Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003345.1 Hibiscus syriacus cultivar Beakdansim tig00007043_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: 605145
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:461 original size:14 final size:14
Alignment explanation
Indices: 442--484 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
432 TGAAATTACC
442 ATTTTTTTATTTTT
1 ATTTTTTTATTTTT
*
456 ATTTTTTTATTGTT
1 ATTTTTTTATTTTT
*
470 A--TTGTTATTTTT
1 ATTTTTTTATTTTT
482 ATT
1 ATT
485 ATTATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.42
14 14 0.58
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (14 bp):
ATTTTTTTATTTTT
Found at i:477 original size:20 final size:21
Alignment explanation
Indices: 448--487 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
438 TACCATTTTT
*
448 TTATTTTTATTTTT-TTATTG
1 TTATTGTTATTTTTATTATTG
468 TTATTGTTATTTTTATTATT
1 TTATTGTTATTTTTATTATT
488 ATAATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (21 bp):
TTATTGTTATTTTTATTATTG
Found at i:497 original size:26 final size:26
Alignment explanation
Indices: 448--498 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
438 TACCATTTTT
* * * *
448 TTATTTTTATTTTTTTATTGTTATTG
1 TTATTTTTATTATTATAATATTATTG
474 TTATTTTTATTATTATAATATTATT
1 TTATTTTTATTATTATAATATTATT
499 ATTGTTGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (26 bp):
TTATTTTTATTATTATAATATTATTG
Found at i:509 original size:23 final size:22
Alignment explanation
Indices: 469--513 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
459 TTTTTATTGT
* *
469 TATTGTTATTTTTATTATTATAA
1 TATTATTATTGTTATTA-TATAA
*
492 TATTATTATTGTTGTTATATAA
1 TATTATTATTGTTATTATATAA
514 CAAAAATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
TATTATTATTGTTATTATATAA
Found at i:1049 original size:15 final size:16
Alignment explanation
Indices: 1029--1065 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
1019 TCGAATACCT
1029 AAAAATAA-TTTTAAG
1 AAAAATAATTTTTAAG
1044 AAAAATAATTTTTAAG
1 AAAAATAATTTTTAAG
1060 ACAAAA
1 A-AAAA
1066 GCTGGTCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 8 0.40
17 4 0.20
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAAATAATTTTTAAG
Found at i:1868 original size:2 final size:2
Alignment explanation
Indices: 1819--1853 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1809 TTAAATTAAT
1819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1854 TCGAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3351 original size:3 final size:3
Alignment explanation
Indices: 3336--3381 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
3326 TAAATACACT
* *
3336 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3382 TTTTTAACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3668 original size:104 final size:105
Alignment explanation
Indices: 3547--3795 Score: 274
Period size: 104 Copynumber: 2.4 Consensus size: 105
3537 TCTCGTGGAT
* * *
3547 GAGTTCTTTCTCATTATGAACTCTTTTGGAAATGTTGATCCAAAT-CTTTTGCGATGGACTTAGA
1 GAGTTC-TTCTCATTATGAACTCTTTTGGAAATGTTGATCCAAATCCATCTGCGAT-GAATTAGA
* *
3611 AA-GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
64 AAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
** * * ** * * *
3652 GAGTTCTTCTCATTATGAACTCTTCAGGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTTTGGAAATGTTGATCCAAATCCATCTGCGATGAATTAGAAA
* *
3717 GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGAT
66 GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
*
3757 GAG---TTCTCATTATGAACTCTTCATTGGAAATGTCGATCC
1 GAGTTCTTCTCATTATGAACTCTT--TTGGAAATGTTGATCC
3796 CTCAAGCGAG
Statistics
Matches: 119, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
102 18 0.15
104 51 0.43
105 50 0.42
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTTTGGAAATGTTGATCCAAATCCATCTGCGATGAATTAGAAA
GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
Found at i:4099 original size:221 final size:218
Alignment explanation
Indices: 3718--4146 Score: 564
Period size: 221 Copynumber: 2.0 Consensus size: 218
3708 AATTTGAAAG
* *
3718 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTCATTATGAACTCTTCATTG
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTCATTATGAACTCTTCACTG
** * ** * * *
3783 GAAATGTCGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAA
66 GAAAAATCAATCCCTCAAGCGAGGCGTCACTGATTAAAAATGTCATAAATCAAGTGATAAGTCAA
* * *
3848 AAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATTGGATGAGTTCTTTTCATTATGAACTCT
131 AAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-GTCGATGAGTTCTTCTCA-TATGAACTCT
3913 CCA-TGAAAATGTTGATGCGAAGTT
194 CCATTGAAAATGTTGATGCGAAGTT
*
3937 GAACAAGTTCTTCTCATTATGAACTTCTTTTCCTCGTT-GGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAAC-T-TTCTCCT--TTAGGATGAG---TTCTCATTATGAACTC
* *
4001 -TC-CT-GAAAAATCAAT-CCTCAAGCGAGGTGTCACTGATTAAAAATGTCATAAATCGAGTGAT
59 TTCACTGGAAAAATCAATCCCTCAAGCGAGGCGTCACTGATTAAAAATGTCATAAATCAAGTGAT
* *
4062 AAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGATGAGTTCTTCTCATATGA
124 AAGTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGATGAGTTCTTCTCATATGA
*
4127 ACTCTCCATTGGAAATGTTG
189 ACTCTCCATTGAAAATGTTG
4147 GTTCACCTCC
Statistics
Matches: 183, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
219 37 0.20
220 26 0.14
221 85 0.46
222 14 0.08
223 3 0.02
224 2 0.01
225 16 0.09
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (218 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTCATTATGAACTCTTCACTG
GAAAAATCAATCCCTCAAGCGAGGCGTCACTGATTAAAAATGTCATAAATCAAGTGATAAGTCAA
AAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGATGAGTTCTTCTCATATGAACTCTCC
ATTGAAAATGTTGATGCGAAGTT
Found at i:5043 original size:17 final size:16
Alignment explanation
Indices: 5002--5086 Score: 70
Period size: 17 Copynumber: 5.3 Consensus size: 16
4992 CCTTTTTCTC
5002 TTTTTATTTTTTCATTT
1 TTTTTA-TTTTTCATTT
*
5019 CTTTTTTTTTTTCA--T
1 -TTTTTATTTTTCATTT
*
5034 TTTTCA-TTTTCATTT
1 TTTTTATTTTTCATTT
*
5049 TTTTTCATTTTTCA-TC
1 TTTTT-ATTTTTCATTT
*
5065 TTTTTATTTGTTCCTTT
1 TTTTTATTT-TTCATTT
5082 TTTTT
1 TTTTT
5087 TCTTCAAGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
13 6 0.11
14 4 0.07
15 10 0.19
16 10 0.19
17 19 0.35
18 5 0.09
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTTCATTT
Found at i:5044 original size:30 final size:31
Alignment explanation
Indices: 5010--5073 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5000 TCTTTTTATT
*
5010 TTTTCATTTCTTTTT-TTTTTTCAT-TTTTCA
1 TTTTCATTT-TTTTTCATTTTTCATCTTTTCA
*
5040 TTTTCATTTTTTTTCATTTTTCATCTTTTTA
1 TTTTCATTTTTTTTCATTTTTCATCTTTTCA
5071 TTT
1 TTT
5074 GTTCCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 17 0.57
31 8 0.27
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTCATTTTTTTTCATTTTTCATCTTTTCA
Found at i:16109 original size:15 final size:16
Alignment explanation
Indices: 16089--16125 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
16079 TCGAATACCT
16089 AAAAATAA-TTTTAAG
1 AAAAATAATTTTTAAG
16104 AAAAATAATTTTTAAG
1 AAAAATAATTTTTAAG
16120 ACAAAA
1 A-AAAA
16126 GCTGGTCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 8 0.40
17 4 0.20
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAAATAATTTTTAAG
Found at i:16948 original size:2 final size:2
Alignment explanation
Indices: 16891--16933 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
16881 TTAAATTAAT
16891 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
16933 T
1 T
16934 TCGAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18458 original size:3 final size:3
Alignment explanation
Indices: 18443--18488 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
18433 ATAAAACACT
* *
18443 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18489 TTTTTTAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:19557 original size:29 final size:28
Alignment explanation
Indices: 19525--19637 Score: 113
Period size: 29 Copynumber: 3.9 Consensus size: 28
19515 AGGATTAGAT
19525 TTTTTACACTTAGGTCCCTATACTTTATA
1 TTTTTACACTTA-GTCCCTATACTTTATA
*
19554 TTTTTACACATAGTCCCTATACTTTAGT-
1 TTTTTACACTTAGTCCCTATACTTTA-TA
* * *
19582 TTTTTACACTTAGGTACTTATAATTTA-A
1 TTTTTACACTTA-GTCCCTATACTTTATA
* *
19610 TTTTTTATACTTTAGTCCCTAGACTTTA
1 -TTTTTACAC-TTAGTCCCTATACTTTA
19638 GAGTTCTCAC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
28 25 0.36
29 41 0.59
30 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (28 bp):
TTTTTACACTTAGTCCCTATACTTTATA
Found at i:19590 original size:57 final size:59
Alignment explanation
Indices: 19519--19639 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 59
19509 CCCTCTAGGA
* * *
19519 TTAGATTTTTTACACTTAGGTCCCTATACTTT-ATATTTTTACAC-ATAGTCCCTATACT
1 TTAGATTTTTTACACTTAGGTACCTATAATTTAAT-TTTTTACACTATAGTCCCTAGACT
* * *
19577 TTAG-TTTTTTACACTTAGGTACTTATAATTTAATTTTTTATACTTTAGTCCCTAGACT
1 TTAGATTTTTTACACTTAGGTACCTATAATTTAATTTTTTACACTATAGTCCCTAGACT
19635 TTAGA
1 TTAGA
19640 GTTCTCACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 32 0.59
58 22 0.41
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (59 bp):
TTAGATTTTTTACACTTAGGTACCTATAATTTAATTTTTTACACTATAGTCCCTAGACT
Found at i:22691 original size:16 final size:17
Alignment explanation
Indices: 22656--22693 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
22646 ATTTCAAATC
