Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001004.1 Hibiscus syriacus cultivar Beakdansim tig00002006_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: 116780
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:211 original size:20 final size:19
Alignment explanation
Indices: 177--216 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
167 TTTTTATATT
* *
177 ATAAAATATTTTAAATAAA
1 ATAAAATAATTTAAACAAA
196 ATAAATATAATTTAAACAAA
1 ATAAA-ATAATTTAAACAAA
216 A
1 A
217 CATTAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAATAATTTAAACAAA
Found at i:4205 original size:64 final size:64
Alignment explanation
Indices: 4104--4255 Score: 304
Period size: 64 Copynumber: 2.4 Consensus size: 64
4094 TCCCAAATCC
4104 ATTTGAACATTTTTTGTTTTGTATATACAAGAATATAAGTACCTATTATTAAATAGTTAAAAGT
1 ATTTGAACATTTTTTGTTTTGTATATACAAGAATATAAGTACCTATTATTAAATAGTTAAAAGT
4168 ATTTGAACATTTTTTGTTTTGTATATACAAGAATATAAGTACCTATTATTAAATAGTTAAAAGT
1 ATTTGAACATTTTTTGTTTTGTATATACAAGAATATAAGTACCTATTATTAAATAGTTAAAAGT
4232 ATTTGAACATTTTTTGTTTTGTAT
1 ATTTGAACATTTTTTGTTTTGTAT
4256 TCCCTCCAGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 88 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (64 bp):
ATTTGAACATTTTTTGTTTTGTATATACAAGAATATAAGTACCTATTATTAAATAGTTAAAAGT
Found at i:9256 original size:2 final size:2
Alignment explanation
Indices: 9249--9288 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9239 ATATAGTTTA
9249 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
9289 TAAGCCTATT
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):
AT
Found at i:15580 original size:20 final size:18
Alignment explanation
Indices: 15555--15594 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
15545 TATCGTCTTT
*
15555 AAAATAATTAACTAATTAAA
1 AAAATAAATAAC-AA-TAAA
15575 AAAATAAATAACAATAAA
1 AAAATAAATAACAATAAA
15593 AA
1 AA
15595 TGGCTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATAAATAACAATAAA
Found at i:18961 original size:34 final size:34
Alignment explanation
Indices: 18923--19000 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
18913 ACAATAGAAA
*
18923 AAAAATCAAAACTAAAAGTAAATATGAAAAGATT
1 AAAAATCAAAACTAAAAATAAATATGAAAAGATT
18957 AAAAATCAAAACTAAAAATAAATATGAAAAGATT
1 AAAAATCAAAACTAAAAATAAATATGAAAAGATT
*
18991 AAGAATCAAA
1 AAAAATCAAA
19001 TTGAATCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (34 bp):
AAAAATCAAAACTAAAAATAAATATGAAAAGATT
Found at i:19826 original size:2 final size:2
Alignment explanation
Indices: 19821--19872 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
19811 ACTTAAATCA
19821 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
19863 AT AT AT AT AT
1 AT AT AT AT AT
19873 TTTTTATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20379 original size:17 final size:18
Alignment explanation
Indices: 20354--20398 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
20344 AATAAATTAA
* *
20354 AAATATAAAAAAT-AATT
1 AAATTTAAAAAATGAAAT
20371 AAATTTAAAAAATGAAAT
1 AAATTTAAAAAATGAAAT
20389 AATATTTAAA
1 AA-ATTTAAA
20399 GGACAAGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTTAAAAAATGAAAT
Found at i:20380 original size:24 final size:25
Alignment explanation
Indices: 20346--20398 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
20336 AATCATAAAA
*
20346 TAAATTAAAAATAT-AAAAAATAAT
1 TAAATTAAAAAAATGAAAAAATAAT
* * *
20370 TAAATTTAAAAAATGAAATAATATT
1 TAAATTAAAAAAATGAAAAAATAAT
20395 TAAA
1 TAAA
20399 GGACAAGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAATTAAAAAAATGAAAAAATAAT
Found at i:34985 original size:173 final size:173
Alignment explanation
Indices: 34744--35257 Score: 728
Period size: 173 Copynumber: 3.0 Consensus size: 173
34734 CAACAAGATG
* *
34744 ATTAAGTCACTAGGTTGCTCAGGTAACCGCTCAGGATCAACACAATGGTAAAAAGTTTCATCAAG
1 ATTAAGTCACTAGGTTGCTCAGGTAACCGCTCAGGATCGACACAATGGTCAAAAGTTTCATCAAG
** * *
34809 CATTCAATGAATGCCTTCCACTGATTCTGAAACCTCGTCATTGCAACCCAATGGTCAAAATAACA
66 CATTCAATGAATGCCTTCCACTGATTCCAAAACCTCATCATTGTAACCCAATGGTCAAAATAACA
* *
34874 TTCAATAACACAAATAAAATAAAGATGAATATGTAGCATGGCA
131 TTCAATAACACAAATAAAATAAAGATGAATAGGTAGCATGACA
* *
34917 ATTAATTCACGAGGTTGCTCAGGTAACCGCTCAGGATCGACACAA-GAGTCAAAAGTTTCATCAA
1 ATTAAGTCACTAGGTTGCTCAGGTAACCGCTCAGGATCGACACAATG-GTCAAAAGTTTCATCAA
*
34981 GCATTCAATGAATGCCTTCCACTGATTCCAAAACCTCATCATTGTAACCCAATGTTCAAAATAAC
65 GCATTCAATGAATGCCTTCCACTGATTCCAAAACCTCATCATTGTAACCCAATGGTCAAAATAAC
* * *
35046 ATTCTACAACACGAATAAAA-AAAGATGAATAGGTAGCATGACA
130 ATTCAATAACACAAATAAAATAAAGATGAATAGGTAGCATGACA
* * * *
35089 ATTAAGTCACTAGGTTGCTCAGCTAACCGCTCAGGACCGACACAATGGTCGAAAGTTTCATCAAA
1 ATTAAGTCACTAGGTTGCTCAGGTAACCGCTCAGGATCGACACAATGGTCAAAAGTTTCATCAAG
** * ** * *
35154 CATTCAACAAATGCCTTCCACTGATCCCAAAAAATCATCACTGTAACCCAATGGTCGAAA-AACA
66 CATTCAATGAATGCCTTCCACTGATTCCAAAACCTCATCATTGTAACCCAATGGTCAAAATAACA
* * *
35218 TTGAATAAAACATAAATAAAATAAAGATGAAAAGGTAGCA
131 TTCAAT--AACACAAATAAAATAAAGATGAATAGGTAGCA
35258 AGATGATAAA
Statistics
Matches: 302, Mismatches: 34, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
171 7 0.02
172 131 0.43
173 147 0.49
174 17 0.06
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (173 bp):
ATTAAGTCACTAGGTTGCTCAGGTAACCGCTCAGGATCGACACAATGGTCAAAAGTTTCATCAAG
CATTCAATGAATGCCTTCCACTGATTCCAAAACCTCATCATTGTAACCCAATGGTCAAAATAACA
TTCAATAACACAAATAAAATAAAGATGAATAGGTAGCATGACA
Found at i:36369 original size:20 final size:20
Alignment explanation
Indices: 36340--36499 Score: 124
Period size: 20 Copynumber: 7.9 Consensus size: 20
36330 GATTTTCCAG
* *
36340 AATCGTAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
36360 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* ** * *
36380 TATCGCAACAAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
