Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007727.1 Hibiscus syriacus cultivar Beakdansim tig00109978_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: 640948
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:901 original size:21 final size:21
Alignment explanation
Indices: 875--957 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
865 CAGATCCCCA
*
875 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
896 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * *
916 CAAAGGGGGAATCGGTTCCCTCAG-
1 ---GGGGGGAATCGATTCCC-CTGT
940 GGGGAGGAATCGATTCCC
1 GGGG-GGAATCGATTCCC
958 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 20 0.40
22 12 0.24
23 16 0.32
24 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:936 original size:22 final size:22
Alignment explanation
Indices: 897--958 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
887 TTCCCCTGTG
897 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTTCAAA
**
920 GGGGGAATCGGTTCCC-TCAGG
1 GGGGGAATCGGTTCCCTTCAAA
*
941 GGGAGGAATCGATTCCCT
1 GGG-GGAATCGGTTCCCT
959 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 15 0.44
23 13 0.38
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:7258 original size:113 final size:112
Alignment explanation
Indices: 7061--7876 Score: 971
Period size: 113 Copynumber: 7.2 Consensus size: 112
7051 TTCAACAAAT
* * ** * * ** *
7061 TTGTTCAACCTTTTGCTTAAATCCATCACCCGATGGATCAGCAGTGCCAGTTAGAGTTCATAATG
1 TTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATG
**
7126 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGT
65 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
** * *
7174 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATG
1 TTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATG
* *
7239 AGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAT
65 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* **
7287 TTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATTACCAG-GTCGAGTTCATAA
1 TTGTTCAACTTTT-GCTTGAATTCATCACTT-GATGGATCAGCATTTCCAGAG-AAAGTTCATAA
7350 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--G-AGAAC
63 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* **
7397 TTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATTGCCAG-GTCGAGTTCATAA
1 TTGTTCAACTTTT-GCTTGAATTCATCACTT-GATGGATCAGCATTTCCAGAG-AAAGTTCATAA
*
7460 TGAGAATAACTCATCTGAAGAA-G--GAAGAAGTTCATAATGAGAAGAAC
63 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
***
7507 TTGTTCAACTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATCAACATTGCCAG-AAGTTCA
1 TTGTTCAACTTTT-GCTTGAATTCATCACTT-GATGGATCAGCATTTCCA--G--AGAAAGTTCA
* * *
7570 TAATGAGAATAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAT
60 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
** * * *
7623 TTGTTCAACCTTTTGCTCAAATCCATTACTTGATGGATCAGCATTTTCAGAGGAAA-TTCATAAT
1 TTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGA-GAAAGTTCATAAT
7687 GAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAAC
64 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * * * *
7735 TTGTTCAAATTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAA-TTCATAAT
1 TTGTTC-AACTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGA-AAGTTCATAAT
7799 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
64 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
*
7848 TTGTTCAATCTTTTGCATG-ATTCTATCAC
1 TTGTTCAA-CTTTTGCTTGAATTC-ATCAC
7877 AGAAGGAGAT
Statistics
Matches: 632, Mismatches: 48, Indels: 46
0.87 0.07 0.06
Matches are distributed among these distances:
107 15 0.02
109 2 0.00
110 138 0.22
111 3 0.00
112 112 0.18
113 294 0.47
114 4 0.01
115 1 0.00
116 56 0.09
117 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (112 bp):
TTGTTCAACTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGA
GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
Found at i:7685 original size:336 final size:334
Alignment explanation
Indices: 7061--7863 Score: 1070
Period size: 336 Copynumber: 2.4 Consensus size: 334
7051 TTCAACAAAT
* * * * *
7061 TTGTTCAACCTTTTGCTTAAATCCATCACCCGATGGATCAGCAGTGCCAGTTAGAGTTCATAATG
1 TTGTTCAA-CTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATG
**
7126 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCT
65 AGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
* ***
7191 CAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
129 CAAATCCATCACTTGATGGATCAGCATCAACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
** *
7256 GAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTTGAATTCATCATTCGAT
194 GAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCAAATCCATCATTCGAT
*
7321 GGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
259 GGATCAGCATTACCAGG-CGAATTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTC
7386 ATAAT-G-AGAAC
322 ATAATAGAAGAAC
* *
7397 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATG
1 TTGTTCAACTTTT-GCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATG
*
7462 AGAATAACTCATCTGAAGAA-G-GAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCT
65 AGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCT
** * *
7524 TGAATTCATCA-TTCGATGGATCAGCATCAACATTGCCAG-AAGTTCATAATGAGAATAACTCAT
129 CAAATCCATCACTT-GATGGATCAGCATCAACA--G--AGAAAGTTCATAATGAGAAGAACTCAT
*
7587 CTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCAAATCCATTA
189 CTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGCTCAAATCCATCA
**
7651 CTT-GATGGATCAGCATTTTCAGAG-GAAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA
253 -TTCGATGGATCAGCATTACCAG-GCG-AATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA
7714 GAAGTTCATAATGAGAAGAAC
315 GAAGTTCATAAT-AGAAGAAC
* * * * * *
7735 TTGTTCAAATTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG-AGAATTCATAAT
1 TTGTTC-AACTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG-GTAGAGTTCATAAT
*
7799 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
64 GAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
7864 ATGATTCTAT
Statistics
Matches: 413, Mismatches: 34, Indels: 35
0.86 0.07 0.07
Matches are distributed among these distances:
332 7 0.02
333 55 0.13
335 28 0.07
336 193 0.47
337 11 0.03
338 72 0.17
339 8 0.02
341 34 0.08
342 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (334 bp):
TTGTTCAACTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGA
GAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCA
AATCCATCACTTGATGGATCAGCATCAACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
ATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCAAATCCATCATTCGATGG
ATCAGCATTACCAGGCGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TAGAAGAAC
Found at i:8218 original size:3 final size:3
Alignment explanation
Indices: 8210--8271 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
8200 TTTGTTTTAT
* *
8210 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8255 -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
8272 CAAACAGGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 8 0.15
3 45 0.85
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:8236 original size:22 final size:22
Alignment explanation
Indices: 8200--8267 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
8190 TTTTATTTCA
*
8200 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-ATATTATTATTAT
8223 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTAATATTATTATTAT
* *
8245 TATTATATT-ATATTATTATTAT
1 T-TTGTTTTAATATTATTATTAT
8267 T
1 T
8268 ATTACAAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
22 27 0.66
23 14 0.34
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTGTTTTAATATTATTATTAT
Found at i:8258 original size:19 final size:20
Alignment explanation
Indices: 8206--8269 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 20
8196 TTCATTTGTT
8206 TTATT-TATTATTATTATT-
1 TTATTATATTATTATTATTA
* * *
8224 TTGTTTTAATATTATTATTA
1 TTATTATATTATTATTATTA
8244 TTATTATATTA-TATTATTA
1 TTATTATATTATTATTATTA
8263 TTATTAT
1 TTATTAT
8270 TACAAACAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 4 0.10
19 27 0.69
20 8 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTATATTATTATTATTA
Found at i:8268 original size:22 final size:22
Alignment explanation
Indices: 8207--8271 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
8197 TCATTTGTTT
*
8207 TATT-TATTATTATTATT-TTG
1 TATTATATTATTATTATTATTA
*
8227 TTTTAATATTATTATTATTATTA
1 TATT-ATATTATTATTATTATTA
8250 TATTATATTATTATTATTATTA
1 TATTATATTATTATTATTATTA
8272 CAAACAGGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 3 0.08
22 31 0.79
