Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007914.1 Hibiscus syriacus cultivar Beakdansim tig00110317_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: 500553
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:262216 original size:31 final size:31
Alignment explanation
Indices: 262169--262227 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
262159 AAAGTAACAA
* *
262169 ATTAATTTTATCGATTTATAATAAATAAATT
1 ATTAATATTATCGATTTATAACAAATAAATT
* *
262200 ATTAATATTATTGATTTATTACAAATAA
1 ATTAATATTATCGATTTATAACAAATAA
262228 GGAACCCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTAATATTATCGATTTATAACAAATAAATT
Found at i:263847 original size:17 final size:18
Alignment explanation
Indices: 263812--263852 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
263802 ATATTATGTA
*
263812 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
263830 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
263847 TTTACT
1 TTTACT
263853 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:265543 original size:18 final size:18
Alignment explanation
Indices: 265516--265557 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
265506 ACAGCATCCA
*
265516 CCGCAACCATTTATGATG
1 CCGCAACCATATATGATG
* *
265534 TCGCAGCCATATATGATG
1 CCGCAACCATATATGATG
265552 CCGCAA
1 CCGCAA
265558 TCGCCTTTCC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:265905 original size:3 final size:3
Alignment explanation
Indices: 265897--265925 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
265887 ACCTGCTCAG
265897 GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
265926 TGATGACAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:267301 original size:18 final size:18
Alignment explanation
Indices: 267278--267320 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
267268 AAAATGTATA
* *
267278 ACTTACTAATTTGCTTTC
1 ACTTACCAACTTGCTTTC
*
267296 ACTTACCCACTTGCTTTC
1 ACTTACCAACTTGCTTTC
267314 ACTTACC
1 ACTTACC
267321 CATGCGCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.42
Consensus pattern (18 bp):
ACTTACCAACTTGCTTTC
Found at i:267321 original size:18 final size:18
Alignment explanation
Indices: 267288--267322 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
267278 ACTTACTAAT
267288 TTGCTTTCACTTACCCAC
1 TTGCTTTCACTTACCCAC
267306 TTGCTTTCACTTACCCA
1 TTGCTTTCACTTACCCA
267323 TGCGCACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (18 bp):
TTGCTTTCACTTACCCAC
Found at i:267683 original size:17 final size:16
Alignment explanation
Indices: 267661--267702 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
267651 TCATCAGTTC
267661 TTATCAATCAAAATCA
1 TTATCAATCAAAATCA
* *
267677 TTAATCAATCAAATTCC
1 TT-ATCAATCAAAATCA
267694 TTATCAATC
1 TTATCAATC
267703 TTTAATTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (16 bp):
TTATCAATCAAAATCA
Found at i:270106 original size:20 final size:21
Alignment explanation
Indices: 270067--270106 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
270057 ATGTCACGAG
270067 AAACACACATATCATTATATCA
1 AAACACACATAT-ATTATATCA
*
270089 AAACATACATAT-TTATAT
1 AAACACACATATATTATAT
270107 ACAATCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
AAACACACATATATTATATCA
Found at i:270373 original size:23 final size:23
Alignment explanation
Indices: 270337--270428 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
270327 CACCACAGAT
* * *
270337 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * *
270360 CGTAGAATTACACCGTAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
** *
270383 CGTAGAAATACACCTTAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
*
270406 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
270429 TATAATAATG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:271868 original size:21 final size:21
Alignment explanation
Indices: 271844--271888 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
271834 TTTTGTTCGT
271844 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
271865 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
271886 TTG
1 TTG
271889 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:274016 original size:41 final size:41
Alignment explanation
Indices: 273971--274065 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
273961 GCCCACTGAT
*
273971 CCGCGCTATACCCCTATGTGATGTATAGCACGGATCAGGGG
1 CCGCGCTATACCCCTATGTGACGTATAGCACGGATCAGGGG
**
274012 CCGCGCTATACCCCTATGTGACGTATAGCGTGGATCAGGGG
1 CCGCGCTATACCCCTATGTGACGTATAGCACGGATCAGGGG
*
274053 CTGCGCTATACCC
1 CCGCGCTATACCC
274066 ACGTGTAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.22
Consensus pattern (41 bp):
CCGCGCTATACCCCTATGTGACGTATAGCACGGATCAGGGG
Found at i:276030 original size:18 final size:17
Alignment explanation
Indices: 275993--276043 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
275983 TCAGATTCAT
*
275993 ATTCCAATTCCT-ACAG
1 ATTCCAATTCCTCATAG
276009 ATTCCAATTCCTTCATAG
1 ATTCCAATTCC-TCATAG
*
276027 ATTCTAATTCCCTCATA
1 ATTCCAATT-CCTCATA
276044 AACATTCCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 11 0.37
17 1 0.03
18 16 0.53
19 2 0.07
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.37
Consensus pattern (17 bp):
ATTCCAATTCCTCATAG
Found at i:279724 original size:14 final size:14
Alignment explanation
Indices: 279707--279747 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
279697 ACTGCTTACA
279707 ACATAACACTTAAT
1 ACATAACACTTAAT
* *
279721 ACATAACACTGATT
1 ACATAACACTTAAT
279735 ACATAACACTTAA
1 ACATAACACTTAA
279748 ACCAAAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (14 bp):
ACATAACACTTAAT
Found at i:289755 original size:21 final size:21
Alignment explanation
Indices: 289731--289773 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
289721 AAACCCCTTG
289731 TTCTCTATCTCTCTCTTATGT
1 TTCTCTATCTCTCTCTTATGT
289752 TTCTCTATCTCTCTCTTATGT
1 TTCTCTATCTCTCTCTTATGT
289773 T
1 T
289774 ATGAAGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.28, G:0.05, T:0.58
Consensus pattern (21 bp):
TTCTCTATCTCTCTCTTATGT
Found at i:292775 original size:30 final size:30
Alignment explanation
Indices: 292694--292775 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
292684 ATAATAATTC
* *
292694 ATTTGATCTCACAATTGTAATTAAAAGTTT
1 ATTTGATCTCGCAATTCTAATTAAAAGTTT
* * * *
292724 ATTTGA-CCCTGTAGTTTTAATTAAAAGTTT
1 ATTTGATCTC-GCAATTCTAATTAAAAGTTT
292754 ATTTGATCTCGCAATTCTAATT
1 ATTTGATCTCGCAATTCTAATT
292776 TTATTACAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 2 0.05
30 37 0.90
31 2 0.05
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (30 bp):
ATTTGATCTCGCAATTCTAATTAAAAGTTT
Found at i:294095 original size:22 final size:21
Alignment explanation
Indices: 294058--294103 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
294048 TTTTAGTCTT
294058 AAAATAATTTCAAAACAATTTAC
1 AAAATAATTTCAAAAC-ATTT-C
*
294081 AAAAT-ATTTCGAAACATTTC
1 AAAATAATTTCAAAACATTTC
294101 AAA
1 AAA
294104 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 9 0.41
23 5 0.23
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAATTTCAAAACATTTC
Found at i:299957 original size:23 final size:21
Alignment explanation
Indices: 299931--299992 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 21
299921 AATCTCATGA
299931 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTT--AG
*
299954 GGGAACCGATTCCCCCCTTAG
1 GGGAACCGATTCCCCCTTTAG
* *
299975 GGGAATCGATACCCCCTT
1 GGGAACCGATTCCCCCTT
299993 GGGGTTATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 17 0.49
23 18 0.51
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTTTAG
Found at i:304363 original size:32 final size:32
Alignment explanation
Indices: 304323--304407 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 32
304313 CTTTATTTTG
*
304323 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGTAATA
*
304355 TTCGGGTCGGATCGGGTTTTTTTAAGTGTAATA
1 TTCGGGTCGGGTCGGG-TTTTTTAAGTGTAATA
304388 TTCGGGTCGGGTTCGGGTTT
1 TTCGGGTCGGG-TCGGGTTT
304408 AGGATGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
32 15 0.31
33 28 0.58
34 5 0.10
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.41
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGGTTTTTTAAGTGTAATA
Found at i:304628 original size:38 final size:38
Alignment explanation
Indices: 304567--304653 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
304557 TTTATTTTGT
304567 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC-GAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAG-G
304604 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGG
304642 TCGGGTCGGGTT
1 TCGGGTCGGGTT
304654 CGGGTGTAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 10 0.21
38 37 0.77
39 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.38
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGG
Found at i:304638 original size:243 final size:236
Alignment explanation
Indices: 304113--304647 Score: 713
Period size: 238 Copynumber: 2.2 Consensus size: 236
304103 TTTATTTTGG
* * *
304113 TCGGGCCGGATC-GGATTTTTTAAGTGTGATATTTGGGTCGGGTCGGGTTTAGGTTTAGGGTTAA
1 TCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTTAGG--TA--G-TAA
**
304177 AAAAAACAGACCGACCCGAAAATATATATAATTCGGGTCAGGTCAGATTAAGTCACTGTTTTTAT
61 AAAAAACAGACCGACCCGAAAATATATATAATTCGGACCAGGTCAGATTAAGTCACTGTTTTTAT
* *
304242 TAAATAAAAATATTTTTTTATTATTTCGGGTCGGTTCGGATTTCTAATTCATATATTCGGGTCGG
126 TAAATAAAAATATTTTTTTATTATTTCGGGTCGGTTCGGATTTCTAATTCATAGAGTCGGGTCGG
304307 ATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
191 ATGAAACTTTATTTTGTT---GTCGGGTCGGGTTTTTTAAGTGTGATAT
* *
304356 TCGGGTCGGATCGGGTTTTTTTAAGTGTAATATTCGGGTCGGGTTCGGGTTTAGG-A-T-GAAAA
1 TCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG-TCGGGTTTAGGTAGTAAAAAA
* *
304418 AACCGTACCGACCCGAAAATATATATAATTCGGACCGGGTCAGATTAAGTCACTGTTTTTATTAA
65 AACAG-ACCGACCCGAAAATATATATAATTCGGACCAGGTCAGATTAAGTCACTGTTTTTATTAA
* *
304483 ATAAAAATATTTTTTTATTATTTTGGGTCGAGTCGGGTCGGATTTCTAATTCATAGGGTCGGGTC
129 ATAAAAATATTTTTTTATTATTTCGGGTCG-GT----TCGGATTTCTAATTCATAGAGTCGGGTC
304548 GGATGAAACTTTATTTTG-T-TCGGGTCGGGTTTTTTAAGTGTGATAT
189 GGATGAAACTTTATTTTGTTGTCGGGTCGGGTTTTTTAAGTGTGATAT
* *
304594 TCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGT
1 TC--G--G-GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGT
304648 CGGGTTCGGG
Statistics
Matches: 263, Mismatches: 16, Indels: 27
0.86 0.05 0.09
Matches are distributed among these distances:
237 8 0.03
238 115 0.44
239 2 0.01
240 1 0.00
242 9 0.03
243 90 0.34
244 27 0.10
245 11 0.04
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (236 bp):
TCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTTAGGTAGTAAAAAAA
ACAGACCGACCCGAAAATATATATAATTCGGACCAGGTCAGATTAAGTCACTGTTTTTATTAAAT
AAAAATATTTTTTTATTATTTCGGGTCGGTTCGGATTTCTAATTCATAGAGTCGGGTCGGATGAA
ACTTTATTTTGTTGTCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:305267 original size:18 final size:17
Alignment explanation
Indices: 305230--305276 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
305220 ATATGTAATT
305230 AGATTCCAATT-CTTAC
1 AGATTCCAATTCCTTAC
*
305246 AGATTCTAATTCCTTAAC
1 AGATTCCAATTCCTT-AC
305264 AGATTCCAATTCC
1 AGATTCCAATTCC
305277 CTCATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 10 0.37
17 3 0.11
18 14 0.52
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (17 bp):
AGATTCCAATTCCTTAC
Found at i:315824 original size:253 final size:253
Alignment explanation
Indices: 315376--315881 Score: 1003
Period size: 253 Copynumber: 2.0 Consensus size: 253
315366 AGACTCCTTT
315376 GGTTCTAAGTTTCGTAGTTTGTGCAGCTTTCATGTTGGAAATGGTAAGAATATTAGATTTTGGCA
1 GGTTCTAAGTTTCGTAGTTTGTGCAGCTTTCATGTTGGAAATGGTAAGAATATTAGATTTTGGCA
315441 GGATAGTTGGGCTGCTGATTATCCGTTCCAGATTTTGTTCCCTAGACTGTTTTGCCTTTCTACTA
66 GGATAGTTGGGCTGCTGATTATCCGTTCCAGATTTTGTTCCCTAGACTGTTTTGCCTTTCTACTA
315506 ATAAATATGGTAAGCTTTGTGAGTTTGGAGAATTTCTCTCATCGGGTTGGATTTGGAATGTCCAA
131 ATAAATATGGTAAGCTTTGTGAGTTTGGAGAATTTCTCTCATCGGGTTGGATTTGGAATGTCCAA
315571 GTAAGAAGAAACTTAAATGATTGGGAGCTTGAATAATGGTGTAATCTGGTGAGCATAA
196 GTAAGAAGAAACTTAAATGATTGGGAGCTTGAATAATGGTGTAATCTGGTGAGCATAA
315629 GGTTCTAAGTTTCGTAGTTTGTGCAGCTTTCATGTTGGAAATGGTAAGAATATTAGATTTTGGCA
1 GGTTCTAAGTTTCGTAGTTTGTGCAGCTTTCATGTTGGAAATGGTAAGAATATTAGATTTTGGCA
315694 GGATAGTTGGGCTGCTGATTATCCGTTCCAGATTTTGTTCCCTAGACTGTTTTGCCTTTCTACTA
66 GGATAGTTGGGCTGCTGATTATCCGTTCCAGATTTTGTTCCCTAGACTGTTTTGCCTTTCTACTA
*
315759 ATAAATATGGTAAGCTTTGTGAGTTTGGAGAATTTCTCTCATCGGGTTGGATTTGGGATGTCCAA
131 ATAAATATGGTAAGCTTTGTGAGTTTGGAGAATTTCTCTCATCGGGTTGGATTTGGAATGTCCAA
315824 GTAAGAAGAAACTTAAATGATTGGGAGCTTGAATAATGGTGTAATCTGGTGAGCATAA
196 GTAAGAAGAAACTTAAATGATTGGGAGCTTGAATAATGGTGTAATCTGGTGAGCATAA
315882 TTTCTTCTTT
Statistics
Matches: 252, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 252 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (253 bp):
GGTTCTAAGTTTCGTAGTTTGTGCAGCTTTCATGTTGGAAATGGTAAGAATATTAGATTTTGGCA
GGATAGTTGGGCTGCTGATTATCCGTTCCAGATTTTGTTCCCTAGACTGTTTTGCCTTTCTACTA
ATAAATATGGTAAGCTTTGTGAGTTTGGAGAATTTCTCTCATCGGGTTGGATTTGGAATGTCCAA
GTAAGAAGAAACTTAAATGATTGGGAGCTTGAATAATGGTGTAATCTGGTGAGCATAA
Found at i:322404 original size:20 final size:20
Alignment explanation
Indices: 322361--322405 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
322351 CCGCCTACGC
*
322361 AAGAAAGAAAAAGGAAGAAT
1 AAGAAAGAAAAAGAAAGAAT
*
322381 AAGAAAGGAAAAGAAAAGAA-
1 AAGAAAGAAAAAG-AAAGAAT
322401 AAGAA
1 AAGAA
322406 TAAACGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AAGAAAGAAAAAGAAAGAAT
Found at i:335390 original size:25 final size:23
Alignment explanation
Indices: 335362--335415 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
335352 TATCATAAAT
335362 AATATTATAAT-TAAAATTATGAAAA
1 AATATTA-AATAT-AAATTATG-AAA
* *
335387 AATAGTAAATATAAATTTTGAAA
1 AATATTAAATATAAATTATGAAA
335410 AATATT
1 AATATT
335416 CATTTAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 8 0.32
24 10 0.40
25 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (23 bp):
AATATTAAATATAAATTATGAAA
Found at i:336185 original size:22 final size:22
Alignment explanation
Indices: 336160--336203 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
336150 ACATTTTTAC
336160 AACATTTTAAATTCAACAAAAT
1 AACATTTTAAATTCAACAAAAT
* *
336182 AACATTTTAAGTTGAACAAAAT
1 AACATTTTAAATTCAACAAAAT
336204 CATCTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (22 bp):
AACATTTTAAATTCAACAAAAT
Found at i:341335 original size:31 final size:32
Alignment explanation
Indices: 341300--341379 Score: 119
Period size: 31 Copynumber: 2.5 Consensus size: 32
341290 CACTAGAAAA
*
341300 TATGTTCCTTCAAGTGAGT-CTCTTGAAAGG-C
1 TATGTTCCTTCTAGTGAGTCCT-TTGAAAGGCC
341331 TATGTTCCTTCTAGTGAGTCCTTTGAAAGGCC
1 TATGTTCCTTCTAGTGAGTCCTTTGAAAGGCC
*
341363 TAGGTTCCTTCTAGTGA
1 TATGTTCCTTCTAGTGA
341380 CTGTTTTAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 26 0.58
32 19 0.42
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (32 bp):
TATGTTCCTTCTAGTGAGTCCTTTGAAAGGCC
Found at i:345948 original size:22 final size:22
Alignment explanation
Indices: 345906--345950 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
345896 CACTTTGCTC
*
345906 ATATTCAATTTTTTTTATAAAT
1 ATATTCAATTTGTTTTATAAAT
345928 ATATTCAATTTAGTTTT-TAAAT
1 ATATTCAATTT-GTTTTATAAAT
345950 A
1 A
345951 ATATGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTCAATTTGTTTTATAAAT
Found at i:348568 original size:30 final size:31
Alignment explanation
Indices: 348515--348577 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
348505 GATTAATATG
*
348515 TAACAGATTGATAAATTGAATAATCATTTTA
1 TAACAGATTAATAAATTGAATAATCATTTTA
* * *
348546 TAACAGTTTAATATATT-AATAATTATTTTA
1 TAACAGATTAATAAATTGAATAATCATTTTA
348576 TA
1 TA
348578 GTTGTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (31 bp):
TAACAGATTAATAAATTGAATAATCATTTTA
Found at i:349154 original size:4 final size:4
Alignment explanation
Indices: 349147--350400 Score: 2417
Period size: 4 Copynumber: 314.5 Consensus size: 4
349137 CACTATATAT
* *
349147 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
349195 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349243 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349291 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-- ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349337 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349385 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349433 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349481 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349529 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349577 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349625 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349673 ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349719 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349767 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349815 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349863 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349911 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
349959 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
350007 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
350055 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
350103 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
350151 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
350199 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
350247 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
350295 ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
