Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008642.1 Hibiscus syriacus cultivar Beakdansim tig00111618_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: 212011
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:156261 original size:157 final size:156
Alignment explanation
Indices: 155975--156269 Score: 475
Period size: 157 Copynumber: 1.9 Consensus size: 156
155965 TTCTTTTATC
* * *
155975 ATTCAAACTTAAATATGTATTATTTTAATTTAAAATATACAAAAGTATATAATATCTTTAATATT
1 ATTCAAACTTAAACATATATAATTTTAATTTAAAATATACAAAAGTATATAATATCTTTAATATT
* * * *
156040 CAAAATTAAAAAGGTAACAAATACCTTTTTAAGTTGACATATTCAAAGAGTAATTATCCTACTAA
66 CAAAATTAAAAAGATAACAAATACCTTTTTAAATTAACATATTAAAAGAGTAATTATCCTACTAA
156105 TATTCAAAGAGTAAACTAATTTTACT
131 TATTCAAAGAGTAAACTAATTTTACT
*
156131 ATTCAAACTTAAACATATATAATTTTAATTTGAAATATACAAAAGTATATAATTATCTTTTAATA
1 ATTCAAACTTAAACATATATAATTTTAATTTAAAATATACAAAAGTATATAA-TATC-TTTAATA
* *
156196 TTCAAAA-TAAAAAGATAATAAATACCTTTTTAAATTAACTTATTAAAAGAGTAATTATCCTACT
64 TTCAAAATTAAAAAGATAACAAATACCTTTTTAAATTAACATATTAAAAGAGTAATTATCCTACT
156260 AATATTCAAA
129 AATATTCAAA
156270 TTAAAAATTA
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
156 48 0.38
157 65 0.51
158 14 0.11
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (156 bp):
ATTCAAACTTAAACATATATAATTTTAATTTAAAATATACAAAAGTATATAATATCTTTAATATT
CAAAATTAAAAAGATAACAAATACCTTTTTAAATTAACATATTAAAAGAGTAATTATCCTACTAA
TATTCAAAGAGTAAACTAATTTTACT
Found at i:161322 original size:72 final size:72
Alignment explanation
Indices: 161229--161372 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
161219 TCTTTTAATT
161229 TGCAATATTCAAAAGGACTATGAATTTAATATAAATATTAAATCCATCAATTAAATTCATCCATT
1 TGCAATATTCAAAAGGACTATGAATTTAATATAAATATTAAATCCATCAATTAAATTCATCCATT
161294 TCTTCCA
66 TCTTCCA
*
161301 TGCAATATTCAAAAGGACTATGAATTTAATATAAATATTAAATCCATCAATTAAATTCATCCCTT
1 TGCAATATTCAAAAGGACTATGAATTTAATATAAATATTAAATCCATCAATTAAATTCATCCATT
161366 TCTTCCA
66 TCTTCCA
161373 ACATCGTACA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (72 bp):
TGCAATATTCAAAAGGACTATGAATTTAATATAAATATTAAATCCATCAATTAAATTCATCCATT
TCTTCCA
Found at i:162611 original size:25 final size:25
Alignment explanation
Indices: 162581--162629 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
162571 TTAAAATAAT
162581 ATTTATATAATT-ATTATTTATTTAA
1 ATTTAT-TAATTAATTATTTATTTAA
*
162606 ATTTATTAATTAATTATTTTTTTA
1 ATTTATTAATTAATTATTTATTTA
162630 TACTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTATTAATTAATTATTTATTTAA
Found at i:162786 original size:22 final size:24
Alignment explanation
Indices: 162738--162786 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
162728 TTTTTTATAA
* * *
162738 TTAATGTTAATATTTATTATTATT
1 TTAATGTTAATATTTATAATGAAT
162762 TTAAT-TTAA-ATTTATAATGAAT
1 TTAATGTTAATATTTATAATGAAT
162784 TTA
1 TTA
162787 TATTCATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 4 0.18
24 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAATGTTAATATTTATAATGAAT
Found at i:164414 original size:21 final size:21
Alignment explanation
Indices: 164390--164429 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
164380 ATCTCCGCAG
*
164390 GGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
164411 GGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
164430 AGGATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:165855 original size:14 final size:14
Alignment explanation
Indices: 165836--165880 Score: 90
Period size: 14 Copynumber: 3.2 Consensus size: 14
165826 TTTTATCCTT
165836 AACATATACATTAA
1 AACATATACATTAA
165850 AACATATACATTAA
1 AACATATACATTAA
165864 AACATATACATTAA
1 AACATATACATTAA
165878 AAC
1 AAC
165881 CAACTTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.27
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:165977 original size:23 final size:23
Alignment explanation
Indices: 165950--166153 Score: 114
Period size: 23 Copynumber: 9.4 Consensus size: 23
165940 ATGCTCACAA
* *
165950 CCAATTTATCACTTCACA-TTTAT
1 CCAATTTATC-CATAACATTTTAT
*
165973 TCAATTTATCCATAACATTTTAT
1 CCAATTTATCCATAACATTTTAT
*
165996 CCAATTTATTCA-AACA----A-
1 CCAATTTATCCATAACATTTTAT
* * * *
166013 CCAACTGATCACTTCACA-TTTAT
1 CCAATTTATC-CATAACATTTTAT
*
166036 TCAATTTATCCATAACATTTTAT
1 CCAATTTATCCATAACATTTTAT
* *
166059 CCAATATATTCA-AACA----A-
1 CCAATTTATCCATAACATTTTAT
* * * * *
166076 ACAACTGATCACTTCACA-TTTAT
1 CCAATTTATC-CATAACATTTTAT
*
166099 TCAATTTATCCATAACATTTTAT
1 CCAATTTATCCATAACATTTTAT
*
166122 CCAATTTATTCATAACATTTTAT
1 CCAATTTATCCATAACATTTTAT
166145 CCAATTTAT
1 CCAATTTAT
166154 TCAAACTTCA
Statistics
Matches: 134, Mismatches: 32, Indels: 30
0.68 0.16 0.15
Matches are distributed among these distances:
17 12 0.09
18 4 0.03
19 6 0.04
22 25 0.19
23 87 0.65
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.41
Consensus pattern (23 bp):
CCAATTTATCCATAACATTTTAT
Found at i:166045 original size:63 final size:63
Alignment explanation
Indices: 165946--166138 Score: 341
Period size: 63 Copynumber: 3.0 Consensus size: 63