23 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TATTATATTATTATTATTATTA
Found at i:9594 original size:18 final size:16
Alignment explanation
Indices: 9563--9616 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 16
9553 TTATTTGCAA
9563 TATTATTTATTATTAT
1 TATTATTTATTATTAT
9579 TATTACTTTAATTATTAT
1 TATTA-TTT-ATTATTAT
*
9597 T-TCA-TTATTATTAT
1 TATTATTTATTATTAT
*
9611 TTTTAT
1 TATTAT
9617 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 9 0.28
15 4 0.12
16 5 0.16
17 5 0.16
18 9 0.28
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTATTATTAT
Found at i:9605 original size:11 final size:10
Alignment explanation
Indices: 9563--9608 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
9553 TTATTTGCAA
9563 TATTATTTAT
1 TATTATTTAT
9573 TATTA-TTAT
1 TATTATTTAT
* *
9582 TACT-TTAAT
1 TATTATTTAT
9591 TATTATTTCAT
1 TATTATTT-AT
9602 TATTATT
1 TATTATT
9609 ATTTTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 13 0.45
10 7 0.24
11 9 0.31
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTATTTAT
Found at i:13021 original size:93 final size:93
Alignment explanation
Indices: 12908--13081 Score: 271
Period size: 92 Copynumber: 1.9 Consensus size: 93
12898 TGTCAAAAAA
* *
12908 ATAATATATGGTTTTTGAAAATATATAGTATAGTTTTTAAAAACATATGGTGTAGTTTTTGAAAA
1 ATAATATA-GGTTTTTGAAAATATATAATATAG-TTTTAAAAACATATGGTATAGTTTTTGAAAA
*
12973 CATGT-TATATAGTTTTTTTTAAAAAAACAC
64 CATATATATATA-TTTTTTTTAAAAAAACAC
*
13003 ATAATATA-GTTTTTGAAAATATATAATATAGTTTTAAAAACATATGGTATAGTTTTTTAAAACA
1 ATAATATAGGTTTTTGAAAATATATAATATAGTTTTAAAAACATATGGTATAGTTTTTGAAAACA
13067 TATATATATATTTTT
66 TATATATATATTTTT
13082 GAAAATATCT
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
92 38 0.51
93 28 0.38
95 8 0.11
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (93 bp):
ATAATATAGGTTTTTGAAAATATATAATATAGTTTTAAAAACATATGGTATAGTTTTTGAAAACA
TATATATATATTTTTTTTAAAAAAACAC
Found at i:13042 original size:21 final size:22
Alignment explanation
Indices: 12889--13108 Score: 126
Period size: 22 Copynumber: 9.7 Consensus size: 22
12879 ATCATATAAC
12889 ATATAGTTTTGTCAAAAA-A-ATA
1 ATATAGTTTT-T-AAAAATATATA
*
12911 ATATATGGTTTTTGAAAATATATA
1 ATATA--GTTTTTAAAAATATATA
* * *
12935 GTATAGTTTTTAAAAACATATG
1 ATATAGTTTTTAAAAATATATA
* * * * * *
12957 GTGTAGTTTTTGAAAACATGTT
1 ATATAGTTTTTAAAAATATATA
* *
12979 ATATAGTTTTTTTTAAAAAAACACATA
1 ATATAG---TTTTT--AAAAATATATA
*
13006 ATATAGTTTTTGAAAATATATA
1 ATATAGTTTTTAAAAATATATA
* *
13028 ATATAG-TTTTAAAAACATATG
1 ATATAGTTTTTAAAAATATATA
*
13049 GTATAGTTTTTTAAAACATATAT-
1 ATATAG-TTTTTAAAA-ATATATA
* *
13072 ATATA-TTTTTGAAAATATCTA
1 ATATAGTTTTTAAAAATATATA
**
13093 GCATAGTTTTTAAAAA
1 ATATAGTTTTTAAAAA
13109 AAAACATATT
Statistics
Matches: 155, Mismatches: 29, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
20 5 0.03
21 28 0.18
22 68 0.44
23 14 0.09
24 22 0.14
25 5 0.03
27 13 0.08
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (22 bp):
ATATAGTTTTTAAAAATATATA
Found at i:13076 original size:44 final size:45
Alignment explanation
Indices: 12918--13086 Score: 170
Period size: 49 Copynumber: 3.8 Consensus size: 45
12908 ATAATATATG
*
12918 GTTTTTG-AAA-ATATATAGTATAGTTTTTAAAAACATATGGTGTA
1 GTTTTTGAAAACATATATA-TATAGTTTTTAAAAACATATGGTATA
* * **
12962 GTTTTTGAAAACATGT-TATATAGTTTTTTTTAAAAAAACACATAATATA
1 GTTTTTGAAAACATATATATATAG---TTTTT--AAAAACATATGGTATA
*
13011 GTTTTTGAAAATATATA-ATATAG-TTTTAAAAACATATGGTATA
1 GTTTTTGAAAACATATATATATAGTTTTTAAAAACATATGGTATA
* *
13054 GTTTTTTAAAACATATATATATA-TTTTTGAAAA
1 GTTTTTGAAAACATATATATATAGTTTTTAAAAA
13087 TATCTAGCAT
Statistics
Matches: 102, Mismatches: 13, Indels: 20
0.76 0.10 0.15
Matches are distributed among these distances:
43 28 0.27
44 25 0.25
45 9 0.09
46 3 0.03
47 5 0.05
49 32 0.31
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (45 bp):
GTTTTTGAAAACATATATATATAGTTTTTAAAAACATATGGTATA
Found at i:13189 original size:21 final size:21
Alignment explanation
Indices: 13163--13215 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
13153 TATGTAATAT
13163 ATATATATATATATATTGAAAA
1 ATATATATATATAT-TTGAAAA
*
13185 CATAT-TATATA-ATTTTAAAA
1 -ATATATATATATATTTGAAAA
13205 ATATA-ATATAT
1 ATATATATATAT
13216 TATATAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.33
20 6 0.22
21 2 0.07
22 6 0.22
23 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATATATATATTTGAAAA
Found at i:13215 original size:26 final size:27
Alignment explanation
Indices: 13186--13248 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
13176 TATTGAAAAC
13186 ATATTATATAATTTTAAAAATATA-AT
1 ATATTATATAATTTTAAAAATATATAT
* * *
13212 ATATTATATAGTTTTTAGAATATATAT
1 ATATTATATAATTTTAAAAATATATAT
13239 ATATATATAT
1 ATAT-TATAT
13249 TAAGCTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 21 0.66
27 6 0.19
28 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTATATAATTTTAAAAATATATAT
Found at i:15453 original size:12 final size:12
Alignment explanation
Indices: 15436--15468 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
15426 ACCTAGGATG
15436 CTTGATTTATTT
1 CTTGATTTATTT
15448 CTTGATTTATTT
1 CTTGATTTATTT
*
15460 CTTGCTTTA
1 CTTGATTTA
15469 GTTTTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.64
Consensus pattern (12 bp):
CTTGATTTATTT
Found at i:17662 original size:13 final size:13
Alignment explanation
Indices: 17644--17712 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 13
17634 CATTGAATTT
17644 GTTAAAGTAAAGA
1 GTTAAAGTAAAGA
***
17657 GTTAAA-TAATTT
1 GTTAAAGTAAAGA
17669 GTTAAAGTAAAGA
1 GTTAAAGTAAAGA
***
17682 GTTAAA-TAATTT
1 GTTAAAGTAAAGA
17694 GTTAAAGTAAAGA
1 GTTAAAGTAAAGA
17707 GTTAAA
1 GTTAAA
17713 TAATTTTGTT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 18 0.43
13 24 0.57
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.33
Consensus pattern (13 bp):
GTTAAAGTAAAGA
Found at i:17673 original size:25 final size:25
Alignment explanation
Indices: 17639--17723 Score: 161
Period size: 25 Copynumber: 3.4 Consensus size: 25
17629 TTCCCCATTG
17639 AATTTGTTAAAGTAAAGAGTTAAAT
1 AATTTGTTAAAGTAAAGAGTTAAAT
17664 AATTTGTTAAAGTAAAGAGTTAAAT
1 AATTTGTTAAAGTAAAGAGTTAAAT
17689 AATTTGTTAAAGTAAAGAGTTAAAT
1 AATTTGTTAAAGTAAAGAGTTAAAT
17714 AATTTTGTTA
1 AA-TTTGTTA
17724 GTAAATCTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 52 0.88
26 7 0.12
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (25 bp):
AATTTGTTAAAGTAAAGAGTTAAAT
Found at i:23972 original size:12 final size:12
Alignment explanation
Indices: 23951--23984 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
23941 ACCACATTTC
*
23951 CAATACCAAACA
1 CAATATCAAACA
23963 CAATATCAAACA
1 CAATATCAAACA
*
23975 CAATCTCAAA
1 CAATATCAAA
23985 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:26440 original size:18 final size:18
Alignment explanation
Indices: 26417--26452 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
26407 AAGCAAAAGG
*
26417 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
26435 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
26453 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:26882 original size:20 final size:20
Alignment explanation
Indices: 26857--26894 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26847 ACGCTTATTT
*
26857 CGCGTTGTGAATTTACCTTC
1 CGCGTTGCGAATTTACCTTC
26877 CGCGTTGCGAATTTACCT
1 CGCGTTGCGAATTTACCT
26895 ACAACATGTC
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:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGAATTTACCTTC
Found at i:26978 original size:25 final size:25
Alignment explanation
Indices: 26940--26989 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
26930 TTGAAAATTA
*
26940 AACATTGTCGTGGGTACATTATTTG
1 AACATTGTCATGGGTACATTATTTG
*
26965 AACATTGTTATGGGTACATTATTTG
1 AACATTGTCATGGGTACATTATTTG
26990 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (25 bp):
AACATTGTCATGGGTACATTATTTG
Found at i:27384 original size:24 final size:25
Alignment explanation
Indices: 27357--27411 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
27347 TTTCAAATTC
*
27357 ATTTCATATGT-AATTAGAGTTTGA
1 ATTTCAAATGTCAATTAGAGTTTGA
* *
27381 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTAGAGTTTGA
27405 ATTTCAA
1 ATTTCAA
27412 TATAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTAGAGTTTGA
Found at i:27397 original size:18 final size:18
Alignment explanation
Indices: 27376--27412 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27366 GTAATTAGAG
27376 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
27394 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
27412 T
1 T
