Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005203.1 Hibiscus syriacus cultivar Beakdansim tig00011761_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: 1490345
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:127078 original size:25 final size:23
Alignment explanation
Indices: 127033--127078 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
127023 AGTTATTATT
**
127033 TAAAAAAATAAAATTTTTAATAC
1 TAAAAAAATAAAATTAATAATAC
127056 TAAAATAAATTAAAATTAATAAT
1 TAAAA-AAA-TAAAATTAATAAT
127079 TTAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 3 0.16
25 11 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAAAAATAAAATTAATAATAC
Found at i:131673 original size:45 final size:45
Alignment explanation
Indices: 131624--131711 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
131614 GAACATCGAA
*
131624 TGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACA-AGCCATGCATCGATGCACTCAG
131669 TGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTC
1 TGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTC
131712 TGGCTATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAG
Found at i:131770 original size:109 final size:109
Alignment explanation
Indices: 131565--131779 Score: 267
Period size: 109 Copynumber: 2.0 Consensus size: 109
131555 TTTTTCAAAG
*
131565 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGGAATTAATTGAACATCGAATGCATT
1 TGATGCACCGATGCACCAAGCCATGCATCGATGCACCATGGAATT-ATTGAACATCGAATGCATT
* * *
131630 TTATGCATCGATGCACATACCATGCATCGATGCACTCAGTGCATT
65 TTATGCATCGATGCACATACCATGCACCGATGAACTAAGTGCATT
* * *
131675 TGATGCATCGATGCA-CAAGCCATGCATCGATGCACTC-TGGCTATT-TTGAAATATCGAATGCA
1 TGATGCACCGATGCACCAAGCCATGCATCGATGCAC-CATGG-AATTATTG-AACATCGAATGCA
***
131737 TTTTATGCATCGATGCACACT-TGGTGCACCGATGAACTAAGTG
63 TTTTATGCATCGATGCACA-TACCATGCACCGATGAACTAAGTG
131780 TCCAACGGTC
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
108 3 0.03
109 69 0.76
110 19 0.21
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (109 bp):
TGATGCACCGATGCACCAAGCCATGCATCGATGCACCATGGAATTATTGAACATCGAATGCATTT
TATGCATCGATGCACATACCATGCACCGATGAACTAAGTGCATT
Found at i:137704 original size:13 final size:13
Alignment explanation
Indices: 137686--137710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
137676 AATTCTAAAA
137686 TCTAAATTTAATT
1 TCTAAATTTAATT
137699 TCTAAATTTAAT
1 TCTAAATTTAAT
137711 GTTTTTGATT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TCTAAATTTAATT
Found at i:146838 original size:22 final size:22
Alignment explanation
Indices: 146813--146854 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
146803 GCGACATCTA
146813 TCCCCATCTCCGACGAAATCAG
1 TCCCCATCTCCGACGAAATCAG
*
146835 TCCCCATCTCCGGCGAAATC
1 TCCCCATCTCCGACGAAATC
146855 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.43, G:0.14, T:0.19
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAG
Found at i:147286 original size:20 final size:20
Alignment explanation
Indices: 147242--147315 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
147232 GCGATTTTAG
*
147242 TTTCGCGTTGCGATAGTTAA
1 TTTCGCGTTGCGATAGTTAT
* *
147262 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTTAT
* **
147282 TTTCGTGTTGCGATTTTTAT
1 TTTCGCGTTGCGATAGTTAT
*
147302 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
147316 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTTAT
Found at i:147316 original size:20 final size:20
Alignment explanation
Indices: 147231--147318 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
147221 AGCATCGCAA
*
147231 TGCGA-TTTTAGTTTCGCGT
1 TGCGATTTTTATTTTCGCGT
** **
147250 TGCGATAGTTAAATTCGCGT
1 TGCGATTTTTATTTTCGCGT
** * *
147270 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTTATTTTCGCGT
*
147290 TGCGATTTTTATTTTCGTGT
1 TGCGATTTTTATTTTCGCGT
147310 TGCGATTTT
1 TGCGATTTT
147319 AAGTTTCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 5 0.09
20 52 0.91
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.48
Consensus pattern (20 bp):
TGCGATTTTTATTTTCGCGT
Found at i:149069 original size:18 final size:18
Alignment explanation
Indices: 149046--149095 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
149036 TTTACTCATA
149046 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
149064 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
149082 ATTTCACTTAGATT
1 ATTTCACTTAGATT
149096 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:149267 original size:20 final size:20
Alignment explanation
Indices: 149242--149309 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
149232 TAGTTTACTT
149242 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
149262 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
149282 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
149302 TCACAACG
1 TCGCAACG
149310 AAAGAATCGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:149319 original size:34 final size:38
Alignment explanation
Indices: 149242--149328 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 38
149232 TAGTTTACTT
*
149242 TCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTATCACAAC-CGAAAATGAC-A
149282 TCGCAACGCGAAAATGACTATCACAA-CG-AAA-GA-A
1 TCGCAACGCGAAAATGACTATCACAACCGAAAATGACA
*
149316 TCGCAATGCGAAA
1 TCGCAACGCGAAA
149329 TGAAAATCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 13 0.29
36 2 0.04
37 3 0.07
38 2 0.04
40 25 0.56
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (38 bp):
TCGCAACGCGAAAATGACTATCACAACCGAAAATGACA
Found at i:149377 original size:20 final size:20
Alignment explanation
Indices: 149352--149458 Score: 139
Period size: 20 Copynumber: 5.5 Consensus size: 20
149342 GCGATTCTCT
149352 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
149372 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
149392 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
149412 CGTTGCGATAAT-AATTTTCG
1 CGTTGCGATAGTCAA-ATTCG
149432 CGTTGCGATAGTC--ATTCG
1 CGTTGCGATAGTCAAATTCG
*
149450 TGTTGCGAT
1 CGTTGCGAT
149459 TTTAAGTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
18 12 0.15
19 1 0.01
20 65 0.83
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:150039 original size:21 final size:21
Alignment explanation
Indices: 149948--150052 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
149938 GACTCACCTG
*
149948 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
149970 T-ATCGTTCAAGAGACCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
149990 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
150011 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
150032 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
150053 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:150045 original size:42 final size:42
Alignment explanation
Indices: 149945--150055 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
149935 CCCGACTCAC
* * * *
149945 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGACCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGACCA
* ** *
149987 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGACCA
*
150029 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
150056 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGACCA
Found at i:150406 original size:12 final size:12
Alignment explanation
Indices: 150389--150413 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
150379 GGGGGGTAAG
150389 TCTTATATTTCA
1 TCTTATATTTCA
150401 TCTTATATTTCA
1 TCTTATATTTCA
150413 T
1 T
150414 TTTGATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TCTTATATTTCA
Found at i:151490 original size:14 final size:14
Alignment explanation
Indices: 151453--151514 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
151443 TTGCTTGTTT
*
151453 AATTGATTTATAAA
1 AATTGATTTGTAAA
151467 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
151481 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
151496 TATTGATGTGTAAA
1 AATTGATTTGTAAA
151510 TAATT
1 -AATT
151515 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:151638 original size:20 final size:20
Alignment explanation
Indices: 151613--151665 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
151603 AGGTATACTT
* *
151613 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACACAAAA
* *
151633 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAACACAAAA
*
151653 TCGCAATGCGAAA
1 TCGCAACGCGAAA
151666 GTCAATTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACACAAAA
Found at i:151666 original size:20 final size:20
Alignment explanation
