Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 24
Found at i:2408646 original size:25 final size:25
Alignment explanation
Indices: 2408618--2408669 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2408608 CAAGCATCCG
2408618 AACCATTCACAACAAAACCAAAACT
1 AACCATTCACAACAAAACCAAAACT
*
2408643 AACCATTCACAATAAAACCAAAACT
1 AACCATTCACAACAAAACCAAAACT
2408668 AA
1 AA
2408670 GTATAGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.58, C:0.29, G:0.00, T:0.13
Consensus pattern (25 bp):
AACCATTCACAACAAAACCAAAACT
Found at i:2422757 original size:29 final size:30
Alignment explanation
Indices: 2422709--2422775 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
2422699 TGTTTATTTA
*
2422709 TTTATTTTTCAGCACCTTAA-TTTCAGTAT
1 TTTATTTTTCAGCACCTTAACTTTCAGCAT
*
2422738 TTTATTTTTCTGC-CCTTTAACTTTTCAGCAT
1 TTTATTTTTCAGCACC-TTAAC-TTTCAGCAT
2422769 TTTATTT
1 TTTATTT
2422776 CAGTCCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 16 0.48
31 15 0.45
ACGTcount: A:0.19, C:0.18, G:0.06, T:0.57
Consensus pattern (30 bp):
TTTATTTTTCAGCACCTTAACTTTCAGCAT
Found at i:2429594 original size:15 final size:14
Alignment explanation
Indices: 2429556--2429594 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2429546 TCATGACAAC
*
2429556 CATTTTTTTTGTTT
1 CATTTTTTTTGATT
*
2429570 CATTTCTTTTGAATT
1 CATTTTTTTTG-ATT
2429585 CATTTTTTTT
1 CATTTTTTTT
2429595 CTTCATTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.13, C:0.10, G:0.05, T:0.72
Consensus pattern (14 bp):
CATTTTTTTTGATT
Found at i:2433211 original size:18 final size:18
Alignment explanation
Indices: 2433174--2433219 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
2433164 CTAATTAGAG
*
2433174 AAAAGAGAAAAAGAAC-A
1 AAAAGAAAAAAAGAACAA
*
2433191 AAAAGAAAAAAGAGAAGAA
1 AAAAGAAAAAA-AGAACAA
2433210 AAAAGAAAAA
1 AAAAGAAAAA
2433220 TAAGGTGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 4 0.16
19 11 0.44
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAGAACAA
Found at i:2435950 original size:31 final size:31
Alignment explanation
Indices: 2435915--2435977 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2435905 AATTCGATGA
* *
2435915 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACACCC
*
2435946 ATTCAATATGTCATTCTCATTAGGAACACCC
1 ATTCAATATGTCATTCTCACTAGGAACACCC
2435977 A
1 A
2435978 AACTCTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACACCC
Found at i:2438038 original size:18 final size:18
Alignment explanation
Indices: 2438015--2438051 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2438005 CATACTAGAG
2438015 TAAAGTTTGTTATGAGTT
1 TAAAGTTTGTTATGAGTT
2438033 TAAAGTTTGTTATGAGTT
1 TAAAGTTTGTTATGAGTT
2438051 T
1 T
2438052 TAGCCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (18 bp):
TAAAGTTTGTTATGAGTT
Found at i:2441382 original size:39 final size:39
Alignment explanation
Indices: 2441322--2441431 Score: 159
Period size: 39 Copynumber: 2.8 Consensus size: 39
2441312 TGTATTTGCC
*
2441322 ACACCATGACAA-TTTCTTTCTTGGACCCCACGTGAGTGT
1 ACACCATGACAATTTTC-TTCTTGGACCCCACGTGAATGT
* *
2441361 ACACCATGCCAATTTTCTTCTTGGATCCCACGTGAATGT
1 ACACCATGACAATTTTCTTCTTGGACCCCACGTGAATGT
* *
2441400 GCACCATGACAATTTCCTTCTTGGACCCCACG
1 ACACCATGACAATTTTCTTCTTGGACCCCACG
2441432 CGAGATGCCA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
39 59 0.94
40 4 0.06
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (39 bp):
ACACCATGACAATTTTCTTCTTGGACCCCACGTGAATGT
Found at i:2441698 original size:30 final size:30
Alignment explanation
Indices: 2441664--2441722 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2441654 GAACCTATGC
2441664 GCATTGGA-CCAATGCATATTGGATTCATGT
1 GCATTGGATCC-ATGCATATTGGATTCATGT
* *
2441694 GCATTGGATTCATGCGTATTGGATTCATG
1 GCATTGGATCCATGCATATTGGATTCATG
2441723 CGCACCAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (30 bp):
GCATTGGATCCATGCATATTGGATTCATGT
Found at i:2441699 original size:15 final size:15
Alignment explanation
Indices: 2441681--2441726 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
2441671 ACCAATGCAT
*
2441681 ATTGGATTCATGTGC
1 ATTGGATTCATGCGC
*
2441696 ATTGGATTCATGCGT
1 ATTGGATTCATGCGC
2441711 ATTGGATTCATGCGC
1 ATTGGATTCATGCGC
2441726 A
1 A
2441727 CCAATACGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (15 bp):
ATTGGATTCATGCGC
Found at i:2445122 original size:42 final size:42
Alignment explanation
Indices: 2445063--2445148 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
2445053 TTGATAATCC
*
2445063 ATTGTTAAAAATTTAACAACGATATTGATGCATCACCATAAG
1 ATTGTTAAAAATTTAACAACGATATTAATGCATCACCATAAG
* *
2445105 ATTGTTAAAAATTTAACAATGATTTTAATGCATCACCATAAG
1 ATTGTTAAAAATTTAACAACGATATTAATGCATCACCATAAG
2445147 AT
1 AT
2445149 AATGTCATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (42 bp):
ATTGTTAAAAATTTAACAACGATATTAATGCATCACCATAAG
Found at i:2451904 original size:23 final size:24
Alignment explanation
Indices: 2451877--2451938 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
2451867 CTCATCTGAA
*
2451877 TTGAAAAAGT-AAATCATCCACAT
1 TTGAAAAACTAAAATCATCCACAT
*
2451900 TTG--AAACTAAAATCATCTACAT
1 TTGAAAAACTAAAATCATCCACAT
2451922 TTG--AAACTAAAATCATC
1 TTGAAAAACTAAAATCATC
2451939 TACACATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 4 0.11
22 29 0.81
23 3 0.08
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (24 bp):
TTGAAAAACTAAAATCATCCACAT
Found at i:2451939 original size:22 final size:22
Alignment explanation
Indices: 2451887--2451942 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2451877 TTGAAAAAGT
*
2451887 AAATCATCCACATTTGAAACTA
1 AAATCATCTACATTTGAAACTA
2451909 AAATCATCTACATTTGAAACTA
1 AAATCATCTACATTTGAAACTA
2451931 AAATCATCTACA
1 AAATCATCTACA
2451943 CATATGAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATCATCTACATTTGAAACTA
Found at i:2455734 original size:2 final size:2
Alignment explanation
Indices: 2455727--2455804 Score: 138
Period size: 2 Copynumber: 39.0 Consensus size: 2
2455717 TGTAAACTTC
2455727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2455769 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2455805 GAAAAAGATG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2462800 original size:23 final size:20
Alignment explanation
Indices: 2462769--2462822 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
2462759 ATCCCGATAC
2462769 TATTATTATTTATTATTTTCATA
1 TATT-TTATTTATT-TTTT-ATA
* *
2462792 TTTTTTTATTCATTTTTTATA
1 -TATTTTATTTATTTTTTATA
2462813 TATTTTATTT
1 TATTTTATTT
2462823 TCATTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 4 0.15
23 8 0.31
24 3 0.12
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTATTTATTTTTTATA
Found at i:2462872 original size:2 final size:2
Alignment explanation
Indices: 2462865--2462892 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2462855 CTTTATCATG
2462865 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
2462893 AAAGTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2467080 original size:93 final size:92
Alignment explanation
Indices: 2466920--2467151 Score: 231
Period size: 93 Copynumber: 2.6 Consensus size: 92
2466910 ATATTATTTA
* * * * *
2466920 TATACAATAAATCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACGCCCCAGCATTATGGATAAT
*
2466985 TCAGCTAGCCTGATAAAGATGATTATAC
66 TCAGCTA-ACTGATAAAGATGATTATAC
* * *
2467013 TATACAATAAAGCTTGAGCTGTTCCTCTAAGGAAATTGGTTAAATG-CCCAG-ATTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACGCCCCAGCATTATGGAT-A-
2467076 ATTCAGCTAACTGATAAAG--G--TAT--
64 ATTCAGCTAACTGATAAAGATGATTATAC
* * *
2467099 T-TAC-AT--A--TTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATG
1 TATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACGCCCCAGCATTATG
2467152 ATTCACCTAG
Statistics
Matches: 120, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
80 28 0.23
81 5 0.04
82 6 0.05
84 2 0.02
85 3 0.03
86 1 0.01
88 3 0.03
90 1 0.01
91 8 0.07
92 14 0.12
93 49 0.41
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (92 bp):
TATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACGCCCCAGCATTATGGATAAT
TCAGCTAACTGATAAAGATGATTATAC
Found at i:2468363 original size:71 final size:71
Alignment explanation
Indices: 2468183--2468412 Score: 295
Period size: 71 Copynumber: 3.2 Consensus size: 71
2468173 AATACGATGA
* * ** *
2468183 TTTGTCTCACTTGAGATTGTTTTACTTGAAAGAATATTTATTTCCCCTTGAGATTGTCATTCTTA
1 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTT-CCCTCAAGATTGT-TTTCTTA
2468248 AAACAGAC
64 AAACAGAC
*
2468256 ATTGTCTCACTT--G-CTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTCTTAAA
1 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTCTTAAA
*
2468318 ACATAC
66 ACAGAC
* *
2468324 TTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCCCTCAATATTGTTTTTCTTAA
1 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTG-TTTTCTTAA
*
2468389 AACAAGAG
65 AAC-AGAC
* *
2468397 TTTATCTCGCTTGAGA
1 TTTGTCTCACTTGAGA
2468413 TAGTTTCCCT
Statistics
Matches: 138, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
68 24 0.17
69 11 0.08
70 26 0.19
71 38 0.28
72 12 0.09
73 27 0.20
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (71 bp):
TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTCTTAAA
ACAGAC
Found at i:2468562 original size:36 final size:37
Alignment explanation
Indices: 2468494--2468566 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
2468484 ATTTCCCTTG
* *
2468494 AAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 AAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACA
*
2468531 AAATTTTGTCTC-CTTGAGACAATTTCTCTTGAAACA
1 AAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACA
2468567 TAACATTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 21 0.64
37 12 0.36
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (37 bp):
AAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACA
Found at i:2468719 original size:101 final size:98
Alignment explanation
Indices: 2468401--2468885 Score: 582
Period size: 96 Copynumber: 4.9 Consensus size: 98
2468391 CAAGAGTTTA
* *
2468401 TCTCGCTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAA
1 TCTCTCTTGAGATAGTTTCCCTTGAA-C--AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAA
2468466 ACATAAACATTGAAAAACATTTCCCTTG-A--AATTTTG
63 ACAT-AACATTG--AAACATTTCCCTTGAATGAATTTTG
*
2468502 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCT-CCTTGAGACAATTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTG-AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
2468566 ATAACATTGAAAACATTTCCCTTGAAATGAATTTTG
65 ATAACATTG-AAACATTTCCCTTG-AATGAATTTTG
* *
2468602 TCT-TCTTGAGATAGTTTCCCTCGAAGCAGGAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAA
1 TCTCTCTTGAGATAGTTTCCCTTGAA-CA--AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAA
* *
2468666 ACATAACATTGAAATATTT-CCTTGAAATTAATTTTG
63 ACATAACATTGAAACATTTCCCTTG-AATGAATTTTG
* *
2468702 TTTCTCTTGAGATAGTTTACCTTGAA-ACAAA--TTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
* * *
2468764 ATAACGTTGAAAAATATCCCTTGAATGAA--TTG
65 ATAACATTGAAACATTTCCCTTGAATGAATTTTG
** *
2468796 AATCTCTTGAGATAGTTTCCCTTGAAC-AAATTTTGTCTCCCTTGAGAGAGTTTCTCTTGAAA-A
1 TCTCTCTTGAGATAGTTTCCCTTGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
*
2468859 TAAACTTTGAAAACAGTTTCCCTTGAA
66 T-AACATTG-AAACA-TTTCCCTTGAA
2468886 ACAAAATCTT
Statistics
Matches: 343, Mismatches: 24, Indels: 38
0.85 0.06 0.09
Matches are distributed among these distances:
93 3 0.01
94 28 0.08
95 35 0.10
96 68 0.20
97 22 0.06
98 31 0.09
99 34 0.10
100 28 0.08
101 61 0.18
102 33 0.10
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (98 bp):
TCTCTCTTGAGATAGTTTCCCTTGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
TAACATTGAAACATTTCCCTTGAATGAATTTTG
Found at i:2468941 original size:93 final size:92
Alignment explanation
Indices: 2468436--2468943 Score: 391
Period size: 96 Copynumber: 5.3 Consensus size: 92
2468426 AGCAGAAAAT
* * ***
2468436 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAACATTTCCCTTGAAATTTT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT-AACGTTG-AAAA-ATATCCCTTGAAACAAT
** *
2468501 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
63 -AATCTCTTGAGATAGTTTACCTT-AAAC-AAA
* * * *
2468534 TTTTGTCT-CCTTGAGACAATTTCTCTTGAAACATAACATTGAAAACATTTCCCTTGAAATGAAT
1 -TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAACGTTGAAAA-ATATCCCTTGAAA-CAA-
** * * *
2468598 TTTGTCTTCTTGAGATAGTTTCCCTCGAAGCAGGAAA
62 -TAATC-TCTTGAGATAGTTTACCT-TAA--A-CAAA
* * * * *
2468635 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAACATTGAAATAT-TTCCTTGAAATTAATT
1 -TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAACGTTGAAAAATATCCCTTGAAA-CAA--
**
2468699 TTGTTTCTCTTGAGATAGTTTACCTTGAAACAAA
62 -T-AATCTCTTGAGATAGTTTACCTT-AAACAAA
**
2468733 -TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAACGTTGAAAAATATCCCTTGAATGAATTGA
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAACGTTGAAAAATATCCCTTGAAACAA-T-A
* *
2468797 ATCTCTTGAGATAGTTTCCCTTGAACAAA
64 ATCTCTTGAGATAGTTTACCTTAAACAAA
* * *
2468826 TTTTGTCTCCCTTGAGAGAGTTTCTCTTGAAA-ATAAACTTTGAAAACAGTTTCCCTTGAAACAA
1 -TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT-AACGTTGAAAA-A-TATCCCTTGAAACAA
*
2468890 -AATCT-TTGA-ATATGTTTACATTAAACAAA
62 TAATCTCTTGAGATA-GTTTACCTTAAACAAA
*
2468919 TTTCGTCTCCCTTGAGATAGTTTCT
1 TTT-GTCTCCCTTGAGACAGTTTCT
2468944 TTGGAAGTTT
Statistics
Matches: 354, Mismatches: 35, Indels: 46
0.81 0.08 0.11
Matches are distributed among these distances:
92 6 0.02
93 43 0.12
94 30 0.08
95 39 0.11
96 64 0.18
97 27 0.08
98 31 0.09
99 29 0.08
100 12 0.03
101 36 0.10
102 37 0.10
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (92 bp):
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAACGTTGAAAAATATCCCTTGAAACAATAAT
CTCTTGAGATAGTTTACCTTAAACAAA
Found at i:2469041 original size:32 final size:30
Alignment explanation
Indices: 2468971--2469049 Score: 99
Period size: 32 Copynumber: 2.6 Consensus size: 30
2468961 CTTGAGACAG
*
2468971 TTCTCTTGAAAC-AATACCTTTGAAATCGT
1 TTCTCTTGAAACAAAAACCTTTGAAATCGT
2469000 TT-TCTTTGAACACAGAAAACCTTTGAAATCGT
1 TTCTC-TTGAA-ACA-AAAACCTTTGAAATCGT
2469032 TTCTCTTGAAACATAAAA
1 TTCTCTTGAAACA-AAAA
2469050 AAAAATCTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 2 0.05
29 7 0.16
30 2 0.05
31 7 0.16
32 23 0.53
33 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (30 bp):
TTCTCTTGAAACAAAAACCTTTGAAATCGT
Found at i:2469077 original size:27 final size:28
Alignment explanation
Indices: 2469047--2469105 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
2469037 TTGAAACATA
* *
2469047 AAAAAAAATC-TTG-AATTGTTTCTCTTG
1 AAAAAAAACCGTTGAAAATGTTTCT-TTG
2469074 -AAAAAAACCGTTGAAAATGTTTCTTTG
1 AAAAAAAACCGTTGAAAATGTTTCTTTG
2469101 AAAAA
1 AAAAA
2469106 TCGAATCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 8 0.30
27 6 0.22
28 13 0.48
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (28 bp):
AAAAAAAACCGTTGAAAATGTTTCTTTG
Found at i:2470775 original size:19 final size:18
Alignment explanation
Indices: 2470730--2470788 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
2470720 CCTATACTAT
2470730 TATTATTTATTATTTTCA
1 TATTATTTATTATTTTCA
*
2470748 TATTATTTATTCATTTTTA
1 TATTATTTATT-ATTTTCA
2470767 TA-TA-TT-TTATTTTCA
1 TATTATTTATTATTTTCA
2470782 T-TTATTT
1 TATTATTT
2470789 TTACCTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 9 0.25
16 4 0.11
17 2 0.06
18 13 0.36
19 8 0.22
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTATTTATTATTTTCA
Found at i:2473578 original size:178 final size:176
Alignment explanation
Indices: 2473249--2473606 Score: 682
Period size: 178 Copynumber: 2.0 Consensus size: 176
2473239 ATCATTCATA
2473249 TCTT-GTTGTCGAGCTCCCAAGGTAGAGAGCTGGACTCAATAAATGTGAAGCGCGAATCCATGGA
1 TCTTGGTTGTCGAGCTCCCAAGGTAGAGAGCTGGACTCAATAAATGTGAAGCGCGAATCCATGGA
*
2473313 CGCATACCGTAAATCAAATGTCTCCAAAACGAACAAAAATACGGAGGCATTTGATCTTCTTGTGG
66 CGCATACCGTAAATCAAATGTCTCCAAAACGAAAAAAAATACGGAGGCATTTGATCTTCTTGTGG
2473378 AGCTAGTTCCGGTACAGGCTCGTCATCAGGTACGTGATCATCGATG
131 AGCTAGTTCCGGTACAGGCTCGTCATCAGGTACGTGATCATCGATG
2473424 TCTTGGTTGTCGAGCTCCCAAGGTAGAGAGCTGGGACTCAATAAATGTGAAGCGCGAATCCATGG
1 TCTTGGTTGTCGAGCTCCCAAGGTAGAGAGCT-GGACTCAATAAATGTGAAGCGCGAATCCATGG
2473489 ACGCATACCGTAAATCAAATGTCTCCAAAAACGAAAAAAAATACGGAGGCATTTGATCTTCTTGT
65 ACGCATACCGTAAATCAAATGTCTCC-AAAACGAAAAAAAATACGGAGGCATTTGATCTTCTTGT
2473554 GGAGCTAGTTCCGGTACAGGCTCGTCATCAGGTACGTGATCATCGATG
129 GGAGCTAGTTCCGGTACAGGCTCGTCATCAGGTACGTGATCATCGATG
2473602 TCTTG
1 TCTTG
2473607 CATAATTTGT
Statistics
Matches: 179, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
175 4 0.02
176 27 0.15
177 58 0.32
178 90 0.50
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (176 bp):
TCTTGGTTGTCGAGCTCCCAAGGTAGAGAGCTGGACTCAATAAATGTGAAGCGCGAATCCATGGA
CGCATACCGTAAATCAAATGTCTCCAAAACGAAAAAAAATACGGAGGCATTTGATCTTCTTGTGG
AGCTAGTTCCGGTACAGGCTCGTCATCAGGTACGTGATCATCGATG
Found at i:2481104 original size:65 final size:64
Alignment explanation
Indices: 2480971--2481130 Score: 186
Period size: 65 Copynumber: 2.5 Consensus size: 64
2480961 TGAACTAAGA
*
2480971 GTGCATTGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGACTG
1 GTGCATTGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCA-AGTGCATCGATGCATGACTG
* * *
2481035 GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAACATA-CTC-AGTGCATCGGTGCATGGT
1 GTGCATTGATGCATCAAATGCATTCGATGTTTTCA-AA-ATAGC-CAAGTGCATCGATGCAT-G-
2481098 A-T-
61 ACTG
*
2481100 GTGCATTGATGCATGAAATGCATTCGATGTT
1 GTGCATTGATGCATCAAATGCATTCGATGTT
2481131 CAATTTAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
64 26 0.31
65 47 0.57
66 5 0.06
67 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATTGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAGTGCATCGATGCATGACTG
Found at i:2484036 original size:42 final size:43
Alignment explanation
Indices: 2483949--2484045 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 43
2483939 CGAACATGTT
*
2483949 GCGGCATTTTAGAATACAAAAGCCGCTATATAACCTAACCTTTA
1 GCGGCGTTTTAGAATACAAAAGCCGC-ATATAACCTAACCTTTA
* * * *
2483993 GCGGCGTTTTAGTATACAAACGCCGC-TATAACCTGACTTTTA
1 GCGGCGTTTTAGAATACAAAAGCCGCATATAACCTAACCTTTA
*
2484035 GCGGGGTTTTA
1 GCGGCGTTTTA
2484046 TTAGTAGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 24 0.51
44 23 0.49
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTTAGAATACAAAAGCCGCATATAACCTAACCTTTA
Found at i:2486845 original size:24 final size:24
Alignment explanation
Indices: 2486818--2486879 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
2486808 CGTTCGTGAA
*
2486818 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
2486842 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
2486866 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
2486880 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:2488412 original size:16 final size:16
Alignment explanation
Indices: 2488389--2488443 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