27413 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:27419 original size:24 final size:24
Alignment explanation
Indices: 27368--27420 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
27358 TTTCATATGT
* * *
27368 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
27392 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
27416 AATTT
1 AATTT
27421 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:27765 original size:39 final size:39
Alignment explanation
Indices: 27722--27808 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
27712 TCCGATGCTC
27722 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
27761 ATCAAAATCCAAATCTCATATGGTGCCAAGCGAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
27800 ATCAAAATC
1 ATCAAAATC
27809 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:28033 original size:20 final size:20
Alignment explanation
Indices: 27989--28026 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27979 GCAATCAATG
*
27989 CGAAATTCAAATTCGCAACA
1 CGAAAGTCAAATTCGCAACA
28009 CGAAAGTCAAATTCGCAA
1 CGAAAGTCAAATTCGCAA
28027 ACCGAAAATC
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:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCAACA
Found at i:28060 original size:20 final size:20
Alignment explanation
Indices: 28035--28162 Score: 92
Period size: 20 Copynumber: 6.8 Consensus size: 20
28025 AAACCGAAAA
28035 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
* *
28055 TCGCGTTGCAAATTTGACTA
1 TCGCGTTGCGAATTTGACTT
** *
28075 TCGC--AAC--ACTT-A-TT
1 TCGCGTTGCGAATTTGACTT
28089 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
* *
28109 T--CGTTGTGAATTTAACTT
1 TCGCGTTGCGAATTTGACTT
* * *
28127 TTGCATTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTT
* *
28147 TCGCGCTACGAATTTG
1 TCGCGTTGCGAATTTG
28163 TACCTTCAAC
Statistics
Matches: 81, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 4 0.05
18 20 0.25
19 1 0.01
20 50 0.62
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:28119 original size:18 final size:18
Alignment explanation
Indices: 28092--28141 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
28082 ACTTATTTCG
*
28092 CGTTGCGAATTTGACTTT
1 CGTTGCGAATTTAACTTT
*
28110 CGTTGTGAATTTAACTTTT
1 CGTTGCGAATTTAAC-TTT
*
28129 GCATTGCGAATTT
1 -CGTTGCGAATTT
28142 GACTATCGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 10 0.38
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (18 bp):
CGTTGCGAATTTAACTTT
Found at i:29494 original size:21 final size:21
Alignment explanation
Indices: 29433--29528 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
29423 ATGAATCAGG
* *
29433 CTCTTGAACGGT-GGACGGGAC
1 CTCTTGAACGATGGGA-GGGGC
* *
29454 CTCTTAAACGATGACG-GGGGC
1 CTCTTGAACGATG-GGAGGGGC
*
29475 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * *
29496 TTCTTCG-ATGATGAGAGGGGC
1 CTCTT-GAACGATGGGAGGGGC
29517 CTCTTGAACGAT
1 CTCTTGAACGAT
29529 AAGAGGAACC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 1 0.02
23 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:29533 original size:21 final size:21
Alignment explanation
Indices: 29453--29545 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
29443 GTGGACGGGA
* *
29453 CCTCTTAAACGATGACG-GGGG
1 CCTCTTGAACGAT-AAGAGGGG
* **
29474 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATAAGAGGGG
* * *
29495 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATAAGAGGGG
**
29516 CCTCTTGAACGATAAGAGGAA
1 CCTCTTGAACGATAAGAGGGG
29537 CCTCTTGAA
1 CCTCTTGAA
29546 TGATGATAGG
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.04
21 53 0.95
22 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATAAGAGGGG
Found at i:30068 original size:21 final size:21
Alignment explanation
Indices: 30051--30090 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30041 TTTTCAAAGG
30051 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
30072 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
30091 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:30140 original size:19 final size:19
Alignment explanation
Indices: 30116--30154 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
30106 TCGAATGCAT
30116 TCCATGCACCGATACACTC
1 TCCATGCACCGATACACTC
* *
30135 TCCATGCATCGATGCACTC
1 TCCATGCACCGATACACTC
30154 T
1 T
30155 GATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATACACTC
Found at i:30179 original size:64 final size:65
Alignment explanation
Indices: 30051--30215 Score: 199
Period size: 64 Copynumber: 2.5 Consensus size: 65
30041 TTTTCAAAGG
* *
30051 CATGCACCGATGCATCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCA
1 CATGCACCGATACA-CAAT-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGCA
30115 TTC
63 TTC
** * * *
30118 CATGCACCGATACACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATACACAATCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
* * *
30182 GATGCATCGATGCACAATCCATGCATCGATGCAC
1 CATGCACCGATACACAATCCATGCATCGATGCAC
30216 CAGGCTATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 53 0.62
65 15 0.18
66 4 0.05
67 13 0.15
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (65 bp):
CATGCACCGATACACAATCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
Found at i:30252 original size:18 final size:17
Alignment explanation
Indices: 30226--30261 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
30216 CAGGCTATTT
30226 TTCAAGCATCGAATGCAC
1 TTCAAGCATCG-ATGCAC
*
30244 TTCATGCATCGATGCAC
1 TTCAAGCATCGATGCAC
30261 T
1 T
30262 CTTAGTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (17 bp):
TTCAAGCATCGATGCAC
Found at i:42117 original size:43 final size:43
Alignment explanation
Indices: 42056--42141 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
42046 ATGCCAACGG
42056 ACTGGAAACATCTCCAGACAACATGAGATGCCGCTGCAAAATA
1 ACTGGAAACATCTCCAGACAACATGAGATGCCGCTGCAAAATA
*
42099 ACTGGAAACATCTCCAGACAACATGAGATGCCGCTGTAAAATA
1 ACTGGAAACATCTCCAGACAACATGAGATGCCGCTGCAAAATA
42142 TTTTGGAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (43 bp):
ACTGGAAACATCTCCAGACAACATGAGATGCCGCTGCAAAATA
Found at i:43490 original size:19 final size:21
Alignment explanation
Indices: 43453--43495 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
43443 TAACTTTTTC
43453 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
43473 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
43493 TTT
1 TTT
43496 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:43501 original size:19 final size:20
Alignment explanation
Indices: 43452--43501 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
43442 TTAACTTTTT
*
43452 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
43472 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
43491 CTTTTACCTTT
1 CTTTTACCTTT
43502 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:48026 original size:24 final size:22
Alignment explanation
Indices: 47998--48077 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
47988 CACTTAACAA
47998 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
48022 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
48042 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
48066 TGCATCGATGCA
1 TGCATCGATGCA
48078 CAAGATCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 13 0.27
24 17 0.35
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:50581 original size:21 final size:21
Alignment explanation
Indices: 50557--50596 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
50547 TTTTCAAAGG
50557 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
50578 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
50597 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:50646 original size:19 final size:19
Alignment explanation
Indices: 50622--50660 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
50612 TCGAATGCAT
50622 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
50641 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
50660 T
1 T
50661 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:50685 original size:64 final size:64
Alignment explanation
Indices: 50557--50786 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 64
50547 TTTTCAAAGG
* * *
50557 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGC
50620 ATT
62 ATT
50623 CCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCA-T
50687 T
64 T
* * ** * *
50688 AATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCA-
50750 TT
63 TT
* * *
50752 CATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
50787 AGGAGTCCAA
Statistics
Matches: 140, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
