Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004037.1 Hibiscus syriacus cultivar Beakdansim tig00008818_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: 77540
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4545 original size:35 final size:35
Alignment explanation
Indices: 4477--4550 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
4467 TTAAAATATT
* * *
4477 TATTTTTTTTAAAATTATTTACTTATTTGAAATAA
1 TATTATTTTTAAAATTATCTACTTATTTCAAATAA
*
4512 TATTATTTTT-AAATTATCTATTTAATTTCAAATAA
1 TATTATTTTTAAAATTATCTACTT-ATTTCAAATAA
4547 TATT
1 TATT
4551 GCACATAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 11 0.32
35 23 0.68
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
TATTATTTTTAAAATTATCTACTTATTTCAAATAA
Found at i:4711 original size:22 final size:21
Alignment explanation
Indices: 4686--4740 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
4676 AAATAAATAA
4686 ATATTTTTATAA-TATTATAA-
1 ATATTTTTATAATTATT-TAAT
*
4706 ATATATTTTATAATTATTTCAT
1 ATAT-TTTTATAATTATTTAAT
4728 ATAATTTTTATAA
1 AT-ATTTTTATAA
4741 AAAAAACATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.13
21 10 0.33
22 14 0.47
23 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTTATAATTATTTAAT
Found at i:6286 original size:20 final size:18
Alignment explanation
Indices: 6257--6312 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 18
6247 ATATTTAATG
6257 AAAAGATATCAATTGTTA
1 AAAAGATATCAATTGTTA
6275 ACAAAGGATATCAATTGTTA
1 A-AAA-GATATCAATTGTTA
* *
6295 AAAATATACCAATTGTTA
1 AAAAGATATCAATTGTTA
6313 CCAGTTGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 13 0.38
19 6 0.18
20 15 0.44
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (18 bp):
AAAAGATATCAATTGTTA
Found at i:9003 original size:34 final size:33
Alignment explanation
Indices: 8955--9023 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 33
8945 TTACAAACTC
* * *
8955 CCTAGTTTTTCACGGGATAAACTAGAGCCTTTT
1 CCTAGTTTTACACGGGATAAACTAGAACATTTT
* *
8988 CCTAGCTTTTACACGGGCTTAACTAGAACATTTT
1 CCTAG-TTTTACACGGGATAAACTAGAACATTTT
9022 CC
1 CC
9024 CTTTACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (33 bp):
CCTAGTTTTACACGGGATAAACTAGAACATTTT
Found at i:10298 original size:30 final size:30
Alignment explanation
Indices: 10262--10331 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
10252 ACTCAACAGG
*
10262 GACTAATTTGTAAAAGAAAGAATCCGTTTT
1 GACTAATTTGTAAAAGAAAGAATACGTTTT
*
10292 GACTAATTTGTAAAAGAAAGAATATGTTTT
1 GACTAATTTGTAAAAGAAAGAATACGTTTT
10322 GACTAATTTG
1 GACTAATTTG
10332 CAAATCTCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (30 bp):
GACTAATTTGTAAAAGAAAGAATACGTTTT
Found at i:20250 original size:17 final size:17
Alignment explanation
Indices: 20224--20263 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
20214 TCCTCTTCTT
*
20224 CTCCCTTCTTCTTCCTC
1 CTCCCCTCTTCTTCCTC
*
20241 CTCCCCTCTTCTTTCTC
1 CTCCCCTCTTCTTCCTC
20258 CTCCCC
1 CTCCCC
20264 GTGAAAGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.42
Consensus pattern (17 bp):
CTCCCCTCTTCTTCCTC
Found at i:20696 original size:21 final size:21
Alignment explanation
Indices: 20672--20719 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
20662 GAATTTAAGC
20672 TGAAAAAGATGAATTTTCGGG
1 TGAAAAAGATGAATTTTCGGG
*
20693 TGAAAATGATGAATTTTCGGG
1 TGAAAAAGATGAATTTTCGGG
20714 TGAAAA
1 TGAAAA
20720 GGCTTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.27, T:0.29
Consensus pattern (21 bp):
TGAAAAAGATGAATTTTCGGG
Found at i:22565 original size:23 final size:23
Alignment explanation
Indices: 22538--22606 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 23
22528 AATCTTATAT
22538 GGCACTAT-GGTGCATTTCTACGC
1 GGCACT-TCGGTGCATTTCTACGC
* *
22561 GGCACTTCGGTGCAAATTCTACGT
1 GGCACTTCGGTGC-ATTTCTACGC
*
22585 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
22607 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 18 0.45
24 21 0.52
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:23803 original size:29 final size:29
Alignment explanation
Indices: 23762--24099 Score: 173
Period size: 29 Copynumber: 11.8 Consensus size: 29
23752 TTAAATTATT
*
23762 AAATATATTTTATTAT-TGTTTTATCCTAA
1 AAATATATTTTATT-TCTATTTTATCCTAA
23791 AAATATATTTTATTTCTATTTTATCCTAA
1 AAATATATTTTATTTCTATTTTATCCTAA
* *
23820 AAATATATTTTATTTCTATTTTAACTTAA
1 AAATATATTTTATTTCTATTTTATCCTAA
* ** * *
23849 AAATATATTTTA-ATCTTATCATAACTTAA
1 AAATATATTTTATTTC-TATTTTATCCTAA
* * * *
23878 AAATATATTTTATTTTTATCTTAACTTTCAA
1 AAATATATTTTATTTCTATTTTATC-CT-AA
** * * *
23909 AAATATA-TCCA---C-ATATTAACATTAA
1 AAATATATTTTATTTCTATTTTATC-CTAA
* **
23934 AAATATTTTTTTATTT-TAAATTAT--T--
1 AAATA-TATTTTATTTCTATTTTATCCTAA
*
23959 AAATATATTTTATTAT-TGTTTTATCCTAA
1 AAATATATTTTATT-TCTATTTTATCCTAA
* * *
23988 AAATTTATTTTATTTCTATTTTAACTTAA
1 AAATATATTTTATTTCTATTTTATCCTAA
* ** * *
24017 AAATATATTTTGATCT-TATCATAACTTAA
1 AAATATATTTT-ATTTCTATTTTATCCTAA
* * **
24046 AAATATATTTTATTTTTATCTTAACTTTTAA
1 AAATATATTTTATTTCTAT-TTTA-TCCTAA
* *
24077 AAATATATCTTATTTTTATTTTA