350343 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
350391 ATAC ATAC AT
1 ATAC ATAC AT
350401 GTTATTATCA
Statistics
Matches: 1232, Mismatches: 14, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
2 4 0.00
4 1228 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:350812 original size:38 final size:38
Alignment explanation
Indices: 350765--350841 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
350755 AACTGAATAT
*
350765 TTGTCCCGAATAACCACTATGTCCCGAATGACCACTGA
1 TTGTCCCGAATAACCACTATGTCCCGAAGGACCACTGA
*
350803 TTGTTCCGAATAACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAATAACCACTATGTCCCGAAGGACCACTGA
350841 T
1 T
350842 AATCCCTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (38 bp):
TTGTCCCGAATAACCACTATGTCCCGAAGGACCACTGA
Found at i:350838 original size:18 final size:18
Alignment explanation
Indices: 350766--350830 Score: 94
Period size: 18 Copynumber: 3.5 Consensus size: 18
350756 ACTGAATATT
350766 TGTCCCGAATAACCACTA
1 TGTCCCGAATAACCACTA
*
350784 TGTCCCGAATGACCACTGA
1 TGTCCCGAATAACCACT-A
*
350803 TTGTTCCGAATAACCACTA
1 -TGTCCCGAATAACCACTA
350822 TGTCCCGAA
1 TGTCCCGAA
350831 GGACCACTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 24 0.59
19 2 0.05
20 15 0.37
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (18 bp):
TGTCCCGAATAACCACTA
Found at i:351311 original size:19 final size:20
Alignment explanation
Indices: 351282--351327 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
351272 ATTATCTAAA
351282 CCTATATTCACATATGATTT
1 CCTATATTCACATATGATTT
351302 CCTA-ATTCACATATGATTT
1 CCTATATTCACATATGATTT
351321 CCTATAT
1 CCTATAT
351328 AATTCTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (20 bp):
CCTATATTCACATATGATTT
Found at i:352197 original size:20 final size:24
Alignment explanation
Indices: 352172--352226 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
352162 GAAGGTATGC
352172 ATCGATGCACT-C-T-ACA-GTGT
1 ATCGATGCACTCCTTAACATGTGT
*
352192 ATCGATGCATTCCTTAACATGTGT
1 ATCGATGCACTCCTTAACATGTGT
352216 ATCGATGCACT
1 ATCGATGCACT
352227 ACCTGTGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.34
21 1 0.03
22 1 0.03
23 3 0.10
24 14 0.48
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (24 bp):
ATCGATGCACTCCTTAACATGTGT
Found at i:356156 original size:20 final size:20
Alignment explanation
Indices: 356065--356160 Score: 74
Period size: 18 Copynumber: 5.0 Consensus size: 20
356055 GCACTGAATA
*
356065 TTTGTCCCAAAGGACCAC--
1 TTTGTCCCGAAGGACCACTG
*
356083 TATGTCCCGAAGGACCACTG
1 TTTGTCCCGAAGGACCACTG
* * * * *
356103 ATTGTTCTGAAGAACTAC--
1 TTTGTCCCGAAGGACCACTG
* *
356121 TATGTCCTGAAGGACCACTG
1 TTTGTCCCGAAGGACCACTG
*
356141 TTTGTCCCGAATGACCACTG
1 TTTGTCCCGAAGGACCACTG
356161 ATAATCCCTC
Statistics
Matches: 58, Mismatches: 16, Indels: 6
0.73 0.20 0.08
Matches are distributed among these distances:
18 29 0.50
20 29 0.50
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (20 bp):
TTTGTCCCGAAGGACCACTG
Found at i:357129 original size:2 final size:2
Alignment explanation
Indices: 357122--357148 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
357112 ACATGAATTT
357122 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
357149 TCATATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:358940 original size:21 final size:22
Alignment explanation
Indices: 358903--358949 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
358893 CATTTTGGTT
358903 ATTAAACTTTCAAATTTTAT-AA
1 ATTAAACTTTCAAA-TTTATCAA
*
358925 ATTAATCTTT-AAATTTATCAA
1 ATTAAACTTTCAAATTTATCAA
358946 ATTA
1 ATTA
358950 TTATAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 9 0.39
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAAACTTTCAAATTTATCAA
Found at i:359008 original size:31 final size:30
Alignment explanation
Indices: 358933--359008 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
358923 AAATTAATCT
* **
358933 TTAAATTTATCAAATTATTATAAAATGACG
1 TTAAATTTATCAAATTATTACAAAATGAAA
* * *
358963 TTAATTTTTTTCAAATTGTTACAAAATGATAA
1 TTAA-ATTTATCAAATTATTACAAAATGA-AA
358995 TTAAATTTATCAAA
1 TTAAATTTATCAAA
359009 CTTTATTATT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 4 0.11
31 28 0.78
32 4 0.11
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (30 bp):
TTAAATTTATCAAATTATTACAAAATGAAA
Found at i:360339 original size:36 final size:36
Alignment explanation
Indices: 360292--360363 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
360282 TGTGAGGACC
* *
360292 ACGTATCGATCATGTATGTAGTTATACATCATTTTG
1 ACGTATAGATCATGTATGTAGTTATACATCACTTTG
360328 ACGTATAGATCATGTATGTAGTTATACATCACTTTG
1 ACGTATAGATCATGTATGTAGTTATACATCACTTTG
360364 TCAATGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (36 bp):
ACGTATAGATCATGTATGTAGTTATACATCACTTTG
Found at i:360358 original size:19 final size:19
Alignment explanation
Indices: 360300--360358 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
360290 CCACGTATCG
360300 ATCATGTATGTAGTTATAC
1 ATCATGTATGTAGTTATAC
* *
360319 ATCAT-TTTG-ACG-TATAG
1 ATCATGTATGTA-GTTATAC
360336 ATCATGTATGTAGTTATAC
1 ATCATGTATGTAGTTATAC
360355 ATCA
1 ATCA
360359 CTTTGTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 10 0.31
18 8 0.25
19 14 0.44
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (19 bp):
ATCATGTATGTAGTTATAC
Found at i:360502 original size:36 final size:36
Alignment explanation
Indices: 360453--360557 Score: 201
Period size: 36 Copynumber: 2.9 Consensus size: 36
360443 ATAAAAAAAA
*
360453 TTAATTTGGGCATGAAGGAAGGCTTGTATAGTCTTC
1 TTAATTTGAGCATGAAGGAAGGCTTGTATAGTCTTC
360489 TTAATTTGAGCATGAAGGAAGGCTTGTATAGTCTTC
1 TTAATTTGAGCATGAAGGAAGGCTTGTATAGTCTTC
360525 TTAATTTGAGCATGAAGGAAGGCTTGTATAGTC
1 TTAATTTGAGCATGAAGGAAGGCTTGTATAGTC
360558 ATCAAGTCTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.35
Consensus pattern (36 bp):
TTAATTTGAGCATGAAGGAAGGCTTGTATAGTCTTC
Found at i:362747 original size:22 final size:22
Alignment explanation
Indices: 362722--362766 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
362712 GATATATTGT
* *
362722 AAAGTATCGATCCTTTTTATAA
1 AAAGGATCGATACTTTTTATAA
*
362744 AAAGGATCGATACTTTTTTTAA
1 AAAGGATCGATACTTTTTATAA
362766 A
1 A
362767 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
AAAGGATCGATACTTTTTATAA
Found at i:363148 original size:23 final size:23
Alignment explanation
Indices: 363122--363194 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
363112 ATATTTTACA
*
363122 ATATAAACACTACCTATTATATT
1 ATATAAACACTACCTATTACATT
*
363145 ATATAAACGCTACCTATTACATT
1 ATATAAACACTACCTATTACATT
*** *
363168 ATATAAGTGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
363191 ATAT
1 ATAT
363195 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:363648 original size:23 final size:23
Alignment explanation
Indices: 363622--363684 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
363612 ATATAAGCAT
363622 TACCTATTACATTATATAAACGC
1 TACCTATTACATTATATAAACGC
* *
363645 TACCTATTATATTATATAAGCGC
1 TACCTATTACATTATATAAACGC
*
363668 TACCTATTACATCATAT
1 TACCTATTACATTATAT
363685 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGC
Found at i:363736 original size:22 final size:22
Alignment explanation
Indices: 363702--363746 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
363692 TATTCTATTG
*
363702 AAAGTATCCATACTTTTTATAA
1 AAAGGATCCATACTTTTTATAA
* *
363724 AAAGGATCGATACTTTTTTTAA
1 AAAGGATCCATACTTTTTATAA
363746 A
1 A
363747 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAGGATCCATACTTTTTATAA
Found at i:364125 original size:23 final size:23
Alignment explanation
Indices: 364090--364162 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
364080 ATACTTTACA
*
364090 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
364113 ATAT-AGACGCTACCTATTACATT
1 ATATAAG-CGCTACCTATTACATT
*
364136 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
364159 ATAT
1 ATAT
364163 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.04
23 42 0.91
24 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:364530 original size:479 final size:479
Alignment explanation
Indices: 362662--365112 Score: 4287
Period size: 479 Copynumber: 5.1 Consensus size: 479
362652 CAAATATAAT
362662 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTGA-TATATTGTAAAG
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT-ATTATATTG-AAAG
* *
362726 TATCGATCCTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
64 TATCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
* *
362791 TTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
129 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
*
362856 TTATTTAATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
194 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
*
362921 AGATAATAATAAATATGTAATAAATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAA
259 AG---ATAAT--A-A--T-AT--ATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAA
*
362986 CGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
313 CGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
* * * * *
363051 TAACCTTAAATTAACGTTTTCTACGGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATAT
378 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATATATAC
* *
363116 TTTACAATATAAACACTACCTATTATATTATATAAAC
443 TTTACAATATAAGCACTACCTATTACATTATATAAAC
* *
363153 GCTACCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTG
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
* *
363218 TCCATACTTTTTATAAAAATGATCAATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
66 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTT
* *
363283 TTTTAATAGTGTTTTATGTTTTCCACCTACAATATTAATTTAATAACTTCATTTGCAC-AAAAAT
130 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
*
363347 TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAA
195 TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
*
363412 GATAATAATAAATATGAAATATATATGGTTATTGTTTTTAATTTAATAATAATATATATCGTAAC
260 G------AT--A-AT--AATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAAC
363477 GTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
314 GTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
* *
363542 AACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTATAAAAAGGATATATACT
379 AACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATATATACT
*
363607 TTACAATATAAGCATTACCTATTACATTATATAAAC
444 TTACAATATAAGCACTACCTATTACATTATATAAAC
* *
363643 GCTACCTATTATATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTCTATTGAAAGTA
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
363708 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTT
66 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
363772 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
131 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
363837 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
196 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
363902 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
261 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
363967 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
*
364032 ATGTTTTCCACAGTGAAAAAAGTATGAACACTTTTATAAAAATGATATATACTTTACAATATAAG
391 ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATATATACTTTACAATATAAG
*
364097 CACTACCTATTACATTATATAGAC
456 CACTACCTATTACATTATATAAAC
364121 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
*
364186 TCCATATTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
66 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
364251 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
131 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
*
364316 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATGTAACAATATTAACCAAAG
196 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
364381 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
261 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
*
364446 TCATTAGACGCCTATAATTACTAAATTAATATCTTAGAACTCACTCAAAAGATAACCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
* * *
364511 ATGTTTTCCACAGTGAAAAAAATATGGACACTTTTATAAAAAGGATATATATTTTACAATATAAG
391 ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATATATACTTTACAATATAAG
364576 CACTACCTATTACATTATATAAAC
456 CACTACCTATTACATTATATAAAC
364600 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
* * *
364665 TCCATACTTTTTATAAAAATGATCAATACTTTTTTTAAAGTTATGTAATTTATATTTCAATTTTT
66 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
364730 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
131 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
364795 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
196 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
364860 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
261 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
364925 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
* *
364990 ATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAG
391 ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATATATACTTTACAATATAAG
365055 CACTACCTATTACATTATATAAAC
456 CACTACCTATTACATTATATAAAC
*
365079 GCTACCTATTATATTATATAAGCGCTACCTATTA
1 GCTACCTATTACATTATATAAGCGCTACCTATTA
365113 TGGGATCGAT
Statistics
Matches: 1887, Mismatches: 63, Indels: 32
0.95 0.03 0.02
Matches are distributed among these distances:
478 330 0.17
479 847 0.45
480 2 0.00
481 1 0.00
483 2 0.00
488 59 0.03
489 71 0.04
490 447 0.24
491 114 0.06
492 2 0.00
493 6 0.00
495 2 0.00
496 4 0.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (479 bp):
GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATATATACTTTACAATATAAG
CACTACCTATTACATTATATAAAC
Found at i:364595 original size:23 final size:23
Alignment explanation
Indices: 364569--364641 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
364559 ATATTTTACA
*
364569 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
364592 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
364615 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
364638 ATAT
1 ATAT
364642 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:365061 original size:958 final size:962
Alignment explanation
Indices: 362662--365112 Score: 4333
Period size: 968 Copynumber: 2.5 Consensus size: 962
362652 CAAATATAAT
362662 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTGA-TATATTGTAAAG
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT-ATTATATTG-AAAG
* *
362726 TATCGATCCTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
64 TATCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
* *
362791 TTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
129 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
*
362856 TTATTTAATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
194 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
*
362921 AGATAATAATAAATATGTAATAAATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAA
259 AG---ATAAT--A-A--T-AT--ATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAA
*
362986 CGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
313 CGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
* *
363051 TAACCTTAAATTAACG-TTTTCTACGGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATA
378 TAACCTTAAATTAATGTTTTTC-ACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATA
* * * *
363115 TTTTACAATATAAACACTACCTATTATATTATATAAACGCTACCTATTACATTATATAAGTGCTA
442 CTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTA
* *
363180 CCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCAAT
507 CCTATTACATCATATTTTTACCTATTATATTGAAAGTATCCATACTTTTTATAAAAAGGATCAAT
*
363245 ACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTTAATAGTGTTTTATGTTTTCCACC
572 ACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACC
363310 TACAATATTAATTTAATAACTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAAAA
637 TACAATATTAATTTAATAACTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAAAA
*
363375 TAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGAAATATATATGG
702 TAATATTTAGAATTTAAATGTAACAATATTAACCAAAG-----AAT-AATAT-AAATATATATGG
363440 TTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATA
760 TTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATA
363505 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
825 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
*
363570 AAAAAATATGGACACTTTTATAAAAAGGATATATACTTTACAATATAAGCATTACCTATTACATT
890 AAAAAATATGGACACTTTTATAAAAAGGATATATACTTTACAATATAAGCACTACCTATTACATT
363635 ATATAAAC
955 ATATAAAC
* *
363643 GCTACCTATTATATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTCTATTGAAAGTA
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
363708 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTT
66 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
363772 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
131 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
363837 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
196 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
363902 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
261 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
363967 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
* * *
364032 ATGTTTTCCACAGTGAAAAAAGTATGAACACTTTTATAAAAATGATATATACTTTACAATATAAG
391 ATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAG
*
364097 CACTACCTATTACATTATATAGACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATA
456 CACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATA
* *
364162 TTTTTACCTATTATATTGAAAGTATCCATATTTTTTATAAAAAGGATCGATACTTTTTTTAAAGT
