Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 95 of 150
Found at i:29787135 original size:30 final size:31
Alignment explanation
Indices: 29787101--29787160 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
29787091 AAACTTTTTG
*
29787101 TTTTCCTCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTCC-CCTAAAACTTTTACTCCCTTCCCAC
*
29787131 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
29787161 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 19 0.73
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:29787295 original size:19 final size:16
Alignment explanation
Indices: 29787251--29787295 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
29787241 ACTTTCCCTT
29787251 AAACTTTTATTCCCCA
1 AAACTTTTATTCCCCA
29787267 AAACTTTTTATTTTCCCCCA
1 AAAC-TTTTA--TT-CCCCA
29787287 AAACTTTTA
1 AAACTTTTA
29787296 CTTCTCACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.16
17 5 0.20
19 7 0.28
20 9 0.36
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (16 bp):
AAACTTTTATTCCCCA
Found at i:29791258 original size:20 final size:20
Alignment explanation
Indices: 29791235--29791310 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
29791225 GGTAAATTAG
29791235 TAAGTAAACCTAAAATAAAC
1 TAAGTAAACCTAAAATAAAC
* *
29791255 TAAGTAAATGCTATAAATGGTAAATTAG
1 TAAGTAAA-CCTA-AAA---T-AA--AC
29791283 TAAGTAAACCTAAAATAAAC
1 TAAGTAAACCTAAAATAAAC
29791303 TAAGTAAA
1 TAAGTAAA
29791311 TGCTATCATC
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
20 17 0.39
21 3 0.07
22 5 0.11
23 1 0.02
25 1 0.02
26 5 0.11
27 3 0.07
28 9 0.20
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (20 bp):
TAAGTAAACCTAAAATAAAC
Found at i:29791277 original size:48 final size:48
Alignment explanation
Indices: 29791221--29791316 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
29791211 AATAAGGGTA
29791221 AAATGGTAAATTAGTAAGTAAACCTAAAATAAACTAAGTAAATGCTAT
1 AAATGGTAAATTAGTAAGTAAACCTAAAATAAACTAAGTAAATGCTAT
29791269 AAATGGTAAATTAGTAAGTAAACCTAAAATAAACTAAGTAAATGCTAT
1 AAATGGTAAATTAGTAAGTAAACCTAAAATAAACTAAGTAAATGCTAT
29791317 CATCTTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.27
Consensus pattern (48 bp):
AAATGGTAAATTAGTAAGTAAACCTAAAATAAACTAAGTAAATGCTAT
Found at i:29797124 original size:31 final size:31
Alignment explanation
Indices: 29797061--29797124 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
29797051 TGTTGATTTA
* *
29797061 TTTTTATATTATTTATTGTAAAATTTATTTC
1 TTTTTATATTATTTATTGTAAAATATAATTC
* *
29797092 TTTTTATTATTATTTA-TGTGAACTATAATTC
1 TTTTTA-TATTATTTATTGTAAAATATAATTC
29797123 TT
1 TT
29797125 CAAATAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTTTATATTATTTATTGTAAAATATAATTC
Found at i:29800010 original size:21 final size:21
Alignment explanation
Indices: 29799978--29800039 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
29799968 TCAATTGATA
*
29799978 TGAGTTTTAGTTTAACCCTTC
1 TGAGTTTCAGTTTAACCCTTC
* *
29799999 T-AGGTTTCAGTTTAGCTCTTC
1 TGA-GTTTCAGTTTAACCCTTC
* *
29800020 TGAGCTTCAGATTAACCCTT
1 TGAGTTTCAGTTTAACCCTT
29800040 ATTAATTTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (21 bp):
TGAGTTTCAGTTTAACCCTTC
Found at i:29810534 original size:21 final size:22
Alignment explanation
Indices: 29810510--29810552 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29810500 TTACATGTAA
* *
29810510 TTATTTAG-TAAATTATATTGT
1 TTATATAGTTAAATAATATTGT
29810531 TTATATAGTTAAATAATATTGT
1 TTATATAGTTAAATAATATTGT
29810553 ACTTCGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TTATATAGTTAAATAATATTGT
Found at i:29812001 original size:19 final size:19
Alignment explanation
Indices: 29811977--29812019 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
29811967 TTTTAAATCA
29811977 TGAGATATAATAGATTTTG
1 TGAGATATAATAGATTTTG
29811996 TGAGATATAATAGATTTTG
1 TGAGATATAATAGATTTTG
29812015 TGAGA
1 TGAGA
29812020 CAATGTCAGA
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:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (19 bp):
TGAGATATAATAGATTTTG
Found at i:29816350 original size:25 final size:23
Alignment explanation
Indices: 29816322--29816426 Score: 91
Period size: 25 Copynumber: 4.7 Consensus size: 23
29816312 TAAGTTTGTG
29816322 AATAGATGAAATTTTTAGCAGTACA
1 AATAGATGAAATTTTTA-CA-TACA
29816347 AATAGATGAAATTTTT--A-ACA
1 AATAGATGAAATTTTTACATACA
29816367 AATAGATGAAA--TTT-CAT-CA
1 AATAGATGAAATTTTTACATACA
* * *
29816386 ACTACAT-CAATTTTTAGCAGTACA
1 AATAGATGAAATTTTTA-CA-TACA
29816410 AATAGATGAAATTTTTA
1 AATAGATGAAATTTTTA
29816427 ACAAAACGGA
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
18 5 0.08
19 8 0.12
20 17 0.26
22 3 0.05
23 1 0.02
24 7 0.11
25 24 0.37
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (23 bp):
AATAGATGAAATTTTTACATACA
Found at i:29820927 original size:2 final size:2
Alignment explanation
Indices: 29820920--29820950 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29820910 ATTTTAACCC
29820920 AT AT 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 A
29820951 GTAATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29825874 original size:18 final size:18
Alignment explanation
Indices: 29825853--29825887 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29825843 TTGTAAAATT
*
29825853 AAAGCTTAAATTAAATGC
1 AAAGATTAAATTAAATGC
29825871 AAAGATTAAATTAAATG
1 AAAGATTAAATTAAATG
29825888 ATAAAGGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAGATTAAATTAAATGC
Found at i:29826027 original size:18 final size:17
Alignment explanation
Indices: 29826006--29826050 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
29825996 ATATTATGTT
29826006 TATATATATATAAATATA
1 TATATATATATAAAT-TA
*
29826024 TATATATATATAACTTA
1 TATATATATATAAATTA
29826041 TATAT-TATAT
1 TATATATATAT
29826051 TTAATTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 5 0.19
17 7 0.27
18 14 0.54
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATATATATAAATTA
Found at i:29826045 original size:2 final size:2
Alignment explanation
Indices: 29826006--29826035 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29825996 ATATTATGTT
*
29826006 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29826036 ACTTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:29827165 original size:36 final size:36
Alignment explanation
Indices: 29827117--29827233 Score: 114
Period size: 36 Copynumber: 3.3 Consensus size: 36
29827107 ATCGGTTATC
*
29827117 CGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTT
1 CGACTAGTGCTGGGCGCAATAATTTGTCGACTCGTT
* * ** *
29827153 CGACTAGTGCTGGGCACAACT-A-TCGTCGA-TTATC
1 CGACTAGTGCTGGGCGCAA-TAATTTGTCGACTCGTT
* * *
29827187 CGACTAGTGCTAGGCGCAATAATTTTTCAACTCGTT
1 CGACTAGTGCTGGGCGCAATAATTTGTCGACTCGTT
*
29827223 TGACTAGTGCT
1 CGACTAGTGCT
29827234 AGGCACAACT
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
33 1 0.02
34 20 0.32
35 10 0.16
36 30 0.48
37 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (36 bp):
CGACTAGTGCTGGGCGCAATAATTTGTCGACTCGTT
Found at i:29827195 original size:34 final size:34
Alignment explanation
Indices: 29827098--29827197 Score: 94
Period size: 36 Copynumber: 2.9 Consensus size: 34
29827088 TCGCGGATGA
* * *
29827098 ACAACTATCATCGGTTATCCGACTAGCGCTGGGC
1 ACAACTATCGTCGATTATCCGACTAGTGCTGGGC
* * ** *
29827132 GCAA-TAATTTGTCGACTCGTTCGACTAGTGCTGGGC
1 ACAACT-A-TCGTCGA-TTATCCGACTAGTGCTGGGC
29827168 ACAACTATCGTCGATTATCCGACTAGTGCT
1 ACAACTATCGTCGATTATCCGACTAGTGCT
29827198 AGGCGCAATA
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
33 1 0.02
34 17 0.35
35 10 0.20
36 20 0.41
37 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (34 bp):
ACAACTATCGTCGATTATCCGACTAGTGCTGGGC
Found at i:29827211 original size:70 final size:70
Alignment explanation
Indices: 29827098--29827350 Score: 335
Period size: 70 Copynumber: 3.6 Consensus size: 70
29827088 TCGCGGATGA
*
29827098 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTCGACTAGTGC
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
29827163 TGGGC
66 TGGGC
* * * * * *
29827168 ACAACTATCGTCGATTATCCGACTAGTGCTAGGCGCAATAATTTTTCAACTCGTTTGACTAGTGC
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
*
29827233 TAGGC
66 TGGGC
* * * *
29827238 ACAACTATCATCGGTTATCCGACTAACGCTGGGCGTAATAATTTGTTGACTCGTTTGACTAGTGT
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
*
29827303 TGGGA
66 TGGGC
* ** * * *
29827308 AAAACTATCGCCGGTTATCCGACTAGCGTTGGGCACAAAAATT
1 ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATT
29827351 AATTCACGGT
Statistics
Matches: 155, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
70 155 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (70 bp):
ACAACTATCATCGGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCGACTCGTTTGACTAGTGC
TGGGC
Found at i:29830238 original size:42 final size:42
Alignment explanation
Indices: 29830177--29830298 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 42
29830167 GATTTGAGAT
* *
29830177 TTACGTGTAAGACCATGTCTGGGACATTGGCGTTGTATATGA
1 TTACGTGTAAGACCCTGTCTGGGACATTGGCATTGTATATGA
* * *
29830219 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACATTGGCATTG-TATATGA
* * *
29830262 TTACATGTAAGACCAC-GTCTAGGACGTTGGCATTGTA
1 TTACGTGTAAGACC-CTGTCTGGGACATTGGCATTGTA
29830299 CGAGCTTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.49
43 34 0.50
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (42 bp):
TTACGTGTAAGACCCTGTCTGGGACATTGGCATTGTATATGA
Found at i:29832101 original size:42 final size:42
Alignment explanation
Indices: 29832049--29832185 Score: 186
Period size: 42 Copynumber: 3.3 Consensus size: 42
29832039 TATGATTACG
* * *
29832049 TGTAAGACCATGTCTGAGACATTGGCTTCGTTATGTGATTCA
1 TGTAAGACCATGTCTGGGACATTGGCTTCGATATGAGATTCA
* *
29832091 TGTAAGACCATGTCTGGGACATTGACATCGATATGAGATTCA
1 TGTAAGACCATGTCTGGGACATTGGCTTCGATATGAGATTCA
* * *
29832133 CGTAAGACCATGTCTGGGACATTGG-TATCGATATGAGAATCG
1 TGTAAGACCATGTCTGGGACATTGGCT-TCGATATGAGATTCA
29832175 TGTAAGACCAT
