Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 38
Found at i:4531282 original size:12 final size:13
Alignment explanation
Indices: 4531244--4531290 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 13
4531234 CCGGTTTTTT
*
4531244 ACCGGATAAAAAA
1 ACCGGTTAAAAAA
4531257 ACCGGTTTGAAAAAA
1 ACCGG-TT-AAAAAA
4531272 ACCGGTT-AAAAA
1 ACCGGTTAAAAAA
4531284 ACCGGTT
1 ACCGGTT
4531291 TTTATCCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 12 0.39
13 5 0.16
14 3 0.10
15 11 0.35
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (13 bp):
ACCGGTTAAAAAA
Found at i:4533609 original size:21 final size:21
Alignment explanation
Indices: 4533585--4533624 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4533575 TTTATTTTAT
4533585 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
4533606 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
4533625 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:4533672 original size:33 final size:33
Alignment explanation
Indices: 4533619--4533717 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
4533609 TTTGTTTCAA
4533619 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
4533651 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
4533684 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
4533717 T
1 T
4533718 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:4534192 original size:17 final size:18
Alignment explanation
Indices: 4534172--4534205 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4534162 ATTTTTTTAT
4534172 AACCG-TTTTTTTAAAAA
1 AACCGATTTTTTTAAAAA
4534189 AACCGATTTTTTTAAAA
1 AACCGATTTTTTTAAAA
4534206 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (18 bp):
AACCGATTTTTTTAAAAA
Found at i:4534205 original size:15 final size:15
Alignment explanation
Indices: 4534153--4534209 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
4534143 ATCTGGAATA
*
4534153 TTAAAATCGATTTTT
1 TTAAAACCGATTTTT
*
4534168 TTATAACCG-TTTTT
1 TTAAAACCGATTTTT
4534182 TTAAAAAAACCGATTTTT
1 TT---AAAACCGATTTTT
4534200 TTAAAACCGA
1 TTAAAACCGA
4534210 AACCGGTTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 15 0.43
17 6 0.17
18 7 0.20
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:4534324 original size:15 final size:17
Alignment explanation
Indices: 4534298--4534329 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4534288 TTCTATGGGA
4534298 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
4534314 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
4534330 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:4534471 original size:16 final size:16
Alignment explanation
Indices: 4534450--4534480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4534440 TCTAGGGTCC
4534450 CTTTACATCATACACT
1 CTTTACATCATACACT
*
4534466 CTTTACATCTTACAC
1 CTTTACATCATACAC
4534481 AAACCAAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (16 bp):
CTTTACATCATACACT
Found at i:4534915 original size:19 final size:19
Alignment explanation
Indices: 4534889--4534933 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
4534879 CAACAGGAGA
4534889 GCAACCATTAAAAGAGAGG
1 GCAACCATTAAAAGAGAGG
*
4534908 GTAACCATTAAAAGAGAGG
1 GCAACCATTAAAAGAGAGG
4534927 GCAACCA
1 GCAACCA
4534934 CAGAAACAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (19 bp):
GCAACCATTAAAAGAGAGG
Found at i:4540866 original size:12 final size:11
Alignment explanation
Indices: 4540840--4540934 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 11
4540830 CATCATGAAG
*
4540840 AGAAAGAAGAA
1 AGAAAAAAGAA
4540851 AGAAAAAAGAAA
1 AGAAAAAAG-AA
*
4540863 AGAAAAAA-AG
1 AGAAAAAAGAA
*
4540873 AGAAAAATTGGAA
1 AGAAAAA--AGAA
*
4540886 AGGAGAAAA-AA
1 A-GAAAAAAGAA
* * *
4540897 TGAAAATAGAT
1 AGAAAAAAGAA
*
4540908 GGAAAAAAG-A
1 AGAAAAAAGAA
4540918 AGAAAGAAAGAA
1 AGAAA-AAAGAA
4540930 AGAAA
1 AGAAA
4540935 GAAAACTCAC
Statistics
Matches: 62, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
10 17 0.27
11 22 0.35
12 16 0.26
13 2 0.03
14 5 0.08
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (11 bp):
AGAAAAAAGAA
Found at i:4540876 original size:15 final size:16
Alignment explanation
Indices: 4540846--4540878 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4540836 GAAGAGAAAG
4540846 AAGAAAGAAAAAAGAA
1 AAGAAAGAAAAAAGAA
*
4540862 AAGAAA-AAAAGAGAA
1 AAGAAAGAAAAAAGAA
4540877 AA
1 AA
4540879 ATTGGAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAAAGAA
Found at i:4543527 original size:36 final size:37
Alignment explanation
Indices: 4543470--4543543 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
4543460 TGAGATTGGG
*
4543470 GCAAGTCAACTTTAAGCCTTCACCAAAGAGTAGTGAA
1 GCAAGTCAACTTTAAGCCTTCACCAAAGAGGAGTGAA
* **
4543507 GCAA-TCAATTTTAAGCCTTCACTGAAGAGGAGTGAA
1 GCAAGTCAACTTTAAGCCTTCACCAAAGAGGAGTGAA
4543543 G
1 G
4543544 AAAATCCATC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (37 bp):
GCAAGTCAACTTTAAGCCTTCACCAAAGAGGAGTGAA
Found at i:4543826 original size:131 final size:133
Alignment explanation
Indices: 4543577--4543857 Score: 422
Period size: 132 Copynumber: 2.1 Consensus size: 133
4543567 AGCAAGATGA
* *
4543577 TAAGTCCTTCGGGCTATCCATAAAACCTTTGGGTAGGATGTTTTCATATGAATTCGAAAATGAAA
1 TAAGTCCTTCGGGCCATCCATAAAACCTTTGGGTAGGATGTTTTCAAATGAATTCGAAAATGAAA
* * *
4543642 AAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAATTTTCAC-TT
66 AAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGATTTTCAAAATTTCACACT
*
4543706 TAG
131 TAC
* * * * *
4543709 TAAGTCATTCGGGCCATCTATAAGACCTTTGGGTAGGATGTTTTCAAATGAATTTGAAAATG-AG
1 TAAGTCCTTCGGGCCATCCATAAAACCTTTGGGTAGGATGTTTTCAAATGAATTCGAAAATGAAA
* * *
4543773 AAAATTATGTTTTAAGATGATGACATTTTTGAAAACTAAGAAGGCGATTTTCAAAATTTCACACT
66 AAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGATTTTCAAAATTTCACACT
4543838 TAC
131 TAC
4543841 TAAGTCCTTCGGGCCAT
1 TAAGTCCTTCGGGCCAT
4543858 AAATAAGTCT
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
131 58 0.44
132 75 0.56
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (133 bp):
TAAGTCCTTCGGGCCATCCATAAAACCTTTGGGTAGGATGTTTTCAAATGAATTCGAAAATGAAA
AAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAAGGCGATTTTCAAAATTTCACACT
TAC
Found at i:4543952 original size:42 final size:42
Alignment explanation
Indices: 4543861--4543941 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
4543851 GGGCCATAAA
* *
4543861 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCAG
1 TAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTAATCAG
*
4543903 TAAGTCTTTCGAGCATGATGCTTAAAACCTTTGGGTAAT
1 TAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTAAT
4543942 TTTTAAGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (42 bp):
TAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTAATCAG
Found at i:4544576 original size:16 final size:16
Alignment explanation
Indices: 4544555--4544585 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4544545 TCTAGGGTTC
4544555 CTTTACATCATACACT
1 CTTTACATCATACACT
*
4544571 CTTTACATCTTACAC
1 CTTTACATCATACAC
4544586 AAACCAAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (16 bp):
CTTTACATCATACACT
Found at i:4553366 original size:35 final size:35
Alignment explanation
Indices: 4553256--4553454 Score: 135
Period size: 35 Copynumber: 5.8 Consensus size: 35
4553246 ATATTTTAAA
* * *
4553256 TAAAAGATATTTATTATCTCTTTACATTTGAATAT
1 TAAAAGATATTTATTATCTTTTTAAATTTGTATAT
* * * * * *
4553291 TAATATGATAATTA-TAT-TCTTTTAAATATCTCAAAG
1 TAA-AAGATATTTATTATCT-TTTTAAATTTGT-ATAT
4553327 TAAAAGATATTTATTATCTTTTTAAATTTGTATAT
1 TAAAAGATATTTATTATCTTTTTAAATTTGTATAT
* * *
4553362 TAAAAGATA-TTA--ATTTTTTTGAATATT-TAAAT
1 TAAAAGATATTTATTATCTTTTTAAAT-TTGTATAT
* * **
4553394 TAAAACATATTT-TTATCTTTTCAAATTTAAATAT
1 TAAAAGATATTTATTATCTTTTTAAATTTGTATAT
* *
4553428 TAAAA-ATATAGTAATATCTTTTTAAAT
1 TAAAAGATAT-TTATTATCTTTTTAAAT
4553455 ATTTCAAATT
Statistics
Matches: 125, Mismatches: 27, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
32 22 0.18
33 10 0.08
34 22 0.18
35 44 0.35
36 26 0.21
37 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (35 bp):
TAAAAGATATTTATTATCTTTTTAAATTTGTATAT
Found at i:4553476 original size:66 final size:63
Alignment explanation
Indices: 4553338--4553477 Score: 158
Period size: 66 Copynumber: 2.1 Consensus size: 63
4553328 AAAAGATATT
* ** *
4553338 TATTATCTTTTTAAATTTGTATATTAAAAGATATTAATTTTTTTGAATATTTAAATTAAAACA
1 TATTATCTTTTCAAATTTAAATATTAAAAGATATTAATTTTTTTAAATATTTAAATTAAAACA
4553401 TATTTTTATCTTTTCAAATTTAAATATTAAAA-ATATAGTAATATCTTTTTAAATATTTCAAATT
1 TA---TTATCTTTTCAAATTTAAATATTAAAAGATAT--TAAT-T-TTTTTAAATATTT-AAATT
4553465 AAAA-A
58 AAAACA
4553470 TATTATCT
1 TATTATCT
4553478 ATTAAAAGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
63 2 0.03
65 4 0.06
66 30 0.46
67 4 0.06
68 1 0.02
69 15 0.23
70 9 0.14
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (63 bp):
TATTATCTTTTCAAATTTAAATATTAAAAGATATTAATTTTTTTAAATATTTAAATTAAAACA
Found at i:4553481 original size:16 final size:17
Alignment explanation
Indices: 4553462--4553494 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4553452 AATATTTCAA
4553462 ATTAAAA-ATATTATCT
1 ATTAAAAGATATTATCT
4553478 ATTAAAAGATATTATCT
1 ATTAAAAGATATTATCT
4553495 TTTTGAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTAAAAGATATTATCT
Found at i:4565026 original size:272 final size:268
Alignment explanation