Indices: 151628--151666 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
151618 ACGCTAAACT
151628 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAATGCGAAAGA
151648 CAAAATCGCAATGCGAAAG
1 CAAAATCGCAATGCGAAAG
151667 TCAATTCGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (20 bp):
CAAAATCGCAATGCGAAAGA
Found at i:151735 original size:20 final size:20
Alignment explanation
Indices: 151709--151973 Score: 261
Period size: 20 Copynumber: 13.8 Consensus size: 20
151699 GCAATTTTCT
*
151709 CGTTGCGATAGTCAAATAC-
1 CGTTGCGATAGTCAAATTCG
* *
151728 CTGTTGCGATAATAAAATTCG
1 C-GTTGCGATAGTCAAATTCG
*
151749 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
151763 CGTTGCAATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
151782 CCGTTGCGATAATCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
151803 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
151823 CGTTGCGATAGGCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
151843 CATTGCGATAGGCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
151863 CATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
151883 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
151903 CGTTGCGAT-TTC----T-G
1 CGTTGCGATAGTCAAATTCG
* *
151917 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
151937 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
151957 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
151974 GAATGTGTAA
Statistics
Matches: 205, Mismatches: 25, Indels: 31
0.79 0.10 0.12
Matches are distributed among these distances:
14 20 0.10
15 3 0.01
16 1 0.00
18 1 0.00
19 5 0.02
20 172 0.84
21 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:151760 original size:54 final size:54
Alignment explanation
Indices: 151697--151811 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 54
151687 CTAATACGCT
* *
151697 TTGCAATTTTCTCGTTGCGATAGTCAAATA-CCTGTTGCGATAATAAAATTCGCG
1 TTGCGATTTTCTCGTTGCAATAGTCAAATAGCC-GTTGCGATAATAAAATTCGCG
*
151751 TTGCGATTTTCTCGTTGCAATAGTCAAATAGCCGTTGCGATAATCAAATTCGCG
1 TTGCGATTTTCTCGTTGCAATAGTCAAATAGCCGTTGCGATAATAAAATTCGCG
151805 TTGCGAT
1 TTGCGAT
151812 AGTCAAATTC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 55 0.96
55 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (54 bp):
TTGCGATTTTCTCGTTGCAATAGTCAAATAGCCGTTGCGATAATAAAATTCGCG
Found at i:151859 original size:60 final size:58
Alignment explanation
Indices: 151709--151966 Score: 236
Period size: 54 Copynumber: 4.5 Consensus size: 58
151699 GCAATTTTCT
* * *
151709 CGTTGCGATAGTCAAATAC-CTGTTGCGATAATAAAATTCGCGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCGC-GTTGCGAT-A-CAAATTCGCGTTGCGATAGTCAAATTCG
* *
151763 CGTTGCAATAGTCAAA-TAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG-CGTTGCGAT-A-CAAATTCGCGTTGCGATAGTCAAATTCG
* * * *
151823 CGTTGCGATAGGCAAATTCGCATTGCGATAGGCAAATTCGCATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATA--CAAATTCGCGTTGCGATAGTCAAATTCG
* * *
151883 TGTTGCGATAGTCAAATTCGCGTTGCGAT-----TTCTGAGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATACAAATTC-GCGTTGCGATAGTCAAATTCG
151937 CGTTGCGATAGTCAAATTCGCGTTGCGATA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATA
151967 TTCAAATGAA
Statistics
Matches: 172, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
53 3 0.02
54 87 0.51
55 1 0.01
56 1 0.01
59 1 0.01
60 77 0.45
61 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (58 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATACAAATTCGCGTTGCGATAGTCAAATTCG
Found at i:152196 original size:140 final size:140
Alignment explanation
Indices: 151944--152213 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
151934 TCGCGTTGCG
*
151944 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
152009 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
152074 AATACACATA
131 AATACACATA
*
152084 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
*
152149 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
152214 TACAATGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAACAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:152296 original size:18 final size:18
Alignment explanation
Indices: 152273--152307 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
152263 AAGCCGGTTG
*
152273 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
152291 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
152308 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:154585 original size:24 final size:24
Alignment explanation
Indices: 154551--154604 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
154541 CTGAAACATC
154551 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
154575 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
154599 ATCAAA
1 ATCAAA
154605 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:154839 original size:14 final size:14
Alignment explanation
Indices: 154820--154846 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
154810 TGAGCACCAT
154820 AAACTGGGGTTGAA
1 AAACTGGGGTTGAA
154834 AAACTGGGGTTGA
1 AAACTGGGGTTGA
154847 TTACTACCCG
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:0.33, C:0.07, G:0.37, T:0.22
Consensus pattern (14 bp):
AAACTGGGGTTGAA
Found at i:155451 original size:20 final size:20
Alignment explanation
Indices: 155426--155533 Score: 171
Period size: 20 Copynumber: 5.4 Consensus size: 20
155416 GAAATTCAGT
155426 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
155446 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
155466 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
155486 GTTGCGATAGTCCGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
155506 GTTGCGATAGTCCGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
155526 ATTGCGAT
1 GTTGCGAT
155534 TTACATATTC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:155545 original size:20 final size:20
Alignment explanation
Indices: 155522--155613 Score: 175
Period size: 20 Copynumber: 4.6 Consensus size: 20
155512 ATAGTCCGAA
155522 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
155542 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
155562 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
155582 TCGCATTGTGATTTACATAT
1 TCGCATTGCGATTTACATAT
155602 TCGCATTGCGAT
1 TCGCATTGCGAT
155614 AGTCGGAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:155551 original size:60 final size:60
Alignment explanation
Indices: 155427--155617 Score: 167
Period size: 60 Copynumber: 3.2 Consensus size: 60
155417 AAATTCAGTG
* * * * ** * * *
155427 TTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCGTTGCGACAGT-CAGAATCGCG
1 TTGCGATAGTCCGAATCGCGTTGCGATAGTCCGAATCGCATTGCGA-TTTACATATTCGCA
155487 TTGCGATAGTCCGAATCGCGTTGCGATAGTCCGAATCGCATTGCGATTTACATATTCGCA
1 TTGCGATAGTCCGAATCGCGTTGCGATAGTCCGAATCGCATTGCGATTTACATATTCGCA
* * * * * *
155547 TTGCGAT-TTAC-ATATTCGCATTGCGAT-TTAC-ATATTCGCATTGTGATTTACATATTCGCA
1 TTGCGATAGTCCGA-A-TCGCGTTGCGATAGTCCGA-A-TCGCATTGCGATTTACATATTCGCA
155607 TTGCGATAGTC
1 TTGCGATAGTC
155618 GGAAAATCGC
Statistics
Matches: 108, Mismatches: 17, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 7 0.06
60 98 0.91
61 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (60 bp):
TTGCGATAGTCCGAATCGCGTTGCGATAGTCCGAATCGCATTGCGATTTACATATTCGCA
Found at i:155843 original size:17 final size:17
Alignment explanation
Indices: 155821--155857 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
155811 TTTAAAGACA
155821 AAACAAAGACAAATACT
1 AAACAAAGACAAATACT
155838 AAACAAAGACAAATACT
1 AAACAAAGACAAATACT
155855 AAA
1 AAA
155858 TTCACAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (17 bp):
AAACAAAGACAAATACT
Found at i:156146 original size:22 final size:22
Alignment explanation
Indices: 156116--156173 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
156106 AGATGGAGAT
*
156116 AGACGGATTTTGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* *
156138 AGACTGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* * *
156160 GGATGGATGTCGCC
1 AGACGGATTTCGCC
156174 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:157738 original size:3 final size:3
Alignment explanation
Indices: 157730--157754 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
157720 GGCGACGATA
157730 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
157755 TGGTAGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:163241 original size:23 final size:23
Alignment explanation
Indices: 163197--163241 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
163187 AAATTTTTTA
* *
163197 CTTTTATTTTTTTTACTCTTAAC
