTCCTGATGAGA
65 TAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACC-CATCTTCTTGATGAGA
* * * *
110653 TATAGAGAAATGGATCAAAATAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTGGA-C-
129 TATAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCA
** ** *
110716 ACTTTAAACCCCATTTTC-T-TG
194 ACAATAAACCCCA-GCTCATGCG
*
110737 ATGAGATATAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGT
1 ATGAGATATAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGT
* * * *
110802 GGACCAAATCAACGAAGCGAAGCTCAATGTGAGTAAAACTTTAAACCCCATCTTCTTGATGAGAT
66 AGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAA-CCCATCTTCTTGATGAGAT
* *
110867 ACAGAGAAGT-GAGTCAAAATAATGAAGTGGTCATCTTTCTAATGAGATACAGAGAAGTAGACCA
130 ATAGAGAAGTGGA-TCAAAATAATGAAGTGGTCATCTTCCTAATGAGATACAGAGAAGTAGACC-
* * **
110931 AAACAATGAAGCGGAGCTCAATGCG
193 -AACAATAAACCCCAGCTC-ATGCG
* * ** **** **** *
110956 A-GCGAATCTTCA-AACCCCATCTTCCTGATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAG
1 ATGAG-ATATAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAG
* *
111019 TAGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACACCATCTTCTTGATAAGA
65 TAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAAC-CCATCTTCTTGATGAGA
* * *
111084 TATAGAGAAGTGGGTCAAAATAATAAAGTGGTCATCTTCCTAATAAGATACAGAGAAGTAGACCA
129 TATAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCA
111149 A
194 A
111150 AACAATGAAG
Statistics
Matches: 347, Mismatches: 53, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
212 3 0.01
213 164 0.47
214 3 0.01
216 4 0.01
217 8 0.02
218 158 0.46
219 7 0.02
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (215 bp):
ATGAGATATAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGT
AGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCATCTTCTTGATGAGATA
TAGAGAAGTGGATCAAAATAATGAAGTGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAC
AATAAACCCCAGCTCATGCG
Found at i:111048 original size:218 final size:218
Alignment explanation
Indices: 110765--111204 Score: 709
Period size: 218 Copynumber: 2.0 Consensus size: 218
110755 GATCAAAATA
* *
110765 ATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTGGACCAAATCAACGAAGCGAAGCTCAAT
1 ATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAACGAAGCGAAGCTCAAT
* * * *
110830 GTGAGTAAAACTTTAAACCCCATCTTCTTGATGAGATACAGAGAAGTGAGTCAAAATAATGAAGT
66 GTGAGTAAAACTTCAAACACCATCTTCTTGATAAGATACAGAGAAGTGAGTCAAAATAATAAAGT
* * * *
110895 GGTCATCTTTCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGGAGCTCAATGCGAGCG
131 GGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAATACGAGCG
*
110960 AATCTTCAAACCCCATCTTCCTG
196 AAACTTCAAACCCCATCTTCCTG
* *
110983 ATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAAT
1 ATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAACGAAGCGAAGCTCAAT
* * *
111048 GTGAGTGAAACTTCAAACACCATCTTCTTGATAAGATATAGAGAAGTGGGTCAAAATAATAAAGT
66 GTGAGTAAAACTTCAAACACCATCTTCTTGATAAGATACAGAGAAGTGAGTCAAAATAATAAAGT
* *
111113 GGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCACTACGAGTG
131 GGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAATACGAGCG
*
111178 AAACTTCAAACCCCATCTTCTTG
196 AAACTTCAAACCCCATCTTCCTG
111201 ATGA
1 ATGA
111205 GATACAAAGA
Statistics
Matches: 203, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
218 203 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (218 bp):
ATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAACGAAGCGAAGCTCAAT
GTGAGTAAAACTTCAAACACCATCTTCTTGATAAGATACAGAGAAGTGAGTCAAAATAATAAAGT
GGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAATACGAGCG
AAACTTCAAACCCCATCTTCCTG
Found at i:111062 original size:95 final size:95
Alignment explanation
Indices: 110888--111079 Score: 312
Period size: 95 Copynumber: 2.0 Consensus size: 95
110878 AGTCAAAATA
* *
110888 ATGAAGTGGTCATCTTTCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGGAGCTCAAT
1 ATGAAGTGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAAT
* *
110953 GCGAGCGAATCTTCAAACCCCATCTTCCTG
66 GCGAGCGAAACTTCAAACACCATCTTCCTG
*
110983 ATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAAT
1 ATGAAGTGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAAT
* * *
111048 GTGAGTGAAACTTCAAACACCATCTTCTTG
66 GCGAGCGAAACTTCAAACACCATCTTCCTG
111078 AT
1 AT
111080 AAGATATAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (95 bp):
ATGAAGTGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAAT
GCGAGCGAAACTTCAAACACCATCTTCCTG
Found at i:111152 original size:123 final size:123
Alignment explanation
Indices: 110986--111208 Score: 383
Period size: 123 Copynumber: 1.8 Consensus size: 123
110976 CTTCCTGATG
* * **
110986 AAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAATGTG
1 AAGTGGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAATACG
111051 AGTGAAACTTCAAACACCATCTTCTTGATAAGATATAGAGAAGTGGGTCAAAATAATA
66 AGTGAAACTTCAAACACCATCTTCTTGATAAGATATAGAGAAGTGGGTCAAAATAATA
*
111109 AAGTGGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCACTACG
1 AAGTGGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAATACG
* *
111174 AGTGAAACTTCAAACCCCATCTTCTTGATGAGATA
66 AGTGAAACTTCAAACACCATCTTCTTGATAAGATA
111209 CAAAGAAATG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 93 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (123 bp):
AAGTGGTCATCTTCCTAATAAGATACAGAGAAGTAGACCAAAACAATGAAGCGAAGCTCAATACG
AGTGAAACTTCAAACACCATCTTCTTGATAAGATATAGAGAAGTGGGTCAAAATAATA
Found at i:111367 original size:46 final size:46
Alignment explanation
Indices: 111291--111600 Score: 295
Period size: 46 Copynumber: 6.8 Consensus size: 46
111281 CATCATTCAG
* * * * **
111291 TCTTTTATCCCTAAGTCAATAGAGGCAGATTGAAGCCATCGTCCAA
1 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACATTATCCAA
*
111337 TCTTTTACCCCTAAGTCAAGAGGGGTAGATTGAAGACATTATCCAA
1 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACATTATCCAA
* * * * * *
111383 TCTCTTACCCTTAAGTCAAGAAGGGCATATTGGAGACATAATCCAA
1 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACATTATCCAA
* * ** * *
111429 TCTTTTACCCTTAAGTCAATAAAGGCATATTGAAGACATTATTCAA
1 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACATTATCCAA
* * * * * *
111475 TCTCTTACCAC-GA-CCATG-GGAG-AGATTGAAGACATTATCCAA
1 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACATTATCCAA
* * * *
111517 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGTCATCATCTAA
1 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACATTATCCAA
* ** *
111563 TCTTTTACCCTTAAGTCAAGAAAGGCGGATTGAAGACA
1 TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACA
111601 CCATTCAATC
Statistics
Matches: 212, Mismatches: 48, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
42 27 0.13
43 2 0.01
44 5 0.02
45 4 0.02
46 174 0.82
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (46 bp):
TCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGACATTATCCAA
Found at i:111628 original size:134 final size:134
Alignment explanation
Indices: 111363--111615 Score: 380
Period size: 134 Copynumber: 1.9 Consensus size: 134
111353 CAAGAGGGGT
* * **
111363 AGATTGAAGACATTATCCAATCTCTTACCCTTAAGTCAAGAAGGGCATATTGGAGACATAATCCA
1 AGATTGAAGACATTATCCAATCTCTTACCCCTAAGTCAAGAAGGGCAGATTAAAGACATAATCCA
