Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004932.1 Hibiscus syriacus cultivar Beakdansim tig00011096_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: 116796
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:94 original size:3 final size:3
Alignment explanation
Indices: 81--144 Score: 64
Period size: 3 Copynumber: 22.7 Consensus size: 3
71 ATTATTATTC
* *
81 AAT AAT GAT AAT AAT AAT AAT AAT -AT AAT ATT AAT AA- AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
126 ATT AAT AAT ATT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AA
145 AATGGGAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 8 0.16
3 42 0.84
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:131 original size:27 final size:25
Alignment explanation
Indices: 90--147 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
80 CAATAATGAT
90 AATAATAATAATAAT-ATAATATTAA
1 AATAA-AATAATAATAATAATATTAA
*
115 TAA-AAAATAATATTAATAATATTAA
1 -AATAAAATAATAATAATAATATTAA
140 AATAAAAT
1 AATAAAAT
148 GGGAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 10 0.34
25 17 0.59
26 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AATAAAATAATAATAATAATATTAA
Found at i:7928 original size:2 final size:2
Alignment explanation
Indices: 7921--7946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7911 CAGTTCACTC
7921 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
7947 TCCCCCACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8253 original size:15 final size:16
Alignment explanation
Indices: 8228--8257 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8218 AAGTTAACGC
8228 CGTTAAACTTTGACGG
1 CGTTAAACTTTGACGG
8244 CGTT-AACTTTGACG
1 CGTTAAACTTTGACG
8258 TGTGAGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (16 bp):
CGTTAAACTTTGACGG
Found at i:10063 original size:15 final size:15
Alignment explanation
Indices: 10039--10073 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10029 ATGATCCAAT
* *
10039 TCTTTTAGCTGAATC
1 TCTTTCAGCTAAATC
10054 TCTTTCAGCTAAATC
1 TCTTTCAGCTAAATC
10069 TCTTT
1 TCTTT
10074 ACATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (15 bp):
TCTTTCAGCTAAATC
Found at i:16413 original size:21 final size:22
Alignment explanation
Indices: 16374--16414 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16364 TTCTATTTTA
*
16374 TTTATTTAAATTGAGAATTAAG
1 TTTATTTAAATTGACAATTAAG
*
16396 TTTATTT-ATTTGACAATTA
1 TTTATTTAAATTGACAATTA
16415 CGATGCTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTAAG
Found at i:19114 original size:3 final size:3
Alignment explanation
Indices: 19106--19169 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
19096 TCCCGACACC
19106 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
19154 ATT AAT GTT ATT ATT A
1 ATT ATT ATT ATT ATT A
19170 ATGGGTTTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:21390 original size:131 final size:131
Alignment explanation
Indices: 21147--21511 Score: 505
Period size: 131 Copynumber: 2.8 Consensus size: 131
21137 CTCGATATTG
* * * *
21147 AAAATAATAATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGATTTAAGACATAAGAGGTCA
1 AAAATAATGACATCTTTTCATTTCGATTGGAGTAATAAATGATTGATTTAAGACATGAGAGGTCA
* * * *
21212 TTTATTCTCGATTGGAAATAATTAGATATTACCGTTTTCTCCCGAATCAATATTGATTTTTAAGA
66 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACCAGAATCAATATTGACTTTTAAGA
21277 C
131 C
** * * * * * *
21278 GGAATAATGGCATCTCTTCATTTCGATTGGAGTAATAAATAACTGTTTTAAGACATGAGATGTCA
1 AAAATAATGACATCTTTTCATTTCGATTGGAGTAATAAATGATTGATTTAAGACATGAGAGGTCA
* *
21343 TTTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTAGAATCAATATTGACTTTTAAGA
66 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACCAGAATCAATATTGACTTTTAAGA
21408 C
131 C
* * * * * * *
21409 AAAATAGTGATATCTTTTCATTTTGATCGGAGTAATAAATGATTGCTTTAAGGCCTGAGAGGTCA
1 AAAATAATGACATCTTTTCATTTCGATTGGAGTAATAAATGATTGATTTAAGACATGAGAGGTCA
21474 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTT
66 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTT
21512 TTCTTAAATT
Statistics
Matches: 201, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
131 201 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (131 bp):
AAAATAATGACATCTTTTCATTTCGATTGGAGTAATAAATGATTGATTTAAGACATGAGAGGTCA
TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACCAGAATCAATATTGACTTTTAAGA
C
Found at i:23906 original size:23 final size:22
Alignment explanation
Indices: 23880--23922 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
23870 ATATTTTATA
* *
23880 TATATGTATATAGATTTAAGATT
1 TATATATATATA-ACTTAAGATT
23903 TATATATATATAACTTAAGA
1 TATATATATATAACTTAAGA
23923 ATTCAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (22 bp):
TATATATATATAACTTAAGATT
Found at i:24340 original size:18 final size:17
Alignment explanation
Indices: 24319--24363 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
24309 ACATTAAATG
*
24319 ATATTAAAATTATAATAA
1 ATATTAAAATT-TAAGAA
24337 ATATTAAAAATTTAAGAA
1 ATATT-AAAATTTAAGAA
*
24355 ATATGAAAA
1 ATATTAAAA
24364 ACGTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 14 0.58
19 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
ATATTAAAATTTAAGAA
Found at i:24364 original size:18 final size:19
Alignment explanation
Indices: 24324--24364 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
24314 AAATGATATT
* *
24324 AAAATTATAATAAATATTA
1 AAAATTATAAGAAATATGA
24343 AAAATT-TAAGAAATATGA
1 AAAATTATAAGAAATATGA
24361 AAAA
1 AAAA
24365 CGTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATTATAAGAAATATGA
Found at i:24443 original size:19 final size:20
Alignment explanation
Indices: 24421--24462 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
24411 TAAAATCTTG
24421 AAAT-TTATTAAAAATT-TAA
1 AAATATTATT-AAAATTGTAA
24440 AAATATTATTAAAATTGTAA
1 AAATATTATTAAAATTGTAA
24460 AAA
1 AAA
24463 AAGGATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATATTATTAAAATTGTAA
Found at i:24699 original size:17 final size:18
Alignment explanation
Indices: 24662--24708 Score: 87
Period size: 17 Copynumber: 2.7 Consensus size: 18
24652 TGTTTATGAG
24662 GGAATTGGAATCTGTTCA
1 GGAATTGGAATCTGTTCA
24680 GGAATTGGAATCTG-TCA
1 GGAATTGGAATCTGTTCA
24697 GGAATTGGAATC
1 GGAATTGGAATC
24709 CAATTCCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTTCA
Found at i:25479 original size:259 final size:254
Alignment explanation
Indices: 25065--25668 Score: 922
Period size: 259 Copynumber: 2.4 Consensus size: 254
25055 CTCCATTCGA
* * *
25065 GACCCGACCCGAACAAAATAAAGTTTCACCCGACCCAACCAGAATATATGAATTAG-AA--ACCC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCACCC
*
25127 GACCCGAAATAATAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAATATATATAT
66 GACCCGAAATAATAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATATATAT
* * *
25192 ATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATAT-TTTTTGGGTCG
131 ATAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATATTCGGGTCG
* * *
25256 GGTGTTTTTCACCCTAAACCCGAACCCGACTCGACCCGAATATCACACTTAAAAAAAATT
196 GGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCAAACTT-AAAAAAATT
*
25316 GACCCGACCCGACCAAAATAAAGTTTCACCCGAACCGACCCGAATATATGAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA-CC-AC
*
25381 CCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGGCTTAATTGAAAAAA-A
64 CCGACCCGAAATAAT--AAAAAA-TATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATA
*
25445 TTATATATAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATATTC
126 -TATATATAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATATTC
*
25510 GGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCAAACTTAAAAAAATT
190 GGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCAAACTTAAAAAAATT
* *
25575 GACCCGACCTGACCAAAATAAAGTTTCA-CCGACCCGACCCAAATATATGAATTAG-AA--ACCC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCACCC
*
25636 TACCCGAAATAAT-AAAAATATTTTTATTCAATA
66 GACCCGAAATAATAAAAAATATTTTTATTCAATA
25669 TATGAATAAG
Statistics
Matches: 325, Mismatches: 18, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
249 15 0.05
250 5 0.02
251 52 0.16
252 2 0.01
253 16 0.05
256 17 0.05
257 2 0.01
258 32 0.10
259 129 0.40
260 55 0.17
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (254 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCACCC
GACCCGAAATAATAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATATATAT
ATAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATATTCGGGTCG
GGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCAAACTTAAAAAAATT
Found at i:26720 original size:13 final size:13
Alignment explanation
Indices: 26704--26734 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
26694 TTTAATTGCG
26704 AAAATTAAAAATT
1 AAAATTAAAAATT
*
26717 AAAATTAAAATTT
1 AAAATTAAAAATT
26730 AAAAT
1 AAAAT
26735 ATTCGATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:26954 original size:33 final size:32
Alignment explanation
Indices: 26895--26965 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
26885 TAATTTTAAA
26895 AAATAAAAATAAAAACAAAGGAAAAAATAATG
1 AAATAAAAATAAAAACAAAGGAAAAAATAATG
* * *
26927 AAATTAAAATAAAAA-ACAGGAACAAA-AAT-
1 AAATAAAAATAAAAACAAAGGAAAAAATAATG
26956 AAGATAAAAA
1 AA-ATAAAAA
26966 GGAATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 9 0.26
31 9 0.26
32 14 0.41
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (32 bp):
AAATAAAAATAAAAACAAAGGAAAAAATAATG
Found at i:27078 original size:2 final size:2
Alignment explanation
Indices: 27073--27138 Score: 123
Period size: 2 Copynumber: 32.5 Consensus size: 2
27063 AAAATAAAGA
27073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27115 AT AT AGT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT A
27139 CAAATATTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 61 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27273 original size:25 final size:24
Alignment explanation
Indices: 27245--27325 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 24
27235 AAAACGTATG
27245 GAAAATAAATAATAAAAACCAAAAA
1 GAAAATAAATAATAAAAA-CAAAAA
*
27270 GAAAAT-AGTAA-AAAAACAATAAA
1 GAAAATAAATAATAAAAACAA-AAA
* * *
27293 -ATAATAAGTAATAAAAA-TAAAA
1 GAAAATAAATAATAAAAACAAAAA
27315 G-AAATAAATAA
1 GAAAATAAATAA
27326 AATATATAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 18 0.38
23 14 0.30
24 9 0.19
25 6 0.13
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (24 bp):
GAAAATAAATAATAAAAACAAAAA
Found at i:27434 original size:4 final size:4
Alignment explanation
Indices: 27425--27464 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
27415 AATATTAATA
*
27425 AAAT AAAT AAAAT AAAT GAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
27465 ATATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:28346 original size:11 final size:11
Alignment explanation
Indices: 28330--28363 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28320 TTTAAGTAAT
*
28330 ATATATATGTG
1 ATATATATATG
28341 ATATATATATG
1 ATATATATATG
28352 ATATTATATATG
1 ATA-TATATATG
28364 GATGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (11 bp):
ATATATATATG
Found at i:29599 original size:106 final size:106
Alignment explanation
Indices: 29176--30022 Score: 1303
Period size: 106 Copynumber: 8.0 Consensus size: 106
29166 GTATTGTTCC
* * * *
29176 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
29240 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * * *
29282 GAGTCTAATATCATTCGCTATGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
29341 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * *
29382 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTTTTTTTTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG-TTGTTTGTTGACA
29447 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * *
29489 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTTTTTTTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
29554 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
**
29595 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
29660 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
*
29701 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
29766 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
**
29807 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
29872 CCAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* *
29913 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
29978 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
30019 GAGT
1 GAGT
30023 GGCACGATAT
Statistics
Matches: 692, Mismatches: 41, Indels: 16
0.92 0.05 0.02
Matches are distributed among these distances:
100 82 0.12
101 3 0.00
102 4 0.01
104 3 0.00
105 2 0.00
106 497 0.72
107 101 0.15
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
Found at i:31693 original size:16 final size:17
Alignment explanation
Indices: 31674--31719 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
31664 TCTTTTTGAT
*
31674 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
31690 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
31707 TTTTTCT-TTGTTT
1 TTTTGCTCTTGTTT
31720 TTTTTTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:31729 original size:13 final size:14
Alignment explanation
Indices: 31707--31758 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 14
31697 CTTGTTTCTC
31707 TTTTTCTTTG-TTT
1 TTTTTCTTTGCTTT
*
31720 TTTTTTTTTGCTTT
1 TTTTTCTTTGCTTT
*
31734 TTTCCTTCTTTTCTTT
1 TTT--TTCTTTGCTTT
31750 TTTGTTCTT
1 TTT-TTCTT
31759 GATTGGATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.28
14 6 0.19
15 5 0.16
16 12 0.38
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTGCTTT
Found at i:31749 original size:16 final size:16
Alignment explanation
Indices: 31680--31752 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
31670 TGATTTTTGC
31680 TCTTTTTTCCTT-TTGT
1 TCTTTTTTCCTTCTT-T
*
31696 TCTTGTTT-C-TCTTTT
1 TCTTTTTTCCTTC-TTT
** *
31711 TCTTTGTTTTTTTTTTT
1 TCTTT-TTTCCTTCTTT
31728 TGCTTTTTTCCTTCTTT
1 T-CTTTTTTCCTTCTTT
31745 TCTTTTTT
1 TCTTTTTT
31753 GTTCTTGATT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 1 0.02
15 6 0.14
16 19 0.43
17 13 0.30
18 5 0.11
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (16 bp):
TCTTTTTTCCTTCTTT
Found at i:34662 original size:13 final size:13
Alignment explanation
Indices: 34644--34673 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34634 TTTAATTGCG
34644 AAATTAAAAATTA
1 AAATTAAAAATTA
*
34657 AAATTAAAATTTA
1 AAATTAAAAATTA
34670 AAAT
1 AAAT
34674 ATTCGATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTAAAAATTA
Found at i:35017 original size:2 final size:2
Alignment explanation
Indices: 35012--35056 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35002 AAAATAAAGA
35012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35054 AT A
1 AT A
35057 CAAATATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35225 original size:24 final size:24
Alignment explanation
Indices: 35162--35226 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 24
35152 AAAACGTATG
*
35162 GAAAATAAATAATAAAAACCAAAAA
1 GAAAAT-AGTAATAAAAACCAAAAA
35187 GAAAATAGTAA-AAAAA-CAATAAA
1 GAAAATAGTAATAAAAACCAA-AAA
*
35210 -ATAATCAGTAATAAAAA
1 GAAAAT-AGTAATAAAAA
35227 TAAAAGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 7 0.20
23 13 0.37
24 9 0.26
25 6 0.17
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (24 bp):
GAAAATAGTAATAAAAACCAAAAA
Found at i:35352 original size:9 final size:9
Alignment explanation
Indices: 35338--35376 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
35328 TTAGAATATT
35338 AATAAAATA
1 AATAAAATA
35347 AATAAAATA
1 AATAAAATA
35356 AATGAATAAATA
1 AAT--A-AAATA
35368 AATAAAATA
1 AATAAAATA
35377 TAAAAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 17 0.63
10 1 0.04
11 1 0.04
12 8 0.30
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (9 bp):
AATAAAATA
Found at i:36216 original size:11 final size:11
Alignment explanation
Indices: 36200--36233 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
36190 TTTAAGTAAT
*
36200 ATATATATGTG
1 ATATATATATG
36211 ATATATATATG
1 ATATATATATG
36222 ATAATATATATG
1 AT-ATATATATG
36234 GATGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (11 bp):
ATATATATATG
Found at i:38145 original size:15 final size:15
Alignment explanation
Indices: 38125--38154 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38115 ATACTTCAAG
38125 GGAAAATAACCTCAC
1 GGAAAATAACCTCAC
38140 GGAAAATAACCTCAC
1 GGAAAATAACCTCAC
38155 ATCAAGCTTC
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:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (15 bp):
GGAAAATAACCTCAC
Found at i:38537 original size:3 final size:3
Alignment explanation
Indices: 38529--38569 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
38519 TCCTTTTTAA
* *
38529 ATT ATT ATT ATT ATT ATT AAT ATC A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38570 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 32 0.97
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:38584 original size:26 final size:27
Alignment explanation
Indices: 38528--38585 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
38518 TTCCTTTTTA
**
38528 AATTATTATTATTATTATTAATATCAT
1 AATTATTATTATTATTATTAATAAAAT
*
38555 -ATTATTATTATTATTTTTAA-AAAAT
1 AATTATTATTATTATTATTAATAAAAT
38580 AATTAT
1 AATTAT
38586 AAATTACAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTATTATTATTATTATTAATAAAAT
Found at i:42063 original size:4 final size:4
Alignment explanation
Indices: 42054--42078 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42044 ATTGATTTCT
42054 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
