Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000933.1 Hibiscus syriacus cultivar Beakdansim tig00001860_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: 84456
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4484 original size:27 final size:26
Alignment explanation
Indices: 4431--4537 Score: 90
Period size: 27 Copynumber: 4.0 Consensus size: 26
4421 TCTCGTTAAC
* * *
4431 CCCGACGACGTTCATCTT-TTCGTCAA
1 CCCGACGTCGTTCGTCTTCTT-GCCAA
*
4457 CTCCAACGTCGTTCGTCTTCTTGCCAA
1 C-CCGACGTCGTTCGTCTTCTTGCCAA
* *
4484 CCACGACGTTGTTTGTCTTCTTGCCAA
1 CC-CGACGTCGTTCGTCTTCTTGCCAA
* * *
4511 CCCCGACGACGTTCGTTTTCTCGCCAA
1 -CCCGACGTCGTTCGTCTTCTTGCCAA
4538 GCTTAACGCC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
26 2 0.03
27 59 0.91
28 4 0.06
ACGTcount: A:0.16, C:0.36, G:0.17, T:0.32
Consensus pattern (26 bp):
CCCGACGTCGTTCGTCTTCTTGCCAA
Found at i:9888 original size:308 final size:305
Alignment explanation
Indices: 9301--9911 Score: 1041
Period size: 308 Copynumber: 2.0 Consensus size: 305
9291 AAAGTGTTAG
*
9301 AGTCTCCACCGATCACTTTAAAAACATTTAGGTGGATCGGACACCATCTTACCTGATCTGCGTTT
1 AGTCGCCACCGATCACTTTAAAAACATTTAGGTGGATCGGACACCATCTTACCTGATCTGCGTTT
* * *
9366 TACCAGAAATGTGTCGGGTTCAGGAGTCGGTTACAGTCAAGGAATGATTAGCACCCTTGTACTGC
66 TACCAGAAATGTGTCGGGTTCAGGAGTCGGTTACAGTCAAGGAAGGAATAACACCCTTGTACTGC
9431 CCTTTCGGTACCAATTAATTTGTCGGTTGTCTTAATTACGAAAATTAAAATTAAAATTTAAAAAT
131 CCTTTCGGTACCAATTAATTTGTCGGTTGTCTTAATTACGAAAATT---ATTAAAATTTAAAAAT
*
9496 TCGATCATAATTATTTACCTTTTGATCAATTAAAATTATCCTAAAAAAATATCATAAATAAAGTT
193 TCGATCATAATTATTTACCTTTTGATCAATTAAAATTATCCTAAAAAAAGATCATAAATAAAGTT
9561 AAAAAAATAAAACAAACAAAAACCAAGAGTTAATATTAAGATCGAAAT
258 AAAAAAATAAAACAAACAAAAACCAAGAGTTAATATTAAGATCGAAAT
* * *
9609 AGTCGCCACCGATCACTTTAAAAGCATTTAGGTGTATCGGACATCATCTTACCTGATCTGCGTTT
1 AGTCGCCACCGATCACTTTAAAAACATTTAGGTGGATCGGACACCATCTTACCTGATCTGCGTTT
9674 TACCAGAAATGTGTCGGGTTC-GGAAGTCGGTTACAGTCAAGGAAGGAATAACACCCTTGTACTG
66 TACCAGAAATGTGTCGGGTTCAGG-AGTCGGTTACAGTCAAGGAAGGAATAACACCCTTGTACTG
* *
9738 CTCTTTCGGTACCAATTAATTTGTCGGTTGTCTTAATTGCGAAAA-T-TT-AAATTTAAAAATTC
130 CCCTTTCGGTACCAATTAATTTGTCGGTTGTCTTAATTACGAAAATTATTAAAATTTAAAAATTC
*
9800 GATCATAATTATTTACCTTTTGATCAATTAAAATTATTCTAAAAAAAGATCATAAATAAAGTTAA
195 GATCATAATTATTTACCTTTTGATCAATTAAAATTATCCTAAAAAAAGATCATAAATAAAGTTAA
* *
9865 AAAAATAAAACAAACAAAAACAAAGAGTTAGTATTAAGATCGAAAT
260 AAAAATAAAACAAACAAAAACCAAGAGTTAATATTAAGATCGAAAT
9911 A
1 A
9912 AAAAAATAAA
Statistics
Matches: 289, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
302 122 0.42
303 2 0.01
307 3 0.01
308 162 0.56
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (305 bp):
AGTCGCCACCGATCACTTTAAAAACATTTAGGTGGATCGGACACCATCTTACCTGATCTGCGTTT
TACCAGAAATGTGTCGGGTTCAGGAGTCGGTTACAGTCAAGGAAGGAATAACACCCTTGTACTGC
CCTTTCGGTACCAATTAATTTGTCGGTTGTCTTAATTACGAAAATTATTAAAATTTAAAAATTCG
ATCATAATTATTTACCTTTTGATCAATTAAAATTATCCTAAAAAAAGATCATAAATAAAGTTAAA
AAAATAAAACAAACAAAAACCAAGAGTTAATATTAAGATCGAAAT
Found at i:9958 original size:16 final size:16
Alignment explanation
Indices: 9937--9979 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
9927 GGAATGAAAG
9937 AAAATTAAAATTAAAA
1 AAAATTAAAATTAAAA
*
9953 AAAATT-AAATTGAAA
1 AAAATTAAAATTAAAA
*
9968 AGAATTAAAATT
1 AAAATTAAAATT
9980 CATGGATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAATTAAAATTAAAA
Found at i:10077 original size:24 final size:23
Alignment explanation
Indices: 10036--10082 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
10026 ACTTAAGGGA
* *
10036 TTAAATAGCAAAAAAACATAAAT
1 TTAAATACCAAAAAAACACAAAT
*
10059 TTAAAGTACCAAAATAACACAAAT
1 TTAAA-TACCAAAAAAACACAAAT
10083 AGAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (23 bp):
TTAAATACCAAAAAAACACAAAT
Found at i:12636 original size:30 final size:31
Alignment explanation
Indices: 12569--12655 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
12559 AGTCGAGGGT
* * *
12569 TACCTATGTCTTTCGAGACATATGGACAGTT
1 TACCTATGTCCTTCGGGACATATGGACAGTG
*
12600 TACCTATGTCCTTCGGGACATATGGGCAG-G
1 TACCTATGTCCTTCGGGACATATGGACAGTG
* *
12630 TACCTATGTTCTTCGGTACATATGGA
1 TACCTATGTCCTTCGGGACATATGGA
12656 TAGGTCCTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 23 0.47
31 26 0.53
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (31 bp):
TACCTATGTCCTTCGGGACATATGGACAGTG
Found at i:14025 original size:3 final size:3
Alignment explanation
Indices: 14002--14055 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
13992 CAAACAAAAT
*
14002 TAA TAA TAT TAA T-A TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14048 TAA TAA TA
1 TAA TAA TA
14056 TATATATTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:15065 original size:13 final size:14
Alignment explanation
Indices: 15047--15109 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
15037 CTATACTTAC
*
15047 CCCTAACTTA-AAA
1 CCCTAAATTATAAA
15060 CCCTAAATTATAAA
1 CCCTAAATTATAAA
***
15074 CCCTAAACCCTAAA
1 CCCTAAATTATAAA
* *
15088 CCTATAAATCATAAA
1 CC-CTAAATTATAAA
15103 CCCTAAA
1 CCCTAAA
15110 CCCAAAACTC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
13 9 0.22
14 20 0.50
15 11 0.28
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:15074 original size:14 final size:14
Alignment explanation
Indices: 15057--15109 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
15047 CCCTAACTTA
*
15057 AAACCCTAAATTAT
1 AAACCCTAAATCAT
* *
15071 AAACCCTAAACCCT
1 AAACCCTAAATCAT
*
15085 AAACCTATAAATCAT
1 AAACC-CTAAATCAT
15100 AAACCCTAAA
1 AAACCCTAAA
15110 CCCAAAACTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:15080 original size:7 final size:7