1 TGTAAGACCAT
29832186 AACTAGCTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCTTCGATATGAGATTCA
Found at i:29832222 original size:84 final size:84
Alignment explanation
Indices: 29832035--29832235 Score: 212
Period size: 84 Copynumber: 2.4 Consensus size: 84
29832025 TTAAGATACT
* * * * *
29832035 GATATATGATTACGTGTAAGACCATGTCTGAGACATTGGCTTCGTTATGTGATTCATGTAAGACC
1 GATATATGA-TACATGTAAGACCATGTCTGGGACATTGGCTTCGATATGAGAATCATGTAAGACC
** *
29832100 ATGTCTGGGACATTGACATC
65 ATAACTGAGACATTGACATC
* * *
29832120 GATATGA-GATTCACGTAAGACCATGTCTGGGACATTGG-TATCGATATGAGAATCGTGTAAGAC
1 GATAT-ATGATACATGTAAGACCATGTCTGGGACATTGGCT-TCGATATGAGAATCATGTAAGAC
*
29832183 CATAACT-AG-CTATTGGCATC
64 CATAACTGAGAC-ATTGACATC
*
29832203 GATATATGATAGCATGTAAGACCATATCTGGGA
1 GATATATGATA-CATGTAAGACCATGTCTGGGA
29832236 TATGGCATTG
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
82 2 0.02
83 18 0.19
84 68 0.71
85 7 0.07
86 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (84 bp):
GATATATGATACATGTAAGACCATGTCTGGGACATTGGCTTCGATATGAGAATCATGTAAGACCA
TAACTGAGACATTGACATC
Found at i:29832242 original size:42 final size:43
Alignment explanation
Indices: 29832035--29832243 Score: 184
Period size: 42 Copynumber: 5.0 Consensus size: 43
29832025 TTAAGATACT
* * *
29832035 GATATATGAT-TACGTGTAAGACCATGTCTGAGACATTGGCTTC
1 GATATATGATAT-CATGTAAGACCATGTCTGGGACATTGGCATC
* * *
29832078 GTTATGTGAT-TCATGTAAGACCATGTCTGGGACATTGACATC
1 GATATATGATATCATGTAAGACCATGTCTGGGACATTGGCATC
* *
29832120 GATATGA-GAT-TCACGTAAGACCATGTCTGGGACATTGGTATC
1 GATAT-ATGATATCATGTAAGACCATGTCTGGGACATTGGCATC
* ** *
29832162 GATATGA-GA-ATCGTGTAAGACCATAACT-AG-CTATTGGCATC
1 GATAT-ATGATATCATGTAAGACCATGTCTGGGAC-ATTGGCATC
* * *
29832203 GATATATGATAGCATGTAAGACCATATCTGGGATA-TGGCAT
1 GATATATGATATCATGTAAGACCATGTCTGGGACATTGGCAT
29832244 TGTGTGAGTT
Statistics
Matches: 137, Mismatches: 22, Indels: 15
0.79 0.13 0.09
Matches are distributed among these distances:
40 2 0.01
41 16 0.12
42 108 0.79
43 11 0.08
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (43 bp):
GATATATGATATCATGTAAGACCATGTCTGGGACATTGGCATC
Found at i:29839301 original size:33 final size:33
Alignment explanation
Indices: 29839259--29839325 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29839249 ATGGGGGACC
29839259 TCTCATCTCGGTGCCAACGCCATGTCCCAGACA
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACA
*
29839292 TCTCATCTCGGTGCCAACGCCATGTCCCATACA
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACA
29839325 T
1 T
29839326 GGTCTTACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.39, G:0.16, T:0.24
Consensus pattern (33 bp):
TCTCATCTCGGTGCCAACGCCATGTCCCAGACA
Found at i:29843193 original size:20 final size:21
Alignment explanation
Indices: 29843154--29843199 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
29843144 CTATCAAAGC
*
29843154 ATTTAGAGAATCTTTTTTTTAT
1 ATTTAGAGAA-CTATTTTTTAT
29843176 ATTTAGAGAA-TATTTTTTAT
1 ATTTAGAGAACTATTTTTTAT
29843196 ATTT
1 ATTT
29843200 TCTAAACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
22 10 0.43
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (21 bp):
ATTTAGAGAACTATTTTTTAT
Found at i:29851212 original size:40 final size:40
Alignment explanation
Indices: 29851168--29851304 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 40
29851158 CTATAGGTCA
* *
29851168 AGCATTAGCAGCGCTTTTTGAAAAATGCCGCTATAAATCG
1 AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCG
* * *
29851208 AGCATTAGCGGCTCTTTTTGAAAAACGCTGCTATAGATC-
1 AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCG
* * *
29851247 ATGTATTAGCGGCG-TTTCTCGAAAAACGCCGCAAT-AATCG
1 A-GCATTAGCGGCGCTTT-TTGAAAAACGCCGCTATAAATCG
* *
29851287 AGTATTAGCGGTGCTTTT
1 AGCATTAGCGGCGCTTTT
29851305 CGGAAAACAC
Statistics
Matches: 81, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
39 19 0.23
40 62 0.77
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (40 bp):
AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCG
Found at i:29851312 original size:39 final size:39
Alignment explanation
Indices: 29851171--29851319 Score: 140
Period size: 40 Copynumber: 3.8 Consensus size: 39
29851161 TAGGTCAAGC
* * * * *
29851171 ATTAGCAGCGCTTTTTGAAAAATGCCGCTATAAATCGAGC
1 ATTAGCGGCGCTTTTCGAAAAACGCCGCAAT-AATCGAGT
* * * *
29851211 ATTAGCGGCTCTTTTTGAAAAACGCTGCTATAGATC-ATGT
1 ATTAGCGGCGCTTTTCGAAAAACGCCGCAATA-ATCGA-GT
29851251 ATTAGCGGCG-TTTCTCGAAAAACGCCGCAATAATCGAGT
1 ATTAGCGGCGCTTT-TCGAAAAACGCCGCAATAATCGAGT
* * *
29851290 ATTAGCGGTGCTTTTCGGAAAACACCGCAA
1 ATTAGCGGCGCTTTTCGAAAAACGCCGCAA
29851320 AAAATTTAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
39 33 0.36
40 59 0.64
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (39 bp):
ATTAGCGGCGCTTTTCGAAAAACGCCGCAATAATCGAGT
Found at i:29851407 original size:193 final size:195
Alignment explanation
Indices: 29851169--29851611 Score: 492
Period size: 193 Copynumber: 2.3 Consensus size: 195
29851159 TATAGGTCAA
* * * * *
29851169 GCATTAGCAGCGCTTTTTGAAAAATGCCGCTATAAATCGAGCATTAGCGGCTCTTTTTGAAAAAC
1 GCATTAGCGGCACTTTTTGAAAAATGCCGCTATAGATCGAGCATTAGCGGCACTTTTTAAAAAAC
* * * * *
29851234 GCTGCTATAGATC-ATGTATTAGC-G-GCGTTTCTCGAAAAACGCCG-CAATA-ATCGAGTATTA
66 GCCGCAATAGATCGA-GAATTAGCTGTGC-TTTCTC-AAAAAC-ACGTCAATAGATCGAGCATTA
*** *
29851294 GCGGTGCTTTTC-GGAAAACACCGCAAAAAATTTAAGCAAAAC-ACGTCGTTTGTTGTTGAGCTT
127 GCGACACTTTTCAGAAAAACACCGCAAAAAA-TTAAGCAAAACGACGTCGTTTGTTGTTGAGCTT
29851357 TAGTG
191 TAGTG
* * * *
29851362 GCATTAGTGGCACTTTTTAAAAAATGCCG-TAATAGATCGAGCATTA-CGACGC-TTTTAAAAAA
1 GCATTAGCGGCACTTTTTGAAAAATGCCGCT-ATAGATCGAGCATTAGCGGCACTTTTTAAAAAA
* * *
29851424 TGCCGCAATAGATCGAGAATTAGCTGTGCTTTGTCAAAAACACGTCTATAGATCGAGCATTAGCG
65 CGCCGCAATAGATCGAGAATTAGCTGTGCTTTCTCAAAAACACGTCAATAGATCGAGCATTAGCG
* * * *
29851489 ACACTTTTCAGAAAAATACCGCAAAAAATTGAGCAAAACGATGTCGTTTGTTTTTGAGCTTTAGT
130 ACACTTTTCAGAAAAACACCGCAAAAAATTAAGCAAAACGACGTCGTTTGTTGTTGAGCTTTAGT
*
29851554 T
195 G
** * *
29851555 GCATTAGCGGCGGTTGTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCACTTTT
1 GCATTAGCGGCACTTTTTGAAAAATGCCGCTATAGATCGAGCATTAGCGGCACTTTT
29851612 CGCAAAATGC
Statistics
Matches: 206, Mismatches: 33, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
190 2 0.01
191 37 0.18
192 41 0.20
193 118 0.57
194 5 0.02
195 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (195 bp):
GCATTAGCGGCACTTTTTGAAAAATGCCGCTATAGATCGAGCATTAGCGGCACTTTTTAAAAAAC
GCCGCAATAGATCGAGAATTAGCTGTGCTTTCTCAAAAACACGTCAATAGATCGAGCATTAGCGA
CACTTTTCAGAAAAACACCGCAAAAAATTAAGCAAAACGACGTCGTTTGTTGTTGAGCTTTAGTG
Found at i:29851677 original size:114 final size:115
Alignment explanation
Indices: 29851469--29851680 Score: 338
Period size: 114 Copynumber: 1.9 Consensus size: 115
29851459 AAAAACACGT
*
29851469 CTATAGATCGAGCATTAGCGACACTTTTCAGAAAAATACCGCAAAAAATTGAGCAAAACGATGTC
1 CTATAGATCGAGCATTAGCGACACTTTTCAGAAAAATACCGCAAAAAATTGAGCAAAACGACGTC
* * *
29851534 GTTTGTTTTTGAGCTTTAGTTGCATTAGCGGCGGTTGTTGAAAAACGCCG
66 GTTTCTTGTTGAGCTTTAGTGGCATTAGCGGCGGTTGTTGAAAAACGCCG
* * *
29851584 CTATAGATCGAGCATTAGCGGCACTTTTC-GCAAAATGCCGCAAAAAAGTTGAG-AAAACGACGT
1 CTATAGATCGAGCATTAGCGACACTTTTCAGAAAAATACCGCAAAAAA-TTGAGCAAAACGACGT
29851647 CGTTTCTTGTTGAGCTTTAGTGGCATTAGCGGCG
65 CGTTTCTTGTTGAGCTTTAGTGGCATTAGCGGCG
29851681 TAAAAAAATC
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
114 56 0.63
115 33 0.37
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (115 bp):
CTATAGATCGAGCATTAGCGACACTTTTCAGAAAAATACCGCAAAAAATTGAGCAAAACGACGTC
GTTTCTTGTTGAGCTTTAGTGGCATTAGCGGCGGTTGTTGAAAAACGCCG
Found at i:29851713 original size:7 final size:7
Alignment explanation
Indices: 29851698--29851758 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
29851688 ATCATTTTAT
29851698 TTTAAGG
1 TTTAAGG
*
29851705 TTTAGGG
1 TTTAAGG
**
29851712 TTTAATA
1 TTTAAGG
29851719 TTTAAGG
1 TTTAAGG
*
29851726 TTTAATG
1 TTTAAGG
* *
29851733 TCTATGG
1 TTTAAGG
29851740 TTTAAGG
1 TTTAAGG
29851747 TTTTAAGG
1 -TTTAAGG
29851755 TTTA
1 TTTA
29851759 TGATATAATA
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
7 34 0.83
8 7 0.17
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:29855542 original size:43 final size:43
Alignment explanation
Indices: 29855495--29855665 Score: 150
Period size: 43 Copynumber: 4.0 Consensus size: 43
29855485 GAACGGTACT
29855495 TTTAGCGACGTTTGTGATAAAAACGCCACTAAAGATCATGTTC
1 TTTAGCGACGTTTGTGATAAAAACGCCACTAAAGATCATGTTC
* * * *
29855538 TTTAGCGGCGTTTGTGAAAAAAAAGTCACTAAA-AGTCAT-TCTC
1 TTTAGCGACGTTTGTGATAAAAACGCCACTAAAGA-TCATGT-TC
* * * * * * *
29855581 TATAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTTAAGTTC
1 TTTAGCGACGTTTGTGATAAAAACGCCACTAAAGATCATGTTC
* * * * *
29855624 TTTAGCAACATTTGTGGGT-AAAGCGCCACTAAAGGTCATGTT
1 TTTAGCGACGTTTGT-GATAAAAACGCCACTAAAGATCATGTT
29855666 TTATAGCAGC
Statistics
Matches: 102, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
42 2 0.02
43 97 0.95
44 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (43 bp):
TTTAGCGACGTTTGTGATAAAAACGCCACTAAAGATCATGTTC
Found at i:29857712 original size:3 final size:3
Alignment explanation
Indices: 29857704--29857754 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
29857694 ATAGAAAAGA
29857704 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
29857753 AA
1 AA
29857755 GAAGCATTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29858720 original size:36 final size:36
Alignment explanation
Indices: 29858648--29858722 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
29858638 CTAATGTAAT
* * * **
29858648 TGTTAATTTAATTGAATGAAAGTTTATGGATGTATA
1 TGTTAATTCAATTAAATGAAAGTTTATAGAAATATA
* *
29858684 TGTTAATTCAATTAAATGGAATTTTATAGAAATATA
1 TGTTAATTCAATTAAATGAAAGTTTATAGAAATATA
29858720 TGT
1 TGT
29858723 ATTTAGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.44
Consensus pattern (36 bp):
TGTTAATTCAATTAAATGAAAGTTTATAGAAATATA
Found at i:29858921 original size:70 final size:70
Alignment explanation