Indices: 4564491--4565031 Score: 1030
Period size: 272 Copynumber: 2.0 Consensus size: 268
4564481 AGTCATCGAA
4564491 ACTATTCTTAGTATGCCCAGCATACCTATCTTTCTGTATATTTTTCCCAATTATCCTTTAGTTTT
1 ACTATTCTTAGTATGCCCAGCATACCTATCTTTCTGTATATTTTTCCCAATTATCCTTTAGTTTT
4564556 CCCAATGTATGTCAAATGAGAATGTAAGGTACAGCATTGCACCGAAGTGCCGAAATGGTCATTCA
66 CCCAATGTATGTCAAATGAGAATGTAAGGTACAGCATTGCACCGAAGTGCCGAAATGGTCATTCA
4564621 CTTTTTATAATACCATGAGTGGCACCTTTATGCTGAAAATGCAGTTATGCACTAAACAAAATCAA
131 CTTTTTATAATACCATGAGTGGCACCTTTATGCTGAAAATGCAGTTATGCACTAAACAAAATCAA
4564686 TCGATAACTTTCATACACGAAGTATGTCAAAATGGTAATTCACCTTTTATGAATACCATGGGTGG
196 TCGATAACTTTCATACACGAAGTATGTCAAAATGGTAATTCACCTTTTATGAATACCATGGGTGG
4564751 CACCTTTT
261 CACCTTTT
4564759 ACTATT-TTAGTATGCCCAGCATACCTATCTTTCTGTATATTTTTCCCAATTATCCTTTAGTTTT
1 ACTATTCTTAGTATGCCCAGCATACCTATCTTTCTGTATATTTTTCCCAATTATCCTTTAGTTTT
4564823 CCCAATGTATGTCAAATGAGAATGTAAGGTACATGCATTGCACCGAAGTGCCGAAATGGTCATTC
66 CCCAATGTATGTCAAATGAGAATGTAAGGTACA-GCATTGCACCGAAGTGCCGAAATGGTCATTC
4564888 ACTTTTTATTAATACCATGAGTGGCACCTTTTATGCTGAAAATGCACCGTTATGCACTAAACAAA
130 ACTTTTTA-TAATACCATGAGTGGCACC-TTTATGCTGAAAATGCA--GTTATGCACTAAACAAA
4564953 ATCAATCGATAACTTTCATACACGAAGTATGTCAAAATGGTAATTCACCTTTTATGAATACCATG
191 ATCAATCGATAACTTTCATACACGAAGTATGTCAAAATGGTAATTCACCTTTTATGAATACCATG
4565018 GGTGGCACCTTTT
256 GGTGGCACCTTTT
4565031 A
1 A
4565032 TGCCGAAAAT
Statistics
Matches: 268, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
267 91 0.34
268 45 0.17
269 19 0.07
270 17 0.06
272 96 0.36
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (268 bp):
ACTATTCTTAGTATGCCCAGCATACCTATCTTTCTGTATATTTTTCCCAATTATCCTTTAGTTTT
CCCAATGTATGTCAAATGAGAATGTAAGGTACAGCATTGCACCGAAGTGCCGAAATGGTCATTCA
CTTTTTATAATACCATGAGTGGCACCTTTATGCTGAAAATGCAGTTATGCACTAAACAAAATCAA
TCGATAACTTTCATACACGAAGTATGTCAAAATGGTAATTCACCTTTTATGAATACCATGGGTGG
CACCTTTT
Found at i:4565076 original size:111 final size:111
Alignment explanation
Indices: 4564876--4565082 Score: 342
Period size: 111 Copynumber: 1.9 Consensus size: 111
4564866 CGAAGTGCCG
* * * *
4564876 AAATGGTCATTCACTTTTTATTAATACCATGAGTGGCACCTTTTATGCTGAAAATGCACCGTTAT
1 AAATGGTAATTCACCTTTTATGAATACCATGAGTGGCACCTTTTATGCCGAAAATGCACCGTTAT
*
4564941 GCACTAAACAAAATCAATCGATAACTTTCATACACGAAGTATGTCA
66 GCACTAAACAAAATCAATCAATAACTTTCATACACGAAGTATGTCA
*
4564987 AAATGGTAATTCACCTTTTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACCGTTAT
1 AAATGGTAATTCACCTTTTATGAATACCATGAGTGGCACCTTTTATGCCGAAAATGCACCGTTAT
* *
4565052 GCATTAAACAAAATCGATCAATAACTTTCAT
66 GCACTAAACAAAATCAATCAATAACTTTCAT
4565083 TAGTGGCACC
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 88 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (111 bp):
AAATGGTAATTCACCTTTTATGAATACCATGAGTGGCACCTTTTATGCCGAAAATGCACCGTTAT
GCACTAAACAAAATCAATCAATAACTTTCATACACGAAGTATGTCA
Found at i:4568831 original size:15 final size:15
Alignment explanation
Indices: 4568764--4568841 Score: 53
Period size: 15 Copynumber: 5.4 Consensus size: 15
4568754 TATCACTATT
4568764 ATTATA-ATATTATAA
1 ATTATATATA-TATAA
4568779 TATT-TAT-TAT-TAA
1 -ATTATATATATATAA
* *
4568792 ACTATATAAAT-TAA
1 ATTATATATATATAA
4568806 A-TATATATATAATAA
1 ATTATATATAT-ATAA
4568821 ATTATAT-TATATATA
1 ATTATATATATATA-A
4568836 ATTATA
1 ATTATA
4568842 AAAATAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
12 2 0.04
13 14 0.27
14 10 0.19
15 18 0.35
16 8 0.15
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATATATATATAA
Found at i:4568831 original size:19 final size:20
Alignment explanation
Indices: 4568797--4568837 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
4568787 ATTAAACTAT
4568797 ATAAATTAAATATATATATA
1 ATAAATTAAATATATATATA
*
4568817 ATAAATTATAT-TATATATA
1 ATAAATTAAATATATATATA
4568836 AT
1 AT
4568838 TATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATTAAATATATATATA
Found at i:4568869 original size:31 final size:30
Alignment explanation
Indices: 4568789--4568870 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
4568779 TATTTATTAT
* * * *
4568789 TAAACTATA-TAAATTAAATATATATATAA
1 TAAATTATATTAAATTAATTATAAAAATAA
*
4568818 TAAATTATATTATATATAATTATAAAAATAA
1 TAAATTATATTAAAT-TAATTATAAAAATAA
4568849 T-AATTAATATTAAAATTAATTA
1 TAAATT-ATATT-AAATTAATTA
4568871 ACATAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 8 0.19
30 8 0.19
31 24 0.56
32 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAATTATATTAAATTAATTATAAAAATAA
Found at i:4581479 original size:8 final size:8
Alignment explanation
Indices: 4581466--4581545 Score: 55
Period size: 8 Copynumber: 10.1 Consensus size: 8
4581456 ATATCGCTAT
4581466 TATTATAA
1 TATTATAA
4581474 TATTATAA
1 TATTATAA
*
4581482 TATT-TAT
1 TATTATAA
4581489 TATTA-AA
1 TATTATAA
*
4581496 CTA-CATAA
1 -TATTATAA
4581504 -ATTA-AA
1 TATTATAA
4581510 TTATTATAA
1 -TATTATAA
4581519 TATATATAA
1 TAT-TATAA
4581528 T-TATACTAA
1 TAT-TA-TAA
4581537 TATTATAA
1 TATTATAA
4581545 T
1 T
4581546 TAGATTCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
6 3 0.05
7 9 0.16
8 31 0.53
9 14 0.24
10 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (8 bp):
TATTATAA
Found at i:4581531 original size:18 final size:17
Alignment explanation
Indices: 4581504--4581547 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
4581494 AACTACATAA
4581504 ATTA-AATTATTA-TAAT
1 ATTATAATTA-TACTAAT
4581520 ATATATAATTATACTAAT
1 AT-TATAATTATACTAAT
4581538 ATTATAATTA
1 ATTATAATTA
4581548 GATTCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 12 0.48
18 11 0.44
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTATAATTATACTAAT
Found at i:4582921 original size:18 final size:18
Alignment explanation
Indices: 4582876--4582931 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
4582866 AATAATAATA
*
4582876 ATAATAAT-ATTATATTT
1 ATAATAATAATTATATAT
* * *
4582893 ATTATATTAATTATGTAT
1 ATAATAATAATTATATAT
*
4582911 ATAATAATAATAATA-AT
1 ATAATAATAATTATATAT
4582928 ATAA
1 ATAA
4582932 ATACAATAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAATAATAATTATATAT
Found at i:4585407 original size:12 final size:12
Alignment explanation
Indices: 4585390--4585414 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4585380 ATGTGAATTG
4585390 CAACTTTTTCTT
1 CAACTTTTTCTT
4585402 CAACTTTTTCTT
1 CAACTTTTTCTT
4585414 C
1 C
4585415 GCTGGAACTT
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:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (12 bp):
CAACTTTTTCTT
Found at i:4585898 original size:12 final size:12
Alignment explanation
Indices: 4585872--4585905 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4585862 AGGATATTTC
4585872 AATGGTGAT-GA
1 AATGGTGATGGA
*
4585883 AATGGTAATGGA
1 AATGGTGATGGA
4585895 AATGGTGATGG
1 AATGGTGATGG
4585906 TGTAGGCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.26
Consensus pattern (12 bp):
AATGGTGATGGA
Found at i:4595777 original size:31 final size:31
Alignment explanation
Indices: 4595733--4595829 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
4595723 GATTAACCTG
* * *
4595733 TTATGAATCGATAATATTAGTGACCGATTTA
1 TTATAAATAGATAAAATTAGTGACCGATTTA
* * *
4595764 TTATAAATAGATAACGA-TAGTGATCAATTTA
1 TTATAAATAGATAA-AATTAGTGACCGATTTA
* * * *
4595795 TTATAAATTGATAAAATTAGCGACTGATTTG
1 TTATAAATAGATAAAATTAGTGACCGATTTA
4595826 TTAT
1 TTAT
4595830 TTTTTAAACT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
30 1 0.02
31 50 0.96
32 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (31 bp):
TTATAAATAGATAAAATTAGTGACCGATTTA
Found at i:4597577 original size:13 final size:13
Alignment explanation
Indices: 4597559--4597584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4597549 TAGTTAACCC
4597559 AAATATATTTATT
1 AAATATATTTATT
4597572 AAATATATTTATT
1 AAATATATTTATT
4597585 GTTAATGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATATATTTATT
Found at i:4602409 original size:21 final size:21
Alignment explanation
Indices: 4602385--4602440 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
4602375 ACGATGAATT
* *
4602385 TATCGATACTGATGCACTTAG
1 TATCGATACTGATGCAATAAG
4602406 TATCGATACTGATGCAATAAG
1 TATCGATACTGATGCAATAAG
4602427 TATCGATACTGATG
1 TATCGATACTGATG
4602441 TGGGTATCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (21 bp):
TATCGATACTGATGCAATAAG
Found at i:4603020 original size:44 final size:44
Alignment explanation
Indices: 4602971--4603323 Score: 438
Period size: 44 Copynumber: 8.0 Consensus size: 44
4602961 CTGCTCTAAA
*
4602971 ATAAATGAAAATGCATAAAGGTGCATTATTGACAGAAAGGTGCC
1 ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
* *
4603015 ATAAATGAAAATGCATAAAGGTGAATTATTGGCATAAAGGTGCC
1 ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
* * * * *
4603059 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGTACT
1 ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
* * * *
4603103 ATAAATGAAAATGCATAATGATGCATTATTGGAATAAAGGTGCC
1 ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
* * * *
4603147 ATAAATGAAAATGTATAACGGTGCATTATTGGTAGAAATGTGCC
1 ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
* * * * *
4603191 ATAAATGACAATGAATAACGGTCCATTATTGGAAGAAAGGTGCC
1 ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
* * * *
4603235 ACAAATGAAAATGCATAATGATGCATTATTGGTAGAAAGGTGCC
1 ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
* * *
4603279 ATAAATGAAAATGCATACCA-GTGCATTATTGGCAAAAATGTGCC