165936 TTTCATGCTC
* *
165946 ACAACCAATTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
*
166009 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
*
166072 ACAAACAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCATA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCA-A
166136 ACA
1 ACA
166139 TTTTATCCAA
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 120 0.97
64 4 0.03
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (63 bp):
ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
Found at i:166102 original size:31 final size:31
Alignment explanation
Indices: 165999--166102 Score: 77
Period size: 31 Copynumber: 3.3 Consensus size: 31
165989 ATTTTATCCA
*
165999 ATTTATTCAAACAACCAACTGATCACTTCAC
1 ATTTATTCAAACAAACAACTGATCACTTCAC
*** * * * * *
166030 ATTTATTCAATTTATCCA-T-AACATTTTATCC
1 ATTTATTCAAACAAACAACTGATCACTTCA--C
*
166061 AATATATTCAAACAAACAACTGATCACTTCAC
1 -ATTTATTCAAACAAACAACTGATCACTTCAC
166093 ATTTATTCAA
1 ATTTATTCAA
166103 TTTATCCATA
Statistics
Matches: 50, Mismatches: 18, Indels: 10
0.64 0.23 0.13
Matches are distributed among these distances:
29 6 0.12
30 1 0.02
31 23 0.46
32 13 0.26
33 1 0.02
34 6 0.12
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (31 bp):
ATTTATTCAAACAAACAACTGATCACTTCAC
Found at i:166449 original size:138 final size:138
Alignment explanation
Indices: 166201--166834 Score: 1072
Period size: 138 Copynumber: 4.6 Consensus size: 138
166191 ATCCAATTTC
* * *
166201 ACATGAGTGACATAATAGGGCAATGATAAAATATTCTCTGACAAAATTATGGAAGGCACGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
* * * * *
166266 AGGAACGCGCTTTCACAACTTTTCCAAGTCCCCTAAAAAATAATAGGTACTGACATGAATAGTTC
66 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
166331 TCTGGGGG
131 TCTGGGGG
166339 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
*
166404 GGGAATGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
66 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
166469 TCTGGGGG
131 TCTGGGGG
166477 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
* **
166542 AGGAATACGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
66 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
166607 TCTGGGGG
131 TCTGGGGG
**
166615 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCTT
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
* * *
166680 GGGGACGCGCTTTAACCACTTTACCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
66 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
166745 T-TCGGGGG
131 TCT-GGGGG
*
166753 ACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
* *
166818 GAGAACGCGCCTTCACC
66 GGGAACGCGCTTTCACC
166835 TAAATAGTAC
Statistics
Matches: 469, Mismatches: 26, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
137 1 0.00
138 468 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (138 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
TCTGGGGG
Found at i:171394 original size:21 final size:20
Alignment explanation
Indices: 171308--171465 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
171298 AAATGACCAA
**
171308 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
171327 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
171347 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
171367 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
171388 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
171409 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
171429 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
171450 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
171466 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:171458 original size:20 final size:20
Alignment explanation
Indices: 171433--171626 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
171423 GATTTTCAAT
* *
171433 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
171453 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
171473 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
171493 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
171513 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
171533 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
171553 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
171573 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
171594 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
171614 AATCGCAACGCGA
1 AATCGCAACGCGA
171627 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:171478 original size:40 final size:39
Alignment explanation
Indices: 171433--171626 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
171423 GATTTTCAAT
* ** *
171433 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
171473 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
171513 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
171553 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
171594 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
171627 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:171516 original size:60 final size:60