1 CTTTTATTCTTTTTACTATTAAC
163220 CTTTTA-TCTTTTTACATATTAA
1 CTTTTATTCTTTTTAC-TATTAA
163242 ATCAATTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (23 bp):
CTTTTATTCTTTTTACTATTAAC
Found at i:165120 original size:60 final size:59
Alignment explanation
Indices: 165017--165129 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
165007 AAATGGTCCC
** * * *
165017 CTGACTATAGGTACTGCTTTATTAAGTCCCTTGAGTATTAAAAGTTATAAAATGATCAT
1 CTGACTATAGGTACTGCTTTATTAAGTCCCTCAACTATGAAAAGTTACAAAATGATCAT
* *
165076 CTGACTATAGAGTA-TCGCTTTGTTGAGTCCCTCAACTATGAAAAGTTACAAAAT
1 CTGACTATAG-GTACT-GCTTTATTAAGTCCCTCAACTATGAAAAGTTACAAAAT
165130 AGTCACCCGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 11 0.24
60 34 0.76
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (59 bp):
CTGACTATAGGTACTGCTTTATTAAGTCCCTCAACTATGAAAAGTTACAAAATGATCAT
Found at i:172566 original size:34 final size:32
Alignment explanation
Indices: 172486--172574 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
172476 TTAGTATTTT
* * *
172486 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
172518 TTTATGTAAATATTATTTTATTAT-TAAAATAATA
1 TTTATATAATTATTATTTT-TTATAT-AAAT-ATA
172552 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
172575 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 16 0.35
33 7 0.15
34 22 0.48
35 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Found at i:174325 original size:21 final size:21
Alignment explanation
Indices: 174295--174342 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
174285 GCAGGGGTAC
* *
174295 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
174316 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
174337 ATGCCA
1 ATGCCA
174343 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:174372 original size:21 final size:21
Alignment explanation
Indices: 174346--174439 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
174336 TATGCCATCT
* *
174346 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
174367 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
*
174388 CCGCCA-GGTTATATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
174409 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
174430 CCGCAGGGTT
1 CCGCAGGGTT
174440 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:175205 original size:126 final size:126
Alignment explanation
Indices: 174980--175331 Score: 659
Period size: 126 Copynumber: 2.8 Consensus size: 126
174970 TTAAGTTATT
*
174980 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
* *
175045 TGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
175106 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
* *
175171 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTGT
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
175232 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
175297 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
175332 CCGATTATAG
Statistics
Matches: 221, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 221 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (126 bp):
CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
Found at i:175412 original size:8 final size:8
Alignment explanation
Indices: 175399--175439 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
175389 TCACAATCTT
175399 TCAAATTC
1 TCAAATTC
175407 TCAAATTC
1 TCAAATTC
* *
175415 CCAAACTC
1 TCAAATTC
175423 T-AAATTC
1 TCAAATTC
175430 TCAAATTC
1 TCAAATTC
175438 TC
1 TC
175440 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:178450 original size:13 final size:11
Alignment explanation
Indices: 178429--178469 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
178419 AAATACATAA
178429 ATATATTTAAT
1 ATATATTTAAT
178440 ATATTTATTTAAT
1 ATA--TATTTAAT
178453 ATATATTTAAT
1 ATATATTTAAT
178464 AT-TATT
1 ATATATT
178470 AGTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.14
11 13 0.46
13 11 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:178517 original size:23 final size:23
Alignment explanation
Indices: 178479--178536 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
178469 TAGTTATAAT
178479 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
178500 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
178523 TTTTACATAATATA
1 TTTTACATAATATA
178537 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:181483 original size:29 final size:30
Alignment explanation
Indices: 181429--181488 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
181419 CTCATAAAAA
*
181429 TAAATTTGAAAACTCTTATTTTCTTA-TGT
1 TAAATTTGAAAACTCTTATTTGCTTACTGT
*
181458 TAAATTTGAAAACT-TTCTTCTGCTTACTGT
1 TAAATTTGAAAACTCTTATT-TGCTTACTGT
181488 T
1 T
181489 TAGTGGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 19 0.70
30 4 0.15
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.50
Consensus pattern (30 bp):
TAAATTTGAAAACTCTTATTTGCTTACTGT
Found at i:181725 original size:15 final size:15
Alignment explanation
Indices: 181705--181733 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
181695 AGATTAATTT
181705 ATATGTTTATTGATG
1 ATATGTTTATTGATG
181720 ATATGTTTATTGAT
1 ATATGTTTATTGAT
181734 AGAATATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (15 bp):
ATATGTTTATTGATG
Found at i:181751 original size:17 final size:17
Alignment explanation
Indices: 181720--181785 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
181710 TTTATTGATG
181720 ATATGTTTATTGATAGAAT
1 ATATG-TTA-TGATAGAAT
*
181739 ATATGTTACGATAGAAT
1 ATATGTTATGATAGAAT
* *
181756 AATTTGTT-TTATAGAAT
1 -ATATGTTATGATAGAAT
181773 ATATGTTATGATA
1 ATATGTTATGATA
181786 TATTTATTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.15
17 19 0.49
18 9 0.23
19 5 0.13
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (17 bp):
ATATGTTATGATAGAAT
Found at i:181917 original size:17 final size:17
Alignment explanation
Indices: 181877--181918 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
181867 CATGAAATCA
181877 ATGAATATATGTACTGC
1 ATGAATATATGTACTGC
*
181894 ATG--TATATGTTCTGC
1 ATGAATATATGTACTGC
181909 ATGAATATAT
1 ATGAATATAT
181919 ATGTTTAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 14 0.64
17 8 0.36
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (17 bp):
ATGAATATATGTACTGC
Found at i:182537 original size:30 final size:32
Alignment explanation
Indices: 182501--182654 Score: 157
Period size: 30 Copynumber: 5.1 Consensus size: 32
182491 GATGAAGAAA
**
182501 AACCAGAAATTAG-TGAACCCA-AAATTAATG
1 AACCAGAAACCAGCTGAACCCAGAAATTAATG
* * * *
182531 AACCAG-AACTAGTTG-AGCCAAAAATTAATG
1 AACCAGAAACCAGCTGAACCCAGAAATTAATG
*
182561 AACCA-AAACCAGCTG-AGCCAGAAATTAATG
1 AACCAGAAACCAGCTGAACCCAGAAATTAATG
*
182591 AACCAG-AACCAGCT-AAGCCAGAAATTAATG
1 AACCAGAAACCAGCTGAACCCAGAAATTAATG
*
182621 AACCAG-AACCAGCT-AAGCCAGAAATTAATG
1 AACCAGAAACCAGCTGAACCCAGAAATTAATG
182651 AACC
1 AACC
182655 TAAAATTGAT
Statistics
Matches: 114, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
29 9 0.08
30 105 0.92
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (32 bp):
AACCAGAAACCAGCTGAACCCAGAAATTAATG
Found at i:182590 original size:60 final size:60
Alignment explanation
Indices: 182522--182654 Score: 212
Period size: 60 Copynumber: 2.2 Consensus size: 60
182512 AGTGAACCCA
* * * *
182522 AAATTAATGAACCAGAACTAGTTGAGCCAAAAATTAATGAACCAAAACCAGCTGAGCCAG
1 AAATTAATGAACCAGAACCAGCTAAGCCAAAAATTAATGAACCAAAACCAGCTAAGCCAG
* *
182582 AAATTAATGAACCAGAACCAGCTAAGCCAGAAATTAATGAACCAGAACCAGCTAAGCCAG
1 AAATTAATGAACCAGAACCAGCTAAGCCAAAAATTAATGAACCAAAACCAGCTAAGCCAG
182642 AAATTAATGAACC
1 AAATTAATGAACC
182655 TAAAATTGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (60 bp):
AAATTAATGAACCAGAACCAGCTAAGCCAAAAATTAATGAACCAAAACCAGCTAAGCCAG
Found at i:182598 original size:15 final size:15
Alignment explanation
Indices: 182501--182673 Score: 78
Period size: 15 Copynumber: 11.5 Consensus size: 15
182491 GATGAAGAAA
*
182501 AACCAGAAATTAGTG
1 AACCAGAAATTAATG
182516 AACCCA-AAATTAATG
1 AA-CCAGAAATTAATG
* *
182531 AACCAG-AACTAGTTG
1 AACCAGAAATTA-ATG
* *
182546 AGCCAAAAATTAATG
1 AACCAGAAATTAATG
** *
182561 AACCA-AAACCAGCTG
1 AACCAGAAATTA-ATG
*
182576 AGCCAGAAATTAATG
1 AACCAGAAATTAATG
*
182591 AACCAGAACCAGCTAA-G
1 AACCAGAA--A-TTAATG
182608 --CCAGAAATTAATG
1 AACCAGAAATTAATG
*
182621 AACCAGAACCAGCTAA-G
1 AACCAGAA--A-TTAATG
182638 --CCAGAAATTAATG
1 AACCAGAAATTAATG
*
182651 AACCTA-AAATTGATG
1 AACC-AGAAATTAATG
182666 AACCAGAA
1 AACCAGAA
182674 CCTGCTGAGG
Statistics
Matches: 117, Mismatches: 21, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