1 AAATATATTTTATTTCTATTTTA
24100 ACTTATTACA
Statistics
Matches: 249, Mismatches: 39, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
24 8 0.03
25 18 0.07
26 10 0.04
27 4 0.02
28 7 0.03
29 154 0.62
30 17 0.07
31 31 0.12
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (29 bp):
AAATATATTTTATTTCTATTTTATCCTAA
Found at i:23828 original size:58 final size:58
Alignment explanation
Indices: 23762--24084 Score: 218
Period size: 58 Copynumber: 5.6 Consensus size: 58
23752 TTAAATTATT
* * * ** *
23762 AAATATATTTTATTAT-TGTTTTATCCTAAAAATATATTTT-ATTTCTATTTTATCCTAA
1 AAATATATTTTATT-TCTATTTTAACCTAAAAATATATTTTAATCT-TATCATAACCTAA
* *
23820 AAATATATTTTATTTCTATTTTAACTTAAAAATATATTTTAATCTTATCATAACTTAA
1 AAATATATTTTATTTCTATTTTAACCTAAAAATATATTTTAATCTTATCATAACCTAA
* * * ** * * *
23878 AAATATATTTTATTTTTATCTTAACTTTCAAAAATATA--TCCA-CATAT--TAACATTA
1 AAATATATTTTATTTCTATTTTAAC-CT-AAAAATATATTTTAATCTTATCATAACCTAA
** * * * * ** *
23933 AAA-ATA-TTT-TTT-TATTTTAAATTATTAAATATATTTTATTATTGTTTTATCCTAA
1 AAATATATTTTATTTCTATTTTAACCTA-AAAATATATTTTAATCTTATCATAACCTAA
* * * *
23988 AAATTTATTTTATTTCTATTTTAACTTAAAAATATATTTTGATCTTATCATAACTTAA
1 AAATATATTTTATTTCTATTTTAACCTAAAAATATATTTTAATCTTATCATAACCTAA
* * *
24046 AAATATATTTTATTTTTATCTTAACTTTTAAAAATATAT
1 AAATATATTTTATTTCTATTTTAAC--CTAAAAATATAT
24085 CTTATTTTTA
Statistics
Matches: 208, Mismatches: 41, Indels: 30
0.75 0.15 0.11
Matches are distributed among these distances:
49 1 0.00
50 9 0.04
51 7 0.03
52 4 0.02
53 5 0.02
54 3 0.01
55 17 0.08
56 2 0.01
57 8 0.04
58 115 0.55
59 16 0.08
60 21 0.10
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (58 bp):
AAATATATTTTATTTCTATTTTAACCTAAAAATATATTTTAATCTTATCATAACCTAA
Found at i:24009 original size:197 final size:199
Alignment explanation
Indices: 23717--24103 Score: 627
Period size: 197 Copynumber: 1.9 Consensus size: 199
23707 TTTAACTTAA
23717 ATCCACACATTAACATTAAAAATATTTTTTTTATTTTAAATTATTAAATATATTTTATTATTGTT
1 ATCCACACATTAACATTAAAAATATTTTTTTTATTTTAAATTATTAAATATATTTTATTATTGTT
* * **
23782 TTATCCTAAAAATATATTTTATTTCTATTTTATCCTAAAAATATATTTT-ATTTCTATTTTAACT
66 TTATCCTAAAAATATATTTTATTTCTATTTTAACCTAAAAATATATTTTGATCT-TATCATAACT
*
23846 TAAAAATATATTTTAATCTTATCATAAC-TTAAAAATATATTTTATTTTTATCTTAACTTTCAAA
130 TAAAAATATATTTTAATCTTATCATAACTTTAAAAATATATCTTATTTTTATCTTAACTTTCAAA
23910 AATAT
195 AATAT
*
23915 ATCCACATATTAACATTAAAAATA-TTTTTTTATTTTAAATTATTAAATATATTTTATTATTGTT
1 ATCCACACATTAACATTAAAAATATTTTTTTTATTTTAAATTATTAAATATATTTTATTATTGTT
* *
23979 TTATCCTAAAAATTTATTTTATTTCTATTTTAACTTAAAAATATATTTTGATCTTATCATAACTT
66 TTATCCTAAAAATATATTTTATTTCTATTTTAACCTAAAAATATATTTTGATCTTATCATAACTT
* * * *
24044 AAAAATATATTTTATTTTTATCTTAACTTTTAAAAATATATCTTATTTTTATTTTAACTT
131 AAAAATATATTTTAATCTTATCATAAC-TTTAAAAATATATCTTATTTTTATCTTAACTT
24104 ATTACATATA
Statistics
Matches: 174, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
197 119 0.68
198 26 0.15
199 29 0.17
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.53
Consensus pattern (199 bp):
ATCCACACATTAACATTAAAAATATTTTTTTTATTTTAAATTATTAAATATATTTTATTATTGTT
TTATCCTAAAAATATATTTTATTTCTATTTTAACCTAAAAATATATTTTGATCTTATCATAACTT
AAAAATATATTTTAATCTTATCATAACTTTAAAAATATATCTTATTTTTATCTTAACTTTCAAAA
ATAT
Found at i:24136 original size:30 final size:30
Alignment explanation
Indices: 24097--24184 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
24087 TATTTTTATT
* *
24097 TTAACTTATTACATATATTATATTCTTAAC
1 TTAAATTATTAAATATATTATATTCTTAAC
* * *
24127 TTATATTATTAAATATATTCT-TGTCTTACC
1 TTAAATTATTAAATATATTATAT-TCTTAAC
* *
24157 TTAAATTATTAAATATAATATATCCTTA
1 TTAAATTATTAAATATATTATATTCTTA
24185 TTTTAACATA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.96
31 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (30 bp):
TTAAATTATTAAATATATTATATTCTTAAC
Found at i:24244 original size:26 final size:26
Alignment explanation
Indices: 24207--24280 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
24197 ATATATATTT
* *
24207 TATTATTATTTTTAACTTAAAAATGTA
1 TATT-TTATTTTTAATTTAAAAATGAA
*
24234 TATTTTATTTTTTATTTAAAAATGAA
1 TATTTTATTTTTAATTTAAAAATGAA
24260 TATTTTATTTTTTAATTTAAA
1 TATTTTA-TTTTTAATTTAAA
24281 TATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 26 0.62
27 16 0.38
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (26 bp):
TATTTTATTTTTAATTTAAAAATGAA
Found at i:24254 original size:25 final size:25
Alignment explanation
Indices: 24207--24296 Score: 87
Period size: 26 Copynumber: 3.6 Consensus size: 25
24197 ATATATATTT
* *
24207 TATTATTATTTTTAACTTAAAAATGTA
1 TATT-TTATTTTTTA-TTTAAAATGTA
*
24234 TATTTTATTTTTTATTTAAAAATGAA
1 TATTTTATTTTTTATTT-AAAATGTA
24260 TATTTTATTTTTTAATTT-AAA--TA
1 TATTTTATTTTTT-ATTTAAAATGTA
*
24283 TATATTATTTTTTA
1 TATTTTATTTTTTA
24297 AAATTTCAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
22 1 0.02
23 13 0.23
25 5 0.09
26 29 0.52
27 8 0.14
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTTATTTTTTATTTAAAATGTA
Found at i:24301 original size:25 final size:24
Alignment explanation