42079 TTGGACTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:45041 original size:258 final size:259
Alignment explanation
Indices: 44545--45220 Score: 966
Period size: 258 Copynumber: 2.6 Consensus size: 259
44535 CCCGATTTAC
* * * *
44545 TGATGGCT-GAAGGACTTACCAATTTTGGAAATAGTTTATTAGGTAAGAAACTTTGGAAACCGTT
1 TGATGGCTCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCT
* *
44609 TTCTTACTTTTTCAAAAATTTCATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATTGCTTTT
66 TTCTTAC-TTTTCAAAATTTTCATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGC-TTT
** *
44674 CTCATTTTTTACAAACATCATATAAAAACATCATGCCTGAAGGTCTTATAGATGACCCGAATGAT
129 CTCA-TTTTTACAAACATCATATAAAAACATCATGCCCAAAGGTCTTATAGATGACCCGAATGAC
* * * * * *
44739 TTATCATCTCGCTCGAAATACTGTCAGACAACCTGAATGATTTAATCATCATGCTCGAAAGACTT
193 TTATCATCTCACTCGAAAGACTGACAGACAACCCGAAGGATTTAATCATCATACTCGAAAGACTT
*
44804 GT
258 AT
* * *
44806 TGATGGCTCAAAGGACTTACCAATTATGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCGCT
1 TGATGGCTCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCT
*
44871 TTCTTACTTTTCAAAATTTTCATTTTTTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCT
66 TTCTTACTTTTCAAAATTTTCATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCT
* * * *
44936 CATTTTT-GAAACATCATATGAAAGCAT-ATTGCCCAAAGGTCTTATAGATGGCCCGAATGACTT
131 CATTTTTACAAACATCATATAAAAACATCA-TGCCCAAAGGTCTTATAGATGACCCGAATGACTT
* **
44999 ATCATCTTACTCGAAAGACTGACAGATGACCCGAAGGATTTAATCATCATACTCGAAAGACTTAT
195 ATCATCTCACTCGAAAGACTGACAGACAACCCGAAGGATTTAATCATCATACTCGAAAGACTTAT
*
45064 TGATGGAC-CAAAGGACTTACCAATTTTGAAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGC
1 TGATGG-CTCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGC
* *
45128 TTTCTTACTCTTCAAAATTTTCATTTTCTGAAAATATTAAATGAGAAACTTTGGAAATCGCTTTC
65 TTTCTTACTTTTCAAAATTTTCATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTC
* * *
45193 TTATTTTT-CAAAAATTATCATAAAAACA
130 TCATTTTTACAAACATCAT-ATAAAAACA
45221 ACTTAATGGT
Statistics
Matches: 371, Mismatches: 40, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
257 1 0.00
258 236 0.64
259 13 0.04
260 7 0.02
261 58 0.16
262 56 0.15
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (259 bp):
TGATGGCTCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCT
TTCTTACTTTTCAAAATTTTCATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCT
CATTTTTACAAACATCATATAAAAACATCATGCCCAAAGGTCTTATAGATGACCCGAATGACTTA
TCATCTCACTCGAAAGACTGACAGACAACCCGAAGGATTTAATCATCATACTCGAAAGACTTAT
Found at i:45052 original size:42 final size:41
Alignment explanation
Indices: 44981--45060 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
44971 AAGGTCTTAT
* * *
44981 AGATGGCCCGAATGACTTATCATCTTACTCGAAAGACTGAC
1 AGATGACCCGAAGGACTTATCATCATACTCGAAAGACTGAC
*
45022 AGATGACCCGAAGGATTTAATCATCATACTCGAAAGACT
1 AGATGACCCGAAGGACTT-ATCATCATACTCGAAAGACT
45061 TATTGATGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (41 bp):
AGATGACCCGAAGGACTTATCATCATACTCGAAAGACTGAC
Found at i:46312 original size:64 final size:64
Alignment explanation
Indices: 46244--46365 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
46234 ATTGTTCAAG
* * * * *
46244 GTGTATCGATGCACATG-AGGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCAATGCACAAGTA-GTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
**
46308 GTGTATCAATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATGCAAACATCGAATG
1 GTGTATCAATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATG
46366 GGATTTATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 49 0.98
65 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCAATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
Found at i:47041 original size:18 final size:18
Alignment explanation
Indices: 46972--47041 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
46962 AGGGATTATC
* *
46972 AGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACAT
* **
46990 AGTGGTTCTTCGAAACAAT
1 AGTGGTCCTTCGGGAC-AT
47009 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
47028 AGTGGTCCTTCGGG
1 AGTGGTCCTTCGGG
47042 CCAAATATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 25 0.60
19 4 0.10
20 13 0.31
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:50266 original size:22 final size:22
Alignment explanation
Indices: 50239--50288 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
50229 CCGACCCGTT
50239 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
50261 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
50283 GACCCG
1 GACCCG
50289 TTGACCGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.50, G:0.24, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:50288 original size:17 final size:17
Alignment explanation
Indices: 50225--50269 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
50215 TGACCGGTCA
50225 CGACCCGACCCGTTGACC
1 CGACCCGA-CCGTTGACC
50243 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
50260 CGACCCGACC
1 CGACCCGACC
50270 CGACCGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (17 bp):
CGACCCGACCGTTGACC
Found at i:50364 original size:28 final size:29
Alignment explanation
Indices: 50324--50388 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
50314 ATTTGGTTTT
* **
50324 GGTGCTATTTTGGGAATTAATTCGAAAA-
1 GGTGCTATATTGGGAATTAATTAAAAAAG
* *
50352 GGTGCTATATTGGTAATTATTTAAAAAAG
1 GGTGCTATATTGGGAATTAATTAAAAAAG
50381 GGTGCTAT
1 GGTGCTAT
50389 TTGTGTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (29 bp):
GGTGCTATATTGGGAATTAATTAAAAAAG
Found at i:57449 original size:19 final size:19
Alignment explanation
Indices: 57422--57459 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
57412 GAACGCTGGA
57422 AACCAGTTTTGACCGGTTT
1 AACCAGTTTTGACCGGTTT
*
57441 AACCGGTTTTGACCGGTTT
1 AACCAGTTTTGACCGGTTT
57460 GACTGGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (19 bp):
AACCAGTTTTGACCGGTTT
Found at i:57455 original size:10 final size:10