Indices: 29858818--29858949 Score: 183
Period size: 70 Copynumber: 1.9 Consensus size: 70
29858808 TGCTGGGCAC
* * *
29858818 AACTATCGTCGGATATCCAACTAGCGCTAGGCGCAATAATTTGTTGACTCGTTCAACTAGTGTCG
1 AACTATCGTCGGATATCCAACTAACGCTAGGCGCAATAACTTGTCGACTCGTTCAACTAGTGTCG
29858883 GACAT
66 GACAT
* *** * *
29858888 AACTATCGTCGGTTATTTGACTAACGCTTGGCGCAATAACTTGTCGACTCGTTCGACTAGTG
1 AACTATCGTCGGATATCCAACTAACGCTAGGCGCAATAACTTGTCGACTCGTTCAACTAGTG
29858950 CTGGGCACAC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
70 53 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (70 bp):
AACTATCGTCGGATATCCAACTAACGCTAGGCGCAATAACTTGTCGACTCGTTCAACTAGTGTCG
GACAT
Found at i:29860999 original size:19 final size:18
Alignment explanation
Indices: 29860972--29861016 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
29860962 AACAAAAATA
* * *
29860972 TTGAGAGAGTTGATAGAG
1 TTGAAAGAGCTGAGAGAG
29860990 TTTGAAAGAGCTGAGAGAG
1 -TTGAAAGAGCTGAGAGAG
29861009 TTGAAAGA
1 TTGAAAGA
29861017 AAGATACGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.36, T:0.24
Consensus pattern (18 bp):
TTGAAAGAGCTGAGAGAG
Found at i:29861839 original size:3 final size:3
Alignment explanation
Indices: 29861831--29861855 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29861821 TTGAGAAGCT
29861831 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
29861856 ACAGAAAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29874051 original size:28 final size:27
Alignment explanation
Indices: 29874011--29874065 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
29874001 ATGAAAATAA
29874011 AAAATATATGTGTACATATACATAGTTAT
1 AAAATATATGTGT--ATATACATAGTTAT
*
29874040 AAAA-ATATGTGTATATATATAGTTAT
1 AAAATATATGTGTATATACATAGTTAT
29874066 GAATCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 13 0.52
28 8 0.32
29 4 0.16
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (27 bp):
AAAATATATGTGTATATACATAGTTAT
Found at i:29874155 original size:24 final size:22
Alignment explanation
Indices: 29874123--29874172 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
29874113 ATAAAAAACG
*
29874123 TGTATATATAAATTATATAATATA
1 TGTACATATAAA-TATAT-ATATA
29874147 TGTACATATAAATATATATATA
1 TGTACATATAAATATATATATA
29874169 TGTA
1 TGTA
29874173 TGCGTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
23 5 0.20
24 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (22 bp):
TGTACATATAAATATATATATA
Found at i:29876267 original size:252 final size:252
Alignment explanation
Indices: 29875822--29876341 Score: 790
Period size: 252 Copynumber: 2.1 Consensus size: 252
29875812 ACTGTAACTA
* * * **
29875822 CTCCACTGCAACTTCAGGGAAATAAGGTTTGTGGTTGTACTCTGCTCTATGGTTCAACCTACTCC
1 CTCCACTGCAACTTCAGGGAAATAAGGTTTGTGGTTGTAATCTACTCCATACTTCAACCTACTCC
* *
29875887 GCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAATCGCTATCTACTGTCCGCTCCACTAC
66 GCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGTCCACTCCACTAC
* * * *
29875952 AACTTTAGGGAGACACGACTTGTTGTTTTCAGTCTACTCTACTGGATCTTCAGGGAAATAAGACT
131 AACTTTAGGGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATCTTCAGGGAAATAAGACC
29876017 TATATCTTCAACCTGCTCCACTACAACTTCAGGAAAATAAGATTCATAGCCGATCTG
196 TATATCTTCAACCTGCTCCACTACAACTTCAGGAAAATAAGATTCATAGCCGATCTG
* ** *
29876074 CTCCACTG-AATCTTTAGGGAGGTAAGGTTTGTGGTTTTAATCTACTCCATACTTCAACCTACTC
1 CTCCACTGCAA-CTTCAGGGAAATAAGGTTTGTGGTTGTAATCTACTCCATACTTCAACCTACTC
* *
29876138 CGCTGCAATTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGTCTACTCCACTA
65 CGCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGTCCACTCCACTA
*
29876203 CAACTTTAGGGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATTTTCAGGGAAATAAGAC
130 CAACTTTAGGGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATCTTCAGGGAAATAAGAC
* * * * * *
29876268 CTGTATCTTCAACCTGCTCGACTGCAACTTCAGGGAAATAGGATTCGTAGCCGATCTG
195 CTATATCTTCAACCTGCTCCACTACAACTTCAGGAAAATAAGATTCATAGCCGATCTG
* *
29876326 CTCCACTACATCTTCA
1 CTCCACTGCAACTTCA
29876342 AGAAGATACG
Statistics
Matches: 239, Mismatches: 27, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
251 2 0.01
252 236 0.99
253 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (252 bp):
CTCCACTGCAACTTCAGGGAAATAAGGTTTGTGGTTGTAATCTACTCCATACTTCAACCTACTCC
GCTGCAACTTCAGGGAAATAAGATTCGACATGATAAGAACCGCTATCTACTGTCCACTCCACTAC
AACTTTAGGGAGACACAACTTGTTGTTTTCAGTCTACTCCACTGCATCTTCAGGGAAATAAGACC
TATATCTTCAACCTGCTCCACTACAACTTCAGGAAAATAAGATTCATAGCCGATCTG
Found at i:29895414 original size:16 final size:16
Alignment explanation
Indices: 29895381--29895415 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29895371 TTTTATAATG
* *
29895381 AAATGCCATGTAGTCA
1 AAATGCCATGCAGCCA
29895397 AAATGCCATGCAGCCA
1 AAATGCCATGCAGCCA
29895413 AAA
1 AAA
29895416 CAAAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:29897061 original size:20 final size:20
Alignment explanation
Indices: 29897036--29897074 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29897026 GACGATAAAT
29897036 AAAATAAAT-AAAACTATATA
1 AAAATAAATGAAAA-TATATA
*
29897056 AAAATATATGAAAATATAT
1 AAAATAAATGAAAATATAT
29897075 GTATGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATAAATGAAAATATATA
Found at i:29897141 original size:30 final size:30
Alignment explanation
Indices: 29897105--29897201 Score: 104
Period size: 30 Copynumber: 3.1 Consensus size: 30
29897095 TATGAAAATA
*
29897105 AAAAATATATGTGTACATATACATAGTTAT
1 AAAAATATATGTGTATATATACATAGTTAT
*
29897135 AAAAATATATGTGTATATATATCGTTATGAATTAT
1 AAAAATATATGTGTATATATA-C---AT-AGTTAT
* * *
29897170 AAAAATATATGTATATATGTAGATAGTTAT
1 AAAAATATATGTGTATATATACATAGTTAT
29897200 AA
1 AA
29897202 GATATATAGG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 27 0.48
31 3 0.05
34 2 0.04
35 24 0.43
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.39
Consensus pattern (30 bp):
AAAAATATATGTGTATATATACATAGTTAT
Found at i:29921364 original size:29 final size:29
Alignment explanation
Indices: 29921332--29921387 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
29921322 ATTAGTCTTA
* *
29921332 TATTTAATTTTAAAATAATATTTTTTAAT
1 TATTTAATTTAAAAATAATATGTTTTAAT
* *
29921361 TATTTTATTTAAAAATTATATGTTTTA
1 TATTTAATTTAAAAATAATATGTTTTA
29921388 TTCTATAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TATTTAATTTAAAAATAATATGTTTTAAT
Found at i:29922418 original size:16 final size:15
Alignment explanation
Indices: 29922371--29922418 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
29922361 AAATAAAAAC
*
29922371 ATAAAAAAATTTAAA
1 ATAAAAAATTTTAAA
* *
29922386 ATTATAATATTTTAAA
1 A-TAAAAAATTTTAAA
29922402 ATAAAAAATTTTGAAA
1 ATAAAAAATTTT-AAA
29922418 A
1 A
29922419 ATAATTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATAAAAAATTTTAAA
Found at i:29922423 original size:30 final size:31
Alignment explanation
Indices: 29922371--29922442 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
29922361 AAATAAAAAC
29922371 ATAAAAAAATTTAAAATTATAA-TATTTTAAA
1 ATAAAAAAATTTAAAA-TATAATTATTTTAAA
* *
29922402 ATAAAAAATTTTGAAAA-ATAATTTTTTTAAA
1 ATAAAAAAATTT-AAAATATAATTATTTTAAA
29922433 ATTAAAAAAA
1 A-TAAAAAAA
29922443 ATAAAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.11
31 20 0.57
32 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (31 bp):
ATAAAAAAATTTAAAATATAATTATTTTAAA
Found at i:29927739 original size:16 final size:17
Alignment explanation
Indices: 29927713--29927746 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29927703 TAAAATTTTC
29927713 AAAATAATATTTAATAT
1 AAAATAATATTTAATAT
*
29927730 AAAA-AATATTTATTAT
1 AAAATAATATTTAATAT
29927746 A
1 A
29927747 TTTATTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATATTTAATAT
Found at i:29927769 original size:39 final size:38
Alignment explanation
Indices: 29927722--29927810 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 38
29927712 CAAAATAATA
*
29927722 TTTAATATAAAAAATATTTATTATATTTAT-TTTAGTATT
1 TTTAATATAAAAAACATTTA-TATATTTATATTT-GTATT
* *
29927761 TTTTATATAATAAAACATTTATATATTTATATTTGTGTT
1 TTTAATATAA-AAAACATTTATATATTTATATTTGTATT
29927800 TTTAATATAAA
1 TTTAATATAAA
29927811 TATTTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
38 1 0.02
39 31 0.70
40 12 0.27
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (38 bp):
TTTAATATAAAAAACATTTATATATTTATATTTGTATT
Found at i:29934333 original size:25 final size:25
Alignment explanation
Indices: 29934305--29934365 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
29934295 CTGAGCTCAT
*
29934305 AGCTTGCACTTCTCGCTAAGCTCGC
1 AGCTTGCACATCTCGCTAAGCTCGC
* * *
29934330 AGCTTTG-ACATCTTGCTGAGCTTGC
1 AGC-TTGCACATCTCGCTAAGCTCGC
29934355 AGCTTGCACAT
1 AGCTTGCACAT
29934366 TGGAAAGCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 3 0.10
25 24 0.80
26 3 0.10
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (25 bp):
AGCTTGCACATCTCGCTAAGCTCGC
Found at i:29946098 original size:3 final size:3
Alignment explanation
Indices: 29946092--29946141 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
29946082 CTCGTCGTCG
* * *
29946092 TCA TCA TCA TCA TCA TCA TCT TGA TCA TCA TCA -GA GTCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA -TCA TCA TCA
29946137 TCA TC
1 TCA TC
29946142 TTTACCCTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:29954135 original size:25 final size:25
Alignment explanation
Indices: 29954107--29954161 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29954097 TTACTGTATT
*
29954107 ATTGCCCAGATAAGCTTCCCGTTAC
1 ATTGCCCACATAAGCTTCCCGTTAC
* * *
29954132 ATTGCTCACATGAGCTTCCCGTTAT
1 ATTGCCCACATAAGCTTCCCGTTAC
29954157 ATTGC
1 ATTGC
29954162 TTGAGAGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (25 bp):
ATTGCCCACATAAGCTTCCCGTTAC
Found at i:29959142 original size:22 final size:23
Alignment explanation
Indices: 29959101--29959148 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
29959091 TTTTAGGTAA
*
29959101 AAAAATAGGTGTTTTAAAGGGTT
1 AAAAATAGGTGTATTAAAGGGTT
*