2488379 GGGTCTCCAA
2488389 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
2488405 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
2488421 CGTTTATG-TCTGTGTT
1 CGTTTATGTTC-GTGTT
2488437 CGTTTAT
1 CGTTTAT
2488444 TTATTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 2 0.06
16 34 0.94
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:2488530 original size:16 final size:16
Alignment explanation
Indices: 2488509--2488540 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2488499 AAAGAATTTT
2488509 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2488525 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2488541 CTTATTTATT
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:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2490385 original size:2 final size:2
Alignment explanation
Indices: 2490380--2490498 Score: 176
Period size: 2 Copynumber: 62.0 Consensus size: 2
2490370 TTTTTTGTTT
*
2490380 TA TA TA TA TA TA TA T- TA T- TT TA TA T- TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2490418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2490460 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2490499 GTAATATAGT
Statistics
Matches: 107, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
1 5 0.05
2 102 0.95
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2490633 original size:27 final size:27
Alignment explanation
Indices: 2490603--2490656 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2490593 TATTTTTAAA
2490603 ATATAATGTATAATTTTGAAAACATTT
1 ATATAATGTATAATTTTGAAAACATTT
* * *
2490630 ATATACTGTATAGTTTTTAAAACATTT
1 ATATAATGTATAATTTTGAAAACATTT
2490657 TGAAAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (27 bp):
ATATAATGTATAATTTTGAAAACATTT
Found at i:2490643 original size:135 final size:135
Alignment explanation
Indices: 2490520--2490767 Score: 288
Period size: 135 Copynumber: 1.8 Consensus size: 135
2490510 TGTGAAATGT
* * * *
2490520 TTTTGACAAA-ATATAATATATAATTTTCAGAAAACA-ATTTTCAAAAATTTATATATTATATAG
1 TTTTGA-AAATATATAATATAT-AGTTTAAAAAAACATATTTTCAAAAA-TTATATAATATATAG
* * *
2490583 TTTTTGAAAATATTTTT-AAA-ATATAATGTATAATTTTGAAAACATTTATATACTGTATAGTTT
63 TTTTTAAAAATATTTTTAAAATATATAATATATAATTTTAAAAACATTTATATACTGTATAGTTT
*
2490646 TTAAAACA
128 TGAAAACA
* * * *
2490654 TTTTGAAAACTTATATAATATATAGTTTAAAAAAATATTTTTTGAAAGATTATATAATATATAGT
1 TTTTGAAAA--TATATAATATATAGTTTAAAAAAACATATTTTCAAAAATTATATAATATATAGT
*
2490719 TTTTAAAAATATTTTTGAAAATTATATAATATATAGTTTTAAAAACATT
64 TTTTAAAAATATTTTT-AAAA-TATATAATATATAATTTTAAAAACATT
2490768 GTTTGAAATC
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
133 3 0.03
134 6 0.06
135 40 0.43
136 19 0.20
137 3 0.03
139 23 0.24
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (135 bp):
TTTTGAAAATATATAATATATAGTTTAAAAAAACATATTTTCAAAAATTATATAATATATAGTTT
TTAAAAATATTTTTAAAATATATAATATATAATTTTAAAAACATTTATATACTGTATAGTTTTGA
AAACA
Found at i:2490707 original size:39 final size:37
Alignment explanation
Indices: 2490628--2490788 Score: 184
Period size: 39 Copynumber: 4.3 Consensus size: 37
2490618 TTGAAAACAT
* * * *
2490628 TTATATACTGTATAGTTTTTAAAACA--TTTTGAAAA
1 TTATATAATATATAGTTTTAAAAATATTTTTTGAAAA
*
2490663 CTTATATAATATATAGTTTAAAAAAATATTTTTTGAAAGA
1 -TTATATAATATATAGTTT-TAAAAATATTTTTTGAAA-A
2490703 TTATATAATATATAGTTTTTAAAAATA-TTTTTGAAAA
1 TTATATAATATATAG-TTTTAAAAATATTTTTTGAAAA
* * *
2490740 TTATATAATATATAGTTTTAAAAACATTGTTTGAAATC
1 TTATATAATATATAGTTTTAAAAATATTTTTTGAAA-A
2490778 TTATATAATAT
1 TTATATAATAT
2490789 TTTTAAAACA
Statistics
Matches: 109, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
36 26 0.24
37 29 0.27
38 20 0.18
39 30 0.28
40 4 0.04
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
TTATATAATATATAGTTTTAAAAATATTTTTTGAAAA
Found at i:2490717 original size:75 final size:75
Alignment explanation
Indices: 2490628--2490788 Score: 218
Period size: 75 Copynumber: 2.1 Consensus size: 75
2490618 TTGAAAACAT
* * *
2490628 TTATATACTGTATAGTTTTT-AAAACA-TTTTGAAAACTTATATAATATATAGTTTAAAAAAATA
1 TTATATAATATATAGTTTTTAAAAACATTTTTGAAAA-TTATATAATATATAGTTT-AAAAAACA
*
2490691 TTTTTTGAAAGA
64 TTGTTTGAAAGA
* *
2490703 TTATATAATATATAGTTTTTAAAAATATTTTTGAAAATTATATAATATATAGTTTTAAAAACATT
1 TTATATAATATATAGTTTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTAAAAAACATT
**
2490768 GTTTGAAATC
66 GTTTGAAAGA
2490778 TTATATAATAT
1 TTATATAATAT
2490789 TTTTAAAACA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 44 0.58
76 23 0.30
77 9 0.12
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (75 bp):
TTATATAATATATAGTTTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTAAAAAACATT
GTTTGAAAGA
Found at i:2490783 original size:31 final size:30
Alignment explanation
Indices: 2490748--2490869 Score: 81
Period size: 31 Copynumber: 3.9 Consensus size: 30
2490738 AATTATATAA
2490748 TATATAGTTTTAAAAACATTGTTTGAAATCT
1 TATATAGTTTTAAAAACATT-TTTGAAATCT
* * *
2490779 TATATAATATTTTTAAAACA--TTTGAAACTAT
1 TATAT-A-GTTTTAAAAACATTTTTGAAA-TCT
* * *
2490810 ATATATAGTTTTGAAAAC-TTTTTAAAATACAA
1 -TATATAGTTTTAAAAACATTTTTGAAAT-C-T
*
2490842 TATATAGTTTT-AAAACGTATTTTGAAAT
1 TATATAGTTTTAAAAACAT-TTTTGAAAT
2490870 ATATATATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
30 22 0.31
31 26 0.36
32 14 0.19
33 10 0.14
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (30 bp):
TATATAGTTTTAAAAACATTTTTGAAATCT
Found at i:2490821 original size:63 final size:61
Alignment explanation
Indices: 2490742--2490877 Score: 152
Period size: 63 Copynumber: 2.2 Consensus size: 61
2490732 TTTGAAAATT
* * *
2490742 ATATAATATATAGTTTTAAAAACATTGTTTGAAAT-CTTATATAATATTTTTAAAAC-A-TTTGA
1 ATAT-ATATATAGTTTTAAAAAC-TT-TTTAAAATAC-AATAT-ATAGTTTTAAAACGATTTTGA
2490804 A
61 A
*
2490805 ACTATATATATAGTTTTGAAAACTTTTTAAAATACAATATATAGTTTTAAAACGTATTTTGAA
1 A-TATATATATAGTTTTAAAAACTTTTTAAAATACAATATATAGTTTTAAAACG-ATTTTGAA
2490868 ATATATATAT
1 ATATATATAT
2490878 TATATAAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
60 12 0.19
61 11 0.17
62 13 0.20
63 25 0.39
64 3 0.05
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (61 bp):
ATATATATATAGTTTTAAAAACTTTTTAAAATACAATATATAGTTTTAAAACGATTTTGAA
Found at i:2490876 original size:31 final size:30
Alignment explanation
Indices: 2490705--2490877 Score: 118
Period size: 30 Copynumber: 5.3 Consensus size: 30
2490695 TTGAAAGATT
*
2490705 ATATAATATATAGTTTTTAAAAATATTTTTGAAAA
1 ATAT-ATATATAG-TTTTAAAAA-CTTTTTG--AA
2490740 TTATATAATATATAGTTTTAAAAACATTGTTTGAA
1 --ATAT-ATATATAGTTTTAAAAAC-TT-TTTGAA
* * *
2490775 ATCTTATATAATA-TTTTTAAAAC-ATTTGAA
1 AT-ATATAT-ATAGTTTTAAAAACTTTTTGAA
* *
2490805 ACTATATATATAGTTTTGAAAACTTTTTAAA
1 A-TATATATATAGTTTTAAAAACTTTTTGAA
*
2490836 ATACAATATATAGTTTT-AAAACGTATTTTGAA
1 ATA-TATATATAGTTTTAAAAAC-T-TTTTGAA
2490868 ATATATATAT
1 ATATATATAT
2490878 TATATAAATT
Statistics
Matches: 115, Mismatches: 11, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
29 3 0.03
30 28 0.24
31 26 0.23
32 9 0.08
33 15 0.13
34 4 0.03
35 2 0.02
36 11 0.10
37 17 0.15
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (30 bp):
ATATATATATAGTTTTAAAAACTTTTTGAA
Found at i:2490926 original size:5 final size:5
Alignment explanation
Indices: 2490898--2490984 Score: 85
Period size: 5 Copynumber: 18.2 Consensus size: 5
2490888 ATATTTAGTA
*
2490898 TATTAT TATTT T-TTT TA-TT T-TTT TATTT TATTT TA-TT CATTT TATTT
1 TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
* * * *
2490945 AATTT TA-TT TAATT TATTT TAATT TATTT GATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
2490985 TCTTTTCCAG
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
4 17 0.25
5 46 0.69
6 4 0.06
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:2490940 original size:19 final size:18
Alignment explanation
Indices: 2490898--2490984 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 18
2490888 ATATTTAGTA
2490898 TATTATTATTTT-TTTTAT
1 TATT-TTATTTTATTTTAT
*
2490916 TTTTTTATTTTATTTTAT
1 TATTTTATTTTATTTTAT
*
2490934 TCATTTTATTTAATTTTATT
1 T-ATTTTATTTTATTTTA-T
* *
2490954 TAATTTATTTTAATTTATT
1 TATTTTATTTTATTTTA-T
2490973 TGATTTTATTTT
1 T-ATTTTATTTT
2490985 TCTTTTCCAG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
17 7 0.12
18 10 0.17
19 30 0.52
20 11 0.19
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.75
Consensus pattern (18 bp):
TATTTTATTTTATTTTAT
Found at i:2492212 original size:16 final size:17
Alignment explanation
Indices: 2492193--2492234 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2492183 TTTGACTTTT
2492193 TTTATTCATTTATTT-A
1 TTTATTCATTTATTTGA
*
2492209 TTTATTC-TTTCTTTGA
1 TTTATTCATTTATTTGA
2492225 TTTATT-ATTT
1 TTTATTCATTT
2492235 TGGTGTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTCATTTATTTGA
Found at i:2493348 original size:3 final size:3
Alignment explanation
Indices: 2493340--2493368 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2493330 AATCGTTTAA
2493340 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2493369 ATAAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2493873 original size:18 final size:18
Alignment explanation
Indices: 2493847--2493887 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2493837 TGCTCCGACA
* *
2493847 AAGAGACGAAAGTCATCG
1 AAGAAACGAAAGTCACCG
2493865 AAGAAACGAAAGTCACCG
1 AAGAAACGAAAGTCACCG
2493883 AAGAA
1 AAGAA
2493888 GAATATCGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.24, T:0.07
Consensus pattern (18 bp):
AAGAAACGAAAGTCACCG