**
22656 TTAAATTAATTTATGGA
1 TTAAATTAATTTATAAA
22673 TTAAA-TAATTTATAAA
1 TTAAATTAATTTATAAA
22689 TTAAA
1 TTAAA
22694 GATATCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TTAAATTAATTTATAAA
Found at i:24632 original size:26 final size:26
Alignment explanation
Indices: 24601--24652 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
24591 ATTCTCCAGC
*
24601 TTCTTTTTCTTCACTTTTATTCTTCT
1 TTCTTTCTCTTCACTTTTATTCTTCT
*
24627 TTCTTTCTCTTCACTTTTCTTCTTCT
1 TTCTTTCTCTTCACTTTTATTCTTCT
24653 CCTCTTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (26 bp):
TTCTTTCTCTTCACTTTTATTCTTCT
Found at i:26064 original size:15 final size:15
Alignment explanation
Indices: 26044--26087 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
26034 TACGTGAAGA
26044 AAAGTGAAGAGAAAG
1 AAAGTGAAGAGAAAG
26059 AAAGTG-A-AG--A-
1 AAAGTGAAGAGAAAG
26069 AAAGTGAAGAGAAAG
1 AAAGTGAAGAGAAAG
26084 AAAG
1 AAAG
26088 AAGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
10 6 0.25
11 2 0.08
12 2 0.08
13 2 0.08
14 2 0.08
15 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (15 bp):
AAAGTGAAGAGAAAG
Found at i:26071 original size:25 final size:25
Alignment explanation
Indices: 26037--26104 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
26027 ATTCAGATAC
26037 GTGAAGAAAAGTGAAGAGAAAGAAA
1 GTGAAGAAAAGTGAAGAGAAAGAAA
26062 GTGAAGAAAAGTGAAGAGAAAGAAA
1 GTGAAGAAAAGTGAAGAGAAAGAAA
*
26087 GAAGAAGAAAAGTGAAGA
1 G-TGAAGAAAAGTGAAGA
26105 AAAATATGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 26 0.63
26 15 0.37
ACGTcount: A:0.60, C:0.00, G:0.32, T:0.07
Consensus pattern (25 bp):
GTGAAGAAAAGTGAAGAGAAAGAAA
Found at i:26366 original size:8 final size:8
Alignment explanation
Indices: 26353--26406 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
26343 ATTTGATACT
26353 ATATATAA
1 ATATATAA
26361 ATATATAA
1 ATATATAA
* * *
26369 TGTATTTGA
1 -ATATATAA
26378 ATATATAA
1 ATATATAA
26386 ATATATAA
1 ATATATAA
*
26394 TATATTTAA
1 -ATATATAA
26403 ATAT
1 ATAT
26407 GATTATCTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 25 0.68
9 12 0.32
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (8 bp):
ATATATAA
Found at i:26381 original size:25 final size:25
Alignment explanation
Indices: 26353--26406 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
26343 ATTTGATACT
* *
26353 ATATATAAATATATAATGTATTTGA
1 ATATATAAATATATAATATATTTAA
26378 ATATATAAATATATAATATATTTAA
1 ATATATAAATATATAATATATTTAA
26403 ATAT
1 ATAT
26407 GATTATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
ATATATAAATATATAATATATTTAA
Found at i:28160 original size:45 final size:45
Alignment explanation
Indices: 28097--28848 Score: 585
Period size: 45 Copynumber: 16.2 Consensus size: 45
28087 CGTTGGAGGC
* *
28097 TTCTTTGGATGT-TCATAGACTGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTGT-ATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * *
28142 TTCTTCGGTGGTGTATAGACCGGTGGCTTTGGTGGTTTAGGTTCATACGTCGGAGGT
1 TTCTTTGGAGGTGTATAGACCGGTGG-TTT-G-GGTTCAGG--C-TTC-TC-----T
* *
28199 TTCTTTGGAGGCT-CATAGACTGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGG-TGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * *
28244 TTCTTTGGTGGTGCATAAACCGGTGGCTTTGGGGGCTT-AGGCTCATACGTTGGTGGT
1 TTCTTTGGAGGTGTATAGACCGGTGG-TTT--GGG-TTCAGGCT--T-C-----T-CT
* *
28301 TTCTTTGGCGGCT-CATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGG-TGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * * * *
28346 TTCTTTGGAGGTGTATAAACCGGTGGCTTAGGCTCGGGTTTCTCT
1 TTCTTTGGAGGTGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
28391 TTCTTTGG-GG-GCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTG-T-ATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * * * *
28436 TTCTTTGGAGGTGTATAAACCGGTGGCTTAGGCTCGGGTTTCTCT
1 TTCTTTGGAGGTGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
28481 TTCTTTGG-GG-GCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTG-T-ATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * * * * *
28526 TTCTTTGGAGGAGTATAAACCGGTGGCTTAGGCTCGGGTTTCTCT
1 TTCTTTGGAGGTGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
*
28571 TTCTTTGGGGGT-TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTGT-ATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * * * *
28616 TTCTTTGGAGGTGTATAAACCGGTGGCTTAGGCTCGGGTTTCTCT
1 TTCTTTGGAGGTGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
28661 TTCTTTGG-GG-GCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTG-T-ATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * * * *
28706 TTCTTTGGAGGTGTATAAACCGGTGGCTTAGGCTCGGGTTTCTCT
1 TTCTTTGGAGGTGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* *
28751 TTCTTTGGGGGT-TCATAGACCGGTGGTTTGGGTTCAAGCTTCTCT
1 TTCTTTGGAGGTGT-ATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
* * * * * * *
28796 TTCTTTGGTGGCT-CATGGACCGGTGGCTTAGGCTCAGGTTTCTCT
1 TTCTTTGGAGG-TGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
28841 TTCTTTGG
1 TTCTTTGG
28849 TGGTTCATAA
Statistics
Matches: 566, Mismatches: 94, Indels: 94
0.75 0.12 0.12
Matches are distributed among these distances:
43 3 0.01
44 13 0.02
45 425 0.75
46 19 0.03
47 4 0.01
48 15 0.03
49 2 0.00
50 4 0.01
51 6 0.01
52 4 0.01
53 2 0.00
54 15 0.03
55 1 0.00
56 7 0.01
57 44 0.08
58 2 0.00
ACGTcount: A:0.11, C:0.18, G:0.32, T:0.38
Consensus pattern (45 bp):
TTCTTTGGAGGTGTATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
Found at i:28433 original size:90 final size:90
Alignment explanation
Indices: 28300--28857 Score: 992
Period size: 90 Copynumber: 6.2 Consensus size: 90
28290 ACGTTGGTGG
*
28300 TTTCTTTGGCGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
1 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
28365 CCGGTGGCTTAGGCTCGGGTTTCTC
66 CCGGTGGCTTAGGCTCGGGTTTCTC
28390 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
1 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
28455 CCGGTGGCTTAGGCTCGGGTTTCTC
66 CCGGTGGCTTAGGCTCGGGTTTCTC
*
28480 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGAGTATAAA
1 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
28545 CCGGTGGCTTAGGCTCGGGTTTCTC
66 CCGGTGGCTTAGGCTCGGGTTTCTC
*
28570 TTTCTTTGGGGGTTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
1 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
28635 CCGGTGGCTTAGGCTCGGGTTTCTC
66 CCGGTGGCTTAGGCTCGGGTTTCTC
28660 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
1 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
28725 CCGGTGGCTTAGGCTCGGGTTTCTC
66 CCGGTGGCTTAGGCTCGGGTTTCTC
* * * * **
28750 TTTCTTTGGGGGTTCATAGACCGGTGGTTTGGGTTCAAGCTTCTCTTTCTTTGGTGGCT-CATGG
1 TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGG-TGTATAA
*
28814 ACCGGTGGCTTAGGCTCAGGTTTCTC
65 ACCGGTGGCTTAGGCTCGGGTTTCTC
* *
28840 TTTCTTTGGTGGTTCATA
1 TTTCTTTGGGGGCTCATA
28858 ATTTGGAGGT
Statistics
Matches: 454, Mismatches: 13, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
90 453 1.00
91 1 0.00
ACGTcount: A:0.11, C:0.19, G:0.32, T:0.39
Consensus pattern (90 bp):
TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
CCGGTGGCTTAGGCTCGGGTTTCTC
Found at i:28602 original size:180 final size:180
Alignment explanation
Indices: 28109--28857 Score: 1007
Period size: 180 Copynumber: 4.0 Consensus size: 180
28099 CTTTGGATGT
* * * * *
28109 TCATAGACTGGTGGTTTGGGTTCAGGCTTCTCTTTCTTCGGTGGTGTATAGACCGGTGGCTTTGG
1 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTAGG
* * *
28174 -TGGTTTAGGTTCATACGTCGGAGGTTTCTTTGGAGGCTCATAGACTGGTGGTTTGGGTTCAGGC
66 CTCG----GGTT--T-C-TC-----TTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGC
* * ** *
28238 TTCTCTTTCTTTGGTGGTGCATAAACCGGTGGCTTTGGGGGCTTAGGCTCATACGTTGGTGGTTT
118 TTCTCTTTCTTTGGAGGTGCATAAACC---GG---T---GGCTTAGGCTC--AGGTTTCT-CTTT
*
28303 CTTTGGCGGC
171 CTTTGGGGGC
28313 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTAGG
1 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTAGG
28378 CTCGGGTTTCTCTTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTG
66 CTCGGGTTTCTCTTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTG
* *
28443 GAGGTGTATAAACCGGTGGCTTAGGCTCGGGTTTCTCTTTCTTTGGGGGC
131 GAGGTGCATAAACCGGTGGCTTAGGCTCAGGTTTCTCTTTCTTTGGGGGC
*
28493 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGAGTATAAACCGGTGGCTTAGG
1 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTAGG
*
28558 CTCGGGTTTCTCTTTCTTTGGGGGTTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTG
66 CTCGGGTTTCTCTTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTG
* *
28623 GAGGTGTATAAACCGGTGGCTTAGGCTCGGGTTTCTCTTTCTTTGGGGGC
131 GAGGTGCATAAACCGGTGGCTTAGGCTCAGGTTTCTCTTTCTTTGGGGGC
28673 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTAGG
1 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTAGG
* *
28738 CTCGGGTTTCTCTTTCTTTGGGGGTTCATAGACCGGTGGTTTGGGTTCAAGCTTCTCTTTCTTTG
66 CTCGGGTTTCTCTTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTG
* ** * *
28803 GTGGCT-CATGGACCGGTGGCTTAGGCTCAGGTTTCTCTTTCTTTGGTGGT
131 GAGG-TGCATAAACCGGTGGCTTAGGCTCAGGTTTCTCTTTCTTTGGGGGC
28853 TCATA
1 TCATA
28858 ATTTGGAGGT
Statistics
Matches: 516, Mismatches: 27, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
180 364 0.71
181 5 0.01
183 11 0.02
186 1 0.00
189 2 0.00
192 63 0.12
197 2 0.00
198 1 0.00
199 1 0.00
201 4 0.01
204 60 0.12
205 2 0.00