Alignment explanation
Indices: 171433--171625 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
171423 GATTTTCAAT
* ** * *
171433 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
171493 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
171553 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
171614 AATCGCAACGCG
1 AATCGCAACGCG
171626 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:171797 original size:21 final size:22
Alignment explanation
Indices: 171771--171824 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
171761 CTCTCTACGG
171771 CGAAGAAATCCGT-CCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
171792 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
171814 CGGCGAAATCC
1 CGAAGAAATCC
171825 CTCACAACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:172045 original size:33 final size:33
Alignment explanation
Indices: 172006--172113 Score: 171
Period size: 33 Copynumber: 3.3 Consensus size: 33
171996 TTCACTTAGA
* *
172006 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
*
172039 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
* *
172072 TGTCATCTCGCGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
172105 TTTCATTTC
1 TTTCATTTC
172114 AACCAAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
Found at i:172054 original size:19 final size:18
Alignment explanation
Indices: 172030--172111 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 18
172020 ACGATTCTGT
172030 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCA-TTCG
* *
172049 CGTTGC--TATTC--TCT
1 CGTTGCGATTTTCATTCG
*
172063 CGTTGCGATTGTCATCTCG
1 CGTTGCGATTTTCAT-TCG
*
172082 CGTTGCGA--TTC--TCT
1 CGTTGCGATTTTCATTCG
172096 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
172112 TCAACCAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 19
0.64 0.10 0.26
Matches are distributed among these distances:
14 18 0.38
16 6 0.13
17 6 0.13
18 1 0.02
19 16 0.34
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTCATTCG
Found at i:172068 original size:14 final size:14
Alignment explanation
Indices: 172049--172105 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
172039 TTTCATTTCG
*
172049 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
172063 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
172080 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
172096 CGTTGCGATT
1 CGTTGCGATT
172106 TTCATTTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 17 0.46
15 1 0.03
16 5 0.14
17 5 0.14
18 1 0.03
19 8 0.22
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:174102 original size:90 final size:92
Alignment explanation
Indices: 173808--174168 Score: 625
Period size: 90 Copynumber: 4.0 Consensus size: 92
173798 TTGCTTAGTA
*
173808 AATTTATTCGGTTGCTGCC-ATTC-GCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
173871 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
*
173898 AAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG--ATA-TATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
173960 TCTTTGTTTTGTC-TTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
173986 AAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATA-TATTT
1 -AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT
174049 GTCTTTGTTTTGTCTTTTGGTTGAAAGT
65 GTCTTTGTTTTGTCTTTTGGTTGAAAGT
174077 AATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
174140 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
174167 AA
1 AA
174169 ATTTATCCAT
Statistics
Matches: 261, Mismatches: 3, Indels: 14
0.94 0.01 0.05
Matches are distributed among these distances:
88 32 0.12
89 75 0.29
90 109 0.42
91 17 0.07
92 28 0.11
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (92 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGT
Found at i:174104 original size:179 final size:180
Alignment explanation
Indices: 173804--174174 Score: 644
Period size: 179 Copynumber: 2.1 Consensus size: 180
173794 TAGATTGCTT
173804 AGTAAATTTATTCGGTTGCTGCCATTCGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATT
1 AGTAAATTTATTCGGTTGCTGCCATTCGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATT
173869 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTG
66 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAAC--TG
173934 TATTCTTTAACACTGTG-ATA-TATTTGTCTTTGTTTTGTC-TTTGGTTGAA
129 TATTCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
173983 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATA-TA
1 AGTAAATTTATTCGGTTGCTGCC-ATTC-GCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
174046 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
64 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTG
174111 TATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 TATTCTTTAACACTGTG-AATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
174164 AGTAAATTTAT
1 AGTAAATTTAT
174175 CCATTCAAGT
Statistics
Matches: 183, Mismatches: 3, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
177 19 0.10
179 89 0.49