Found at i:2495026 original size:9 final size:9
Alignment explanation
Indices: 2495014--2495082 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
2495004 AGCAATATTA
2495014 ATAATAATT
1 ATAATAATT
2495023 ATAAT--TT
1 ATAATAATT
* **
2495030 TTAATTGTT
1 ATAATAATT
*
2495039 ATAATAATA
1 ATAATAATT
*
2495048 ATAATAGTT
1 ATAATAATT
*
2495057 ATAATATAAT
1 ATAATA-ATT
2495067 ATTAATAATT
1 A-TAATAATT
2495077 ATAATA
1 ATAATA
2495083 TAATATTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
7 6 0.13
9 30 0.65
10 5 0.11
11 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (9 bp):
ATAATAATT
Found at i:2495088 original size:20 final size:20
Alignment explanation
Indices: 2495042--2495094 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2495032 AATTGTTATA
* *
2495042 ATAATAATAATAGTTATAAT
1 ATAATATTAATAATTATAAT
2495062 ATAATATTAATAATTATAAT
1 ATAATATTAATAATTATAAT
*
2495082 ATAATATTTATAA
1 ATAATATTAATAA
2495095 CTCGGACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTAATAATTATAAT
Found at i:2515400 original size:12 final size:12
Alignment explanation
Indices: 2515383--2515407 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2515373 GAACTAACCT
2515383 TATTTGGTGGGG
1 TATTTGGTGGGG
2515395 TATTTGGTGGGG
1 TATTTGGTGGGG
2515407 T
1 T
2515408 TGTTTTAATG
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:0.08, C:0.00, G:0.48, T:0.44
Consensus pattern (12 bp):
TATTTGGTGGGG
Found at i:2520852 original size:21 final size:23
Alignment explanation
Indices: 2520812--2520862 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
2520802 CGATTTCTCC
*
2520812 TCATCTGCATTTGAAAACT-AAA
1 TCATCTACATTTGAAAACTAAAA
2520834 TCATCTACATTTG-AAACTAAAA
1 TCATCTACATTTGAAAACTAAAA
2520856 TCATCTA
1 TCATCTA
2520863 GTATTGCTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (23 bp):
TCATCTACATTTGAAAACTAAAA
Found at i:2524402 original size:19 final size:17
Alignment explanation
Indices: 2524380--2524427 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
2524370 ATAATATTTA
2524380 TTAATAAATAGTAAAATAT
1 TTAATAAA-A-TAAAATAT
2524399 TTAATAAAATAAAATA-
1 TTAATAAAATAAAATAT
*
2524415 ATAATAATAATAA
1 TTAATAA-AATAA
2524428 GCCAAAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 6 0.22
17 12 0.44
18 1 0.04
19 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TTAATAAAATAAAATAT
Found at i:2524588 original size:31 final size:30
Alignment explanation
Indices: 2524553--2524625 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
2524543 ATTTCAGTCC
*
2524553 CTTATATTATTAATTTATTAAATTTTGATCA
1 CTTATATTATCAA-TTATTAAATTTTGATCA
* * *
2524584 CTTATGTTATCGATTATTATATTTTGATCA
1 CTTATATTATCAATTATTAAATTTTGATCA
*
2524614 CTGAT-TTATCAA
1 CTTATATTATCAA
2524626 CTTCCTTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 6 0.17
30 20 0.56
31 10 0.28
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (30 bp):
CTTATATTATCAATTATTAAATTTTGATCA
Found at i:2524608 original size:30 final size:29
Alignment explanation
Indices: 2524567--2524623 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
2524557 TATTATTAAT
*
2524567 TTATTAAATTTTGATCACTTATGTTATCGA
1 TTATTAAATTTTGATCACTGAT-TTATCGA
*
2524597 TTATTATATTTTGATCACTGATTTATC
1 TTATTAAATTTTGATCACTGATTTATC
2524624 AACTTCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (29 bp):
TTATTAAATTTTGATCACTGATTTATCGA
Found at i:2524832 original size:24 final size:24
Alignment explanation
Indices: 2524805--2524856 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2524795 CGTTCATTTA
* *
2524805 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
2524829 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
2524853 CGTT
1 CGTT
2524857 TATGTTCTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:2524843 original size:14 final size:14
Alignment explanation
Indices: 2524826--2524856 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2524816 GTTCGGTTAT
*
2524826 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
2524840 GTTCGATTATGTTC
1 GTTCGATTATGTTC
2524854 GTT
1 GTT
2524857 TATGTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:2524857 original size:24 final size:24
Alignment explanation
Indices: 2524815--2524876 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
2524805 CGTTCGTGAA
*
2524815 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
2524839 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
2524863 CTTTC-ATTTATGTT
1 CGTTCGA-TTATGTT
2524877 TAACCCAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.11, C:0.13, G:0.19, T:0.56
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:2525877 original size:10 final size:10
Alignment explanation
Indices: 2525862--2525931 Score: 60
Period size: 10 Copynumber: 7.2 Consensus size: 10
2525852 TCCAGTGTTG
2525862 ATGTTCGTTT
1 ATGTTCGTTT
2525872 ATGTTCGTGTT
1 ATGTTCGT-TT
* *
2525883 CAT-TTATGTTC
1 -ATGTT-CGTTT
2525894 ATGTTCGTTT
1 ATGTTCGTTT
2525904 ATGTTCG---
1 ATGTTCGTTT
2525911 -TGTTCGTTT
1 ATGTTCGTTT
2525920 ATGTTCGTTT
1 ATGTTCGTTT
2525930 AT
1 AT
2525932 TTATTAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
6 6 0.12
10 31 0.65
11 7 0.15
12 4 0.08
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:2525882 original size:16 final size:16
Alignment explanation
Indices: 2525863--2525927 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
2525853 CCAGTGTTGA
2525863 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
2525879 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
2525895 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2525911 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2525927 T
1 T
2525928 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2526018 original size:16 final size:16
Alignment explanation
Indices: 2525997--2526027 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2525987 AAAAAAAATT
2525997 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2526013 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
2526028 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2526215 original size:2 final size:2
Alignment explanation
Indices: 2526208--2526260 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2526198 GGTACTTACT
2526208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2526250 TA TA TA TA TA T
1 TA TA TA TA TA T
2526261 GAAAAGTACT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2528292 original size:26 final size:26
Alignment explanation
Indices: 2528241--2528308 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
2528231 TACATTAAAT
*
2528241 ATTTAATACATAGCA-TTTTTGTTAC
1 ATTTATTACATAGCATTTTTTGTTAC
*
2528266 ATTTATTATATAGCATTTTTTGTTAC
1 ATTTATTACATAGCATTTTTTGTTAC
2528292 ATTTATTACATAGCATT
1 ATTTATTACATAGCATT
2528309 AAAATTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 13 0.33
26 26 0.67
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.51
Consensus pattern (26 bp):
ATTTATTACATAGCATTTTTTGTTAC
Found at i:2529257 original size:3 final size:3
Alignment explanation
Indices: 2529246--2529279 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2529236 AAAAAAATAA
2529246 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2529280 AAATTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2535505 original size:89 final size:89
Alignment explanation
Indices: 2535354--2535561 Score: 321
Period size: 89 Copynumber: 2.3 Consensus size: 89
2535344 GCAAAAATAT
* * *
2535354 AACCAACCTAAGGATATTCCTTGGGGCCTATGGGCCTACCCAAGGGTATCATTAGATCCGTAGGG
1 AACCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCAAAGGGCATCATTAGATCCGTAGGG
** *
2535419 TTACCCT-AAGCAC-CTAGTAAAGGG
66 TTA-CCTGAAGCACAC-AACAAAGGA
*
2535443 AACCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCAAAGGGCATCCTTAGATCCGTAGGG
1 AACCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCAAAGGGCATCATTAGATCCGTAGGG
2535508 TTACCTGAAGCACACAACAAAGGA
66 TTACCTGAAGCACACAACAAAGGA
2535532 AACCAACCTAAGGATATGCCTTGGGGCCTA
1 AACCAACCTAAGGATATGCCTTGGGGCCTA
2535562 CCCAAGGATA
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
88 3 0.03
89 106 0.96
90 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (89 bp):
AACCAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCAAAGGGCATCATTAGATCCGTAGGG
TTACCTGAAGCACACAACAAAGGA
Found at i:2548757 original size:54 final size:54
Alignment explanation
Indices: 2548692--2548850 Score: 264
Period size: 54 Copynumber: 2.9 Consensus size: 54
2548682 CACTGACAAG
* *
2548692 AAATCTGGGCAGAAGCCATAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
1 AAATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGA
*
2548746 AAATCTAGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGA
1 AAATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGA
* * *
2548800 AAATCTGGGTAGAAACCACAGGAAATGATGCATGTGTTGTCAAATGTTTTA
1 AAATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTA
2548851 TGAACCAATG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (54 bp):
AAATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGA
Found at i:2549396 original size:25 final size:25
Alignment explanation
Indices: 2549362--2549420 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
2549352 GAGTTCCACA
2549362 AATGAAACATTTCTTTTGAGGCTTT
1 AATGAAACATTTCTTTTGAGGCTTT
2549387 AATGAAACATTTCTTTTGAGGCTTT
1 AATGAAACATTTCTTTTGAGGCTTT
2549412 AATGAAACA
1 AATGAAACA
2549421 AAGAAAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (25 bp):
AATGAAACATTTCTTTTGAGGCTTT
Found at i:2549857 original size:54 final size:54