Indices: 24232--24309 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 24
24222 CTTAAAAATG
* *
24232 TATATTTTATTTTTT-ATTTAAAAA
1 TATATATTATTTTTTAATTT-CAAA
*
24256 TGAATATTTTATTTTTTAATTT-AAA
1 T--ATATATTATTTTTTAATTTCAAA
24281 TATATATTATTTTTTAAAATTTCAAA
1 TATATATTATTTTTT--AATTTCAAA
24307 TAT
1 TAT
24310 TATAAGAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
23 13 0.28
24 1 0.02
25 9 0.19
26 20 0.43
27 4 0.09
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (24 bp):
TATATATTATTTTTTAATTTCAAA
Found at i:24324 original size:23 final size:22
Alignment explanation
Indices: 24295--24337 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
24285 TATTATTTTT
24295 TAAAATT-TCAAATATTATAAGAA
1 TAAAATTAT-AAATATT-TAAGAA
24318 TAAAATTATAAATATTTAAG
1 TAAAATTATAAATATTTAAG
24338 TTAAGGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
TAAAATTATAAATATTTAAGAA
Found at i:30705 original size:37 final size:37
Alignment explanation
Indices: 30632--30706 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
30622 GTTAGAAAAC
* * *
30632 ATTTATATATTTTCTTTATAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTACAAAATTGAAAATCATAAA
*
30669 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTACAAAATTGAAAATCATAAA
30706 A
1 A
30707 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTACAAAATTGAAAATCATAAA
Found at i:32714 original size:228 final size:228
Alignment explanation
Indices: 32317--32806 Score: 849
Period size: 228 Copynumber: 2.1 Consensus size: 228
32307 GTTATATTGT
* * * *
32317 AAAGTATTTATCCTTTTTATAAAAATGTCCATACTTATTTCACTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
*
32382 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
66 TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
32447 TAATTTTGTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAA
131 TAATTTTGTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATT-A
32512 AAAAAATTGAAACATAAATTACATAACTTT-AAA
195 AAAAAATTGAAACATAAATTACATAACTTTAAAA
*
32545 AAAGTATATATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTG-AAAACATATTTATTATT
*
32610 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAA
65 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
* * * *
32674 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACGCTATTA
130 ATAATTTTGTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTA
32739 AAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAATTGAAACATAAATTACATAACTTTAAAA
32773 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
32807 GTATAAAAGT
Statistics
Matches: 248, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
227 31 0.12
228 148 0.60
229 69 0.28
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (228 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
TAATTTTGTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAA
AAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:33236 original size:181 final size:182
Alignment explanation
Indices: 32874--33348 Score: 686
Period size: 181 Copynumber: 2.6 Consensus size: 182
32864 TCGATCCAAA
* * * * * *
32874 TAAAAAATGTGTCCATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATG
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACTGGT-TACAAAATG
* * * * *
32938 ATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACAC
65 ATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
*
33003 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTT
130 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTT
*
33056 TAAAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACTGGTTACAAAATGA
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACTGGTTACAAAATGA
* * * *
33121 TAAAACCGATAAAACGTTACCAGATATATTGAAAGTGTCGCTACTTT-ATATAAGGATCGACACT
66 TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
* ** *
33185 TTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTT
131 TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTT
* * *
33237 AAAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACTGG-TATCAAAATG
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACTGGTTA-CAAAATG
*
33301 ATAAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
65 ATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
33349 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 28, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
180 2 0.01
181 166 0.63
182 95 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACTGGTTACAAAATGA
TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTT
Found at i:33292 original size:20 final size:19
Alignment explanation
Indices: 33269--33315 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
33259 CGATATAACA
*
33269 GGTAAAAATATGATAAAACT
1 GGTAAAAA-ATGATAAAACC
*
33289 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
33309 GGTAAAA
1 GGTAAAA
33316 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:35550 original size:21 final size:21
Alignment explanation
Indices: 35526--35569 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
35516 AAGACAATCA