Alignment explanation
Indices: 15070--15122 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
15060 CCCTAAATTA
15070 TAAACCC
1 TAAACCC
15077 TAAACCC
1 TAAACCC
*
15084 TAAACCTA
1 TAAACC-C
* *
15092 TAAATCA
1 TAAACCC
15099 TAAACCC
1 TAAACCC
15106 TAAACCC
1 TAAACCC
* *
15113 AAAACTC
1 TAAACCC
15120 TAA
1 TAA
15123 CAGGGGCAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 33 0.87
8 5 0.13
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:15093 original size:22 final size:22
Alignment explanation
Indices: 15057--15111 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
15047 CCCTAACTTA
* *
15057 AAACCCTAAA-TTATAAACCCT
1 AAACCCTAAACCTATAAACCAT
*
15078 AAACCCTAAACCTATAAATCAT
1 AAACCCTAAACCTATAAACCAT
15100 AAACCCTAAACC
1 AAACCCTAAACC
15112 CAAAACTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACCCTAAACCTATAAACCAT
Found at i:16153 original size:27 final size:27
Alignment explanation
Indices: 16118--16174 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
16108 GACTTGGGCA
*
16118 AAGACGAACGACGTCGGAGTTGACAAG
1 AAGACGAACGACGTCAGAGTTGACAAG
* * *
16145 AAGATGAACGGCGTCAGAGTTGACGAG
1 AAGACGAACGACGTCAGAGTTGACAAG
16172 AAG
1 AAG
16175 GCAAATGGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.35, T:0.12
Consensus pattern (27 bp):
AAGACGAACGACGTCAGAGTTGACAAG
Found at i:16312 original size:20 final size:19
Alignment explanation
Indices: 16273--16312 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16263 TTAAGCCACC
* *
16273 ATTAATTTAAATTATCATT
1 ATTAAATTAAATTATAATT
16292 ATTAAATTAAATTAATAATT
1 ATTAAATTAAATT-ATAATT
16312 A
1 A
16313 AAATTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAAATTAAATTATAATT
Found at i:18705 original size:18 final size:18
Alignment explanation
Indices: 18682--18719 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
18672 GCCATTGTCA
18682 TCGCCAGCCAAAATGGGT
1 TCGCCAGCCAAAATGGGT
18700 TCGCCAGCCAAAATGGGT
1 TCGCCAGCCAAAATGGGT
18718 TC
1 TC
18720 CTCGGTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TCGCCAGCCAAAATGGGT
Found at i:30323 original size:36 final size:36
Alignment explanation
Indices: 30158--30356 Score: 238
Period size: 36 Copynumber: 5.5 Consensus size: 36
30148 GATTGGAGAA
*
30158 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
*
30194 AAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
30230 AATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * * *
30266 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * * *
30302 AAAGCATCTTAAGTCTTCACC-AAAAAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAA-TAGTGAAGC
* *
30338 AGATCCATTTTAAGCCTTC
1 A-AACCATCTTAAGCCTTC
30357 TCAGAAGAGT
Statistics
Matches: 141, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
35 2 0.01
36 126 0.89
37 13 0.09
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (36 bp):
AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:30812 original size:51 final size:52
Alignment explanation
Indices: 30728--31420 Score: 517
Period size: 51 Copynumber: 12.9 Consensus size: 52
30718 TGAAGCAAAT
* * * *
30728 GAAGATTATTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT-
1 GAAGA-TATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTGTA
* *
30780 GAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTGT-
1 GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTGTA
* *
30831 GAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTGT-
1 GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTGTA
* * * * *
30882 GAAGATATGCGAGTTCTATACTCCTTGAAGAAAGAGAGAGCGAGCCCGTTTTCA
1 GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCG-TGT-A
* * * * *
30936 GAAGATCATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGTGAGCCCATTTGTA
1 GAAGAT-ATTCGAGTTCTATAC-TCCTTAAAGAAAGAGGGAGCGAACCC--GTGTA
* * * *
30992 AAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGAAGCGAACCCGTTTTTA
1 GAAGA-TATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCG--TGTA
* * * * *
31047 GAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCCCGTTTTCA
1 GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCG-TGT-A
* * *
31101 GAAGATCATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCA
1 GAAGAT-ATTCGAGTTCTATAC-TCCTTAAAGAAAGAGGGAGCGAACCCGTGT--A
* * ** *
31157 AAAGATTATTCGAGTTCTATACTCCTTAAAGAAA-A---AGGGAATTCGTTTATA
1 GAAGA-TATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCG--TGTA
* * * *
31208 GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAA
1 GAAGA-TATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGT--GTA
* * * * * * * *
31263 GAAGATGTTCGAGTTCCATAATCCCTAGAGAAATAGGGAG-TAGACCCGATTGTT
1 GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGA-ACCCG--TGTA
* * * * * *
31317 GAAGTTTGTTCGAG-TCTTATACTCTCTGAAAG-AATAGGGAGC-AGACACGATTGTT
1 GAAG-ATATTCGAGTTC-TATACTC-CTTAAAGAAAGAGGGAGCGA-ACCCG--TGTA
* * *
31372 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCCG
1 GAAGA-TATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCG
31421 ATTATTGAAG
Statistics
Matches: 529, Mismatches: 78, Indels: 65
0.79 0.12 0.10
Matches are distributed among these distances:
51 173 0.33
52 8 0.02
53 8 0.02
54 99 0.19
55 146 0.28
56 91 0.17
57 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (52 bp):
GAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTGTA
Found at i:31052 original size:55 final size:55
Alignment explanation
Indices: 30728--31450 Score: 598
Period size: 55 Copynumber: 13.4 Consensus size: 55
30718 TGAAGCAAAT
* * * *
30728 GAAGATTATTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGT-