180 27 0.15
181 48 0.26
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (180 bp):
AGTAAATTTATTCGGTTGCTGCCATTCGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATT
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGTA
TTCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:174240 original size:19 final size:19
Alignment explanation
Indices: 174216--174343 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
174206 TAGTTTACTT
* *
174216 TCGCAACACGAAACTTAAA
1 TCGCAACGCGAAACTAAAA
*
174235 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
174254 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
174273 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
174287 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
174306 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACTAAAA
*
174320 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
174339 TCGCA
1 TCGCA
174344 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
14 18 0.20
15 3 0.03
16 4 0.04
17 4 0.04
18 4 0.04
19 56 0.63
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:174294 original size:33 final size:32
Alignment explanation
Indices: 174251--174343 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
174241 CGCGAAACCA
**
174251 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
174283 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
174316 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
174344 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:174341 original size:52 final size:51
Alignment explanation
Indices: 174216--174343 Score: 136
Period size: 52 Copynumber: 2.5 Consensus size: 51
174206 TAGTTTACTT
**
174216 TCGCAACACGAAACTTAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
174267 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC--CAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
174320 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACACGAAACCAAAATCGCA
174344 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
49 3 0.05
50 6 0.10
51 1 0.02
52 40 0.66
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:174361 original size:19 final size:19
Alignment explanation
Indices: 174339--174473 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
174329 GAAACCAAAA
*
174339 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
174358 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
174374 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
174391 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
174407 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
174424 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
174443 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
174463 TCGTGTTGCGA
1 TCGCGTTGCGA
174474 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:174380 original size:14 final size:14
Alignment explanation
Indices: 174361--174417 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
174351 TTTCATTTCG
174361 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
174375 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
174392 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
174408 CGTTGCGATT
1 CGTTGCGATT
174418 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:174386 original size:33 final size:33
Alignment explanation
Indices: 174344--174436 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
174334 CAAAATCGCA
*
174344 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
174377 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
174410 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
174437 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:176373 original size:14 final size:14
Alignment explanation
Indices: 176354--176389 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
176344 TTGCGATAAT
176354 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
176368 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
176382 TGATTTGT
1 TGATTTGT
176390 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:176561 original size:20 final size:19
Alignment explanation
Indices: 176493--176575 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
176483 AAAAATGACT
176493 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
176512 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
176526 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
176545 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
176565 ATCGCAATGCG
1 ATCGCAATGCG
176576 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
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 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:176628 original size:19 final size:19
Alignment explanation
Indices: 176604--176858 Score: 325
Period size: 19 Copynumber: 14.4 Consensus size: 19
176594 GATTATCTCG
176604 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
176623 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
176642 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