Alignment explanation
Indices: 2549799--2549971 Score: 199
Period size: 54 Copynumber: 3.2 Consensus size: 54
2549789 TGTGTTTTTT
2549799 AGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATCATTTT-AAATGAGTTTTCAA
1 AGAAACTAAGTCCGATTTTCAGAAGTTTCTTGAT-ATTTTCAAATGAGTTTTCAA
* *
2549853 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGAAGATTTTCAAAT-ATGTTTT-AA
1 AGAAACTAAGTCCGATTTTCAGAAGTTTCTTG-ATATTTTCAAATGA-GTTTTCAA
* * * * * ***
2549907 AGAAACTAAGTCCAATTTTTAAAAGTTTCATGATTTTTATCAAATGAACATTCAA
1 AGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATATTT-TCAAATGAGTTTTCAA
2549962 AGAAACTAAG
1 AGAAACTAAG
2549972 CTTTCGGGGG
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
53 4 0.04
54 74 0.73
55 23 0.23
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (54 bp):
AGAAACTAAGTCCGATTTTCAGAAGTTTCTTGATATTTTCAAATGAGTTTTCAA
Found at i:2550571 original size:105 final size:105
Alignment explanation
Indices: 2550366--2550886 Score: 731
Period size: 105 Copynumber: 4.9 Consensus size: 105
2550356 AAAGATTATG
* * * *
2550366 ATTCACCATAGAA-AAGGTAAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTA
1 ATTCACCACAGAATGAGGTGAACCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCGTCCTA
* * *
2550430 AAGGAGAAAGTTCATAATGAGAAGAACTTTTTCCTTTAAA
66 AAGGAGAAAGTTCATAATGAGAAGAACTTGTCCCTTTCAA
2550470 ATTCACCACAGAATGAGGTGAACCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCGTCCTA
1 ATTCACCACAGAATGAGGTGAACCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCGTCCTA
*
2550535 AAGAAGAAAGTTCATAATGAGAAGAACTTGTCCCTTTCAA
66 AAGGAGAAAGTTCATAATGAGAAGAACTTGTCCCTTTCAA
* * *
2550575 ATTCACCACAGAATGAGGTGAACCAATATTTCCAGAGGAGTTTATAATGAAAAGAACTCGTCCTA
1 ATTCACCACAGAATGAGGTGAACCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCGTCCTA
2550640 AAGGAGAAAGTTCATAATGAGAAGAACTTGTCCCTTTCAA
66 AAGGAGAAAGTTCATAATGAGAAGAACTTGTCCCTTTCAA
* * * * * * * **
2550680 GTCCACCGCAGAAGGAGATGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCACCCTA
1 ATTCACCACAGAATGAGGTGAACCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCGTCCTA
*
2550745 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
66 AAGGAGAAAGTTCATAATGAGAAGAACTTGTCCCTTTCAA
* * * * *
2550785 ATTCACCACAGAATGAGGTGGATCAACATTTCCAGTTGAGAGTTTATAATGAGAAGAACTCATCC
1 ATTCACCACAGAATGAGGTGAACCAACATTTCCAG-AG-GAGTTCATAATGAGAAGAACTCGTCC
2550850 -AATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
64 TAA--AGG-AG-A-AAGTTCATAATGAGAAGAACTTGT
2550887 TCAACCTTGC
Statistics
Matches: 374, Mismatches: 35, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
104 12 0.03
105 306 0.82
106 2 0.01
107 24 0.06
108 3 0.01
109 2 0.01
110 1 0.00
111 24 0.06
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (105 bp):
ATTCACCACAGAATGAGGTGAACCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCGTCCTA
AAGGAGAAAGTTCATAATGAGAAGAACTTGTCCCTTTCAA
Found at i:2550917 original size:91 final size:91
Alignment explanation
Indices: 2550813--2551208 Score: 702
Period size: 91 Copynumber: 4.4 Consensus size: 91
2550803 TGGATCAACA
* *
2550813 TTTCCAGTTGAGAGTTTATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGA
2550878 AGAACTTGTTCAACCTTGCATCAGTG
66 AGAACTTGTTCAACCTTGCATCAGTG
* *
2550904 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCAATGAGGAATAAGAAGTTCATAATGAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGA
*
2550969 ATAACTTGTTCAACCTTGCATCAGTG
66 AGAACTTGTTCAACCTTGCATCAGTG
* *
2550995 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGTGGAAGAAGAAGTTCATAATTAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGA
2551060 AGAACTTGTTCAACCTTGCATCAGTG
66 AGAACTTGTTCAACCTTGCATCAGTG
* *
2551086 TTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGA
2551151 AGAACTTGTTCAACCTTGCATCAGTG
66 AGAACTTGTTCAACCTTGCATCAGTG
*
2551177 TTTCCAGTGAAGAGTTCATAATGAGAAGAACT
1 TTTCCAGTGGAGAGTTCATAATGAGAAGAACT
2551209 TGTTCAATCC
Statistics
Matches: 289, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 289 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (91 bp):
TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTGCATCAGTG
Found at i:2550979 original size:20 final size:20
Alignment explanation
Indices: 2550916--2550980 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
2550906 TCCAGTGGAG
*
2550916 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAATAACT
**
2550936 CA-TTC--AATGAGGAATAAGA
1 -AGTTCATAATGA-GAATAACT
2550955 AGTTCATAATGAGAATAACT
1 AGTTCATAATGAGAATAACT
*
2550975 TGTTCA
1 AGTTCA
2550981 ACCTTGCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 14 0.41
21 6 0.18
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTTCATAATGAGAATAACT
Found at i:2553097 original size:42 final size:42
Alignment explanation
Indices: 2553050--2553160 Score: 186
Period size: 42 Copynumber: 2.6 Consensus size: 42
2553040 CCGAAATCTT
* * *
2553050 GTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATATTTTCCC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATTTTCCC
*
2553092 GTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATTTTCCC
2553134 GTGTTTGTTTCACGTAATTCGTTTTCC
1 GTGTTTGTTTCACGTAATTCGTTTTCC
2553161 AGAATGTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATTTTCCC
Found at i:2553379 original size:10 final size:10
Alignment explanation
Indices: 2553364--2553409 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
2553354 TATTTAAAAT
2553364 ATATTTATTA
1 ATATTTATTA
2553374 ATATTTATAATA
1 ATATTTAT--TA
2553386 ATATTATATT-
1 ATATT-TATTA
2553396 ATATTT-TTA
1 ATATTTATTA
2553405 ATATT
1 ATATT
2553410 ATATAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 13 0.41
11 1 0.03
12 7 0.22
13 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTATTA
Found at i:2553389 original size:22 final size:23
Alignment explanation
Indices: 2553344--2553413 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
2553334 CAAAATATTA
*
2553344 ATTAT-TTAAATATTTAAAAT-AT
1 ATTATATT-AATATTTATAATAAT
2553366 ATT-TATTAATATTTATAATAAT
1 ATTATATTAATATTTATAATAAT
2553388 ATTATATT-ATATTT-T--TAAT
1 ATTATATTAATATTTATAATAAT
2553407 ATTATAT
1 ATTATAT
2553414 AAAATAATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 11 0.25
21 13 0.30
22 16 0.36
23 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTATATTAATATTTATAATAAT
Found at i:2553397 original size:26 final size:24
Alignment explanation
Indices: 2553335--2553397 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 24
2553325 TATTTTCATC
2553335 AAAATATTA-ATTATTTAAATATTT
1 AAAATATTATATTA-TTAAATATTT
2553359 AAAATA-TAT-TTATT-AATATTTAT
1 AAAATATTATATTATTAAATA-TT-T
2553382 AATAATATTATATTAT
1 AA-AATATTATATTAT
2553398 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 8 0.24
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAAATATTATATTATTAAATATTT
Found at i:2553409 original size:31 final size:31
Alignment explanation
Indices: 2553363--2553530 Score: 133
Period size: 31 Copynumber: 5.6 Consensus size: 31
2553353 ATATTTAAAA
*
2553363 TATATTTATTAATATTTATAATAATATTATAT
1 TATATTT-TTAATATATATAATAATATTATAT
*
2553395 TATATTTTTAATATTATATAA-AATAATCA-AT
1 TATATTTTTAATA-TATATAATAAT-ATTATAT
*
2553426 TATA-TTATAATA-ATATAA-AATATTATAT
1 TATATTTTTAATATATATAATAATATTATAT
* * *
2553454 T-TTTATTTTAATAATATATAATAA-ATTTTTT
1 TATAT-TTTTAAT-ATATATAATAATATTATAT
* *
2553485 TATATATTTAATA-AT-GAATAATATTAT-T
1 TATATTTTTAATATATATAATAATATTATAT
2553513 TATATATTTTAATA-ATAT
1 TATAT-TTTTAATATATAT
2553531 TTTAATAAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 26
0.73 0.09 0.17
Matches are distributed among these distances:
27 4 0.04
28 23 0.21
29 21 0.19
30 9 0.08
31 33 0.30
32 20 0.18
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TATATTTTTAATATATATAATAATATTATAT
Found at i:2553496 original size:28 final size:29
Alignment explanation
Indices: 2553426--2553528 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 29
2553416 AATAATCAAT
* *
2553426 TATATTATAATAAT-ATAAAATATTATATT-
1 TATATTTTAATAATGA-ATAATATTAT-TTA
* *
2553455 TTTATTTTAATAAT-ATATAATAAATT-TTTT
1 TATATTTTAATAATGA-ATAAT--ATTATTTA
2553485 TATATATTTAATAATGAATAATATTATTTA
1 TATAT-TTTAATAATGAATAATATTATTTA
2553515 TATATTTTAATAAT
1 TATATTTTAATAAT
2553529 ATTTTAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
29 32 0.51
30 13 0.21
31 17 0.27
32 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TATATTTTAATAATGAATAATATTATTTA
Found at i:2553508 original size:19 final size:19
Alignment explanation
Indices: 2553486--2553538 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
2553476 AAATTTTTTT
2553486 ATATATTTAATAATGAATA
1 ATATATTTAATAATGAATA
* *
2553505 ATATTATTTATATATTTTAATA
1 ATA-TATTTA-ATA-ATGAATA
2553527 ATAT-TTTAATAA
1 ATATATTTAATAA
2553539 AAATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATATTTAATAATGAATA
Found at i:2553530 original size:11 final size:11
Alignment explanation
Indices: 2553501--2553538 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2553491 TTTAATAATG
2553501 AATAATATTATT
1 AATAATATT-TT
*
2553513 TAT-ATATTTT
1 AATAATATTTT
2553523 AATAATATTTT
1 AATAATATTTT
2553534 AATAA
1 AATAA
2553539 AAATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:2553559 original size:23 final size:23
Alignment explanation
Indices: 2553533--2553577 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2553523 AATAATATTT
2553533 TAATAAAAATATTTAAAATATAC
1 TAATAAAAATATTTAAAATATAC
* * *
2553556 TAATTAATATTTTTAAAATATA
1 TAATAAAAATATTTAAAATATA