35526 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
35547 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
35568 AG
1 AG
35570 GCATAAGGGG
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:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:35645 original size:33 final size:33
Alignment explanation
Indices: 35603--35668 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
35593 AAATAGATGG
*
35603 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
35636 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
35669 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:37479 original size:19 final size:19
Alignment explanation
Indices: 37455--37503 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
37445 AATGTAGGGT
37455 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
37474 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
37493 TATTTTTGTAT
1 TAATTTTGTAT
37504 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:37966 original size:198 final size:198
Alignment explanation
Indices: 37622--38201 Score: 1090
Period size: 198 Copynumber: 2.9 Consensus size: 198
37612 CAATATGGCC
*
37622 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
*
37687 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATAAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
37752 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAA
37817 TGGAA
194 TGGAA
*
37822 AAC-TGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
37886 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
37951 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
38016 GAA
196 GAA
38019 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
38084 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
38149 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGT
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGT
38202 TAAATAGTTC
Statistics
Matches: 373, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
197 42 0.11
198 272 0.73
199 56 0.15
200 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
GAA
Found at i:38816 original size:18 final size:18
Alignment explanation
Indices: 38795--38831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38785 GTAATTGGAG
38795 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
38813 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
38831 T
1 T
38832 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:38839 original size:24 final size:24
Alignment explanation
Indices: 38787--38833 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
38777 TTTCATAAGT
* *
38787 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
38811 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
38834 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:39145 original size:39 final size:39
Alignment explanation
Indices: 39102--39188 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
39092 TCCGATGCTC
* *
39102 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
*
39141 ATCAAAATCCAAATCTCATATGATGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
39180 ATCAAAATC
1 ATCAAAATC
39189 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
Found at i:39669 original size:23 final size:23
Alignment explanation
Indices: 39609--39681 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
39599 ATAGGTAAAA
* *
39609 ATATGATGTAATAGATAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
39632 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
39655 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
39678 ATAT
1 ATAT
39682 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:39955 original size:21 final size:21
Alignment explanation
Indices: 39937--40010 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
39927 GTGGAAAACA
39937 TGAAACACTATTAAAAAAAAT
1 TGAAACACTATTAAAAAAAAT
* *
39958 TGAAACA-TAAATTACATAACTTACA-
1 TGAAACACT--ATTA-A-AA--AAAAT
39983 TGAAACACTATTAAAAAAAAT
1 TGAAACACTATTAAAAAAAAT
40004 TGAAACA
1 TGAAACA
40011 TAAATTACAT
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
20 3 0.07
21 14 0.34
22 6 0.15
23 2 0.05
24 6 0.15
25 7 0.17
26 3 0.07
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.24
Consensus pattern (21 bp):
TGAAACACTATTAAAAAAAAT
Found at i:39987 original size:46 final size:46
Alignment explanation
Indices: 39934--40025 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
39924 TAGGTGGAAA
39934 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTT
39980 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTT
40026 TAAAAGAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (46 bp):
ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTT
Found at i:40117 original size:23 final size:23
Alignment explanation
Indices: 40086--40158 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
40076 ATAGGTAAAA
*
40086 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
40109 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
40132 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
40155 ATAT