63 2 0.01
64 98 0.70
65 17 0.12
66 7 0.05
67 14 0.10
68 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATT
Found at i:50766 original size:17 final size:19
Alignment explanation
Indices: 50738--50786 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
50728 ATTTTTCAAA
50738 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
50756 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
50775 CACCGATGCACT
1 CATCGATGCACT
50787 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:53265 original size:36 final size:36
Alignment explanation
Indices: 53213--53286 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
53203 TTGGTTGAAG
53213 AAATACAATTCATTCAAGTTTCAATTTGCAGAATAA
1 AAATACAATTCATTCAAGTTTCAATTTGCAGAATAA
*
53249 AAATGCAATTCATTCAAGTTTCAATTTGCAGAATAA
1 AAATACAATTCATTCAAGTTTCAATTTGCAGAATAA
53285 AA
1 AA
53287 GAAGTTTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (36 bp):
AAATACAATTCATTCAAGTTTCAATTTGCAGAATAA
Found at i:53372 original size:20 final size:19
Alignment explanation
Indices: 53334--53373 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
53324 AAATCGCAAC
*
53334 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCACGTT
*
53353 GCGATTTTCATTTTCACGTT
1 GCGATTTT-AGTTTCACGTT
53373 G
1 G
53374 TGAATTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCACGTT
Found at i:53423 original size:13 final size:13
Alignment explanation
Indices: 53405--53436 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
53395 GGGTTTCTTC
53405 AACAAAAAGACAA
1 AACAAAAAGACAA
53418 AACAAAAAGACAA
1 AACAAAAAGACAA
53431 AACAAA
1 AACAAA
53437 GATAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:53680 original size:22 final size:22
Alignment explanation
Indices: 53648--53695 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
53638 GGAGATAGAT
53648 GGATTTCGTCGGAAATGAGGAC
1 GGATTTCGTCGGAAATGAGGAC
* * *
53670 GGATTTTGTCGGAGATGGGGAC
1 GGATTTCGTCGGAAATGAGGAC
53692 GGAT
1 GGAT
53696 GTCACCATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.10, G:0.42, T:0.25
Consensus pattern (22 bp):
GGATTTCGTCGGAAATGAGGAC
Found at i:53848 original size:20 final size:20
Alignment explanation
Indices: 53823--53871 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
53813 GCGTAAAAAC
53823 ATTTGACTTTCGCGTTGCAA
1 ATTTGACTTTCGCGTTGCAA
* *
53843 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCAA
53863 ATTTGACTT
1 ATTTGACTT
53872 CTGTGTTGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCAA
Found at i:53879 original size:20 final size:20
Alignment explanation
Indices: 53823--53882 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
53813 GCGTAAAAAC
*
53823 ATTTGACTT-TCGCGTTGCAA
1 ATTTGACTTCT-GCGTTGCGA
53843 ATTTGACTATC-GCGTTGCGA
1 ATTTGACT-TCTGCGTTGCGA
*
53863 ATTTGACTTCTGTGTTGCGA
1 ATTTGACTTCTGCGTTGCGA
53883 TTTACAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 32 0.91
21 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTTGACTTCTGCGTTGCGA
Found at i:53916 original size:21 final size:21
Alignment explanation
Indices: 53901--53944 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
53891 TTCGCGTTGT
53901 GAATTTGGCAAATCGCAATGC
1 GAATTTGGCAAATCGCAATGC
* *
53922 GAATTTGGAAAATCGAAATGC
1 GAATTTGGCAAATCGCAATGC
53943 GA
1 GA
53945 TTTACATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (21 bp):
GAATTTGGCAAATCGCAATGC
Found at i:56071 original size:16 final size:16
Alignment explanation
Indices: 56050--56080 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56040 ATTCAAATAT
*
56050 TTAATAATCATTTATA
1 TTAATAATAATTTATA
56066 TTAATAATAATTTAT
1 TTAATAATAATTTAT
56081 GTAGTTTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATAATAATTTATA
Found at i:56384 original size:28 final size:28
Alignment explanation
Indices: 56344--56400 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
56334 TTTTAGGGAG
56344 AAAACTAAGAAAAAGTCTCTGTTTCTCT
1 AAAACTAAGAAAAAGTCTCTGTTTCTCT
56372 AAAACTAAGAAAAAGTCTCTGTTTCTCT
1 AAAACTAAGAAAAAGTCTCTGTTTCTCT
56400 A
1 A
56401 CAACGATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (28 bp):
AAAACTAAGAAAAAGTCTCTGTTTCTCT
Found at i:60248 original size:2 final size:2
Alignment explanation
Indices: 60241--60268 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60231 TGTTTAAAGA
60241 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
60269 GGTTAGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61303 original size:229 final size:227
Alignment explanation
Indices: 60898--61346 Score: 799
Period size: 229 Copynumber: 2.0 Consensus size: 227
60888 GTAAATTATC
* * *
60898 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
60963 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
61028 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
61093 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
61126 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
61191 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
61256 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
61321 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
61347 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 40 0.19
229 171 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:61434 original size:20 final size:19
Alignment explanation
Indices: 61411--61455 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
61401 CGATATACCA
61411 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
61431 GGTAACAAATGATAAAACC
1 GGTAAAAAATGATAAAACC
61450 GGTAAA
1 GGTAAA
61456 TTTAAAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:63901 original size:21 final size:21
Alignment explanation
Indices: 63854--63918 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
63844 AAGACAATCA
* *
63854 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
63876 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
63896 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
63917 AG
1 AG
63919 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:63993 original size:33 final size:33
Alignment explanation
Indices: 63951--64016 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
63941 AAATAGATGG
*
63951 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
63984 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
64017 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:65837 original size:19 final size:19
Alignment explanation
Indices: 65813--65861 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
65803 AATGTAGGGT
65813 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
65832 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
65851 TATTTTTGTAT
1 TAATTTTGTAT
65862 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:66476 original size:198 final size:198
Alignment explanation
Indices: 65980--66950 Score: 1843
Period size: 198 Copynumber: 4.9 Consensus size: 198
65970 CAATATGGCC
* *
65980 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
66045 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
66110 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGA
66175 ATGGAA
193 ATGGAA
*
66181 AACAGGGTGCACCCACAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66246 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
66311 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
66376 GAA
196 GAA
*
66379 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66444 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66509 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
66574 GAA
196 GAA
*
66577 AACATGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66642 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
66707 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCATAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
66772 GAA
196 GAA
66775 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66840 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66905 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
66951 CTAATTTAAA
Statistics
Matches: 758, Mismatches: 12, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
198 587 0.77
199 113 0.15
200 24 0.03
201 34 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:68432 original size:18 final size:18
Alignment explanation
Indices: 68411--68472 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
68401 AGCGGTCGCA
68411 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
68429 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
68447 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
68465 GAAGATGA
1 GAAGATGA