36401 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
36421 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATACG-AA
* * *
36442 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
36462 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
36482 AATCGCAACGCGAATACG
1 AATCGCAACGCGAATACG
36500 TATTCGCATT
Statistics
Matches: 111, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
19 2 0.02
20 74 0.67
21 35 0.32
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:36403 original size:41 final size:41
Alignment explanation
Indices: 36381--36493 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 41
36371 GATTCTGACT
* *
36381 ATCGCAACAAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACAAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
36422 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACAAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
36463 ATCGCAACGAGAATACGT-AAATCGCAACGCG
1 ATCGCAACAAGAATACGTAAAATCGCAACGCG
36494 AATACGTATT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 13 0.19
41 56 0.81
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
ATCGCAACAAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:36407 original size:21 final size:20
Alignment explanation
Indices: 36381--36491 Score: 141
Period size: 20 Copynumber: 5.5 Consensus size: 20
36371 GATTCTGACT
*
36381 ATCGCAACAAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
36402 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
36422 ATCGCAACGAGAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
36443 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
36463 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
36483 ATCGCAACG
1 ATCGCAACG
36492 CGAATACGTA
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
20 45 0.58
21 33 0.42
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:36412 original size:61 final size:60
Alignment explanation
Indices: 36340--36501 Score: 173
Period size: 61 Copynumber: 2.6 Consensus size: 60
36330 GATTTTCCAG
* * * * **
36340 AATCGTAACGCGAATATGAAAATCGCAACGCGATTC-TGACTATCGCAACAAGTATCCGTAA
1 AATCGCAACGCGAATACGTAAATCGCAACGCGATACGT-AAAATCGCAACAAGTATCCGT-A
* * * **
36401 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTAAATCGCAACGCG-ATACGTAAAATCGCAACAAGTATCCGTA
*
36462 AATCGCAACGAGAATACGTAAATCGCAACGCGAATACGTA
1 AATCGCAACGCGAATACGTAAATCGCAACGCG-ATACGTA
36502 TTCGCATTGC
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
61 63 0.75
62 20 0.24
63 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATACGTAAATCGCAACGCGATACGTAAAATCGCAACAAGTATCCGTA
Found at i:36519 original size:20 final size:20
Alignment explanation
Indices: 36496--36547 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
36486 GCAACGCGAA
*
36496 TACGTATTCGCATTGCGATT
1 TACGTAATCGCATTGCGATT
*
36516 TACGTAATCGCGTTGCGATT
1 TACGTAATCGCATTGCGATT
36536 TA-GTAAATCGCA
1 TACGT-AATCGCA
36548 ACGAGATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (20 bp):
TACGTAATCGCATTGCGATT
Found at i:37437 original size:24 final size:24
Alignment explanation
Indices: 37410--37463 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
37400 GTATTCGAAA
37410 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
37434 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
37458 TTTGAT
1 TTTGAT
37464 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:40125 original size:19 final size:19
Alignment explanation
Indices: 39977--40133 Score: 136
Period size: 19 Copynumber: 8.7 Consensus size: 19
39967 CTTAATGTCT
*
39977 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
39996 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
40010 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
40029 ATCGCAACGCGAATATGAAT
1 ATCGCAATGCGAA-ATGAAA
**
40049 ATCGCAATGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
*
40069 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
40088 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
40102 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40121 ATCGCAACGCGAA
1 ATCGCAATGCGAA
40134 TTTAGTTTCG
Statistics
Matches: 112, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
14 18 0.16
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 50 0.45
20 29 0.26
21 3 0.03
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40186 original size:33 final size:33
Alignment explanation
Indices: 40139--40218 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
40129 GCGAATTTAG
* * * * *
40139 TTTCGCGTTCCGATTTTGTCGTTGCGCTTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
40172 TTTCGCATTGCGATTCTCTCGTTGCGATTTTTA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
40205 TTTCGTATTGCGAT
1 TTTCGCATTGCGAT
40219 AGTCTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.10, C:0.21, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:40344 original size:14 final size:14
Alignment explanation
Indices: 40325--40361 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
40315 CATCAATTAA
40325 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
40339 ACAAATCATCTTTT
1 ACAAATCAACTTTT
40353 ACAAATCAA
1 ACAAATCAA
40362 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41776 original size:21 final size:21
Alignment explanation
Indices: 41710--41776 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
41700 GTGAATCGGG
*
41710 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
41730 CATCTTCAACGATGACAGTGGC
1 C-TCTTGAACGGTGGGAGGGGA
41752 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
41773 CTCT
1 CTCT
41777 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:41795 original size:42 final size:41
Alignment explanation