* * **
111428 ATCTTTTACCCTTAAGTCAATAAAGGCATATTGAAGACATTATTCAATCTCTTACCACGACCATG
66 ATCTTTTACCCTTAAGTCAAGAAAGGCAGATTGAAGACACCATTCAATCTCTTACCACGACCATG
111493 GGAG
131 GGAG
* * * * *
111497 AGATTGAAGACATTATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGTCATCATCTA
1 AGATTGAAGACATTATCCAATCTCTTACCCCTAAGTCAAGAAGGGCAGATTAAAGACATAATCCA
*
111562 ATCTTTTACCCTTAAGTCAAGAAAGGCGGATTGAAGACACCATTCAATCTCTTA
66 ATCTTTTACCCTTAAGTCAAGAAAGGCAGATTGAAGACACCATTCAATCTCTTA
111616 ACCCGGTCAT
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
134 105 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (134 bp):
AGATTGAAGACATTATCCAATCTCTTACCCCTAAGTCAAGAAGGGCAGATTAAAGACATAATCCA
ATCTTTTACCCTTAAGTCAAGAAAGGCAGATTGAAGACACCATTCAATCTCTTACCACGACCATG
GGAG
Found at i:112228 original size:16 final size:17
Alignment explanation
Indices: 112207--112243 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
112197 CCCAAATAAT
112207 AAATTT-TTTTAAATTA
1 AAATTTATTTTAAATTA
*
112223 AAATTTATTTTAATTTA
1 AAATTTATTTTAAATTA
112240 AAAT
1 AAAT
112244 GTCTAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAATTA
Found at i:112313 original size:16 final size:16
Alignment explanation
Indices: 112277--112329 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
112267 AACTACCCAA
*
112277 CAATTAAACCCAAACC
1 CAATTACACCCAAACC
*
112293 CAATTACACCCAAGCC
1 CAATTACACCCAAACC
*
112309 TAATTAC-CCAACAAACC
1 CAATTACACC--CAAACC
112326 CAAT
1 CAAT
112330 AAGCCCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 2 0.07
16 20 0.67
17 8 0.27
ACGTcount: A:0.45, C:0.38, G:0.02, T:0.15
Consensus pattern (16 bp):
CAATTACACCCAAACC
Found at i:113243 original size:12 final size:14
Alignment explanation
Indices: 113216--113247 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
113206 GAGAAGTTTT
113216 TTTTTTTAAAATGA
1 TTTTTTTAAAATGA
113230 TTTTTTT-AAA-GA
1 TTTTTTTAAAATGA
113242 TTTTTT
1 TTTTTT
113248 AAACTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 3 0.17
14 7 0.39
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (14 bp):
TTTTTTTAAAATGA
Found at i:113610 original size:29 final size:30
Alignment explanation
Indices: 113573--113643 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
113563 CCCCTTAACT
* *
113573 TTTTGAAAATTTAG-ATTTGGCCCTCGAAC
1 TTTTCAAAATTTAGAATTTGGCCCTCAAAC
* *
113602 TTTTCAAAAATTCGAATTTGGCCCTCAAAC
1 TTTTCAAAATTTAGAATTTGGCCCTCAAAC
113632 TTTTCAAAATTT
1 TTTTCAAAATTT
113644 CCTTTTTGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 11 0.31
30 25 0.69
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (30 bp):
TTTTCAAAATTTAGAATTTGGCCCTCAAAC
Found at i:116726 original size:84 final size:87
Alignment explanation
Indices: 116624--116817 Score: 225
Period size: 88 Copynumber: 2.3 Consensus size: 87
116614 TTTAAGCATC
* * * *
116624 AAAGGTGTTCAAACTTTTTCAAAAAAATAATTAA-AT-T-ATTTT-TTTTACATTTATTTGGATA
1 AAAGGTCTTCAAACTTTTTCAAAAAAA-AATTAAGATCTGATTTTATTTTACACTCAATTGGATA
*
116685 CTTAAACTTTTAAAATGCATCAA
65 CTTAAACTTTTAAAATGCATAAA
* * * * * *
116708 AAAGGTCTTCAAATTTTTTCAAGAAAAAATTAAGTTCCTGTTTTTATTTTGCACTCAATTGGGTA
1 AAAGGTCTTCAAACTTTTTCAAAAAAAAATTAAGAT-CTGATTTTATTTTACACTCAATTGGATA
116773 CTTAAACTTTTAAAATGCATAAA
65 CTTAAACTTTTAAAATGCATAAA
* *
116796 AAAAGCCTTCAAACTTTTTCAA
1 AAAGGTCTTCAAACTTTTTCAA
116818 CCAATGATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
83 6 0.07
84 25 0.27
86 1 0.01
87 4 0.04
88 55 0.60
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (87 bp):
AAAGGTCTTCAAACTTTTTCAAAAAAAAATTAAGATCTGATTTTATTTTACACTCAATTGGATAC
TTAAACTTTTAAAATGCATAAA
Found at i:117281 original size:65 final size:65
Alignment explanation
Indices: 117205--117332 Score: 175
Period size: 65 Copynumber: 2.0 Consensus size: 65
117195 TTGTTTTTTT
* * * *
117205 TGAAAAAATTTGAGGGCCTTTTTTATGCATTTTTAAAGTTCAAATACCCAATTGAATGCAAAATA
1 TGAAAAAATTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAATACCCAAATGAATGCAAAATA
* * * * *
117270 TGAAATAATTTGAAGGTCTTTTTGATGTATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAA
1 TGAAAAAATTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAATACCCAAATGAATGCAAAA
117333 AAAAAAAAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (65 bp):
TGAAAAAATTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAATACCCAAATGAATGCAAAATA
Found at i:117739 original size:11 final size:11
Alignment explanation
Indices: 117708--117755 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
117698 TCACATTAAC
*
117708 AAATAATTTTA
1 AAATTATTTTA
117719 AAATTA--TTA
1 AAATTATTTTA
117728 AAATTATTTTA
1 AAATTATTTTA
117739 AAATTAATTTTTA
1 AAATT-A-TTTTA
117752 AAAT
1 AAAT
117756 AATAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 9 0.28
11 13 0.41
12 1 0.03
13 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:118730 original size:9 final size:9
Alignment explanation
Indices: 118716--118744 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
118706 GATGATGATG
118716 ATTTTAATA
1 ATTTTAATA
118725 ATTTTAATA
1 ATTTTAATA
118734 ATTTTAA-A
1 ATTTTAATA
118742 ATT
1 ATT
118745 ATTTGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTTTAATA
Found at i:131033 original size:18 final size:18
Alignment explanation
Indices: 131002--131043 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
130992 CTTGTACTTC
131002 CTTTT-CTTTCTGTTTTT
1 CTTTTCCTTTCTGTTTTT
*
131019 CTTTTCCTTTTTGTTTTT
1 CTTTTCCTTTCTGTTTTT
*
131037 ATTTTCC
1 CTTTTCC
131044 CTCTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (18 bp):
CTTTTCCTTTCTGTTTTT
Found at i:133488 original size:11 final size:11
Alignment explanation
Indices: 133472--133515 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
133462 TCATTAATAA
133472 ATAAACAAGTC
1 ATAAACAAGTC
*
133483 ATAAACAAGCTT
1 ATAAACAAG-TC
*
133495 ATAAACGAGTC
1 ATAAACAAGTC
133506 AATAAACAAG
1 -ATAAACAAG
133516 CTTGTTTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (11 bp):
ATAAACAAGTC
Found at i:133505 original size:23 final size:24
Alignment explanation
Indices: 133472--133518 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
133462 TCATTAATAA
133472 ATAAACAAGTC-ATAAACAAGCTT
1 ATAAACAAGTCAATAAACAAGCTT
*
133495 ATAAACGAGTCAATAAACAAGCTT
1 ATAAACAAGTCAATAAACAAGCTT
133519 GTTTGTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (24 bp):
ATAAACAAGTCAATAAACAAGCTT
Found at i:138342 original size:29 final size:29
Alignment explanation
Indices: 138256--138343 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 29
138246 AATACAGAAA
* * *
138256 AAGTGCGAGCTGTCACAA-TAAAGCTACA
1 AAGTGCGAACTGTCACAAGTGAAGCTACG
* * *
138284 AAGTGTGAACTATTAC-AGTGAAGCTACG
1 AAGTGCGAACTGTCACAAGTGAAGCTACG
* *
138312 AAGTGCGAACTGTCACAAGTGAATCTGCG
1 AAGTGCGAACTGTCACAAGTGAAGCTACG
138341 AAG
1 AAG
138344 CAACTGAAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
27 1 0.02
28 33 0.70
29 13 0.28
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (29 bp):
AAGTGCGAACTGTCACAAGTGAAGCTACG
Found at i:138440 original size:22 final size:22
Alignment explanation
Indices: 138408--138455 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
138398 CTTTCAAAAG