1 ATAAATGAAAATGCATA-AAGGTGCATTATTGGCAGAAAGGTGCC
4603323 A
1 A
4603324 CTAATGGTAT
Statistics
Matches: 267, Mismatches: 41, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 267 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAAAGGTGCATTATTGGCAGAAAGGTGCC
Found at i:4603209 original size:132 final size:132
Alignment explanation
Indices: 4602971--4603323 Score: 492
Period size: 132 Copynumber: 2.7 Consensus size: 132
4602961 CTGCTCTAAA
* * *
4602971 ATAAATGAAAATGCATAAAGGTGCATTATT-GACAGAAAGGTGCCATAAATGAAAATGCATAAAG
1 ATAAATGAAAATGCATAATGATGCATTATTGGA-AGAAAGGTGCCATAAATGAAAATGCATAACG
* * * * * * *
4603035 GTGAATTATTGGCATAAAGGTGCCATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGT
65 GTGCATTATTGGCAAAAATGTGCCATAAATGAAAATGAATAACGATCCATTATTGGAAGAAAGGT
*
4603100 ACT
130 ACC
* *
4603103 ATAAATGAAAATGCATAATGATGCATTATTGGAATAAAGGTGCCATAAATGAAAATGTATAACGG
1 ATAAATGAAAATGCATAATGATGCATTATTGGAAGAAAGGTGCCATAAATGAAAATGCATAACGG
* * * * *
4603168 TGCATTATTGGTAGAAATGTGCCATAAATGACAATGAATAACGGTCCATTATTGGAAGAAAGGTG
66 TGCATTATTGGCAAAAATGTGCCATAAATGAAAATGAATAACGATCCATTATTGGAAGAAAGGTA
4603233 CC
131 CC
* * * *
4603235 ACAAATGAAAATGCATAATGATGCATTATTGGTAGAAAGGTGCCATAAATGAAAATGCATACCAG
1 ATAAATGAAAATGCATAATGATGCATTATTGGAAGAAAGGTGCCATAAATGAAAATGCATAACGG
4603300 TGCATTATTGGCAAAAATGTGCCA
66 TGCATTATTGGCAAAAATGTGCCA
4603324 CTAATGGTAT
Statistics
Matches: 195, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
132 193 0.99
133 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.25
Consensus pattern (132 bp):
ATAAATGAAAATGCATAATGATGCATTATTGGAAGAAAGGTGCCATAAATGAAAATGCATAACGG
TGCATTATTGGCAAAAATGTGCCATAAATGAAAATGAATAACGATCCATTATTGGAAGAAAGGTA
CC
Found at i:4607953 original size:44 final size:44
Alignment explanation
Indices: 4607881--4608189 Score: 431
Period size: 44 Copynumber: 7.0 Consensus size: 44
4607871 ATTGCTCTAA
* *
4607881 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
** * * * *
4607925 ATTCATGAAAATGCATAACGACGTATTATTGGCATAAAGGTTCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* *
4607969 ATAAATGAAAATGCATAAC-AGTGCATTATTAGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGTGCC
* *
4608013 ATAAATGAAATTACATAACGATGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * *
4608057 ATAAATGAAAATGCATAACGGTGCATTATTGGCAAAAAGGTTCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* *
4608101 ATAAATGAAAATGCATAACGATACATTATTGGCAGAAAGGTTCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* *
4608145 ATAAATGAAAATGCATAACGATACATTATTGGCAAAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
4608189 A
1 A
4608190 CTCATGGTAT
Statistics
Matches: 233, Mismatches: 30, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
43 1 0.00
44 231 0.99
45 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
Found at i:4609932 original size:13 final size:13
Alignment explanation
Indices: 4609914--4609940 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4609904 AAGCAAGATG
4609914 GACTTTATTATAA
1 GACTTTATTATAA
4609927 GACTTTATTATAA
1 GACTTTATTATAA
4609940 G
1 G
4609941 TCTAGGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (13 bp):
GACTTTATTATAA
Found at i:4613508 original size:21 final size:21
Alignment explanation
Indices: 4613478--4613518 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4613468 GATAAATAAA
*
4613478 TTATCTAAAATATTATTATTT
1 TTATCAAAAATATTATTATTT
4613499 TTATCAAAAATATTATTATT
1 TTATCAAAAATATTATTATT
4613519 AGACGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATCAAAAATATTATTATTT
Found at i:4613638 original size:22 final size:23
Alignment explanation
Indices: 4613610--4613653 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4613600 TAAAACATCC
4613610 AATAATAATA-TTTTCGATAAAA
1 AATAATAATATTTTTCGATAAAA
4613632 AATAATAATATTTTTCGATAAA
1 AATAATAATATTTTTCGATAAA
4613654 TTTTTATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (23 bp):
AATAATAATATTTTTCGATAAAA
Found at i:4620888 original size:15 final size:15
Alignment explanation
Indices: 4620868--4620896 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4620858 AATTTAATTG
4620868 TGTAACTATATGTTT
1 TGTAACTATATGTTT
4620883 TGTAACTATATGTT
1 TGTAACTATATGTT
4620897 ATACTAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (15 bp):
TGTAACTATATGTTT
Found at i:4621034 original size:54 final size:53
Alignment explanation
Indices: 4620975--4621684 Score: 785
Period size: 54 Copynumber: 12.9 Consensus size: 53
4620965 CAATTCACGG
* * * * *
4620975 AATTCATCACATGTTGATGAATAATCGTTTTGACACTAAGTGTGTAAAGTACGA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
*
4621029 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAACGTACA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACA
*
4621082 TAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGGAAAGTACAA
1 -AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
* * *
4621137 AATTCATCATATGTTGATGAATAACCATGTT-GATG-AATAACCGTTTCGACACTAAGTGTGCAA
1 AATTCATCATATGTTGATGAATAACCGT-TTCG--GCACTAA--GTGT-G-CA--AA--GT---A
*
4621200 AGTACAA
52 C-----A
*
4621207 AATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGTACA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACA
* * * **
4621260 GATTCATCATATGCTGATGAATAACCGTTTCGGTACTAAGTGTGCAAAGTATGG
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTA-CA
* * * * *
4621314 AACTCATCATAGGCTGATGAATAACCGTTTCGGTACTAAGTGTGCAAAGTACGG
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
** * * *
4621368 AATTCATCATACATTGATGAATAACCATTTCGGTACTAAGTGTGCAAAGTACGG
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
*
4621422 AATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGTACGA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
*
4621476 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACGG
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
* *
4621530 AATTCATCATATGTAGATGAATAATCGTTTCGGCACTAAGTGTGCAAAGTACGA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
* * *
4621584 AATTCATCATATGTTGATGAATAAACGTTTCGACACTAATTGTGCAAAGTACAA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTAC-A
* * * * * *
4621638 AATTCATTATACGTTGATGAATAACCCTTTTGGCACTACGAGTGCAA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAA
4621685 CCCACGAAAT
Statistics
Matches: 574, Mismatches: 58, Indels: 48
0.84 0.09 0.07
Matches are distributed among these distances:
53 49 0.09
54 460 0.80
55 7 0.01
56 1 0.00
57 3 0.01
58 2 0.00
59 1 0.00
61 4 0.01
63 4 0.01
65 2 0.00
66 2 0.00
67 3 0.01
69 6 0.01
70 30 0.05
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (53 bp):
AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACA
Found at i:4621168 original size:16 final size:16
Alignment explanation
Indices: 4621147--4621178 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4621137 AATTCATCAT
4621147 ATGTTGATGAATAACC
1 ATGTTGATGAATAACC
4621163 ATGTTGATGAATAACC
1 ATGTTGATGAATAACC
4621179 GTTTCGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTGATGAATAACC
Found at i:4621206 original size:70 final size:70
Alignment explanation
Indices: 4621093--4621232 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
4621083 AATTCATCAT
* *
4621093 ATGTTGATGAATAACCGTTTCGGCACTAAGTGTGGAAAGTACAAAATTCATCATATGTTGATGAA
1 ATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGTACAAAATTCATCATATGTTGATGAA
4621158 TAACC
66 TAACC
4621163 ATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGTACAAAATTCATCATATGTTGATGAA
1 ATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGTACAAAATTCATCATATGTTGATGAA
4621228 TAACC
66 TAACC
4621233 GTTTCGACAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (70 bp):
ATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGTACAAAATTCATCATATGTTGATGAA
TAACC
Found at i:4627500 original size:111 final size:111
Alignment explanation
Indices: 4627171--4627500 Score: 489
Period size: 111 Copynumber: 3.0 Consensus size: 111
4627161 ACTATAAAAC
* * *
4627171 AACATGCTATAACCGGATATAAAGTTTCTTACCAATATACTTACCATTTATCCCATAAGCTCGTA
1 AACATGATATAACCGAATACAAAGTTTCTTACCAATATACTTACCATTTATCCCATAAGCTCGTA
* * * *
4627236 AGCTTATTTGCATGCTTACCATTTATTAACCAATAAACCATAAATT
66 AGCTTATTTGCATGTTTATCATTCATTAACCAATAAACCATAGATT
** * * *
4627282 AACATGATATAATAGAATACAAAGTTTCTTACCAATATACTTTCCATTTATCCCATAATCTCATA
1 AACATGATATAACCGAATACAAAGTTTCTTACCAATATACTTACCATTTATCCCATAAGCTCGTA
* * *
4627347 AGTTTATTTTCATGTTTATCATTCATTATCCAATAAACCATAGATT
66 AGCTTATTTGCATGTTTATCATTCATTAACCAATAAACCATAGATT
* *
4627393 AACATGATATAACCGAATGCAAAGTTTCTTACCAATATACTTGCCATTTATCCCATAAGCTCGTA
1 AACATGATATAACCGAATACAAAGTTTCTTACCAATATACTTACCATTTATCCCATAAGCTCGTA
* *
4627458 TGCTTATTTGCATGTTTGTCATTCATTAACCAATAAACCATAG
66 AGCTTATTTGCATGTTTATCATTCATTAACCAATAAACCATAG
4627501 CCCAAAGTAT
Statistics
Matches: 193, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
111 193 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.36
Consensus pattern (111 bp):
AACATGATATAACCGAATACAAAGTTTCTTACCAATATACTTACCATTTATCCCATAAGCTCGTA
AGCTTATTTGCATGTTTATCATTCATTAACCAATAAACCATAGATT
Found at i:4628054 original size:24 final size:24
Alignment explanation
Indices: 4628022--4628070 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
4628012 AGTCTTCTTG
*
4628022 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATATATGTAC
4628046 ATGATGTATAAAACATATATGTAC
1 ATGATGTATAAAACATATATGTAC
4628070 A
1 A