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * * *
30780 GAAGA-TATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCG--TGT-
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * * *
30831 GAAGA-TATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCG--TGT-
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * * * * *
30882 GAAGA-TATGCGAGTTCTATACTCCTTGAAGAAAGAGAGAGCGAGCCCGTTTTCA
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * * * * * *
30936 GAAGATCATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGTGAGCCCATTTGTA
1 GAAGATTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTTTA
* *
30992 AAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGAAGCGAACCCGTTTTTA
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * *
31047 GAAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCCCGTTTTCA
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * * **
31101 GAAGATCATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCA
1 GAAGATTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTTTA
* * * ** *
31157 AAAGATTATTCGAGTTCTATACTCCTTAAAGAAA-A---AGGGAATTCGTTTATA
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * ****
31208 GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAA
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
* * * * * * *
31263 GAAGA-TGTTCGAGTTCCATAATCCCTAGAGAAATAGGGAG-TAGACCCGATTGTT-
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGA-ACCCG-TTTTTA
* * * * * *
31317 GAAGTTTGTTCGAG-TCTTATACTCTCTGAAAG-AATAGGGAGC-AGACACGATTGTT-
1 GAAGATTATTCGAGTTC-TATACTCCCT-AAAGAAAGAGGGAGCGA-ACCCG-TTTTTA
* * *
31372 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCCGATTATT-
1 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTTTTA
*
31427 GAAGATTGTTCGAG-TCTTATACTC
1 GAAGATTATTCGAGTTC-TATACTC
31451 TTTGAAGAAA
Statistics
Matches: 561, Mismatches: 89, Indels: 39
0.81 0.13 0.06
Matches are distributed among these distances:
51 176 0.31
52 6 0.01
53 2 0.00
54 101 0.18
55 179 0.32
56 97 0.17
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (55 bp):
GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTTA
Found at i:31331 original size:216 final size:216
Alignment explanation
Indices: 30781--31412 Score: 567
Period size: 216 Copynumber: 2.9 Consensus size: 216
30771 AACCCGTGTG
* * * * *
30781 AAGA-TATGCGAGTTCTATACTCCTTAAAGAAAGAAGG-AGCGAACCCGT--G-TGAAGATATGC
1 AAGATTATTCGAGTTCTATACTCCCTAAAGAAAG-AGGAAGCGAACCCGTAAGAAGAAGATGTTC
* * * * * * * * *
30841 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCG-TGT-GAAGAT-ATGCGAGTTCTATAC
65 GAGTTCCATAATCCCTGAAGAAAGAGGGAGAGAGCCCGTTTTAGAAGATCATTCGAGTTCTATAC
* * * * * * *
30903 TCCTTG-AAGAAAGAGAGAGCGAGCCCGTTTTCAGAAGATCATTCAAGTTCTATACTTCCTGAAA
130 TCC-TGAAAGAAAGAGGGAGCAAACCCGTTTCCAGAAGATTATTCGAGTTCTATAC-TCCTTAAA
*
30967 GAAAGAGGGAGTGAGCCCATTTGTAA
193 GAAAGAGGGA--GAGCCCATTTATAA
**** *
30993 AAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGAAGCGAACCCGTTTTTAGAAGATTTTCG
1 AAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGAAGCGAACCCGTAAGAAGAAGATGTTCG
* * *
31058 AGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCCCGTTTTCAGAAGATCATTCGAGTTCTATAC
66 AGTTCCATAATCCCTGAAGAAAGAGGGAGAGAGCCCGTTTT-AGAAGATCATTCGAGTTCTATAC
*
31123 TTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATTCGAGTTCTATACTCCTTAAAG
130 -TCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAGAAGATTATTCGAGTTCTATACTCCTTAAAG
* ** * *
31188 AAAAAGGGA-A-TTCGTTTATAG
194 AAAGAGGGAGAGCCCATTTATAA
* * *
31209 AAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTTCG
1 AAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGAAGCGAACCCGTAAGAAGAAGATGTTCG
* * **
31274 AGTTCCATAATCCCT-AGAGAAATAGGGAGTAGA-CCCGATTGTT-GAAGTTTGTTCGAG-TCTT
66 AGTTCCATAATCCCTGA-AGAAAGAGGGAG-AGAGCCCG-TT-TTAGAAGATCATTCGAGTTC-T
* * * * *** *
31335 ATACTCTCTGAAAG-AATAGGGAGCAGACACGATTGTTGAAGATTATTCGAGTTCTATACTCCCT
126 ATACTC-CTGAAAGAAAGAGGGAGCAAACCCGTTTCCAGAAGATTATTCGAGTTCTATACTCCTT
*
31399 GAAGAAAGAGGGAG
190 AAAGAAAGAGGGAG
31413 CGGACCCGAT
Statistics
Matches: 350, Mismatches: 52, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
212 7 0.02
213 38 0.11
215 57 0.16
216 156 0.45
217 7 0.02
218 2 0.01
219 6 0.02
220 32 0.09
221 45 0.13
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (216 bp):
AAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGAAGCGAACCCGTAAGAAGAAGATGTTCG
AGTTCCATAATCCCTGAAGAAAGAGGGAGAGAGCCCGTTTTAGAAGATCATTCGAGTTCTATACT
CCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAGAAGATTATTCGAGTTCTATACTCCTTAAAGAA
AGAGGGAGAGCCCATTTATAA
Found at i:31419 original size:110 final size:110
Alignment explanation
Indices: 30936--31512 Score: 329
Period size: 110 Copynumber: 5.3 Consensus size: 110
30926 CCCGTTTTCA
* * * * *
30936 GAAGATCATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAG-TGAGCCC-ATT-TGTAAAAGAT
1 GAAGATTATTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCAGA-CCCGATTAT-T-GAAGAT
* * * * * * *
30998 TATTCGAGT-TCTATACTCCCTAAAGAAA-GAGGAAGCGAACCCG-TTTTT
62 TGTTCGAGTCT-TATACTCTCTGAAGAAATAAGGAA-CAAACACGATTGTT
31046 AGAAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGC-GAGCCCG-TT-TTCAGAAGAT
1 -GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGA-CCCGATTATT--GAAGAT
** * * * * * ***
31107 CATTCGAGT-TCTATACT-TCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCA
62 TGTTCGAGTCT-TATACTCT-CTG-AAGAAATAAGGAACAAACACGATTGTT
* * * * ** * * *
31157 AAAGATTATTCGAGTTCTATACTCCTTAAAGAAA-AAGG-G-A-ATTCGTTTATAGAAGATTATT
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTATTGAAGATTGTT
* * * * * * **
31218 CGAGT-TCTATACTCCCT-AGAGAAAGAGGGAGCGAAC-CTG-TAAGAA
66 CGAGTCT-TATACTCTCTGA-AGAAATAAGGAACAAACAC-GAT-TGTT
* * * * * * *
31263 GAAGA-TGTTCGAGTTCCATAATCCCT-AGAGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGT
1 GAAGATTATTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCAGACCCGATTATTGAAGATTGT
* * *
31326 TCGAGTCTTATACTCTCTGAA-AGAATAGGGAGCAGACACGATTGTT
65 TCGAGTCTTATACTCTCTGAAGA-AATAAGGAACAAACACGATTGTT
*
31372 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCCGATTATTGAAGATTGTT
1 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTATTGAAGATTGTT
*
31437 CGAGTCTTATACTCTTTGAAGAAATAAGGAACAAACACGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAAGGAACAAACACGATTGTT
* *
31482 GAAGATTGTTCGAG-TCTTATACTCTCTGAAG
1 GAAGATTATTCGAGTTC-TATACTCCCTGAAG
31513 CACAGAGAAC
Statistics
Matches: 376, Mismatches: 61, Indels: 59
0.76 0.12 0.12
Matches are distributed among these distances:
104 1 0.00
105 25 0.07
106 25 0.07
107 27 0.07
108 6 0.02
109 97 0.26
110 158 0.42
111 37 0.10
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (110 bp):
GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACCCGATTATTGAAGATTGTT
CGAGTCTTATACTCTCTGAAGAAATAAGGAACAAACACGATTGTT
Found at i:31457 original size:55 final size:55
Alignment explanation
Indices: 31291--31512 Score: 295
Period size: 55 Copynumber: 4.0 Consensus size: 55
31281 TAATCCCTAG
* * *
31291 AGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* *
31346 A-AGAATAGGGAGCAGACACGATTGTTGAAGATTATTCGAGT-TCTATACTCCCTGA
1 AGA-AATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGA
* * * * *
31401 AGAAAGAGGGAGCGGACCCGATTATTGAAGATTGTTCGAGTCTTATACTCTTTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
31456 AGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
31511 AG
1 AG
31513 CACAGAGAAC
Statistics
Matches: 143, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
54 2 0.01
55 139 0.97
56 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
Found at i:31499 original size:165 final size:164
Alignment explanation
Indices: 31208--31511 Score: 400
Period size: 165 Copynumber: 1.8 Consensus size: 164
31198 TTCGTTTATA
*
31208 GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTTC
1 GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
* ** * * *
31273 GAGTTCCATAATCCCTAGAGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATA
66 GAGTTCCATAATCCCTAGAGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTCTTATA
31338 CTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
131 CTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
* * **
31372 GAAGATTATTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGGACCCGATTA-TTGAAGATTG
1 GAAGATTATTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCG-TAAGAAGAAGA-TG
* * * *
31435 TTCGAG-TCTTATACT-CTTTGAAGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTC
63 TTCGAGTTC-CATAATCCCTAG-AGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTC
31498 TTATACTCTCTGAA
126 TTATACTCTCTGAA
31512 GCACAGAGAA
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
163 1 0.01
164 55 0.46
165 64 0.53
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (164 bp):
GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
GAGTTCCATAATCCCTAGAGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTCTTATA
CTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
Found at i:31537 original size:164 final size:164
Alignment explanation
Indices: 31208--31551 Score: 392
Period size: 164 Copynumber: 2.1 Consensus size: 164
31198 TTCGTTTATA
*
31208 GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATGTTC
1 GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
* ** * * *
31273 GAGTTCCATAATCCCTAGAGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATA
66 GAGTTCCATAATCCCTAGAGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTCTTATA
* * *
31338 CTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
131 CTCTCTGAAAGAACAGAGAACAGACACGATTGTT
* * **
31372 GAAGATTATTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGGACCCGATTA-TTGAAGATTG
1 GAAGATTATTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCG-TAAGAAGAAGA-TG
* * * *
31435 TTCGAG-TCTTATACT-CTTTGAAGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTC
63 TTCGAGTTC-CATAATCCCTAG-AGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTC
* * * *
31498 TTATACTCTCTG-AAGCACAGAGAACAGAGATGTTTGTT
126 TTATACTCTCTGAAAGAACAGAGAACAGACACGATTGTT
* *
31536 GAAGATTGTGCGAGTT
1 GAAGATTATTCGAGTT
31552 TCATGCATCC
Statistics
Matches: 151, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
163 1 0.01
164 88 0.58
165 62 0.41
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (164 bp):
GAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
GAGTTCCATAATCCCTAGAGAAATAAGGAACAAACACGATTGTTGAAGATTGTTCGAGTCTTATA
CTCTCTGAAAGAACAGAGAACAGACACGATTGTT
Found at i:41468 original size:75 final size:75
Alignment explanation
Indices: 41382--41714 Score: 429
Period size: 75 Copynumber: 4.4 Consensus size: 75
41372 TTTAATCGAT
* * * * * *
41382 TAAAATAAAATAGGTGTTACCTATTATGTTAAACTATCTA-TCGATTTGTTTGAAGGTTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACT-GATTTGTTTAAAGATTACTAAT
41446 AATGTAAACGG
65 AATGTAAACGG
* * * *
41457 TAAAATAAAATAGGAGCTACATATTACGTTAAAATACCTACTGGTTTGTTTAAAGATTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGATTTGTTTAAAGATTACTAATA
*
41522 ATGTAAAAGG
66 ATGTAAACGG
* * * *
41532 TAGAATAAAATAGGCACTACCTATTACGTTTAACTACCTA-TCAGTTTGTTTAAAGATTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGA-TTTGTTTAAAGATTACTAAT