1 ATAT
40159 TGTAAAGTAT
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:40413 original size:477 final size:475
Alignment explanation
Indices: 39504--40455 Score: 1814
Period size: 477 Copynumber: 2.0 Consensus size: 475
39494 TAGGTGGAAA
*
39504 ACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATT
1 ACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATT
39569 TTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTAT
66 TTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTAT
39634 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCT
131 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCT
39699 TTTTATAAAAGTGTACATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGTG
196 TTTTATAAAAGTGTACATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGTG
39764 AGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATAT
261 AGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATAT
39829 ATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
326 ATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
39894 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
391 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATT
39959 GAAACATAAATTACATAACTT
455 GAAACATAAATTACATAACTT
*
39980 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCT
1 ACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
* *
40045 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
65 TTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTA
40110 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
130 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
* * *
40175 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAATGTTATCTTTTGAGT
195 TTTTTATAAAAGTGTACATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGT
40240 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
260 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
40305 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
325 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
40370 TTGTGCAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
390 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
40435 GAAACATAAATTACATAACTT
455 GAAACATAAATTACATAACTT
40456 TAAAAGAAGT
Statistics
Matches: 467, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
476 44 0.09
477 423 0.91
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (475 bp):
ACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATT
TTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTAT
ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCT
TTTTATAAAAGTGTACATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGTG
AGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATAT
ATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTT
Found at i:40547 original size:23 final size:23
Alignment explanation
Indices: 40516--40588 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
40506 ATAGGTAAAA
*
40516 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
** * *
40539 ATATAATGTAATATATATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
40562 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
40585 ATAT
1 ATAT
40589 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:40613 original size:46 final size:45
Alignment explanation
Indices: 40516--40613 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
40506 ATAGGTAAAA
* *
40516 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATATATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATATATCCTTT
* * *
40562 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATATATCCTTT
*
40608 TTATAA
1 ATATAA
40614 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATATATCCTTT
Found at i:40978 original size:23 final size:23
Alignment explanation
Indices: 40947--41019 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
40937 ATAGGTAAAA
*
40947 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
40970 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
40993 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
41016 ATAT
1 ATAT
41020 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:41044 original size:46 final size:45
Alignment explanation
Indices: 40947--41044 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
40937 ATAGGTAAAA
* * *
40947 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTATCATTT
* *
40993 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCATTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTATCATTT
*
41039 TTATAA
1 ATATAA
41045 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTATCATTT
Found at i:41084 original size:431 final size:431
Alignment explanation
Indices: 39980--42661 Score: 5118
Period size: 430 Copynumber: 6.2 Consensus size: 431
39970 TACATAACTT
*
39980 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
40045 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
*
40110 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
*