Indices: 41710--41832 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
41700 GTGAATCGGG
* * * *
41710 CTCTTGAATGGTGGGA-GGGACATCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGAC-TC-TCGAGGATGACAGGGGC
*
41752 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
41794 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
41833 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.84
43 7 0.10
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:42269 original size:19 final size:19
Alignment explanation
Indices: 42229--42316 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
42219 TCTGGAACTT
*
42229 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
42250 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
42269 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
42283 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
42302 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
42317 TTATAGTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 28 0.51
21 11 0.20
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:42335 original size:19 final size:20
Alignment explanation
Indices: 42313--42395 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 20
42303 AAATCGCAAC
42313 GCGATTAT-AGTTTCGCGTT
1 GCGATTATAAGTTTCGCGTT
**
42332 GCGATT-TTGGTTTCGCGTT
1 GCGATTATAAGTTTCGCGTT
** *
42351 GCGA-TAGTCATTTTTCACGTT
1 GCGATTA-T-AAGTTTCGCGTT
* *
42372 GCGATTTTAAGTTTCGTGTT
1 GCGATTATAAGTTTCGCGTT
42392 GCGA
1 GCGA
42396 AAGTAAACTA
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
18 2 0.04
19 20 0.41
20 13 0.27
21 13 0.27
22 1 0.02
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (20 bp):
GCGATTATAAGTTTCGCGTT
Found at i:42589 original size:94 final size:94
Alignment explanation
Indices: 42450--42665 Score: 378
Period size: 94 Copynumber: 2.3 Consensus size: 94
42440 GCATTACTTA
* *
42450 AACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGCATTAAAGAATACACAGTTTAGCAGA
42515 ATTGGCAGCAACCGAACAAATTTACTTTC
66 ATTGGCAGCAACCGAACAAATTTACTTTC
* * *
42544 AACCAAAAGATAAAAAAAAGACAAATACTAACTTCACAGCGTTAAAGAATACACAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGCATTAAAGAATACACAGTTTAGCAGA
42609 ATTGGCAGCAACCGAACAAATTTACTTTC
66 ATTGGCAGCAACCGAACAAATTTACTTTC
*
42638 AACCAAAAGACAAAACAAAGACGAATAC
1 AACCAAAAGACAAAACAAAGACAAATAC
42666 ACAATTTAGC
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 114 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.18
Consensus pattern (94 bp):
AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGCATTAAAGAATACACAGTTTAGCAGA
ATTGGCAGCAACCGAACAAATTTACTTTC
Found at i:42703 original size:70 final size:70
Alignment explanation
Indices: 42590--42735 Score: 249
Period size: 70 Copynumber: 2.1 Consensus size: 70
42580 CAGCGTTAAA
*
42590 GAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-
1 GAATACACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTAC-TTCAACCAAAAGACAAAACA
42654 AAAGAC
65 AAAGAC
*
42660 GAATACACAATTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAA
1 GAATACACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTCAACCAAAAGACAAAACAA
42725 AAGAC
66 AAGAC
*
42730 AAATAC
1 GAATAC
42736 TAACTTCACA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
69 19 0.26
70 53 0.74
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (70 bp):
GAATACACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTCAACCAAAAGACAAAACAA
AAGAC
Found at i:42767 original size:164 final size:164
Alignment explanation
Indices: 42496--42798 Score: 527
Period size: 164 Copynumber: 1.8 Consensus size: 164
42486 GAGTATTAAA
* *
42496 GAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGATAAAAAA
1 GAATACACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAAA
*
42561 AAGACAAATACTAACTTCACAGCGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
66 AAGACAAATACTAACTTCACAGCGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAAC
42626 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC
131 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC
*
42660 GAATACACAATTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACA
1 GAATACACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA-A
* *
42724 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAA
65 AAAGACAAATACTAACTTCACAGCGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAA
*
42789 TAAATTTACT
130 CAAATTTACT
42799 AAGCAATCTA
Statistics
Matches: 131, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
163 17 0.13
164 114 0.87
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (164 bp):
GAATACACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAAA
AAGACAAATACTAACTTCACAGCGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAAC
AAATTTACTTTCAACCAAAAGACAAAACAAAGAC
Found at i:43180 original size:21 final size:21
Alignment explanation
Indices: 43156--43230 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
43146 GTGACGGGAT
43156 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* ** *
43177 AGGTGTATAG-TCGGGTTG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
43198 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
43216 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
43231 AAGTGGAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.15, C:0.13, G:0.41, T:0.31
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:44548 original size:33 final size:34
Alignment explanation
Indices: 44497--44562 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
44487 TTGAAATGAA
* **
44497 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCACAACGCGGAAATGAAAATCGCAACGAGAG
44531 AATCACAACGC-GAAATGAAAATCGCAACGAGA
1 AATCACAACGCGGAAATGAAAATCGCAACGAGA
44563 AATTAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (34 bp):