41596 AATGTAAACGG
65 AATGTAAACGG
** * *
41607 TAAAATAAAATAGGCATTACCTATTACGTTAAACTACCTACTGGTGTGTTTAAATG-TTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGATTTGTTTAAA-GATTACTAAT
41671 AATGTAAACGG
65 AATGTAAACGG
* *
41682 TAAAATAAAATAGGCGCTACATATTATGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA
41715 TAGGTGCTAC
Statistics
Matches: 225, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
74 1 0.00
75 221 0.98
76 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGATTTGTTTAAAGATTACTAATA
ATGTAAACGG
Found at i:41657 original size:150 final size:150
Alignment explanation
Indices: 41382--41714 Score: 474
Period size: 150 Copynumber: 2.2 Consensus size: 150
41372 TTTAATCGAT
* * * * * *
41382 TAAAATAAAATAGGTGTTACCTATTATGTTAAACTATCTATCGATTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTATCGATTTGTTTAAAGATTACTAATA
*
41447 ATGTAAACGGTAAAATAAAATAGGAGCTACATATTACGTTAAAATACCTACTGGTTTGTTTAAA-
66 ATGTAAACGGTAAAATAAAATAGGAGCTACATATTACGTTAAAATACCTACTGGTGTGTTTAAAT
41511 GATTACTAATAATGTAAAAGG
131 G-TTACTAATAATGTAAAAGG
* * *
41532 TAGAATAAAATAGGCACTACCTATTACGTTTAACTACCTATC-AGTTTGTTTAAAGATTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTATCGA-TTTGTTTAAAGATTACTAAT
* * *
41596 AATGTAAACGGTAAAATAAAATAGGCA-TTACCTATTACGTTAAACTACCTACTGGTGTGTTTAA
65 AATGTAAACGGTAAAATAAAATAGG-AGCTACATATTACGTTAAAATACCTACTGGTGTGTTTAA
*
41660 ATGTTACTAATAATGTAAACGG
129 ATGTTACTAATAATGTAAAAGG
* *
41682 TAAAATAAAATAGGCGCTACATATTATGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA
41715 TAGGTGCTAC
Statistics
Matches: 161, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
149 1 0.01
150 158 0.98
151 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (150 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTATCGATTTGTTTAAAGATTACTAATA
ATGTAAACGGTAAAATAAAATAGGAGCTACATATTACGTTAAAATACCTACTGGTGTGTTTAAAT
GTTACTAATAATGTAAAAGG
Found at i:41718 original size:23 final size:23
Alignment explanation
Indices: 41689--41760 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
41679 CGGTAAAATA
*
41689 AAATAGGCGCTACATATTATGTT
1 AAATAGGTGCTACATATTATGTT
*
41712 AAATAGGTGCTACATATTACGTT
1 AAATAGGTGCTACATATTATGTT
* *
41735 AAATAAGTGCTACATGTTATGTT
1 AAATAGGTGCTACATATTATGTT
41758 AAA
1 AAA
41761 CTAACTACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (23 bp):
AAATAGGTGCTACATATTATGTT
Found at i:41836 original size:23 final size:23
Alignment explanation
Indices: 41810--41860 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
41800 CGGCAAAATA
41810 AAATAGGCGCTACCTATTACGTT
1 AAATAGGCGCTACCTATTACGTT
*
41833 AAATAGGTGCTACCTATTACGTT
1 AAATAGGCGCTACCTATTACGTT
41856 AAATA
1 AAATA
41861 AGTGATACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTACGTT
Found at i:41873 original size:23 final size:23
Alignment explanation
Indices: 41820--41881 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
41810 AAATAGGCGC
* *
41820 TACCTATTACGTTAAATAGGTGC
1 TACCTATTACGTTAAATAAGTGA
41843 TACCTATTACGTTAAATAAGTGA
1 TACCTATTACGTTAAATAAGTGA
* *
41866 TACTTATTACATTAAA
1 TACCTATTACGTTAAA
41882 CTAGCTACCG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (23 bp):
TACCTATTACGTTAAATAAGTGA
Found at i:41929 original size:121 final size:121
Alignment explanation
Indices: 41628--41930 Score: 444
Period size: 121 Copynumber: 2.5 Consensus size: 121
41618 AGGCATTACC
* * * * *
41628 TATTACGTTAAACTACCTACTGGTGTGTTTAAATGTTACTAATAATGTAAACGGTAAAATAAAAT
1 TATTACGTTAAACTAACTACCGGTTTGTTTAAAAGTTAATAATAATGTAAACGGTAAAATAAAAT
* *
41693 AGGCGCTACATATTATGTTAAATAGGTGCTACATATTACGTTAAATAAGTGCTACA
66 AGGCGCTACATATTACGTTAAATAGGTGCTACATATTACGTTAAATAAGTGATACA
* * * * *
41749 TGTTATGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATAATAATGCAAACGGCAAAATAAAAT
1 TATTACGTTAAACTAACTACCGGTTTGTTTAAAAGTTAATAATAATGTAAACGGTAAAATAAAAT
* * *
41814 AGGCGCTACCTATTACGTTAAATAGGTGCTACCTATTACGTTAAATAAGTGATACT
66 AGGCGCTACATATTACGTTAAATAGGTGCTACATATTACGTTAAATAAGTGATACA
* * *
41870 TATTACATTAAACTAGCTACCGGTTTGTTTAAAAGTTAATAATAATGTAAACGATAAAATA
1 TATTACGTTAAACTAACTACCGGTTTGTTTAAAAGTTAATAATAATGTAAACGGTAAAATA
41931 TATAATCGTT
Statistics
Matches: 160, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
121 160 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (121 bp):
TATTACGTTAAACTAACTACCGGTTTGTTTAAAAGTTAATAATAATGTAAACGGTAAAATAAAAT
AGGCGCTACATATTACGTTAAATAGGTGCTACATATTACGTTAAATAAGTGATACA
Found at i:41943 original size:42 final size:42
Alignment explanation
Indices: 41896--41976 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
41886 CTACCGGTTT
*
41896 GTTTAAAAGTTAATAATAATGTAAACGATAAAATATATAATC
1 GTTTAAAAGTCAATAATAATGTAAACGATAAAATATATAATC
41938 GTTTAAAAGTCAATAATAATGTAAACGATAAAATATATA
1 GTTTAAAAGTCAATAATAATGTAAACGATAAAATATATA
41977 CAACTTAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (42 bp):
GTTTAAAAGTCAATAATAATGTAAACGATAAAATATATAATC
Found at i:42665 original size:107 final size:107
Alignment explanation
Indices: 42535--42774 Score: 349
Period size: 107 Copynumber: 2.2 Consensus size: 107
42525 TATTGGACGC
* *
42535 AACCTTATTTTGTTGTCGTCGGATTTCGAATTACCCATCA-TCTAAACTTTGGTAACATTTTAGG
1 AACC-TATTTTGTTATCGTCGGATTTCGAA-GACCCATCAGTCTAAACTTTGGTAACATTTTAGG
42599 CGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATT
64 CGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATT
* * * * * *
42643 AACCTATTTTGTTATCGCCGGATTTCTAAGGCCCATCAGTTTAAACTTTGTTAATATTTTAGGCG
1 AACCTATTTTGTTATCGTCGGATTTCGAAGACCCATCAGTCTAAACTTTGGTAACATTTTAGGCG
* *
42708 CTACCTAATATGTTGATAATATTGATAACAAATTAAGTAATT