29959124 AAAATTAGGTGTATT-AAGGGTT
1 AAAAATAGGTGTATTAAAGGGTT
29959146 AAA
1 AAA
29959149 CCATCGAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (23 bp):
AAAAATAGGTGTATTAAAGGGTT
Found at i:29971832 original size:31 final size:31
Alignment explanation
Indices: 29971797--29971873 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
29971787 GTGAAAATGG
*
29971797 GCCCACAAGCCCATGACATTT-CCTCGTGTGA
1 GCCCACACGCCCATGACATTTGCC-CGTGTGA
*
29971828 GCCCACACGCCCATGACATTTGCCCGTGTGG
1 GCCCACACGCCCATGACATTTGCCCGTGTGA
29971859 GCCCACACGCCCATG
1 GCCCACACGCCCATG
29971874 TGGCCCACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 41 0.95
32 2 0.05
ACGTcount: A:0.19, C:0.40, G:0.22, T:0.18
Consensus pattern (31 bp):
GCCCACACGCCCATGACATTTGCCCGTGTGA
Found at i:29978492 original size:20 final size:20
Alignment explanation
Indices: 29978465--29978515 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
29978455 ATTTACCTCG
*
29978465 AGTATCGATACTTGAGC-AA
1 AGTATCGATACTCGAGCAAA
29978484 AGATATCGATACTCGAGCAAA
1 AG-TATCGATACTCGAGCAAA
29978505 AGTATCGATAC
1 AGTATCGATAC
29978516 CAAATCTCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 23 0.79
21 4 0.14
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (20 bp):
AGTATCGATACTCGAGCAAA
Found at i:29984207 original size:29 final size:29
Alignment explanation
Indices: 29984143--29984208 Score: 98
Period size: 28 Copynumber: 2.2 Consensus size: 29
29984133 GTTTGACTAG
*
29984143 ATTATAATTAATTATTTTATTAAGATAAAT
1 ATTA-AATTAATCATTTTATTAAGATAAAT
29984173 ATTAAATTAATCA-TTTATTAAGATAAAT
1 ATTAAATTAATCATTTTATTAAGATAAAT
29984201 ATCTAAAT
1 AT-TAAAT
29984209 AAATATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 17 0.50
29 13 0.38
30 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (29 bp):
ATTAAATTAATCATTTTATTAAGATAAAT
Found at i:29984230 original size:29 final size:29
Alignment explanation
Indices: 29984198--29984293 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
29984188 TATTAAGATA
29984198 AATATCTAAATAAATATTAAATTACATTT
1 AATATCTAAATAAATATTAAATTACATTT
* * ** **
29984227 AATATCTCATATTAATATTGCATTACTAAAAT
1 AATATCT-AAATAAATATTAAATTAC--ATTT
* * * *
29984259 ACTATCTAGATAAATATTAAATGAAATTT
1 AATATCTAAATAAATATTAAATTACATTT
29984288 AATATC
1 AATATC
29984294 AGATATTAAT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 14 0.29
30 14 0.29
31 12 0.25
32 8 0.17
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (29 bp):
AATATCTAAATAAATATTAAATTACATTT
Found at i:29986112 original size:46 final size:47
Alignment explanation
Indices: 29986043--29986152 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 47
29986033 ACAGTAGTTT
** * * *
29986043 AGATAAACTATCAATAGTCAAAATTGTGAAC-AGCCACCAAAATCGC
1 AGATAAACTGCCAATAATCAAAATCGTGAACAAGCCACCAAAATCAC
* * *
29986089 AGATATACTGCTAATAATCAAAATCGTGGACAAGCCACCAAAATCAC
1 AGATAAACTGCCAATAATCAAAATCGTGAACAAGCCACCAAAATCAC
29986136 AGATAAACTGCCAATAA
1 AGATAAACTGCCAATAA
29986153 CTTTCACCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
46 24 0.45
47 29 0.55
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.19
Consensus pattern (47 bp):
AGATAAACTGCCAATAATCAAAATCGTGAACAAGCCACCAAAATCAC
Found at i:29988674 original size:188 final size:188
Alignment explanation
Indices: 29988352--29988725 Score: 658
Period size: 188 Copynumber: 2.0 Consensus size: 188
29988342 CAAGACTAGC
29988352 CATCTTCCTAATCGAAATTGTAAAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCAC
1 CATCTTCCTAATCGAAATTGTAAAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCAC
* * *
29988417 TTTGATTCTTTTATAGGATTACGAACGCATTTAGATTATTTTCTAAAGTAATTTATTCTTCTCGC
66 TTTGATTCTTTTACAGGATTACGAACGCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCGC
*
29988482 AATGAAAATATTCTTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATGTT
131 AATGAAAATATTATTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATGTT
* * * *
29988540 CATCTTCCTAATTGAAATTGTAGACGACATAATAATCCTTTTATATATTTGAATCAAATGTTCAC
1 CATCTTCCTAATCGAAATTGTAAAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCAC
* *
29988605 TTTGATTCTTTTACAGGATTACGAACTCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTTGC
66 TTTGATTCTTTTACAGGATTACGAACGCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCGC
29988670 AATGAAAATATTATTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATG
131 AATGAAAATATTATTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATG
29988726 AGCTAATATG
Statistics
Matches: 176, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
188 176 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (188 bp):
CATCTTCCTAATCGAAATTGTAAAAGACATAATAATCCTTCTATATATTTGAATCAAATGTTCAC
TTTGATTCTTTTACAGGATTACGAACGCATTTAGATTATTTGCTAAAGTAAGTTATTCTTCTCGC
AATGAAAATATTATTGCAGTGCCACTTATCATCAGCTTGAACTTAGACAAACAATGTT
Found at i:29992161 original size:36 final size:37
Alignment explanation
Indices: 29992055--29992459 Score: 410
Period size: 36 Copynumber: 11.0 Consensus size: 37
29992045 AAAAATGGAA
*
29992055 TACTGATTCTACT-AAAGTACTC-AACGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
*
29992090 TACTGATTCTACTAAAAGTGCTTAAACGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
*
29992127 TACTGATTTTACTAAAAGTGCTC-AACGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* * **
29992163 TACTGA-TCTTACTGAATGTGCTC-AGTGAGCAATATC
1 TACTGATTC-TACTAAAAGTGCTCAAACGAGCAATATC
* * * *
29992199 TACTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* * *
29992236 TATTGATTCTACTGAAAGTGCTCAAATGAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* *
29992273 TACTAATTCTACTAAAAGTGCTC-AACAAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* * * * * * *
29992309 TACCGATCCTATTGAATGTGCTCAAATGAGCAATGTC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
* * * *
29992346 TACTGATTCTGCT-GAACTGCTCAAACAAGCAATATC
1 TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
*
29992382 TACTGATTCTACTAAATAGTTGCTCAAATGAGCAATATC
1 TACTGATTCTACTAAA-AG-TGCTCAAACGAGCAATATC
* * * * * *
29992421 CATTGATTATACTGAATGCTTGCTCAAACGAGCATTATC
1 TACTGATTCTACTAAAAG--TGCTCAAACGAGCAATATC
29992460 CAATGATTAT
Statistics
Matches: 306, Mismatches: 54, Indels: 16
0.81 0.14 0.04
Matches are distributed among these distances:
35 14 0.05
36 126 0.41
37 117 0.38
38 2 0.01
39 47 0.15
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (37 bp):
TACTGATTCTACTAAAAGTGCTCAAACGAGCAATATC
Found at i:29992184 original size:73 final size:72
Alignment explanation
Indices: 29992055--29992476 Score: 443
Period size: 73 Copynumber: 5.7 Consensus size: 72
29992045 AAAAATGGAA
* * * * *
29992055 TACTGATTCTACTAAAGTACTCAACGAGCAATATCTACTGATTCTACTAAAAGTGCTTAAACGAG
1 TACTGATTCTACTAAAGTGCTCAACGAGCAATATCTACTGATTCTACTGAATGTGCTCAAATGAG
29992120 CAATATC
66 CAATATC
* *
29992127 TACTGATTTTACTAAAAGTGCTCAACGAGCAATATCTACTGA-TCTTACTGAATGTGCTC-AGTG
1 TACTGATTCTACT-AAAGTGCTCAACGAGCAATATCTACTGATTC-TACTGAATGTGCTCAAATG
29992190 AGCAATATC
64 AGCAATATC
* * * * *
29992199 TACTGATCCTACTGAATGTGCTCAAACGAGCAATGTCTATTGATTCTACTGAAAGTGCTCAAATG
1 TACTGATTCTACT-AAAGTGCTC-AACGAGCAATATCTACTGATTCTACTGAATGTGCTCAAATG
29992264 AGCAATATC
64 AGCAATATC
* * * * *
29992273 TACTAATTCTACTAAAAGTGCTCAACAAGCAATATCTACCGATCCTATTGAATGTGCTCAAATGA
1 TACTGATTCTACT-AAAGTGCTCAACGAGCAATATCTACTGATTCTACTGAATGTGCTCAAATGA
*
29992338 GCAATGTC
65 GCAATATC
* * * * *
29992346 TACTGATTCTGCTGAACTGCTCAAACAAGCAATATCTACTGATTCTACTAAATAGTTGCTCAAAT
1 TACTGATTCTACTAAAGTGCTC-AACGAGCAATATCTACTGATTCTACTGAAT-G-TGCTCAAAT
29992411 GAGCAATATC
63 GAGCAATATC
* * * * * * * *
29992421 CATTGATTATACTGAATGCTTGCTCAAACGAGCATTATCCAATGATTATACTGAAT
1 TACTGATTCTACT-AAAG--TGCTC-AACGAGCAATATCTACTGATTCTACTGAAT
29992477 AAGATTTTTT
Statistics
Matches: 290, Mismatches: 49, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
72 51 0.18
73 147 0.51
74 34 0.12
75 27 0.09
76 1 0.00
78 30 0.10
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (72 bp):
TACTGATTCTACTAAAGTGCTCAACGAGCAATATCTACTGATTCTACTGAATGTGCTCAAATGAG
CAATATC
Found at i:29992367 original size:146 final size:145
Alignment explanation
Indices: 29992055--29992420 Score: 518
Period size: 146 Copynumber: 2.5 Consensus size: 145
29992045 AAAAATGGAA
* * * *
29992055 TACTGATTCTACTAAAGTACTC-AACGAGCAATATCTACTGATTCTACTAAAAGTGCTTAAACGA
1 TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATGA
* * * * *
29992119 GCAATATCTACTGATTTTACTAAAAGTGCTCAACGAGCAATATCTACTGATCTTACTGAATGTGC
66 GCAATATCTACTAATTCTACTAAAAGTGCTCAACAAGCAATATCTACCGATCCTACTGAATGTGC
*
29992184 TCAGTGAGCAATATC
131 TCAATGAGCAATATC
* * * *
29992199 TACTGATCCTACTGAATGTGCTCAAACGAGCAATGTCTATTGATTCTACTGAAAGTGCTCAAATG
1 TACTGATTCTACTGAA-GTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATG
*
29992264 AGCAATATCTACTAATTCTACTAAAAGTGCTCAACAAGCAATATCTACCGATCCTATTGAATGTG
65 AGCAATATCTACTAATTCTACTAAAAGTGCTCAACAAGCAATATCTACCGATCCTACTGAATGTG
*
29992329 CTCAAATGAGCAATGTC
130 CTC-AATGAGCAATATC
* * *
29992346 TACTGATTCTGCTGAACTGCTCAAACAAGCAATATCTACTGATTCTACTAAATAGTTGCTCAAAT
1 TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAA-AG-TGCTCAAAT
29992411 GAGCAATATC
64 GAGCAATATC
29992421 CATTGATTAT
Statistics
Matches: 194, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
144 14 0.07
145 5 0.03
146 129 0.66
147 27 0.14
148 19 0.10
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (145 bp):
TACTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAATGA
GCAATATCTACTAATTCTACTAAAAGTGCTCAACAAGCAATATCTACCGATCCTACTGAATGTGC
TCAATGAGCAATATC
Found at i:30003480 original size:56 final size:56
Alignment explanation
Indices: 30003374--30003574 Score: 240
Period size: 56 Copynumber: 3.6 Consensus size: 56
30003364 TATTTGTAAA
* * * * * * **
30003374 ATAGCCTTGACAAATTTCCACTTATAATATATTTCTGAAAAACTTTCACATATAAG
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTCTGATGAACTTTCACATATAAG
** * * *
30003430 ATAGTCTTGATGGACTTCCACATATAAGATAGTTTTGATGGACTTCCACATATAAG
