Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 21
Found at i:3645656 original size:15 final size:15
Alignment explanation
Indices: 3645631--3645673 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3645621 CCCCCTGCAT
*
3645631 CCGCACCGCATCCAC
1 CCGCCCCGCATCCAC
* *
3645646 CCGTCCCGCATCCGC
1 CCGCCCCGCATCCAC
*
3645661 CCGCCCCACATCC
1 CCGCCCCGCATCC
3645674 GCCTGCCCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.14, C:0.63, G:0.14, T:0.09
Consensus pattern (15 bp):
CCGCCCCGCATCCAC
Found at i:3645674 original size:15 final size:15
Alignment explanation
Indices: 3645639--3645681 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3645629 ATCCGCACCG
* * *
3645639 CATCCACCCGTCCCG
1 CATCCGCCCGCCCCA
3645654 CATCCGCCCGCCCCA
1 CATCCGCCCGCCCCA
*
3645669 CATCCGCCTGCCC
1 CATCCGCCCGCCC
3645682 AACTATATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.63, G:0.14, T:0.12
Consensus pattern (15 bp):
CATCCGCCCGCCCCA
Found at i:3648763 original size:3 final size:3
Alignment explanation
Indices: 3648757--3648806 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
3648747 GTATTTTATT
* * *
3648757 ATA ATA ATA ATA GTA GTA ATA ATAA ATA A-A ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
3648802 ATA AT
1 ATA AT
3648807 TAAAACTCGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3648789 original size:12 final size:12
Alignment explanation
Indices: 3648774--3648811 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3648764 TAATAGTAGT
3648774 AATAATAAATAA
1 AATAATAAATAA
3648786 AATAAT-AATAA
1 AATAATAAATAA
*
3648797 CAATAATAATTAA
1 -AATAATAAATAA
3648810 AA
1 AA
3648812 CTCGGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 5 0.22
12 14 0.61
13 4 0.17
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATAAATAA
Found at i:3652430 original size:12 final size:11
Alignment explanation
Indices: 3652407--3652463 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
3652397 TACTTGATCA
*
3652407 TTTTTCTTTCT
1 TTTTTTTTTCT
3652418 TTTATTTTTTCT
1 TTT-TTTTTTCT
**
3652430 TCTTTTTTCACT
1 T-TTTTTTTTCT
3652442 TTTTTTTTTGCT
1 TTTTTTTTT-CT
*
3652454 TTTTGTTTTC
1 TTTTTTTTTC
3652464 GCCTTGATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 10 0.27
12 25 0.68
13 2 0.05
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:3656174 original size:2 final size:2
Alignment explanation
Indices: 3656167--3656211 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
3656157 CTTATCTTGG
**
3656167 AT AT AT AT AT AT AT AT AT AT AT GGG AT A- 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
3656209 AT A
1 AT A
3656212 GGGGCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3659836 original size:57 final size:57
Alignment explanation
Indices: 3659767--3659885 Score: 229
Period size: 57 Copynumber: 2.1 Consensus size: 57
3659757 AATATCTAGT
*
3659767 ACGAATTAGCGAATTGAGAAGTGGGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
1 ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
3659824 ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
1 ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
3659881 ACGAA
1 ACGAA
3659886 GGGCTGCCGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.24
Consensus pattern (57 bp):
ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
Found at i:3662510 original size:32 final size:32
Alignment explanation
Indices: 3662443--3662503 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3662433 TGACATGGAT
* *
3662443 TATGTCATATCATTACTTTAAGTGATGTTCTA
1 TATGTCATATCATCACTTTAAGTGATGTGCTA
**
3662475 TATGTCATATCATCACTTTGGGTGATGTG
1 TATGTCATATCATCACTTTAAGTGATGTG
3662504 GCATATGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (32 bp):
TATGTCATATCATCACTTTAAGTGATGTGCTA
Found at i:3671449 original size:15 final size:15
Alignment explanation
Indices: 3671425--3671473 Score: 89
Period size: 15 Copynumber: 3.3 Consensus size: 15
3671415 TTGCAGTCTC
*
3671425 CGGCATTCAGTATTT
1 CGGCAATCAGTATTT
3671440 CGGCAATCAGTATTT
1 CGGCAATCAGTATTT
3671455 CGGCAATCAGTATTT
1 CGGCAATCAGTATTT
3671470 CGGC
1 CGGC
3671474 TTAGGAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (15 bp):
CGGCAATCAGTATTT
Found at i:3672006 original size:16 final size:17
Alignment explanation
Indices: 3671985--3672016 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3671975 CCGGTTTCGG
3671985 TTTTAAAAAA-CGGTTT
1 TTTTAAAAAACCGGTTT
3672001 TTTTAAAAAACCGGTT
1 TTTTAAAAAACCGGTT
3672017 AAAAAAACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAACCGGTTT
Found at i:3672369 original size:13 final size:13
Alignment explanation
Indices: 3672348--3672377 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3672338 AAGTTCGATA
3672348 AATTCAAATACTT
1 AATTCAAATACTT
*
3672361 AATTGAAATACTT
1 AATTCAAATACTT
3672374 AATT
1 AATT
3672378 AACTCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (13 bp):
AATTCAAATACTT
Found at i:3672484 original size:32 final size:33
Alignment explanation
Indices: 3672388--3672486 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3672378 AACTCAAAAT
* * *
3672388 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3672421 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3672454 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3672486 A
1 A
3672487 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:3675900 original size:22 final size:23
Alignment explanation
Indices: 3675874--3675925 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3675864 TATAATAAAA
3675874 ATATAAA-TTATTTTT-TATTCAT
1 ATATAAATTTATTTTTATA-TCAT
*
3675896 ATATATATTTATTTTTATATCAT
1 ATATAAATTTATTTTTATATCAT
*
3675919 AAATAAA
1 ATATAAA
3675926 ACATAATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 6 0.24
23 17 0.68
24 2 0.08
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATAAATTTATTTTTATATCAT
Found at i:3686247 original size:12 final size:12
Alignment explanation
Indices: 3686203--3686265 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
3686193 GGTCAAGTAT
3686203 CATATCAGAATC
1 CATATCAGAATC
*
3686215 CA-AGTCAAGTAT-
1 CATA-TC-AGAATC
*
3686227 CAGATCAGAATC
1 CATATCAGAATC
3686239 CATATCAGATAT-
1 CATATCAGA-ATC
*
3686251 CATATCATAATC
1 CATATCAGAATC
3686263 CAT
1 CAT
3686266 GTCAAGTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
11 7 0.17
12 27 0.66
13 7 0.17
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (12 bp):
CATATCAGAATC
Found at i:3686282 original size:24 final size:24
Alignment explanation
Indices: 3686160--3686285 Score: 155
Period size: 24 Copynumber: 5.2 Consensus size: 24
3686150 AAAATCAAAA
* *
3686160 CATAATTCATGTTAAGTATCATAT
1 CATAATCCATGTCAAGTATCATAT
* *
3686184 CAAAATCCAGGTCAAGTATCATAT
1 CATAATCCATGTCAAGTATCATAT
* * *
3686208 CAGAATCCAAGTCAAGTATCAGAT
1 CATAATCCATGTCAAGTATCATAT
* *
3686232 CAGAATCCATATC-AGATATCATAT
1 CATAATCCATGTCAAG-TATCATAT
3686256 CATAATCCATGTCAAGTATCATAT
1 CATAATCCATGTCAAGTATCATAT
3686280 CATAAT
1 CATAAT
3686286 TCAAATCGAA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 84 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (24 bp):
CATAATCCATGTCAAGTATCATAT
Found at i:3687305 original size:26 final size:26
Alignment explanation
Indices: 3687276--3687345 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
3687266 TCAGTTTTAT
* * *
3687276 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCACTCATTCCAGAGCTCAAGGATA
*
3687302 TCCACTCATTCCTGAGCTCAAGGATA
1 TCCACTCATTCCAGAGCTCAAGGATA
*
3687328 TCCACTCATTCCTGAGCT
1 TCCACTCATTCCAGAGCT
3687346 TGATGATACT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (26 bp):
TCCACTCATTCCAGAGCTCAAGGATA
Found at i:3687353 original size:26 final size:26
Alignment explanation
Indices: 3687289--3687345 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
3687279 ATTCATTTCA
3687289 GAGCTCGAGGATATCCACTCATTCCT
1 GAGCTCGAGGATATCCACTCATTCCT
*
3687315 GAGCTCAAGGATATCCACTCATTCCT
1 GAGCTCGAGGATATCCACTCATTCCT
3687341 GAGCT
1 GAGCT
3687346 TGATGATACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (26 bp):
GAGCTCGAGGATATCCACTCATTCCT
Found at i:3689684 original size:13 final size:13
Alignment explanation
Indices: 3689666--3689699 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
3689656 ATTGACATTA
3689666 AGGCATACTAGAG
1 AGGCATACTAGAG
3689679 AGGCATACTAGAG
1 AGGCATACTAGAG
3689692 AGGCATAC
1 AGGCATAC
3689700 CAGGTGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (13 bp):
AGGCATACTAGAG
Found at i:3691776 original size:13 final size:13
Alignment explanation
Indices: 3691758--3691782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3691748 TAAAAATAAA
3691758 ATTATTTAAAAAT
1 ATTATTTAAAAAT
3691771 ATTATTTAAAAA
1 ATTATTTAAAAA
3691783 AAATCTGAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTATTTAAAAAT
Found at i:3693150 original size:22 final size:22
Alignment explanation
Indices: 3693123--3693169 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3693113 AAAACATAAT
3693123 AGATTACACAGAGAAAAAAGAA
1 AGATTACACAGAGAAAAAAGAA
3693145 AGATTACACAGAGAAAAAAGAA
1 AGATTACACAGAGAAAAAAGAA
3693167 AGA
1 AGA
3693170 GGAACCGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.64, C:0.09, G:0.19, T:0.09
Consensus pattern (22 bp):
AGATTACACAGAGAAAAAAGAA
Found at i:3699030 original size:44 final size:44
Alignment explanation
Indices: 3698967--3699066 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 44
3698957 ATATATTTGG
* * *
3698967 ATTAGTGCTATGACACTTTAGTATCAGTTCTAAGGCACTTCATT
1 ATTAGTGCTATGAAACTTTAGTATCAGTGCTAAGACACTTCATT
* *
3699011 ATTAGTGTTATGAAACTTTAGTATCAGTGCTAAGACATTTCATT