66 CTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATT
*
42750 AACCTATTTT-TTATCGTCAGATTTC
1 AACCTATTTTGTTATCGTCGGATTTC
42775 TAAGGTCTCA
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
106 20 0.17
107 95 0.80
108 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (107 bp):
AACCTATTTTGTTATCGTCGGATTTCGAAGACCCATCAGTCTAAACTTTGGTAACATTTTAGGCG
CTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATT
Found at i:44711 original size:18 final size:18
Alignment explanation
Indices: 44688--44729 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
44678 AAGAAGAAAT
*
44688 TGATAATCCA-ATTGATGA
1 TGATAAT-CATATAGATGA
44706 TGATAATCATATAGATGA
1 TGATAATCATATAGATGA
44724 TGATAA
1 TGATAA
44730 GATTGGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (18 bp):
TGATAATCATATAGATGA
Found at i:50992 original size:18 final size:18
Alignment explanation
Indices: 50971--51025 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
50961 AAAAGTTTTC
*
50971 TCTTTTTACTTTTCAAGT
1 TCTTTTCACTTTTCAAGT
50989 TCTTTTCACTTTTCAAGT
1 TCTTTTCACTTTTCAAGT
*
51007 TCTTTTCATTTTTCAAGT
1 TCTTTTCACTTTTCAAGT
51025 T
1 T
51026 TTGGTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.60
Consensus pattern (18 bp):
TCTTTTCACTTTTCAAGT
Found at i:53096 original size:11 final size:11
Alignment explanation
Indices: 53080--53112 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
53070 CTAATTATAC
53080 AAAAAATATTT
1 AAAAAATATTT
53091 AAAAAATATTT
1 AAAAAATATTT
53102 AAAAAATATTT
1 AAAAAATATTT
53113 TAATTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAAAATATTT
Found at i:53393 original size:2 final size:2
Alignment explanation
Indices: 53386--53416 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
53376 ATTATTAATC
*
53386 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53417 GTATTTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56727 original size:62 final size:61
Alignment explanation
Indices: 56628--56750 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 61
56618 GGCGACCGAT
* * *
56628 CAAATAATTCAAATGTTGAGTGCTACAACTGTGGCAAGCATGGGCACTATGCAAAAGAGTG
1 CAAATAAATCAAATGTCGAGTGCTACAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTG
* * *
56689 CAAATCAAATCAAATGTCGAGTGCTATAATTGCGGCAAGCATGGGCACTATGCAAAGGAGTG
1 CAAAT-AAATCAAATGTCGAGTGCTACAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTG
56751 TTATTCCGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
61 5 0.09
62 50 0.91
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (61 bp):
CAAATAAATCAAATGTCGAGTGCTACAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTG
Found at i:70471 original size:42 final size:41
Alignment explanation
Indices: 70419--70506 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
70409 TTCCAAAATC
* * *
70419 AATAATTCCTTCGGACCATCAATAAGTCTTTCGAGCATGAT
1 AATAAATCCTTCGGACAATCAATAAGTCTTTCGAGCAAGAT
** **
70460 GAATAAATCCTTCGGGTAATTTATAAGTCTTTCGAGCAAGAT
1 -AATAAATCCTTCGGACAATCAATAAGTCTTTCGAGCAAGAT
70502 AATAA
1 AATAA
70507 GTCATCGGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 5 0.13
42 34 0.87
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (41 bp):
AATAAATCCTTCGGACAATCAATAAGTCTTTCGAGCAAGAT
Found at i:70526 original size:41 final size:42
Alignment explanation
Indices: 70435--70527 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
70425 TCCTTCGGAC
* * *
70435 CATCAATAAGTCTTTCGAGCATGATGAATAAATCCTTCGGGT
1 CATCTATAAGTCTTTCGAGCAAGATGAATAAATCCATCGGGT
* * *
70477 AATTTATAAGTCTTTCGAGCAAGAT-AATAAGT-CATCGGGGT
1 CATCTATAAGTCTTTCGAGCAAGATGAATAAATCCATC-GGGT
70518 CATCTATAAG
1 CATCTATAAG
70528 AACTTCAGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
40 3 0.07
41 18 0.43
42 21 0.50
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (42 bp):
CATCTATAAGTCTTTCGAGCAAGATGAATAAATCCATCGGGT
Found at i:71108 original size:88 final size:87
Alignment explanation
Indices: 70914--71153 Score: 248
Period size: 88 Copynumber: 2.7 Consensus size: 87
70904 AGATCAGTTA
* * * *
70914 CATCACAGAATGAGGTAGATCAACATTCTCTTTTACTTGATTCTATCACATAAGGAGTTGGATCA
1 CATCACAGAATGAGGTGGATCAACATTCTCTTTTACTAGATTCCATCACACAAGGAGTTGGATCA
* *
70979 ACATCACTTTTTTGTTTAATAC
66 ACATCACCTTTTTGTTCAATAC
** * * * * * *
71001 CATTGCAAAAGGAGGTGGATCAATATTCTATTTTTTCTAGATTCCATCACACAAGGAGTTTGATC
1 CATCACAGAATGAGGTGGATCAACATTCT-CTTTTACTAGATTCCATCACACAAGGAGTTGGATC
* **
71066 GACATCACCTTTTTGTTCAATTT
65 AACATCACCTTTTTGTTCAATAC
* * * * * *
71089 CATCACAGAATGAGATGGATCAACGTTCCCTTTTGCTAGATTCCATCATAGAAGGA-TATGGATC
1 CATCACAGAATGAGGTGGATCAACATTCTCTTTTACTAGATTCCATCACACAAGGAGT-TGGATC
71153 A
65 A
71154 GCACGATCAA
Statistics
Matches: 120, Mismatches: 31, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
86 1 0.01
87 51 0.43
88 68 0.57
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (87 bp):
CATCACAGAATGAGGTGGATCAACATTCTCTTTTACTAGATTCCATCACACAAGGAGTTGGATCA
ACATCACCTTTTTGTTCAATAC
Found at i:72873 original size:20 final size:20
Alignment explanation
Indices: 72848--72982 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
72838 AATTGGGAAA
72848 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
72868 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
72888 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
72909 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
72929 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
72949 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
72969 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
72983 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:72910 original size:61 final size:61