AATCACAACGCGGAAATGAAAATCGCAACGAGAG
Found at i:44558 original size:19 final size:19
Alignment explanation
Indices: 44489--44600 Score: 117
Period size: 19 Copynumber: 6.1 Consensus size: 19
44479 TCTTTTGGTT
44489 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
44508 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
44526 G--A-GAGAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
44542 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
44561 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
44580 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
44599 GA
1 GA
44601 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
14 8 0.11
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 47 0.63
20 14 0.19
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:44636 original size:20 final size:20
Alignment explanation
Indices: 44607--44660 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
44597 GCGATTTTGG
*
44607 TTTCGCGTTGCGATAGTCAT
1 TTTCGTGTTGCGATAGTCAT
**
44627 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATAGTCAT
*
44647 TTTCATGTTGCGAT
1 TTTCGTGTTGCGAT
44661 TTTAAGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
TTTCGTGTTGCGATAGTCAT
Found at i:44661 original size:20 final size:20
Alignment explanation
Indices: 44613--44663 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
44603 TTGGTTTCGC
** *
44613 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
44633 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
44653 GTTGCGATTTT
1 GTTGCGATTTT
44664 AAGTTTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:45220 original size:20 final size:19
Alignment explanation
Indices: 45197--45412 Score: 166
Period size: 20 Copynumber: 10.7 Consensus size: 19
45187 CGCTTTAAAA
45197 ATCGCGTTGCGATTTTACGT
1 ATCGCGTTGCGA-TTTACGT
*
45217 ATCGTCGTTGCGATTTACGG
1 ATCG-CGTTGCGATTTACGT
*
45237 ATACGCATTGCGATTTACGT
1 AT-CGCGTTGCGATTTACGT
*
45257 ATTCTCGTTGCGATTTACAG-
1 A-TCGCGTTGCGATTTAC-GT
*
45277 ATACGCATTGCGATTTACGT
1 AT-CGCGTTGCGATTTACGT
* *
45297 ATTCTCGTTGCGATTTACGG
1 A-TCGCGTTGCGATTTACGT
45317 ATACGCGTTGCGATTTTACGT
1 AT-CGCGTTGCGA-TTTACGT
* * *
45338 ATTCTCGTTGCAATTTACGG
1 A-TCGCGTTGCGATTTACGT
* * *
45358 ATACTCGTTGCGATAGT-CAGA
1 AT-CGCGTTGCGAT-TTAC-GT
* *
45379 ATCGCGTTGCGATTTTCAT
1 ATCGCGTTGCGATTTACGT
45398 ATTCGCGTTGCGATT
1 A-TCGCGTTGCGATT
45413 CTAGAAAATC
Statistics
Matches: 159, Mismatches: 22, Indels: 30
0.75 0.10 0.14
Matches are distributed among these distances:
19 6 0.04
20 120 0.75
21 32 0.20
22 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (19 bp):
ATCGCGTTGCGATTTACGT
Found at i:45347 original size:41 final size:41
Alignment explanation
Indices: 45199--45371 Score: 271
Period size: 40 Copynumber: 4.3 Consensus size: 41
45189 CTTTAAAAAT
45199 CGCGTTGCGATTTTACGTA-TCGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTC-TCGTTGCGATTTACGGATA
* *
45240 CGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
45280 CGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
45320 CGCGTTGCGATTTTACGTATTCTCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
45361 CTCGTTGCGAT
1 CGCGTTGCGAT
45372 AGTCAGAATC
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 74 0.60
41 50 0.40
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:45387 original size:81 final size:81
Alignment explanation
Indices: 45203--45412 Score: 239
Period size: 81 Copynumber: 2.6 Consensus size: 81
45193 AAAAATCGCG
* *
45203 TTGCGATTTTACGT-ATCGTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCGTT
1 TTGCGA-TTCACGTAATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTT
*
45266 GCGATTTACAGATACGCA
64 GCAATTTACAGATACGCA
* * *
45284 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
1 TTGCGATTCACGTAATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
* * *
45349 AATTTACGGATACTCG
66 AATTTACAGATACGCA
* ** *
45365 TTGCGATAGTCA-G-AATCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGAT--TCACGTAATCGCGTTGCGATTTACGGATACGCGTTGCGATT
45413 CTAGAAAATC
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
80 34 0.31
81 74 0.67
82 1 0.01
83 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (81 bp):
TTGCGATTCACGTAATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
AATTTACAGATACGCA
Found at i:48842 original size:2 final size:2
Alignment explanation
Indices: 48835--48905 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
48825 TTTTTAAAAC
48835 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
48877 AT AT 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 AT AT A
48906 CCCCCATCCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49097 original size:24 final size:24
Alignment explanation
Indices: 49070--49118 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
49060 TATATCAAAA
*
49070 ATCAAAAAATAAATCAGGTCAAGT
1 ATCAAAAAAGAAATCAGGTCAAGT
* **
49094 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAAAAGAAATCAGGTCAAGT
49118 A
1 A
49119 ACAGATCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAAAAGAAATCAGGTCAAGT
Found at i:49202 original size:24 final size:24
Alignment explanation
Indices: 49087--49202 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
49077 AATAAATCAG
* *
49087 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
49111 GTCAAGTAACAGATCATAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
49135 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
49159 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
49183 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
49203 TCAAATCGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 75 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:49218 original size:48 final size:48
Alignment explanation