40175 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAATGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
40240 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
40305 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
40370 TTGTGCAAATTAAATTATTAAATTAATATTGTAGGTGGAAA
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
40411 ACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
40475 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
*
40540 TATAATGTAATATATATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
*
40605 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
40670 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
40735 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
40800 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGAAAA
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
40841 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
40906 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
*
40971 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCA
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
*
41036 TTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
41101 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
41165 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
41230 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
* *
41271 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
41336 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
*
41401 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
*
41466 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAAAATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
41531 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
*
41596 TATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
41661 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
41702 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
41767 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
* *
41832 TATAATGTAATATATATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTATCTATCC
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
* *
41897 TTTTTATAAAAGTGTTCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
41962 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
*
42027 TATTTTTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
42092 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGAAAA
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
*
42133 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
42198 TTTTATAAAAAGT-TGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
42262 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
* *
42327 TTTTTATAAAAGTGTCCAAACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
42392 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
*
42457 TATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
42522 TTGTGGAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
42563 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
42628 TTTTATAAAAAGTATGGACACTTTCAATATAATA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATA
42662 TAATGTAATA
Statistics
Matches: 2208, Mismatches: 40, Indels: 6
0.98 0.02 0.00
Matches are distributed among these distances:
430 1267 0.57
431 941 0.43
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (431 bp):
ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
Found at i:41321 original size:861 final size:862
Alignment explanation
Indices: 39980--42661 Score: 5136
Period size: 861 Copynumber: 3.1 Consensus size: 862
39970 TACATAACTT
*
39980 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
40045 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
*
40110 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
* *
40175 TTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAATGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
40240 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
40305 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
40370 TTGTGCAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAAT
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
40434 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
456 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
*
40499 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATATATCGTTTAT
521 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTAT
40564 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
586 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
*
40629 TTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTAAGATATTAATTTAGTA
651 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTA
40694 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCT
716 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCT
*
40759 AAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATT
781 AAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATT
*
40824 AATATTGTAGGTGAAAA
846 AATATTGTAGGTGGAAA
40841 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