Alignment explanation
Indices: 72845--72982 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
72835 GTGAATTGGG
* * *
72845 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
72906 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
72967 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
72983 TTTCAAAGCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:73488 original size:20 final size:20
Alignment explanation
Indices: 73434--73492 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
73424 GCGATTCTCT
**
73434 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
73454 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
73474 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
73493 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:74833 original size:18 final size:18
Alignment explanation
Indices: 74812--74856 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
74802 TCCACTTCGG
*
74812 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
74830 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
74848 GAGCCATCA
1 GAGCCATCA
74857 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:75391 original size:19 final size:20
Alignment explanation
Indices: 75337--75403 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
75327 TAGTTTACTT
* *
75337 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
75357 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
75377 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
75396 TCGCAACG
1 TCGCAACG
75404 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:75439 original size:32 final size:33
Alignment explanation
Indices: 75376--75440 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
75366 GGAAATGGCT
75376 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
75409 ATCGCAATGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
75441 TGAAAATCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:75449 original size:19 final size:19
Alignment explanation
Indices: 75376--75457 Score: 97
Period size: 19 Copynumber: 4.6 Consensus size: 19
75366 GGAAATGGCT
75376 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
75395 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
75409 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
75427 ATCGCAATGAC-AAATGAAA
1 ATCGCAATG-CGAAATGAAA
75446 ATCGCAATGCGA
1 ATCGCAATGCGA
75458 TCTGTGTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.34
19 20 0.38
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:75518 original size:14 final size:14
Alignment explanation
Indices: 75469--75524 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
75459 CTGTGTTTCG
75469 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
75483 CGTT--GATTTCATTT
1 CGTTGCGATTT--TGT
75497 CGTATTGCGATTTTGT
1 CG--TTGCGATTTTGT
75513 CGTTGCGATTTT
1 CGTTGCGATTTT
75525 TATTTCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
12 5 0.15
14 18 0.53
16 6 0.18
18 5 0.15
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:75537 original size:33 final size:30
Alignment explanation
Indices: 75471--75540 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
75461 GTGTTTCGCG
**
75471 TTGCGATTTTGTCGTTGATTTCATTTCGTA
1 TTGCGATTTTGTCGTTGATTTCATTTCACA
*
75501 TTGCGATTTTGTCGTTGCGATTTTTATTTCACA
1 TTGCGATTTTGTCGTT--GA-TTTCATTTCACA
75534 TTGCGAT
1 TTGCGAT
75541 AGCCATTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 16 0.47
32 2 0.06
33 16 0.47
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.51
Consensus pattern (30 bp):
TTGCGATTTTGTCGTTGATTTCATTTCACA
Found at i:75576 original size:20 final size:20
Alignment explanation
Indices: 75534--75580 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
75524 TTATTTCACA
*
75534 TTGCGATAGCCATTTCTGTG
1 TTGCGATAGCCATTTCTGCG
*
75554 TTGCGATAGTCATTT-TCGCG
1 TTGCGATAGCCATTTCT-GCG
75574 TTGCGAT
1 TTGCGAT
75581 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.40
Consensus pattern (20 bp):
TTGCGATAGCCATTTCTGCG
Found at i:77451 original size:14 final size:14
Alignment explanation
Indices: 77432--77467 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
77422 ATTGTTTAAT
77432 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
77446 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
77460 TGATTTGT
1 TGATTTGT
77468 TATATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:77575 original size:20 final size:20
Alignment explanation
Indices: 77550--77588 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
77540 ATGTTGAAGG
77550 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
77570 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
77589 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:77618 original size:19 final size:19
Alignment explanation
Indices: 77594--77658 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
77584 GCAACGAGAG
77594 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
77613 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
77632 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
77646 AATCGCAATGCGA
1 AATCGCAATGCGA
77659 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:77708 original size:19 final size:20
Alignment explanation
Indices: 77684--77733 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
77674 GCGATTTTGT
77684 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
77703 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
77723 CGTTGCGATAG
1 CGTTGCGATAG
77734 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:78739 original size:23 final size:23