*
138408 ATTTAGTCTTTATTAGAATAAT
1 ATTTAGACTTTATTAGAATAAT
* *
138430 ATTTAGACTTTATTAGTATCAT
1 ATTTAGACTTTATTAGAATAAT
138452 ATTT
1 ATTT
138456 TTAGCATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (22 bp):
ATTTAGACTTTATTAGAATAAT
Found at i:138913 original size:21 final size:21
Alignment explanation
Indices: 138889--138938 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
138879 TTTATTTAAG
138889 AGTTTGTTTTTAATTCAAATA
1 AGTTTGTTTTTAATTCAAATA
* **
138910 AGTTTG-ATTTAATTTGAATA
1 AGTTTGTTTTTAATTCAAATA
*
138930 AATTTGTTT
1 AGTTTGTTT
138939 AGATAATTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (21 bp):
AGTTTGTTTTTAATTCAAATA
Found at i:149922 original size:2 final size:2
Alignment explanation
Indices: 149915--149939 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
149905 GTTCCCTTTG
149915 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
149940 CATCTGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:152471 original size:6 final size:6
Alignment explanation
Indices: 152454--152483 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
152444 CTTAAATCCA
152454 AACCCAT AACCCT AACCCT AACCCT AACCC
1 AACCC-T AACCCT AACCCT AACCCT AACCC
152484 CTTGAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.37, C:0.50, G:0.00, T:0.13
Consensus pattern (6 bp):
AACCCT
Found at i:152911 original size:14 final size:14
Alignment explanation
Indices: 152892--152918 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
152882 GCTTGAAACA
152892 AAAGCAAAAACAGT
1 AAAGCAAAAACAGT
152906 AAAGCAAAAACAG
1 AAAGCAAAAACAG
152919 AATACACAAC
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:0.67, C:0.15, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAGCAAAAACAGT
Found at i:161087 original size:13 final size:13
Alignment explanation
Indices: 161039--161152 Score: 54
Period size: 13 Copynumber: 8.4 Consensus size: 13
161029 GACCGACTCG
*
161039 TTGACCGTTAACT
1 TTGACCGTTGACT
*
161052 TTGACCTTTGA-T
1 TTGACCGTTGACT
* *
161064 TTTA--ATTGACT
1 TTGACCGTTGACT
161075 TTGACCGTTGACT
1 TTGACCGTTGACT
* *
161088 CTGACTAGCCGTTGAGT
1 TTG---A-CCGTTGACT
*
161105 TTGACCATTGACT
1 TTGACCGTTGACT
*
161118 TTGACTTGACGTTGAGT
1 TTGAC----CGTTGACT
*
161135 TTGACCATTGACT
1 TTGACCGTTGACT
161148 TTGAC
1 TTGAC
161153 TTTGACCGTT
Statistics
Matches: 75, Mismatches: 15, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
10 4 0.05
11 4 0.05
12 4 0.05
13 40 0.53
14 1 0.01
16 1 0.01
17 21 0.28
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:161121 original size:6 final size:6
Alignment explanation
Indices: 161112--161158 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
161102 AGTTTGACCA
* * *
161112 TTGACT TTGAC- TTGACG TTGAGT TTGACCA TTGACT TTGACT TTGAC
1 TTGACT TTGACT TTGACT TTGACT TTGA-CT TTGACT TTGACT TTGAC
161159 CGTTAACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
5 5 0.15
6 25 0.74
7 4 0.12
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (6 bp):
TTGACT
Found at i:161151 original size:19 final size:19
Alignment explanation
Indices: 161112--161159 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
161102 AGTTTGACCA
161112 TTGACTTTGA-C-TTGACG
1 TTGACTTTGACCATTGACG
* *
161129 TTGAGTTTGACCATTGACT
1 TTGACTTTGACCATTGACG
161148 TTGACTTTGACC
1 TTGACTTTGACC
161160 GTTAACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 9 0.35
18 1 0.04
19 16 0.62
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (19 bp):
TTGACTTTGACCATTGACG
Found at i:161154 original size:30 final size:30
Alignment explanation
Indices: 161069--161154 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 30
161059 TTGATTTTAA
* * * * *
161069 TTGACTTTGACCGTTGACTCTGACTAGCCG
1 TTGAGTTTGACCATTGACTTTGACTTGACG
161099 TTGAGTTTGACCATTGACTTTGACTTGACG
1 TTGAGTTTGACCATTGACTTTGACTTGACG
161129 TTGAGTTTGACCATTGACTTTGACTT
1 TTGAGTTTGACCATTGACTTTGACTT
161155 TGACCGTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (30 bp):
TTGAGTTTGACCATTGACTTTGACTTGACG
Found at i:166308 original size:66 final size:68
Alignment explanation
Indices: 166237--166366 Score: 201
Period size: 66 Copynumber: 1.9 Consensus size: 68
166227 ATTTAAGTAA
* *
166237 TTACATGATGTTTATCATAAAATACTTATACTAA-TTT-TAAATTACATAATGTTTATATTATTT
1 TTACATAATGTTTACCATAAAATACTTATACTAATTTTATAAATTACATAATGTTTATATTATTT
166300 TTT
66 TTT
*
166303 TTACATAATGTTTACCATAAAATATTTATACTAATTTTAACTAAATTACATAATGTTTATATTA
1 TTACATAATGTTTACCATAAAATACTTATACTAATTTT-A-TAAATTACATAATGTTTATATTA
166367 ATTATTTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
66 31 0.54
67 3 0.05
70 23 0.40
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.48
Consensus pattern (68 bp):
TTACATAATGTTTACCATAAAATACTTATACTAATTTTATAAATTACATAATGTTTATATTATTT
TTT
Found at i:169686 original size:112 final size:111
Alignment explanation
Indices: 169482--169691 Score: 276
Period size: 112 Copynumber: 1.9 Consensus size: 111
169472 TGGACGTGTA
*** * *
169482 TGTTAAATCCTCCCAGGGAAATATGAAAATAGCAATACAACTCAAAAAAATATAAGAAGTAATTT
1 TGTTAAATCCTCCCACAAAAATATGAAAATAGCAATACAACTCAAAAAAATATAAGAAGTAACTC
* * *
169547 TAAGATGATTGATTAACTGAACCTGCTCAATTAGCTGTATGTTAAT
66 CAAGATGATTGATCAACTAAACCTGCTCAATTAGCTGTATGTTAAT
** * **
169593 TGTTAAATCCTCCCACAAAAATATGAAAATAGTGATAACAACTCGATCAAATATAAGAAGTAACT
1 TGTTAAATCCTCCCACAAAAATATGAAAATAGCAAT-ACAACTCAAAAAAATATAAGAAGTAACT
* *
169658 CCAGGATGATTGATCAACTAAACTTGCTCAATTA
65 CCAAGATGATTGATCAACTAAACCTGCTCAATTA
169692 CAAATATCTA
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
111 31 0.37
112 52 0.63
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (111 bp):
TGTTAAATCCTCCCACAAAAATATGAAAATAGCAATACAACTCAAAAAAATATAAGAAGTAACTC
CAAGATGATTGATCAACTAAACCTGCTCAATTAGCTGTATGTTAAT
Found at i:174433 original size:27 final size:27
Alignment explanation
Indices: 174377--174433 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
174367 GTACCCAATT
* **
174377 TTTTTTTATATATTTTTTCTTTTCTTA
1 TTTTTTTATATATTTTTTCTTTACACA
*
174404 TTTTTTTCTAT-TTTTTTCATTTACACA
1 TTTTTTTATATATTTTTTC-TTTACACA
174431 TTT
1 TTT
174434 CTTAAGACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTTTTTATATATTTTTTCTTTACACA
Found at i:177304 original size:10 final size:10
Alignment explanation
Indices: 177289--177331 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
177279 AGGGTTTGAA
177289 TTTTTTTTCC
1 TTTTTTTTCC
*
177299 TTTTTTCTCC
1 TTTTTTTTCC
*
177309 TTTTTCTTCC
1 TTTTTTTTCC
177319 TTTTTCTTTCC
1 TTTTT-TTTCC
177330 TT
1 TT
177332 CTTTGCCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 22 0.79
11 6 0.21
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTTTCC
Found at i:190599 original size:9 final size:9
Alignment explanation
Indices: 190583--190663 Score: 87
Period size: 9 Copynumber: 9.1 Consensus size: 9
190573 GTTTGTAAAC
190583 TGTTATGTA
1 TGTTATGTA
*
190592 TATTATGTA
1 TGTTATGTA
190601 TGTTATGTA
1 TGTTATGTA
190610 CTGTTATGTA
1 -TGTTATGTA
* *
190620 TATTATTTA
1 TGTTATGTA
*
190629 TGTTATGTT
1 TGTTATGTA
190638 TGTATAT-T-
1 TGT-TATGTA
190646 TG-TATGTA
1 TGTTATGTA
190654 TGTTATGTA
1 TGTTATGTA
190663 T
1 T
190664 ATTTTTTATG
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
