Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 54
Found at i:7710291 original size:59 final size:60
Alignment explanation
Indices: 7710180--7710293 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 60
7710170 GGCGTGTCCC
* * * *
7710180 CGGGGATGCGCCTTACCCCCGTGGCATCCGACTCAGTAAAACCCCGTGAAAGCGCATCCT
1 CGGGGATGCACCTTACCCCCGTGGAATCCGACTCAGCAAAACCCAGTGAAAGCGCATCCT
7710240 CGGGGATGCACCTTA-CCCCGT-GAATCCGACTCAGCATAAACCCAAGT-AAAGCGC
1 CGGGGATGCACCTTACCCCCGTGGAATCCGACTCAGCA-AAACCC-AGTGAAAGCGC
7710294 GTCCCCAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 13 0.27
59 19 0.40
60 16 0.33
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (60 bp):
CGGGGATGCACCTTACCCCCGTGGAATCCGACTCAGCAAAACCCAGTGAAAGCGCATCCT
Found at i:7710306 original size:59 final size:60
Alignment explanation
Indices: 7710183--7710308 Score: 141
Period size: 59 Copynumber: 2.1 Consensus size: 60
7710173 GTGTCCCCGG
* * * * * **
7710183 GGATGCGCCTTACCCCCGTGGCATCCGACTCAGTAAAACCCCGTGAAAGCGCATCCTCGG
1 GGATGCACCTTACCCCCGTGGAATCCGACTCAGCAAAACCCAGTGAAAGCGCATCCCCAA
*
7710243 GGATGCACCTTA-CCCCGT-GAATCCGACTCAGCATAAACCCAAGT-AAAGCGCGTCCCCAA
1 GGATGCACCTTACCCCCGTGGAATCCGACTCAGCA-AAACCC-AGTGAAAGCGCATCCCCAA
7710302 GGATGCA
1 GGATGCA
7710309 ACTTTGTGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 13 0.23
59 30 0.54
60 13 0.23
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (60 bp):
GGATGCACCTTACCCCCGTGGAATCCGACTCAGCAAAACCCAGTGAAAGCGCATCCCCAA
Found at i:7710816 original size:12 final size:12
Alignment explanation
Indices: 7710799--7710855 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
7710789 CTTAAGAATT
7710799 TTATTTTAATAA
1 TTATTTTAATAA
*
7710811 TTATTTTAAGTAT
1 TTATTTTAA-TAA
7710824 TTATTACTTAATAA
1 TTATT--TTAATAA
*
7710838 CTATTTTAAT--
1 TTATTTTAATAA
7710848 TTATTTTA
1 TTATTTTA
7710856 TATTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 7 0.18
12 14 0.37
13 7 0.18
14 6 0.16
15 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATTTTAATAA
Found at i:7710866 original size:37 final size:39
Alignment explanation
Indices: 7710781--7710855 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
7710771 ATTAAAAATA
*
7710781 ATTTATTACTTAAGAATTTTATTTTAATAATTATTTTAAGT
1 ATTTATTACTTAAGAA-TCTATTTTAAT-ATTATTTTAAGT
*
7710822 ATTTATTACTTAATAA-CTATTTTAAT-TTATTTTA
1 ATTTATTACTTAAGAATCTATTTTAATATTATTTTA
7710856 TATTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 8 0.25
39 9 0.28
41 15 0.47
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (39 bp):
ATTTATTACTTAAGAATCTATTTTAATATTATTTTAAGT
Found at i:7710948 original size:9 final size:9
Alignment explanation
Indices: 7710931--7710967 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
7710921 TTAAATTTTA
7710931 TATTTTAAT
1 TATTTTAAT
*
7710940 TATTATAAT
1 TATTTTAAT
7710949 TATTTTAAT
1 TATTTTAAT
7710958 ATATTTTAAT
1 -TATTTTAAT
7710968 AATATACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTTTAAT
Found at i:7715257 original size:27 final size:26
Alignment explanation
Indices: 7715205--7715263 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
7715195 ATATTATTTG
* * *
7715205 AATTGATTTTTTTAATATAATTAATA
1 AATTTATTTTTTTAATAAAATAAATA
* *
7715231 ATTTTATTTTTTTATTAAAATAAAATA
1 AATTTATTTTTTTAATAAAAT-AAATA
7715258 AATTTA
1 AATTTA
7715264 ATATTTTCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
AATTTATTTTTTTAATAAAATAAATA
Found at i:7715960 original size:31 final size:32
Alignment explanation
Indices: 7715925--7715986 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
7715915 GACGAGTCCG
7715925 AATAAAAATA-TATTTTGGAAATTTAAAAAAC
1 AATAAAAATAGTATTTTGGAAATTTAAAAAAC
*
7715956 AATAAAAATAGTTTTTTTGGAAATTTAAAAA
1 AATAAAAATAG-TATTTTGGAAATTTAAAAA
7715987 CATTGTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 10 0.36
33 18 0.64
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (32 bp):
AATAAAAATAGTATTTTGGAAATTTAAAAAAC
Found at i:7717390 original size:18 final size:18
Alignment explanation
Indices: 7717367--7717406 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
7717357 GATGCAATTA
*
7717367 GTATCGATGCTGCTGTGG
1 GTATCGATGCTACTGTGG
7717385 GTATCGATGCTACTGTGG
1 GTATCGATGCTACTGTGG
7717403 GTAT
1 GTAT
7717407 TGATACTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (18 bp):
GTATCGATGCTACTGTGG
Found at i:7729057 original size:54 final size:54
Alignment explanation
Indices: 7728970--7729253 Score: 369
Period size: 54 Copynumber: 5.3 Consensus size: 54
7728960 ATAAGTTCTT
* * *
7728970 TGGGGTGCACACATAGTGCCGATTAA-GTCGTTCATAAACTTATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCC-AATAAGGTCGTTCATAAACTTATTATGAATTTCG
7729024 TGGGTTGCACACTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATTAT-G
1 TGGGTTGCACACTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATT-TCG
* * * *
7729078 TGGGTTGCACACTTAGTGCCAATACGGTCATTCATAAACTTATTATTAATTTTG
1 TGGGTTGCACACTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATTTCG
* *
7729132 TGGGTTGCACACTT-GTGTCGATACA-GTCGTTCATAAACTTATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCAATA-AGGTCGTTCATAAACTTATTATGAATTTCG
* * * * * *
7729185 TGGGTTGCACACTTAGAGCCGATATGATCGTTCATAAACTTATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATTTCG
*
7729239 TGGGTTGTACACTTA
1 TGGGTTGCACACTTA
7729254 TACATTAAAC
Statistics
Matches: 205, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
53 51 0.25
54 153 0.75
55 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATTTCG
Found at i:7729219 original size:107 final size:108
Alignment explanation
Indices: 7728970--7729253 Score: 378
Period size: 107 Copynumber: 2.6 Consensus size: 108
7728960 ATAAGTTCTT
* * *
7728970 TGGGGTGCACACATAGTGCCGAT-TAAGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCAC
1 TGGGTTGCACACTTAGTGCCGATATGA-TCGTTCATAAACTTATTATGAATTTCGTGGGTTGCAC
7729034 ACTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATTATG
65 ACTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATTATG
* * * * * *
7729078 TGGGTTGCACACTTAGTGCCAATACGGTCATTCATAAACTTATTATTAATTTTGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATATGATCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
* *
7729143 CTT-GTGTCGATACA-GTCGTTCATAAACTTATTATGAATT-TCG
66 CTTAGTGCCAATA-AGGTCGTTCATAAACTTATTATGAATTAT-G
* * * *
7729185 TGGGTTGCACACTTAGAGCCGATATGATCGTTCATAAACTTATTATGAATTCCATGGGTTGTACA
1 TGGGTTGCACACTTAGTGCCGATATGATCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
7729250 CTTA
66 CTTA
7729254 TACATTAAAC
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
106 1 0.01
107 91 0.60
108 59 0.39
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (108 bp):
TGGGTTGCACACTTAGTGCCGATATGATCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
CTTAGTGCCAATAAGGTCGTTCATAAACTTATTATGAATTATG
Found at i:7735784 original size:54 final size:54
Alignment explanation
Indices: 7735700--7736087 Score: 447
Period size: 54 Copynumber: 7.2 Consensus size: 54
7735690 TTCTTTGGTG
* * ** *
7735700 TGCACACGTAGTGCCAATACGGTAATTCATAAACTTATTAAGAATTCTATGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTATGGGT
* * ** *
7735754 TACACACTTAGTGTCGATATAGTCATTCATAAACTTATTATGAATTCTATGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTATGGGT
* * *
7735808 TGCACACTTTGTACCGATACGGTCGTTCATAAACTTATTATGAATTCCATGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTATGGGT
* * * **
7735862 TGCACACTTAGTGTCGATACCGTCGTTCATAAACTTATTATGAATTCTGTTAGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTATGGGT
* * **
7735916 TGCACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATT-TCGTCAGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCT-ATGGGT
* * * *
7735970 TGCACACTTAGTGCCGATGCAGTCGTTCATAAACTTATTATGAATTATGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTATGGGT
* * ** * * *
7736024 TACATACTTAGTTTCGATATGGTCGTTCATAAACTTATTATGAATT-TCGTGGGA
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCT-ATGGGT
7736078 TGCACACTTA
1 TGCACACTTA
7736088 TACATTAAAC
Statistics
Matches: 288, Mismatches: 43, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
53 2 0.01
54 285 0.99
55 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTATGGGT
Found at i:7737432 original size:13 final size:14
Alignment explanation
Indices: 7737414--7737442 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7737404 TGGGCTGGCA
7737414 AACCCTTGATC-CT
1 AACCCTTGATCTCT
7737427 AACCCTTGATCTCT
1 AACCCTTGATCTCT
7737441 AA
1 AA
7737443 GGCTAGTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.34, G:0.07, T:0.31
Consensus pattern (14 bp):
AACCCTTGATCTCT
Found at i:7740073 original size:33 final size:33
Alignment explanation
Indices: 7740031--7740096 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
7740021 TGACGATGGA
*
7740031 GATAGTGCGACACTGAGGGAAAATAATGAAACC
1 GATAGTGCGACACTGAGGGAAAAGAATGAAACC
7740064 GATAGTGCGACACTGAGGGAAAAGAATGAAACC
1 GATAGTGCGACACTGAGGGAAAAGAATGAAACC
7740097 CTAGCTCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.29, T:0.14
Consensus pattern (33 bp):
GATAGTGCGACACTGAGGGAAAAGAATGAAACC
Found at i:7740225 original size:3 final size:3
Alignment explanation
Indices: 7740213--7740282 Score: 79
Period size: 3 Copynumber: 22.7 Consensus size: 3
7740203 TTGTTTATTT
* *
7740213 ATA ATAA ATA ATA ATA ATA ATA ATT GTA ATA ATA ATA ATA ATAA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