176656 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
176675 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
176694 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
176713 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
176732 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
176746 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
176765 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
176784 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
176798 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
176818 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
176832 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
176851 TTGCGATT
1 TTGCGATT
176859 GTATTTTCCG
Statistics
Matches: 209, Mismatches: 6, Indels: 42
0.81 0.02 0.16
Matches are distributed among these distances:
14 29 0.14
16 24 0.11
17 21 0.10
18 3 0.01
19 120 0.57
20 12 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:176644 original size:52 final size:52
Alignment explanation
Indices: 176582--176791 Score: 255
Period size: 52 Copynumber: 3.9 Consensus size: 52
176572 TGCGTTTATA
176582 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
176634 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
176686 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
176745 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
176792 CTCTCGTTGC
Statistics
Matches: 141, Mismatches: 9, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
52 91 0.65
54 4 0.03
55 5 0.04
56 2 0.01
57 27 0.19
58 3 0.02
59 9 0.06
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:176709 original size:90 final size:90
Alignment explanation
Indices: 176582--176858 Score: 398
Period size: 90 Copynumber: 3.2 Consensus size: 90
176572 TGCGTTTATA
*
176582 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
176642 TTGCGATTCTTTCGTTGCGATTTTC
66 TTGCGATTCTTTCGTTGCGATTTTC
176667 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
*
176732 TTGCGATTCTCTCGTTGCGATTTTC
66 TTGCGATTCTTTCGTTGCGATTTTC
*
176757 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGC
*
176817 ATTGCGA-T-TTTCATGTTGGGATTTTC
65 ATTGCGATTCTTTC--GTTGCGATTTTC
*
176843 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
176859 GTATTTTCCG
Statistics
Matches: 178, Mismatches: 6, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
84 3 0.02
85 30 0.17
86 36 0.20
87 6 0.03
88 8 0.04
90 95 0.53
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (90 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
TTGCGATTCTTTCGTTGCGATTTTC
Found at i:176792 original size:52 final size:55
Alignment explanation
Indices: 176604--176830 Score: 314
Period size: 52 Copynumber: 4.2 Consensus size: 55
176594 GATTATCTCG
*
176604 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCG-ATTGCGATTTTCATTTCGCA
*
176656 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCG-ATTGCGATTTTCATTTCGCA
176713 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCGATTGCGATTTTCATTTCGCA
176765 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCGATTGCGATTTTCATTT-CGCA
176818 TTGCGATTTTCAT
1 TTGCGATTTTCAT
176831 GTTGGGATTT
Statistics
Matches: 168, Mismatches: 1, Indels: 11
0.93 0.01 0.06
Matches are distributed among these distances:
52 111 0.66
53 17 0.10
54 7 0.04
55 8 0.05
57 25 0.15
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (55 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCGATTGCGATTTTCATTTCGCA
Found at i:176802 original size:33 final size:33
Alignment explanation
Indices: 176623--176858 Score: 210
Period size: 33 Copynumber: 6.8 Consensus size: 33
176613 TCATTTCGCA
*
176623 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
176656 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
176692 CATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
176730 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
176765 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
176798 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
176832 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
176859 GTATTTTCCG
Statistics
Matches: 176, Mismatches: 14, Indels: 26
0.81 0.06 0.12
Matches are distributed among these distances:
31 9 0.05
32 5 0.03
33 62 0.35
34 29 0.16
35 6 0.03
36 5 0.03
37 2 0.01
38 46 0.26
39 3 0.02
40 9 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:177782 original size:20 final size:20
Alignment explanation
Indices: 177754--178142 Score: 448
Period size: 20 Copynumber: 19.4 Consensus size: 20
177744 AAATTTCAGT
* * * *
177754 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
177774 GTTGCGA-TTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
177793 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
177813 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
177833 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
177853 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
177873 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