Alignment explanation
Indices: 57427--57459 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
57417 CTGGAAACCA
57427 GTTTTGACCG
1 GTTTTGACCG
*
57437 G-TTTAACCG
1 GTTTTGACCG
57446 GTTTTGACCG
1 GTTTTGACCG
57456 GTTT
1 GTTT
57460 GACTGGTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.42
Consensus pattern (10 bp):
GTTTTGACCG
Found at i:57460 original size:9 final size:9
Alignment explanation
Indices: 57429--57462 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
57419 GGAAACCAGT
57429 TTTGACCGG
1 TTTGACCGG
*
57438 TTTAACCGG
1 TTTGACCGG
57447 TTTTGACCGG
1 -TTTGACCGG
57457 TTTGAC
1 TTTGAC
57463 TGGTCACGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (9 bp):
TTTGACCGG
Found at i:57488 original size:13 final size:13
Alignment explanation
Indices: 57470--57521 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
57460 GACTGGTCAC
57470 GACCCGACCCGTT
1 GACCCGACCCGTT
57483 GACCCGACCC---
1 GACCCGACCCGTT
57493 GACCCGA-CCGTT
1 GACCCGACCCGTT
57505 GACCCGACCCGTT
1 GACCCGACCCGTT
57518 GACC
1 GACC
57522 GGTGCTATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.06
10 7 0.20
12 7 0.20
13 19 0.54
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:57506 original size:22 final size:23
Alignment explanation
Indices: 57469--57515 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
57459 TGACTGGTCA
57469 CGACCCGACCCGTTGACCCGACC
1 CGACCCGACCCGTTGACCCGACC
57492 CGACCCGA-CCGTTGACCCGACC
1 CGACCCGACCCGTTGACCCGACC
57514 CG
1 CG
57516 TTGACCGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.17, C:0.51, G:0.23, T:0.09
Consensus pattern (23 bp):
CGACCCGACCCGTTGACCCGACC
Found at i:57583 original size:29 final size:29
Alignment explanation
Indices: 57551--57618 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
57541 ATTTGGTTTT
*
57551 GGTGCTATTTTGGGAATTAATTAGAAAAG
1 GGTGCTATTTTGGGAATTAATTAAAAAAG
* * *
57580 GGTGCTATATTGGTAATTATTTAAAAAAG
1 GGTGCTATTTTGGGAATTAATTAAAAAAG
57609 GGTGCTATTT
1 GGTGCTATTT
57619 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.38
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTAAAAAAG
Found at i:61136 original size:54 final size:54
Alignment explanation
Indices: 61073--61440 Score: 522
Period size: 54 Copynumber: 6.8 Consensus size: 54
61063 TACCAAATAG
* *
61073 GCACTAAGTGTGCATTTCACTGAATTCATCATATGTTGATGAATAATCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* ** * *
61127 GCACTAAGTGTGCATTTTACATAATTCATCATATGTTGATGAATAACCATTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* * *
61181 GCACTAAGTGTGCATTTCATGGAATTCATCATATGTTGATGAATAATCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* *
61235 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACTGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* *
61289 GTACTAAGTGTGAATTTCACGGAATTCATCATATGTTGATGAATAACCGTTT-A
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
*
61342 GGCACTAAGTGTGTATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
1 -GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* *** * * *
61397 GCACTATGTGTGCAAAACAAGGAATTCATAATATGTTTATGAAT
1 GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAAT
61441 GACCATATGG
Statistics
Matches: 283, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
54 282 1.00
55 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
Found at i:67759 original size:3 final size:3
Alignment explanation
Indices: 67751--67849 Score: 81
Period size: 3 Copynumber: 31.0 Consensus size: 3
67741 AAAAAACATG
* *
67751 TAA TAA TAA TAAA TGAA TAA TGA TAA TAG TAA TAA TAAA TGAA TAA TAA
1 TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA
* * * * *
67800 TAG TAG TAA TAT TAAA TAA TAA TAA TAA TAT TAAA TAT TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
67847 TAA
1 TAA
67850 CCCGAACAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
3 62 0.79
4 16 0.21
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:67819 original size:19 final size:19
Alignment explanation
Indices: 67751--67848 Score: 82
Period size: 19 Copynumber: 5.4 Consensus size: 19
67741 AAAAAACATG
*
67751 TAATAATAATAAATGAATAA
1 TAATAATATTAAAT-AATAA
* *
67771 TGATAATAGT-AATAAT-A
1 TAATAATATTAAATAATAA
* *
67788 -AATGA-A-T-AATAATAG
1 TAATAATATTAAATAATAA
*
67803 TAGTAATATTAAATAATAA
1 TAATAATATTAAATAATAA
*
67822 TAATAATATTAAATATTAA
1 TAATAATATTAAATAATAA
67841 TAATAATA
1 TAATAATA
67849 ACCCGAACAA
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
14 7 0.11
15 1 0.02
16 6 0.10
17 2 0.03
18 4 0.06
19 35 0.56
20 8 0.13
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (19 bp):
TAATAATATTAAATAATAA
Found at i:67840 original size:26 final size:26
Alignment explanation
Indices: 67754--67829 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
67744 AAACATGTAA
*
67754 TAATAATAAATGAATAATGATAATAG
1 TAATAATAAATGAATAATAATAATAG
*
67780 TAATAATAAATGAATAATAATAGTAG
1 TAATAATAAATGAATAATAATAATAG
*
67806 TAATATTAAAT-AATAATAATAATA
1 TAATAATAAATGAATAATAATAATA
67830 TTAAATATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 12 0.26
26 34 0.74
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (26 bp):
TAATAATAAATGAATAATAATAATAG
Found at i:68263 original size:41 final size:41
Alignment explanation
Indices: 68144--68264 Score: 104
Period size: 41 Copynumber: 3.0 Consensus size: 41
68134 TTTTTATGGC
* * ** *
68144 GTTTTTAGACAAACGTCGCTTTAGACTCGTACATTAATGGT
1 GTTTTTATATAAACGTCGCTAAAGACTCGTACATTAGTGGT
* * * *
68185 GTTTTT-TAATAAATGTTGC-AATA-TCTAAGTACATTAGTGGT
1 GTTTTTAT-ATAAACGTCGCTAA-AGACT-CGTACATTAGTGGT
*
68226 GTTTTTATATAAACGTCGCTAAAGACTCGTACTTTAGTG
1 GTTTTTATATAAACGTCGCTAAAGACTCGTACATTAGTG
68265 ACGCTTTTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
40 2 0.03
41 53 0.88
42 5 0.08
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (41 bp):
GTTTTTATATAAACGTCGCTAAAGACTCGTACATTAGTGGT
Found at i:69776 original size:21 final size:21