*
7740260 TTA ATTA AT- ATA ATA ATA ATA AT
1 ATA A-TA ATA ATA ATA ATA ATA AT
7740283 TATTATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
2 2 0.04
3 46 0.81
4 9 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:7740287 original size:3 final size:3
Alignment explanation
Indices: 7740281--7740315 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7740271 AATAATAATA
7740281 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
7740316 AAATACAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7741019 original size:41 final size:41
Alignment explanation
Indices: 7740950--7741136 Score: 203
Period size: 41 Copynumber: 4.6 Consensus size: 41
7740940 GATCGGGATT
* * * * *
7740950 TAAAGCACGAGTCTATAGTGGCGTTTGTATAAAAATGTCAT
1 TAAAGTACGAGTCTATAGAGGCGTTTGTATAAAAACGCCAC
* * * * ***
7740991 TAAAGTATGAGTCTTTAGCGGCGCTTGTATAAAAATATCAC
1 TAAAGTACGAGTCTATAGAGGCGTTTGTATAAAAACGCCAC
* * *
7741032 TAAAGTACAAGTCTTTAGTGGCGTTTGTATAAAAACGCCAC
1 TAAAGTACGAGTCTATAGAGGCGTTTGTATAAAAACGCCAC
* *
7741073 TAAAGTACGATTCTATAGAGACGTTTGTATAAAAACGCCAC
1 TAAAGTACGAGTCTATAGAGGCGTTTGTATAAAAACGCCAC
* *
7741114 TAAAGTATGATTCTATAGAGGCG
1 TAAAGTACGAGTCTATAGAGGCG
7741137 CCGCTGAAGT
Statistics
Matches: 125, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (41 bp):
TAAAGTACGAGTCTATAGAGGCGTTTGTATAAAAACGCCAC
Found at i:7741233 original size:40 final size:40
Alignment explanation
Indices: 7741143--7741236 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
7741133 GGCGCCGCTG
* *
7741143 AAGTACAATCTTTAGCGGAGTTTGTATAAAAACGCTACTA
1 AAGTACAGTCTTTAACGGAGTTTGTATAAAAACGCTACTA
* * *
7741183 AAGTACAGTCTTTAACGGTGTTTTTATAGAAAC-CTACTA
1 AAGTACAGTCTTTAACGGAGTTTGTATAAAAACGCTACTA
*
7741222 AAGTGCGAGTCTTTA
1 AAGTAC-AGTCTTTA
7741237 GTTGCGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 11 0.23
40 36 0.77
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (40 bp):
AAGTACAGTCTTTAACGGAGTTTGTATAAAAACGCTACTA
Found at i:7744327 original size:18 final size:18
Alignment explanation
Indices: 7744304--7744343 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7744294 GATACAAAGC
* *
7744304 AACTGAATTTACGTTAGA
1 AACTGAACTTAAGTTAGA
*
7744322 AACTGAACTTAATTTAGA
1 AACTGAACTTAAGTTAGA
7744340 AACT
1 AACT
7744344 ATATTGAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (18 bp):
AACTGAACTTAAGTTAGA
Found at i:7745997 original size:20 final size:20
Alignment explanation
Indices: 7745972--7746024 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
7745962 GACCCGAACT
*
7745972 TGGTATTGATACTTGGCT-AA
1 TGGTATTGATACTT-GATGAA
*
7745992 TGGTATCGATACTTGATGAA
1 TGGTATTGATACTTGATGAA
7746012 TGAGTATTGATAC
1 TG-GTATTGATAC
7746025 CCTCAATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 17 0.61
21 9 0.32
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (20 bp):
TGGTATTGATACTTGATGAA
Found at i:7747829 original size:28 final size:28
Alignment explanation
Indices: 7747789--7747845 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
7747779 TGATCAAATT
7747789 TAGAACCCCATATAACTTCAATATCTCA
1 TAGAACCCCATATAACTTCAATATCTCA
7747817 TAGAACCCCATATAACTTCAATATCTCA
1 TAGAACCCCATATAACTTCAATATCTCA
7747845 T
1 T
7747846 GGATGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.30
Consensus pattern (28 bp):
TAGAACCCCATATAACTTCAATATCTCA
Found at i:7757704 original size:22 final size:22
Alignment explanation
Indices: 7757679--7757743 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
7757669 ATATTTCGAA
7757679 TACCACTATGTTTTGGATTTGG
1 TACCACTATGTTTTGGATTTGG
7757701 TACCACTATGTTTTGGATTTGG
1 TACCACTATGTTTTGGATTTGG
*
7757723 TACCACTATATTTTGGATTTG
1 TACCACTATGTTTTGGATTTG
7757744 AGTTTGTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (22 bp):
TACCACTATGTTTTGGATTTGG
Found at i:7757804 original size:2 final size:2
Alignment explanation
Indices: 7757799--7757864 Score: 78
Period size: 2 Copynumber: 33.0 Consensus size: 2
7757789 ATACACATAC
* * * * * *
7757799 AT AT AT AC AT AC AT AT AT AT AT AT AC AC AC AT AC 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
7757841 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
7757865 TAGTTTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:7757810 original size:18 final size:18
Alignment explanation
Indices: 7757787--7757839 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
7757777 TGACAATCAC
7757787 ACATACACATACATATAT
1 ACATACACATACATATAT
* *
7757805 ACATACATATATATATAT
1 ACATACACATACATATAT
7757823 AC--ACACATACATATAT
1 ACATACACATACATATAT
7757839 A
1 A
7757840 TATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 13 0.42
18 18 0.58
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (18 bp):
ACATACACATACATATAT
Found at i:7759288 original size:35 final size:35
Alignment explanation
Indices: 7759233--7759335 Score: 154
Period size: 35 Copynumber: 2.9 Consensus size: 35
7759223 TTAATCTACG
7759233 TCTGATAACTGTAAAA-CATATGATAATTGTAAACA
1 TCTGATAACTG-AAAATCATATGATAATTGTAAACA
*
7759268 TCTGATAACTGAAAATCATATGATAATTGTAAATA
1 TCTGATAACTGAAAATCATATGATAATTGTAAACA
* * *
7759303 TTTGATAACTAAAAATCATCTGATAATTGTAAA
1 TCTGATAACTGAAAATCATATGATAATTGTAAA
7759336 TATTTAGAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
34 4 0.06
35 59 0.94
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.34
Consensus pattern (35 bp):
TCTGATAACTGAAAATCATATGATAATTGTAAACA
Found at i:7759336 original size:18 final size:18
Alignment explanation
Indices: 7759233--7759336 Score: 104
Period size: 18 Copynumber: 5.9 Consensus size: 18
7759223 TTAATCTACG
*
7759233 TCTGATAACTGTAAAACA
1 TCTGATAACTGTAAATCA
* *
7759251 TATGATAATTGTAAA-CA
1 TCTGATAACTGTAAATCA
*
7759268 TCTGATAACTGAAAATCA
1 TCTGATAACTGTAAATCA
* *
7759286 TATGATAATTGTAAAT-A
1 TCTGATAACTGTAAATCA
* **
7759303 TTTGATAACTAAAAATCA
1 TCTGATAACTGTAAATCA
*
7759321 TCTGATAATTGTAAAT
1 TCTGATAACTGTAAAT
7759337 ATTTAGAATT
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
17 27 0.40
18 41 0.60
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.35
Consensus pattern (18 bp):
TCTGATAACTGTAAATCA
Found at i:7761029 original size:30 final size:30
Alignment explanation
Indices: 7760995--7761080 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 30
7760985 TAAAATCTAT
* * *
7760995 AACTTTTCAAAATTACATTTTTTGTCTTTA
1 AACTTTTCAAAATTACATTTTTAGTCCTCA
* *
7761025 AACTTTTACAAAGTT-TATATTTTAGTCCTCA
1 AACTTTT-CAAAATTACAT-TTTTAGTCCTCA
7761056 AAC-TTTCAAAATTTACA-TTTTAGTC
1 AACTTTTCAAAA-TTACATTTTTAGTC
7761081 ACTAATCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
29 12 0.27
30 14 0.31
31 19 0.42
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.48
Consensus pattern (30 bp):
AACTTTTCAAAATTACATTTTTAGTCCTCA
Found at i:7761061 original size:31 final size:29
Alignment explanation
Indices: 7760999--7761080 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
7760989 ATCTATAACT
* * *
7760999 TTTCAAAA-TTACATTTTTTGTCTTTAAAC
1 TTTCAAAATTTACA-TTTTAGTCCTCAAAC
* *
7761028 TTTTACAAAGTTTATATTTTAGTCCTCAAAC
1 -TTT-CAAAATTTACATTTTAGTCCTCAAAC
7761059 TTTCAAAATTTACATTTTAGTC
1 TTTCAAAATTTACATTTTAGTC
7761081 ACTAATCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 17 0.40
30 6 0.14
31 16 0.37
32 4 0.09
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.49
Consensus pattern (29 bp):
TTTCAAAATTTACATTTTAGTCCTCAAAC
Found at i:7773610 original size:9 final size:9
Alignment explanation
Indices: 7773596--7773621 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
7773586 ATTAAGCTTC
7773596 TTTTTTTTA
1 TTTTTTTTA
7773605 TTTTTTTTA
1 TTTTTTTTA
7773614 TTTTTTTT
1 TTTTTTTT
7773622 TATTAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:7773611 original size:10 final size:10
Alignment explanation
Indices: 7773596--7773625 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
7773586 ATTAAGCTTC
7773596 TTTTTTTTA-
1 TTTTTTTTAT
7773605 TTTTTTTTAT
1 TTTTTTTTAT
7773615 TTTTTTTTAT
1 TTTTTTTTAT
7773625 T
1 T
7773626 AACAATCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:7777087 original size:12 final size:13
Alignment explanation
Indices: 7777070--7777101 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
7777060 TCATTGCAAG
7777070 TGCAAATGTA-AA
1 TGCAAATGTAGAA
7777082 TGCAAATGTAGAA
1 TGCAAATGTAGAA
7777095 TGCAAAT
1 TGCAAAT
7777102 ATGCAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (13 bp):
TGCAAATGTAGAA
Found at i:7781717 original size:6 final size:6
Alignment explanation
Indices: 7781706--7781744 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
7781696 AACATTCTCC
*
7781706 TCCTCT TCCTCT CCCTCT TCCTCT TCCTCT TCCTCT TCC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCC
7781745 ATCTGTCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (6 bp):
TCCTCT
Found at i:7784338 original size:25 final size:25
Alignment explanation
Indices: 7784322--7784378 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
7784312 TAACATTTCT
7784322 ATATAATAAATAATATAAATATATA
1 ATATAATAAATAATATAAATATATA
*
7784347 ATATTATAAATAATATTAATATATATA
1 ATATAATAAATAATA-TAA-ATATATA
7784374 ATATA
1 ATATA
7784379 TTTTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 14 0.50
26 3 0.11
27 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAATAAATAATATAAATATATA
Found at i:7784341 original size:9 final size:9
Alignment explanation
Indices: 7784327--7784374 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
7784317 TTTCTATATA
7784327 ATAAATAAT
1 ATAAATAAT
7784336 ATAAAT-AT
1 ATAAATAAT
*
7784344 AT-AATATT
1 ATAAATAAT
7784352 ATAAATAAT
1 ATAAATAAT
*
7784361 ATTAATATAT
1 ATAAATA-AT
7784371 ATAA
1 ATAA
7784375 TATATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
7 3 0.09
8 7 0.22
9 17 0.53
10 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATAAATAAT
Found at i:7784344 original size:20 final size:21
Alignment explanation
Indices: 7784321--7784378 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
7784311 ATAACATTTC
7784321 TATATAATA-AATAATATAAA
1 TATATAATATAATAATATAAA
*
7784341 TATATAATATTATAA-AT-AA
1 TATATAATATAATAATATAAA
7784360 TAT-TAATATATATAATATA
1 TATATAATATA-ATAATATA
7784379 TTTTTATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 6 0.19
19 9 0.28
20 13 0.41
21 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATATAATATAATAATATAAA
Found at i:7784379 original size:17 final size:17
Alignment explanation
Indices: 7784334--7784392 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
7784324 ATAATAAATA
7784334 ATATA-AATATA-TAAT
1 ATATATAATATATTAAT
7784349 AT-TATAAATAATATTAAT
1 ATATAT-AAT-ATATTAAT
**
7784367 ATATATAATATATTTTT
1 ATATATAATATATTAAT
7784384 ATATATAAT
1 ATATATAAT
7784393 TTATAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 2 0.05
16 3 0.08
17 18 0.49
18 9 0.24
19 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATAATATATTAAT
Found at i:7785519 original size:21 final size:21
Alignment explanation
Indices: 7785490--7785542 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
7785480 ATTCTGACTA
7785490 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
7785511 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
7785532 TCGCAATGCGA
1 TCGCATTGCGA
7785543 ATCTGACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:7786157 original size:33 final size:33
Alignment explanation
Indices: 7786117--7786188 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
7786107 GGAAAGGACT
* **
7786117 ATCGCAACGAGAGAATTGCAACGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAACCAAA
*
7786150 ATCGCAACGAGATAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAACCAAA
7786183 ATCGCA
1 ATCGCA
7786189 TTGCGCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACGCGAAACCAAA
Found at i:7786259 original size:20 final size:19
Alignment explanation
Indices: 7786184--7786261 Score: 111
Period size: 19 Copynumber: 4.1 Consensus size: 19
7786174 GAAACCAAAA
* *
7786184 TCGCATTGCGCTTTTCATT
1 TCGCGTTGCGATTTTCATT
7786203 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
7786222 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
7786241 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
7786261 T
1 T
7786262 TAACCAAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 35 0.67
20 17 0.33
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:7788098 original size:93 final size:93
Alignment explanation
Indices: 7787924--7788204 Score: 419
Period size: 94 Copynumber: 3.1 Consensus size: 93
7787914 TAGATTGCTT
* * * *
7787924 AGTAAATTTATTCAGTTGTTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
7787985 AGTT-TCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
7788013 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
7788078 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
7788107 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTTTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
7788172 ATTTGTCTTTGTTTTGTCTTTTGGTTAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
7788200 AGTAA
1 AGTAA
7788205 TGCAATCCAT
Statistics
Matches: 175, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
89 33 0.19
91 3 0.02
92 2 0.01
93 47 0.27
94 90 0.51
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:7788320 original size:20 final size:19
Alignment explanation
Indices: 7788293--7788350 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 19
7788283 TCTTTTAGTT
7788293 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
7788312 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
**
7788332 GAAACAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
7788351 CAAAATCGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.52, C:0.19, G:0.21, T:0.09
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:7788889 original size:39 final size:41
Alignment explanation
Indices: 7788844--7788929 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
7788834 TCCTATTGTG
*
7788844 AAGAGGCC-C-TCATTCCTTG-AGA-GTCCCATCCCACCGTTC
1 AAGAGGCCACGTCA-TCCTTGAAGAGGTCCC-TCCCACCATTC
*
7788883 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCAC-GTCATCCTTGAAGAGGTCCCTCCCACCATTC
7788925 AAGAG
1 AAGAG
7788930 CCTGATTCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 8 0.20
40 1 0.03
41 5 0.12
42 21 0.52
43 5 0.12
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (41 bp):
AAGAGGCCACGTCATCCTTGAAGAGGTCCCTCCCACCATTC
Found at i:7790131 original size:14 final size:14
Alignment explanation
Indices: 7790112--7790147 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
7790102 ATTGTTTAAT
7790112 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
7790126 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
7790140 TGATTTGT
1 TGATTTGT
7790148 TTAATTGATG
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:7790334 original size:19 final size:19
Alignment explanation
Indices: 7790254--7790324 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
7790244 AAAAATGACT
*
7790254 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
7790273 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAAA
7790292 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
7790311 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
7790325 CTAAATTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 47 0.98
20 1 0.02
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:7790341 original size:19 final size:19
Alignment explanation
Indices: 7790254--7790334 Score: 103
Period size: 19 Copynumber: 4.3 Consensus size: 19
7790244 AAAAATGACT
*
7790254 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
*
7790273 ATCGCAACGAGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
7790292 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
7790311 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
7790330 TTCGC
1 ATCGC
7790335 GTTGCGATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
19 56 0.98
20 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:7790352 original size:19 final size:19
Alignment explanation
Indices: 7790330--7790447 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
7790320 CGAAACTAAA
7790330 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
7790349 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
7790364 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
7790382 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
7790397 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
7790415 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
7790434 TTCCACGTTGCGAT
1 TT-CGCGTTGCGAT
7790448 AGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 35 0.48
20 9 0.12
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:7790376 original size:33 final size:33
Alignment explanation
Indices: 7790334--7790427 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
7790324 ACTAAATTCG
*
7790334 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
7790367 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
7790400 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
7790428 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:7790446 original size:20 final size:21
Alignment explanation
Indices: 7790400--7790454 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
7790390 GCGATTCTCT
**
7790400 CGTTGCGATTTTCATTTCGCA
1 CGTTGCGATAGTCATTTCGCA
7790421 --TTGCGATAGTCATTTC-CA
1 CGTTGCGATAGTCATTTCGCA
*
7790439 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
7790455 AAGATGATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 14 0.48
20 13 0.45
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCATTTCGCA
Found at i:7790493 original size:20 final size:20
Alignment explanation
Indices: 7790421--7790493 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
7790411 TCATTTCGCA
**
7790421 TTGCGATAGTCATTTCCACG
1 TTGCGATAGTCATTTCCGTG
* **
7790441 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
7790461 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
7790482 TTGCGATAGTCA
1 TTGCGATAGTCA
7790494 AATGAATGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 2 0.05
20 23 0.57
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:7792989 original size:23 final size:23
Alignment explanation
Indices: 7792947--7793022 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
7792937 TCTGAAAATC
*
7792947 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCG-GTATTGACCAAG
7792971 ATCAAAGTCCGGTATTGACCAAG
1 ATCAAAGTCCGGTATTGACCAAG
7792994 ATCAAAGTCCGGTATTGACCAAG
1 ATCAAAGTCCGGTATTGACCAAG
7793017 ATCAAA
1 ATCAAA
7793023 TTTCGAATAC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 41 0.80