1 ATTAGTGCTATGAAACTTTAGTATCAGTGCTAAGACACTTCATT
3699055 ATATGAGTGCTA
1 AT-T-AGTGCTA
3699067 CGACATTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 41 0.85
45 1 0.02
46 6 0.12
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (44 bp):
ATTAGTGCTATGAAACTTTAGTATCAGTGCTAAGACACTTCATT
Found at i:3699039 original size:22 final size:22
Alignment explanation
Indices: 3698970--3699039 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
3698960 TATTTGGATT
*
3698970 AGTGCTATGACACTTTAGTATC
1 AGTGTTATGACACTTTAGTATC
* * * * *
3698992 AGT-TCTAAGGCACTTCATTATT
1 AGTGT-TATGACACTTTAGTATC
*
3699014 AGTGTTATGAAACTTTAGTATC
1 AGTGTTATGACACTTTAGTATC
3699036 AGTG
1 AGTG
3699040 CTAAGACATT
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (22 bp):
AGTGTTATGACACTTTAGTATC
Found at i:3699081 original size:24 final size:24
Alignment explanation
Indices: 3699036--3699081 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3699026 CTTTAGTATC
* *
3699036 AGTGCTAAGACATTTCATTATATG
1 AGTGCTAAGACATTGCAGTATATG
*
3699060 AGTGCTACGACATTGCAGTATA
1 AGTGCTAAGACATTGCAGTATA
3699082 AAATACTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (24 bp):
AGTGCTAAGACATTGCAGTATATG
Found at i:3699797 original size:32 final size:33
Alignment explanation
Indices: 3699754--3699825 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
3699744 TTTTTATAAC
* ** *
3699754 TTTTTACTGTGACTGAATAAT-TTTGTTACAAT
1 TTTTTATTGTGAAAGAATAATATTTGTCACAAT
* *
3699786 TTTTTATTGTGAAAGAATATTATTTGTCACATT
1 TTTTTATTGTGAAAGAATAATATTTGTCACAAT
3699819 TTTTTAT
1 TTTTTAT
3699826 AATGATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (33 bp):
TTTTTATTGTGAAAGAATAATATTTGTCACAAT
Found at i:3703118 original size:13 final size:15
Alignment explanation
Indices: 3703097--3703134 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
3703087 AGCACTATCA
3703097 TTGTGTGTGTGATGC
1 TTGTGTGTGTGATGC
3703112 TTGTGTGTGTGATGC
1 TTGTGTGTGTGATGC
3703127 TTGTGTGT
1 TTGTGTGT
3703135 TGCATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.05, G:0.39, T:0.50
Consensus pattern (15 bp):
TTGTGTGTGTGATGC
Found at i:3712440 original size:51 final size:51
Alignment explanation
Indices: 3712334--3712662 Score: 270
Period size: 51 Copynumber: 6.5 Consensus size: 51
3712324 AATGGAATTA
* * * ** * *
3712334 TATGTTAAGTTTCACTTTTAGAATTTAAGTGCTAATTTCACTAATCTAAGCC
1 TATGTTAAGTTTCACTGTTGGAA-TTAAGTGTTAATTTCACCGATGTAAGTC
* *
3712386 TATGTTAAGTTTCACTGTTGTAATTAAGTATTAATTTCACCGATGTAAGTC
1 TATGTTAAGTTTCACTGTTGGAATTAAGTGTTAATTTCACCGATGTAAGTC
* * * *
3712437 TATGTAAAGTTACAATGCTT-GAGTTAAGTGTTAATTTCACCTG-TGTAAGTC
1 TATGTTAAGTTTCACTG-TTGGAATTAAGTGTTAATTTCACC-GATGTAAGTC
* * ** * *
3712488 TATATTAAGTTCCACTGTTGGAATTATCTGTTAATTTCATCGCTGTAAGTC
1 TATGTTAAGTTTCACTGTTGGAATTAAGTGTTAATTTCACCGATGTAAGTC
*** ** ** *
3712539 TATGTTAAGTTTTGTTACTGGAATTAAGTGTTAATTAGA-CTAGTGTAAGTC
1 TATGTTAAGTTTCACTGTTGGAATTAAGTGTTAATTTCACCGA-TGTAAGTC
* * * * * * *
3712590 TATGTTGAG-TTCACTATTGGAATTAAGTGATAATTTAACTGGTGTAAGTA
1 TATGTTAAGTTTCACTGTTGGAATTAAGTGTTAATTTCACCGATGTAAGTC
* *
3712640 TATGTTAGGTTTCACTGGTGGAA
1 TATGTTAAGTTTCACTGTTGGAA
3712663 ATATATGATA
Statistics
Matches: 218, Mismatches: 52, Indels: 15
0.76 0.18 0.05
Matches are distributed among these distances:
50 40 0.18
51 155 0.71
52 23 0.11
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.42
Consensus pattern (51 bp):
TATGTTAAGTTTCACTGTTGGAATTAAGTGTTAATTTCACCGATGTAAGTC
Found at i:3712907 original size:69 final size:68
Alignment explanation
Indices: 3712740--3713037 Score: 210
Period size: 69 Copynumber: 4.3 Consensus size: 68
3712730 ATGGTATGCA
** * * * *
3712740 AAGA-CACCTAATCATATTTATTCCACGTAACTCACAATGGAGCCCCAAAGGATTAGAGTCACTC
1 AAGAGCACCTAATCATATTTATTATAGGTGACTCAC-ATGGAGCCCCAAATGATTAGAGTGACTC
* *
3712804 ACAT
65 ATAC
* * * * * * * * *
3712808 GATAGCATCTAATCATACTTGTTTTGGGTGACTCGTACAT-GAGCCCC-GATGAATTAGAGTTAC
1 AAGAGCACCTAATCATATTTATTATAGGTGACTC--ACATGGAGCCCCAAATG-ATTAGAGTGAC
3712871 TCATA-
63 TCATAC
* *
3712876 AGAGAGCACCTAGTCATGTTTATTATAGGTGACTCACATGGGAGCCCCAAATGATTAGAGTGACT
1 A-AGAGCACCTAATCATATTTATTATAGGTGACTCACAT-GGAGCCCCAAATGATTAGAGTGACT
*
3712941 CGTAC
64 CATAC
* * * * * * *
3712946 AAGAGCACCTAATCATATTTATTTTGGGTGACTCATGAGGGAGTCACAAAGGATTCA-AGTGACT
1 AAGAGCACCTAATCATATTTATTATAGGTGACTCA-CATGGAGCCCCAAATGATT-AGAGTGACT
*
3713010 CACAC
64 CATAC
** *
3713015 GGGAGCACATAATCATATTTATT
1 AAGAGCACCTAATCATATTTATT
3713038 TCGGGTGAAT
Statistics
Matches: 179, Mismatches: 40, Indels: 21
0.75 0.17 0.09
Matches are distributed among these distances:
67 4 0.02
68 4 0.02
69 161 0.90
70 8 0.04
71 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (68 bp):
AAGAGCACCTAATCATATTTATTATAGGTGACTCACATGGAGCCCCAAATGATTAGAGTGACTCA
TAC
Found at i:3715269 original size:22 final size:22
Alignment explanation
Indices: 3715244--3715296 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
3715234 GTGGTATGAA
3715244 ACTTTAGTATCAGTGCTAAGAC
1 ACTTTAGTATCAGTGCTAAGAC
* * * * *
3715266 ACTTGAATATTAGTGCTTAGAT
1 ACTTTAGTATCAGTGCTAAGAC
*
3715288 AATTTAGTA
1 ACTTTAGTA
3715297 CGCTAGTCGA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
ACTTTAGTATCAGTGCTAAGAC
Found at i:3724153 original size:22 final size:23
Alignment explanation
Indices: 3724085--3724162 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 23
3724075 TTTTAATCAA
* *
3724085 AATATTAATTATTAAAATATTTAA-
1 AATA-TAA-TATTAATATTTTTAAT
* *
3724109 AATATATTATTAATATTTCTAAT
1 AATATAATATTAATATTTTTAAT
3724132 AATATAATATT-ATATTTTTAAT
1 AATATAATATTAATATTTTTAAT
*
3724154 ATTATAATA
1 AATATAATA
3724163 AATAATCAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 30 0.65
23 12 0.26
24 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATAATATTAATATTTTTAAT
Found at i:3724153 original size:31 final size:30
Alignment explanation
Indices: 3724111--3724229 Score: 93
Period size: 29 Copynumber: 4.0 Consensus size: 30
3724101 ATATTTAAAA
*
3724111 TATATTATTAATATTTCTAATAATATAAT-AT
1 TATATTATTAATA-TTATAATAA-ATAATAAT
*
3724142 TATATTTTTAATATTATAATAAATAATCAAT
1 TATATTATTAATATTATAATAAATAAT-AAT
* * * * *
3724173 TATATTA--AATAATATAAGATATTATATT
1 TATATTATTAATATTATAATAAATAATAAT
* * *
3724201 TTTATT-TTAATAATATAATAAATATTAAT
1 TATATTATTAATATTATAATAAATAATAAT
3724230 AAAATTTATA
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
28 7 0.10
29 35 0.50
30 8 0.11
31 20 0.29
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (30 bp):
TATATTATTAATATTATAATAAATAATAAT
Found at i:3724155 original size:51 final size:49
Alignment explanation
Indices: 3724104--3724299 Score: 127
Period size: 53 Copynumber: 3.9 Consensus size: 49
3724094 TATTAAAATA
3724104 TTTAAAATATATTATTAATATTTCTAATAATATAATATTATATTTTTAAT
1 TTTAAAATATATTATTAATATTT-TAATAATATAATATTATATTTTTAAT
* * * * * *
3724154 ATTATAATAAATAATCAATTATATTAAATAATATAAGATATTATATTTTT-AT
1 TTTAAAATATATTATTAA-TAT-TTTAATAATAT-A-ATATTATATTTTTAAT
* * * *
3724206 TTTAATAATATA--A-TAA-ATATTAATAAAATTTATATTAT-TTATTAAT
1 TTTAA-AATATATTATTAATATTTTAATAATA-TAATATTATATTTTTAAT
3724252 TTCATAGAAATAATATTATTAA-ATTATTAATAATGAATAATATTATAT
1 TT--TA-AAAT-ATATTATTAATATT-TTAATAAT--ATAATATTATAT
3724300 ATATATATAA
Statistics
Matches: 110, Mismatches: 18, Indels: 31
0.69 0.11 0.19
Matches are distributed among these distances:
45 4 0.04
46 11 0.10
47 7 0.06
48 8 0.07
49 4 0.04
50 15 0.14
51 13 0.12
52 13 0.12
53 25 0.23
54 8 0.07
55 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (49 bp):
TTTAAAATATATTATTAATATTTTAATAATATAATATTATATTTTTAAT
Found at i:3724432 original size:31 final size:28
Alignment explanation
Indices: 3724405--3724477 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 28
3724395 TTATATAATT
3724405 TATAATATTTTTATTTCAATAAAATATACCAA
1 TATAATATTTTTA-TT-AATAAAATATA--AA
3724437 TATTAATATTTTTATTAATAAAATTATAAAA
1 TA-TAATATTTTTATTAATAAAA-TAT-AAA
3724468 TATAATATTT
1 TATAATATTT
3724478 AATAATAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
30 8 0.21
31 11 0.29
32 7 0.18
33 12 0.32
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (28 bp):
TATAATATTTTTATTAATAAAATATAAA
Found at i:3724476 original size:30 final size:32
Alignment explanation
Indices: 3724405--3724477 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
3724395 TTATATAATT
*
3724405 TATAATATTTTTATTTCAATAAAATATACCAA
1 TATAATATTTTTATTTCAATAAAATATACAAA
3724437 TATTAATATTTTTA-TT-AATAAAATTATA-AAA
1 TA-TAATATTTTTATTTCAATAAAA-TATACAAA
3724468 TATAATATTT
1 TATAATATTT
3724478 AATAATAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
30 8 0.21
31 11 0.29
32 8 0.21
33 11 0.29
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAATATTTTTATTTCAATAAAATATACAAA
Found at i:3724520 original size:25 final size:26
Alignment explanation
Indices: 3724492--3724547 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
3724482 ATAAACAAAT
* *
3724492 TATTTTAATTTT-TTAAAAATAATAA
1 TATTTAAATTTTATGAAAAATAATAA
* *
3724517 TA-TTAAATTTTATGATAAATAATAT
1 TATTTAAATTTTATGAAAAATAATAA
3724542 TATTTA
1 TATTTA
3724548 TTGTATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 8 0.32
25 14 0.56
26 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TATTTAAATTTTATGAAAAATAATAA
Found at i:3724697 original size:14 final size:14
Alignment explanation
Indices: 3724680--3724710 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3724670 TTATTTTACG
3724680 GAAAACATTTTCCA
1 GAAAACATTTTCCA
*
3724694 GAAAACGTTTTCCA
1 GAAAACATTTTCCA
3724708 GAA
1 GAA
3724711 TTGTAATTCA
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:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (14 bp):