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTCTGATGAACTTTCACATATAAG
* * *
30003486 ATAGTTTTGACAAACTTTCACATATAAGATAGTTCTGATGAACTTTCACATATAAG
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTCTGATGAACTTTCACATATAAG
* *
30003542 ATAGTCTTGGCAGACTTCTACATATAAGATAGT
1 ATAGTCTTGACAGACTTCCACATATAAGATAGT
30003575 CCTTACGAAC
Statistics
Matches: 119, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (56 bp):
ATAGTCTTGACAGACTTCCACATATAAGATAGTTCTGATGAACTTTCACATATAAG
Found at i:30003536 original size:84 final size:85
Alignment explanation
Indices: 30003374--30003574 Score: 255
Period size: 84 Copynumber: 2.4 Consensus size: 85
30003364 TATTTGTAAA
* * * * *
30003374 ATAGCCTTGACAAATTTCCACTTATAATATA-TTTCTGAAAAACTTTCACATATAAGATAGTCTT
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTTCTGAAAAACTTTCACATATAAGATAGTCTT
*
30003438 GATGGACTTCCACATATAAG
66 GATGAACTTCCACATATAAG
* ** *
30003458 ATAGTTTTGATGGACTTCCACATATAAGATAGTTT-TGACAAACTTTCACATATAAGATAGT-TC
1 ATAGTCTTGACAGACTTCCACATATAAGATAGTTTCTGAAAAACTTTCACATATAAGATAGTCT-
*
30003521 TGATGAACTTTCACATATAAG
65 TGATGAACTTCCACATATAAG
* *
30003542 ATAGTCTTGGCAGACTTCTACATATAAGATAGT
1 ATAGTCTTGACAGACTTCCACATATAAGATAGT
30003575 CCTTACGAAC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
83 1 0.01
84 95 0.96
85 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (85 bp):
ATAGTCTTGACAGACTTCCACATATAAGATAGTTTCTGAAAAACTTTCACATATAAGATAGTCTT
GATGAACTTCCACATATAAG
Found at i:30003545 original size:28 final size:28
Alignment explanation
Indices: 30003396--30003546 Score: 178
Period size: 28 Copynumber: 5.4 Consensus size: 28
30003386 AATTTCCACT
* * **
30003396 TATAATATATTTCTGAAAAACTTTCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
* *
30003424 TATAAGATAG-TCTTGATGGACTTCCACA
1 TATAAGATAGTTC-TGATGAACTTTCACA
* * *
30003452 TATAAGATAGTTTTGATGGACTTCCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
* **
30003480 TATAAGATAGTTTTGACAAACTTTCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
30003508 TATAAGATAGTTCTGATGAACTTTCACA
1 TATAAGATAGTTCTGATGAACTTTCACA
30003536 TATAAGATAGT
1 TATAAGATAGT
30003547 CTTGGCAGAC
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 2 0.02
28 104 0.97
29 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (28 bp):
TATAAGATAGTTCTGATGAACTTTCACA
Found at i:30003558 original size:28 final size:28
Alignment explanation
Indices: 30003415--30003575 Score: 175
Period size: 28 Copynumber: 5.8 Consensus size: 28
30003405 TTTCTGAAAA
**
30003415 ACTTTCACATATAAGATAGTCTTGATGG
1 ACTTTCACATATAAGATAGTCTTGACAG
* * **
30003443 ACTTCCACATATAAGATAGTTTTGATGG
1 ACTTTCACATATAAGATAGTCTTGACAG
* * *
30003471 ACTTCCACATATAAGATAGTTTTGACAA
1 ACTTTCACATATAAGATAGTCTTGACAG
*
30003499 ACTTTCACATATAAGATAGT-TCTGA-TG
1 ACTTTCACATATAAGATAGTCT-TGACAG
*
30003526 AACTTTCACATATAAGATAGTCTTGGCAG
1 -ACTTTCACATATAAGATAGTCTTGACAG
30003555 AC-TTCTACATATAAGATAGTC
1 ACTTTC-ACATATAAGATAGTC
30003576 CTTACGAACT
Statistics
Matches: 118, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.03
28 112 0.95
29 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (28 bp):
ACTTTCACATATAAGATAGTCTTGACAG
Found at i:30003586 original size:28 final size:28
Alignment explanation
Indices: 30003421--30003595 Score: 164
Period size: 28 Copynumber: 6.2 Consensus size: 28
30003411 AAAAACTTTC
* *
30003421 ACATATAAGATAGTCTTGATGGACTTCC
1 ACATATAAGATAGTCTTGATGAACTTCT
* * *
30003449 ACATATAAGATAGTTTTGATGGACTTCC
1 ACATATAAGATAGTCTTGATGAACTTCT
* **
30003477 ACATATAAGATAGTTTTGACAAACTT-T
1 ACATATAAGATAGTCTTGATGAACTTCT
30003504 CACATATAAGATAGT-TCTGATGAACTT-T
1 -ACATATAAGATAGTCT-TGATGAACTTCT
30003532 CACATATAAGATAGTCTTG--GCAGACTTCT
1 -ACATATAAGATAGTCTTGATG-A-ACTTCT
*
30003561 ACATATAAGATAGTCCTT-ACGAACTTCT
1 ACATATAAGATAGT-CTTGATGAACTTCT
*
30003589 GCATATA
1 ACATATA
30003596 TTTCATAACT
Statistics
Matches: 130, Mismatches: 8, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 120 0.92
29 6 0.05
30 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (28 bp):
ACATATAAGATAGTCTTGATGAACTTCT
Found at i:30003594 original size:56 final size:55
Alignment explanation
Indices: 30003421--30003595 Score: 183
Period size: 56 Copynumber: 3.1 Consensus size: 55
30003411 AAAAACTTTC
** * * * *
30003421 ACATATAAGATAGTCTTGATGGACTTCCACATATAAGATAGTTTTGATGGACTTCC
1 ACATATAAGATAGTCTTGACAGACTTCTACATATAAGATAGTCTT-ATGAACTTCT
* * *
30003477 ACATATAAGATAGTTTTGACAAACTT-TCACATATAAGATAGTTCTGATGAACTT-T
1 ACATATAAGATAGTCTTGACAGACTTCT-ACATATAAGATAG-TCTTATGAACTTCT
* *
30003532 CACATATAAGATAGTCTTGGCAGACTTCTACATATAAGATAGTCCTTACGAACTTCT
1 -ACATATAAGATAGTCTTGACAGACTTCTACATATAAGATAGT-CTTATGAACTTCT
*
30003589 GCATATA
1 ACATATA
30003596 TTTCATAACT
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
55 1 0.01
56 93 0.95
57 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (55 bp):
ACATATAAGATAGTCTTGACAGACTTCTACATATAAGATAGTCTTATGAACTTCT
Found at i:30004948 original size:27 final size:27
Alignment explanation
Indices: 30004910--30004964 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
30004900 TGGTGCCACA
30004910 AATTAACTCGACATCAACTTAGTATTG
1 AATTAACTCGACATCAACTTAGTATTG
30004937 AATTAACTCGACATCAACTTAGTATTG
1 AATTAACTCGACATCAACTTAGTATTG
30004964 A
1 A
30004965 TAACAACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (27 bp):
AATTAACTCGACATCAACTTAGTATTG
Found at i:30006420 original size:108 final size:108
Alignment explanation
Indices: 30006231--30006447 Score: 407
Period size: 108 Copynumber: 2.0 Consensus size: 108
30006221 GAGTAAAGCG
* *
30006231 TGCCGACTATGGGGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGTTCCATTGCCAT
1 TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGCCAT
30006296 CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
66 CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
*
30006339 TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGTCAT
1 TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGCCAT
30006404 CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
66 CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
30006447 T
1 T
30006448 AAGTTATATT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (108 bp):
TGCCGACTATGGAGCGGTGATGGATTTAGCAATATTCACCCCACCTCGTCCCGCTCCATTGCCAT
CCCTACTTAGAAAAACTACGAAAATGTCATTCCGTATTTAAAA
Found at i:30009619 original size:22 final size:21
Alignment explanation
Indices: 30009575--30009629 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
30009565 TATTCACTAA
*
30009575 TTAATTTCTATAATGGATGTT
1 TTAATTTCTATAATGAATGTT
30009596 TTAATTTCTTGATAAT-AATGTT
1 TTAATTTC-T-ATAATGAATGTT
*
30009618 TT-ATTTCAATAA
1 TTAATTTCTATAA
30009630 CTTCACTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.13
21 13 0.43
22 8 0.27
23 5 0.17
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (21 bp):
TTAATTTCTATAATGAATGTT
Found at i:30010092 original size:18 final size:18
Alignment explanation
Indices: 30010052--30010094 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
30010042 AATATTGCTT
* * *
30010052 CTAAAAGGTATTTTTGGG
1 CTAAAAAGTACTTTTGAG
*
30010070 ATAAAAAGTACTTTTGAG
1 CTAAAAAGTACTTTTGAG
30010088 CTAAAAA
1 CTAAAAA
30010095 TATTGCTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.33
Consensus pattern (18 bp):
CTAAAAAGTACTTTTGAG
Found at i:30010601 original size:30 final size:30
Alignment explanation
Indices: 30010567--30010628 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
30010557 ACTTATTTTT
30010567 ACATGACTCAAATATGAAATACATTTCGAA
1 ACATGACTCAAATATGAAATACATTTCGAA
30010597 ACATGACTCAAATATGAAATACATTTCGAA
1 ACATGACTCAAATATGAAATACATTTCGAA
30010627 AC
1 AC
30010629 TCAGGAGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.26
Consensus pattern (30 bp):
ACATGACTCAAATATGAAATACATTTCGAA
Found at i:30011182 original size:31 final size:30
Alignment explanation
Indices: 30011125--30011182 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
30011115 ATAAATATTA
**
30011125 AATTTATAAATGAACTTTTCTCTGATGTAT
1 AATTTATAAATGAACTTTGATCTGATGTAT
* *
30011155 AATTTGATACATGAACTTTGATTTGATG
1 AATTT-ATAAATGAACTTTGATCTGATG
30011183 CATTGCGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.22
31 18 0.78
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (30 bp):
AATTTATAAATGAACTTTGATCTGATGTAT
Found at i:30019778 original size:16 final size:16
Alignment explanation
Indices: 30019757--30019788 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30019747 TTTATAACTG
*
30019757 CTATGTATTTATATAT
1 CTATGTATGTATATAT
30019773 CTATGTATGTATATAT
1 CTATGTATGTATATAT
30019789 TTGAAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53
Consensus pattern (16 bp):
CTATGTATGTATATAT
Found at i:30024048 original size:2 final size:2
Alignment explanation
Indices: 30024041--30024084 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
30024031 CACAATGTAC
*
30024041 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30024083 AT
1 AT
30024085 TGAATCAGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30032317 original size:27 final size:27
Alignment explanation
Indices: 30032274--30032325 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
30032264 TTTTCGCCTT
* *
30032274 TTTTATTTTCATTTTCTTCTTTTTCAC
1 TTTTATTTTCATCTTCTCCTTTTTCAC
30032301 TTTTATTTTTC-TCTTCTCCTTTTTC
1 TTTTA-TTTTCATCTTCTCCTTTTTC
30032326 TTTTTCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTATTTTCATCTTCTCCTTTTTCAC
Found at i:30038181 original size:21 final size:21
Alignment explanation
Indices: 30038152--30038192 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30038142 TTGGAGTAAC
* *
30038152 TCTATCATTAGCGCTAGTTGA
1 TCTAGCATTACCGCTAGTTGA
*
30038173 TCTAGCATTACCTCTAGTTG
1 TCTAGCATTACCGCTAGTTG
30038193 TTCGAATATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (21 bp):
TCTAGCATTACCGCTAGTTGA
Found at i:30040666 original size:14 final size:14
Alignment explanation
Indices: 30040621--30040684 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