521 TTTTTACCTATTATATTGAAAGTATCCATACTTTTTATAAAAAGGATCAATACTTTTTTTAAAGT
364227 TATGTAATTTATGTTTCAA-TTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTT
586 TATGTAATTTATGTTTCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTT
* *
364291 AATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAAT
651 AATAACTTCATTTGCAC-AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAAT
*
364356 TTAAATGTAACAATATTAACCAAAG-AT-A-AT-AATATATATGTTTATTGTTTTTAATTTAATA
715 TTAAATGTAACAATATTAACCAAAGAATAATATAAATATATATGGTTATTGTTTTTAATTTAATA
364417 ATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTA
780 ATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTA
*
364482 GAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTA
845 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTA
*
364547 TAAAAAGGATATATATTTTACAATATAAGCACTACCTATTACATTATATAAAC
910 TAAAAAGGATATATACTTTACAATATAAGCACTACCTATTACATTATATAAAC
364600 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
1 GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
* * *
364665 TCCATACTTTTTATAAAAATGATCAATACTTTTTTTAAAGTTATGTAATTTATATTTCAATTTTT
66 TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
364730 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
131 TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
364795 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
196 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
364860 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
261 ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
364925 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
364990 ATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAG
391 ATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAG
*
365055 CACTACCTATTACATTATATAAACGCTACCTATTATATTATATAAGCGCTACCTATTA
456 CACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTA
365113 TGGGATCGAT
Statistics
Matches: 1425, Mismatches: 41, Indels: 31
0.95 0.03 0.02
Matches are distributed among these distances:
957 330 0.23
958 382 0.27
959 2 0.00
960 1 0.00
962 2 0.00
967 60 0.04
968 383 0.27
969 4 0.00
970 2 0.00
971 1 0.00
973 1 0.00
974 1 0.00
976 5 0.00
979 131 0.09
980 65 0.05
981 55 0.04
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (962 bp):
GCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTA
TCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
ATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAG
CACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATA
TTTTTACCTATTATATTGAAAGTATCCATACTTTTTATAAAAAGGATCAATACTTTTTTTAAAGT
TATGTAATTTATGTTTCAATTTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTT
AATAACTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATT
TAAATGTAACAATATTAACCAAAGAATAATATAAATATATATGGTTATTGTTTTTAATTTAATAA
TAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAA
AACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTAT
AAAAAGGATATATACTTTACAATATAAGCACTACCTATTACATTATATAAAC
Found at i:365113 original size:23 final size:23
Alignment explanation
Indices: 365048--365113 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
365038 ATACTTTACA
* *
365048 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTATATT
*
365071 ATATAAACGCTACCTATTATATT
1 ATATAAGCGCTACCTATTATATT
365094 ATATAAGCGCTACCTATTAT
1 ATATAAGCGCTACCTATTAT
365114 GGGATCGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTATATT
Found at i:365448 original size:199 final size:200
Alignment explanation
Indices: 365182--365748 Score: 992
Period size: 199 Copynumber: 2.8 Consensus size: 200
365172 CATTCTGGAC
* * *
365182 CAAAAATATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCTGTTAGA
1 CAAAAGTATCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGA
365247 TTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATA
66 TTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATA
* * *
365312 TATTGATCGACATTTTATTGTTGCACCCTGTTTGCCATTCATTCTGAACCAAAAATATCGACACA
131 TATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTATGAACCAAAAATATCGACACA
*
365377 GACTA
196 AACTA
365382 CAAAAGTATCGATACATTATTTAGACATATTCTCTCAT-AAACCGGTATACTTGTACCGGTTAGA
1 CAAAAGTATCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGA
*
365446 TTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATA
66 TTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATA
*
365511 TATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTATGGACCAAAAATATCGACACA
131 TATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTATGAACCAAAAATATCGACACA
365576 AACTA
196 AACTA
* * * *
365581 CAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGATTAGA
1 CAAAAGTATCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGA
*
365646 TTGAAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATA
66 TTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATA
*
365711 TATGGATCGACACTTTATAGTTGCACCCTGTTTGCCAT
131 TATGGATCGACACTTTATTGTTGCACCCTGTTTGCCAT
365749 ATTGTAAATT
Statistics
Matches: 350, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
199 190 0.54
200 160 0.46
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (200 bp):
CAAAAGTATCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGA
TTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATA
TATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTATGAACCAAAAATATCGACACA
AACTA
Found at i:366010 original size:19 final size:19
Alignment explanation
Indices: 365986--366030 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
365976 ATTCACATAA
365986 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
* *
366005 AAAATTATAAATCTTATAG
1 AAAATTATAAATCGTATAC
366024 AAAATTA
1 AAAATTA
366031 ACCCTACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:367847 original size:33 final size:33
Alignment explanation
Indices: 367810--367875 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
367800 CATCTTAATA
*
367810 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
367843 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
367876 CCATCTATTT
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:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:367934 original size:21 final size:21
Alignment explanation
Indices: 367909--367973 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
367899 CCCCTTATGC
* * *
367909 CTCTCAAGTGTATCTTAGACT
1 CTCTCAAGTTTCTCTTCGACT
367930 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
367951 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
367972 CT
1 CT
367974 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:370415 original size:20 final size:19
Alignment explanation
Indices: 370369--370415 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
370359 TCCGGTAACG
370369 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
370388 TTAATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
370409 TTTTACC
1 TTTTACC
370416 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:370642 original size:182 final size:179
Alignment explanation
Indices: 370156--370627 Score: 719
Period size: 180 Copynumber: 2.6 Consensus size: 179
370146 CGTACTTACG
* * *
370156 AAAGTATCGACACTTTCAATATATCCGATATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
*
370221 TATCATATTTTCACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGACACATTATA
66 TATCATATTTT-ACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAGTATCGACACATTATA
*
370286 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
370336 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
* *
370401 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACTTTAT
66 TATCATA-TTTTACCTGTTATATCGTTTTGGATCGATATATTTTTT-AAAGTATCGACACATTAT
** *
370466 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
129 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * * *
370518 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
* * *
370583 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATA-TTTTACCTGTTATATCGTTTTGGATCGATATATTTTT
370628 AATTTAGATC
Statistics
Matches: 267, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
180 101 0.38
181 67 0.25
182 99 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (179 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
TATCATATTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAGTATCGACACATTATAG
GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:372738 original size:2 final size:2
Alignment explanation
Indices: 372731--372755 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
372721 GCTCTTTCTG
372731 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
372756 CCACAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:380674 original size:13 final size:13
Alignment explanation
Indices: 380656--380680 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