2553578 ACATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAAATATTTAAAATATAC
Found at i:2553941 original size:15 final size:15
Alignment explanation
Indices: 2553905--2553960 Score: 87
Period size: 15 Copynumber: 3.8 Consensus size: 15
2553895 TTCCGGAAAT
2553905 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
2553920 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
2553934 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
2553949 GTAATTCATTTT
1 GTAATTCATTTT
2553961 GAAAAACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 12 0.33
15 24 0.67
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:2560704 original size:24 final size:24
Alignment explanation
Indices: 2560677--2560724 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2560667 AAAAATTCAA
2560677 CAATTTCCAACTACTTTTCGGTGC
1 CAATTTCCAACTACTTTTCGGTGC
*
2560701 CAATTTCCAGCTACTTTTCGGTGC
1 CAATTTCCAACTACTTTTCGGTGC
2560725 TTTAATTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.38
Consensus pattern (24 bp):
CAATTTCCAACTACTTTTCGGTGC
Found at i:2561564 original size:17 final size:17
Alignment explanation
Indices: 2561542--2561585 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2561532 ATGTAAAAAT
2561542 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
2561559 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
2561576 AAATATTTAA
1 AAATATTTAA
2561586 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:2568004 original size:2 final size:2
Alignment explanation
Indices: 2567999--2568032 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2567989 TTATTGAACA
2567999 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
2568033 TTGTAAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2568161 original size:14 final size:13
Alignment explanation
Indices: 2568128--2568160 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2568118 TAAGCTAAAA
*
2568128 ATATTTTTATTAT
1 ATATTTTTAATAT
2568141 ATATTTTTAATAT
1 ATATTTTTAATAT
2568154 -TATTTTT
1 ATATTTTT
2568161 TGGAATAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATATTTTTAATAT
Found at i:2572463 original size:17 final size:18
Alignment explanation
Indices: 2572438--2572471 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2572428 ATCTTATAAT
2572438 AATACATTTA-TTGAATA
1 AATACATTTATTTGAATA
*
2572455 AATATATTTATTTGAAT
1 AATACATTTATTTGAAT
2572472 TCAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (18 bp):
AATACATTTATTTGAATA
Found at i:2572711 original size:4 final size:4
Alignment explanation
Indices: 2572702--2572798 Score: 178
Period size: 4 Copynumber: 24.5 Consensus size: 4
2572692 GTGAACCGGC
2572702 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
*
2572750 AGTG AGTG AGTG AGTG ACTG AGT- AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
2572797 AG
1 AG
2572799 AGTTGTTCAC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 3 0.03
4 87 0.97
ACGTcount: A:0.26, C:0.01, G:0.48, T:0.25
Consensus pattern (4 bp):
AGTG
Found at i:2574022 original size:27 final size:28
Alignment explanation
Indices: 2573972--2574028 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
2573962 AAAATAGGAG
2573972 TAAACTTATGACACACGACTAATCTCATA
1 TAAACTTATGACACAC-ACTAATCTCATA
2574001 TAAACTTATGACACA-ACTAATCTCATA
1 TAAACTTATGACACACACTAATCTCATA
2574028 T
1 T
2574029 CCAATTGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 13 0.46
29 15 0.54
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (28 bp):
TAAACTTATGACACACACTAATCTCATA
Found at i:2574961 original size:2 final size:2
Alignment explanation
Indices: 2574954--2574979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2574944 ATTATTATTA
2574954 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
2574980 TACAAGCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2576898 original size:17 final size:18
Alignment explanation
Indices: 2576862--2576900 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2576852 TCATTTTCTG
2576862 ATATTTCTATATAAATAA
1 ATATTTCTATATAAATAA
* *
2576880 ATATTT-TATTTATATAA
1 ATATTTCTATATAAATAA
2576897 ATAT
1 ATAT
2576901 ATATAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTCTATATAAATAA
Found at i:2576907 original size:31 final size:31
Alignment explanation
Indices: 2576869--2576929 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2576859 CTGATATTTC
*
2576869 TATATAAATAAATATTTTAT-TTATATAAATA
1 TATATAAATAAATATATTATATTA-ATAAATA
*
2576900 TATATAAATTAATATATTATATTAATAAAT
1 TATATAAATAAATATATTATATTAATAAAT
2576930 TTGAAATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TATATAAATAAATATATTATATTAATAAATA
Found at i:2577432 original size:28 final size:27
Alignment explanation
Indices: 2577401--2577454 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
2577391 TAATTCTTTC
*
2577401 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
*
2577429 TTTTCATAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
2577455 TTATTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:2577462 original size:24 final size:22
Alignment explanation
Indices: 2577423--2577477 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
2577413 TTATATATAC
2577423 TTATTATTTTCATAATATTTATA
1 TTATTATTTTCATAATATTT-TA
*
2577446 TATATTATTTT-ATTAATGTTTTA
1 T-TATTATTTTCA-TAATATTTTA
2577469 TT-TTATTTT
1 TTATTATTTT
2577478 TCAAGTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
23 5 0.17
24 16 0.55
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTTTCATAATATTTTA
Found at i:2581831 original size:7 final size:8
Alignment explanation
Indices: 2581812--2581861 Score: 55
Period size: 8 Copynumber: 5.8 Consensus size: 8
2581802 TACTTGAAAA
2581812 AAAAAAGG
1 AAAAAAGG
2581820 AAAAAAGG
1 AAAAAAGG
*
2581828 AAAAAAAAAGA
1 ---AAAAAAGG
2581839 AAAAAAGGG
1 AAAAAA-GG
2581848 AAAAAAGG
1 AAAAAAGG
2581856 AAAAAA
1 AAAAAA
2581862 TTGAACCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 22 0.61
9 7 0.19
11 7 0.19
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:2581833 original size:19 final size:19
Alignment explanation
Indices: 2581809--2581861 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
2581799 TTATACTTGA
2581809 AAAAAAAAAGGAAAAAAGG
1 AAAAAAAAAGGAAAAAAGG
*
2581828 AAAAAAAAAGAAAAAAAGG
1 AAAAAAAAAGGAAAAAAGG
*
2581847 --GAAAAAAGGAAAAAA
1 AAAAAAAAAGGAAAAAA
2581862 TTGAACCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 13 0.42
19 18 0.58
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGGAAAAAAGG
Found at i:2586215 original size:20 final size:22
Alignment explanation
Indices: 2586169--2586248 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
2586159 TACATCTACA
*
2586169 CTCTTCAAAGATGATAGATTCT
1 CTCTCCAAAGATGATAGATTCT
2586191 CTCTCCAAAGATGATAGATTCT
1 CTCTCCAAAGATGATAGATTCT
2586213 CTCTCCAAAGATGATAGATTCT
1 CTCTCCAAAGATGATAGATTCT
* *
2586235 CTTTTCAAAGATGA
1 CTCTCCAAAGATGA
2586249 AAGTTTTATT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCTCCAAAGATGATAGATTCT
Found at i:2587262 original size:113 final size:113
Alignment explanation
Indices: 2587064--2587691 Score: 837
Period size: 113 Copynumber: 5.6 Consensus size: 113
2587054 TTTCCAGAAG
* *
2587064 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
** * *
2587128 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGCATTGCCAGGTAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTGCCAGGTAA
*
2587176 AGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * **
2587241 AACCTTTTGCTTGAATTCATCACTCGATGGATCAACATTTCCAGAAAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTGCCAGGTAA
* * ** *
2587289 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCCTAATGAGAAGAGCTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
2587354 AACCCTTTGTTTGAATTCATCATTTGATGGATCAGCGTTACCAGGTAG
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTGCCAGGTAA
*
2587402 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
2587467 AA-C--TT--TT---TTCATCATTTGATGGATCAGCGTTGCCAGGTAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTGCCAGGTAA
* * *
2587507 AGCTCATAATGAGAAGAACTCATCTTAAGAAGGAAGAAGAAGTTCATAATGAAAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * *
2587572 AACCTTTTGTTTGAATTCATCACTCGATGGATCA-AATTTTCCAGATAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCAGCA-TTGCCAGGTAA
* *
2587620 GAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTT
1 -AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
2587684 CAACCTTT
65 CAACCTTT
2587692 GTTTGACTCT
Statistics
Matches: 454, Mismatches: 51, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
105 94 0.21
106 1 0.00
108 4 0.01
110 4 0.01
112 29 0.06
113 296 0.65
114 26 0.06
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTGCCAGGTAA
Found at i:2587656 original size:218 final size:221
Alignment explanation
Indices: 2587067--2587687 Score: 815
Period size: 218 Copynumber: 2.8 Consensus size: 221
2587057 CCAGAAGAGT
*
2587067 TCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* ** * * * *
2587131 CTTTTGCTCAAATCCATCACTTGATGGATTAGCATTGCCAGGTAA-AGTTCATAATGAGAAGAAC
66 CTTTTGTTTGAATTCATCACTTGATGGATCA-AATTACCAGGTAAGAGTTCATAATGAGAAGAAC
*
2587195 TCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCA
130 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-C-TTT-CTT--ATTCA
* *
2587260 TCACTCGATGGATCAACATTTCCAGAAAAAGT
190 TCACTCGATGGATCAACATTGCCAGAAAAAGC
* * * *
2587292 TCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCCTAATGAGAAGAGCTTGTTTAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * **
2587357 CCTTTGTTTGAATTCATCATTTGATGGATCAGCGTTACCAGGT-AGAGTTCATAATGAGAAGAAC
66 CTTTTGTTTGAATTCATCACTTGATGGATCA-AATTACCAGGTAAGAGTTCATAATGAGAAGAAC
* *
2587421 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC-TT-TT-TTCATCATT
130 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTCTTATTCATCACT
* * * **
2587483 TGATGGATCAGCGTTGCCAGGTAAAGC
195 CGATGGATCAACATTGCCAGAAAAAGC
* * *
2587510 TCATAATGAGAAGAACTCATCTTAAGAAGGAAGAAGAAGTTCATAATGAAAAGAATTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * *
2587575 CTTTTGTTTGAATTCATCACTCGATGGATCAAATTTTCCAGATAAGAGTTCATAATGAGAAGAAC
66 CTTTTGTTTGAATTCATCACTTGATGGATCAAA-TTACCAGGTAAGAGTTCATAATGAGAAGAAC
* *
2587640 TTATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAAC
130 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
2587688 CTTTGTTTGA
Statistics
Matches: 351, Mismatches: 41, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
218 157 0.45
219 30 0.09
221 2 0.01
223 2 0.01
225 27 0.08
226 133 0.38
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (221 bp):
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTTGTTTGAATTCATCACTTGATGGATCAAATTACCAGGTAAGAGTTCATAATGAGAAGAACT
CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTCTTATTCATCACTC
GATGGATCAACATTGCCAGAAAAAGC
Found at i:2588308 original size:124 final size:122
Alignment explanation
Indices: 2588009--2588326 Score: 408
Period size: 124 Copynumber: 2.6 Consensus size: 122
2587999 AACGTTGCCG
* * *
2588009 GAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTT
1 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTT
* * * * * *
2588074 GTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAATACCAACTTTTCCA
66 GTTCAACCTTTTGCATGATCCTATCACAAAAAGAAATAAAGCAATACCAAC-TTTCCA
* *
2588132 GAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTT
1 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTT
* * * *
2588197 GTTCAACCTTTTGCTTGACTCCATTTC-CAAAAAGAAATAAAGCAGCATAGCTA-TTTCCA
66 GTTCAACCTTTTGCATGA-TCC-TATCACAAAAAGAAATAAAGCA--ATACCAACTTTCCA
* *
2588256 G-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATAAGAAGAACT
1 GAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACT
2588320 TGTTCAA
65 TGTTCAA
2588327 TCTTGCATTG
Statistics
Matches: 171, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
123 78 0.46
124 85 0.50
125 3 0.02
126 5 0.03
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (122 bp):
GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTT
GTTCAACCTTTTGCATGATCCTATCACAAAAAGAAATAAAGCAATACCAACTTTCCA
Found at i:2590633 original size:17 final size:18
Alignment explanation
Indices: 2590597--2590635 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2590587 TCCTTTTCTG
2590597 ATATTTCTATATAAATAA
1 ATATTTCTATATAAATAA
* *
2590615 ATATTT-TATTTATATAA
1 ATATTTCTATATAAATAA
2590632 ATAT
1 ATAT
2590636 ATATAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTCTATATAAATAA
Found at i:2590642 original size:31 final size:31
Alignment explanation
Indices: 2590604--2590664 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2590594 CTGATATTTC
*
2590604 TATATAAATAAATATTTTAT-TTATATAAATA
1 TATATAAATAAATATATTATATTA-ATAAATA
*
2590635 TATATAAATTAATATATTATATTAATAAAT
1 TATATAAATAAATATATTATATTAATAAAT
2590665 TTGAAATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TATATAAATAAATATATTATATTAATAAATA
Found at i:2593496 original size:25 final size:25
Alignment explanation
Indices: 2593466--2593514 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2593456 CACTATTGAT
**
2593466 TTAGGCACAACGTCGTAATTGATGC
1 TTAGGCACAACGTCACAATTGATGC
*
2593491 TTAGGCACAGCGTCACAATTGATG
1 TTAGGCACAACGTCACAATTGATG
2593515 TTTTACACGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (25 bp):
TTAGGCACAACGTCACAATTGATGC
Found at i:2595858 original size:16 final size:18
Alignment explanation
Indices: 2595837--2595869 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2595827 ATTTAAGTAT
2595837 TAAA-TTTATT-ATTATA
1 TAAATTTTATTAATTATA
2595853 TAAATTTTATTAATTAT
1 TAAATTTTATTAATTAT
2595870 TATATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAAATTTTATTAATTATA
Found at i:2598077 original size:39 final size:39
Alignment explanation
Indices: 2598034--2598111 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
2598024 GTCTGCTATC
2598034 GAAACATATATCTTCTTTTCTTTTCTCAAGGTTGAATTT
1 GAAACATATATCTTCTTTTCTTTTCTCAAGGTTGAATTT
*
2598073 GAAACATGTATCTTCTTTTCTTTTCTCAAGGTTGAATTT
1 GAAACATATATCTTCTTTTCTTTTCTCAAGGTTGAATTT
2598112 AGCCATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (39 bp):
GAAACATATATCTTCTTTTCTTTTCTCAAGGTTGAATTT
Found at i:2600000 original size:35 final size:35
Alignment explanation
Indices: 2599961--2600029 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
2599951 GAAGTCTTTG
2599961 TAGGTTCAGCACCGAT-AAGCTAGTAATTCCTTATA
1 TAGGTTCAGCACCGATCAA-CTAGTAATTCCTTATA
* *
2599996 TAGGTTCAGCACCGATCAACTGGTAATTTCTTAT
1 TAGGTTCAGCACCGATCAACTAGTAATTCCTTAT
2600030 GGACCTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 29 0.94
36 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (35 bp):
TAGGTTCAGCACCGATCAACTAGTAATTCCTTATA
Found at i:2600898 original size:365 final size:365
Alignment explanation
Indices: 2600228--2600953 Score: 1443
Period size: 365 Copynumber: 2.0 Consensus size: 365
2600218 GGTGCTCCCT
2600228 TAGGTTGACACCTAGGCCCTTTGGGCCTAGGGTAAGTCCTTATGGATGCAGTTCTGGAAAACTGC
1 TAGGTTGACACCTAGGCCCTTTGGGCCTAGGGTAAGTCCTTATGGATGCAGTTCTGGAAAACTGC
2600293 ATATGATGTTCGATTGGAGGGCGATTCTATATTTTAAGCTAAAAACACTACTGACGTTTTCATAA
66 ATATGATGTTCGATTGGAGGGCGATTCTATATTTTAAGCTAAAAACACTACTGACGTTTTCATAA
2600358 CTTGAAGTTGAACTGATTTGGAAACTTAACTGTAAGTTTTATTTCTGCATTGTTGGAACACACTG
131 CTTGAAGTTGAACTGATTTGGAAACTTAACTGTAAGTTTTATTTCTGCATTGTTGGAACACACTG
2600423 AGCTCCCTAGCTCACTCCCCCCAAACTTTTCTCTTTCAGATACTTTTTGATAGGCGACCCAGACC
196 AGCTCCCTAGCTCACTCCCCCCAAACTTTTCTCTTTCAGATACTTTTTGATAGGCGACCCAGACC
2600488 TGGTACTTGGAGGATCGACACATTCGTACAAGATTATTTTGTTGTAATGATTTTATCTTATGAGT
261 TGGTACTTGGAGGATCGACACATTCGTACAAGATTATTTTGTTGTAATGATTTTATCTTATGAGT
2600553 TACATTTATTTTGGGTGGCATGTGCCTATATTTTGACACC
326 TACATTTATTTTGGGTGGCATGTGCCTATATTTTGACACC
*
2600593 TAGGTTGACACCTAGGCCCTTTGGGCCTAGGGTAAGTCCTTATGGATGCAGTTCTGGGAAACTGC
1 TAGGTTGACACCTAGGCCCTTTGGGCCTAGGGTAAGTCCTTATGGATGCAGTTCTGGAAAACTGC
2600658 ATATGATGTTCGATTGGAGGGCGATTCTATATTTTAAGCTAAAAACACTACTGACGTTTTCATAA
66 ATATGATGTTCGATTGGAGGGCGATTCTATATTTTAAGCTAAAAACACTACTGACGTTTTCATAA
2600723 CTTGAAGTTGAACTGATTTGGAAACTTAACTGTAAGTTTTATTTCTGCATTGTTGGAACACACTG
131 CTTGAAGTTGAACTGATTTGGAAACTTAACTGTAAGTTTTATTTCTGCATTGTTGGAACACACTG
2600788 AGCTCCCTAGCTCACTCCCCCCAAACTTTTCTCTTTCAGATACTTTTTGATAGGCGACCCAGACC
196 AGCTCCCTAGCTCACTCCCCCCAAACTTTTCTCTTTCAGATACTTTTTGATAGGCGACCCAGACC
2600853 TGGTACTTGGAGGATCGACACATTCGTACAAGATTATTTTGTTGTAATGATTTTATCTTATGAGT
261 TGGTACTTGGAGGATCGACACATTCGTACAAGATTATTTTGTTGTAATGATTTTATCTTATGAGT
2600918 TACATTTATTTTGGGTGGCATGTGCCTATATTTTGA
326 TACATTTATTTTGGGTGGCATGTGCCTATATTTTGA
2600954 AAATACTTGT
Statistics
Matches: 360, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
365 360 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (365 bp):
TAGGTTGACACCTAGGCCCTTTGGGCCTAGGGTAAGTCCTTATGGATGCAGTTCTGGAAAACTGC
ATATGATGTTCGATTGGAGGGCGATTCTATATTTTAAGCTAAAAACACTACTGACGTTTTCATAA
CTTGAAGTTGAACTGATTTGGAAACTTAACTGTAAGTTTTATTTCTGCATTGTTGGAACACACTG
AGCTCCCTAGCTCACTCCCCCCAAACTTTTCTCTTTCAGATACTTTTTGATAGGCGACCCAGACC
TGGTACTTGGAGGATCGACACATTCGTACAAGATTATTTTGTTGTAATGATTTTATCTTATGAGT
TACATTTATTTTGGGTGGCATGTGCCTATATTTTGACACC
Found at i:2603184 original size:42 final size:40
Alignment explanation
Indices: 2603074--2603184 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 40
2603064 TTATTGTCGT
* * *
2603074 TACAAATCACCAATTAAGACTAGTGACAAAAACAATTATC
1 TACAAATCAACAACTAAGACTAGTGACAAAAACAATTAGC
*
2603114 TAC--A-CAACTTACTAAGACTAGTGACAAAAACAATTAGC
1 TACAAATCAAC-AACTAAGACTAGTGACAAAAACAATTAGC
*
2603152 GTCACAAATCAACAACTAAGACTAGTGCCAAAA
1 -T-ACAAATCAACAACTAAGACTAGTGACAAAA
2603185 TGTTTTCATC
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
37 3 0.05
38 27 0.46
39 1 0.02
40 5 0.08
42 19 0.32
43 4 0.07
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.20
Consensus pattern (40 bp):
TACAAATCAACAACTAAGACTAGTGACAAAAACAATTAGC
Found at i:2608063 original size:19 final size:19
Alignment explanation
Indices: 2608022--2608067 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2608012 ATGATTTCCT
* *
2608022 TTTGAAAACAAAATTAGAT
1 TTTGAAAACAAAATAAGAC
2608041 TTTGAAAACAAAATGAAG-C
1 TTTGAAAACAAAAT-AAGAC
2608060 TTTGAAAA
1 TTTGAAAA
2608068 ATGATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (19 bp):
TTTGAAAACAAAATAAGAC
Found at i:2608361 original size:25 final size:25
Alignment explanation
Indices: 2608327--2608378 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2608317 CCGTATAGGA
2608327 CCCAAAGCAATTTGGGTACCAAAAT
1 CCCAAAGCAATTTGGGTACCAAAAT
2608352 CCCAAAGCAATTTGGGTACCAAAAT
1 CCCAAAGCAATTTGGGTACCAAAAT
2608377 CC
1 CC
2608379 AAATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (25 bp):
CCCAAAGCAATTTGGGTACCAAAAT
Found at i:2608889 original size:24 final size:24
Alignment explanation
Indices: 2608862--2608908 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2608852 TCTCTCTAAT
2608862 AATTGATATCTATATCAAATGCAC
1 AATTGATATCTATATCAAATGCAC
2608886 AATTGATATCTATATCAAATGCA
1 AATTGATATCTATATCAAATGCA