Indices: 49120--49220 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
49110 GGTCAAGTAA
* ** *
49120 CAGATCATAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* *
49168 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
49216 CAGAT
1 CAGAT
49221 AAAATATTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:50348 original size:18 final size:18
Alignment explanation
Indices: 50327--50361 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50317 TGCCATCCGG
*
50327 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
50345 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
50362 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:51584 original size:8 final size:8
Alignment explanation
Indices: 51526--51611 Score: 63
Period size: 8 Copynumber: 10.5 Consensus size: 8
51516 TCAAAGTTTT
51526 GGTCAACGG
1 GGTCAAC-G
51535 TGGTCAACG
1 -GGTCAACG
51544 CCGGTCAAC-
1 --GGTCAACG
51553 GGTCAACG
1 GGTCAACG
*
51561 AGTCAACG
1 GGTCAACG
51569 GGT---CG
1 GGTCAACG
*
51574 GGTCAATG
1 GGTCAACG
*
51582 GGTCAGGTCG
1 GGTCA--ACG
51592 GGTCAACG
1 GGTCAACG
51600 GGTCAACG
1 GGTCAACG
51608 GGTC
1 GGTC
51612 GGGTCGGGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
5 5 0.08
7 7 0.11
8 29 0.47
9 1 0.02
10 20 0.32
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:51620 original size:18 final size:18
Alignment explanation
Indices: 51569--51604 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51559 CGAGTCAACG
*
51569 GGTCGGGTCAATGGGTCA
1 GGTCGGGTCAACGGGTCA
51587 GGTCGGGTCAACGGGTCA
1 GGTCGGGTCAACGGGTCA
51605 ACGGGTCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.44, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCA
Found at i:58976 original size:19 final size:18
Alignment explanation
Indices: 58941--58982 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
58931 TTTTTTTTGT
58941 AATTTTTCTGAATTTTTA
1 AATTTTTCTGAATTTTTA
* *
58959 TATTTTTCTGACTTTTTTA
1 AATTTTTCTGA-ATTTTTA
58978 AATTT
1 AATTT
58983 GTAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (18 bp):
AATTTTTCTGAATTTTTA
Found at i:59178 original size:15 final size:15
Alignment explanation
Indices: 59158--59209 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
59148 TGAGACATTA
59158 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
59173 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
* *
59188 CCCACCCCACATCCG
1 CCCGCCCCGCATCCG
*
59203 TCCGCCC
1 CCCGCCC
59210 AGCTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.10, C:0.67, G:0.15, T:0.08
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:66876 original size:7 final size:7
Alignment explanation
Indices: 66864--66905 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
66854 TTTCTTATTT
66864 ATTTTTA
1 ATTTTTA
66871 ATTTTTA
1 ATTTTTA
66878 ATTTTTA
1 ATTTTTA
66885 ATTTTTA
1 ATTTTTA
66892 ATTTTTA
1 ATTTTTA
66899 ATTTTTA
1 ATTTTTA
66906 TTTGGGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:67433 original size:111 final size:112
Alignment explanation
Indices: 67217--67678 Score: 692
Period size: 112 Copynumber: 4.1 Consensus size: 112
67207 TTGTTGGTTT
* * *
67217 GTGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
67282 GGTTTATAAATGACAAAACAGATAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* * *
67329 GTGTCGATACTTTATAAAAATATATTGATCTATAACAATATAACA-GTTAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
67393 GGTCTATAAATGACAAAACAGGTAAAGCGCTACAATATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* *
67440 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
67505 GGTCTATAAATGACAAAACAGGTAAAGTGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* * * * *
67552 ATGTCGGTACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAACAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
67617 GGTCTATAAATGACAAAACAAGTAAAGCTCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
*
67664 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
67679 GTAACCCCCT
Statistics
Matches: 321, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
111 101 0.31
112 220 0.69
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:69238 original size:22 final size:22
Alignment explanation
Indices: 69211--69272 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
69201 AACGATCAAC
69211 GGTCAACGGTCGGGTCGGGTCA
1 GGTCAACGGTCGGGTCGGGTCA
69233 GGTCAACGGTCGGGTC--G---
1 GGTCAACGGTCGGGTCGGGTCA
69250 GGTCAACGGTCGGGTCGGGTCA
1 GGTCAACGGTCGGGTCGGGTCA
69272 G
1 G
69273 ACCGGTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 16 0.46
19 1 0.03
20 1 0.03
22 17 0.49
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCA
Found at i:69243 original size:17 final size:17
Alignment explanation
Indices: 69223--69271 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
69213 TCAACGGTCG
*
69223 GGTCGGGTCAGGTCAAC
1 GGTCGGGTCGGGTCAAC
69240 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
69257 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
69272 GACCGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:69339 original size:29 final size:31
Alignment explanation
Indices: 69307--69376 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 31
69297 TTCAGATCGG
69307 TCAAACCGGTTC-GAACCGATTG-AAACCGA
1 TCAAACCGGTTCAGAACCGATTGAAAACCGA
* * *
69336 TCAAGCCGG-TCAGAACCGGTTGAAAACCGG
1 TCAAACCGGTTCAGAACCGATTGAAAACCGA
*
69366 TTAAACCGGTT
1 TCAAACCGGTT
69377 TCCAGCAGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 2 0.06
29 17 0.52
30 13 0.39
31 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (31 bp):
TCAAACCGGTTCAGAACCGATTGAAAACCGA
Found at i:70421 original size:182 final size:182
Alignment explanation
Indices: 70107--70564 Score: 749
Period size: 182 Copynumber: 2.5 Consensus size: 182