6 3 0.05
7 1 0.02
8 4 0.07
9 40 0.67
10 12 0.20
ACGTcount: A:0.23, C:0.01, G:0.17, T:0.58
Consensus pattern (9 bp):
TGTTATGTA
Found at i:190616 original size:28 final size:28
Alignment explanation
Indices: 190581--190636 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
190571 AAGTTTGTAA
190581 ACTGTTATGTATATTATGTATGTTATGT
1 ACTGTTATGTATATTATGTATGTTATGT
*
190609 ACTGTTATGTATATTATTTATGTTATGT
1 ACTGTTATGTATATTATGTATGTTATGT
190637 TTGTATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (28 bp):
ACTGTTATGTATATTATGTATGTTATGT
Found at i:190631 original size:13 final size:14
Alignment explanation
Indices: 190583--190679 Score: 78
Period size: 13 Copynumber: 6.9 Consensus size: 14
190573 GTTTGTAAAC
190583 TGTTATGTATATTA
1 TGTTATGTATATTA
190597 TG-TATGT-TATGTA
1 TGTTATGTATAT-TA
190610 CTGTTATGTATATTA
1 -TGTTATGTATATTA
*
190625 T-TTATGT-TATGTT
1 TGTTATGTATAT-TA
* *
190638 TGTATATTTGTATGTA
1 TGT-TATGTATAT-TA
190654 TGTTATGTATATT-
1 TGTTATGTATATTA
*
190667 TTTTATGTATATT
1 TGTTATGTATATT
190680 TGTATGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
12 6 0.09
13 27 0.39
14 7 0.10
15 18 0.26
16 11 0.16
ACGTcount: A:0.24, C:0.01, G:0.15, T:0.60
Consensus pattern (14 bp):
TGTTATGTATATTA
Found at i:190636 original size:5 final size:5
Alignment explanation
Indices: 190583--190661 Score: 55
Period size: 5 Copynumber: 16.6 Consensus size: 5
190573 GTTTGTAAAC
* *
190583 TGTTA TG-TA TATTA TG-TA TGTTA TG-TA CTGTTA TG-TA TATTA T-TTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA -TGTTA TGTTA TGTTA TGTTA
*
190629 TGTTA TGTT- TGTATA TTTGTA TG-TA TGTTA TGT
1 TGTTA TGTTA TGT-TA TGT-TA TGTTA TGTTA TGT
190662 ATATTTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
4 23 0.39
5 29 0.49
6 7 0.12
ACGTcount: A:0.23, C:0.01, G:0.18, T:0.58
Consensus pattern (5 bp):
TGTTA
Found at i:190680 original size:13 final size:13
Alignment explanation
Indices: 190656--190698 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
190646 TGTATGTATG
190656 TTATGTATATTTT
1 TTATGTATATTTT
190669 TTATGTATA-TTT
1 TTATGTATATTTT
* *
190681 GTATGT-TTTTTT
1 TTATGTATATTTT
190693 TTATGT
1 TTATGT
190699 GTTATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 1 0.04
12 16 0.62
13 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.70
Consensus pattern (13 bp):
TTATGTATATTTT
Found at i:190692 original size:22 final size:22
Alignment explanation
Indices: 190603--190691 Score: 85
Period size: 21 Copynumber: 4.1 Consensus size: 22
190593 ATTATGTATG
* *
190603 TTATGTACTGTTATGTATATTAT
1 TTATGTA-TATTATGTATATTTT
*
190626 TTATGT-TATGTTTGTATA-TTT
1 TTATGTATAT-TATGTATATTTT
* *
190647 GTATGTATGTTATGTATATTTT
1 TTATGTATATTATGTATATTTT
*
190669 TTATGTATATT-TGTATGTTTT
1 TTATGTATATTATGTATATTTT
190690 TT
1 TT
190692 TTTATGTGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
21 27 0.50
22 21 0.39
23 6 0.11
ACGTcount: A:0.21, C:0.01, G:0.15, T:0.63
Consensus pattern (22 bp):
TTATGTATATTATGTATATTTT
Found at i:193638 original size:5 final size:5
Alignment explanation
Indices: 193628--193669 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
193618 AAAAAATATT
193628 TTCCA TTCCA TTCCA TTCCA TTCCA TTCCA TTCCA TT-CA TTC
1 TTCCA TTCCA TTCCA TTCCA TTCCA TTCCA TTCCA TTCCA TTC
193670 ATCCTTAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.43
Consensus pattern (5 bp):
TTCCA
Found at i:203264 original size:40 final size:39
Alignment explanation
Indices: 203220--203337 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 39
203210 TGATATGTGT
* * *
203220 AAGTCTTACAGAAAAGAAGAAAAACCATCTAAACATTCCC
1 AAGTC-TATAGAAGAGAAGAAAAACCATCCAAACATTCCC
*
203260 AAGTCCTATAGAAGAGAAGAAAAACCATCCAAACATTCTC
1 AAGT-CTATAGAAGAGAAGAAAAACCATCCAAACATTCCC
* * *
203300 AAATACCATAGATGAGAAGAAAAACCATCCAAACATTC
1 AAGT-CTATAGAAGAGAAGAAAAACCATCCAAACATTC
203338 TCAAATACCA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 68 0.99
41 1 0.01
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (39 bp):
AAGTCTATAGAAGAGAAGAAAAACCATCCAAACATTCCC
Found at i:203338 original size:40 final size:40
Alignment explanation
Indices: 203234--203356 Score: 194
Period size: 40 Copynumber: 3.1 Consensus size: 40
203224 CTTACAGAAA
* * * *
203234 AGAAGAAAAACCATCTAAACATTCCCAAGT-CCTATAGAAG
1 AGAAGAAAAACCATCCAAACATTCTCAAATACC-ATAGATG
203274 AGAAGAAAAACCATCCAAACATTCTCAAATACCATAGATG
1 AGAAGAAAAACCATCCAAACATTCTCAAATACCATAGATG
203314 AGAAGAAAAACCATCCAAACATTCTCAAATACCATAGATG
1 AGAAGAAAAACCATCCAAACATTCTCAAATACCATAGATG
203354 AGA
1 AGA
203357 CCCCAAACAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 76 0.97
41 2 0.03
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (40 bp):
AGAAGAAAAACCATCCAAACATTCTCAAATACCATAGATG
Found at i:206985 original size:31 final size:31
Alignment explanation
Indices: 206947--207009 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
206937 TGTTCAGTGC
*
206947 TGAGACAGGAGTCTAACTTCGTGACGAAGGT
1 TGAGACAGGAGTCTAACCTCGTGACGAAGGT
206978 TGAGACAGGAGTCTAACCTCGTGACGAAGGT
1 TGAGACAGGAGTCTAACCTCGTGACGAAGGT
207009 T
1 T
207010 TTGAGTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (31 bp):
TGAGACAGGAGTCTAACCTCGTGACGAAGGT
Found at i:208930 original size:30 final size:30
Alignment explanation
Indices: 208896--208969 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 30
208886 AAAATTTGAT
*
208896 AAAAAAAAATTT-GGCCT-TTAAAAATAAA
1 AAAAAAAAATTTAGACCTCTTAAAAATAAA
208924 AAAAAAAAATTTAGACCTCTTAAAAATTAAA
1 AAAAAAAAATTTAGACCTCTTAAAAA-TAAA
*
208955 AAACAAAAATTTAGA
1 AAAAAAAAATTTAGA
208970 TTTTTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.29
29 4 0.10
30 7 0.17
31 18 0.44
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (30 bp):
AAAAAAAAATTTAGACCTCTTAAAAATAAA
Found at i:213634 original size:3 final size:3
Alignment explanation
Indices: 213628--213669 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
213618 AACAAAATAC
213628 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
213670 TTCAATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:213714 original size:6 final size:6
Alignment explanation
Indices: 213703--213859 Score: 72
Period size: 6 Copynumber: 27.3 Consensus size: 6
213693 CAAAGTAAAT
* **
213703 TTGAAA TTGAAA TT--AA TAGAGT TTGAAA TT-AAA GTTGAAA -TGAAAA
1 TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA -TTGAAA TTG-AAA
* *
213749 TT-AAA GTTGAAA TTGAAA TT-AAA TT-ATAA TTTAAA TTG--A GTGATAA
1 TTGAAA -TTGAAA TTGAAA TTGAAA TTGA-AA TTGAAA TTGAAA TTGA-AA
* * *
213795 TTGAAA TTGAAA TT-AAA TT-ATAC TTTAAA TTG--A GTGATAA TTGAAA
1 TTGAAA TTGAAA TTGAAA TTGA-AA TTGAAA TTGAAA TTGA-AA TTGAAA
*
213841 TTGAAA TT-AAG TTGAAA TT
1 TTGAAA TTGAAA TTGAAA TT
213860 AATTTTAAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 38
0.68 0.09 0.22
Matches are distributed among these distances:
4 9 0.08
5 24 0.21
6 66 0.57
7 17 0.15
ACGTcount: A:0.47, C:0.01, G:0.15, T:0.38
Consensus pattern (6 bp):
TTGAAA
Found at i:213742 original size:12 final size:11
Alignment explanation
Indices: 213725--213861 Score: 68
Period size: 11 Copynumber: 11.9 Consensus size: 11
213715 TTAATAGAGT
213725 TTGAAATTAAA