Alignment explanation
Indices: 69750--69805 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
69740 TGATTTATTA
69750 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
69771 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
69792 TTATGGATGTCAAG
1 TTATGGATTTCAAG
69806 ATTATTGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.48
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:72802 original size:29 final size:31
Alignment explanation
Indices: 72768--72837 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 31
72758 AGGGATTCAA
72768 TTAGAAT-T-TTCAAAAGTTTAAGGACTAAT
1 TTAGAATATGTTCAAAAGTTTAAGGACTAAT
*
72797 TTAGAATAGGATGTTCAAAAGTTTAAGGATTAAT
1 TTAGAAT---ATGTTCAAAAGTTTAAGGACTAAT
72831 TTAGAAT
1 TTAGAAT
72838 GAGAGTCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 7 0.20
33 1 0.03
34 27 0.77
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (31 bp):
TTAGAATATGTTCAAAAGTTTAAGGACTAAT
Found at i:74648 original size:15 final size:15
Alignment explanation
Indices: 74630--74676 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
74620 CTTTAACCCT
74630 CTTTTGTTTAAGTAC
1 CTTTTGTTTAAGTAC
74645 CTTTTGTTTAAGTAC
1 CTTTTGTTTAAGTAC
74660 CTTTTGTTTAAGTAC
1 CTTTTGTTTAAGTAC
74675 CT
1 CT
74677 AACATGGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (15 bp):
CTTTTGTTTAAGTAC
Found at i:75913 original size:57 final size:59
Alignment explanation
Indices: 75762--75920 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 59
75752 GTTAGGTGAT
* *
75762 CATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAATAATGTCCCATAGTTAGGAGAC
1 CATTTTGTAATTTTTAATAGTTGAGGGACTCAACAAAATATTGTCCCATAGTTA-GAGAC
* * * *
75822 CATTTTGTAATTTTGAATAGTCGAGGGACACAACAAAATATTGTCCCATAGTTA-AG-G
1 CATTTTGTAATTTTTAATAGTTGAGGGACTCAACAAAATATTGTCCCATAGTTAGAGAC
75879 CATTTTGTAATTTTTAATAGTTGAGGGACTCAACAAAGATAT
1 CATTTTGTAATTTTTAATAGTTGAGGGACTCAACAAA-ATAT
75921 ACTCTATAGT
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
57 34 0.38
58 6 0.07
60 49 0.55
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (59 bp):
CATTTTGTAATTTTTAATAGTTGAGGGACTCAACAAAATATTGTCCCATAGTTAGAGAC
Found at i:77514 original size:36 final size:36
Alignment explanation
Indices: 77467--77538 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
77457 ATACCTGAAA
* *
77467 GTGTGTTGCAGAGAACCCCTGGGGATAATGGAAGGC
1 GTGTGTTGCAGAGAACCCCTGCGGATAATAGAAGGC
77503 GTGTGTTGCAGAGAACCCCTGCGGATAATAGAAGGC
1 GTGTGTTGCAGAGAACCCCTGCGGATAATAGAAGGC
77539 ACTTTCCTCC
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:0.26, C:0.18, G:0.36, T:0.19
Consensus pattern (36 bp):
GTGTGTTGCAGAGAACCCCTGCGGATAATAGAAGGC
Found at i:78727 original size:30 final size:29
Alignment explanation
Indices: 78682--78749 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
78672 TGTTCATAAT
* *
78682 TATTTCTTAATTATTAACATATGTAAACA
1 TATTTTTTAACTATTAACATATGTAAACA
78711 GTATTTTTTAACTATTAACATATGTAAACA
1 -TATTTTTTAACTATTAACATATGTAAACA
78741 TAGTTTTTT
1 TA-TTTTTT
78750 TCAGAAAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (29 bp):
TATTTTTTAACTATTAACATATGTAAACA
Found at i:85985 original size:47 final size:48
Alignment explanation
Indices: 85923--86044 Score: 201
Period size: 47 Copynumber: 2.6 Consensus size: 48
85913 TTATAGCACA
85923 AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAG-CCG
1 AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
* *
85970 AGTTTGACGTCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
1 AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
* *
86018 AGTCTGACTTCTATGTGACGGTGGTGC
1 AGTCTGACATCTGTGTGACGGTGGTGC
86045 GTTGGTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 42 0.61
48 27 0.39
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (48 bp):
AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
Found at i:88396 original size:37 final size:36
Alignment explanation
Indices: 88321--88396 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
88311 TTTTTATATT
*
88321 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
88357 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
88394 TTT
1 TTT
88397 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:88579 original size:20 final size:20
Alignment explanation
Indices: 88543--88580 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
88533 ATCCTATTCC
**
88543 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
88563 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
88581 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:93660 original size:3 final size:3
Alignment explanation
Indices: 93654--93715 Score: 67
Period size: 3 Copynumber: 20.3 Consensus size: 3
93644 TGTTTTGCAA
93654 TAT TAT T-T TAT TAT TAT TAT TAT T-T T-T TAAT TAT TACT TCCAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T T--AT TAT
93700 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
93716 TTCATCTTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.11
3 40 0.75
4 4 0.08
5 2 0.04
6 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:93735 original size:2 final size:2
Alignment explanation
Indices: 93728--93769 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
93718 CATCTTAGTC
93728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93770 TTGTTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94043 original size:27 final size:26
Alignment explanation
Indices: 93992--94050 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
93982 ATATTTCTAA
*
93992 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTACTTATAAAT-T
94019 ATAAATAAATAGATTTT-CTTA-AAATT
1 ATAAATAAAT--ATTTTACTTATAAATT
94045 ATAAAT
1 ATAAAT
94051 TTGAAATAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.24
27 14 0.48
28 3 0.10
29 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAAATAAATATTTTACTTATAAATT
Found at i:94043 original size:134 final size:132
Alignment explanation