ACGTcount: A:0.11, C:0.18, G:0.32, T:0.38
Consensus pattern (180 bp):
TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTAGG
CTCGGGTTTCTCTTTCTTTGGGGGCTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTG
GAGGTGCATAAACCGGTGGCTTAGGCTCAGGTTTCTCTTTCTTTGGGGGC
Found at i:36093 original size:16 final size:16
Alignment explanation
Indices: 36068--36098 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36058 TAATAAATAA
36068 ACGAACATAAACGAAT
1 ACGAACATAAACGAAT
*
36084 ACGAATATAAACGAA
1 ACGAACATAAACGAA
36099 CAATTTTTTT
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:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (16 bp):
ACGAACATAAACGAAT
Found at i:36227 original size:23 final size:23
Alignment explanation
Indices: 36162--36227 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
36152 CATTTAATTA
* * *
36162 ATAAACGAACACGAACGAACGAAC
1 ATAAACGAACA-TAACAAACAAAC
*
36186 ATAAACGAACATAATAAACAAAC
1 ATAAACGAACATAACAAACAAAC
*
36209 ATAAATGAACA-ACACAAAC
1 ATAAACGAACATA-ACAAAC
36228 CCACACAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 1 0.03
23 23 0.66
24 11 0.31
ACGTcount: A:0.61, C:0.21, G:0.09, T:0.09
Consensus pattern (23 bp):
ATAAACGAACATAACAAACAAAC
Found at i:36512 original size:24 final size:26
Alignment explanation
Indices: 36483--36534 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
36473 GCCCTCTGTT
*
36483 CGAACATAAATGAACATA-AAT-GAA
1 CGAACATAAACGAACATATAATCGAA
36507 CGAACATAAACGAACATATAATCGAA
1 CGAACATAAACGAACATATAATCGAA
36533 CG
1 CG
36535 TTCACGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (26 bp):
CGAACATAAACGAACATATAATCGAA
Found at i:37035 original size:60 final size:59
Alignment explanation
Indices: 36963--37128 Score: 235
Period size: 60 Copynumber: 2.8 Consensus size: 59
36953 AGATATTGAG
* * * *
36963 TTTTATTTTAAATTAGTAT-TTAAATTTTTAAATATTTTAATTTCATAATTGAATTATTAT
1 TTTTATTCTAAATT--TATCTTAAACTTTTAAATATTTTAATTTCATAATTGAATTATGAA
*
37023 TTTTATTCTAAATTTATCCTTAAACTTTTAAATATTTTAATTTCATTATTGAATTATGAA
1 TTTTATTCTAAATTTAT-CTTAAACTTTTAAATATTTTAATTTCATAATTGAATTATGAA
*
37083 TTTTATTCTAAATTTATTCTTAAACTTTTAAATATTTCAATTTCAT
1 TTTTATTCTAAATTTA-TCTTAAACTTTTAAATATTTTAATTTCAT
37129 TCCCAAACTA
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
58 3 0.03
60 93 0.96
61 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (59 bp):
TTTTATTCTAAATTTATCTTAAACTTTTAAATATTTTAATTTCATAATTGAATTATGAA
Found at i:37129 original size:60 final size:60
Alignment explanation
Indices: 36982--37129 Score: 242
Period size: 60 Copynumber: 2.5 Consensus size: 60
36972 AAATTAGTAT
* * * *
36982 TTAAATTTTTAAATATTTTAATTTCATAATTGAATTATTATTTTTATTCTAAATTTATCC
1 TTAAACTTTTAAATATTTTAATTTCATTATTGAATTATGAATTTTATTCTAAATTTATCC
*
37042 TTAAACTTTTAAATATTTTAATTTCATTATTGAATTATGAATTTTATTCTAAATTTATTC
1 TTAAACTTTTAAATATTTTAATTTCATTATTGAATTATGAATTTTATTCTAAATTTATCC
*
37102 TTAAACTTTTAAATATTTCAATTTCATT
1 TTAAACTTTTAAATATTTTAATTTCATT
37130 CCCAAACTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.55
Consensus pattern (60 bp):
TTAAACTTTTAAATATTTTAATTTCATTATTGAATTATGAATTTTATTCTAAATTTATCC
Found at i:37141 original size:60 final size:60
Alignment explanation
Indices: 36982--37188 Score: 184
Period size: 60 Copynumber: 3.5 Consensus size: 60
36972 AAATTAGTAT
* * * *** * * * *
36982 TTAAATTTTTAAATATTTTAATTTCATAATTGAATTATTATTTTTATTCTAAATTTATCC
1 TTAAACTTTTAAATATTTCAATTTCATTACCAAACTATGAATTTTATTCTAAATTTATTC
* *** *
37042 TTAAACTTTTAAATATTTTAATTTCATTATTGAATTATGAATTTTATTCTAAATTTATTC
1 TTAAACTTTTAAATATTTCAATTTCATTACCAAACTATGAATTTTATTCTAAATTTATTC
* * * *
37102 TTAAACTTTTAAATATTTCAATTTCATTCCCAAACTATGACTCTCATTCTAAA-TTATTC
1 TTAAACTTTTAAATATTTCAATTTCATTACCAAACTATGAATTTTATTCTAAATTTATTC
* * *
37161 TCCAAACTTTTGAAT-CTTCTAATTTCAT
1 T-TAAACTTTTAAATATTTC-AATTTCAT
37189 CCCTAAATTC
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
59 10 0.08
60 118 0.92
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (60 bp):
TTAAACTTTTAAATATTTCAATTTCATTACCAAACTATGAATTTTATTCTAAATTTATTC
Found at i:38396 original size:27 final size:26
Alignment explanation
Indices: 38331--38400 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
38321 CCGTAAGGTG
* *
38331 GTTCATACACCGGTGGCTTCTTTGGA
1 GTTCATAGACTGGTGGCTTCTTTGGA
*
38357 GTCTCGT-GTACTGGTGGCTTCTTTGGA
1 GT-TCATAG-ACTGGTGGCTTCTTTGGA
38384 TGTTCATAGACTGGTGG
1 -GTTCATAGACTGGTGG
38401 TTTGGGTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
26 2 0.06
27 31 0.86
28 3 0.08
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (26 bp):
GTTCATAGACTGGTGGCTTCTTTGGA
Found at i:38436 original size:45 final size:45
Alignment explanation
Indices: 38375--38721 Score: 390
Period size: 45 Copynumber: 7.7 Consensus size: 45
38365 TACTGGTGGC
* * * * *
38375 TTCTTTGGAT-GTTCATAGACTGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGG-TGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* *
38420 TTCTTTGGTGGTTCATAGACCGGGGGCTTAGGCTTAGGTTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * * *
38465 TTCTTTGGTGGTTCATAAACTGGGGGCTTAGGCTCGGGTTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * *
38510 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCGGGTTTTTCC
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * * * * * ** *
38555 TTCTTCGGGGGCTCATAGACCGGTGGTTTGGGTTGTGGCTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * * *
38600 TTCTTCGGTGGTTCATAGACCGGGGGCTTAGGCTCAAGTTTCTTT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* *
38645 TTCTTTGGTGGTTCATACACCGGTGGCTTAGGCTCGGGTTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * *
38690 TTCTTTGGAGGTTCATAGACAGGGGGCTTAGG
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGG
38722 TAATTTGCCA
Statistics
Matches: 253, Mismatches: 48, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
44 1 0.00
45 252 1.00
ACGTcount: A:0.11, C:0.18, G:0.31, T:0.39
Consensus pattern (45 bp):
TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
Found at i:38650 original size:180 final size:180
Alignment explanation
Indices: 38387--38721 Score: 553
Period size: 180 Copynumber: 1.9 Consensus size: 180
38377 CTTTGGATGT
* *
38387 TCATAGACTGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTTCATAGACCGGGGGCTTAGG
1 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTCGGTGGTTCATAGACCGGGGGCTTAGG
* * *
38452 CTTAGGTTTCTCTTTCTTTGGTGGTTCATAAACTGGGGGCTTAGGCTCGGGTTTCTCTTTCTTTG
66 CTCAAGTTTCTCTTTCTTTGGTGGTTCATAAACCGGGGGCTTAGGCTCGGGTTTCTCTTTCTTTG
* * *
38517 GTGGTTCATAGACCGGTGGCTTAGGCTCGGGTTTTTCCTTCTTCGGGGGC
131 GAGGTTCATAGACAGGGGGCTTAGGCTCGGGTTTTTCCTTCTTCGGGGGC
**
38567 TCATAGACCGGTGGTTTGGGTTGTGGCTTCTCTTTCTTCGGTGGTTCATAGACCGGGGGCTTAGG
1 TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTCGGTGGTTCATAGACCGGGGGCTTAGG
* * *
38632 CTCAAGTTTCTTTTTCTTTGGTGGTTCATACACCGGTGGCTTAGGCTCGGGTTTCTCTTTCTTTG
66 CTCAAGTTTCTCTTTCTTTGGTGGTTCATAAACCGGGGGCTTAGGCTCGGGTTTCTCTTTCTTTG
38697 GAGGTTCATAGACAGGGGGCTTAGG
131 GAGGTTCATAGACAGGGGGCTTAGG
38722 TAATTTGCCA
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
180 142 1.00
ACGTcount: A:0.11, C:0.19, G:0.32, T:0.39
Consensus pattern (180 bp):
TCATAGACCGGTGGTTTGGGTTCAGGCTTCTCTTTCTTCGGTGGTTCATAGACCGGGGGCTTAGG
CTCAAGTTTCTCTTTCTTTGGTGGTTCATAAACCGGGGGCTTAGGCTCGGGTTTCTCTTTCTTTG
GAGGTTCATAGACAGGGGGCTTAGGCTCGGGTTTTTCCTTCTTCGGGGGC
Found at i:39056 original size:2 final size:2
Alignment explanation
Indices: 39049--39073 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39039 GACATGAAAA
39049 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39074 AAAGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39544 original size:76 final size:76
Alignment explanation
Indices: 39418--39569 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
39408 GACCCTCAGT
39418 GTTTCATTTTATGGTAAAAAGGTCTTTAATATTTGATATAATTATCGCTTTGTCCCTTATTCTTT
1 GTTTCATTTTATGGTAAAAAGGTCTTTAATATTTGATATAATTATCGCTTTGTCCCTTATTCTTT
39483 TTTTATGAGGC
66 TTTTATGAGGC
39494 GTTTCATTTTATGGTAAAAAGGTCTTTAATATTTGATATAATTATCGCTTTGTCCCTTATTCTTT
1 GTTTCATTTTATGGTAAAAAGGTCTTTAATATTTGATATAATTATCGCTTTGTCCCTTATTCTTT
39559 TTTTATGAGGC
66 TTTTATGAGGC
39570 ATTTTAACCC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (76 bp):
GTTTCATTTTATGGTAAAAAGGTCTTTAATATTTGATATAATTATCGCTTTGTCCCTTATTCTTT
TTTTATGAGGC
Found at i:41932 original size:17 final size:17
Alignment explanation
Indices: 41910--41942 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41900 TTATGCATTA
41910 TTAATATAT-ATATAATT
1 TTAATA-ATCATATAATT
41927 TTAATAATCATATAAT
1 TTAATAATCATATAAT
41943 ATAACATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATAATCATATAATT
Found at i:43550 original size:12 final size:14
Alignment explanation
Indices: 43527--43558 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
43517 GGGGGGGGGG
43527 GAGAAGAACAAAAA
1 GAGAAGAACAAAAA
43541 -AGAA-AACAAAAA
1 GAGAAGAACAAAAA
43553 GAGAAG
1 GAGAAG
43559 GGAGAGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 4
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (14 bp):
GAGAAGAACAAAAA
Found at i:46365 original size:27 final size:27
Alignment explanation
Indices: 46316--46412 Score: 135
Period size: 27 Copynumber: 3.6 Consensus size: 27
46306 CCGTAAGGTG
* *
46316 GTTCATACACCGGTGGCTTCTTTGGA-
1 GTTCATAGACTGGTGGCTTCTTTGGAT
*
46342 GTCTCGT-GTACTGGTGGCTTCTTTGGAT