4628071 ATTTCATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATATATGTAC
Found at i:4639720 original size:10 final size:10
Alignment explanation
Indices: 4639705--4639779 Score: 60
Period size: 10 Copynumber: 6.9 Consensus size: 10
4639695 TGAATGGATG
4639705 TAAACGAACA
1 TAAACGAACA
4639715 TAAACGAACACA
1 TAAACG-A-ACA
*
4639727 TTAAACGAACG
1 -TAAACGAACA
*
4639738 TAAACAAACA
1 TAAACGAACA
*
4639748 TAAATGAACACAA
1 TAAACG-A-AC-A
4639761 TAAACGAACA
1 TAAACGAACA
*
4639771 TAAATGAAC
1 TAAACGAAC
4639780 CTGCACAAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
10 27 0.52
11 6 0.12
12 7 0.13
13 12 0.23
ACGTcount: A:0.59, C:0.19, G:0.09, T:0.13
Consensus pattern (10 bp):
TAAACGAACA
Found at i:4639748 original size:33 final size:33
Alignment explanation
Indices: 4639704--4639774 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
4639694 ATGAATGGAT
* *
4639704 GTAAACGAACATAAACGAACACATTAAACGAAC
1 GTAAACAAACATAAACGAACACAATAAACGAAC
*
4639737 GTAAACAAACATAAATGAACACAATAAACGAAC
1 GTAAACAAACATAAACGAACACAATAAACGAAC
*
4639770 ATAAA
1 GTAAA
4639775 TGAACCTGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.13
Consensus pattern (33 bp):
GTAAACAAACATAAACGAACACAATAAACGAAC
Found at i:4639769 original size:13 final size:12
Alignment explanation
Indices: 4639712--4639770 Score: 54
Period size: 13 Copynumber: 5.1 Consensus size: 12
4639702 ATGTAAACGA
4639712 ACATAAACGAAC
1 ACATAAACGAAC
4639724 ACATTAAACG-A-
1 ACA-TAAACGAAC
*
4639735 ACGTAAAC-AA-
1 ACATAAACGAAC
*
4639745 ACATAAATGAAC
1 ACATAAACGAAC
4639757 ACAATAAACGAAC
1 AC-ATAAACGAAC
4639770 A
1 A
4639771 TAAATGAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 12 0.32
11 4 0.11
12 6 0.16
13 16 0.42
ACGTcount: A:0.59, C:0.20, G:0.08, T:0.12
Consensus pattern (12 bp):
ACATAAACGAAC
Found at i:4639811 original size:23 final size:23
Alignment explanation
Indices: 4639784--4639840 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
4639774 ATGAACCTGC
4639784 ACAAACATAAAAAATGAACATAA
1 ACAAACATAAAAAATGAACATAA
* * * *
4639807 TCAAACACAATAAATGAACGTAA
1 ACAAACATAAAAAATGAACATAA
*
4639830 ACGAACATAAA
1 ACAAACATAAA
4639841 CAACAACAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.63, C:0.16, G:0.07, T:0.14
Consensus pattern (23 bp):
ACAAACATAAAAAATGAACATAA
Found at i:4647058 original size:42 final size:42
Alignment explanation
Indices: 4647012--4647091 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
4647002 TATTTTTCAA
* *
4647012 AAAATATTTTCTAGTGTTTGATAGTTGTAATTGGTTTTATGG
1 AAAATATTTTCTAGCGTTTGATAGTTGTAATTGATTTTATGG
* *
4647054 AAAATGTTTTTTAGCGTTTGATAGTTGTAATTGATTTT
1 AAAATATTTTCTAGCGTTTGATAGTTGTAATTGATTTT
4647092 CCCAATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.51
Consensus pattern (42 bp):
AAAATATTTTCTAGCGTTTGATAGTTGTAATTGATTTTATGG
Found at i:4648079 original size:3 final size:3
Alignment explanation
Indices: 4648073--4648098 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4648063 GAAGAAGAAA
4648073 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
4648099 TGAGAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:4648239 original size:28 final size:28
Alignment explanation
Indices: 4648208--4648274 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
4648198 AAAAAATGTT
*
4648208 TTAAATATATGTATGAATTTGAGTTTAG
1 TTAAATATATGTATGAATTCGAGTTTAG
4648236 TTAAATATATGTATGAATTCGAGTTTAG
1 TTAAATATATGTATGAATTCGAGTTTAG
4648264 TTAAATATATG
1 TTAAATATATG
4648275 GTTATTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.45
Consensus pattern (28 bp):
TTAAATATATGTATGAATTCGAGTTTAG
Found at i:4651918 original size:148 final size:147
Alignment explanation
Indices: 4651574--4651994 Score: 488
Period size: 148 Copynumber: 2.9 Consensus size: 147
4651564 GTTTTAGCTA
** * *
4651574 AAAAATGTCAAAACATGTAACTAATAATCTTCAGAACGAGCCATTAATAATGCAAGATGCTAGAA
1 AAAAATGTCAAAACATGCCATTAATAATCTTCAGAACGA-CCATTAATAATGCAAGATGCCAGAA
* * * *
4651639 AATGCCAGCAACGTTTT-AGTG-TCCCATCAATCATCTTCAGCAACTTTTCAGTGAAA-GTCATC
65 AATGCCAACAA-ATTTTCAGTGCT-CCATCAATCATCTTCAGCAACTTTTCAGTAAAATGTCATA
* * *
4651701 TCTAATAATGTATCACACCT
128 TCTAATAATGCACCACACCC
* * *** * * * *
4651721 GAAAATGTTAAAATGGGCCATTAATAATCTTCAGAACGGGCAATTAATAATACAAGATGCCAGAG
1 AAAAATGTCAAAACATGCCATTAATAATCTTCAGAAC-GACCATTAATAATGCAAGATGCCAGAA
* * * *
4651786 AATGCCAACAAATTTTCAGTGCTCGATCAATCATCTTCAGCAACTTTTCAATTAAATGTTATATC
65 AATGCCAACAAATTTTCAGTGCTCCATCAATCATCTTCAGCAACTTTTCAGTAAAATGTCATATC
**
4651851 TAATAATGCACCATGCCC
130 TAATAATGCACCACACCC
* * *
4651869 AAAAATGTCAAAACATGCCATTAATACTCTTCAGAACAGACCATTAATAATGTAGGATGCCAGAA
1 AAAAATGTCAAAACATGCCATTAATAATCTTCAGAAC-GACCATTAATAATGCAAGATGCCAGAA
* * *
4651934 AATGCCAACAACTTTTCAGTACCCCATCAATCATCTTCAGCAACTTTTCAGTAAAATGTCA
65 AATGCCAACAAATTTTCAGTGCTCCATCAATCATCTTCAGCAACTTTTCAGTAAAATGTCA
4651995 ACTCATTTCT
Statistics
Matches: 225, Mismatches: 45, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
146 4 0.02
147 94 0.42
148 127 0.56
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (147 bp):
AAAAATGTCAAAACATGCCATTAATAATCTTCAGAACGACCATTAATAATGCAAGATGCCAGAAA
ATGCCAACAAATTTTCAGTGCTCCATCAATCATCTTCAGCAACTTTTCAGTAAAATGTCATATCT
AATAATGCACCACACCC
Found at i:4652933 original size:2 final size:2
Alignment explanation
Indices: 4652926--4652965 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4652916 TTAATTAATA
4652926 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
4652966 TAATGAATAA
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:4653426 original size:17 final size:17
Alignment explanation
Indices: 4653404--4653439 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4653394 AAGACTGAGG
*
4653404 ACCAAAATACAACATGC
1 ACCAAAAAACAACATGC
4653421 ACCAAAAAACAACATGC
1 ACCAAAAAACAACATGC
4653438 AC
1 AC
4653440 AACTTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.31, G:0.06, T:0.08
Consensus pattern (17 bp):
ACCAAAAAACAACATGC
Found at i:4654088 original size:23 final size:23
Alignment explanation
Indices: 4654034--4654091 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
4654024 CCTCTATTTC
* *
4654034 TCAAATGGACACCACAACTTCTT
1 TCAAATGGCCACCACAACTTCAT
4654057 TCAAATGGCCACCACAACTTCAT
1 TCAAATGGCCACCACAACTTCAT
4654080 TCAAATGGCCAC
1 TCAAATGGCCAC
4654092 ACACTATCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.22
Consensus pattern (23 bp):
TCAAATGGCCACCACAACTTCAT
Found at i:4655426 original size:3 final size:3
Alignment explanation
Indices: 4655418--4655466 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
4655408 TAACAAAAAT
* *
4655418 ATA ATA ATA ATA TTA ATG AT- ATA ATA ATA ATA ATA ATA TATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA
4655464 ATA
1 ATA
4655467 TTTATAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:4655441 original size:20 final size:19
Alignment explanation
Indices: 4655416--4655476 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
4655406 TGTAACAAAA
*
4655416 ATATAATAATAATATTAAT
1 ATATAATAATAATAATAAT
4655435 GATATAATAATAATAATAAT
1 -ATATAATAATAATAATAAT
* *
4655455 ATATAATTAATATTTATAAT
1 ATATAA-TAATAATAATAAT
4655475 AT
1 AT
4655477 TTTTTAATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 6 0.16
20 31 0.84
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATATAATAATAATAATAAT
Found at i:4655443 original size:17 final size:17
Alignment explanation
Indices: 4655421--4655466 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
4655411 CAAAAATATA
* *
4655421 ATAATAATATTAATGAT
1 ATAATAATAATAATAAT
4655438 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
4655455 AT-ATAATTAATA
1 ATAATAA-TAATA
4655467 TTTATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:4655465 original size:23 final size:23
Alignment explanation
Indices: 4655418--4655475 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
4655408 TAACAAAAAT
* *
4655418 ATAATAATAATATTAATGATATA
1 ATAATAATAATAATAATAATATA
4655441 ATAATAATAATAATATATAAT-TA
1 ATAATAATAATAATA-ATAATATA
* *
4655464 ATATTTATAATA
1 ATAATAATAATA
4655476 TTTTTTAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAATAATAATAATAATAATATA
Found at i:4657504 original size:21 final size:21
Alignment explanation
Indices: 4657475--4657516 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4657465 GGCTACCCGG
*
4657475 TTGGGCTCTGTTTTTGGACCT
1 TTGGACTCTGTTTTTGGACCT
*
4657496 TTGGACTCTTTTTTTGGACCT
1 TTGGACTCTGTTTTTGGACCT
4657517 GCAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.19, G:0.24, T:0.50
Consensus pattern (21 bp):
TTGGACTCTGTTTTTGGACCT
Found at i:4657534 original size:3 final size:3
Alignment explanation
Indices: 4657521--4657607 Score: 79
Period size: 3 Copynumber: 26.7 Consensus size: 3
4657511 GGACCTGCAA
4657521 AAT ATAT AAT AAT AAT AAT AAT AAAT AAT AAAT AA- ATAT AAT ATAT
1 AAT A-AT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT A-AT AAT A-AT
4657567 AAT GAAT AAT AAT AAT ATAT AAT AAAT AA- ATAT AAT AAT AA
1 AAT -AAT AAT AAT AAT A-AT AAT -AAT AAT A-AT AAT AAT AA
4657608 AAACTATATA
Statistics
Matches: 73, Mismatches: 0, Indels: 22
0.77 0.00 0.23
Matches are distributed among these distances:
2 2 0.03
3 48 0.66
4 23 0.32
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4657561 original size:20 final size:20
Alignment explanation
Indices: 4657521--4657626 Score: 114
Period size: 20 Copynumber: 5.3 Consensus size: 20
4657511 GGACCTGCAA