Indices: 93786--94042 Score: 327
Period size: 134 Copynumber: 1.9 Consensus size: 132
93776 AAATAACAAT
* *
93786 ATTTATTTATTTTTTATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCCCTTTTCTGATA
1 ATTTATTTATTTTTTATATCGAAGAAAAGAGCTGTCTTAAGACACCTAGAAGCCATTTTCTGATA
* * *** **
93851 TTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTTATTATCTTAAAAAATGTTTTA
66 TTTCTAAATAAATAAATATCTTACTATATAAAAATAATAAATAGATTATCTT-AAAAATGTTTTA
93916 GTC
130 GTC
* * *
93919 ATTTATTTATTTTTTAATATCGAAGACAATAGCTGTCTTAAGACACCTAGAAGTCATTTTCTGAT
1 ATTTATTTATTTTTT-ATATCGAAGAAAAGAGCTGTCTTAAGACACCTAGAAGCCATTTTCTGAT
* * *
93984 ATTTCTAAATAAATAAATATTTTA-TTTATAAATATATAAATAAATAGATTTTCTTAAAA
65 ATTTCTAAATAAATAAATATCTTACTATATAAA-A-AT-AATAAATAGATTATCTTAAAA
94043 TTATAAATTT
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
133 21 0.20
134 67 0.64
135 6 0.06
136 11 0.10
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (132 bp):
ATTTATTTATTTTTTATATCGAAGAAAAGAGCTGTCTTAAGACACCTAGAAGCCATTTTCTGATA
TTTCTAAATAAATAAATATCTTACTATATAAAAATAATAAATAGATTATCTTAAAAATGTTTTAG
TC
Found at i:94597 original size:26 final size:26
Alignment explanation
Indices: 94541--94620 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
94531 TTTTCATTAC
94541 TTATTATTTTCATAATATTTATATGT
1 TTATTATTTTCATAATATTTATATGT
* *
94567 ATATTATTTTCATTAATATTTTTAT-T
1 TTATTATTTTCA-TAATATTTATATGT
* * *
94593 TTATTTAAATTTCATATTATTTGTATGT
1 TTA-TT-ATTTTCATAATATTTATATGT
94621 CGGAGGGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 14 0.32
27 23 0.52
28 7 0.16
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TTATTATTTTCATAATATTTATATGT
Found at i:99853 original size:7 final size:7
Alignment explanation
Indices: 99832--99908 Score: 77
Period size: 7 Copynumber: 10.3 Consensus size: 7
99822 TCCAATAAAG
99832 AAAG-AA
1 AAAGAAA
99838 AAAGAAAA
1 AAAG-AAA
99846 AAAGAAA
1 AAAGAAA
99853 AAAGAAA
1 AAAGAAA
99860 AAAGATGAA
1 AAAGA--AA
99869 AAAGGAAA
1 AAA-GAAA
99877 AATGAGAAA
1 AA--AGAAA
99886 AAA-AAA
1 AAAGAAA
99892 AAAGAGAA
1 AAAGA-AA
99900 AAAGAAA
1 AAAGAAA
99907 AA
1 AA
99909 GGGGAGAAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 17
0.78 0.00 0.22
Matches are distributed among these distances:
6 10 0.16
7 21 0.34
8 17 0.27
9 11 0.18
10 3 0.05
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:99856 original size:15 final size:16
Alignment explanation
Indices: 99834--99908 Score: 102
Period size: 15 Copynumber: 4.8 Consensus size: 16
99824 CAATAAAGAA
99834 AGAAAAAGAAAAAAAG
1 AGAAAAAGAAAAAAAG
99850 A-AAAAAG-AAAAAAG
1 AGAAAAAGAAAAAAAG
* *
99864 ATGAAAAAGGAAAAATG
1 A-GAAAAAGAAAAAAAG
99881 AGAAAAA-AAAAAAAG
1 AGAAAAAGAAAAAAAG
99896 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
99909 GGGGAGAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
14 8 0.15
15 19 0.37
16 18 0.35
17 7 0.13
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AGAAAAAGAAAAAAAG
Found at i:99870 original size:31 final size:30
Alignment explanation
Indices: 99834--99908 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 30
99824 CAATAAAGAA
99834 AGAAAAAGAAAAA-AAGAAAAAAGAAAAAAG
1 AGAAAAAGAAAAATAAGAAAAAA-AAAAAAG
*
99864 ATGAAAAAGGAAAAATGAGAAAAAAAAAAAAG
1 A-GAAAAA-GAAAAATAAGAAAAAAAAAAAAG
99896 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
99909 GGGGAGAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
30 7 0.17
31 12 0.29
32 14 0.34
33 8 0.20
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (30 bp):
AGAAAAAGAAAAATAAGAAAAAAAAAAAAG
Found at i:99909 original size:14 final size:14
Alignment explanation
Indices: 99834--99909 Score: 80
Period size: 16 Copynumber: 5.0 Consensus size: 14
99824 CAATAAAGAA
*
99834 AGAAAAAGAAAAAA
1 AGAAAAAGAAAAAG
99848 AGAAAAAAGAAAAAAG
1 AG-AAAAAG-AAAAAG
99864 ATGAAAAAGGAAAAATG
1 A-GAAAAA-GAAAAA-G
*
99881 AGAAAAAAAAAAAAG
1 AG-AAAAAGAAAAAG
99896 AGAAAAAGAAAAAG
1 AGAAAAAGAAAAAG
99910 GGGAGAAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
14 13 0.25
15 9 0.17
16 22 0.42
17 9 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AGAAAAAGAAAAAG
Found at i:104692 original size:22 final size:22
Alignment explanation
Indices: 104663--104717 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
104653 ATCTATACTC
104663 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
104685 TTTAAAGATGATAGATTTTCTT
1 TTCAAAGATGATAGATTCTCTT
104707 TTCAAAGATGA
1 TTCAAAGATGA
104718 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:106183 original size:76 final size:76
Alignment explanation
Indices: 105395--106182 Score: 1276
Period size: 76 Copynumber: 10.4 Consensus size: 76
105385 CTATTTCTCA
* *
105395 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTACGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
105460 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
105471 CATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCTTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
105536 AGCCTTA-GGT
66 AGCCTTAGGGT
** *
105546 CATCTACAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
105610 AGCCTTAGGGT
66 AGCCTTAGGGT
105621 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
105685 AGCCTTAGGGT
66 AGCCTTAGGGT
*
105696 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
105761 AGCCATAGGGT
66 AGCCTTAGGGT
**
105772 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGGAGCTTTTTGAAATTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GGGAGCTTTTTGATGTTTTCA
*
105837 AAACCTTAGGGT
65 AAGCCTTAGGGT
* * * *
105849 CATCTTTAAGTCCTACAATGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
105914 AACCTTTGGGT
66 AGCCTTAGGGT
* *
105925 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
105990 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
106001 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
106066 AACCTTAGGGT
66 AGCCTTAGGGT
*
106077 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