1 TTGAAATTAAA
*
213736 GTTGAAATGAAAA
1 -TTGAAAT-TAAA
213749 TT-AAAGTTGAAA
1 TTGAAA-TT-AAA
213761 TTGAAATTAAA
1 TTGAAATTAAA
213772 TT-ATAATTTAAA
1 TTGA-AA-TTAAA
* *
213784 TTG-AGTGATAA
1 TTGAAATTA-AA
213795 TTGAAATTGAAA
1 TTGAAATT-AAA
*
213807 TT-AAATTATAC
1 TTGAAATTA-AA
* *
213818 TTTAAATT-GA
1 TTGAAATTAAA
*
213828 GTGATAATTGAAA
1 TTGA-AATT-AAA
*
213841 TTGAAATTAAG
1 TTGAAATTAAA
213852 TTGAAATTAA
1 TTGAAATTAA
213862 TTTTAAAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
10 6 0.06
11 40 0.42
12 39 0.41
13 11 0.11
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37
Consensus pattern (11 bp):
TTGAAATTAAA
Found at i:213751 original size:18 final size:18
Alignment explanation
Indices: 213698--213771 Score: 82
Period size: 18 Copynumber: 4.2 Consensus size: 18
213688 TTATACAAAG
*
213698 TAAATTTGAAATTGAAAT
1 TAAAGTTGAAATTGAAAT
* **
213716 T-AA-TAGAGTTTGAAAT
1 TAAAGTTGAAATTGAAAT
213732 TAAAGTTGAAA-TGAAAAT
1 TAAAGTTGAAATTG-AAAT
213750 TAAAGTTGAAATTGAAAT
1 TAAAGTTGAAATTGAAAT
213768 TAAA
1 TAAA
213772 TTATAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 11 0.24
17 6 0.13
18 27 0.59
19 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (18 bp):
TAAAGTTGAAATTGAAAT
Found at i:213784 original size:23 final size:23
Alignment explanation
Indices: 213731--213827 Score: 64
Period size: 23 Copynumber: 4.4 Consensus size: 23
213721 GAGTTTGAAA
*
213731 TTAAAGTTGAAATGAAAATTA-AAGT
1 TTAAA-TTGAAAT-TAAATTATAA-T
*
213756 TGAAATTGAAATTAAATTATAAT
1 TTAAATTGAAATTAAATTATAAT
* *
213779 TTAAATTG------AGTGATAAT
1 TTAAATTGAAATTAAATTATAAT
* *
213796 TGAAATTGAAATTAAATTATACT
1 TTAAATTGAAATTAAATTATAAT
213819 TTAAATTGA
1 TTAAATTGA
213828 GTGATAATTG
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
17 14 0.25
23 28 0.51
24 9 0.16
25 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.38
Consensus pattern (23 bp):
TTAAATTGAAATTAAATTATAAT
Found at i:213805 original size:40 final size:40
Alignment explanation
Indices: 213755--213850 Score: 183
Period size: 40 Copynumber: 2.4 Consensus size: 40
213745 AAAATTAAAG
213755 TTGAAATTGAAATTAAATTATAATTTAAATTGAGTGATAA
1 TTGAAATTGAAATTAAATTATAATTTAAATTGAGTGATAA
*
213795 TTGAAATTGAAATTAAATTATACTTTAAATTGAGTGATAA
1 TTGAAATTGAAATTAAATTATAATTTAAATTGAGTGATAA
213835 TTGAAATTGAAATTAA
1 TTGAAATTGAAATTAA
213851 GTTGAAATTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.47, C:0.01, G:0.12, T:0.40
Consensus pattern (40 bp):
TTGAAATTGAAATTAAATTATAATTTAAATTGAGTGATAA
Found at i:213847 original size:23 final size:23
Alignment explanation
Indices: 213776--213848 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 23
213766 ATTAAATTAT
*
213776 AATTTAAATTGAGTGATAATTGA
1 AATTGAAATTGAGTGATAATTGA
213799 AATTGAAA-T---T-A-AATT-A
1 AATTGAAATTGAGTGATAATTGA
* *
213815 TACTTTAAATTGAGTGATAATTGA
1 -AATTGAAATTGAGTGATAATTGA
213839 AATTGAAATT
1 AATTGAAATT
213849 AAGTTGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 16
0.64 0.09 0.28
Matches are distributed among these distances:
16 1 0.03
17 10 0.27
18 2 0.05
19 1 0.03
21 1 0.03
22 2 0.05
23 19 0.51
24 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.14, T:0.40
Consensus pattern (23 bp):
AATTGAAATTGAGTGATAATTGA
Found at i:213855 original size:17 final size:17
Alignment explanation
Indices: 213703--213859 Score: 77
Period size: 17 Copynumber: 9.5 Consensus size: 17
213693 CAAAGTAAAT
213703 TTGAAATTGAAATTAA-
1 TTGAAATTGAAATTAAG
* **
213719 TAGAGTTTGAAATTAAAG
1 TTGAAATTGAAATT-AAG
213737 TTGAAA-TGAAAATTAAAG
1 TTGAAATTG-AAATT-AAG
*
213755 TTGAAATTGAAATTAAA
1 TTGAAATTGAAATTAAG
* *
213772 TT-ATAATTTAAATTGAG
1 TTGA-AATTGAAATTAAG
213789 -TGATAATTG--A--AA-
1 TTGA-AATTGAAATTAAG
*
213801 TTGAAATT-AAATTATAC
1 TTGAAATTGAAATTA-AG
* *
213818 TTTAAATTG-AGTGATAA-
1 TTGAAATTGAAAT--TAAG
213835 TTGAAATTGAAATTAAG
1 TTGAAATTGAAATTAAG
213852 TTGAAATT
1 TTGAAATT
213860 AATTTTAAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 35
0.68 0.10 0.22
Matches are distributed among these distances:
12 4 0.04
13 5 0.05
15 2 0.02
16 17 0.16
17 49 0.46
18 26 0.24
19 4 0.04
ACGTcount: A:0.47, C:0.01, G:0.15, T:0.38
Consensus pattern (17 bp):
TTGAAATTGAAATTAAG
Found at i:213937 original size:19 final size:19
Alignment explanation
Indices: 213915--213970 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
213905 AATAAAACAC
*
213915 TAGTTTGAATTTAAAATTA
1 TAGTTTGAAATTAAAATTA
*
213934 TAGTTTAAAATTAAAATTA
1 TAGTTTGAAATTAAAATTA
* *
213953 CA-TTTGAAATGAAAATTA
1 TAGTTTGAAATTAAAATTA
213971 AATATGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (19 bp):
TAGTTTGAAATTAAAATTA
Found at i:213967 original size:18 final size:18
Alignment explanation
Indices: 213927--213980 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
213917 GTTTGAATTT
* * *
213927 AAAATTATAGTTTAAAATT
1 AAAATTA-AATTTGAAATG
*
213946 AAAATTACATTTGAAATG
1 AAAATTAAATTTGAAATG
*
213964 AAAATTAAATATGAAAT
1 AAAATTAAATTTGAAAT
213981 TGGAATTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (18 bp):
AAAATTAAATTTGAAATG
Found at i:214103 original size:11 final size:11
Alignment explanation
Indices: 214083--214162 Score: 61
Period size: 12 Copynumber: 6.8 Consensus size: 11
214073 TAATTTTAAA
214083 TTAAATTGAAAT
1 TTAAA-TGAAAT
*
214095 TTCAATGAAAT
1 TTAAATGAAAT
* *
214106 TTAAATTTAATT
1 TTAAA-TGAAAT
*
214118 TTCAAATGAATT
1 TT-AAATGAAAT
214130 TTAAATGAAAT
1 TTAAATGAAAT
* *
214141 TGAAATCTAAAT
1 TTAAAT-GAAAT
214153 TTAAAATGAA
1 TT-AAATGAA
214163 GTTGAAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
11 23 0.43
12 24 0.44
13 7 0.13
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (11 bp):
TTAAATGAAAT
Found at i:214111 original size:23 final size:24
Alignment explanation
Indices: 214083--214141 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
214073 TAATTTTAAA
214083 TTAAATTGAAATTTC-AATGAAAT
1 TTAAATTGAAATTTCAAATGAAAT
* * *
214106 TTAAATTTAATTTTCAAATGAATT
1 TTAAATTGAAATTTCAAATGAAAT
214130 TTAAA-TGAAATT
1 TTAAATTGAAATT
214142 GAAATCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (24 bp):
TTAAATTGAAATTTCAAATGAAAT
Found at i:214137 original size:35 final size:35
Alignment explanation
Indices: 214079--214180 Score: 98
Period size: 35 Copynumber: 2.9 Consensus size: 35
214069 CTTATAATTT
* * *
214079 TAAA-TTAAATTGAAATTTCAATGAAATTTAAATT
1 TAAATTTAAAATGAAATTTAAATGAAATTTAAATC
* * * *
214113 TAATTTTCAAATGAATTTTAAATGAAATTGAAATC
1 TAAATTTAAAATGAAATTTAAATGAAATTTAAATC
* * **
214148 TAAATTTAAAATGAAGTTGAAATTTAATTTAAA
1 TAAATTTAAAATGAAATTTAAATGAAATTTAAA
214181 ATATTTAAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
34 3 0.06
35 50 0.94
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (35 bp):
TAAATTTAAAATGAAATTTAAATGAAATTTAAATC
Found at i:214144 original size:17 final size:17
Alignment explanation
Indices: 214077--214152 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 17
214067 AACTTATAAT
*
214077 TTTAAATTAAATTGAAA
1 TTTAAATGAAATTGAAA
* *
214094 TTTCAATGAAATTTAAA
1 TTTAAATGAAATTGAAA
* * *
214111 TTTAATTTTCAAA-TGAAT
1 TTTAA--ATGAAATTGAAA
214129 TTTAAATGAAATTGAAA
1 TTTAAATGAAATTGAAA
*
214146 TCTAAAT
1 TTTAAAT