4657521 AATATATAAT-AATAATAAT
1 AATATATAATAAATAATAAT
*
4657540 AATAAATAATAAATAA-ATAT
1 AATATATAATAAATAATA-AT
*
4657560 AATATATAATGAATAATAAT
1 AATATATAATAAATAATAAT
4657580 AATATATAATAAATAA-ATAT
1 AATATATAATAAATAATA-AT
4657600 AATA-ATAA-AAACTATATAAT
1 AATATATAATAAA-TA-ATAAT
*
4657620 ACTATAT
1 AATATAT
4657627 TTTCAAAAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.04
19 17 0.23
20 50 0.68
21 4 0.05
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (20 bp):
AATATATAATAAATAATAAT
Found at i:4657589 original size:40 final size:39
Alignment explanation
Indices: 4657521--4657607 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 39
4657511 GGACCTGCAA
4657521 AATATATAATAATAATAATAATAAATAATAAATAAATAT
1 AATATATAATAATAATAATAATAAATAATAAATAAATAT
*
4657560 AATATATAATGAATAATAATAATATATAATAAATAAATAT
1 AATATATAAT-AATAATAATAATAAATAATAAATAAATAT
4657600 AATA-ATAA
1 AATATATAA
4657608 AAACTATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 14 0.30
40 32 0.70
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (39 bp):
AATATATAATAATAATAATAATAAATAATAAATAAATAT
Found at i:4657619 original size:40 final size:40
Alignment explanation
Indices: 4657521--4657626 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
4657511 GGACCTGCAA
*
4657521 AATATATAAT-AATAATAATAATAAATAATAAATAAATAT
1 AATATATAATAAATAATAATAATATATAATAAATAAATAT
*
4657560 AATATATAATGAATAATAATAATATATAATAAATAAATAT
1 AATATATAATAAATAATAATAATATATAATAAATAAATAT
*
4657600 AATA-ATAA-AAACTATATAATACTATAT
1 AATATATAATAAA-TA-ATAATAATATAT
4657627 TTTCAAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
38 2 0.03
39 16 0.26
40 43 0.70
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (40 bp):
AATATATAATAAATAATAATAATATATAATAAATAAATAT
Found at i:4657697 original size:33 final size:35
Alignment explanation
Indices: 4657646--4657735 Score: 87
Period size: 34 Copynumber: 2.6 Consensus size: 35
4657636 TATGTTTTCT
*
4657646 AAAATCGTTTTTCAAAACTACATAATATA-TTTTA
1 AAAATCGTTTTTCAAAACTACATAATATACGTTTA
* * * *
4657680 AAAATTGTTTTT-GAAACTATATATTATACGTTTAAA
1 AAAATCGTTTTTCAAAACTACATAATATACGTTT--A
4657716 AAAAT-GTGTTTTCAAAACTA
1 AAAATCGT-TTTTCAAAACTA
4657736 TATCATGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
33 13 0.29
34 14 0.31
35 2 0.04
36 10 0.22
37 6 0.13
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (35 bp):
AAAATCGTTTTTCAAAACTACATAATATACGTTTA
Found at i:4657810 original size:39 final size:37
Alignment explanation
Indices: 4657763--4657868 Score: 113
Period size: 39 Copynumber: 2.7 Consensus size: 37
4657753 AAAAAAATTC
*
4657763 AAAACTATATAATATATTTTTTCAAAATTTTGTTTTTA
1 AAAACTATATAATATATTTTTTCAAAATTGT-TTTTTA
* ** *
4657801 AAAATCTATATATTATACATTTTCGAAATTGTTTTTTAA
1 AAAA-CTATATAATATATTTTTTCAAAATTGTTTTTT-A
*
4657840 AAAACTATATATTATATATTTTTTTAAAA
1 AAAACTATATA--ATATATTTTTTCAAAA
4657869 ATTATATTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
38 16 0.30
39 27 0.50
40 11 0.20
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (37 bp):
AAAACTATATAATATATTTTTTCAAAATTGTTTTTTA
Found at i:4657848 original size:38 final size:39
Alignment explanation
Indices: 4657763--4657861 Score: 137
Period size: 38 Copynumber: 2.6 Consensus size: 39
4657753 AAAAAAATTC
* * *
4657763 AAAACTATATAATATATTTTTTCAAAATTTTGTTTTTAA
1 AAAACTATATATTATATATTTTCAAAATTGTGTTTTTAA
* * *
4657802 AAATCTATATATTATACATTTTCGAAATTGT-TTTTTAA
1 AAAACTATATATTATATATTTTCAAAATTGTGTTTTTAA
4657840 AAAACTATATATTATATATTTT
1 AAAACTATATATTATATATTTT
4657862 TTTAAAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 27 0.52
39 25 0.48
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (39 bp):
AAAACTATATATTATATATTTTCAAAATTGTGTTTTTAA
Found at i:4679667 original size:13 final size:13
Alignment explanation
Indices: 4679650--4679713 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
4679640 ATAATAATAA
4679650 ATAATAAATAAAT
1 ATAATAAATAAAT
* **
4679663 CTAATATTTAAAT
1 ATAATAAATAAAT
*
4679676 AATAAT-ACTAATAT
1 -ATAATAAATAA-AT
4679690 ATAATAAATAAAT
1 ATAATAAATAAAT
4679703 ATAAT-AATAAA
1 ATAATAAATAAA
4679714 AACTATATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
12 6 0.15
13 25 0.61
14 10 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATAAATAAAT
Found at i:4679679 original size:20 final size:20
Alignment explanation
Indices: 4679644--4679712 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
4679634 AAAGAAATAA
*
4679644 TAATAAATAATAAATAAATC
1 TAATATATAATAAATAAATC
*
4679664 TAATATTTAA-ATAAT-AATAC
1 TAATATATAATA-AATAAAT-C
*
4679684 TAATATATAATAAATAAATA
1 TAATATATAATAAATAAATC
4679704 TAATA-ATAA
1 TAATATATAA
4679713 AAACTATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
19 8 0.20
20 29 0.71
21 4 0.10
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATATATAATAAATAAATC
Found at i:4679731 original size:40 final size:40
Alignment explanation
Indices: 4679639--4679731 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
4679629 CCTGAAAAGA
* * *
4679639 AATAATAATAAATAATAAATAAATCTAATATTTAAATAAT
1 AATAATAATATATAATAAATAAATATAATATATAAATAAT
*
4679679 AATACTAATATATAATAAATAAATATAATA-ATAAA-AACT
1 AATAATAATATATAATAAATAAATATAATATATAAATAA-T
*
4679718 ATATAATACTATAT
1 A-ATAATAATATAT
4679732 TTTCAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.04
39 6 0.13
40 37 0.82
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (40 bp):
AATAATAATATATAATAAATAAATATAATATATAAATAAT
Found at i:4679789 original size:34 final size:33
Alignment explanation
Indices: 4679746--4679851 Score: 97
Period size: 34 Copynumber: 3.0 Consensus size: 33
4679736 AAAAATATGT
*
4679746 TTTCTAAAATCGTTTTTCAAAACTATATAATATA
1 TTTCAAAAAT-GTTTTTCAAAACTATATAATATA
* * *
4679780 TTTCAAAAATTGTTTATT-GAAACTATATATTATGCG
1 TTTCAAAAA-TGTTT-TTCAAAACTATATAATAT--A
*
4679816 TTTAAAAAAATGTGTTTTCAAAACTATATAATATA
1 TTT-CAAAAATGT-TTTTCAAAACTATATAATATA
4679851 T
1 T
4679852 ATGTTTTCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
34 25 0.44
35 4 0.07
36 8 0.14
37 20 0.35
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (33 bp):
TTTCAAAAATGTTTTTCAAAACTATATAATATA
Found at i:4679864 original size:38 final size:36
Alignment explanation
Indices: 4679740--4679979 Score: 163
Period size: 38 Copynumber: 6.4 Consensus size: 36
4679730 ATTTTCAAAA
4679740 ATATGTTTTCTAAAATCGTTTTTCAAAACTATATA-AT
1 ATATGTTTTC-AAAAT-GTTTTTCAAAACTATATATAT
*
4679777 ATA---TTTCAAAAATTGTTTATT-GAAACTATATAT-T
1 ATATGTTTTC-AAAA-TGTTT-TTCAAAACTATATATAT
** **
4679811 ATGCGTTTAAAAAAATGTGTTTTCAAAACTATATAATAT
1 ATATGTTT-TCAAAATGT-TTTTCAAAACTATAT-ATAT
* *
4679850 ATATGTTTTCAAAATTTCTTTTCAAAACTATCTA-AT
1 ATATGTTTTCAAAATGT-TTTTCAAAACTATATATAT
*
4679886 ATATGTTTTCAAAATTTGTTTTTTTTTAAAACTATATAT-T
1 ATATGTTTTCAAAA--TG---TTTTTCAAAACTATATATAT
*
4679926 ATATGTTTTCGAAACTGATTTTTCAAAAACTATATATTAT
1 ATATGTTTTC-AAAATG-TTTTTC-AAAACTATATA-TAT
* *
4679966 ATATTTTTTTAAAA
1 ATATGTTTTCAAAA
4679980 ATTAAATTAT
Statistics
Matches: 160, Mismatches: 22, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
34 25 0.16
35 3 0.02
36 21 0.13
37 26 0.16
38 34 0.21
39 13 0.08
40 34 0.21
41 4 0.03
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.47
Consensus pattern (36 bp):
ATATGTTTTCAAAATGTTTTTCAAAACTATATATAT
Found at i:4679895 original size:36 final size:38
Alignment explanation
Indices: 4679830--4679979 Score: 130
Period size: 40 Copynumber: 3.9 Consensus size: 38
4679820 AAAAAATGTG
4679830 TTTTCAAAACTATATAATATATATGTTTTCAAAATTTC
1 TTTTCAAAACTATATAATATATATGTTTTCAAAATTTC
* *
4679868 TTTTCAAAACTATCT-A-ATATATGTTTTCAAAATTTGTTTT
1 TTTTCAAAACTATATAATATATATGTTTTCAAAA----TTTC
* * *
4679908 TTTTTAAAACTATAT-AT-TATATGTTTTCGAAACTGAT-
1 TTTTCAAAACTATATAATATATATGTTTTC-AAAAT-TTC
* * *
4679945 TTTTCAAAAACTATATATTATATATTTTTTTAAAA
1 TTTTC-AAAACTATATAATATATATGTTTTCAAAA
4679980 ATTAAATTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
36 16 0.18
37 6 0.07
38 25 0.27
39 4 0.04
40 37 0.41
41 3 0.03
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (38 bp):
TTTTCAAAACTATATAATATATATGTTTTCAAAATTTC
Found at i:4681428 original size:14 final size:14
Alignment explanation
Indices: 4681409--4681496 Score: 70
Period size: 14 Copynumber: 5.9 Consensus size: 14
4681399 AATAGTAAGT
*
4681409 AAAATAAATATAAA
1 AAAATAAAAATAAA
4681423 AAAATAAAGAA-AAA
1 AAAATAAA-AATAAA
* **
4681437 GAAGGAAAACATAAA
1 AAAATAAAA-ATAAA
4681452 AAAATAAAACAAGTAAA
1 AAAAT-AAA-AA-TAAA
4681469 TAAAATAAAAATAAA
1 -AAAATAAAAATAAA
*
4681484 AAAGTAAAAATAA
1 AAAATAAAAATAA
4681497 TATATATATA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
13 1 0.02
14 29 0.49
15 10 0.17
16 6 0.10
17 8 0.14
18 5 0.08
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:4681501 original size:2 final size:2
Alignment explanation
Indices: 4681496--4681551 Score: 71
Period size: 2 Copynumber: 28.5 Consensus size: 2
4681486 AGTAAAAATA
* *
4681496 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT A- AT AGT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
4681537 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
4681552 AATTAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 2 0.04
2 43 0.91
3 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4681570 original size:41 final size:38
Alignment explanation
Indices: 4681495--4681593 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 38
4681485 AAGTAAAAAT
* *