70097 GTTGTTATAT
* * *
70107 TTTATTATAAGTATCGAAACTTTTGAAATTTAAAAGAGAATAAGTTATAGCGTTAATAAAGTGTC
1 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
* * *
70172 GATACTTTATAAATATGTATCGATCCATAACAATAAAACAGGTAAAACTATGACAAAACCGGTCT
66 GATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAATATGACAAAACCAGTCT
* *
70237 CGAAATGACAAAA-TCGGTAAAGCA-CTATCGGATATGTTGAAAGTGTCGATAC
131 CGAAATGACAAAACT-GATAAAG-AGCTACCGGATATGTTGAAAGTGTCGATAC
* *
70289 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAAAGTGTC
1 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
* **
70354 GATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATTAGTCT
66 GATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAATATGACAAAACCAGTCT
70419 CGAAATGACAAAACTGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATAC
131 CGAAATGACAAAACTGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATAC
* *
70471 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTCGATAAAGTGTC
1 TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
70536 GATACTTTATAAAAATGTATCGATCCATA
66 GATACTTTATAAAAATGTATCGATCCATA
70565 TGTAACACCC
Statistics
Matches: 257, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
181 1 0.00
182 255 0.99
183 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (182 bp):
TTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGTCAATAAAGTGTC
GATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAATATGACAAAACCAGTCT
CGAAATGACAAAACTGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATAC
Found at i:71383 original size:13 final size:13
Alignment explanation
Indices: 71336--71372 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
71326 GTCACAACCC
71336 GACCCGACCCGTT
1 GACCCGACCCGTT
71349 GACCCGACCCGTT
1 GACCCGACCCGTT
*
71362 GAACCGACCCG
1 GACCCGACCCG
71373 ACCCGTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:71396 original size:15 final size:15
Alignment explanation
Indices: 71372--71405 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
71362 GAACCGACCC
*
71372 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
71387 GACCCATTGACCGTT
1 GACCCATTGACCGTT
71402 GACC
1 GACC
71406 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:72744 original size:18 final size:18
Alignment explanation
Indices: 72718--72753 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
72708 TCGAAAGGAC
*
72718 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
72736 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
72754 CAGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:73946 original size:12 final size:12
Alignment explanation
Indices: 73931--74000 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
73921 GATAAATGAC
73931 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
73943 CTGATTTCTGAT
1 CTGAATTCTGTT
*
73955 CTGGATTCTGTT
1 CTGAATTCTGTT
*
73967 ATG-ATATCTGTT
1 CTGAAT-TCTGTT
73979 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
73991 TTGATTTCTG
1 CTGAATTCTG
74001 ATATCTTCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:73962 original size:24 final size:24
Alignment explanation
Indices: 73894--74002 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
73884 AAATATTTTA
*
73894 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** *
73918 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
73942 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
73966 TATGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
73990 TTTGATTTCTGAT
1 TCTGATTTCTGAT
74003 ATCTTCGTTT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 67 0.99
25 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:79207 original size:12 final size:12
Alignment explanation
Indices: 79190--79214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
79180 TCCTATAGCG
79190 GCCGTTAAAAAT
1 GCCGTTAAAAAT
79202 GCCGTTAAAAAT
1 GCCGTTAAAAAT
79214 G
1 G
79215 TTGTCGGCAC
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:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GCCGTTAAAAAT
Found at i:84011 original size:2 final size:2
Alignment explanation
Indices: 84004--84035 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83994 TATTTTAAGA
84004 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
84036 TATTTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90004 original size:43 final size:42
Alignment explanation
Indices: 89850--90089 Score: 226
Period size: 43 Copynumber: 5.7 Consensus size: 42
89840 TTGAGGCTTA
* * *
89850 AATTATAAAAGTAAAAAGT-ATAATTAAAAAAAATTAGGAACCTC
1 AATTATAAAGGTAAAAAGTGA-GATTAAAAAAAA-TA-GAGCCTC
* *
89894 AATTATAAAGGTAAAAAGT-ATA-TAAAAATAA-AGA-CCTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAAATAGAGCCTC
* *
89932 AATT-TAAAGGTAAAAAGTGAGATTGAAAAAAGTAGGAGCCTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAAATA-GAGCCTC
* *
89974 AATTATAAATGT-AAAAGTGAGATTAAAAAAAATTAGAGGCTCC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAAA-TAGAGCCT-C
* * * *
90017 AATTTTAAAAGTAAAAAGTGAGATT-GAAAAAATCAAATGCCTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAAAT-AGA-GCCTC
*
90060 AATTATAAAGGTAAAAAGTGAGATTGAAAA
1 AATTATAAAGGTAAAAAGTGAGATTAAAAA
90090 TTATTAAGGT
Statistics
Matches: 165, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
37 14 0.08
38 10 0.06
39 8 0.05
40 2 0.01
41 2 0.01
42 40 0.24
43 52 0.32
44 37 0.22
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (42 bp):
AATTATAAAGGTAAAAAGTGAGATTAAAAAAAATAGAGCCTC
Found at i:90048 original size:86 final size:85
Alignment explanation
Indices: 89837--90089 Score: 256
Period size: 86 Copynumber: 3.0 Consensus size: 85
89827 AAAAATGATT
* * * * *
89837 AAATT-GAGGCTTAAATTATAAAAGTAAAAAGT-ATAATTAAAAAAAATTAGGAACCTCAATTAT