380646 GATCAGATTT
380656 TTTTAACCGGTTA
1 TTTTAACCGGTTA
380669 TTTTAACCGGTT
1 TTTTAACCGGTT
380681 TGGAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:383070 original size:21 final size:21
Alignment explanation
Indices: 383046--383087 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
383036 AGTTTATTTT
383046 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
383067 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
383088 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:383136 original size:33 final size:32
Alignment explanation
Indices: 383082--383180 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
383072 TTTGTTTCAA
383082 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
383114 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
383147 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
383180 T
1 T
383181 ATGTTGAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:384323 original size:17 final size:18
Alignment explanation
Indices: 384303--384336 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
384293 ATTTTTTTAT
384303 AACC-GATTTTTTAAAAA
1 AACCGGATTTTTTAAAAA
*
384320 AACCGGTTTTTTTAAAA
1 AACCGGATTTTTTAAAA
384337 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGGATTTTTTAAAAA
Found at i:384336 original size:15 final size:15
Alignment explanation
Indices: 384284--384340 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
384274 TTTAATAATA
*
384284 TTAAAATCGATTTTT
1 TTAAAACCGATTTTT
*
384299 TTATAACCGATTTTT
1 TTAAAACCGATTTTT
* *
384314 TAAAAAAACCGGTTTTT
1 T--TAAAACCGATTTTT
384331 TTAAAACCGA
1 TTAAAACCGA
384341 AACCGGTTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 21 0.64
17 12 0.36
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:397053 original size:19 final size:19
Alignment explanation
Indices: 397029--397089 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
397019 TTTTGGTGCA
*
397029 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
397048 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCC-CT
397069 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
397090 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:403997 original size:13 final size:13
Alignment explanation
Indices: 403979--404023 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
403969 ATGATAAATA
*
403979 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
403992 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
404005 AAACAACTACAAT
1 AAAAAACTACAAT
404018 AAAAAA
1 AAAAAA
404024 GTACTAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:404174 original size:3 final size:3
Alignment explanation
Indices: 404168--404192 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
404158 GTCGTCGTCG
404168 TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC T
404193 GAGTAGGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:407315 original size:13 final size:12
Alignment explanation
Indices: 407288--407312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
407278 ATATTTTAAA
407288 TAATTTTTTTAT
1 TAATTTTTTTAT
407300 TAATTTTTTTAT
1 TAATTTTTTTAT
407312 T
1 T
407313 TAAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TAATTTTTTTAT
Found at i:407992 original size:14 final size:14
Alignment explanation
Indices: 407973--408008 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
407963 CGTTCGATTA
407973 TATGTTCGTTTATT
1 TATGTTCGTTTATT
*
407987 TATGTTCATTTATT
1 TATGTTCGTTTATT
408001 TATGTTCG
1 TATGTTCG
408009 AACAGAGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.08, G:0.14, T:0.61
Consensus pattern (14 bp):
TATGTTCGTTTATT
Found at i:420011 original size:20 final size:19
Alignment explanation
Indices: 419953--420012 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
419943 AAAAGAAAAC
**
419953 AAAT-TAAGTAAAATGATA
1 AAATGTAAGTAAAAAAATA
*
419971 AAATG-AAGAAAACAAAGATA
1 AAATGTAAGTAAA-AAA-ATA
419991 AAATAGTAAGTAAAAAAATA
1 AAAT-GTAAGTAAAAAAATA
420011 AA
1 AA
420013 TAATAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 10 0.30
19 1 0.03
20 12 0.36
21 4 0.12
22 6 0.18
ACGTcount: A:0.68, C:0.02, G:0.12, T:0.18
Consensus pattern (19 bp):
AAATGTAAGTAAAAAAATA
Found at i:420031 original size:11 final size:12
Alignment explanation
Indices: 420005--420135 Score: 51
Period size: 11 Copynumber: 10.9 Consensus size: 12
419995 AGTAAGTAAA
420005 AAAATAAATAAT
1 AAAATAAATAAT
420017 AAAATATATATAA-
1 AAAATA-A-ATAAT
* *
420030 AAAAGAAA-AAG
1 AAAATAAATAAT
*
420041 AAAATAAATAAA
1 AAAATAAATAAT
*
420053 ACAAATAAACAA-
1 A-AAATAAATAAT
*
420065 AATAAT-AATAAC
1 AA-AATAAATAAT
* *
420077 AAAGTACA-AAT
1 AAAATAAATAAT
* *
420088 AATATATAT-AT
1 AAAATAAATAAT
*
420099 ATAATAAATAA-
1 AAAATAAATAAT
420110 AAAAGTAAATATAT
1 AAAA-TAAATA-AT
*
420124 ATAAATTAATAA
1 A-AAATAAATAA
420136 ATTAAATGAC
Statistics
Matches: 89, Mismatches: 16, Indels: 27
0.67 0.12 0.20
Matches are distributed among these distances:
10 2 0.02
11 33 0.37
12 24 0.27
13 17 0.19
14 10 0.11
15 3 0.03
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:420205 original size:2 final size:2
Alignment explanation
Indices: 420194--420222 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
420184 TAAAGATAAT
420194 TA TA -A 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
420223 GTAACAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:420659 original size:12 final size:11
Alignment explanation
Indices: 420631--420671 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
420621 TAACAAAATA
* *
420631 AATAATATAAA
1 AATAATACAAG
420642 AATAATACAAG
1 AATAATACAAG
420653 TAATAATACAAG
1 -AATAATACAAG
420665 AATAATA
1 AATAATA
420672 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:420776 original size:12 final size:12
Alignment explanation
Indices: 420754--420798 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
420744 GAATAAAAGG
420754 AAAATATAATAGT
1 AAAA-ATAATAGT
*
420767 AAAAATAATAAT
1 AAAAATAATAGT
*
420779 AAATATAATAGT
1 AAAAATAATAGT
*
420791 AATAATAA
1 AAAAATAA
420799 AAATGTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:421392 original size:37 final size:37
Alignment explanation
Indices: 421351--421455 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
421341 GTGCTTGTGG
* *
421351 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
421388 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
421425 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
421456 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:422400 original size:106 final size:105
Alignment explanation
Indices: 422186--423666 Score: 2127
Period size: 106 Copynumber: 14.0 Consensus size: 105
422176 GCATTGTTCT
* ** * ** *
422186 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTAACTCTGGAACCGAGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTATTGACA
* * *
422250 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
422292 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T-GAAA-T-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTATTGACAAC
* * * *
422352 CAGCCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
422393 G-GTTCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAA
*
422457 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
422498 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAA
* *
422563 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
422604 GAGTCCAATATCCTACGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAA
*
422669 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
422710 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAA
*
422775 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
422816 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAA
*
422881 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
422922 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTATTGACAA
* * *
422987 CCAGCGGTCCCTTTGTCATAAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
423028 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTATTGACAA
* * *
423093 CCAGAGGTCCTTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
423134 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAA
*
423199 CCAGCGGTCCCTTCCTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
423240 GAGTCCAATATCATTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTATTGACAA
423305 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
423346 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAA-TTGTTTATTGACAA
*
423411 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
423452 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTATTGACAA
*
423517 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
423558 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAATTGTTTATTGACAA
* * * * *