4681495 AATATATATATATATATATATATATAATAAATAATAGTA
1 AATATATATATATATATAAATATATAATAAATAATA-AA
4681534 AATATATATATATATATAAAT-TAATAA-AACTGATAATAAA
1 AATATATATATATATATAAATAT-ATAATAA---ATAATAAA
*
4681574 AATAATATATATATCTATAA
1 AAT-ATATATATATATATAA
4681594 TCTAAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
38 3 0.06
39 24 0.46
40 4 0.08
41 21 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (38 bp):
AATATATATATATATATAAATATATAATAAATAATAAA
Found at i:4682995 original size:106 final size:106
Alignment explanation
Indices: 4682687--4684152 Score: 2243
Period size: 106 Copynumber: 13.9 Consensus size: 106
4682677 GCATTGTTCC
* * * ** * *
4682687 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGACTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * *
4682751 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
4682793 GAGTACAATATCCTTTGTTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * *
4682852 TCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* *
4682894 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
4682958 CCAGCGGTCCCTTCGACGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
4682999 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
4683064 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4683105 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
4683170 CTAGTGGTCCCTTCGTCGTGAAGTTGAAGTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
4683211 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
4683276 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTGGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
4683317 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
4683382 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4683423 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
4683488 CCAACGGTCCCTTCGTCGTGAATTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
4683529 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
4683594 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
4683635 GAGTCCAATATCTTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
4683700 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4683741 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
4683806 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
4683847 TAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
4683912 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
4683953 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
4684018 CCA-CTGGTCCCTTCGTTGTGAAGTTGAACTTGC-TTGTCTG
66 CCAGC-GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4684058 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
4684123 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
4684153 CTACTCTCGA
Statistics
Matches: 1242, Mismatches: 106, Indels: 25
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.00
100 75 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 101 0.08
106 1052 0.85
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:4684475 original size:18 final size:19
Alignment explanation
Indices: 4684446--4684482 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4684436 TGTTAAATCC
4684446 CCAAATAATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
*
4684465 CCAAA-AATGCCCTAATAT
1 CCAAATAATGCCCCAATAT
4684483 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:4684921 original size:22 final size:22
Alignment explanation
Indices: 4684895--4684971 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
4684885 TTATGTTTGG
4684895 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
4684917 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
4684939 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
4684961 TCAACGGTTTG
1 TCAAAGGTTTG
4684972 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:4685593 original size:21 final size:21
Alignment explanation
Indices: 4685569--4685609 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4685559 TGCATGTGCT
4685569 TTTTGTCCTT-TTTTCTTTTGA
1 TTTT-TCCTTCTTTTCTTTTGA
*
4685590 TTTTTGCTTCTTTTCTTTTG
1 TTTTTCCTTCTTTTCTTTTG
4685610 TTCTTGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.02, C:0.15, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTTCCTTCTTTTCTTTTGA
Found at i:4685626 original size:44 final size:45
Alignment explanation
Indices: 4685576--4685664 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 45
4685566 GCTTTTTGTC
* *
4685576 CTTTTTTCTTTTGATTTTTGCTTCTTT-TCTTTTGTTCTTGATTCT
1 CTTTTTT-ATTTGACTTTTGCTTCTTTCTCTTTTGTTCTTGATTCT
* *
4685621 CTTTTTTATTTGCCTTTTGCTTCTTTGCTTTTTTGTTCTTGATT
1 CTTTTTTATTTGACTTTTGCTTCTTT-CTCTTTTGTTCTTGATT
4685665 GGATCTTCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 16 0.42
45 7 0.18
46 15 0.39
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (45 bp):
CTTTTTTATTTGACTTTTGCTTCTTTCTCTTTTGTTCTTGATTCT
Found at i:4688715 original size:2 final size:2
Alignment explanation
Indices: 4688710--4688765 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
4688700 AGTAAAAATA
* * *
4688710 AT AT AT AT AT AT AT A- AT AA AT AA AT A- AT AGT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
4688751 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
4688766 AATTAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:4688729 original size:43 final size:42
Alignment explanation
Indices: 4688681--4688819 Score: 114
Period size: 38 Copynumber: 3.3 Consensus size: 42
4688671 AAAACAAGTA
4688681 AATAAAATAATAATAAAAAAGTAAAAATAATATATATATATAT
1 AATAAAATAA-AATAAAAAAGTAAAAATAATATATATATATAT
* *
4688724 AAT-AAAT-AAAT--AATAGTAAATAT-ATATATATATATAT
1 AATAAAATAAAATAAAAAAGTAAAAATAATATATATATATAT
* * *
4688761 -ATATAAAT-TAATAAAACTGATAATAAAAATAATATATATATAATCT
1 AATA-AAATAAAATAAAA---A-AGTAAAAATAATATATATAT-ATAT
4688807 AA-AAAATAAAATA
1 AATAAAATAAAATA
4688820 TATACTAAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
36 2 0.03
37 14 0.18
38 17 0.22
40 5 0.07
41 1 0.01
42 4 0.05
43 3 0.04
44 7 0.09
45 14 0.18
46 8 0.11
47 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (42 bp):
AATAAAATAAAATAAAAAAGTAAAAATAATATATATATATAT
Found at i:4688738 original size:29 final size:29
Alignment explanation
Indices: 4688685--4688753 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
4688675 CAAGTAAATA
4688685 AAATA-ATA-ATAAAAAAGTAAAAATAAT
1 AAATATATATATAAAAAAGTAAAAATAAT
* * *
4688712 ATATATATATATAATAAA-TAAATAATAGT
1 AAATATATATATAAAAAAGTAAA-AATAAT
4688741 AAATATATATATA
1 AAATATATATATA
4688754 TATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.11
28 7 0.20
29 24 0.69
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (29 bp):
AAATATATATATAAAAAAGTAAAAATAAT
Found at i:4688749 original size:35 final size:36
Alignment explanation
Indices: 4688705--4688773 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
4688695 AAAAAAGTAA
4688705 AAATAATATATATATATATAATAAATAAA-TAATAGT
1 AAATAATATATATATATAT-ATAAATAAATTAATAGT
*
4688741 AAAT-ATATATATATATATATATATAAATTAATA
1 AAATAATATATATATATATATAAATAAATTAATA
4688774 AAACTGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 8 0.26
35 19 0.61
36 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (36 bp):
AAATAATATATATATATATATAAATAAATTAATAGT
Found at i:4688815 original size:41 final size:40
Alignment explanation
Indices: 4688684--4688828 Score: 132
Period size: 41 Copynumber: 3.5 Consensus size: 40
4688674 ACAAGTAAAT
*
4688684 AAAATAATAATAAAAAAGTAAAAATAATATATATAT-ATATAA
1 AAAATAA-AAT-AATAA-TAAAAATAATATATATATAATATAA
* * *
4688726 TAAAT-AAATAATAGTAAATATATATATATATATATATATAA
1 AAAATAAAATAATAATAAAAATA-ATATATATATA-ATATAA
* * *
4688767 ATTAATAAAACTGATAATAAAAATAATATATATATAATCTAA
1 A-AAATAAAA-TAATAATAAAAATAATATATATATAATATAA
*
4688809 AAAATAAAATATATACTAAA
1 AAAATAAAATA-ATAATAAA
4688829 GTAAAAAGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
38 7 0.08
39 13 0.16
40 4 0.05
41 21 0.25
42 13 0.16
43 14 0.17
44 11 0.13
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (40 bp):
AAAATAAAATAATAATAAAAATAATATATATATAATATAA
Found at i:4688834 original size:23 final size:22
Alignment explanation
Indices: 4688784--4688841 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
4688774 AAACTGATAA
* *
4688784 TAAAAATAATATATATATAATC
1 TAAAAATAAAATATATATAAAC
*
4688806 TAAAAAATAAAATATATACTAAAG
1 T-AAAAATAAAATATATA-TAAAC
*
4688830 TAAAAAGAAAAT
1 TAAAAATAAAAT
4688842 GCATAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.03
23 25 0.83
24 4 0.13
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (22 bp):
TAAAAATAAAATATATATAAAC
Found at i:4688835 original size:25 final size:23
Alignment explanation
Indices: 4688785--4688835 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
4688775 AACTGATAAT
* *
4688785 AAAAATAATATATATATAATCTA
1 AAAAATAAAATATATATAAACTA
*
4688808 AAAAATAAAATATATACTAAAGTA
1 AAAAATAAAATATATA-TAAACTA
4688832 AAAA
1 AAAA
4688836 GAAAATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAAATAAAATATATATAAACTA
Found at i:4689927 original size:17 final size:17
Alignment explanation
Indices: 4689905--4689940 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4689895 AGAAACTATC
*
4689905 TAAAATATATGATAATT
1 TAAAATATATCATAATT
*
4689922 TAAAATCTATCATAATT
1 TAAAATATATCATAATT
4689939 TA
1 TA
4689941 TTAATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAAATATATCATAATT
Found at i:4690164 original size:62 final size:62