GAAAACATTTTCCA
Found at i:3724738 original size:20 final size:20
Alignment explanation
Indices: 3724702--3724739 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3724692 CAGAAAACGT
**
3724702 TTTCCAGAATTGTAATTCAA
1 TTTCCAGAATTCAAATTCAA
3724722 TTTCCAGAATTCAAATTC
1 TTTCCAGAATTCAAATTC
3724740 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
TTTCCAGAATTCAAATTCAA
Found at i:3724747 original size:15 final size:14
Alignment explanation
Indices: 3724715--3724773 Score: 91
Period size: 14 Copynumber: 4.1 Consensus size: 14
3724705 CCAGAATTGT
3724715 AATTCAATTTCCAG
1 AATTCAATTTCCAG
*
3724729 AATTCAAATTCCAG
1 AATTCAATTTCCAG
*
3724743 TAATTCATTTTCCAG
1 -AATTCAATTTCCAG
3724758 AATTCAATTTCCAG
1 AATTCAATTTCCAG
3724772 AA
1 AA
3724774 AACCAATTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 28 0.70
15 12 0.30
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:3724748 original size:29 final size:29
Alignment explanation
Indices: 3724713--3724771 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3724703 TTCCAGAATT
3724713 GTAATTCAATTTCCAGAATTCAAATTCCA
1 GTAATTCAATTTCCAGAATTCAAATTCCA
* *
3724742 GTAATTCATTTTCCAGAATTCAATTTCCA
1 GTAATTCAATTTCCAGAATTCAAATTCCA
3724771 G
1 G
3724772 AAAACCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (29 bp):
GTAATTCAATTTCCAGAATTCAAATTCCA
Found at i:3728036 original size:33 final size:33
Alignment explanation
Indices: 3727994--3728060 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3727984 TATATAAATA
3727994 ACCAAGGGAGATGTAATACCCCAAAATTTGGTC
1 ACCAAGGGAGATGTAATACCCCAAAATTTGGTC
3728027 ACCAAGGGAGATGTAATACCCCAAAATTTGGTC
1 ACCAAGGGAGATGTAATACCCCAAAATTTGGTC
3728060 A
1 A
3728061 ATGACTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (33 bp):
ACCAAGGGAGATGTAATACCCCAAAATTTGGTC
Found at i:3728074 original size:33 final size:33
Alignment explanation
Indices: 3728004--3728075 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
3727994 ACCAAGGGAG
* * * *
3728004 ATGTAATACCCCAAAATTTGGTCACCAAGGGAG
1 ATGTAATACCCCAAAATTTGGTCAACAACGAAA
** *
3728037 ATGTAATACCCCAAAATTTGGTCAATGACTAAA
1 ATGTAATACCCCAAAATTTGGTCAACAACGAAA
3728070 ATGTAA
1 ATGTAA
3728076 GTTTTAAAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (33 bp):
ATGTAATACCCCAAAATTTGGTCAACAACGAAA
Found at i:3733729 original size:45 final size:45
Alignment explanation
Indices: 3733671--3733850 Score: 351
Period size: 45 Copynumber: 4.0 Consensus size: 45
3733661 AAAAAATAAA
3733671 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
1 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
3733716 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
1 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
3733761 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
1 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
*
3733806 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTGGAAAATT
1 GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
3733851 TTCTCTAAGC
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (45 bp):
GTGTTCGCCCTTAAGGAAGAGATTAGGGAAACATTTTAGAAAATT
Found at i:3734963 original size:20 final size:20
Alignment explanation
Indices: 3734900--3734955 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
3734890 TAGCGTTGCA
* *
3734900 AAATTAGCGTTTCGAAAATG
1 AAATTCGCGTTGCGAAAATG
*
3734920 AAATTCGCGTTGCGAAAACG
1 AAATTCGCGTTGCGAAAATG
3734940 AAATTCGCGTTGCGAA
1 AAATTCGCGTTGCGAA
3734956 TTTGAAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (20 bp):
AAATTCGCGTTGCGAAAATG
Found at i:3735014 original size:72 final size:72
Alignment explanation
Indices: 3734938--3735147 Score: 174
Period size: 72 Copynumber: 3.1 Consensus size: 72
3734928 GTTGCGAAAA
*
3734938 CGAAATTCGCGTTGCGAATTTGAAATCTGAGTTGCAAATAGTTGTGTTTACCTATATCGGTTATT
1 CGAAATTCGCGTTGCGAATTTGAAATCTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTTATT
3735003 AGCGTTG
66 AGCGTTG
** *** * * * **
3735010 CGAAATTCAAGTTGCGAAAACGAAATTTGTGTTGCGAAT--TTG-G---A--GA-ATCGCGTTGC
1 CGAAATTCGCGTTGCGAATTTGAAATCTGAGTTGCGAATAGTTGTGTTTACCTATATCG-GTTAT
* **
3735066 GA-TTTTG
65 TAGCGTTG
* *
3735073 -GAGAA-TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAAT
1 CGA-AATTCGCGTTGCGAATTTGAAATCTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTTAT
3735136 TAGCGTTG
65 TAGCGTTG
3735144 CGAA
1 CGAA
3735148 TTTGAGAATC
Statistics
Matches: 96, Mismatches: 29, Indels: 27
0.63 0.19 0.18
Matches are distributed among these distances:
62 27 0.28
63 9 0.09
64 8 0.08
65 1 0.01
66 1 0.01
68 1 0.01
69 1 0.01
70 7 0.07
71 8 0.08
72 33 0.34
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (72 bp):
CGAAATTCGCGTTGCGAATTTGAAATCTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTTATT
AGCGTTG
Found at i:3735066 original size:21 final size:21
Alignment explanation
Indices: 3735040--3735093 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
3735030 CGAAATTTGT
3735040 GTTGCGAATTTGGAGAATCGC
1 GTTGCGAATTTGGAGAATCGC
*
3735061 GTTGCGATTTTGGAGAATCGC
1 GTTGCGAATTTGGAGAATCGC
3735082 GTTGCGAATTTG
1 GTTGCGAATTTG
3735094 AAAACTGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (21 bp):
GTTGCGAATTTGGAGAATCGC
Found at i:3735166 original size:20 final size:20
Alignment explanation
Indices: 3735141--3735193 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
3735131 GTAATTAGCG
3735141 TTGCGAATTTGAGAATCGCA
1 TTGCGAATTTGAGAATCGCA
* * *
3735161 TTGCGATTTTGGTGAATCGCG
1 TTGCGAATTT-GAGAATCGCA
*
3735182 TTGCGAGTTTGA
1 TTGCGAATTTGA
3735194 AACGATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (20 bp):
TTGCGAATTTGAGAATCGCA
Found at i:3735179 original size:21 final size:21
Alignment explanation
Indices: 3735153--3735192 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3735143 GCGAATTTGA
*
3735153 GAATCGCATTGCGATTTTGGT
1 GAATCGCATTGCGAGTTTGGT
*
3735174 GAATCGCGTTGCGAGTTTG
1 GAATCGCATTGCGAGTTTG
3735193 AAACGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.15, G:0.33, T:0.35
Consensus pattern (21 bp):
GAATCGCATTGCGAGTTTGGT
Found at i:3735200 original size:32 final size:32
Alignment explanation
Indices: 3735164--3735227 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
3735154 AATCGCATTG
* *
3735164 CGATTTTGGTGAATCGCGTTGCGAGTTTGAAA
1 CGATTTTGGAGAATCGCGTTGCGAATTTGAAA
3735196 CGATTTTGGAGAATCGCGTTGCGAATTTGAAA
1 CGATTTTGGAGAATCGCGTTGCGAATTTGAAA
3735228 ACTATGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (32 bp):
CGATTTTGGAGAATCGCGTTGCGAATTTGAAA
Found at i:3739934 original size:19 final size:19
Alignment explanation
Indices: 3739907--3739969 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
3739897 ATAAATGTTT
3739907 AACCGGCTAGACTGGTCTG
1 AACCGGCTAGACTGGTCTG
* * *
3739926 AACCAGCTAGATTGGTCTA
1 AACCGGCTAGACTGGTCTG
* *
3739945 AACCGGCTTGACCGGTCTG
1 AACCGGCTAGACTGGTCTG
3739964 AACCGG
1 AACCGG
3739970 TCTGACCCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.21
Consensus pattern (19 bp):
AACCGGCTAGACTGGTCTG
Found at i:3740037 original size:29 final size:29
Alignment explanation
Indices: 3739995--3740158 Score: 217
Period size: 29 Copynumber: 5.7 Consensus size: 29
3739985 TGACCTGACC
* *
3739995 CGATGCTATTTTGGGAATTATTTTTAAAA
1 CGATGATATTTTGGTAATTATTTTTAAAA
3740024 CGATGATATTTTGGTAATTATATTTTAAAA
1 CGATGATATTTTGGTAATTAT-TTTTAAAA
* *
3740054 CGGTGATATTTTGGTAATTATTTTCAAAA
1 CGATGATATTTTGGTAATTATTTTTAAAA
*
3740083 CGATGATATTTTGGTAATTATTTTCAAAA
1 CGATGATATTTTGGTAATTATTTTTAAAA
3740112 C-AGTGATATTTTGGTAATTA-TTTTAAAA
1 CGA-TGATATTTTGGTAATTATTTTTAAAA
* *
3740140 AGGTGATATTTCT-GTAATT
1 CGATGATATTT-TGGTAATT
3740159 TTTGACTGTG
Statistics
Matches: 123, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
28 22 0.18
29 73 0.59
30 28 0.23
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (29 bp):
CGATGATATTTTGGTAATTATTTTTAAAA
Found at i:3740093 original size:59 final size:57
Alignment explanation
Indices: 3740001--3740158 Score: 228
Period size: 59 Copynumber: 2.7 Consensus size: 57
3739991 GACCCGATGC
* * *
3740001 TATTTTGGGAATTATTTTTAAAACGATGATATTTTGGTAATTATATTTTAAAACGGTGA
1 TATTTTGGTAATTA-TTTTAAAACGATGATATTTTGGTAATTAT-TTTCAAAACAGTGA
3740060 TATTTTGGTAATTATTTTCAAAACGATGATATTTTGGTAATTATTTTCAAAACAGTGA
1 TATTTTGGTAATTATTTT-AAAACGATGATATTTTGGTAATTATTTTCAAAACAGTGA
* *
3740118 TATTTTGGTAATTATTTTAAAAAGGTGATATTTCT-GTAATT
1 TATTTTGGTAATTATTTTAAAACGATGATATTT-TGGTAATT
3740159 TTTGACTGTG
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
57 19 0.21
58 35 0.38
59 38 0.41
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (57 bp):
TATTTTGGTAATTATTTTAAAACGATGATATTTTGGTAATTATTTTCAAAACAGTGA
Found at i:3740278 original size:76 final size:78
Alignment explanation
Indices: 3740187--3740339 Score: 292
Period size: 76 Copynumber: 2.0 Consensus size: 78
3740177 AACCCCTTTG
3740187 ACCATAACTTTGACCAGCTTTAAATGGCCATTAAACGACATTTGATTTTATTCGAGTATA-CTA-
1 ACCATAACTTTGACCAGCTTTAAATGGCCATTAAACGACATTTGATTTTATTCGAGTATACCTAT
3740250 TTTGACATTTTTT
66 TTTGACATTTTTT
3740263 ACCATAACTTTGACCAGCTTTAAATGGCCATTAAACGACATTTGATTTTATTCGAGTATACCTAT
1 ACCATAACTTTGACCAGCTTTAAATGGCCATTAAACGACATTTGATTTTATTCGAGTATACCTAT
3740328 TTTGACATTTTT
66 TTTGACATTTTT
3740340 CGACATGCCA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
76 60 0.80
77 3 0.04
78 12 0.16
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.41
Consensus pattern (78 bp):
ACCATAACTTTGACCAGCTTTAAATGGCCATTAAACGACATTTGATTTTATTCGAGTATACCTAT
TTTGACATTTTTT
Found at i:3740909 original size:2 final size:2
Alignment explanation