30040611 CTAATTTTAT
*
30040621 ATTTTCAATCTTCAA
1 ATTTTCAAT-TTCCA
*
30040636 ATTTT-AATTT-TA
1 ATTTTCAATTTCCA
*
30040648 ATTTTCACTTTCCA
1 ATTTTCAATTTCCA
*
30040662 ATTTTCAATTTCAA
1 ATTTTCAATTTCCA
*
30040676 AATTTCAAT
1 ATTTTCAAT
30040685 CCTCAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
12 6 0.15
13 6 0.15
14 24 0.59
15 5 0.12
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTCAATTTCCA
Found at i:30040672 original size:7 final size:7
Alignment explanation
Indices: 30040606--30040672 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 7
30040596 TCCAATCCCC
30040606 ATTTTCTA
1 ATTTTC-A
30040614 ATTTT-A
1 ATTTTCA
30040620 TATTTTCA
1 -ATTTTCA
*
30040628 ATCTTCAA
1 ATTTTC-A
30040636 ATTTT-A
1 ATTTTCA
30040642 ATTTT-A
1 ATTTTCA
30040648 ATTTTCA
1 ATTTTCA
* *
30040655 CTTTCCA
1 ATTTTCA
30040662 ATTTTCA
1 ATTTTCA
30040669 ATTT
1 ATTT
30040673 CAAAATTTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
6 13 0.27
7 25 0.51
8 11 0.22
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTTCA
Found at i:30051592 original size:20 final size:19
Alignment explanation
Indices: 30051546--30051592 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
30051536 TACAAAAAGT
*
30051546 TTCAAAATAATTTTTAAAA
1 TTCAAAATAATTTATAAAA
30051565 TTCAAAAT-ATTTATAGAAA
1 TTCAAAATAATTTATA-AAA
30051584 TTACAAAAT
1 TT-CAAAAT
30051593 TTATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 13 0.52
20 6 0.24
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (19 bp):
TTCAAAATAATTTATAAAA
Found at i:30054946 original size:15 final size:16
Alignment explanation
Indices: 30054915--30054947 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30054905 TTCATATATG
*
30054915 TAATTTTAATTATTTT
1 TAATTTTAATAATTTT
30054931 TAATTTT-ATAATTTT
1 TAATTTTAATAATTTT
30054946 TA
1 TA
30054948 TAACAGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTTTAATAATTTT
Found at i:30055919 original size:20 final size:18
Alignment explanation
Indices: 30055879--30055915 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
30055869 TTATGCCAGG
*
30055879 TGTGTATCCTATCCCTTA
1 TGTGTATCCTAACCCTTA
30055897 TGTGTATCCTAACCCTTA
1 TGTGTATCCTAACCCTTA
30055915 T
1 T
30055916 ATGTTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTGTATCCTAACCCTTA
Found at i:30055924 original size:18 final size:18
Alignment explanation
Indices: 30055881--30055924 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
30055871 ATGCCAGGTG
* *
30055881 TGTATCCTATCCCTTATG
1 TGTATCCTAACCCTTATA
30055899 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
30055917 TGTTTCCT
1 TGTATCCT
30055925 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:30059796 original size:126 final size:126
Alignment explanation
Indices: 30059438--30059815 Score: 535
Period size: 127 Copynumber: 3.0 Consensus size: 126
30059428 TAAGGTCAAA
30059438 TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
1 TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
*
30059503 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAATCGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * * * * * * *
30059564 CAGGAACTACTATAAAAAAAAGAGCGTCCACATAGGAGCTTTTTTCATCAGTTTTACTGACAGTA
1 TAGGAACTACTGT-AGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTG
* * *
30059629 CATCTTGCTTGAAGCATTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTATTTTTT
65 CATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * *
30059691 TAGGAACTACGGTAGAAAAAGAGCATCCACGTGGGAGCTCTTTTCAGT-AATTTTGCTGACAGTG
1 TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCA-TCAATTTTGCTGACAGTG
* * * * *
30059755 CATCCTACTTGAAGCGTTTTTCACATTATCTT-TTCAGAACCGTCTTTTCAAAATTAATTTT
65 CATCCTGCTTGAAGCGTTTTTGACACTAT-TTGTTCAGAACCGTCTTCTCAAAATTATTTTT
30059816 CCTAAAACAA
Statistics
Matches: 218, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
126 102 0.47
127 116 0.53
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (126 bp):
TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGC
ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:30059926 original size:34 final size:34
Alignment explanation
Indices: 30059884--30060015 Score: 130
Period size: 34 Copynumber: 4.0 Consensus size: 34
30059874 CTAAACACAA
30059884 AATTATTTTTTTTTAAAA-ACTAAACCCTAATTT
1 AATTATTTTTTTTTAAAACACTAAACCCTAATTT
* * * * *
30059917 AATTAATTTTCTTAAAAACTCTAAACTCTAATTT
1 AATTATTTTTTTTTAAAACACTAAACCCTAATTT
* * * * *
30059951 TATT-TATTTATTTAAAACCCCTAAAACCTAATTT
1 AATTATTTTTTTTTAAAA-CACTAAACCCTAATTT
30059985 -A--ATTTTTTTTTAAAACACTAAACCCTAATTT
1 AATTATTTTTTTTTAAAACACTAAACCCTAATTT
30060016 TAAAAAAAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
31 14 0.18
32 11 0.14
33 25 0.32
34 29 0.37
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (34 bp):
AATTATTTTTTTTTAAAACACTAAACCCTAATTT
Found at i:30060062 original size:20 final size:20
Alignment explanation
Indices: 30060039--30060097 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
30060029 AAACCCTAAA
30060039 CCTAAATTATTTTAACAAAC
1 CCTAAATTATTTTAACAAAC
* *
30060059 CCTACCACTA---TAACCATAAC
1 CCTA-AATTATTTTAA-CA-AAC
30060079 CCTAAATTATTTTAACAAA
1 CCTAAATTATTTTAACAAA
30060098 AATCTAACCC
Statistics
Matches: 29, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 13 0.45
21 5 0.17
22 3 0.10
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (20 bp):
CCTAAATTATTTTAACAAAC
Found at i:30065974 original size:14 final size:15
Alignment explanation
Indices: 30065940--30065978 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
30065930 TATGTATATT
30065940 TTTTATTAAATTGAA
1 TTTTATTAAATTGAA
* *
30065955 TGTTATTATA-TGAA
1 TTTTATTAAATTGAA
30065969 TTTTATTAAA
1 TTTTATTAAA
30065979 AATGAATCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (15 bp):
TTTTATTAAATTGAA
Found at i:30067939 original size:12 final size:12
Alignment explanation
Indices: 30067922--30067951 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30067912 CCGTGTGTGA
30067922 CACACGGCCTAG
1 CACACGGCCTAG
*
30067934 CACACGGCCTGG
1 CACACGGCCTAG
30067946 CACACG
1 CACACG
30067952 AGTGTGTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.43, G:0.27, T:0.07
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:30076759 original size:2 final size:2
Alignment explanation
Indices: 30076752--30076780 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30076742 TCGATTTTTA
30076752 AT 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 A
30076781 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30079074 original size:16 final size:18
Alignment explanation
Indices: 30079053--30079097 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
30079043 CTAAGCCTTG
*
30079053 AATATTTTT-TTAATAT-
1 AATATTTTTGTTAAAATC
30079069 AATATTTTTGTTAAAATC
1 AATATTTTTGTTAAAATC
30079087 AATATTATTTG
1 AATATT-TTTG
30079098 ATGTTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 6 0.24
19 4 0.16
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
AATATTTTTGTTAAAATC
Found at i:30082932 original size:20 final size:19
Alignment explanation
Indices: 30082890--30082933 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
30082880 TCCAAACATC
*
30082890 AGAAAAGTAAATTATTTCT
1 AGAAAAGTAAATTATTTCG
30082909 AGAAAAGTAAATTATTTTCG
1 AGAAAAGTAAATTA-TTTCG
30082929 AGAAA
1 AGAAA
30082934 TTATTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (19 bp):
AGAAAAGTAAATTATTTCG
Found at i:30082949 original size:15 final size:15
Alignment explanation
Indices: 30082917--30082954 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
30082907 CTAGAAAAGT
30082917 AAATTA-TTTTCGAG
1 AAATTATTTTTCGAG
30082931 AAATTATTTTTC-AG
1 AAATTATTTTTCGAG
*
30082945 AAAATATTTT
1 AAATTATTTT
30082955 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (15 bp):
AAATTATTTTTCGAG
Found at i:30086060 original size:19 final size:19
Alignment explanation
Indices: 30086030--30086074 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
30086020 TTTACGAGGA
30086030 AATTTAGAGCATGGTGTGCC
1 AATTT-GAGCATGGTGTGCC
*
30086050 AGTTTGAGCATGGTGTGCC
1 AATTTGAGCATGGTGTGCC
30086069 AATTTG
1 AATTTG
30086075 TTTGGGGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.22, C:0.13, G:0.31, T:0.33
Consensus pattern (19 bp):
AATTTGAGCATGGTGTGCC
Found at i:30090345 original size:29 final size:28
Alignment explanation
Indices: 30090272--30090443 Score: 127
Period size: 29 Copynumber: 5.8 Consensus size: 28
30090262 TTTCTTTCCA
*
30090272 TTTATTTTTGAAGCCCTTGTTTCACTTATTTT
1 TTTATTTTT-AAGCCCTTATTTCA---ATTTT
30090304 TTT-TCTTTTAAGCCCTTATTTCAATTTT
1 TTTAT-TTTTAAGCCCTTATTTCAATTTT
30090332 TTTATTTTTGAAGCCCTTATTT-AACCTTTT
1 TTTATTTTT-AAGCCCTTATTTCAA--TTTT
* *
30090362 TTT-TGCTTTTAAGTCCTTATTTCACTTTT
1 TTTAT--TTTTAAGCCCTTATTTCAATTTT
* *
30090391 TTAATTTTTAAAGCCCTAATTT-AACTTATT
1 TTTATTTTT-AAGCCCTTATTTCAA-TT-TT
** *
30090421 TTTGCTTTTAAGTCCTTATTTCA
1 TTTATTTTTAAGCCCTTATTTCA
30090444 CTACTTTTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
28 19 0.17
29 42 0.37
30 28 0.24
31 19 0.17
32 7 0.06
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.58
Consensus pattern (28 bp):
TTTATTTTTAAGCCCTTATTTCAATTTT
Found at i:30090384 original size:59 final size:59
Alignment explanation
Indices: 30090272--30090443 Score: 238
Period size: 59 Copynumber: 2.9 Consensus size: 59
30090262 TTTCTTTCCA
* * * * *
30090272 TTTATTTTTGAAGCCCTTGTTTCACTTATTTTTTTTCTTTTAAGCCCTTATTTCAATTTT
1 TTTATTTTTGAAGCCCTTATTTAACCT-TTTTTTTGCTTTTAAGTCCTTATTTCAATTTT
*
30090332 TTTATTTTTGAAGCCCTTATTTAACCTTTTTTTTGCTTTTAAGTCCTTATTTCACTTTT
1 TTTATTTTTGAAGCCCTTATTTAACCTTTTTTTTGCTTTTAAGTCCTTATTTCAATTTT
* * * *
30090391 TTAATTTTTAAAGCCCTAATTTAA-CTTATTTTTGCTTTTAAGTCCTTATTTCA
1 TTTATTTTTGAAGCCCTTATTTAACCTTTTTTTTGCTTTTAAGTCCTTATTTCA
30090444 CTACTTTTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 28 0.27
59 50 0.49
60 24 0.24
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.58