Alignment explanation
Indices: 4690017--4690164 Score: 181
Period size: 62 Copynumber: 2.4 Consensus size: 62
4690007 GTCCGTGAGG
* * * *
4690017 AATTTTGTTCATTTCAATTAAAAATACCAATTTAATTTATGTCATAATAATAATTATGTCGAA
1 AATTTTGTTCATTTCAA-TAAAAATACCAATTTAATTTACGACATAACAATAATTATATCGAA
** * *
4690080 AATTTCATTCATTTCAACAAAAATACCAATTTAATTTACGACATAACAATAATTCTATC-AA
1 AATTTTGTTCATTTCAATAAAAATACCAATTTAATTTACGACATAACAATAATTATATCGAA
* *
4690141 AATTTTTGTTAATTTTAATAAAAA
1 AA-TTTTGTTCATTTCAATAAAAA
4690165 AATATACTAA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
61 4 0.06
62 52 0.73
63 15 0.21
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (62 bp):
AATTTTGTTCATTTCAATAAAAATACCAATTTAATTTACGACATAACAATAATTATATCGAA
Found at i:4691589 original size:15 final size:16
Alignment explanation
Indices: 4691569--4691606 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4691559 AATAGTAGTT
*
4691569 AAAATTTA-TTATTTA
1 AAAATTTACTAATTTA
4691584 AAAATTTACTAATTTA
1 AAAATTTACTAATTTA
*
4691600 AATATTT
1 AAAATTT
4691607 TAATGACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AAAATTTACTAATTTA
Found at i:4692800 original size:32 final size:31
Alignment explanation
Indices: 4692743--4692804 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
4692733 GGAGTTTTTG
4692743 GGGTTTTGGTGAGTAGAAAAGAGAGGAAAGTT
1 GGGTTTTGGTGAG-AGAAAAGAGAGGAAAGTT
*
4692775 GGGTTTTGGTGA-AGAACATGAAGAGGAAAG
1 GGGTTTTGGTGAGAGAA-AAG-AGAGGAAAG
4692805 GCTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 4 0.15
31 2 0.07
32 21 0.78
ACGTcount: A:0.35, C:0.02, G:0.40, T:0.23
Consensus pattern (31 bp):
GGGTTTTGGTGAGAGAAAAGAGAGGAAAGTT
Found at i:4693550 original size:22 final size:22
Alignment explanation
Indices: 4693507--4693551 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4693497 CGGATCTAGC
*
4693507 AAATTTTTAAATACTTTCTATA
1 AAATTTTTAAATACTTTATATA
*
4693529 AAATTTTTATAA-ATTTTATATA
1 AAATTTTTA-AATACTTTATATA
4693551 A
1 A
4693552 GTTTACTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTTTAAATACTTTATATA
Found at i:4700926 original size:18 final size:18
Alignment explanation
Indices: 4700881--4700929 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
4700871 TTTTCAGGAT
*
4700881 TAATTTAAA-ATTTAAAA
1 TAATTTAAATATTTTAAA
* *
4700898 TGA-TTATATATTTTAAA
1 TAATTTAAATATTTTAAA
4700915 TAATTTAAATATTTT
1 TAATTTAAATATTTT
4700930 TTATTAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 4 0.16
17 11 0.44
18 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATTTAAATATTTTAAA
Found at i:4700938 original size:14 final size:15
Alignment explanation
Indices: 4700919--4700951 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
4700909 TTTAAATAAT
4700919 TTAAATA-TTTTTTA
1 TTAAATATTTTTTTA
4700933 TTAAATATTTTTTTA
1 TTAAATATTTTTTTA
4700948 TTAA
1 TTAA
4700952 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAAATATTTTTTTA
Found at i:4704935 original size:5 final size:5
Alignment explanation
Indices: 4704927--4704957 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
4704917 TAAATAACAA
*
4704927 TAAAA TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
4704958 TAAGGCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:4707485 original size:41 final size:42
Alignment explanation
Indices: 4707440--4707740 Score: 249
Period size: 41 Copynumber: 7.3 Consensus size: 42
4707430 GGTACATATA
* * *
4707440 TAGTGGTATTTTTAGATAAACGCCGCTAAA-ACCTAGTAGTT
1 TAGTGGCATTTTTAGACAAACGCCGCTAAATACCTAGTACTT
* * * * *
4707481 TAGTGGCGTTTTAAGCAAAAATGCCGCTAAATA-CTCGTACTT
1 TAGTGGCATTTTTAG-ACAAACGCCGCTAAATACCTAGTACTT
*
4707523 TAGTGGCATTTTTAGACAAACGCCGCTTAA-ACCTAGTACTT
1 TAGTGGCATTTTTAGACAAACGCCGCTAAATACCTAGTACTT
* * * ** * *
4707564 TAATTGC-TTTTTTGATGAATGCCGCTAAATACTTA-TACTT
1 TAGTGGCATTTTTAGACAAACGCCGCTAAATACCTAGTACTT
* * * *
4707604 TAGAGGCGTTTTTAGACAAACACCGCTAAA-ACCTAGTTCTT
1 TAGTGGCATTTTTAGACAAACGCCGCTAAATACCTAGTACTT
* * *
4707645 TAGTGGCATTTTTTGACAAACGGCGCTAAATA-CTTGTACTT
1 TAGTGGCATTTTTAGACAAACGCCGCTAAATACCTAGTACTT
* * * * * * *
4707686 TAGTGGCGTTTTAAGCAAAAACACTGCTAAATA-CTCGTACAT
1 TAGTGGCATTTTTAG-ACAAACGCCGCTAAATACCTAGTACTT
*
4707728 TAGTGGCGTTTTT
1 TAGTGGCATTTTT
4707741 TATTTACAAA
Statistics
Matches: 204, Mismatches: 48, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
40 31 0.15
41 106 0.52
42 66 0.32
43 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (42 bp):
TAGTGGCATTTTTAGACAAACGCCGCTAAATACCTAGTACTT
Found at i:4707616 original size:81 final size:82
Alignment explanation
Indices: 4707448--4707741 Score: 313
Period size: 83 Copynumber: 3.6 Consensus size: 82
4707438 TATAGTGGTA
* * * **
4707448 TTTTTAGATAAACGCCGCTAAAACCTAGTAGTTTAGTGGCGTTTTAAGCAAAAATGCCGCTAAAT
1 TTTTTAGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCATTTTTTG-AAAAATGCCGCTAAAT
* *
4707513 ACTCGTACTTTAGTGGCA
65 ACTTGTACTTTAGTGGCG
* * * **
4707531 TTTTTAGACAAACGCCGCTTAAACCTAGTACTTTAATTGC-TTTTTTGATGAATGCCGCTAAATA
1 TTTTTAGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCATTTTTTGAAAAATGCCGCTAAATA
* *
4707595 CTTATACTTTAGAGGCG
66 CTTGTACTTTAGTGGCG
* * * * *
4707612 TTTTTAGACAAACACCGCTAAAACCTAGTTCTTTAGTGGCATTTTTTGACAAACGGCGCTAAATA
1 TTTTTAGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCATTTTTTGAAAAATGCCGCTAAATA
4707677 CTTGTACTTTAGTGGCG
66 CTTGTACTTTAGTGGCG
* * * * * * *
4707694 TTTTAAGCAAAAACACTGCTAAATA-CTCGTACATTAGTGGCGTTTTTT
1 TTTTTAG-ACAAACGCCGCTAAA-ACCTAGTACTTTAGTGGCATTTTTT
4707742 ATTTACAAAT
Statistics
Matches: 177, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
81 63 0.36
82 46 0.26
83 67 0.38
84 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (82 bp):
TTTTTAGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCATTTTTTGAAAAATGCCGCTAAATA
CTTGTACTTTAGTGGCG
Found at i:4712029 original size:43 final size:42
Alignment explanation
Indices: 4711853--4712032 Score: 189
Period size: 43 Copynumber: 4.2 Consensus size: 42
4711843 ATTTGTATAA
*
4711853 AAAAATGCCGCTATAGATATAACCTTTTGCGGCGTTTGTTCC
1 AAAAATGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* * * * *
4711895 CAAAACGCCGCTGTAAGATCTGACCTTTTGCGACGTTTGTATCC
1 AAAAATGCCGCTAT-AGATATGACCTTTTGCGGCGTTTGT-TCC
** * * * * **
4711939 AAAAACACCTCTATAGATCTGACCTTTTGCTGTGTTTGTTTT
1 AAAAATGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* *
4711981 GAAAATGCCGCTATAGATATCGACCTTTTGCGGCATTTGTTCC
1 AAAAATGCCGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCC
4712024 AAAAATGCC
1 AAAAATGCC
4712033 ACGATAAATC
Statistics
Matches: 109, Mismatches: 26, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
42 27 0.25
43 69 0.63
44 13 0.12
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (42 bp):
AAAAATGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
Found at i:4712049 original size:43 final size:42
Alignment explanation
Indices: 4711874--4712061 Score: 146
Period size: 43 Copynumber: 4.4 Consensus size: 42
4711864 TATAGATATA
*
4711874 ACCTTTTGCGGCGTTTGTTCCCAAAACGCCGCTG-TAAGATCTG
1 ACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC-GATAA-ATCTG
* * * * *
4711917 ACCTTTTGCGACGTTTGTATCCAAAAACACCTCTATAGATCTG
1 ACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGCGATAAATCTG
* * *** * *
4711960 ACCTTTTGCTGTGTTTGTTTTGAAAATGCCGCTATAGATATC-G
1 ACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCGATA-A-ATCTG
* * *
4712003 ACCTTTTGCGGCATTTGTTCCAAAAATGCCACGATAAATCTTG
1 ACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCGATAAATC-TG
* *
4712046 ACCTATGGCGGCGTTT
1 ACCTTTTGCGGCGTTT
4712062 TTTGTTCTCA
Statistics
Matches: 112, Mismatches: 27, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
41 3 0.03
42 13 0.12
43 80 0.71
44 16 0.14
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (42 bp):
ACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCGATAAATCTG
Found at i:4712870 original size:24 final size:23
Alignment explanation
Indices: 4712824--4712870 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
4712814 AACGATTTTA
* * *
4712824 AAAAAATTAGTTTTTAGTGATTT
1 AAAAAATTAGTTTTAAATAATTT
4712847 AAAAAATCTAGTTTTAAATAATTT
1 AAAAAAT-TAGTTTTAAATAATTT
4712871 GGTGTTTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (23 bp):
AAAAAATTAGTTTTAAATAATTT
Found at i:4714254 original size:17 final size:17
Alignment explanation
Indices: 4714232--4714275 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
4714222 TTCTCACTCC
*
4714232 TTTTCTTGTTTCTTTTT
1 TTTTCTTCTTTCTTTTT
4714249 TTTTCTGGTCTTTCTTTTT
1 TTTTCT--TCTTTCTTTTT
4714268 TTCTTCTT
1 TT-TTCTT
4714276 TTTTTCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 12 0.52
20 4 0.17
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (17 bp):
TTTTCTTCTTTCTTTTT
Found at i:4714800 original size:3 final size:3
Alignment explanation
Indices: 4714783--4714849 Score: 50
Period size: 3 Copynumber: 22.3 Consensus size: 3
4714773 CATGTAAAAA
* * *
4714783 AAT AA- AAT AAA AAT AAT -AT AGTT AAAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT AAT
*
4714828 AAT AATT AAT ATT AAT AA- AAT A
1 AAT AA-T AAT AAT AAT AAT AAT A
4714850 TCTGGACGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
2 6 0.12
3 36 0.72
4 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4714837 original size:22 final size:20
Alignment explanation
Indices: 4714785--4714844 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