214153 TTAAAATGAA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
16 4 0.09
17 28 0.64
18 8 0.18
19 4 0.09
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (17 bp):
TTTAAATGAAATTGAAA
Found at i:214464 original size:17 final size:18
Alignment explanation
Indices: 214428--214470 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
214418 TACTTCGAAA
214428 TTTATCAATCCCAAATAT
1 TTTATCAATCCCAAATAT
*
214446 TTTATCAATCTCAAA-AT
1 TTTATCAATCCCAAATAT
*
214463 TTTTTCAA
1 TTTATCAA
214471 ACTTTGACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATCAATCCCAAATAT
Found at i:214549 original size:20 final size:21
Alignment explanation
Indices: 214526--214569 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
214516 AATAAATAGT
*
214526 AATTTA-AATAAAATTTAAAA
1 AATTTACAATAAAATGTAAAA
*
214546 AA-TTACAATAACATGTAAAA
1 AATTTACAATAAAATGTAAAA
214566 AATT
1 AATT
214570 ATATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.15
20 16 0.80
21 1 0.05
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
AATTTACAATAAAATGTAAAA
Found at i:217760 original size:42 final size:42
Alignment explanation
Indices: 217701--217787 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
217691 TGAAATTATT
* *
217701 TATATTGATACTTTATTAAATTATTTGAATGCTACATAGTCA
1 TATATTGATACTTTATTAAATTATTTGAATACTACATAATCA
*
217743 TATATTGATACTTTATTAAATTATTTGAATACTATATAATCA
1 TATATTGATACTTTATTAAATTATTTGAATACTACATAATCA
217785 TAT
1 TAT
217788 TTATTAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (42 bp):
TATATTGATACTTTATTAAATTATTTGAATACTACATAATCA
Found at i:217774 original size:21 final size:21
Alignment explanation
Indices: 217700--217775 Score: 52
Period size: 21 Copynumber: 3.6 Consensus size: 21
217690 ATGAAATTAT
217700 TTATATTGATACTTTATTAAA
1 TTATATTGATACTTTATTAAA
* ** *
217721 TTAT-TTGAATGCTACA-T-AG
1 TTATATTG-ATACTTTATTAAA
217740 TCATATATTGATACTTTATTAAA
1 T--TATATTGATACTTTATTAAA
217763 TTAT-TTGAATACT
1 TTATATTG-ATACT
217776 ATATAATCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
19 2 0.05
20 7 0.17
21 25 0.62
22 4 0.10
23 2 0.05
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (21 bp):
TTATATTGATACTTTATTAAA
Found at i:217788 original size:21 final size:21
Alignment explanation
Indices: 217722--217789 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
217712 TTTATTAAAT
* * *
217722 TATTTGAATGCTACATAGTCA
1 TATTTGAATACTATATAATCA
*
217743 TATATTG-ATACTTTATTAA--A
1 TAT-TTGAATACTATA-TAATCA
217763 TTATTTGAATACTATATAATCA
1 -TATTTGAATACTATATAATCA
217785 TATTT
1 TATTT
217790 ATTAAATTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
20 7 0.19
21 23 0.64
22 6 0.17
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (21 bp):
TATTTGAATACTATATAATCA
Found at i:220775 original size:17 final size:17
Alignment explanation
Indices: 220729--220775 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
220719 ACAACCTTAA
**
220729 ATTCAAATTAAAAAACT
1 ATTCAAATTAAAGTACT
*
220746 ATTTAAATT-AAGTACT
1 ATTCAAATTAAAGTACT
220762 ATTCAAATTAAAGT
1 ATTCAAATTAAAGT
220776 GTTGATGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (17 bp):
ATTCAAATTAAAGTACT
Found at i:220890 original size:20 final size:21
Alignment explanation
Indices: 220867--220908 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
220857 AATAAATAAT
*
220867 AATTTAAATAA-ATTTTAAAA
1 AATTAAAATAACATTTTAAAA
220887 AATTAAAATAACATTTTAAAA
1 AATTAAAATAACATTTTAAAA
220908 A
1 A
220909 TTATATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAAAATAACATTTTAAAA
Found at i:220907 original size:19 final size:19
Alignment explanation
Indices: 220848--220911 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
220838 AATTATTTAC
** *
220848 ATTAAAATAAATAAATAATA
1 ATTAAAATAAAT-TTTAAAA
*
220868 ATTTAAATAAATTTTAAAAA
1 ATTAAAATAAATTTT-AAAA
220888 ATTAAAATAACATTTTAAAA
1 ATTAAAATAA-ATTTTAAAA
220908 ATTA
1 ATTA
220912 TATTAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.84
21 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAATAAATTTTAAAA
Found at i:221066 original size:16 final size:16
Alignment explanation
Indices: 221030--221075 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
221020 TAATGTTTAA
*
221030 ATTCAAATTTAAAAAACT
1 ATTCAAA-TT-AAATACT
*
221048 ATTTAAATTAAATACT
1 ATTCAAATTAAATACT
221064 ATTCAAATTAAA
1 ATTCAAATTAAA
221076 GTGTTGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 17 0.68
17 2 0.08
18 6 0.24
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTCAAATTAAATACT
Found at i:222162 original size:35 final size:37
Alignment explanation
Indices: 222121--222213 Score: 163
Period size: 37 Copynumber: 2.6 Consensus size: 37
222111 ATTTTTAAAA
*
222121 TTATATTTTCGAAATATTTTTTTACAT-T-TATTTTT
1 TTATATTTTCGAAATATTTTTTCACATATATATTTTT
222156 TTATATTTTCGAAATATTTTTTCACATATATATTTTT
1 TTATATTTTCGAAATATTTTTTCACATATATATTTTT
222193 TTATATTTTCGAAATATTTTT
1 TTATATTTTCGAAATATTTTT
222214 AGCTTTTCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 26 0.47
36 1 0.02
37 28 0.51
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (37 bp):
TTATATTTTCGAAATATTTTTTCACATATATATTTTT
Found at i:222228 original size:37 final size:36
Alignment explanation
Indices: 222073--222230 Score: 142
Period size: 37 Copynumber: 4.2 Consensus size: 36
222063 TTTAAAATTT
* * *
222073 TTTTTTTCTATTTTTGAAATATTTTTTATATTTTCAAAA
1 TTTTTTTATATTTTCGAAATATTTTTTACA-TTT--AAA
222112 TTTTTAAAATTATATTTTCGAAATATTTTTTTACATTT--A
1 TTTTT----TTATATTTTCGAAATA-TTTTTTACATTTAAA
* *
222151 TTTTTTTATATTTTCGAAATATTTTTTCACATATATA
1 TTTTTTTATATTTTCGAAATATTTTTT-ACATTTAAA
*
222188 TTTTTTTATATTTTCGAAATA-TTTTTAGCTTTTCAAA
1 TTTTTTTATATTTTCGAAATATTTTTTA-CATTT-AAA
222225 TTTTTT
1 TTTTTT
222231 GTAAAATATT
Statistics
Matches: 102, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
34 6 0.06
35 22 0.22
36 8 0.08
37 30 0.29
39 11 0.11
43 17 0.17
44 8 0.08
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (36 bp):
TTTTTTTATATTTTCGAAATATTTTTTACATTTAAA
Found at i:222309 original size:34 final size:34
Alignment explanation
Indices: 222271--222378 Score: 85
Period size: 34 Copynumber: 3.2 Consensus size: 34
222261 AATTTTTTAC
222271 ATATTTTTTTTATATTTTTGAAATATTAAAAAAT
1 ATATTTTTTTTATATTTTTGAAATATTAAAAAAT
** * ** * *
222305 ATATTTTCGTAATATTTTTTTCAA-ATTAGAAATT
1 ATATTTTTTTTATA-TTTTTGAAATATTAAAAAAT
* * * *
222339 TTATATTTTTTACATTTTCGAAATATT-AAAAAT
1 ATATTTTTTTTATATTTTTGAAATATTAAAAAAT
*
222372 ACATTTT
1 ATATTTT
222379 CAAAATATTT
Statistics
Matches: 51, Mismatches: 21, Indels: 5
0.66 0.27 0.06
Matches are distributed among these distances:
33 14 0.27
34 30 0.59
35 7 0.14
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (34 bp):
ATATTTTTTTTATATTTTTGAAATATTAAAAAAT
Found at i:222431 original size:69 final size:69
Alignment explanation
Indices: 222275--222434 Score: 252
Period size: 68 Copynumber: 2.3 Consensus size: 69
222265 TTTTACATAT
* * * **
222275 TTTTTTTATATTTTTGAAATATTAAAAAATATATTTTCGTAATATTTTTTTCAAATTAGAAATTT
1 TTTTTTTACATTTTCGAAATATTAAAAAATACATTTTCAAAATATTTTTTTCAAATTAGAAATTT
222340 TATA
66 TATA
222344 -TTTTTTACATTTTCGAAATATT-AAAAATACATTTTCAAAATATTTTTTTACAAATTAGAAATT