Consensus pattern (59 bp):
TTTATTTTTGAAGCCCTTATTTAACCTTTTTTTTGCTTTTAAGTCCTTATTTCAATTTT
Found at i:30090491 original size:58 final size:56
Alignment explanation
Indices: 30090300--30090480 Score: 172
Period size: 59 Copynumber: 3.1 Consensus size: 56
30090290 GTTTCACTTA
* * * * * *
30090300 TTTTTTTT-CTTTTAAGCCCTTATTTCAATTTTTTTATTTTTGAAGCCCTTATTTAACC
1 TTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTAACTTTTAAAG-CC-AATTTAA-C
*
30090358 TTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTAATTTTTAAAGCCCTAATTTAAC
1 TTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTAACTTTTAAAG-CC-AATTTAAC
* *
30090416 TTATTTTTGCTTTTAAGTCCTTATTTCACTACTTTTTTTAACTTTTAATG-C-A-TTAAC
1 TTTTTTTTGCTTTTAAGTCCTTATTT--C-AC-TTTTTTAACTTTTAAAGCCAATTTAAC
30090473 TTTTTTTT
1 TTTTTTTT
30090481 TAGTTTTAAG
Statistics
Matches: 109, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
57 12 0.11
58 35 0.32
59 43 0.39
60 2 0.02
61 2 0.02
62 15 0.14
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.59
Consensus pattern (56 bp):
TTTTTTTTGCTTTTAAGTCCTTATTTCACTTTTTTAACTTTTAAAGCCAATTTAAC
Found at i:30092631 original size:121 final size:121
Alignment explanation
Indices: 30092412--30092632 Score: 280
Period size: 121 Copynumber: 1.8 Consensus size: 121
30092402 TTATTTAATA
* * * * *
30092412 TTTTTTTTGGAACTTTTATGTCATTATTTCATTAATTTTACAGTTATAAAACAAAATATGCCAAA
1 TTTTTTTTGGAACTTTTAAGCCATTATTTCACTAATTTTACAGTTATAAAACAAAATAGGCAAAA
* * * **
30092477 ATATTAAAATATTTCTTGAACTATTTCCTTCTTTTAAAAACAAATTTTTTAAATGC
66 AAAGTAAAATAATTCTTGAACTATTTCAATCTTTTAAAAACAAATTTTTTAAATGC
* * * * * *
30092533 TTTTTTTTGGAACTTTTAAGCCCTTATTTCACTAATTTTATAGTTGTCAAATAAAATAGGGAAAA
1 TTTTTTTTGGAACTTTTAAGCCATTATTTCACTAATTTTACAGTTATAAAACAAAATAGGCAAAA
* *
30092598 AAAGTAAAATAATTCTTGAATTATTTTAATCTTTT
66 AAAGTAAAATAATTCTTGAACTATTTCAATCTTTT
30092633 TTAAATAAAT
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
121 82 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (121 bp):
TTTTTTTTGGAACTTTTAAGCCATTATTTCACTAATTTTACAGTTATAAAACAAAATAGGCAAAA
AAAGTAAAATAATTCTTGAACTATTTCAATCTTTTAAAAACAAATTTTTTAAATGC
Found at i:30096069 original size:71 final size:70
Alignment explanation
Indices: 30095966--30096113 Score: 199
Period size: 71 Copynumber: 2.1 Consensus size: 70
30095956 TTTTTATATG
* * * * *
30095966 TCAAATATTTATTTTTTCACCTACATTGTAGATATGGTAAATTTTAATATTATAAAATCAACTAA
1 TCAAATATTTATTTTTTCACCTACACTCTAGATATAGTAAACTTTAATATTATAAAATCAAATAA
30096031 TTATT
66 TTATT
* *
30096036 TCAAATATCATTA-TTTTTCACCTTCACTCTAGATATAGTAAACTTTAATATTATAAAATTAAAT
1 TCAAATAT--TTATTTTTTCACCTACACTCTAGATATAGTAAACTTTAATATTATAAAATCAAAT
30096100 AATTATT
64 AATTATT
*
30096107 TCGAATA
1 TCAAATA
30096114 CACATACAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 8 0.12
71 57 0.84
72 3 0.04
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (70 bp):
TCAAATATTTATTTTTTCACCTACACTCTAGATATAGTAAACTTTAATATTATAAAATCAAATAA
TTATT
Found at i:30103900 original size:16 final size:16
Alignment explanation
Indices: 30103879--30103909 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30103869 ATTTCATATA
*
30103879 TAAAAATTATATTTAC
1 TAAAAATAATATTTAC
30103895 TAAAAATAATATTTA
1 TAAAAATAATATTTA
30103910 AAATAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAATAATATTTAC
Found at i:30104573 original size:5 final size:5
Alignment explanation
Indices: 30104563--30104587 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
30104553 GCACATAAAA
30104563 CAAAC CAAAC CAAAC CAAAC CAAAC
1 CAAAC CAAAC CAAAC CAAAC CAAAC
30104588 TTATTCTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:30107880 original size:30 final size:30
Alignment explanation
Indices: 30107816--30107880 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
30107806 CATATGGTCA
* ***
30107816 ATTTTTTTTAATATTTATGATTCTAGGCTT
1 ATTTTTTATAATATTTATGAGAATAGGCTT
30107846 -TTTTTTATATATATTTATGAGAATAGG-TT
1 ATTTTTTATA-ATATTTATGAGAATAGGCTT
30107875 ATTTTT
1 ATTTTT
30107881 GGAGAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (30 bp):
ATTTTTTATAATATTTATGAGAATAGGCTT
Found at i:30108602 original size:18 final size:18
Alignment explanation
Indices: 30108579--30108613 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30108569 ATCAAAATTT
* *
30108579 TAAAAATTAAATTTAAAC
1 TAAAAATCAAATATAAAC
30108597 TAAAAATCAAATATAAA
1 TAAAAATCAAATATAAA
30108614 TGAATTACAG
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:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATCAAATATAAAC
Found at i:30108683 original size:29 final size:29
Alignment explanation
Indices: 30108650--30108714 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
30108640 AAAATAATTT
*
30108650 AATCTTTATCCAGCCAATTTCAAATCTTC
1 AATCTTTATCCAGCCAACTTCAAATCTTC
30108679 AATCTTTATCCAGCCAACTTCAAATCTTC
1 AATCTTTATCCAGCCAACTTCAAATCTTC
30108708 AATCTTT
1 AATCTTT
30108715 CAATCTACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (29 bp):
AATCTTTATCCAGCCAACTTCAAATCTTC
Found at i:30109184 original size:19 final size:19
Alignment explanation
Indices: 30109146--30109189 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
30109136 TTTAATATGT
**
30109146 ATTTTTTATTTGTTGTTTAA
1 ATTTTTTATTTGTTAATT-A
30109166 ATTTTTTATTT-TTAATTA
1 ATTTTTTATTTGTTAATTA
30109184 ATTTTT
1 ATTTTT
30109190 ATAATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
20 11 0.50
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (19 bp):
ATTTTTTATTTGTTAATTA
Found at i:30110923 original size:20 final size:20
Alignment explanation
Indices: 30110900--30110938 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
30110890 AATAAAAGAG
30110900 TTATTAATTA-AAAATATTAT
1 TTATTAATTATAAAA-ATTAT
30110920 TTATTAATTATAAAAATTA
1 TTATTAATTATAAAAATTA
30110939 ATTAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAATTATAAAAATTAT
Found at i:30111611 original size:18 final size:18
Alignment explanation
Indices: 30111571--30111613 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30111561 GTTTAATGTG
30111571 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
30111589 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
30111607 TAATTAA
1 TAATTAA
30111614 AAACCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:30114109 original size:23 final size:23
Alignment explanation
Indices: 30114083--30114128 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
30114073 CAAGGTCTGG
* *
30114083 AATAGGTGCGGAGACGGGTTCAT
1 AATAAGTGCGAAGACGGGTTCAT
**
30114106 AATAAGTGTTAAGACGGGTTCAT
1 AATAAGTGCGAAGACGGGTTCAT
30114129 CATCGAGTCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.26
Consensus pattern (23 bp):
AATAAGTGCGAAGACGGGTTCAT
Found at i:30114556 original size:6 final size:6
Alignment explanation
Indices: 30114539--30114607 Score: 68
Period size: 6 Copynumber: 11.5 Consensus size: 6
30114529 CGGAGGAAGG
* * *
30114539 AGATGA AAATGA AGATGA AGATGA AGATGA AGATGA GGATCG- AGGTGA
1 AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGAT-GA AGATGA
* * *
30114587 CGATGA AGACGA AGATAA AGA
1 AGATGA AGATGA AGATGA AGA
30114608 GGAGGAGGAG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
5 1 0.02
6 48 0.96
7 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.33, T:0.14
Consensus pattern (6 bp):
AGATGA
Found at i:30117130 original size:29 final size:29
Alignment explanation
Indices: 30117098--30117163 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
30117088 CCAAAATCAA
*
30117098 CCTATTCCAATAAATATGCCAAAAACTAG
1 CCTATTCCAATAAATATACCAAAAACTAG
* * *
30117127 CCTATTCCGATAAATATACCAGAAACTGG
1 CCTATTCCAATAAATATACCAAAAACTAG
30117156 CCTATTCC
1 CCTATTCC
30117164 CTCAATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.26
Consensus pattern (29 bp):
CCTATTCCAATAAATATACCAAAAACTAG
Found at i:30124549 original size:175 final size:174
Alignment explanation
Indices: 30124257--30124651 Score: 553
Period size: 175 Copynumber: 2.3 Consensus size: 174
30124247 AAATTTGGTC
* *
30124257 AAAATTAAATATAGTGATAAAATTTCAAATTTGAGTGTAGTATAATGACTAAAACTAAAATTGGA
1 AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAGTATAATAACTAAAACTAAAATTGGA
* ** *
30124322 CCATTGTTTTATATTAAAGAATGTAAAGGGATCAAAATTGAAATTATACCATCATCTTAT-GAGA
66 CCATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTATACCATCATCTTATAGAGA
*
30124386 GAGAGAATAG-AAAAGCGTGT-ATCGTTTGAGGTACCAAATTATGTTA
131 GAGAGAATAGCAAAA-CGTGTCA-C--TCGAGGTACCAAATTATGTTA
* *
30124432 AAAATTAAATATAGAGATAAAATTTCAAATTTGAATGTAGTATAATAACTAAAACTAAAATTTGA
1 AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAGTATAATAACTAAAACTAAAATTGGA
* *
30124497 CTATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTGTACCATCATCTTATAAGAG
66 CCATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTATACCATCATCTTAT-AGAG
* *
30124562 AGAGAGAATAGCAGAATGTGTCACTCGAGGTACCAAATTATGTTA
130 AGAGAGAATAGCAAAACGTGTCACTCGAGGTACCAAATTATGTTA
* * * * * *
30124607 AAAATTATATATAAATATGAAATCTCAAATTTGAGTGTAATATAA
1 AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAGTATAA
30124652 AGACCGAAAC
Statistics
Matches: 196, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
175 173 0.88
177 19 0.10
178 4 0.02
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.32
Consensus pattern (174 bp):
AAAATTAAATATAGAGATAAAATTTCAAATTTGAGTGTAGTATAATAACTAAAACTAAAATTGGA
CCATTGTTTTATAATAAAGAAAATAAAGGGATCAAAATTAAAATTATACCATCATCTTATAGAGA
GAGAGAATAGCAAAACGTGTCACTCGAGGTACCAAATTATGTTA
Found at i:30135883 original size:21 final size:21
Alignment explanation
Indices: 30135857--30135899 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30135847 ATAAACAATA
**
30135857 TAATGGTTTTGCCTTTTAACT
1 TAATGGTTTTAACTTTTAACT
30135878 TAATGGTTTTAACTTTTAACT
1 TAATGGTTTTAACTTTTAACT
30135899 T
1 T
30135900 TTAAAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (21 bp):
TAATGGTTTTAACTTTTAACT
Found at i:30140293 original size:16 final size:17
Alignment explanation