68473 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:68435 original size:6 final size:6
Alignment explanation
Indices: 68411--68502 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
68401 AGCGGTCGCA
* * * * * *
68411 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
68459 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
68503 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:68446 original size:3 final size:3
Alignment explanation
Indices: 68426--68506 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
68416 TGAAGCTGAC
* * * * * ** *
68426 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
68474 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
68507 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:68465 original size:36 final size:36
Alignment explanation
Indices: 68414--68490 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
68404 GGTCGCAGAA
*
68414 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
68450 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
68486 GATGA
1 GATGA
68491 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:68506 original size:12 final size:12
Alignment explanation
Indices: 68414--68502 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
68404 GGTCGCAGAA
*
68414 GATGAAGCTGAC
1 GATGAAGATGAC
68426 GATGAAGATGAC
1 GATGAAGATGAC
*
68438 GATGATGATGAC
1 GATGAAGATGAC
* *
68450 GATGAAGCTGGC
1 GATGAAGATGAC
*
68462 GATGAAGATGAT
1 GATGAAGATGAC
* * *
68474 GACGATGATGAT
1 GATGAAGATGAC
* *
68486 GATGATGATGAA
1 GATGAAGATGAC
68498 GATGA
1 GATGA
68503 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:68506 original size:18 final size:18
Alignment explanation
Indices: 68411--68502 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
68401 AGCGGTCGCA
*
68411 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
68429 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
68447 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
68465 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
68483 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
68501 GA
1 GA
68503 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:70240 original size:183 final size:183
Alignment explanation
Indices: 69932--70823 Score: 1649
Period size: 183 Copynumber: 4.9 Consensus size: 183
69922 CTTTCAACAT
** * * * * *
69932 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGATTTTATGCTCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
69997 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
70062 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
70115 ATTATAATGTAATAGATAATTTAGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
70180 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
70245 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
70298 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
70363 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
70428 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
70481 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
70546 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
70611 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* *
70664 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
70729 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
70794 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
70824 GTAATTTTAA
Statistics
Matches: 692, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 692 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:72512 original size:18 final size:18
Alignment explanation
Indices: 72491--72527 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
72481 GTAATTGGAG
72491 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
72509 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
72527 T
1 T
72528 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:72535 original size:24 final size:24
Alignment explanation
Indices: 72483--72529 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
72473 TTTCATATGT
* *
72483 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
72507 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
72530 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:72829 original size:39 final size:39
Alignment explanation
Indices: 72786--72872 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
72776 TCCGATGCTC
*
72786 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
72825 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
72864 ATCAAAATC
1 ATCAAAATC
72873 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:73308 original size:23 final size:23
Alignment explanation
Indices: 73277--73349 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
73267 ATAGGTAAAC
*
73277 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
73300 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
73323 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
73346 ATAT
1 ATAT
73350 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:79506 original size:35 final size:35
Alignment explanation
Indices: 79467--79801 Score: 217
Period size: 35 Copynumber: 9.4 Consensus size: 35
79457 TTCGAAAATT
* *
79467 TATATATTATATAGTTTTTGAAAATATTTTTAAAA
1 TATATAATATATAGTTTTTAAAAATATTTTTAAAA
* *
79502 TATATAATATATAG-TTTTGAAAATATTTTGAAAACA
1 TATATAATATATAGTTTTTAAAAATATTTT-TAAA-A
* *
79538 TGTATATATTATATAGTTTTT-AAAATAATTTTGAAAA
1 --TATATAATATATAGTTTTTAAAAAT-ATTTTTAAAA
* * *
79575 CTTATATAGTATATAG-TTTTAAAAACATTTTTGAAAT
1 --TATATAATATATAGTTTTTAAAAATATTTTT-AAAA
** *
79612 TATATAATATATAGTTTAAAAAAACATATTTTGAAAAA
1 TATATAATATATAGTTT-TTAAAA-ATATTTT-TAAAA
79650 TTATATAATATATAG-TTTTAAAAATATTTTTTGAAAA
1 -TATATAATATATAGTTTTTAAAAATA-TTTTT-AAAA
** * *
79687 CCTAT-ATA-ATA-TTTTT-AAAACATTTTGAAAA
1 TATATAATATATAGTTTTTAAAAATATTTTTAAAA
* * * * *
79718 CTATATAATGTATAGGTTTGAAAACTTTTTTTAAAA
1 -TATATAATATATAGTTTTTAAAAATATTTTTAAAA
* *
79754 AATATAATAT-T-G--TTTAAAAATATTTTTTTGAAA
1 TATATAATATATAGTTTTTAAAAATA--TTTTTAAAA
*
79787 TATATATTATATAGT
1 TATATAATATATAGT
79802 ATTATTATTA
Statistics
Matches: 234, Mismatches: 40, Indels: 51
0.72 0.12 0.16
Matches are distributed among these distances:
31 11 0.05
32 7 0.03
33 24 0.10
34 27 0.12
35 44 0.19
36 29 0.12
37 37 0.16
38 32 0.14
39 23 0.10
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAAATATTTTTAAAA
Found at i:79574 original size:110 final size:106
Alignment explanation
Indices: 79454--79801 Score: 331
Period size: 110 Copynumber: 3.2 Consensus size: 106
79444 CCAGAAAACG
*
79454 ATTTTCGAAAATTTATATATTATATAGTTTTTGAAAATATTTTTAAAATATATAATATATAGTTT
1 ATTTT-GAAAA-TTATATA-TATATAGTTTTT-AAAACATTTTTAAAATATATAATATATAGTTT
* *
79519 TGAAAATATTTTGAAAACATGTATATATTATATAGTTTTTAAAATA-
62 TGAAAATATTTTGAAAA-AT-TATATAATATATAGTTTTAAAAATAT
* *
79565 ATTTTGAAAACTTATATAGTATATAGTTTTAAAAACATTTTTGAAATTATATAATATATAGTTTA
1 ATTTTGAAAA-TTATATA-TATATAGTTTTTAAAACATTTTT-AAAATATATAATATATAGTTT-
**
79630 AAAAAACATATTTTGAAAAATTATATAATATATAGTTTTAAAAATAT
62 -TGAAA-ATATTTTGAAAAATTATATAATATATAGTTTTAAAAATAT
* ** * * *
79677 TTTTTGAAAA-CCTATATA-ATA-TTTTTAAAACATTTTGAAAACTATATAATGTATAGGTTTGA
1 ATTTTGAAAATTATATATATATAGTTTTTAAAACATTTTTAAAA-TATATAATATATAGTTTTGA
* *
79739 AAACTTTTTTTAAAAA--ATATAATAT-T-G-TTTAAAAATATT
65 AAA-TATTTTGAAAAATTATATAATATATAGTTTTAAAAATA-T
*
79778 TTTTTG-AAA-TATATATTATATAGT
1 ATTTTGAAAATTATATA-TATATAGT
79802 ATTATTATTA
Statistics
Matches: 203, Mismatches: 23, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
100 17 0.08
101 10 0.05
102 4 0.02
103 10 0.05
104 1 0.00
105 13 0.06
106 3 0.01
107 29 0.14
108 3 0.01
109 12 0.06
110 47 0.23
111 28 0.14
112 14 0.07
113 12 0.06
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (106 bp):
ATTTTGAAAATTATATATATATAGTTTTTAAAACATTTTTAAAATATATAATATATAGTTTTGAA
AATATTTTGAAAAATTATATAATATATAGTTTTAAAAATAT
Found at i:79590 original size:37 final size:37
Alignment explanation
Indices: 79454--79741 Score: 251
Period size: 38 Copynumber: 7.9 Consensus size: 37
79444 CCAGAAAACG
* * *
79454 ATTTTCGAAAATTTATATATTATATAGTTTTTGAAAAT-
1 ATTTT-GAAAACTTATATAATATATAG-TTTTAAAAATA
* *
79492 ATTTTTAAAA--TATATAATATATAGTTTTGAAAAT-
1 ATTTTGAAAACTTATATAATATATAGTTTTAAAAATA
* *
79526 ATTTTGAAAACATGTATATATTATATAGTTTTTAAAATA
1 ATTTTGAAAAC-T-TATATAATATATAGTTTTAAAAATA
* *
79565 ATTTTGAAAACTTATATAGTATATAGTTTTAAAAACA
1 ATTTTGAAAACTTATATAATATATAGTTTTAAAAATA
* * *
79602 TTTTTG-AAA-TTATATAATATATAGTTTAAAAAAACA
1 ATTTTGAAAACTTATATAATATATAGTTT-TAAAAATA
*
79638 TATTTTGAAAAATTATATAATATATAGTTTTAAAAATA
1 -ATTTTGAAAACTTATATAATATATAGTTTTAAAAATA
* * *