12 6 0.05
13 4 0.03
14 12 0.10
15 73 0.62
16 12 0.10
17 4 0.03
18 6 0.05
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (15 bp):
AACCAGAAATTAATG
Found at i:184577 original size:13 final size:13
Alignment explanation
Indices: 184561--184658 Score: 92
Period size: 13 Copynumber: 7.5 Consensus size: 13
184551 ATTCTTCATC
* *
184561 CATAGTGTTATTA
1 CATATTGTTATTG
*
184574 CATATTGTTACTG
1 CATATTGTTATTG
*
184587 CATAATGTTATTG
1 CATATTGTTATTG
184600 CATATTGTTCA-TG
1 CATATTGTT-ATTG
* *
184613 CATACTGTTATTA
1 CATATTGTTATTG
184626 CATATTGTTCA-TG
1 CATATTGTT-ATTG
* *
184639 CATACTATTATTG
1 CATATTGTTATTG
184652 CATATTG
1 CATATTG
184659 GAATAATTGA
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
12 2 0.03
13 63 0.94
14 2 0.03
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (13 bp):
CATATTGTTATTG
Found at i:184590 original size:26 final size:26
Alignment explanation
Indices: 184546--184707 Score: 148
Period size: 26 Copynumber: 6.0 Consensus size: 26
184536 AACTTGCTAA
* * *
184546 TACATATTCTTCATCCATAGTGTTAT
1 TACATATTGTTCATGCATACTGTTAT
*
184572 TACATATTGTT-ACTGCATAATGTTAT
1 TACATATTGTTCA-TGCATACTGTTAT
*
184598 TGCATATTGTTCATGCATACTGTTAT
1 TACATATTGTTCATGCATACTGTTAT
*
184624 TACATATTGTTCATGCATACTATTAT
1 TACATATTGTTCATGCATACTGTTAT
* * * *
184650 TGCATATTGGAATAATTGAATACTGTTAT
1 TACATATT-G-TTCA-TGCATACTGTTAT
*
184679 TACATAACTTGTT-AGTGCAGACTGTTAT
1 TACAT-A-TTGTTCA-TGCATACTGTTAT
184707 T
1 T
184708 GTGTTAATAT
Statistics
Matches: 112, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.01
26 74 0.66
27 2 0.02
28 15 0.13
29 16 0.14
30 2 0.02
31 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (26 bp):
TACATATTGTTCATGCATACTGTTAT
Found at i:184626 original size:52 final size:52
Alignment explanation
Indices: 184548--184708 Score: 171
Period size: 52 Copynumber: 3.0 Consensus size: 52
184538 CTTGCTAATA
* * * *
184548 CATATTCTTCATCCATAGTGTTATTACATATTGTTACTGCATAATGTTATTG
1 CATATTGTTCATGCATACTGTTATTACATATTGTTACTGCATACTGTTATTG
*
184600 CATATTGTTCATGCATACTGTTATTACATATTGTT-CATGCATACTATTATTG
1 CATATTGTTCATGCATACTGTTATTACATATTGTTAC-TGCATACTGTTATTG
* * * * *
184652 CATATTGGAATAATTGAATACTGTTATTACATAACTTGTTAGTGCAGACTGTTATTG
1 CATATT-G-TTCA-TGCATACTGTTATTACAT-A-TTGTTACTGCATACTGTTATTG
184709 TGTTAATATT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
51 1 0.01
52 51 0.56
53 1 0.01
54 2 0.02
55 17 0.19
56 1 0.01
57 18 0.20
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (52 bp):
CATATTGTTCATGCATACTGTTATTACATATTGTTACTGCATACTGTTATTG
Found at i:185406 original size:16 final size:16
Alignment explanation
Indices: 185374--185488 Score: 92
Period size: 16 Copynumber: 7.2 Consensus size: 16
185364 TTTCTTATTG
185374 ATTGCATTTGTTTTTTT
1 ATTGCATTTG-TTTTTT
185391 ATTG-AGTTTGTTTTTT
1 ATTGCA-TTTGTTTTTT
**
185407 ATTGCATTT-TTTTAG
1 ATTGCATTTGTTTTTT
**
185422 ATTG-ACTTTGTTTTAG
1 ATTGCA-TTTGTTTTTT
* *
185438 CTTGCATTTGTTTTAT
1 ATTGCATTTGTTTTTT
* * *
185454 ATTGAATTTGTTATTG
1 ATTGCATTTGTTTTTT
*
185470 ATTGTATTTGTTTTTT
1 ATTGCATTTGTTTTTT
185486 ATT
1 ATT
185489 ACAGTTTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
14 1 0.01
15 11 0.14
16 59 0.73
17 10 0.12
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.64
Consensus pattern (16 bp):
ATTGCATTTGTTTTTT
Found at i:185458 original size:32 final size:31
Alignment explanation
Indices: 185359--185488 Score: 127
Period size: 32 Copynumber: 4.1 Consensus size: 31
185349 TATGTTGCAG
* *
185359 TTGAATTTCTTATTGATTGCATTTGTTTTTTTA
1 TTGAATTTGTT-TTGATTGCATTTG-TTTTATA
* * *
185392 TTGAGTTTGTTTTTTATTGCATTT-TTTTAGA
1 TTGAATTTG-TTTTGATTGCATTTGTTTTATA
* *
185423 TTGACTTTGTTTTAGCTTGCATTTGTTTTATA
1 TTGAATTTGTTTT-GATTGCATTTGTTTTATA
* *
185455 TTGAATTTGTTATTGATTGTATTTGTTTTTTA
1 TTGAATTTGTT-TTGATTGCATTTGTTTTATA
185487 TT
1 TT
185489 ACAGTTTAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
30 4 0.05
31 21 0.26
32 33 0.41
33 20 0.25
34 2 0.03
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.64
Consensus pattern (31 bp):
TTGAATTTGTTTTGATTGCATTTGTTTTATA
Found at i:187631 original size:26 final size:22
Alignment explanation
Indices: 187591--187648 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 22
187581 GACCATAAAT
*
187591 TATGTAAATAGGAATAATTTAAGTGA
1 TATGTATATAGGAAT-ATTT--G-GA
*
187617 TATGTATATATGAATATTTGGA
1 TATGTATATAGGAATATTTGGA
187639 TATGTATATA
1 TATGTATATA
187649 AGTGATGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 12 0.40
23 1 0.03
25 4 0.13
26 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (22 bp):
TATGTATATAGGAATATTTGGA
Found at i:188179 original size:21 final size:21
Alignment explanation
Indices: 188126--188179 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 21
188116 TTGAGACACC
188126 TATGTGGTCCTT-GGCATATG
1 TATGTGGTCCTTAGGCATATG
* *
188146 TATATGGTTCTTAAGG-A-ATG
1 TATGTGGTCCTT-AGGCATATG
188166 ATATGTGGTCCTTA
1 -TATGTGGTCCTTA
188180 TGGACATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 14 0.52
21 11 0.41
22 2 0.07
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (21 bp):
TATGTGGTCCTTAGGCATATG
Found at i:188223 original size:23 final size:23
Alignment explanation
Indices: 188193--188238 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
188183 ACATTATTAT
188193 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
*
188216 ATGGCACTATGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
188239 GCGGTACTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:188252 original size:23 final size:24
Alignment explanation
Indices: 188195--188254 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
188185 ATTATTATAT
*
188195 GGCACTA-CGGTGCAATTCTACAT
1 GGCACTATCGGTGCAATTCTACAC
*
188218 GGCACTAT-GGTGCAATTCTACGC
1 GGCACTATCGGTGCAATTCTACAC
*
188241 GGTACT-TCGGTGCA
1 GGCACTATCGGTGCA
188255 TTTATACGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (24 bp):
GGCACTATCGGTGCAATTCTACAC
Found at i:188368 original size:2 final size:2
Alignment explanation
Indices: 188361--188397 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
188351 TAACAAATAC
188361 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 T
188398 GTGATGGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:188571 original size:15 final size:13
Alignment explanation
Indices: 188536--188573 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
188526 TAATTCGATG
188536 ATAATGAT-ATAA
1 ATAATGATAATAA
188548 ATAATGATAATAA
1 ATAATGATAATAA
188561 TATATATGATAAT
1 -ATA-ATGATAAT
188574 GCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 3 0.13
15 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
ATAATGATAATAA
Found at i:193323 original size:23 final size:23
Alignment explanation
Indices: 193296--193353 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
193286 TTTTATATGA
* *
193296 CACTATGGTGTAATTCTACGTGG
1 CACTATGGTGCAATTCTACGCGG
193319 CACTATGGTGCAATTCTACGCGG
1 CACTATGGTGCAATTCTACGCGG
193342 CACT-TCGGTGCA
1 CACTAT-GGTGCA
193354 TTTATACGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (23 bp):
CACTATGGTGCAATTCTACGCGG
Found at i:193361 original size:23 final size:23
Alignment explanation
Indices: 193296--193361 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
193286 TTTTATATGA
* * *
193296 CACTATGGTGTAATTCTACGTGG
1 CACTATGGTGCAATTATACGCGG
*
193319 CACTATGGTGCAATTCTACGCGG
1 CACTATGGTGCAATTATACGCGG
*
193342 CACT-TCGGTGCATTTATACG
1 CACTAT-GGTGCAATTATACG
193362 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (23 bp):
CACTATGGTGCAATTATACGCGG
Found at i:193467 original size:2 final size:2
Alignment explanation
Indices: 193460--193486 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
193450 TAACAAATAC
193460 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 T
193487 GATGGATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:193658 original size:15 final size:13
Alignment explanation
Indices: 193623--193660 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
193613 TAATTTGATG
193623 ATAATGAT-ATAA
1 ATAATGATAATAA
193635 ATAATGATAATAA
1 ATAATGATAATAA
193648 TATATATGATAAT
1 -ATA-ATGATAAT
193661 GCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 3 0.13
15 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
ATAATGATAATAA
Found at i:195328 original size:30 final size:29
Alignment explanation
Indices: 195294--195387 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
195284 TTAACGAAGA
195294 GTGGTCTGATTGAATTAATTAAAAAGTTTG
1 GTGGTCTGATTGAATTAA-TAAAAAGTTTG
*
195324 GTGGTCTGATTGAGA--CA-AAAAAGTTTG
1 GTGGTCTGATTGA-ATTAATAAAAAGTTTG