Indices: 3740902--3740940 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3740892 GATTTGATAA
* *
3740902 AT AT AT AT GT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3740941 CACATGTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3742189 original size:23 final size:22
Alignment explanation
Indices: 3742137--3742197 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
3742127 TACCCTCATG
3742137 GGGGGTATCGGTACCCATTCAA
1 GGGGGTATCGGTACCCATTCAA
** *
3742159 GTATGGTATCGGTATCCATTCAAA
1 G-GGGGTATCGGTACCCATTC-AA
*
3742183 GGGGGTATCGATACC
1 GGGGGTATCGGTACC
3742198 TAGCACGCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 1 0.03
23 26 0.87
24 3 0.10
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGGTACCCATTCAA
Found at i:3746009 original size:22 final size:21
Alignment explanation
Indices: 3745967--3746006 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3745957 GATATTATTT
*
3745967 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTAAAATA
3745988 TCATTTTTGT-ATTTTAAAA
1 TCATTTTT-TAATTTTAAAA
3746007 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTAAAATA
Found at i:3747892 original size:21 final size:21
Alignment explanation
Indices: 3747838--3747886 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3747828 TAGGAGCATG
*
3747838 GGGTATAAATACCACTCCATA
1 GGGTATCAATACCACTCCATA
3747859 GGGTATCAATACCACTCCATA
1 GGGTATCAATACCACTCCATA
3747880 GGGTATC
1 GGGTATC
3747887 TGTACCTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (21 bp):
GGGTATCAATACCACTCCATA
Found at i:3748030 original size:19 final size:19
Alignment explanation
Indices: 3748006--3748045 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3747996 AATTTACATT
3748006 GGGGTATCGGTACCATCTG
1 GGGGTATCGGTACCATCTG
*
3748025 GGGGTATCGGTACCATTTG
1 GGGGTATCGGTACCATCTG
3748044 GG
1 GG
3748046 CAATCTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.40, T:0.28
Consensus pattern (19 bp):
GGGGTATCGGTACCATCTG
Found at i:3751450 original size:16 final size:17
Alignment explanation
Indices: 3751419--3751451 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3751409 AAAGATCAAT
3751419 CTTTTTTGAAAAGGATC
1 CTTTTTTGAAAAGGATC
*
3751436 CTTTTTT-AAAGGGATC
1 CTTTTTTGAAAAGGATC
3751452 GATCCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (17 bp):
CTTTTTTGAAAAGGATC
Found at i:3751922 original size:31 final size:31
Alignment explanation
Indices: 3751876--3751939 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3751866 TTTGGAAACT
3751876 TTTAGGGGACTAAAAGGATTA-TTTTCTAAAAG
1 TTTAGGGGACTAAAA-GATTAGTTTT-TAAAAG
* *
3751908 TTTA-GGGCCTAAAAGTTTAGTTTTTAAAAG
1 TTTAGGGGACTAAAAGATTAGTTTTTAAAAG
3751938 TT
1 TT
3751940 AGGTGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 12 0.41
31 13 0.45
32 4 0.14
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.39
Consensus pattern (31 bp):
TTTAGGGGACTAAAAGATTAGTTTTTAAAAG
Found at i:3757236 original size:30 final size:29
Alignment explanation
Indices: 3757172--3757267 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 29
3757162 TTTAGTTATT
*
3757172 GACCAAAATATAAATTTTGAAA-TTTAGTG
1 GACCAAAGTATAAATTTTGAAAGTTTAG-G
*
3757201 G-CCAAAGTATAAAGTTTGGAAAGTTTAGG
1 GACCAAAGTATAAA-TTTTGAAAGTTTAGG
* *
3757230 GACCAAAAGGATAAATTTCTAAAAGTTTAGG
1 GACC-AAAGTATAAATTT-TGAAAGTTTAGG
*
3757261 AACCAAA
1 GACCAAA
3757268 AGTGTAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
28 11 0.20
29 10 0.18
30 13 0.23
31 22 0.39
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (29 bp):
GACCAAAGTATAAATTTTGAAAGTTTAGG
Found at i:3757284 original size:30 final size:31
Alignment explanation
Indices: 3757220--3757286 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3757210 TAAAGTTTGG
*
3757220 AAAGTTTAGGGACCAAAAGGATAAATTTCTA
1 AAAGTTTAGGAACCAAAAGGATAAATTTCTA
*
3757251 AAAGTTTAGGAACCAAAAGTG-TAATTTTC-A
1 AAAGTTTAGGAACCAAAAG-GATAAATTTCTA
3757281 AAAGTT
1 AAAGTT
3757287 AGGTGTTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 7 0.21
31 25 0.76
32 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGTTTAGGAACCAAAAGGATAAATTTCTA
Found at i:3778733 original size:21 final size:21
Alignment explanation
Indices: 3778707--3778756 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3778697 AGCTGAACAA
3778707 TATCGATATTGATACAATTAG
1 TATCGATATTGATACAATTAG
3778728 TATCGATATTGATACAATTAG
1 TATCGATATTGATACAATTAG
*
3778749 TATTGATA
1 TATCGATA
3778757 CTATGAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (21 bp):
TATCGATATTGATACAATTAG
Found at i:3779322 original size:54 final size:54
Alignment explanation
Indices: 3779258--3779372 Score: 180
Period size: 54 Copynumber: 2.1 Consensus size: 54
3779248 GATTACCGAA
* *
3779258 TGGCACTATGTGTGCAACTTAAGAAATTC-ATAATGAGTTTATGAATTTCCT-TAT
1 TGGCACTATGTGTGCAACTTAAGAAATTCTA-AATAAGTTTATAAATTT-CTGTAT
3779312 TGGCACTATGTGTGCAACTTAAGAAATTCTAAATAAGTTTATAAATTTCTGTAT
1 TGGCACTATGTGTGCAACTTAAGAAATTCTAAATAAGTTTATAAATTTCTGTAT
3779366 TGGCACT
1 TGGCACT
3779373 GGAGTGCAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
53 2 0.04
54 54 0.95
55 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (54 bp):
TGGCACTATGTGTGCAACTTAAGAAATTCTAAATAAGTTTATAAATTTCTGTAT
Found at i:3783550 original size:3 final size:3
Alignment explanation
Indices: 3783542--3783566 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3783532 GAATAAGGTT
3783542 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
3783567 ATGCATCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:3788576 original size:72 final size:73
Alignment explanation
Indices: 3788446--3788582 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 73
3788436 ACTATAAGGG
* * * * * * * *
3788446 AGGTATCGATACCATTGATTTCAGAATGCAGAAATGGTTTTGATACTGTAATATAGTATCGGTAC
1 AGGTATCGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAGAGAGTATCGGTAC
3788511 TAAGAGAA
66 TAAGAGAA
* * *
3788519 AGGTATTGATACCATGGA-TCCAGAATATAGAAATGGTATCGATACTGAAAGGGAGTATCGGTAC
1 AGGTATCGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAGAGAGTATCGGTAC
3788583 CACAGTATAG
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
72 37 0.70
73 16 0.30
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (73 bp):
AGGTATCGATACCATGGATTCCAGAATACAGAAATGGTATCGATACTGAAAGAGAGTATCGGTAC
TAAGAGAA
Found at i:3792132 original size:24 final size:25
Alignment explanation
Indices: 3792105--3792159 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
3792095 AAAATCATGG
*
3792105 CTTTTGGAA-AACCAAAAGATGTGA
1 CTTTTGGAAGAACCAAAAGATATGA
* *
3792129 CTTTT-GAAGAACCAATAGTTATGA
1 CTTTTGGAAGAACCAAAAGATATGA
3792153 CTTTTGG
1 CTTTTGG
3792160 TGATTCACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.12
24 22 0.85
25 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (25 bp):
CTTTTGGAAGAACCAAAAGATATGA
Found at i:3794687 original size:54 final size:54
Alignment explanation
Indices: 3794597--3795092 Score: 769
Period size: 54 Copynumber: 9.2 Consensus size: 54
3794587 CACCTTATAT
* * * * *
3794597 CACTATGTGTGCAACTTAATAAATTCATAATTAGTTTATGAATTTCCATATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
3794651 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
3794705 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
* * * *
3794759 CACCGTGTGTGAAACTTAATAAATTCATAATGAGATTATGAATTTTCGTATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
* *
3794813 CACTGTGTGTGCAACTTAAGAAATTCATAATGTGTTTATGAATTTCCGTATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
* *
3794867 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTGTTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
* *
3794921 CACTGTGTGTGCAACTTAAAAAATTCATAATGAGTTTATGAATTTTTGTATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
* *
3794975 CACTGTGTGTGCAACTTAAGAAATTCATAATTAGTTTACGAATTTTCGTATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
* * * * *
3795029 CACTATATGTGCAACTTAAGAAATTCATAATAAGTTT-TTAAATTTCTGTATTGG
1 CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTC-GTATTGG
*
3795083 CACTGGGTGT
1 CACTGTGTGT
3795093 ACAAACTACT
Statistics
Matches: 407, Mismatches: 34, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
53 6 0.01
54 401 0.99
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (54 bp):
CACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
Found at i:3796999 original size:2 final size:2
Alignment explanation
Indices: 3796994--3797096 Score: 206
Period size: 2 Copynumber: 51.5 Consensus size: 2
3796984 ATTACATGAT
3796994 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
3797036 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
3797078 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3797097 TTTTATTATC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 101 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3797380 original size:17 final size:17
Alignment explanation
Indices: 3797334--3797383 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
3797324 AAATCTCAGG
3797334 TTTATTGA-TTTTTAAA
1 TTTATTGATTTTTTAAA
* * *
3797350 TCATATTG-TGTTTTCAA
1 T-TTATTGATTTTTTAAA
3797367 TTTATTGATTTTTTAAA
1 TTTATTGATTTTTTAAA
3797384 AATATTTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (17 bp):
TTTATTGATTTTTTAAA
Found at i:3800067 original size:16 final size:16
Alignment explanation
Indices: 3800046--3800083 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3800036 TGCATTTGAT
3800046 TTTTTTCT-TTTTCACA
1 TTTTTTCTGTTTTC-CA
*
3800062 TTTTTTTTGTTTTCCA
1 TTTTTTCTGTTTTCCA
3800078 TTTTTT
1 TTTTTT
3800084 TCACGTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTTCTGTTTTCCA
Found at i:3800084 original size:16 final size:17
Alignment explanation
Indices: 3800044--3800085 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3800034 AATGCATTTG
3800044 ATTTTTTTCTTTTTCAC
1 ATTTTTTTCTTTTTCAC
3800061 ATTTTTTT-TGTTTTC-C
1 ATTTTTTTCT-TTTTCAC
3800077 ATTTTTTTC
1 ATTTTTTTC
3800086 ACGTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTTTCTTTTTCAC
Found at i:3805993 original size:17 final size:17
Alignment explanation
Indices: 3805971--3806003 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3805961 TACGTGTCGA
3805971 TTTTACGCCTTCTTCGG
1 TTTTACGCCTTCTTCGG
3805988 TTTTACGCCTTCTTCG
1 TTTTACGCCTTCTTCG
3806004 ATTTGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.30, G:0.15, T:0.48
Consensus pattern (17 bp):
TTTTACGCCTTCTTCGG
Found at i:3809622 original size:26 final size:26
Alignment explanation
Indices: 3809577--3809655 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
3809567 CTAGAAGGCG
* * * *
3809577 CGCTGACTAGATCTTCTAGAAACTGT
1 CGCTGACTGGACCTTTTAGAAACTGC
*
3809603 CGCTGACTGGACTTTTTAGAAACTGC
1 CGCTGACTGGACCTTTTAGAAACTGC
3809629 CGCTGACTGGACCTTTTAGAAACTGC
1 CGCTGACTGGACCTTTTAGAAACTGC
3809655 C
1 C
3809656 ACGTCAGACC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (26 bp):
CGCTGACTGGACCTTTTAGAAACTGC
Found at i:3813465 original size:17 final size:17
Alignment explanation
Indices: 3813443--3813476 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3813433 TTAAATGCTT
3813443 AAGGAAGAACATTTGAA
1 AAGGAAGAACATTTGAA
3813460 AAGGAAGAACATTTGAA
1 AAGGAAGAACATTTGAA
3813477 GATGCAAATC
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:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (17 bp):
AAGGAAGAACATTTGAA
Found at i:3814150 original size:59 final size:60
Alignment explanation
Indices: 3814068--3814188 Score: 226
Period size: 59 Copynumber: 2.0 Consensus size: 60
3814058 TGTGACTCTA
3814068 AGTCGCATGTACCAATTTGATTATCAGGGAACAAAATTAAACAAATGATAATTGTTTTCC
1 AGTCGCATGTACCAATTTGATTATCAGGGAACAAAATTAAACAAATGATAATTGTTTTCC
*
3814128 AGTCGCATGTA-CAATTTGATTATCAGGGAACAAAATTAAACAAATGTTAATTGTTTTCC
1 AGTCGCATGTACCAATTTGATTATCAGGGAACAAAATTAAACAAATGATAATTGTTTTCC
3814187 AG
1 AG
3814189 GAGTGTCTGC
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 49 0.82
60 11 0.18
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (60 bp):
AGTCGCATGTACCAATTTGATTATCAGGGAACAAAATTAAACAAATGATAATTGTTTTCC
Found at i:3818479 original size:30 final size:30
Alignment explanation
Indices: 3818392--3818547 Score: 162
Period size: 30 Copynumber: 5.3 Consensus size: 30
3818382 AACCTATTAG
* *
3818392 TATAATTGAAACAAAAAATC-AAGTTTAATGC
1 TATAATTGAAAC--GAAATCAAAGTTCAATGC
* *
3818423 TATAATTGAAAC--TATTAAAG-TCAATGC
1 TATAATTGAAACGAAATCAAAGTTCAATGC
*
3818450 TATAAATGAAACGAAATCAAAGTTCAATGC
1 TATAATTGAAACGAAATCAAAGTTCAATGC
*
3818480 TATAATTGAAACGGAAATC-AAGTT-TATGC
1 TATAATTGAAAC-GAAATCAAAGTTCAATGC
* **
3818509 TATAATTGAAAAGAAATCAAAGTTCAATAT
1 TATAATTGAAACGAAATCAAAGTTCAATGC
3818539 TATAATTGA
1 TATAATTGA
3818548 TAAAATTAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
27 19 0.18
28 9 0.08
29 26 0.25
30 34 0.32
31 18 0.17
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (30 bp):
TATAATTGAAACGAAATCAAAGTTCAATGC
Found at i:3818528 original size:59 final size:57
Alignment explanation
Indices: 3818392--3818547 Score: 170
Period size: 59 Copynumber: 2.7 Consensus size: 57
3818382 AACCTATTAG
* * * *
3818392 TATAATTGAAACAAAAAATC-AAGTTTAATGCTATAATTGAAACTATTAAAGTCAATGC
1 TATAATTG-AA-AAGAAATCAAAGTTCAATGCTATAATTGAAACAAATAAAGTCAATGC
* * * **
3818450 TATAAATGAAACGAAATCAAAGTTCAATGCTATAATTGAAACGGAAATCAAGTTTATGC
1 TATAATTGAAAAGAAATCAAAGTTCAATGCTATAATTGAAAC--AAATAAAGTCAATGC
**
3818509 TATAATTGAAAAGAAATCAAAGTTCAATATTATAATTGA
1 TATAATTGAAAAGAAATCAAAGTTCAATGCTATAATTGA
3818548 TAAAATTAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
56 6 0.07
57 24 0.29
58 7 0.09
59 45 0.55
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (57 bp):
TATAATTGAAAAGAAATCAAAGTTCAATGCTATAATTGAAACAAATAAAGTCAATGC
Found at i:3819563 original size:69 final size:70
Alignment explanation
Indices: 3819452--3819586 Score: 263
Period size: 69 Copynumber: 1.9 Consensus size: 70
3819442 TAAAAATATA
3819452 CTAGTTAAGCATTACTTTAGAAACTTCATTATAACTTTTGATATTTGTTTCTTTT-ATAAAACTA
1 CTAGTTAAGCATTACTTTAGAAACTTCATTATAACTTTTGATATTTGTTTCTTTTAATAAAACTA
3819516 GCGGC
66 GCGGC
3819521 CTAGTTAAGCATTACTTTAGAAACTTCATTATAACTTTTGATATTTGTTTCTTTTAATAAAACTA
1 CTAGTTAAGCATTACTTTAGAAACTTCATTATAACTTTTGATATTTGTTTCTTTTAATAAAACTA
3819586 G
66 G
3819587 GCACTATTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
69 55 0.85
70 10 0.15
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (70 bp):
CTAGTTAAGCATTACTTTAGAAACTTCATTATAACTTTTGATATTTGTTTCTTTTAATAAAACTA
GCGGC
Found at i:3820439 original size:2 final size:2
Alignment explanation
Indices: 3820432--3820472 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3820422 ATGATTTTAC
3820432 TA TA TA 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 TA TA TA T
3820473 TAATTTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3821967 original size:18 final size:17
Alignment explanation
Indices: 3821929--3821967 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3821919 ATGTTTTTTC
*
3821929 ATTTTAAATAAAAGTCA
1 ATTTTAAATAAAAGACA
*
3821946 ATTTTAATTAAAACGACA
1 ATTTTAAATAAAA-GACA
3821964 ATTT
1 ATTT
3821968 AAAGTATGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (17 bp):
ATTTTAAATAAAAGACA
Found at i:3822117 original size:25 final size:27
Alignment explanation
Indices: 3822063--3822119 Score: 91
Period size: 25 Copynumber: 2.1 Consensus size: 27
3822053 CTCGTCGATT
3822063 AATTAATGTCTTTGCAATGAAATTTACA
1 AATTAATG-CTTTGCAATGAAATTTACA
3822091 AATTAATG-TTTGCAATG-AATTTACA
1 AATTAATGCTTTGCAATGAAATTTACA
3822116 AATT
1 AATT
3822120 CGAGTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 12 0.41
26 9 0.31
28 8 0.28
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (27 bp):
AATTAATGCTTTGCAATGAAATTTACA
Found at i:3823710 original size:19 final size:19
Alignment explanation
Indices: 3823688--3823730 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3823678 TGGTCAATTT
3823688 CCCCTTTTGCTCGTGAACC
1 CCCCTTTTGCTCGTGAACC
3823707 CCCCTTTTGCTCGTGAACC
1 CCCCTTTTGCTCGTGAACC
3823726 CCCCT
1 CCCCT
3823731 GTCCTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.47, G:0.14, T:0.30
Consensus pattern (19 bp):
CCCCTTTTGCTCGTGAACC
Found at i:3824845 original size:3 final size:3
Alignment explanation
Indices: 3824839--3824874 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3824829 ACATTATTAT
3824839 TAA TAA TAA -AA TAA TAA T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3824875 TCCCAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3824855 original size:11 final size:11
Alignment explanation
Indices: 3824839--3824874 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3824829 ACATTATTAT
3824839 TAATAATAAAA
1 TAATAATAAAA
*
3824850 TAATAATATAA
1 TAATAATAAAA
3824861 TAATAATAATAA
1 TAATAATAA-AA
3824873 TA
1 TA
3824875 TCCCAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:3829976 original size:140 final size:139
Alignment explanation
Indices: 3829607--3830132 Score: 621
Period size: 140 Copynumber: 3.8 Consensus size: 139
3829597 TGGACTTTCG
* * *
3829607 GTGGATGACATTGTTCCTACGTGATTAGGACATCTAGCCATCTTTAGGGATAATTTGGGAGACAA
1 GTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGACAA
* *
3829672 CACGGTTCCTACGTGATGAA-GAAGTATGGTTATCTGAAAATGACG-TTGCTCTTACGTGATGAG
66 CACGGTTCCTACGTGAT-AAGGAAGTCTGGTTATCTGAGAATGACGCTT-CTCTTACGTGATGAG
3829735 GAGATCTGGTC
129 GAGATCTGGTC
* * * * *
3829746 GATGGACGACATTATTCCT-CGTGATGAGGAAGTCTAACCATATTTAAGGATAATTTGGGAGACA
1 G-TGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGACA
* * * * * *
3829810 ACACGGGTCCTACGTGATGAGAAAGTCTGGTTATCTGAGAATGATGCTTCTCCTATGTGATGAGG
65 ACACGGTTCCTACGTGATAAGGAAGTCTGGTTATCTGAGAATGACGCTTCTCTTACGTGATGAGG
*
3829875 AGATCTCGTC
130 AGATCTGGTC
* * * * *
3829885 TGTGGACGATATTGTTCCTATGTGATGAGGACGTCTGGCCATCTGTAGGGATAATTTCGGAGACA
1 -GTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGACA
* * * * * ** *
3829950 ACATGGTTCCTACGTGATAAGGAAGTCTGGTTAT-TAAAGGATGACACTGCTCTTACACGTTGAG
65 ACACGGTTCCTACGTGATAAGGAAGTCTGGTTATCT-GAGAATGACGCTTCTCTTACGTGATGAG
3830014 GAGATCTGGTC
129 GAGATCTGGTC
* * * *
3830025 GGTGGATGACATTGTTCCTACGTGATGAGGATGTCTAGCCGTCTTTAGGGATAATTT-AGAGACA
1 -GTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGACA
* * * *
3830089 ACATGGTTCCTATGTGATGAGGAAGTCTGGTTATCTGAGGATGA
65 ACACGGTTCCTACGTGATAAGGAAGTCTGGTTATCTGAGAATGA
3830133 AGTTGCTCCT
Statistics
Matches: 326, Mismatches: 54, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
138 1 0.00
139 162 0.50
140 163 0.50
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (139 bp):
GTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGACAA
CACGGTTCCTACGTGATAAGGAAGTCTGGTTATCTGAGAATGACGCTTCTCTTACGTGATGAGGA
GATCTGGTC
Found at i:3830117 original size:279 final size:279
Alignment explanation
Indices: 3829607--3830132 Score: 727
Period size: 279 Copynumber: 1.9 Consensus size: 279
3829597 TGGACTTTCG
* * * *
3829607 GTGGATGACATTGTTCCTACGTGATTAGGACATCTAGCCATCTTTAGGGATAATTTGGGAGACAA
1 GTGGACGACATTGTTCCTACGTGATGAGGACATCTAGCCATCTGTAGGGATAATTTCGGAGACAA
** **
3829672 CACGGTTCCTACGTGATGAAGAAGTATGGTTATCTGAAAATGACGTTGCTCTTACGTGATGAGGA
66 CACGGTTCCTACGTGATGAAGAAGTATGGTTATCTGAAAATGACACTGCTCTTACACGATGAGGA
3829737 GATCTGGTCGATGGACGACATTATTCCTCGTGATGAGGAAGTCTAACCATATTTAAGGATAATTT