1 GT-TCATAG-ACTGGTGGCTTCTTTGGAT
46370 GTTCATAGACTGGTGGCTTCTTTGGAT
1 GTTCATAGACTGGTGGCTTCTTTGGAT
46397 GTTCATAGACTGGTGG
1 GTTCATAGACTGGTGG
46413 TTTGGGTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
26 2 0.03
27 58 0.92
28 3 0.05
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (27 bp):
GTTCATAGACTGGTGGCTTCTTTGGAT
Found at i:46438 original size:45 final size:45
Alignment explanation
Indices: 46387--46821 Score: 521
Period size: 45 Copynumber: 9.7 Consensus size: 45
46377 GACTGGTGGC
* * * *
46387 TTCTTTGGAT-GTTCATAGACTGGTGGTTTGGGTTCAGGTTTCTCT
1 TTCTTTGG-TGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* *
46432 TTCTTTGGTGGTTCATAGACCGGGGGCTTAGGCTTAGGTTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * * * *
46477 TTCTTTGGTGGTTCATAAACTGGGGGCTTAGGCTCGGGTTTCTCC
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * * * *
46522 TTCTTTGGTGGTTCATAAACTGGGGGCTTAGGCTCGGGTTTCTCC
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
** * * *
46567 TTCTTTGGTGGTTCATAGACTAGTGGCTTATGCTCGGGTTTCTCC
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * *
46612 TTCTTTGGTGGTTCATAGACCGGTGGCTTATGCTCGGGTTTCTCC
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * *
46657 TTCTTTGGGGGCTCATAGACCGGTGGTTTAGGCTCAGGTTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * * *
46702 TTCTTTGGTGGTTCATAGACCGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* * * *
46747 TTCTTTGGAGGTTCATAGACAGGCGGCTTAGGCTCTGGTTTCTCT
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
* *
46792 TTCTTTGGTGGTTCATAGACAGGGGGCTTA
1 TTCTTTGGTGGTTCATAGACCGGTGGCTTA
46822 TGTTGATAAG
Statistics
Matches: 351, Mismatches: 38, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
44 1 0.00
45 350 1.00
ACGTcount: A:0.11, C:0.19, G:0.30, T:0.40
Consensus pattern (45 bp):
TTCTTTGGTGGTTCATAGACCGGTGGCTTAGGCTCAGGTTTCTCT
Found at i:49045 original size:5 final size:5
Alignment explanation
Indices: 49035--49075 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
49025 AACGGTCAAC
*
49035 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
49076 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:49090 original size:9 final size:9
Alignment explanation
Indices: 49072--49189 Score: 74
Period size: 9 Copynumber: 12.3 Consensus size: 9
49062 GGTCGGGTCG
*
49072 GGTCAGACC
1 GGTCAAACC
49081 GGTCAAACC
1 GGTCAAACC
*
49090 GGTTCAGACC
1 GG-TCAAACC
49100 GGTCAAACC
1 GGTCAAACC
* * *
49109 GTTTCAGATC
1 G-GTCAAACC
*
49119 GGTCAAACT
1 GGTCAAACC
*
49128 GGTTCGAACC
1 GG-TCAAACC
* *
49138 GGTTGAAATC
1 GG-TCAAACC
49148 GGTCAAACC
1 GGTCAAACC
49157 GGTCAGAACC
1 GGTCA-AACC
*
49167 GGTTGAAAACC
1 GG-T-CAAACC
*
49178 GGTTAAACC
1 GGTCAAACC
49187 GGT
1 GGT
49190 TTCCAGCAGC
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
9 41 0.49
10 35 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:49096 original size:19 final size:19
Alignment explanation
Indices: 49074--49190 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
49064 TCGGGTCGGG
49074 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
49093 TCAGACCGGTCAAACCGTT
1 TCAGACCGGTCAAACCGGT
* *
49112 TCAGATCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
* *
49131 TC-GAACCGGTTGAAATCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
49150 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
49170 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
49190 T
1 T
49191 TCCAGCAGCC
Statistics
Matches: 79, Mismatches: 13, Indels: 11
0.77 0.13 0.11
Matches are distributed among these distances:
18 3 0.04
19 52 0.66
20 15 0.19
21 9 0.11
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:49188 original size:20 final size:21
Alignment explanation
Indices: 49152--49190 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49142 GAAATCGGTC
49152 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
49173 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
49191 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:52045 original size:23 final size:23
Alignment explanation
Indices: 52027--52087 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
52017 CTCGTATAAA
*
52027 TGCACCGAAGTGCCACGTAGAGT
1 TGCACCGAAGTGCCACGTAGAAT
52050 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
52073 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
52088 TATAAGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:52879 original size:64 final size:63
Alignment explanation
Indices: 52770--52889 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
52760 TATAAATCTC
* *
52770 ATTCGATGTTTGTATTTAATAGGGTGCATTGATGCACTACTTGTGCATCGATACACTAATGAT
1 ATTCGATGTTTGTATTTAATAGGGTGCATCGATGCACTACATGTGCATCGATACACTAATGAT
* *
52833 ATTCGATGTTTTTATTTTAA-AGGAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 ATTCGATGTTTGTA-TTTAATAGG-GTGCATCGATGCACTACATGTGCATCGATACAC
52890 CTTGAACAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 16 0.31
64 35 0.69
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (63 bp):
ATTCGATGTTTGTATTTAATAGGGTGCATCGATGCACTACATGTGCATCGATACACTAATGAT
Found at i:53416 original size:13 final size:14
Alignment explanation
Indices: 53398--53427 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
53388 TCTTCACGGT
53398 GAAGAAGAAGAA-A
1 GAAGAAGAAGAAGA
53411 GAAGAAGAAGAAGA
1 GAAGAAGAAGAAGA
53425 GAA
1 GAA
53428 ATCTGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAGAAGA
Found at i:54296 original size:13 final size:13
Alignment explanation
Indices: 54275--54308 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
54265 TATCTTATTT
*
54275 TTATATTTAGGAA
1 TTATCTTTAGGAA
54288 TTATCTTTAGGAA
1 TTATCTTTAGGAA
54301 TTATCTTT
1 TTATCTTT
54309 TGTTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (13 bp):
TTATCTTTAGGAA
Found at i:54813 original size:12 final size:11
Alignment explanation
Indices: 54788--54824 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
54778 AAAGAATTCC
54788 TTTGAATTGGTT
1 TTTGAATT-GTT
*
54800 TTTGAGTTGTT
1 TTTGAATTGTT
54811 TTTGAATTGTT
1 TTTGAATTGTT
54822 TTT
1 TTT
54825 AACCTAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.14, C:0.00, G:0.22, T:0.65
Consensus pattern (11 bp):
TTTGAATTGTT
Found at i:57589 original size:15 final size:15
Alignment explanation
Indices: 57569--57601 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
57559 AGTGGAGGAC
57569 GCCCTCTAGGTGGGA
1 GCCCTCTAGGTGGGA
57584 GCCCTCTAGGTGGGA
1 GCCCTCTAGGTGGGA
57599 GCC
1 GCC
57602 TGGGAGAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.30, G:0.39, T:0.18
Consensus pattern (15 bp):
GCCCTCTAGGTGGGA
Found at i:58319 original size:60 final size:60
Alignment explanation
Indices: 58193--58322 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 60
58183 ACAAATAGTC
* * * *
58193 CCCTAACTATATAATATTGCTTTGTTAAGTCTCTCGACTATTAAAAATTATGAAATGAAT
1 CCCTGACTATAGAATATTGCTTTGTTAAGTCCCTCAACTATTAAAAATTATGAAATGAAT
* * *
58253 CTCTGACTATAGAATATTGCTTTGTTAAGTCCCTTAACTATTAAAAATTATGAAATG-GT
1 CCCTGACTATAGAATATTGCTTTGTTAAGTCCCTCAACTATTAAAAATTATGAAATGAAT
58312 CACCTGACTAT
1 C-CCTGACTAT
58323 TCATTATGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.03
60 59 0.97
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (60 bp):
CCCTGACTATAGAATATTGCTTTGTTAAGTCCCTCAACTATTAAAAATTATGAAATGAAT
Found at i:59510 original size:20 final size:20
Alignment explanation
Indices: 59471--59512 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
59461 ACATATATTG
*
59471 AAAAAAATTGGACTTCTAAT
1 AAAAAAATTGGAATTCTAAT
59491 AAAAAAATT-GAATTCATAAT
1 AAAAAAATTGGAATTC-TAAT
59511 AA
1 AA
59513 CAAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (20 bp):
AAAAAAATTGGAATTCTAAT
Found at i:60171 original size:3 final size:3
Alignment explanation
Indices: 60163--60190 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
60153 TCATTTATCC
60163 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
60191 GTTAGCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:61150 original size:12 final size:12
Alignment explanation
Indices: 61135--61166 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
61125 GAAAGGCAAC
61135 AACAACAACAAT
1 AACAACAACAAT
61147 AACAACAACAAT
1 AACAACAACAAT
*
61159 CACAACAA
1 AACAACAA
61167 TTTGAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.06
Consensus pattern (12 bp):
AACAACAACAAT
Found at i:69959 original size:60 final size:60
Alignment explanation
Indices: 69829--69962 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
69819 TTTCGTATTG
* * * *
69829 GTCCATAAGCTTTTAAACATTTTAATTTCATCCTTTAATTATGACTATCATTCTAAATTA
1 GTCCATAAACTTTTAAACATTTCAATTTCATCCCTAAATTATGACTATCATTCTAAATTA
* * * * * *
69889 GT-CTTCAAACTTTTAAACATTTCATTTTCATCCCTAAATTATTATCT-TCCTTTTACATTA
1 GTCCAT-AAACTTTTAAACATTTCAATTTCATCCCTAAATTATGA-CTATCATTCTAAATTA
*
69949 GTCCCTAAACTTTT
1 GTCCATAAACTTTT
69963 TAAATATAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
59 2 0.03
60 54 0.90
61 4 0.07
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (60 bp):
GTCCATAAACTTTTAAACATTTCAATTTCATCCCTAAATTATGACTATCATTCTAAATTA
Found at i:70995 original size:17 final size:16
Alignment explanation
Indices: 70975--71031 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
70965 TACTTTTATA
*
70975 TATTCATACTATTTTT
1 TATTCATACTAATTTT
*
70991 GTATTCCTACTAATTTT