24 10 0.20
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (23 bp):
ATCAAAGTCCGGTATTGACCAAG
Found at i:7793890 original size:20 final size:21
Alignment explanation
Indices: 7793865--7794222 Score: 238
Period size: 20 Copynumber: 17.3 Consensus size: 21
7793855 CAGATCTCGT
*
7793865 TGCGATTTTC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
7793885 TGCGA-TTACGTAAATCG-AA
1 TGCGATTTACGTAAATCGCAA
* * * *
7793904 GTACGAATTAGGAAAATCGCAA
1 -TGCGATTTACGTAAATCGCAA
7793926 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * * *
7793946 TGTGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
7793967 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
7793987 AGCGA-TTGCGTAAATCACAA
1 TGCGATTTACGTAAATCGCAA
*
7794007 TGCG-GTTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
7794027 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
7794048 TGCGA-TTACGTAAATACGTAATCGCA
1 TGCGATTTACGTAAAT-CG----C-AA
* * *
7794074 TGCGATTTTCCT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
*
7794094 TGCGATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* * * *
7794114 TGCGATTTTCCTAATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
7794135 TACGATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
7794155 TGCGATTTACGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* * *
7794175 TGCGAATTATGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
7794196 CGCGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
7794217 TGCGAT
1 TGCGAT
7794223 AGTCAGAATC
Statistics
Matches: 271, Mismatches: 50, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.02
20 155 0.57
21 90 0.33
22 5 0.02
25 3 0.01
26 9 0.03
27 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:7793920 original size:21 final size:21
Alignment explanation
Indices: 7793896--7793966 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
7793886 GCGATTACGT
7793896 AAATCG-AAGTACGAATTAGGA
1 AAATCGCAAGT-CGAATTAGGA
* *
7793917 AAATCGCAA-TGCG-ATTACGT
1 AAATCGCAAGT-CGAATTAGGA
7793937 AAATCGCAATGT-GAATTAGGA
1 AAATCGCAA-GTCGAATTAGGA
7793958 AAATCGCAA
1 AAATCGCAA
7793967 TGCGATTACG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 15 0.37
21 23 0.56
22 3 0.07
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (21 bp):
AAATCGCAAGTCGAATTAGGA
Found at i:7793922 original size:41 final size:41
Alignment explanation
Indices: 7793876--7794062 Score: 265
Period size: 41 Copynumber: 4.6 Consensus size: 41
7793866 GCGATTTTCT
7793876 AAATCGCAATGCGATTACGTAAATCG-AAGTACGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TACGAATTAGGA
**
7793917 AAATCGCAATGCGATTACGTAAATCGCAATGTGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATACGAATTAGGA
*
7793958 AAATCGCAATGCGATTACGTAAATCGCAA-AGCG-ATT-GCGT
1 AAATCGCAATGCGATTACGTAAATCGCAATA-CGAATTAG-GA
* * *
7793998 AAATCACAATGCGGTTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATACGAATTAGGA
7794039 AAATCGCAATGCGATTACGTAAAT
1 AAATCGCAATGCGATTACGTAAAT
7794063 ACGTAATCGC
Statistics
Matches: 129, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 1 0.01
40 33 0.26
41 92 0.71
42 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGCAATACGAATTAGGA
Found at i:7794025 original size:81 final size:81
Alignment explanation
Indices: 7793876--7794062 Score: 281
Period size: 81 Copynumber: 2.3 Consensus size: 81
7793866 GCGATTTTCT
*
7793876 AAATCGCAATGCGATTACGTAAATCGAAGTACGAATTAGGAAAATCGCAATGCGATTACGTAAAT
1 AAATCGCAATGCGATTACGTAAATCGAAG-ACGAATTAGGAAAATCACAATGCGATTACGTAAAT
*
7793941 CGCAATGTGAATTAGGA
65 CGCAATGCGAATTAGGA
* *
7793958 AAATCGCAATGCGATTACGTAAATCGCAA-AGCG-ATT-GCGTAAATCACAATGCGGTTACGTAA
1 AAATCGCAATGCGATTACGTAAATCG-AAGA-CGAATTAG-GAAAATCACAATGCGATTACGTAA
7794020 ATCGCAATGCGAATTAGGA
63 ATCGCAATGCGAATTAGGA
7794039 AAATCGCAATGCGATTACGTAAAT
1 AAATCGCAATGCGATTACGTAAAT
7794063 ACGTAATCGC
Statistics
Matches: 98, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
80 1 0.01
81 67 0.68
82 28 0.29
83 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (81 bp):
AAATCGCAATGCGATTACGTAAATCGAAGACGAATTAGGAAAATCACAATGCGATTACGTAAATC
GCAATGCGAATTAGGA
Found at i:7794194 original size:41 final size:40
Alignment explanation
Indices: 7794062--7794179 Score: 184
Period size: 41 Copynumber: 3.0 Consensus size: 40
7794052 ATTACGTAAA
*
7794062 TACGTAATCGCA-TGCGATTTTCCTAATCGCATTGCGATT
1 TACGTAATCGCATTGCGATTTTCCTATTCGCATTGCGATT
*
7794101 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTACGATT
1 TACGTAATCGCATTGCGATTTTCCT-ATTCGCATTGCGATT
* *
7794142 TACGTAATCGCATTGCGATTTACGTATTCGCATTGCGA
1 TACGTAATCGCATTGCGATTTTCCTATTCGCATTGCGA
7794180 ATTATGAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
39 12 0.17
40 24 0.33
41 36 0.50
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (40 bp):
TACGTAATCGCATTGCGATTTTCCTATTCGCATTGCGATT
Found at i:7794194 original size:61 final size:60
Alignment explanation
Indices: 7794067--7794194 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 60
7794057 GTAAATACGT
* * * *
7794067 AATCGCATGCGATTTTCCTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTA
1 AATCGCATACGATTTACCTAATCGCATTGCGATTTACGTAATCGCATTGCGATTATCCAA
* * * *
7794127 ATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAT-GAA
1 AATCGCA-TACGATTTACCTAATCGCATTGCGATTTACGTAATCGCATTGCG-ATTATCCAA
7794188 AATCGCA
1 AATCGCA
7794195 ACGCGAATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 6 0.11
61 47 0.82
62 4 0.07
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (60 bp):
AATCGCATACGATTTACCTAATCGCATTGCGATTTACGTAATCGCATTGCGATTATCCAA
Found at i:7794200 original size:21 final size:21
Alignment explanation
Indices: 7794176--7794221 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7794166 TATTCGCATT
7794176 GCGAATTAT-GAAAATCGCAAC
1 GCGAATT-TGGAAAATCGCAAC
* *
7794197 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
7794218 GCGA
1 GCGA
7794222 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:7796123 original size:29 final size:29
Alignment explanation
Indices: 7796081--7796240 Score: 120
Period size: 29 Copynumber: 5.7 Consensus size: 29
7796071 CCTTTTAAGC
* * *
7796081 AATATTTATCAAAATATCACCATTTTCAA
1 AATAATTACCAAAATATCACCATTTTTAA
* *
7796110 AATAATTACTAAAATATCA--TTTTTTAA
1 AATAATTACCAAAATATCACCATTTTTAA
*
7796137 GAA-AATTA--AGAAAT-T-ATCATTTTTAA
1 -AATAATTACCA-AAATATCACCATTTTTAA
** *
7796163 AA-AATTATGAAAATAGCACCATTTTTAA
1 AATAATTACCAAAATATCACCATTTTTAA
* ** *
7796191 AATAATTACCATAATATCATTATTTTCAA
1 AATAATTACCAAAATATCACCATTTTTAA
*
7796220 AATAATTACCAAAATACCACC
1 AATAATTACCAAAATATCACC
7796241 CAGTCAACGG
Statistics
Matches: 103, Mismatches: 19, Indels: 18
0.74 0.14 0.13
Matches are distributed among these distances:
24 1 0.01
25 9 0.09
26 15 0.15
27 12 0.12
28 14 0.14
29 52 0.50
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (29 bp):
AATAATTACCAAAATATCACCATTTTTAA
Found at i:7796176 original size:26 final size:26
Alignment explanation
Indices: 7796101--7796176 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
7796091 AAAATATCAC
*
7796101 CATTTTCAAAATAATTACT-AAAA-TAT
1 CATTTTTAAAA-AATTA-TGAAAATTAT
*
7796127 CATTTTTTAAGAAAATTAAG-AAATTAT
1 CA-TTTTTAA-AAAATTATGAAAATTAT
7796154 CATTTTTAAAAAATTATGAAAAT
1 CATTTTTAAAAAATTATGAAAAT
7796177 AGCACCATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
25 8 0.19
26 16 0.38
27 16 0.38
28 2 0.05
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (26 bp):
CATTTTTAAAAAATTATGAAAATTAT
Found at i:7804770 original size:24 final size:24
Alignment explanation
Indices: 7804740--7804788 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
7804730 AATTATTTAT
7804740 TTTTATTACTATGCAA-TAATCTTA
1 TTTTATTAC-ATGCAATTAATCTTA
* *
7804764 TTTTATTTCATGTAATTAATCTTA
1 TTTTATTACATGCAATTAATCTTA
7804788 T
1 T
7804789 CAGCCATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTATTACATGCAATTAATCTTA
Found at i:7809665 original size:25 final size:25
Alignment explanation
Indices: 7809637--7809684 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
7809627 TTAAAAGTCC
7809637 TATTTTATATTTCAAATTTTATTCT
1 TATTTTATATTTCAAATTTTATTCT
*
7809662 TATTTTATATTTTAAATTTTATT
1 TATTTTATATTTCAAATTTTATT
7809685 TGGAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTATATTTCAAATTTTATTCT
Found at i:7809888 original size:57 final size:58
Alignment explanation
Indices: 7809826--7809940 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
7809816 TTTATAATTC
* * *
7809826 ATACGATATATATATTT-TTTCATAT-TTTTTATTTATGATATACAAATATCATATAAA
1 ATACGACATATATATTTCTTT-ATATCCTTTTATATATGATATACAAATATCATATAAA
*
7809883 ATACGACATATATATTTCTTTATATCCTTTTATATATGATATACATATATCATATAAA
1 ATACGACATATATATTTCTTTATATCCTTTTATATATGATATACAAATATCATATAAA
7809941 GTTAAGAGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 20 0.38
58 32 0.62
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (58 bp):
ATACGACATATATATTTCTTTATATCCTTTTATATATGATATACAAATATCATATAAA
Found at i:7814652 original size:13 final size:13
Alignment explanation
Indices: 7814634--7814661 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7814624 ATTACAGTAG
7814634 CCCCCTTAGCAGC
1 CCCCCTTAGCAGC
7814647 CCCCCTTAGCAGC
1 CCCCCTTAGCAGC
7814660 CC
1 CC
7814662 ATGTGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.57, G:0.14, T:0.14