1 TTTTTTTACATTTTCGAAATATTAAAAAATACATTTTCAAAATATTTTTTT-CAAATTAGAAATT
222407 TTATA
65 TTATA
222412 TTTTTTTACATTTTCGAAATATT
1 TTTTTTTACATTTTCGAAATATT
222435 TTTTTTACAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
67 24 0.29
68 38 0.45
69 22 0.26
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (69 bp):
TTTTTTTACATTTTCGAAATATTAAAAAATACATTTTCAAAATATTTTTTTCAAATTAGAAATTT
TATA
Found at i:222440 original size:22 final size:22
Alignment explanation
Indices: 222344--222443 Score: 76
Period size: 22 Copynumber: 4.4 Consensus size: 22
222334 AAATTTTATA
222344 TTTTTTACATTTTCGAAATATT
1 TTTTTTACATTTTCGAAATATT
***** *
222366 AAAAATACATTTTCAAAATA-T
1 TTTTTTACATTTTCGAAATATT
** *
222387 TTTTTTACAAATTAGAAATTTTATAT
1 TTTTTTACATTTTCGAAA---TAT-T
222413 TTTTTTACATTTTCGAAATATT
1 TTTTTTACATTTTCGAAATATT
222435 TTTTTTACA
1 TTTTTTACA
222444 AATGAAATGA
Statistics
Matches: 55, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
21 10 0.18
22 24 0.44
23 3 0.05
24 2 0.04
26 16 0.29
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (22 bp):
TTTTTTACATTTTCGAAATATT
Found at i:223529 original size:23 final size:23
Alignment explanation
Indices: 223503--223547 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
223493 TTCATTATAT
*
223503 TTTA-AATTTAATTTGTAATTTCG
1 TTTATAATTTAAATT-TAATTTCG
*
223526 TTTATATTTTAAATTTAATTTC
1 TTTATAATTTAAATTTAATTTC
223548 TAATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTATAATTTAAATTTAATTTCG
Found at i:223581 original size:7 final size:6
Alignment explanation
Indices: 223473--223582 Score: 59
Period size: 6 Copynumber: 18.3 Consensus size: 6
223463 TTTGTTTATT
* * * *
223473 TTTTAA ATTTAA TTTGTAA -TTTCA TTAT-A TTTTAA ATTTAA TTTGTAA
1 TTTTAA TTTTAA TTT-TAA TTTTAA TTTTAA TTTTAA TTTTAA TTT-TAA
* * * *
223521 -TTT-C GTTTATA TTTTAA ATTTAA TTTCTAA TTTAAA TTTT-A TTTTAA
1 TTTTAA TTTTA-A TTTTAA TTTTAA TTT-TAA TTTTAA TTTTAA TTTTAA
*
223568 ATTTAA TTTCTAA TT
1 TTTTAA TTT-TAA TT
223583 ATTATTTTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
5 15 0.19
6 42 0.54
7 21 0.27
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (6 bp):
TTTTAA
Found at i:223590 original size:30 final size:29
Alignment explanation
Indices: 223473--223582 Score: 157
Period size: 30 Copynumber: 3.7 Consensus size: 29
223463 TTTGTTTATT
* *
223473 TTTTAAATTTAATTTGTAATTTCATTATA
1 TTTTAAATTTAATTTCTAATTTCATTTTA
* *
223502 TTTTAAATTTAATTTGTAATTTCGTTTATA
1 TTTTAAATTTAATTTCTAATTTCATTT-TA
*
223532 TTTTAAATTTAATTTCTAATTTAAATTTTA
1 TTTTAAATTTAATTTCTAATTT-CATTTTA
223562 TTTTAAATTTAATTTCTAATT
1 TTTTAAATTTAATTTCTAATT
223583 ATTATTTTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 25 0.34
30 46 0.62
31 3 0.04
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTTAAATTTAATTTCTAATTTCATTTTA
Found at i:224906 original size:96 final size:96
Alignment explanation
Indices: 224722--224913 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
224712 ACTTTTGCAA
** *
224722 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
224787 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAGAAAACATTGCCTCGATT
* * *
224818 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
* *
224882 GGAACTCGAA-ATAA-AATAATATTGCCTCGATT
65 AGAA-TCGAAGATAAGAA-AACATTGCCTCGATT
224914 TTTTAAAGAT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 2 0.02
96 77 0.92
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAGAAAACATTGCCTCGATT
Found at i:225259 original size:29 final size:29
Alignment explanation
Indices: 225220--225320 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
225210 TTTGAGGTTA
225220 AAAATGG-AATTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTTAGACATTCGGGGGT
* * ** * *
225248 AAAAGGGTAATTTTGAGAGTTTCGAGGTT
1 AAAATGGTAATTTTTAGACATTCGGGGGT
* *
225277 GAAAATGG--AGTTTTAGGACATCCGGGGGT
1 -AAAATGGTAATTTTTA-GACATTCGGGGGT
225306 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
225321 GGAAGTTTCG
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
28 18 0.34
29 24 0.45
30 11 0.21
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGACATTCGGGGGT
Found at i:225282 original size:58 final size:59
Alignment explanation
Indices: 225195--225350 Score: 176
Period size: 58 Copynumber: 2.6 Consensus size: 59
225185 GGGAGGAATA
* * *
225195 GTAATTTTGGGAAAATTT-GAGGTTAAAAATGGAATTTTTA-GACATTCGGGGGTAAAAGG
1 GTAATTTTTGG-AAGTTTCGAGGTTAAAAATGG-ATTTTTAGGACATCCGGGGGTAAAAGG
* * *
225254 GTAA-TTTT-GAGAGTTTCGAGGTTGAAAATGGAGTTTTAGGACATCCGGGGGTAAAATG
1 GTAATTTTTGGA-AGTTTCGAGGTTAAAAATGGATTTTTAGGACATCCGGGGGTAAAAGG
* *
225312 GTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTT
1 GTAATTTTTGGAAGTTTCGAGGTTAAAAAT-GGATTTTT
225351 GGAAGTTCGA
Statistics
Matches: 81, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
56 1 0.01
57 11 0.14
58 37 0.46
59 23 0.28
60 9 0.11
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (59 bp):
GTAATTTTTGGAAGTTTCGAGGTTAAAAATGGATTTTTAGGACATCCGGGGGTAAAAGG
Found at i:225349 original size:30 final size:30
Alignment explanation
Indices: 225306--225623 Score: 355
Period size: 30 Copynumber: 10.7 Consensus size: 30
225296 ATCCGGGGGT
*
225306 AAAATGGTAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGG-GATTTTTGGAAGTTTCGGGGTCA
*
225337 AAAATGGGATTTTTGGAAG-TTCGAGG-CTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGTC-A
** * *
225366 AAAATGAAATTTTTGGGAGTTTCATGGGT-A
1 AAAATGGGATTTTTGGAAGTTTC-GGGGTCA
* *
225396 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGGGGTCA
* * *
225426 AAAATGGGATTTCTGGAAGTATCGGGGTAA
1 AAAATGGGATTTTTGGAAGTTTCGGGGTCA
*
225456 AAAATGGGATTTTTGGAAGTCT-GAGGGT-A
1 AAAATGGGATTTTTGGAAGTTTCG-GGGTCA
* *
225485 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGGGGTCA
*
225515 AAAATGGGATTTTTGGAAGTTTCGAGGT-A
1 AAAATGGGATTTTTGGAAGTTTCGGGGTCA
* *
225544 AAAATGGGATTTTTTGAAGTTTTGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGGGGTCA
*
225574 AAAATGGGATTTTTGGAAG-TTCGAGGT-A
1 AAAATGGGATTTTTGGAAGTTTCGGGGTCA
* **
225602 AAAACGAAATTTTTGGAAGTTT
1 AAAATGGGATTTTTGGAAGTTT
225624 AGGGACCTCC
Statistics
Matches: 245, Mismatches: 32, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.07
29 86 0.35
30 132 0.54
31 9 0.04
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (30 bp):
AAAATGGGATTTTTGGAAGTTTCGGGGTCA
Found at i:225368 original size:59 final size:58
Alignment explanation
Indices: 225306--225623 Score: 424
Period size: 59 Copynumber: 5.4 Consensus size: 58
225296 ATCCGGGGGT
225306 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGCTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG-TA
* * * *
225366 AAAATGAAATTTTTGGGAGTTTCATGGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGT-A
* * * *
225426 AAAATGGGATTTCTGGAAGTATCGGGGTAAAAAATGGGATTTTTGGAAG-TCTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-GA-GGTA
*
225485 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTCGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGTA
* * *
225544 AAAATGGGATTTTTTGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTA
* *
225602 AAAACGAAATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
225624 AGGGACCTCC
Statistics