1 -TATTCATACTAATTTT
* *
71008 TATTCTTACTAGTATTT
1 TATTCATACTAAT-TTT
71025 T-TTCATA
1 TATTCATA
71032 TTTACGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 16 0.47
17 18 0.53
ACGTcount: A:0.25, C:0.14, G:0.04, T:0.58
Consensus pattern (16 bp):
TATTCATACTAATTTT
Found at i:71017 original size:16 final size:17
Alignment explanation
Indices: 70975--71018 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
70965 TACTTTTATA
*
70975 TATTCATACTATTTTTG
1 TATTCATACTAATTTTG
*
70992 TATTCCTACTAATTTT-
1 TATTCATACTAATTTTG
*
71008 TATTCTTACTA
1 TATTCATACTA
71019 GTATTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTCATACTAATTTTG
Found at i:79455 original size:37 final size:38
Alignment explanation
Indices: 79353--79457 Score: 123
Period size: 33 Copynumber: 2.9 Consensus size: 38
79343 AATTCGACCA
* *
79353 GACCTGAATATCACACTTAAAAAAACCTGA--C-A--C
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTC
*
79386 GACCCGAATATCACACTTAAAAAAATCCGACCCGACTC
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTC
**
79424 GACCCGAATATCATGCTT-AAAAAACCCGACCCGA
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGA
79458 ACAAAATAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
33 27 0.44
35 1 0.02
36 1 0.02
37 15 0.25
38 17 0.28
ACGTcount: A:0.41, C:0.31, G:0.11, T:0.16
Consensus pattern (38 bp):
GACCCGAATATCACACTTAAAAAAACCCGACCCGACTC
Found at i:79712 original size:31 final size:31
Alignment explanation
Indices: 79641--79716 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
79631 AACTCGAACT
*
79641 CGACCCGACCCGAATATCACACTTAAAAAAA
1 CGACCCGACCCGAATATCACAATTAAAAAAA
* * * **
79672 CGACTCGACCCGAATAT-ATGAATTAGAAACC
1 CGACCCGACCCGAATATCA-CAATTAAAAAAA
79703 CGACCCGACCCGAA
1 CGACCCGACCCGAA
79717 ATAATAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.39, C:0.33, G:0.14, T:0.13
Consensus pattern (31 bp):
CGACCCGACCCGAATATCACAATTAAAAAAA
Found at i:80890 original size:16 final size:14
Alignment explanation
Indices: 80857--80890 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
80847 TCAGCATAAT
*
80857 GCGCGTTTCAGAGG
1 GCGCGCTTCAGAGG
80871 GCGCGCTTCAGAGG
1 GCGCGCTTCAGAGG
80885 GCGCGC
1 GCGCGC
80891 CTTACCCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.29, G:0.44, T:0.15
Consensus pattern (14 bp):
GCGCGCTTCAGAGG
Found at i:83164 original size:4 final size:4
Alignment explanation
Indices: 83155--83313 Score: 318
Period size: 4 Copynumber: 39.8 Consensus size: 4
83145 TATTCTATTC
83155 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
83203 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
83251 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
83299 TATG TATG TATG TAT
1 TATG TATG TATG TAT
83314 ATGCATGGTA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 155 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:84734 original size:12 final size:12
Alignment explanation
Indices: 84717--84741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84707 AGTGAATCGA
84717 TAAAATAAAGTT
1 TAAAATAAAGTT
84729 TAAAATAAAGTT
1 TAAAATAAAGTT
84741 T
1 T
84742 TTATATTTAT
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAAATAAAGTT
Found at i:86377 original size:21 final size:21
Alignment explanation
Indices: 86353--86397 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
86343 CGCCCGGAGT
*
86353 TATTTTATTTTTATATATATA
1 TATTTTATTTATATATATATA
86374 TATTTTATTTATATATATATA
1 TATTTTATTTATATATATATA
86395 TAT
1 TAT
86398 AATATAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTATTTATATATATATA
Found at i:86496 original size:35 final size:36
Alignment explanation
Indices: 86434--86693 Score: 226
Period size: 37 Copynumber: 7.0 Consensus size: 36
86424 AAAATATAAT
*
86434 ATATTTTGAAAACATTTATATATTATATAGTTTTTAAAA
1 ATATTTTG-AAACA--TATATAATATATAGTTTTTAAAA
86473 ATATTTTGAAA-ATATATAATATATAGTTTTT-AAA
1 ATATTTTGAAACATATATAATATATAGTTTTTAAAA
* *
86507 ATCATTTTGAGA-ATATATAATATATAGTTTTTTTAAAC
1 AT-ATTTTGAAACATATATAATATATAG--TTTTTAAAA
* * *
86545 AT-TTTTAAAATATATATAATATATAGTTTTTGAAA
1 ATATTTTGAAACATATATAATATATAGTTTTTAAAA
* * *
86580 ACATTTGTGAAAACATATATATTATATAG-TTTTGAAA
1 ATATTT-TG-AAACATATATAATATATAGTTTTTAAAA
* *
86617 ATATTTTTGAAAACATTTATATATTATATAATTTTT-AAA
1 ATA-TTTTG-AAACA--TATATAATATATAGTTTTTAAAA
* * *
86656 ATATTTTTGAAAACTTATATAATATATAATTTTGAAAA
1 ATA-TTTTG-AAACATATATAATATATAGTTTTTAAAA
86694 CATTTAAACG
Statistics
Matches: 192, Mismatches: 16, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
34 5 0.03
35 49 0.26
36 9 0.05
37 57 0.30
38 30 0.16
39 38 0.20
40 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
ATATTTTGAAACATATATAATATATAGTTTTTAAAA
Found at i:87933 original size:8 final size:7
Alignment explanation
Indices: 87916--87961 Score: 51
Period size: 8 Copynumber: 6.4 Consensus size: 7
87906 TTTCCCTTAA
87916 ATTTATT
1 ATTTATT
87923 ATTTCATT
1 ATTT-ATT
87931 ATTT-TT
1 ATTTATT
87937 ATTT-TT
1 ATTTATT
87943 ATTTTATT
1 A-TTTATT
87951 ATTTTATT
1 A-TTTATT
87959 ATT
1 ATT
87962 AGTATTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 9 0.25
7 9 0.25
8 18 0.50
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTATT
Found at i:87946 original size:20 final size:21
Alignment explanation
Indices: 87916--87962 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
87906 TTTCCCTTAA
87916 ATTTATTATTTCATTATTTTT
1 ATTTATTATTTCATTATTTTT
*
87937 ATTT-TTATTTTATTA-TTTT
1 ATTTATTATTTCATTATTTTT
87956 A-TTATTA
1 ATTTATTA
87963 GTATTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
20 10 0.42
21 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTATTATTTCATTATTTTT
Found at i:87953 original size:28 final size:28
Alignment explanation
Indices: 87917--87970 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
87907 TTCCCTTAAA
**
87917 TTTATTATTTCATTATTTTTATTTTTAT
1 TTTATTATTTCATTATTAGTATTTTTAT
*
87945 TTTATTATTTTATTATTAGTATTTTT
1 TTTATTATTTCATTATTAGTATTTTT
87971 TGTTCCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTATTATTTCATTATTAGTATTTTTAT
Found at i:93186 original size:8 final size:8
Alignment explanation
Indices: 93173--93199 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
93163 GCATATGTAC
93173 TGATAAAA
1 TGATAAAA
93181 TGATAAAA
1 TGATAAAA
93189 TGATAAAA
1 TGATAAAA
93197 TGA
1 TGA
93200 GAAACACCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (8 bp):
TGATAAAA
Found at i:93373 original size:9 final size:9
Alignment explanation
Indices: 93361--93411 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
93351 TAATTCATAT
93361 AAAATATAA
1 AAAATATAA
93370 AAAA-ATACA
1 AAAATATA-A
93379 TAAAATATAA
1 -AAAATATAA
93389 AAAA-ATACA
1 AAAATATA-A
93398 TAAAATATAA
1 -AAAATATAA
93408 AAAA
1 AAAA
93412 ATTTAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
8 6 0.17
9 14 0.39
10 10 0.28
11 6 0.17
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATATAA
Found at i:93376 original size:10 final size:10
Alignment explanation
Indices: 93361--93419 Score: 59
Period size: 10 Copynumber: 6.1 Consensus size: 10
93351 TAATTCATAT
93361 AAAATATAAA
1 AAAATATAAA
* *
93371 AAAATA-CAT
1 AAAATATAAA
93380 AAAATATAAA
1 AAAATATAAA
* *
93390 AAAATA-CAT
1 AAAATATAAA
93399 AAAATATAAA
1 AAAATATAAA
*
93409 AAAATTTAAA
1 AAAATATAAA
93419 A
1 A
93420 TTTCTAAGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
9 14 0.37
10 24 0.63
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAATATAAA
Found at i:93383 original size:19 final size:19
Alignment explanation
Indices: 93359--93413 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
93349 GATAATTCAT
93359 ATAAAATATAAAAAAATAC
1 ATAAAATATAAAAAAATAC
93378 ATAAAATATAAAAAAATAC
1 ATAAAATATAAAAAAATAC
93397 ATAAAATATAAAAAAAT
1 ATAAAATATAAAAAAAT
93414 TTAAAATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAAATATAAAAAAATAC
Found at i:94678 original size:38 final size:38
Alignment explanation
Indices: 94598--94679 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 38
94588 TATAAGTTAG
* * *
94598 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCCT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTAAAAATCAT
* *
94637 AAAAATTTATATAATTTTTTTTACAAAATTAAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTAAAAATCAT
94675 AAAAA
1 AAAAA
94680 ATGTTTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 14 0.38
39 23 0.62
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:98415 original size:26 final size:26
Alignment explanation
Indices: 98358--98411 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
98348 GAATAAAGTT
98358 TTGTTGTTGTTGTTAAGTCATTTTTG
1 TTGTTGTTGTTGTTAAGTCATTTTTG
98384 TTGTTGTTGTTGTTAAGTCA-TTTTG
1 TTGTTGTTGTTGTTAAGTCATTTTTG
98409 TTG
1 TTG
98412 GTTGATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.11, C:0.04, G:0.24, T:0.61
Consensus pattern (26 bp):
TTGTTGTTGTTGTTAAGTCATTTTTG
Found at i:103092 original size:23 final size:23
Alignment explanation
Indices: 103059--103103 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
103049 ATTGTTGATT
103059 CAATTTCACAT-TCTTAAATTTTA
1 CAATTTCACATCT-TTAAATTTTA
*
103082 CAATTTTACATCTTTAAATTTT
1 CAATTTCACATCTTTAAATTTT
103104 TAATATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (23 bp):
CAATTTCACATCTTTAAATTTTA
Found at i:105298 original size:17 final size:17
Alignment explanation