131 GATCTGGTCGATGGACGACATTATTCCTCGTGATGAGGAAGTCTAACCATATTTAAGGATAATTT
*
3829802 GGGAGACAACACGGGTCCTACGTGATGAGAAAGTCTGGTTATCTGAGAATGATGCTTCTCCTATG
196 GAGAGACAACACGGGTCCTACGTGATGAGAAAGTCTGGTTATCTGAGAATGATGCTTCTCCTATG
3829867 TGATGAGGAGATCTCGTCT
261 TGATGAGGAGATCTCGTCT
* * * *
3829886 GTGGACGATATTGTTCCTATGTGATGAGGACGTCTGGCCATCTGTAGGGATAATTTCGGAGACAA
1 GTGGACGACATTGTTCCTACGTGATGAGGACATCTAGCCATCTGTAGGGATAATTTCGGAGACAA
* * *
3829951 CATGGTTCCTACGTGAT-AAGGAAGTCTGGTTAT-T-AAAGGATGACACTGCTCTTACACGTTGA
66 CACGGTTCCTACGTGATGAA-GAAGTATGGTTATCTGAAA--ATGACACTGCTCTTACACGATGA
* * * * * * * *
3830013 GGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGATGTCTAGCCGTCTTTAGGGATA
128 GGAGATCTGGTCGATGGACGACATTATTCCT-CGTGATGAGGAAGTCTAACCATATTTAAGGATA
* * * * *
3830078 ATTT-AGAGACAACATGGTTCCTATGTGATGAGGAAGTCTGGTTATCTGAGGATGA
192 ATTTGAGAGACAACACGGGTCCTACGTGATGAGAAAGTCTGGTTATCTGAGAATGA
3830133 AGTTGCTCCT
Statistics
Matches: 214, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
277 3 0.01
278 3 0.01
279 176 0.82
280 32 0.15
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (279 bp):
GTGGACGACATTGTTCCTACGTGATGAGGACATCTAGCCATCTGTAGGGATAATTTCGGAGACAA
CACGGTTCCTACGTGATGAAGAAGTATGGTTATCTGAAAATGACACTGCTCTTACACGATGAGGA
GATCTGGTCGATGGACGACATTATTCCTCGTGATGAGGAAGTCTAACCATATTTAAGGATAATTT
GAGAGACAACACGGGTCCTACGTGATGAGAAAGTCTGGTTATCTGAGAATGATGCTTCTCCTATG
TGATGAGGAGATCTCGTCT
Found at i:3830140 original size:139 final size:140
Alignment explanation
Indices: 3829604--3830172 Score: 662
Period size: 139 Copynumber: 4.1 Consensus size: 140
3829594 CTTTGGACTT
* *
3829604 TCGGTGGATGACATTGTTCCTACGTGATTAGGACATCTAGCCATCTTTAGGGATAATTTGGGAGA
1 TCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGA
* * * * * *
3829669 CAACACGGTTCCTACGTGATGAAGAAGTATGGTTATCTGAAAATGACGTTGCTCTTACGTGATGA
66 CAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGAATGAAGTTGCTCCTACGCGATGA
3829734 GGAGATCTGG
131 GGAGATCTGG
* * * * * * *
3829744 TCGATGGACGACATTATTCCT-CGTGATGAGGAAGTCTAACCATATTTAAGGATAATTTGGGAGA
1 TCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGA
* * * * *
3829808 CAACACGGGTCCTACGTGATGAGAAAGTCTGGTTATCTGAGAATGATGCTT-CTCCTATGTGATG
66 CAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGAATGAAG-TTGCTCCTACGCGATG
*
3829872 AGGAGATCTCG
130 AGGAGATCTGG
* * * * * * *
3829883 TCTGTGGACGATATTGTTCCTATGTGATGAGGACGTCTGGCCATCTGTAGGGATAATTTCGGAGA
1 TCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGA
* * * * * * * *
3829948 CAACATGGTTCCTACGTGATAAGGAAGTCTGGTTAT-TAAAGGATGACA-CTGCTCTTACACGTT
66 CAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCT-GAGAATGA-AGTTGCTCCTACGCGAT
3830011 GAGGAGATCTGG
129 GAGGAGATCTGG
* * *
3830023 TCGGTGGATGACATTGTTCCTACGTGATGAGGATGTCTAGCCGTCTTTAGGGATAATTT-AGAGA
1 TCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGA
* * * * *
3830087 CAACATGGTTCCTATGTGATGAGGAAGTCTGGTTATCTGAGGATGAAGTTGCTCCTACGCGTTAA
66 CAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGAATGAAGTTGCTCCTACGCGATGA
*
3830152 GGAGATATGG
131 GGAGATCTGG
*
3830162 TCGGTTGATGA
1 TCGGTGGATGA
3830173 TGATTGACTT
Statistics
Matches: 360, Mismatches: 62, Indels: 15
0.82 0.14 0.03
Matches are distributed among these distances:
138 1 0.00
139 196 0.54
140 163 0.45
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (140 bp):
TCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGA
CAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGAATGAAGTTGCTCCTACGCGATGA
GGAGATCTGG
Found at i:3830428 original size:67 final size:67
Alignment explanation
Indices: 3830339--3830523 Score: 253
Period size: 67 Copynumber: 2.7 Consensus size: 67
3830329 AGAATTTACA
* ** * * * *
3830339 TTTCAAGGGAAAACTAAGTCAAGGGAGACGAAACTTTGTTTCTAGAGAAACAATCTCAAAGGTTT
1 TTTCAAGAG-AAACTATCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTC
3830404 ATG
65 ATG
* *
3830407 TTTCAAGAGAAACTATCTCAAGCGACACAAAACTTTGTTTCAAGAGAAACAATCTCAGAGGTTCA
1 TTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTCA
3830472 TG
66 TG
* * *
3830474 TTTCAAGAGAAACTGTCTCAAGCAAGACAAAACTTTGTTTCAAGAAAAAC
1 TTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAAC
3830524 TGTCTCAAGC
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 96 0.92
68 8 0.08
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (67 bp):
TTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTCA
TG
Found at i:3830455 original size:37 final size:37
Alignment explanation
Indices: 3830405--3830699 Score: 221
Period size: 37 Copynumber: 8.4 Consensus size: 37
3830395 CAAAGGTTTA
* *
3830405 TGTTTCAAGAGAAACTATCTCAAGCGACACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
** **
3830442 TGTTTCAAGAGAAACAATCTCAGAG-G-TTC---A---
1 TGTTTCAAGAGAAACTGTCTCA-AGCGAGACAAAACTT
*
3830472 TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* *
3830509 TGTTTCAAGAAAAACTGTCTCAAGCAAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* ** **
3830546 TGTTTCGAGAGAAACAATCTCAA---AG-----GTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* *
3830575 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAA-TT
1 -TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* * * *
3830612 TGTTTCAAGAGAAACTGTTTTAAGTGAAACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* * *
3830648 TGTTTCAAGAGAAACTGTTTCAAGTGAAACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* *
3830685 TGTTTCGAGATAAAC
1 TGTTTCAAGAGAAAC
3830700 AATCTCAAAG
Statistics
Matches: 211, Mismatches: 28, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
29 4 0.02
30 39 0.18
31 1 0.00
33 3 0.01
34 3 0.01
36 65 0.31
37 94 0.45
38 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
Found at i:3830517 original size:22 final size:22
Alignment explanation
Indices: 3830491--3830551 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 22
3830481 AGAAACTGTC
3830491 TCAAGCAAGACAAAACTTTGTT
1 TCAAGCAAGACAAAACTTTGTT
*
3830513 T----CAAGA-AAAAC--TGTC
1 TCAAGCAAGACAAAACTTTGTT
3830528 TCAAGCAAGACAAAACTTTGTT
1 TCAAGCAAGACAAAACTTTGTT
3830550 TC
1 TC
3830552 GAGAGAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
15 4 0.13
17 5 0.17
18 5 0.17
19 5 0.17
20 5 0.17
22 6 0.20
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (22 bp):
TCAAGCAAGACAAAACTTTGTT
Found at i:3830548 original size:104 final size:102
Alignment explanation
Indices: 3830405--3830662 Score: 365
Period size: 104 Copynumber: 2.5 Consensus size: 102
3830395 CAAAGGTTTA
* * *
3830405 TGTTTCAAGAGAAACTATCTCAAGCGACACAAAACTTTGTTTCAAGAGAAACAATCTCAGAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGC-AAACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
3830470 CATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAACTT
65 CATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAA-TT
* *
3830509 TGTTTCAAGAAAAACTGTCTCAAGCAAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCAA-ACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
* * **
3830574 TATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
65 CATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATT
* * *
3830612 TGTTTCAAGAGAAACTGTTTTAAGTGAAACAAAA-TTTGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAACTGTCTCAAG-CAAACAAAACTTTGTTTCAAGAGAAAC
3830663 TGTTTCAAGT
Statistics
Matches: 138, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
102 16 0.12
103 30 0.22
104 92 0.67
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGCAAACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTC
ATGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATT
Found at i:3830623 original size:36 final size:37
Alignment explanation
Indices: 3830576--3830699 Score: 135
Period size: 36 Copynumber: 3.4 Consensus size: 37
3830566 CAAAGGTTTA
* *
3830576 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* * * *
3830612 TGTTTCAAGAGAAACTGTTTTAAGTGAAACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* * *
3830648 TGTTTCAAGAGAAACTGTTTCAAGTGAAACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* *
3830685 TGTTTCGAGATAAAC
1 TGTTTCAAGAGAAAC
3830700 AATCTCAAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 64 0.81
37 15 0.19
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.31
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
Found at i:3830661 original size:21 final size:21
Alignment explanation
Indices: 3830590--3830701 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 21
3830580 TCAAGAGAAA
* * *
3830590 TTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGAGAAACAAAAT
3830611 TTGTTTCAAGAGAAAC-----
1 TTGTTTCAAGAGAAACAAAAT
* *
3830627 -TGTTTTAAGTGAAACAAAAT
1 TTGTTTCAAGAGAAACAAAAT
3830647 TTGTTTCAAGAGAAAC-----
1 TTGTTTCAAGAGAAACAAAAT
*
3830663 -TGTTTCAAGTGAAACAAAACT
1 TTGTTTCAAGAGAAACAAAA-T
* *
3830684 TTGTTTCGAGATAAACAA
1 TTGTTTCAAGAGAAACAA
3830702 TCTCAAAGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 25
0.65 0.11 0.24
Matches are distributed among these distances:
15 27 0.40
21 26 0.39
22 14 0.21
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (21 bp):
TTGTTTCAAGAGAAACAAAAT
Found at i:3830807 original size:68 final size:66
Alignment explanation
Indices: 3830733--3830859 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
3830723 GTTTCAAGTG
* * *
3830733 AAACAATTTCAAAATATT-GTGTTTTGAGGGAAAACTGTCTCAAGTGAGACGAAGTTTTTTTTTA
1 AAACAATCT-AAAATATTCGTGTCTT-AAGGAAAACTGTCTCAAGTGAGACGAA-TTTTTTTTTA
3830797 AGAA
63 AGAA
* *
3830801 AAACAATCTAAAATGTTCGTGTCTTAAGGAAGACTGTCTCAAGTGAGACGAATTTTTTT
1 AAACAATCTAAAATATTCGTGTCTTAAGGAAAACTGTCTCAAGTGAGACGAATTTTTTT
3830860 AGAAAATTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