177893 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
177913 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
177933 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
177953 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
177973 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
177994 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
178014 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
178034 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
178054 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
178074 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
178094 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
178114 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
178134 GTTGCGATT
1 GTTGCGATT
178143 ATTGAAAATC
Statistics
Matches: 321, Mismatches: 36, Indels: 24
0.84 0.09 0.06
Matches are distributed among these distances:
19 22 0.07
20 279 0.87
21 18 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:179837 original size:13 final size:13
Alignment explanation
Indices: 179819--179843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179809 GGTTAACAAC
179819 TTTAAATTAAATG
1 TTTAAATTAAATG
179832 TTTAAATTAAAT
1 TTTAAATTAAAT
179844 TAAACCTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTAAATTAAATG
Found at i:180112 original size:37 final size:37
Alignment explanation
Indices: 180022--180126 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
180012 CCTTTTCGTC
180022 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
180059 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * * *
180096 CTACTATTATTTAAACTCATAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
180127 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:180848 original size:20 final size:20
Alignment explanation
Indices: 180799--180848 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
180789 TATACATACA
180799 TTTTTATATTTTTATATATAT
1 TTTTTAT-TTTTTATATATAT
* *
180820 TTTTAATTTTTTAT-TTTAT
1 TTTTTATTTTTTATATATAT
180839 TATTTTATTT
1 T-TTTTATTT
180849 ATACTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTATTTTTTATATATAT
Found at i:180879 original size:55 final size:55
Alignment explanation
Indices: 180776--180879 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
180766 TACTATTTAG
*
180776 TATTTTATTATATTATACATACATTTTTATATTTTTATATATATTTTTAATTTTT
1 TATTTTATTATATTATACATACATTTTTATATTTTCATATATATTTTTAATTTTT
* ** *
180831 TATTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATGTTTTTA
1 TATTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATTTTTA
180880 GTTTCTTTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
55 28 0.67
56 12 0.29
57 2 0.05
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (55 bp):
TATTTTATTATATTATACATACATTTTTATATTTTCATATATATTTTTAATTTTT
Found at i:185602 original size:11 final size:10
Alignment explanation
Indices: 185588--185627 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
185578 CAAAAACAAA
185588 AAAAAAGAAG
1 AAAAAAGAAG
185598 CAAAAAAGAAG
1 -AAAAAAGAAG
185609 AAAACAA-AAG
1 AAAA-AAGAAG
185619 AAAAAAGAA
1 AAAAAAGAA
185628 AGAACAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.07
10 13 0.48
11 12 0.44
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:185612 original size:21 final size:20
Alignment explanation
Indices: 185588--185644 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
185578 CAAAAACAAA
185588 AAAAAAGAAGCAAAAAAGAAG
1 AAAAAA-AAGCAAAAAAGAAG
185609 AAAACAAAAG-AAAAAAGAAAG
1 AAAA-AAAAGCAAAAAAG-AAG
* *
185630 AACAAAAATCAAAAA
1 AAAAAAAAGCAAAAA
185645 GAAAAAGGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 11 0.35
21 18 0.58
22 2 0.06
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGCAAAAAAGAAG
Found at i:185622 original size:19 final size:19
Alignment explanation
Indices: 185579--185650 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
185569 CAAAAAGGGC
* *
185579 AAAAACAAAAAAAAAGAAGCA
1 AAAAAGAAAAAACAA-AAG-A
185600 AAAAAGAAGAAAACAAAAGA
1 AAAAAGAA-AAAACAAAAGA
*
185620 AAAAAGAAAGAACAAAA-A
1 AAAAAGAAAAAACAAAAGA
185638 TCAAAAAGAAAAA
1 --AAAAAGAAAAA
185651 GGGACAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.02
19 8 0.18
20 19 0.43
21 10 0.23
22 6 0.14
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.01
Consensus pattern (19 bp):
AAAAAGAAAAAACAAAAGA
Found at i:185629 original size:11 final size:11
Alignment explanation
Indices: 185579--185636 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 11
185569 CAAAAAGGGC
*
185579 AAAAACAAA-A
1 AAAAAGAAAGA
185589 AAAAAG-AAGCA
1 AAAAAGAAAG-A
185600 AAAAAG-AAGA
1 AAAAAGAAAGA
*
185610 AAACA-AAAGA
1 AAAAAGAAAGA
185620 AAAAAGAAAGA
1 AAAAAGAAAGA
185631 ACAAAA
1 A-AAAA
185637 ATCAAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 2 0.05
10 18 0.45
11 16 0.40
12 4 0.10
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:185629 original size:24 final size:24
Alignment explanation
Indices: 185582--185650 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