79676 TTTTTTGAAAACCTATAT-A-ATAT--TTTT-AAAA-C
1 -ATTTTGAAAACTTATATAATATATAGTTTTAAAAATA
* * *
79708 ATTTTGAAAAC-TATATAATGTATAGGTTTGAAAA
1 ATTTTGAAAACTTATATAATATATAGTTTTAAAAA
79742 CTTTTTTTAA
Statistics
Matches: 215, Mismatches: 21, Indels: 31
0.81 0.08 0.12
Matches are distributed among these distances:
30 5 0.02
31 11 0.05
32 3 0.01
33 4 0.02
34 26 0.12
35 34 0.16
36 14 0.07
37 37 0.17
38 52 0.24
39 29 0.13
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (37 bp):
ATTTTGAAAACTTATATAATATATAGTTTTAAAAATA
Found at i:81106 original size:2 final size:2
Alignment explanation
Indices: 81099--81153 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
81089 TTAGTACCAT
81099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81141 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
81154 CATTTTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82568 original size:16 final size:16
Alignment explanation
Indices: 82547--82583 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
82537 GTCTCCAACG
82547 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
82563 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
82579 TTTAT
1 TTTAT
82584 TTTTGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:85233 original size:57 final size:57
Alignment explanation
Indices: 85145--85257 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
85135 GGTATCTTCT
* * * *
85145 TCGCCATTAGTATGAGAACTTGGAATATGAGAAAAGTTCATGTTATCCATGTCGAAG
1 TCGCCATCAGTATCAGAACTTGGAAAATGAGAAAAGTTCATGTCATCCATGTCGAAG
* *
85202 TCGCCATCAGTATCAGAACTTTGAAAATGAGAAGAGTTCATGTCATCCATGTCGAA
1 TCGCCATCAGTATCAGAACTTGGAAAATGAGAAAAGTTCATGTCATCCATGTCGAA
85258 ATGAATCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (57 bp):
TCGCCATCAGTATCAGAACTTGGAAAATGAGAAAAGTTCATGTCATCCATGTCGAAG
Found at i:88594 original size:17 final size:18
Alignment explanation
Indices: 88572--88605 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
88562 TCTTTAAGGT
88572 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
88589 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
88606 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:94790 original size:40 final size:40
Alignment explanation
Indices: 94711--94790 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
94701 AGAATGTCAG
** *
94711 GAAGGCGCGGCCCATGCACCGCGCCTTACCCTACGTGGCA
1 GAAGGCGCAACCCATGCACCGCGCCTTACCCTACATGGCA
94751 GAAGGCGCAACCCATGCACCGCGCCTTACCC-AGCATGGCA
1 GAAGGCGCAACCCATGCACCGCGCCTTACCCTA-CATGGCA
94791 CCATGTCAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.03
40 35 0.97
ACGTcount: A:0.21, C:0.40, G:0.28, T:0.11
Consensus pattern (40 bp):
GAAGGCGCAACCCATGCACCGCGCCTTACCCTACATGGCA
Found at i:96996 original size:53 final size:53
Alignment explanation
Indices: 96911--97026 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 53
96901 GTTGCACCTA
* * * *
96911 AGTGTCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCATACAT
1 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACAT
* * *
96964 AGTGCCGAAATGGTCATTCATAAACTCATTATGAATACAATGGGTGCACACAT
1 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACAT
*
97017 AGTGCAGAAA
1 AGTGCCGAAA
97027 GTACATATAG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (53 bp):
AGTGCCGAAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACAT
Found at i:97189 original size:48 final size:48
Alignment explanation
Indices: 97042--97170 Score: 231
Period size: 48 Copynumber: 2.7 Consensus size: 48
97032 TATAGTACTG
* *
97042 ATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAATAATC
1 ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAATCATC
97090 ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAATCATC
1 ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAATCATC
*
97138 ATACGAAAATGCAACTTATACATTAAACAAAAT
1 ATACGAAAATGCAACTTATGCATTAAACAAAAT
97171 ATGTCGATAC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (48 bp):
ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAATCATC
Found at i:100751 original size:14 final size:14
Alignment explanation
Indices: 100732--100767 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
100722 CGTTCGATTA
100732 TATGTTCGTCCATT
1 TATGTTCGTCCATT
*
100746 TATGTTCGTTCATT
1 TATGTTCGTCCATT
100760 TATGTTCG
1 TATGTTCG
100768 AACAGAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.53
Consensus pattern (14 bp):
TATGTTCGTCCATT
Found at i:102900 original size:3 final size:3
Alignment explanation
Indices: 102892--102922 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
102882 AGCAGAAACT
102892 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
102923 GACCCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:108402 original size:34 final size:32
Alignment explanation
Indices: 108340--108409 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
108330 ACCTTACAAC
* *
108340 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
108372 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
108406 TCCC
1 TCCC
108410 CTTTACAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:108839 original size:29 final size:31
Alignment explanation
Indices: 108807--108866 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
108797 AAATTTTGAA
*
108807 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
108836 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
108867 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:116969 original size:20 final size:22
Alignment explanation
Indices: 116924--116981 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
116914 GCATGGGTAG
116924 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
116948 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
116968 TGCATCGATGCACT
1 TGCATCGATGCACT
116982 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:121010 original size:21 final size:21
Alignment explanation
Indices: 120984--121035 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
120974 GGCAAGGTGT
120984 ATCGATGCATATTGAATATGC
1 ATCGATGCATATTGAATATGC
121005 ATCGATGCATATTGAATATGC
1 ATCGATGCATATTGAATATGC
121026 ATCGATGCAT
1 ATCGATGCAT
121036 TCTTTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (21 bp):
ATCGATGCATATTGAATATGC
Found at i:121177 original size:24 final size:20
Alignment explanation
Indices: 121150--121207 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
121140 GCATGGGTAG
121150 TGCATCGATACACATGTTAAAGAA
1 TGCATCGATACAC-TG-T--AGAA
*
121174 TGCATCGATGCACTGTAGAA
1 TGCATCGATACACTGTAGAA
*
121194 TGCATCGATGCACT
1 TGCATCGATACACT
121208 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
22 1 0.03
23 2 0.06
24 12 0.36
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATACACTGTAGAA
Found at i:121195 original size:20 final size:20
Alignment explanation
Indices: 121170--121207 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
121160 CACATGTTAA
121170 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
121190 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
121208 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:131862 original size:20 final size:20
Alignment explanation
Indices: 131837--131880 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
131827 GGGTAATAAG
131837 TTTGGGTTTGGTTTAGATAT
1 TTTGGGTTTGGTTTAGATAT
*
131857 TTTGGGTTTGGTTTGGATAT
1 TTTGGGTTTGGTTTAGATAT
131877 TTTG
1 TTTG
131881 TAATAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.57
Consensus pattern (20 bp):
TTTGGGTTTGGTTTAGATAT
Found at i:132976 original size:114 final size:114
Alignment explanation
Indices: 132795--133018 Score: 349
Period size: 114 Copynumber: 2.0 Consensus size: 114
132785 GAATCAAATA
132795 ATCTCAGTGATTAAGAGATAATTGTTATTCTTAAAAGTCTTAAATTCGAGCACGATACTTGTAAG
1 ATCTCAGTGATTAAGAGATAATTGTTATTCTTAAAAGTCTTAAATTCGAGCACGATACTTGTAAG
132860 GATCTTTGAATGTTCATTTTCTAAATTATTGAAAGCCTTTCAAATGAAT
66 GATCTTTGAATGTTCATTTTCTAAATTATTGAAAGCCTTTCAAATGAAT
* * * * * * *
132909 ATCTTAGTGATTAAGAGATAATTGTTATTCTTAGAAGTCTTAAGTTTGAGCATGATATTTGTTAG
1 ATCTCAGTGATTAAGAGATAATTGTTATTCTTAAAAGTCTTAAATTCGAGCACGATACTTGTAAG
* * * *
132974 GATTTTTTAATGTTCATTTTCTAAATTATTTAAAGCCTTTTAAAT
66 GATCTTTGAATGTTCATTTTCTAAATTATTGAAAGCCTTTCAAAT
133019 TGATATTATC
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (114 bp):
ATCTCAGTGATTAAGAGATAATTGTTATTCTTAAAAGTCTTAAATTCGAGCACGATACTTGTAAG
GATCTTTGAATGTTCATTTTCTAAATTATTGAAAGCCTTTCAAATGAAT
Found at i:134020 original size:54 final size:54
Alignment explanation
Indices: 133956--134065 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
133946 ATCCAACTTC