Consensus pattern (13 bp):
CCCCCTTAGCAGC
Found at i:7817951 original size:15 final size:16
Alignment explanation
Indices: 7817923--7817954 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
7817913 AAAATCTTTC
7817923 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
7817939 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
7817954 T
1 T
7817955 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:7818729 original size:16 final size:16
Alignment explanation
Indices: 7818705--7818738 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
7818695 TATCGCCGAC
*
7818705 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
7818721 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
7818737 CG
1 CG
7818739 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:7819400 original size:54 final size:54
Alignment explanation
Indices: 7819357--7819800 Score: 591
Period size: 54 Copynumber: 8.2 Consensus size: 54
7819347 TCCCATAGTT
* * *
7819357 TGCACACATAGTACCGAAACGGTTATTCATCCACATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
7819411 TGTACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
7819465 TGCACACTTAGTGTCGAAATGATTATTCATCCACATAGGATGAATTCCGTAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
7819519 TGCACACTTAGTGCCAAAACAGTTATTCATCCACATAGGATCAATTCTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
7819573 TGCACATTTAGTACCGAAACGGTTATTCATCCATATAGAATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
7819627 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGAACGAACTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * *
7819681 CGTACACTTAATGCCGAAACGGTTATTCATCTACATAGGATGAATTCCGTGAAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* ** * * *
7819735 TGCACACTTAGTGCCGAAACGATTATTCATCCACATATAATGGATTTCGTGAAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
*
7819789 TGCACATTTAGT
1 TGCACACTTAGT
7819801 TCCTAGTTGG
Statistics
Matches: 338, Mismatches: 52, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 338 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:7826907 original size:3 final size:3
Alignment explanation
Indices: 7826899--7826947 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
7826889 TATTAAACAT
* * *
7826899 TTA TTA TTA TTA TTA TGGTA TTA TTT TTA TTA TTT TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA T--TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7826946 TT
1 TT
7826948 TTTTTTGTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 35 0.92
5 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:7826953 original size:9 final size:9
Alignment explanation
Indices: 7826898--7826952 Score: 69
Period size: 9 Copynumber: 6.3 Consensus size: 9
7826888 ATATTAAACA
7826898 TTTATTATT
1 TTTATTATT
*
7826907 ATTATTA-T
1 TTTATTATT
**
7826915 GGTATTATT
1 TTTATTATT
7826924 TTTATTATT
1 TTTATTATT
7826933 TTTATTATT
1 TTTATTATT
7826942 TTTATT-TT
1 TTTATTATT
7826950 TTT
1 TTT
7826953 TGTAGGTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
8 11 0.28
9 29 0.73
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTATTATT
Found at i:7826953 original size:18 final size:18
Alignment explanation
Indices: 7826898--7826952 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 18
7826888 ATATTAAACA
*
7826898 TTTATTATTATTATTA-T
1 TTTATTATTTTTATTATT
**
7826915 GGTATTATTTTTATTATT
1 TTTATTATTTTTATTATT
7826933 TTTATTATTTTTATT-TT
1 TTTATTATTTTTATTATT
7826950 TTT
1 TTT
7826953 TGTAGGTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTATTATTTTTATTATT
Found at i:7828477 original size:16 final size:16
Alignment explanation
Indices: 7828456--7828488 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
7828446 TCACGAACAA
7828456 ATGGCGATCTATAGGG
1 ATGGCGATCTATAGGG
7828472 ATGGCGATCTATAGGG
1 ATGGCGATCTATAGGG
7828488 A
1 A
7828489 AAACGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.36, T:0.24
Consensus pattern (16 bp):
ATGGCGATCTATAGGG
Found at i:7828646 original size:37 final size:35
Alignment explanation
Indices: 7828597--7828677 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 35
7828587 TTGTTACATT
*
7828597 TTATTTATTTTATGT-ATTTTTTTACTATTTGTTTAG
1 TTATTTATTTTAT-TCATTTATTTA-TATTTGTTTAG
*
7828633 TTATTGTATTTTATTCATTTATTTATCTTTGTTTAG
1 TTATT-TATTTTATTCATTTATTTATATTTGTTTAG
7828669 TTATATTAT
1 TTAT-TTAT
7828678 ATTTTATTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 23 0.57
37 17 0.43
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.68
Consensus pattern (35 bp):
TTATTTATTTTATTCATTTATTTATATTTGTTTAG
Found at i:7828664 original size:36 final size:37
Alignment explanation
Indices: 7828596--7828690 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 37
7828586 TTTGTTACAT
*
7828596 TTTATTTATTTTATGT-ATTTTTTTACTATTTGTTTAG
1 TTTATTTATTTTAT-TCATTTATTTACTATTTGTTTAG
*
7828633 -TTATTGTATTTTATTCATTTATTTA-TCTTTGTTTAG
1 TTTATT-TATTTTATTCATTTATTTACTATTTGTTTAG
7828669 TTATATTATATTTTATTACATT
1 TT-TATT-TATTTTATT-CATT
7828691 GATATTTCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
36 16 0.32
37 17 0.34
38 13 0.26
39 4 0.08
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.67
Consensus pattern (37 bp):
TTTATTTATTTTATTCATTTATTTACTATTTGTTTAG
Found at i:7833919 original size:25 final size:25
Alignment explanation
Indices: 7833885--7833986 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
7833875 AGGGGCACCA
*
7833885 TTTTTCAAATAACTT-CATCAAACAT
1 TTTTTAAAAT-ACTTCCATCAAACAT
*
7833910 TTTTTAAAATTCTTCCATCAAACAT
1 TTTTTAAAATACTTCCATCAAACAT
* * *
7833935 TATTTAAAATTCTTTCAT-AAAGCA-
1 TTTTTAAAATACTTCCATCAAA-CAT
* *
7833959 -TTTTAAAACTTCTT-CATAAAACAT
1 TTTTTAAAA-TACTTCCATCAAACAT
7833983 TTTT
1 TTTT
7833987 GCCTTTTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
23 12 0.18
24 14 0.21
25 40 0.61
ACGTcount: A:0.38, C:0.17, G:0.01, T:0.44
Consensus pattern (25 bp):
TTTTTAAAATACTTCCATCAAACAT
Found at i:7833924 original size:24 final size:24
Alignment explanation
Indices: 7833897--7833986 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 24
7833887 TTTCAAATAA
7833897 CTTCATCAAACATTTTTTAAAATT
1 CTTCATCAAACATTTTTTAAAATT
*
7833921 CTTCCATCAAACATTATTTAAAATT
1 CTT-CATCAAACATTTTTTAAAATT
7833946 CTTTCAT-AAAGCA--TTTTAAAACTT
1 C-TTCATCAAA-CATTTTTTAAAA-TT
*
7833970 CTTCATAAAACATTTTT
1 CTTCATCAAACATTTTT
7833987 GCCTTTTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
23 14 0.25
24 12 0.21
25 29 0.51
26 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (24 bp):
CTTCATCAAACATTTTTTAAAATT
Found at i:7835045 original size:175 final size:175
Alignment explanation
Indices: 7834749--7835158 Score: 532
Period size: 175 Copynumber: 2.3 Consensus size: 175
7834739 ATTAGACGTA
* * * * *
7834749 CTCATCAAGTAGGAACAATGTCATCCCCTGACTAGACCTCTTTAACATGAATGAAAAATGTCATC
1 CTCATCAAGTAGGAACAATGTCATCCACTGACTAGACCTCCTTAACATGAAGGAGAAATGGCATC
* * * * *
7834814 ATAAGCGACCAAATTCTTTTCATCGCGGATGAACAATGCTGTTTATCTTTAGGCAACCATATTTC
66 ATAAGCGACCAAATTCTCTTCATCGCGGATGAACAATGCCGTTTATCTTCAGGCAACCAGATTGC
* *
7834879 CTCAGCAATAAGGAACAATGTTACCTTCAAACACGACTAGATGTC
131 ATCAGCAAGAAGGAACAATGTTACCTTCAAACACGACTAGATGTC
* * *
7834924 CTCATCAAGTAGGAACAATGTCGTCCACTGACTAGATCTCCTCAACATGAAGGAGAAATGGCATC
1 CTCATCAAGTAGGAACAATGTCATCCACTGACTAGACCTCCTTAACATGAAGGAGAAATGGCATC
** * * * *
7834989 ATAAGCGACCAGTTTCTCTTCATTGTGGATGAACAGTTCCGTTTATCTTCAGGCAACCAGATTGC
66 ATAAGCGACCAAATTCTCTTCATCGCGGATGAACAATGCCGTTTATCTTCAGGCAACCAGATTGC
* ** * * *
7835054 ATCAGTAAGAAGGAACAATGTTGTCTTTAGACGCGACTAGATGTC
131 ATCAGCAAGAAGGAACAATGTTACCTTCAAACACGACTAGATGTC
* * * * *
7835099 CTCATCAACTAGGAAAAATGTTATCTACTGACTAGACCTCCTTAACATGAAGTAGAAATG
1 CTCATCAAGTAGGAACAATGTCATCCACTGACTAGACCTCCTTAACATGAAGGAGAAATG
7835159 TTCTCTTTAT
Statistics
Matches: 200, Mismatches: 35, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
175 200 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (175 bp):
CTCATCAAGTAGGAACAATGTCATCCACTGACTAGACCTCCTTAACATGAAGGAGAAATGGCATC
ATAAGCGACCAAATTCTCTTCATCGCGGATGAACAATGCCGTTTATCTTCAGGCAACCAGATTGC
ATCAGCAAGAAGGAACAATGTTACCTTCAAACACGACTAGATGTC
Found at i:7835578 original size:16 final size:17
Alignment explanation
Indices: 7835557--7835589 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7835547 TTATGTCTTG
*
7835557 CTTAAAATTTAT-TTCT
1 CTTAAAAGTTATATTCT
7835573 CTTAAAAGTTATATTCT
1 CTTAAAAGTTATATTCT
7835590 TTTTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (17 bp):
CTTAAAAGTTATATTCT
Found at i:7835826 original size:7 final size:7
Alignment explanation
Indices: 7835816--7835841 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
7835806 TTTATTTATT
7835816 ATATTAA
1 ATATTAA
7835823 ATATTAA
1 ATATTAA
7835830 ATATTAA
1 ATATTAA
7835837 ATATT
1 ATATT
7835842 TATTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATTAA
Found at i:7835849 original size:3 final size:3
Alignment explanation
Indices: 7835841--7835899 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
7835831 TATTAAATAT
* * *
7835841 TTA TTA TTA TTA TTA TGGTA TTA TTT TTA TT- TTA TTA -TG TTA ATA
1 TTA TTA TTA TTA TTA T--TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
7835886 TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TT
7835900 TGGTTTGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
5 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:7837682 original size:15 final size:17