Indices: 105276--105309 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
105266 CTATGATTCA
105276 TTTCCTCCCCCTTCAAC
1 TTTCCTCCCCCTTCAAC
105293 TTTCCTCCCCCTTCAAC
1 TTTCCTCCCCCTTCAAC
105310 AACATCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTCCTCCCCCTTCAAC
Found at i:113893 original size:60 final size:60
Alignment explanation
Indices: 113724--113876 Score: 270
Period size: 60 Copynumber: 2.5 Consensus size: 60
113714 ATCAGGTAAA
*
113724 TATTTTGTAATTTTTAATAATTGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
1 TATTTTATAATTTTTAATAATTGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
*
113784 TATTTTATAATTTTTAATAATCGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
1 TATTTTATAATTTTTAATAATTGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
* *
113844 TGTTTTATAACTTTTAATAATTGAGGGACTCAA
1 TATTTTATAATTTTTAATAATTGAGGGACTCAA
113877 TAAAGTAATA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 88 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (60 bp):
TATTTTATAATTTTTAATAATTGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
Found at i:114177 original size:21 final size:21
Alignment explanation
Indices: 114153--114201 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
114143 AAAGTGTCAT
114153 AAAATAACAAAACCGATAGAA
1 AAAATAACAAAACCGATAGAA
* *
114174 AAAATAACAAAATCGGTAGAA
1 AAAATAACAAAACCGATAGAA
*
114195 ATAATAA
1 AAAATAA
114202 TGTTTTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAATAACAAAACCGATAGAA
Found at i:114566 original size:16 final size:16
Alignment explanation
Indices: 114545--114575 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
114535 ATGGTTAAAC
*
114545 GCTGAATGATTCAAAT
1 GCTGAACGATTCAAAT
114561 GCTGAACGATTCAAA
1 GCTGAACGATTCAAA
114576 GGTTCTATAT
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:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (16 bp):
GCTGAACGATTCAAAT
Found at i:117370 original size:41 final size:41
Alignment explanation
Indices: 117276--117659 Score: 271
Period size: 41 Copynumber: 9.4 Consensus size: 41
117266 AGCGTTTACA
* * *
117276 TAACAAACGCCACAA-AATGGT-A-ACTTTAGCGGCATTTTT
1 TAACAAACGCCGCAATAA-GGTAATACTTTAGTGGCGTTTTT
*
117315 ATAA-AAACGCCGCAATAAGGTAAT-CTATAGTGGCGTTTTAT
1 -TAACAAACGCCGCAATAAGGTAATACTTTAGTGGCGTTTT-T
*
117356 TAACAAACGCCGCAA-AAGAGTAATAC-TTAGCGGCG-TTTT
1 TAACAAACGCCGCAATAAG-GTAATACTTTAGTGGCGTTTTT
* *
117395 TATACAAACGCCGCAAT-AGAGTAGTACTTTAGCGGCG-TTTT
1 TA-ACAAACGCCGCAATAAG-GTAATACTTTAGTGGCGTTTTT
*
117436 TATACAAACGCCGCAAT-AGAGTATTACTTTAGTGGCG-TTTT
1 TA-ACAAACGCCGCAATAAG-GTAATACTTTAGTGGCGTTTTT
* * * * *
117477 TATACAAACGCCACAATAGGGTTCAT-CTGTAGTGGTGGTTTTT
1 TA-ACAAACGCCGCAATAAGG-TAATACTTTAGTGG-CGTTTTT
* *
117520 CAACAAACGCCGCAAT-AGAGTAGTACTTTAGTGGCGTTTTT
1 TAACAAACGCCGCAATAAG-GTAATACTTTAGTGGCGTTTTT
* * * *
117561 ATAA-AAACGCCACAATAGGGTTCAT-CTTTAGTGGCATTTTT
1 -TAACAAACGCCGCAATAAGG-TAATACTTTAGTGGCGTTTTT
* * * * * * *
117602 TCAACAAACACCGTAATAAAGTAGTACTTTAGCGGCATTTTA
1 T-AACAAACGCCGCAATAAGGTAATACTTTAGTGGCGTTTTT
*
117644 T-ACAAAAGCCGCAATA
1 TAACAAACGCCGCAATA
117660 GTTTGGTATG
Statistics
Matches: 282, Mismatches: 40, Indels: 44
0.77 0.11 0.12
Matches are distributed among these distances:
39 16 0.06
40 62 0.22
41 141 0.50
42 58 0.21
43 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
TAACAAACGCCGCAATAAGGTAATACTTTAGTGGCGTTTTT
Found at i:117541 original size:83 final size:81
Alignment explanation
Indices: 117298--117660 Score: 410
Period size: 83 Copynumber: 4.4 Consensus size: 81
117288 CAAAATGGTA
* * * * * *
117298 ACTTTAGCGGCATTTTTATAAAAACGCCGCAATAAGGTAATCTATAGTGGCGTTTTATTAACAAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTCATCTTTAGTGGCGTTTT-TCAACAAA
* *
117363 CGCCGCAAAAGAGTAAT
65 CGCCGCAATAGAGTAGT
* *
117380 AC-TTAGCGGCGTTTTTATACAAACGCCGCAATAGAGT-AGTACTTTAGCGGCGTTTTT-ATACA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTCA-T-CTTTAGTGGCGTTTTTCA-ACA
*
117442 AACGCCGCAATAGAGTATT
63 AACGCCGCAATAGAGTAGT
* * * *
117461 ACTTTAGTGGCGTTTTTATACAAACGCCACAATAGGGTTCATCTGTAGTGGTGGTTTTTCAACAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGG-TCATCTTTAGTGG-CGTTTTTCAACAA
117526 ACGCCGCAATAGAGTAGT
64 ACGCCGCAATAGAGTAGT
* * * *
117544 ACTTTAGTGGCGTTTTTATAAAAACGCCACAATAGGGTTCATCTTTAGTGGCATTTTTTCAACAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGG-TCATCTTTAGTGGC-GTTTTTCAACAA
* * *
117609 ACACCGTAATAAAGTAGT
64 ACGCCGCAATAGAGTAGT
* *
117627 ACTTTAGCGGC-ATTTTATACAAAAGCCGCAATAG
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAG
117661 TTTGGTATGT
Statistics
Matches: 245, Mismatches: 27, Indels: 18
0.84 0.09 0.06
Matches are distributed among these distances:
80 2 0.01
81 55 0.22
82 72 0.29
83 114 0.47
84 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (81 bp):
ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTCATCTTTAGTGGCGTTTTTCAACAAAC
GCCGCAATAGAGTAGT
Found at i:117550 original size:124 final size:124
Alignment explanation
Indices: 117298--117660 Score: 379
Period size: 124 Copynumber: 3.0 Consensus size: 124
117288 CAAAATGGTA
* * *
117298 ACTTTAGCGGCATTTTTATAAAAACGCCGCAATA-AGGTAAT-CTATAGTGGCG-TTTTATTAAC
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGA-GTATTACTTTAGTGGCGTTTTTATTAAC
*
117360 AAACGCCGCAAAAGAGTAATACTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAGT
65 AAACGCCACAAAAGAGTAATACTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAGT
*
117420 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTATTACTTTAGTGGCGTTTTTA-T-ACA
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGAGTATTACTTTAGTGGCGTTTTTATTAACA
* * * * *
117483 AACGCCACAATAGGGTTCAT-CTGTAGTGGTGGTTTTTCA-ACAAACGCCGCAATAGAGTAGT
66 AACGCCACAAAAGAG-TAATACT-TAGCGG-CGTTTTT-ATACAAACGCCGCAATAGAGTAGT
* * * * * *
117544 ACTTTAGTGGCGTTTTTATAAAAACGCCACAATAGGGT-TCATCTTTAGTGGCATTTTT-TCAAC
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGAGTATTA-CTTTAGTGGCGTTTTTATTAAC
* ** * * *
117607 AAACACCGTAATAA-AGTAGTACTTTAGCGGC-ATTTTATACAAAAGCCGCAATAG
65 AAACGCCACAA-AAGAGTAATAC-TTAGCGGCGTTTTTATACAAACGCCGCAATAG
117661 TTTGGTATGT
Statistics
Matches: 199, Mismatches: 28, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
122 54 0.27
123 41 0.21
124 84 0.42
125 18 0.09
126 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (124 bp):
ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGAGTATTACTTTAGTGGCGTTTTTATTAACA
AACGCCACAAAAGAGTAATACTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAGT
Found at i:119500 original size:3 final size:3
Alignment explanation
Indices: 119492--119519 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
119482 CATAACCTTC
119492 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
119520 TTTTAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:120752 original size:20 final size:22
Alignment explanation
Indices: 120729--120787 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
120719 TGATTTATTA
120729 TTATGGATTTCAA-TTTCTTG-
1 TTATGGATTTCAAGTTTCTTGT
* *
120749 TTATGGATTTTAAGTTTGTTGT
1 TTATGGATTTCAAGTTTCTTGT
*
120771 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
120788 ATTGGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.36
21 6 0.18
22 15 0.45
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.54
Consensus pattern (22 bp):
TTATGGATTTCAAGTTTCTTGT
Found at i:120985 original size:43 final size:43
Alignment explanation
Indices: 120899--120995 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
120889 GAGGTAATTA
* *
120899 GCGGCGTTTGTATCTTAAAACGCCGCTATAGATATGACATTTT
1 GCGGCGTTTGTATCTAAAAACGCCGCTATAGACATGACATTTT
*
120942 GCGGCGTTTGT-TCTAAAAAGCGCCGCTATATACCA-GATC-TTTT
1 GCGGCGTTTGTATCTAAAAA-CGCCGCTATAGA-CATGA-CATTTT
120985 GCGGCGTTTGT
1 GCGGCGTTTGT
120996 GGGAAAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 7 0.15
43 39 0.81
44 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTGTATCTAAAAACGCCGCTATAGACATGACATTTT
Found at i:121395 original size:15 final size:15
Alignment explanation
Indices: 121377--121410 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
121367 TTTGTTGACC
121377 CCCTTTTGATCAAGT
1 CCCTTTTGATCAAGT
* *
121392 CCCTTTTGTTTAAGT
1 CCCTTTTGATCAAGT
121407 CCCT
1 CCCT
121411 AACATGGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.29, G:0.12, T:0.44
Consensus pattern (15 bp):
CCCTTTTGATCAAGT
Found at i:143335 original size:19 final size:20
Alignment explanation
Indices: 143311--143348 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
143301 TGCAAACTTA
143311 TAGAAAAAA-AATGTGTAAC
1 TAGAAAAAAGAATGTGTAAC
*
143330 TAGAAAAAAGAATTTGTAA
1 TAGAAAAAAGAATGTGTAA
143349 AAAAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.03, G:0.16, T:0.24
Consensus pattern (20 bp):
TAGAAAAAAGAATGTGTAAC
Found at i:151496 original size:18 final size:19
Alignment explanation
Indices: 151469--151504 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
151459 TTTTTTTAAT
*
151469 GGTTCGGGTTTTTCGGTTC
1 GGTTCGGGTTTATCGGTTC
151488 GGTTC-GGTTTATCGGTT
1 GGTTCGGGTTTATCGGTT
151505 TTTCAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.03, C:0.14, G:0.36, T:0.47
Consensus pattern (19 bp):
GGTTCGGGTTTATCGGTTC
Found at i:153621 original size:20 final size:22
Alignment explanation
Indices: 153587--153633 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