66 7 0.13
67 32 0.60
68 14 0.26
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (66 bp):
AAACAATCTAAAATATTCGTGTCTTAAGGAAAACTGTCTCAAGTGAGACGAATTTTTTTTTAAGA
A
Found at i:3835141 original size:19 final size:19
Alignment explanation
Indices: 3835117--3835161 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3835107 GGGTCAGACT
*
3835117 GGTCAAACCGGTTC-ATACC
1 GGTCAAACCAGTTCGA-ACC
3835136 GGTCAAACCAGTTCGAACC
1 GGTCAAACCAGTTCGAACC
3835155 GGTCAAA
1 GGTCAAA
3835162 ACTGTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (19 bp):
GGTCAAACCAGTTCGAACC
Found at i:3835189 original size:21 final size:19
Alignment explanation
Indices: 3835133--3835189 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3835123 ACCGGTTCAT
*
3835133 ACCGGTCAAACCAGTTCGA
1 ACCGGTCAAACCAGTTTGA
* *
3835152 ACCGGTCAAAACTGTTTGAAA
1 ACCGGTCAAACCAGTTTG--A
*
3835173 ATCGGTCAAACCAGTTT
1 ACCGGTCAAACCAGTTT
3835190 CCAGCCCTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (19 bp):
ACCGGTCAAACCAGTTTGA
Found at i:3842373 original size:14 final size:14
Alignment explanation
Indices: 3842324--3842366 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
3842314 ACAGTCAACG
3842324 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
3842338 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
*
3842352 GTCGGGTCCGGTCA
1 GTCGGGTCGGGTCA
3842366 G
1 G
3842367 ACCGGTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.07, C:0.23, G:0.49, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:3842419 original size:21 final size:21
Alignment explanation
Indices: 3842393--3842432 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3842383 CGAACCGGTC
3842393 AAAACCAGTCAAACCGGTTAA
1 AAAACCAGTCAAACCGGTTAA
*
3842414 AAAACCGGTCAAACCGGTT
1 AAAACCAGTCAAACCGGTT
3842433 TCCAGCCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (21 bp):
AAAACCAGTCAAACCGGTTAA
Found at i:3842429 original size:9 final size:9
Alignment explanation
Indices: 3842359--3842431 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
3842349 TCAGTCGGGT
*
3842359 CCGGTCAGA
1 CCGGTCAAA
3842368 CCGGTCAAA
1 CCGGTCAAA
* *
3842377 CTGGTTCGAA
1 CCGG-TCAAA
3842387 CCGGTCAAAA
1 CCGGTC-AAA
*
3842397 CCAGTCAAA
1 CCGGTCAAA
*
3842406 CCGGTTAAAAAA
1 CCGG-T--CAAA
3842418 CCGGTCAAA
1 CCGGTCAAA
3842427 CCGGT
1 CCGGT
3842432 TTCCAGCCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
9 27 0.54
10 15 0.30
11 1 0.02
12 7 0.14
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.15
Consensus pattern (9 bp):
CCGGTCAAA
Found at i:3859953 original size:28 final size:28
Alignment explanation
Indices: 3859922--3859981 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
3859912 TCAGTATCAA
* *
3859922 TTTTAATATAAGAA-ACCAAGTAGCGCCT
1 TTTTAATATAACAATA-CAAGTAGCACCT
*
3859950 TTTT-ATATAACAATACAGGTAGCACCT
1 TTTTAATATAACAATACAAGTAGCACCT
3859977 TTTTA
1 TTTTA
3859982 TATTGTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (28 bp):
TTTTAATATAACAATACAAGTAGCACCT
Found at i:3860180 original size:101 final size:101
Alignment explanation
Indices: 3860052--3860364 Score: 251
Period size: 101 Copynumber: 3.1 Consensus size: 101
3860042 AAAGGGTTTT
* **
3860052 ATTTATAACAATATAGGTAGCATCTTTTTATAGTGTCAATCATTTACGTAATATGTTTGAAACTT
1 ATTTATAACAATAAAGGTAGCGCCTTTTTATAGTGTCAATCATTTACGTAATATGTTTGAAACTT
3860117 TTATTATTAAGAAACTATAAGAGAAAAAA-GGCTTAA
66 TTATTATTAAGAAACTATAAGAGAAAAAATGG-TTAA
* * * * * * * * * ** *
3860153 ATTTATAACAATACATGTAACGCCTTTTTAT-GTTGTTAATCGTGTAAGTTATAT-CTACAAAAT
1 ATTTATAACAATAAAGGTAGCGCCTTTTTATAG-TGTCAATCATTTACGTAATATGTTTGAAACT
* * * * * **
3860216 TTGTTTTATTATG-GACATGTAAGACAAAAAATGGTTTT
65 TT-TATTATTAAGAAAC-TATAAGAGAAAAAATGGTTAA
* * * * *
3860254 ATTTATAACAGA-AAAGGTAGTGCCTTTTTATAATGTCAACCATTTACGTGATA-GTTTGAAACC
1 ATTTATAACA-ATAAAGGTAGCGCCTTTTTATAGTGTCAATCATTTACGTAATATGTTTGAAACT
* ** *
3860317 TTTATTATTAAGAAACTATAACAGAAAATGTGTTTAA
65 TTTATTATTAAGAAACTATAAGAGAAAAAATGGTTAA
3860354 ATTTATGAACA
1 ATTTAT-AACA
3860365 TGTAAGATAG
Statistics
Matches: 155, Mismatches: 48, Indels: 18
0.70 0.22 0.08
Matches are distributed among these distances:
100 37 0.24
101 115 0.74
102 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (101 bp):
ATTTATAACAATAAAGGTAGCGCCTTTTTATAGTGTCAATCATTTACGTAATATGTTTGAAACTT
TTATTATTAAGAAACTATAAGAGAAAAAATGGTTAA
Found at i:3860359 original size:201 final size:201
Alignment explanation
Indices: 3859955--3860344 Score: 550
Period size: 201 Copynumber: 1.9 Consensus size: 201
3859945 CGCCTTTTTA
* * *
3859955 TATAACAATACAGGTAGCACCTTTTTATATTGTTAATTGTCTAAGTTATATATGCAAAACATGTT
1 TATAACAATACAGGTAACACCTTTTTATATTGTTAATCGTCTAAGTTATATATACAAAACATGTT
* * *
3860020 TCATTAAGGACATGTAAGACAAAAAGGGTTTTATTTATAACAATATAGGTAGCATCTTTTTATAG
66 TCATTAAGGACATGTAAGACAAAAAGGGTTTTATTTATAACAATAAAGGTAGCACCTTTTTATAA
* * *
3860085 TGTCAATCATTTACGTAATATGTTTGAAACTTTTATTATTAAGAAACTATAAGAGAAAAAAGGCT
131 TGTCAACCATTTACGTAATATGTTTGAAACCTTTATTATTAAGAAACTATAACAGAAAAAAGGCT
3860150 TAAATT
196 TAAATT
* * * * * **
3860156 TATAACAATACATGTAACGCCTTTTTATGTTGTTAATCGTGTAAGTTATATCTACAAAATTTGTT
1 TATAACAATACAGGTAACACCTTTTTATATTGTTAATCGTCTAAGTTATATATACAAAACATGTT
* * * **
3860221 TTATTATGGACATGTAAGACAAAAAATGGTTTTATTTATAACAGA-AAAGGTAGTGCCTTTTTAT
66 TCATTAAGGACATGTAAGAC-AAAAAGGGTTTTATTTATAACA-ATAAAGGTAGCACCTTTTTAT
*
3860285 AATGTCAACCATTTACGTGATA-GTTTGAAACCTTTATTATTAAGAAACTATAACAGAAAA
129 AATGTCAACCATTTACGTAATATGTTTGAAACCTTTATTATTAAGAAACTATAACAGAAAA
3860345 TGTGTTTAAA
Statistics
Matches: 165, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
201 109 0.66
202 55 0.33
203 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (201 bp):
TATAACAATACAGGTAACACCTTTTTATATTGTTAATCGTCTAAGTTATATATACAAAACATGTT
TCATTAAGGACATGTAAGACAAAAAGGGTTTTATTTATAACAATAAAGGTAGCACCTTTTTATAA
TGTCAACCATTTACGTAATATGTTTGAAACCTTTATTATTAAGAAACTATAACAGAAAAAAGGCT
TAAATT
Found at i:3860770 original size:98 final size:97
Alignment explanation
Indices: 3860521--3860793 Score: 259
Period size: 98 Copynumber: 2.7 Consensus size: 97
3860511 ATTCCAACCT
*
3860521 TTTAAGTTATATGTGTGAAACATTTTTCATTATGAAAATGTAAAACAAAACAATGTTATATTTTT
1 TTTAAGTTATATGTGTGAAACCTTTTTCATTAT-AAAATGTAAAA-AAAAC-ATGTTATATTTTT
* * * *
3860586 AACAACACATGTAGCGCTTTCATTTACTGTGAACAT
63 AACAATACATGTAGCGCCTTCA-TTACTGTCAACAG
* * * * *
3860622 TTTACA-TGATAAGTTTGAAACCTTTTTCATTA-AGAAACTGTAAGAGAAAACATGTTTAAATTT
1 TTTA-AGTTATATGTGTGAAACCTTTTTCATTATA-AAA-TGTAA-AAAAAACATG-TTATATTT
* *
3860685 TTAACAATAC-TAGTAGCTCCTT-A-TATTGTCAACAG
61 TTAACAATACAT-GTAGCGCCTTCATTACTGTCAACAG
* * *
3860720 TTTAAGTTATATGTGTGAAACCTTTTTCATTATAATTATGTACAAAAAAACAGGGTTATATTTAT
1 TTTAAGTTATATGTGTGAAACCTTTTTCATTATAA-AATGTA-AAAAAAACA-TGTTATATTTTT
3860785 AACAATACA
63 AACAATACA
3860794 GCTCCTTTTT
Statistics
Matches: 140, Mismatches: 20, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
97 1 0.01
98 64 0.46
99 5 0.04
100 8 0.06
101 60 0.43
102 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (97 bp):
TTTAAGTTATATGTGTGAAACCTTTTTCATTATAAAATGTAAAAAAAACATGTTATATTTTTAAC
AATACATGTAGCGCCTTCATTACTGTCAACAG
Found at i:3861467 original size:61 final size:61
Alignment explanation
Indices: 3861360--3861519 Score: 232
Period size: 61 Copynumber: 2.6 Consensus size: 61
3861350 TCCCGTGAAC
* *
3861360 TCTAGGACTTGATTAATCAAATACTGACTTT-CTCGTGAATTATGAGGAACACAGTAAAGAT
1 TCTATGACTTGATTAATCAAATACTGACTTTCCT-GTGAACTATGAGGAACACAGTAAAGAT
* *
3861421 TCTATGACTTGATTAATCAAATAATGACTTTCCTGTGAACTCTGAGGAACACAGTAAAGAT
1 TCTATGACTTGATTAATCAAATACTGACTTTCCTGTGAACTATGAGGAACACAGTAAAGAT
* * * *
3861482 TCCATGACATGATTAATCAAATTCTGACTTTCCCGTGA
1 TCTATGACTTGATTAATCAAATACTGACTTTCCTGTGA
3861520 TCCTAGTTCA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
61 87 0.98
62 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (61 bp):
TCTATGACTTGATTAATCAAATACTGACTTTCCTGTGAACTATGAGGAACACAGTAAAGAT
Found at i:3867646 original size:14 final size:14
Alignment explanation
Indices: 3867627--3867660 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3867617 TTTAGTTCTA
3867627 TGGCATATCATTTT
1 TGGCATATCATTTT
3867641 TGGCATATCATTTT
1 TGGCATATCATTTT
*
3867655 TAGCAT
1 TGGCAT
3867661 GAGTCGATGT
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:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (14 bp):
TGGCATATCATTTT
Found at i:3871196 original size:94 final size:94
Alignment explanation
Indices: 3871034--3871239 Score: 394
Period size: 94 Copynumber: 2.2 Consensus size: 94
3871024 TTGGGAGCGT
3871034 GGGGTGCATCGGTACACTCTCAGGGTGTATCGATACACTATGTGTAAAATTAAAATATTTCGAAT
1 GGGGTGCATCGGTACACTCTCAGGGTGTATCGATACACTATGTGTAAAATTAAAATATTTCGAAT
3871099 GTTATAAGACTTAGTGCATCGGTAAACTA
66 GTTATAAGACTTAGTGCATCGGTAAACTA
*
3871128 GGGGTGCATCGGTACACTCTCAGGGTGTATCGATACACTATGTGTAAAATTAAAATATTTCGACT
1 GGGGTGCATCGGTACACTCTCAGGGTGTATCGATACACTATGTGTAAAATTAAAATATTTCGAAT
3871193 GTTATAAGACTTAGTGCATCGGTAAACTA
66 GTTATAAGACTTAGTGCATCGGTAAACTA
*
3871222 GAGGTGCATCGGTACACT
1 GGGGTGCATCGGTACACT
3871240 AATTACATTC
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 110 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (94 bp):
GGGGTGCATCGGTACACTCTCAGGGTGTATCGATACACTATGTGTAAAATTAAAATATTTCGAAT
GTTATAAGACTTAGTGCATCGGTAAACTA
Found at i:3874009 original size:23 final size:22
Alignment explanation
Indices: 3873982--3874046 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
3873972 CATAGCATAG
3873982 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* *
3874005 TGCATCGGTGCATC-TTC-ATGA
1 TGCATCGATGCA-CATTCAAGGA
* *
3874026 GGTATCGATGCACATTCAAGG
1 TGCATCGATGCACATTCAAGG