Indices: 30140260--30140301 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
30140250 ACAGAGTTAG
30140260 AATTGAATTGAGAAAATT
1 AATT-AATTGAGAAAATT
*
30140278 ATTTAATTGA-AAAATT
1 AATTAATTGAGAAAATT
30140294 AATTAATT
1 AATTAATT
30140302 TAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
17 6 0.27
18 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (17 bp):
AATTAATTGAGAAAATT
Found at i:30147678 original size:2 final size:2
Alignment explanation
Indices: 30147673--30147699 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30147663 TCAAGGGTTT
30147673 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 T
30147700 GCATCAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30149489 original size:19 final size:19
Alignment explanation
Indices: 30149467--30149508 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
30149457 CAAAATTTGG
30149467 AATAAATAAATAATAAA-AT
1 AATAAA-AAATAATAAATAT
*
30149486 AATAAAAACTAATAAATAT
1 AATAAAAAATAATAAATAT
30149505 AATA
1 AATA
30149509 TTGTGCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAATAAATAT
Found at i:30151624 original size:19 final size:19
Alignment explanation
Indices: 30151598--30151650 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
30151588 AACCTAAAAG
30151598 AAAT-CTAAAATT-ATTCTTA
1 AAATCCTAAAATTAATTC--A
30151617 AAA-CCT-AAATTAATTCA
1 AAATCCTAAAATTAATTCA
30151634 AAATCCTAAAATCTAAT
1 AAATCCTAAAAT-TAAT
30151651 ATCTAACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.14
18 8 0.28
19 13 0.45
20 4 0.14
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATCCTAAAATTAATTCA
Found at i:30161500 original size:88 final size:88
Alignment explanation
Indices: 30161384--30162137 Score: 1118
Period size: 88 Copynumber: 8.6 Consensus size: 88
30161374 GGACCATTGG
* *
30161384 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGACCTACTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
30161449 ACTGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * * ** *
30161472 CTTTGATTTACTTCGTTGTCGATGCAGGAAGGTAAGATCTGCTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
30161537 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * *
30161560 CTTCAATCTGCTTCACTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACTTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
**
30161625 ATTGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* *
30161648 CTTCAATCTGCTTCATTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
30161713 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * * *
30161736 CTTCGATCTGTTTCACTGTCGATGTAGGAAGGCAAGATATGCTATCTTCAACCTACTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
30161801 ACCGATGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * *
30161824 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTACTATCTTCAACTTGCTCCACTATA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
30161889 ATCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
** * * * * *
30161912 CTTTAATCTGCTTCGCCGCCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
* *
30161977 ACTGAGGGAGGCAAGACTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* *
30162000 CTTCGATCTGCTTCACTGTC-AGTACAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTAC
1 CTTCGATCTGCTTCACTGTCGA-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
*
30162064 AACCGAGGGAGGCAAGGCTTATGT
65 AACCGAGGGAGGCAAGGCTTGTGT
*
30162088 CTTTGATCTGCTTCACTGTCAGTAT--AGGAAGGCAAGATCTGCTATCTTCA
1 CTTCGATCTGCTTCACTGTC-G-ATGCAGGAAGGCAAGATCTGCTATCTTCA
30162138 CTGATCTGTT
Statistics
Matches: 594, Mismatches: 68, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
87 1 0.00
88 591 0.99
90 1 0.00
91 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (88 bp):
CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
ACCGAGGGAGGCAAGGCTTGTGT
Found at i:30163452 original size:51 final size:50
Alignment explanation
Indices: 30163396--30163495 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 50
30163386 CTTTCGTTTA
* *
30163396 TTTTTTTT-GGACTCAAAGCACCCTTTGCGGGTTTTCACTTTGGTTCCCTT
1 TTTTTTTTAGGAATCAAAGCACCCTTTGCGGGTTTTCACCTTGG-TCCCTT
* *
30163446 TTTTTTTTAGGAATCAAGGCGCCCTTTGCGGGTTTTCACCTTGGTCCCTT
1 TTTTTTTTAGGAATCAAAGCACCCTTTGCGGGTTTTCACCTTGGTCCCTT
30163496 CTCCTTCTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 14 0.31
51 31 0.69
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (50 bp):
TTTTTTTTAGGAATCAAAGCACCCTTTGCGGGTTTTCACCTTGGTCCCTT
Found at i:30171118 original size:19 final size:20
Alignment explanation
Indices: 30171082--30171119 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30171072 ATCAAAATCA
*
30171082 TTTTTTCTTGATTCAAAAGT
1 TTTTTTCTTGAATCAAAAGT
*
30171102 TTTTTTTTTGAAT-AAAAG
1 TTTTTTCTTGAATCAAAAG
30171120 CAATATTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTTTCTTGAATCAAAAGT
Found at i:30173670 original size:22 final size:22
Alignment explanation
Indices: 30173645--30173689 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30173635 TGAGCAAATG
30173645 TTCTTTCATTCTTTACGATTTT
1 TTCTTTCATTCTTTACGATTTT
**
30173667 TTCTTTCATTCTTTTGGATTTT
1 TTCTTTCATTCTTTACGATTTT
30173689 T
1 T
30173690 CTGTCAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.07, T:0.67
Consensus pattern (22 bp):
TTCTTTCATTCTTTACGATTTT
Found at i:30174175 original size:22 final size:22
Alignment explanation
Indices: 30174147--30174299 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
30174137 TGTTGATAGT
*
30174147 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
30174169 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
30174191 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
30174213 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
30174235 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
30174257 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
30174279 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
30174300 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:30174724 original size:14 final size:14
Alignment explanation
Indices: 30174698--30174739 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
30174688 AGAAGTGATG
*
30174698 TGAAAAATGAAAAGA
1 TGAAAAAT-AAAAAA
30174713 T-AAAAATAAAAAA
1 TGAAAAATAAAAAA
30174726 TGAAAAAGTAAAAA
1 TGAAAAA-TAAAAA
30174740 TGGAGAGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 11 0.46
15 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (14 bp):
TGAAAAATAAAAAA
Found at i:30174726 original size:21 final size:21
Alignment explanation
Indices: 30174700--30174740 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30174690 AAGTGATGTG
30174700 AAAAATG-AAAAGATAAAAATA
1 AAAAATGAAAAAG-TAAAAATA
30174721 AAAAATGAAAAAGTAAAAAT
1 AAAAATGAAAAAGTAAAAAT
30174741 GGAGAGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAAATGAAAAAGTAAAAATA
Found at i:30176464 original size:50 final size:50
Alignment explanation
Indices: 30176003--30176456 Score: 304
Period size: 50 Copynumber: 9.1 Consensus size: 50
30175993 TCCTTAGCAG
* * * *
30176003 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
** * * ** * *
30176053 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAG
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGA-CAT
* * * *
30176103 TGTAGTGGAACAGATTGAAGCTACGACGGCGGAT-TTGGTTTCCCTGATAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTT-GTTTCCCTGACAT
** * * * * ** * *
30176153 TGCAATTAAAAAGGTTGAAGCCACAACGGTGGATCTTACTT-CCTTAGCAG
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGA-CAT
* * * * * *
30176203 TGCAGTGGAATAGATTGAAGCTATGACGGCAGATCTAGTTTCCCTGATAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
** * * ** * *
30176253 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAG
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGA-CAT
* * * * *
30176303 CGCAATGGAATAGATTGAAACTACGACGGCGGATCTAGTTTTCCTGACAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
** * * ** * **
30176353 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACGG
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
** * * * *
30176403 TGCGGTGGAACAGATTGAAGCTACGACAGCGGATCTGGTTTCCCCGACAT
1 TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
30176453 TGCA
1 TGCA
30176457 GTTGAACAAA
Statistics
Matches: 286, Mismatches: 110, Indels: 16
0.69 0.27 0.04
Matches are distributed among these distances:
49 14 0.05
50 258 0.90
51 14 0.05
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (50 bp):
TGCAATGGAAAAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
Found at i:30176472 original size:100 final size:100
Alignment explanation
Indices: 30175984--30176456 Score: 748
Period size: 100 Copynumber: 4.7 Consensus size: 100
30175974 CGGAACCACA
30175984 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
30176049 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
* *
30176084 GATCTTACTTCCTTAGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGGATTTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
* *
30176149 ATATTGCAATTAAAAAGGTTGAAGCCACAACGGTG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
* * * *
30176184 GATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGCTATGACGGCAGATCTAGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
30176249 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
* * * * * *
30176284 GATCTTACTTCCTTAGCAGCGCAATGGAATAGATTGAAACTACGACGGCGGATCTAGTTTTCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
*
30176349 ACATTGCAATTAAAAAGATTGAAGCCACAACGGCG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
* * * * * *
30176384 GATCTTACTTCCCTAACGGTGCGGTGGAACAGATTGAAGCTACGACAGCGGATCTGGTTTCCCCG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
*
30176449 ACATTGCA
66 ATATTGCA
30176457 GTTGAACAAA
Statistics
Matches: 342, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 342 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (100 bp):
GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
Done.