133956 ATTTCCCACCTTTCTATAGGACAATTTCATTAGTTCGAATTTACATGTGGAATG
1 ATTTCCCACCTTTCTATAGGACAATTTCATTAGTTCGAATTTACATGTGGAATG
* * *
134010 ATTTCCCACCTTTCTTTAGGACTATTTCATTAGTTCGAATTTACATGTGGGATG
1 ATTTCCCACCTTTCTATAGGACAATTTCATTAGTTCGAATTTACATGTGGAATG
134064 AT
1 AT
134066 AACACTAAGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (54 bp):
ATTTCCCACCTTTCTATAGGACAATTTCATTAGTTCGAATTTACATGTGGAATG
Found at i:134211 original size:16 final size:16
Alignment explanation
Indices: 134190--134225 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
134180 TTGAAATCTG
134190 TGAAGGAATTGGAATC
1 TGAAGGAATTGGAATC
134206 TGAAGGAATTGGAATC
1 TGAAGGAATTGGAATC
134222 TGAA
1 TGAA
134226 TCTGAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.25
Consensus pattern (16 bp):
TGAAGGAATTGGAATC
Found at i:134533 original size:10 final size:10
Alignment explanation
Indices: 134518--134548 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
134508 GGGATGGCCA
134518 TGGGTCGGGT
1 TGGGTCGGGT
134528 TGGGTCGGGT
1 TGGGTCGGGT
134538 TGGGTCGGGT
1 TGGGTCGGGT
134548 T
1 T
134549 TTTGGTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.58, T:0.32
Consensus pattern (10 bp):
TGGGTCGGGT
Found at i:134858 original size:28 final size:29
Alignment explanation
Indices: 134796--134864 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
134786 CCTAAACCCG
*
134796 AACCCGACCTGAATATCACACTTTAAAAA
1 AACCCGACCCGAATATCACACTTTAAAAA
134825 AACCCGACCCGAATATCACAC-TTAAAAA
1 AACCCGACCCGAATATCACACTTTAAAAA
134853 AACCCGACCCGA
1 AACCCGACCCGA
134865 CCCTGATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 19 0.49
29 20 0.51
ACGTcount: A:0.43, C:0.33, G:0.09, T:0.14
Consensus pattern (29 bp):
AACCCGACCCGAATATCACACTTTAAAAA
Found at i:134884 original size:31 final size:31
Alignment explanation
Indices: 134846--134915 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
134836 AATATCACAC
*
134846 TTAAAAAAACCCGACCC-GACCCTGATTTTTT
1 TTAAAAAAACCCGACCCGGACCC-AATTTTTT
* *
134877 TT-AAAAAATCCGACCCGGTCCCAATTTTTT
1 TTAAAAAAACCCGACCCGGACCCAATTTTTT
134907 TTAAAAAAA
1 TTAAAAAAA
134916 ACCTTGACCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 22 0.65
31 12 0.35
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (31 bp):
TTAAAAAAACCCGACCCGGACCCAATTTTTT
Found at i:135003 original size:38 final size:36
Alignment explanation
Indices: 134924--135015 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 36
134914 AAACCTTGAC
* **
134924 CGACCCGACCCAACCCGAATATCACGCTTAAAAAAA
1 CGACCCGACCCGACCCGAATATCAAACTTAAAAAAA
134960 --A-CCGACCCGACCCGAATATCAAACTTTAAAAAACA
1 CGACCCGACCCGACCCGAATATCAAAC-TTAAAAAA-A
134995 CGACCCGACCCGAACCCGAAT
1 CGACCCGACCCG-ACCCGAAT
135016 TTTTTTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
33 20 0.43
34 9 0.19
35 1 0.02
37 1 0.02
38 8 0.17
39 8 0.17
ACGTcount: A:0.40, C:0.37, G:0.12, T:0.11
Consensus pattern (36 bp):
CGACCCGACCCGACCCGAATATCAAACTTAAAAAAA
Found at i:139247 original size:28 final size:30
Alignment explanation
Indices: 139215--139271 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
139205 TAAACTTAAC
139215 TTAAAAG-TT-TATTA-TCTTTTTATTATAT
1 TTAAAAGTTTATATTAGT-TTTTTATTATAT
139243 TTAAAAGTTTATATTAGTTTTTTATTATA
1 TTAAAAGTTTATATTAGTTTTTTATTATA
139272 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 7 0.27
29 2 0.08
30 16 0.62
31 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (30 bp):
TTAAAAGTTTATATTAGTTTTTTATTATAT
Found at i:139364 original size:2 final size:2
Alignment explanation
Indices: 139359--139385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
139349 TATATATATA
139359 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
139386 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:143774 original size:20 final size:20
Alignment explanation
Indices: 143732--143774 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
143722 GATCACGTTT
*
143732 ATAATTACAAATTTCAATAA
1 ATAATTACAAAATTCAATAA
*
143752 ATAATTATAAAATT-AATAGA
1 ATAATTACAAAATTCAATA-A
143772 ATA
1 ATA
143775 TATATACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAATTACAAAATTCAATAA
Found at i:144035 original size:20 final size:19
Alignment explanation
Indices: 144010--144063 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
144000 GCGAAATAAA
144010 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
144030 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
144050 AATCGCAACGCGAT
1 AATCGCAACGCGAT
144064 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:144198 original size:20 final size:20
Alignment explanation
Indices: 144113--144327 Score: 179
Period size: 20 Copynumber: 10.7 Consensus size: 20
144103 GATTTTCCAT
* **
144113 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
144133 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
144152 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
144174 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
144194 AATCGCAACG-GCAATACGTAA
1 AATCGCAACGCG-AATACGT-A
144215 AATCGCAACGAC-AATACGTA
1 AATCGCAACG-CGAATACGTA
* *
144235 AATCACAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
144255 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
144275 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
144295 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
144315 AATCGCAACGCGA
1 AATCGCAACGCGA
144328 TTTTTAAAGC
Statistics
Matches: 161, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.01
19 5 0.03
20 114 0.71
21 39 0.24
22 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:144199 original size:41 final size:40
Alignment explanation
Indices: 144154--144326 Score: 206
Period size: 40 Copynumber: 4.3 Consensus size: 40
144144 GATTCTGACT
* * *
144154 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGCGAATACGTAA
* *
144195 ATCGCAACG-GCAATACGTAAAATCGCAACGAC-AATACGTAA
1 ATCGCAACGCG-TATCCGT-AAATCGCAACG-CGAATACGTAA
* * *
144236 ATCACAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAA
* *
144276 ATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAA
144316 ATCGCAACGCG
1 ATCGCAACGCG
144327 ATTTTTAAAG
Statistics
Matches: 113, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
40 66 0.58
41 45 0.40
42 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAA
Found at i:144597 original size:27 final size:27
Alignment explanation
Indices: 144540--144592 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
144530 CATCTCCGGC
* *
144540 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
144567 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
144593 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:144821 original size:21 final size:21
Alignment explanation
Indices: 144763--144838 Score: 88
Period size: 20 Copynumber: 3.7 Consensus size: 21
144753 TCCAACTCAG
144763 ATCGCAAC-ATGA-AAATGAAA
1 ATCGCAACGA-GAGAAATGAAA
**
144783 ATCGCAAC-ACGA-AAATGACT
1 ATCGCAACGA-GAGAAATGAAA
144803 ATCGCAACGAGAGAAATGAAA
1 ATCGCAACGAGAGAAATGAAA
144824 ATCGCAACGAGAGAA
1 ATCGCAACGAGAGAA
144839 TCGCAACGCG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 27 0.55
21 22 0.45
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.12
Consensus pattern (21 bp):
ATCGCAACGAGAGAAATGAAA
Found at i:144947 original size:20 final size:19
Alignment explanation
Indices: 144858--144970 Score: 119
Period size: 20 Copynumber: 6.1 Consensus size: 19
144848 GAAACCAAAA
*
144858 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
144877 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
144896 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
144910 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
144929 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
144949 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
144969 TC
1 TC
144971 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 2 0.03
19 31 0.40
20 32 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:148415 original size:14 final size:14
Alignment explanation
Indices: 148396--148431 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
148386 ATTGTTTAAT
148396 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
148410 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
148424 TGATTTGT
1 TGATTTGT
148432 TTAATTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:148560 original size:19 final size:17
Alignment explanation
Indices: 148538--148646 Score: 68
Period size: 19 Copynumber: 6.3 Consensus size: 17
148528 AAAAATGACT
148538 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAAT-AAA
* *
148557 ATCGCAA-CG--AGAGA
1 ATCGCAAGCGAAATAAA