423622 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
423663 GAGT
1 GAGT
423667 GGCAAGATAT
Statistics
Matches: 1265, Mismatches: 92, Indels: 37
0.91 0.07 0.03
Matches are distributed among these distances:
99 3 0.00
100 74 0.06
101 4 0.00
102 5 0.00
104 3 0.00
105 60 0.05
106 1107 0.88
107 9 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:424517 original size:22 final size:22
Alignment explanation
Indices: 424491--424546 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
424481 TTGTGTTTGG
424491 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
424513 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
424535 TCAAAGGTTTGA
1 TCAAAGGTTTGA
424547 TGGGGTAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:425179 original size:15 final size:16
Alignment explanation
Indices: 425148--425180 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
425138 TTTTTGTCCC
425148 TTTTTCTTTCGATTTT
1 TTTTTCTTTCGATTTT
425164 TTTTTCTTTCGATTTT
1 TTTTTCTTTCGATTTT
425180 T
1 T
425181 GTTCTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTCGATTTT
Found at i:425185 original size:15 final size:16
Alignment explanation
Indices: 425151--425187 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
425141 TTGTCCCTTT
*
425151 TTCTTTCGATTTTTTT
1 TTCTTTCGATTTTTTG
425167 TTCTTTCGA-TTTTTG
1 TTCTTTCGATTTTTTG
425182 TTCTTT
1 TTCTTT
425188 TGTTCTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.05, C:0.14, G:0.08, T:0.73
Consensus pattern (16 bp):
TTCTTTCGATTTTTTG
Found at i:425218 original size:6 final size:7
Alignment explanation
Indices: 425177--425227 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
425167 TTCTTTCGAT
425177 TTTTGTTC
1 TTTT-TTC
425185 TTTTGTTC
1 TTTT-TTC
*
425193 TTTTGT-
1 TTTTTTC
*
425199 TTTTTCC
1 TTTTTTC
425206 TTCTTTTC
1 TT-TTTTC
425214 TTTTTTC
1 TTTTTTC
425221 TTTTTTC
1 TTTTTTC
425228 CCTTTTTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 4 0.11
7 15 0.41
8 18 0.49
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:425231 original size:24 final size:24
Alignment explanation
Indices: 425182--425228 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
425172 TCGATTTTTG
* *
425182 TTCTTTTGTTCTTTTGTTTTTTCC
1 TTCTTTTCTTCTTTTCTTTTTTCC
425206 TTCTTTTCTT-TTTTCTTTTTTCC
1 TTCTTTTCTTCTTTTCTTTTTTCC
425229 CTTTTTGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (24 bp):
TTCTTTTCTTCTTTTCTTTTTTCC
Found at i:430047 original size:2 final size:2
Alignment explanation
Indices: 430040--430079 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
430030 TAAAGATAAT
430040 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
430080 GTAACAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:430277 original size:2 final size:2
Alignment explanation
Indices: 430234--430258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
430224 CTTGTGTCGA
430234 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
430259 ATAGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:430493 original size:12 final size:11
Alignment explanation
Indices: 430465--430505 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
430455 TAACAAAATA
* *
430465 AATAATATAAA
1 AATAATACAAG
430476 AATAATACAAG
1 AATAATACAAG
430487 TAATAATACAAG
1 -AATAATACAAG
430499 AATAATA
1 AATAATA
430506 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:430602 original size:12 final size:12
Alignment explanation
Indices: 430585--430624 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
430575 TAAAGGAAAT
430585 ATAATAGTAAAA
1 ATAATAGTAAAA
* *
430597 ATAATAATAAAT
1 ATAATAGTAAAA
*
430609 ATAATAGTAATA
1 ATAATAGTAAAA
430621 ATAA
1 ATAA
430625 AAATGCAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (12 bp):
ATAATAGTAAAA
Found at i:431223 original size:37 final size:37
Alignment explanation
Indices: 431182--431286 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
431172 GTGCTTGTGG
* *
431182 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
** * *
431219 ATCCTATTTTTAGGAGTTTAAATCCTAACAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
431256 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
431287 GACGAAAAGG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:434028 original size:19 final size:19
Alignment explanation
Indices: 434004--434041 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
433994 AATGGAATGG
* *
434004 ATTTTATTTTTATGCTATT
1 ATTTTATATTTATACTATT
434023 ATTTTATATTTATACTATT
1 ATTTTATATTTATACTATT
434042 TAAAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTATATTTATACTATT
Found at i:436224 original size:42 final size:42
Alignment explanation
Indices: 436177--436261 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
436167 CAACTAACAT
436177 TAAAATTGATGCTGCCATTAATTAAATAAAATCAAAAGGAAA
1 TAAAATTGATGCTGCCATTAATTAAATAAAATCAAAAGGAAA
436219 TAAAATTGATGCTGCCATTAATTAAATAAAATCAAAAGGAAA
1 TAAAATTGATGCTGCCATTAATTAAATAAAATCAAAAGGAAA
436261 T
1 T
436262 TGAAAGGCAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (42 bp):
TAAAATTGATGCTGCCATTAATTAAATAAAATCAAAAGGAAA
Found at i:443641 original size:2 final size:2
Alignment explanation
Indices: 443634--443706 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
443624 ATTCTCAAAC
443634 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
443676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
443707 TAAGATTTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:445467 original size:20 final size:20
Alignment explanation
Indices: 445428--445467 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
445418 TCCATTCTAT
* *
445428 GATGGAATTTAATTTTCTTG
1 GATGGAATTCAATTTCCTTG
*
445448 GATGGAATTCACTTTCCTTG
1 GATGGAATTCAATTTCCTTG
445468 TTGAAGGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (20 bp):
GATGGAATTCAATTTCCTTG
Found at i:446003 original size:219 final size:223
Alignment explanation
Indices: 445617--446074 Score: 714
Period size: 219 Copynumber: 2.1 Consensus size: 223
445607 TTTATTTTGG
*
445617 TCGGGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGGTTTAGGGTAAAAAATAC
1 TCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGGTTTAGGGTAAAAAATAC
* *
445682 CCGATCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
66 CCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
*
445747 TTATATATATATAATTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATA-TTTTTT-TTATT
131 CTATATATATATAATTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATT
445810 TC-G-AGTCGGGTTTCTAATTCATATAT
196 TCGGCAGTCGGGTTTCTAATTCATATAT
* *
445836 TCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCGGGTCGGGGTT-GGGTTTAGGGTGAAAAAT
1 TCGGGTCGGGTCGG-TTTTTTTAAGTGTGATATTCGGGTC-GAGTTCGGGTTTAGGGTAAAAAAT
445900 ACCCGACCCGACCC-AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAC
64 ACCCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAC
* *
445964 CCCTATATATATA-ATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATATTTTTTTTAT
129 CCCTATATATATATA-ATTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATA-TTTTTTTAT
* *
446028 TATTTCGGGTCGGTCGGGTTTTTAATTCATATAT
192 TATTTC-GG-CAGTCGGGTTTCTAATTCATATAT
*
446062 TCGGGCCGGGTCG
1 TCGGGTCGGGTCG
446075 AGTCTCGGAT
Statistics
Matches: 218, Mismatches: 11, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
218 1 0.00
219 111 0.51
220 55 0.25
221 10 0.05
222 7 0.03
224 1 0.00
226 33 0.15
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.41
Consensus pattern (223 bp):
TCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGGTTTAGGGTAAAAAATAC
CCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
CTATATATATATAATTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATT
TCGGCAGTCGGGTTTCTAATTCATATAT
Found at i:446474 original size:18 final size:17
Alignment explanation
Indices: 446435--446487 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
446425 TATGGAATTG
* *
446435 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCATA
446452 GATTCCAATTCCTTCATA
1 GATTCCAATTCC-TCATA
446470 GATTCCAATTCCCTCATA
1 GATTCCAATT-CCTCATA
446488 AACATTCCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 12 0.38
18 18 0.56
19 2 0.06
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (17 bp):
GATTCCAATTCCTCATA
Found at i:450496 original size:22 final size:22
Alignment explanation
Indices: 450470--450524 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
450460 AATTTATATA
450470 AATTTTGATAATTGTATATTTC
1 AATTTTGATAATTGTATATTTC
450492 AATTTTGATAATTGTATATTTC
1 AATTTTGATAATTGTATATTTC
450514 AATTTTGATAA
1 AATTTTGATAA
450525 AATTGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (22 bp):
AATTTTGATAATTGTATATTTC
Found at i:452008 original size:15 final size:15
Alignment explanation
Indices: 451980--452019 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