106142 AACCTTCGGGT
66 AGCCTTAGGGT
* * * *
106153 AATCCGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
106183 TTAAGACCTC
Statistics
Matches: 662, Mismatches: 47, Indels: 6
0.93 0.07 0.01
Matches are distributed among these distances:
74 22 0.03
75 170 0.26
76 402 0.61
77 68 0.10
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:106354 original size:9 final size:9
Alignment explanation
Indices: 106336--106412 Score: 68
Period size: 9 Copynumber: 8.4 Consensus size: 9
106326 TTTTACTTAA
*
106336 ATTATTATT
1 ATTATAATT
*
106345 ATTAAAATT
1 ATTATAATT
*
106354 ATTATTATT
1 ATTATAATT
106363 ATTATAATT
1 ATTATAATT
*
106372 ATTATTATT
1 ATTATAATT
106381 A-TATATATT
1 ATTATA-ATT
*
106390 A-TATTATT
1 ATTATAATT
106398 ATTAAATAATT
1 ATT--ATAATT
106409 ATTA
1 ATTA
106413 CAAGCCCAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
8 7 0.13
9 40 0.73
11 8 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTATAATT
Found at i:106354 original size:15 final size:16
Alignment explanation
Indices: 106333--106412 Score: 92
Period size: 18 Copynumber: 4.8 Consensus size: 16
106323 TCATTTTACT
106333 TAAATTATTATTATTA
1 TAAATTATTATTATTA
106349 -AAATTATTATTATTA
1 TAAATTATTATTATTA
106364 TTATAATTATTATTATTA
1 -TA-AATTATTATTATTA
106382 TATATATTA-TATTATTA
1 TA-A-ATTATTATTATTA
*
106399 TTAAATAATTATTA
1 -TAAATTATTATTA
106413 CAAGCCCAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
15 15 0.26
16 3 0.05
17 19 0.33
18 20 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATTATTATTATTA
Found at i:106412 original size:3 final size:3
Alignment explanation
Indices: 106336--106401 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
106326 TTTTACTTAA
** *
106336 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
106383 ATAT ATT A-T ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
106402 AATAATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:107788 original size:3 final size:3
Alignment explanation
Indices: 107775--107833 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
107765 TTATTTGCAA
* *
107775 TAT TAT T-T TAT TAT TAT T-T T-T TTT TAAT TAT TACT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
107818 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
107834 TCTTTCATCT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 7 0.15
3 37 0.77
4 4 0.08
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:107863 original size:2 final size:2
Alignment explanation
Indices: 107856--107880 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
107846 GTCATATAAT
107856 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
107881 TTGTTTAAAT
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:109901 original size:15 final size:15
Alignment explanation
Indices: 109883--109933 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
109873 CGCAAGGCTA
*
109883 TCCTCAGGGTTATCC
1 TCCTCAGGGATATCC
*
109898 TCCTCAGGGATACCC
1 TCCTCAGGGATATCC
*
109913 GCCTCAGGGATATCC
1 TCCTCAGGGATATCC
109928 TCCTCA
1 TCCTCA
109934 ATATGCTCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.18, C:0.37, G:0.20, T:0.25
Consensus pattern (15 bp):
TCCTCAGGGATATCC
Found at i:110008 original size:2 final size:2
Alignment explanation
Indices: 109995--110032 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
109985 CTGGTCAGTA
* *
109995 CT CT CC CT CT CT CT CG CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
110033 ATATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Found at i:110501 original size:26 final size:26
Alignment explanation
Indices: 110465--110514 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
110455 TGGATCAGTA
*
110465 ATCATCTAAAATTTTATAAGTTTGTT
1 ATCATCTAAAATTTTATAAATTTGTT
110491 ATCATCTAAAATTTTATAAATTTG
1 ATCATCTAAAATTTTATAAATTTG
110515 CCTTAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (26 bp):
ATCATCTAAAATTTTATAAATTTGTT
Found at i:112671 original size:25 final size:24
Alignment explanation
Indices: 112617--112697 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 24
112607 ATAAATTGCA
* * *
112617 CCGAAGTGCCGTGTAGAGTTTTTGC
1 CCGAAGTGCCGCGTAGAATTTGT-C
112642 ACCGAAGTGCCGCGTAGAAATTTGTC
1 -CCGAAGTGCCGCGTAG-AATTTGTC
112668 CCGAAG-GACCGCGTAGAATTTGTC
1 CCGAAGTG-CCGCGTAGAATTTGTC
112692 CCGAAG
1 CCGAAG
112698 GACATATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
24 15 0.30
25 14 0.28
26 16 0.32
27 5 0.10
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (24 bp):
CCGAAGTGCCGCGTAGAATTTGTC
Found at i:112692 original size:24 final size:25
Alignment explanation
Indices: 112643--112700 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
112633 AGTTTTTGCA
112643 CCGAAGTG-CCGCGTAGAAATTTGTC
1 CCGAAG-GACCGCGTAGAAATTTGTC
112668 CCGAAGGACCGCGTAG-AATTTGTC
1 CCGAAGGACCGCGTAGAAATTTGTC
112692 CCGAAGGAC
1 CCGAAGGAC
112701 ATATAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAAATTTGTC
Found at i:112936 original size:30 final size:31
Alignment explanation
Indices: 112887--112970 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
112877 ACATAATTTA
* *
112887 TATCGCATAGACATATCA-TTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
*
112917 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
* *
112948 TATCACATAATCATAAC-TTTTCC
1 TATCACATAAACATATCATTTTCC
112971 TGCATATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 21 0.45
31 26 0.55
ACGTcount: A:0.32, C:0.26, G:0.02, T:0.39
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTCCATACCTT
Found at i:113384 original size:21 final size:20
Alignment explanation
Indices: 113360--113399 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
113350 TTCATATTCG
*
113360 TTGAGGGGGTATCGATTCCCT
1 TTGAAGGGGTA-CGATTCCCT
*
113381 TTGAATGGGTACGATTCCC
1 TTGAAGGGGTACGATTCCC
113400 CTAGCCCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (20 bp):
TTGAAGGGGTACGATTCCCT
Done.