148571 ATCGCAATGCGAAATTAAA
1 ATCGCAA-GCGAAA-TAAA
148590 ATCGCAA-CG--ATAAA
1 ATCGCAAGCGAAATAAA
*
148604 ATCGCAACACGAAACTAAA
1 ATCGCAA-GCGAAA-TAAA
148623 ATCGCAACGCGAAACTAAA
1 ATCGCAA-GCGAAA-TAAA
*
148642 TTCGC
1 ATCGC
148647 GTTGCGATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
14 20 0.27
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 42 0.57
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (17 bp):
ATCGCAAGCGAAATAAA
Found at i:148580 original size:33 final size:32
Alignment explanation
Indices: 148538--148636 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 32
148528 AAAAATGACT
*
148538 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGAGAAA
*
148571 ATCGCAATGCGAAATTAAAATCGCAACGATAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGAGAAA
** *
148604 ATCGCAACACGAAACTAAAATCGCAACGCGAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGAGAAA
148637 CTAAATTCGC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 57 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGAGAAA
Found at i:148605 original size:14 final size:14
Alignment explanation
Indices: 148554--148611 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
148544 ATGCGAAATG
*
148554 AAAATCGCAACGAG
1 AAAATCGCAACGAT
*
148568 AGAATCGCAATGCGAAATT
1 AAAATCGCAA--CG--A-T
148587 AAAATCGCAACGAT
1 AAAATCGCAACGAT
148601 AAAATCGCAAC
1 AAAATCGCAAC
148612 ACGAAACTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:148664 original size:19 final size:19
Alignment explanation
Indices: 148642--148707 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
148632 CGAAACTAAA
*
148642 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
148661 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
148677 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
148694 TTCGCATTGCGATT
1 TTCGCATTGCGATT
148708 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 6 0.16
19 19 0.51
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:148688 original size:33 final size:33
Alignment explanation
Indices: 148646--148717 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
148636 ACTAAATTCG
148646 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
148679 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
148712 CGTTGC
1 CGTTGC
148718 AATAGTAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:152176 original size:20 final size:19
Alignment explanation
Indices: 152155--152374 Score: 129
Period size: 20 Copynumber: 10.9 Consensus size: 19
152145 GCGATAGTCA
*
152155 GAATCTCGTTGCGATTTAC
1 GAATCGCGTTGCGATTTAC
* *
152174 AGATTCGCATTGCGATTTAC
1 -GAATCGCGTTGCGATTTAC
*
152194 -ATATTCGCATTGCGATTTAC
1 GA-A-TCGCGTTGCGATTTAC
* **
152214 GTATTCGTATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* *
152234 GGATACGCATTGCGATTTAC
1 GAAT-CGCGTTGCGATTTAC
* *
152254 GTATTCTCGTTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
*
152274 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* * *
152295 GTATTCTCATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
*
152315 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* * *
152336 GGATACTCGTTGCGATAGT-C
1 GAAT-CGCGTTGCGAT-TTAC
152356 AGAATCGCGTTGCGATTTA
1 -GAATCGCGTTGCGATTTA
152375 TATGTTCGCG
Statistics
Matches: 157, Mismatches: 29, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 112 0.71
21 38 0.24
22 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (19 bp):
GAATCGCGTTGCGATTTAC
Found at i:152207 original size:40 final size:40
Alignment explanation
Indices: 152161--152412 Score: 231
Period size: 40 Copynumber: 6.2 Consensus size: 40
152151 GTCAGAATCT
* *
152161 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACATATTCG
1 CGTTGCGATTTAC-GTATTCGCATTGCGATTTACAGATACG
* * *
152201 CATTGCGATTTACGTATTCGTATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
* * * *
152241 CATTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
* *
152281 CGTTGCGATTTTACGTATTCTCATTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCGCATTGCGATTTACAGATACG
* * * * *
152322 CGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGA-TTTACGTATTCGCATTGCGAT-TTACAGATA-CG
** * * * * *
152363 CGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
152403 CGTTGCGATT
1 CGTTGCGATT
152413 ATGGAAAATC
Statistics
Matches: 182, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.01
40 108 0.59
41 71 0.39
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
Found at i:152308 original size:41 final size:40
Alignment explanation
Indices: 152161--152351 Score: 242
Period size: 40 Copynumber: 4.7 Consensus size: 40
152151 GTCAGAATCT
* ** *
152161 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACATATTCG
1 CGTTGCGATTTAC-GTATTCTCATTGCGATTTACGGATACG
*
152201 CATTGCGATTTACGTATTCGT-ATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTC-TCATTGCGATTTACGGATACG
* *
152241 CATTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCATTGCGATTTACGGATACG
152281 CGTTGCGATTTTACGTATTCTCATTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCATTGCGATTTACGGATACG
* * *
152322 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTACGTATTCTCATTGCGAT
152352 AGTCAGAATC
Statistics
Matches: 136, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.01
40 76 0.56
41 58 0.43
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCATTGCGATTTACGGATACG
Found at i:152369 original size:61 final size:61
Alignment explanation
Indices: 152178--152374 Score: 168
Period size: 61 Copynumber: 3.2 Consensus size: 61
152168 ATTTACAGAT
** * * * * ** * *
152178 TCGCATTGCGATTTACATATTCGCATTGCGATTTACGTATTCGTATTGCGAT-TTACG-GA
1 TCGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATGTCACGTAA
* * * * * *
152237 TACGCATTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 T-CGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATGTCACGTAA
* *
152299 TCTCATTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-G-AA
1 TCGCATTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACGCGTTGCGAT-GTCACGTAA
*
152360 TCGCGTTGCGATTTA
1 TCGCATTGCGATTTA
152375 TATGTTCGCG
Statistics
Matches: 114, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 1 0.01
60 44 0.39
61 45 0.39
62 22 0.19
63 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (61 bp):
TCGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATGTCACGTAA
Found at i:152383 original size:20 final size:20
Alignment explanation
Indices: 152360--152412 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
152350 ATAGTCAGAA
*
152360 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
152380 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
152400 TCGCGTTGCGATT
1 TCGCGTTGCGATT
152413 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:152490 original size:20 final size:20
Alignment explanation
Indices: 152441--152494 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
152431 AATTTGTACT
152441 ATCGCATTGCGATTCTAGGA
1 ATCGCATTGCGATTCTAGGA
152461 A-CTG-ATTTGCGATTCT-GGA
1 ATC-GCA-TTGCGATTCTAGGA
152480 GATCGCATTGCGATT
1 -ATCGCATTGCGATT
152495 TTTATTTCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
19 5 0.17
20 22 0.76
21 2 0.07
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTCTAGGA
Found at i:158012 original size:18 final size:20
Alignment explanation
Indices: 157976--158012 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
157966 GTTTCATTCT
157976 ACTAGACTAATTATGAAATG
1 ACTAGACTAATTATGAAATG
157996 ACTA-ACTAATT-TGAAAT
1 ACTAGACTAATTATGAAAT
158013 AAATACTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (20 bp):
ACTAGACTAATTATGAAATG
Found at i:166754 original size:31 final size:31
Alignment explanation
Indices: 166713--166788 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
166703 TAGGATAAAC
* *
166713 TATGTATTTAGTCATTCAATTATTTAAATGAT
1 TATGT-TTTAGTCATACAATTATTCAAATGAT
* *
166745 T-TCGTTTTAGTCATACTATTATTCAAGTGAT
1 TAT-GTTTTAGTCATACAATTATTCAAATGAT
166776 TATGTTTTAGTCA
1 TATGTTTTAGTCA
166789 CGTAACTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (31 bp):
TATGTTTTAGTCATACAATTATTCAAATGAT
Found at i:173430 original size:19 final size:18
Alignment explanation
Indices: 173406--173462 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
173396 TCTAAAGAGT
* *
173406 TAAATAGAAGAAATCATAA
1 TAAATAAAAGAAAT-AAAA
173425 TAAATAAAAGAAGATAAAA
1 TAAATAAAAGAA-ATAAAA
*
173444 TAAAGTACAAGAAATAAAA
1 TAAA-TAAAAGAAATAAAA
173463 CTCATCACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 24 0.73
20 9 0.27
ACGTcount: A:0.68, C:0.04, G:0.11, T:0.18
Consensus pattern (18 bp):
TAAATAAAAGAAATAAAA
Done.