451970 TTCTTCTAGC
451980 TCATAGTCATATATA
1 TCATAGTCATATATA
451995 TCATA-TCATA-ATA
1 TCATAGTCATATATA
*
452008 T-ATATTCATATA
1 TCATAGTCATATA
452020 ATTCATAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 9 0.39
14 6 0.26
15 5 0.22
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (15 bp):
TCATAGTCATATATA
Found at i:453678 original size:21 final size:18
Alignment explanation
Indices: 453634--453705 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
453624 GTTCTTAAGG
453634 AGTGGTCATTCGGGATAT
1 AGTGGTCATTCGGGATAT
*
453652 AGTGGTCATTTGGGATAAAT
1 AGTGGTCATTCGGGAT--AT
**
453672 CAGTGGTTC-TTCGGGACGT
1 -AGTGG-TCATTCGGGATAT
453691 AGTGGTCATTCGGGA
1 AGTGGTCATTCGGGA
453706 CAAATATACA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.04
18 27 0.60
19 1 0.02
20 2 0.04
21 11 0.24
22 2 0.04
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.32
Consensus pattern (18 bp):
AGTGGTCATTCGGGATAT
Found at i:453694 original size:39 final size:39
Alignment explanation
Indices: 453634--453710 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
453624 GTTCTTAAGG
* * *
453634 AGTGGTCATTCGGGATATAGTGGTCATTTGGGATAAATC
1 AGTGGTCATTCGGGACATAGTGGTCATTCGGGACAAATC
*
453673 AGTGGTTC-TTCGGGACGTAGTGGTCATTCGGGACAAAT
1 AGTGG-TCATTCGGGACATAGTGGTCATTCGGGACAAAT
453711 ATACAGTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.31
Consensus pattern (39 bp):
AGTGGTCATTCGGGACATAGTGGTCATTCGGGACAAATC
Found at i:454125 original size:21 final size:21
Alignment explanation
Indices: 454099--454139 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
454089 TTAATTAAGG
454099 AAAAGG-TATATAGATAAGTAT
1 AAAAGGATAT-TAGATAAGTAT
*
454120 AAAAGGATATTATATAAGTA
1 AAAAGGATATTAGATAAGTA
454140 GTGCAGGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (21 bp):
AAAAGGATATTAGATAAGTAT
Found at i:458783 original size:21 final size:21
Alignment explanation
Indices: 458754--458795 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
458744 GTTCATTTAT
*
458754 TTGAGAGTGCATCGATACACA
1 TTGAAAGTGCATCGATACACA
* *
458775 TTGAAAGTGTATCGATGCACA
1 TTGAAAGTGCATCGATACACA
458796 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (21 bp):
TTGAAAGTGCATCGATACACA
Found at i:462945 original size:24 final size:24
Alignment explanation
Indices: 462912--462962 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
462902 TATACATGAA
*
462912 CTGTATAACGTATTTCTTGCGGAG
1 CTGTAGAACGTATTTCTTGCGGAG
462936 CTGTAGAACGTATTTCTTGCGGAG
1 CTGTAGAACGTATTTCTTGCGGAG
462960 CTG
1 CTG
462963 ATGTAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (24 bp):
CTGTAGAACGTATTTCTTGCGGAG
Found at i:463848 original size:65 final size:65
Alignment explanation
Indices: 463710--463872 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
463700 AATTTTTCAA
* * *
463710 TGTGTATCGATGCACAGGAAGTGCATCGATACA-CCCATTAAAAATGAAAACATCGAATACAATT
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGACAATT
* * * * ***
463774 AGTGCATCGATGCATA-AAGAGTGCATCGATGCACCCCCTTAAAAATGAAAACATCGAAGGTGAT
1 TGTGTATCGATGCATAGGA-AGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGACAAT
463838 T
65 T
* *
463839 TGTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCAC
463873 TTCAAGGGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 26 0.32
65 54 0.67
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (65 bp):
TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGACAATT
Found at i:464984 original size:2 final size:2
Alignment explanation
Indices: 464977--465036 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
464967 AGGAAAAATG
*
464977 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
465019 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
465037 TTAGGAAGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:465573 original size:23 final size:23
Alignment explanation
Indices: 465516--465576 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
465506 CAACCTTATA
* * *
465516 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGATGCAATTCTACG
* * *
465539 CGGTACTACGATGCAATTCTACG
1 TGGCACTTCGATGCAATTCTACG
465562 TGGCACTTCGATGCA
1 TGGCACTTCGATGCA
465577 TTTATGCGAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGATGCAATTCTACG
Found at i:473166 original size:20 final size:20
Alignment explanation
Indices: 473143--473189 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
473133 GTCCCGGAGG
473143 ACCACTGATTGT-TCTGAAGA
1 ACCACTGATTGTCT-TGAAGA
*
473163 ACCACT-A-TGTCTTGAAGG
1 ACCACTGATTGTCTTGAAGA
473181 ACCACTGAT
1 ACCACTGAT
473190 AATCTCTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 14 0.61
19 3 0.13
20 6 0.26
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (20 bp):
ACCACTGATTGTCTTGAAGA
Found at i:473904 original size:21 final size:21
Alignment explanation
Indices: 473875--473916 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
473865 GTTCATTTAT
*
473875 TTGAGAGTGCATCGATACACA
1 TTGAAAGTGCATCGATACACA
*
473896 TTGAAAGTGCATCGATGCACA
1 TTGAAAGTGCATCGATACACA
473917 CAACCTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (21 bp):
TTGAAAGTGCATCGATACACA
Found at i:477333 original size:21 final size:21
Alignment explanation
Indices: 477307--477347 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
477297 TTAATTAAGG
477307 AAAAGG-TATATAGATAAGTAT
1 AAAAGGATAT-TAGATAAGTAT
477328 AAAAGGATATTAGATAAGTA
1 AAAAGGATATTAGATAAGTA
477348 GTGCAGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (21 bp):
AAAAGGATATTAGATAAGTAT
Found at i:479718 original size:31 final size:30
Alignment explanation
Indices: 479672--479762 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
479662 CCGTATTAAT
*
479672 AGATCAAATTTATATTTTATCTAAAATTTA
1 AGATCAAATTAATATTTTATCTAAAATTTA
*
479702 AGGATTAAATTAATATTTTATCT-AAATTTCA
1 A-GATCAAATTAATATTTTATCTAAAATTT-A
*
479733 AGATCAAATTAATATTCTATCTAAAATTTA
1 AGATCAAATTAATATTTTATCTAAAATTTA
479763 GGAGATATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
30 27 0.50
31 27 0.50
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (30 bp):
AGATCAAATTAATATTTTATCTAAAATTTA
Found at i:479775 original size:31 final size:32
Alignment explanation
Indices: 479672--479780 Score: 111
Period size: 31 Copynumber: 3.5 Consensus size: 32
479662 CCGTATTAAT
*
479672 AGATCAAATTTATATTTTATCTAAAATTTAAGG
1 AGAT-AAATTAATATTTTATCTAAAATTTAAGG
* *
479705 A-TTAAATTAATATTTTATCT-AAATTTCA--
1 AGATAAATTAATATTTTATCTAAAATTTAAGG
*
479733 AGATCAAATTAATATTCTATCTAAAATTT-AGG
1 AGAT-AAATTAATATTTTATCTAAAATTTAAGG
* *
479765 AGATATATTAAAATTT
1 AGATAAATTAATATTT
479781 GTATATTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 24 0.38
31 31 0.49
32 5 0.08
33 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (32 bp):
AGATAAATTAATATTTTATCTAAAATTTAAGG
Found at i:489968 original size:87 final size:87
Alignment explanation
Indices: 489822--489998 Score: 338
Period size: 87 Copynumber: 2.0 Consensus size: 87
489812 ACTTATTTCT
489822 TTTAACTTGGATGATATTGTTGCTTTATTAAATGAGAGTGTAGTACAAGTTATAAATGTTTTTTT
1 TTTAACTTGGATGATATTGTTGCTTTATTAAATGAGAGTGTAGTACAAGTTATAAATGTTTTTTT
489887 TTACATTTTTATGGTATTTAAC
66 TTACATTTTTATGGTATTTAAC
489909 TTTAACTTGGATGATATTGTTGCTTTATTAAATGAGAGTGTCA-TACAAGTTATAAATGTTTTTT
1 TTTAACTTGGATGATATTGTTGCTTTATTAAATGAGAGTGT-AGTACAAGTTATAAATGTTTTTT
489973 TTTACATTTTTATGGTATTTAAC
65 TTTACATTTTTATGGTATTTAAC
489996 TTT
1 TTT
489999 TAGCGTTTAT
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 88 0.99
88 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.50
Consensus pattern (87 bp):
TTTAACTTGGATGATATTGTTGCTTTATTAAATGAGAGTGTAGTACAAGTTATAAATGTTTTTTT
TTACATTTTTATGGTATTTAAC
Found at i:490878 original size:23 final size:23
Alignment explanation
Indices: 490830--490886 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
490820 TAGGATACTC
*
490830 GCTCCATTGTAAGTATTAATTAG
1 GCTCCGTTGTAAGTATTAATTAG
* * *
490853 GCTCCGTTGTAAGTTTTAGTTGG
1 GCTCCGTTGTAAGTATTAATTAG
*
490876 GCTCTGTTGTA
1 GCTCCGTTGTA
490887 GTCCAGTTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (23 bp):
GCTCCGTTGTAAGTATTAATTAG
Found at i:497170 original size:15 final size:15
Alignment explanation
Indices: 497150--497179 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
497140 ATACTTCTGC
497150 ATTGGAGAACAACTG
1 ATTGGAGAACAACTG
497165 ATTGGAGAACAACTG
1 ATTGGAGAACAACTG
497180 CTACTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (15 bp):
ATTGGAGAACAACTG
Found at i:497673 original size:15 final size:15
Alignment explanation
Indices: 497653--497682 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
497643 GAAGAAACAT
*
497653 GCCCAACCTGCTCAG
1 GCCCAACCTCCTCAG
497668 GCCCAACCTCCTCAG
1 GCCCAACCTCCTCAG
497683 ATCTACCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.50, G:0.17, T:0.13
Consensus pattern (15 bp):
GCCCAACCTCCTCAG
Done.