Matches: 228, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
58 29 0.13
59 137 0.60
60 60 0.26
61 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTA
Found at i:225414 original size:89 final size:87
Alignment explanation
Indices: 225302--225622 Score: 400
Period size: 89 Copynumber: 3.6 Consensus size: 87
225292 GGACATCCGG
*
225302 GGGT-AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGCTA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGG-TA
** *
225366 AAAATGAAATTTTTGGGAGTTTCAT
64 AAAATGGGATTTTTGGAAGTTT-AT
* *
225391 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTCTGGAAGTATCGGGGTAA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGT-TCGAGGT-A
*
225456 AAAATGGGATTTTTGGAAGTCTGA-
64 AAAATGGGATTTTTGGAAGT-TTAT
* *
225480 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTCGAGGTAA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGTAA
*
225545 AAATGGGATTTTTTGAAGTTT-T
65 AAATGGGATTTTTGGAAGTTTAT
* * **
225567 GGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGT-AAAAACGAAATTTTTGGAAGTT
1 -GGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
225623 TAGGGACCTC
Statistics
Matches: 205, Mismatches: 19, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
86 2 0.01
87 18 0.09
88 30 0.15
89 122 0.60
90 32 0.16
91 1 0.00
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (87 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTAAA
AATGGGATTTTTGGAAGTTTAT
Found at i:227370 original size:17 final size:18
Alignment explanation
Indices: 227350--227396 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
227340 AAATGAATTT
*
227350 TAAATTTAAATTT-AGAA
1 TAAATTTAAATTTCAAAA
*
227367 TAAACTT-AATTTCAAAA
1 TAAATTTAAATTTCAAAA
227384 TAAATTTAAATTT
1 TAAATTTAAATTT
227397 GTTGGGCCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 5 0.20
17 15 0.60
18 5 0.20
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAATTTAAATTTCAAAA
Found at i:227816 original size:56 final size:56
Alignment explanation
Indices: 227658--227989 Score: 314
Period size: 56 Copynumber: 6.0 Consensus size: 56
227648 AGGGTTTCGA
* * * * *
227658 CCATGGCATGGGTGACACCAAGAAAAATATCTTTTTATCAGATAAGGGTGGTGTCGG
1 CCATGGCATGGATGACA-CAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGG
* ** * * *
227715 CCTTGGCATGGGCGTCACAAATAAAAA-ATATTTTTTATCTGATAAAGGTGATGTTGG
1 CCATGGCATGGATGACACAAA-AAAAATAT-TTTTTTATCTGATAAAGGTGGTGTCGG
* * *
227772 CCACGGCATGGATGACACAAAAAAAATATTTTTTTATTTGATAAAGGTGGTGTCGA
1 CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGG
** ** * *
227828 CCATGGCATGGACAACACAAAAAATTTATTTTTTTACCTGATAAAGGTGGTGTCAG
1 CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGG
* * * * * *
227884 TCATGCCATGGCTGACACAAAAAAATTCTTTTTTTATCTGATAAAGGTAGTGTCGG
1 CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGG
* * ** * *
227940 TCATGCCATGGCCGACAC---CAAAA-ATTTTTTTATCTGATAAAAGTGGTGTC
1 CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTC
227990 AACCATGTCA
Statistics
Matches: 229, Mismatches: 43, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
52 24 0.10
53 3 0.01
56 143 0.62
57 59 0.26
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (56 bp):
CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGG
Found at i:227906 original size:112 final size:109
Alignment explanation
Indices: 227658--228002 Score: 350
Period size: 112 Copynumber: 3.1 Consensus size: 109
227648 AGGGTTTCGA
* * * * * *
227658 CCATGGCATGGGTGACACCAAGAAAAATATCTTTTTATCAGATAAGGGTGGTGTCGGCCTTGGCA
1 CCATGGCATGGATGACA-CAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGGCCATGGCA
* * * **
227723 TGGGCGTCACAAATAAAAAATATTTTTTATCTGATAAAGGTGATGTTGG
65 TGGACG--ACACA-AAAAAAT-TTTTTTATCTGATAAAGGTGGTGTCAG
* * *
227772 CCACGGCATGGATGACACAAAAAAAATATTTTTTTATTTGATAAAGGTGGTGTCGACCATGGCAT
1 CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGGCCATGGCAT
* *
227837 GGACAACACAAAAAATTTATTTTTTTACCTGATAAAGGTGGTGTCAG
66 GGACGACACAAAAAA---ATTTTTTTATCTGATAAAGGTGGTGTCAG
* * * * * * * *
227884 TCATGCCATGGCTGACACAAAAAAATTCTTTTTTTATCTGATAAAGGTAGTGTCGGTCATGCCAT
1 CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGGCCATGGCAT
* * * *
227949 GGCCGACAC-CAAAAATTTTTTTATCTGATAAAAGTGGTGTCAA
66 GGACGACACAAAAAAATTTTTTTATCTGATAAAGGTGGTGTCAG
*
227992 CCATGTCATGG
1 CCATGGCATGG
228003 CCAACACCAT
Statistics
Matches: 193, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
108 35 0.18
110 5 0.03
111 8 0.04
112 84 0.44
113 46 0.24
114 15 0.08
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (109 bp):
CCATGGCATGGATGACACAAAAAAAATATTTTTTTATCTGATAAAGGTGGTGTCGGCCATGGCAT
GGACGACACAAAAAAATTTTTTTATCTGATAAAGGTGGTGTCAG
Found at i:228022 original size:52 final size:53
Alignment explanation
Indices: 227799--228012 Score: 151
Period size: 56 Copynumber: 3.9 Consensus size: 53
227789 CAAAAAAAAT
* * * * * * * *
227799 ATTTTTTTATTTGATAAAGGTGGTGTCGACCATGGCATGGACAACACAAAAAA
1 ATTTTTTTATCTGATAAAAGTAGTGTCAACCATGCCATGGCCAACACCATAAA
* * * ** ** * *
227852 TTTATTTTTTTACCTGATAAAGGTGGTGTCAGTCATGCCATGGCTGACACAAAAAA
1 ---ATTTTTTTATCTGATAAAAGTAGTGTCAACCATGCCATGGCCAACACCATAAA
* *** *
227908 ATTCTTTTTTTATCTGATAAAGGTAGTGTCGGTCATGCCATGGCCGACACCA-AAA
1 A---TTTTTTTATCTGATAAAAGTAGTGTCAACCATGCCATGGCCAACACCATAAA
* *
227963 ATTTTTTTATCTGATAAAAGTGGTGTCAACCATGTCATGGCCAACACCAT
1 ATTTTTTTATCTGATAAAAGTAGTGTCAACCATGCCATGGCCAACACCAT
228013 TTTTTTTTTT
Statistics
Matches: 133, Mismatches: 21, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
52 41 0.31
53 1 0.01
55 4 0.03
56 87 0.65
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (53 bp):
ATTTTTTTATCTGATAAAAGTAGTGTCAACCATGCCATGGCCAACACCATAAA
Found at i:228072 original size:52 final size:49
Alignment explanation
Indices: 227912--228075 Score: 139
Period size: 52 Copynumber: 3.1 Consensus size: 49
227902 AAAAAAATTC
* * * *
227912 TTTTTTTATCTGATAAAGGTAGTGTCGGTCATGCCATGGCCGACACCAAAAA
1 TTTTTTTATCTGATAAA-GTAGTGTCGGCCAT-TCATGGCCAACACC-AAAT
* ** **
227964 TTTTTTTATCTGATAAAAGTGGTGTCAACCATGTCATGGCCAACACCATTTTT
1 TTTTTTTATCTGAT-AAAGTAGTGTCGGCCAT-TCATGGCCAACACCA--AAT
* *
228017 TTTTTTTATCTAATAAAGTTAGTGTCGGCCATTACATGACCAACACTCAAAT
1 TTTTTTTATCTGATAAAG-TAGTGTCGGCCATT-CATGGCCAACAC-CAAAT
228069 TTTTTTT
1 TTTTTTT
228076 TCAAAATATC
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
51 1 0.01
52 50 0.56
53 37 0.41
54 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (49 bp):
TTTTTTTATCTGATAAAGTAGTGTCGGCCATTCATGGCCAACACCAAAT
Found at i:230305 original size:23 final size:23
Alignment explanation
Indices: 230272--230315 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
230262 AGTCAAGTAA
*
230272 TCCAAAAGGCTAATTTTATTTTT
1 TCCAAAAGGCTAATTTAATTTTT
*
230295 TCCAAATGGCTAATTTAATTT
1 TCCAAAAGGCTAATTTAATTT
230316 CTATATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (23 bp):
TCCAAAAGGCTAATTTAATTTTT
Found at i:234939 original size:2 final size:2
Alignment explanation
Indices: 234932--234959 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
234922 TTTATCAATT
234932 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
234960 TGCATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.