* * *
195351 GTGGTCAGATTG-ATTAATGACCATAGTTTG
1 GTGGTCTGATTGAATTAAT-A-AAAAGTTTG
195381 GTGGTCT
1 GTGGTCT
195388 CCCGTGTAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
25 1 0.02
27 22 0.42
29 2 0.04
30 26 0.50
31 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.28, T:0.36
Consensus pattern (29 bp):
GTGGTCTGATTGAATTAATAAAAAGTTTG
Found at i:195602 original size:16 final size:16
Alignment explanation
Indices: 195581--195612 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
195571 AAGATATTAT
*
195581 AATGACTTCATTAATA
1 AATGACTTAATTAATA
195597 AATGACTTAATTAATA
1 AATGACTTAATTAATA
195613 GAAGGAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (16 bp):
AATGACTTAATTAATA
Found at i:196697 original size:35 final size:35
Alignment explanation
Indices: 196581--196720 Score: 97
Period size: 35 Copynumber: 3.9 Consensus size: 35
196571 TTTTATATAG
* * * *
196581 TATAATATAT-A-TAATAAATATAGTTTTTAAAATA
1 TATAATATATAATTATTAAA-ACAGTTTTGAAAACA
* * * * * *
196615 TATAATATATAGTTTTTGGAAACTTACTTTTAAAAACG
1 TATAATATATAATTATT-AAAAC--AGTTTTGAAAACA
*
196653 TATAATATATAGTTATTAAAAC-GATTTTGAAAACA
1 TATAATATATAATTATTAAAACAG-TTTTGAAAACA
* *
196688 TATAGTATATAATTTTTAAAACAGTTTTGAAAA
1 TATAATATATAATTATTAAAACAGTTTTGAAAA
196721 TATGTATATA
Statistics
Matches: 82, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
34 10 0.12
35 37 0.45
36 4 0.05
37 6 0.07
38 25 0.30
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.41
Consensus pattern (35 bp):
TATAATATATAATTATTAAAACAGTTTTGAAAACA
Found at i:196819 original size:28 final size:30
Alignment explanation
Indices: 196763--196827 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
196753 TTGAAAACGA
196763 TTTTTGAAAATATATTAATATATTATATAG
1 TTTTTGAAAATATATTAATATATTATATAG
*
196793 TTTTTGAAAA-ATA-TAATATATGTTATACAG
1 TTTTTGAAAATATATTAATATA--TTATATAG
196823 TTTTT
1 TTTTT
196828 ATTATTTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.22
29 3 0.09
30 22 0.69
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTTTGAAAATATATTAATATATTATATAG
Found at i:203394 original size:42 final size:42
Alignment explanation
Indices: 203347--203439 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
203337 CGAAATCACA
*
203347 TGTTTGGTTCA-TGTAATTCGTTTTTTC-AAAAATATTTTCTC-G
1 TGTTTGGTTCACT-TAATTCG-TTTTCCGAAAAATATTTTC-CAG
* *
203389 TGTTTGTTTCACTTAATTCGTTTTCCGAAAAATGTTTTCCAG
1 TGTTTGGTTCACTTAATTCGTTTTCCGAAAAATATTTTCCAG
203431 TGTTTGGTT
1 TGTTTGGTT
203440 GGAAGAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
41 6 0.14
42 37 0.84
43 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (42 bp):
TGTTTGGTTCACTTAATTCGTTTTCCGAAAAATATTTTCCAG
Found at i:203809 original size:28 final size:26
Alignment explanation
Indices: 203765--203827 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 26
203755 TTTAATAAAT
*
203765 ATATAATAA-ATTTTTTATATATTTA
1 ATATAATAATATTATTTATATATTTA
203790 ATAATGAATAATATTATTTATATATTTA
1 AT-AT-AATAATATTATTTATATATTTA
203818 ATATAATAAT
1 ATATAATAAT
203828 CTAATAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 2 0.06
26 8 0.24
27 7 0.21
28 17 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATAATAATATTATTTATATATTTA
Found at i:203859 original size:23 final size:23
Alignment explanation
Indices: 203809--203883 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
203799 AATATTATTT
*
203809 ATATATTTAATATAATA-ATCTAATA
1 ATAT-TTTAATA-AATATATTTAA-A
203834 ATATTTTAATAAATATATTTAAA
1 ATATTTTAATAAATATATTTAAA
** * *
203857 ATATACTAATTAATATTTTTAAA
1 ATATTTTAATAAATATATTTAAA
203880 ATAT
1 ATAT
203884 AATATAACAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 28 0.64
24 12 0.27
25 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTTTAATAAATATATTTAAA
Found at i:203866 original size:34 final size:37
Alignment explanation
Indices: 203809--203884 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
203799 AATATTATTT
*
203809 ATATATTTAATATAATAATCTAA-TAATATTTTAATAA
1 ATATATTTAAAATAATAATCTAATTAATATTTTAA-AA
*
203846 ATATATTTAAAAT-AT-A-CTAATTAATATTTTTAAA
1 ATATATTTAAAATAATAATCTAATTAATATTTTAAAA
203880 ATATA
1 ATATA
203885 ATATAACACT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
34 11 0.31
35 11 0.31
36 2 0.06
37 12 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (37 bp):
ATATATTTAAAATAATAATCTAATTAATATTTTAAAA
Found at i:203884 original size:23 final size:23
Alignment explanation
Indices: 203840--203884 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
203830 AATAATATTT
203840 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
203863 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
203885 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:204255 original size:15 final size:15
Alignment explanation
Indices: 204235--204264 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
204225 TCAAATTCAA
204235 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
204250 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
204265 AAAACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:204386 original size:15 final size:15
Alignment explanation
Indices: 204330--204387 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
204320 TCCATAAATA
*
204330 TAATTCATTTTCCA-
1 TAATTCATATTCCAG
* *
204344 AAATTCAAATTCCAG
1 TAATTCATATTCCAG
*
204359 TAATTCACATTCCAG
1 TAATTCATATTCCAG
*
204374 TAATTCATTTTCCA
1 TAATTCATATTCCA
204388 AAAAACCAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
14 11 0.31
15 25 0.69
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (15 bp):
TAATTCATATTCCAG
Found at i:204424 original size:124 final size:123
Alignment explanation
Indices: 204173--204424 Score: 344
Period size: 124 Copynumber: 2.0 Consensus size: 123
204163 AAAAAAAATG
* * * * *
204173 TAATTCATTTTTCGAAAAACGTTTTCCATAAATGTAACTCATTTTATAGAATTCAAATTCAATAA
1 TAATTCATTTTACGAAAAACATTTTCCATAAATATAACTCATTTTACAAAATTCAAATTCAATAA
** * * * *
204238 TTCATTTTCCAGTAATTCATTTTCCAGAAAACTAATTACAGCAAAACAAGCAGACCCG
66 TTCACATTCCAGTAATTCATTTTCCAAAAAACCAATTACAGCAAAACAAACAGACCCA
* * *
204296 TAATTCATTTTACGAAAAACATTTTCCATAAATATAATTCATTTTCCAAAATTCAAATTCCAGTA
1 TAATTCATTTTACGAAAAACATTTTCCATAAATATAACTCATTTTACAAAATTCAAATT-CAATA
*
204361 ATTCACATTCCAGTAATTCATTTTCCAAAAAACCAATTACAGTC-AAACAAACATACCCA
65 ATTCACATTCCAGTAATTCATTTTCCAAAAAACCAATTACAG-CAAAACAAACAGACCCA
204420 TAATT
1 TAATT
204425 TCGGGTGTTG
Statistics
Matches: 112, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
123 52 0.46
124 59 0.53
125 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34
Consensus pattern (123 bp):
TAATTCATTTTACGAAAAACATTTTCCATAAATATAACTCATTTTACAAAATTCAAATTCAATAA
TTCACATTCCAGTAATTCATTTTCCAAAAAACCAATTACAGCAAAACAAACAGACCCA
Found at i:208291 original size:47 final size:48
Alignment explanation
Indices: 208209--208304 Score: 185
Period size: 47 Copynumber: 2.0 Consensus size: 48
208199 TTGAATTGAA
208209 TGGACAACTTACACTTCTTAGGTTCATTGACGTTCTCGAAGCCCACAC
1 TGGACAACTTACACTTCTTAGGTTCATTGACGTTCTCGAAGCCCACAC
208257 TGGACAACTTACACTTC-TAGGTTCATTGACGTTCTCGAAGCCCACAC
1 TGGACAACTTACACTTCTTAGGTTCATTGACGTTCTCGAAGCCCACAC
208304 T
1 T
208305 TTTTTGGTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 31 0.65
48 17 0.35
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (48 bp):
TGGACAACTTACACTTCTTAGGTTCATTGACGTTCTCGAAGCCCACAC
Found at i:217567 original size:20 final size:20
Alignment explanation
Indices: 217542--217584 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
217532 TCTAAAGGCC
217542 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
217562 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
217582 CAT
1 CAT
217585 GTGGTAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:222821 original size:23 final size:23
Alignment explanation
Indices: 222782--222839 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
222772 ATCCAAATTT
*
222782 GAAGAGGAAGAATAATAGAGTATG
1 GAAG-GGAAGAAAAATAGAGTATG
222806 GAAGGGAAGAAAAATAGAGTATG
1 GAAGGGAAGAAAAATAGAGTATG
222829 GAAGGGAAGAA
1 GAAGGGAAGAA
222840 GGAATAAGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 29 0.88
24 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (23 bp):
GAAGGGAAGAAAAATAGAGTATG
Found at i:224959 original size:26 final size:26
Alignment explanation
Indices: 224930--224981 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
224920 ATTGTGTTAT
* *
224930 GATATTTAGATTTGTATTATATTTTA
1 GATATTTAAAGTTGTATTATATTTTA
224956 GATATTTAAAGTTGTATTATATTTTA
1 GATATTTAAAGTTGTATTATATTTTA
224982 ATTAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (26 bp):