185572 AAAGGGCAAA
*
185582 AACAAAAA-AAAAGAAGCAAAAAAG
1 AACAAAAACAAAAGAA-AAAAAAAG
*
185606 AA-GAAAACAAAAGAAAAAAGAAAG
1 AACAAAAACAAAAGAAAAAA-AAAG
185630 AACAAAAATCAAAAAGAAAAA
1 AACAAAAA-C-AAAAGAAAAA
185651 GGGACAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.19
24 15 0.41
25 4 0.11
26 1 0.03
27 10 0.27
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (24 bp):
AACAAAAACAAAAGAAAAAAAAAG
Found at i:185649 original size:13 final size:13
Alignment explanation
Indices: 185579--185650 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 13
185569 CAAAAAGGGC
185579 AAAAACAAAAA-A
1 AAAAACAAAAAGA
185591 AAAGAAGCAAAAAAGA
1 AAA-AA-C-AAAAAGA
185607 AGAAAAC-AAAAGA
1 A-AAAACAAAAAGA
* *
185620 AAAAAGAAAGAACA
1 AAAAACAAA-AAGA
*
185634 AAAATCAAAAAGA
1 AAAAACAAAAAGA
185647 AAAA
1 AAAA
185651 GGGACAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
12 7 0.15
13 18 0.38
14 11 0.23
15 6 0.12
16 4 0.08
17 2 0.04
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.01
Consensus pattern (13 bp):
AAAAACAAAAAGA
Found at i:186281 original size:22 final size:22
Alignment explanation
Indices: 186253--186307 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
186243 GCTACCCCAT
*
186253 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAACATCAAATGC
186275 CAAACCTTTGAACATCAAATGC
1 CAAACCTTTGAACATCAAATGC
186297 CAAACCTTTGA
1 CAAACCTTTGA
186308 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAACATCAAATGC
Found at i:187379 original size:106 final size:105
Alignment explanation
Indices: 187254--188208 Score: 1438
Period size: 106 Copynumber: 9.0 Consensus size: 105
187244 ATATCGTGCC
*
187254 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
187319 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
187360 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGA-TGCTCGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTT-CC
*
187424 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
187465 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTT-CC
* * *
187530 AATTTTAGAGCCAATTTCAA---CACAGTGAAAGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
187568 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTT-CC
*
187633 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
187674 ACTAC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
1 ACT-CGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTC-
187738 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
187780 ACTCGAGACAACACAAGTTTAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGGTTGTCAACAAACAATTT-C
*
187844 CAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
187886 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
*
187951 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
187992 ACTCAAGACAACACAAGTTCAACTTCACAAGGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
*
188057 AATTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
188098 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAAATTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGGTTGTCAACAAAC-AATTTC
* * * *
188162 CAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
188204 ACTCG
1 ACTCG
188209 GAACAATACA
Statistics
Matches: 773, Mismatches: 62, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
103 94 0.12
104 3 0.00
105 99 0.13
106 568 0.73
107 9 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:188610 original size:84 final size:83
Alignment explanation
Indices: 188399--188728 Score: 353
Period size: 83 Copynumber: 3.9 Consensus size: 83
188389 AAGGAGTATC
* * * * * *
188399 TGTCAACAAAGACGTTCAAGTTCGATTACACTCAGCTCCAAGGCGCATCATTTACAGCATAGCTC
1 TGTCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTC
188464 AAGGCTAGAAGGGCTATT
66 AAGGCTAGAAGGGCTATT
* *
188482 TGTCAGCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTC
1 TGTCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTC
188547 AAGG-TAAGAAGGGCTATT
66 AAGGCT-AGAAGGGCTATT
* * * * * *
188565 T-TCCAACAAAAGACCTTCGAGTTCGACTACGCTTAACTCTAAGGCATATCATTTGCAGTATAAC
1 TGT-CAAC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAAC
188629 TCAAGGCTAGAAGGG-TGATT
64 TCAAGGCTAGAAGGGCT-ATT
* * * * * * * *
188649 TGTCATCAAAAACCTTCGAGTTCGATTATATTCAACT-CAGAGGCAAATCAAATTTACAGCATAA
1 TGTCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCA-AGGCACATC--ATTTGCAGCATAA
* *
188713 CTCAAGACGAGAAGGG
63 CTCAAGGCTAGAAGGG
188729 TTATCTACCA
Statistics
Matches: 209, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
82 3 0.01
83 110 0.53
84 69 0.33
85 27 0.13
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (83 bp):
TGTCAACAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTC
AAGGCTAGAAGGGCTATT
Found at i:189299 original size:37 final size:37
Alignment explanation
Indices: 189209--189313 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
189199 CATTTTCGTC
*
189209 CTACTAGTATTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAGTATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