40906 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
*
40971 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCA
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
41036 TTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
41101 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
41165 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
41230 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
* *
41295 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTT
456 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
*
41360 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTAT
521 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTAT
41425 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
586 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
*
41490 TTTCACTGTGGAAAAAATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTA
651 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTA
41555 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCT
716 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCT
41620 AAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATT
781 AAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATT
41685 AATATTGTAGGTGGAAA
846 AATATTGTAGGTGGAAA
41702 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
41767 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
* *
41832 TATAATGTAATATATATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTATCTATCC
131 TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
*
41897 TTTTTATAAAAGTGTTCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
196 TTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
41962 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
261 GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
*
42027 TATTTTTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
326 TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
42092 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAAAT
391 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
*
42157 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGT-TGGACACTTT
456 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
42221 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTAT
521 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTAT
*
42286 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCAAACTTT
586 ATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
*
42351 TTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTA
651 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTA
42416 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCT
716 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCT
*
42481 AAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGGAAATGAAATTATTAAATT
781 AAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATT
42546 AATATTGTAGGTGGAAA
846 AATATTGTAGGTGGAAA
42563 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
1 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
42628 TTTTATAAAAAGTATGGACACTTTCAATATAATA
66 TTTTATAAAAAGTATGGACACTTTCAATATAATA
42662 TAATGTAATA
Statistics
Matches: 1792, Mismatches: 27, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
860 138 0.08
861 1456 0.81
862 198 0.11
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (862 bp):
ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCAT
TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
TATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCC
TTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
GAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
TATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTAT
ATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTA
ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCT
AAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATT
AATATTGTAGGTGGAAA
Found at i:41408 original size:23 final size:23
Alignment explanation
Indices: 41377--41449 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
41367 ATAGGTAAAA
*
41377 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
41400 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
41423 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
41446 ATAT
1 ATAT
41450 TGTAAAGTAT
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:41839 original size:23 final size:23
Alignment explanation
Indices: 41808--41870 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
41798 ATAGGTAAAA
*
41808 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
** * *
41831 ATATAATGTAATATATATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
41854 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
41871 ATGGTTATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:41878 original size:23 final size:23
Alignment explanation
Indices: 41808--41880 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
41798 ATAGGTAAAA
* **
41808 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAATGCTT
*
41831 ATATAATGTAATA--TATATCGTTT
1 ATATAATGTAATAGGTA-AT-GCTT