GATATTTAAAGTTGTATTATATTTTA
Found at i:245591 original size:2 final size:2
Alignment explanation
Indices: 245584--245612 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
245574 TTCGATTCAA
245584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
245613 CTCGATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:248925 original size:18 final size:18
Alignment explanation
Indices: 248902--248949 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
248892 TAGGCCAAGC
248902 TCCTCCTAC-TCCTAGTAA
1 TCCTCCTACAT-CTAGTAA
248920 TCCTCCTACATCTAGTAA
1 TCCTCCTACATCTAGTAA
248938 TCCTCCTACATC
1 TCCTCCTACATC
248950 CACGCCGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.33
Consensus pattern (18 bp):
TCCTCCTACATCTAGTAA
Found at i:249144 original size:51 final size:51
Alignment explanation
Indices: 249081--249189 Score: 182
Period size: 51 Copynumber: 2.1 Consensus size: 51
249071 GTGACAACTT
* *
249081 CTCCACCCCCGGTTTCAGCTCCTCCTCCAGCAACACCCCCACCCGTCAGCA
1 CTCCTCCCCCGGTTTCAACTCCTCCTCCAGCAACACCCCCACCCGTCAGCA
* *
249132 CTCCTCCCCCGGTTTCAACTCCTCCTCCAGCAACTCCCCCACCCGTCAGCT
1 CTCCTCCCCCGGTTTCAACTCCTCCTCCAGCAACACCCCCACCCGTCAGCA
249183 CTCCTCC
1 CTCCTCC
249190 TCCTGCTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.15, C:0.56, G:0.10, T:0.19
Consensus pattern (51 bp):
CTCCTCCCCCGGTTTCAACTCCTCCTCCAGCAACACCCCCACCCGTCAGCA
Found at i:249207 original size:51 final size:51
Alignment explanation
Indices: 249081--249207 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 51
249071 GTGACAACTT
* * * *
249081 CTCCACCCCCGGTTTCAGCTCCTCCTCCAGCAACACCCCCACCCGTCAGCA
1 CTCCTCCCCCGGCTTCAACGCCTCCTCCAGCAACACCCCCACCCGTCAGCA
* * * *
249132 CTCCTCCCCCGGTTTCAACTCCTCCTCCAGCAACTCCCCCACCCGTCAGCT
1 CTCCTCCCCCGGCTTCAACGCCTCCTCCAGCAACACCCCCACCCGTCAGCA
* * **
249183 CTCCTCCTCCTGCTTCCCCGCCTCC
1 CTCCTCCCCCGGCTTCAACGCCTCC
249208 AGCCTCTCCT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.13, C:0.57, G:0.10, T:0.20
Consensus pattern (51 bp):
CTCCTCCCCCGGCTTCAACGCCTCCTCCAGCAACACCCCCACCCGTCAGCA
Found at i:249215 original size:30 final size:30
Alignment explanation
Indices: 249181--249270 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
249171 CACCCGTCAG
* * * *
249181 CTCTCCTCCTCCTGCTTCCCCGCCTCCAGC
1 CTCTCCTCCACCGGCTTCTCCACCTCCAGC
249211 CTCTCCTCCACCGGCTTCTCCACCTCCAGC
1 CTCTCCTCCACCGGCTTCTCCACCTCCAGC
*
249241 CACTCCTCCACCGGCTTCTCCACCTCCAGC
1 CTCTCCTCCACCGGCTTCTCCACCTCCAGC
249271 TACCCCTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.09, C:0.58, G:0.10, T:0.23
Consensus pattern (30 bp):
CTCTCCTCCACCGGCTTCTCCACCTCCAGC
Found at i:251777 original size:17 final size:18
Alignment explanation
Indices: 251737--251777 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
251727 TATATTTTTT
251737 AAAAATTCTAAGAAAAAA
1 AAAAATTCTAAGAAAAAA
251755 ATAAAATT-T-AGAAAATAA
1 A-AAAATTCTAAGAAAA-AA
251773 AAAAA
1 AAAAA
251778 CATTTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 6 0.29
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAATTCTAAGAAAAAA
Found at i:254011 original size:24 final size:26
Alignment explanation
Indices: 253966--254017 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
253956 CGTTCGTGAA
*
253966 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
253992 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
254016 CG
1 CG
254018 AACAGAGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:255628 original size:41 final size:41
Alignment explanation
Indices: 255568--255653 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
255558 TTTCCTGCAG
255568 AATATAGACATGATATTATGTTAAATATATAATCAATAGAA
1 AATATAGACATGATATTATGTTAAATATATAATCAATAGAA
*
255609 AATATAGACATGATCTTATGTTAAATATATAATCAATAGAA
1 AATATAGACATGATATTATGTTAAATATATAATCAATAGAA
255650 AATA
1 AATA
255654 AAAAAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (41 bp):
AATATAGACATGATATTATGTTAAATATATAATCAATAGAA
Found at i:259353 original size:25 final size:25
Alignment explanation
Indices: 259324--259371 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
259314 GGTTATAGAC
* * *
259324 AGTTCATCTTTTTTGATTTAGATAG
1 AGTTCACCTCTTTTAATTTAGATAG
259349 AGTTCACCTCTTTTAATTTAGAT
1 AGTTCACCTCTTTTAATTTAGAT
259372 GGAGAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (25 bp):
AGTTCACCTCTTTTAATTTAGATAG
Found at i:261544 original size:87 final size:87
Alignment explanation
Indices: 261398--261558 Score: 295
Period size: 87 Copynumber: 1.9 Consensus size: 87
261388 TGTTATATTA
261398 TTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAG
1 TTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAG
261463 AGCTTATATAATAAAATAGGTT
66 AGCTTATATAATAAAATAGGTT
* *
261485 TTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAG
1 TTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAG
*
261550 CGCTTATAT
66 AGCTTATAT
261559 TGACCTATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (87 bp):
TTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAG
AGCTTATATAATAAAATAGGTT
Found at i:262001 original size:182 final size:182
Alignment explanation
Indices: 261711--262351 Score: 1146
Period size: 182 Copynumber: 3.5 Consensus size: 182
261701 ATTAATAGAT
*
261711 CGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA
1 CGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA
261776 CTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGATACTTATAATAAATTAT
66 CTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGATACTTATAATAAATTAT
*
261841 CGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
131 CGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
* * *
261893 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAAATTTTTATAAAGTATCGACA
1 CGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA
261958 CTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCGATACTTATAATAAATTA
66 CTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCGATACTTATAATAAATTA
262022 TCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
130 TCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
*
262075 CGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA
1 CGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA
*
262140 CGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAA--GTCGATACTTATAATAAATTAT
66 CTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGATACTTATAATAAATTAT
262203 CGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
131 CGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
* *
262255 CGATTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA
1 CGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA
* *
262320 CTTTATTGACGATATAACTTCTTCTCTT-TTAA
66 CTTTATTGGCGCTATAACTTCTTCTCTTATTAA
262352 AAAATGTAAA
Statistics
Matches: 443, Mismatches: 14, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
179 4 0.01
180 161 0.36
181 2 0.00
182 274 0.62
183 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
CGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA
CTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGATACTTATAATAAATTAT
CGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
Found at i:265369 original size:184 final size:184
Alignment explanation
Indices: 265052--265400 Score: 592
Period size: 184 Copynumber: 1.9 Consensus size: 184
265042 GCGTTACTTA
265052 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
1 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
* * * *
265117 TATATTTATATCGGTTATATTAAAAAATTACCTATTACATTATAATTGTGGGTTCTGATGTTTTT
66 TATATCTATACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
* *
265182 TCAATCGATACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
131 TCAATCGACACTTTTTGAAAAGGTATCAACACTTTTTTCATCCATTCTGGACAT
* *
265236 AAAGTA-GCGACACAATATTAAAAAGTGTCGATATAGGTTGTATACCTATTCTCTCATAAAACTG
1 AAAGTATG-GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
* *
265300 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGGTGTTTT
65 GTATATCTATACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
265365 TTCAATCGACACTTTTTGAAAAGGTATCAACACTTT
130 TTCAATCGACACTTTTTGAAAAGGTATCAACACTTT
265401 ATGCTGATAT
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
183 1 0.01
184 153 0.99
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (184 bp):
AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
TATATCTATACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
TCAATCGACACTTTTTGAAAAGGTATCAACACTTTTTTCATCCATTCTGGACAT
Found at i:266706 original size:12 final size:12