4714775 TGTAAAAAAA
*
4714785 TAAAATAAAAATAAT-ATAG
1 TAAAATAATAATAATAATAG
*
4714804 TTAAATAATAATAATAATAG
1 TAAAATAATAATAATAATAG
*
4714824 TAATAATAATTAATATTAATA
1 TAA-AATAA-TAATAATAATA
4714845 AAATATCTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.38
20 6 0.18
21 5 0.15
22 10 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TAAAATAATAATAATAATAG
Found at i:4728645 original size:18 final size:18
Alignment explanation
Indices: 4728618--4728670 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 18
4728608 AAGATGATGA
4728618 ATAC-GATGAAAATATCG
1 ATACTGATGAAAATATCG
4728635 ATACTGATGAAAATAGTATCG
1 ATACTGATG-AAA-A-TATCG
4728656 ATACTGATGAAAATA
1 ATACTGATGAAAATA
4728671 GTATCAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.12
18 6 0.19
19 4 0.12
20 4 0.12
21 14 0.44
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.26
Consensus pattern (18 bp):
ATACTGATGAAAATATCG
Found at i:4728656 original size:21 final size:21
Alignment explanation
Indices: 4728630--4728685 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
4728620 ACGATGAAAA
4728630 TATCGATACTGATGAAAATAG
1 TATCGATACTGATGAAAATAG
4728651 TATCGATACTGATGAAAATAG
1 TATCGATACTGATGAAAATAG
*
4728672 TATCAATACTGATG
1 TATCGATACTGATG
4728686 TGGAGGTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (21 bp):
TATCGATACTGATGAAAATAG
Found at i:4728826 original size:20 final size:20
Alignment explanation
Indices: 4728801--4728849 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
4728791 AGAGAAATAT
4728801 CGATACTATAGGAGGGGTAC
1 CGATACTATAGGAGGGGTAC
4728821 CGATACTATAGGAGGGGTAC
1 CGATACTATAGGAGGGGTAC
*
4728841 TGATACTAT
1 CGATACTAT
4728850 TCAGTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (20 bp):
CGATACTATAGGAGGGGTAC
Found at i:4729456 original size:65 final size:64
Alignment explanation
Indices: 4729387--4729546 Score: 250
Period size: 65 Copynumber: 2.5 Consensus size: 64
4729377 GAATAAATTG
* * *
4729387 AACATCGAATGCATTTTATGCATCGATGCACATGCCATGCATCGATGCACTCAGGGT-TTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTT-TG-
4729451 A
64 A
*
4729452 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGA
*
4729516 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
4729547 TCTTAGTGCA
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
64 30 0.34
65 56 0.63
66 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGA
Found at i:4729546 original size:17 final size:19
Alignment explanation
Indices: 4729518--4729566 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4729508 TATTTTGAAA
4729518 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
4729536 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
4729555 CACCGATGCACT
1 CATCGATGCACT
4729567 AACGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:4738109 original size:20 final size:20
Alignment explanation
Indices: 4738080--4738117 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4738070 TTTCAAAGGG
4738080 ATGCACCGATGCACCAATTC
1 ATGCACCGATGCACCAATTC
*
4738100 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
4738118 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATTC
Found at i:4738538 original size:18 final size:18
Alignment explanation
Indices: 4738515--4738556 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4738505 GGTTTGCGCA
4738515 ATTCAA-AGTCTATTTTTC
1 ATTCAATAGTC-ATTTTTC
*
4738533 ATTCAATATTCATTTTTC
1 ATTCAATAGTCATTTTTC
*
4738551 TTTCAA
1 ATTCAA
4738557 GAACACTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTCAATAGTCATTTTTC
Found at i:4744054 original size:53 final size:53
Alignment explanation
Indices: 4743971--4744156 Score: 273
Period size: 53 Copynumber: 3.5 Consensus size: 53
4743961 GGGTGTTATA
* * * * *
4743971 GAGTTTATGAATTACCATTTCGGTAGTATGTGTGCAACCATGATATTCATAAT
1 GAGTTTGTGAATTACCATTTCAGCACTATGTGTGCAACCATGGTATTCATAAT
*
4744024 GAGTTTGTTAATTACCATTTCAGCACTATGTGTGCAACCATGGTATTCATAAT
1 GAGTTTGTGAATTACCATTTCAGCACTATGTGTGCAACCATGGTATTCATAAT
* ** * *
4744077 GAGTTTGTGAATTACTATTTTGGTACTATGTGTGCATCCATGGTATTCATAAT
1 GAGTTTGTGAATTACCATTTCAGCACTATGTGTGCAACCATGGTATTCATAAT
4744130 GAGTTTGTGAATTACCATTTCAGCACT
1 GAGTTTGTGAATTACCATTTCAGCACT
4744157 TAGGTTCAAC
Statistics
Matches: 117, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 117 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (53 bp):
GAGTTTGTGAATTACCATTTCAGCACTATGTGTGCAACCATGGTATTCATAAT
Found at i:4750845 original size:43 final size:43
Alignment explanation
Indices: 4750784--4750870 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
4750774 TACTTCTAGA
* * ** * *
4750784 TGATATTGTCCTTAAAAATGTTCCAACATTTATTATTTCTTGC
1 TGATATGGACCTTAAAAATGCACCAACATTCATCATTTCTTGC
*
4750827 TGATATGGACCTTCAAAATGCACCAACATTCATCATTTCTTGC
1 TGATATGGACCTTAAAAATGCACCAACATTCATCATTTCTTGC
4750870 T
1 T
4750871 CCAACAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (43 bp):
TGATATGGACCTTAAAAATGCACCAACATTCATCATTTCTTGC
Found at i:4751759 original size:3 final size:3
Alignment explanation
Indices: 4751751--4751794 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4751741 TGTATAATCT
4751751 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4751795 TTATTAACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4764954 original size:13 final size:14
Alignment explanation
Indices: 4764923--4764955 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4764913 AATAAATAGA
4764923 AAAATACAAAATGG
1 AAAATACAAAATGG
4764937 AAAATACAAAAT-G
1 AAAATACAAAATGG
4764950 AAAATA
1 AAAATA
4764956 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.70, C:0.06, G:0.09, T:0.15
Consensus pattern (14 bp):
AAAATACAAAATGG
Found at i:4764970 original size:17 final size:18
Alignment explanation
Indices: 4764939--4764972 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4764929 CAAAATGGAA
*
4764939 AATACAAAATGAAAATAT
1 AATACAAAATAAAAATAT
4764957 AATA-AAAATAAAAATA
1 AATACAAAATAAAAATA
4764973 GTTAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AATACAAAATAAAAATAT
Found at i:4767665 original size:30 final size:30
Alignment explanation
Indices: 4767631--4767718 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 30
4767621 TATGTGTGCA
4767631 ACCATGGTATTCATAATGAGTTTGTGAATT
1 ACCATGGTATTCATAATGAGTTTGTGAATT
*** * * *
4767661 ACCAT--T-TTGGCACT-A-TGTGTGCA--
1 ACCATGGTATTCATAATGAGTTTGTGAATT
4767684 ACCATGGTATTCATAATGAGTTTGTGAATT
1 ACCATGGTATTCATAATGAGTTTGTGAATT
4767714 ACCAT
1 ACCAT
4767719 TTTAGCACCA
Statistics
Matches: 39, Mismatches: 12, Indels: 14
0.60 0.18 0.22
Matches are distributed among these distances:
23 5 0.13
25 7 0.18
26 5 0.13
27 5 0.13
28 7 0.18
30 10 0.26
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (30 bp):
ACCATGGTATTCATAATGAGTTTGTGAATT
Found at i:4767679 original size:53 final size:53
Alignment explanation
Indices: 4767617--4767826 Score: 357
Period size: 53 Copynumber: 4.0 Consensus size: 53
4767607 TGTACTTTCA
4767617 GCACTATGTGTGCAACCATGGTATTCATAATGAGTTTGTGAATTACCATTTTG
1 GCACTATGTGTGCAACCATGGTATTCATAATGAGTTTGTGAATTACCATTTTG
*
4767670 GCACTATGTGTGCAACCATGGTATTCATAATGAGTTTGTGAATTACCATTTTA
1 GCACTATGTGTGCAACCATGGTATTCATAATGAGTTTGTGAATTACCATTTTG
* * *
4767723 GCACCATGTGTGCAACCATGGTATTCATAATGAGTTTTTGAATTACCATTTCG
1 GCACTATGTGTGCAACCATGGTATTCATAATGAGTTTGTGAATTACCATTTTG
* * *
4767776 ACACTATGTGTGCATCCATGGTATTCATAATAAGTTTGTGAATTACCATTT
1 GCACTATGTGTGCAACCATGGTATTCATAATGAGTTTGTGAATTACCATTT
4767827 CAGCACTTAG
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 147 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (53 bp):
GCACTATGTGTGCAACCATGGTATTCATAATGAGTTTGTGAATTACCATTTTG
Found at i:4768386 original size:2 final size:2
Alignment explanation
Indices: 4768381--4768411 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4768371 TATATATATA
4768381 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4768412 ATTTGAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4770951 original size:18 final size:19
Alignment explanation
Indices: 4770928--4770970 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
4770918 AGGTAATCCT
4770928 ATTCC-CTAGTAATCTTAC
1 ATTCCACTAGTAATCTTAC
*
4770946 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTAGTAATCTTAC
4770966 ATTCC
1 ATTCC
4770971 GTGAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTAGTAATCTTAC
Found at i:4771570 original size:60 final size:60
Alignment explanation
Indices: 4771476--4771615 Score: 201
Period size: 60 Copynumber: 2.3 Consensus size: 60
4771466 ATCATTTTAT
*
4771476 AACTTTTATTATTAGAGTGACTTAACAAAACAACACTCTATAATTGAAAAATAATTTTGA
1 AACTTTTAATATTAGAGTGACTTAACAAAACAACACTCTATAATTGAAAAATAATTTTGA
* * * * * *
4771536 AACTTTTAATATTAGAGTGACTTAATAAAGCAACATTCTATAATTGGAGAATAATTTTGT
1 AACTTTTAATATTAGAGTGACTTAACAAAACAACACTCTATAATTGAAAAATAATTTTGA
4771596 AACTTTTAATAGTT-GAGTGA
1 AACTTTTAATA-TTAGAGTGA
4771616 GTATCCTTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 70 0.97
61 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (60 bp):
AACTTTTAATATTAGAGTGACTTAACAAAACAACACTCTATAATTGAAAAATAATTTTGA
Found at i:4772376 original size:3 final size:3
Alignment explanation
Indices: 4772361--4772400 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
4772351 GATTAAAGAA
*
4772361 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4772401 AGTGTGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Done.