1 AAATTAGAGGC-TCAATTTTAAAAGTAAAAAGTGA-GATT-GAAAAAA-TAGGAGCCTCAATTAT
*
89900 AAAGGTAAAAAGT-ATA-TAAAAA
62 AAAGGTAAAAAGTGAGATTAAAAA
* * *
89922 TAA--AGA-CCTCAA-TTTAAAGGTAAAAAGTGAGATTGAAAAAAGTAGGAGCCTCAATTATAAA
1 AAATTAGAGGCTCAATTTTAAAAGTAAAAAGTGAGATTGAAAAAA-TAGGAGCCTCAATTATAAA
*
89983 TGT-AAAAGTGAGATTAAAAA
65 GGTAAAAAGTGAGATTAAAAA
*
90003 AAATTAGAGGCTCCAATTTTAAAAGTAAAAAGTGAGATTGAAAAAATCA-AATGCCTCAATTATA
1 AAATTAGAGGCT-CAATTTTAAAAGTAAAAAGTGAGATTGAAAAAAT-AGGA-GCCTCAATTATA
*
90067 AAGGTAAAAAGTGAGATTGAAAA
63 AAGGTAAAAAGTGAGATTAAAAA
90090 TTATTAAGGT
Statistics
Matches: 139, Mismatches: 17, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
79 6 0.04
80 28 0.20
81 25 0.18
82 4 0.03
83 4 0.03
84 4 0.03
85 7 0.05
86 45 0.32
87 16 0.12
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.25
Consensus pattern (85 bp):
AAATTAGAGGCTCAATTTTAAAAGTAAAAAGTGAGATTGAAAAAATAGGAGCCTCAATTATAAAG
GTAAAAAGTGAGATTAAAAA
Found at i:90206 original size:87 final size:86
Alignment explanation
Indices: 89893--90207 Score: 201
Period size: 86 Copynumber: 3.7 Consensus size: 86
89883 TTAGGAACCT
* * * * **
89893 CAATTATAAAGGTAAAAAGT-ATA-T-AAAAA-TAAAGACCTCAATT-TAAAGGT-AAAAAGTGA
1 CAATTATAAAGATAAAAAGTGAGATTCAAAAATTAGAGACTTCAATTATAAATATAAAAAAGTGA
* * *
89952 GATTGAAAAAAGT-AGGA-GCCT
66 GATTGAAAAAA-TCA-AATACCC
* * * *
89973 CAATTATAAATG-T-AAAAGTGAGATTAAAAAAAATTAGAGGCTCCAATTTTAAA-AGT-AAAAA
1 CAATTATAAA-GATAAAAAGTGAGATT--CAAAAATTAGAGACTTCAATTATAAATA-TAAAAAA
* *
90034 GTGAGATTGAAAAAATCAAATGCCT
62 GTGAGATTGAAAAAATCAAATACCC
* * * * * **
90059 CAATTATAAAGGTAAAAAGTGAGATTGAAAATTATTA-AGGTCATCAAGTGGAAATATAAAAAAG
1 CAATTATAAAGATAAAAAGTGAGATTCAAAA--ATTAGA-GACTTCAATTATAAATATAAAAAAG
*
90123 TGAGATT-AAAAATATTAAA-ACCC
63 TGAGATTGAAAAA-ATCAAATACCC
* *
90146 CAATTATAAAGATAAAAAGTGGGATTTCAAAAATTAGAGACTTCAATTATAAATATTAAAAA
1 CAATTATAAAGATAAAAAGTGAGA-TTCAAAAATTAGAGACTTCAATTATAAATATAAAAAA
90208 TAAAATTGAA
Statistics
Matches: 188, Mismatches: 26, Indels: 36
0.75 0.10 0.14
Matches are distributed among these distances:
79 6 0.03
80 13 0.07
81 2 0.01
84 5 0.03
85 17 0.09
86 64 0.34
87 56 0.30
88 25 0.13
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.25
Consensus pattern (86 bp):
CAATTATAAAGATAAAAAGTGAGATTCAAAAATTAGAGACTTCAATTATAAATATAAAAAAGTGA
GATTGAAAAAATCAAATACCC
Found at i:92433 original size:22 final size:23
Alignment explanation
Indices: 92408--92456 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
92398 TCACTAATTC
92408 CAAACT-TTAAA-TTCATAAATCT
1 CAAACTCTTAAATTTCA-AAATCT
92430 CAAA-TCTTAAATTTCAAAATCT
1 CAAACTCTTAAATTTCAAAATCT
92452 CAAAC
1 CAAAC
92457 GGATTTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (23 bp):
CAAACTCTTAAATTTCAAAATCT
Found at i:94343 original size:21 final size:21
Alignment explanation
Indices: 94297--94343 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
94287 ATTGAAATTC
94297 TTATTTTACTCGTTATATTTT
1 TTATTTTACTCGTTATATTTT
*
94318 ATATTTTATCTC-TTAT-TTTAT
1 TTATTTTA-CTCGTTATATTT-T
94339 TTATT
1 TTATT
94344 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.14
21 16 0.73
22 3 0.14
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (21 bp):
TTATTTTACTCGTTATATTTT
Found at i:94942 original size:84 final size:84
Alignment explanation
Indices: 94801--94968 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
94791 CTTTTGCTTC
*
94801 TTTCTTCTAGCGGCATGTGTAAGTTCCATTGCTCTCAAAGGACAGATCGTGTTTGTCATCGGAAC
1 TTTCTTCTAGCGGCATGTGCAAGTTCCATTGCTCTCAAAGGACAGATCGTGTTTGTCATCGGAAC
94866 AGCAACATGACGCATGGGG
66 AGCAACATGACGCATGGGG
*
94885 TTTCTTCTAGCGGCATGTGCAAGTTCCATTGCTCTCAAAGGAGAGATCGTGTTTGTCATCGGAAC
1 TTTCTTCTAGCGGCATGTGCAAGTTCCATTGCTCTCAAAGGACAGATCGTGTTTGTCATCGGAAC
94950 AGCAACATGACGCATGGGG
66 AGCAACATGACGCATGGGG
94969 GGGGGGCTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (84 bp):
TTTCTTCTAGCGGCATGTGCAAGTTCCATTGCTCTCAAAGGACAGATCGTGTTTGTCATCGGAAC
AGCAACATGACGCATGGGG
Found at i:96198 original size:18 final size:18
Alignment explanation
Indices: 96150--96200 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
96140 TTACAATATG
96150 ATAATTTTAAAAAATTAT
1 ATAATTTTAAAAAATTAT
**
96168 ATAAAATTAAAAAATTAT
1 ATAATTTTAAAAAATTAT
*
96186 ATATTTTTTAAAAAA
1 ATA-ATTTTAAAAAA
96201 GAAAACACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATTTTAAAAAATTAT
Found at i:103801 original size:5 final size:5
Alignment explanation
Indices: 103791--103820 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
103781 CACAAGGTAT
103791 TCAAC TCAAC TCAAC TCAAC TCAAC TCAAC
1 TCAAC TCAAC TCAAC TCAAC TCAAC TCAAC
103821 AGAACTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
TCAAC
Found at i:103826 original size:15 final size:15
Alignment explanation
Indices: 103792--103826 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
103782 ACAAGGTATT
*
103792 CAACTCAACTCAACT
1 CAACTCAACTCAACA
103807 CAACTCAACTCAACA
1 CAACTCAACTCAACA
*
103822 GAACT
1 CAACT
103827 ATCAATCGTG
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:0.43, C:0.37, G:0.03, T:0.17
Consensus pattern (15 bp):
CAACTCAACTCAACA
Found at i:107003 original size:20 final size:20
Alignment explanation
Indices: 106960--107167 Score: 222
Period size: 20 Copynumber: 10.2 Consensus size: 20
106950 CTGACTATAA
*
106960 CAACGAGTATCCGTAAAATCG
1 CAACGCGTATCCGT-AAATCG
*
106981 CAACGCGTATCCGTAAATTG
1 CAACGCGTATCCGTAAATCG
* *
107001 CAACGAC-AATACGTAAAATCG
1 CAACG-CGTATCCGT-AAATCG
*
107022 CAACGCGTATCCGTAAATCA
1 CAACGCGTATCCGTAAATCG
* * *
107042 CAACGAGAATACGTAAATCG
1 CAACGCGTATCCGTAAATCG
*
107062 CAACGCGTATCTGTAAATCG
1 CAACGCGTATCCGTAAATCG
* * *
107082 CAACGAGAATACGTAAATCG
1 CAACGCGTATCCGTAAATCG
*
107102 CAATGCGTATCCGTAAATCG
1 CAACGCGTATCCGTAAATCG
* *
107122 CAACGAC-AATACGTAAAATCG