Alignment explanation
Indices: 266685--266724 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
266675 ATTTGGATCA
*
266685 TCATCATCATCG
1 TCATCTTCATCG
266697 TCATCTTCATCG
1 TCATCTTCATCG
* *
266709 TCAGCTTCATCT
1 TCATCTTCATCG
266721 TCAT
1 TCAT
266725 TGACCGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:268841 original size:19 final size:19
Alignment explanation
Indices: 268814--268862 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
268804 TTACATTCAC
268814 ATACAAAATTATAAATCGT-
1 ATACAAAATTATAAATC-TA
*
268833 ATGCAAAATTATAAATCTA
1 ATACAAAATTATAAATCTA
268852 ATACAAAATTA
1 ATACAAAATTA
268863 ACCCTACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCTA
Found at i:270465 original size:33 final size:33
Alignment explanation
Indices: 270413--270500 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
270403 ATGACATCGA
* *
270413 CTTTCTTCCT-CCTCATTTCTTTCATCTCTTCTT
1 CTTTC-TCCTCCCTCTTTTCTTCCATCTCTTCTT
270446 CTTTCTCCTCCCTCTTTTCTTCCATCTCTTCTT
1 CTTTCTCCTCCCTCTTTTCTTCCATCTCTTCTT
*
270479 CTTCCTCCTCCCTCTTTTCTTC
1 CTTTCTCCTCCCTCTTTTCTTC
270501 TTCATATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 4 0.08
33 47 0.92
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (33 bp):
CTTTCTCCTCCCTCTTTTCTTCCATCTCTTCTT
Found at i:270733 original size:34 final size:33
Alignment explanation
Indices: 270686--270750 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
270676 CATCTTAAGA
* * *
270686 TCACCCCTTAACACCTCAACTTTTTTTCACCACT
1 TCACCCATCAACACCTCAAC-TTCTTTCACCACT
*
270720 TCACCCATCAACACCTCTACTTCTTTCACCA
1 TCACCCATCAACACCTCAACTTCTTTCACCA
270751 GTCCATCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.25, C:0.43, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCATCAACACCTCAACTTCTTTCACCACT
Found at i:270813 original size:21 final size:21
Alignment explanation
Indices: 270789--270829 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
270779 CTTATGCCTC
270789 TCAAGTGTATCTTCGACTCTA
1 TCAAGTGTATCTTCGACTCTA
* *
270810 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTATCTTCGACTCT
270830 TGATTGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTATCTTCGACTCTA
Found at i:270931 original size:15 final size:15
Alignment explanation
Indices: 270911--270943 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
270901 ACTCTGTTTT
*
270911 CCCTCACCGTCGTCC
1 CCCTCACCGTCATCC
270926 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
270941 CCC
1 CCC
270944 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.64, G:0.09, T:0.18
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:273404 original size:181 final size:182
Alignment explanation
Indices: 273052--273525 Score: 707
Period size: 182 Copynumber: 2.6 Consensus size: 182
273042 CGTACTTACG
* * * * *
273052 AAAGTATCGAAACTTTTAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
273117 TATCATATTTTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTG-TTGATCGATACATTTTTTGAAAGTATCGACACTTTA
* *
273182 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 TAAGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * *
273234 AAAGTTTCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATACCAGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
273299 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTAT
*
273364 AAGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
131 AAGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * ** *
273416 AAAGTACCTACACTTTAAATATATTCGGTACCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
273481 TGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTT
273526 AATTTGGATC
Statistics
Matches: 262, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
181 82 0.31
182 180 0.69
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTAT
AAGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
Found at i:274827 original size:2 final size:2
Alignment explanation
Indices: 274822--274847 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
274812 AAAAAAATTA
274822 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
274848 TCCAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:275157 original size:29 final size:29
Alignment explanation
Indices: 275040--275448 Score: 164
Period size: 30 Copynumber: 14.1 Consensus size: 29
275030 ACACACATAT
* * *
275040 TTAACTTATTAAATATATTTTATTTTTGTC
1 TTAACTTA-AAAATATATTTTATTCTTATC
* * * * * *
275070 TCAATTTATTAAATATATATTATTTTTATT
1 TTAACTTA-AAAATATATTTTATTCTTATC
* *
275100 TTTA-TGTAAAAAATATATTTCA-TCTTTATC
1 TTAACT-T-AAAAATATATTTTATTC-TTATC
* *
275130 TTCACTTAAAAGTATATTTTATTCTTATC
1 TTAACTTAAAAATATATTTTATTCTTATC
** * ***
275159 TTGATTTTTAAAAATATTTTTTA-AAATATC
1 TT-A-ACTTAAAAATATATTTTATTCTTATC
* * *
275189 TTAA-TTTAAAATAT-GTTTA--ATTA--
1 TTAACTTAAAAATATATTTTATTCTTATC
* *
275212 TTAATTTAAAAA-ATATATTATTCTTATC
1 TTAACTTAAAAATATATTTTATTCTTATC
* * * * *
275240 CTCAC-TAAAAATATATGTTATACTTATT
1 TTAACTTAAAAATATATTTTATTCTTATC
* *
275268 TTAAATTTAAAAAATATATTTTATTATTATC
1 TT-AACTT-AAAAATATATTTTATTCTTATC
* * *
275299 TTAAATTCTAAAAATATATTTTTATTTTTTTC
1 TT-AACT-TAAAAATATA-TTTTATTCTTATC
* * *
275331 TTAACCTATTAAATATATTTTATTTTTAT-
1 TTAACTTA-AAAATATATTTTATTCTTATC
* * * *
275360 TTTA--TAAGAATATATGTTTCAATCTTATA
1 TTAACTTAAAAATATAT-TTT-ATTCTTATC
* * *
275389 TTCACTTAAAAGTATATTTTATTCTTATTT
1 TTAACTTAAAAATATATTTTATTCTTA-TC
*
275419 TTAACTT-AAAATATATTTTATTTTTATC
1 TTAACTTAAAAATATATTTTATTCTTATC
275447 TT
1 TT
275449 GACTATTAAT
Statistics
Matches: 289, Mismatches: 64, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
23 6 0.02
24 9 0.03
25 3 0.01
26 14 0.05
27 20 0.07
28 25 0.09
29 52 0.18
30 78 0.27
31 68 0.24
32 14 0.05
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTCTTATC
Found at i:275284 original size:31 final size:31
Alignment explanation
Indices: 275244--275324 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
275234 CTTATCCTCA
*
275244 CTAAAAATATATGTTA-TACTTATTTTAAATT
1 CTAAAAATATATGTTATTA-TTATCTTAAATT
*
275275 -TAAAAAATATATTTTATTATTATCTTAAATT
1 CT-AAAAATATATGTTATTATTATCTTAAATT
275306 CTAAAAATATAT-TT-TTATT
1 CTAAAAATATATGTTATTATT
275325 TTTTTCTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 5 0.11
30 3 0.07
31 34 0.76
32 3 0.07
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (31 bp):
CTAAAAATATATGTTATTATTATCTTAAATT
Found at i:275322 original size:32 final size:32
Alignment explanation
Indices: 275244--275334 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
275234 CTTATCCTCA
* *
275244 CTAAAAATATA-TGTTA-TACTTATTTTAAATT
1 CTAAAAATATATTTTTATTA-TTATCTTAAATT
275275 -TAAAAA-ATATATTTTATTATTATCTTAAATT
1 CTAAAAATATAT-TTTTATTATTATCTTAAATT
* *
275306 CTAAAAATATATTTTTATTTTTTTCTTAA
1 CTAAAAATATATTTTTATTATTATCTTAA
275335 CCTATTAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
29 3 0.06
30 6 0.12
31 15 0.29
32 23 0.45
33 4 0.08
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (32 bp):
CTAAAAATATATTTTTATTATTATCTTAAATT
Found at i:279316 original size:20 final size:20
Alignment explanation
Indices: 279276--279336 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
279266 ACCTGACCCG
* *
279276 TTGATCATTAACCGTTAACT
1 TTGATCATTAACTGTTGACT
** *
279296 TTGATTGTTGACTGTTGACT
1 TTGATCATTAACTGTTGACT
279316 TTGATCATTAACTGTTGACT
1 TTGATCATTAACTGTTGACT
279336 T
1 T
279337 CTGCCGTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (20 bp):
TTGATCATTAACTGTTGACT
Found at i:280037 original size:29 final size:29
Alignment explanation
Indices: 279972--280045 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
279962 ATCTCTAATT
* **
279972 TGCATGAGATT-TATCCTCGTCTTGATTT
1 TGCATGAGATTATATCCTCGTCTTAATGA
*
280000 TGCAGGAGATTATATCCTCGTCTTAATGA
1 TGCATGAGATTATATCCTCGTCTTAATGA
*
280029 TGTATGAGATTATATCC
1 TGCATGAGATTATATCC
280046 CCATCCTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 10 0.26
29 29 0.74
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (29 bp):
TGCATGAGATTATATCCTCGTCTTAATGA
Found at i:280068 original size:29 final size:29
Alignment explanation
Indices: 280036--280104 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
280026 TGATGTATGA
*
280036 GATTATATCCCCATCCTGATTCTGCATAT-
1 GATTATATCCCCATCCTGACTCTGCAT-TG
*
280065 GATTATATCCCCGTCCTGACTCTGCATTG
1 GATTATATCCCCATCCTGACTCTGCATTG
*
280094 GATTTTATCCC
1 GATTATATCCC
280105 TGTCTTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.03
29 35 0.97
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (29 bp):
GATTATATCCCCATCCTGACTCTGCATTG
Found at i:282041 original size:23 final size:20