Alignment explanation
Indices: 7837657--7837690 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
7837647 TTTATCATTG
7837657 TTTAGTTATATT-ATAT
1 TTTAGTTATATTGATAT
7837673 TTTA-TTATATTGATAT
1 TTTAGTTATATTGATAT
7837689 TT
1 TT
7837691 CATTCATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTAGTTATATTGATAT
Found at i:7841347 original size:22 final size:20
Alignment explanation
Indices: 7841315--7841354 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
7841305 TTTAAAGTTG
7841315 TTTATTCAAAATATGATTTTAA
1 TTTATTCAAAA-ATG-TTTTAA
*
7841337 TTTATTGAAAAATGTTTT
1 TTTATTCAAAAATGTTTT
7841355 GGAGAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTATTCAAAAATGTTTTAA
Found at i:7846512 original size:21 final size:19
Alignment explanation
Indices: 7846474--7846519 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
7846464 AATTAATCCT
7846474 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
7846494 ACTAATATTAAGTAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
7846515 A-TAAT
1 ACTAAT
7846520 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:7856685 original size:21 final size:20
Alignment explanation
Indices: 7856647--7856688 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
7856637 AATTAATCCT
7856647 ACTAAGTATTAAAGCTAAGA
1 ACTAAGTATTAAAGCTAAGA
7856667 ACTAA-TATTAAGGAGCTAAGA
1 ACTAAGTATTAA--AGCTAAGA
7856688 A
1 A
7856689 TAACGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.24
Consensus pattern (20 bp):
ACTAAGTATTAAAGCTAAGA
Found at i:7867367 original size:23 final size:23
Alignment explanation
Indices: 7867341--7867394 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
7867331 GTTTCCCCAT
7867341 AGAATATTTATCATATGTTTACA
1 AGAATATTTATCATATGTTTACA
*
7867364 AGAATGTTTATCATATGTTTACA
1 AGAATATTTATCATATGTTTACA
*
7867387 AGTATATT
1 AGAATATT
7867395 AGAGTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (23 bp):
AGAATATTTATCATATGTTTACA
Found at i:7869671 original size:12 final size:12
Alignment explanation
Indices: 7869654--7869680 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7869644 ATCTCTGTAG
7869654 AAAAAAGGAAAA
1 AAAAAAGGAAAA
7869666 AAAAAAGGAAAA
1 AAAAAAGGAAAA
7869678 AAA
1 AAA
7869681 GTGAAGCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGGAAAA
Found at i:7869802 original size:18 final size:17
Alignment explanation
Indices: 7869779--7869834 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
7869769 CTAAAAGACA
7869779 TTTTATTGTATAATTATT
1 TTTTATTGT-TAATTATT
*
7869797 TTTTATT-TTTATTATT
1 TTTTATTGTTAATTATT
7869813 ATTATTATTGTTAA-TATT
1 -TT-TTATTGTTAATTATT
7869831 TTTT
1 TTTT
7869835 TTAATTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 9 0.27
17 5 0.15
18 16 0.48
19 3 0.09
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTATTGTTAATTATT
Found at i:7870836 original size:24 final size:24
Alignment explanation
Indices: 7870800--7870854 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
7870790 TATTTTTTAA
7870800 TTATTT-TTCTTTT-TTACTAACTT
1 TTATTTATTCTTTTGTTACTAA-TT
* * *
7870823 TTATTTATTGTTTTGTTATTTATT
1 TTATTTATTCTTTTGTTACTAATT
7870847 TTATTTAT
1 TTATTTAT
7870855 CATTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.22
24 16 0.59
25 5 0.19
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (24 bp):
TTATTTATTCTTTTGTTACTAATT
Found at i:7874395 original size:106 final size:106
Alignment explanation
Indices: 7874210--7874424 Score: 430
Period size: 106 Copynumber: 2.0 Consensus size: 106
7874200 GAAAAACATT
7874210 CTCAAGCAGAACAGTCTCAGATATGAAAGGTCTGTAAAGCCAAAGCTCGGGAAGCAAATGGGGCA
1 CTCAAGCAGAACAGTCTCAGATATGAAAGGTCTGTAAAGCCAAAGCTCGGGAAGCAAATGGGGCA
7874275 CGATCCATTTCAAGGACCAGATTGACAGGCCAAACATGAGA
66 CGATCCATTTCAAGGACCAGATTGACAGGCCAAACATGAGA
7874316 CTCAAGCAGAACAGTCTCAGATATGAAAGGTCTGTAAAGCCAAAGCTCGGGAAGCAAATGGGGCA
1 CTCAAGCAGAACAGTCTCAGATATGAAAGGTCTGTAAAGCCAAAGCTCGGGAAGCAAATGGGGCA
7874381 CGATCCATTTCAAGGACCAGATTGACAGGCCAAACATGAGA
66 CGATCCATTTCAAGGACCAGATTGACAGGCCAAACATGAGA
7874422 CTC
1 CTC
7874425 CATCCAAGAG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 109 1.00
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.16
Consensus pattern (106 bp):
CTCAAGCAGAACAGTCTCAGATATGAAAGGTCTGTAAAGCCAAAGCTCGGGAAGCAAATGGGGCA
CGATCCATTTCAAGGACCAGATTGACAGGCCAAACATGAGA
Found at i:7875031 original size:106 final size:106
Alignment explanation
Indices: 7874653--7875724 Score: 1597
Period size: 106 Copynumber: 10.2 Consensus size: 106
7874643 TTCAGTTTCA
* * * *
7874653 TTCAGAACCAATTTCAACTTCACAGAGAAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
7874718 CGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* *
7874758 TTCATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
7874823 CGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
*
7874863 TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * **
7874928 TGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCGGT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* * * *
7874969 TCCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
7875034 CGACGAAGGGACCGTTGGTTGTCAAAAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
*
7875075 TTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
7875140 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
*
7875181 TTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
7875246 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
*
7875287 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
7875352 CGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* * * * *
7875393 TTCAGAGCCAATTTCGACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTC
* * * **
7875457 ACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT--TTA-
65 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* * * *
7875493 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
7875558 CAAACGAAGGGACGGCTGGTTGTCAACAAGCAACTTCCCAAT
66 C-GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
* *
7875600 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * **
7875665 CAACGAAGGGA-TGACTGGTTGTCAACAAACAATTTCCCGGT
66 CGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAAT
*
7875706 TCCAGAGCCAATTTCAACT
1 TTCAGAGCCAATTTCAACT
7875725 CCACGACGGA
Statistics
Matches: 884, Mismatches: 72, Indels: 21
0.90 0.07 0.02
Matches are distributed among these distances:
100 57 0.06
101 24 0.03
102 1 0.00
103 4 0.00
104 4 0.00
105 191 0.22
106 539 0.61
107 64 0.07
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT
Found at i:7878441 original size:45 final size:45
Alignment explanation
Indices: 7878387--7878520 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 45
7878377 TTTCATAGAA
7878387 GAAGATAGATCAGCATCAACCCTTGTGCTTGATTCCATCACAACAG
1 GAAG-TAGATCAGCATCAACCCTTGTGCTTGATTCCATCACAACAG
* *** * * * *
7878433 GAGGTAGATCAGCA-CCTTCGTCGTG-TTAGATTCTATCATAACAG
1 GAAGTAGATCAGCATCAACCCTTGTGCTT-GATTCCATCACAACAG
*** *
7878477 GAAGTAGATCAATGTCAACCCTTGTGCTTGATTCCAACACAACA
1 GAAGTAGATCAGCATCAACCCTTGTGCTTGATTCCATCACAACA
7878521 TGAGTGGATC
Statistics
Matches: 65, Mismatches: 20, Indels: 7
0.71 0.22 0.08
Matches are distributed among these distances:
43 2 0.03
44 30 0.46
45 28 0.43
46 5 0.08
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
GAAGTAGATCAGCATCAACCCTTGTGCTTGATTCCATCACAACAG
Found at i:7878443 original size:89 final size:89
Alignment explanation
Indices: 7878323--7878520 Score: 283
Period size: 89 Copynumber: 2.2 Consensus size: 89
7878313 GTAGTCATTT
** * * *
7878323 TGCTTGATTATATCACAACATGTGGTAGATCAGCACCTTCGTCGTGTTAGATTCTTTCATAGA-A
1 TGCTTGATTCCATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTAGATTCTATCATA-ACA
*
7878387 -GAAGATAGATCAGCATCAACCCTTG
65 GGAAG-TAGATCAACATCAACCCTTG
7878412 TGCTTGATTCCATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTAGATTCTATCATAACAG
1 TGCTTGATTCCATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTAGATTCTATCATAACAG
**
7878477 GAAGTAGATCAATGTCAACCCTTG
66 GAAGTAGATCAACATCAACCCTTG
*
7878501 TGCTTGATTCCAACACAACA
1 TGCTTGATTCCATCACAACA
7878521 TGAGTGGATC
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 1 0.01
89 93 0.95
90 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (89 bp):
TGCTTGATTCCATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTAGATTCTATCATAACAG
GAAGTAGATCAACATCAACCCTTG
Found at i:7878476 original size:44 final size:44
Alignment explanation
Indices: 7878328--7878487 Score: 144
Period size: 44 Copynumber: 3.6 Consensus size: 44
7878318 CATTTTGCTT
* * *
7878328 GATTATATCACAACATGTGGTAGATCAGCACCTTCGTCGTGTTA
1 GATTCTATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTA
* * * * *** * *
7878372 GATTCTTTCATAGA-AGAAGATAGATCAGCATCAACCCTTGTGCTT-
1 GATTCTATCACA-ACAGGAGGTAGATCAGCA-CCTTCGTCGTG-TTA
*
7878417 GATTCCATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTA
1 GATTCTATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTA
* *
7878461 GATTCTATCATAACAGGAAGTAGATCA
1 GATTCTATCACAACAGGAGGTAGATCA
7878488 ATGTCAACCC
Statistics
Matches: 86, Mismatches: 25, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
43 2 0.02
44 52 0.60
45 30 0.35
46 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
GATTCTATCACAACAGGAGGTAGATCAGCACCTTCGTCGTGTTA
Found at i:7878704 original size:44 final size:43