153577 AATTAAATCG
153587 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
* *
153609 TATTTTT-TT-AATAAATATAT
1 TATTTTTATTGAATAAAAATAA
153629 TATTT
1 TATTT
153634 CAGTCCGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTTTATTGAATAAAAATAA
Found at i:155995 original size:61 final size:62
Alignment explanation
Indices: 155847--155999 Score: 163
Period size: 61 Copynumber: 2.5 Consensus size: 62
155837 TTAAATTATA
* * *
155847 ACCCTCATTT-TAAATTTGTCCTTAAACTTTT-GAATATTCTAATTTCATCCCTAAACTATTG
1 ACCCTC-TTTCTAAATTAGTCCTTAAACTTTTGGAATATTCTAATTTCACCCCTAAACTACTG
* * ** *
155908 -CTCTCATTCTAAACCAATCCTTAAACTTTTGGAA-ATTCTAATTTCACCCCCTAAACT-CTG
1 ACCCTCTTTCTAAATTAGTCCTTAAACTTTTGGAATATTCTAATTTCA-CCCCTAAACTACTG
**
155968 ACCCTCTTTCTAAATTAGTCCCCAAACTTTTG
1 ACCCTCTTTCTAAATTAGTCCTTAAACTTTTG
156000 TATATTCCAA
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
59 2 0.03
60 35 0.48
61 36 0.49
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (62 bp):
ACCCTCTTTCTAAATTAGTCCTTAAACTTTTGGAATATTCTAATTTCACCCCTAAACTACTG
Found at i:158376 original size:20 final size:20
Alignment explanation
Indices: 158353--158404 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
158343 AACGCGATCC
158353 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
158373 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
158393 CCAAAATCGCAA
1 CCAGAATCGCAA
158405 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:158421 original size:21 final size:20
Alignment explanation
Indices: 158394--158492 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
158384 AATCAGTTTC
158394 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
158415 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
158436 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
158456 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
158477 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
158493 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:158521 original size:20 final size:20
Alignment explanation
Indices: 158459--158652 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
158449 CGATTTTCCA
* ** *
158459 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
158479 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
158499 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
158519 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
158539 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
158559 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
158579 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
158599 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
158619 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
158640 AAATCGCAACGCG
1 AAATCGCAACGCG
158653 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:158543 original size:60 final size:60
Alignment explanation
Indices: 158459--158652 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
158449 CGATTTTCCA
* ** * *
158459 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
158519 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
158579 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
158640 AAATCGCAACGCG
1 AAATCGCAACGCG
158653 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:159069 original size:33 final size:33
Alignment explanation
Indices: 159030--159100 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
159020 TTCACTTAGA
*
159030 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
159063 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
159096 TTTCA
1 TTTCA
159101 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:159239 original size:14 final size:14
Alignment explanation
Indices: 159220--159274 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
159210 AGAATGACTG
159220 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
159234 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
159253 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
159267 TCGCAACG
1 TCGCAACG
159275 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:159287 original size:33 final size:33
Alignment explanation
Indices: 159220--159290 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
159210 AGAATGACTG
***
159220 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
159253 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
159286 TCGCA
1 TCGCA
159291 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:159308 original size:19 final size:19
Alignment explanation
Indices: 159286--159350 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
159276 GAAACCAAAA
*
159286 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
159305 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
159319 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
159338 TCGCGTTGCGATT
1 TCGCGTTGCGATT
159351 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:159327 original size:14 final size:14
Alignment explanation
Indices: 159308--159397 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
159298 TTTCATTTCG
159308 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
159322 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
159341 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
159355 CGTTGCGACAGTCATCTCG
1 CGTTGCG--A-T--TCTCT
159374 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
159388 CGTTGCGATT
1 CGTTGCGATT
159398 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 31 0.50
16 5 0.08
17 5 0.08
19 21 0.34
ACGTcount: A:0.10, C:0.27, G:0.23, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:159333 original size:33 final size:33
Alignment explanation
Indices: 159291--159405 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
159281 CAAAATCGCA
159291 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
159324 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*** *
159357 TTGCGACAGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
159390 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
159406 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:159747 original size:13 final size:13
Alignment explanation
Indices: 159712--159764 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
159702 TGATTCAATA
159712 GTTTAATTGA-TT
1 GTTTAATTGATTT
*
159724 GTTT-TTTGATTT
1 GTTTAATTGATTT
159736 GTTTAATTGATTT
1 GTTTAATTGATTT
**
159749 GTAAAAGTTGATTT
1 GTTTAA-TTGATTT
159763 GT
1 GT
159765 ATGTTTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 10 0.29
13 11 0.32
14 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (13 bp):
GTTTAATTGATTT
Found at i:159761 original size:38 final size:37
Alignment explanation
Indices: 159718--159866 Score: 113
Period size: 38 Copynumber: 4.2 Consensus size: 37
159708 AATAGTTTAA
159718 TTGATTGTTTTTTGATTTGTTTAATTGATTTGTAAAAG
1 TTGATTGTTTTTTGA-TTGTTTAATTGATTTGTAAAAG
* * *
159756 TTGA----TTTGT-A-TGTTT-TTTGA-TT-CAATAA-
1 TTGATTGTTTTTTGATTGTTTAATTGATTTGTAA-AAG
159784 TCTG-TATGTGTTTTTGATTGTTTAATTGATTTGTAAAAG
1 T-TGAT-TGT-TTTTTGATTGTTTAATTGATTTGTAAAAG
**
159823 TTGATTCAATTTTTGATTGTTTAATTGATTTGTAAAAG
1 TTGATT-GTTTTTTGATTGTTTAATTGATTTGTAAAAG
*
159861 ATGATT
1 TTGATT
159867 TGTAAAAGTT
Statistics
Matches: 86, Mismatches: 9, Indels: 32
0.68 0.07 0.25
Matches are distributed among these distances:
28 3 0.03
29 6 0.07
30 4 0.05
31 5 0.06
33 1 0.01
34 8 0.09
35 1 0.01
36 5 0.06
37 4 0.05
38 45 0.52
39 4 0.05
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (37 bp):
TTGATTGTTTTTTGATTGTTTAATTGATTTGTAAAAG
Found at i:159853 original size:19 final size:19
Alignment explanation
Indices: 159794--159853 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
159784 TCTGTATGTG
159794 TTTTTGATTGTTTAATTGA
1 TTTTTGATTGTTTAATTGA
* * ** * *
159813 TTTGTAAAAG-TTGATTCAA
1 TTTTTGATTGTTTAATT-GA
159832 TTTTTGATTGTTTAATTGA
1 TTTTTGATTGTTTAATTGA
159851 TTT
1 TTT
159854 GTAAAAGATG
Statistics
Matches: 27, Mismatches: 12, Indels: 4
0.63 0.28 0.09
Matches are distributed among these distances:
18 5 0.19
19 17 0.63
20 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
TTTTTGATTGTTTAATTGA
Found at i:159867 original size:14 final size:14
Alignment explanation
Indices: 159848--159883 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
159838 ATTGTTTAAT
159848 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
159862 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
159876 TGATTTGT
1 TGATTTGT
159884 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:160006 original size:19 final size:19
Alignment explanation
Indices: 159990--160091 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
159980 AAAAATGACT
159990 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
160009 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
160028 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
160042 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
160061 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
160081 ATCGCAATGCG
1 ATCGCAATGCG
160092 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:160140 original size:33 final size:33
Alignment explanation
Indices: 160098--160425 Score: 313
Period size: 33 Copynumber: 9.5 Consensus size: 33
160088 TGCGTTTATA
160098 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