Alignment explanation
Indices: 282002--282059 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 20
281992 GTCATATTTT
282002 ATTATTTTAATTTTATTATA
1 ATTATTTTAATTTTATTATA
282022 ATTATTTATAATATTATATTATA
1 ATTATTT-TAAT-TT-TATTATA
*
282045 TATTGGTTTTAATTT
1 -ATT-ATTTTAATTT
282060 CTCAACTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.22
21 4 0.12
22 2 0.06
23 9 0.28
24 7 0.22
25 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTATTTTAATTTTATTATA
Found at i:282085 original size:2 final size:2
Alignment explanation
Indices: 282078--282123 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
282068 TTTCCTCACC
282078 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
282120 AT AT
1 AT AT
282124 TCATATTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:290680 original size:105 final size:105
Alignment explanation
Indices: 290497--290704 Score: 326
Period size: 105 Copynumber: 2.0 Consensus size: 105
290487 ATACTCCTAT
* *
290497 ATTCTGATGTCAGCATCTATTCCTAAACAACTTGCTAGCAATACCTCTCTTTGACTTCAGTCAAC
1 ATTCTGATGTCAGCATCTATTCCTAAACAACTGGCTAGAAATACCTCTCTTTGACTTCAGTCAAC
*
290562 AATTAGATAATGACAACTTCCTAACTAGCAACAGTAAACA
66 AATTAGATAATGACAACTTCATAACTAGCAACAGTAAACA
* * * * *
290602 ATTCTGATGTCGGCATCTATTTCTAAGCAACTGGCTAGAAATACCTCTCTTTGGCTTCAGTCAAT
1 ATTCTGATGTCAGCATCTATTCCTAAACAACTGGCTAGAAATACCTCTCTTTGACTTCAGTCAAC
* *
290667 AATTAGATTATGACAACTTCATAACTAGCACCAGTAAA
66 AATTAGATAATGACAACTTCATAACTAGCAACAGTAAA
290705 TAAAATGCTG
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 93 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (105 bp):
ATTCTGATGTCAGCATCTATTCCTAAACAACTGGCTAGAAATACCTCTCTTTGACTTCAGTCAAC
AATTAGATAATGACAACTTCATAACTAGCAACAGTAAACA
Found at i:300807 original size:43 final size:43
Alignment explanation
Indices: 300742--300824 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
300732 GCACTATACC
**
300742 CACGTGGCGCCAGCTCACCGTATAGCGCGGTGCAGGGGGCACG
1 CACGTGGCGCCAAATCACCGTATAGCGCGGTGCAGGGGGCACG
*
300785 CACGTGGCGCCAAATCATCGTATAGCGCGGTGCAGGGGGC
1 CACGTGGCGCCAAATCACCGTATAGCGCGGTGCAGGGGGC
300825 GCACTTTACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.18, C:0.30, G:0.39, T:0.13
Consensus pattern (43 bp):
CACGTGGCGCCAAATCACCGTATAGCGCGGTGCAGGGGGCACG
Found at i:301892 original size:33 final size:32
Alignment explanation
Indices: 301852--301913 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
301842 TCCTAATTTT
*
301852 AATAAATTAAA-ATAAATTTACCTACAAATATAA
1 AATAAATTAAAGA-AAA-TTACATACAAATATAA
301885 AATAAATTAAAGAAAATTACATACAAATA
1 AATAAATTAAAGAAAATTACATACAAATA
301914 GTCCATGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (32 bp):
AATAAATTAAAGAAAATTACATACAAATATAA
Found at i:306325 original size:32 final size:32
Alignment explanation
Indices: 306284--306355 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
306274 CCCATGATTA
* * *
306284 ACCCAAGAAAGTGCCTTGGGGCCTGAGAGTCT
1 ACCCAAGAAAGTGCCTCGGGGCCTCAGAGCCT
**
306316 ACCCAAGAAAGTTTCTCGGGGCCTCAGAGCCT
1 ACCCAAGAAAGTGCCTCGGGGCCTCAGAGCCT
*
306348 ACCTAAGA
1 ACCCAAGA
306356 GTCACCTTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (32 bp):
ACCCAAGAAAGTGCCTCGGGGCCTCAGAGCCT
Found at i:308267 original size:16 final size:15
Alignment explanation
Indices: 308246--308275 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
308236 TTAAATACAT
308246 AAAAAAGAAAGAAAGA
1 AAAAAAGAAA-AAAGA
308262 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
308276 GAAGGGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:312524 original size:35 final size:35
Alignment explanation
Indices: 312478--312604 Score: 166
Period size: 35 Copynumber: 3.6 Consensus size: 35
312468 CTTAGATCCG
312478 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
* ***
312513 TAAGGAATTACCAGTTTGATCGAG-CTGAACCTGCCG
1 TAAGGAATTACCAGTTCGATCG-GTCTGAACCT-ATA
*
312549 TAAGGAATTACCAGTTCGATCGGTCTGAAACTATA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
* *
312584 TAAGAAATTACCAGTTTGATC
1 TAAGGAATTACCAGTTCGATC
312605 AAGTTGAACC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
35 49 0.63
36 29 0.37
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (35 bp):
TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
Found at i:312593 original size:71 final size:71
Alignment explanation
Indices: 312475--312617 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
312465 CACCTTAGAT
* * *
312475 CCGTAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAGTTTGATCGAGCTG
1 CCGTAAGGAATTACCAGTTCGATCGGTCTGAAACTATATAAGAAATTACCAGTTTGATCAAGCTG
312540 AACCTG
66 AACCTG
*
312546 CCGTAAGGAATTACCAGTTCGATCGGTCTGAAACTATATAAGAAATTACCAGTTTGATCAAGTTG
1 CCGTAAGGAATTACCAGTTCGATCGGTCTGAAACTATATAAGAAATTACCAGTTTGATCAAGCTG
312611 AACCTG
66 AACCTG
312617 C
1 C
312618 AGAGACTTCA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (71 bp):
CCGTAAGGAATTACCAGTTCGATCGGTCTGAAACTATATAAGAAATTACCAGTTTGATCAAGCTG
AACCTG
Found at i:313670 original size:27 final size:27
Alignment explanation
Indices: 313613--313670 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
313603 TAATATAGTC
* * ** *
313613 ATTTTACACTTTAAGGGCATTTTGGTT
1 ATTTTACACTTCAAGGGCAATTTCATA
*
313640 ATTTTACACTTCAGGGGCAATTTCATA
1 ATTTTACACTTCAAGGGCAATTTCATA
313667 ATTT
1 ATTT
313671 CATAATCAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.45
Consensus pattern (27 bp):
ATTTTACACTTCAAGGGCAATTTCATA
Found at i:314647 original size:23 final size:23
Alignment explanation
Indices: 314580--314647 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
314570 GTGCCATATA
*
314580 TTTGTCCCGAATGACCACATAAT
1 TTTGTCCCGAATGACCACATAGT
** *
314603 TTTGTCCTAAATGACCGCATAGT
1 TTTGTCCCGAATGACCACATAGT
*
314626 TTTGTCCCGAAGGACCACATAG
1 TTTGTCCCGAATGACCACATAG
314648 AACCCTCGAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (23 bp):
TTTGTCCCGAATGACCACATAGT
Found at i:315600 original size:20 final size:20
Alignment explanation
Indices: 315571--315608 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
315561 TTTCAAAGTG
315571 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
315591 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
315609 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:315675 original size:45 final size:46
Alignment explanation
Indices: 315626--315717 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 46
315616 TCAAACATTG
* *
315626 AATGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
315671 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
315717 A
1 A
315718 GGCTTTTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 23 0.52
46 21 0.48
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (46 bp):
AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:318510 original size:22 final size:22
Alignment explanation
Indices: 318481--318531 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
318471 TGGTAGATGA
318481 CTATTCTAGATATACTTGAGTT
1 CTATTCTAGATATACTTGAGTT
*
318503 GTATTCTAGATATACTTGAGTT
1 CTATTCTAGATATACTTGAGTT
318525 CTATTCT
1 CTATTCT
318532 TAAGTACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (22 bp):
CTATTCTAGATATACTTGAGTT
Found at i:321233 original size:24 final size:23
Alignment explanation
Indices: 321188--321268 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
321178 ACACTTAACA
*
321188 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CATTTGAAT
*
321212 GTGCATCGATTCATCATGTTG-A-
1 GTGCATCGATGCATCAT-TTGAAT
* *
321234 -TGCACCGATGCA-CGTCTTGAAT
1 GTGCATCGATGCATCAT-TTGAAT
321256 GTGCATCGATGCA
1 GTGCATCGATGCA
321269 CAGGGTCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 5 0.11
21 11 0.24
23 14 0.30
24 16 0.35
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (23 bp):
GTGCATCGATGCATCATTTGAAT
Found at i:321395 original size:17 final size:18
Alignment explanation
Indices: 321369--321403 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
321359 AGTCGTACAC
*
321369 CTCTTTTCTT-CTCTAAA
1 CTCTTCTCTTGCTCTAAA
321386 CTCTTCTCTTGCTCTAAA
1 CTCTTCTCTTGCTCTAAA
321404 TTAACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.17, C:0.31, G:0.03, T:0.49
Consensus pattern (18 bp):
CTCTTCTCTTGCTCTAAA
Found at i:322845 original size:21 final size:21
Alignment explanation
Indices: 322803--322846 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
322793 ACCCCGGGAG
* *
322803 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
322824 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
322845 CT
1 CT
322847 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Done.