Alignment explanation
Indices: 78713--78757 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
78703 AGTCAGTATT
* *
78713 CGAAATTTATCTTGGTCAATACC
1 CGAAATTGATATTGGTCAATACC
*
78736 CGAACTTGATATTGGTCAATAC
1 CGAAATTGATATTGGTCAATAC
78758 TCGGATTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (23 bp):
CGAAATTGATATTGGTCAATACC
Found at i:78961 original size:12 final size:12
Alignment explanation
Indices: 78944--78968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
78934 ATATAATCCT
78944 GAAGAAGAAAAA
1 GAAGAAGAAAAA
78956 GAAGAAGAAAAA
1 GAAGAAGAAAAA
78968 G
1 G
78969 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:81264 original size:19 final size:19
Alignment explanation
Indices: 81242--81372 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
81232 GGAAATTACT
81242 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
81261 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
81275 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
81294 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
81308 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
81327 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
81341 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
81360 ATCGCAACGCGAA
1 ATCGCAATGCGAA
81373 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:81284 original size:33 final size:33
Alignment explanation
Indices: 81242--81368 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
81232 GGAAATTACT
81242 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
81275 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
81307 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
81341 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
81369 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:81349 original size:66 final size:66
Alignment explanation
Indices: 81243--81375 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
81233 GAAATTACTA
*
81243 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
81308 T
66 T
*
81309 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
81374 T
66 T
81375 T
1 T
81376 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:81395 original size:14 final size:14
Alignment explanation
Indices: 81378--81423 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
81368 GCGAATTTAA
*
81378 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
81392 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
*
81406 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
81420 TTTC
1 TTTC
81424 ATTTCGCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.07, C:0.24, G:0.22, T:0.48
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:81564 original size:14 final size:14
Alignment explanation
Indices: 81545--81581 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
81535 CATCAATTAA
81545 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
81559 ACAAATCACCTTTT
1 ACAAATCAACTTTT
81573 ACAAATCAA
1 ACAAATCAA
81582 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:83088 original size:42 final size:42
Alignment explanation
Indices: 82975--83125 Score: 205
Period size: 42 Copynumber: 3.6 Consensus size: 42
82965 CTGAACGGTG
82975 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATA
1 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATA
* * * * * * *
83017 GGA-GGGACTCTTGAGGGATGACAGTGGCCTCTTGAACGGTG
1 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATA
83058 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATA
1 GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATA
* * *
83100 GGAGTGGACTCTTGAGGGATGATAGG
1 GGAGGGGACTCTCGAGGAATGATAGG
83126 CGAGTCGGGC
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 34 0.37
42 57 0.63
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATA
Found at i:83089 original size:83 final size:83
Alignment explanation
Indices: 82951--83121 Score: 326
Period size: 83 Copynumber: 2.1 Consensus size: 83
82941 ACCTTTCAAC
82951 GATGACAGTGGCCTCTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
1 GATGACAGTGGCCTCTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
83016 AGGAG-GGACTCTTGAGG
66 AGGAGTGGACTCTTGAGG
83033 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTC-TGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
83098 TAGGAGTGGACTCTTGAGG
65 TAGGAGTGGACTCTTGAGG
83117 GATGA
1 GATGA
83122 TAGGCGAGTC
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
82 15 0.17
83 55 0.63
84 17 0.20
ACGTcount: A:0.23, C:0.18, G:0.39, T:0.20
Consensus pattern (83 bp):
GATGACAGTGGCCTCTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
AGGAGTGGACTCTTGAGG
Found at i:83453 original size:92 final size:88
Alignment explanation
Indices: 83335--83515 Score: 283
Period size: 92 Copynumber: 2.0 Consensus size: 88
83325 ATTTCAAACT
* *
83335 TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGATACACAGTTTAGCAG
1 TTCAACCAAAGACAAAACAAAAACAAATACTAACTTCACAGTGTT--A-ATAAACAGTTTAGCAG
83400 AATTGGCAGCAACCGAATAAA-TTTAC
63 AATTGGCAGCAACCG-ATAAAGTTTAC
*
83426 TTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGTA
1 TTCAACC-AAAGACAAAACAAAAACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAA
83491 TTGGCAGCAACCGATAAAGTTTAC
65 TTGGCAGCAACCGATAAAGTTTAC
83515 T
1 T
83516 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
88 5 0.06
89 35 0.41
90 1 0.01
91 7 0.08
92 37 0.44
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (88 bp):
TTCAACCAAAGACAAAACAAAAACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGAAT
TGGCAGCAACCGATAAAGTTTAC
Done.