160131 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
160164 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
160202 ATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
160240 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
160273 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
160313 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
160344 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
160377 ATTTCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
*
160410 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
160426 GTATTTTCCG
Statistics
Matches: 254, Mismatches: 24, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 136 0.54
34 1 0.00
35 10 0.04
36 11 0.04
37 2 0.01
38 68 0.27
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:160144 original size:19 final size:19
Alignment explanation
Indices: 160120--160425 Score: 374
Period size: 19 Copynumber: 17.4 Consensus size: 19
160110 GATTATCTCG
160120 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160139 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
160153 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160172 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
160191 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
160210 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
160229 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
160248 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
160262 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
160300 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
160314 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160333 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
160352 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
160366 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160385 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
160399 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
160418 TTGCGATT
1 TTGCGATT
160426 GTATTTTCCG
Statistics
Matches: 250, Mismatches: 12, Indels: 50
0.80 0.04 0.16
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 31 0.12
19 153 0.61
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:160425 original size:52 final size:52
Alignment explanation
Indices: 160120--160397 Score: 484
Period size: 52 Copynumber: 5.2 Consensus size: 52
160110 GATTATCTCG
*
160120 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* *
160172 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
160229 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
160281 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
160333 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
160385 TTGCGATTTTCAT
1 TTGCGATTTTCAT
160398 GTTGGGATTT
Statistics
Matches: 218, Mismatches: 3, Indels: 10
0.94 0.01 0.04
Matches are distributed among these distances:
52 160 0.73
54 7 0.03
55 8 0.04
57 43 0.20
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:162745 original size:12 final size:12
Alignment explanation
Indices: 162728--162752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
162718 TCTTCGGGGA
162728 CTTTTTCTTCTT
1 CTTTTTCTTCTT
162740 CTTTTTCTTCTT
1 CTTTTTCTTCTT
162752 C
1 C
162753 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:162961 original size:24 final size:24
Alignment explanation
Indices: 162927--162973 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
162917 CTGAAACATC
162927 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
162951 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
162974 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:163674 original size:20 final size:20
Alignment explanation
Indices: 163646--164014 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
163636 AAATTTCAGT
* * * *
163646 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
163666 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
163686 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
163706 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
163726 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163746 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
163766 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
163786 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163806 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163826 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
163846 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
163866 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163886 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
163906 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
163926 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
163946 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
163966 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
163986 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
164006 GTTGCGATT
1 GTTGCGATT
164015 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:174289 original size:2 final size:2
Alignment explanation
Indices: 174282--174323 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
174272 TTCTCAAACC
174282 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
174324 TAATCTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:182526 original size:2 final size:2
Alignment explanation
Indices: 182519--182549 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
182509 TGATTTTAAT
182519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
182550 GATTATGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:185589 original size:21 final size:21
Alignment explanation
Indices: 185565--185638 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
185555 AATGGTTTCT
*
185565 TCATTTCCGAGAACCCGGATA
1 TCATTTCCGAGCACCCGGATA
*
185586 TCATTTCCGGGCACCCGGATA
1 TCATTTCCGAGCACCCGGATA
*
185607 TCATTTCCGGGCACCCGGATA
1 TCATTTCCGAGCACCCGGATA
185628 TCCA-TTCCGAG
1 T-CATTTCCGAG
185639 GTTTCATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 47 0.96
22 2 0.04
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (21 bp):
TCATTTCCGAGCACCCGGATA
Found at i:189781 original size:31 final size:30
Alignment explanation
Indices: 189746--189803 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
189736 AATTGTACGT
*
189746 TTAGTACCTAAACTATCAGTTTTGTTCAGTC
1 TTAGTACCTAAACTATCAATTTT-TTCAGTC
* *
189777 TTAGTATCTAAACTTTCAATTTTTTCA
1 TTAGTACCTAAACTATCAATTTTTTCA
189804 AAATCATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (30 bp):
TTAGTACCTAAACTATCAATTTTTTCAGTC
Found at i:195090 original size:54 final size:54
Alignment explanation
Indices: 195015--195135 Score: 188
Period size: 54 Copynumber: 2.2 Consensus size: 54
195005 TAGTAACCCC
* * *
195015 TGCCCACGCCTTAACTAAAGACCTCTTCTGCGATAGCTTAGAATGAATAAGCCG
1 TGCCCACGCCTTAACTAAAGACCTCTTCTGCAATAGCTCAAAATGAATAAGCCG
* *
195069 TGCCCACGCCTTAACTGAAGACCTTTTCTGCAATAGCTCAAAATGAATAAGCCG
1 TGCCCACGCCTTAACTAAAGACCTCTTCTGCAATAGCTCAAAATGAATAAGCCG
*
195123 TGCCCATGCCTTA
1 TGCCCACGCCTTA
195136 TGCGGAAACC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (54 bp):
TGCCCACGCCTTAACTAAAGACCTCTTCTGCAATAGCTCAAAATGAATAAGCCG
Found at i:202583 original size:54 final size:54
Alignment explanation
Indices: 202505--202645 Score: 194
Period size: 54 Copynumber: 2.6 Consensus size: 54
202495 AACTAGTAAC
* * *
202505 CCGTGCCCACGCCTTAACTAAAGACCTCTTCTGCGATAGCTTAGAATGAATAAG
1 CCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAAAATGAATAAG
* *
202559 CCGTGCCCACGCCTTAACTGAAGACCTTTTTTGCGATAGCTCAAAATGAATAAG
1 CCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAAAATGAATAAG
* * *
202613 CCGTGCCAACGCCTTATGC-GAAAACCTCTTCTG
1 CCGTGCCCACGCCTTA-ACTGAAGACCTCTTCTG
202646 GTCTTTTTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 75 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (54 bp):
CCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAAAATGAATAAG
Found at i:202775 original size:19 final size:19
Alignment explanation
Indices: 202734--202775 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
202724 GAATGTGAGT
* *
202734 ATATGTGTCATATGTTATT
1 ATATGTGACATATGTTATG
202753 ATATGTGACATGAT-TTATG
1 ATATGTGACAT-ATGTTATG
202772 ATAT
1 ATAT
202776 ATGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (19 bp):
ATATGTGACATATGTTATG
Found at i:205981 original size:2 final size:2
Alignment explanation
Indices: 205925--205967 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
205915 ACACACACAG
205925 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
205967 A
1 A
205968 CCATCAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:206418 original size:2 final size:2
Alignment explanation
Indices: 206411--206447 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
206401 TGCCATGCGT
206411 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
206448 TTTAGGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:211733 original size:17 final size:17
Alignment explanation
Indices: 211711--211744 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
211701 TGTTGAACCC
*
211711 TAATTTGTTTTTTTATT
1 TAATTTATTTTTTTATT
211728 TAATTTATTTTTTTATT
1 TAATTTATTTTTTTATT
211745 CACTATAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TAATTTATTTTTTTATT
Done.