Alignment explanation
Indices: 7878585--7878704 Score: 109
Period size: 44 Copynumber: 2.7 Consensus size: 43
7878575 ATTGACATTT
* * *
7878585 TGTTCGATTC-ATCACAGAAGGAGGTGGATCAACATGGTTATTT
1 TGTTCGATTCTATCACAGAA-GAGGTAGATCAACATCGTTATTG
* * * * * *
7878628 TGCTCGATTCTATCATAGTAGGAGATATATCAACATTCG-TGTTG
1 TGTTCGATTCTATCACAG-AAGAGGTAGATCAACA-TCGTTATTG
7878672 TGTTCGATTCTATCACAGCAAGAGGTAGATCAA
1 TGTTCGATTCTATCACAG-AAGAGGTAGATCAA
7878705 TGTCAACCTT
Statistics
Matches: 59, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
43 9 0.15
44 47 0.80
45 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (43 bp):
TGTTCGATTCTATCACAGAAGAGGTAGATCAACATCGTTATTG
Found at i:7879880 original size:46 final size:45
Alignment explanation
Indices: 7879814--7879938 Score: 189
Period size: 46 Copynumber: 2.8 Consensus size: 45
7879804 TATAAAATTT
7879814 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
7879859 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * * * *
7879905 CTTGCCA-GTATTCCATATGCTCGTAAACTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
7879939 GCATGGTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
44 22 0.30
45 11 0.15
46 41 0.55
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:7880111 original size:40 final size:40
Alignment explanation
Indices: 7880043--7880166 Score: 169
Period size: 40 Copynumber: 3.0 Consensus size: 40
7880033 ACCGTAGTGC
*
7880043 TACACATAAGGTCATGCCCATCATATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCA-C-CATATACACCGAAGTGTAT
* *
7880085 TACACATAAGGTCGTGCCCACCATATACATCGAAGCT-TAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAG-TGTAT
* *
7880125 TACACATAAGGTCATGCCCACCATATAAACTGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
7880165 TA
1 TA
7880167 TAAACCTGCA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
40 51 0.70
41 2 0.03
42 19 0.26
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
Found at i:7882673 original size:21 final size:23
Alignment explanation
Indices: 7882618--7882673 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
7882608 TAAACCCAAA
* * *
7882618 CCATTTTTCATAAATAAATGAGT
1 CCATTTTACAAAAATAAATGAGC
7882641 CCA-TTTAC-AAAATAAAT-A-C
1 CCATTTTACAAAAATAAATGAGC
7882660 CCATTTTACAAAAA
1 CCATTTTACAAAAA
7882674 AATATATACG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.11
20 6 0.21
21 12 0.43
22 4 0.14
23 3 0.11
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (23 bp):
CCATTTTACAAAAATAAATGAGC
Found at i:7884548 original size:11 final size:12
Alignment explanation
Indices: 7884534--7884573 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
7884524 TTTATTATTT
7884534 TTTTTAAAGA-A
1 TTTTTAAAGACA
*
7884545 -TTTTAATGACA
1 TTTTTAAAGACA
7884556 TTTTTAAA-ACA
1 TTTTTAAAGACA
7884567 TTTTTAA
1 TTTTTAA
7884574 TTCAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.32
11 11 0.44
12 6 0.24
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (12 bp):
TTTTTAAAGACA
Found at i:7885775 original size:141 final size:139
Alignment explanation
Indices: 7885521--7885800 Score: 542
Period size: 141 Copynumber: 2.0 Consensus size: 139
7885511 CAAAAGAATA
7885521 GAATAACATGGCAGGAATTTGTTTCGATCATATGCCATAGGTTTTGTGGCATGAATTTTTTAGAT
1 GAATAACATGGCAGGAATTTGTTTCGATCATATGCCATAGGTTTTGTGGCATGAATTTTTTAGAT
7885586 GTCACGACTGTGGAAGGGGATTTAGGATTTCATCGCGAAGCATGAATGGGTTGGGGGATTGAAAA
66 GTCACGACTGTGGAAGGGGATTTAGGATTTCATCGCGAAGCATGAATGGGTT-GGGGATTG-AAA
7885651 CAAACTTGGGG
129 CAAACTTGGGG
7885662 GAATAACATGGCAGGAATTTGTTTCGATCATATGCCATAGGTTTTGTGGCATGAATTTTTTAGAT
1 GAATAACATGGCAGGAATTTGTTTCGATCATATGCCATAGGTTTTGTGGCATGAATTTTTTAGAT
7885727 GTCACGACTGTGGAAGGGGATTTAGGATTTCATCGCGAAGCATGAATGGGTTGGGGATTGAAACA
66 GTCACGACTGTGGAAGGGGATTTAGGATTTCATCGCGAAGCATGAATGGGTTGGGGATTGAAACA
7885792 AACTTGGGG
131 AACTTGGGG
7885801 TTTTAATAAA
Statistics
Matches: 139, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
139 14 0.10
140 8 0.06
141 117 0.84
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (139 bp):
GAATAACATGGCAGGAATTTGTTTCGATCATATGCCATAGGTTTTGTGGCATGAATTTTTTAGAT
GTCACGACTGTGGAAGGGGATTTAGGATTTCATCGCGAAGCATGAATGGGTTGGGGATTGAAACA
AACTTGGGG
Found at i:7887224 original size:23 final size:23
Alignment explanation
Indices: 7887151--7887225 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
7887141 AAGAATGTGA
7887151 CACAAGAGTAGAGAAAAAGCGTGC
1 CACAAGAGTAGAGAAAAA-CGTGC
* * *
7887175 CACAAGAATAGAGAAAAACATAC
1 CACAAGAGTAGAGAAAAACGTGC
* *
7887198 CACAAGAGTAGAGAAAAATGTGT
1 CACAAGAGTAGAGAAAAACGTGC
7887221 CACAA
1 CACAA
7887226 TGACATAGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 26 0.60
24 17 0.40
ACGTcount: A:0.52, C:0.16, G:0.21, T:0.11
Consensus pattern (23 bp):
CACAAGAGTAGAGAAAAACGTGC
Found at i:7893244 original size:172 final size:172
Alignment explanation
Indices: 7892958--7893302 Score: 690
Period size: 172 Copynumber: 2.0 Consensus size: 172
7892948 TTCCCGAACC
7892958 TTCTCTAATCTTGAAATGATTCGTTAACAGACTTCTAGTATCTTGCATAAACCCTCTTGGGGTTA
1 TTCTCTAATCTTGAAATGATTCGTTAACAGACTTCTAGTATCTTGCATAAACCCTCTTGGGGTTA
7893023 AAAACTGGTTATCCAAAATTTCCAAGTAAAACTAACATTTCTTATGCACATCAGTAGTTATATCG
66 AAAACTGGTTATCCAAAATTTCCAAGTAAAACTAACATTTCTTATGCACATCAGTAGTTATATCG
7893088 GATCAATATGTCTTTTCAAAGTTATTAACCAACTTCCAGGGA
131 GATCAATATGTCTTTTCAAAGTTATTAACCAACTTCCAGGGA
7893130 TTCTCTAATCTTGAAATGATTCGTTAACAGACTTCTAGTATCTTGCATAAACCCTCTTGGGGTTA
1 TTCTCTAATCTTGAAATGATTCGTTAACAGACTTCTAGTATCTTGCATAAACCCTCTTGGGGTTA
7893195 AAAACTGGTTATCCAAAATTTCCAAGTAAAACTAACATTTCTTATGCACATCAGTAGTTATATCG
66 AAAACTGGTTATCCAAAATTTCCAAGTAAAACTAACATTTCTTATGCACATCAGTAGTTATATCG
7893260 GATCAATATGTCTTTTCAAAGTTATTAACCAACTTCCAGGGA
131 GATCAATATGTCTTTTCAAAGTTATTAACCAACTTCCAGGGA
7893302 T
1 T
7893303 AATTCTTGTC
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 173 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (172 bp):
TTCTCTAATCTTGAAATGATTCGTTAACAGACTTCTAGTATCTTGCATAAACCCTCTTGGGGTTA
AAAACTGGTTATCCAAAATTTCCAAGTAAAACTAACATTTCTTATGCACATCAGTAGTTATATCG
GATCAATATGTCTTTTCAAAGTTATTAACCAACTTCCAGGGA
Found at i:7895655 original size:80 final size:80
Alignment explanation
Indices: 7895500--7895889 Score: 557
Period size: 80 Copynumber: 4.8 Consensus size: 80
7895490 TTGCCCTCAA
* ** * *
7895500 CACACAGCAAAAAGGGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGA
1 CACACAGC--AAA-GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGG
*
7895564 TCCGTAGGGTTACCTTAAG
62 TCCGTAGGGTTACCTTATG
* * *
7895583 CACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCTAAGATATCCTTAGGTCCA
1 CACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCG
*
7895648 TAAGGTTACCTTATG
66 TAGGGTTACCTTATG
* * * *
7895663 CACACAACAAAGGAAACCAACTTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCG
1 CACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCG
7895728 TAGGGTTACCTTATG
66 TAGGGTTACCTTATG
* * * *
7895743 CACATAGCAAAGGGAACCAACCTAAGGATATGCGTTGGGGCCTACCCAAGATATCCTTAGGTTCG
1 CACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCG
7895808 TAGGGTTACCTTATG
66 TAGGGTTACCTTATG
* *
7895823 CACACATCAAAGGGAACCAACCTAAGGATATTCCTTGGGGCCTACCCAAGATATCCTTAGGTCCG
1 CACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCG
7895888 TA
66 TA
7895890 AGGACTTACA
Statistics
Matches: 275, Mismatches: 31, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
80 256 0.93
81 11 0.04
83 8 0.03
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (80 bp):
CACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCG
TAGGGTTACCTTATG
Found at i:7897554 original size:17 final size:18
Alignment explanation
Indices: 7897521--7897554 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7897511 TCTATTATGT
*
7897521 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
7897539 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
7897555 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:7900672 original size:23 final size:23
Alignment explanation
Indices: 7900646--7900690 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
7900636 CACCACAGCT
*
7900646 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
7900669 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
7900691 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:7900908 original size:149 final size:149
Alignment explanation
Indices: 7900658--7900972 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
7900648 TATAATTGCA
7900658 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
7900722 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTT
* *
7900787 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
7900807 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
* *
7900872 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTTC
7900937 CAAAGAATATACATATATC
131 CAAAGAATATACATATATC
7900956 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
7900973 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTTC
CAAAGAATATACATATATC
Found at i:7905548 original size:22 final size:21
Alignment explanation
Indices: 7905523--7905573 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
7905513 CACCACAGCT
7905523 CGTATAATTGCACCGAAGTGC
1 CGTATAATTGCACCGAAGTGC
* *
7905544 GCGTAGAATTGCACCGTAGTGC
1 -CGTATAATTGCACCGAAGTGC
*
7905566 CATATAAT
1 CGTATAAT