1 CAACG-CGTATCCGT-AAATCG
107143 CAACGCGTATCCGTAAATCG
1 CAACGCGTATCCGTAAATCG
107163 CAACG
1 CAACG
107168 TGATTTTTAA
Statistics
Matches: 152, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
20 106 0.70
21 46 0.30
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAACGCGTATCCGTAAATCG
Found at i:107071 original size:40 final size:41
Alignment explanation
Indices: 106960--107167 Score: 330
Period size: 41 Copynumber: 5.1 Consensus size: 41
106950 CTGACTATAA
* * *
106960 CAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATTG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* *
107001 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCA
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
107042 CAACGAGAATACGT-AAATCGCAACGCGTATCTGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
107082 CAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
107122 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
107163 CAACG
1 CAACG
107168 TGATTTTTAA
Statistics
Matches: 154, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.49
41 79 0.51
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
Found at i:109450 original size:24 final size:24
Alignment explanation
Indices: 109416--109469 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
109406 CTGAAAAATC
109416 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
109440 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
109464 ATCAAA
1 ATCAAA
109470 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:109483 original size:24 final size:24
Alignment explanation
Indices: 109416--109483 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
109406 CTGAAAAATC
* * *
109416 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
109440 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
109464 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
109484 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:110344 original size:19 final size:19
Alignment explanation
Indices: 110320--110371 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
110310 CGATACCGGA
110320 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
* *
110339 GATCGCGTTGCGATTTATG
1 GATCGCGTTGCGAATTATC
110358 GATACGCGTTGCGA
1 GAT-CGCGTTGCGA
110372 TTTTACGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:110367 original size:20 final size:20
Alignment explanation
Indices: 110323--110554 Score: 197
Period size: 20 Copynumber: 11.6 Consensus size: 20
110313 TACCGGAGAT
*
110323 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
*
110342 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
110362 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
110382 TGTCGTTTGCGATTTACGGATA
1 CG-CG-TTGCGATTTACGGATA
* * *
110404 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
110424 CTCGTTGCGATTTACATATA
1 CGCGTTGCGATTTACGGATA
* *
110444 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
110464 CTCGTTGC-AATTACGGATA
1 CGCGTTGCGATTTACGGATA
110483 CGCGTTGCGATTTTAC-G-TA
1 CGCGTTGCGA-TTTACGGATA
*
110502 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
110523 CGCATTGCAATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
110544 CTCGTTGCGAT
1 CGCGTTGCGAT
110555 AGTCAGAATC
Statistics
Matches: 171, Mismatches: 30, Indels: 23
0.76 0.13 0.10
Matches are distributed among these distances:
19 39 0.23
20 83 0.49
21 42 0.25
22 7 0.04
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:110445 original size:40 final size:41
Alignment explanation
Indices: 110344--110554 Score: 286
Period size: 40 Copynumber: 5.2 Consensus size: 41
110334 TTATCGATCG
* *
110344 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
110385 CGTTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CG-TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
110426 CGTTGCGATTTACATATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
110466 CGTTGC-AATTACGGATACGCGTTGCGATTTTACGTA-TGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
110505 CGTTGCGATTTACGGATACGCATTGCAATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
110546 CGTTGCGAT
1 CGTTGCGAT
110555 AGTCAGAATC
Statistics
Matches: 150, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 26 0.17
40 75 0.50
41 25 0.17
42 24 0.16
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:110586 original size:20 final size:20
Alignment explanation
Indices: 110563--110611 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
110553 ATAGTCAGAA
*
110563 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
110583 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
110603 TCGCGTTGC
1 TCGCGTTGC
110612 AATTCTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:110714 original size:20 final size:20
Alignment explanation
Indices: 110644--110718 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
110634 AATTTGTACT
** *
110644 ATCGCATTGCGATTCTTCATA
1 ATCGCATTGCGATTCTGGA-G
*
110665 ATCGCGTTGCGATTCTGG-G
1 ATCGCATTGCGATTCTGGAG
*
110684 AACTG-ATTTGCGATTCTGGAG
1 ATC-GCA-TTGCGATTCTGGAG
110705 ATCGCATTGCGATT
1 ATCGCATTGCGATT
110719 TTTATTTCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.05
20 22 0.51
21 19 0.44
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTCTGGAG
Found at i:116748 original size:22 final size:23
Alignment explanation
Indices: 116708--116762 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
116698 TTAGAACTAC
* * *
116708 AAATTATAATTATACAATTTTAT
1 AAATTATAAGTATAAAATTATAT
116731 AAATT-TAAGTATAAAATTATAT
1 AAATTATAAGTATAAAATTATAT
*
116753 ATTATTATAA
1 A-AATTATAA
116763 AAATTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 15 0.58
23 8 0.31
24 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATTATAAGTATAAAATTATAT
Done.