*
41854 ATATAATGTAATAGGTAATGGTT
1 ATATAATGTAATAGGTAATGCTT
41877 ATAT
1 ATAT
41881 TGTAAAGTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.05
23 35 0.85
24 2 0.05
25 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAATGCTT
Found at i:42269 original size:23 final size:23
Alignment explanation
Indices: 42238--42310 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
42228 ATAGGTAAAA
*
42238 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
42261 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
42284 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
42307 ATAT
1 ATAT
42311 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:42335 original size:46 final size:45
Alignment explanation
Indices: 42238--42335 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
42228 ATAGGTAAAA
* * *
42238 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTATCCTTT
* *
42284 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTATCCTTT
*
42330 TTATAA
1 ATATAA
42336 AAGTGTCCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTATCCTTT
Found at i:49942 original size:12 final size:13
Alignment explanation
Indices: 49924--49953 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
49914 TCACGTTTGG
49924 GAGAAGAAGATGA
1 GAGAAGAAGATGA
49937 -AGAAGAAGATGA
1 GAGAAGAAGATGA
49949 GAGAA
1 GAGAA
49954 TTGCTTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (13 bp):
GAGAAGAAGATGA
Found at i:50645 original size:31 final size:31
Alignment explanation
Indices: 50609--50667 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
50599 AACTTAAAAG
*
50609 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
50640 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
50668 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:52783 original size:65 final size:64
Alignment explanation
Indices: 52650--52809 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 64
52640 TGCACTAAGA
* * *
52650 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTAAGTGCATCGATGCATGTCTT
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTTCAAAATAACCTAAGTGCATCGATGCATGTCAT
*
52714 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTGAGTGCATCGATGCATGGT-
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTTCA-AAATAACCTAAGTGCATCGATGCAT-GTC
52777 AT
63 AT
52779 GTGCATCGATGCATATAATGCATTCGATGTT
1 GTGCATCGATGCATA-AATGCATTCGATGTT
52810 CAATTTATTC
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 28 0.32
65 54 0.62
66 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTTCAAAATAACCTAAGTGCATCGATGCATGTCAT
Found at i:59377 original size:218 final size:218
Alignment explanation
Indices: 58999--59429 Score: 862
Period size: 218 Copynumber: 2.0 Consensus size: 218
58989 GAGCTCTATG
58999 AACCGGCTTTTGTCTCCGGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAGTTTGAGTT
1 AACCGGCTTTTGTCTCCGGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAGTTTGAGTT
59064 TGTTTCTAGTGCCTTGTAGCAATGCTCATTTTCCTACAAACATAGATTAATTTTTTATTTTTGGT
66 TGTTTCTAGTGCCTTGTAGCAATGCTCATTTTCCTACAAACATAGATTAATTTTTTATTTTTGGT
59129 ACCCAAATTCTTTTGGGTCCATATTCATTAGTTTCCAAAATCCTAGTCCCCATAGGTATCCATTT
131 ACCCAAATTCTTTTGGGTCCATATTCATTAGTTTCCAAAATCCTAGTCCCCATAGGTATCCATTT
59194 GTGTAGGATATCATTATCCTACA
196 GTGTAGGATATCATTATCCTACA
59217 AACCGGCTTTTGTCTCCGGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAGTTTGAGTT
1 AACCGGCTTTTGTCTCCGGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAGTTTGAGTT
59282 TGTTTCTAGTGCCTTGTAGCAATGCTCATTTTCCTACAAACATAGATTAATTTTTTATTTTTGGT
66 TGTTTCTAGTGCCTTGTAGCAATGCTCATTTTCCTACAAACATAGATTAATTTTTTATTTTTGGT
59347 ACCCAAATTCTTTTGGGTCCATATTCATTAGTTTCCAAAATCCTAGTCCCCATAGGTATCCATTT
131 ACCCAAATTCTTTTGGGTCCATATTCATTAGTTTCCAAAATCCTAGTCCCCATAGGTATCCATTT
59412 GTGTAGGATATCATTATC
196 GTGTAGGATATCATTATC
59430 TTTAGTAGTA
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 213 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (218 bp):
AACCGGCTTTTGTCTCCGGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAGTTTGAGTT
TGTTTCTAGTGCCTTGTAGCAATGCTCATTTTCCTACAAACATAGATTAATTTTTTATTTTTGGT
ACCCAAATTCTTTTGGGTCCATATTCATTAGTTTCCAAAATCCTAGTCCCCATAGGTATCCATTT
GTGTAGGATATCATTATCCTACA
Found at i:61835 original size:65 final size:64
Alignment explanation
Indices: 61713--61871 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 64
61703 GCACTAAGAG
* * * *
61713 TGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGTATCGATGCAT-GTCTT
1 TGCATCGATGCAT-AAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCGATGCATGGT-AT
61776 A
64 A
*
61777 TGCATCGATGCATCAAATGCTTTCGATGTTTTCATAAA-AACCTGAGTGCATCGATGCATGGTAT
1 TGCATCGATGCAT-AAATGCATTCGATGTTTTCA-AAATAACCTGAGTGCATCGATGCATGGTAT
*
61841 G
64 A
61842 TGCATCGATGCATATAATGCATTCGATGTT
1 TGCATCGATGCATA-AATGCATTCGATGTT
61872 CAATTTATTC
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 26 0.31
65 52 0.63
66 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCATAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCGATGCATGGTATA
Done.