2608909 TGACATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (24 bp):
AATTGATATCTATATCAAATGCAC
Found at i:2609585 original size:31 final size:31
Alignment explanation
Indices: 2609550--2609611 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2609540 AAAGAGGAGA
2609550 GGTTCTAGTTTAGCC-TTAGAAAA-ACTAGAGT
1 GGTTCTAGTTTAGCCATT-GAAAAGA-TAGAGT
*
2609581 GGTTCTATTTTAGCCATTGAAAAGATAGAGT
1 GGTTCTAGTTTAGCCATTGAAAAGATAGAGT
2609612 TGTAAGGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (31 bp):
GGTTCTAGTTTAGCCATTGAAAAGATAGAGT
Found at i:2611380 original size:196 final size:196
Alignment explanation
Indices: 2611041--2611430 Score: 681
Period size: 196 Copynumber: 2.0 Consensus size: 196
2611031 AAATATTTTG
* *
2611041 TCTAAATATGAAATATCAATAGAGCATCTGATATCTTGAGATAAGGTTCAAGTGTGTTCAAATTT
1 TCTAAATATGAAATATCAATAGAGCATCTGATATCTTGAAATAAGATTCAAGTGTGTTCAAATTT
* *
2611106 ATTATTATTTTGGTTATCTTTTAATTAAATTAAAAGATAAATTAAGAGAAATTGATTGGTTGACA
66 ATTATTATTTTGGTAATCTTGTAATTAAATTAAAAGATAAATTAAGAGAAATTGATTGGTTGACA
* *
2611171 CTATTTATATGGTTTTATTTATATTATTAATGTAATATATGTATATATTCAATTTGGTTTTTCAT
131 ATATTTATATGGTTTTATTTATATTATTAATGCAATATATGTATATATTCAATTTGGTTTTTCAT
2611236 T
196 T
* * *
2611237 TCTAAATATGATATATTAATAGAGCATCTGATATCTTGAAATAAGATTTAAGTGTGTTCAAATTT
1 TCTAAATATGAAATATCAATAGAGCATCTGATATCTTGAAATAAGATTCAAGTGTGTTCAAATTT
2611302 ATTATTATTTTGGTAATCTTGTAATTAAATTAAAAGATAAATTAAGAGAAATTGATTGGTTGACA
66 ATTATTATTTTGGTAATCTTGTAATTAAATTAAAAGATAAATTAAGAGAAATTGATTGGTTGACA
* *
2611367 ATATTTCTATGGTTTTATTTATATTGTTAATGCAATATATGTATATATTCAATTTGGTTTTTCA
131 ATATTTATATGGTTTTATTTATATTATTAATGCAATATATGTATATATTCAATTTGGTTTTTCA
2611431 GTTTTGATTG
Statistics
Matches: 183, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
196 183 1.00
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (196 bp):
TCTAAATATGAAATATCAATAGAGCATCTGATATCTTGAAATAAGATTCAAGTGTGTTCAAATTT
ATTATTATTTTGGTAATCTTGTAATTAAATTAAAAGATAAATTAAGAGAAATTGATTGGTTGACA
ATATTTATATGGTTTTATTTATATTATTAATGCAATATATGTATATATTCAATTTGGTTTTTCAT
T
Found at i:2615246 original size:24 final size:23
Alignment explanation
Indices: 2615213--2615268 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
2615203 TACTTTGCTA
2615213 TTTTGAGATTTCAATATTTGGTTGT
1 TTTTG-GATTTCAATATTTGG-TGT
** *
2615238 TTTTGGATTTGGATATTTTGTGT
1 TTTTGGATTTCAATATTTGGTGT
2615261 TTTTGGAT
1 TTTTGGAT
2615269 GATTATTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 11 0.39
24 12 0.43
25 5 0.18
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.59
Consensus pattern (23 bp):
TTTTGGATTTCAATATTTGGTGT
Found at i:2615267 original size:17 final size:17
Alignment explanation
Indices: 2615245--2615293 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
2615235 TGTTTTTGGA
2615245 TTTGGATATTTTGTGTT
1 TTTGGATATTTTGTGTT
2615262 TTTGGATGATTATTTGTGTT
1 TTTGGAT-A-T-TTTGTGTT
*
2615282 TTATAGATATTT
1 TT-TGGATATTT
2615294 ATGGGCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 7 0.26
18 3 0.11
19 2 0.07
20 11 0.41
21 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.20, T:0.61
Consensus pattern (17 bp):
TTTGGATATTTTGTGTT
Found at i:2616388 original size:24 final size:24
Alignment explanation
Indices: 2616334--2616388 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2616324 CCACAGCTAG
* * *
2616334 TATAAATTGCACCGAAGTGTCGCG
1 TATAAATTGCACCGAAGTGCCACA
*
2616358 TAGAAATTGCACCGAAGTGCCACA
1 TATAAATTGCACCGAAGTGCCACA
2616382 TATAAAT
1 TATAAAT
2616389 GTCTTGAAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (24 bp):
TATAAATTGCACCGAAGTGCCACA
Found at i:2616454 original size:23 final size:23
Alignment explanation
Indices: 2616394--2616455 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2616384 TAAATGTCTT
* *
2616394 GAAGGACCACATAGTATTATCCC
1 GAAGGACTACATAGAATTATCCC
* *
2616417 GAAGGACTACGTAGAATTGTCCC
1 GAAGGACTACATAGAATTATCCC
* *
2616440 GAATGACTATATAGAA
1 GAAGGACTACATAGAA
2616456 CCTTCGACTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (23 bp):
GAAGGACTACATAGAATTATCCC
Found at i:2621659 original size:24 final size:21
Alignment explanation
Indices: 2621617--2621659 Score: 50
Period size: 21 Copynumber: 1.9 Consensus size: 21
2621607 TTCTAATATG
*
2621617 TTTTTGTCTTCTTTATTGACC
1 TTTTGGTCTTCTTTATTGACC
2621638 TTTTGGTCGTTCTCTTAGTTGA
1 TTTTGGTC-TTCT-TTA-TTGA
2621660 ATTTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 3 0.17
24 4 0.22
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.58
Consensus pattern (21 bp):
TTTTGGTCTTCTTTATTGACC
Found at i:2635016 original size:3 final size:3
Alignment explanation
Indices: 2635008--2635044 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2634998 TTAAAAAATC
2635008 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2635045 TTGAATTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2635662 original size:11 final size:12
Alignment explanation
Indices: 2635642--2635673 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2635632 TTATAAATTT
2635642 TAATTAATTAAA
1 TAATTAATTAAA
2635654 TAA-TAATT-AA
1 TAATTAATTAAA
2635664 TAATTAATTA
1 TAATTAATTA
2635674 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.28
11 10 0.56
12 3 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTAATTAAA
Found at i:2637313 original size:31 final size:29
Alignment explanation
Indices: 2637269--2637331 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
2637259 AGTTTTGAAG
*
2637269 GTTTGAGGGCTAAAGTATAAACTTTGTAAAA
1 GTTTGAGGGCTAAAATAT-AA-TTTGTAAAA
*
2637300 GTTT-AGGGACTAAAATATAATTTTTAAAA
1 GTTTGAGGG-CTAAAATATAATTTGTAAAA
2637329 GTT
1 GTT
2637332 ATATATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 11 0.38
30 6 0.21
31 12 0.41
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (29 bp):
GTTTGAGGGCTAAAATATAATTTGTAAAA
Found at i:2640002 original size:18 final size:17
Alignment explanation
Indices: 2639965--2640098 Score: 108
Period size: 18 Copynumber: 7.6 Consensus size: 17
2639955 ATTCTAAATG
* *
2639965 TTTACAGTTATCAGACA
1 TTTACAGTTATAAGATA
2639982 TTTCACAGTTATAAGATA
1 TTT-ACAGTTATAAGATA
* *
2640000 TTTACATTTATTAGATGA
1 TTTACAGTTATAAGAT-A
*
2640018 TTTTCAGTTATTAA-ATA
1 TTTACAGTTA-TAAGATA
* *
2640035 TTTAGAGTTATCAGATGA
1 TTTACAGTTATAAGAT-A
* * * *
2640053 TTTTCAATTATCAGATG
1 TTTACAGTTATAAGATA
*
2640070 TTTACAGTAATAAGATA
1 TTTACAGTTATAAGATA
2640087 TTTTACAGTTAT
1 -TTTACAGTTAT
2640099 CAAATGTAGA
Statistics
Matches: 91, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
16 2 0.02
17 37 0.41
18 50 0.55
19 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTACAGTTATAAGATA
Found at i:2640074 original size:70 final size:70
Alignment explanation
Indices: 2639959--2640103 Score: 161
Period size: 70 Copynumber: 2.1 Consensus size: 70
2639949 TGATAGATTC
* * * *
2639959 TAAATGTTTACAGTTATCAGACATTTCACAGTTATAAGATATTTACATTTATTAGATGATTTT-C
1 TAAATATTTACAGTTATCAGACATTTCACAGTTATAAGATATTTACAGTAATAAGAT-ATTTTAC
2640023 AGTTAT
65 AGTTAT
* * * *
2640029 TAAATATTTAGAGTTATCAGATGATTTTCA-A-TTATCAGATGTTTACAGTAATAAGATATTTTA
1 TAAATATTTACAGTTATCAGA-CA-TTTCACAGTTATAAGATATTTACAGTAATAAGATATTTTA
2640092 CAGTTAT
64 CAGTTAT
*
2640099 CAAAT
1 TAAAT
2640104 GTAGATTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
69 5 0.08
70 51 0.81
71 2 0.03
72 5 0.08
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (70 bp):
TAAATATTTACAGTTATCAGACATTTCACAGTTATAAGATATTTACAGTAATAAGATATTTTACA
GTTAT
Found at i:2640099 original size:35 final size:35
Alignment explanation
Indices: 2639960--2640105 Score: 136
Period size: 35 Copynumber: 4.2 Consensus size: 35
2639950 GATAGATTCT
* *
2639960 AAATGTTTACAGTTATCAGA-CATTTCACAGTTAT-
1 AAATGTTTACAGTTATCAGATGATTT-TCAGTTATC
* * * *
2639994 AAGATATTTACATTTATTAGATGATTTTCAGTTATT
1 AA-ATGTTTACAGTTATCAGATGATTTTCAGTTATC
* * *
2640030 AAATATTTAGAGTTATCAGATGATTTTCAATTATC
1 AAATGTTTACAGTTATCAGATGATTTTCAGTTATC
* * *
2640065 AGATGTTTACAGTAATAAGAT-ATTTTACAGTTATC
1 AAATGTTTACAGTTATCAGATGATTTT-CAGTTATC
2640100 AAATGT
1 AAATGT
2640106 AGATTAATAA
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
34 7 0.08
35 78 0.86
36 6 0.07
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (35 bp):
AAATGTTTACAGTTATCAGATGATTTTCAGTTATC
Found at i:2640703 original size:23 final size:23
Alignment explanation
Indices: 2640652--2640703 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2640642 TTATGTTTTA
**
2640652 GCTAT-ACTTACATATATATTTT
1 GCTATAACTTACATATATATTGG
* *
2640674 ACGATAACTTACATATATATTGG
1 GCTATAACTTACATATATATTGG
2640697 GCTATAA
1 GCTATAA
2640704 TTTTCAGTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (23 bp):
GCTATAACTTACATATATATTGG
Found at i:2641823 original size:21 final size:21
Alignment explanation
Indices: 2641794--2641840 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2641784 ATTCTGACTA
*
2641794 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGACTTTCCAAAT
* *
2641815 TCGCGTTGCGACTTTCCTAAT
1 TCGCATTGCGACTTTCCAAAT
2641836 TCGCA
1 TCGCA
2641841 ATATGAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGACTTTCCAAAT
Found at i:2641861 original size:20 final size:20
Alignment explanation
Indices: 2641845--2641908 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
2641835 TTCGCAATAT
*
2641845 GAATTCGTAAATCGCAATGC
1 GAATACGTAAATCGCAATGC
2641865 GAATACGTAAATCGCAATGC
1 GAATACGTAAATCGCAATGC
* *
2641885 GAATACGTAGATCGCAACGC
1 GAATACGTAAATCGCAATGC
2641905 GAAT
1 GAAT
2641909 CTGACTATCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (20 bp):
GAATACGTAAATCGCAATGC
Done.