189246 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGTATTCAAACTCCTAAAAATAGGATAGAATT
* * *
189283 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGTATTCAAACTCCTAAAAATAGGAT
189314 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGTATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:189752 original size:12 final size:13
Alignment explanation
Indices: 189730--189764 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
189720 TATATATATA
189730 ATTATATTTTATTT
1 ATTATA-TTTATTT
189744 ATT-TATTTATTT
1 ATTATATTTATTT
189756 ATTATATTT
1 ATTATATTT
189765 TTTCATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 10 0.50
13 7 0.35
14 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTATATTTATTT
Found at i:190028 original size:9 final size:9
Alignment explanation
Indices: 190008--190059 Score: 65
Period size: 8 Copynumber: 5.9 Consensus size: 9
189998 TATACATACA
190008 TTTTTATA-
1 TTTTTATAT
190016 TTTTTATAT
1 TTTTTATAT
190025 TTTTATATAT
1 TTTT-TATAT
190035 TTTTTAT-T
1 TTTTTATAT
190043 TTTTTAT-T
1 TTTTTATAT
190051 TTATTTATA
1 TT-TTTATA
190060 CTATTTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
8 19 0.47
9 12 0.30
10 9 0.22
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTATAT
Found at i:190057 original size:17 final size:16
Alignment explanation
Indices: 190007--190058 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
189997 TTATACATAC
*
190007 ATTTTTATATTTTTAT
1 ATTTTTATATTTTTTT
190023 ATTTTTATATATTTTTT
1 ATTTTTATAT-TTTTTT
*
190040 ATTTTTTTATTTTATTT
1 ATTTTTATATTTT-TTT
190057 AT
1 AT
190059 ACTATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTTATATTTTTTT
Found at i:190071 original size:30 final size:29
Alignment explanation
Indices: 189948--190074 Score: 111
Period size: 27 Copynumber: 4.4 Consensus size: 29
189938 TATGTAAATT
* *
189948 TATTTTTCATTTATTTATTATTATTGT-TAC
1 TATTTTTTATTTTTTTA-TATTATT-TATAC
** * **
189978 TATTTAGTATTTTATTATATTATACATAC
1 TATTTTTTATTTTTTTATATTATTTATAC
*
190007 -A-TTTTTATATTTTTATATT-TTTATA-
1 TATTTTTTATTTTTTTATATTATTTATAC
*
190032 TATTTTTTATTTTTTTATTTTATTTATAC
1 TATTTTTTATTTTTTTATATTATTTATAC
190061 TATTTATTTATTTT
1 TATTT-TTTATTTT
190075 CATTATGTTT
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
26 5 0.07
27 30 0.39
28 7 0.09
29 14 0.18
30 20 0.26
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (29 bp):
TATTTTTTATTTTTTTATATTATTTATAC
Found at i:190074 original size:27 final size:28
Alignment explanation
Indices: 189956--190074 Score: 83
Period size: 26 Copynumber: 4.3 Consensus size: 28
189946 TTTATTTTTC
*
189956 ATTTA-TTTATTATTATTGT-TACTATTT
1 ATTTATTTTATT-TTATTATATACTATTT
* *
189983 A-GTATTTTATTATATTATACATAC-ATTT
1 ATTTATTTTATTTTATTAT--ATACTATTT
* *
190011 -TTATATTTTTATATTT-TTATATATTTTTT
1 ATT-TA-TTTTAT-TTTATTATATACTATTT
190040 ATTT-TTTTATTTTATT-TATACTATTT
1 ATTTATTTTATTTTATTATATACTATTT
190066 ATTTATTTT
1 ATTTATTTT
190075 CATTATGTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
26 22 0.31
27 19 0.27
28 7 0.10
29 9 0.13
30 12 0.17
31 2 0.03
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
ATTTATTTTATTTTATTATATACTATTT
Found at i:196830 original size:2 final size:2
Alignment explanation
Indices: 196823--196854 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
196813 TACATTCTTT
196823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
196855 ATTACCTAAG
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):
TA
Found at i:198430 original size:92 final size:92
Alignment explanation
Indices: 198327--198598 Score: 338
Period size: 91 Copynumber: 3.0 Consensus size: 92
198317 GAGGAAAATA
*
198327 AAAAAACAAAAGCAATCAAAAGCACCATCAAGAGAAGAATCAAAAGGTTTTCTTTGACAGAAACG
1 AAAAAACAAAAGCAATCAAAAGCACCATTAAGAGAAGAATCAAAAGGTTTTCTTTGACAGAAAC-
*
198392 AAAGCACACAAGC-A-GGAAACTAAGAAT
65 AAAGCACA-AAACTATGGAAACTAAGAAT
* * * *
198419 CAAAAATAAAAGCAATCAAAAGCACCATTAGGAGAAGAATCAAAAGGTTTTCTTTAACAGAAACA
1 AAAAAACAAAAGCAATCAAAAGCACCATTAAGAGAAGAATCAAAAGGTTTTCTTTGACAGAAACA
*
198484 AAAC-CAAAACTATGGAAACTAAGAAT
66 AAGCACAAAACTATGGAAACTAAGAAT
* * * * * *
198510 AAAAAACAAAAACAA-CTAAAAGCACCATTAACAAAAGAATCAAAAGATGTTCTTTGACATAAAC
1 AAAAAACAAAAGCAATC-AAAAGCACCATTAAGAGAAGAATCAAAAGGTTTTCTTTGACAGAAAC
* *
198574 AAAGCAAAAAAATAT-GACAACTAAG
65 AAAGCACAAAACTATGGA-AACTAAG
198599 TATTATTAAT
Statistics
Matches: 155, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
89 3 0.02
90 4 0.03
91 75 0.48
92 73 0.47
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.15
Consensus pattern (92 bp):
AAAAAACAAAAGCAATCAAAAGCACCATTAAGAGAAGAATCAAAAGGTTTTCTTTGACAGAAACA
AAGCACAAAACTATGGAAACTAAGAAT
Found at i:209777 original size:29 final size:29
Alignment explanation
Indices: 209745--209803 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
209735 CCAGGGAGTT
209745 CAATATTTTATCCATTAAAGCCCATTTTC
1 CAATATTTTATCCATTAAAGCCCATTTTC
209774 CAATATTTTATCCATTAAAGCCCATTTTC
1 CAATATTTTATCCATTAAAGCCCATTTTC
209803 C
1 C
209804 TTTAGGACCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (29 bp):
CAATATTTTATCCATTAAAGCCCATTTTC
Done.