3874047 GAGCATCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 13 0.39
22 4 0.12
23 14 0.42
24 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:3874075 original size:43 final size:44
Alignment explanation
Indices: 3873977--3874080 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
3873967 CAATGCATAG
* ** *
3873977 CATAGTGCATCGATGCACATTCAAGGAATGCATCGGTGCATCTT
1 CATAGTGTATCGATGCACATTCAAGGAATGCATCAATACATCTT
*
3874021 CATGAG-GTATCGATGCACATTCAAGGGA-GCATCAATACA-CTGT
1 CAT-AGTGTATCGATGCACATTCAAGGAATGCATCAATACATCT-T
3874064 CATAGTGTATCGATGCA
1 CATAGTGTATCGATGCA
3874081 TTGTGCATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 4 0.08
43 23 0.44
44 23 0.44
45 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGGAATGCATCAATACATCTT
Found at i:3874185 original size:23 final size:22
Alignment explanation
Indices: 3874158--3874222 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
3874148 CATAGCATAG
3874158 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* *
3874181 TGCATCGGTGCATC-TTC-ATGA
1 TGCATCGATGCA-CATTCAAGGA
* *
3874202 GGTATCGATGCACATTCAAGG
1 TGCATCGATGCACATTCAAGG
3874223 GAGCATCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 13 0.39
22 4 0.12
23 14 0.42
24 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:3874211 original size:176 final size:177
Alignment explanation
Indices: 3873916--3874268 Score: 699
Period size: 176 Copynumber: 2.0 Consensus size: 177
3873906 AAAGGGTTTT
3873916 GAAAAAATAAGAAATATTTAGGGATTTAACCCTAAAACCCGACGAGTGTATCAATGCATAGCATA
1 GAAAAAATAAGAAATATTTAGGGATTTAACCCTAAAACCCGACGAGTGTATCAATGCATAGCATA
3873981 GTGCATCGATGCACATTCAAGGAATGCATCGGTGCATCTTCATGAGGTATCGATGCACATTCAAG
66 GTGCATCGATGCACATTCAAGGAATGCATCGGTGCATCTTCATGAGGTATCGATGCACATTCAAG
3874046 GGAGCATCAATACACTGTCATAGTGTATCGATGCATTGTGCATAAAA
131 GGAGCATCAATACACTGTCATAGTGTATCGATGCATTGTGCATAAAA
3874093 GAAAAAATAAGAAATATTTAGGGATTT-ACCCTAAAACCCGACGAGTGTATCAATGCATAGCATA
1 GAAAAAATAAGAAATATTTAGGGATTTAACCCTAAAACCCGACGAGTGTATCAATGCATAGCATA
3874157 GTGCATCGATGCACATTCAAGGAATGCATCGGTGCATCTTCATGAGGTATCGATGCACATTCAAG
66 GTGCATCGATGCACATTCAAGGAATGCATCGGTGCATCTTCATGAGGTATCGATGCACATTCAAG
3874222 GGAGCATCAATACACTGTCATAGTGTATCGATGCATTGTGCATAAAA
131 GGAGCATCAATACACTGTCATAGTGTATCGATGCATTGTGCATAAAA
3874269 ATGTTAAAAT
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 149 0.85
177 27 0.15
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (177 bp):
GAAAAAATAAGAAATATTTAGGGATTTAACCCTAAAACCCGACGAGTGTATCAATGCATAGCATA
GTGCATCGATGCACATTCAAGGAATGCATCGGTGCATCTTCATGAGGTATCGATGCACATTCAAG
GGAGCATCAATACACTGTCATAGTGTATCGATGCATTGTGCATAAAA
Found at i:3874251 original size:43 final size:44
Alignment explanation
Indices: 3874153--3874256 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
3874143 CAATGCATAG
* ** *
3874153 CATAGTGCATCGATGCACATTCAAGGAATGCATCGGTGCATCTT
1 CATAGTGTATCGATGCACATTCAAGGAATGCATCAATACATCTT
*
3874197 CATGAG-GTATCGATGCACATTCAAGGGA-GCATCAATACA-CTGT
1 CAT-AGTGTATCGATGCACATTCAAGGAATGCATCAATACATCT-T
3874240 CATAGTGTATCGATGCA
1 CATAGTGTATCGATGCA
3874257 TTGTGCATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 4 0.08
43 23 0.44
44 23 0.44
45 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGGAATGCATCAATACATCTT
Found at i:3879368 original size:20 final size:21
Alignment explanation
Indices: 3879343--3879381 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3879333 ACTCTTGGGT
*
3879343 AAAAATGA-TTAATTATTTAA
1 AAAAATGACTAAATTATTTAA
3879363 AAAAATGACTAAATTATTT
1 AAAAATGACTAAATTATTT
3879382 GTACTTAACG
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:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAATGACTAAATTATTTAA
Found at i:3880269 original size:18 final size:18
Alignment explanation
Indices: 3880230--3880266 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3880220 TAATAGTGAG
3880230 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
3880248 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
3880265 TT
1 TT
3880267 TATATTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:3880339 original size:51 final size:52
Alignment explanation
Indices: 3880252--3880356 Score: 131
Period size: 51 Copynumber: 2.0 Consensus size: 52
3880242 ATATTTTTAT
* * * * *
3880252 TATAATTATATTTTTTATATTTGTATTATTGTTTAAAGTGATATAAGTCATA
1 TATAATAATATTTTTTAAAATTGCATTATAGTTTAAAGTGATATAAGTCATA
* * *
3880304 TATAATAATATTTTTTAAAATT-CATTATAGTTTAAATTGATATGATTCATA
1 TATAATAATATTTTTTAAAATTGCATTATAGTTTAAAGTGATATAAGTCATA
3880355 TA
1 TA
3880357 AAGTGTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 26 0.58
52 19 0.42
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (52 bp):
TATAATAATATTTTTTAAAATTGCATTATAGTTTAAAGTGATATAAGTCATA
Found at i:3919162 original size:117 final size:117
Alignment explanation
Indices: 3918950--3919192 Score: 450
Period size: 117 Copynumber: 2.1 Consensus size: 117
3918940 TTTAAAATCA
*
3918950 ATTTTAAAAGTACTTTAAAATTCCAGTGTTTAATATTGTTATTATAAAATATTTTTAATAAGATA
1 ATTTT-AAAGTACTTTAAAATTCCAGTGTTTAATATTGTTATTATAAAATATTTTTAAAAAGATA
3919015 AAATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATT
65 AAATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATT
*
3919068 ATTTTAAAGTACTTTAAAATTCTAGTGTTTAATATTGTTATTATAAAATATTTTTAAAAAGATAA
1 ATTTTAAAGTACTTTAAAATTCCAGTGTTTAATATTGTTATTATAAAATATTTTTAAAAAGATAA
*
3919133 AATATATGCTTTACACATTATATTATAAATTCAAAATATGTTAACTTAAATT
66 AATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATT
3919185 ATTTTAAA
1 ATTTTAAA
3919193 TTTATTAATA
Statistics
Matches: 122, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
117 117 0.96
118 5 0.04
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (117 bp):
ATTTTAAAGTACTTTAAAATTCCAGTGTTTAATATTGTTATTATAAAATATTTTTAAAAAGATAA
AATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATT
Found at i:3919244 original size:117 final size:116
Alignment explanation
Indices: 3919009--3919249 Score: 288
Period size: 117 Copynumber: 2.1 Consensus size: 116
3918999 TATTTTTAAT
3919009 AAGATAAAATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATTATTTTA
1 AAGATAAAATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATTATTTTA
* * * * * * * ** *
3919074 AAGTACTTTAAAATTCTAGTGTTTAATATTGTTATTATAAAATATTTTTAAA
66 AAGTAC-TTAAAATTCTAATATATAAAATAGTAATTATAAAAGATAATAAAA
*
3919126 AAGATAAAATATATGCTTTACACATTATATTATAAATTCAAAATATGTTAACTTAAATTATTTTA
1 AAGATAAAATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATTATTTTA
* * * *
3919191 AATTTA-TTAATATTTTAATATATAAAATAGATCAATT-TAACAGATAATAAAA
66 AA-GTACTTAAAATTCTAATATATAAAATAG-T-AATTATAAAAGATAATAAAA
*
3919243 AATATAA
1 AAGATAA
3919250 TTATAATAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
116 17 0.16
117 83 0.79
118 5 0.05
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (116 bp):
AAGATAAAATATATGCTTTACACATTATATTATAAATTCAAAATATATTAACTTAAATTATTTTA
AAGTACTTAAAATTCTAATATATAAAATAGTAATTATAAAAGATAATAAAA
Found at i:3920121 original size:21 final size:20
Alignment explanation
Indices: 3920095--3920137 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3920085 TTTTATAATG
* *
3920095 AATCCTAAACCTTAAACCTTA
1 AATCCT-AACCCTAAACCCTA
3920116 AATCCTAACCCTAAACCCTA
1 AATCCTAACCCTAAACCCTA
3920136 AA
1 AA
3920138 ATATAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (20 bp):
AATCCTAACCCTAAACCCTA
Found at i:3920132 original size:7 final size:7
Alignment explanation
Indices: 3920098--3920186 Score: 54
Period size: 7 Copynumber: 12.9 Consensus size: 7
3920088 TATAATGAAT
3920098 CCTAAAC
1 CCTAAAC
*
3920105 CTTAAAC
1 CCTAAAC
* *
3920112 CTTAAAT
1 CCTAAAC
3920119 CCT-AAC
1 CCTAAAC
3920125 CCTAAAC
1 CCTAAAC
*
3920132 CCTAAAA
1 CCTAAAC
** *
3920139 TATAAAT
1 CCTAAAC
* *
3920146 CATAAAG
1 CCTAAAC
*
3920153 TCTAAAC
1 CCTAAAC
* *
3920160 TCTAAAT
1 CCTAAAC
*
3920167 CCTAAAT
1 CCTAAAC
3920174 CCTAAAC
1 CCTAAAC
3920181 CCTAAA
1 CCTAAA
3920187 TTATACTTAC
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
6 5 0.08
7 60 0.92
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (7 bp):
CCTAAAC
Found at i:3920180 original size:21 final size:21
Alignment explanation
Indices: 3920125--3920187 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3920115 AAATCCTAAC
* * *
3920125 CCTAAACCCTAAAATATAAAT
1 CCTAAATCCTAAACTCTAAAT
*
3920146 CATAAAGT-CTAAACTCTAAAT
1 CCTAAA-TCCTAAACTCTAAAT
*
3920167 CCTAAATCCTAAACCCTAAAT
1 CCTAAATCCTAAACTCTAAAT
3920188 TATACTTACC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (21 bp):
CCTAAATCCTAAACTCTAAAT
Found at i:3920184 original size:14 final size:14
Alignment explanation
Indices: 3920098--3920187 Score: 60
Period size: 14 Copynumber: 6.5 Consensus size: 14
3920088 TATAATGAAT
3920098 CCTAAA-CCTTAAAC
1 CCTAAATCC-TAAAC
*
3920112 CTTAAATCCT-AAC
1 CCTAAATCCTAAAC
* *
3920125 CCTAAACCCTAAAA
1 CCTAAATCCTAAAC
** * *
3920139 TATAAATCATAAAG
1 CCTAAATCCTAAAC
* *
3920153 TCTAAA-CTCTAAAT
1 CCTAAATC-CTAAAC
3920167 CCTAAATCCTAAAC
1 CCTAAATCCTAAAC
3920181 CCTAAAT
1 CCTAAAT
3920188 TATACTTACC
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
13 12 0.21
14 43 0.74
15 3 0.05
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.26
Consensus pattern (14 bp):
CCTAAATCCTAAAC
Found at i:3920285 original size:14 final size:14
Alignment explanation
Indices: 3920268--3920300 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3920258 CATAAATCCT
*
3920268 AAACTCTAAACTAC
1 AAACCCTAAACTAC
3920282 AAACCCTAAACTAC
1 AAACCCTAAACTAC
3920296 AAACC
1 AAACC
3920301 TTAATCCGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAACTAC
Done.