7905574 GATGTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (21 bp):
CGTATAATTGCACCGAAGTGC
Found at i:7905810 original size:139 final size:142
Alignment explanation
Indices: 7905545--7905827 Score: 400
Period size: 139 Copynumber: 2.0 Consensus size: 142
7905535 CCGAAGTGCG
7905545 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCATAGAATTCCTTAAGAATCA
1 CGTAGAATTGCACC--AGTGCCATATAATGATGTCCA-AAGGACCATAGAATTCCTTAAGAATCA
* * *
7905610 TATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTTCACAGAATATATAT
63 TACACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTTCAAAGAATATACAT
7905675 ATATCCCGAAGGACCT
128 ATATCCCG-AGGACCT
7905691 CGTAGAATTGCACC-GTGCCATATAAT-ATGT-C-AA-GACCACATAGAATTCCTTAAGAATCAT
1 CGTAGAATTGCACCAGTGCCATATAATGATGTCCAAAGGA-C-CATAGAATTCCTTAAGAATCAT
* *
7905751 ACACATATGCTA-GGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAG-ATATACAT
64 ACACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTT-CAAAGAATATACAT
*
7905814 ATGTCCCGAGGACC
128 ATATCCCGAGGACC
7905828 GTGTAGACCT
Statistics
Matches: 128, Mismatches: 6, Indels: 14
0.86 0.04 0.09
Matches are distributed among these distances:
138 8 0.06
139 52 0.41
140 37 0.29
141 1 0.01
142 4 0.03
143 12 0.09
146 14 0.11
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (142 bp):
CGTAGAATTGCACCAGTGCCATATAATGATGTCCAAAGGACCATAGAATTCCTTAAGAATCATAC
ACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACAAATGTTCAAAGAATATACATATA
TCCCGAGGACCT
Found at i:7907473 original size:21 final size:21
Alignment explanation
Indices: 7907449--7907493 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7907439 TGTTGTTCGT
* *
7907449 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
7907470 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
7907491 TTG
1 TTG
7907494 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:7910659 original size:54 final size:55
Alignment explanation
Indices: 7910577--7910686 Score: 213
Period size: 54 Copynumber: 2.0 Consensus size: 55
7910567 AGCCCTACCA
7910577 AAGTGCCTTCCACATGGGTATGTATGGCAATGAAATAGGATATAC-TTTGTTATT
1 AAGTGCCTTCCACATGGGTATGTATGGCAATGAAATAGGATATACTTTTGTTATT
7910631 AAGTGCCTTCCACATGGGTATGTATGGCAATGAAATAGGATATACTTTTGTTATT
1 AAGTGCCTTCCACATGGGTATGTATGGCAATGAAATAGGATATACTTTTGTTATT
7910686 A
1 A
7910687 TTCGGGGATA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 45 0.82
55 10 0.18
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (55 bp):
AAGTGCCTTCCACATGGGTATGTATGGCAATGAAATAGGATATACTTTTGTTATT
Found at i:7913966 original size:54 final size:54
Alignment explanation
Indices: 7913811--7913969 Score: 210
Period size: 54 Copynumber: 2.9 Consensus size: 54
7913801 CACCGAAGTG
** * * * * *** *
7913811 CCAAAATGGAAATTCACAAACTCATTATGAATTCCATGGATTGCACGCATAGTG
1 CCAAAATGGTTATTCATAAACACATTATGAATACCATGGGTTGCACATTTAGTA
*
7913865 CCGAAATGGTTATTCATAAACACATTATGAATACCATGGGTTGCACATTTAGTA
1 CCAAAATGGTTATTCATAAACACATTATGAATACCATGGGTTGCACATTTAGTA
*
7913919 CCAAAATGGTTATTCATAAACACATTATGAATACCAAGGGTTGCACATTTA
1 CCAAAATGGTTATTCATAAACACATTATGAATACCATGGGTTGCACATTTA
7913970 ATGTCGAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (54 bp):
CCAAAATGGTTATTCATAAACACATTATGAATACCATGGGTTGCACATTTAGTA
Found at i:7920866 original size:54 final size:54
Alignment explanation
Indices: 7920719--7920878 Score: 194
Period size: 54 Copynumber: 2.9 Consensus size: 54
7920709 CGAAATGGAA
* * * * ** *
7920719 ATTCACAAACTCATTATGAATTCCATAGATTGCACACATAGTGCCGAAATGGTT
1 ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTGCCAAAATGGTT
* *
7920773 ATTCATAAACACATTATGCATACCATGGGTTGCACATTTAGTGCCAAAATGGTT
1 ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTGCCAAAATGGTT
* * * *
7920827 ATTCATAAACACGTTATGAATACCATGGATTGTATATTTAGTGTCGAAAATG
1 ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTG-CCAAAATG
7920879 CACCGTTATG
Statistics
Matches: 90, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 83 0.92
55 7 0.08
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (54 bp):
ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTGCCAAAATGGTT
Found at i:7922272 original size:3 final size:3
Alignment explanation
Indices: 7922257--7922304 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
7922247 GCACGGGACG
7922257 AGA AGA ATG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
7922302 AGA
1 AGA
7922305 TAACTTGGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 1 0.02
3 41 0.95
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:7924456 original size:55 final size:55
Alignment explanation
Indices: 7924372--7924480 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
7924362 CTCCGACAGT
7924372 TCCCCTGGTCATGCAATGACAAATCTTACAAAAGAAATAAAGAAAACAAACAAGA
1 TCCCCTGGTCATGCAATGACAAATCTTACAAAAGAAATAAAGAAAACAAACAAGA
*
7924427 TCCCCTGGTCATGCAATGATAAATCTTACAAAAGAAATAAAGAAAACAAACAAG
1 TCCCCTGGTCATGCAATGACAAATCTTACAAAAGAAATAAAGAAAACAAACAAG
7924481 TAAAACTACA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.17
Consensus pattern (55 bp):
TCCCCTGGTCATGCAATGACAAATCTTACAAAAGAAATAAAGAAAACAAACAAGA
Found at i:7928168 original size:18 final size:19
Alignment explanation
Indices: 7928145--7928208 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 19
7928135 TTCATTGAAA
*
7928145 AACCGATAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
7928163 AACCGAAAAACCCGAACC-
1 AACCGAAAAACCCGAACCG
*** *
7928181 -ATTAAAAAAACCGAACCG
1 AACCGAAAAACCCGAACCG
7928199 AACCGAAAAA
1 AACCGAAAAA
7928209 ACCAGTTTCG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 13 0.37
18 9 0.26
19 13 0.37
ACGTcount: A:0.53, C:0.30, G:0.12, T:0.05
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:7928683 original size:18 final size:18
Alignment explanation
Indices: 7928653--7928701 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
7928643 GAACCGAACC
*
7928653 ATTTTACTCGATTCGTGTCG
1 ATTTT-CTCGATT-GTCTCG
*
7928673 ATTTT-TCGATTTTCTCG
1 ATTTTCTCGATTGTCTCG
7928690 ATTTTCTCGATT
1 ATTTTCTCGATT
7928702 TCGTTCCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
20 5 0.19
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.53
Consensus pattern (18 bp):
ATTTTCTCGATTGTCTCG
Found at i:7928703 original size:8 final size:9
Alignment explanation
Indices: 7928670--7928702 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
7928660 TCGATTCGTG
7928670 TCGATTTT-
1 TCGATTTTC
7928678 TCGATTTTC
1 TCGATTTTC
7928687 TCGATTTTC
1 TCGATTTTC
7928696 TCGATTT
1 TCGATTT
7928703 CGTTCCTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (9 bp):
TCGATTTTC
Found at i:7931459 original size:23 final size:24
Alignment explanation
Indices: 7931408--7931470 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
7931398 TGGTTGCAAG
* **
7931408 GTAAATTTTTAACTTTATTTTTTA
1 GTAAATTTTTAAATTTATAGTTTA
*
7931432 ATAAATTTTTAAATTTATAGTTT-
1 GTAAATTTTTAAATTTATAGTTTA
*
7931455 GTAAATTTTTTAATTT
1 GTAAATTTTTAAATTT
7931471 TTAATTATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (24 bp):
GTAAATTTTTAAATTTATAGTTTA
Found at i:7938841 original size:19 final size:20
Alignment explanation
Indices: 7938819--7938867 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
7938809 AATGATTTTC
* *
7938819 TTTTGAAAAACAAAGTGGA-
1 TTTTGAAAAACAAAATGAAG
7938838 TTTTGAAAAACAAAATGAAG
1 TTTTGAAAAACAAAATGAAG
7938858 TTTTGAAAAA
1 TTTTGAAAAA
7938868 TGATTTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAG
Found at i:7942835 original size:18 final size:18
Alignment explanation
Indices: 7942801--7942835 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7942791 ATACATAGTA
*
7942801 GTATCGGTACCCCTTTGG
1 GTATCGGTACCACTTTGG
*
7942819 GTATCGGTACCATTTTG
1 GTATCGGTACCACTTTG
7942836 CATTATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (18 bp):
GTATCGGTACCACTTTGG
Found at i:7943732 original size:18 final size:18
Alignment explanation
Indices: 7943709--7943751 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
7943699 TTGAAAGGTT
7943709 GATATCAATTGTTAGAGA
1 GATATCAATTGTTAGAGA
7943727 GATATCAATTGTTAGAGA
1 GATATCAATTGTTAGAGA
7943745 GATATCA
1 GATATCA
7943752 TTTGCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (18 bp):
GATATCAATTGTTAGAGA
Found at i:7945921 original size:19 final size:19
Alignment explanation
Indices: 7945886--7945922 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7945876 GAAGCTTGGG
*
7945886 GAGCCGTTTGAGCCGAGCT
1 GAGCCGTTTAAGCCGAGCT
*
7945905 GAGCCGTTTAAGTCGAGC
1 GAGCCGTTTAAGCCGAGC
7945923 CGCCTCGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (19 bp):
GAGCCGTTTAAGCCGAGCT
Found at i:7949841 original size:20 final size:20
Alignment explanation
Indices: 7949816--7949858 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
7949806 TCTAAGATCT
* *
7949816 CATTTAGGACCATTTAGATG
1 CATTTAGGAACATATAGATG
*
7949836 CATTTAGGAACATATAGTTG
1 CATTTAGGAACATATAGATG
7949856 CAT
1 CAT
7949859 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAGGAACATATAGATG
Found at i:7951368 original size:22 final size:20
Alignment explanation
Indices: 7951328--7951369 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
7951318 CACTACCACT
*
7951328 ATTCCATTTTCACATCATTC
1 ATTCCATTTTCACAACATTC
7951348 ATTCCATTTTGCCACAACATTC
1 ATTCCATTTT--CACAACATTC
7951370 TCATTTGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTCCATTTTCACAACATTC
Done.